diff --git a/.flake8 b/.flake8 index c186519..d8fd042 100644 --- a/.flake8 +++ b/.flake8 @@ -1,16 +1,12 @@ [flake8] -max-line-length = 120 -extend-ignore = E203, W503, E501 +ignore = E501, E203, E121, E123, E126, W503, W504 exclude = .git, - __pycache__, - docs/source/conf.py, - old, - build, - dist, - venv, - env, .venv, - ./venv-docs, + __pycache__, + api/Archive, + data, docs, - .env + instance, + output, + venv diff --git a/.github/workflows/bar-api.yml b/.github/workflows/bar-api.yml index f6a68dc..b04383e 100644 --- a/.github/workflows/bar-api.yml +++ b/.github/workflows/bar-api.yml @@ -12,6 +12,7 @@ jobs: runs-on: ubuntu-24.04 strategy: + fail-fast: false matrix: python-version: [3.10.18, 3.11, 3.12, 3.13] diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml index c97b361..efaa815 100644 --- a/.github/workflows/codeql.yml +++ b/.github/workflows/codeql.yml @@ -29,16 +29,16 @@ jobs: # Initializes the CodeQL tools for scanning. - name: Initialize CodeQL - uses: github/codeql-action/init@v2 + uses: github/codeql-action/init@v3 with: languages: ${{ matrix.language }} # Autobuild attempts to build any compiled languages (C/C++, C#, or Java). # If this step fails, then you should remove it and run the build manually (see below) - name: Autobuild - uses: github/codeql-action/autobuild@v2 + uses: github/codeql-action/autobuild@v3 - name: Perform CodeQL Analysis - uses: github/codeql-action/analyze@v2 + uses: github/codeql-action/analyze@v3 with: category: "/language:${{matrix.language}}" \ No newline at end of file diff --git a/.gitignore b/.gitignore index 7e08bbb..34ddd49 100644 --- a/.gitignore +++ b/.gitignore @@ -141,3 +141,6 @@ dmypy.json output/* !output !output/placeholder.txt + +# Local sqlite mirrors generated from MySQL dumps +config/databases/*.db diff --git a/README.md b/README.md index c354f9e..b6db475 100644 --- a/README.md +++ b/README.md @@ -4,4 +4,4 @@ [![Website Status](https://img.shields.io/website?url=http%3A%2F%2Fbar.utoronto.ca%2Fapi%2F)](http://bar.utoronto.ca/api/) ![GitHub repo size](https://img.shields.io/github/repo-size/BioAnalyticResource/BAR_API) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![Documentation Status](https://readthedocs.org/projects/bar-api/badge/?version=latest)](https://bar-api.readthedocs.io/en/latest/?badge=latest) -This is the official repository for the Bio-Analytic Resource API. The API documentation can be found [here](https://bar-api.readthedocs.io/en/latest/). +This is the official repository for the Bio-Analytic Resource API. The API documentation can be found [here](https://bar-api.readthedocs.io/en/latest/). \ No newline at end of file diff --git a/api/Archive/efp_tables_structure_sample_data_dump_01_28_25.csv b/api/Archive/efp_tables_structure_sample_data_dump_01_28_25.csv new file mode 100644 index 0000000..fe26873 --- /dev/null +++ b/api/Archive/efp_tables_structure_sample_data_dump_01_28_25.csv @@ -0,0 +1,1128 @@ +database_name,ORDINAL_POSITION,COLUMN_NAME,COLUMN_TYPE,IS_NULLABLE,COLUMN_DEFAULT +hnahal,7,channel,varchar(5),YES,NULL +meristem_db,7,channel,varchar(5),YES,NULL +meristem_db_new,7,channel,varchar(5),YES,NULL +actinidia_bud_development,5,data_bot_id,varchar(8),NO,NULL +actinidia_flower_fruit_development,5,data_bot_id,varchar(16),NO,NULL +actinidia_postharvest,5,data_bot_id,varchar(24),NO,NULL +actinidia_vegetative_growth,5,data_bot_id,varchar(16),NO,NULL +affydb,9,data_bot_id,tinytext,YES,NULL +apple,5,data_bot_id,varchar(12),YES,NULL +arabidopsis_ecotypes,8,data_bot_id,varchar(16),YES,NULL +arachis,5,data_bot_id,varchar(65),NO,NULL +atgenexp,8,data_bot_id,varchar(50),NO,NULL +atgenexp_hormone,7,data_bot_id,varchar(50),YES,NULL +atgenexp_pathogen,7,data_bot_id,varchar(50),YES,NULL +atgenexp_plus,8,data_bot_id,varchar(50),NO,NULL +atgenexp_stress,7,data_bot_id,varchar(40),YES,NULL +barley_mas,8,data_bot_id,varchar(24),NO,NULL +barley_rma,8,data_bot_id,varchar(24),NO,NULL +barley_seed,5,data_bot_id,varchar(12),NO,NULL +barley_spike_meristem,5,data_bot_id,varchar(24),NO,NULL +barley_spike_meristem_v3,5,data_bot_id,varchar(24),NO,NULL +brachypodium,5,data_bot_id,varchar(50),NO,NULL +brachypodium_Bd21,5,data_bot_id,varchar(32),NO,NULL +brachypodium_embryogenesis,5,data_bot_id,varchar(50),NO,NULL +brachypodium_grains,5,data_bot_id,varchar(32),NO,NULL +brachypodium_metabolites_map,5,data_bot_id,varchar(45),NO,NULL +brachypodium_photo_thermocycle,5,data_bot_id,varchar(12),NO,NULL +brassica_rapa,5,data_bot_id,varchar(10),YES,NULL +cacao_developmental_atlas,5,data_bot_id,varchar(16),YES,NULL +cacao_developmental_atlas_sca,5,data_bot_id,varchar(16),YES,NULL +cacao_drought_diurnal_atlas,5,data_bot_id,varchar(16),YES,NULL +cacao_drought_diurnal_atlas_sca,5,data_bot_id,varchar(16),YES,NULL +cacao_infection,5,data_bot_id,varchar(24),YES,NULL +cacao_leaf,5,data_bot_id,varchar(12),YES,NULL +cacao_meristem_atlas_sca,5,data_bot_id,varchar(24),YES,NULL +cacao_seed_atlas_sca,5,data_bot_id,varchar(24),YES,NULL +camelina,6,data_bot_id,varchar(40),NO,NULL +camelina_tpm,6,data_bot_id,varchar(40),NO,NULL +cannabis,5,data_bot_id,varchar(8),NO,NULL +canola,8,data_bot_id,tinytext,NO,NULL +canola_original,8,data_bot_id,tinytext,NO,NULL +canola_original_v2,8,data_bot_id,tinytext,NO,NULL +canola_seed,5,data_bot_id,varchar(12),NO,NULL +cassava_atlas,5,data_bot_id,varchar(24),NO,NULL +cassava_cbb,5,data_bot_id,varchar(24),NO,NULL +cassava_eacmv,5,data_bot_id,varchar(24),NO,NULL +circadian_mutants,5,data_bot_id,varchar(18),NO,NULL +cuscuta,5,data_bot_id,varchar(12),YES,NULL +cuscuta_early_haustoriogenesis,5,data_bot_id,varchar(8),NO,NULL +cuscuta_lmd,5,data_bot_id,varchar(8),NO,NULL +dna_damage,5,data_bot_id,varchar(32),YES,NULL +durum_wheat_abiotic_stress,5,data_bot_id,varchar(32),NO,NULL +durum_wheat_biotic_stress,5,data_bot_id,varchar(42),NO,NULL +durum_wheat_development,5,data_bot_id,varchar(24),NO,NULL +embryo,5,data_bot_id,varchar(8),NO,NULL +eucalyptus,5,data_bot_id,varchar(42),NO,NULL +euphorbia,5,data_bot_id,varchar(24),NO,NULL +gc_drought,5,data_bot_id,varchar(12),NO,NULL +germination,5,data_bot_id,varchar(16),NO,NULL +grape_developmental,8,data_bot_id,varchar(50),NO,NULL +guard_cell,8,data_bot_id,varchar(24),NO,NULL +gynoecium,5,data_bot_id,varchar(16),NO,NULL +heterodera_schachtii,5,data_bot_id,varchar(16),NO,NULL +hnahal,6,data_bot_id,tinytext,NO,NULL +human_body_map_2,8,data_bot_id,varchar(20),NO,NULL +human_developmental,8,data_bot_id,varchar(24),YES,NULL +human_developmental_SpongeLab,8,data_bot_id,tinytext,NO,NULL +human_diseased,8,data_bot_id,tinytext,NO,NULL +kalanchoe,5,data_bot_id,varchar(16),NO,NULL +kalanchoe_time_course_analysis,5,data_bot_id,varchar(16),NO,NULL +klepikova,5,data_bot_id,varchar(16),NO,NULL +lateral_root_initiation,6,data_bot_id,varchar(64),YES,NULL +light_series,8,data_bot_id,varchar(30),NO,NULL +lipid_map,5,data_bot_id,varchar(16),NO,NULL +little_millet,5,data_bot_id,varchar(12),YES,NULL +lupin_lcm_leaf,5,data_bot_id,varchar(32),NO,NULL +lupin_lcm_pod,5,data_bot_id,varchar(32),NO,NULL +lupin_lcm_stem,5,data_bot_id,varchar(32),NO,NULL +lupin_pod_seed,5,data_bot_id,varchar(32),NO,NULL +lupin_whole_plant,5,data_bot_id,varchar(32),NO,NULL +maize_RMA_linear,8,data_bot_id,varchar(30),NO,NULL +maize_RMA_log,8,data_bot_id,varchar(30),NO,NULL +maize_atlas,5,data_bot_id,varchar(40),NO,NULL +maize_atlas_v5,5,data_bot_id,varchar(40),NO,NULL +maize_buell_lab,5,data_bot_id,varchar(50),NO,NULL +maize_early_seed,5,data_bot_id,varchar(50),NO,NULL +maize_ears,8,data_bot_id,varchar(16),NO,NULL +maize_embryonic_leaf_development,5,data_bot_id,varchar(24),NO,NULL +maize_enzyme,8,data_bot_id,varchar(8),NO,NULL +maize_gdowns,5,data_bot_id,varchar(40),NO,NULL +maize_iplant,8,data_bot_id,varchar(16),NO,NULL +maize_kernel_v5,5,data_bot_id,varchar(8),NO,NULL +maize_leaf_gradient,8,data_bot_id,varchar(12),NO,NULL +maize_lipid_map,5,data_bot_id,varchar(12),NO,NULL +maize_metabolite,8,data_bot_id,varchar(5),NO,NULL +maize_nitrogen_use_efficiency,5,data_bot_id,varchar(24),NO,NULL +maize_rice_comparison,8,data_bot_id,varchar(12),NO,NULL +maize_root,5,data_bot_id,varchar(255),NO,NULL +maize_stress_v5,5,data_bot_id,varchar(20),NO,NULL +mangosteen_aril_vs_rind,5,data_bot_id,varchar(8),NO,NULL +mangosteen_callus,5,data_bot_id,varchar(8),NO,NULL +mangosteen_diseased_vs_normal,5,data_bot_id,varchar(12),NO,NULL +mangosteen_fruit_ripening,5,data_bot_id,varchar(8),NO,NULL +mangosteen_seed_development,5,data_bot_id,varchar(12),NO,NULL +mangosteen_seed_development_germination,5,data_bot_id,varchar(8),NO,NULL +mangosteen_seed_germination,5,data_bot_id,varchar(12),NO,NULL +marchantia_organ_stress,5,data_bot_id,varchar(32),NO,NULL +medicago_mas,8,data_bot_id,varchar(22),NO,NULL +medicago_rma,8,data_bot_id,varchar(22),NO,NULL +medicago_root,6,data_bot_id,varchar(16),NO,NULL +medicago_root_v5,5,data_bot_id,varchar(16),NO,NULL +medicago_seed,6,data_bot_id,varchar(15),NO,NULL +meristem_db,6,data_bot_id,varchar(18),NO,NULL +meristem_db_new,6,data_bot_id,tinytext,NO,NULL +mouse_db,3,data_bot_id,varchar(18),NO,NULL +oat,8,data_bot_id,varchar(24),NO,NULL +phelipanche,5,data_bot_id,varchar(32),NO,NULL +physcomitrella_db,5,data_bot_id,varchar(40),NO,NULL +poplar,9,data_bot_id,varchar(40),YES,NULL +poplar_hormone,5,data_bot_id,varchar(12),NO,NULL +poplar_leaf,5,data_bot_id,varchar(40),YES,NULL +poplar_xylem,5,data_bot_id,varchar(40),YES,NULL +potato_dev,5,data_bot_id,varchar(15),NO,NULL +potato_stress,5,data_bot_id,varchar(12),NO,NULL +potato_wounding,5,data_bot_id,varchar(12),NO,NULL +rice_abiotic_stress_sc_pseudobulk,5,data_bot_id,varchar(64),NO,NULL +rice_drought_heat_stress,5,data_bot_id,varchar(12),NO,NULL +rice_leaf_gradient,8,data_bot_id,varchar(12),NO,NULL +rice_maize_comparison,8,data_bot_id,varchar(12),NO,NULL +rice_mas,8,data_bot_id,varchar(26),NO,NULL +rice_metabolite,8,data_bot_id,varchar(6),NO,NULL +rice_rma,8,data_bot_id,varchar(26),NO,NULL +rice_root,5,data_bot_id,varchar(8),NO,NULL +rohan,8,data_bot_id,tinytext,NO,NULL +root,8,data_bot_id,varchar(24),NO,NULL +root_Schaefer_lab,5,data_bot_id,varchar(20),YES,NULL +rpatel,8,data_bot_id,tinytext,NO,NULL +seed_db,8,data_bot_id,varchar(64),NO,NULL +seedcoat,8,data_bot_id,varchar(12),NO,NULL +selaginella,5,data_bot_id,varchar(36),NO,NULL +shoot_apex,8,data_bot_id,varchar(8),NO,NULL +silique,5,data_bot_id,varchar(64),NO,NULL +single_cell,5,data_bot_id,varchar(32),NO,NULL +sorghum_atlas_w_BS_cells,5,data_bot_id,varchar(24),NO,NULL +sorghum_comparative_transcriptomics,5,data_bot_id,varchar(40),NO,NULL +sorghum_developmental,5,data_bot_id,varchar(12),NO,NULL +sorghum_developmental_2,5,data_bot_id,varchar(32),NO,NULL +sorghum_flowering_activation,5,data_bot_id,varchar(32),NO,NULL +sorghum_low_phosphorus,5,data_bot_id,varchar(16),NO,NULL +sorghum_nitrogen_stress,5,data_bot_id,varchar(32),NO,NULL +sorghum_nitrogen_use_efficiency,5,data_bot_id,varchar(12),NO,NULL +sorghum_phosphate_stress,5,data_bot_id,varchar(32),NO,NULL +sorghum_plasma,5,data_bot_id,varchar(16),NO,NULL +sorghum_saline_alkali_stress,5,data_bot_id,varchar(32),NO,NULL +sorghum_stress,5,data_bot_id,varchar(12),NO,NULL +sorghum_strigolactone_variation,5,data_bot_id,varchar(32),NO,NULL +sorghum_sulfur_stress,5,data_bot_id,varchar(32),NO,NULL +sorghum_temperature_stress,5,data_bot_id,varchar(32),NO,NULL +sorghum_vascularization_and_internode,5,data_bot_id,varchar(32),NO,NULL +soybean,8,data_bot_id,varchar(22),NO,NULL +soybean_embryonic_development,5,data_bot_id,varchar(42),NO,NULL +soybean_heart_cotyledon_globular,5,data_bot_id,varchar(42),NO,NULL +soybean_senescence,5,data_bot_id,varchar(8),NO,NULL +soybean_severin,8,data_bot_id,varchar(18),NO,NULL +spruce,5,data_bot_id,varchar(24),NO,NULL +strawberry,5,data_bot_id,varchar(24),NO,NULL +striga,5,data_bot_id,varchar(42),NO,NULL +sugarcane_culms,5,data_bot_id,varchar(16),YES,NULL +sugarcane_leaf,5,data_bot_id,varchar(32),YES,NULL +sunflower,5,data_bot_id,varchar(16),YES,NULL +thellungiella_db,6,data_bot_id,varchar(40),NO,NULL +tomato,8,data_bot_id,varchar(18),YES,NULL +tomato_ils,6,data_bot_id,varchar(12),YES,NULL +tomato_ils2,6,data_bot_id,varchar(12),YES,NULL +tomato_ils3,6,data_bot_id,varchar(16),YES,NULL +tomato_meristem,5,data_bot_id,varchar(24),YES,NULL +tomato_renormalized,8,data_bot_id,varchar(18),YES,NULL +tomato_root,5,data_bot_id,varchar(12),YES,NULL +tomato_root_field_pot,5,data_bot_id,varchar(12),YES,NULL +tomato_s_pennellii,6,data_bot_id,varchar(24),YES,NULL +tomato_seed,5,data_bot_id,varchar(16),NO,NULL +tomato_shade_mutants,5,data_bot_id,varchar(20),NO,NULL +tomato_shade_timecourse,5,data_bot_id,varchar(16),NO,NULL +tomato_trait,8,data_bot_id,tinytext,NO,NULL +triphysaria,5,data_bot_id,varchar(32),NO,NULL +triticale,8,data_bot_id,varchar(18),NO,NULL +triticale_mas,8,data_bot_id,varchar(30),NO,NULL +tung_tree,5,data_bot_id,varchar(16),YES,NULL +wheat,5,data_bot_id,varchar(16),NO,NULL +wheat_abiotic_stress,5,data_bot_id,varchar(16),NO,NULL +wheat_embryogenesis,5,data_bot_id,varchar(50),NO,NULL +wheat_meiosis,5,data_bot_id,varchar(24),NO,NULL +wheat_root,5,data_bot_id,varchar(16),NO,NULL +willow,5,data_bot_id,varchar(16),NO,NULL +affydb,7,data_call,tinytext,NO,NULL +arabidopsis_ecotypes,6,data_call,tinytext,YES,NULL +atgenexp,6,data_call,tinytext,NO,NULL +atgenexp_hormone,5,data_call,tinytext,YES,NULL +atgenexp_pathogen,5,data_call,tinytext,YES,NULL +atgenexp_plus,6,data_call,tinytext,YES,NULL +atgenexp_stress,5,data_call,varchar(20),YES,NULL +barley_mas,6,data_call,tinytext,YES,NULL +barley_rma,6,data_call,tinytext,YES,NULL +canola,6,data_call,tinytext,YES,NULL +canola_original,6,data_call,tinytext,YES,NULL +canola_original_v2,6,data_call,tinytext,YES,NULL +grape_developmental,6,data_call,tinytext,NO,NULL +guard_cell,6,data_call,tinytext,YES,NULL +human_body_map_2,6,data_call,tinytext,YES,NULL +human_developmental,6,data_call,tinytext,YES,NULL +human_developmental_SpongeLab,6,data_call,tinytext,YES,NULL +human_diseased,6,data_call,tinytext,YES,NULL +klepikova,6,data_call,varchar(2),YES,NULL +light_series,6,data_call,tinytext,YES,NULL +maize_RMA_linear,6,data_call,tinytext,YES,NULL +maize_RMA_log,6,data_call,tinytext,YES,NULL +maize_ears,6,data_call,tinytext,YES,NULL +maize_enzyme,6,data_call,tinytext,YES,NULL +maize_iplant,6,data_call,tinytext,YES,NULL +maize_leaf_gradient,6,data_call,tinytext,YES,NULL +maize_metabolite,6,data_call,tinytext,YES,NULL +maize_rice_comparison,6,data_call,tinytext,YES,NULL +medicago_mas,6,data_call,tinytext,YES,NULL +medicago_rma,6,data_call,tinytext,YES,NULL +poplar,7,data_call,varchar(12),NO,NULL +rice_leaf_gradient,6,data_call,tinytext,YES,NULL +rice_maize_comparison,6,data_call,tinytext,YES,NULL +rice_mas,6,data_call,tinytext,YES,NULL +rice_metabolite,6,data_call,tinytext,YES,NULL +rice_rma,6,data_call,tinytext,YES,NULL +rohan,6,data_call,tinytext,YES,NULL +root,6,data_call,tinytext,YES,NULL +rpatel,6,data_call,tinytext,YES,NULL +seed_db,6,data_call,varchar(40),YES,NULL +seedcoat,6,data_call,tinytext,YES,NULL +shoot_apex,6,data_call,varchar(2),YES,NULL +soybean,6,data_call,tinytext,NO,NULL +soybean_severin,6,data_call,tinytext,NO,NULL +tomato,6,data_call,tinytext,YES,NULL +tomato_renormalized,6,data_call,tinytext,YES,NULL 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+grape_developmental,3,sample_file_name,tinytext,NO,NULL +guard_cell,3,sample_file_name,tinytext,YES,NULL +hnahal,3,sample_file_name,tinytext,YES,NULL +human_body_map_2,3,sample_file_name,tinytext,YES,NULL +human_developmental,3,sample_file_name,tinytext,YES,NULL +human_developmental_SpongeLab,3,sample_file_name,tinytext,YES,NULL +human_diseased,3,sample_file_name,tinytext,YES,NULL +lateral_root_initiation,3,sample_file_name,varchar(80),YES,NULL +light_series,3,sample_file_name,tinytext,YES,NULL +maize_RMA_linear,3,sample_file_name,tinytext,YES,NULL +maize_RMA_log,3,sample_file_name,tinytext,YES,NULL +maize_ears,3,sample_file_name,tinytext,YES,NULL +maize_enzyme,3,sample_file_name,tinytext,YES,NULL +maize_iplant,3,sample_file_name,tinytext,YES,NULL +maize_leaf_gradient,3,sample_file_name,tinytext,YES,NULL +maize_metabolite,3,sample_file_name,tinytext,YES,NULL +maize_rice_comparison,3,sample_file_name,tinytext,YES,NULL +medicago_mas,3,sample_file_name,tinytext,YES,NULL +medicago_rma,3,sample_file_name,tinytext,YES,NULL +meristem_db,3,sample_file_name,tinytext,YES,NULL +meristem_db_new,3,sample_file_name,tinytext,YES,NULL +poplar,3,sample_file_name,varchar(40),NO,NULL +rice_leaf_gradient,3,sample_file_name,tinytext,YES,NULL +rice_maize_comparison,3,sample_file_name,tinytext,YES,NULL +rice_mas,3,sample_file_name,tinytext,YES,NULL +rice_metabolite,3,sample_file_name,tinytext,YES,NULL +rice_rma,3,sample_file_name,tinytext,YES,NULL +rohan,3,sample_file_name,tinytext,YES,NULL +root,3,sample_file_name,tinytext,YES,NULL +rpatel,3,sample_file_name,tinytext,YES,NULL +seed_db,3,sample_file_name,varchar(100),YES,NULL +seedcoat,3,sample_file_name,tinytext,YES,NULL +shoot_apex,3,sample_file_name,varchar(16),YES,NULL +soybean,3,sample_file_name,tinytext,NO,NULL +soybean_severin,3,sample_file_name,tinytext,NO,NULL +thellungiella_db,3,sample_file_name,varchar(80),YES,NULL +tomato,3,sample_file_name,tinytext,YES,NULL +tomato_renormalized,3,sample_file_name,tinytext,YES,NULL +tomato_trait,3,sample_file_name,tinytext,YES,NULL +triticale,3,sample_file_name,tinytext,YES,NULL +triticale_mas,3,sample_file_name,tinytext,YES,NULL +actinidia_bud_development,2,sample_id,int unsigned,NO,0 +actinidia_flower_fruit_development,2,sample_id,int unsigned,NO,0 +actinidia_postharvest,2,sample_id,int unsigned,NO,0 +actinidia_vegetative_growth,2,sample_id,int unsigned,NO,0 +affydb,1,sample_id,int unsigned,NO,0 +apple,1,sample_id,int unsigned,NO,0 +arabidopsis_ecotypes,1,sample_id,int unsigned,NO,0 +arachis,1,sample_id,varchar(5),NO,NULL +atgenexp,1,sample_id,int unsigned,NO,0 +atgenexp_hormone,1,sample_id,int unsigned,NO,0 +atgenexp_pathogen,1,sample_id,int unsigned,NO,0 +atgenexp_plus,1,sample_id,int unsigned,NO,0 +atgenexp_stress,1,sample_id,int unsigned,NO,0 +barley_mas,1,sample_id,int unsigned,NO,0 +barley_rma,1,sample_id,int unsigned,NO,0 +barley_seed,2,sample_id,int unsigned,NO,0 +barley_spike_meristem,2,sample_id,int unsigned,NO,0 +barley_spike_meristem_v3,2,sample_id,int unsigned,NO,0 +brachypodium,2,sample_id,int unsigned,NO,0 +brachypodium_Bd21,2,sample_id,int unsigned,NO,0 +brachypodium_embryogenesis,2,sample_id,int unsigned,NO,0 +brachypodium_grains,2,sample_id,int unsigned,NO,0 +brachypodium_metabolites_map,2,sample_id,int unsigned,NO,0 +brachypodium_photo_thermocycle,2,sample_id,int unsigned,NO,0 +brassica_rapa,1,sample_id,int unsigned,NO,0 +cacao_developmental_atlas,1,sample_id,int unsigned,NO,0 +cacao_developmental_atlas_sca,1,sample_id,int unsigned,NO,0 +cacao_drought_diurnal_atlas,1,sample_id,int unsigned,NO,0 +cacao_drought_diurnal_atlas_sca,1,sample_id,int unsigned,NO,0 +cacao_infection,1,sample_id,int unsigned,NO,0 +cacao_leaf,1,sample_id,int unsigned,NO,0 +cacao_meristem_atlas_sca,1,sample_id,int unsigned,NO,0 +cacao_seed_atlas_sca,1,sample_id,int unsigned,NO,0 +camelina,1,sample_id,varchar(5),NO,NULL +camelina_tpm,1,sample_id,varchar(5),NO,NULL +cannabis,2,sample_id,int unsigned,NO,0 +canola,1,sample_id,int unsigned,NO,0 +canola_original,1,sample_id,int unsigned,NO,0 +canola_original_v2,1,sample_id,int unsigned,NO,0 +canola_seed,2,sample_id,int unsigned,NO,0 +cassava_atlas,2,sample_id,int unsigned,NO,0 +cassava_cbb,2,sample_id,int unsigned,NO,0 +cassava_eacmv,2,sample_id,int unsigned,NO,0 +circadian_mutants,2,sample_id,int unsigned,NO,0 +cuscuta,1,sample_id,int unsigned,NO,0 +cuscuta_early_haustoriogenesis,2,sample_id,int unsigned,NO,0 +cuscuta_lmd,2,sample_id,int unsigned,NO,0 +dna_damage,1,sample_id,int unsigned,NO,0 +durum_wheat_abiotic_stress,2,sample_id,int unsigned,NO,0 +durum_wheat_biotic_stress,2,sample_id,int unsigned,NO,0 +durum_wheat_development,2,sample_id,int unsigned,NO,0 +embryo,2,sample_id,int unsigned,NO,0 +eucalyptus,2,sample_id,int unsigned,NO,0 +euphorbia,2,sample_id,int unsigned,NO,0 +gc_drought,2,sample_id,int unsigned,NO,0 +germination,2,sample_id,int unsigned,NO,0 +grape_developmental,1,sample_id,int,NO,NULL +guard_cell,1,sample_id,int unsigned,NO,0 +gynoecium,2,sample_id,int unsigned,NO,0 +heterodera_schachtii,2,sample_id,int unsigned,NO,0 +hnahal,1,sample_id,int unsigned,NO,0 +human_body_map_2,1,sample_id,int unsigned,NO,0 +human_developmental,1,sample_id,int unsigned,NO,0 +human_developmental_SpongeLab,1,sample_id,int unsigned,NO,0 +human_diseased,1,sample_id,int unsigned,NO,0 +kalanchoe,2,sample_id,int unsigned,NO,0 +kalanchoe_time_course_analysis,2,sample_id,int unsigned,NO,0 +klepikova,2,sample_id,int unsigned,NO,0 +lateral_root_initiation,1,sample_id,varchar(30),NO,NULL +light_series,1,sample_id,int unsigned,NO,0 +lipid_map,2,sample_id,int unsigned,NO,0 +little_millet,1,sample_id,int unsigned,NO,0 +lupin_lcm_leaf,2,sample_id,int unsigned,NO,0 +lupin_lcm_pod,2,sample_id,int unsigned,NO,0 +lupin_lcm_stem,2,sample_id,int unsigned,NO,0 +lupin_pod_seed,2,sample_id,int unsigned,NO,0 +lupin_whole_plant,2,sample_id,int unsigned,NO,0 +maize_RMA_linear,1,sample_id,int unsigned,NO,0 +maize_RMA_log,1,sample_id,int unsigned,NO,0 +maize_atlas,1,sample_id,varchar(5),NO,NULL +maize_atlas_v5,2,sample_id,int unsigned,NO,0 +maize_buell_lab,1,sample_id,int unsigned,NO,0 +maize_early_seed,1,sample_id,int unsigned,NO,0 +maize_ears,1,sample_id,int unsigned,NO,0 +maize_embryonic_leaf_development,2,sample_id,int unsigned,NO,0 +maize_enzyme,1,sample_id,int unsigned,NO,0 +maize_gdowns,1,sample_id,varchar(30),NO,NULL +maize_iplant,1,sample_id,int unsigned,NO,0 +maize_kernel_v5,2,sample_id,int unsigned,NO,0 +maize_leaf_gradient,1,sample_id,int unsigned,NO,0 +maize_lipid_map,2,sample_id,int unsigned,NO,0 +maize_metabolite,1,sample_id,int unsigned,NO,0 +maize_nitrogen_use_efficiency,2,sample_id,int unsigned,NO,0 +maize_rice_comparison,1,sample_id,int unsigned,NO,0 +maize_root,1,sample_id,int unsigned,NO,0 +maize_stress_v5,2,sample_id,int unsigned,NO,0 +mangosteen_aril_vs_rind,2,sample_id,int unsigned,NO,0 +mangosteen_callus,2,sample_id,int unsigned,NO,0 +mangosteen_diseased_vs_normal,2,sample_id,int unsigned,NO,0 +mangosteen_fruit_ripening,2,sample_id,int unsigned,NO,0 +mangosteen_seed_development,2,sample_id,int unsigned,NO,0 +mangosteen_seed_development_germination,2,sample_id,int unsigned,NO,0 +mangosteen_seed_germination,2,sample_id,int unsigned,NO,0 +marchantia_organ_stress,2,sample_id,int unsigned,NO,0 +medicago_mas,1,sample_id,int unsigned,NO,0 +medicago_rma,1,sample_id,int unsigned,NO,0 +medicago_root,1,sample_id,int unsigned,NO,0 +medicago_root_v5,1,sample_id,int unsigned,NO,0 +medicago_seed,1,sample_id,int unsigned,NO,0 +meristem_db,1,sample_id,int unsigned,NO,0 +meristem_db_new,1,sample_id,int unsigned,NO,0 +oat,1,sample_id,int unsigned,NO,0 +phelipanche,2,sample_id,int unsigned,NO,0 +physcomitrella_db,1,sample_id,varchar(30),NO, +poplar,1,sample_id,int unsigned,NO,0 +poplar_hormone,2,sample_id,int unsigned,NO,0 +poplar_leaf,1,sample_id,int unsigned,NO,0 +poplar_xylem,1,sample_id,int unsigned,NO,0 +potato_dev,1,sample_id,int unsigned,NO,0 +potato_stress,1,sample_id,int unsigned,NO,0 +potato_wounding,1,sample_id,int unsigned,NO,0 +rice_abiotic_stress_sc_pseudobulk,2,sample_id,int unsigned,NO,0 +rice_drought_heat_stress,2,sample_id,int unsigned,NO,0 +rice_leaf_gradient,1,sample_id,int unsigned,NO,0 +rice_maize_comparison,1,sample_id,int unsigned,NO,0 +rice_mas,1,sample_id,int unsigned,NO,0 +rice_metabolite,1,sample_id,int unsigned,NO,0 +rice_rma,1,sample_id,int unsigned,NO,0 +rice_root,1,sample_id,int unsigned,NO,0 +rohan,1,sample_id,int unsigned,NO,0 +root,1,sample_id,int unsigned,NO,0 +root_Schaefer_lab,1,sample_id,int unsigned,NO,0 +rpatel,1,sample_id,int unsigned,NO,0 +seed_db,1,sample_id,int unsigned,NO,0 +seedcoat,1,sample_id,int unsigned,NO,0 +selaginella,1,sample_id,int unsigned,NO,0 +shoot_apex,1,sample_id,int unsigned,NO,0 +silique,2,sample_id,int unsigned,NO,0 +single_cell,2,sample_id,int unsigned,NO,0 +sorghum_atlas_w_BS_cells,2,sample_id,int unsigned,NO,0 +sorghum_comparative_transcriptomics,2,sample_id,int unsigned,NO,0 +sorghum_developmental,2,sample_id,int unsigned,NO,0 +sorghum_developmental_2,2,sample_id,int unsigned,NO,0 +sorghum_flowering_activation,2,sample_id,int unsigned,NO,0 +sorghum_low_phosphorus,2,sample_id,int unsigned,NO,0 +sorghum_nitrogen_stress,2,sample_id,int unsigned,NO,0 +sorghum_nitrogen_use_efficiency,2,sample_id,int unsigned,NO,0 +sorghum_phosphate_stress,2,sample_id,int unsigned,NO,0 +sorghum_plasma,2,sample_id,int unsigned,NO,0 +sorghum_saline_alkali_stress,2,sample_id,int unsigned,NO,0 +sorghum_stress,2,sample_id,int unsigned,NO,0 +sorghum_strigolactone_variation,2,sample_id,int unsigned,NO,0 +sorghum_sulfur_stress,2,sample_id,int unsigned,NO,0 +sorghum_temperature_stress,2,sample_id,int unsigned,NO,0 +sorghum_vascularization_and_internode,2,sample_id,int unsigned,NO,0 +soybean,1,sample_id,int,NO,NULL +soybean_embryonic_development,2,sample_id,int unsigned,NO,0 +soybean_heart_cotyledon_globular,2,sample_id,int unsigned,NO,0 +soybean_senescence,2,sample_id,int unsigned,NO,0 +soybean_severin,1,sample_id,int,NO,NULL +spruce,2,sample_id,int unsigned,NO,0 +strawberry,2,sample_id,int unsigned,NO,0 +striga,2,sample_id,int unsigned,NO,0 +sugarcane_culms,1,sample_id,int unsigned,NO,0 +sugarcane_leaf,1,sample_id,int unsigned,NO,0 +sunflower,1,sample_id,int unsigned,NO,0 +thellungiella_db,1,sample_id,varchar(30),NO,NULL +tomato,1,sample_id,int unsigned,NO,0 +tomato_ils,1,sample_id,int unsigned,NO,0 +tomato_ils2,1,sample_id,int unsigned,NO,0 +tomato_ils3,1,sample_id,int unsigned,NO,0 +tomato_meristem,1,sample_id,int unsigned,NO,0 +tomato_renormalized,1,sample_id,int unsigned,NO,0 +tomato_root,1,sample_id,int unsigned,NO,0 +tomato_root_field_pot,1,sample_id,int unsigned,NO,0 +tomato_s_pennellii,1,sample_id,int unsigned,NO,0 +tomato_seed,2,sample_id,int unsigned,NO,0 +tomato_shade_mutants,2,sample_id,int unsigned,NO,0 +tomato_shade_timecourse,2,sample_id,int unsigned,NO,0 +tomato_trait,1,sample_id,int unsigned,NO,0 +triphysaria,2,sample_id,int unsigned,NO,0 +triticale,1,sample_id,int unsigned,NO,0 +triticale_mas,1,sample_id,int unsigned,NO,0 +tung_tree,1,sample_id,int unsigned,NO,0 +wheat,2,sample_id,int unsigned,NO,0 +wheat_abiotic_stress,2,sample_id,int unsigned,NO,0 +wheat_embryogenesis,2,sample_id,int unsigned,NO,0 +wheat_meiosis,2,sample_id,int unsigned,NO,0 +wheat_root,2,sample_id,int unsigned,NO,0 +willow,2,sample_id,int unsigned,NO,0 +barley_mas,9,sample_tissue,varchar(20),YES,NULL +canola,9,sample_tissue,text,NO,NULL +canola_original,9,sample_tissue,text,NO,NULL +canola_original_v2,9,sample_tissue,text,NO,NULL +grape_developmental,9,sample_tissue,text,NO,NULL +maize_RMA_linear,9,sample_tissue,text,NO,NULL +medicago_mas,9,sample_tissue,text,NO,NULL +rice_mas,9,sample_tissue,text,NO,NULL +oat,3,version,varchar(2),NO,NULL diff --git a/api/Archive/efp_tables_structure_sample_data_dump_01_28_25.sql b/api/Archive/efp_tables_structure_sample_data_dump_01_28_25.sql new file mode 100644 index 0000000..f0133c2 --- /dev/null +++ b/api/Archive/efp_tables_structure_sample_data_dump_01_28_25.sql @@ -0,0 +1,1128 @@ +database_name ORDINAL_POSITION COLUMN_NAME COLUMN_TYPE IS_NULLABLE COLUMN_DEFAULT +hnahal 7 channel varchar(5) YES NULL +meristem_db 7 channel varchar(5) YES NULL +meristem_db_new 7 channel varchar(5) YES NULL +actinidia_bud_development 5 data_bot_id varchar(8) NO NULL +actinidia_flower_fruit_development 5 data_bot_id varchar(16) NO NULL +actinidia_postharvest 5 data_bot_id varchar(24) NO NULL +actinidia_vegetative_growth 5 data_bot_id varchar(16) NO NULL +affydb 9 data_bot_id tinytext YES NULL +apple 5 data_bot_id varchar(12) YES NULL +arabidopsis_ecotypes 8 data_bot_id varchar(16) YES NULL +arachis 5 data_bot_id varchar(65) NO NULL +atgenexp 8 data_bot_id varchar(50) NO NULL +atgenexp_hormone 7 data_bot_id varchar(50) YES NULL +atgenexp_pathogen 7 data_bot_id varchar(50) YES NULL +atgenexp_plus 8 data_bot_id varchar(50) NO NULL +atgenexp_stress 7 data_bot_id varchar(40) YES NULL +barley_mas 8 data_bot_id varchar(24) NO NULL +barley_rma 8 data_bot_id varchar(24) NO NULL +barley_seed 5 data_bot_id varchar(12) NO NULL +barley_spike_meristem 5 data_bot_id varchar(24) NO NULL +barley_spike_meristem_v3 5 data_bot_id varchar(24) NO NULL +brachypodium 5 data_bot_id varchar(50) NO NULL +brachypodium_Bd21 5 data_bot_id varchar(32) NO NULL +brachypodium_embryogenesis 5 data_bot_id varchar(50) NO NULL +brachypodium_grains 5 data_bot_id varchar(32) NO NULL +brachypodium_metabolites_map 5 data_bot_id varchar(45) NO NULL +brachypodium_photo_thermocycle 5 data_bot_id varchar(12) NO NULL +brassica_rapa 5 data_bot_id varchar(10) YES NULL +cacao_developmental_atlas 5 data_bot_id varchar(16) YES NULL +cacao_developmental_atlas_sca 5 data_bot_id varchar(16) YES NULL +cacao_drought_diurnal_atlas 5 data_bot_id varchar(16) YES NULL +cacao_drought_diurnal_atlas_sca 5 data_bot_id varchar(16) YES NULL +cacao_infection 5 data_bot_id varchar(24) YES NULL +cacao_leaf 5 data_bot_id varchar(12) YES NULL +cacao_meristem_atlas_sca 5 data_bot_id varchar(24) YES NULL +cacao_seed_atlas_sca 5 data_bot_id varchar(24) YES NULL +camelina 6 data_bot_id varchar(40) NO NULL +camelina_tpm 6 data_bot_id varchar(40) NO NULL +cannabis 5 data_bot_id varchar(8) NO NULL +canola 8 data_bot_id tinytext NO NULL +canola_original 8 data_bot_id tinytext NO NULL +canola_original_v2 8 data_bot_id tinytext NO NULL +canola_seed 5 data_bot_id varchar(12) NO NULL +cassava_atlas 5 data_bot_id varchar(24) NO NULL +cassava_cbb 5 data_bot_id varchar(24) NO NULL +cassava_eacmv 5 data_bot_id varchar(24) NO NULL +circadian_mutants 5 data_bot_id varchar(18) NO NULL +cuscuta 5 data_bot_id varchar(12) YES NULL +cuscuta_early_haustoriogenesis 5 data_bot_id varchar(8) NO NULL +cuscuta_lmd 5 data_bot_id varchar(8) NO NULL +dna_damage 5 data_bot_id varchar(32) YES NULL +durum_wheat_abiotic_stress 5 data_bot_id varchar(32) NO NULL +durum_wheat_biotic_stress 5 data_bot_id varchar(42) NO NULL +durum_wheat_development 5 data_bot_id varchar(24) NO NULL +embryo 5 data_bot_id varchar(8) NO NULL +eucalyptus 5 data_bot_id varchar(42) NO NULL +euphorbia 5 data_bot_id varchar(24) NO NULL +gc_drought 5 data_bot_id varchar(12) NO NULL +germination 5 data_bot_id varchar(16) NO NULL +grape_developmental 8 data_bot_id varchar(50) NO NULL +guard_cell 8 data_bot_id varchar(24) NO NULL +gynoecium 5 data_bot_id varchar(16) NO NULL +heterodera_schachtii 5 data_bot_id varchar(16) NO NULL +hnahal 6 data_bot_id tinytext NO NULL +human_body_map_2 8 data_bot_id varchar(20) NO NULL +human_developmental 8 data_bot_id varchar(24) YES NULL +human_developmental_SpongeLab 8 data_bot_id tinytext NO NULL +human_diseased 8 data_bot_id tinytext NO NULL +kalanchoe 5 data_bot_id varchar(16) NO NULL +kalanchoe_time_course_analysis 5 data_bot_id varchar(16) NO NULL +klepikova 5 data_bot_id varchar(16) NO NULL +lateral_root_initiation 6 data_bot_id varchar(64) YES NULL +light_series 8 data_bot_id varchar(30) NO NULL +lipid_map 5 data_bot_id varchar(16) NO NULL +little_millet 5 data_bot_id varchar(12) YES NULL +lupin_lcm_leaf 5 data_bot_id varchar(32) NO NULL +lupin_lcm_pod 5 data_bot_id varchar(32) NO NULL +lupin_lcm_stem 5 data_bot_id varchar(32) NO NULL +lupin_pod_seed 5 data_bot_id varchar(32) NO NULL +lupin_whole_plant 5 data_bot_id varchar(32) NO NULL +maize_RMA_linear 8 data_bot_id varchar(30) NO NULL +maize_RMA_log 8 data_bot_id varchar(30) NO NULL +maize_atlas 5 data_bot_id varchar(40) NO NULL +maize_atlas_v5 5 data_bot_id varchar(40) NO NULL +maize_buell_lab 5 data_bot_id varchar(50) NO NULL +maize_early_seed 5 data_bot_id varchar(50) NO NULL +maize_ears 8 data_bot_id varchar(16) NO NULL +maize_embryonic_leaf_development 5 data_bot_id varchar(24) NO NULL +maize_enzyme 8 data_bot_id varchar(8) NO NULL +maize_gdowns 5 data_bot_id varchar(40) NO NULL +maize_iplant 8 data_bot_id varchar(16) NO NULL +maize_kernel_v5 5 data_bot_id varchar(8) NO NULL +maize_leaf_gradient 8 data_bot_id varchar(12) NO NULL +maize_lipid_map 5 data_bot_id varchar(12) NO NULL +maize_metabolite 8 data_bot_id varchar(5) NO NULL +maize_nitrogen_use_efficiency 5 data_bot_id varchar(24) NO NULL +maize_rice_comparison 8 data_bot_id varchar(12) NO NULL +maize_root 5 data_bot_id varchar(255) NO NULL +maize_stress_v5 5 data_bot_id varchar(20) NO NULL +mangosteen_aril_vs_rind 5 data_bot_id varchar(8) NO NULL +mangosteen_callus 5 data_bot_id varchar(8) NO NULL +mangosteen_diseased_vs_normal 5 data_bot_id varchar(12) NO NULL +mangosteen_fruit_ripening 5 data_bot_id varchar(8) NO NULL +mangosteen_seed_development 5 data_bot_id varchar(12) NO NULL +mangosteen_seed_development_germination 5 data_bot_id varchar(8) NO NULL +mangosteen_seed_germination 5 data_bot_id varchar(12) NO NULL +marchantia_organ_stress 5 data_bot_id varchar(32) NO NULL +medicago_mas 8 data_bot_id varchar(22) NO NULL +medicago_rma 8 data_bot_id varchar(22) NO NULL +medicago_root 6 data_bot_id varchar(16) NO NULL +medicago_root_v5 5 data_bot_id varchar(16) NO NULL +medicago_seed 6 data_bot_id varchar(15) NO NULL +meristem_db 6 data_bot_id varchar(18) NO NULL +meristem_db_new 6 data_bot_id tinytext NO NULL +mouse_db 3 data_bot_id varchar(18) NO NULL +oat 8 data_bot_id varchar(24) NO NULL +phelipanche 5 data_bot_id varchar(32) NO NULL +physcomitrella_db 5 data_bot_id varchar(40) NO NULL +poplar 9 data_bot_id varchar(40) YES NULL +poplar_hormone 5 data_bot_id varchar(12) NO NULL +poplar_leaf 5 data_bot_id varchar(40) YES NULL +poplar_xylem 5 data_bot_id varchar(40) YES NULL +potato_dev 5 data_bot_id varchar(15) NO NULL +potato_stress 5 data_bot_id varchar(12) NO NULL +potato_wounding 5 data_bot_id varchar(12) NO NULL +rice_abiotic_stress_sc_pseudobulk 5 data_bot_id varchar(64) NO NULL +rice_drought_heat_stress 5 data_bot_id varchar(12) NO NULL +rice_leaf_gradient 8 data_bot_id varchar(12) NO NULL +rice_maize_comparison 8 data_bot_id varchar(12) NO NULL +rice_mas 8 data_bot_id varchar(26) NO NULL +rice_metabolite 8 data_bot_id varchar(6) NO NULL +rice_rma 8 data_bot_id varchar(26) NO NULL +rice_root 5 data_bot_id varchar(8) NO NULL +rohan 8 data_bot_id tinytext NO NULL +root 8 data_bot_id varchar(24) NO NULL +root_Schaefer_lab 5 data_bot_id varchar(20) YES NULL +rpatel 8 data_bot_id tinytext NO NULL +seed_db 8 data_bot_id varchar(64) NO NULL +seedcoat 8 data_bot_id varchar(12) NO NULL +selaginella 5 data_bot_id varchar(36) NO NULL +shoot_apex 8 data_bot_id varchar(8) NO NULL +silique 5 data_bot_id varchar(64) NO NULL +single_cell 5 data_bot_id varchar(32) NO NULL +sorghum_atlas_w_BS_cells 5 data_bot_id varchar(24) NO NULL +sorghum_comparative_transcriptomics 5 data_bot_id varchar(40) NO NULL +sorghum_developmental 5 data_bot_id varchar(12) NO NULL +sorghum_developmental_2 5 data_bot_id varchar(32) NO NULL +sorghum_flowering_activation 5 data_bot_id varchar(32) NO NULL +sorghum_low_phosphorus 5 data_bot_id varchar(16) NO NULL +sorghum_nitrogen_stress 5 data_bot_id varchar(32) NO NULL +sorghum_nitrogen_use_efficiency 5 data_bot_id varchar(12) NO NULL +sorghum_phosphate_stress 5 data_bot_id varchar(32) NO NULL +sorghum_plasma 5 data_bot_id varchar(16) NO NULL +sorghum_saline_alkali_stress 5 data_bot_id varchar(32) NO NULL +sorghum_stress 5 data_bot_id varchar(12) NO NULL +sorghum_strigolactone_variation 5 data_bot_id varchar(32) NO NULL +sorghum_sulfur_stress 5 data_bot_id varchar(32) NO NULL +sorghum_temperature_stress 5 data_bot_id varchar(32) NO NULL +sorghum_vascularization_and_internode 5 data_bot_id varchar(32) NO NULL +soybean 8 data_bot_id varchar(22) NO NULL +soybean_embryonic_development 5 data_bot_id varchar(42) NO NULL +soybean_heart_cotyledon_globular 5 data_bot_id varchar(42) NO NULL +soybean_senescence 5 data_bot_id varchar(8) NO NULL +soybean_severin 8 data_bot_id 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YES NULL +maize_metabolite 5 data_signal float YES 0 +maize_nitrogen_use_efficiency 4 data_signal float YES 0 +maize_rice_comparison 5 data_signal float YES 0 +maize_root 4 data_signal float YES 0 +maize_stress_v5 4 data_signal float YES 0 +mangosteen_aril_vs_rind 4 data_signal float YES 0 +mangosteen_callus 4 data_signal float YES 0 +mangosteen_diseased_vs_normal 4 data_signal float YES 0 +mangosteen_fruit_ripening 4 data_signal float YES 0 +mangosteen_seed_development 4 data_signal float YES 0 +mangosteen_seed_development_germination 4 data_signal float YES 0 +mangosteen_seed_germination 4 data_signal float YES 0 +marchantia_organ_stress 4 data_signal float YES 0 +medicago_mas 5 data_signal float YES 0 +medicago_rma 5 data_signal float YES 0 +medicago_root 4 data_signal float YES 0 +medicago_root_v5 4 data_signal float YES 0 +medicago_seed 4 data_signal float YES 0 +meristem_db 5 data_signal float YES 0 +meristem_db_new 5 data_signal float YES 0 +mouse_db 2 data_signal float NO 0 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0 +shoot_apex 5 data_signal float NO NULL +silique 4 data_signal float YES 0 +single_cell 4 data_signal float YES 0 +sorghum_atlas_w_BS_cells 4 data_signal float YES 0 +sorghum_comparative_transcriptomics 4 data_signal float YES 0 +sorghum_developmental 4 data_signal float YES 0 +sorghum_developmental_2 4 data_signal float YES 0 +sorghum_flowering_activation 4 data_signal float YES 0 +sorghum_low_phosphorus 4 data_signal float YES 0 +sorghum_nitrogen_stress 4 data_signal float YES 0 +sorghum_nitrogen_use_efficiency 4 data_signal float YES 0 +sorghum_phosphate_stress 4 data_signal float YES 0 +sorghum_plasma 4 data_signal float YES 0 +sorghum_saline_alkali_stress 4 data_signal float YES 0 +sorghum_stress 4 data_signal float YES 0 +sorghum_strigolactone_variation 4 data_signal float YES 0 +sorghum_sulfur_stress 4 data_signal float YES 0 +sorghum_temperature_stress 4 data_signal float YES 0 +sorghum_vascularization_and_internode 4 data_signal float YES 0 +soybean 5 data_signal float NO NULL +soybean_embryonic_development 4 data_signal float YES 0 +soybean_heart_cotyledon_globular 4 data_signal float YES 0 +soybean_senescence 4 data_signal float YES 0 +soybean_severin 5 data_signal float NO NULL +spruce 4 data_signal float YES 0 +strawberry 4 data_signal float YES 0 +striga 4 data_signal float YES 0 +sugarcane_culms 4 data_signal float NO 0 +sugarcane_leaf 4 data_signal float NO 0 +sunflower 4 data_signal float NO 0 +thellungiella_db 5 data_signal float NO NULL +tomato 5 data_signal float YES 0 +tomato_ils 4 data_signal float YES 0 +tomato_ils2 4 data_signal float YES 0 +tomato_ils3 4 data_signal float YES 0 +tomato_meristem 4 data_signal float YES 0 +tomato_renormalized 5 data_signal float YES 0 +tomato_root 4 data_signal float YES 0 +tomato_root_field_pot 4 data_signal float YES 0 +tomato_s_pennellii 4 data_signal float YES 0 +tomato_seed 4 data_signal float YES 0 +tomato_shade_mutants 4 data_signal float YES 0 +tomato_shade_timecourse 4 data_signal float YES 0 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NULL +atgenexp 2 proj_id int unsigned NO 0 +atgenexp_hormone 2 proj_id int unsigned NO 0 +atgenexp_pathogen 2 proj_id varchar(15) NO 0 +atgenexp_plus 2 proj_id varchar(15) NO 0 +atgenexp_stress 2 proj_id varchar(15) NO 0 +barley_mas 2 proj_id varchar(15) NO 0 +barley_rma 2 proj_id varchar(15) NO 0 +barley_seed 1 proj_id varchar(5) NO NULL +barley_spike_meristem 1 proj_id varchar(5) NO NULL +barley_spike_meristem_v3 1 proj_id varchar(5) NO NULL +brachypodium 1 proj_id varchar(5) NO NULL +brachypodium_Bd21 1 proj_id varchar(5) NO NULL +brachypodium_embryogenesis 1 proj_id varchar(5) NO NULL +brachypodium_grains 1 proj_id varchar(5) NO NULL +brachypodium_metabolites_map 1 proj_id varchar(5) NO NULL +brachypodium_photo_thermocycle 1 proj_id varchar(5) NO NULL +brassica_rapa 2 proj_id varchar(5) NO 0 +cacao_developmental_atlas 2 proj_id varchar(5) NO 0 +cacao_developmental_atlas_sca 2 proj_id varchar(5) NO 0 +cacao_drought_diurnal_atlas 2 proj_id varchar(5) NO 0 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NO NULL +mangosteen_aril_vs_rind 1 proj_id varchar(2) NO NULL +mangosteen_callus 1 proj_id varchar(2) NO NULL +mangosteen_diseased_vs_normal 1 proj_id varchar(2) NO NULL +mangosteen_fruit_ripening 1 proj_id varchar(2) NO NULL +mangosteen_seed_development 1 proj_id varchar(2) NO NULL +mangosteen_seed_development_germination 1 proj_id varchar(2) NO NULL +mangosteen_seed_germination 1 proj_id varchar(2) NO NULL +marchantia_organ_stress 1 proj_id varchar(5) NO NULL +medicago_mas 2 proj_id varchar(15) NO 0 +medicago_rma 2 proj_id varchar(15) NO 0 +medicago_root 2 proj_id varchar(5) NO NULL +medicago_root_v5 2 proj_id varchar(5) NO NULL +medicago_seed 2 proj_id varchar(5) NO NULL +meristem_db 2 proj_id varchar(15) NO 0 +meristem_db_new 2 proj_id varchar(15) NO 0 +phelipanche 1 proj_id varchar(5) NO NULL +physcomitrella_db 2 proj_id varchar(30) NO +poplar 2 proj_id varchar(15) NO 0 +poplar_hormone 1 proj_id varchar(5) NO NULL +poplar_leaf 2 proj_id varchar(5) NO 0 +poplar_xylem 2 proj_id varchar(5) NO 0 +potato_dev 2 proj_id varchar(15) NO 0 +potato_stress 2 proj_id varchar(15) NO 0 +potato_wounding 2 proj_id varchar(15) NO 0 +rice_abiotic_stress_sc_pseudobulk 1 proj_id varchar(5) NO NULL +rice_drought_heat_stress 1 proj_id varchar(5) NO NULL +rice_leaf_gradient 2 proj_id varchar(15) NO 0 +rice_maize_comparison 2 proj_id varchar(15) NO 0 +rice_mas 2 proj_id varchar(15) NO 0 +rice_metabolite 2 proj_id varchar(15) NO 0 +rice_rma 2 proj_id varchar(15) NO 0 +rice_root 2 proj_id varchar(2) NO 0 +rohan 2 proj_id varchar(15) NO 0 +root 2 proj_id varchar(15) NO 0 +root_Schaefer_lab 2 proj_id varchar(5) NO 0 +rpatel 2 proj_id varchar(15) NO 0 +seed_db 2 proj_id varchar(20) NO 0 +seedcoat 2 proj_id varchar(15) NO 0 +selaginella 2 proj_id varchar(5) NO 0 +shoot_apex 2 proj_id varchar(2) YES NULL +silique 1 proj_id varchar(5) NO NULL +single_cell 1 proj_id varchar(5) NO NULL +sorghum_atlas_w_BS_cells 1 proj_id varchar(5) NO NULL +sorghum_comparative_transcriptomics 1 proj_id varchar(5) NO NULL +sorghum_developmental 1 proj_id varchar(5) NO NULL +sorghum_developmental_2 1 proj_id varchar(5) NO NULL +sorghum_flowering_activation 1 proj_id varchar(5) NO NULL +sorghum_low_phosphorus 1 proj_id varchar(5) NO NULL +sorghum_nitrogen_stress 1 proj_id varchar(5) NO NULL +sorghum_nitrogen_use_efficiency 1 proj_id varchar(5) NO NULL +sorghum_phosphate_stress 1 proj_id varchar(5) NO NULL +sorghum_plasma 1 proj_id varchar(5) NO NULL +sorghum_saline_alkali_stress 1 proj_id varchar(5) NO NULL +sorghum_stress 1 proj_id varchar(5) NO NULL +sorghum_strigolactone_variation 1 proj_id varchar(5) NO NULL +sorghum_sulfur_stress 1 proj_id varchar(5) NO NULL +sorghum_temperature_stress 1 proj_id varchar(5) NO NULL +sorghum_vascularization_and_internode 1 proj_id varchar(5) NO NULL +soybean 2 proj_id varchar(15) NO NULL +soybean_embryonic_development 1 proj_id varchar(5) NO NULL +soybean_heart_cotyledon_globular 1 proj_id varchar(5) NO NULL +soybean_senescence 1 proj_id varchar(5) NO NULL +soybean_severin 2 proj_id varchar(15) NO NULL +spruce 1 proj_id varchar(5) NO NULL +strawberry 1 proj_id varchar(5) NO NULL +striga 1 proj_id varchar(5) NO NULL +sugarcane_culms 2 proj_id varchar(5) NO 0 +sugarcane_leaf 2 proj_id varchar(12) NO 0 +sunflower 2 proj_id varchar(5) NO 0 +thellungiella_db 2 proj_id varchar(30) NO NULL +tomato 2 proj_id varchar(15) NO 0 +tomato_ils 2 proj_id varchar(15) NO 0 +tomato_ils2 2 proj_id varchar(15) NO 0 +tomato_ils3 2 proj_id varchar(15) NO 0 +tomato_meristem 2 proj_id varchar(2) NO 0 +tomato_renormalized 2 proj_id varchar(15) NO 0 +tomato_root 2 proj_id varchar(2) NO 0 +tomato_root_field_pot 2 proj_id varchar(2) NO 0 +tomato_s_pennellii 2 proj_id varchar(15) NO 0 +tomato_seed 1 proj_id varchar(5) NO NULL +tomato_shade_mutants 1 proj_id varchar(5) NO NULL +tomato_shade_timecourse 1 proj_id varchar(5) NO NULL +tomato_trait 2 proj_id varchar(30) NO 0 +triphysaria 1 proj_id varchar(5) NO NULL +triticale 2 proj_id varchar(15) NO 0 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3 sample_file_name tinytext NO NULL +guard_cell 3 sample_file_name tinytext YES NULL +hnahal 3 sample_file_name tinytext YES NULL +human_body_map_2 3 sample_file_name tinytext YES NULL +human_developmental 3 sample_file_name tinytext YES NULL +human_developmental_SpongeLab 3 sample_file_name tinytext YES NULL +human_diseased 3 sample_file_name tinytext YES NULL +lateral_root_initiation 3 sample_file_name varchar(80) YES NULL +light_series 3 sample_file_name tinytext YES NULL +maize_RMA_linear 3 sample_file_name tinytext YES NULL +maize_RMA_log 3 sample_file_name tinytext YES NULL +maize_ears 3 sample_file_name tinytext YES NULL +maize_enzyme 3 sample_file_name tinytext YES NULL +maize_iplant 3 sample_file_name tinytext YES NULL +maize_leaf_gradient 3 sample_file_name tinytext YES NULL +maize_metabolite 3 sample_file_name tinytext YES NULL +maize_rice_comparison 3 sample_file_name tinytext YES NULL +medicago_mas 3 sample_file_name tinytext YES NULL +medicago_rma 3 sample_file_name tinytext YES NULL +meristem_db 3 sample_file_name tinytext YES NULL +meristem_db_new 3 sample_file_name tinytext YES NULL +poplar 3 sample_file_name varchar(40) NO NULL +rice_leaf_gradient 3 sample_file_name tinytext YES NULL +rice_maize_comparison 3 sample_file_name tinytext YES NULL +rice_mas 3 sample_file_name tinytext YES NULL +rice_metabolite 3 sample_file_name tinytext YES NULL +rice_rma 3 sample_file_name tinytext YES NULL +rohan 3 sample_file_name tinytext YES NULL +root 3 sample_file_name tinytext YES NULL +rpatel 3 sample_file_name tinytext YES NULL +seed_db 3 sample_file_name varchar(100) YES NULL +seedcoat 3 sample_file_name tinytext YES NULL +shoot_apex 3 sample_file_name varchar(16) YES NULL +soybean 3 sample_file_name tinytext NO NULL +soybean_severin 3 sample_file_name tinytext NO NULL +thellungiella_db 3 sample_file_name varchar(80) YES NULL +tomato 3 sample_file_name tinytext YES NULL +tomato_renormalized 3 sample_file_name tinytext YES NULL +tomato_trait 3 sample_file_name tinytext YES NULL +triticale 3 sample_file_name tinytext YES NULL +triticale_mas 3 sample_file_name tinytext YES NULL +actinidia_bud_development 2 sample_id int unsigned NO 0 +actinidia_flower_fruit_development 2 sample_id int unsigned NO 0 +actinidia_postharvest 2 sample_id int unsigned NO 0 +actinidia_vegetative_growth 2 sample_id int unsigned NO 0 +affydb 1 sample_id int unsigned NO 0 +apple 1 sample_id int unsigned NO 0 +arabidopsis_ecotypes 1 sample_id int unsigned NO 0 +arachis 1 sample_id varchar(5) NO NULL +atgenexp 1 sample_id int unsigned NO 0 +atgenexp_hormone 1 sample_id int unsigned NO 0 +atgenexp_pathogen 1 sample_id int unsigned NO 0 +atgenexp_plus 1 sample_id int unsigned NO 0 +atgenexp_stress 1 sample_id int unsigned NO 0 +barley_mas 1 sample_id int unsigned NO 0 +barley_rma 1 sample_id int unsigned NO 0 +barley_seed 2 sample_id int unsigned NO 0 +barley_spike_meristem 2 sample_id int unsigned NO 0 +barley_spike_meristem_v3 2 sample_id int unsigned NO 0 +brachypodium 2 sample_id int unsigned NO 0 +brachypodium_Bd21 2 sample_id int unsigned NO 0 +brachypodium_embryogenesis 2 sample_id int unsigned NO 0 +brachypodium_grains 2 sample_id int unsigned NO 0 +brachypodium_metabolites_map 2 sample_id int unsigned NO 0 +brachypodium_photo_thermocycle 2 sample_id int unsigned NO 0 +brassica_rapa 1 sample_id int unsigned NO 0 +cacao_developmental_atlas 1 sample_id int unsigned NO 0 +cacao_developmental_atlas_sca 1 sample_id int unsigned NO 0 +cacao_drought_diurnal_atlas 1 sample_id int unsigned NO 0 +cacao_drought_diurnal_atlas_sca 1 sample_id int unsigned NO 0 +cacao_infection 1 sample_id int unsigned NO 0 +cacao_leaf 1 sample_id int unsigned NO 0 +cacao_meristem_atlas_sca 1 sample_id int unsigned NO 0 +cacao_seed_atlas_sca 1 sample_id int unsigned NO 0 +camelina 1 sample_id varchar(5) NO NULL +camelina_tpm 1 sample_id varchar(5) NO NULL +cannabis 2 sample_id int unsigned NO 0 +canola 1 sample_id int unsigned NO 0 +canola_original 1 sample_id int unsigned NO 0 +canola_original_v2 1 sample_id int unsigned NO 0 +canola_seed 2 sample_id int unsigned NO 0 +cassava_atlas 2 sample_id int unsigned NO 0 +cassava_cbb 2 sample_id int unsigned NO 0 +cassava_eacmv 2 sample_id int unsigned NO 0 +circadian_mutants 2 sample_id int unsigned NO 0 +cuscuta 1 sample_id int unsigned NO 0 +cuscuta_early_haustoriogenesis 2 sample_id int unsigned NO 0 +cuscuta_lmd 2 sample_id int unsigned NO 0 +dna_damage 1 sample_id int unsigned NO 0 +durum_wheat_abiotic_stress 2 sample_id int unsigned NO 0 +durum_wheat_biotic_stress 2 sample_id int unsigned NO 0 +durum_wheat_development 2 sample_id int unsigned NO 0 +embryo 2 sample_id int unsigned NO 0 +eucalyptus 2 sample_id int unsigned NO 0 +euphorbia 2 sample_id int unsigned NO 0 +gc_drought 2 sample_id int unsigned NO 0 +germination 2 sample_id int unsigned NO 0 +grape_developmental 1 sample_id int NO NULL +guard_cell 1 sample_id int unsigned NO 0 +gynoecium 2 sample_id int unsigned NO 0 +heterodera_schachtii 2 sample_id int unsigned NO 0 +hnahal 1 sample_id int unsigned NO 0 +human_body_map_2 1 sample_id int unsigned NO 0 +human_developmental 1 sample_id int unsigned NO 0 +human_developmental_SpongeLab 1 sample_id int unsigned NO 0 +human_diseased 1 sample_id int unsigned NO 0 +kalanchoe 2 sample_id int unsigned NO 0 +kalanchoe_time_course_analysis 2 sample_id int unsigned NO 0 +klepikova 2 sample_id int unsigned NO 0 +lateral_root_initiation 1 sample_id varchar(30) NO NULL +light_series 1 sample_id int unsigned NO 0 +lipid_map 2 sample_id int unsigned NO 0 +little_millet 1 sample_id int unsigned NO 0 +lupin_lcm_leaf 2 sample_id int unsigned NO 0 +lupin_lcm_pod 2 sample_id int unsigned NO 0 +lupin_lcm_stem 2 sample_id int unsigned NO 0 +lupin_pod_seed 2 sample_id int unsigned NO 0 +lupin_whole_plant 2 sample_id int unsigned NO 0 +maize_RMA_linear 1 sample_id int unsigned NO 0 +maize_RMA_log 1 sample_id int unsigned NO 0 +maize_atlas 1 sample_id varchar(5) NO NULL +maize_atlas_v5 2 sample_id int unsigned NO 0 +maize_buell_lab 1 sample_id int unsigned NO 0 +maize_early_seed 1 sample_id int unsigned NO 0 +maize_ears 1 sample_id int unsigned NO 0 +maize_embryonic_leaf_development 2 sample_id int unsigned NO 0 +maize_enzyme 1 sample_id int unsigned NO 0 +maize_gdowns 1 sample_id varchar(30) NO NULL +maize_iplant 1 sample_id int unsigned NO 0 +maize_kernel_v5 2 sample_id int unsigned NO 0 +maize_leaf_gradient 1 sample_id int unsigned NO 0 +maize_lipid_map 2 sample_id int unsigned NO 0 +maize_metabolite 1 sample_id int unsigned NO 0 +maize_nitrogen_use_efficiency 2 sample_id int unsigned NO 0 +maize_rice_comparison 1 sample_id int unsigned NO 0 +maize_root 1 sample_id int unsigned NO 0 +maize_stress_v5 2 sample_id int unsigned NO 0 +mangosteen_aril_vs_rind 2 sample_id int unsigned NO 0 +mangosteen_callus 2 sample_id int unsigned NO 0 +mangosteen_diseased_vs_normal 2 sample_id int unsigned NO 0 +mangosteen_fruit_ripening 2 sample_id int unsigned NO 0 +mangosteen_seed_development 2 sample_id int unsigned NO 0 +mangosteen_seed_development_germination 2 sample_id int unsigned NO 0 +mangosteen_seed_germination 2 sample_id int unsigned NO 0 +marchantia_organ_stress 2 sample_id int unsigned NO 0 +medicago_mas 1 sample_id int unsigned NO 0 +medicago_rma 1 sample_id int unsigned NO 0 +medicago_root 1 sample_id int unsigned NO 0 +medicago_root_v5 1 sample_id int unsigned NO 0 +medicago_seed 1 sample_id int unsigned NO 0 +meristem_db 1 sample_id int unsigned NO 0 +meristem_db_new 1 sample_id int unsigned NO 0 +oat 1 sample_id int unsigned NO 0 +phelipanche 2 sample_id int unsigned NO 0 +physcomitrella_db 1 sample_id varchar(30) NO +poplar 1 sample_id int unsigned NO 0 +poplar_hormone 2 sample_id int unsigned NO 0 +poplar_leaf 1 sample_id int unsigned NO 0 +poplar_xylem 1 sample_id int unsigned NO 0 +potato_dev 1 sample_id int unsigned NO 0 +potato_stress 1 sample_id int unsigned NO 0 +potato_wounding 1 sample_id int unsigned NO 0 +rice_abiotic_stress_sc_pseudobulk 2 sample_id int unsigned NO 0 +rice_drought_heat_stress 2 sample_id int unsigned NO 0 +rice_leaf_gradient 1 sample_id int unsigned NO 0 +rice_maize_comparison 1 sample_id int unsigned NO 0 +rice_mas 1 sample_id int unsigned NO 0 +rice_metabolite 1 sample_id int unsigned NO 0 +rice_rma 1 sample_id int unsigned NO 0 +rice_root 1 sample_id int unsigned NO 0 +rohan 1 sample_id int unsigned NO 0 +root 1 sample_id int unsigned NO 0 +root_Schaefer_lab 1 sample_id int unsigned NO 0 +rpatel 1 sample_id int unsigned NO 0 +seed_db 1 sample_id int unsigned NO 0 +seedcoat 1 sample_id int unsigned NO 0 +selaginella 1 sample_id int unsigned NO 0 +shoot_apex 1 sample_id int unsigned NO 0 +silique 2 sample_id int unsigned NO 0 +single_cell 2 sample_id int unsigned NO 0 +sorghum_atlas_w_BS_cells 2 sample_id int unsigned NO 0 +sorghum_comparative_transcriptomics 2 sample_id int unsigned NO 0 +sorghum_developmental 2 sample_id int unsigned NO 0 +sorghum_developmental_2 2 sample_id int unsigned NO 0 +sorghum_flowering_activation 2 sample_id int unsigned NO 0 +sorghum_low_phosphorus 2 sample_id int unsigned NO 0 +sorghum_nitrogen_stress 2 sample_id int unsigned NO 0 +sorghum_nitrogen_use_efficiency 2 sample_id int unsigned NO 0 +sorghum_phosphate_stress 2 sample_id int unsigned NO 0 +sorghum_plasma 2 sample_id int unsigned NO 0 +sorghum_saline_alkali_stress 2 sample_id int unsigned NO 0 +sorghum_stress 2 sample_id int unsigned NO 0 +sorghum_strigolactone_variation 2 sample_id int unsigned NO 0 +sorghum_sulfur_stress 2 sample_id int unsigned NO 0 +sorghum_temperature_stress 2 sample_id int unsigned NO 0 +sorghum_vascularization_and_internode 2 sample_id int unsigned NO 0 +soybean 1 sample_id int NO NULL +soybean_embryonic_development 2 sample_id int unsigned NO 0 +soybean_heart_cotyledon_globular 2 sample_id int unsigned NO 0 +soybean_senescence 2 sample_id int unsigned NO 0 +soybean_severin 1 sample_id int NO NULL +spruce 2 sample_id int unsigned NO 0 +strawberry 2 sample_id int unsigned NO 0 +striga 2 sample_id int unsigned NO 0 +sugarcane_culms 1 sample_id int unsigned NO 0 +sugarcane_leaf 1 sample_id int unsigned NO 0 +sunflower 1 sample_id int unsigned NO 0 +thellungiella_db 1 sample_id varchar(30) NO NULL +tomato 1 sample_id int unsigned NO 0 +tomato_ils 1 sample_id int unsigned NO 0 +tomato_ils2 1 sample_id int unsigned NO 0 +tomato_ils3 1 sample_id int unsigned NO 0 +tomato_meristem 1 sample_id int unsigned NO 0 +tomato_renormalized 1 sample_id int unsigned NO 0 +tomato_root 1 sample_id int unsigned NO 0 +tomato_root_field_pot 1 sample_id int unsigned NO 0 +tomato_s_pennellii 1 sample_id int unsigned NO 0 +tomato_seed 2 sample_id int unsigned NO 0 +tomato_shade_mutants 2 sample_id int unsigned NO 0 +tomato_shade_timecourse 2 sample_id int unsigned NO 0 +tomato_trait 1 sample_id int unsigned NO 0 +triphysaria 2 sample_id int unsigned NO 0 +triticale 1 sample_id int unsigned NO 0 +triticale_mas 1 sample_id int unsigned NO 0 +tung_tree 1 sample_id int unsigned NO 0 +wheat 2 sample_id int unsigned NO 0 +wheat_abiotic_stress 2 sample_id int unsigned NO 0 +wheat_embryogenesis 2 sample_id int unsigned NO 0 +wheat_meiosis 2 sample_id int unsigned NO 0 +wheat_root 2 sample_id int unsigned NO 0 +willow 2 sample_id int unsigned NO 0 +barley_mas 9 sample_tissue varchar(20) YES NULL +canola 9 sample_tissue text NO NULL +canola_original 9 sample_tissue text NO NULL +canola_original_v2 9 sample_tissue text NO NULL +grape_developmental 9 sample_tissue text NO NULL +maize_RMA_linear 9 sample_tissue text NO NULL +medicago_mas 9 sample_tissue text NO NULL +rice_mas 9 sample_tissue text NO NULL +oat 3 version varchar(2) NO NULL diff --git a/api/Archive/schema.sql b/api/Archive/schema.sql new file mode 100644 index 0000000..3271efd --- /dev/null +++ b/api/Archive/schema.sql @@ -0,0 +1,23169 @@ +-- MySQL dump 10.13 Distrib 8.4.8, for Linux (x86_64) +-- +-- Host: localhost Database: +-- ------------------------------------------------------ +-- Server version 8.4.8 + +/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */; +/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */; +/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */; +/*!50503 SET NAMES utf8mb4 */; +/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */; +/*!40103 SET TIME_ZONE='+00:00' */; +/*!50606 SET @OLD_INNODB_STATS_AUTO_RECALC=@@INNODB_STATS_AUTO_RECALC */; +/*!50606 SET GLOBAL INNODB_STATS_AUTO_RECALC=OFF */; +/*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */; +/*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */; +/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO' */; +/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */; + +-- +-- Current Database: `mysql` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `mysql` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `mysql`; + +-- +-- Table structure for table `columns_priv` +-- + +DROP TABLE IF EXISTS `columns_priv`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `columns_priv` ( + `Host` char(255) CHARACTER SET ascii COLLATE ascii_general_ci NOT NULL DEFAULT '', + `Db` char(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `User` char(32) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `Table_name` char(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `Column_name` char(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `Timestamp` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP, + `Column_priv` set('Select','Insert','Update','References') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT '', + PRIMARY KEY (`Host`,`User`,`Db`,`Table_name`,`Column_name`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='Column privileges'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `component` +-- + +DROP TABLE IF EXISTS `component`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `component` ( + `component_id` int unsigned NOT NULL AUTO_INCREMENT, + `component_group_id` int unsigned NOT NULL, + `component_urn` text NOT NULL, + PRIMARY KEY (`component_id`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB AUTO_INCREMENT=2 DEFAULT CHARSET=utf8mb3 ROW_FORMAT=DYNAMIC COMMENT='Components'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `db` +-- + +DROP TABLE IF EXISTS `db`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `db` ( + `Host` char(255) CHARACTER SET ascii COLLATE ascii_general_ci NOT NULL DEFAULT '', + `Db` char(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `User` char(32) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `Select_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Insert_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Update_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Delete_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Create_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Drop_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Grant_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `References_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Index_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Alter_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Create_tmp_table_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Lock_tables_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Create_view_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Show_view_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Create_routine_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Alter_routine_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Execute_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Event_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Trigger_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + PRIMARY KEY (`Host`,`User`,`Db`), + KEY `User` (`User`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='Database privileges'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `default_roles` +-- + +DROP TABLE IF EXISTS `default_roles`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `default_roles` ( + `HOST` char(255) CHARACTER SET ascii COLLATE ascii_general_ci NOT NULL DEFAULT '', + `USER` char(32) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `DEFAULT_ROLE_HOST` char(255) CHARACTER SET ascii COLLATE ascii_general_ci NOT NULL DEFAULT '%', + `DEFAULT_ROLE_USER` char(32) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + PRIMARY KEY (`HOST`,`USER`,`DEFAULT_ROLE_HOST`,`DEFAULT_ROLE_USER`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='Default roles'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `engine_cost` +-- + +DROP TABLE IF EXISTS `engine_cost`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `engine_cost` ( + `engine_name` varchar(64) NOT NULL, + `device_type` int NOT NULL, + `cost_name` varchar(64) NOT NULL, + `cost_value` float DEFAULT NULL, + `last_update` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP, + `comment` varchar(1024) DEFAULT NULL, + `default_value` float GENERATED ALWAYS AS ((case `cost_name` when _utf8mb3'io_block_read_cost' then 1.0 when _utf8mb3'memory_block_read_cost' then 0.25 else NULL end)) VIRTUAL, + PRIMARY KEY (`cost_name`,`engine_name`,`device_type`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `func` +-- + +DROP TABLE IF EXISTS `func`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `func` ( + `name` char(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `ret` tinyint NOT NULL DEFAULT '0', + `dl` char(128) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `type` enum('function','aggregate') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL, + PRIMARY KEY (`name`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='User defined functions'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `global_grants` +-- + +DROP TABLE IF EXISTS `global_grants`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `global_grants` ( + `USER` char(32) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `HOST` char(255) CHARACTER SET ascii COLLATE ascii_general_ci NOT NULL DEFAULT '', + `PRIV` char(32) CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT '', + `WITH_GRANT_OPTION` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + PRIMARY KEY (`USER`,`HOST`,`PRIV`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='Extended global grants'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gtid_executed` +-- + +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE IF NOT EXISTS `gtid_executed` ( + `source_uuid` char(36) NOT NULL COMMENT 'uuid of the source where the transaction was originally executed.', + `interval_start` bigint NOT NULL COMMENT 'First number of interval.', + `interval_end` bigint NOT NULL COMMENT 'Last number of interval.', + `gtid_tag` char(32) NOT NULL COMMENT 'GTID Tag.', + PRIMARY KEY (`source_uuid`,`gtid_tag`,`interval_start`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `help_category` +-- + +DROP TABLE IF EXISTS `help_category`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `help_category` ( + `help_category_id` smallint unsigned NOT NULL, + `name` char(64) NOT NULL, + `parent_category_id` smallint unsigned DEFAULT NULL, + `url` text NOT NULL, + PRIMARY KEY (`help_category_id`), + UNIQUE KEY `name` (`name`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='help categories'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `help_keyword` +-- + +DROP TABLE IF EXISTS `help_keyword`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `help_keyword` ( + `help_keyword_id` int unsigned NOT NULL, + `name` char(64) NOT NULL, + PRIMARY KEY (`help_keyword_id`), + UNIQUE KEY `name` (`name`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='help keywords'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `help_relation` +-- + +DROP TABLE IF EXISTS `help_relation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `help_relation` ( + `help_topic_id` int unsigned NOT NULL, + `help_keyword_id` int unsigned NOT NULL, + PRIMARY KEY (`help_keyword_id`,`help_topic_id`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='keyword-topic relation'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `help_topic` +-- + +DROP TABLE IF EXISTS `help_topic`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `help_topic` ( + `help_topic_id` int unsigned NOT NULL, + `name` char(64) NOT NULL, + `help_category_id` smallint unsigned NOT NULL, + `description` text NOT NULL, + `example` text NOT NULL, + `url` text NOT NULL, + PRIMARY KEY (`help_topic_id`), + UNIQUE KEY `name` (`name`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='help topics'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `ndb_binlog_index` +-- + +DROP TABLE IF EXISTS `ndb_binlog_index`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `ndb_binlog_index` ( + `Position` bigint unsigned NOT NULL, + `File` varchar(255) NOT NULL, + `epoch` bigint unsigned NOT NULL, + `inserts` int unsigned NOT NULL, + `updates` int unsigned NOT NULL, + `deletes` int unsigned NOT NULL, + `schemaops` int unsigned NOT NULL, + `orig_server_id` int unsigned NOT NULL, + `orig_epoch` bigint unsigned NOT NULL, + `gci` int unsigned NOT NULL, + `next_position` bigint unsigned NOT NULL, + `next_file` varchar(255) NOT NULL, + PRIMARY KEY (`epoch`,`orig_server_id`,`orig_epoch`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=latin1 STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `password_history` +-- + +DROP TABLE IF EXISTS `password_history`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `password_history` ( + `Host` char(255) CHARACTER SET ascii COLLATE ascii_general_ci NOT NULL DEFAULT '', + `User` char(32) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `Password_timestamp` timestamp(6) NOT NULL DEFAULT CURRENT_TIMESTAMP(6), + `Password` text COLLATE utf8mb3_bin, + PRIMARY KEY (`Host`,`User`,`Password_timestamp` DESC) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='Password history for user accounts'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `plugin` +-- + +DROP TABLE IF EXISTS `plugin`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `plugin` ( + `name` varchar(64) NOT NULL DEFAULT '', + `dl` varchar(128) NOT NULL DEFAULT '', + PRIMARY KEY (`name`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='MySQL plugins'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `procs_priv` +-- + +DROP TABLE IF EXISTS `procs_priv`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `procs_priv` ( + `Host` char(255) CHARACTER SET ascii COLLATE ascii_general_ci NOT NULL DEFAULT '', + `Db` char(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `User` char(32) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `Routine_name` char(64) CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT '', + `Routine_type` enum('FUNCTION','PROCEDURE') COLLATE utf8mb3_bin NOT NULL, + `Grantor` varchar(288) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `Proc_priv` set('Execute','Alter Routine','Grant') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT '', + `Timestamp` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP, + PRIMARY KEY (`Host`,`User`,`Db`,`Routine_name`,`Routine_type`), + KEY `Grantor` (`Grantor`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='Procedure privileges'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `proxies_priv` +-- + +DROP TABLE IF EXISTS `proxies_priv`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proxies_priv` ( + `Host` char(255) CHARACTER SET ascii COLLATE ascii_general_ci NOT NULL DEFAULT '', + `User` char(32) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `Proxied_host` char(255) CHARACTER SET ascii COLLATE ascii_general_ci NOT NULL DEFAULT '', + `Proxied_user` char(32) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `With_grant` tinyint(1) NOT NULL DEFAULT '0', + `Grantor` varchar(288) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `Timestamp` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP, + PRIMARY KEY (`Host`,`User`,`Proxied_host`,`Proxied_user`), + KEY `Grantor` (`Grantor`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='User proxy privileges'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `replication_asynchronous_connection_failover` +-- + +DROP TABLE IF EXISTS `replication_asynchronous_connection_failover`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `replication_asynchronous_connection_failover` ( + `Channel_name` char(64) CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL COMMENT 'The replication channel name that connects source and replica.', + `Host` char(255) CHARACTER SET ascii COLLATE ascii_general_ci NOT NULL COMMENT 'The source hostname that the replica will attempt to switch over the replication connection to in case of a failure.', + `Port` int unsigned NOT NULL COMMENT 'The source port that the replica will attempt to switch over the replication connection to in case of a failure.', + `Network_namespace` char(64) NOT NULL COMMENT 'The source network namespace that the replica will attempt to switch over the replication connection to in case of a failure. If its value is empty, connections use the default (global) namespace.', + `Weight` tinyint unsigned NOT NULL COMMENT 'The order in which the replica shall try to switch the connection over to when there are failures. Weight can be set to a number between 1 and 100, where 100 is the highest weight and 1 the lowest.', + `Managed_name` char(64) CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT '' COMMENT 'The name of the group which this server belongs to.', + PRIMARY KEY (`Channel_name`,`Host`,`Port`,`Network_namespace`,`Managed_name`), + KEY `Channel_name` (`Channel_name`,`Managed_name`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='The source configuration details'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `replication_asynchronous_connection_failover_managed` +-- + +DROP TABLE IF EXISTS `replication_asynchronous_connection_failover_managed`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `replication_asynchronous_connection_failover_managed` ( + `Channel_name` char(64) CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL COMMENT 'The replication channel name that connects source and replica.', + `Managed_name` char(64) CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT '' COMMENT 'The name of the source which needs to be managed.', + `Managed_type` char(64) CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT '' COMMENT 'Determines the managed type.', + `Configuration` json DEFAULT NULL COMMENT 'The data to help manage group. For Managed_type = GroupReplication, Configuration value should contain {"Primary_weight": 80, "Secondary_weight": 60}, so that it assigns weight=80 to PRIMARY of the group, and weight=60 for rest of the members in mysql.replication_asynchronous_connection_failover table.', + PRIMARY KEY (`Channel_name`,`Managed_name`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='The managed source configuration details'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `replication_group_configuration_version` +-- + +DROP TABLE IF EXISTS `replication_group_configuration_version`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `replication_group_configuration_version` ( + `name` char(255) CHARACTER SET ascii COLLATE ascii_general_ci NOT NULL COMMENT 'The configuration name.', + `version` bigint unsigned NOT NULL COMMENT 'The version of the configuration name.', + PRIMARY KEY (`name`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='The group configuration version.'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `replication_group_member_actions` +-- + +DROP TABLE IF EXISTS `replication_group_member_actions`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `replication_group_member_actions` ( + `name` char(255) CHARACTER SET ascii COLLATE ascii_general_ci NOT NULL COMMENT 'The action name.', + `event` char(64) CHARACTER SET ascii COLLATE ascii_general_ci NOT NULL COMMENT 'The event that will trigger the action.', + `enabled` tinyint(1) NOT NULL COMMENT 'Whether the action is enabled.', + `type` char(64) CHARACTER SET ascii COLLATE ascii_general_ci NOT NULL COMMENT 'The action type.', + `priority` tinyint unsigned NOT NULL COMMENT 'The order on which the action will be run, value between 1 and 100, lower values first.', + `error_handling` char(64) CHARACTER SET ascii COLLATE ascii_general_ci NOT NULL COMMENT 'On errors during the action will be handled: IGNORE, CRITICAL.', + PRIMARY KEY (`name`,`event`), + KEY `event` (`event`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='The member actions configuration.'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `role_edges` +-- + +DROP TABLE IF EXISTS `role_edges`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `role_edges` ( + `FROM_HOST` char(255) CHARACTER SET ascii COLLATE ascii_general_ci NOT NULL DEFAULT '', + `FROM_USER` char(32) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `TO_HOST` char(255) CHARACTER SET ascii COLLATE ascii_general_ci NOT NULL DEFAULT '', + `TO_USER` char(32) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `WITH_ADMIN_OPTION` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + PRIMARY KEY (`FROM_HOST`,`FROM_USER`,`TO_HOST`,`TO_USER`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='Role hierarchy and role grants'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `server_cost` +-- + +DROP TABLE IF EXISTS `server_cost`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `server_cost` ( + `cost_name` varchar(64) NOT NULL, + `cost_value` float DEFAULT NULL, + `last_update` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP, + `comment` varchar(1024) DEFAULT NULL, + `default_value` float GENERATED ALWAYS AS ((case `cost_name` when _utf8mb3'disk_temptable_create_cost' then 20.0 when _utf8mb3'disk_temptable_row_cost' then 0.5 when _utf8mb3'key_compare_cost' then 0.05 when _utf8mb3'memory_temptable_create_cost' then 1.0 when _utf8mb3'memory_temptable_row_cost' then 0.1 when _utf8mb3'row_evaluate_cost' then 0.1 else NULL end)) VIRTUAL, + PRIMARY KEY (`cost_name`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `servers` +-- + +DROP TABLE IF EXISTS `servers`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `servers` ( + `Server_name` char(64) NOT NULL DEFAULT '', + `Host` char(255) CHARACTER SET ascii COLLATE ascii_general_ci NOT NULL DEFAULT '', + `Db` char(64) NOT NULL DEFAULT '', + `Username` char(64) NOT NULL DEFAULT '', + `Password` char(64) NOT NULL DEFAULT '', + `Port` int NOT NULL DEFAULT '0', + `Socket` char(64) NOT NULL DEFAULT '', + `Wrapper` char(64) NOT NULL DEFAULT '', + `Owner` char(64) NOT NULL DEFAULT '', + PRIMARY KEY (`Server_name`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='MySQL Foreign Servers table'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `slave_master_info` +-- + +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE IF NOT EXISTS `slave_master_info` ( + `Number_of_lines` int unsigned NOT NULL COMMENT 'Number of lines in the file.', + `Master_log_name` text CHARACTER SET utf8mb3 COLLATE utf8mb3_bin NOT NULL COMMENT 'The name of the master binary log currently being read from the master.', + `Master_log_pos` bigint unsigned NOT NULL COMMENT 'The master log position of the last read event.', + `Host` varchar(255) CHARACTER SET ascii COLLATE ascii_general_ci DEFAULT NULL COMMENT 'The host name of the source.', + `User_name` text CHARACTER SET utf8mb3 COLLATE utf8mb3_bin COMMENT 'The user name used to connect to the master.', + `User_password` text CHARACTER SET utf8mb3 COLLATE utf8mb3_bin COMMENT 'The password used to connect to the master.', + `Port` int unsigned NOT NULL COMMENT 'The network port used to connect to the master.', + `Connect_retry` int unsigned NOT NULL COMMENT 'The period (in seconds) that the slave will wait before trying to reconnect to the master.', + `Enabled_ssl` tinyint(1) NOT NULL COMMENT 'Indicates whether the server supports SSL connections.', + `Ssl_ca` text CHARACTER SET utf8mb3 COLLATE utf8mb3_bin COMMENT 'The file used for the Certificate Authority (CA) certificate.', + `Ssl_capath` text CHARACTER SET utf8mb3 COLLATE utf8mb3_bin COMMENT 'The path to the Certificate Authority (CA) certificates.', + `Ssl_cert` text CHARACTER SET utf8mb3 COLLATE utf8mb3_bin COMMENT 'The name of the SSL certificate file.', + `Ssl_cipher` text CHARACTER SET utf8mb3 COLLATE utf8mb3_bin COMMENT 'The name of the cipher in use for the SSL connection.', + `Ssl_key` text CHARACTER SET utf8mb3 COLLATE utf8mb3_bin COMMENT 'The name of the SSL key file.', + `Ssl_verify_server_cert` tinyint(1) NOT NULL COMMENT 'Whether to verify the server certificate.', + `Heartbeat` float NOT NULL, + `Bind` text CHARACTER SET utf8mb3 COLLATE utf8mb3_bin COMMENT 'Displays which interface is employed when connecting to the MySQL server', + `Ignored_server_ids` text CHARACTER SET utf8mb3 COLLATE utf8mb3_bin COMMENT 'The number of server IDs to be ignored, followed by the actual server IDs', + `Uuid` text CHARACTER SET utf8mb3 COLLATE utf8mb3_bin COMMENT 'The master server uuid.', + `Retry_count` bigint unsigned NOT NULL COMMENT 'Number of reconnect attempts, to the master, before giving up.', + `Ssl_crl` text CHARACTER SET utf8mb3 COLLATE utf8mb3_bin COMMENT 'The file used for the Certificate Revocation List (CRL)', + `Ssl_crlpath` text CHARACTER SET utf8mb3 COLLATE utf8mb3_bin COMMENT 'The path used for Certificate Revocation List (CRL) files', + `Enabled_auto_position` tinyint(1) NOT NULL COMMENT 'Indicates whether GTIDs will be used to retrieve events from the master.', + `Channel_name` varchar(64) CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL COMMENT 'The channel on which the replica is connected to a source. Used in Multisource Replication', + `Tls_version` text CHARACTER SET utf8mb3 COLLATE utf8mb3_bin COMMENT 'Tls version', + `Public_key_path` text CHARACTER SET utf8mb3 COLLATE utf8mb3_bin COMMENT 'The file containing public key of master server.', + `Get_public_key` tinyint(1) NOT NULL COMMENT 'Preference to get public key from master.', + `Network_namespace` text CHARACTER SET utf8mb3 COLLATE utf8mb3_bin COMMENT 'Network namespace used for communication with the master server.', + `Master_compression_algorithm` varchar(64) CHARACTER SET utf8mb3 COLLATE utf8mb3_bin NOT NULL COMMENT 'Compression algorithm supported for data transfer between source and replica.', + `Master_zstd_compression_level` int unsigned NOT NULL COMMENT 'Compression level associated with zstd compression algorithm.', + `Tls_ciphersuites` text CHARACTER SET utf8mb3 COLLATE utf8mb3_bin COMMENT 'Ciphersuites used for TLS 1.3 communication with the master server.', + `Source_connection_auto_failover` tinyint(1) NOT NULL DEFAULT '0' COMMENT 'Indicates whether the channel connection failover is enabled.', + `Gtid_only` tinyint(1) NOT NULL DEFAULT '0' COMMENT 'Indicates if this channel only uses GTIDs and does not persist positions.', + PRIMARY KEY (`Channel_name`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='Master Information'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `slave_relay_log_info` +-- + +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE IF NOT EXISTS `slave_relay_log_info` ( + `Number_of_lines` int unsigned NOT NULL COMMENT 'Number of lines in the file or rows in the table. Used to version table definitions.', + `Relay_log_name` text CHARACTER SET utf8mb3 COLLATE utf8mb3_bin COMMENT 'The name of the current relay log file.', + `Relay_log_pos` bigint unsigned DEFAULT NULL COMMENT 'The relay log position of the last executed event.', + `Master_log_name` text CHARACTER SET utf8mb3 COLLATE utf8mb3_bin COMMENT 'The name of the master binary log file from which the events in the relay log file were read.', + `Master_log_pos` bigint unsigned DEFAULT NULL COMMENT 'The master log position of the last executed event.', + `Sql_delay` int DEFAULT NULL COMMENT 'The number of seconds that the slave must lag behind the master.', + `Number_of_workers` int unsigned DEFAULT NULL, + `Id` int unsigned DEFAULT NULL COMMENT 'Internal Id that uniquely identifies this record.', + `Channel_name` varchar(64) CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL COMMENT 'The channel on which the replica is connected to a source. Used in Multisource Replication', + `Privilege_checks_username` varchar(32) CHARACTER SET utf8mb3 COLLATE utf8mb3_bin DEFAULT NULL COMMENT 'Username part of PRIVILEGE_CHECKS_USER.', + `Privilege_checks_hostname` varchar(255) CHARACTER SET ascii COLLATE ascii_general_ci DEFAULT NULL COMMENT 'Hostname part of PRIVILEGE_CHECKS_USER.', + `Require_row_format` tinyint(1) NOT NULL COMMENT 'Indicates whether the channel shall only accept row based events.', + `Require_table_primary_key_check` enum('STREAM','ON','OFF','GENERATE') NOT NULL DEFAULT 'STREAM' COMMENT 'Indicates what is the channel policy regarding tables without primary keys on create and alter table queries', + `Assign_gtids_to_anonymous_transactions_type` enum('OFF','LOCAL','UUID') NOT NULL DEFAULT 'OFF' COMMENT 'Indicates whether the channel will generate a new GTID for anonymous transactions. OFF means that anonymous transactions will remain anonymous. LOCAL means that anonymous transactions will be assigned a newly generated GTID based on server_uuid. UUID indicates that anonymous transactions will be assigned a newly generated GTID based on Assign_gtids_to_anonymous_transactions_value', + `Assign_gtids_to_anonymous_transactions_value` text CHARACTER SET utf8mb3 COLLATE utf8mb3_bin COMMENT 'Indicates the UUID used while generating GTIDs for anonymous transactions', + PRIMARY KEY (`Channel_name`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='Relay Log Information'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `slave_worker_info` +-- + +DROP TABLE IF EXISTS `slave_worker_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `slave_worker_info` ( + `Id` int unsigned NOT NULL, + `Relay_log_name` text CHARACTER SET utf8mb3 COLLATE utf8mb3_bin NOT NULL, + `Relay_log_pos` bigint unsigned NOT NULL, + `Master_log_name` text CHARACTER SET utf8mb3 COLLATE utf8mb3_bin NOT NULL, + `Master_log_pos` bigint unsigned NOT NULL, + `Checkpoint_relay_log_name` text CHARACTER SET utf8mb3 COLLATE utf8mb3_bin NOT NULL, + `Checkpoint_relay_log_pos` bigint unsigned NOT NULL, + `Checkpoint_master_log_name` text CHARACTER SET utf8mb3 COLLATE utf8mb3_bin NOT NULL, + `Checkpoint_master_log_pos` bigint unsigned NOT NULL, + `Checkpoint_seqno` int unsigned NOT NULL, + `Checkpoint_group_size` int unsigned NOT NULL, + `Checkpoint_group_bitmap` blob NOT NULL, + `Channel_name` varchar(64) CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL COMMENT 'The channel on which the replica is connected to a source. Used in Multisource Replication', + PRIMARY KEY (`Channel_name`,`Id`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='Worker Information'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `tables_priv` +-- + +DROP TABLE IF EXISTS `tables_priv`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `tables_priv` ( + `Host` char(255) CHARACTER SET ascii COLLATE ascii_general_ci NOT NULL DEFAULT '', + `Db` char(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `User` char(32) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `Table_name` char(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `Grantor` varchar(288) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `Timestamp` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP, + `Table_priv` set('Select','Insert','Update','Delete','Create','Drop','Grant','References','Index','Alter','Create View','Show view','Trigger') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT '', + `Column_priv` set('Select','Insert','Update','References') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT '', + PRIMARY KEY (`Host`,`User`,`Db`,`Table_name`), + KEY `Grantor` (`Grantor`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='Table privileges'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `time_zone` +-- + +DROP TABLE IF EXISTS `time_zone`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `time_zone` ( + `Time_zone_id` int unsigned NOT NULL AUTO_INCREMENT, + `Use_leap_seconds` enum('Y','N') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + PRIMARY KEY (`Time_zone_id`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='Time zones'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `time_zone_leap_second` +-- + +DROP TABLE IF EXISTS `time_zone_leap_second`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `time_zone_leap_second` ( + `Transition_time` bigint NOT NULL, + `Correction` int NOT NULL, + PRIMARY KEY (`Transition_time`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='Leap seconds information for time zones'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `time_zone_name` +-- + +DROP TABLE IF EXISTS `time_zone_name`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `time_zone_name` ( + `Name` char(64) NOT NULL, + `Time_zone_id` int unsigned NOT NULL, + PRIMARY KEY (`Name`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='Time zone names'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `time_zone_transition` +-- + +DROP TABLE IF EXISTS `time_zone_transition`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `time_zone_transition` ( + `Time_zone_id` int unsigned NOT NULL, + `Transition_time` bigint NOT NULL, + `Transition_type_id` int unsigned NOT NULL, + PRIMARY KEY (`Time_zone_id`,`Transition_time`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='Time zone transitions'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `time_zone_transition_type` +-- + +DROP TABLE IF EXISTS `time_zone_transition_type`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `time_zone_transition_type` ( + `Time_zone_id` int unsigned NOT NULL, + `Transition_type_id` int unsigned NOT NULL, + `Offset` int NOT NULL DEFAULT '0', + `Is_DST` tinyint unsigned NOT NULL DEFAULT '0', + `Abbreviation` char(8) NOT NULL DEFAULT '', + PRIMARY KEY (`Time_zone_id`,`Transition_type_id`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='Time zone transition types'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `user` +-- + +DROP TABLE IF EXISTS `user`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `user` ( + `Host` char(255) CHARACTER SET ascii COLLATE ascii_general_ci NOT NULL DEFAULT '', + `User` char(32) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `Select_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Insert_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Update_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Delete_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Create_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Drop_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Reload_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Shutdown_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Process_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `File_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Grant_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `References_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Index_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Alter_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Show_db_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Super_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Create_tmp_table_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Lock_tables_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Execute_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Repl_slave_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Repl_client_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Create_view_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Show_view_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Create_routine_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Alter_routine_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Create_user_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Event_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Trigger_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Create_tablespace_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `ssl_type` enum('','ANY','X509','SPECIFIED') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT '', + `ssl_cipher` blob NOT NULL, + `x509_issuer` blob NOT NULL, + `x509_subject` blob NOT NULL, + `max_questions` int unsigned NOT NULL DEFAULT '0', + `max_updates` int unsigned NOT NULL DEFAULT '0', + `max_connections` int unsigned NOT NULL DEFAULT '0', + `max_user_connections` int unsigned NOT NULL DEFAULT '0', + `plugin` char(64) COLLATE utf8mb3_bin NOT NULL DEFAULT 'caching_sha2_password', + `authentication_string` text COLLATE utf8mb3_bin, + `password_expired` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `password_last_changed` timestamp NULL DEFAULT NULL, + `password_lifetime` smallint unsigned DEFAULT NULL, + `account_locked` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Create_role_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Drop_role_priv` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT 'N', + `Password_reuse_history` smallint unsigned DEFAULT NULL, + `Password_reuse_time` smallint unsigned DEFAULT NULL, + `Password_require_current` enum('N','Y') CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci DEFAULT NULL, + `User_attributes` json DEFAULT NULL, + PRIMARY KEY (`Host`,`User`) +) /*!50100 TABLESPACE `mysql` */ ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin STATS_PERSISTENT=0 ROW_FORMAT=DYNAMIC COMMENT='Users and global privileges'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `general_log` +-- + +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE IF NOT EXISTS `general_log` ( + `event_time` timestamp(6) NOT NULL DEFAULT CURRENT_TIMESTAMP(6) ON UPDATE CURRENT_TIMESTAMP(6), + `user_host` mediumtext NOT NULL, + `thread_id` bigint unsigned NOT NULL, + `server_id` int unsigned NOT NULL, + `command_type` varchar(64) NOT NULL, + `argument` mediumblob NOT NULL +) ENGINE=CSV DEFAULT CHARSET=utf8mb3 COMMENT='General log'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `slow_log` +-- + +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE IF NOT EXISTS `slow_log` ( + `start_time` timestamp(6) NOT NULL DEFAULT CURRENT_TIMESTAMP(6) ON UPDATE CURRENT_TIMESTAMP(6), + `user_host` mediumtext NOT NULL, + `query_time` time(6) NOT NULL, + `lock_time` time(6) NOT NULL, + `rows_sent` int NOT NULL, + `rows_examined` int NOT NULL, + `db` varchar(512) NOT NULL, + `last_insert_id` int NOT NULL, + `insert_id` int NOT NULL, + `server_id` int unsigned NOT NULL, + `sql_text` mediumblob NOT NULL, + `thread_id` bigint unsigned NOT NULL +) ENGINE=CSV DEFAULT CHARSET=utf8mb3 COMMENT='Slow log'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `3ddi_wiki` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `3ddi_wiki` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `3ddi_wiki`; + +-- +-- Table structure for table `actor` +-- + +DROP TABLE IF EXISTS `actor`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `actor` ( + `actor_id` bigint unsigned NOT NULL AUTO_INCREMENT, + `actor_user` int unsigned DEFAULT NULL, + `actor_name` varbinary(255) NOT NULL, + PRIMARY KEY (`actor_id`), + UNIQUE KEY `actor_name` (`actor_name`), + UNIQUE KEY `actor_user` (`actor_user`) +) ENGINE=InnoDB AUTO_INCREMENT=4 DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `archive` +-- + +DROP TABLE IF EXISTS `archive`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `archive` ( + `ar_id` int unsigned NOT NULL AUTO_INCREMENT, + `ar_namespace` int NOT NULL DEFAULT '0', + `ar_title` varbinary(255) NOT NULL DEFAULT '', + `ar_comment_id` bigint unsigned NOT NULL, + `ar_actor` bigint unsigned NOT NULL, + `ar_timestamp` binary(14) NOT NULL, + `ar_minor_edit` tinyint NOT NULL DEFAULT '0', + `ar_rev_id` int unsigned NOT NULL, + `ar_deleted` tinyint unsigned NOT NULL DEFAULT '0', + `ar_len` int unsigned DEFAULT NULL, + `ar_page_id` int unsigned DEFAULT NULL, + `ar_parent_id` int unsigned DEFAULT NULL, + `ar_sha1` varbinary(32) NOT NULL DEFAULT '', + PRIMARY KEY (`ar_id`), + UNIQUE KEY `ar_revid_uniq` (`ar_rev_id`), + KEY `ar_actor_timestamp` (`ar_actor`,`ar_timestamp`), + KEY `ar_name_title_timestamp` (`ar_namespace`,`ar_title`,`ar_timestamp`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `bot_passwords` +-- + +DROP TABLE IF EXISTS `bot_passwords`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `bot_passwords` ( + `bp_user` int unsigned NOT NULL, + `bp_app_id` varbinary(32) NOT NULL, + `bp_password` tinyblob NOT NULL, + `bp_token` binary(32) NOT NULL DEFAULT '\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0', + `bp_restrictions` blob NOT NULL, + `bp_grants` blob NOT NULL, + PRIMARY KEY (`bp_user`,`bp_app_id`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `category` +-- + +DROP TABLE IF EXISTS `category`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `category` ( + `cat_id` int unsigned NOT NULL AUTO_INCREMENT, + `cat_title` varbinary(255) NOT NULL, + `cat_pages` int NOT NULL DEFAULT '0', + `cat_subcats` int NOT NULL DEFAULT '0', + `cat_files` int NOT NULL DEFAULT '0', + PRIMARY KEY (`cat_id`), + UNIQUE KEY `cat_title` (`cat_title`), + KEY `cat_pages` (`cat_pages`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `categorylinks` +-- + +DROP TABLE IF EXISTS `categorylinks`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `categorylinks` ( + `cl_from` int unsigned NOT NULL DEFAULT '0', + `cl_to` varbinary(255) NOT NULL DEFAULT '', + `cl_sortkey` varbinary(230) NOT NULL DEFAULT '', + `cl_timestamp` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP, + `cl_sortkey_prefix` varbinary(255) NOT NULL DEFAULT '', + `cl_collation` varbinary(32) NOT NULL DEFAULT '', + `cl_type` enum('page','subcat','file') NOT NULL DEFAULT 'page', + PRIMARY KEY (`cl_from`,`cl_to`), + KEY `cl_timestamp` (`cl_to`,`cl_timestamp`), + KEY `cl_sortkey` (`cl_to`,`cl_type`,`cl_sortkey`,`cl_from`), + KEY `cl_collation_ext` (`cl_collation`,`cl_to`,`cl_type`,`cl_from`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `change_tag` +-- + +DROP TABLE IF EXISTS `change_tag`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `change_tag` ( + `ct_id` int unsigned NOT NULL AUTO_INCREMENT, + `ct_rc_id` int DEFAULT NULL, + `ct_log_id` int unsigned DEFAULT NULL, + `ct_rev_id` int unsigned DEFAULT NULL, + `ct_params` blob, + `ct_tag_id` int unsigned NOT NULL, + PRIMARY KEY (`ct_id`), + UNIQUE KEY `ct_rc_tag_id` (`ct_rc_id`,`ct_tag_id`), + UNIQUE KEY `ct_log_tag_id` (`ct_log_id`,`ct_tag_id`), + UNIQUE KEY `ct_rev_tag_id` (`ct_rev_id`,`ct_tag_id`), + KEY `ct_tag_id_id` (`ct_tag_id`,`ct_rc_id`,`ct_rev_id`,`ct_log_id`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `change_tag_def` +-- + +DROP TABLE IF EXISTS `change_tag_def`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `change_tag_def` ( + `ctd_id` int unsigned NOT NULL AUTO_INCREMENT, + `ctd_name` varbinary(255) NOT NULL, + `ctd_user_defined` tinyint(1) NOT NULL, + `ctd_count` bigint unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`ctd_id`), + UNIQUE KEY `ctd_name` (`ctd_name`), + KEY `ctd_count` (`ctd_count`), + KEY `ctd_user_defined` (`ctd_user_defined`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `comment` +-- + +DROP TABLE IF EXISTS `comment`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `comment` ( + `comment_id` bigint unsigned NOT NULL AUTO_INCREMENT, + `comment_hash` int NOT NULL, + `comment_text` blob NOT NULL, + `comment_data` blob, + PRIMARY KEY (`comment_id`), + KEY `comment_hash` (`comment_hash`) +) ENGINE=InnoDB AUTO_INCREMENT=7 DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `content` +-- + +DROP TABLE IF EXISTS `content`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `content` ( + `content_id` bigint unsigned NOT NULL AUTO_INCREMENT, + `content_size` int unsigned NOT NULL, + `content_sha1` varbinary(32) NOT NULL, + `content_model` smallint unsigned NOT NULL, + `content_address` varbinary(255) NOT NULL, + PRIMARY KEY (`content_id`) +) ENGINE=InnoDB AUTO_INCREMENT=23 DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `content_models` +-- + +DROP TABLE IF EXISTS `content_models`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `content_models` ( + `model_id` int NOT NULL AUTO_INCREMENT, + `model_name` varbinary(64) NOT NULL, + PRIMARY KEY (`model_id`), + UNIQUE KEY `model_name` (`model_name`) +) ENGINE=InnoDB AUTO_INCREMENT=3 DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `externallinks` +-- + +DROP TABLE IF EXISTS `externallinks`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `externallinks` ( + `el_id` int unsigned NOT NULL AUTO_INCREMENT, + `el_from` int unsigned NOT NULL DEFAULT '0', + `el_to` blob NOT NULL, + `el_index` blob NOT NULL, + `el_index_60` varbinary(60) NOT NULL, + PRIMARY KEY (`el_id`), + KEY `el_from` (`el_from`,`el_to`(40)), + KEY `el_to` (`el_to`(60),`el_from`), + KEY `el_index` (`el_index`(60)), + KEY `el_index_60` (`el_index_60`,`el_id`), + KEY `el_from_index_60` (`el_from`,`el_index_60`,`el_id`) +) ENGINE=InnoDB AUTO_INCREMENT=658440 DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `filearchive` +-- + +DROP TABLE IF EXISTS `filearchive`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `filearchive` ( + `fa_id` int unsigned NOT NULL AUTO_INCREMENT, + `fa_name` varbinary(255) NOT NULL DEFAULT '', + `fa_archive_name` varbinary(255) DEFAULT '', + `fa_storage_group` varbinary(16) DEFAULT NULL, + `fa_storage_key` varbinary(64) DEFAULT '', + `fa_deleted_user` int DEFAULT NULL, + `fa_deleted_timestamp` binary(14) DEFAULT NULL, + `fa_deleted_reason_id` bigint unsigned NOT NULL, + `fa_size` int unsigned DEFAULT '0', + `fa_width` int DEFAULT '0', + `fa_height` int DEFAULT '0', + `fa_metadata` mediumblob, + `fa_bits` int DEFAULT '0', + `fa_media_type` enum('UNKNOWN','BITMAP','DRAWING','AUDIO','VIDEO','MULTIMEDIA','OFFICE','TEXT','EXECUTABLE','ARCHIVE','3D') DEFAULT NULL, + `fa_major_mime` enum('unknown','application','audio','image','text','video','message','model','multipart','chemical') DEFAULT 'unknown', + `fa_minor_mime` varbinary(100) DEFAULT 'unknown', + `fa_description_id` bigint unsigned NOT NULL, + `fa_actor` bigint unsigned NOT NULL, + `fa_timestamp` binary(14) DEFAULT NULL, + `fa_deleted` tinyint unsigned NOT NULL DEFAULT '0', + `fa_sha1` varbinary(32) NOT NULL DEFAULT '', + PRIMARY KEY (`fa_id`), + KEY `fa_name` (`fa_name`,`fa_timestamp`), + KEY `fa_storage_group` (`fa_storage_group`,`fa_storage_key`), + KEY `fa_deleted_timestamp` (`fa_deleted_timestamp`), + KEY `fa_sha1` (`fa_sha1`(10)), + KEY `fa_actor_timestamp` (`fa_actor`,`fa_timestamp`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `image` +-- + +DROP TABLE IF EXISTS `image`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `image` ( + `img_name` varbinary(255) NOT NULL DEFAULT '', + `img_size` int unsigned NOT NULL DEFAULT '0', + `img_width` int NOT NULL DEFAULT '0', + `img_height` int NOT NULL DEFAULT '0', + `img_metadata` mediumblob NOT NULL, + `img_bits` int NOT NULL DEFAULT '0', + `img_media_type` enum('UNKNOWN','BITMAP','DRAWING','AUDIO','VIDEO','MULTIMEDIA','OFFICE','TEXT','EXECUTABLE','ARCHIVE','3D') DEFAULT NULL, + `img_major_mime` enum('unknown','application','audio','image','text','video','message','model','multipart','chemical') NOT NULL DEFAULT 'unknown', + `img_minor_mime` varbinary(100) NOT NULL DEFAULT 'unknown', + `img_description_id` bigint unsigned NOT NULL, + `img_actor` bigint unsigned NOT NULL, + `img_timestamp` binary(14) NOT NULL, + `img_sha1` varbinary(32) NOT NULL DEFAULT '', + PRIMARY KEY (`img_name`), + KEY `img_size` (`img_size`), + KEY `img_timestamp` (`img_timestamp`), + KEY `img_sha1` (`img_sha1`), + KEY `img_media_mime` (`img_media_type`,`img_major_mime`,`img_minor_mime`), + KEY `img_actor_timestamp` (`img_actor`,`img_timestamp`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `imagelinks` +-- + +DROP TABLE IF EXISTS `imagelinks`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `imagelinks` ( + `il_from` int unsigned NOT NULL DEFAULT '0', + `il_to` varbinary(255) NOT NULL DEFAULT '', + `il_from_namespace` int NOT NULL DEFAULT '0', + PRIMARY KEY (`il_from`,`il_to`), + KEY `il_backlinks_namespace` (`il_from_namespace`,`il_to`,`il_from`), + KEY `il_to` (`il_to`,`il_from`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interwiki` +-- + +DROP TABLE IF EXISTS `interwiki`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interwiki` ( + `iw_prefix` varchar(32) NOT NULL, + `iw_url` blob NOT NULL, + `iw_local` tinyint(1) NOT NULL, + `iw_trans` tinyint NOT NULL DEFAULT '0', + `iw_api` blob NOT NULL, + `iw_wikiid` varchar(64) NOT NULL, + PRIMARY KEY (`iw_prefix`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `ip_changes` +-- + +DROP TABLE IF EXISTS `ip_changes`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `ip_changes` ( + `ipc_rev_id` int unsigned NOT NULL DEFAULT '0', + `ipc_rev_timestamp` binary(14) NOT NULL, + `ipc_hex` varbinary(35) NOT NULL DEFAULT '', + PRIMARY KEY (`ipc_rev_id`), + KEY `ipc_rev_timestamp` (`ipc_rev_timestamp`), + KEY `ipc_hex_time` (`ipc_hex`,`ipc_rev_timestamp`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; 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`user_email` (`user_email`(50)) +) ENGINE=InnoDB AUTO_INCREMENT=5049 DEFAULT CHARSET=binary; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `user_autocreate_serial` +-- + +DROP TABLE IF EXISTS `user_autocreate_serial`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `user_autocreate_serial` ( + `uas_shard` int unsigned NOT NULL, + `uas_value` int unsigned NOT NULL, + PRIMARY KEY (`uas_shard`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `user_former_groups` +-- + +DROP TABLE IF EXISTS `user_former_groups`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `user_former_groups` ( + `ufg_user` int unsigned NOT NULL DEFAULT '0', + `ufg_group` varbinary(255) NOT NULL DEFAULT '', + PRIMARY KEY (`ufg_user`,`ufg_group`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `user_groups` +-- + +DROP TABLE IF EXISTS `user_groups`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `user_groups` ( + `ug_user` int unsigned NOT NULL DEFAULT '0', + `ug_group` varbinary(255) NOT NULL DEFAULT '', + `ug_expiry` varbinary(14) DEFAULT NULL, + PRIMARY KEY (`ug_user`,`ug_group`), + KEY `ug_group` (`ug_group`), + KEY `ug_expiry` (`ug_expiry`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `user_newtalk` +-- + +DROP TABLE IF EXISTS `user_newtalk`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `user_newtalk` ( + `user_id` int unsigned NOT NULL DEFAULT '0', + `user_ip` varbinary(40) NOT NULL DEFAULT '', + `user_last_timestamp` binary(14) DEFAULT NULL, + KEY `un_user_id` (`user_id`), + KEY `un_user_ip` (`user_ip`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `user_properties` +-- + +DROP TABLE IF EXISTS `user_properties`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `user_properties` ( + `up_user` int unsigned NOT NULL, + `up_property` varbinary(255) NOT NULL, + `up_value` blob, + PRIMARY KEY (`up_user`,`up_property`), + KEY `up_property` (`up_property`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `watchlist` +-- + +DROP TABLE IF EXISTS `watchlist`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `watchlist` ( + `wl_id` int unsigned NOT NULL AUTO_INCREMENT, + `wl_user` int unsigned NOT NULL, + `wl_namespace` int NOT NULL DEFAULT '0', + `wl_title` varbinary(255) NOT NULL DEFAULT '', + `wl_notificationtimestamp` binary(14) DEFAULT NULL, + PRIMARY KEY (`wl_id`), + UNIQUE KEY `wl_user` (`wl_user`,`wl_namespace`,`wl_title`), + KEY `wl_user_notificationtimestamp` (`wl_user`,`wl_notificationtimestamp`), + KEY `wl_namespace_title` (`wl_namespace`,`wl_title`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `watchlist_expiry` +-- + +DROP TABLE IF EXISTS `watchlist_expiry`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `watchlist_expiry` ( + `we_item` int unsigned NOT NULL, + `we_expiry` binary(14) NOT NULL, + PRIMARY KEY (`we_item`), + KEY `we_expiry` (`we_expiry`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `AnnoJ` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `AnnoJ` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `AnnoJ`; + +-- +-- Current Database: `BAR_Search` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `BAR_Search` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `BAR_Search`; + +-- +-- Table structure for table `arrays` +-- + +DROP TABLE IF EXISTS `arrays`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `arrays` ( + `array_id` int DEFAULT NULL, + `array_platform` varchar(50) DEFAULT NULL, + `array_name` varchar(50) DEFAULT NULL, + KEY `array_id` (`array_id`), + CONSTRAINT `arrays_ibfk_1` FOREIGN KEY (`array_id`) REFERENCES `species_array` (`array_id`) ON DELETE CASCADE ON UPDATE RESTRICT +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `species_array` +-- + +DROP TABLE IF EXISTS `species_array`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `species_array` ( + `identifier` varchar(40) NOT NULL, + `species_id` int NOT NULL, + `array_id` int NOT NULL, + PRIMARY KEY (`identifier`), + UNIQUE KEY `species_id` (`species_id`), + UNIQUE KEY `array_id` (`array_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `species_template_tool` +-- + +DROP TABLE IF EXISTS `species_template_tool`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `species_template_tool` ( + `species_id` int DEFAULT NULL, + `species_name` varchar(50) DEFAULT NULL, + `tool_name` varchar(50) DEFAULT NULL, + `base_url` varchar(500) DEFAULT NULL, + `on_array` int DEFAULT NULL, + `image_name` varchar(255) DEFAULT NULL, + KEY `species_id` (`species_id`), + CONSTRAINT `species_template_tool_ibfk_1` FOREIGN KEY (`species_id`) REFERENCES `species_array` (`species_id`) ON DELETE CASCADE ON UPDATE RESTRICT +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `CDD3D` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `CDD3D` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `CDD3D`; + +-- +-- Table structure for table `SWISSVAR_06052015` +-- + +DROP TABLE IF EXISTS `SWISSVAR_06052015`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `SWISSVAR_06052015` ( + `EntryID` int NOT NULL AUTO_INCREMENT, + `SV_ID` varchar(100) NOT NULL, + `SP_ID` varchar(10) NOT NULL, + `ANNOT` varchar(100) NOT NULL, + `MUTN` mediumtext NOT NULL, + `DESCR` text, + `PDB_ID` varchar(4) NOT NULL, + `PDB_CHAIN` varchar(1) NOT NULL, + `SITE` int NOT NULL, + PRIMARY KEY (`EntryID`), + KEY `PDB_ID` (`PDB_ID`,`PDB_CHAIN`) +) ENGINE=InnoDB AUTO_INCREMENT=529208 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `NASCArrays` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `NASCArrays` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `NASCArrays`; + +-- +-- Table structure for table `Experiments` +-- + +DROP TABLE IF EXISTS `Experiments`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `Experiments` ( + `ExpID` int NOT NULL, + `Title` varchar(100) NOT NULL, + `Description` text, + `ExpDate` date DEFAULT NULL, + `Link` varchar(100) DEFAULT NULL, + PRIMARY KEY (`ExpID`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `Slides` +-- + +DROP TABLE IF EXISTS `Slides`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `Slides` ( + `ExpID` int NOT NULL, + `SlideID` varchar(100) NOT NULL, + `Slide_Name` int DEFAULT NULL, + `Genetic_Background` varchar(50) DEFAULT NULL, + `Tissue` varchar(200) DEFAULT NULL, + `Treatment` text, + `Stock_Code` varchar(100) DEFAULT NULL, + `Cel_File` varchar(100) DEFAULT NULL, + PRIMARY KEY (`SlideID`), + KEY `ExpID` (`ExpID`), + CONSTRAINT `Slides_ibfk_1` FOREIGN KEY (`ExpID`) REFERENCES `Experiments` (`ExpID`) ON DELETE RESTRICT ON UPDATE RESTRICT +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `NGM` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `NGM` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `NGM`; + +-- +-- Table structure for table `chr_seq_annotation` +-- + +DROP TABLE IF EXISTS `chr_seq_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `chr_seq_annotation` ( + `SeqID` varchar(20) NOT NULL, + `Source` varchar(10) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(20) DEFAULT NULL, + `geneId` varchar(20) DEFAULT NULL, + `Parent` varchar(40) DEFAULT NULL, + `Attributes` varchar(256) DEFAULT NULL, + KEY `range` (`Source`,`SeqID`,`Start`,`End`), + KEY `seqend` (`Source`,`SeqID`,`End`), + KEY `typeid` (`SeqID`,`Source`,`Type`,`Parent`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `known_snps` +-- + +DROP TABLE IF EXISTS `known_snps`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `known_snps` ( + `source` varchar(10) NOT NULL DEFAULT 'TAIR9', + `seqId` varchar(10) NOT NULL, + `pos` int NOT NULL, + PRIMARY KEY (`source`,`seqId`,`pos`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='known SNPs in gene sequence'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `TRTCFungarium` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `TRTCFungarium` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `TRTCFungarium`; + +-- +-- Table structure for table `collections` +-- + +DROP TABLE IF EXISTS `collections`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `collections` ( + `Rev_Date` varchar(250) DEFAULT NULL, + `Collection` varchar(250) NOT NULL DEFAULT '', + `Coll_ID` varchar(250) NOT NULL DEFAULT '', + PRIMARY KEY (`Collection`,`Coll_ID`), + KEY `coll_id` (`Coll_ID`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `link` +-- + +DROP TABLE IF EXISTS `link`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `link` ( + `Rev_Date` varchar(250) DEFAULT NULL, + `Accession_No` varchar(250) NOT NULL DEFAULT '', + `Coll_ID` varchar(250) NOT NULL DEFAULT '', + PRIMARY KEY (`Accession_No`,`Coll_ID`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `main` +-- + +DROP TABLE IF EXISTS `main`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `main` ( + `Rev_Date` varchar(250) DEFAULT NULL, + `Reviewer` varchar(250) DEFAULT NULL, + `Rec_Enter` varchar(250) DEFAULT NULL, + `Rec_Date` varchar(250) DEFAULT NULL, + `TRTC_Loc` varchar(250) DEFAULT NULL, + `Qtyr` varchar(250) DEFAULT NULL, + `TRTC` varchar(250) DEFAULT NULL, + `Accession_No` varchar(250) NOT NULL DEFAULT '', + `Museum_Coll` varchar(250) DEFAULT NULL, + `Kingdom` varchar(250) DEFAULT NULL, + `Phyllum` varchar(250) DEFAULT NULL, + `Class` varchar(250) DEFAULT NULL, + `Organism` varchar(250) DEFAULT NULL, + `Family` varchar(250) DEFAULT NULL, + `Genus` varchar(250) DEFAULT NULL, + `Species` varchar(250) DEFAULT NULL, + `Species_Auth` varchar(250) DEFAULT NULL, + `Subspecies` varchar(250) DEFAULT NULL, + `Subspecies_Auth` varchar(250) DEFAULT NULL, + `Variety` varchar(250) DEFAULT NULL, + `Variety_Auth` varchar(250) DEFAULT NULL, + `Formae` varchar(250) DEFAULT NULL, + `Formae_Auth` varchar(250) DEFAULT NULL, + `Other_Tax_Level` varchar(250) DEFAULT NULL, + `Other_Tax_Lev_Auth` varchar(250) DEFAULT NULL, + `Image` varchar(250) DEFAULT NULL, + `Notes_Image` varchar(250) DEFAULT NULL, + `Sequence` varchar(250) DEFAULT NULL, + `Sampled_for_DNA` varchar(250) DEFAULT NULL, + `Specimen_status` varchar(250) DEFAULT NULL, + `Exsiccatae` varchar(250) DEFAULT NULL, + `Exsic_No` varchar(250) DEFAULT NULL, + `Host_Genus` varchar(250) DEFAULT NULL, + `Host_sp` varchar(250) DEFAULT NULL, + `Collector` varchar(250) DEFAULT NULL, + `Coll_no` varchar(250) DEFAULT NULL, + `Other_Coll` varchar(250) DEFAULT NULL, + `Coll_Date` varchar(250) DEFAULT NULL, + `Id_Name` varchar(250) DEFAULT NULL, + `Herb_Name` varchar(250) DEFAULT NULL, + `Cross_Ref` varchar(250) DEFAULT NULL, + `Country` varchar(250) DEFAULT NULL, + `Province` varchar(250) DEFAULT NULL, + `District` varchar(250) DEFAULT NULL, + `County` varchar(250) DEFAULT NULL, + `Township` varchar(250) DEFAULT NULL, + `Other` varchar(250) DEFAULT NULL, + `LatN` varchar(250) DEFAULT NULL, + `LatS` varchar(250) DEFAULT NULL, + `LongE` varchar(250) DEFAULT NULL, + `LongW` varchar(250) DEFAULT NULL, + `UTM_E` varchar(250) DEFAULT NULL, + `UTM_N` varchar(250) DEFAULT NULL, + `UTM_Z` varchar(250) DEFAULT NULL, + `Map_Ref` varchar(250) DEFAULT NULL, + `Elevation` varchar(250) DEFAULT NULL, + `Units_Elevation` varchar(250) DEFAULT NULL, + `Location` varchar(250) DEFAULT NULL, + `Loc_Description` varchar(250) DEFAULT NULL, + `Habitat` varchar(250) DEFAULT NULL, + `Substrate` varchar(250) DEFAULT NULL, + `Notes_Other` varchar(250) DEFAULT NULL, + `Notes_on_specimen` varchar(250) DEFAULT NULL, + `Notes` varchar(250) DEFAULT NULL, + `Publications` varchar(250) DEFAULT NULL, + PRIMARY KEY (`Accession_No`), + KEY `image` (`Image`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `actinidia_bud_development` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `actinidia_bud_development` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `actinidia_bud_development`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(12) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(8) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `actinidia_flower_fruit_development` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `actinidia_flower_fruit_development` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `actinidia_flower_fruit_development`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(12) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(16) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `actinidia_postharvest` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `actinidia_postharvest` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `actinidia_postharvest`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(12) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(24) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `actinidia_vegetative_growth` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `actinidia_vegetative_growth` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `actinidia_vegetative_growth`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(12) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(16) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `affydb` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `affydb` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `affydb`; + +-- +-- Table structure for table `proj_info` +-- + +DROP TABLE IF EXISTS `proj_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_info` ( + `proj_id` int unsigned NOT NULL AUTO_INCREMENT, + `proj_date_submit` date NOT NULL DEFAULT '0000-00-00', + `proj_date_ready` date NOT NULL DEFAULT '0000-00-00', + `proj_date_complete` date NOT NULL DEFAULT '0000-00-00', + `proj_paid_date` date NOT NULL DEFAULT '0000-00-00', + `proj_paid_amount` decimal(6,2) NOT NULL DEFAULT '0.00', + `proj_title` tinytext, + `proj_pi` tinytext, + `proj_pi_title` tinytext, + `proj_pi_inst` tinytext, + `proj_pi_addr` tinytext, + `proj_pi_tel` tinytext, + `proj_pi_fax` tinytext, + `proj_pi_email` tinytext, + `proj_keyw1` tinytext, + `proj_keyw2` tinytext, + `proj_keyw3` tinytext, + `proj_keyw4` tinytext, + `proj_keyw5` tinytext, + `proj_res_area` tinytext, + `proj_abstr` text, + `proj_prop` text, + `proj_fund_src` text, + `proj_num_samps` tinyint unsigned NOT NULL DEFAULT '0', + `proj_num_arrays` tinyint unsigned NOT NULL DEFAULT '0', + `proj_ht3_array` tinytext, + PRIMARY KEY (`proj_id`) +) ENGINE=InnoDB AUTO_INCREMENT=53 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `proj_res_area` +-- + +DROP TABLE IF EXISTS `proj_res_area`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_res_area` ( + `proj_res_index` text, + `proj_res_area` tinytext +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_biosource_info` +-- + +DROP TABLE IF EXISTS `sample_biosource_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_biosource_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned DEFAULT NULL, + `sample_bio_name` tinytext, + `sample_organism` tinytext, + `sample_alias` tinytext, + `sample_stock_code` tinytext, + `sample_genetic_var` tinytext, + `sample_tissue` tinytext, + `sample_diseased` tinytext, + `sample_growth_cond` tinytext, + `sample_growth_stage` tinytext, + `sample_time_point` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned NOT NULL DEFAULT '0', + `sample_file_name` tinytext NOT NULL, + `data_num` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(30) DEFAULT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_call` tinytext NOT NULL, + `data_p_val` float NOT NULL DEFAULT '0', + `data_bot_id` tinytext +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_ext_param` +-- + +DROP TABLE IF EXISTS `sample_ext_param`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_ext_param` ( + `sample_param_type` tinytext, + `sample_param_index` tinytext NOT NULL, + `sample_param_data` tinytext NOT NULL, + `sample_param_ontology` tinytext +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_extraction_info` +-- + +DROP TABLE IF EXISTS `sample_extraction_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_extraction_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned DEFAULT NULL, + `sample_protocol_name` tinytext NOT NULL, + `sample_protocol_method` tinytext, + `sample_amplification` tinytext, + `sample_other_info` tinytext, + `sample_type` tinytext, + PRIMARY KEY (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_general_info` +-- + +DROP TABLE IF EXISTS `sample_general_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_general_info` ( + `sample_id` int unsigned NOT NULL AUTO_INCREMENT, + `proj_id` int unsigned DEFAULT NULL, + `sample_repl` tinytext, + `sample_ctrl` tinytext, + `sample_name` tinytext, + `sample_desc` longtext, + `sample_od` decimal(10,3) unsigned NOT NULL DEFAULT '0.000', + `sample_mass` decimal(10,3) unsigned NOT NULL DEFAULT '0.000', + `sample_vol` decimal(10,3) unsigned NOT NULL DEFAULT '0.000', + `sample_file_name` tinytext, + `sample_bot_id` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB AUTO_INCREMENT=486 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_hybrid_blocking_agent` +-- + +DROP TABLE IF EXISTS `sample_hybrid_blocking_agent`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_hybrid_blocking_agent` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned DEFAULT NULL, + `blocking_agent` tinytext, + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_hybrid_solution` +-- + +DROP TABLE IF EXISTS `sample_hybrid_solution`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_hybrid_solution` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned DEFAULT NULL, + `solution` tinytext, + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_hybrid_wash` +-- + +DROP TABLE IF EXISTS `sample_hybrid_wash`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_hybrid_wash` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned DEFAULT NULL, + `step_num` int DEFAULT NULL, + `wash_step` tinytext, + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_hybridization_info` +-- + +DROP TABLE IF EXISTS `sample_hybridization_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_hybridization_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned DEFAULT NULL, + `sample_protocol_name` tinytext, + `sample_amount` tinytext, + `sample_time` int DEFAULT NULL, + `sample_concentration` int DEFAULT NULL, + `sample_volume` int DEFAULT NULL, + `sample_temperature` int DEFAULT NULL, + PRIMARY KEY (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_image_analysis_info` +-- + +DROP TABLE IF EXISTS `sample_image_analysis_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_image_analysis_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned DEFAULT NULL, + `sample_image_name` tinytext, + `sample_scaling_factor` float DEFAULT NULL, + `sample_software_name` tinytext, + PRIMARY KEY (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_label_info` +-- + +DROP TABLE IF EXISTS `sample_label_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_label_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned DEFAULT NULL, + `sample_protocol_name` tinytext, + `sample_label_amount` int unsigned DEFAULT NULL, + `sample_label_name` tinytext, + `sample_label_method` tinytext, + `sample_other_info` tinytext, + PRIMARY KEY (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_norm_info` +-- + +DROP TABLE IF EXISTS `sample_norm_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_norm_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned DEFAULT NULL, + `sample_strategy` tinytext, + `sample_algorithm` tinytext, + `sample_ctrl_elem` tinytext, + PRIMARY KEY (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_scan_info` +-- + +DROP TABLE IF EXISTS `sample_scan_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_scan_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned DEFAULT NULL, + `sample_protocol_name` tinytext, + `sample_image_width` int unsigned DEFAULT NULL, + `sample_image_height` int unsigned DEFAULT NULL, + `sample_x_res` int unsigned DEFAULT NULL, + `sample_y_res` int unsigned DEFAULT NULL, + `sample_scanner_name` tinytext, + `sample_software_name` tinytext, + PRIMARY KEY (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_slide_info` +-- + +DROP TABLE IF EXISTS `sample_slide_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_slide_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned DEFAULT NULL, + `sample_date_hybridized` tinytext, + `sample_slide_design_name` tinytext, + `sample_array_source` tinytext, + `sample_array_type` tinytext, + `sample_num_array_spots` tinytext, + PRIMARY KEY (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_temp_data` +-- + +DROP TABLE IF EXISTS `sample_temp_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_temp_data` ( + `data_probeset_id` tinytext, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned NOT NULL DEFAULT '0', + `data_signal` float NOT NULL DEFAULT '0', + `data_call` tinytext NOT NULL, + `data_p_val` float NOT NULL DEFAULT '0', + `data_bot_id` tinytext +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `annotations_lookup` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `annotations_lookup` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `annotations_lookup`; + +-- +-- Table structure for table `agi_alias` +-- + +DROP TABLE IF EXISTS `agi_alias`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `agi_alias` ( + `agi` varchar(30) NOT NULL, + `alias` varchar(30) NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`agi`,`alias`,`date`), + KEY `alias_date_agi` (`alias`,`date`,`agi`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `agi_annotation` +-- + +DROP TABLE IF EXISTS `agi_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `agi_annotation` ( + `agi` varchar(11) NOT NULL, + `annotation` longtext NOT NULL, + `date` date NOT NULL DEFAULT '0000-00-00', + PRIMARY KEY (`agi`,`date`), + KEY `date_agi` (`date`,`agi`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `agi_ncbi_geneid` +-- + +DROP TABLE IF EXISTS `agi_ncbi_geneid`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `agi_ncbi_geneid` ( + `agi` varchar(30) NOT NULL, + `geneid` varchar(30) NOT NULL, + `date` date NOT NULL, + KEY `gene_gi` (`geneid`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `agi_ncbi_ids` +-- + +DROP TABLE IF EXISTS `agi_ncbi_ids`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `agi_ncbi_ids` ( + `agi` varchar(30) NOT NULL DEFAULT '', + `geneid` varchar(30) DEFAULT NULL, + `protid` varchar(30) DEFAULT NULL, + `date` date NOT NULL, + KEY `agi_geneid_prot_id_date` (`agi`,`geneid`,`protid`,`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `agi_ncbi_mrnaid` +-- + +DROP TABLE IF EXISTS `agi_ncbi_mrnaid`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `agi_ncbi_mrnaid` ( + `agi` varchar(30) NOT NULL, + `mrnaid` varchar(30) NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`mrnaid`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `agi_ncbi_protid` +-- + +DROP TABLE IF EXISTS `agi_ncbi_protid`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `agi_ncbi_protid` ( + `agi` varchar(30) NOT NULL, + `protid` varchar(30) NOT NULL, + `date` date NOT NULL, + KEY `prot_gi` (`protid`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `agi_uniprot_lookup` +-- + +DROP TABLE IF EXISTS `agi_uniprot_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `agi_uniprot_lookup` ( + `agi` varchar(30) NOT NULL, + `uniprot` varchar(30) NOT NULL, + `date` date NOT NULL, + KEY `date_agi_uniport` (`date`,`agi`,`uniprot`), + KEY `date_uniport_agi` (`date`,`uniprot`,`agi`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `araport11_gff3` +-- + +DROP TABLE IF EXISTS `araport11_gff3`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `araport11_gff3` ( + `SeqID` varchar(20) NOT NULL, + `Source` varchar(10) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(20) DEFAULT NULL, + `geneId` varchar(20) DEFAULT NULL, + `Parent` varchar(512) DEFAULT NULL, + `Attributes` varchar(256) DEFAULT NULL, + KEY `geneId_idx` (`geneId`), + KEY `Start_idx` (`Start`), + KEY `End_idx` (`End`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `at_agi_lookup` +-- + +DROP TABLE IF EXISTS `at_agi_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `at_agi_lookup` ( + `probeset` varchar(60) NOT NULL DEFAULT '', + `agi` varchar(30) NOT NULL DEFAULT '', + `date` date NOT NULL DEFAULT '0000-00-00', + PRIMARY KEY (`probeset`,`agi`,`date`), + KEY `date_agi_probeset` (`date`,`agi`,`probeset`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `chr_seq_annotation` +-- + +DROP TABLE IF EXISTS `chr_seq_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `chr_seq_annotation` ( + `SeqID` varchar(20) NOT NULL, + `Source` varchar(10) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(20) DEFAULT NULL, + `geneId` varchar(20) DEFAULT NULL, + `Parent` varchar(40) DEFAULT NULL, + `Attributes` varchar(256) DEFAULT NULL, + KEY `range` (`Source`,`SeqID`,`Start`,`End`), + KEY `seqend` (`Source`,`SeqID`,`End`), + KEY `typeid` (`SeqID`,`Source`,`Type`,`Parent`), + KEY `Start_idx` (`Start`), + KEY `End_idx` (`End`), + KEY `Id_idx` (`Id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `chr_upload` +-- + +DROP TABLE IF EXISTS `chr_upload`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `chr_upload` ( + `SeqID` varchar(20) NOT NULL, + `Source` varchar(10) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(20) DEFAULT NULL, + `geneId` varchar(20) DEFAULT NULL, + `Parent` varchar(40) DEFAULT NULL, + `Attributes` varchar(256) DEFAULT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gene_annotations` +-- + +DROP TABLE IF EXISTS `gene_annotations`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene_annotations` ( + `agi` varchar(12) NOT NULL, + `annotation` longtext NOT NULL, + `source` varchar(10) NOT NULL, + PRIMARY KEY (`agi`,`source`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pbi_agi_lookup` +-- + +DROP TABLE IF EXISTS `pbi_agi_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pbi_agi_lookup` ( + `probeset` varchar(60) NOT NULL DEFAULT '', + `agi` varchar(30) NOT NULL DEFAULT '', + `date` date NOT NULL DEFAULT '0000-00-00', + PRIMARY KEY (`probeset`,`agi`,`date`), + KEY `agi` (`agi`), + KEY `date` (`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `tair_ncbi_refseq_mapping_prot` +-- + +DROP TABLE IF EXISTS `tair_ncbi_refseq_mapping_prot`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `tair_ncbi_refseq_mapping_prot` ( + `agi` varchar(30) NOT NULL, + `ncbi` varchar(30) NOT NULL, + `refseq_acc` varchar(30) NOT NULL, + `date` date NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `tair_ncbi_refseq_mapping_rna` +-- + +DROP TABLE IF EXISTS `tair_ncbi_refseq_mapping_rna`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `tair_ncbi_refseq_mapping_rna` ( + `agi` varchar(30) NOT NULL, + `ncbi` varchar(30) NOT NULL, + `refseq_acc` varchar(30) NOT NULL, + `date` date NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `apple` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `apple` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `apple`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(5) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(18) NOT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_bot_id` varchar(12) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `arabidopsis_ecotypes` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `arabidopsis_ecotypes` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `arabidopsis_ecotypes`; + +-- +-- Table structure for table `proj_info` +-- + +DROP TABLE IF EXISTS `proj_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_info` ( + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `proj_title` tinytext, + `proj_pi` tinytext, + `proj_pi_title` tinytext, + `proj_pi_inst` tinytext, + `proj_pi_addr` tinytext, + `proj_keyw1` tinytext, + `proj_keyw2` tinytext, + `proj_keyw3` tinytext, + `proj_keyw4` tinytext, + `proj_keyw5` tinytext, + `proj_res_area` tinytext, + `proj_num_samps` tinyint unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`proj_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_biosource_info` +-- + +DROP TABLE IF EXISTS `sample_biosource_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_biosource_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_bio_name` tinytext, + `sample_organism` tinytext, + `sample_alias` tinytext, + `sample_stock_code` tinytext, + `sample_genetic_var` tinytext, + `sample_tissue` tinytext, + `sample_diseased` tinytext, + `sample_growth_cond` tinytext, + `sample_growth_stage` tinytext, + `sample_time_point` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(30) DEFAULT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(16) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_general_info` +-- + +DROP TABLE IF EXISTS `sample_general_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_general_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_repl` tinytext, + `sample_ctrl` tinytext, + `sample_desc` tinytext, + `sample_file_name` tinytext, + `sample_bot_id` tinytext NOT NULL, + `sample_name` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `arabidopsis_proteomics` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `arabidopsis_proteomics` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `arabidopsis_proteomics`; + +-- +-- Table structure for table `abundance` +-- + +DROP TABLE IF EXISTS `abundance`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `abundance` ( + `genotype` int NOT NULL, + `AGI` text NOT NULL, + `replicant` int NOT NULL, + `zt` int NOT NULL, + `value` decimal(10,8) NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `rhythmicity` +-- + +DROP TABLE IF EXISTS `rhythmicity`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `rhythmicity` ( + `genotype` int NOT NULL, + `AGI` text NOT NULL, + `cs_acrophase` decimal(10,8) NOT NULL, + `cs_amplitude` decimal(10,8) NOT NULL, + `cs_pval` decimal(25,23) NOT NULL, + `cs_qval` decimal(25,23) NOT NULL, + `cs_mean` decimal(25,18) NOT NULL, + `jtk_acrophase` decimal(10,8) NOT NULL, + `jtk_amplitude` decimal(10,8) NOT NULL, + `jtk_pval` decimal(25,23) NOT NULL, + `jtk_qval` decimal(25,23) NOT NULL, + `jtk_mean` decimal(25,18) NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `arabidopsis_transcriptomics` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `arabidopsis_transcriptomics` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `arabidopsis_transcriptomics`; + +-- +-- Table structure for table `abundance` +-- + +DROP TABLE IF EXISTS `abundance`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `abundance` ( + `genotype` int NOT NULL, + `AGI` varchar(12) NOT NULL, + `replicant` int NOT NULL, + `zt` int NOT NULL, + `value` float NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `rhythmicity` +-- + +DROP TABLE IF EXISTS `rhythmicity`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `rhythmicity` ( + `genotype` int NOT NULL, + `AGI` text NOT NULL, + `cs_acrophase` decimal(10,8) NOT NULL, + `cs_amplitude` decimal(10,8) NOT NULL, + `cs_pval` decimal(25,23) NOT NULL, + `cs_qval` decimal(25,23) NOT NULL, + `cs_mean` decimal(25,18) NOT NULL, + `jtk_acrophase` decimal(10,8) NOT NULL, + `jtk_amplitude` decimal(10,8) NOT NULL, + `jtk_pval` decimal(25,23) NOT NULL, + `jtk_qval` decimal(25,23) NOT NULL, + `jtk_mean` decimal(25,18) NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `arachis` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `arachis` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `arachis`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` varchar(5) NOT NULL, + `proj_id` varchar(24) NOT NULL, + `data_probeset_id` varchar(30) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(65) NOT NULL, + PRIMARY KEY (`sample_id`,`proj_id`,`data_probeset_id`), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `atgenexp` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `atgenexp` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `atgenexp`; + +-- +-- Table structure for table `proj_info` +-- + +DROP TABLE IF EXISTS `proj_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_info` ( + `proj_id` int unsigned NOT NULL DEFAULT '0', + `proj_title` tinytext, + `proj_pi` tinytext, + `proj_pi_title` tinytext, + `proj_pi_inst` tinytext, + `proj_pi_addr` tinytext, + `proj_keyw1` tinytext, + `proj_keyw2` tinytext, + `proj_keyw3` tinytext, + `proj_keyw4` tinytext, + `proj_keyw5` tinytext, + `proj_res_area` tinytext, + `proj_num_samps` tinyint unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`proj_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `proj_res_area` +-- + +DROP TABLE IF EXISTS `proj_res_area`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_res_area` ( + `proj_res_index` tinytext, + `proj_res_area` tinytext +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_biosource_info` +-- + +DROP TABLE IF EXISTS `sample_biosource_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_biosource_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned NOT NULL DEFAULT '0', + `sample_bio_name` tinytext, + `sample_organism` tinytext, + `sample_alias` tinytext, + `sample_stock_code` tinytext, + `sample_genetic_var` tinytext, + `sample_tissue` tinytext, + `sample_diseased` tinytext, + `sample_growth_cond` tinytext, + `sample_growth_stage` tinytext, + `sample_time_point` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned NOT NULL DEFAULT '0', + `sample_file_name` tinytext NOT NULL, + `data_probeset_id` varchar(30) DEFAULT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_call` tinytext NOT NULL, + `data_p_val` float NOT NULL DEFAULT '0', + `data_bot_id` varchar(50) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_ext_param` +-- + +DROP TABLE IF EXISTS `sample_ext_param`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_ext_param` ( + `sample_param_type` tinytext, + `sample_param_index` tinytext NOT NULL, + `sample_param_data` tinytext NOT NULL, + `sample_param_ontology` tinytext +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_general_info` +-- + +DROP TABLE IF EXISTS `sample_general_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_general_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned NOT NULL DEFAULT '0', + `sample_repl` tinytext, + `sample_ctrl` tinytext, + `sample_desc` tinytext, + `sample_file_name` tinytext, + `sample_bot_id` tinytext NOT NULL, + `sample_name` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_temp_data` +-- + +DROP TABLE IF EXISTS `sample_temp_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_temp_data` ( + `data_probeset_id` tinytext, + KEY `data_probeset_id` (`data_probeset_id`(12)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `atgenexp_hormone` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `atgenexp_hormone` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `atgenexp_hormone`; + +-- +-- Table structure for table `proj_info` +-- + +DROP TABLE IF EXISTS `proj_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_info` ( + `proj_id` int unsigned NOT NULL DEFAULT '0', + `proj_title` tinytext, + `proj_pi` tinytext, + `proj_pi_title` tinytext, + `proj_pi_inst` tinytext, + `proj_pi_addr` tinytext, + `proj_keyw1` tinytext, + `proj_keyw2` tinytext, + `proj_keyw3` tinytext, + `proj_keyw4` tinytext, + `proj_keyw5` tinytext, + `proj_res_area` tinytext, + `proj_num_samps` tinyint unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`proj_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `proj_res_area` +-- + +DROP TABLE IF EXISTS `proj_res_area`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_res_area` ( + `proj_res_index` tinytext, + `proj_res_area` tinytext +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_biosource_info` +-- + +DROP TABLE IF EXISTS `sample_biosource_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_biosource_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned NOT NULL DEFAULT '0', + `sample_bio_name` tinytext, + `sample_organism` tinytext, + `sample_alias` tinytext, + `sample_stock_code` tinytext, + `sample_genetic_var` tinytext, + `sample_tissue` tinytext, + `sample_diseased` tinytext, + `sample_growth_condition` tinytext, + `sample_growth_stage` tinytext, + `sample_time_point` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(30) DEFAULT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(50) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_ext_param` +-- + +DROP TABLE IF EXISTS `sample_ext_param`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_ext_param` ( + `sample_param_type` tinytext NOT NULL, + `sample_param_index` tinytext, + `sample_param_data` tinytext, + `sample_param_ontology` tinytext NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_general_info` +-- + +DROP TABLE IF EXISTS `sample_general_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_general_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned NOT NULL DEFAULT '0', + `sample_repl` tinytext, + `sample_ctrl` tinytext, + `sample_desc` tinytext, + `sample_file_name` tinytext, + `sample_bot_id` tinytext NOT NULL, + `sample_name` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_temp_data` +-- + +DROP TABLE IF EXISTS `sample_temp_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_temp_data` ( + `data_probeset_id` tinytext, + KEY `data_probeset_id` (`data_probeset_id`(12)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `seed_data` +-- + +DROP TABLE IF EXISTS `seed_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `seed_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` tinytext, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` tinytext, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(6)), + KEY `data_probeset_id` (`data_probeset_id`(6),`data_bot_id`(20)), + KEY `data_bot_id` (`data_bot_id`(20)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `atgenexp_pathogen` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `atgenexp_pathogen` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `atgenexp_pathogen`; + +-- +-- Table structure for table `proj_info` +-- + +DROP TABLE IF EXISTS `proj_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_info` ( + `proj_id` varchar(15) NOT NULL, + `proj_title` tinytext, + `proj_pi` tinytext, + `proj_pi_title` tinytext, + `proj_pi_inst` tinytext, + `proj_pi_addr` tinytext, + `proj_keyw1` tinytext, + `proj_keyw2` tinytext, + `proj_keyw3` tinytext, + `proj_keyw4` tinytext, + `proj_keyw5` tinytext, + `proj_res_area` tinytext, + `proj_num_samps` tinytext, + PRIMARY KEY (`proj_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `proj_res_area` +-- + +DROP TABLE IF EXISTS `proj_res_area`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_res_area` ( + `proj_res_index` tinytext, + `proj_res_area` tinytext +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_biosource_info` +-- + +DROP TABLE IF EXISTS `sample_biosource_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_biosource_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_bio_name` tinytext, + `sample_organism` tinytext, + `sample_alias` tinytext, + `sample_stock_code` tinytext, + `sample_genetic_var` tinytext, + `sample_tissue` tinytext, + `sample_diseased` tinytext, + `sample_growth_condition` tinytext, + `sample_growth_stage` tinytext, + `sample_time_point` tinytext, + PRIMARY KEY (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(30) DEFAULT NULL, + `data_signal` float DEFAULT NULL, + `data_call` tinytext, + `data_p_val` float DEFAULT NULL, + `data_bot_id` varchar(50) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_ext_param` +-- + +DROP TABLE IF EXISTS `sample_ext_param`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_ext_param` ( + `sample_param_type` tinytext NOT NULL, + `sample_param_index` tinytext, + `sample_param_data` tinytext, + `sample_param_ontology` tinytext NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_general_info` +-- + +DROP TABLE IF EXISTS `sample_general_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_general_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_repl` tinytext, + `sample_ctrl` tinytext, + `sample_desc` tinytext, + `sample_file_name` tinytext, + `sample_bot_id` tinytext, + `sample_name` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_temp_data` +-- + +DROP TABLE IF EXISTS `sample_temp_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_temp_data` ( + `data_probeset_id` tinytext, + KEY `data_probeset_id` (`data_probeset_id`(12)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `atgenexp_plus` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `atgenexp_plus` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `atgenexp_plus`; + +-- +-- Table structure for table `proj_info` +-- + +DROP TABLE IF EXISTS `proj_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_info` ( + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `proj_title` tinytext, + `proj_pi` tinytext, + `proj_pi_title` tinytext, + `proj_pi_inst` tinytext, + `proj_pi_addr` tinytext, + `proj_keyw1` tinytext, + `proj_keyw2` tinytext, + `proj_keyw3` tinytext, + `proj_keyw4` tinytext, + `proj_keyw5` tinytext, + `proj_res_area` tinytext, + `proj_num_samps` tinyint unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`proj_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `proj_res_area` +-- + +DROP TABLE IF EXISTS `proj_res_area`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_res_area` ( + `proj_res_index` tinytext, + `proj_res_area` tinytext +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `ranks` +-- + +DROP TABLE IF EXISTS `ranks`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `ranks` ( + `expression` float DEFAULT NULL, + `rank` int NOT NULL DEFAULT '0', + PRIMARY KEY (`rank`), + KEY `expression_idx` (`expression`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_biosource_info` +-- + +DROP TABLE IF EXISTS `sample_biosource_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_biosource_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_bio_name` tinytext, + `sample_organism` tinytext, + `sample_alias` tinytext, + `sample_stock_code` tinytext, + `sample_genetic_var` tinytext, + `sample_tissue` tinytext, + `sample_diseased` tinytext, + `sample_growth_cond` tinytext, + `sample_growth_stage` tinytext, + `sample_time_point` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(30) DEFAULT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(50) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_ext_param` +-- + +DROP TABLE IF EXISTS `sample_ext_param`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_ext_param` ( + `sample_param_type` tinytext, + `sample_param_index` tinytext NOT NULL, + `sample_param_data` tinytext NOT NULL, + `sample_param_ontology` tinytext +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_general_info` +-- + +DROP TABLE IF EXISTS `sample_general_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_general_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_repl` tinytext, + `sample_ctrl` tinytext, + `sample_desc` tinytext, + `sample_file_name` tinytext, + `sample_bot_id` tinytext NOT NULL, + `sample_name` tinytext, + PRIMARY KEY (`sample_id`), + KEY `proj_id` (`proj_id`), + KEY `idx` (`proj_id`,`sample_repl`(12),`sample_ctrl`(12),`sample_bot_id`(12)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_temp_data` +-- + +DROP TABLE IF EXISTS `sample_temp_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_temp_data` ( + `data_probeset_id` tinytext, + KEY `data_probeset_id` (`data_probeset_id`(12)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `atgenexp_stress` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `atgenexp_stress` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `atgenexp_stress`; + +-- +-- Table structure for table `proj_info` +-- + +DROP TABLE IF EXISTS `proj_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_info` ( + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `proj_title` tinytext, + `proj_pi` tinytext, + `proj_pi_title` tinytext, + `proj_pi_inst` tinytext, + `proj_pi_addr` tinytext, + `proj_keyw1` tinytext, + `proj_keyw2` tinytext, + `proj_keyw3` tinytext, + `proj_keyw4` tinytext, + `proj_keyw5` tinytext, + `proj_res_area` tinytext, + `proj_num_samps` tinyint unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`proj_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `proj_res_area` +-- + +DROP TABLE IF EXISTS `proj_res_area`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_res_area` ( + `proj_res_index` tinytext, + `proj_res_area` tinytext +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_biosource_info` +-- + +DROP TABLE IF EXISTS `sample_biosource_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_biosource_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_bio_name` tinytext, + `sample_organism` tinytext, + `sample_alias` tinytext, + `sample_stock_code` tinytext, + `sample_genetic_var` tinytext, + `sample_tissue` tinytext, + `sample_diseased` tinytext, + `sample_growth_cond` tinytext, + `sample_growth_stage` tinytext, + `sample_time_point` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(30) DEFAULT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_call` varchar(20) DEFAULT NULL, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(40) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_ext_param` +-- + +DROP TABLE IF EXISTS `sample_ext_param`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_ext_param` ( + `sample_param_type` tinytext, + `sample_param_index` tinytext NOT NULL, + `sample_param_data` tinytext NOT NULL, + `sample_param_ontology` tinytext +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_general_info` +-- + +DROP TABLE IF EXISTS `sample_general_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_general_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_repl` tinytext, + `sample_ctrl` tinytext, + `sample_desc` tinytext, + `sample_file_name` tinytext, + `sample_bot_id` tinytext NOT NULL, + `sample_name` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_temp_data` +-- + +DROP TABLE IF EXISTS `sample_temp_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_temp_data` ( + `data_probeset_id` tinytext, + KEY `data_probeset_id` (`data_probeset_id`(12)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `bar_api_db_api_test` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `bar_api_db_api_test` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `bar_api_db_api_test`; + +-- +-- Current Database: `barley_annotations_lookup` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `barley_annotations_lookup` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `barley_annotations_lookup`; + +-- +-- Table structure for table `at_bar_lookup` +-- + +DROP TABLE IF EXISTS `at_bar_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `at_bar_lookup` ( + `bar` varchar(30) NOT NULL, + `probeset` varchar(30) NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`probeset`,`bar`,`date`), + KEY `date_gene` (`bar`,`probeset`,`date`), + KEY `date` (`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `bar_annotation` +-- + +DROP TABLE IF EXISTS `bar_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `bar_annotation` ( + `bar` varchar(60) NOT NULL, + `annotation` longtext NOT NULL, + `go_annotation` mediumtext NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`bar`,`date`), + KEY `date` (`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `barley_seed_lookup` +-- + +DROP TABLE IF EXISTS `barley_seed_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `barley_seed_lookup` ( + `gene` varchar(32) NOT NULL, + `probeset` varchar(32) NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`probeset`,`gene`,`date`), + KEY `date_gene` (`gene`,`probeset`,`date`), + KEY `date` (`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `barley_mas` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `barley_mas` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `barley_mas`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(30) NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(24) NOT NULL, + `sample_tissue` varchar(20) DEFAULT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(12)), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `barley_rma` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `barley_rma` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `barley_rma`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(30) NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(24) NOT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(12)), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `barley_seed` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `barley_seed` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `barley_seed`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(32) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(12) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `barley_spike_meristem` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `barley_spike_meristem` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `barley_spike_meristem`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(24) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `barley_spike_meristem_v3` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `barley_spike_meristem_v3` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `barley_spike_meristem_v3`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(32) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(24) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `bayer_canola_expressolog` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `bayer_canola_expressolog` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `bayer_canola_expressolog`; + +-- +-- Table structure for table `annotations` +-- + +DROP TABLE IF EXISTS `annotations`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `annotations` ( + `gene` varchar(60) NOT NULL, + `annotation` longtext NOT NULL, + `date` date NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `arabidopsis` +-- + +DROP TABLE IF EXISTS `arabidopsis`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `arabidopsis` ( + `gene` varchar(30) NOT NULL, + `sequence` mediumtext NOT NULL, + `date` date NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `arabidopsis_canola_expressolog` +-- + +DROP TABLE IF EXISTS `arabidopsis_canola_expressolog`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `arabidopsis_canola_expressolog` ( + `Cluster` int NOT NULL DEFAULT '0', + `Gene_A` varchar(60) NOT NULL DEFAULT '', + `Probeset_A` varchar(60) NOT NULL DEFAULT '', + `Genome_A` varchar(30) DEFAULT NULL, + `Gene_B` varchar(60) NOT NULL DEFAULT '', + `Probeset_B` varchar(60) NOT NULL DEFAULT '', + `Genome_B` varchar(30) DEFAULT NULL, + `SCC_Value` float DEFAULT NULL, + `Seq_Similarity` int DEFAULT NULL, + PRIMARY KEY (`Cluster`,`Gene_A`,`Probeset_A`,`Gene_B`,`Probeset_B`), + KEY `Gene_A` (`Gene_A`,`Gene_B`), + KEY `Gene_B` (`Gene_B`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `canola` +-- + +DROP TABLE IF EXISTS `canola`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `canola` ( + `gene` varchar(30) NOT NULL, + `sequence` mediumtext NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`gene`), + KEY `gene` (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `tissue_equivalency` +-- + +DROP TABLE IF EXISTS `tissue_equivalency`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `tissue_equivalency` ( + `Tissue_A` varchar(100) DEFAULT NULL, + `Species_A` varchar(100) DEFAULT NULL, + `Tissue_B` varchar(100) DEFAULT NULL, + `Species_B` varchar(100) DEFAULT NULL, + `SCC_Value` float DEFAULT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `brachypodium` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `brachypodium` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `brachypodium`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(18) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(50) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `brachypodium_Bd21` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `brachypodium_Bd21` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `brachypodium_Bd21`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(18) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(32) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `brachypodium_embryogenesis` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `brachypodium_embryogenesis` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `brachypodium_embryogenesis`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(18) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(50) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `brachypodium_grains` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `brachypodium_grains` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `brachypodium_grains`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(18) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(32) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `brachypodium_metabolites_map` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `brachypodium_metabolites_map` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_unicode_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `brachypodium_metabolites_map`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) CHARACTER SET utf8mb4 COLLATE utf8mb4_unicode_ci NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(64) CHARACTER SET utf8mb4 COLLATE utf8mb4_unicode_ci NOT NULL, + `data_signal` float DEFAULT NULL, + `data_bot_id` varchar(45) CHARACTER SET utf8mb4 COLLATE utf8mb4_unicode_ci NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_unicode_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `brachypodium_photo_thermocycle` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `brachypodium_photo_thermocycle` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `brachypodium_photo_thermocycle`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(18) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(12) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `brassica_rapa` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `brassica_rapa` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `brassica_rapa`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(5) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(16) NOT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_bot_id` varchar(10) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `cacao_developmental_atlas` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `cacao_developmental_atlas` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `cacao_developmental_atlas`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(5) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_bot_id` varchar(16) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `cacao_developmental_atlas_sca` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `cacao_developmental_atlas_sca` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `cacao_developmental_atlas_sca`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(5) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_bot_id` varchar(16) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `cacao_drought_diurnal_atlas` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `cacao_drought_diurnal_atlas` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `cacao_drought_diurnal_atlas`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(5) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_bot_id` varchar(16) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `cacao_drought_diurnal_atlas_sca` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `cacao_drought_diurnal_atlas_sca` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `cacao_drought_diurnal_atlas_sca`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(5) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_bot_id` varchar(16) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `cacao_infection` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `cacao_infection` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `cacao_infection`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(5) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(18) NOT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_bot_id` varchar(24) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `cacao_leaf` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `cacao_leaf` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `cacao_leaf`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(5) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(18) NOT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_bot_id` varchar(12) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `cacao_meristem_atlas_sca` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `cacao_meristem_atlas_sca` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `cacao_meristem_atlas_sca`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(5) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_bot_id` varchar(24) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `cacao_seed_atlas_sca` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `cacao_seed_atlas_sca` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `cacao_seed_atlas_sca`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(5) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_bot_id` varchar(24) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `camelina` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `camelina` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `camelina`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` varchar(5) NOT NULL, + `proj_id` varchar(5) NOT NULL, + `sample_file_name` varchar(20) DEFAULT NULL, + `data_probeset_id` varchar(20) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`proj_id`,`data_probeset_id`), + KEY `data_bot_id` (`data_bot_id`), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `camelina_annotations_lookup` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `camelina_annotations_lookup` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `camelina_annotations_lookup`; + +-- +-- Table structure for table `camelina_lookup` +-- + +DROP TABLE IF EXISTS `camelina_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `camelina_lookup` ( + `camelina_gene` varchar(30) NOT NULL, + `arabidopsis_gene` varchar(15) NOT NULL, + `date` date NOT NULL, + KEY `agi` (`arabidopsis_gene`), + KEY `camelina` (`camelina_gene`), + KEY `date` (`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `camelina_tpm` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `camelina_tpm` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `camelina_tpm`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` varchar(5) NOT NULL, + `proj_id` varchar(5) NOT NULL, + `sample_file_name` varchar(20) DEFAULT NULL, + `data_probeset_id` varchar(20) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`proj_id`,`data_probeset_id`), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`), + KEY `data_bot_id` (`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `cannabis` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `cannabis` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `cannabis`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(2) NOT NULL DEFAULT '0', + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(8) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `canola` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `canola` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `canola`; + +-- +-- Table structure for table `proj_info` +-- + +DROP TABLE IF EXISTS `proj_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_info` ( + `proj_id` varchar(100) NOT NULL DEFAULT '0', + `proj_title` tinytext, + `proj_pi` tinytext, + `proj_pi_title` tinytext, + `proj_pi_inst` tinytext, + `proj_pi_addr` tinytext, + `proj_keyw1` tinytext, + `proj_keyw2` tinytext, + `proj_keyw3` tinytext, + `proj_keyw4` tinytext, + `proj_keyw5` tinytext, + `proj_res_area` tinytext, + `proj_num_samps` tinyint unsigned NOT NULL DEFAULT '0' +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_biosource_info` +-- + +DROP TABLE IF EXISTS `sample_biosource_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_biosource_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(200) NOT NULL DEFAULT '0', + `sample_bio_name` tinytext, + `sample_organism` tinytext, + `sample_alias` tinytext, + `sample_stock_code` tinytext, + `sample_genetic_var` tinytext, + `sample_tissue` tinytext, + `sample_diseased` tinytext, + `sample_growth_cond` tinytext, + `sample_growth_stage` tinytext, + `sample_time_point` tinytext +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` tinytext NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` tinytext NOT NULL, + `sample_tissue` text NOT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(100)), + KEY `data_probeset_id` (`data_probeset_id`(30),`data_bot_id`(20)), + KEY `data_bot_id` (`data_bot_id`(12)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_general_info` +-- + +DROP TABLE IF EXISTS `sample_general_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_general_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(100) NOT NULL DEFAULT '0', + `sample_repl` tinytext, + `sample_ctrl` tinytext, + `sample_desc` tinytext, + `sample_file_name` tinytext, + `sample_bot_id` tinytext NOT NULL, + `sample_name` tinytext +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `canola_annotations_lookup` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `canola_annotations_lookup` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `canola_annotations_lookup`; + +-- +-- Table structure for table `gene_annotation_lookup` +-- + +DROP TABLE IF EXISTS `gene_annotation_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene_annotation_lookup` ( + `gene` varchar(60) NOT NULL, + `annotation` longtext NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gene_annotation_lookup_v5` +-- + +DROP TABLE IF EXISTS `gene_annotation_lookup_v5`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene_annotation_lookup_v5` ( + `gene` varchar(60) NOT NULL, + `annotation` longtext NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `canola_nssnp` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `canola_nssnp` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `canola_nssnp`; + +-- +-- Table structure for table `protein_reference` +-- + +DROP TABLE IF EXISTS `protein_reference`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `protein_reference` ( + `protein_reference_id` int NOT NULL AUTO_INCREMENT, + `gene_name` varchar(45) NOT NULL, + `gene_identifier` varchar(45) DEFAULT NULL, + PRIMARY KEY (`protein_reference_id`) +) ENGINE=InnoDB AUTO_INCREMENT=101041 DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `snps_to_protein` +-- + +DROP TABLE IF EXISTS `snps_to_protein`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `snps_to_protein` ( + `snps_reference_id` int NOT NULL AUTO_INCREMENT, + `protein_reference_id` int NOT NULL, + `transcript_pos` int NOT NULL, + `chromosome` varchar(25) NOT NULL, + `chromosomal_loci` int NOT NULL, + `ref_DNA` varchar(1) NOT NULL, + `alt_DNA` varchar(45) NOT NULL, + `aa_pos` int NOT NULL, + `ref_aa` varchar(3) NOT NULL, + `alt_aa` varchar(3) NOT NULL, + `type` varchar(50) NOT NULL, + `effect_impact` varchar(50) NOT NULL, + `transcript_biotype` varchar(45) DEFAULT NULL, + `alt_freq` decimal(10,5) NOT NULL, + PRIMARY KEY (`snps_reference_id`,`protein_reference_id`), + KEY `protein_fk_idx` (`protein_reference_id`), + CONSTRAINT `protein_fk` FOREIGN KEY (`protein_reference_id`) REFERENCES `protein_reference` (`protein_reference_id`) +) ENGINE=InnoDB AUTO_INCREMENT=398050 DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `canola_original` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `canola_original` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `canola_original`; + +-- +-- Table structure for table `proj_info` +-- + +DROP TABLE IF EXISTS `proj_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_info` ( + `proj_id` varchar(100) NOT NULL DEFAULT '0', + `proj_title` tinytext, + `proj_pi` tinytext, + `proj_pi_title` tinytext, + `proj_pi_inst` tinytext, + `proj_pi_addr` tinytext, + `proj_keyw1` tinytext, + `proj_keyw2` tinytext, + `proj_keyw3` tinytext, + `proj_keyw4` tinytext, + `proj_keyw5` tinytext, + `proj_res_area` tinytext, + `proj_num_samps` tinyint unsigned NOT NULL DEFAULT '0' +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_biosource_info` +-- + +DROP TABLE IF EXISTS `sample_biosource_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_biosource_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(200) NOT NULL DEFAULT '0', + `sample_bio_name` tinytext, + `sample_organism` tinytext, + `sample_alias` tinytext, + `sample_stock_code` tinytext, + `sample_genetic_var` tinytext, + `sample_tissue` tinytext, + `sample_diseased` tinytext, + `sample_growth_cond` tinytext, + `sample_growth_stage` tinytext, + `sample_time_point` tinytext +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` tinytext NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` tinytext NOT NULL, + `sample_tissue` text NOT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(100)), + KEY `data_probeset_id` (`data_probeset_id`(100)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_general_info` +-- + +DROP TABLE IF EXISTS `sample_general_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_general_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(100) NOT NULL DEFAULT '0', + `sample_repl` tinytext, + `sample_ctrl` tinytext, + `sample_desc` tinytext, + `sample_file_name` tinytext, + `sample_bot_id` tinytext NOT NULL, + `sample_name` tinytext +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `canola_original_v2` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `canola_original_v2` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `canola_original_v2`; + +-- +-- Table structure for table `proj_info` +-- + +DROP TABLE IF EXISTS `proj_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_info` ( + `proj_id` varchar(100) NOT NULL DEFAULT '0', + `proj_title` tinytext, + `proj_pi` tinytext, + `proj_pi_title` tinytext, + `proj_pi_inst` tinytext, + `proj_pi_addr` tinytext, + `proj_keyw1` tinytext, + `proj_keyw2` tinytext, + `proj_keyw3` tinytext, + `proj_keyw4` tinytext, + `proj_keyw5` tinytext, + `proj_res_area` tinytext, + `proj_num_samps` tinyint unsigned NOT NULL DEFAULT '0' +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_biosource_info` +-- + +DROP TABLE IF EXISTS `sample_biosource_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_biosource_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(200) NOT NULL DEFAULT '0', + `sample_bio_name` tinytext, + `sample_organism` tinytext, + `sample_alias` tinytext, + `sample_stock_code` tinytext, + `sample_genetic_var` tinytext, + `sample_tissue` tinytext, + `sample_diseased` tinytext, + `sample_growth_cond` tinytext, + `sample_growth_stage` tinytext, + `sample_time_point` tinytext +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` tinytext NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` tinytext NOT NULL, + `sample_tissue` text NOT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(100)), + KEY `data_probeset_id` (`data_probeset_id`(100)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_general_info` +-- + +DROP TABLE IF EXISTS `sample_general_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_general_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(100) NOT NULL DEFAULT '0', + `sample_repl` tinytext, + `sample_ctrl` tinytext, + `sample_desc` tinytext, + `sample_file_name` tinytext, + `sample_bot_id` tinytext NOT NULL, + `sample_name` tinytext +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `canola_seed` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `canola_seed` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `canola_seed`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(16) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(12) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `cassava_atlas` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `cassava_atlas` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `cassava_atlas`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(24) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `cassava_cbb` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `cassava_cbb` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `cassava_cbb`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(24) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `cassava_eacmv` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `cassava_eacmv` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `cassava_eacmv`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(24) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `circadian_mutants` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `circadian_mutants` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `circadian_mutants`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(12) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(18) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `cistome` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `cistome` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `cistome`; + +-- +-- Table structure for table `agis` +-- + +DROP TABLE IF EXISTS `agis`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `agis` ( + `uniq` int NOT NULL, + `id` int NOT NULL, + `motif` varchar(30) NOT NULL, + `agi` varchar(30) NOT NULL, + `alias` varchar(30) DEFAULT NULL, + PRIMARY KEY (`uniq`), + KEY `agi` (`agi`), + KEY `motif_agi_alias` (`motif`,`agi`,`alias`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `cluster_agis` +-- + +DROP TABLE IF EXISTS `cluster_agis`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `cluster_agis` ( + `id` varchar(4) NOT NULL, + `cluster` varchar(50) NOT NULL, + `agis` varchar(200) NOT NULL, + PRIMARY KEY (`id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `data` +-- + +DROP TABLE IF EXISTS `data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `data` ( + `id` int NOT NULL, + `cluster` varchar(100) NOT NULL, + `pssm` text NOT NULL, + `consensus` varchar(200) NOT NULL, + `agis` mediumtext NOT NULL, + `ref_free_text` varchar(100) DEFAULT NULL, + `ref_pubmed_id` varchar(50) NOT NULL, + PRIMARY KEY (`id`), + KEY `data_pssm_idx` (`pssm`(20)), + KEY `cluster_agis` (`cluster`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `jaspar_consensus` +-- + +DROP TABLE IF EXISTS `jaspar_consensus`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `jaspar_consensus` ( + `ID` varchar(10) NOT NULL, + `consensus` varchar(30) NOT NULL, + `alias` varchar(10) DEFAULT NULL, + PRIMARY KEY (`ID`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `premapped_jaspar_motifs` +-- + +DROP TABLE IF EXISTS `premapped_jaspar_motifs`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `premapped_jaspar_motifs` ( + `SeqID` varchar(15) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Strand` char(1) DEFAULT NULL, + `Score` float DEFAULT NULL, + `pvalue` float DEFAULT NULL, + `qvalue` float DEFAULT NULL, + `match_seq` varchar(40) DEFAULT NULL, + `motif` varchar(20) DEFAULT NULL, + `ic` float DEFAULT NULL, + `fd` float DEFAULT NULL, + `Attribute` varchar(50) DEFAULT NULL, + KEY `premapped_idx` (`SeqID`,`End`,`Start`,`qvalue`,`pvalue`,`Strand`,`match_seq`,`motif`,`ic`,`fd`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `premapped_weirauch_motifs` +-- + +DROP TABLE IF EXISTS `premapped_weirauch_motifs`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `premapped_weirauch_motifs` ( + `SeqID` varchar(15) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Strand` char(1) DEFAULT NULL, + `Score` float DEFAULT NULL, + `pvalue` float DEFAULT NULL, + `qvalue` float DEFAULT NULL, + `match_seq` varchar(40) DEFAULT NULL, + `motif` varchar(20) DEFAULT NULL, + `ic` float DEFAULT NULL, + `fd` float DEFAULT NULL, + `Attribute` varchar(50) DEFAULT NULL, + KEY `premapped_idx` (`SeqID`,`End`,`Start`,`qvalue`,`pvalue`,`Strand`,`match_seq`,`motif`,`ic`,`fd`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `premapped_yu_motifs` +-- + +DROP TABLE IF EXISTS `premapped_yu_motifs`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `premapped_yu_motifs` ( + `SeqID` varchar(15) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Strand` char(1) DEFAULT NULL, + `Score` float DEFAULT NULL, + `pvalue` float DEFAULT NULL, + `qvalue` float DEFAULT NULL, + `match_seq` varchar(40) DEFAULT NULL, + `motif` varchar(20) DEFAULT NULL, + `ic` float DEFAULT NULL, + `fd` float DEFAULT NULL, + `Attribute` varchar(50) DEFAULT NULL, + KEY `premapped_idx` (`SeqID`,`End`,`Start`,`qvalue`,`pvalue`,`Strand`,`match_seq`,`motif`,`ic`,`fd`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pssm_consensus` +-- + +DROP TABLE IF EXISTS `pssm_consensus`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pssm_consensus` ( + `id` int NOT NULL, + `cluster` varchar(40) NOT NULL, + `pssm` varchar(100) NOT NULL, + `consensus` varchar(100) NOT NULL, + `agis` tinytext NOT NULL, + PRIMARY KEY (`id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `cistome_legacy` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `cistome_legacy` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `cistome_legacy`; + +-- +-- Table structure for table `cluster_agis` +-- + +DROP TABLE IF EXISTS `cluster_agis`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `cluster_agis` ( + `id` varchar(4) NOT NULL, + `cluster` varchar(50) NOT NULL, + `agis` varchar(200) NOT NULL, + PRIMARY KEY (`id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `data` +-- + +DROP TABLE IF EXISTS `data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `data` ( + `id` int NOT NULL, + `cluster` varchar(100) NOT NULL, + `pssm` varchar(300) NOT NULL, + `consensus` varchar(200) NOT NULL, + `agis` mediumtext NOT NULL, + `ref_free_text` varchar(100) DEFAULT NULL, + `ref_pubmed_id` varchar(50) NOT NULL, + PRIMARY KEY (`id`), + KEY `cluster_agis` (`cluster`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pssm_consensus` +-- + +DROP TABLE IF EXISTS `pssm_consensus`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pssm_consensus` ( + `id` int NOT NULL, + `cluster` varchar(40) NOT NULL, + `pssm` varchar(100) NOT NULL, + `consensus` varchar(100) NOT NULL, + `agis` tinytext NOT NULL, + PRIMARY KEY (`id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `cort_db` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `cort_db` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `cort_db`; + +-- +-- Table structure for table `Metadata` +-- + +DROP TABLE IF EXISTS `Metadata`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `Metadata` ( + `ID` varchar(10) CHARACTER SET utf8mb3 COLLATE utf8mb3_unicode_ci NOT NULL, + `BSG_94_percent` varchar(50) CHARACTER SET utf8mb3 COLLATE utf8mb3_unicode_ci NOT NULL, + `GenBank_Accession` varchar(8) CHARACTER SET utf8mb3 COLLATE utf8mb3_unicode_ci DEFAULT NULL, + `Herbarium_Accession` varchar(20) CHARACTER SET utf8mb3 COLLATE utf8mb3_unicode_ci DEFAULT NULL, + `Collection_Number` varchar(20) CHARACTER SET utf8mb3 COLLATE utf8mb3_unicode_ci DEFAULT NULL, + `Genus` varchar(20) CHARACTER SET utf8mb3 COLLATE utf8mb3_unicode_ci DEFAULT NULL, + `Species` varchar(200) CHARACTER SET utf8mb3 COLLATE utf8mb3_unicode_ci NOT NULL, + `Continent` varchar(20) CHARACTER SET utf8mb3 COLLATE utf8mb3_unicode_ci DEFAULT NULL, + `Country` varchar(20) CHARACTER SET utf8mb3 COLLATE utf8mb3_unicode_ci DEFAULT NULL, + `Province/State` varchar(50) CHARACTER SET utf8mb3 COLLATE utf8mb3_unicode_ci DEFAULT NULL, + `Location` varchar(200) CHARACTER SET utf8mb3 COLLATE utf8mb3_unicode_ci DEFAULT NULL, + `Habitat` varchar(200) CHARACTER SET utf8mb3 COLLATE utf8mb3_unicode_ci DEFAULT NULL, + `Source` varchar(20) CHARACTER SET utf8mb3 COLLATE utf8mb3_unicode_ci DEFAULT NULL, + `Date_of_Collection` text CHARACTER SET utf8mb3 COLLATE utf8mb3_unicode_ci, + `Collector` varchar(50) CHARACTER SET utf8mb3 COLLATE utf8mb3_unicode_ci DEFAULT NULL, + `Determiner` varchar(50) CHARACTER SET utf8mb3 COLLATE utf8mb3_unicode_ci DEFAULT NULL, + `Type_Specimen` varchar(20) CHARACTER SET utf8mb3 COLLATE utf8mb3_unicode_ci DEFAULT NULL, + `Sequence_Location` varchar(20) CHARACTER SET utf8mb3 COLLATE utf8mb3_unicode_ci DEFAULT NULL, + `Publications` text CHARACTER SET utf8mb3 COLLATE utf8mb3_unicode_ci, + `Sequence` text CHARACTER SET utf8mb3 COLLATE utf8mb3_unicode_ci NOT NULL, + PRIMARY KEY (`ID`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `current_mappings` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `current_mappings` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `current_mappings`; + +-- +-- Table structure for table `lookups` +-- + +DROP TABLE IF EXISTS `lookups`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `lookups` ( + `organism` varchar(50) NOT NULL, + `geneid_column_name` varchar(12) NOT NULL, + `annot_db_name` varchar(40) NOT NULL, + `lookup_file_name` varchar(100) DEFAULT NULL, + `lookup_source` varchar(50) DEFAULT NULL, + `lookup_file_date` date DEFAULT NULL, + `lookup_version` varchar(30) DEFAULT NULL, + `lookup_table_name` varchar(50) DEFAULT NULL, + `annotation_file_name` varchar(100) DEFAULT NULL, + `annotation_source` varchar(40) DEFAULT NULL, + `annot_file_date` date NOT NULL, + `annot_version` varchar(30) DEFAULT NULL, + `annot_table_name` varchar(50) NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `cuscuta` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `cuscuta` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `cuscuta`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(2) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(16) DEFAULT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(12) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `cuscuta_early_haustoriogenesis` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `cuscuta_early_haustoriogenesis` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `cuscuta_early_haustoriogenesis`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(12) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(8) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `cuscuta_lmd` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `cuscuta_lmd` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `cuscuta_lmd`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(12) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(8) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `dna_damage` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `dna_damage` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `dna_damage`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(5) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(10) NOT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_bot_id` varchar(32) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `docking_db` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `docking_db` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `docking_db`; + +-- +-- Table structure for table `results` +-- + +DROP TABLE IF EXISTS `results`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `results` ( + `protein` varchar(20) DEFAULT NULL, + `ligand` varchar(20) DEFAULT NULL, + `data` varchar(65480) DEFAULT NULL, + `predicted` tinyint(1) DEFAULT '1' +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `durum_wheat_abiotic_stress` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `durum_wheat_abiotic_stress` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `durum_wheat_abiotic_stress`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(32) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(32) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `durum_wheat_biotic_stress` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `durum_wheat_biotic_stress` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `durum_wheat_biotic_stress`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(32) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(42) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `durum_wheat_development` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `durum_wheat_development` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `durum_wheat_development`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(32) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(24) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `efp_seq_browser` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `efp_seq_browser` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `efp_seq_browser`; + +-- +-- Table structure for table `data` +-- + +DROP TABLE IF EXISTS `data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `data` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `user_id` int unsigned NOT NULL, + `file` varchar(64) NOT NULL, + `title` varchar(64) NOT NULL, + PRIMARY KEY (`id`), + KEY `data_user_index` (`user_id`), + CONSTRAINT `data_ibfk_1` FOREIGN KEY (`user_id`) REFERENCES `users` (`id`) ON DELETE CASCADE ON UPDATE RESTRICT +) ENGINE=InnoDB AUTO_INCREMENT=64 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `users` +-- + +DROP TABLE IF EXISTS `users`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `users` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `user` varchar(100) NOT NULL, + PRIMARY KEY (`id`) +) ENGINE=InnoDB AUTO_INCREMENT=11 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `efpexpressiondata` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `efpexpressiondata` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `efpexpressiondata`; + +-- +-- Table structure for table `Barley_20131203131233` +-- + +DROP TABLE IF EXISTS `Barley_20131203131233`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `Barley_20131203131233` ( + `sample_id` varchar(30) NOT NULL, + `project_id` varchar(30) NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`), + KEY `Barley_20131203131233_idx` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `Barley_20131203131234` +-- + +DROP TABLE IF EXISTS `Barley_20131203131234`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `Barley_20131203131234` ( + `sample_id` varchar(30) NOT NULL, + `project_id` varchar(30) NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`), + KEY `Barley_20131203131234_idx` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `Barley_20131203131248` +-- + +DROP TABLE IF EXISTS `Barley_20131203131248`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `Barley_20131203131248` ( + `sample_id` varchar(30) NOT NULL, + `project_id` varchar(30) NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`), + KEY `Barley_20131203131248_idx` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `Barley_20131203131256` +-- + +DROP TABLE IF EXISTS `Barley_20131203131256`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `Barley_20131203131256` ( + `sample_id` varchar(30) NOT NULL, + `project_id` varchar(30) NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`), + KEY `Barley_20131203131256_idx` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `Bigfile_test_20120905130928` +-- + +DROP TABLE IF EXISTS `Bigfile_test_20120905130928`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `Bigfile_test_20120905130928` ( + `sample_id` varchar(30) NOT NULL, + `project_id` varchar(30) NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `Bigfile_test_20120905140953` +-- + +DROP TABLE IF EXISTS `Bigfile_test_20120905140953`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `Bigfile_test_20120905140953` ( + `sample_id` varchar(30) NOT NULL, + `project_id` varchar(30) NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `Lateral_Root_Initiation_20120829` +-- + +DROP TABLE IF EXISTS `Lateral_Root_Initiation_20120829`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `Lateral_Root_Initiation_20120829` ( + `sample_id` varchar(30) NOT NULL, + `project_id` varchar(30) NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`), + KEY `Lateral_Root_Initiation_LRI_20120822040812_idx` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `Lateral_Root_Initiation_LRI_20120705050723` +-- + +DROP TABLE IF EXISTS `Lateral_Root_Initiation_LRI_20120705050723`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `Lateral_Root_Initiation_LRI_20120705050723` ( + `sample_id` int NOT NULL, + `project_id` int NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `Lateral_Root_Initiation_LRI_20120821030854` +-- + +DROP TABLE IF EXISTS `Lateral_Root_Initiation_LRI_20120821030854`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `Lateral_Root_Initiation_LRI_20120821030854` ( + `sample_id` varchar(30) NOT NULL, + `project_id` varchar(30) NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`), + KEY `Lateral_Root_Initiation_LRI_20120821030854_idx` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `Lateral_Root_Initiation_LRI_20120821050803` +-- + +DROP TABLE IF EXISTS `Lateral_Root_Initiation_LRI_20120821050803`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `Lateral_Root_Initiation_LRI_20120821050803` ( + `sample_id` varchar(30) NOT NULL, + `project_id` varchar(30) NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`), + KEY `Lateral_Root_Initiation_LRI_20120821050803_idx` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `Lateral_Root_Initiation_LRI_20120821050842` +-- + +DROP TABLE IF EXISTS `Lateral_Root_Initiation_LRI_20120821050842`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `Lateral_Root_Initiation_LRI_20120821050842` ( + `sample_id` varchar(30) NOT NULL, + `project_id` varchar(30) NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`), + KEY `Lateral_Root_Initiation_LRI_20120821050842_idx` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `Lateral_Root_Initiation_LRI_20120822040812` +-- + +DROP TABLE IF EXISTS `Lateral_Root_Initiation_LRI_20120822040812`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `Lateral_Root_Initiation_LRI_20120822040812` ( + `sample_id` varchar(30) NOT NULL, + `project_id` varchar(30) NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`), + KEY `Lateral_Root_Initiation_LRI_20120822040812_idx` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `Lateral_Root_Initiation_LRI_20120822040829` +-- + +DROP TABLE IF EXISTS `Lateral_Root_Initiation_LRI_20120822040829`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `Lateral_Root_Initiation_LRI_20120822040829` ( + `sample_id` varchar(30) NOT NULL, + `project_id` varchar(30) NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`), + KEY `Lateral_Root_Initiation_LRI_20120822040829_idx` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `Lateral_Root_Initiation_LRI_20120822040854` +-- + +DROP TABLE IF EXISTS `Lateral_Root_Initiation_LRI_20120822040854`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `Lateral_Root_Initiation_LRI_20120822040854` ( + `sample_id` varchar(30) NOT NULL, + `project_id` varchar(30) NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`), + KEY `Lateral_Root_Initiation_LRI_20120822040854_idx` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `Lateral_root_initiation_20120711130737` +-- + +DROP TABLE IF EXISTS `Lateral_root_initiation_20120711130737`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `Lateral_root_initiation_20120711130737` ( + `sample_id` varchar(30) NOT NULL, + `project_id` varchar(30) NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`), + KEY `Lateral_root_initiation_20120711130737_idx` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `Medicago_truncatula_20130812080825` +-- + +DROP TABLE IF EXISTS `Medicago_truncatula_20130812080825`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `Medicago_truncatula_20130812080825` ( + `sample_id` varchar(30) NOT NULL, + `project_id` varchar(30) NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + 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(`sample_id`,`project_id`,`data_probeset_id`), + KEY `test_20120209130229_idx` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `test_20120209130237` +-- + +DROP TABLE IF EXISTS `test_20120209130237`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `test_20120209130237` ( + `sample_id` int NOT NULL, + `project_id` int NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`), + KEY `test_20120209130237_idx` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `test_20140729070702` +-- + +DROP TABLE IF EXISTS `test_20140729070702`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `test_20140729070702` ( + `sample_id` varchar(30) NOT NULL, + `project_id` varchar(30) NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`), + KEY `test_20140729070702_idx` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `test_23423904wsd_20120501090505` +-- + +DROP TABLE IF EXISTS `test_23423904wsd_20120501090505`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `test_23423904wsd_20120501090505` ( + `sample_id` int NOT NULL, + `project_id` int NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`), + KEY `test_23423904wsd_20120501090505_idx` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `test_23423904wsd_20120501090511` +-- + +DROP TABLE IF EXISTS `test_23423904wsd_20120501090511`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `test_23423904wsd_20120501090511` ( + `sample_id` int NOT NULL, + `project_id` int NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`), + KEY `test_23423904wsd_20120501090511_idx` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `test_23423904wsd_20120501090515` +-- + +DROP TABLE IF EXISTS `test_23423904wsd_20120501090515`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `test_23423904wsd_20120501090515` ( + `sample_id` int NOT NULL, + `project_id` int NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`), + KEY `test_23423904wsd_20120501090515_idx` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `test_23423904wsd_20120501090523` +-- + +DROP TABLE IF EXISTS 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`sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`), + KEY `test_23423904wsd_20120501090557_idx` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `test_eFP_20140325160308` +-- + +DROP TABLE IF EXISTS `test_eFP_20140325160308`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `test_eFP_20140325160308` ( + `sample_id` varchar(30) NOT NULL, + `project_id` varchar(30) NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`), + KEY `test_eFP_20140325160308_idx` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `test_eFP_20140325160322` +-- + +DROP TABLE IF EXISTS `test_eFP_20140325160322`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `test_eFP_20140325160322` ( + `sample_id` varchar(30) NOT NULL, + `project_id` varchar(30) NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`), + KEY `test_eFP_20140325160322_idx` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `test_eFP_20140325160324` +-- + +DROP TABLE IF EXISTS `test_eFP_20140325160324`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `test_eFP_20140325160324` ( + `sample_id` varchar(30) NOT NULL, + `project_id` varchar(30) NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`), + KEY `test_eFP_20140325160324_idx` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `test_eFP_20140325160337` +-- + +DROP TABLE IF EXISTS `test_eFP_20140325160337`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `test_eFP_20140325160337` ( + `sample_id` varchar(30) NOT NULL, + `project_id` varchar(30) NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`), + KEY `test_eFP_20140325160337_idx` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `testser_20120222140246` +-- + +DROP TABLE IF EXISTS `testser_20120222140246`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `testser_20120222140246` ( + `sample_id` int NOT NULL, + `project_id` int NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`), + KEY `testser_20120222140246_idx` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `thellungiella` +-- + +DROP TABLE IF EXISTS `thellungiella`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `thellungiella` ( + `sample_id` varchar(30) NOT NULL, + `project_id` varchar(30) NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`), + KEY `Lateral_Root_Initiation_LRI_20120822040812_idx` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `tsa_test_20121005151054` +-- + +DROP TABLE IF EXISTS `tsa_test_20121005151054`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `tsa_test_20121005151054` ( + `sample_id` varchar(30) NOT NULL, + `project_id` varchar(30) NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`), + KEY `tsa_test_20121005151054_idx` (`data_probeset_id`,`data_bot_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `zip_upload_20120910150906` +-- + +DROP TABLE IF EXISTS `zip_upload_20120910150906`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `zip_upload_20120910150906` ( + `sample_id` varchar(30) NOT NULL, + `project_id` varchar(30) NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `zip_upload_20120910150949` +-- + +DROP TABLE IF EXISTS `zip_upload_20120910150949`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `zip_upload_20120910150949` ( + `sample_id` varchar(30) NOT NULL, + `project_id` varchar(30) NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `embryo` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `embryo` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `embryo`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(3) NOT NULL DEFAULT '0', + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(16) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(8) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `eplant2` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `eplant2` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `eplant2`; + +-- +-- Table structure for table `1001_genomes_lookup` +-- + +DROP TABLE IF EXISTS `1001_genomes_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `1001_genomes_lookup` ( + `id` varchar(8) CHARACTER SET latin1 COLLATE latin1_swedish_ci NOT NULL, + `lookup` varchar(32) CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci NOT NULL, + PRIMARY KEY (`id`,`lookup`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `TAIR10_functional_descriptions` +-- + +DROP TABLE IF EXISTS `TAIR10_functional_descriptions`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `TAIR10_functional_descriptions` ( + `Model_name` varchar(32) NOT NULL, + `Type` varchar(32) NOT NULL, + `Short_description` text, + `Curator_summary` text, + `Computational_description` text, + KEY `Model_name_idx` (`Model_name`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `agi_alias` +-- + +DROP TABLE IF EXISTS `agi_alias`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `agi_alias` ( + `agi` varchar(30) NOT NULL, + `alias` varchar(30) NOT NULL, + PRIMARY KEY (`agi`,`alias`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `agi_annotation` +-- + +DROP TABLE IF EXISTS `agi_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `agi_annotation` ( + `agi` varchar(11) NOT NULL, + `annotation` mediumtext NOT NULL, + PRIMARY KEY (`agi`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `agi_names` +-- + +DROP TABLE IF EXISTS `agi_names`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `agi_names` ( + `agi` varchar(30) NOT NULL, + `name` varchar(128) NOT NULL, + PRIMARY KEY (`agi`,`name`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `agi_uniprot_lookup` +-- + +DROP TABLE IF EXISTS `agi_uniprot_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `agi_uniprot_lookup` ( + `agi` varchar(30) NOT NULL, + `uniprot` varchar(30) NOT NULL, + KEY `idx_agi` (`agi`), + KEY `idx_uniprot` (`uniprot`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `araport11_gff3` +-- + +DROP TABLE IF EXISTS `araport11_gff3`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `araport11_gff3` ( + `SeqID` varchar(10) NOT NULL, + `Source` varchar(12) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(50) DEFAULT NULL, + `geneId` varchar(50) DEFAULT NULL, + `Parent` varchar(50) DEFAULT NULL, + `Attributes` varchar(50) DEFAULT NULL, + KEY `geneId_idx` (`geneId`), + KEY `Start_idx` (`Start`), + KEY `End_idx` (`End`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `binding` +-- + +DROP TABLE IF EXISTS `binding`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `binding` ( + `id` varchar(25) NOT NULL, + `residue` varchar(5) NOT NULL, + `position` int NOT NULL, + PRIMARY KEY (`id`,`residue`,`position`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `geneRIFs` +-- + +DROP TABLE IF EXISTS `geneRIFs`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `geneRIFs` ( + `gene` varchar(16) NOT NULL, + `pubmed` varchar(16) NOT NULL, + `RIF` text NOT NULL, + KEY `rifs` (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gene_alias` +-- + +DROP TABLE IF EXISTS `gene_alias`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene_alias` ( + `gene` varchar(16) NOT NULL, + `symbol` varchar(32) NOT NULL, + `synonyms` varchar(128) DEFAULT NULL, + KEY `alias_idx` (`gene`,`symbol`,`synonyms`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `hmmpred` +-- + +DROP TABLE IF EXISTS `hmmpred`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `hmmpred` ( + `agi` varchar(16) NOT NULL, + `template` varchar(16) NOT NULL, + `hmmpred_evalue` float NOT NULL, + `link` varchar(128) NOT NULL, + KEY `hmm_index` (`agi`,`template`,`hmmpred_evalue`,`link`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `isoforms` +-- + +DROP TABLE IF EXISTS `isoforms`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `isoforms` ( + `gene` varchar(10) NOT NULL, + `isoform` varchar(12) NOT NULL, + KEY `idx_gene_isoform` (`gene`,`isoform`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pdb_experimental` +-- + +DROP TABLE IF EXISTS `pdb_experimental`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pdb_experimental` ( + `agi` varchar(16) NOT NULL, + `model` varchar(8) NOT NULL, + `isoform` varchar(3) DEFAULT NULL, + KEY `agi_model_isoform` (`agi`,`model`,`isoform`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `publications` +-- + +DROP TABLE IF EXISTS `publications`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `publications` ( + `gene` varchar(12) CHARACTER SET latin1 COLLATE latin1_swedish_ci NOT NULL, + `author` varchar(64) CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci NOT NULL, + `year` varchar(6) CHARACTER SET latin1 COLLATE latin1_swedish_ci NOT NULL, + `journal` varchar(64) CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci NOT NULL, + `title` text CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci NOT NULL, + `pubmed` varchar(16) CHARACTER SET latin1 COLLATE latin1_swedish_ci NOT NULL, + KEY `gene_idx` (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `reactome` +-- + +DROP TABLE IF EXISTS `reactome`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `reactome` ( + `gene_id` varchar(12) NOT NULL, + `pathway_id` varchar(18) NOT NULL, + KEY `reactome_index` (`gene_id`,`pathway_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `reactome_reactions` +-- + +DROP TABLE IF EXISTS `reactome_reactions`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `reactome_reactions` ( + `gene_id` varchar(12) NOT NULL, + `reaction_id` varchar(18) NOT NULL, + KEY `reactome_reactions_index` (`gene_id`,`reaction_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `tair10_gff3` +-- + +DROP TABLE IF EXISTS `tair10_gff3`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `tair10_gff3` ( + `SeqID` varchar(20) NOT NULL, + `Source` varchar(10) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(20) DEFAULT NULL, + `geneId` varchar(20) DEFAULT NULL, + `Parent` varchar(40) DEFAULT NULL, + `Attributes` varchar(256) DEFAULT NULL, + KEY `geneId_idx` (`geneId`), + KEY `Start_idx` (`Start`), + KEY `End_idx` (`End`), + KEY `type_geneId` (`Type`,`geneId`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `eplant_barley` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `eplant_barley` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `eplant_barley`; + +-- +-- Table structure for table `gene_annotation` +-- + +DROP TABLE IF EXISTS `gene_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene_annotation` ( + `gene` varchar(50) NOT NULL, + `annotation` mediumtext NOT NULL, + PRIMARY KEY (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gff3` +-- + +DROP TABLE IF EXISTS `gff3`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gff3` ( + `SeqID` varchar(20) NOT NULL, + `Source` varchar(20) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(50) DEFAULT NULL, + `geneId` varchar(50) DEFAULT NULL, + `Parent` varchar(50) DEFAULT NULL, + `Attributes` varchar(50) DEFAULT NULL, + KEY `geneId_idx` (`geneId`), + KEY `Start_idx` (`Start`), + KEY `End_idx` (`End`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `eplant_barley_legacy` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `eplant_barley_legacy` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `eplant_barley_legacy`; + +-- +-- Table structure for table `functional_descriptions` +-- + +DROP TABLE IF EXISTS `functional_descriptions`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `functional_descriptions` ( + `Model_name` varchar(16) NOT NULL, + `Type` varchar(32) DEFAULT NULL, + `Short_description` text, + `Curator_summary` text, + `Computational_description` text, + KEY `Model_name_idx` (`Model_name`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gff3` +-- + +DROP TABLE IF EXISTS `gff3`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gff3` ( + `SeqID` varchar(20) NOT NULL, + `Source` varchar(20) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(50) DEFAULT NULL, + `geneId` varchar(50) DEFAULT NULL, + `Parent` varchar(50) DEFAULT NULL, + `Attributes` varchar(50) DEFAULT NULL, + KEY `geneId_idx` (`geneId`), + KEY `Start_idx` (`Start`), + KEY `End_idx` (`End`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `eplant_camelina` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `eplant_camelina` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `eplant_camelina`; + +-- +-- Table structure for table `gff3` +-- + +DROP TABLE IF EXISTS `gff3`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gff3` ( + `SeqID` varchar(18) NOT NULL, + `Source` varchar(10) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(50) DEFAULT NULL, + `geneId` varchar(28) DEFAULT NULL, + `Parent` varchar(28) DEFAULT NULL, + `Attributes` varchar(28) DEFAULT NULL, + KEY `geneId_idx` (`geneId`), + KEY `Start_idx` (`Start`), + KEY `End_idx` (`End`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `eplant_cassava` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `eplant_cassava` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `eplant_cassava`; + +-- +-- Table structure for table `gene_annotation` +-- + +DROP TABLE IF EXISTS `gene_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene_annotation` ( + `gene` varchar(50) NOT NULL, + `annotation` mediumtext NOT NULL, + PRIMARY KEY (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gff3` +-- + +DROP TABLE IF EXISTS `gff3`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gff3` ( + `SeqID` varchar(20) NOT NULL, + `Source` varchar(20) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(50) DEFAULT NULL, + `geneId` varchar(50) DEFAULT NULL, + `Parent` varchar(50) DEFAULT NULL, + `Attributes` varchar(50) DEFAULT NULL, + KEY `geneId_idx` (`geneId`), + KEY `Start_idx` (`Start`), + KEY `End_idx` (`End`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `eplant_eucalyptus` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `eplant_eucalyptus` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `eplant_eucalyptus`; + +-- +-- Table structure for table `gene_annotation` +-- + +DROP TABLE IF EXISTS `gene_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene_annotation` ( + `gene` varchar(50) NOT NULL, + `annotation` mediumtext NOT NULL, + PRIMARY KEY (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gff3` +-- + +DROP TABLE IF EXISTS `gff3`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gff3` ( + `SeqID` varchar(20) NOT NULL, + `Source` varchar(20) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(50) DEFAULT NULL, + `geneId` varchar(50) DEFAULT NULL, + `Parent` varchar(50) DEFAULT NULL, + `Attributes` varchar(50) DEFAULT NULL, + KEY `geneId_idx` (`geneId`), + KEY `Start_idx` (`Start`), + KEY `End_idx` (`End`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `eplant_maize` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `eplant_maize` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `eplant_maize`; + +-- +-- Table structure for table `geneRIFs` +-- + +DROP TABLE IF EXISTS `geneRIFs`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `geneRIFs` ( + `gene` varchar(16) NOT NULL, + `pubmed` varchar(16) NOT NULL, + `RIF` text NOT NULL, + KEY `rifs` (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gene_annotation` +-- + +DROP TABLE IF EXISTS `gene_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene_annotation` ( + `gene` varchar(20) NOT NULL, + `annotation` mediumtext NOT NULL, + PRIMARY KEY (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gff3_v3` +-- + +DROP TABLE IF EXISTS `gff3_v3`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gff3_v3` ( + `SeqID` varchar(20) NOT NULL, + `Source` varchar(20) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(50) DEFAULT NULL, + `geneId` varchar(50) DEFAULT NULL, + `Parent` varchar(50) DEFAULT NULL, + `Attributes` varchar(50) DEFAULT NULL, + KEY `geneId_idx` (`geneId`), + KEY `Start_idx` (`Start`), + KEY `End_idx` (`End`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gff3_v4` +-- + +DROP TABLE IF EXISTS `gff3_v4`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gff3_v4` ( + `SeqID` varchar(20) NOT NULL, + `Source` varchar(20) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(50) DEFAULT NULL, + `geneId` varchar(50) DEFAULT NULL, + `Parent` varchar(50) DEFAULT NULL, + `Attributes` varchar(50) DEFAULT NULL, + KEY `geneId_idx` (`geneId`), + KEY `Start_idx` (`Start`), + KEY `End_idx` (`End`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `maize_lookup_v4` +-- + +DROP TABLE IF EXISTS `maize_lookup_v4`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `maize_lookup_v4` ( + `probeset` varchar(24) NOT NULL, + `gene_id` varchar(24) NOT NULL, + KEY `gene_probeset` (`gene_id`,`probeset`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `publications` +-- + +DROP TABLE IF EXISTS `publications`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `publications` ( + `gene` varchar(16) CHARACTER SET latin1 COLLATE latin1_swedish_ci NOT NULL, + `author` varchar(64) CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci NOT NULL, + `year` varchar(6) CHARACTER SET latin1 COLLATE latin1_swedish_ci NOT NULL, + `journal` varchar(64) CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci NOT NULL, + `title` text CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci NOT NULL, + `pubmed` varchar(16) CHARACTER SET latin1 COLLATE latin1_swedish_ci NOT NULL, + KEY `gene_idx` (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `eplant_medicago` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `eplant_medicago` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `eplant_medicago`; + +-- +-- Table structure for table `geneRIFs` +-- + +DROP TABLE IF EXISTS `geneRIFs`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `geneRIFs` ( + `gene` varchar(16) NOT NULL, + `pubmed` varchar(16) NOT NULL, + `RIF` text NOT NULL, + KEY `rifs` (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gene_annotation` +-- + +DROP TABLE IF EXISTS `gene_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene_annotation` ( + `gene` varchar(50) NOT NULL, + `annotation` mediumtext NOT NULL, + PRIMARY KEY (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gff3` +-- + +DROP TABLE IF EXISTS `gff3`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gff3` ( + `SeqID` varchar(20) NOT NULL, + `Source` varchar(20) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(50) DEFAULT NULL, + `geneId` varchar(50) DEFAULT NULL, + `Parent` varchar(50) DEFAULT NULL, + `Attributes` varchar(50) DEFAULT NULL, + KEY `geneId_idx` (`geneId`), + KEY `Start_idx` (`Start`), + KEY `End_idx` (`End`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pdb_predicted_files` +-- + +DROP TABLE IF EXISTS `pdb_predicted_files`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pdb_predicted_files` ( + `gene` varchar(24) NOT NULL, + `template` varchar(6) NOT NULL, + `confidence` float NOT NULL, + KEY `pdb_predicted_index` (`gene`,`template`,`confidence`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `publications` +-- + +DROP TABLE IF EXISTS `publications`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `publications` ( + `gene` varchar(16) NOT NULL, + `author` varchar(64) NOT NULL, + `year` varchar(6) NOT NULL, + `journal` varchar(64) NOT NULL, + `title` text NOT NULL, + `pubmed` varchar(16) NOT NULL, + KEY `gene_idx` (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `eplant_poplar` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `eplant_poplar` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `eplant_poplar`; + +-- +-- Table structure for table `gene_annotation` +-- + +DROP TABLE IF EXISTS `gene_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene_annotation` ( + `gene` varchar(20) NOT NULL, + `annotation` mediumtext NOT NULL, + PRIMARY KEY (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gff3_v3` +-- + +DROP TABLE IF EXISTS `gff3_v3`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gff3_v3` ( + `SeqID` varchar(20) NOT NULL, + `Source` varchar(20) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(50) DEFAULT NULL, + `geneId` varchar(50) DEFAULT NULL, + `Parent` varchar(50) DEFAULT NULL, + `Attributes` varchar(50) DEFAULT NULL, + KEY `geneId_idx` (`geneId`), + KEY `Start_idx` (`Start`), + KEY `End_idx` (`End`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `isoforms` +-- + +DROP TABLE IF EXISTS `isoforms`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `isoforms` ( + `gene` varchar(20) NOT NULL, + `isoform` varchar(24) NOT NULL, + KEY `idx_gene_isoform` (`gene`,`isoform`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pdb_predicted_files` +-- + +DROP TABLE IF EXISTS `pdb_predicted_files`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pdb_predicted_files` ( + `gene` varchar(24) NOT NULL, + `template` varchar(6) NOT NULL, + `confidence` float NOT NULL, + KEY `pdb_predicted_index` (`gene`,`template`,`confidence`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `eplant_potato` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `eplant_potato` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `eplant_potato`; + +-- +-- Table structure for table `gene_annotation` +-- + +DROP TABLE IF EXISTS `gene_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene_annotation` ( + `gene` varchar(50) NOT NULL, + `annotation` mediumtext NOT NULL, + PRIMARY KEY (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gff3` +-- + +DROP TABLE IF EXISTS `gff3`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gff3` ( + `SeqID` varchar(50) NOT NULL, + `Source` varchar(20) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(50) DEFAULT NULL, + `geneId` varchar(50) DEFAULT NULL, + `Parent` varchar(50) DEFAULT NULL, + `Attributes` varchar(50) DEFAULT NULL, + KEY `geneId_idx` (`geneId`), + KEY `Start_idx` (`Start`), + KEY `End_idx` (`End`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `eplant_rice` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `eplant_rice` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `eplant_rice`; + +-- +-- Table structure for table `gene_annotation` +-- + +DROP TABLE IF EXISTS `gene_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene_annotation` ( + `gene` varchar(20) NOT NULL, + `annotation` mediumtext NOT NULL, + PRIMARY KEY (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gff3_msu` +-- + +DROP TABLE IF EXISTS `gff3_msu`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gff3_msu` ( + `SeqID` varchar(20) NOT NULL, + `Source` varchar(20) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(50) DEFAULT NULL, + `geneId` varchar(50) DEFAULT NULL, + `Parent` varchar(50) DEFAULT NULL, + `Attributes` varchar(50) DEFAULT NULL, + KEY `geneId_idx` (`geneId`), + KEY `Start_idx` (`Start`), + KEY `End_idx` (`End`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `eplant_soybean` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `eplant_soybean` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `eplant_soybean`; + +-- +-- Table structure for table `geneRIFs` +-- + +DROP TABLE IF EXISTS `geneRIFs`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `geneRIFs` ( + `gene` varchar(16) NOT NULL, + `pubmed` varchar(16) NOT NULL, + `RIF` text NOT NULL, + KEY `rifs` (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gene_annotation` +-- + +DROP TABLE IF EXISTS `gene_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene_annotation` ( + `gene` varchar(20) NOT NULL, + `annotation` mediumtext NOT NULL, + PRIMARY KEY (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gff3` +-- + +DROP TABLE IF EXISTS `gff3`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gff3` ( + `SeqID` varchar(20) NOT NULL, + `Source` varchar(20) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(50) DEFAULT NULL, + `geneId` varchar(50) DEFAULT NULL, + `Parent` varchar(50) DEFAULT NULL, + `Attributes` varchar(50) DEFAULT NULL, + KEY `geneId_idx` (`geneId`), + KEY `Start_idx` (`Start`), + KEY `End_idx` (`End`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pdb_predicted_files` +-- + +DROP TABLE IF EXISTS `pdb_predicted_files`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pdb_predicted_files` ( + `gene` varchar(24) NOT NULL, + `template` varchar(6) NOT NULL, + `confidence` float NOT NULL, + KEY `pdb_predicted_index` (`gene`,`template`,`confidence`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `publications` +-- + +DROP TABLE IF EXISTS `publications`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `publications` ( + `gene` varchar(16) NOT NULL, + `author` varchar(64) NOT NULL, + `year` varchar(6) NOT NULL, + `journal` varchar(64) NOT NULL, + `title` text NOT NULL, + `pubmed` varchar(16) NOT NULL, + KEY `gene_idx` (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `eplant_spruce` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `eplant_spruce` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `eplant_spruce`; + +-- +-- Table structure for table `ids` +-- + +DROP TABLE IF EXISTS `ids`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `ids` ( + `locus` varchar(24) NOT NULL, + KEY `locus` (`locus`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `eplant_sugarcane` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `eplant_sugarcane` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `eplant_sugarcane`; + +-- +-- Table structure for table `gff3` +-- + +DROP TABLE IF EXISTS `gff3`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gff3` ( + `SeqID` varchar(18) NOT NULL, + `Source` varchar(10) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(50) DEFAULT NULL, + `geneId` varchar(28) DEFAULT NULL, + `Parent` varchar(28) DEFAULT NULL, + `Attributes` varchar(28) DEFAULT NULL, + KEY `geneId_idx` (`geneId`), + KEY `Start_idx` (`Start`), + KEY `End_idx` (`End`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `eplant_sunflower` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `eplant_sunflower` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `eplant_sunflower`; + +-- +-- Table structure for table `geneRIFs` +-- + +DROP TABLE IF EXISTS `geneRIFs`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `geneRIFs` ( + `gene` varchar(24) NOT NULL, + `pubmed` varchar(16) NOT NULL, + `RIF` text NOT NULL, + KEY `rifs` (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gene_annotation` +-- + +DROP TABLE IF EXISTS `gene_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene_annotation` ( + `gene` varchar(32) NOT NULL, + `annotation` text NOT NULL, + PRIMARY KEY (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gene_mapping` +-- + +DROP TABLE IF EXISTS `gene_mapping`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene_mapping` ( + `ha412` varchar(24) NOT NULL, + `haxrq` varchar(32) NOT NULL, + KEY `eplant` (`haxrq`,`ha412`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gff3` +-- + +DROP TABLE IF EXISTS `gff3`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gff3` ( + `SeqID` varchar(24) NOT NULL, + `Source` varchar(20) NOT NULL, + `Type` varchar(20) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(64) DEFAULT NULL, + `geneId` varchar(64) DEFAULT NULL, + `Parent` varchar(64) DEFAULT NULL, + `Attributes` varchar(50) DEFAULT NULL, + KEY `geneId_idx` (`geneId`), + KEY `Start_idx` (`Start`), + KEY `End_idx` (`End`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `publications` +-- + +DROP TABLE IF EXISTS `publications`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `publications` ( + `gene` varchar(24) NOT NULL, + `author` varchar(64) NOT NULL, + `year` varchar(6) NOT NULL, + `journal` varchar(64) NOT NULL, + `title` text NOT NULL, + `pubmed` varchar(16) NOT NULL, + KEY `gene_idx` (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `eplant_tomato` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `eplant_tomato` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `eplant_tomato`; + +-- +-- Table structure for table `gene_annotation` +-- + +DROP TABLE IF EXISTS `gene_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene_annotation` ( + `gene` varchar(20) NOT NULL, + `annotation` mediumtext NOT NULL, + PRIMARY KEY (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gff3` +-- + +DROP TABLE IF EXISTS `gff3`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gff3` ( + `SeqID` varchar(20) NOT NULL, + `Source` varchar(20) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(50) DEFAULT NULL, + `geneId` varchar(50) DEFAULT NULL, + `Parent` varchar(50) DEFAULT NULL, + `Attributes` varchar(50) DEFAULT NULL, + KEY `geneId_idx` (`geneId`), + KEY `Start_idx` (`Start`), + KEY `End_idx` (`End`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `isoforms` +-- + +DROP TABLE IF EXISTS `isoforms`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `isoforms` ( + `gene` varchar(20) NOT NULL, + `isoform` varchar(24) NOT NULL, + KEY `idx_gene_isoform` (`gene`,`isoform`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pdb_predicted_files` +-- + +DROP TABLE IF EXISTS `pdb_predicted_files`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pdb_predicted_files` ( + `gene` varchar(24) NOT NULL, + `template` varchar(6) NOT NULL, + `confidence` float NOT NULL, + KEY `pdb_predicted_index` (`gene`,`template`,`confidence`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `eplant_wheat` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `eplant_wheat` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `eplant_wheat`; + +-- +-- Table structure for table `gff3` +-- + +DROP TABLE IF EXISTS `gff3`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gff3` ( + `SeqID` varchar(3) NOT NULL, + `Source` varchar(6) NOT NULL, + `Type` varchar(16) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(27) DEFAULT NULL, + `geneId` varchar(27) DEFAULT NULL, + `Parent` varchar(27) DEFAULT NULL, + `Attributes` varchar(27) DEFAULT NULL, + KEY `geneId_idx` (`geneId`), + KEY `Start_idx` (`Start`), + KEY `End_idx` (`End`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `eplant_willow` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `eplant_willow` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `eplant_willow`; + +-- +-- Table structure for table `gene_annotation` +-- + +DROP TABLE IF EXISTS `gene_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene_annotation` ( + `gene` varchar(32) NOT NULL, + `annotation` mediumtext NOT NULL, + PRIMARY KEY (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gene_lookup` +-- + +DROP TABLE IF EXISTS `gene_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene_lookup` ( + `subject_id` varchar(24) NOT NULL, + `query_id` varchar(24) NOT NULL, + KEY `subject_idx` (`subject_id`,`query_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gff3` +-- + +DROP TABLE IF EXISTS `gff3`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gff3` ( + `SeqID` varchar(10) NOT NULL, + `Source` varchar(20) NOT NULL, + `Type` varchar(20) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(32) DEFAULT NULL, + `geneId` varchar(128) DEFAULT NULL, + `Parent` varchar(64) DEFAULT NULL, + `Attributes` varchar(50) DEFAULT NULL, + KEY `geneId_idx` (`geneId`), + KEY `Start_idx` (`Start`), + KEY `End_idx` (`End`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `eucalyptus` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `eucalyptus` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `eucalyptus`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(16) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(42) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `euphorbia` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `euphorbia` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `euphorbia`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(18) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(24) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `expression_max_test` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `expression_max_test` /*!40100 DEFAULT CHARACTER SET utf8mb3 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `expression_max_test`; + +-- +-- Table structure for table `max_average_microarray` +-- + +DROP TABLE IF EXISTS `max_average_microarray`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `max_average_microarray` ( + `locus` varchar(10) DEFAULT NULL, + `average` decimal(13,5) DEFAULT NULL, + `standard_deviation` decimal(13,5) DEFAULT NULL, + `sample` varchar(200) NOT NULL, + `compendium` varchar(180) NOT NULL, + KEY `sample` (`sample`,`compendium`), + KEY `locus_index` (`locus`), + CONSTRAINT `sample` FOREIGN KEY (`sample`, `compendium`) REFERENCES `sample` (`sample`, `compendium`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `max_average_rnaseq` +-- + +DROP TABLE IF EXISTS `max_average_rnaseq`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `max_average_rnaseq` ( + `locus` varchar(10) DEFAULT NULL, + `average` decimal(13,5) DEFAULT NULL, + `standard_deviation` decimal(13,5) DEFAULT NULL, + `sample` varchar(200) NOT NULL, + `compendium` varchar(180) NOT NULL, + KEY `sample0` (`sample`,`compendium`), + KEY `locus_index` (`locus`), + CONSTRAINT `sample0` FOREIGN KEY (`sample`, `compendium`) REFERENCES `sample` (`sample`, `compendium`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `max_induction_microarray` +-- + +DROP TABLE IF EXISTS `max_induction_microarray`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `max_induction_microarray` ( + `locus` varchar(10) DEFAULT NULL, + `average` decimal(13,5) DEFAULT NULL, + `induction_value` decimal(13,5) DEFAULT NULL, + `standard_deviation` decimal(10,5) DEFAULT NULL, + `sample` varchar(200) NOT NULL, + `compendium` varchar(180) NOT NULL, + KEY `max_reduction_sample0` (`sample`,`compendium`), + KEY `locus_index` (`locus`), + CONSTRAINT `max_reduction_sample0` FOREIGN KEY (`sample`, `compendium`) REFERENCES `sample` (`sample`, `compendium`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `max_induction_ratio_microarray` +-- + +DROP TABLE IF EXISTS `max_induction_ratio_microarray`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `max_induction_ratio_microarray` ( + `locus` varchar(10) DEFAULT NULL, + `average` decimal(13,5) DEFAULT NULL, + `standard_deviation` decimal(10,5) DEFAULT NULL, + `expression_ratio` decimal(9,5) DEFAULT NULL, + `induction_value` decimal(13,5) DEFAULT NULL, + `sample` varchar(200) NOT NULL, + `compendium` varchar(180) NOT NULL, + KEY `max_reduction_sample10` (`sample`,`compendium`), + KEY `locus_index` (`locus`), + CONSTRAINT `max_reduction_sample10` FOREIGN KEY (`sample`, `compendium`) REFERENCES `sample` (`sample`, `compendium`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `max_induction_ratio_rnaseq` +-- + +DROP TABLE IF EXISTS `max_induction_ratio_rnaseq`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `max_induction_ratio_rnaseq` ( + `locus` varchar(10) DEFAULT NULL, + `average` decimal(13,5) DEFAULT NULL, + `standard_deviation` decimal(10,5) DEFAULT NULL, + `expression_ratio` decimal(9,5) DEFAULT NULL, + `induction_value` decimal(13,5) DEFAULT NULL, + `sample` varchar(200) NOT NULL, + `compendium` varchar(180) NOT NULL, + KEY `max_reduction_sample100` (`sample`,`compendium`), + KEY `locus_index` (`locus`), + CONSTRAINT `max_reduction_sample100` FOREIGN KEY (`sample`, `compendium`) REFERENCES `sample` (`sample`, `compendium`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `max_induction_rnaseq` +-- + +DROP TABLE IF EXISTS `max_induction_rnaseq`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `max_induction_rnaseq` ( + `locus` varchar(10) DEFAULT NULL, + `average` decimal(13,5) DEFAULT NULL, + `induction_value` decimal(13,5) DEFAULT NULL, + `standard_deviation` decimal(10,5) DEFAULT NULL, + `sample` varchar(200) NOT NULL, + `compendium` varchar(180) NOT NULL, + KEY `max_reduction_sample00` (`sample`,`compendium`), + KEY `locus_index` (`locus`), + CONSTRAINT `max_reduction_sample00` FOREIGN KEY (`sample`, `compendium`) REFERENCES `sample` (`sample`, `compendium`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `max_reduction_microarray` +-- + +DROP TABLE IF EXISTS `max_reduction_microarray`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `max_reduction_microarray` ( + `locus` varchar(10) DEFAULT NULL, + `average` decimal(13,5) DEFAULT NULL, + `reduction_value` decimal(13,5) DEFAULT NULL, + `standard_deviation` decimal(10,5) DEFAULT NULL, + `sample` varchar(200) NOT NULL, + `compendium` varchar(180) NOT NULL, + KEY `max_reduction_sample` (`sample`,`compendium`), + KEY `locus_index` (`locus`), + CONSTRAINT `max_reduction_sample` FOREIGN KEY (`sample`, `compendium`) REFERENCES `sample` (`sample`, `compendium`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `max_reduction_ratio_microarray` +-- + +DROP TABLE IF EXISTS `max_reduction_ratio_microarray`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `max_reduction_ratio_microarray` ( + `locus` varchar(10) DEFAULT NULL, + `average` decimal(13,5) DEFAULT NULL, + `standard_deviation` decimal(10,5) DEFAULT NULL, + `expression_ratio` decimal(9,5) DEFAULT NULL, + `reduction_value` decimal(13,5) DEFAULT NULL, + `sample` varchar(200) NOT NULL, + `compendium` varchar(180) NOT NULL, + KEY `max_reduction_sample1` (`sample`,`compendium`), + KEY `locus_index` (`locus`), + CONSTRAINT `max_reduction_sample1` FOREIGN KEY (`sample`, `compendium`) REFERENCES `sample` (`sample`, `compendium`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `max_reduction_ratio_rnaseq` +-- + +DROP TABLE IF EXISTS `max_reduction_ratio_rnaseq`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `max_reduction_ratio_rnaseq` ( + `locus` varchar(10) DEFAULT NULL, + `average` decimal(13,5) DEFAULT NULL, + `standard_deviation` decimal(10,5) DEFAULT NULL, + `expression_ratio` decimal(9,5) DEFAULT NULL, + `reduction_value` decimal(13,5) DEFAULT NULL, + `sample` varchar(200) NOT NULL, + `compendium` varchar(180) NOT NULL, + KEY `max_reduction_sample11` (`sample`,`compendium`), + KEY `locus_index` (`locus`), + CONSTRAINT `max_reduction_sample11` FOREIGN KEY (`sample`, `compendium`) REFERENCES `sample` (`sample`, `compendium`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `max_reduction_rnaseq` +-- + +DROP TABLE IF EXISTS `max_reduction_rnaseq`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `max_reduction_rnaseq` ( + `locus` varchar(10) DEFAULT NULL, + `average` decimal(13,5) DEFAULT NULL, + `reduction_value` decimal(13,5) DEFAULT NULL, + `standard_deviation` decimal(10,5) DEFAULT NULL, + `sample` varchar(200) NOT NULL, + `compendium` varchar(180) NOT NULL, + KEY `max_reduction_sample2` (`sample`,`compendium`), + KEY `locus_index` (`locus`), + CONSTRAINT `max_reduction_sample2` FOREIGN KEY (`sample`, `compendium`) REFERENCES `sample` (`sample`, `compendium`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `min_average_microarray` +-- + +DROP TABLE IF EXISTS `min_average_microarray`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `min_average_microarray` ( + `locus` varchar(10) DEFAULT NULL, + `average` decimal(13,5) DEFAULT NULL, + `standard_deviation` decimal(10,5) DEFAULT NULL, + `sample` varchar(200) NOT NULL, + `compendium` varchar(180) NOT NULL, + KEY `max_average_sample0` (`sample`,`compendium`), + KEY `locus_index` (`locus`), + CONSTRAINT `max_average_sample0` FOREIGN KEY (`sample`, `compendium`) REFERENCES `sample` (`sample`, `compendium`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `min_average_rnaseq` +-- + +DROP TABLE IF EXISTS `min_average_rnaseq`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `min_average_rnaseq` ( + `locus` varchar(10) DEFAULT NULL, + `average` decimal(13,5) DEFAULT NULL, + `standard_deviation` decimal(10,5) DEFAULT NULL, + `sample` varchar(200) NOT NULL, + `compendium` varchar(180) NOT NULL, + KEY `max_average_sample00` (`sample`,`compendium`), + KEY `locus_index` (`locus`), + CONSTRAINT `max_average_sample00` FOREIGN KEY (`sample`, `compendium`) REFERENCES `sample` (`sample`, `compendium`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `provenance` +-- + +DROP TABLE IF EXISTS `provenance`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `provenance` ( + `provenance_id` int NOT NULL AUTO_INCREMENT, + `url` varchar(100) DEFAULT NULL, + `methods` varchar(15) DEFAULT NULL, + PRIMARY KEY (`provenance_id`), + UNIQUE KEY `idProvenance_UNIQUE` (`provenance_id`) +) ENGINE=InnoDB AUTO_INCREMENT=83 DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample` +-- + +DROP TABLE IF EXISTS `sample`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample` ( + `sample` varchar(200) NOT NULL, + `compendium` varchar(180) NOT NULL, + `provenance_id` int DEFAULT NULL, + PRIMARY KEY (`sample`,`compendium`), + KEY `provenance_id_idx` (`provenance_id`), + CONSTRAINT `provenance_id` FOREIGN KEY (`provenance_id`) REFERENCES `provenance` (`provenance_id`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `fastpheno` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `fastpheno` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `fastpheno`; + +-- +-- Table structure for table `band` +-- + +DROP TABLE IF EXISTS `band`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `band` ( + `trees_pk` int NOT NULL, + `month` enum('jan','feb','mar','apr','may','jun','jul','aug','sep','oct','nov','dec') NOT NULL, + `band` varchar(100) NOT NULL, + `value` decimal(20,15) NOT NULL, + PRIMARY KEY (`trees_pk`,`month`,`band`), + KEY `trees_fk_idx` (`trees_pk`), + CONSTRAINT `trees_fk` FOREIGN KEY (`trees_pk`) REFERENCES `trees` (`trees_pk`) ON DELETE RESTRICT ON UPDATE RESTRICT +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `height` +-- + +DROP TABLE IF EXISTS `height`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `height` ( + `trees_pk` int NOT NULL, + `month` enum('jan','feb','mar','apr','may','jun','jul','aug','sep','oct','nov','dec') NOT NULL, + `tree_height_proxy` decimal(20,15) NOT NULL, + `ground_height_proxy` decimal(20,15) NOT NULL, + PRIMARY KEY (`trees_pk`,`month`), + KEY `tree_fk_idx` (`trees_pk`), + CONSTRAINT `tree_fk` FOREIGN KEY (`trees_pk`) REFERENCES `trees` (`trees_pk`) ON DELETE RESTRICT ON UPDATE RESTRICT +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sites` +-- + +DROP TABLE IF EXISTS `sites`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sites` ( + `sites_pk` int NOT NULL AUTO_INCREMENT, + `site_name` varchar(45) NOT NULL, + `site_desc` varchar(999) DEFAULT NULL, + PRIMARY KEY (`sites_pk`), + UNIQUE KEY `site_name` (`site_name`) +) ENGINE=InnoDB AUTO_INCREMENT=2 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `trees` +-- + +DROP TABLE IF EXISTS `trees`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `trees` ( + `trees_pk` int NOT NULL AUTO_INCREMENT, + `sites_pk` int NOT NULL, + `longitude` decimal(25,15) DEFAULT NULL, + `latitude` decimal(25,15) DEFAULT NULL, + `genotype_id` varchar(5) DEFAULT NULL, + `external_link` varchar(200) DEFAULT NULL, + `tree_given_id` varchar(25) DEFAULT NULL, + PRIMARY KEY (`trees_pk`), + KEY `sites_fk_idx` (`sites_pk`), + CONSTRAINT `sites_fk` FOREIGN KEY (`sites_pk`) REFERENCES `sites` (`sites_pk`) ON DELETE RESTRICT ON UPDATE RESTRICT +) ENGINE=InnoDB AUTO_INCREMENT=6309 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `fastpheno2_draft` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `fastpheno2_draft` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `fastpheno2_draft`; + +-- +-- Table structure for table `band` +-- + +DROP TABLE IF EXISTS `band`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `band` ( + `trees_pk` int NOT NULL, + `month` enum('jan','feb','mar','apr','may','jun','jul','aug','sep','oct','nov','dec') NOT NULL, + `band` varchar(100) NOT NULL, + `value` decimal(20,15) NOT NULL, + PRIMARY KEY (`trees_pk`,`month`,`band`), + KEY `trees_fk_idx` (`trees_pk`), + CONSTRAINT `trees_fk` FOREIGN KEY (`trees_pk`) REFERENCES `trees` (`trees_pk`) ON DELETE RESTRICT ON UPDATE RESTRICT +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `height` +-- + +DROP TABLE IF EXISTS `height`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `height` ( + `trees_pk` int NOT NULL, + `month` enum('jan','feb','mar','apr','may','jun','jul','aug','sep','oct','nov','dec') NOT NULL, + `tree_height_proxy` decimal(20,15) NOT NULL, + `ground_height_proxy` decimal(20,15) NOT NULL, + PRIMARY KEY (`trees_pk`,`month`), + KEY `tree_fk_idx` (`trees_pk`), + CONSTRAINT `tree_fk` FOREIGN KEY (`trees_pk`) REFERENCES `trees` (`trees_pk`) ON DELETE RESTRICT ON UPDATE RESTRICT +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sites` +-- + +DROP TABLE IF EXISTS `sites`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sites` ( + `sites_pk` int NOT NULL AUTO_INCREMENT, + `site_name` varchar(45) NOT NULL, + `site_desc` varchar(999) DEFAULT NULL, + PRIMARY KEY (`sites_pk`), + UNIQUE KEY `site_name` (`site_name`) +) ENGINE=InnoDB AUTO_INCREMENT=2 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `trees` +-- + +DROP TABLE IF EXISTS `trees`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `trees` ( + `trees_pk` int NOT NULL AUTO_INCREMENT, + `sites_pk` int NOT NULL, + `longitude` decimal(25,15) DEFAULT NULL, + `latitude` decimal(25,15) DEFAULT NULL, + `genotype_id` varchar(5) DEFAULT NULL, + `external_link` varchar(200) DEFAULT NULL, + `tree_given_id` varchar(25) DEFAULT NULL, + PRIMARY KEY (`trees_pk`), + KEY `sites_fk_idx` (`sites_pk`), + CONSTRAINT `sites_fk` FOREIGN KEY (`sites_pk`) REFERENCES `sites` (`sites_pk`) ON DELETE RESTRICT ON UPDATE RESTRICT +) ENGINE=InnoDB AUTO_INCREMENT=6309 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `fastpheno_draft` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `fastpheno_draft` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `fastpheno_draft`; + +-- +-- Table structure for table `band` +-- + +DROP TABLE IF EXISTS `band`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `band` ( + `trees_pk` int NOT NULL, + `month` enum('jan','feb','mar','apr','may','jun','jul','aug','sep','oct','nov','dec') NOT NULL, + `band` varchar(100) NOT NULL, + `value` decimal(20,15) NOT NULL, + PRIMARY KEY (`trees_pk`,`month`,`band`), + KEY `trees_fk_idx` (`trees_pk`), + CONSTRAINT `trees_fk` FOREIGN KEY (`trees_pk`) REFERENCES `trees` (`trees_pk`) ON DELETE RESTRICT ON UPDATE RESTRICT +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `height` +-- + +DROP TABLE IF EXISTS `height`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `height` ( + `trees_pk` int NOT NULL, + `month` enum('jan','feb','mar','apr','may','jun','jul','aug','sep','oct','nov','dec') NOT NULL, + `tree_height_proxy` decimal(20,15) NOT NULL, + `ground_height_proxy` decimal(20,15) NOT NULL, + PRIMARY KEY (`trees_pk`,`month`), + KEY `tree_fk_idx` (`trees_pk`), + CONSTRAINT `tree_fk` FOREIGN KEY (`trees_pk`) REFERENCES `trees` (`trees_pk`) ON DELETE RESTRICT ON UPDATE RESTRICT +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sites` +-- + +DROP TABLE IF EXISTS `sites`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sites` ( + `sites_pk` int NOT NULL AUTO_INCREMENT, + `site_name` varchar(45) NOT NULL, + `site_desc` varchar(999) DEFAULT NULL, + PRIMARY KEY (`sites_pk`), + UNIQUE KEY `site_name` (`site_name`) +) ENGINE=InnoDB AUTO_INCREMENT=2 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `trees` +-- + +DROP TABLE IF EXISTS `trees`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `trees` ( + `trees_pk` int NOT NULL AUTO_INCREMENT, + `sites_pk` int NOT NULL, + `longitude` decimal(25,15) DEFAULT NULL, + `latitude` decimal(25,15) DEFAULT NULL, + `genotype_id` varchar(5) DEFAULT NULL, + `external_link` varchar(200) DEFAULT NULL, + `tree_given_id` varchar(25) DEFAULT NULL, + PRIMARY KEY (`trees_pk`), + KEY `sites_fk_idx` (`sites_pk`), + CONSTRAINT `sites_fk` FOREIGN KEY (`sites_pk`) REFERENCES `sites` (`sites_pk`) ON DELETE RESTRICT ON UPDATE RESTRICT +) ENGINE=InnoDB AUTO_INCREMENT=6309 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `gAccounts` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `gAccounts` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `gAccounts`; + +-- +-- Current Database: `gaia` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `gaia` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `gaia`; + +-- +-- Table structure for table `aliases` +-- + +DROP TABLE IF EXISTS `aliases`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `aliases` ( + `id` int NOT NULL AUTO_INCREMENT, + `genes_id` int NOT NULL, + `alias` varchar(256) NOT NULL, + PRIMARY KEY (`id`), + KEY `FK_genes` (`genes_id`), + KEY `idx_aliases` (`alias`,`genes_id`), + CONSTRAINT `aliases_ibfk_1` FOREIGN KEY (`genes_id`) REFERENCES `genes` (`id`), + CONSTRAINT `FK_genes` FOREIGN KEY (`genes_id`) REFERENCES `genes` (`id`) ON DELETE CASCADE +) ENGINE=InnoDB AUTO_INCREMENT=2124845 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `author_list` +-- + +DROP TABLE IF EXISTS `author_list`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `author_list` ( + `id` int NOT NULL AUTO_INCREMENT, + `publication_figures_id` int NOT NULL, + `author` varchar(128) NOT NULL, + PRIMARY KEY (`id`), + KEY `FK_publication_figures_author_list` (`publication_figures_id`), + CONSTRAINT `author_list_ibfk_1` FOREIGN KEY (`publication_figures_id`) REFERENCES `publication_figures` (`id`), + CONSTRAINT `FK_publication_figures_author_list` FOREIGN KEY (`publication_figures_id`) REFERENCES `publication_figures` (`id`) ON DELETE CASCADE +) ENGINE=InnoDB AUTO_INCREMENT=38184 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `figure_models` +-- + +DROP TABLE IF EXISTS `figure_models`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `figure_models` ( + `id` int NOT NULL AUTO_INCREMENT, + `data` json DEFAULT NULL, + PRIMARY KEY (`id`) +) ENGINE=InnoDB AUTO_INCREMENT=93239 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `figures` +-- + +DROP TABLE IF EXISTS `figures`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `figures` ( + `id` int NOT NULL AUTO_INCREMENT, + `publication_figures_id` int NOT NULL, + `img_name` varchar(64) NOT NULL, + `caption` text, + `img_url` varchar(265) DEFAULT NULL, + PRIMARY KEY (`id`), + KEY `FK_publication_figures_figures` (`publication_figures_id`), + CONSTRAINT `figures_ibfk_1` FOREIGN KEY (`publication_figures_id`) REFERENCES `publication_figures` (`id`), + CONSTRAINT `FK_publication_figures_figures` FOREIGN KEY (`publication_figures_id`) REFERENCES `publication_figures` (`id`) ON DELETE CASCADE +) ENGINE=InnoDB AUTO_INCREMENT=31955 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `genes` +-- + +DROP TABLE IF EXISTS `genes`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `genes` ( + `id` int NOT NULL AUTO_INCREMENT, + `species` varchar(64) NOT NULL, + `locus` varchar(64) DEFAULT NULL, + `geneid` varchar(32) DEFAULT NULL, + PRIMARY KEY (`id`), + KEY `idx_locus` (`locus`), + KEY `idx_geneid` (`geneid`) +) ENGINE=InnoDB AUTO_INCREMENT=2358285 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pub_ids` +-- + +DROP TABLE IF EXISTS `pub_ids`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pub_ids` ( + `id` int NOT NULL AUTO_INCREMENT, + `publication_figures_id` int NOT NULL, + `pubmed` varchar(16) DEFAULT NULL, + `pmc` varchar(16) DEFAULT NULL, + PRIMARY KEY (`id`), + KEY `FK_publication_figures_pub_ids` (`publication_figures_id`), + CONSTRAINT `FK_publication_figures_pub_ids` FOREIGN KEY (`publication_figures_id`) REFERENCES `publication_figures` (`id`) ON DELETE CASCADE, + CONSTRAINT `pub_ids_ibfk_1` FOREIGN KEY (`publication_figures_id`) REFERENCES `publication_figures` (`id`) +) ENGINE=InnoDB AUTO_INCREMENT=6655 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `publication_figures` +-- + +DROP TABLE IF EXISTS `publication_figures`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `publication_figures` ( + `id` int NOT NULL AUTO_INCREMENT, + `title` varchar(512) DEFAULT NULL, + `abstract` text, + PRIMARY KEY (`id`) +) ENGINE=InnoDB AUTO_INCREMENT=6655 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `gc_drought` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `gc_drought` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `gc_drought`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(12) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(12) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `geneslider` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `geneslider` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `geneslider`; + +-- +-- Table structure for table `data` +-- + +DROP TABLE IF EXISTS `data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `data` ( + `id` int NOT NULL, + `chr` varchar(2) DEFAULT NULL, + `start` int NOT NULL, + `end` int NOT NULL, + `strand` varchar(1) NOT NULL, + `file_name` varchar(80) NOT NULL, + `url` tinytext, + PRIMARY KEY (`id`), + KEY `chr` (`chr`), + KEY `start_end` (`start`,`end`), + KEY `end_start` (`end`,`start`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `tair10_gff3_pssm` +-- + +DROP TABLE IF EXISTS `tair10_gff3_pssm`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `tair10_gff3_pssm` ( + `SeqID` varchar(20) NOT NULL, + `Source` varchar(10) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(20) DEFAULT NULL, + `geneId` varchar(20) DEFAULT NULL, + `Parent` varchar(40) DEFAULT NULL, + `FD` float DEFAULT NULL, + `Attributes` varchar(256) DEFAULT NULL, + KEY `Start` (`Start`), + KEY `End` (`End`), + KEY `geneId` (`geneId`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `germination` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `germination` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `germination`; + +-- +-- Table structure for table `proj_info` +-- + +DROP TABLE IF EXISTS `proj_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_info` ( + `proj_id` int unsigned NOT NULL DEFAULT '0', + `proj_title` tinytext, + `proj_pi` tinytext, + `proj_pi_title` tinytext, + `proj_pi_inst` tinytext, + `proj_pi_addr` tinytext, + `proj_keyw1` tinytext, + `proj_keyw2` tinytext, + `proj_keyw3` tinytext, + `proj_keyw4` tinytext, + `proj_keyw5` tinytext, + `proj_res_area` tinytext, + `proj_num_samps` tinyint unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`proj_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `proj_res_area` +-- + +DROP TABLE IF EXISTS `proj_res_area`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_res_area` ( + `proj_res_index` tinytext, + `proj_res_area` tinytext +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_biosource_info` +-- + +DROP TABLE IF EXISTS `sample_biosource_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_biosource_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned NOT NULL DEFAULT '0', + `sample_bio_name` tinytext, + `sample_organism` tinytext, + `sample_alias` tinytext, + `sample_stock_code` tinytext, + `sample_genetic_var` tinytext, + `sample_tissue` tinytext, + `sample_diseased` tinytext, + `sample_growth_cond` tinytext, + `sample_growth_stage` tinytext, + `sample_time_point` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(3) NOT NULL DEFAULT '0', + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(30) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(16) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_general_info` +-- + +DROP TABLE IF EXISTS `sample_general_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_general_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned NOT NULL DEFAULT '0', + `sample_repl` tinytext, + `sample_ctrl` tinytext, + `sample_desc` tinytext, + `sample_file_name` tinytext, + `sample_bot_id` tinytext NOT NULL, + `sample_name` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `grape_annotations_lookup` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `grape_annotations_lookup` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `grape_annotations_lookup`; + +-- +-- Table structure for table `grape_annotations` +-- + +DROP TABLE IF EXISTS `grape_annotations`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `grape_annotations` ( + `gene` varchar(60) NOT NULL, + `annotation` varchar(128) DEFAULT NULL, + `date` date NOT NULL, + PRIMARY KEY (`gene`,`date`), + KEY `date_annotation` (`date`,`gene`,`annotation`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `grape_probeset_lookup` +-- + +DROP TABLE IF EXISTS `grape_probeset_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `grape_probeset_lookup` ( + `gene` varchar(100) NOT NULL, + `probeset` varchar(100) NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`gene`,`probeset`,`date`), + KEY `probeset` (`probeset`,`gene`,`date`), + KEY `date` (`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `grape_developmental` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `grape_developmental` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `grape_developmental`; + +-- +-- Table structure for table `sample_biosource_info` +-- + +DROP TABLE IF EXISTS `sample_biosource_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_biosource_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_bio_name` tinytext, + `sample_organism` tinytext, + `sample_alias` tinytext, + `sample_stock_code` tinytext, + `sample_genetic_var` tinytext, + `sample_tissue` tinytext, + `sample_diseased` tinytext, + `sample_growth_cond` tinytext, + `sample_growth_stage` tinytext, + `sample_time_point` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int NOT NULL, + `proj_id` int NOT NULL, + `sample_file_name` tinytext NOT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_call` tinytext NOT NULL, + `data_p_val` float NOT NULL, + `data_bot_id` varchar(50) NOT NULL, + `sample_tissue` text NOT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(12)), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `guard_cell` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `guard_cell` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `guard_cell`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(30) NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(24) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `gynoecium` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `gynoecium` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `gynoecium`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(12) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(16) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `heterodera_schachtii` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `heterodera_schachtii` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `heterodera_schachtii`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(12) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(16) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `hnahal` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `hnahal` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `hnahal`; + +-- +-- Table structure for table `agi_annotation` +-- + +DROP TABLE IF EXISTS `agi_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `agi_annotation` ( + `agi` varchar(11) NOT NULL, + `annotation` longtext NOT NULL, + `date` date NOT NULL DEFAULT '0000-00-00', + PRIMARY KEY (`agi`,`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `at_pgi_lookup` +-- + +DROP TABLE IF EXISTS `at_pgi_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `at_pgi_lookup` ( + `probeset` varchar(60) NOT NULL, + `pgi` varchar(60) NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`probeset`,`pgi`,`date`), + KEY `probeset` (`probeset`), + KEY `pgi` (`pgi`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `chr_seq_annotation` +-- + +DROP TABLE IF EXISTS `chr_seq_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `chr_seq_annotation` ( + `SeqID` varchar(20) NOT NULL, + `Source` varchar(10) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(20) DEFAULT NULL, + `geneId` varchar(20) DEFAULT NULL, + `Parent` varchar(40) DEFAULT NULL, + `Attributes` varchar(256) DEFAULT NULL, + KEY `cistome_id` (`Id`), + KEY `cistome_parent` (`Parent`), + KEY `cistome_annotation` (`Source`,`SeqID`,`Type`,`Strand`,`Start`,`End`), + KEY `ngm_index` (`Source`,`SeqID`,`Type`,`geneId`,`Start`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `chr_seq_annotation_c24` +-- + +DROP TABLE IF EXISTS `chr_seq_annotation_c24`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `chr_seq_annotation_c24` ( + `SeqID` varchar(20) NOT NULL, + `Source` varchar(10) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(20) DEFAULT NULL, + `geneId` varchar(20) DEFAULT NULL, + `Parent` varchar(40) DEFAULT NULL, + `Attributes` mediumtext, + KEY `range` (`Source`,`SeqID`,`Start`,`End`), + KEY `seqend` (`Source`,`SeqID`,`End`), + KEY `typeid` (`SeqID`,`Source`,`Type`,`Parent`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `chr_seq_annotation_patens` +-- + +DROP TABLE IF EXISTS `chr_seq_annotation_patens`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `chr_seq_annotation_patens` ( + `SeqID` varchar(20) NOT NULL, + `Source` varchar(10) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(20) DEFAULT NULL, + `geneId` varchar(20) DEFAULT NULL, + `Parent` varchar(40) DEFAULT NULL, + `Attributes` mediumtext, + KEY `myIndex` (`SeqID`,`Source`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gene_annotations` +-- + +DROP TABLE IF EXISTS `gene_annotations`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene_annotations` ( + `agi` varchar(12) NOT NULL, + `annotation` longtext NOT NULL, + `source` varchar(10) NOT NULL, + PRIMARY KEY (`agi`,`source`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `go` +-- + +DROP TABLE IF EXISTS `go`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `go` ( + `agi` varchar(10) NOT NULL DEFAULT '', + `tair_accession` mediumint unsigned NOT NULL DEFAULT '0', + `object_name` varchar(12) NOT NULL, + `go_term` tinytext NOT NULL, + `go_id` varchar(11) NOT NULL DEFAULT '', + `tair_keyword` smallint unsigned NOT NULL DEFAULT '0', + `aspect` varchar(5) NOT NULL DEFAULT '', + `goslim_term` tinytext NOT NULL, + `evidence_code` varchar(4) NOT NULL DEFAULT '', + `reference` tinytext NOT NULL, + `annotating_db` varchar(5) NOT NULL DEFAULT '', + `date` date NOT NULL DEFAULT '0000-00-00', + KEY `agi` (`agi`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interactions` +-- + +DROP TABLE IF EXISTS `interactions`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interactions` ( + `Protein1` varchar(9) NOT NULL DEFAULT '', + `Protein2` varchar(9) NOT NULL DEFAULT '', + `S_cerevisiae` tinyint NOT NULL DEFAULT '0', + `S_pombe` tinyint NOT NULL DEFAULT '0', + `Worm` tinyint NOT NULL DEFAULT '0', + `Fly` tinyint NOT NULL DEFAULT '0', + `Human` tinyint NOT NULL DEFAULT '0', + `Mouse` tinyint NOT NULL DEFAULT '0', + `E_coli` tinyint NOT NULL DEFAULT '0', + `Total_hits` smallint NOT NULL DEFAULT '0', + `Num_species` tinyint NOT NULL DEFAULT '0', + `Quality` smallint NOT NULL DEFAULT '0', + `Index` tinyint NOT NULL DEFAULT '0', + `Pcc` float DEFAULT NULL, + `Bind_id` tinytext, + UNIQUE KEY `Protein1` (`Protein1`,`Protein2`,`Bind_id`(30)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pgi_annotation` +-- + +DROP TABLE IF EXISTS `pgi_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pgi_annotation` ( + `pgi` varchar(60) NOT NULL, + `annotation` longtext NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`pgi`,`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_biosource_info` +-- + +DROP TABLE IF EXISTS `sample_biosource_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_biosource_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) DEFAULT NULL, + `sample_bio_name` tinytext, + `sample_organism` tinytext, + `sample_alias` tinytext, + `sample_stock_code` tinytext, + `sample_genetic_var` tinytext, + `sample_tissue` tinytext, + `sample_diseased` tinytext, + `sample_growth_cond` tinytext, + `sample_growth_stage` tinytext, + `sample_time_point` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` tinytext NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` tinytext NOT NULL, + `channel` varchar(5) DEFAULT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(12)), + KEY `data_probeset_id` (`data_probeset_id`(12)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_general_info` +-- + +DROP TABLE IF EXISTS `sample_general_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_general_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) DEFAULT NULL, + `sample_repl` tinytext, + `sample_ctrl` tinytext, + `sample_name` tinytext, + `sample_desc` longtext, + `sample_od` decimal(10,3) unsigned NOT NULL DEFAULT '0.000', + `sample_mass` decimal(10,3) unsigned NOT NULL DEFAULT '0.000', + `sample_vol` decimal(10,3) unsigned NOT NULL DEFAULT '0.000', + `sample_file_name` tinytext, + `sample_bot_id` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `hnahal_temp` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `hnahal_temp` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `hnahal_temp`; + +-- +-- Table structure for table `agi_annotation` +-- + +DROP TABLE IF EXISTS `agi_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `agi_annotation` ( + `agi` varchar(11) NOT NULL, + `annotation` longtext NOT NULL, + `date` date NOT NULL DEFAULT '0000-00-00', + PRIMARY KEY (`agi`,`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `at_pgi_lookup` +-- + +DROP TABLE IF EXISTS `at_pgi_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `at_pgi_lookup` ( + `probeset` varchar(60) NOT NULL, + `pgi` varchar(60) NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`probeset`,`pgi`,`date`), + KEY `probeset` (`probeset`), + KEY `pgi` (`pgi`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `chr_seq_annotation` +-- + +DROP TABLE IF EXISTS `chr_seq_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `chr_seq_annotation` ( + `SeqID` varchar(20) NOT NULL, + `Source` varchar(10) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(20) DEFAULT NULL, + `geneId` varchar(20) DEFAULT NULL, + `Parent` varchar(40) DEFAULT NULL, + `Attributes` varchar(256) DEFAULT NULL, + KEY `range` (`Source`,`SeqID`,`Start`,`End`), + KEY `seqend` (`Source`,`SeqID`,`End`), + KEY `typeid` (`SeqID`,`Source`,`Type`,`Parent`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `chr_seq_annotation_c24` +-- + +DROP TABLE IF EXISTS `chr_seq_annotation_c24`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `chr_seq_annotation_c24` ( + `SeqID` varchar(20) NOT NULL, + `Source` varchar(10) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(20) DEFAULT NULL, + `geneId` varchar(20) DEFAULT NULL, + `Parent` varchar(40) DEFAULT NULL, + `Attributes` mediumtext, + KEY `range` (`Source`,`SeqID`,`Start`,`End`), + KEY `seqend` (`Source`,`SeqID`,`End`), + KEY `typeid` (`SeqID`,`Source`,`Type`,`Parent`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `chr_seq_annotation_patens` +-- + +DROP TABLE IF EXISTS `chr_seq_annotation_patens`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `chr_seq_annotation_patens` ( + `SeqID` varchar(20) NOT NULL, + `Source` varchar(10) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(20) DEFAULT NULL, + `geneId` varchar(20) DEFAULT NULL, + `Parent` varchar(40) DEFAULT NULL, + `Attributes` mediumtext, + KEY `myIndex` (`SeqID`,`Source`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gene_annotations` +-- + +DROP TABLE IF EXISTS `gene_annotations`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene_annotations` ( + `agi` varchar(12) NOT NULL, + `annotation` longtext NOT NULL, + `source` varchar(10) NOT NULL, + PRIMARY KEY (`agi`,`source`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `go` +-- + +DROP TABLE IF EXISTS `go`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `go` ( + `agi` varchar(10) NOT NULL DEFAULT '', + `tair_accession` mediumint unsigned NOT NULL DEFAULT '0', + `object_name` varchar(12) NOT NULL, + `go_term` tinytext NOT NULL, + `go_id` varchar(11) NOT NULL DEFAULT '', + `tair_keyword` smallint unsigned NOT NULL DEFAULT '0', + `aspect` varchar(5) NOT NULL DEFAULT '', + `goslim_term` tinytext NOT NULL, + `evidence_code` varchar(4) NOT NULL DEFAULT '', + `reference` tinytext NOT NULL, + `annotating_db` varchar(5) NOT NULL DEFAULT '', + `date` date NOT NULL DEFAULT '0000-00-00', + KEY `agi` (`agi`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interactions` +-- + +DROP TABLE IF EXISTS `interactions`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interactions` ( + `Protein1` varchar(9) NOT NULL DEFAULT '', + `Protein2` varchar(9) NOT NULL DEFAULT '', + `S_cerevisiae` tinyint NOT NULL DEFAULT '0', + `S_pombe` tinyint NOT NULL DEFAULT '0', + `Worm` tinyint NOT NULL DEFAULT '0', + `Fly` tinyint NOT NULL DEFAULT '0', + `Human` tinyint NOT NULL DEFAULT '0', + `Mouse` tinyint NOT NULL DEFAULT '0', + `E_coli` tinyint NOT NULL DEFAULT '0', + `Total_hits` smallint NOT NULL DEFAULT '0', + `Num_species` tinyint NOT NULL DEFAULT '0', + `Quality` smallint NOT NULL DEFAULT '0', + `Index` tinyint NOT NULL DEFAULT '0', + `Pcc` float DEFAULT NULL, + `Bind_id` tinytext, + UNIQUE KEY `Protein1` (`Protein1`,`Protein2`,`Bind_id`(30)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pgi_annotation` +-- + +DROP TABLE IF EXISTS `pgi_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pgi_annotation` ( + `pgi` varchar(60) NOT NULL, + `annotation` longtext NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`pgi`,`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `homologs_db` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `homologs_db` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `homologs_db`; + +-- +-- Table structure for table `homologs` +-- + +DROP TABLE IF EXISTS `homologs`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `homologs` ( + `homologs_id` int NOT NULL AUTO_INCREMENT, + `search_protein_name` varchar(45) NOT NULL, + `result_protein_name` varchar(45) NOT NULL, + `search_species_name` varchar(45) NOT NULL, + `result_species_name` varchar(45) NOT NULL, + `Percent_id` decimal(10,5) NOT NULL, + `e_score` varchar(10) NOT NULL, + PRIMARY KEY (`homologs_id`) +) ENGINE=InnoDB AUTO_INCREMENT=1459145 DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `human_annotations_lookup` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `human_annotations_lookup` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `human_annotations_lookup`; + +-- +-- Table structure for table `gene_probeset_lookup` +-- + +DROP TABLE IF EXISTS `gene_probeset_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene_probeset_lookup` ( + `gene` varchar(30) NOT NULL DEFAULT '', + `probeset` varchar(30) NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`gene`,`probeset`,`date`), + KEY `probeset_date_gene` (`probeset`,`date`,`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `human_annotation` +-- + +DROP TABLE IF EXISTS `human_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `human_annotation` ( + `probeset` varchar(30) NOT NULL, + `annotation` longtext, + `date` date NOT NULL, + PRIMARY KEY (`probeset`), + KEY `date` (`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `human_body_map_2` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `human_body_map_2` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `human_body_map_2`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(28) NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(20) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `human_developmental` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `human_developmental` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `human_developmental`; + +-- +-- Table structure for table `proj_info` +-- + +DROP TABLE IF EXISTS `proj_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_info` ( + `proj_id` varchar(20) NOT NULL DEFAULT '0', + `proj_title` tinytext, + `proj_pi` tinytext, + `proj_pi_title` tinytext, + `proj_pi_inst` tinytext, + `proj_pi_addr` tinytext, + `proj_keyw1` tinytext, + `proj_keyw2` tinytext, + `proj_keyw3` tinytext, + `proj_keyw4` tinytext, + `proj_keyw5` tinytext, + `proj_res_area` tinytext, + `proj_num_samps` tinyint unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`proj_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_biosource_info` +-- + +DROP TABLE IF EXISTS `sample_biosource_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_biosource_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(20) NOT NULL DEFAULT '0', + `sample_bio_name` tinytext, + `sample_organism` tinytext, + `sample_alias` tinytext, + `sample_stock_code` tinytext, + `sample_genetic_var` tinytext, + `sample_tissue` tinytext, + `sample_diseased` tinytext, + `sample_growth_cond` tinytext, + `sample_growth_stage` tinytext, + `sample_time_point` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(32) DEFAULT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(24) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_general_info` +-- + +DROP TABLE IF EXISTS `sample_general_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_general_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(20) NOT NULL DEFAULT '0', + `sample_repl` tinytext, + `sample_ctrl` tinytext, + `sample_desc` tinytext, + `sample_file_name` tinytext, + `sample_bot_id` tinytext NOT NULL, + `sample_name` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `human_developmental_SpongeLab` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `human_developmental_SpongeLab` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `human_developmental_SpongeLab`; + +-- +-- Table structure for table `proj_info` +-- + +DROP TABLE IF EXISTS `proj_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_info` ( + `proj_id` varchar(20) NOT NULL DEFAULT '0', + `proj_title` tinytext, + `proj_pi` tinytext, + `proj_pi_title` tinytext, + `proj_pi_inst` tinytext, + `proj_pi_addr` tinytext, + `proj_keyw1` tinytext, + `proj_keyw2` tinytext, + `proj_keyw3` tinytext, + `proj_keyw4` tinytext, + `proj_keyw5` tinytext, + `proj_res_area` tinytext, + `proj_num_samps` tinyint unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`proj_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_biosource_info` +-- + +DROP TABLE IF EXISTS `sample_biosource_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_biosource_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(20) NOT NULL DEFAULT '0', + `sample_bio_name` tinytext, + `sample_organism` tinytext, + `sample_alias` tinytext, + `sample_stock_code` tinytext, + `sample_genetic_var` tinytext, + `sample_tissue` tinytext, + `sample_diseased` tinytext, + `sample_growth_cond` tinytext, + `sample_growth_stage` tinytext, + `sample_time_point` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` tinytext NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` tinytext NOT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(30)), + KEY `data_probeset_id` (`data_probeset_id`(30),`data_bot_id`(30)), + KEY `data_bot_id` (`data_bot_id`(30)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_general_info` +-- + +DROP TABLE IF EXISTS `sample_general_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_general_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(20) NOT NULL DEFAULT '0', + `sample_repl` tinytext, + `sample_ctrl` tinytext, + `sample_desc` tinytext, + `sample_file_name` tinytext, + `sample_bot_id` tinytext NOT NULL, + `sample_name` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `human_diseased` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `human_diseased` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `human_diseased`; + +-- +-- Table structure for table `proj_info` +-- + +DROP TABLE IF EXISTS `proj_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_info` ( + `proj_id` varchar(20) NOT NULL DEFAULT '0', + `proj_title` tinytext, + `proj_pi` tinytext, + `proj_pi_title` tinytext, + `proj_pi_inst` tinytext, + `proj_pi_addr` tinytext, + `proj_keyw1` tinytext, + `proj_keyw2` tinytext, + `proj_keyw3` tinytext, + `proj_keyw4` tinytext, + `proj_keyw5` tinytext, + `proj_res_area` tinytext, + `proj_num_samps` tinyint unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`proj_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_biosource_info` +-- + +DROP TABLE IF EXISTS `sample_biosource_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_biosource_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(20) NOT NULL DEFAULT '0', + `sample_bio_name` tinytext, + `sample_organism` tinytext, + `sample_alias` tinytext, + `sample_stock_code` tinytext, + `sample_genetic_var` tinytext, + `sample_tissue` tinytext, + `sample_diseased` tinytext, + `sample_growth_cond` tinytext, + `sample_growth_stage` tinytext, + `sample_time_point` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` tinytext NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` tinytext NOT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(30)), + KEY `data_probeset_id` (`data_probeset_id`(30),`data_bot_id`(30)), + KEY `data_bot_id` (`data_bot_id`(30)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_general_info` +-- + +DROP TABLE IF EXISTS `sample_general_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_general_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(20) NOT NULL DEFAULT '0', + `sample_repl` tinytext, + `sample_ctrl` tinytext, + `sample_desc` tinytext, + `sample_file_name` tinytext, + `sample_bot_id` tinytext NOT NULL, + `sample_name` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `interactions` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `interactions` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `interactions`; + +-- +-- Table structure for table `interactions` +-- + +DROP TABLE IF EXISTS `interactions`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interactions` ( + `Protein1` varchar(25) DEFAULT NULL, + `Protein2` varchar(25) DEFAULT NULL, + `S_cerevisiae` tinyint NOT NULL DEFAULT '0', + `S_pombe` tinyint NOT NULL DEFAULT '0', + `Worm` tinyint NOT NULL DEFAULT '0', + `Fly` tinyint NOT NULL DEFAULT '0', + `Human` tinyint NOT NULL DEFAULT '0', + `Mouse` tinyint NOT NULL DEFAULT '0', + `E_coli` tinyint NOT NULL DEFAULT '0', + `Total_hits` smallint NOT NULL DEFAULT '0', + `Num_species` tinyint NOT NULL DEFAULT '0', + `Quality` float NOT NULL, + `aiv_index` tinyint DEFAULT NULL, + `Pcc` float DEFAULT NULL, + `Bind_id` tinytext, + `Interactions_detection_mi` varchar(35) DEFAULT NULL, + `Interactions_detection` varchar(125) DEFAULT NULL, + `Interactions_type_mi` varchar(10) DEFAULT NULL, + `Interactions_type` varchar(30) DEFAULT NULL, + UNIQUE KEY `Protein1` (`Protein1`,`Protein2`,`Bind_id`(30)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interactions_eplant` +-- + +DROP TABLE IF EXISTS `interactions_eplant`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interactions_eplant` ( + `Protein1` varchar(25) DEFAULT NULL, + `Protein2` varchar(25) DEFAULT NULL, + `S_cerevisiae` tinyint NOT NULL DEFAULT '0', + `S_pombe` tinyint NOT NULL DEFAULT '0', + `Worm` tinyint NOT NULL DEFAULT '0', + `Fly` tinyint NOT NULL DEFAULT '0', + `Human` tinyint NOT NULL DEFAULT '0', + `Mouse` tinyint NOT NULL DEFAULT '0', + `E_coli` tinyint NOT NULL DEFAULT '0', + `Total_hits` smallint NOT NULL DEFAULT '0', + `Num_species` tinyint NOT NULL DEFAULT '0', + `Quality` float NOT NULL, + `aiv_index` tinyint DEFAULT NULL, + `Pcc` float DEFAULT NULL, + `Bind_id` tinytext, + `Interactions_detection_mi` varchar(35) DEFAULT NULL, + `Interactions_detection` varchar(125) DEFAULT NULL, + `Interactions_type_mi` varchar(10) DEFAULT NULL, + `Interactions_type` varchar(30) DEFAULT NULL, + UNIQUE KEY `interaction` (`Protein1`,`Protein2`,`aiv_index`,`Bind_id`(30)), + KEY `aiv_index` (`aiv_index`), + KEY `protein2` (`Protein2`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interactions_eplant_v2` +-- + +DROP TABLE IF EXISTS `interactions_eplant_v2`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interactions_eplant_v2` ( + `Protein1` varchar(25) DEFAULT NULL, + `Protein2` varchar(25) DEFAULT NULL, + `S_cerevisiae` tinyint NOT NULL DEFAULT '0', + `S_pombe` tinyint NOT NULL DEFAULT '0', + `Worm` tinyint NOT NULL DEFAULT '0', + `Fly` tinyint NOT NULL DEFAULT '0', + `Human` tinyint NOT NULL DEFAULT '0', + `Mouse` tinyint NOT NULL DEFAULT '0', + `E_coli` tinyint NOT NULL DEFAULT '0', + `Total_hits` smallint NOT NULL DEFAULT '0', + `Num_species` tinyint NOT NULL DEFAULT '0', + `Quality` float NOT NULL, + `aiv_index` tinyint DEFAULT NULL, + `Pcc` float DEFAULT NULL, + `Bind_id` tinytext, + `Interactions_detection_mi` varchar(35) DEFAULT NULL, + `Interactions_detection` varchar(125) DEFAULT NULL, + `Interactions_type_mi` varchar(10) DEFAULT NULL, + `Interactions_type` varchar(30) DEFAULT NULL, + UNIQUE KEY `interaction` (`Protein1`,`Protein2`,`aiv_index`,`Bind_id`(30)), + KEY `aiv_index` (`aiv_index`), + KEY `protein2` (`Protein2`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interactions_eplant_v3` +-- + +DROP TABLE IF EXISTS `interactions_eplant_v3`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interactions_eplant_v3` ( + `Protein1` varchar(25) DEFAULT NULL, + `Protein2` varchar(25) DEFAULT NULL, + `S_cerevisiae` tinyint NOT NULL DEFAULT '0', + `S_pombe` tinyint NOT NULL DEFAULT '0', + `Worm` tinyint NOT NULL DEFAULT '0', + `Fly` tinyint NOT NULL DEFAULT '0', + `Human` tinyint NOT NULL DEFAULT '0', + `Mouse` tinyint NOT NULL DEFAULT '0', + `E_coli` tinyint NOT NULL DEFAULT '0', + `Total_hits` smallint NOT NULL DEFAULT '0', + `Num_species` tinyint NOT NULL DEFAULT '0', + `Quality` float NOT NULL, + `aiv_index` tinyint DEFAULT NULL, + `Pcc` float DEFAULT NULL, + `Bind_id` tinytext, + `Interactions_detection_mi` varchar(35) DEFAULT NULL, + `Interactions_detection` varchar(125) DEFAULT NULL, + `Interactions_type_mi` varchar(10) DEFAULT NULL, + `Interactions_type` varchar(30) DEFAULT NULL, + KEY `aiv_index` (`aiv_index`), + KEY `protein2` (`Protein2`), + KEY `interaction` (`Protein1`,`Protein2`,`aiv_index`,`Bind_id`(30)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interactions_eplant_v4` +-- + +DROP TABLE IF EXISTS `interactions_eplant_v4`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interactions_eplant_v4` ( + `Protein1` varchar(25) DEFAULT NULL, + `Protein2` varchar(25) DEFAULT NULL, + `S_cerevisiae` tinyint NOT NULL DEFAULT '0', + `S_pombe` tinyint NOT NULL DEFAULT '0', + `Worm` tinyint NOT NULL DEFAULT '0', + `Fly` tinyint NOT NULL DEFAULT '0', + `Human` tinyint NOT NULL DEFAULT '0', + `Mouse` tinyint NOT NULL DEFAULT '0', + `E_coli` tinyint NOT NULL DEFAULT '0', + `Total_hits` smallint NOT NULL DEFAULT '0', + `Num_species` tinyint NOT NULL DEFAULT '0', + `Quality` float NOT NULL, + `aiv_index` tinyint DEFAULT NULL, + `Pcc` float DEFAULT NULL, + `Bind_id` tinytext, + `Interactions_detection_mi` varchar(64) DEFAULT NULL, + `Interactions_detection` varchar(256) DEFAULT NULL, + `Interactions_type_mi` varchar(64) DEFAULT NULL, + `Interactions_type` varchar(256) DEFAULT NULL, + KEY `aiv_index` (`aiv_index`), + KEY `protein2` (`Protein2`), + KEY `interaction` (`Protein1`,`Protein2`,`aiv_index`,`Bind_id`(30)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `interactions_dapseq` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `interactions_dapseq` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `interactions_dapseq`; + +-- +-- Table structure for table `interactions` +-- + +DROP TABLE IF EXISTS `interactions`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interactions` ( + `Protein1` varchar(25) DEFAULT NULL, + `Protein2` varchar(25) DEFAULT NULL, + `S_cerevisiae` tinyint NOT NULL DEFAULT '0', + `S_pombe` tinyint NOT NULL DEFAULT '0', + `Worm` tinyint NOT NULL DEFAULT '0', + `Fly` tinyint NOT NULL DEFAULT '0', + `Human` tinyint NOT NULL DEFAULT '0', + `Mouse` tinyint NOT NULL DEFAULT '0', + `E_coli` tinyint NOT NULL DEFAULT '0', + `Total_hits` smallint NOT NULL DEFAULT '0', + `Num_species` tinyint NOT NULL DEFAULT '0', + `Quality` float NOT NULL, + `aiv_index` tinyint DEFAULT NULL, + `Pcc` float DEFAULT NULL, + `Bind_id` tinytext, + `Interactions_detection_mi` varchar(35) DEFAULT NULL, + `Interactions_detection` varchar(125) DEFAULT NULL, + `Interactions_type_mi` varchar(10) DEFAULT NULL, + `Interactions_type` varchar(30) DEFAULT NULL, + UNIQUE KEY `Protein1` (`Protein1`,`Protein2`,`Bind_id`(30)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `new_interactions` +-- + +DROP TABLE IF EXISTS `new_interactions`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `new_interactions` ( + `name` varchar(35) NOT NULL DEFAULT '', + `email` varchar(35) NOT NULL DEFAULT '', + `agi1` varchar(12) NOT NULL DEFAULT '', + `agi2` varchar(12) NOT NULL DEFAULT '', + `pubmed` varchar(20) DEFAULT NULL, + `description` mediumtext, + `date` datetime DEFAULT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `interactions_eddi` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `interactions_eddi` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `interactions_eddi`; + +-- +-- Table structure for table `algorithms_lookup_table` +-- + +DROP TABLE IF EXISTS `algorithms_lookup_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `algorithms_lookup_table` ( + `algo_name` varchar(100) NOT NULL, + `algo_desc` varchar(500) NOT NULL, + `algo_ranges` varchar(200) NOT NULL, + PRIMARY KEY (`algo_name`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `detections_mi_lookup_table` +-- + +DROP TABLE IF EXISTS `detections_mi_lookup_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `detections_mi_lookup_table` ( + `detections_mi_id` varchar(200) NOT NULL, + `interactions_detection` varchar(200) DEFAULT NULL, + `interactions_type_mi` varchar(200) DEFAULT NULL, + `interactions_type` varchar(200) DEFAULT NULL, + PRIMARY KEY (`detections_mi_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `external_db_lookup_table` +-- + +DROP TABLE IF EXISTS `external_db_lookup_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `external_db_lookup_table` ( + `ext_db_id` int NOT NULL, + `name_of_db` varchar(100) NOT NULL, + PRIMARY KEY (`ext_db_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `external_source` +-- + +DROP TABLE IF EXISTS `external_source`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `external_source` ( + `source_id` int NOT NULL AUTO_INCREMENT, + `source_name` varchar(500) NOT NULL, + `comments` text, + `date_uploaded` date DEFAULT NULL, + `url` varchar(350) DEFAULT NULL, + `source_type_id` int NOT NULL, + `is_GRN` tinyint(1) NOT NULL, + `tags` varchar(300) DEFAULT NULL, + PRIMARY KEY (`source_id`), + UNIQUE KEY `source_name_UNIQUE` (`source_name`), + KEY `ext_src_type_FK_idx` (`source_type_id`), + CONSTRAINT `ext_src_type_FK` FOREIGN KEY (`source_type_id`) REFERENCES `source_type_lookup_table` (`source_type_id`) +) ENGINE=InnoDB AUTO_INCREMENT=2088 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interaction_lookup_table` +-- + +DROP TABLE IF EXISTS `interaction_lookup_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interaction_lookup_table` ( + `interaction_type_id` int NOT NULL AUTO_INCREMENT, + `description` varchar(100) NOT NULL, + `entity_1_alias` varchar(50) NOT NULL, + `entity_2_alias` varchar(50) NOT NULL, + PRIMARY KEY (`interaction_type_id`), + UNIQUE KEY `description_UNIQUE` (`description`) +) ENGINE=InnoDB AUTO_INCREMENT=3 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interactions` +-- + +DROP TABLE IF EXISTS `interactions`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interactions` ( + `interaction_id` int NOT NULL AUTO_INCREMENT, + `pearson_correlation_coeff` decimal(6,5) DEFAULT NULL, + `entity_1` varchar(50) NOT NULL, + `entity_2` varchar(50) NOT NULL, + `interaction_type_id` int NOT NULL, + PRIMARY KEY (`interaction_id`), + UNIQUE KEY `unique_interaction_index` (`entity_1`,`entity_2`,`interaction_type_id`), + KEY `interaction_type_id_idx` (`interaction_type_id`), + CONSTRAINT `interaction_type_id` FOREIGN KEY (`interaction_type_id`) REFERENCES `interaction_lookup_table` (`interaction_type_id`) +) ENGINE=InnoDB AUTO_INCREMENT=3240894 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interactions_source_mi_join_table` +-- + +DROP TABLE IF EXISTS `interactions_source_mi_join_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interactions_source_mi_join_table` ( + `interaction_id` int NOT NULL, + `detections_mi_id` varchar(100) DEFAULT NULL, + `source_id` int NOT NULL, + `external_db_lookup` int DEFAULT NULL, + `external_db_id` varchar(30) DEFAULT NULL, + `mode_of_action` tinyint(1) NOT NULL, + PRIMARY KEY (`interaction_id`,`source_id`), + KEY `detection_mi_idx` (`detections_mi_id`), + KEY `source_id_idx` (`source_id`), + KEY `external_db_FK_idx` (`external_db_lookup`), + KEY `m_o_a_db_FK_idx` (`mode_of_action`), + CONSTRAINT `detection_mi_FK` FOREIGN KEY (`detections_mi_id`) REFERENCES `detections_mi_lookup_table` (`detections_mi_id`), + CONSTRAINT `external_db_FK` FOREIGN KEY (`external_db_lookup`) REFERENCES `external_db_lookup_table` (`ext_db_id`), + CONSTRAINT `int_id_FK_on_mi_int_src` FOREIGN KEY (`interaction_id`) REFERENCES `interactions` (`interaction_id`), + CONSTRAINT `m_o_a_db_FK` FOREIGN KEY (`mode_of_action`) REFERENCES `modes_of_action_lookup_table` (`m_of_a_pk`), + CONSTRAINT `source_id_FK` FOREIGN KEY (`source_id`) REFERENCES `external_source` (`source_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interolog_confidence_subset_table` +-- + +DROP TABLE IF EXISTS `interolog_confidence_subset_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interolog_confidence_subset_table` ( + `interaction_id` int NOT NULL, + `s_cerevisiae` tinyint NOT NULL, + `s_pombe` tinyint NOT NULL, + `worm` tinyint NOT NULL, + `fly` tinyint NOT NULL, + `human` tinyint NOT NULL, + `mouse` tinyint NOT NULL, + `e_coli` tinyint NOT NULL, + `total_hits` smallint NOT NULL, + `num_species` tinyint NOT NULL, + PRIMARY KEY (`interaction_id`), + KEY `pdi_interaction_id_idx` (`interaction_id`), + CONSTRAINT `interolog_int_id_FK` FOREIGN KEY (`interaction_id`) REFERENCES `interactions` (`interaction_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `modes_of_action_lookup_table` +-- + +DROP TABLE IF EXISTS `modes_of_action_lookup_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `modes_of_action_lookup_table` ( + `m_of_a_pk` tinyint(1) NOT NULL, + `description` varchar(20) NOT NULL, + PRIMARY KEY (`m_of_a_pk`), + UNIQUE KEY `description_UNIQUE` (`description`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `source_type_lookup_table` +-- + +DROP TABLE IF EXISTS `source_type_lookup_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `source_type_lookup_table` ( + `source_type_id` int NOT NULL AUTO_INCREMENT, + `source_type_desc` varchar(100) DEFAULT NULL, + PRIMARY KEY (`source_type_id`) +) ENGINE=InnoDB AUTO_INCREMENT=2 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `interactions_grn_dev_db` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `interactions_grn_dev_db` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `interactions_grn_dev_db`; + +-- +-- Table structure for table `algorithms_lookup_table` +-- + +DROP TABLE IF EXISTS `algorithms_lookup_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `algorithms_lookup_table` ( + `algo_name` varchar(100) NOT NULL COMMENT 'Algorithm name to be used in place of a surrogate key, assume they’re going to be unique. Like “FIMO”.', + `algo_desc` varchar(500) NOT NULL COMMENT 'Describe the named algorithm in algo_name.', + `algo_ranges` varchar(200) NOT NULL COMMENT 'Briefly describe the range of values', + PRIMARY KEY (`algo_name`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `external_source` +-- + +DROP TABLE IF EXISTS `external_source`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `external_source` ( + `source_id` int NOT NULL AUTO_INCREMENT COMMENT 'surrogate key', + `source_name` varchar(500) NOT NULL COMMENT 'name of the source, can be a pubmed identifier like “PMIDXXXXXXX” or “Asher’s sql dump”', + `comments` text NOT NULL COMMENT 'Comments regarding the source', + `date_uploaded` date NOT NULL COMMENT 'When it was uploaded to database', + `url` varchar(350) DEFAULT NULL COMMENT 'URL if available to paper/source (does not have to be a DOI, can be a link to a databases’ source)', + `image_url` varchar(300) DEFAULT NULL, + `grn_title` varchar(200) DEFAULT NULL, + `cyjs_layout` varchar(1000) DEFAULT NULL, + PRIMARY KEY (`source_id`), + UNIQUE KEY `source_name_UNIQUE` (`source_name`) +) ENGINE=InnoDB AUTO_INCREMENT=69 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interaction_lookup_table` +-- + +DROP TABLE IF EXISTS `interaction_lookup_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interaction_lookup_table` ( + `interaction_type_id` int NOT NULL AUTO_INCREMENT COMMENT 'Surrogate key', + `description` varchar(100) NOT NULL COMMENT 'Describe the binary interaction of the entities. For example ‘ppi - protein interaction where entity_1_alias and entity_2_alias represent proteins’', + `entity_1_alias` varchar(50) NOT NULL COMMENT 'Can be a protein, miRNA, etc.', + `entity_2_alias` varchar(50) NOT NULL COMMENT 'Can be a protein, miRNA, etc.', + PRIMARY KEY (`interaction_type_id`), + UNIQUE KEY `description_UNIQUE` (`description`) +) ENGINE=InnoDB AUTO_INCREMENT=10 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interactions` +-- + +DROP TABLE IF EXISTS `interactions`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interactions` ( + `interaction_id` int NOT NULL AUTO_INCREMENT COMMENT 'surrogate key', + `pearson_correlation_coeff` decimal(6,5) DEFAULT NULL COMMENT 'PCC score imported from interactions table', + `entity_1` varchar(50) NOT NULL COMMENT 'Following the interaction_type_id (referencing the lookup table), define the first entity. For example if it is a PPI relationship than the entity 1 shall be a protein with an AGI (ex AT5G01010).', + `entity_2` varchar(50) NOT NULL COMMENT 'Following the interaction_type_id (referencing the lookup table), define the first entity. For example if it is a PPI relationship than the entity 2 shall be a protein with an AGI (ex AT5G01010).', + `interaction_type_id` int NOT NULL COMMENT 'Reference to the lookup of a interactions_lookup_table. Define what type of interaction these two genes are. For example if the value were ‘3’ and it looksup to a PPI, then both members are proteins.', + PRIMARY KEY (`interaction_id`), + UNIQUE KEY `unique_interaction_index` (`entity_1`,`entity_2`,`interaction_type_id`), + KEY `interaction_type_id_idx` (`interaction_type_id`), + CONSTRAINT `interaction_type_id` FOREIGN KEY (`interaction_type_id`) REFERENCES `interaction_lookup_table` (`interaction_type_id`) +) ENGINE=InnoDB AUTO_INCREMENT=10835 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interactions_algo_score_join_table` +-- + +DROP TABLE IF EXISTS `interactions_algo_score_join_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interactions_algo_score_join_table` ( + `algo_score` varchar(30) NOT NULL COMMENT 'Score for that specific algorithm referenced in ‘algo_name’ for a particular binary interaction', + `interaction_id` int NOT NULL COMMENT 'The interaction we are looking at when we are referring to an algorithm score', + `algo_name` varchar(100) NOT NULL COMMENT 'algo_name which will reference the lookup table', + PRIMARY KEY (`algo_name`,`interaction_id`,`algo_score`), + KEY `interaction_id_idx` (`interaction_id`), + CONSTRAINT `algo_name` FOREIGN KEY (`algo_name`) REFERENCES `algorithms_lookup_table` (`algo_name`), + CONSTRAINT `interaction_id` FOREIGN KEY (`interaction_id`) REFERENCES `interactions` (`interaction_id`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interactions_source_mi_join_table` +-- + +DROP TABLE IF EXISTS `interactions_source_mi_join_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interactions_source_mi_join_table` ( + `interaction_id` int NOT NULL COMMENT 'reference the interaction pair via id', + `source_id` int NOT NULL COMMENT 'reference the paper/source where this interaction came from', + `external_db_id` varchar(30) NOT NULL COMMENT 'For the given external_database, like BIOGRID; what is it’s ID?', + `mode_of_action` tinyint(1) NOT NULL COMMENT 'Repression or activation? Reference it here to the lookup.', + `mi_detection_method` varchar(10) NOT NULL, + `mi_detection_type` varchar(10) NOT NULL, + PRIMARY KEY (`mi_detection_method`,`mi_detection_type`,`external_db_id`,`interaction_id`,`source_id`), + KEY `source_id_idx` (`source_id`), + KEY `m_o_a_db_FK_idx` (`mode_of_action`), + KEY `int_id_FK_on_mi_int_src` (`interaction_id`), + CONSTRAINT `int_id_FK_on_mi_int_src` FOREIGN KEY (`interaction_id`) REFERENCES `interactions` (`interaction_id`), + CONSTRAINT `m_o_a_db_FK` FOREIGN KEY (`mode_of_action`) REFERENCES `modes_of_action_lookup_table` (`m_of_a_pk`), + CONSTRAINT `source_id_FK` FOREIGN KEY (`source_id`) REFERENCES `external_source` (`source_id`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interolog_confidence_subset_table` +-- + +DROP TABLE IF EXISTS `interolog_confidence_subset_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interolog_confidence_subset_table` ( + `interaction_id` int NOT NULL COMMENT 'surrogate key', + `s_cerevisiae` tinyint NOT NULL COMMENT 'species score… repeat for all other species', + `s_pombe` tinyint NOT NULL, + `worm` tinyint NOT NULL, + `fly` tinyint NOT NULL, + `human` tinyint NOT NULL, + `mouse` tinyint NOT NULL, + `e_coli` tinyint NOT NULL, + `total_hits` smallint NOT NULL, + `num_species` tinyint NOT NULL, + PRIMARY KEY (`interaction_id`), + KEY `pdi_interaction_id_idx` (`interaction_id`), + CONSTRAINT `interolog_int_id_FK` FOREIGN KEY (`interaction_id`) REFERENCES `interactions` (`interaction_id`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `modes_of_action_lookup_table` +-- + +DROP TABLE IF EXISTS `modes_of_action_lookup_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `modes_of_action_lookup_table` ( + `m_of_a_pk` tinyint(1) NOT NULL AUTO_INCREMENT COMMENT 'surrogate key', + `description` varchar(20) NOT NULL COMMENT 'Describe the mode of action of the interaction, is it repression or activation for example?', + PRIMARY KEY (`m_of_a_pk`), + UNIQUE KEY `description_UNIQUE` (`description`) +) ENGINE=InnoDB AUTO_INCREMENT=4 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `source_tag_join_table` +-- + +DROP TABLE IF EXISTS `source_tag_join_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `source_tag_join_table` ( + `source_id` int NOT NULL, + `tag_name` varchar(45) NOT NULL, + PRIMARY KEY (`source_id`,`tag_name`), + KEY `tag_join_tag_names_FK_idx` (`tag_name`), + CONSTRAINT `tag_join_source_id_FK` FOREIGN KEY (`source_id`) REFERENCES `external_source` (`source_id`), + CONSTRAINT `tag_join_tag_names_FK` FOREIGN KEY (`tag_name`) REFERENCES `tag_lookup_table` (`tag_name`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `tag_lookup_table` +-- + +DROP TABLE IF EXISTS `tag_lookup_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `tag_lookup_table` ( + `tag_name` varchar(45) NOT NULL, + `tag_group` enum('Gene','Experiment','Condition','Misc') NOT NULL, + PRIMARY KEY (`tag_name`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `interactions_vincent` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `interactions_vincent` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `interactions_vincent`; + +-- +-- Table structure for table `algorithms_lookup_table` +-- + +DROP TABLE IF EXISTS `algorithms_lookup_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `algorithms_lookup_table` ( + `algo_name` varchar(100) NOT NULL COMMENT 'Algorithm name to be used in place of a surrogate key, assume they’re going to be unique. Like “FIMO”.', + `algo_desc` varchar(500) NOT NULL COMMENT 'Describe the named algorithm in algo_name.', + `algo_ranges` varchar(200) NOT NULL COMMENT 'Briefly describe the range of values', + PRIMARY KEY (`algo_name`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `external_source` +-- + +DROP TABLE IF EXISTS `external_source`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `external_source` ( + `source_id` int NOT NULL AUTO_INCREMENT COMMENT 'surrogate key', + `source_name` varchar(500) NOT NULL COMMENT 'name of the source, can be a pubmed identifier like “PMIDXXXXXXX” or “Asher’s sql dump”', + `comments` text NOT NULL COMMENT 'Comments regarding the source', + `date_uploaded` date NOT NULL, + `url` varchar(350) DEFAULT NULL COMMENT 'URL if available to paper/source (does not have to be a DOI, can be a link to a databases’ source)', + `tags` varchar(300) DEFAULT NULL COMMENT 'Specific to GRN project, have tags which describe features of a GRN which are relevant. For example, the condition or tissue of Arabidopsis when GRN was constructed, master regulators, what technique used', + `image_url` varchar(300) DEFAULT NULL, + `grn_title` varchar(200) DEFAULT NULL, + PRIMARY KEY (`source_id`), + UNIQUE KEY `source_name_UNIQUE` (`source_name`) +) ENGINE=InnoDB AUTO_INCREMENT=2286 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interaction_lookup_table` +-- + +DROP TABLE IF EXISTS `interaction_lookup_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interaction_lookup_table` ( + `interaction_type_id` int NOT NULL AUTO_INCREMENT COMMENT 'Surrogate key', + `description` varchar(100) NOT NULL COMMENT 'Describe the binary interaction of the entities. For example ‘ppi - protein interaction where entity_1_alias and entity_2_alias represent proteins’', + `entity_1_alias` varchar(50) NOT NULL COMMENT 'Can be a protein, miRNA, etc.', + `entity_2_alias` varchar(50) NOT NULL COMMENT 'Can be a protein, miRNA, etc.', + PRIMARY KEY (`interaction_type_id`), + UNIQUE KEY `description_UNIQUE` (`description`) +) ENGINE=InnoDB AUTO_INCREMENT=4 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interactions` +-- + +DROP TABLE IF EXISTS `interactions`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interactions` ( + `interaction_id` int NOT NULL AUTO_INCREMENT COMMENT 'surrogate key', + `pearson_correlation_coeff` decimal(6,5) DEFAULT NULL COMMENT 'PCC score imported from interactions table', + `entity_1` varchar(50) NOT NULL COMMENT 'Following the interaction_type_id (referencing the lookup table), define the first entity. For example if it is a PPI relationship than the entity 1 shall be a protein with an AGI (ex AT5G01010).', + `entity_2` varchar(50) NOT NULL COMMENT 'Following the interaction_type_id (referencing the lookup table), define the first entity. For example if it is a PPI relationship than the entity 2 shall be a protein with an AGI (ex AT5G01010).', + `interaction_type_id` int NOT NULL COMMENT 'Reference to the lookup of a interactions_lookup_table. Define what type of interaction these two genes are. For example if the value were ‘3’ and it looksup to a PPI, then both members are proteins.', + PRIMARY KEY (`interaction_id`), + UNIQUE KEY `unique_interaction_index` (`entity_1`,`entity_2`,`interaction_type_id`), + KEY `interaction_type_id_idx` (`interaction_type_id`), + KEY `e_1_idx` (`entity_1`), + KEY `e_2_idx` (`entity_2`), + CONSTRAINT `interaction_type_id` FOREIGN KEY (`interaction_type_id`) REFERENCES `interaction_lookup_table` (`interaction_type_id`) +) ENGINE=InnoDB AUTO_INCREMENT=3191448 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interactions_algo_score_join_table` +-- + +DROP TABLE IF EXISTS `interactions_algo_score_join_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interactions_algo_score_join_table` ( + `algo_score` varchar(30) NOT NULL COMMENT 'Score for that specific algorithm referenced in ‘algo_name’ for a particular binary interaction', + `interaction_id` int NOT NULL COMMENT 'The interaction we are looking at when we are referring to an algorithm score', + `algo_name` varchar(100) NOT NULL COMMENT 'algo_name which will reference the lookup table', + PRIMARY KEY (`algo_name`,`interaction_id`,`algo_score`), + KEY `interaction_id_idx` (`interaction_id`), + CONSTRAINT `algo_name` FOREIGN KEY (`algo_name`) REFERENCES `algorithms_lookup_table` (`algo_name`), + CONSTRAINT `interaction_id` FOREIGN KEY (`interaction_id`) REFERENCES `interactions` (`interaction_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interactions_source_mi_join_table` +-- + +DROP TABLE IF EXISTS `interactions_source_mi_join_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interactions_source_mi_join_table` ( + `interaction_id` int NOT NULL COMMENT 'reference the interaction pair via id', + `source_id` int NOT NULL COMMENT 'reference the paper/source where this interaction came from', + `external_db_id` varchar(30) NOT NULL COMMENT 'For the given external_database, like BIOGRID; what is it’s ID?', + `mode_of_action` tinyint(1) NOT NULL COMMENT 'Repression or activation? Reference it here to the lookup.', + `mi_detection_method` varchar(10) NOT NULL, + `mi_detection_type` varchar(10) NOT NULL, + PRIMARY KEY (`mi_detection_method`,`mi_detection_type`,`external_db_id`,`interaction_id`,`source_id`), + KEY `source_id_idx` (`source_id`), + KEY `m_o_a_db_FK_idx` (`mode_of_action`), + KEY `int_id_FK_on_mi_int_src` (`interaction_id`), + CONSTRAINT `int_id_FK_on_mi_int_src` FOREIGN KEY (`interaction_id`) REFERENCES `interactions` (`interaction_id`), + CONSTRAINT `m_o_a_db_FK` FOREIGN KEY (`mode_of_action`) REFERENCES `modes_of_action_lookup_table` (`m_of_a_pk`), + CONSTRAINT `source_id_FK` FOREIGN KEY (`source_id`) REFERENCES `external_source` (`source_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interolog_confidence_subset_table` +-- + +DROP TABLE IF EXISTS `interolog_confidence_subset_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interolog_confidence_subset_table` ( + `interaction_id` int NOT NULL COMMENT 'surrogate key', + `s_cerevisiae` tinyint NOT NULL COMMENT 'species score… repeat for all other species', + `s_pombe` tinyint NOT NULL, + `worm` tinyint NOT NULL, + `fly` tinyint NOT NULL, + `human` tinyint NOT NULL, + `mouse` tinyint NOT NULL, + `e_coli` tinyint NOT NULL, + `total_hits` smallint NOT NULL, + `num_species` tinyint NOT NULL, + PRIMARY KEY (`interaction_id`), + KEY `pdi_interaction_id_idx` (`interaction_id`), + CONSTRAINT `interolog_int_id_FK` FOREIGN KEY (`interaction_id`) REFERENCES `interactions` (`interaction_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `modes_of_action_lookup_table` +-- + +DROP TABLE IF EXISTS `modes_of_action_lookup_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `modes_of_action_lookup_table` ( + `m_of_a_pk` tinyint(1) NOT NULL AUTO_INCREMENT COMMENT 'surrogate key', + `description` varchar(20) NOT NULL COMMENT 'Describe the mode of action of the interaction, is it repression or activation for example?', + PRIMARY KEY (`m_of_a_pk`), + UNIQUE KEY `description_UNIQUE` (`description`) +) ENGINE=InnoDB AUTO_INCREMENT=4 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `interactions_vincent_v2` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `interactions_vincent_v2` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `interactions_vincent_v2`; + +-- +-- Table structure for table `algorithms_lookup_table` +-- + +DROP TABLE IF EXISTS `algorithms_lookup_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `algorithms_lookup_table` ( + `algo_name` varchar(100) NOT NULL COMMENT 'Algorithm name to be used in place of a surrogate key, assume they’re going to be unique. Like “FIMO”.', + `algo_desc` varchar(500) NOT NULL COMMENT 'Describe the named algorithm in algo_name.', + `algo_ranges` varchar(200) NOT NULL COMMENT 'Briefly describe the range of values', + PRIMARY KEY (`algo_name`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `external_source` +-- + +DROP TABLE IF EXISTS `external_source`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `external_source` ( + `source_id` int NOT NULL AUTO_INCREMENT COMMENT 'surrogate key', + `source_name` varchar(500) NOT NULL COMMENT 'name of the source, can be a pubmed identifier like “PMIDXXXXXXX” or “Asher’s sql dump”', + `comments` text NOT NULL COMMENT 'Comments regarding the source', + `date_uploaded` date NOT NULL COMMENT 'When it was uploaded to database', + `url` varchar(350) DEFAULT NULL COMMENT 'URL if available to paper/source (does not have to be a DOI, can be a link to a databases’ source)', + `image_url` varchar(300) DEFAULT NULL, + `grn_title` varchar(200) DEFAULT NULL, + `cyjs_layout` varchar(1000) DEFAULT NULL, + PRIMARY KEY (`source_id`), + UNIQUE KEY `source_name_UNIQUE` (`source_name`) +) ENGINE=InnoDB AUTO_INCREMENT=37 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interaction_lookup_table` +-- + +DROP TABLE IF EXISTS `interaction_lookup_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interaction_lookup_table` ( + `interaction_type_id` int NOT NULL AUTO_INCREMENT COMMENT 'Surrogate key', + `description` varchar(100) NOT NULL COMMENT 'Describe the binary interaction of the entities. For example ‘ppi - protein interaction where entity_1_alias and entity_2_alias represent proteins’', + `entity_1_alias` varchar(50) NOT NULL COMMENT 'Can be a protein, miRNA, etc.', + `entity_2_alias` varchar(50) NOT NULL COMMENT 'Can be a protein, miRNA, etc.', + PRIMARY KEY (`interaction_type_id`), + UNIQUE KEY `description_UNIQUE` (`description`) +) ENGINE=InnoDB AUTO_INCREMENT=4 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interactions` +-- + +DROP TABLE IF EXISTS `interactions`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interactions` ( + `interaction_id` int NOT NULL AUTO_INCREMENT COMMENT 'surrogate key', + `pearson_correlation_coeff` decimal(6,5) DEFAULT NULL COMMENT 'PCC score imported from interactions table', + `entity_1` varchar(50) NOT NULL COMMENT 'Following the interaction_type_id (referencing the lookup table), define the first entity. For example if it is a PPI relationship than the entity 1 shall be a protein with an AGI (ex AT5G01010).', + `entity_2` varchar(50) NOT NULL COMMENT 'Following the interaction_type_id (referencing the lookup table), define the first entity. For example if it is a PPI relationship than the entity 2 shall be a protein with an AGI (ex AT5G01010).', + `interaction_type_id` int NOT NULL COMMENT 'Reference to the lookup of a interactions_lookup_table. Define what type of interaction these two genes are. For example if the value were ‘3’ and it looksup to a PPI, then both members are proteins.', + PRIMARY KEY (`interaction_id`), + UNIQUE KEY `unique_interaction_index` (`entity_1`,`entity_2`,`interaction_type_id`), + KEY `interaction_type_id_idx` (`interaction_type_id`), + CONSTRAINT `interaction_type_id` FOREIGN KEY (`interaction_type_id`) REFERENCES `interaction_lookup_table` (`interaction_type_id`) +) ENGINE=InnoDB AUTO_INCREMENT=9069 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interactions_algo_score_join_table` +-- + +DROP TABLE IF EXISTS `interactions_algo_score_join_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interactions_algo_score_join_table` ( + `algo_score` varchar(30) NOT NULL COMMENT 'Score for that specific algorithm referenced in ‘algo_name’ for a particular binary interaction', + `interaction_id` int NOT NULL COMMENT 'The interaction we are looking at when we are referring to an algorithm score', + `algo_name` varchar(100) NOT NULL COMMENT 'algo_name which will reference the lookup table', + PRIMARY KEY (`algo_name`,`interaction_id`,`algo_score`), + KEY `interaction_id_idx` (`interaction_id`), + CONSTRAINT `algo_name` FOREIGN KEY (`algo_name`) REFERENCES `algorithms_lookup_table` (`algo_name`), + CONSTRAINT `interaction_id` FOREIGN KEY (`interaction_id`) REFERENCES `interactions` (`interaction_id`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interactions_source_mi_join_table` +-- + +DROP TABLE IF EXISTS `interactions_source_mi_join_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interactions_source_mi_join_table` ( + `interaction_id` int NOT NULL COMMENT 'reference the interaction pair via id', + `source_id` int NOT NULL COMMENT 'reference the paper/source where this interaction came from', + `external_db_id` varchar(30) NOT NULL COMMENT 'For the given external_database, like BIOGRID; what is it’s ID?', + `mode_of_action` tinyint(1) NOT NULL COMMENT 'Repression or activation? Reference it here to the lookup.', + `mi_detection_method` varchar(10) NOT NULL, + `mi_detection_type` varchar(10) NOT NULL, + PRIMARY KEY (`mi_detection_method`,`mi_detection_type`,`external_db_id`,`interaction_id`,`source_id`), + KEY `source_id_idx` (`source_id`), + KEY `m_o_a_db_FK_idx` (`mode_of_action`), + KEY `int_id_FK_on_mi_int_src` (`interaction_id`), + CONSTRAINT `int_id_FK_on_mi_int_src` FOREIGN KEY (`interaction_id`) REFERENCES `interactions` (`interaction_id`), + CONSTRAINT `m_o_a_db_FK` FOREIGN KEY (`mode_of_action`) REFERENCES `modes_of_action_lookup_table` (`m_of_a_pk`), + CONSTRAINT `source_id_FK` FOREIGN KEY (`source_id`) REFERENCES `external_source` (`source_id`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interolog_confidence_subset_table` +-- + +DROP TABLE IF EXISTS `interolog_confidence_subset_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interolog_confidence_subset_table` ( + `interaction_id` int NOT NULL COMMENT 'surrogate key', + `s_cerevisiae` tinyint NOT NULL COMMENT 'species score… repeat for all other species', + `s_pombe` tinyint NOT NULL, + `worm` tinyint NOT NULL, + `fly` tinyint NOT NULL, + `human` tinyint NOT NULL, + `mouse` tinyint NOT NULL, + `e_coli` tinyint NOT NULL, + `total_hits` smallint NOT NULL, + `num_species` tinyint NOT NULL, + PRIMARY KEY (`interaction_id`), + KEY `pdi_interaction_id_idx` (`interaction_id`), + CONSTRAINT `interolog_int_id_FK` FOREIGN KEY (`interaction_id`) REFERENCES `interactions` (`interaction_id`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `modes_of_action_lookup_table` +-- + +DROP TABLE IF EXISTS `modes_of_action_lookup_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `modes_of_action_lookup_table` ( + `m_of_a_pk` tinyint(1) NOT NULL AUTO_INCREMENT COMMENT 'surrogate key', + `description` varchar(20) NOT NULL COMMENT 'Describe the mode of action of the interaction, is it repression or activation for example?', + PRIMARY KEY (`m_of_a_pk`), + UNIQUE KEY `description_UNIQUE` (`description`) +) ENGINE=InnoDB AUTO_INCREMENT=4 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `source_tag_join_table` +-- + +DROP TABLE IF EXISTS `source_tag_join_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `source_tag_join_table` ( + `source_id` int NOT NULL, + `tag_name` varchar(20) NOT NULL, + PRIMARY KEY (`source_id`,`tag_name`), + KEY `tag_join_tag_names_FK_idx` (`tag_name`), + CONSTRAINT `tag_join_source_id_FK` FOREIGN KEY (`source_id`) REFERENCES `external_source` (`source_id`), + CONSTRAINT `tag_join_tag_names_FK` FOREIGN KEY (`tag_name`) REFERENCES `tag_lookup_table` (`tag_name`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `tag_lookup_table` +-- + +DROP TABLE IF EXISTS `tag_lookup_table`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `tag_lookup_table` ( + `tag_name` varchar(20) NOT NULL, + `tag_group` enum('Gene','Experiment','Condition','Misc') NOT NULL, + PRIMARY KEY (`tag_name`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `kalanchoe` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `kalanchoe` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `kalanchoe`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(2) NOT NULL DEFAULT '0', + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(16) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `kalanchoe_time_course_analysis` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `kalanchoe_time_course_analysis` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `kalanchoe_time_course_analysis`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(18) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(16) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `klepikova` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `klepikova` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `klepikova`; + +-- +-- Table structure for table `proj_info` +-- + +DROP TABLE IF EXISTS `proj_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_info` ( + `proj_id` int unsigned NOT NULL DEFAULT '0', + `proj_title` tinytext, + `proj_pi` tinytext, + `proj_pi_title` tinytext, + `proj_pi_inst` tinytext, + `proj_pi_addr` tinytext, + `proj_keyw1` tinytext, + `proj_keyw2` tinytext, + `proj_keyw3` tinytext, + `proj_keyw4` tinytext, + `proj_keyw5` tinytext, + `proj_res_area` tinytext, + `proj_num_samps` tinyint unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`proj_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `proj_res_area` +-- + +DROP TABLE IF EXISTS `proj_res_area`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_res_area` ( + `proj_res_index` tinytext, + `proj_res_area` tinytext +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_biosource_info` +-- + +DROP TABLE IF EXISTS `sample_biosource_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_biosource_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned NOT NULL DEFAULT '0', + `sample_bio_name` tinytext, + `sample_organism` tinytext, + `sample_alias` tinytext, + `sample_stock_code` tinytext, + `sample_genetic_var` tinytext, + `sample_tissue` tinytext, + `sample_diseased` tinytext, + `sample_growth_cond` tinytext, + `sample_growth_stage` tinytext, + `sample_time_point` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(3) NOT NULL DEFAULT '0', + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(30) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(16) NOT NULL, + `data_call` varchar(2) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_general_info` +-- + +DROP TABLE IF EXISTS `sample_general_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_general_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned NOT NULL DEFAULT '0', + `sample_repl` tinytext, + `sample_ctrl` tinytext, + `sample_desc` tinytext, + `sample_file_name` tinytext, + `sample_bot_id` tinytext NOT NULL, + `sample_name` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `lateral_root_initiation` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `lateral_root_initiation` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `lateral_root_initiation`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` varchar(30) NOT NULL, + `project_id` varchar(30) NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(64) DEFAULT NULL, + PRIMARY KEY (`sample_id`,`project_id`,`data_probeset_id`), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `light_series` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `light_series` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `light_series`; + +-- +-- Table structure for table `proj_info` +-- + +DROP TABLE IF EXISTS `proj_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_info` ( + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `proj_title` tinytext, + `proj_pi` tinytext, + `proj_pi_title` tinytext, + `proj_pi_inst` tinytext, + `proj_pi_addr` tinytext, + `proj_keyw1` tinytext, + `proj_keyw2` tinytext, + `proj_keyw3` tinytext, + `proj_keyw4` tinytext, + `proj_keyw5` tinytext, + `proj_res_area` tinytext, + `proj_num_samps` tinyint unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`proj_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_biosource_info` +-- + +DROP TABLE IF EXISTS `sample_biosource_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_biosource_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_bio_name` tinytext, + `sample_organism` tinytext, + `sample_alias` tinytext, + `sample_stock_code` tinytext, + `sample_genetic_var` tinytext, + `sample_tissue` tinytext, + `sample_diseased` tinytext, + `sample_growth_cond` tinytext, + `sample_growth_stage` tinytext, + `sample_time_point` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(30) NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(30) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_general_info` +-- + +DROP TABLE IF EXISTS `sample_general_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_general_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_repl` tinytext, + `sample_ctrl` tinytext, + `sample_desc` tinytext, + `sample_file_name` tinytext, + `sample_bot_id` tinytext NOT NULL, + `sample_name` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `lipid_map` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `lipid_map` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `lipid_map`; + +-- +-- Table structure for table `lipids` +-- + +DROP TABLE IF EXISTS `lipids`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `lipids` ( + `lipid_class` varchar(64) NOT NULL, + `lipid` varchar(64) NOT NULL, + KEY `lipids_key` (`lipid_class`,`lipid`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(64) NOT NULL, + `data_signal` float DEFAULT NULL, + `data_bot_id` varchar(16) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `little_millet` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `little_millet` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `little_millet`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(2) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(32) DEFAULT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(12) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `llama3` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `llama3` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `llama3`; + +-- +-- Table structure for table `summaries` +-- + +DROP TABLE IF EXISTS `summaries`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `summaries` ( + `gene_id` varchar(13) DEFAULT NULL, + `summary` longtext, + `bert_score` decimal(8,7) DEFAULT NULL +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `localisations` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `localisations` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `localisations`; + +-- +-- Table structure for table `BAR_suba3` +-- + +DROP TABLE IF EXISTS `BAR_suba3`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `BAR_suba3` ( + `gene_id` varchar(20) NOT NULL, + `alias` mediumtext, + `lab_description` mediumtext, + `gfp` mediumtext, + `mass_spec` mediumtext, + `swissprot` mediumtext, + `amigo` mediumtext, + `tair` mediumtext, + `gs` mediumtext, + `pred_ipsort` mediumtext, + `pred_mitopred` mediumtext, + `pred_mitoprot2` mediumtext, + `pred_predotar` mediumtext, + `pred_subloc` mediumtext, + `pred_targetp` mediumtext, + `pred_wolfpsort` mediumtext, + `pred_multiloc2` mediumtext, + `pred_adaboost` mediumtext, + `pred_atp` mediumtext, + `pred_bacello` mediumtext, + `pred_chlorop` mediumtext, + `pred_epiloc` mediumtext, + `pred_nucleo` mediumtext, + `pred_plantmploc` mediumtext, + `pred_pclr` mediumtext, + `pred_predsl` mediumtext, + `pred_pprowler` mediumtext, + `pred_pts1` mediumtext, + `pred_slpfa` mediumtext, + `pred_slplocal` mediumtext, + `pred_yloc` mediumtext, + PRIMARY KEY (`gene_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `BAR_suba4` +-- + +DROP TABLE IF EXISTS `BAR_suba4`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `BAR_suba4` ( + `gene_id` varchar(20) NOT NULL, + `alias` mediumtext, + `lab_description` mediumtext, + `gfp` mediumtext, + `mass_spec` mediumtext, + `swissprot` mediumtext, + `amigo` mediumtext, + `tair` mediumtext, + `gs` mediumtext, + `pred_ipsort` mediumtext, + `pred_mitopred` mediumtext, + `pred_mitoprot2` mediumtext, + `pred_predotar` mediumtext, + `pred_subloc` mediumtext, + `pred_targetp` mediumtext, + `pred_wolfpsort` mediumtext, + `pred_multiloc2` mediumtext, + `pred_adaboost` mediumtext, + `pred_atp` mediumtext, + `pred_bacello` mediumtext, + `pred_chlorop` mediumtext, + `pred_epiloc` mediumtext, + `pred_nucleo` mediumtext, + `pred_plantmploc` mediumtext, + `pred_pclr` mediumtext, + `pred_predsl` mediumtext, + `pred_pprowler` mediumtext, + `pred_pts1` mediumtext, + `pred_slpfa` mediumtext, + `pred_slplocal` mediumtext, + `pred_yloc` mediumtext, + PRIMARY KEY (`gene_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `Rice_mPLoc` +-- + +DROP TABLE IF EXISTS `Rice_mPLoc`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `Rice_mPLoc` ( + `gene_id` varchar(20) NOT NULL DEFAULT '', + `alias` text, + `lab_description` text, + `gfp` text, + `mass_spec` text, + `swissprot` text, + `amigo` text, + `annotation` text, + `pred_ipsort` text, + `pred_mitopred` text, + `pred_mitopred2` text, + `pred_predator` text, + `pred_peroxp` text, + `pred_subloc` text, + `pred_targetp` text, + `pred_wolfpsort` text, + `pred_multiloc` text, + `pred_loctree` text, + `pred_mPLoc` text, + PRIMARY KEY (`gene_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `cropPAL2_eplant` +-- + +DROP TABLE IF EXISTS `cropPAL2_eplant`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `cropPAL2_eplant` ( + `locus` varchar(64) NOT NULL, + `location_consensus` set('cell plate','cytoskeleton','cytosol','endoplasmic reticulum','extracellular','golgi','mitochondrion','nucleus','peroxisome','plasma membrane','plastid','unclear','vacuole','endosome') DEFAULT NULL, + KEY `locus_location` (`locus`,`location_consensus`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `src_species_exp_34` +-- + +DROP TABLE IF EXISTS `src_species_exp_34`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `src_species_exp_34` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `source` enum('gfp','msms') NOT NULL, + `locus` varchar(255) DEFAULT NULL, + `taxaid` int DEFAULT NULL, + `paper` varchar(32) DEFAULT NULL, + `location` enum('cell plate','cytoskeleton','cytosol','endoplasmic reticulum','extracellular','golgi','mitochondrion','nucleus','peroxisome','plasma membrane','plastid','unclear','vacuole','endosome') DEFAULT NULL, + `match_type` mediumtext, + PRIMARY KEY (`id`), + KEY `ix_src_species_exp_34_source` (`source`), + KEY `locus` (`locus`), + KEY `taxaid` (`taxaid`) +) ENGINE=InnoDB AUTO_INCREMENT=38257 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `suba` +-- + +DROP TABLE IF EXISTS `suba`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `suba` ( + `gene_id` varchar(20) NOT NULL DEFAULT '', + `alias` text, + `lab_description` text, + `gfp` text, + `mass_spec` text, + `swissprot` text, + `amigo` text, + `annotation` text, + `pred_ipsort` text, + `pred_mitopred` text, + `pred_mitopred2` text, + `pred_predator` text, + `pred_peroxp` text, + `pred_subloc` text, + `pred_targetp` text, + `pred_wolfpsort` text, + `pred_multiloc` text, + `pred_loctree` text, + PRIMARY KEY (`gene_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `suba3` +-- + +DROP TABLE IF EXISTS `suba3`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `suba3` ( + `id` int NOT NULL AUTO_INCREMENT, + `locus` varchar(13) DEFAULT NULL, + `chr` enum('1','2','3','4','5','C','M') DEFAULT NULL, + `description` text, + `ests` int DEFAULT '0', + `flcdnas` int DEFAULT '0', + `residues` int DEFAULT '0', + `mwt` float DEFAULT '0', + `pi` float DEFAULT '0', + `gravy` float DEFAULT '0', + `gfp_image` tinyint NOT NULL DEFAULT '0', + `location_all_predictors` set('cell plate','cytoskeleton','cytosol','endoplasmic reticulum','extracellular','golgi','mitochondrion','nucleus','peroxisome','plasma membrane','plastid','unclear','vacuole','endosome') DEFAULT NULL, + `location_adaboost` set('cell plate','cytoskeleton','cytosol','endoplasmic reticulum','extracellular','golgi','mitochondrion','nucleus','peroxisome','plasma membrane','plastid','unclear','vacuole','endosome') DEFAULT NULL, + `location_atp` set('cell plate','cytoskeleton','cytosol','endoplasmic reticulum','extracellular','golgi','mitochondrion','nucleus','peroxisome','plasma membrane','plastid','unclear','vacuole','endosome') DEFAULT NULL, + `location_bacello` set('cell plate','cytoskeleton','cytosol','endoplasmic reticulum','extracellular','golgi','mitochondrion','nucleus','peroxisome','plasma membrane','plastid','unclear','vacuole','endosome') DEFAULT NULL, + `location_chlorop` set('cell plate','cytoskeleton','cytosol','endoplasmic reticulum','extracellular','golgi','mitochondrion','nucleus','peroxisome','plasma membrane','plastid','unclear','vacuole','endosome') DEFAULT NULL, + `location_epiloc` set('cell plate','cytoskeleton','cytosol','endoplasmic reticulum','extracellular','golgi','mitochondrion','nucleus','peroxisome','plasma membrane','plastid','unclear','vacuole','endosome') DEFAULT NULL, + `location_ipsort` set('cell plate','cytoskeleton','cytosol','endoplasmic reticulum','extracellular','golgi','mitochondrion','nucleus','peroxisome','plasma membrane','plastid','unclear','vacuole','endosome') DEFAULT NULL, + `location_mitopred` set('cell plate','cytoskeleton','cytosol','endoplasmic reticulum','extracellular','golgi','mitochondrion','nucleus','peroxisome','plasma membrane','plastid','unclear','vacuole','endosome') DEFAULT NULL, + `location_mitoprot2` set('cell plate','cytoskeleton','cytosol','endoplasmic reticulum','extracellular','golgi','mitochondrion','nucleus','peroxisome','plasma membrane','plastid','unclear','vacuole','endosome') DEFAULT NULL, + `location_multiloc2` set('cell plate','cytoskeleton','cytosol','endoplasmic reticulum','extracellular','golgi','mitochondrion','nucleus','peroxisome','plasma membrane','plastid','unclear','vacuole','endosome') DEFAULT NULL, + `location_nucleo` set('cell plate','cytoskeleton','cytosol','endoplasmic reticulum','extracellular','golgi','mitochondrion','nucleus','peroxisome','plasma membrane','plastid','unclear','vacuole','endosome') DEFAULT NULL, + `location_plantmploc` set('cell plate','cytoskeleton','cytosol','endoplasmic reticulum','extracellular','golgi','mitochondrion','nucleus','peroxisome','plasma membrane','plastid','unclear','vacuole','endosome') DEFAULT NULL, + `location_pclr` set('cell plate','cytoskeleton','cytosol','endoplasmic reticulum','extracellular','golgi','mitochondrion','nucleus','peroxisome','plasma membrane','plastid','unclear','vacuole','endosome') DEFAULT NULL, + `location_predotar` set('cell plate','cytoskeleton','cytosol','endoplasmic reticulum','extracellular','golgi','mitochondrion','nucleus','peroxisome','plasma membrane','plastid','unclear','vacuole','endosome') DEFAULT NULL, + `location_predsl` set('cell plate','cytoskeleton','cytosol','endoplasmic reticulum','extracellular','golgi','mitochondrion','nucleus','peroxisome','plasma membrane','plastid','unclear','vacuole','endosome') DEFAULT NULL, + `location_pprowler` set('cell plate','cytoskeleton','cytosol','endoplasmic reticulum','extracellular','golgi','mitochondrion','nucleus','peroxisome','plasma membrane','plastid','unclear','vacuole','endosome') DEFAULT NULL, + `location_pts1` set('cell plate','cytoskeleton','cytosol','endoplasmic reticulum','extracellular','golgi','mitochondrion','nucleus','peroxisome','plasma membrane','plastid','unclear','vacuole','endosome') DEFAULT NULL, + `location_slpfa` set('cell plate','cytoskeleton','cytosol','endoplasmic reticulum','extracellular','golgi','mitochondrion','nucleus','peroxisome','plasma membrane','plastid','unclear','vacuole','endosome') DEFAULT NULL, + `location_slplocal` set('cell plate','cytoskeleton','cytosol','endoplasmic reticulum','extracellular','golgi','mitochondrion','nucleus','peroxisome','plasma membrane','plastid','unclear','vacuole','endosome') DEFAULT NULL, + `location_subloc` set('cell plate','cytoskeleton','cytosol','endoplasmic reticulum','extracellular','golgi','mitochondrion','nucleus','peroxisome','plasma membrane','plastid','unclear','vacuole','endosome') DEFAULT NULL, + `location_targetp` set('cell plate','cytoskeleton','cytosol','endoplasmic reticulum','extracellular','golgi','mitochondrion','nucleus','peroxisome','plasma membrane','plastid','unclear','vacuole','endosome') DEFAULT NULL, + `location_wolfpsort` set('cell plate','cytoskeleton','cytosol','endoplasmic reticulum','extracellular','golgi','mitochondrion','nucleus','peroxisome','plasma membrane','plastid','unclear','vacuole','endosome') DEFAULT NULL, + `location_yloc` set('cell plate','cytoskeleton','cytosol','endoplasmic reticulum','extracellular','golgi','mitochondrion','nucleus','peroxisome','plasma membrane','plastid','unclear','vacuole','endosome') DEFAULT NULL, + `location_amigo` text NOT NULL, + `location_tair` text NOT NULL, + `location_swissprot` text NOT NULL, + `spid` varchar(8) DEFAULT NULL, + `location_ms` text NOT NULL, + `location_gfp` text NOT NULL, + `location_consensus` set('cell plate','cytoskeleton','cytosol','endoplasmic reticulum','extracellular','golgi','mitochondrion','nucleus','peroxisome','plasma membrane','plastid','unclear','vacuole','endosome') DEFAULT NULL, + `location_gs` text, + PRIMARY KEY (`id`), + UNIQUE KEY `ix_suba3_locus` (`locus`), + FULLTEXT KEY `ft_index` (`description`) +) ENGINE=InnoDB AUTO_INCREMENT=35451 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `lupin_lcm_leaf` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `lupin_lcm_leaf` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `lupin_lcm_leaf`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(32) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(32) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `lupin_lcm_pod` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `lupin_lcm_pod` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `lupin_lcm_pod`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(32) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(32) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `lupin_lcm_stem` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `lupin_lcm_stem` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `lupin_lcm_stem`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(32) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(32) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `lupin_pod_seed` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `lupin_pod_seed` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `lupin_pod_seed`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(32) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(32) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `lupin_whole_plant` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `lupin_whole_plant` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `lupin_whole_plant`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(32) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(32) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `maize_RMA_linear` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `maize_RMA_linear` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `maize_RMA_linear`; + +-- +-- Table structure for table `proj_info` +-- + +DROP TABLE IF EXISTS `proj_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_info` ( + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `proj_title` tinytext, + `proj_pi` tinytext, + `proj_pi_title` tinytext, + `proj_pi_inst` tinytext, + `proj_pi_addr` tinytext, + `proj_keyw1` tinytext, + `proj_keyw2` tinytext, + `proj_keyw3` tinytext, + `proj_keyw4` tinytext, + `proj_keyw5` tinytext, + `proj_res_area` tinytext, + `proj_num_samps` tinyint unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`proj_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `proj_res_area` +-- + +DROP TABLE IF EXISTS `proj_res_area`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_res_area` ( + `proj_res_index` tinytext, + `proj_res_area` tinytext +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_biosource_info` +-- + +DROP TABLE IF EXISTS `sample_biosource_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_biosource_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_bio_name` tinytext, + `sample_organism` tinytext, + `sample_alias` tinytext, + `sample_stock_code` tinytext, + `sample_genetic_var` tinytext, + `sample_tissue` tinytext, + `sample_diseased` tinytext, + `sample_growth_cond` tinytext, + `sample_growth_stage` tinytext, + `sample_time_point` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(20) NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(30) NOT NULL, + `sample_tissue` text NOT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(12)), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_general_info` +-- + +DROP TABLE IF EXISTS `sample_general_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_general_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_repl` tinytext, + `sample_ctrl` tinytext, + `sample_desc` tinytext, + `sample_file_name` tinytext, + `sample_bot_id` tinytext NOT NULL, + `sample_name` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `maize_RMA_log` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `maize_RMA_log` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `maize_RMA_log`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(20) NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(30) NOT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(12)), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `maize_annotations` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `maize_annotations` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `maize_annotations`; + +-- +-- Table structure for table `enzyme_gene_lookup` +-- + +DROP TABLE IF EXISTS `enzyme_gene_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `enzyme_gene_lookup` ( + `data_probeset_id` varchar(60) NOT NULL, + `gene` varchar(60) NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`data_probeset_id`,`gene`,`date`), + KEY `gene_probeset` (`gene`,`data_probeset_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `enzyme_information` +-- + +DROP TABLE IF EXISTS `enzyme_information`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `enzyme_information` ( + `data_probeset_id` varchar(40) NOT NULL, + `unit` text NOT NULL, + `type` text NOT NULL, + `enzyme_class` text, + `pathway` text, + `compound_id` text, + `pathway_name` text NOT NULL, + KEY `probeset` (`data_probeset_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gene_annotations` +-- + +DROP TABLE IF EXISTS `gene_annotations`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene_annotations` ( + `gene` varchar(60) NOT NULL, + `annotation` longtext NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`gene`,`date`), + KEY `date_gene` (`date`,`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `maize_rice_lookup` +-- + +DROP TABLE IF EXISTS `maize_rice_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `maize_rice_lookup` ( + `maize_id` varchar(60) NOT NULL, + `rice_id` varchar(60) NOT NULL, + `date` date NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `maize_v3_v4_lookup` +-- + +DROP TABLE IF EXISTS `maize_v3_v4_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `maize_v3_v4_lookup` ( + `v4` varchar(24) NOT NULL, + `v3` varchar(24) NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`v4`,`v3`), + KEY `v3_v4` (`v3`,`v4`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `maize_v3_v5_lookup` +-- + +DROP TABLE IF EXISTS `maize_v3_v5_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `maize_v3_v5_lookup` ( + `v3` varchar(24) NOT NULL, + `v5` varchar(24) NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`v5`,`v3`), + KEY `v3_v5` (`v3`,`v5`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `metabolite_gene_lookup` +-- + +DROP TABLE IF EXISTS `metabolite_gene_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `metabolite_gene_lookup` ( + `data_probeset_id` varchar(60) NOT NULL, + `gene` varchar(60) NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`data_probeset_id`,`gene`,`date`), + KEY `gene_probeset` (`gene`,`data_probeset_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `metabolite_information` +-- + +DROP TABLE IF EXISTS `metabolite_information`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `metabolite_information` ( + `data_probeset_id` varchar(42) NOT NULL, + `unit` text NOT NULL, + `type` text NOT NULL, + `enzyme_class` text, + `pathway` text, + `compound_id` text, + `pathway_name` text NOT NULL, + KEY `probeset` (`data_probeset_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `maize_atlas` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `maize_atlas` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `maize_atlas`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` varchar(5) NOT NULL, + `proj_id` varchar(5) NOT NULL, + `data_probeset_id` varchar(25) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`proj_id`,`data_probeset_id`), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `maize_atlas_v5` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `maize_atlas_v5` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `maize_atlas_v5`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(25) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(40) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `maize_buell_lab` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `maize_buell_lab` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `maize_buell_lab`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(5) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_bot_id` varchar(50) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `maize_early_seed` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `maize_early_seed` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `maize_early_seed`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(5) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_bot_id` varchar(50) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `maize_ears` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `maize_ears` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `maize_ears`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(20) NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(16) NOT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(12)), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `maize_embryonic_leaf_development` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `maize_embryonic_leaf_development` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `maize_embryonic_leaf_development`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(18) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(24) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `maize_enzyme` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `maize_enzyme` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `maize_enzyme`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(8) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `maize_gdowns` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `maize_gdowns` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `maize_gdowns`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` varchar(30) NOT NULL, + `proj_id` varchar(30) NOT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`data_probeset_id`), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `maize_gdowns_annotations_lookup` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `maize_gdowns_annotations_lookup` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `maize_gdowns_annotations_lookup`; + +-- +-- Table structure for table `maize_gdowns_lookup` +-- + +DROP TABLE IF EXISTS `maize_gdowns_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `maize_gdowns_lookup` ( + `probeset` varchar(60) NOT NULL, + `gene` varchar(60) NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`probeset`,`gene`), + KEY `date_gene` (`date`,`gene`,`probeset`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `maize_interactions` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `maize_interactions` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `maize_interactions`; + +-- +-- Table structure for table `interactions` +-- + +DROP TABLE IF EXISTS `interactions`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interactions` ( + `Protein1` varchar(25) NOT NULL, + `Protein2` varchar(25) NOT NULL, + `Quality` float DEFAULT '0', + `aiv_index` tinyint NOT NULL, + `Pcc` float DEFAULT NULL, + `bind_id` text, + UNIQUE KEY `interactions_eplant` (`Protein1`,`Protein2`,`aiv_index`,`bind_id`(30)), + KEY `aiv_index` (`aiv_index`), + KEY `protein2` (`Protein2`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `maize_interactions_v5` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `maize_interactions_v5` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `maize_interactions_v5`; + +-- +-- Table structure for table `interactions` +-- + +DROP TABLE IF EXISTS `interactions`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interactions` ( + `Protein1` varchar(25) NOT NULL, + `Protein2` varchar(25) NOT NULL, + `Quality` float DEFAULT '0', + `aiv_index` tinyint NOT NULL, + `Pcc` float DEFAULT NULL, + `bind_id` text, + UNIQUE KEY `interactions_eplant` (`Protein1`,`Protein2`,`aiv_index`,`bind_id`(30)), + KEY `aiv_index` (`aiv_index`), + KEY `protein2` (`Protein2`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `maize_iplant` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `maize_iplant` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `maize_iplant`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(20) NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(16) NOT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(12)), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `maize_kernel_v5` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `maize_kernel_v5` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `maize_kernel_v5`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(25) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(8) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `maize_leaf_gradient` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `maize_leaf_gradient` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `maize_leaf_gradient`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(20) NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(12) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `maize_lipid_map` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `maize_lipid_map` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `maize_lipid_map`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float DEFAULT NULL, + `data_bot_id` varchar(12) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `maize_metabolite` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `maize_metabolite` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `maize_metabolite`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(64) NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(5) NOT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(50)), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `maize_nitrogen_use_efficiency` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `maize_nitrogen_use_efficiency` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `maize_nitrogen_use_efficiency`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(24) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `maize_rice_comparison` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `maize_rice_comparison` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `maize_rice_comparison`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(16) NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(12) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `maize_root` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `maize_root` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `maize_root`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(30) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(255) NOT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(12)), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `maize_stress_v5` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `maize_stress_v5` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `maize_stress_v5`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(25) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(20) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `mangosteen_annotations_lookup` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `mangosteen_annotations_lookup` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `mangosteen_annotations_lookup`; + +-- +-- Table structure for table `mangosteen_annotation` +-- + +DROP TABLE IF EXISTS `mangosteen_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `mangosteen_annotation` ( + `gene` varchar(12) NOT NULL, + `annotation` text, + `date` date NOT NULL, + PRIMARY KEY (`gene`), + KEY `date` (`date`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `mangosteen_aril_vs_rind` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `mangosteen_aril_vs_rind` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `mangosteen_aril_vs_rind`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(2) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(8) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(8) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `mangosteen_callus` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `mangosteen_callus` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `mangosteen_callus`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(2) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(8) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(8) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `mangosteen_diseased_vs_normal` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `mangosteen_diseased_vs_normal` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `mangosteen_diseased_vs_normal`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(2) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(8) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(12) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `mangosteen_fruit_ripening` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `mangosteen_fruit_ripening` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `mangosteen_fruit_ripening`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(2) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(8) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(8) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `mangosteen_seed_development` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `mangosteen_seed_development` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `mangosteen_seed_development`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(2) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(8) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(12) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `mangosteen_seed_development_germination` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `mangosteen_seed_development_germination` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `mangosteen_seed_development_germination`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(2) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(8) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(8) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `mangosteen_seed_germination` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `mangosteen_seed_germination` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `mangosteen_seed_germination`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(2) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(8) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(12) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `marchantia_organ_stress` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `marchantia_organ_stress` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `marchantia_organ_stress`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(32) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(32) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `markergen` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `markergen` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `markergen`; + +-- +-- Table structure for table `accession` +-- + +DROP TABLE IF EXISTS `accession`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `accession` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `name` varchar(10) NOT NULL DEFAULT '', + PRIMARY KEY (`id`), + UNIQUE KEY `name` (`name`) +) ENGINE=InnoDB AUTO_INCREMENT=100 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `capsfeedback` +-- + +DROP TABLE IF EXISTS `capsfeedback`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `capsfeedback` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `researcher_id` int unsigned NOT NULL DEFAULT '0', + `capsinstance_id` int unsigned NOT NULL DEFAULT '0', + `observed_fragment_list` varchar(100) NOT NULL DEFAULT '', + `comment_id` int unsigned DEFAULT NULL, + PRIMARY KEY (`id`) +) ENGINE=InnoDB AUTO_INCREMENT=232 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `capsinstance` +-- + +DROP TABLE IF EXISTS `capsinstance`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `capsinstance` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `accession_id` int unsigned NOT NULL DEFAULT '0', + `capsmarker_id` int unsigned NOT NULL DEFAULT '0', + `fragment_list` varchar(100) DEFAULT NULL, + PRIMARY KEY (`id`), + KEY `capsmarker_id` (`capsmarker_id`), + KEY `accession_id` (`accession_id`) +) ENGINE=InnoDB AUTO_INCREMENT=1342063 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `capsmarker` +-- + +DROP TABLE IF EXISTS `capsmarker`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `capsmarker` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `enzyme_id` int unsigned NOT NULL DEFAULT '0', + `pcr_id` int unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`id`), + KEY `enzyme_id` (`enzyme_id`), + KEY `pcr_id` (`pcr_id`) +) ENGINE=InnoDB AUTO_INCREMENT=254982 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `comment` +-- + +DROP TABLE IF EXISTS `comment`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `comment` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `researcher_id` int unsigned NOT NULL DEFAULT '0', + `details` text NOT NULL, + PRIMARY KEY (`id`) +) ENGINE=InnoDB AUTO_INCREMENT=85 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `dataset` +-- + +DROP TABLE IF EXISTS `dataset`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `dataset` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `name` varchar(25) NOT NULL DEFAULT '', + `target_id` int unsigned DEFAULT NULL, + PRIMARY KEY (`id`), + UNIQUE KEY `name` (`name`) +) ENGINE=InnoDB AUTO_INCREMENT=4 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `difference` +-- + +DROP TABLE IF EXISTS `difference`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `difference` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `pattern` text NOT NULL, + PRIMARY KEY (`id`) +) ENGINE=InnoDB AUTO_INCREMENT=61342 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `enzyme` +-- + +DROP TABLE IF EXISTS `enzyme`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `enzyme` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `name` varchar(10) NOT NULL DEFAULT '', + `price` float DEFAULT NULL, + PRIMARY KEY (`id`), + UNIQUE KEY `name` (`name`) +) ENGINE=InnoDB AUTO_INCREMENT=153 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gene` +-- + +DROP TABLE IF EXISTS `gene`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `name` varchar(10) NOT NULL DEFAULT '', + PRIMARY KEY (`id`), + UNIQUE KEY `name` (`name`) +) ENGINE=InnoDB AUTO_INCREMENT=11079 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pcr` +-- + +DROP TABLE IF EXISTS `pcr`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pcr` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `dataset_id` int unsigned NOT NULL DEFAULT '0', + `gene_id` int unsigned NOT NULL DEFAULT '0', + `forward_id` int unsigned NOT NULL DEFAULT '0', + `reverse_id` int unsigned NOT NULL DEFAULT '0', + `product_id` int unsigned NOT NULL DEFAULT '0', + `chromosome` int unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`id`), + UNIQUE KEY `forward_id` (`forward_id`), + UNIQUE KEY `reverse_id` (`reverse_id`), + UNIQUE KEY `product_id` (`product_id`), + KEY `gene_id` (`gene_id`) +) ENGINE=InnoDB AUTO_INCREMENT=23544 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pcrfeedback` +-- + +DROP TABLE IF EXISTS `pcrfeedback`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pcrfeedback` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `researcher_id` int unsigned NOT NULL DEFAULT '0', + `pcr_id` int unsigned NOT NULL DEFAULT '0', + `accession_id` int unsigned NOT NULL DEFAULT '0', + `comment_id` int unsigned DEFAULT NULL, + PRIMARY KEY (`id`) +) ENGINE=InnoDB AUTO_INCREMENT=7 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pickled_search` +-- + +DROP TABLE IF EXISTS `pickled_search`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pickled_search` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `researcher_id` int unsigned NOT NULL DEFAULT '0', + `saved` date NOT NULL DEFAULT '0000-00-00', + `reminder` date DEFAULT NULL, + `pickle` text NOT NULL, + `comment` text, + PRIMARY KEY (`id`) +) ENGINE=InnoDB AUTO_INCREMENT=29 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `polymorphism` +-- + +DROP TABLE IF EXISTS `polymorphism`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `polymorphism` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `accession_id` int unsigned NOT NULL DEFAULT '0', + `product_id` int unsigned NOT NULL DEFAULT '0', + `difference_id` int unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`id`), + KEY `product_id` (`product_id`), + KEY `difference_id` (`difference_id`) +) ENGINE=InnoDB AUTO_INCREMENT=133293 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `primer` +-- + +DROP TABLE IF EXISTS `primer`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `primer` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `seq` varchar(100) NOT NULL DEFAULT '', + `start` int unsigned NOT NULL DEFAULT '0', + `tm` float NOT NULL DEFAULT '0', + `gc` float NOT NULL DEFAULT '0', + PRIMARY KEY (`id`), + KEY `start` (`start`) +) ENGINE=InnoDB AUTO_INCREMENT=47088 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `primerfeedback` +-- + +DROP TABLE IF EXISTS `primerfeedback`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `primerfeedback` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `researcher_id` int unsigned NOT NULL DEFAULT '0', + `primer_id` int unsigned NOT NULL DEFAULT '0', + `accession_id` int unsigned NOT NULL DEFAULT '0', + `comment_id` int unsigned DEFAULT NULL, + PRIMARY KEY (`id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `product` +-- + +DROP TABLE IF EXISTS `product`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `product` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `target_seq` text NOT NULL, + PRIMARY KEY (`id`) +) ENGINE=InnoDB AUTO_INCREMENT=23545 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `researcher` +-- + +DROP TABLE IF EXISTS `researcher`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `researcher` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `first_name` varchar(20) NOT NULL DEFAULT '', + `last_name` varchar(20) NOT NULL DEFAULT '', + `user_name` varchar(20) NOT NULL DEFAULT '', + `passwd` varchar(20) NOT NULL DEFAULT '', + `email` varchar(50) NOT NULL DEFAULT '', + PRIMARY KEY (`id`), + UNIQUE KEY `user_name` (`user_name`) +) ENGINE=InnoDB AUTO_INCREMENT=156 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sslpfeedback` +-- + +DROP TABLE IF EXISTS `sslpfeedback`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sslpfeedback` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `researcher_id` int unsigned NOT NULL DEFAULT '0', + `sslpinstance_id` int unsigned NOT NULL DEFAULT '0', + `observed_product_size` varchar(100) NOT NULL DEFAULT '', + `comment_id` int unsigned DEFAULT NULL, + PRIMARY KEY (`id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sslpinstance` +-- + +DROP TABLE IF EXISTS `sslpinstance`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sslpinstance` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `accession_id` int unsigned NOT NULL DEFAULT '0', + `pcr_id` int unsigned NOT NULL DEFAULT '0', + `product_size` int unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Temporary view structure for view `test` +-- + +DROP TABLE IF EXISTS `test`; +/*!50001 DROP VIEW IF EXISTS `test`*/; +SET @saved_cs_client = @@character_set_client; +/*!50503 SET character_set_client = utf8mb4 */; +/*!50001 CREATE VIEW `test` AS SELECT + 1 AS `name`, + 1 AS `product_id`, + 1 AS `count`*/; +SET character_set_client = @saved_cs_client; + +-- +-- Temporary view structure for view `vie_cvi` +-- + +DROP TABLE IF EXISTS `vie_cvi`; +/*!50001 DROP VIEW IF EXISTS `vie_cvi`*/; +SET @saved_cs_client = @@character_set_client; +/*!50503 SET character_set_client = utf8mb4 */; +/*!50001 CREATE VIEW `vie_cvi` AS SELECT + 1 AS `agi`, + 1 AS `accesion_name`, + 1 AS `difference_id`, + 1 AS `difference_pattern`, + 1 AS `product_id`*/; +SET character_set_client = @saved_cs_client; + +-- +-- Temporary view structure for view `vie_cvi1` +-- + +DROP TABLE IF EXISTS `vie_cvi1`; +/*!50001 DROP VIEW IF EXISTS `vie_cvi1`*/; +SET @saved_cs_client = @@character_set_client; +/*!50503 SET character_set_client = utf8mb4 */; +/*!50001 CREATE VIEW `vie_cvi1` AS SELECT + 1 AS `agi`, + 1 AS `accesion_name`, + 1 AS `difference_id`, + 1 AS `difference_pattern`, + 1 AS `product_id`*/; +SET character_set_client = @saved_cs_client; + +-- +-- Temporary view structure for view `vie_cvi2` +-- + +DROP TABLE IF EXISTS `vie_cvi2`; +/*!50001 DROP VIEW IF EXISTS `vie_cvi2`*/; +SET @saved_cs_client = @@character_set_client; +/*!50503 SET character_set_client = utf8mb4 */; +/*!50001 CREATE VIEW `vie_cvi2` AS SELECT + 1 AS `agi`, + 1 AS `accesion_name`, + 1 AS `difference_id`, + 1 AS `difference_pattern`, + 1 AS `product_id`*/; +SET character_set_client = @saved_cs_client; + +-- +-- Temporary view structure for view `vie_cvi3` +-- + +DROP TABLE IF EXISTS `vie_cvi3`; +/*!50001 DROP VIEW IF EXISTS `vie_cvi3`*/; +SET @saved_cs_client = @@character_set_client; +/*!50503 SET character_set_client = utf8mb4 */; +/*!50001 CREATE VIEW `vie_cvi3` AS SELECT + 1 AS `agi`, + 1 AS `accesion_name`, + 1 AS `difference_id`, + 1 AS `difference_pattern`, + 1 AS `product_id`*/; +SET character_set_client = @saved_cs_client; + +-- +-- Temporary view structure for view `vie_poly` +-- + +DROP TABLE IF EXISTS `vie_poly`; +/*!50001 DROP VIEW IF EXISTS `vie_poly`*/; +SET @saved_cs_client = @@character_set_client; +/*!50503 SET character_set_client = utf8mb4 */; +/*!50001 CREATE VIEW `vie_poly` AS SELECT + 1 AS `name`, + 1 AS `forward_id`, + 1 AS `forward_seq`, + 1 AS `reverse_id`, + 1 AS `reverse_seq`, + 1 AS `product_id`, + 1 AS `target_seq`, + 1 AS `accesion_id`, + 1 AS `accesion_name`, + 1 AS `difference_id`, + 1 AS `difference_pattern`*/; +SET character_set_client = @saved_cs_client; + +-- +-- Temporary view structure for view `vie_poly1` +-- + +DROP TABLE IF EXISTS `vie_poly1`; +/*!50001 DROP VIEW IF EXISTS `vie_poly1`*/; +SET @saved_cs_client = @@character_set_client; +/*!50503 SET character_set_client = utf8mb4 */; +/*!50001 CREATE VIEW `vie_poly1` AS SELECT + 1 AS `name`, + 1 AS `forward_id`, + 1 AS `forward_seq`, + 1 AS `reverse_id`, + 1 AS `reverse_seq`, + 1 AS `product_id`, + 1 AS `target_seq`, + 1 AS `accesion_id`, + 1 AS `accesion_name`, + 1 AS `difference_id`, + 1 AS `difference_pattern`*/; +SET character_set_client = @saved_cs_client; + +-- +-- Current Database: `markergen_pop` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `markergen_pop` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `markergen_pop`; + +-- +-- Table structure for table `accession` +-- + +DROP TABLE IF EXISTS `accession`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `accession` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `name` varchar(10) NOT NULL DEFAULT '', + PRIMARY KEY (`id`), + UNIQUE KEY `name` (`name`) +) ENGINE=InnoDB AUTO_INCREMENT=98 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `capsinstance` +-- + +DROP TABLE IF EXISTS `capsinstance`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `capsinstance` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `accession_id` int unsigned NOT NULL DEFAULT '0', + `capsmarker_id` int unsigned NOT NULL DEFAULT '0', + `fragment_list` varchar(100) DEFAULT NULL, + PRIMARY KEY (`id`), + KEY `capsmarker_id` (`capsmarker_id`), + KEY `accession_id` (`accession_id`) +) ENGINE=InnoDB AUTO_INCREMENT=1467292 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `capsmarker` +-- + +DROP TABLE IF EXISTS `capsmarker`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `capsmarker` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `enzyme_id` int unsigned NOT NULL DEFAULT '0', + `pcr_id` int unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`id`), + KEY `enzyme_id` (`enzyme_id`), + KEY `pcr_id` (`pcr_id`) +) ENGINE=InnoDB AUTO_INCREMENT=437018 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `dataset` +-- + +DROP TABLE IF EXISTS `dataset`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `dataset` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `name` varchar(25) NOT NULL DEFAULT '', + `target_id` int unsigned DEFAULT NULL, + PRIMARY KEY (`id`), + UNIQUE KEY `name` (`name`) +) ENGINE=InnoDB AUTO_INCREMENT=4 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `difference` +-- + +DROP TABLE IF EXISTS `difference`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `difference` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `pattern` text NOT NULL, + PRIMARY KEY (`id`) +) ENGINE=InnoDB AUTO_INCREMENT=106993 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `enzyme` +-- + +DROP TABLE IF EXISTS `enzyme`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `enzyme` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `name` varchar(10) NOT NULL DEFAULT '', + `price` float DEFAULT NULL, + PRIMARY KEY (`id`), + UNIQUE KEY `name` (`name`) +) ENGINE=InnoDB AUTO_INCREMENT=153 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gene` +-- + +DROP TABLE IF EXISTS `gene`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `name` varchar(10) NOT NULL DEFAULT '', + PRIMARY KEY (`id`), + UNIQUE KEY `name` (`name`) +) ENGINE=InnoDB AUTO_INCREMENT=33604 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pcr` +-- + +DROP TABLE IF EXISTS `pcr`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pcr` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `dataset_id` int unsigned NOT NULL DEFAULT '0', + `gene_id` int unsigned NOT NULL DEFAULT '0', + `forward_id` int unsigned NOT NULL DEFAULT '0', + `reverse_id` int unsigned NOT NULL DEFAULT '0', + `product_id` int unsigned NOT NULL DEFAULT '0', + `chromosome` int unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`id`), + UNIQUE KEY `forward_id` (`forward_id`), + UNIQUE KEY `reverse_id` (`reverse_id`), + UNIQUE KEY `product_id` (`product_id`) +) ENGINE=InnoDB AUTO_INCREMENT=48579 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `polymorphism` +-- + +DROP TABLE IF EXISTS `polymorphism`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `polymorphism` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `accession_id` int unsigned NOT NULL DEFAULT '0', + `product_id` int unsigned NOT NULL DEFAULT '0', + `difference_id` int unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`id`) +) ENGINE=InnoDB AUTO_INCREMENT=154252 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `primer` +-- + +DROP TABLE IF EXISTS `primer`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `primer` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `seq` varchar(100) NOT NULL DEFAULT '', + `start` int unsigned NOT NULL DEFAULT '0', + `tm` float NOT NULL DEFAULT '0', + `gc` float NOT NULL DEFAULT '0', + PRIMARY KEY (`id`), + KEY `start` (`start`) +) ENGINE=InnoDB AUTO_INCREMENT=97157 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `product` +-- + +DROP TABLE IF EXISTS `product`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `product` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `target_seq` text NOT NULL, + PRIMARY KEY (`id`) +) ENGINE=InnoDB AUTO_INCREMENT=48579 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `markergen_test` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `markergen_test` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `markergen_test`; + +-- +-- Table structure for table `accession` +-- + +DROP TABLE IF EXISTS `accession`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `accession` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `name` varchar(10) NOT NULL DEFAULT '', + PRIMARY KEY (`id`), + UNIQUE KEY `name` (`name`) +) ENGINE=InnoDB AUTO_INCREMENT=98 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `capsinstance` +-- + +DROP TABLE IF EXISTS `capsinstance`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `capsinstance` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `accession_id` int unsigned NOT NULL DEFAULT '0', + `capsmarker_id` int unsigned NOT NULL DEFAULT '0', + `fragment_list` varchar(100) DEFAULT NULL, + PRIMARY KEY (`id`), + KEY `capsmarker_id` (`capsmarker_id`), + KEY `accession_id` (`accession_id`) +) ENGINE=InnoDB AUTO_INCREMENT=607552 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `capsmarker` +-- + +DROP TABLE IF EXISTS `capsmarker`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `capsmarker` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `enzyme_id` int unsigned NOT NULL DEFAULT '0', + `pcr_id` int unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`id`), + KEY `enzyme_id` (`enzyme_id`), + KEY `pcr_id` (`pcr_id`) +) ENGINE=InnoDB AUTO_INCREMENT=7148 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `dataset` +-- + +DROP TABLE IF EXISTS `dataset`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `dataset` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `name` varchar(25) NOT NULL DEFAULT '', + `target_id` int unsigned DEFAULT NULL, + PRIMARY KEY (`id`), + UNIQUE KEY `name` (`name`) +) ENGINE=InnoDB AUTO_INCREMENT=2 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `difference` +-- + +DROP TABLE IF EXISTS `difference`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `difference` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `pattern` text NOT NULL, + PRIMARY KEY (`id`) +) ENGINE=InnoDB AUTO_INCREMENT=11039 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `enzyme` +-- + +DROP TABLE IF EXISTS `enzyme`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `enzyme` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `name` varchar(10) NOT NULL DEFAULT '', + `price` float DEFAULT NULL, + PRIMARY KEY (`id`), + UNIQUE KEY `name` (`name`) +) ENGINE=InnoDB AUTO_INCREMENT=152 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gene` +-- + +DROP TABLE IF EXISTS `gene`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `name` varchar(10) NOT NULL DEFAULT '', + PRIMARY KEY (`id`), + UNIQUE KEY `name` (`name`) +) ENGINE=InnoDB AUTO_INCREMENT=33604 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pcr` +-- + +DROP TABLE IF EXISTS `pcr`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pcr` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `dataset_id` int unsigned NOT NULL DEFAULT '0', + `gene_id` int unsigned NOT NULL DEFAULT '0', + `forward_id` int unsigned NOT NULL DEFAULT '0', + `reverse_id` int unsigned NOT NULL DEFAULT '0', + `product_id` int unsigned NOT NULL DEFAULT '0', + `chromosome` int unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`id`), + UNIQUE KEY `forward_id` (`forward_id`), + UNIQUE KEY `reverse_id` (`reverse_id`), + UNIQUE KEY `product_id` (`product_id`) +) ENGINE=InnoDB AUTO_INCREMENT=602 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `polymorphism` +-- + +DROP TABLE IF EXISTS `polymorphism`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `polymorphism` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `accession_id` int unsigned NOT NULL DEFAULT '0', + `product_id` int unsigned NOT NULL DEFAULT '0', + `difference_id` int unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`id`) +) ENGINE=InnoDB AUTO_INCREMENT=58298 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `primer` +-- + +DROP TABLE IF EXISTS `primer`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `primer` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `seq` varchar(100) NOT NULL DEFAULT '', + `start` int unsigned NOT NULL DEFAULT '0', + `tm` float NOT NULL DEFAULT '0', + `gc` float NOT NULL DEFAULT '0', + PRIMARY KEY (`id`), + KEY `start` (`start`) +) ENGINE=InnoDB AUTO_INCREMENT=1203 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `product` +-- + +DROP TABLE IF EXISTS `product`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `product` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `target_seq` text NOT NULL, + PRIMARY KEY (`id`) +) ENGINE=InnoDB AUTO_INCREMENT=602 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `medicago_annotations_lookup` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `medicago_annotations_lookup` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `medicago_annotations_lookup`; + +-- +-- Table structure for table `at_mtgi_lookup` +-- + +DROP TABLE IF EXISTS `at_mtgi_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `at_mtgi_lookup` ( + `mtgi` varchar(60) NOT NULL, + `probeset` varchar(60) NOT NULL, + `date` date NOT NULL, + KEY `mtgi` (`mtgi`), + KEY `probeset` (`probeset`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `at_mtgi_lookup_merged` +-- + +DROP TABLE IF EXISTS `at_mtgi_lookup_merged`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `at_mtgi_lookup_merged` ( + `mtgi` varchar(60) NOT NULL, + `probeset` varchar(60) NOT NULL, + `date` date NOT NULL, + KEY `date` (`date`), + KEY `mtgi_probeset` (`mtgi`,`probeset`), + KEY `probeset_mtgi` (`probeset`,`mtgi`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `at_mtgi_v3_5_lookup` +-- + +DROP TABLE IF EXISTS `at_mtgi_v3_5_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `at_mtgi_v3_5_lookup` ( + `mtgi` varchar(60) NOT NULL, + `probeset` varchar(60) NOT NULL, + `date` date NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `at_mtgi_v4_lookup` +-- + +DROP TABLE IF EXISTS `at_mtgi_v4_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `at_mtgi_v4_lookup` ( + `mtgi` varchar(60) NOT NULL, + `probeset` varchar(60) NOT NULL, + `date` date NOT NULL, + KEY `mtgi` (`mtgi`), + KEY `probeset` (`probeset`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `medicago_seed_lookup` +-- + +DROP TABLE IF EXISTS `medicago_seed_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `medicago_seed_lookup` ( + `mtgi` varchar(60) NOT NULL, + `probeset` varchar(60) NOT NULL, + `date` date NOT NULL, + KEY `date` (`date`), + KEY `gi_probe` (`mtgi`,`probeset`), + KEY `probe_gi` (`probeset`,`mtgi`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `mtgi_annotation` +-- + +DROP TABLE IF EXISTS `mtgi_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `mtgi_annotation` ( + `mtgi` varchar(60) NOT NULL, + `annotation` longtext NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`mtgi`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `mtgi_annotation_merged` +-- + +DROP TABLE IF EXISTS `mtgi_annotation_merged`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `mtgi_annotation_merged` ( + `mtgi` varchar(60) NOT NULL, + `annotation` varchar(170) DEFAULT NULL, + `date` date NOT NULL, + KEY `date_gene` (`date`,`mtgi`,`annotation`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `mtgi_v3_5_annotation` +-- + +DROP TABLE IF EXISTS `mtgi_v3_5_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `mtgi_v3_5_annotation` ( + `mtgi` varchar(60) NOT NULL, + `annotation` longtext NOT NULL, + `date` date NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `mtgi_v4_1_annotation` +-- + +DROP TABLE IF EXISTS `mtgi_v4_1_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `mtgi_v4_1_annotation` ( + `mtgi` varchar(60) NOT NULL, + `annotation` longtext NOT NULL, + `date` date NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `new_mtgi_lookup` +-- + +DROP TABLE IF EXISTS `new_mtgi_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `new_mtgi_lookup` ( + `mtgi` varchar(60) NOT NULL, + `probeset` varchar(60) NOT NULL, + `date` date NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `medicago_mas` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `medicago_mas` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `medicago_mas`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(28) NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(22) NOT NULL, + `sample_tissue` text NOT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(12)), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `medicago_rma` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `medicago_rma` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `medicago_rma`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(28) NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(22) NOT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(12)), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `medicago_root` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `medicago_root` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `medicago_root`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(5) NOT NULL, + `data_probeset_id` varchar(18) NOT NULL, + `data_signal` float DEFAULT '0', + `data_p_value` float DEFAULT '0', + `data_bot_id` varchar(16) NOT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(12)), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `medicago_root_v5` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `medicago_root_v5` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `medicago_root_v5`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(5) NOT NULL, + `data_probeset_id` varchar(64) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(16) NOT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(12)), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `medicago_seed` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `medicago_seed` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `medicago_seed`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(5) NOT NULL, + `data_probeset_id` varchar(18) NOT NULL, + `data_signal` float DEFAULT '0', + `data_p_value` float DEFAULT '0', + `data_bot_id` varchar(15) NOT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(12)), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `meristem_db` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `meristem_db` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `meristem_db`; + +-- +-- Table structure for table `proj_info` +-- + +DROP TABLE IF EXISTS `proj_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_info` ( + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `proj_title` tinytext, + `proj_pi` tinytext, + `proj_pi_title` tinytext, + `proj_pi_inst` tinytext, + `proj_pi_addr` tinytext, + `proj_keyw1` tinytext, + `proj_keyw2` tinytext, + `proj_keyw3` tinytext, + `proj_keyw4` tinytext, + `proj_keyw5` tinytext, + `proj_res_area` tinytext, + `proj_num_samps` tinyint unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`proj_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(30) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(18) NOT NULL, + `channel` varchar(5) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `meristem_db_new` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `meristem_db_new` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `meristem_db_new`; + +-- +-- Table structure for table `proj_info` +-- + +DROP TABLE IF EXISTS `proj_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_info` ( + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `proj_title` tinytext, + `proj_pi` tinytext, + `proj_pi_title` tinytext, + `proj_pi_inst` tinytext, + `proj_pi_addr` tinytext, + `proj_keyw1` tinytext, + `proj_keyw2` tinytext, + `proj_keyw3` tinytext, + `proj_keyw4` tinytext, + `proj_keyw5` tinytext, + `proj_res_area` tinytext, + `proj_num_samps` tinyint unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`proj_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` tinytext NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` tinytext NOT NULL, + `channel` varchar(5) DEFAULT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(12)), + KEY `data_probeset_id` (`data_probeset_id`(12),`data_bot_id`(12)), + KEY `data_bot_id` (`data_bot_id`(12)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `mouse_db` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `mouse_db` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `mouse_db`; + +-- +-- Table structure for table `id_lookup` +-- + +DROP TABLE IF EXISTS `id_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `id_lookup` ( + `lookup` varchar(20) NOT NULL, + `probe_id` varchar(15) NOT NULL, + KEY `lookup_id` (`lookup`,`probe_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `data_probeset_id` varchar(15) NOT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_bot_id` varchar(18) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `ngm_nina` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `ngm_nina` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `ngm_nina`; + +-- +-- Table structure for table `agi_annotation` +-- + +DROP TABLE IF EXISTS `agi_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `agi_annotation` ( + `agi` varchar(11) NOT NULL, + `annotation` longtext NOT NULL, + `date` date NOT NULL DEFAULT '0000-00-00', + PRIMARY KEY (`agi`,`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `chr_seq_annotation` +-- + +DROP TABLE IF EXISTS `chr_seq_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `chr_seq_annotation` ( + `SeqID` varchar(20) NOT NULL, + `Source` varchar(15) NOT NULL, + `Type` varchar(30) NOT NULL, + `Start` int NOT NULL, + `End` int NOT NULL, + `Score` float DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Phase` char(1) DEFAULT NULL, + `Id` varchar(20) DEFAULT NULL, + `geneId` varchar(20) DEFAULT NULL, + `Parent` varchar(40) DEFAULT NULL, + `Attributes` varchar(256) DEFAULT NULL, + KEY `range` (`Source`,`SeqID`,`Start`,`End`), + KEY `seqend` (`Source`,`SeqID`,`End`), + KEY `typeid` (`SeqID`,`Source`,`Type`,`Parent`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `oat` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `oat` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `oat`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `genome` varchar(16) NOT NULL, + `version` varchar(2) NOT NULL, + `genome_id` varchar(16) NOT NULL, + `orthogroup` varchar(16) NOT NULL, + `data_probeset_id` varchar(36) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(24) NOT NULL, + KEY `orthogroup_idx` (`orthogroup`,`data_bot_id`,`data_probeset_id`,`data_signal`), + KEY `data_probeset_id_idx` (`data_probeset_id`,`orthogroup`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `ontologies` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `ontologies` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `ontologies`; + +-- +-- Table structure for table `go` +-- + +DROP TABLE IF EXISTS `go`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `go` ( + `agi` varchar(16) NOT NULL, + `tair_accession` mediumint unsigned NOT NULL DEFAULT '0', + `object_name` varchar(16) NOT NULL, + `go_term` tinytext NOT NULL, + `go_id` varchar(11) NOT NULL DEFAULT '', + `tair_keyword` smallint unsigned NOT NULL DEFAULT '0', + `aspect` varchar(5) NOT NULL DEFAULT '', + `goslim_term` tinytext NOT NULL, + `evidence_code` varchar(4) NOT NULL DEFAULT '', + `reference` tinytext NOT NULL, + `annotating_db` varchar(64) DEFAULT NULL, + `date` date NOT NULL DEFAULT '0000-00-00', + KEY `agi` (`agi`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `go_medicago` +-- + +DROP TABLE IF EXISTS `go_medicago`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `go_medicago` ( + `geneID` varchar(20) NOT NULL, + `tair_accession` mediumint unsigned DEFAULT NULL, + `object_name` varchar(20) DEFAULT NULL, + `go_term` tinytext NOT NULL, + `go_id` varchar(11) NOT NULL, + `tair_keyword` smallint unsigned DEFAULT NULL, + `aspect` varchar(5) NOT NULL, + `goslim_term` tinytext NOT NULL, + `evidence_code` varchar(4) DEFAULT NULL, + `reference` tinytext, + `annotating_db` varchar(5) DEFAULT NULL, + `date` date DEFAULT NULL, + KEY `geneID` (`geneID`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `go_medicago_agrigo` +-- + +DROP TABLE IF EXISTS `go_medicago_agrigo`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `go_medicago_agrigo` ( + `geneID` varchar(20) NOT NULL, + `tair_accession` mediumint unsigned DEFAULT NULL, + `object_name` varchar(20) DEFAULT NULL, + `go_term` tinytext NOT NULL, + `go_id` varchar(11) NOT NULL, + `tair_keyword` smallint unsigned DEFAULT NULL, + `aspect` varchar(5) NOT NULL, + `goslim_term` tinytext NOT NULL, + `evidence_code` varchar(4) DEFAULT NULL, + `reference` tinytext, + `annotating_db` varchar(5) DEFAULT NULL, + `date` date DEFAULT NULL, + KEY `geneID` (`geneID`), + KEY `medindex` (`geneID`,`aspect`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `go_medicago_agrigo_latest` +-- + +DROP TABLE IF EXISTS `go_medicago_agrigo_latest`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `go_medicago_agrigo_latest` ( + `geneID` varchar(20) NOT NULL, + `tair_accession` mediumint unsigned DEFAULT NULL, + `object_name` varchar(20) DEFAULT NULL, + `go_term` tinytext NOT NULL, + `go_id` varchar(11) NOT NULL, + `tair_keyword` smallint unsigned DEFAULT NULL, + `aspect` varchar(5) NOT NULL, + `goslim_term` tinytext NOT NULL, + `evidence_code` varchar(4) DEFAULT NULL, + `reference` tinytext, + `annotating_db` varchar(5) DEFAULT NULL, + `date` date DEFAULT NULL, + KEY `geneID` (`geneID`), + KEY `medindex` (`geneID`,`aspect`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `go_medicago_uniprot` +-- + +DROP TABLE IF EXISTS `go_medicago_uniprot`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `go_medicago_uniprot` ( + `geneID` varchar(20) NOT NULL, + `tair_accession` mediumint unsigned DEFAULT NULL, + `object_name` varchar(20) DEFAULT NULL, + `go_term` tinytext NOT NULL, + `go_id` varchar(11) NOT NULL, + `tair_keyword` smallint unsigned DEFAULT NULL, + `aspect` varchar(5) NOT NULL, + `goslim_term` tinytext NOT NULL, + `evidence_code` varchar(4) DEFAULT NULL, + `reference` tinytext, + `annotating_db` varchar(16) DEFAULT NULL, + `date` date DEFAULT NULL, + KEY `geneID` (`geneID`), + KEY `medindex` (`geneID`,`aspect`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `go_medicago_uniprot_latest` +-- + +DROP TABLE IF EXISTS `go_medicago_uniprot_latest`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `go_medicago_uniprot_latest` ( + `geneID` varchar(20) NOT NULL, + `tair_accession` mediumint unsigned DEFAULT NULL, + `object_name` varchar(20) DEFAULT NULL, + `go_term` tinytext NOT NULL, + `go_id` varchar(11) NOT NULL, + `tair_keyword` smallint unsigned DEFAULT NULL, + `aspect` varchar(5) NOT NULL, + `goslim_term` tinytext NOT NULL, + `evidence_code` varchar(4) DEFAULT NULL, + `reference` tinytext, + `annotating_db` varchar(16) DEFAULT NULL, + `date` date DEFAULT NULL, + KEY `geneID` (`geneID`), + KEY `medindex` (`geneID`,`aspect`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `mapman` +-- + +DROP TABLE IF EXISTS `mapman`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `mapman` ( + `maincode` varchar(4) NOT NULL, + `bincode` varchar(15) NOT NULL, + `name` varchar(150) NOT NULL, + `identifier` varchar(20) NOT NULL, + `description` text, + `type` char(1) DEFAULT NULL, + PRIMARY KEY (`bincode`,`identifier`), + KEY `identifier` (`identifier`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `mapman2012` +-- + +DROP TABLE IF EXISTS `mapman2012`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `mapman2012` ( + `maincode` varchar(4) NOT NULL, + `bincode` varchar(15) NOT NULL, + `name` varchar(150) NOT NULL, + `identifier` varchar(20) NOT NULL, + `description` text, + `type` char(1) DEFAULT NULL, + PRIMARY KEY (`bincode`,`identifier`), + KEY `identifier` (`identifier`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='Jan2010'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `mapman_old` +-- + +DROP TABLE IF EXISTS `mapman_old`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `mapman_old` ( + `maincode` varchar(4) NOT NULL, + `bincode` varchar(15) NOT NULL, + `name` varchar(150) NOT NULL, + `identifier` varchar(20) NOT NULL, + `description` text, + `type` char(1) DEFAULT NULL, + PRIMARY KEY (`bincode`,`identifier`), + KEY `identifier` (`identifier`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='Dec2008'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `taggit` +-- + +DROP TABLE IF EXISTS `taggit`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `taggit` ( + `agi` varchar(10) NOT NULL DEFAULT '', + `category` tinytext NOT NULL, + `date` date NOT NULL DEFAULT '0000-00-00' +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `ortholog_db` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `ortholog_db` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `ortholog_db`; + +-- +-- Table structure for table `arabidopsis` +-- + +DROP TABLE IF EXISTS `arabidopsis`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `arabidopsis` ( + `gene` varchar(30) NOT NULL, + `sequence` mediumtext NOT NULL, + PRIMARY KEY (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `arabidopsis_poplar_mcl` +-- + +DROP TABLE IF EXISTS `arabidopsis_poplar_mcl`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `arabidopsis_poplar_mcl` ( + `cluster` int NOT NULL, + `gene` varchar(60) NOT NULL, + `sequence` mediumtext NOT NULL, + `genome` varchar(6) NOT NULL, + `date` date NOT NULL, + `method` varchar(15) NOT NULL, + PRIMARY KEY (`cluster`,`gene`), + KEY `genecluster` (`cluster`,`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `arabidopsis_poplar_scc` +-- + +DROP TABLE IF EXISTS `arabidopsis_poplar_scc`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `arabidopsis_poplar_scc` ( + `Cluster` int NOT NULL, + `Gene_A` varchar(30) NOT NULL, + `Probeset_A` varchar(60) NOT NULL, + `Genome_A` varchar(30) NOT NULL, + `Gene_B` varchar(60) NOT NULL, + `Probeset_B` varchar(60) NOT NULL, + `Genome_B` varchar(30) NOT NULL, + `SCC_Value` float NOT NULL, + PRIMARY KEY (`Cluster`,`Gene_A`,`Probeset_A`,`Gene_B`,`Probeset_B`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `barley` +-- + +DROP TABLE IF EXISTS `barley`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `barley` ( + `gene` varchar(30) NOT NULL, + `sequence` mediumtext NOT NULL, + KEY `gene` (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `medicago` +-- + +DROP TABLE IF EXISTS `medicago`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `medicago` ( + `gene` varchar(30) NOT NULL, + `sequence` mediumtext NOT NULL, + PRIMARY KEY (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `orthologs` +-- + +DROP TABLE IF EXISTS `orthologs`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `orthologs` ( + `cluster` int NOT NULL, + `gene` varchar(100) NOT NULL, + `genome` varchar(10) NOT NULL, + `sequence` mediumtext NOT NULL, + `date` date NOT NULL, + `method` varchar(15) NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `orthologs_scc` +-- + +DROP TABLE IF EXISTS `orthologs_scc`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `orthologs_scc` ( + `Cluster` int NOT NULL, + `Gene_A` varchar(60) NOT NULL, + `Probeset_A` varchar(60) NOT NULL, + `Genome_A` varchar(30) NOT NULL, + `Gene_B` varchar(60) NOT NULL, + `Probeset_B` varchar(60) NOT NULL, + `Genome_B` varchar(30) NOT NULL, + `SCC_Value` float NOT NULL, + PRIMARY KEY (`Cluster`,`Gene_A`,`Probeset_A`,`Gene_B`,`Probeset_B`), + KEY `Cluster` (`Genome_B`,`Probeset_B`,`Genome_A`), + KEY `Genome_A` (`Genome_A`,`Probeset_A`,`Genome_B`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `poplar` +-- + +DROP TABLE IF EXISTS `poplar`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `poplar` ( + `gene` varchar(60) NOT NULL, + `sequence` mediumtext NOT NULL, + PRIMARY KEY (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `rice` +-- + +DROP TABLE IF EXISTS `rice`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `rice` ( + `gene` varchar(30) NOT NULL, + `sequence` mediumtext NOT NULL, + PRIMARY KEY (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sequences` +-- + +DROP TABLE IF EXISTS `sequences`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sequences` ( + `gene` varchar(40) NOT NULL, + `sequence` tinytext NOT NULL, + PRIMARY KEY (`gene`), + KEY `gene_name` (`gene`(20)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `test` +-- + +DROP TABLE IF EXISTS `test`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `test` ( + `cluster` int NOT NULL, + `gene` varchar(40) NOT NULL, + `genome` varchar(6) NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `phelipanche` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `phelipanche` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `phelipanche`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(16) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(32) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `phelipanche_annotations_lookup` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `phelipanche_annotations_lookup` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `phelipanche_annotations_lookup`; + +-- +-- Table structure for table `phelipanche_lookup` +-- + +DROP TABLE IF EXISTS `phelipanche_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `phelipanche_lookup` ( + `phelipanche` varchar(16) NOT NULL, + `arabidopsis` varchar(16) NOT NULL, + `date` date NOT NULL, + KEY `phelipanche` (`phelipanche`), + KEY `arabidopsis` (`arabidopsis`), + KEY `date` (`date`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `phpmyadmin` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `phpmyadmin` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `phpmyadmin`; + +-- +-- Table structure for table `pma__bookmark` +-- + +DROP TABLE IF EXISTS `pma__bookmark`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pma__bookmark` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `dbase` varchar(255) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `user` varchar(255) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `label` varchar(255) CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT '', + `query` text COLLATE utf8mb3_bin NOT NULL, + PRIMARY KEY (`id`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin COMMENT='Bookmarks'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pma__central_columns` +-- + +DROP TABLE IF EXISTS `pma__central_columns`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pma__central_columns` ( + `db_name` varchar(64) COLLATE utf8mb3_bin NOT NULL, + `col_name` varchar(64) COLLATE utf8mb3_bin NOT NULL, + `col_type` varchar(64) COLLATE utf8mb3_bin NOT NULL, + `col_length` text COLLATE utf8mb3_bin, + `col_collation` varchar(64) COLLATE utf8mb3_bin NOT NULL, + `col_isNull` tinyint(1) NOT NULL, + `col_extra` varchar(255) COLLATE utf8mb3_bin DEFAULT '', + `col_default` text COLLATE utf8mb3_bin, + PRIMARY KEY (`db_name`,`col_name`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin COMMENT='Central list of columns'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pma__column_info` +-- + +DROP TABLE IF EXISTS `pma__column_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pma__column_info` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `db_name` varchar(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `table_name` varchar(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `column_name` varchar(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `comment` varchar(255) CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT '', + `mimetype` varchar(255) CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT '', + `transformation` varchar(255) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `transformation_options` varchar(255) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `input_transformation` varchar(255) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `input_transformation_options` varchar(255) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + PRIMARY KEY (`id`), + UNIQUE KEY `db_name` (`db_name`,`table_name`,`column_name`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin COMMENT='Column information for phpMyAdmin'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pma__designer_settings` +-- + +DROP TABLE IF EXISTS `pma__designer_settings`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pma__designer_settings` ( + `username` varchar(64) COLLATE utf8mb3_bin NOT NULL, + `settings_data` text COLLATE utf8mb3_bin NOT NULL, + PRIMARY KEY (`username`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin COMMENT='Settings related to Designer'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pma__export_templates` +-- + +DROP TABLE IF EXISTS `pma__export_templates`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pma__export_templates` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `username` varchar(64) COLLATE utf8mb3_bin NOT NULL, + `export_type` varchar(10) COLLATE utf8mb3_bin NOT NULL, + `template_name` varchar(64) COLLATE utf8mb3_bin NOT NULL, + `template_data` text COLLATE utf8mb3_bin NOT NULL, + PRIMARY KEY (`id`), + UNIQUE KEY `u_user_type_template` (`username`,`export_type`,`template_name`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin COMMENT='Saved export templates'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pma__favorite` +-- + +DROP TABLE IF EXISTS `pma__favorite`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pma__favorite` ( + `username` varchar(64) COLLATE utf8mb3_bin NOT NULL, + `tables` text COLLATE utf8mb3_bin NOT NULL, + PRIMARY KEY (`username`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin COMMENT='Favorite tables'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pma__history` +-- + +DROP TABLE IF EXISTS `pma__history`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pma__history` ( + `id` bigint unsigned NOT NULL AUTO_INCREMENT, + `username` varchar(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `db` varchar(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `table` varchar(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `timevalue` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP, + `sqlquery` text COLLATE utf8mb3_bin NOT NULL, + PRIMARY KEY (`id`), + KEY `username` (`username`,`db`,`table`,`timevalue`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin COMMENT='SQL history for phpMyAdmin'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pma__navigationhiding` +-- + +DROP TABLE IF EXISTS `pma__navigationhiding`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pma__navigationhiding` ( + `username` varchar(64) COLLATE utf8mb3_bin NOT NULL, + `item_name` varchar(64) COLLATE utf8mb3_bin NOT NULL, + `item_type` varchar(64) COLLATE utf8mb3_bin NOT NULL, + `db_name` varchar(64) COLLATE utf8mb3_bin NOT NULL, + `table_name` varchar(64) COLLATE utf8mb3_bin NOT NULL, + PRIMARY KEY (`username`,`item_name`,`item_type`,`db_name`,`table_name`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin COMMENT='Hidden items of navigation tree'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pma__pdf_pages` +-- + +DROP TABLE IF EXISTS `pma__pdf_pages`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pma__pdf_pages` ( + `db_name` varchar(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `page_nr` int unsigned NOT NULL AUTO_INCREMENT, + `page_descr` varchar(50) CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci NOT NULL DEFAULT '', + PRIMARY KEY (`page_nr`), + KEY `db_name` (`db_name`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin COMMENT='PDF relation pages for phpMyAdmin'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pma__recent` +-- + +DROP TABLE IF EXISTS `pma__recent`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pma__recent` ( + `username` varchar(64) COLLATE utf8mb3_bin NOT NULL, + `tables` text COLLATE utf8mb3_bin NOT NULL, + PRIMARY KEY (`username`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin COMMENT='Recently accessed tables'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pma__relation` +-- + +DROP TABLE IF EXISTS `pma__relation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pma__relation` ( + `master_db` varchar(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `master_table` varchar(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `master_field` varchar(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `foreign_db` varchar(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `foreign_table` varchar(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `foreign_field` varchar(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + PRIMARY KEY (`master_db`,`master_table`,`master_field`), + KEY `foreign_field` (`foreign_db`,`foreign_table`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin COMMENT='Relation table'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pma__savedsearches` +-- + +DROP TABLE IF EXISTS `pma__savedsearches`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pma__savedsearches` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `username` varchar(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `db_name` varchar(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `search_name` varchar(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `search_data` text COLLATE utf8mb3_bin NOT NULL, + PRIMARY KEY (`id`), + UNIQUE KEY `u_savedsearches_username_dbname` (`username`,`db_name`,`search_name`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin COMMENT='Saved searches'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pma__table_coords` +-- + +DROP TABLE IF EXISTS `pma__table_coords`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pma__table_coords` ( + `db_name` varchar(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `table_name` varchar(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `pdf_page_number` int NOT NULL DEFAULT '0', + `x` float unsigned NOT NULL DEFAULT '0', + `y` float unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`db_name`,`table_name`,`pdf_page_number`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin COMMENT='Table coordinates for phpMyAdmin PDF output'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pma__table_info` +-- + +DROP TABLE IF EXISTS `pma__table_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pma__table_info` ( + `db_name` varchar(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `table_name` varchar(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + `display_field` varchar(64) COLLATE utf8mb3_bin NOT NULL DEFAULT '', + PRIMARY KEY (`db_name`,`table_name`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin COMMENT='Table information for phpMyAdmin'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pma__table_uiprefs` +-- + +DROP TABLE IF EXISTS `pma__table_uiprefs`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pma__table_uiprefs` ( + `username` varchar(64) COLLATE utf8mb3_bin NOT NULL, + `db_name` varchar(64) COLLATE utf8mb3_bin NOT NULL, + `table_name` varchar(64) COLLATE utf8mb3_bin NOT NULL, + `prefs` text COLLATE utf8mb3_bin NOT NULL, + `last_update` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP, + PRIMARY KEY (`username`,`db_name`,`table_name`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin COMMENT='Tables'' UI preferences'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pma__tracking` +-- + +DROP TABLE IF EXISTS `pma__tracking`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pma__tracking` ( + `db_name` varchar(64) COLLATE utf8mb3_bin NOT NULL, + `table_name` varchar(64) COLLATE utf8mb3_bin NOT NULL, + `version` int unsigned NOT NULL, + `date_created` datetime NOT NULL, + `date_updated` datetime NOT NULL, + `schema_snapshot` text COLLATE utf8mb3_bin NOT NULL, + `schema_sql` text COLLATE utf8mb3_bin, + `data_sql` longtext COLLATE utf8mb3_bin, + `tracking` set('UPDATE','REPLACE','INSERT','DELETE','TRUNCATE','CREATE DATABASE','ALTER DATABASE','DROP DATABASE','CREATE TABLE','ALTER TABLE','RENAME TABLE','DROP TABLE','CREATE INDEX','DROP INDEX','CREATE VIEW','ALTER VIEW','DROP VIEW') COLLATE utf8mb3_bin DEFAULT NULL, + `tracking_active` int unsigned NOT NULL DEFAULT '1', + PRIMARY KEY (`db_name`,`table_name`,`version`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin COMMENT='Database changes tracking for phpMyAdmin'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pma__userconfig` +-- + +DROP TABLE IF EXISTS `pma__userconfig`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pma__userconfig` ( + `username` varchar(64) COLLATE utf8mb3_bin NOT NULL, + `timevalue` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP, + `config_data` text COLLATE utf8mb3_bin NOT NULL, + PRIMARY KEY (`username`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin COMMENT='User preferences storage for phpMyAdmin'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pma__usergroups` +-- + +DROP TABLE IF EXISTS `pma__usergroups`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pma__usergroups` ( + `usergroup` varchar(64) COLLATE utf8mb3_bin NOT NULL, + `tab` varchar(64) COLLATE utf8mb3_bin NOT NULL, + `allowed` enum('Y','N') COLLATE utf8mb3_bin NOT NULL DEFAULT 'N', + PRIMARY KEY (`usergroup`,`tab`,`allowed`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin COMMENT='User groups with configured menu items'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pma__users` +-- + +DROP TABLE IF EXISTS `pma__users`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pma__users` ( + `username` varchar(64) COLLATE utf8mb3_bin NOT NULL, + `usergroup` varchar(64) COLLATE utf8mb3_bin NOT NULL, + PRIMARY KEY (`username`,`usergroup`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_bin COMMENT='Users and their assignments to user groups'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `physcomitrella_annotations_lookup` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `physcomitrella_annotations_lookup` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `physcomitrella_annotations_lookup`; + +-- +-- Table structure for table `physcomitrella_annotation` +-- + +DROP TABLE IF EXISTS `physcomitrella_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `physcomitrella_annotation` ( + `probeset` varchar(60) NOT NULL, + `annotation` longtext NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`probeset`), + KEY `date_probeset` (`date`,`probeset`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `physcomitrella_lookup` +-- + +DROP TABLE IF EXISTS `physcomitrella_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `physcomitrella_lookup` ( + `probeset` varchar(60) NOT NULL, + `gene` varchar(60) NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`probeset`,`gene`), + KEY `gene_probeset` (`gene`,`probeset`), + KEY `date` (`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `physcomitrella_db` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `physcomitrella_db` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `physcomitrella_db`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` varchar(30) NOT NULL DEFAULT '', + `proj_id` varchar(30) NOT NULL DEFAULT '', + `data_probeset_id` varchar(40) NOT NULL DEFAULT '', + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`proj_id`,`data_probeset_id`), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `poplar` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `poplar` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `poplar`; + +-- +-- Table structure for table `proj_info` +-- + +DROP TABLE IF EXISTS `proj_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_info` ( + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `proj_date_submit` date NOT NULL DEFAULT '0000-00-00', + `proj_date_ready` date NOT NULL DEFAULT '0000-00-00', + `proj_date_complete` date NOT NULL DEFAULT '0000-00-00', + `proj_paid_date` date NOT NULL DEFAULT '0000-00-00', + `proj_paid_amount` decimal(6,2) NOT NULL DEFAULT '0.00', + `proj_title` tinytext, + `proj_pi` tinytext, + `proj_pi_title` tinytext, + `proj_pi_inst` tinytext, + `proj_pi_addr` tinytext, + `proj_pi_tel` tinytext, + `proj_pi_fax` tinytext, + `proj_pi_email` tinytext, + `proj_keyw1` tinytext, + `proj_keyw2` tinytext, + `proj_keyw3` tinytext, + `proj_keyw4` tinytext, + `proj_keyw5` tinytext, + `proj_res_area` tinytext, + `proj_abstr` text, + `proj_prop` text, + `proj_fund_src` text, + `proj_num_samps` tinyint unsigned NOT NULL DEFAULT '0', + `proj_num_arrays` tinyint unsigned NOT NULL DEFAULT '0', + `proj_ht3_array` tinytext, + PRIMARY KEY (`proj_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `proj_res_area` +-- + +DROP TABLE IF EXISTS `proj_res_area`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_res_area` ( + `proj_res_index` text, + `proj_res_area` tinytext +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_biosource_info` +-- + +DROP TABLE IF EXISTS `sample_biosource_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_biosource_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) DEFAULT NULL, + `sample_bio_name` tinytext, + `sample_organism` tinytext, + `sample_alias` tinytext, + `sample_stock_code` tinytext, + `sample_genetic_var` tinytext, + `sample_tissue` tinytext, + `sample_diseased` tinytext, + `sample_growth_cond` tinytext, + `sample_growth_stage` tinytext, + `sample_time_point` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` varchar(40) NOT NULL, + `data_num` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(70) NOT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_call` varchar(12) NOT NULL, + `data_p_val` float NOT NULL DEFAULT '0', + `data_bot_id` varchar(40) DEFAULT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(12)), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_ext_param` +-- + +DROP TABLE IF EXISTS `sample_ext_param`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_ext_param` ( + `sample_param_type` tinytext, + `sample_param_index` tinytext NOT NULL, + `sample_param_data` tinytext NOT NULL, + `sample_param_ontology` tinytext +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_extraction_info` +-- + +DROP TABLE IF EXISTS `sample_extraction_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_extraction_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned DEFAULT NULL, + `sample_protocol_name` tinytext NOT NULL, + `sample_protocol_method` tinytext, + `sample_amplification` tinytext, + `sample_other_info` tinytext, + `sample_type` tinytext, + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_general_info` +-- + +DROP TABLE IF EXISTS `sample_general_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_general_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) DEFAULT NULL, + `sample_repl` tinytext, + `sample_ctrl` tinytext, + `sample_name` tinytext, + `sample_desc` longtext, + `sample_od` decimal(10,3) unsigned NOT NULL DEFAULT '0.000', + `sample_mass` decimal(10,3) unsigned NOT NULL DEFAULT '0.000', + `sample_vol` decimal(10,3) unsigned NOT NULL DEFAULT '0.000', + `sample_file_name` tinytext, + `sample_bot_id` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_hybrid_blocking_agent` +-- + +DROP TABLE IF EXISTS `sample_hybrid_blocking_agent`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_hybrid_blocking_agent` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned DEFAULT NULL, + `blocking_agent` tinytext, + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_hybrid_solution` +-- + +DROP TABLE IF EXISTS `sample_hybrid_solution`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_hybrid_solution` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned DEFAULT NULL, + `solution` tinytext, + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_hybrid_wash` +-- + +DROP TABLE IF EXISTS `sample_hybrid_wash`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_hybrid_wash` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned DEFAULT NULL, + `step_num` int DEFAULT NULL, + `wash_step` tinytext, + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_hybridization_info` +-- + +DROP TABLE IF EXISTS `sample_hybridization_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_hybridization_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) DEFAULT NULL, + `sample_protocol_name` tinytext, + `sample_amount` tinytext, + `sample_time` int DEFAULT NULL, + `sample_concentration` int DEFAULT NULL, + `sample_volume` int DEFAULT NULL, + `sample_temperature` int DEFAULT NULL, + PRIMARY KEY (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_image_analysis_info` +-- + +DROP TABLE IF EXISTS `sample_image_analysis_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_image_analysis_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned DEFAULT NULL, + `sample_image_name` tinytext, + `sample_scaling_factor` float DEFAULT NULL, + `sample_software_name` tinytext, + PRIMARY KEY (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_label_info` +-- + +DROP TABLE IF EXISTS `sample_label_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_label_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned DEFAULT NULL, + `sample_protocol_name` tinytext, + `sample_label_amount` int unsigned DEFAULT NULL, + `sample_label_name` tinytext, + `sample_label_method` tinytext, + `sample_other_info` tinytext, + PRIMARY KEY (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_norm_info` +-- + +DROP TABLE IF EXISTS `sample_norm_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_norm_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned DEFAULT NULL, + `sample_strategy` tinytext, + `sample_algorithm` tinytext, + `sample_ctrl_elem` tinytext, + PRIMARY KEY (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_scan_info` +-- + +DROP TABLE IF EXISTS `sample_scan_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_scan_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned DEFAULT NULL, + `sample_protocol_name` tinytext, + `sample_image_width` int unsigned DEFAULT NULL, + `sample_image_height` int unsigned DEFAULT NULL, + `sample_x_res` int unsigned DEFAULT NULL, + `sample_y_res` int unsigned DEFAULT NULL, + `sample_scanner_name` tinytext, + `sample_software_name` tinytext, + PRIMARY KEY (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_slide_info` +-- + +DROP TABLE IF EXISTS `sample_slide_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_slide_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned DEFAULT NULL, + `sample_date_hybridized` tinytext, + `sample_slide_design_name` tinytext, + `sample_array_source` tinytext, + `sample_array_type` tinytext, + `sample_num_array_spots` tinytext, + PRIMARY KEY (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_temp_data` +-- + +DROP TABLE IF EXISTS `sample_temp_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_temp_data` ( + `data_probeset_id` tinytext, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned NOT NULL DEFAULT '0', + `data_signal` float NOT NULL DEFAULT '0', + `data_call` tinytext NOT NULL, + `data_p_val` float NOT NULL DEFAULT '0', + `data_bot_id` tinytext +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `poplar_annotations_lookup` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `poplar_annotations_lookup` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `poplar_annotations_lookup`; + +-- +-- Table structure for table `at_pgi_lookup` +-- + +DROP TABLE IF EXISTS `at_pgi_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `at_pgi_lookup` ( + `probeset` varchar(60) NOT NULL, + `pgi` varchar(60) NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`probeset`,`pgi`,`date`), + KEY `probeset` (`probeset`), + KEY `pgi` (`pgi`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pgi_annotation` +-- + +DROP TABLE IF EXISTS `pgi_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pgi_annotation` ( + `pgi` varchar(60) NOT NULL, + `annotation` longtext NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`pgi`,`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `poplar_hormone` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `poplar_hormone` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `poplar_hormone`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(18) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(12) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `poplar_interactions` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `poplar_interactions` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `poplar_interactions`; + +-- +-- Table structure for table `interactions` +-- + +DROP TABLE IF EXISTS `interactions`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interactions` ( + `Protein1` varchar(25) NOT NULL, + `Protein2` varchar(25) NOT NULL, + `aiv_index` tinyint NOT NULL, + `cv` int DEFAULT NULL, + UNIQUE KEY `interactions_eplant` (`Protein1`,`Protein2`,`aiv_index`,`cv`), + KEY `aiv_index` (`aiv_index`), + KEY `protein2` (`Protein2`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `poplar_leaf` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `poplar_leaf` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `poplar_leaf`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(5) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(70) NOT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_bot_id` varchar(40) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `poplar_new_annotations` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `poplar_new_annotations` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `poplar_new_annotations`; + +-- +-- Table structure for table `at_pgi_lookup` +-- + +DROP TABLE IF EXISTS `at_pgi_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `at_pgi_lookup` ( + `probeset` varchar(60) NOT NULL, + `pgi` varchar(60) NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`probeset`,`pgi`,`date`), + KEY `date` (`date`), + KEY `pgi_probese` (`pgi`,`probeset`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pgi_annotation` +-- + +DROP TABLE IF EXISTS `pgi_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pgi_annotation` ( + `pgi` varchar(60) NOT NULL, + `annotation` longtext NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`pgi`,`date`), + KEY `date` (`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `poplar_nssnp` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `poplar_nssnp` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `poplar_nssnp`; + +-- +-- Table structure for table `protein_reference` +-- + +DROP TABLE IF EXISTS `protein_reference`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `protein_reference` ( + `protein_reference_id` int NOT NULL AUTO_INCREMENT, + `gene_identifier` varchar(45) NOT NULL, + `gene_name` varchar(45) DEFAULT NULL, + PRIMARY KEY (`protein_reference_id`), + UNIQUE KEY `gene_identifier_UNIQUE` (`gene_identifier`) +) ENGINE=InnoDB AUTO_INCREMENT=55981 DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `snps_reference` +-- + +DROP TABLE IF EXISTS `snps_reference`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `snps_reference` ( + `snps_reference_id` int NOT NULL AUTO_INCREMENT, + `chromosome` int NOT NULL, + `chromosomal_loci` int NOT NULL, + `ref_allele` varchar(1) NOT NULL, + `alt_allele` varchar(1) NOT NULL, + `sample_id` varchar(45) NOT NULL, + PRIMARY KEY (`snps_reference_id`), + UNIQUE KEY `preventdupe` (`chromosome`,`chromosomal_loci`,`ref_allele`,`alt_allele`,`sample_id`) +) ENGINE=InnoDB AUTO_INCREMENT=25980390 DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `snps_to_protein` +-- + +DROP TABLE IF EXISTS `snps_to_protein`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `snps_to_protein` ( + `snps_reference_id` int NOT NULL, + `protein_reference_id` int NOT NULL, + `transcript_pos` int NOT NULL, + `ref_DNA` varchar(1) NOT NULL, + `alt_DNA` varchar(45) NOT NULL, + `aa_pos` int NOT NULL, + `ref_aa` varchar(3) NOT NULL, + `alt_aa` varchar(3) NOT NULL, + `type` varchar(50) NOT NULL, + `effect_impact` varchar(50) NOT NULL, + `transcript_biotype` varchar(45) DEFAULT NULL, + PRIMARY KEY (`snps_reference_id`,`protein_reference_id`), + KEY `protein_fk_idx` (`protein_reference_id`), + CONSTRAINT `protein_fk` FOREIGN KEY (`protein_reference_id`) REFERENCES `protein_reference` (`protein_reference_id`), + CONSTRAINT `snp_fk` FOREIGN KEY (`snps_reference_id`) REFERENCES `snps_reference` (`snps_reference_id`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `poplar_xylem` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `poplar_xylem` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `poplar_xylem`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(5) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(70) NOT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_bot_id` varchar(40) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `potato_annotations` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `potato_annotations` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `potato_annotations`; + +-- +-- Table structure for table `gene_annotation` +-- + +DROP TABLE IF EXISTS `gene_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene_annotation` ( + `gene` varchar(25) NOT NULL, + `annotation` tinytext NOT NULL, + `date` date NOT NULL, + KEY `gene_date` (`gene`,`date`), + KEY `date` (`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gene_protein_lookup` +-- + +DROP TABLE IF EXISTS `gene_protein_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene_protein_lookup` ( + `probeset` varchar(25) NOT NULL, + `gene` varchar(25) NOT NULL, + `date` date NOT NULL, + KEY `probeset_gene` (`probeset`,`gene`), + KEY `gene_probeset` (`gene`,`probeset`), + KEY `date` (`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `potato_dev` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `potato_dev` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `potato_dev`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(15) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `potato_stress` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `potato_stress` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `potato_stress`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(12) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `potato_wounding` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `potato_wounding` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `potato_wounding`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(12) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `prot_model_data` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `prot_model_data` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `prot_model_data`; + +-- +-- Table structure for table `AGI_fasta` +-- + +DROP TABLE IF EXISTS `AGI_fasta`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `AGI_fasta` ( + `auto_inc` int NOT NULL AUTO_INCREMENT, + `AGI_id` varchar(30) NOT NULL, + `AGI_fasta` mediumtext NOT NULL, + PRIMARY KEY (`auto_inc`), + KEY `AGI_id` (`AGI_id`) +) ENGINE=InnoDB AUTO_INCREMENT=33412 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `CDD_annotations` +-- + +DROP TABLE IF EXISTS `CDD_annotations`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `CDD_annotations` ( + `auto_inc` int NOT NULL AUTO_INCREMENT, + `CDD_id` varchar(30) NOT NULL, + `CDD_annot` mediumtext NOT NULL, + PRIMARY KEY (`auto_inc`), + KEY `CDD_id` (`CDD_id`) +) ENGINE=InnoDB AUTO_INCREMENT=27049 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `CDD_fasta` +-- + +DROP TABLE IF EXISTS `CDD_fasta`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `CDD_fasta` ( + `auto_inc` int NOT NULL AUTO_INCREMENT, + `CDD_id` varchar(30) NOT NULL, + `CDD_fasta` mediumtext NOT NULL, + PRIMARY KEY (`auto_inc`), + KEY `CDD_id` (`CDD_id`) +) ENGINE=InnoDB AUTO_INCREMENT=979 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `CDD_model_mapping` +-- + +DROP TABLE IF EXISTS `CDD_model_mapping`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `CDD_model_mapping` ( + `auto_inc` int NOT NULL AUTO_INCREMENT, + `model_id` varchar(30) NOT NULL, + `CDD_id` varchar(30) NOT NULL, + PRIMARY KEY (`auto_inc`), + KEY `model_id` (`model_id`,`CDD_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `agi_annotations` +-- + +DROP TABLE IF EXISTS `agi_annotations`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `agi_annotations` ( + `auto_inc` int NOT NULL AUTO_INCREMENT, + `agi_id` varchar(11) NOT NULL, + `agi_nosplice` varchar(9) NOT NULL, + `blast_annotation` mediumtext, + PRIMARY KEY (`auto_inc`), + KEY `agi_id` (`agi_id`), + KEY `agi_nosplice` (`agi_nosplice`) +) ENGINE=InnoDB AUTO_INCREMENT=3942670 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `model_data` +-- + +DROP TABLE IF EXISTS `model_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `model_data` ( + `model_id` varchar(30) NOT NULL, + `model_path` mediumtext NOT NULL, + `implicit_fasta` mediumtext NOT NULL, + `html_alignments_path` mediumtext, + `jmol_scripts_path` mediumtext, + PRIMARY KEY (`model_id`), + KEY `model_id` (`model_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pdb_agi_mapping` +-- + +DROP TABLE IF EXISTS `pdb_agi_mapping`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pdb_agi_mapping` ( + `auto_inc` int NOT NULL AUTO_INCREMENT, + `model_id` varchar(30) NOT NULL, + `agi_id` varchar(11) NOT NULL, + `evalue` varchar(99) NOT NULL, + PRIMARY KEY (`auto_inc`), + KEY `model_id` (`model_id`), + KEY `agi_id` (`agi_id`) +) ENGINE=InnoDB AUTO_INCREMENT=3942670 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pdb_cdd_mapping` +-- + +DROP TABLE IF EXISTS `pdb_cdd_mapping`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pdb_cdd_mapping` ( + `auto_inc` int NOT NULL AUTO_INCREMENT, + `model_id` varchar(30) NOT NULL, + `cdd_id` varchar(200) NOT NULL, + PRIMARY KEY (`auto_inc`), + KEY `model_id` (`model_id`,`cdd_id`) +) ENGINE=InnoDB AUTO_INCREMENT=472999 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `rice_abiotic_stress_sc_pseudobulk` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `rice_abiotic_stress_sc_pseudobulk` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `rice_abiotic_stress_sc_pseudobulk`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(16) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(64) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `rice_annotations_lookup` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `rice_annotations_lookup` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `rice_annotations_lookup`; + +-- +-- Table structure for table `at_loc_lookup` +-- + +DROP TABLE IF EXISTS `at_loc_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `at_loc_lookup` ( + `probeset` varchar(60) NOT NULL, + `loc` varchar(30) NOT NULL, + `date` date NOT NULL, + KEY `date` (`date`), + KEY `loc_probeset` (`loc`,`probeset`), + KEY `probeset_loc` (`probeset`,`loc`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `at_loc_lookup_merged` +-- + +DROP TABLE IF EXISTS `at_loc_lookup_merged`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `at_loc_lookup_merged` ( + `probeset` varchar(60) NOT NULL, + `loc` varchar(30) NOT NULL, + `date` date NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `enzyme_gene_lookup` +-- + +DROP TABLE IF EXISTS `enzyme_gene_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `enzyme_gene_lookup` ( + `data_probeset_id` varchar(60) NOT NULL, + `gene` varchar(60) NOT NULL, + `date` date NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `enzyme_information` +-- + +DROP TABLE IF EXISTS `enzyme_information`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `enzyme_information` ( + `data_probeset_id` text NOT NULL, + `unit` text NOT NULL, + `type` text NOT NULL, + `enzyme_class` text, + `pathway` text, + `compound_id` text, + `pathway_name` text NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `loc_annotation` +-- + +DROP TABLE IF EXISTS `loc_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `loc_annotation` ( + `loc` varchar(30) NOT NULL, + `annotation` longtext NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`loc`,`date`), + KEY `date` (`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `loc_annotation_merged` +-- + +DROP TABLE IF EXISTS `loc_annotation_merged`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `loc_annotation_merged` ( + `loc` varchar(30) NOT NULL, + `annotation` longtext, + `date` date NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `metabolite_gene_lookup` +-- + +DROP TABLE IF EXISTS `metabolite_gene_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `metabolite_gene_lookup` ( + `data_probeset_id` varchar(60) NOT NULL, + `gene` varchar(60) NOT NULL, + `date` date NOT NULL, + KEY `probeset_gene` (`data_probeset_id`,`gene`), + KEY `gene_probeset` (`gene`,`data_probeset_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `metabolite_information` +-- + +DROP TABLE IF EXISTS `metabolite_information`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `metabolite_information` ( + `data_probeset_id` varchar(30) NOT NULL, + `unit` text NOT NULL, + `type` text NOT NULL, + `enzyme_class` text, + `pathway` text, + `compound_id` text, + `pathway_name` text NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `msu_rap` +-- + +DROP TABLE IF EXISTS `msu_rap`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `msu_rap` ( + `msu` varchar(16) DEFAULT NULL, + `rap` varchar(16) DEFAULT NULL, + KEY `msu_rap` (`msu`,`rap`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `new_loc_annotation` +-- + +DROP TABLE IF EXISTS `new_loc_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `new_loc_annotation` ( + `loc` varchar(30) NOT NULL, + `annotation` longtext, + `date` date NOT NULL, + KEY `date_loc` (`date`,`loc`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `new_loc_lookup` +-- + +DROP TABLE IF EXISTS `new_loc_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `new_loc_lookup` ( + `probeset` varchar(60) NOT NULL, + `loc` varchar(30) NOT NULL, + `date` date NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `rice_maize_lookup` +-- + +DROP TABLE IF EXISTS `rice_maize_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `rice_maize_lookup` ( + `rice_ID` varchar(60) NOT NULL, + `maize_ID` varchar(60) NOT NULL, + `date` date NOT NULL, + KEY `date_gene` (`date`,`rice_ID`,`maize_ID`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `rice_drought_heat_stress` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `rice_drought_heat_stress` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `rice_drought_heat_stress`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(12) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `rice_interactions` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `rice_interactions` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `rice_interactions`; + +-- +-- Table structure for table `RGI_annotation` +-- + +DROP TABLE IF EXISTS `RGI_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `RGI_annotation` ( + `loc` varchar(14) NOT NULL, + `annotation` longtext NOT NULL, + `date` date NOT NULL DEFAULT '0000-00-00', + PRIMARY KEY (`loc`,`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `Rice_mPLoc` +-- + +DROP TABLE IF EXISTS `Rice_mPLoc`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `Rice_mPLoc` ( + `gene_id` varchar(20) NOT NULL DEFAULT '', + `alias` text, + `lab_description` text, + `gfp` text, + `mass_spec` text, + `swissprot` text, + `amigo` text, + `annotation` text, + `pred_ipsort` text, + `pred_mitopred` text, + `pred_mitopred2` text, + `pred_predator` text, + `pred_peroxp` text, + `pred_subloc` text, + `pred_targetp` text, + `pred_wolfpsort` text, + `pred_multiloc` text, + `pred_loctree` text, + `pred_mPLoc` text, + PRIMARY KEY (`gene_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `interactions` +-- + +DROP TABLE IF EXISTS `interactions`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `interactions` ( + `Protein1` varchar(14) NOT NULL, + `Protein2` varchar(14) NOT NULL, + `S_cerevisiae` tinyint NOT NULL DEFAULT '0', + `S_pombe` tinyint NOT NULL DEFAULT '0', + `Worm` tinyint NOT NULL DEFAULT '0', + `Fly` tinyint NOT NULL DEFAULT '0', + `Human` tinyint NOT NULL DEFAULT '0', + `Mouse` tinyint NOT NULL DEFAULT '0', + `E_coli` tinyint NOT NULL DEFAULT '0', + `Total_hits` smallint NOT NULL DEFAULT '0', + `Num_species` tinyint NOT NULL DEFAULT '0', + `Quality` smallint NOT NULL DEFAULT '0', + `Index` tinyint NOT NULL DEFAULT '0', + `Pcc` float DEFAULT NULL, + `Bind_id` tinytext, + UNIQUE KEY `Protein1` (`Protein1`,`Protein2`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `suba` +-- + +DROP TABLE IF EXISTS `suba`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `suba` ( + `gene_id` varchar(20) NOT NULL DEFAULT '', + `alias` text, + `lab_description` text, + `gfp` text, + `mass_spec` text, + `swissprot` text, + `amigo` text, + `annotation` text, + `pred_ipsort` text, + `pred_mitopred` text, + `pred_mitopred2` text, + `pred_predator` text, + `pred_peroxp` text, + `pred_subloc` text, + `pred_targetp` text, + `pred_wolfpsort` text, + `pred_multiloc` text, + `pred_loctree` text, + PRIMARY KEY (`gene_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `rice_leaf_gradient` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `rice_leaf_gradient` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `rice_leaf_gradient`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(18) NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(12) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `rice_maize_comparison` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `rice_maize_comparison` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `rice_maize_comparison`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(18) NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(12) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `rice_mas` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `rice_mas` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `rice_mas`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(28) NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(26) NOT NULL, + `sample_tissue` text NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `rice_metabolite` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `rice_metabolite` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `rice_metabolite`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(25) NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(6) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `rice_rma` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `rice_rma` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `rice_rma`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(28) NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(26) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `rice_root` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `rice_root` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `rice_root`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(2) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(16) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(8) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `rohan` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `rohan` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `rohan`; + +-- +-- Table structure for table `arab_soy_check` +-- + +DROP TABLE IF EXISTS `arab_soy_check`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `arab_soy_check` ( + `Cluster` int NOT NULL DEFAULT '0', + `Gene_A` varchar(60) NOT NULL DEFAULT '', + `Probeset_A` varchar(60) NOT NULL DEFAULT '', + `Genome_A` varchar(30) DEFAULT NULL, + `Gene_B` varchar(60) NOT NULL DEFAULT '', + `Probeset_B` varchar(60) NOT NULL DEFAULT '', + `Genome_B` varchar(30) DEFAULT NULL, + `SCC_Value` float DEFAULT NULL, + `Seq_Similarity` int DEFAULT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `arab_stress_wilkins` +-- + +DROP TABLE IF EXISTS `arab_stress_wilkins`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `arab_stress_wilkins` ( + `sample_id` int NOT NULL, + `proj_id` varchar(15) NOT NULL, + `sample_file_name` tinytext NOT NULL, + `data_probeset_id` tinytext NOT NULL, + `data_signal` float NOT NULL, + `data_call` tinytext NOT NULL, + `data_p_val` float NOT NULL, + `data_bot_id` tinytext NOT NULL, + `sample_tissue` varchar(50) NOT NULL, + `sample_repl` varchar(10) NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `arabidopsis` +-- + +DROP TABLE IF EXISTS `arabidopsis`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `arabidopsis` ( + `gene` varchar(30) NOT NULL, + `sequence` mediumtext NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`gene`,`date`), + KEY `date` (`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `arabidopsis_pop_stress` +-- + +DROP TABLE IF EXISTS `arabidopsis_pop_stress`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `arabidopsis_pop_stress` ( + `Cluster` int NOT NULL, + `Gene_A` varchar(60) NOT NULL, + `Probeset_A` varchar(60) NOT NULL, + `Genome_A` varchar(30) NOT NULL, + `Gene_B` varchar(60) NOT NULL, + `Probeset_B` varchar(60) NOT NULL, + `Genome_B` varchar(30) NOT NULL, + `SCC_Value` float NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `arabidopsis_pop_stress_seq` +-- + +DROP TABLE IF EXISTS `arabidopsis_pop_stress_seq`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `arabidopsis_pop_stress_seq` ( + `Cluster` int NOT NULL DEFAULT '0', + `Gene_A` varchar(60) NOT NULL DEFAULT '', + `Probeset_A` varchar(60) NOT NULL DEFAULT '', + `Genome_A` varchar(30) DEFAULT NULL, + `Gene_B` varchar(60) NOT NULL DEFAULT '', + `Probeset_B` varchar(60) NOT NULL DEFAULT '', + `Genome_B` varchar(30) DEFAULT NULL, + `SCC_Value` float DEFAULT NULL, + `Seq_Similarity` int DEFAULT NULL, + PRIMARY KEY (`Cluster`,`Gene_A`,`Probeset_A`,`Gene_B`,`Probeset_B`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `arabidopsis_rice_stress` +-- + +DROP TABLE IF EXISTS `arabidopsis_rice_stress`; +/*!40101 SET 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NULL, + `SCC_Value` float DEFAULT NULL, + `Seq_Similarity` int DEFAULT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `med_data` +-- + +DROP TABLE IF EXISTS `med_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `med_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` tinytext NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` tinytext NOT NULL, + `sample_repl` varchar(50) NOT NULL, + `sample_tissue` varchar(50) NOT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(12)), + KEY `data_probeset_id` (`data_probeset_id`(12)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- 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= @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `medicago_v4_1` ( + `gene` varchar(30) NOT NULL, + `sequence` mediumtext NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `orthologs` +-- + +DROP TABLE IF EXISTS `orthologs`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `orthologs` ( + `cluster` int NOT NULL, + `gene` varchar(100) NOT NULL, + `genome` varchar(10) NOT NULL, + `sequence` mediumtext NOT NULL, + `date` date NOT NULL, + `method` varchar(15) NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pop_stress_wilkins` +-- + +DROP TABLE IF EXISTS `pop_stress_wilkins`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pop_stress_wilkins` ( + `sample_id` int NOT NULL, + `data_probeset_id` varchar(70) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + `timepoint` varchar(50) NOT NULL, + PRIMARY KEY (`sample_id`,`data_probeset_id`,`timepoint`), + KEY `sample_id` (`sample_id`,`data_bot_id`,`timepoint`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `poplar` +-- + +DROP TABLE IF EXISTS `poplar`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `poplar` ( + `gene` varchar(60) NOT NULL, + `sequence` mediumtext NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `potato` +-- + +DROP TABLE IF EXISTS `potato`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `potato` ( + `gene` varchar(30) NOT NULL, + `sequence` mediumtext NOT NULL, + `date` date NOT NULL, + KEY `date` (`date`), + KEY `gene` (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `proj_info` +-- + +DROP TABLE IF EXISTS `proj_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_info` ( + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `proj_title` tinytext, + `proj_pi` tinytext, + `proj_pi_title` tinytext, + `proj_pi_inst` tinytext, + `proj_pi_addr` tinytext, + `proj_keyw1` tinytext, + `proj_keyw2` tinytext, + `proj_keyw3` tinytext, + `proj_keyw4` tinytext, + `proj_keyw5` tinytext, + `proj_res_area` tinytext, + `proj_num_samps` tinyint unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`proj_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `rice` +-- + +DROP TABLE IF EXISTS `rice`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `rice` ( + `gene` varchar(30) NOT NULL, + `sequence` mediumtext NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`gene`,`date`), + KEY `date` (`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `rice_data` +-- + +DROP TABLE IF EXISTS `rice_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `rice_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` tinytext NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` tinytext NOT NULL, + `sample_tissue` varchar(50) NOT NULL, + `sample_repl` varchar(10) NOT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(12)), + KEY `data_probeset_id` (`data_probeset_id`(12)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `rice_new` +-- + +DROP TABLE IF EXISTS `rice_new`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `rice_new` ( + `gene` varchar(30) NOT NULL, + `sequence` mediumtext NOT NULL, + `date` date NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_biosource_info` +-- + +DROP TABLE IF EXISTS `sample_biosource_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_biosource_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_bio_name` tinytext, + `sample_organism` tinytext, + `sample_alias` tinytext, + `sample_stock_code` tinytext, + `sample_genetic_var` tinytext, + `sample_tissue` tinytext, + `sample_diseased` tinytext, + `sample_growth_cond` tinytext, + `sample_growth_stage` tinytext, + `sample_time_point` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` tinytext NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` tinytext NOT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(12)), + KEY `data_probeset_id` (`data_probeset_id`(12)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_general_info` +-- + +DROP TABLE IF EXISTS `sample_general_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_general_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_repl` tinytext, + `sample_ctrl` tinytext, + `sample_desc` tinytext, + `sample_file_name` tinytext, + `sample_bot_id` tinytext NOT NULL, + `sample_name` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sheezy` +-- + +DROP TABLE IF EXISTS `sheezy`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sheezy` ( + `Cluster` int NOT NULL DEFAULT '0', + `Gene_A` varchar(60) NOT NULL DEFAULT '', + `Probeset_A` varchar(60) NOT NULL DEFAULT '', + `Genome_A` varchar(30) DEFAULT NULL, + `Gene_B` varchar(60) NOT NULL DEFAULT '', + `Probeset_B` varchar(60) NOT NULL DEFAULT '', + `Genome_B` varchar(30) DEFAULT NULL, + `SCC_Value` float DEFAULT NULL, + `Seq_Similarity` int DEFAULT NULL, + PRIMARY KEY (`Cluster`,`Gene_A`,`Probeset_A`,`Gene_B`,`Probeset_B`), + KEY `Gene_A` (`Gene_A`,`Gene_B`), + KEY `Gene_B` (`Gene_B`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `soybean` +-- + +DROP TABLE IF EXISTS `soybean`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `soybean` ( + `gene` varchar(30) NOT NULL, + `sequence` mediumtext NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `soybean_merged` +-- + +DROP TABLE IF EXISTS `soybean_merged`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `soybean_merged` ( + `sample_id` int NOT NULL, + `proj_id` varchar(15) NOT NULL, + `sample_file_name` tinytext NOT NULL, + `data_probeset_id` tinytext NOT NULL, + `data_signal` float NOT NULL, + `data_call` tinytext NOT NULL, + `data_p_val` float NOT NULL, + `data_bot_id` tinytext NOT NULL, + PRIMARY KEY (`sample_id`,`proj_id`,`data_probeset_id`(15)), + KEY `data_probeset_id` (`data_probeset_id`(15),`data_bot_id`(20)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `test` +-- + +DROP TABLE IF EXISTS `test`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `test` ( + `gene` varchar(30) NOT NULL, + `sequence` mediumtext NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `test_expressolog` +-- + +DROP TABLE IF EXISTS `test_expressolog`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `test_expressolog` ( + `Cluster` int NOT NULL DEFAULT '0', + `Gene_A` varchar(60) NOT NULL DEFAULT '', + `Probeset_A` varchar(60) NOT NULL DEFAULT '', + `Genome_A` varchar(30) DEFAULT NULL, + `Gene_B` varchar(60) NOT NULL DEFAULT '', + `Probeset_B` varchar(60) NOT NULL DEFAULT '', + `Genome_B` varchar(30) DEFAULT NULL, + `SCC_Value` float DEFAULT NULL, + `Seq_Similarity` int DEFAULT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `tissue_equivalency` +-- + +DROP TABLE IF EXISTS `tissue_equivalency`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `tissue_equivalency` ( + `Tissue_A` varchar(100) DEFAULT NULL, + `Species_A` varchar(100) DEFAULT NULL, + `Tissue_B` varchar(100) DEFAULT NULL, + `Species_B` varchar(100) DEFAULT NULL, + `SCC_Value` float DEFAULT NULL, + `Accession_A` varchar(100) DEFAULT NULL, + `Accession_B` varchar(100) DEFAULT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `tissue_equivalency_v2` +-- + +DROP TABLE IF EXISTS `tissue_equivalency_v2`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `tissue_equivalency_v2` ( + `Tissue_A` varchar(100) DEFAULT NULL, + `Species_A` varchar(100) DEFAULT NULL, + `Tissue_B` varchar(100) DEFAULT NULL, + `Species_B` varchar(100) DEFAULT NULL, + `SCC_Value` float DEFAULT NULL, + `Accession_A` varchar(100) DEFAULT NULL, + `Accession_B` varchar(100) DEFAULT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `tissue_equivalency_v3` +-- + +DROP TABLE IF EXISTS `tissue_equivalency_v3`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `tissue_equivalency_v3` ( + `Tissue_A` varchar(100) DEFAULT NULL, + `Species_A` varchar(100) DEFAULT NULL, + `Tissue_B` varchar(100) DEFAULT NULL, + `Species_B` varchar(100) DEFAULT NULL, + `SCC_Value` float DEFAULT NULL, + `Accession_A` varchar(100) DEFAULT NULL, + `Accession_B` varchar(100) DEFAULT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `tissue_equivalency_v4` +-- + +DROP TABLE IF EXISTS `tissue_equivalency_v4`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `tissue_equivalency_v4` ( + `Tissue_A` varchar(100) DEFAULT NULL, + `Species_A` varchar(100) DEFAULT NULL, + `Tissue_B` varchar(100) DEFAULT NULL, + `Species_B` varchar(100) DEFAULT NULL, + `SCC_Value` float DEFAULT NULL, + `Accession_A` varchar(100) DEFAULT NULL, + `Accession_B` varchar(100) DEFAULT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `tomato` +-- + +DROP TABLE IF EXISTS `tomato`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `tomato` ( + `gene` varchar(30) NOT NULL, + `sequence` mediumtext NOT NULL, + `date` date NOT NULL, + KEY `date` (`date`), + KEY `gene` (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `root` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `root` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `root`; + +-- +-- Table structure for table `proj_info` +-- + +DROP TABLE IF EXISTS `proj_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_info` ( + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `proj_title` tinytext, + `proj_pi` tinytext, + `proj_pi_title` tinytext, + `proj_pi_inst` tinytext, + `proj_pi_addr` tinytext, + `proj_keyw1` tinytext, + `proj_keyw2` tinytext, + `proj_keyw3` tinytext, + `proj_keyw4` tinytext, + `proj_keyw5` tinytext, + `proj_res_area` tinytext, + `proj_num_samps` tinyint unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`proj_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_biosource_info` +-- + +DROP TABLE IF EXISTS `sample_biosource_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_biosource_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_bio_name` tinytext, + `sample_organism` tinytext, + `sample_alias` tinytext, + `sample_stock_code` tinytext, + `sample_genetic_var` tinytext, + `sample_tissue` tinytext, + `sample_diseased` tinytext, + `sample_growth_cond` tinytext, + `sample_growth_stage` tinytext, + `sample_time_point` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(30) NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(24) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_general_info` +-- + +DROP TABLE IF EXISTS `sample_general_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_general_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_repl` tinytext, + `sample_ctrl` tinytext, + `sample_desc` tinytext, + `sample_file_name` tinytext, + `sample_bot_id` tinytext NOT NULL, + `sample_name` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `root_Schaefer_lab` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `root_Schaefer_lab` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `root_Schaefer_lab`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(5) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(16) NOT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_bot_id` varchar(20) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `rpatel` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `rpatel` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `rpatel`; + +-- +-- Table structure for table `arab_stress_wilkins` +-- + +DROP TABLE IF EXISTS `arab_stress_wilkins`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `arab_stress_wilkins` ( + `sample_id` int NOT NULL, + `proj_id` varchar(15) NOT NULL, + `sample_file_name` tinytext NOT NULL, + `data_probeset_id` tinytext NOT NULL, + `data_signal` float NOT NULL, + `data_call` tinytext NOT NULL, + `data_p_val` float NOT NULL, + `data_bot_id` tinytext NOT NULL, + `sample_tissue` varchar(50) NOT NULL, + `sample_repl` varchar(10) NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `arabidopsis` +-- + +DROP TABLE IF EXISTS `arabidopsis`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `arabidopsis` ( + `gene` varchar(30) NOT NULL, + `sequence` mediumtext NOT NULL, + KEY `gene` (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `arabidopsis_pop_stress` +-- + +DROP TABLE IF EXISTS `arabidopsis_pop_stress`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `arabidopsis_pop_stress` ( + `Cluster` int NOT NULL, + `Gene_A` varchar(60) NOT NULL, + `Probeset_A` varchar(60) NOT NULL, + `Genome_A` varchar(30) NOT NULL, + `Gene_B` varchar(60) NOT NULL, + `Probeset_B` varchar(60) NOT NULL, + `Genome_B` varchar(30) NOT NULL, + `SCC_Value` float NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `arabidopsis_pop_stress_seq` +-- + +DROP TABLE IF EXISTS `arabidopsis_pop_stress_seq`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `arabidopsis_pop_stress_seq` ( + `Cluster` int NOT NULL DEFAULT '0', + `Gene_A` varchar(60) NOT NULL DEFAULT '', + `Probeset_A` varchar(60) NOT NULL DEFAULT '', + `Genome_A` varchar(30) DEFAULT NULL, + `Gene_B` varchar(60) NOT NULL DEFAULT '', + `Probeset_B` varchar(60) NOT NULL DEFAULT '', + `Genome_B` varchar(30) DEFAULT NULL, + `SCC_Value` float DEFAULT NULL, + `Seq_Similarity` int DEFAULT NULL, + PRIMARY KEY (`Cluster`,`Gene_A`,`Probeset_A`,`Gene_B`,`Probeset_B`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `arabidopsis_rice_stress` +-- + +DROP TABLE IF EXISTS `arabidopsis_rice_stress`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `arabidopsis_rice_stress` ( + `Cluster` int NOT NULL, + `Gene_A` varchar(60) NOT NULL, + `Probeset_A` varchar(60) NOT NULL, + `Genome_A` varchar(30) NOT NULL, + `Gene_B` varchar(60) NOT NULL, + `Probeset_B` varchar(60) NOT NULL, + `Genome_B` varchar(30) NOT NULL, + `SCC_Value` float NOT NULL, + `Seq_similarity` int DEFAULT NULL, + PRIMARY KEY (`Cluster`,`Gene_A`,`Probeset_A`,`Gene_B`,`Probeset_B`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `arabidopsis_scc_seq` +-- + +DROP TABLE IF EXISTS `arabidopsis_scc_seq`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `arabidopsis_scc_seq` ( + `Cluster` int NOT NULL DEFAULT '0', + `Gene_A` varchar(60) NOT NULL DEFAULT '', + `Probeset_A` varchar(60) NOT NULL DEFAULT '', + `Genome_A` varchar(30) DEFAULT NULL, + `Gene_B` varchar(60) NOT NULL DEFAULT '', + `Probeset_B` varchar(60) NOT NULL DEFAULT '', + `Genome_B` varchar(30) DEFAULT NULL, + `SCC_Value` float DEFAULT NULL, + `Seq_Similarity` int DEFAULT NULL, + PRIMARY KEY (`Cluster`,`Gene_A`,`Probeset_A`,`Gene_B`,`Probeset_B`), + KEY `geneA_cluster` (`Gene_A`,`Cluster`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `arabidopsis_scc_test` +-- + +DROP TABLE IF EXISTS `arabidopsis_scc_test`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `arabidopsis_scc_test` ( + `Cluster` int NOT NULL, + `Gene_A` varchar(60) NOT NULL, + `Probeset_A` varchar(60) NOT NULL, + `Genome_A` varchar(30) NOT NULL, + `Gene_B` varchar(60) NOT NULL, + `Probeset_B` varchar(60) NOT NULL, + `Genome_B` varchar(30) NOT NULL, + `SCC_Value` float NOT NULL, + PRIMARY KEY (`Cluster`,`Gene_A`,`Probeset_A`,`Gene_B`,`Probeset_B`), + KEY `Cluster` (`Cluster`,`Gene_A`,`Probeset_A`,`Gene_B`,`Probeset_B`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `at_bar_lookup` +-- + +DROP TABLE IF EXISTS `at_bar_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `at_bar_lookup` ( + `bar` varchar(60) NOT NULL, + `probeset` varchar(60) NOT NULL, + `date` date NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `barley` +-- + +DROP TABLE IF EXISTS `barley`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `barley` ( + `gene` varchar(30) NOT NULL, + `sequence` mediumtext NOT NULL, + KEY `gene` (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `barley_data` +-- + +DROP TABLE IF EXISTS `barley_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `barley_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` tinytext NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` tinytext NOT NULL, + `sample_tissue` varchar(50) NOT NULL, + `sample_repl` varchar(5) NOT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(12)), + KEY `data_probeset_id` (`data_probeset_id`(12)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `loc_annotation` +-- + +DROP TABLE IF EXISTS `loc_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `loc_annotation` ( + `loc` varchar(30) NOT NULL, + `annotation` longtext NOT NULL, + `date` date NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `med_data` +-- + +DROP TABLE IF EXISTS `med_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `med_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` tinytext NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` tinytext NOT NULL, + `sample_repl` varchar(50) NOT NULL, + `sample_tissue` varchar(50) NOT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(12)), + KEY `data_probeset_id` (`data_probeset_id`(12)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `medicago` +-- + +DROP TABLE IF EXISTS `medicago`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `medicago` ( + `gene` varchar(30) NOT NULL, + `sequence` mediumtext NOT NULL, + KEY `gene` (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `orthologs` +-- + +DROP TABLE IF EXISTS `orthologs`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `orthologs` ( + `cluster` int NOT NULL, + `gene` varchar(100) NOT NULL, + `genome` varchar(10) NOT NULL, + `sequence` mediumtext NOT NULL, + `date` date NOT NULL, + `method` varchar(15) NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pop_stress_wilkins` +-- + +DROP TABLE IF EXISTS `pop_stress_wilkins`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pop_stress_wilkins` ( + `sample_id` int NOT NULL, + `data_probeset_id` varchar(70) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + `timepoint` varchar(50) NOT NULL, + PRIMARY KEY (`sample_id`,`data_probeset_id`,`timepoint`), + KEY `sample_id` (`sample_id`,`data_bot_id`,`timepoint`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `poplar` +-- + +DROP TABLE IF EXISTS `poplar`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `poplar` ( + `gene` varchar(60) NOT NULL, + `sequence` mediumtext NOT NULL, + KEY `gene` (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `proj_info` +-- + +DROP TABLE IF EXISTS `proj_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_info` ( + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `proj_title` tinytext, + `proj_pi` tinytext, + `proj_pi_title` tinytext, + `proj_pi_inst` tinytext, + `proj_pi_addr` tinytext, + `proj_keyw1` tinytext, + `proj_keyw2` tinytext, + `proj_keyw3` tinytext, + `proj_keyw4` tinytext, + `proj_keyw5` tinytext, + `proj_res_area` tinytext, + `proj_num_samps` tinyint unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`proj_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `rice` +-- + +DROP TABLE IF EXISTS `rice`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `rice` ( + `gene` varchar(30) NOT NULL, + `sequence` mediumtext NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `rice_data` +-- + +DROP TABLE IF EXISTS `rice_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `rice_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` tinytext NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` tinytext NOT NULL, + `sample_tissue` varchar(50) NOT NULL, + `sample_repl` varchar(10) NOT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(12)), + KEY `data_probeset_id` (`data_probeset_id`(12)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_biosource_info` +-- + +DROP TABLE IF EXISTS `sample_biosource_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_biosource_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_bio_name` tinytext, + `sample_organism` tinytext, + `sample_alias` tinytext, + `sample_stock_code` tinytext, + `sample_genetic_var` tinytext, + `sample_tissue` tinytext, + `sample_diseased` tinytext, + `sample_growth_cond` tinytext, + `sample_growth_stage` tinytext, + `sample_time_point` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` tinytext NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` tinytext NOT NULL, + KEY `datapoint_id` (`sample_id`,`proj_id`,`data_probeset_id`(12)), + KEY `data_probeset_id` (`data_probeset_id`(12)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_general_info` +-- + +DROP TABLE IF EXISTS `sample_general_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_general_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_repl` tinytext, + `sample_ctrl` tinytext, + `sample_desc` tinytext, + `sample_file_name` tinytext, + `sample_bot_id` tinytext NOT NULL, + `sample_name` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `soybean` +-- + +DROP TABLE IF EXISTS `soybean`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `soybean` ( + `gene` varchar(30) NOT NULL, + `sequence` mediumtext NOT NULL, + KEY `gene` (`gene`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `soybean_merged` +-- + +DROP TABLE IF EXISTS `soybean_merged`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `soybean_merged` ( + `sample_id` int NOT NULL, + `proj_id` varchar(15) NOT NULL, + `sample_file_name` tinytext NOT NULL, + `data_probeset_id` tinytext NOT NULL, + `data_signal` float NOT NULL, + `data_call` tinytext NOT NULL, + `data_p_val` float NOT NULL, + `data_bot_id` tinytext NOT NULL, + PRIMARY KEY (`sample_id`,`proj_id`,`data_probeset_id`(15)), + KEY `data_probeset_id` (`data_probeset_id`(15),`data_bot_id`(20)) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `test` +-- + +DROP TABLE IF EXISTS `test`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `test` ( + `gene` varchar(30) NOT NULL, + `sequence` mediumtext NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `tissue_equivalency` +-- + +DROP TABLE IF EXISTS `tissue_equivalency`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `tissue_equivalency` ( + `Tissue_A` varchar(100) DEFAULT NULL, + `Species_A` varchar(100) DEFAULT NULL, + `Tissue_B` varchar(100) DEFAULT NULL, + `Species_B` varchar(100) DEFAULT NULL, + `SCC_Value` float DEFAULT NULL, + `Accession_A` varchar(100) DEFAULT NULL, + `Accession_B` varchar(100) DEFAULT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `rsvp` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `rsvp` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `rsvp`; + +-- +-- Table structure for table `questions` +-- + +DROP TABLE IF EXISTS `questions`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `questions` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `subjectId` int unsigned DEFAULT NULL, + `testId` tinyint unsigned DEFAULT NULL, + `question` int unsigned DEFAULT NULL, + `time_taken` int unsigned DEFAULT NULL, + `status` tinyint DEFAULT NULL, + `step` int DEFAULT NULL, + `image` int DEFAULT NULL, + `response` int DEFAULT NULL, + PRIMARY KEY (`id`) +) ENGINE=InnoDB AUTO_INCREMENT=31 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `subject_info` +-- + +DROP TABLE IF EXISTS `subject_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `subject_info` ( + `id` int unsigned NOT NULL AUTO_INCREMENT, + `testID` tinyint unsigned DEFAULT NULL, + `name` varchar(64) DEFAULT NULL, + `email` varchar(64) DEFAULT NULL, + `age` int unsigned DEFAULT NULL, + `gender` varchar(8) DEFAULT NULL, + `pointer` varchar(16) DEFAULT NULL, + `red` varchar(16) DEFAULT NULL, + `start` varchar(64) DEFAULT NULL, + `end` varchar(64) DEFAULT NULL, + `total_time` int unsigned DEFAULT NULL, + PRIMARY KEY (`id`) +) ENGINE=InnoDB AUTO_INCREMENT=6 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `seed_db` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `seed_db` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `seed_db`; + +-- +-- Table structure for table `proj_info` +-- + +DROP TABLE IF EXISTS `proj_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_info` ( + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `proj_title` tinytext, + `proj_pi` tinytext, + `proj_pi_title` tinytext, + `proj_pi_inst` tinytext, + `proj_pi_addr` tinytext, + `proj_keyw1` tinytext, + `proj_keyw2` tinytext, + `proj_keyw3` tinytext, + `proj_keyw4` tinytext, + `proj_keyw5` tinytext, + `proj_res_area` tinytext, + `proj_num_samps` tinyint unsigned NOT NULL DEFAULT '0', + PRIMARY KEY (`proj_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_biosource_info` +-- + +DROP TABLE IF EXISTS `sample_biosource_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_biosource_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_bio_name` tinytext, + `sample_organism` tinytext, + `sample_alias` tinytext, + `sample_stock_code` tinytext, + `sample_genetic_var` tinytext, + `sample_tissue` tinytext, + `sample_diseased` tinytext, + `sample_growth_cond` tinytext, + `sample_growth_stage` tinytext, + `sample_time_point` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(20) NOT NULL DEFAULT '0', + `sample_file_name` varchar(100) DEFAULT NULL, + `data_probeset_id` varchar(30) NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` varchar(40) DEFAULT NULL, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(64) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data_test` +-- + +DROP TABLE IF EXISTS `sample_data_test`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data_test` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` int unsigned NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` tinytext NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` tinytext NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_general_info` +-- + +DROP TABLE IF EXISTS `sample_general_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_general_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_repl` tinytext, + `sample_ctrl` tinytext, + `sample_desc` tinytext, + `sample_file_name` tinytext, + `sample_bot_id` tinytext NOT NULL, + `sample_name` tinytext, + PRIMARY KEY (`sample_id`), + KEY `sample_id` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `seedcoat` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `seedcoat` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `seedcoat`; + +-- +-- Table structure for table `proj_info` +-- + +DROP TABLE IF EXISTS `proj_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `proj_info` ( + `proj_id` varchar(15) NOT NULL, + `proj_title` tinytext, + `proj_pi` tinytext, + `proj_pi_title` tinytext, + `proj_pi_inst` tinytext, + `proj_keyw1` tinytext, + `proj_keyw2` tinytext, + `proj_keyw3` tinytext, + `proj_keyw4` tinytext, + `proj_keyw5` tinytext, + `proj_res_area` tinytext, + `proj_num_samps` tinyint unsigned NOT NULL, + PRIMARY KEY (`proj_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_biosource_info` +-- + +DROP TABLE IF EXISTS `sample_biosource_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_biosource_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_bio_name` tinytext, + `sample_organism` tinytext, + `sample_alias` tinytext, + `sample_stock_code` tinytext, + `sample_genetic_var` tinytext, + `sample_tissue` tinytext, + `sample_diseased` tinytext, + `sample_growth_cond` tinytext, + `sample_growth_stage` tinytext, + `sample_time_point` tinytext, + PRIMARY KEY (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(22) NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(12) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_general_info` +-- + +DROP TABLE IF EXISTS `sample_general_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_general_info` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_repl` tinytext, + `sample_ctrl` tinytext, + `sample_desc` tinytext, + `sample_file_name` tinytext, + `sample_bot_id` tinytext NOT NULL, + `sample_name` tinytext, + PRIMARY KEY (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `selaginella` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `selaginella` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `selaginella`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(5) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(18) NOT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_bot_id` varchar(36) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `shoot_apex` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `shoot_apex` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `shoot_apex`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(2) DEFAULT NULL, + `sample_file_name` varchar(16) DEFAULT NULL, + `data_probeset_id` varchar(12) NOT NULL, + `data_signal` float NOT NULL, + `data_call` varchar(2) DEFAULT NULL, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(8) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `silique` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `silique` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `silique`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(12) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(64) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `single_cell` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `single_cell` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `single_cell`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(32) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `sorghum_atlas_w_BS_cells` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `sorghum_atlas_w_BS_cells` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `sorghum_atlas_w_BS_cells`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(24) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `sorghum_bundle_sheath` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `sorghum_bundle_sheath` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `sorghum_bundle_sheath`; + +-- +-- Current Database: `sorghum_comparative_transcriptomics` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `sorghum_comparative_transcriptomics` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `sorghum_comparative_transcriptomics`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(18) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(40) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `sorghum_developmental` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `sorghum_developmental` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `sorghum_developmental`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(16) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(12) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `sorghum_developmental_2` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `sorghum_developmental_2` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `sorghum_developmental_2`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(16) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(32) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `sorghum_flowering_activation` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `sorghum_flowering_activation` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `sorghum_flowering_activation`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(16) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(32) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `sorghum_low_phosphorus` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `sorghum_low_phosphorus` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `sorghum_low_phosphorus`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(16) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `sorghum_nitrogen_stress` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `sorghum_nitrogen_stress` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `sorghum_nitrogen_stress`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(16) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(32) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `sorghum_nitrogen_use_efficiency` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `sorghum_nitrogen_use_efficiency` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `sorghum_nitrogen_use_efficiency`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(12) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `sorghum_phosphate_stress` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `sorghum_phosphate_stress` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `sorghum_phosphate_stress`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(32) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `sorghum_plasma` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `sorghum_plasma` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `sorghum_plasma`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(16) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `sorghum_saline_alkali_stress` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `sorghum_saline_alkali_stress` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `sorghum_saline_alkali_stress`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(16) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(32) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `sorghum_stress` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `sorghum_stress` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `sorghum_stress`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(16) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(12) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `sorghum_strigolactone_variation` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `sorghum_strigolactone_variation` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `sorghum_strigolactone_variation`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(16) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(32) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `sorghum_sulfur_stress` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `sorghum_sulfur_stress` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `sorghum_sulfur_stress`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(32) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `sorghum_temperature_stress` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `sorghum_temperature_stress` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `sorghum_temperature_stress`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(16) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(32) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `sorghum_vascularization_and_internode` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `sorghum_vascularization_and_internode` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `sorghum_vascularization_and_internode`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(32) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `soybean` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `soybean` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `soybean`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int NOT NULL, + `proj_id` varchar(15) NOT NULL, + `sample_file_name` tinytext NOT NULL, + `data_probeset_id` varchar(36) NOT NULL, + `data_signal` float NOT NULL, + `data_call` tinytext NOT NULL, + `data_p_val` float NOT NULL, + `data_bot_id` varchar(22) NOT NULL, + PRIMARY KEY (`sample_id`,`proj_id`,`data_probeset_id`(15)), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `soybean_annotations_lookup` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `soybean_annotations_lookup` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `soybean_annotations_lookup`; + +-- +-- Table structure for table `gene_probeset_lookup` +-- + +DROP TABLE IF EXISTS `gene_probeset_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gene_probeset_lookup` ( + `gene` varchar(100) NOT NULL, + `probeset` varchar(100) NOT NULL, + `date` date NOT NULL, + KEY `gene_probeset` (`gene`,`probeset`), + KEY `probeset_gene` (`probeset`,`gene`), + KEY `date` (`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `gmax_annotation` +-- + +DROP TABLE IF EXISTS `gmax_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `gmax_annotation` ( + `gmax` varchar(30) NOT NULL, + `annotation` longtext NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`gmax`,`date`), + KEY `date` (`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `soybean_embryonic_development` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `soybean_embryonic_development` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `soybean_embryonic_development`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(42) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `soybean_heart_cotyledon_globular` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `soybean_heart_cotyledon_globular` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `soybean_heart_cotyledon_globular`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(42) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `soybean_nssnp` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `soybean_nssnp` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `soybean_nssnp`; + +-- +-- Table structure for table `protein_reference` +-- + +DROP TABLE IF EXISTS `protein_reference`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `protein_reference` ( + `protein_reference_id` int NOT NULL AUTO_INCREMENT, + `gene_name` varchar(45) DEFAULT NULL, + `gene_identifier` varchar(45) NOT NULL, + PRIMARY KEY (`protein_reference_id`), + KEY `protein_gene_id_idx` (`gene_identifier`) +) ENGINE=InnoDB AUTO_INCREMENT=88178 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_lookup` +-- + +DROP TABLE IF EXISTS `sample_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_lookup` ( + `sample_id` varchar(45) NOT NULL, + `dataset` varchar(45) DEFAULT NULL, + `dataset_sample` varchar(45) DEFAULT NULL, + PRIMARY KEY (`sample_id`), + CONSTRAINT `sample_id` FOREIGN KEY (`sample_id`) REFERENCES `snps_reference` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `soybean_senescence` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `soybean_senescence` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `soybean_senescence`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(8) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `soybean_severin` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `soybean_severin` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `soybean_severin`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int NOT NULL, + `proj_id` varchar(15) NOT NULL, + `sample_file_name` tinytext NOT NULL, + `data_probeset_id` varchar(18) NOT NULL, + `data_signal` float NOT NULL, + `data_call` tinytext NOT NULL, + `data_p_val` float NOT NULL, + `data_bot_id` varchar(18) NOT NULL, + PRIMARY KEY (`sample_id`,`proj_id`,`data_probeset_id`(15)), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `spruce` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `spruce` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `spruce`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(16) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(24) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `strawberry` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `strawberry` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `strawberry`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(16) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(24) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `strawberry_annotations_lookup` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `strawberry_annotations_lookup` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `strawberry_annotations_lookup`; + +-- +-- Table structure for table `strawberry_lookup` +-- + +DROP TABLE IF EXISTS `strawberry_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `strawberry_lookup` ( + `v4_0_a1` varchar(24) NOT NULL, + `v2_0_a2` varchar(24) NOT NULL, + `date` date NOT NULL, + KEY `v4` (`v4_0_a1`), + KEY `v2` (`v2_0_a2`), + KEY `date` (`date`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `striga` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `striga` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `striga`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(42) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `striga_annotations_lookup` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `striga_annotations_lookup` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `striga_annotations_lookup`; + +-- +-- Table structure for table `striga_lookup` +-- + +DROP TABLE IF EXISTS `striga_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `striga_lookup` ( + `striga` varchar(24) NOT NULL, + `arabidopsis` varchar(16) NOT NULL, + `date` date NOT NULL, + KEY `striga` (`striga`), + KEY `arabidopsis` (`arabidopsis`), + KEY `date` (`date`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `string` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `string` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `string`; + +-- +-- Table structure for table `actions_sets` +-- + +DROP TABLE IF EXISTS `actions_sets`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `actions_sets` ( + `item_id_a` int NOT NULL, + `item_id_b` int NOT NULL, + `mode` varchar(16) NOT NULL, + `source` varchar(1024) NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `fusion_evidence` +-- + +DROP TABLE IF EXISTS `fusion_evidence`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `fusion_evidence` ( + `target_protein_id_a` int NOT NULL, + `target_protein_id_b` int NOT NULL, + `source_protein` int NOT NULL, + `source_species` int NOT NULL, + `transfer_score_c1` int NOT NULL, + `transfer_score_c2` int NOT NULL, + `fusion_score` int NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sets` +-- + +DROP TABLE IF EXISTS `sets`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sets` ( + `set_id` varchar(32) NOT NULL, + `collection_id` varchar(16) NOT NULL, + `title` varchar(256) NOT NULL, + `comment` varchar(512) NOT NULL, + `url` varchar(256) NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sets_items` +-- + +DROP TABLE IF EXISTS `sets_items`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sets_items` ( + `set_id` varchar(32) NOT NULL, + `item_id` int NOT NULL, + `species_id` int NOT NULL, + `preferred_name` varchar(16) NOT NULL, + `set_type` varchar(8) NOT NULL, + KEY `mike_idx` (`item_id`,`preferred_name`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sets_pubmedrefs` +-- + +DROP TABLE IF EXISTS `sets_pubmedrefs`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sets_pubmedrefs` ( + `set_id` varchar(32) NOT NULL, + `pubmed_id` int NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `sugarcane_culms` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `sugarcane_culms` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `sugarcane_culms`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(5) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(32) NOT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_bot_id` varchar(16) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `sugarcane_leaf` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `sugarcane_leaf` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `sugarcane_leaf`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(12) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(32) NOT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_bot_id` varchar(32) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `summarization` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `summarization` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `summarization`; + +-- +-- Table structure for table `00efbabb92f34e97a082f2d831bf4ca7` +-- + +DROP TABLE IF EXISTS `00efbabb92f34e97a082f2d831bf4ca7`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `00efbabb92f34e97a082f2d831bf4ca7` ( + `index` bigint DEFAULT NULL, + `data_probeset_id` text, + `data_bot_id` text, + `data_signal` double DEFAULT NULL, + KEY `ix_00efbabb92f34e97a082f2d831bf4ca7_index` (`index`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `3048d74091294927a11bee8cd6bd458d` +-- + +DROP TABLE IF EXISTS `3048d74091294927a11bee8cd6bd458d`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `3048d74091294927a11bee8cd6bd458d` ( + `index` bigint DEFAULT NULL, + `Gene` text, + `Sample` text, + `Value` double DEFAULT NULL, + KEY `ix_3048d74091294927a11bee8cd6bd458d_index` (`index`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `3430dfa7e07c4f51abae06e37fc6ba44` +-- + +DROP TABLE IF EXISTS `3430dfa7e07c4f51abae06e37fc6ba44`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; 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COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `cc36786116eb4f83a5c3cb69adfcfcd2` +-- + +DROP TABLE IF EXISTS `cc36786116eb4f83a5c3cb69adfcfcd2`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `cc36786116eb4f83a5c3cb69adfcfcd2` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int NOT NULL, + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(32) NOT NULL, + PRIMARY KEY (`data_probeset_id`,`data_signal`,`data_bot_id`), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `e033b2ad89464e21aec70d4817b72d09` +-- + +DROP TABLE IF EXISTS `e033b2ad89464e21aec70d4817b72d09`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `e033b2ad89464e21aec70d4817b72d09` ( + `index` varchar(42) DEFAULT NULL, + `Gene` varchar(32) DEFAULT NULL, + `Sample` varchar(32) DEFAULT NULL, + `Value` float DEFAULT NULL, + KEY `ix_e033b2ad89464e21aec70d4817b72d09_index` (`index`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `requests` +-- + +DROP TABLE IF EXISTS `requests`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `requests` ( + `first_name` text, + `last_name` text, + `email` text, + `notes` text +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `users` +-- + +DROP TABLE IF EXISTS `users`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `users` ( + `first_name` varchar(32) DEFAULT NULL, + `last_name` varchar(32) DEFAULT NULL, + `email` varchar(120) DEFAULT NULL, + `telephone` varchar(12) DEFAULT NULL, + `contact_type` varchar(5) DEFAULT NULL, + `api_key` varchar(120) NOT NULL, + `status` varchar(32) DEFAULT NULL, + `date_added` date NOT NULL, + `uses_left` int DEFAULT NULL, + PRIMARY KEY (`api_key`), + UNIQUE KEY `ix_users_email` (`email`), + KEY `ix_users_status` (`status`), + KEY `ix_users_last_name` (`last_name`), + KEY `ix_users_uses_left` (`uses_left`), + KEY `ix_users_first_name` (`first_name`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `sunflower` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `sunflower` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `sunflower`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(5) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(16) NOT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_bot_id` varchar(16) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `thellungiella_annotations_lookup` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `thellungiella_annotations_lookup` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `thellungiella_annotations_lookup`; + +-- +-- Table structure for table `test` +-- + +DROP TABLE IF EXISTS `test`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `test` ( + `thellungiella_gene` varchar(40) NOT NULL, + `arabidopsis_gene` varchar(30) NOT NULL, + `date` date NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `tsa_arabidopsis_lookup` +-- + +DROP TABLE IF EXISTS `tsa_arabidopsis_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `tsa_arabidopsis_lookup` ( + `thellungiella_gene` varchar(40) NOT NULL, + `arabidopsis_gene` varchar(30) NOT NULL, + `date` date NOT NULL, + KEY `date` (`date`), + KEY `at_gene` (`thellungiella_gene`,`arabidopsis_gene`,`date`), + KEY `gene_at` (`arabidopsis_gene`,`thellungiella_gene`,`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `thellungiella_db` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `thellungiella_db` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `thellungiella_db`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` varchar(30) NOT NULL, + `proj_id` varchar(30) NOT NULL, + `sample_file_name` varchar(80) DEFAULT NULL, + `data_probeset_id` varchar(40) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(40) NOT NULL, + PRIMARY KEY (`sample_id`,`proj_id`,`data_probeset_id`), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `tomato` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `tomato` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `tomato`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(18) DEFAULT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(18) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `tomato_annotations_lookup` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `tomato_annotations_lookup` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `tomato_annotations_lookup`; + +-- +-- Table structure for table `454_Illumina_lookup` +-- + +DROP TABLE IF EXISTS `454_Illumina_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `454_Illumina_lookup` ( + `454_id` varchar(60) NOT NULL, + `Illumina_id` varchar(60) NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`454_id`,`Illumina_id`,`date`), + KEY `data` (`date`), + KEY `illumina` (`Illumina_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `tomato_annotations` +-- + +DROP TABLE IF EXISTS `tomato_annotations`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `tomato_annotations` ( + `gene` varchar(60) NOT NULL, + `annotation` longtext NOT NULL, + `date` date NOT NULL, + KEY `data` (`date`), + KEY `gene_date` (`gene`,`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `trait_gene_lookup` +-- + +DROP TABLE IF EXISTS `trait_gene_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `trait_gene_lookup` ( + `data_probeset_id` varchar(100) NOT NULL, + `gene` varchar(50) NOT NULL, + `date` date NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `trait_info` +-- + +DROP TABLE IF EXISTS `trait_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `trait_info` ( + `exper` varchar(40) NOT NULL, + `trait` varchar(30) NOT NULL, + `desc` varchar(100) NOT NULL, + `units` varchar(40) NOT NULL, + KEY `desc` (`desc`,`units`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `tomato_ils` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `tomato_ils` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `tomato_ils`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(20) DEFAULT NULL, + `data_signal` float DEFAULT '0', + `data_p_value` float DEFAULT '0', + `data_bot_id` varchar(12) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `tomato_ils2` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `tomato_ils2` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `tomato_ils2`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(20) DEFAULT NULL, + `data_signal` float DEFAULT '0', + `data_p_value` float DEFAULT '0', + `data_bot_id` varchar(12) DEFAULT NULL, + `log` float NOT NULL, + `p_val` float NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `tomato_ils3` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `tomato_ils3` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `tomato_ils3`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(20) DEFAULT NULL, + `data_signal` float DEFAULT '0', + `data_p_value` float DEFAULT '0', + `data_bot_id` varchar(16) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `tomato_meristem` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `tomato_meristem` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `tomato_meristem`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(2) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(18) DEFAULT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(24) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `tomato_nssnp` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `tomato_nssnp` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `tomato_nssnp`; + +-- +-- Table structure for table `lines_lookup` +-- + +DROP TABLE IF EXISTS `lines_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `lines_lookup` ( + `lines_id` varchar(45) NOT NULL, + `species` varchar(35) DEFAULT NULL, + `alias` varchar(35) DEFAULT NULL, + PRIMARY KEY (`lines_id`), + CONSTRAINT `lines_id` FOREIGN KEY (`lines_id`) REFERENCES `snps_reference` (`sample_id`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `protein_reference` +-- + +DROP TABLE IF EXISTS `protein_reference`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `protein_reference` ( + `protein_reference_id` int NOT NULL AUTO_INCREMENT, + `gene_identifier` varchar(45) NOT NULL, + `gene_name` varchar(45) DEFAULT NULL, + PRIMARY KEY (`protein_reference_id`), + UNIQUE KEY `gene_identifier_UNIQUE` (`gene_identifier`) +) ENGINE=InnoDB AUTO_INCREMENT=91149 DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `tomato_renormalized` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `tomato_renormalized` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `tomato_renormalized`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(18) DEFAULT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(18) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `tomato_root` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `tomato_root` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `tomato_root`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(2) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(18) DEFAULT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(12) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `tomato_root_field_pot` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `tomato_root_field_pot` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `tomato_root_field_pot`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(2) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(18) DEFAULT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(12) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `tomato_s_pennellii` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `tomato_s_pennellii` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `tomato_s_pennellii`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(20) DEFAULT NULL, + `data_signal` float DEFAULT '0', + `data_p_value` float DEFAULT '0', + `data_bot_id` varchar(24) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `tomato_seed` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `tomato_seed` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `tomato_seed`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(24) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(16) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `tomato_sequence` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `tomato_sequence` /*!40100 DEFAULT CHARACTER SET utf8mb3 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `tomato_sequence`; + +-- +-- Table structure for table `tomato_3_2_sequence_info` +-- + +DROP TABLE IF EXISTS `tomato_3_2_sequence_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `tomato_3_2_sequence_info` ( + `gene_id` varchar(20) NOT NULL, + `full_seq` varchar(9999) DEFAULT NULL, + `full_seq_len` int DEFAULT NULL, + `phyre2_seq` varchar(9999) DEFAULT NULL, + `phyre2_seq_start` int DEFAULT NULL, + `phyre2_seq_end` int DEFAULT NULL, + PRIMARY KEY (`gene_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `tomato_shade_mutants` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `tomato_shade_mutants` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `tomato_shade_mutants`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(16) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(20) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `tomato_shade_timecourse` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `tomato_shade_timecourse` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `tomato_shade_timecourse`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(16) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(16) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `tomato_trait` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `tomato_trait` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `tomato_trait`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(30) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(100) NOT NULL, + `data_signal` float DEFAULT NULL, + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` tinytext NOT NULL, + `qvalue` float DEFAULT NULL, + KEY `sample_id` (`sample_id`,`proj_id`,`data_probeset_id`), + KEY `data_probeset_id` (`data_probeset_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `triphysaria` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `triphysaria` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `triphysaria`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(5) NOT NULL, + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(16) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(32) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `triphysaria_annotations_lookup` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `triphysaria_annotations_lookup` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `triphysaria_annotations_lookup`; + +-- +-- Table structure for table `triphysaria_lookup` +-- + +DROP TABLE IF EXISTS `triphysaria_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `triphysaria_lookup` ( + `triphysaria` varchar(24) NOT NULL, + `arabidopsis` varchar(16) NOT NULL, + `date` date NOT NULL, + KEY `triphysaria` (`triphysaria`), + KEY `arabidopsis` (`arabidopsis`), + KEY `date` (`date`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `triticale` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `triticale` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `triticale`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(30) NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(18) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `triticale_annotations_lookup` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `triticale_annotations_lookup` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `triticale_annotations_lookup`; + +-- +-- Table structure for table `triticale_annotation` +-- + +DROP TABLE IF EXISTS `triticale_annotation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `triticale_annotation` ( + `gene` varchar(60) NOT NULL, + `annotation` longtext NOT NULL, + `date` date NOT NULL, + PRIMARY KEY (`gene`), + KEY `date` (`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `triticale_lookup` +-- + +DROP TABLE IF EXISTS `triticale_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `triticale_lookup` ( + `gene` varchar(60) NOT NULL, + `probeset` varchar(60) NOT NULL, + `date` date NOT NULL, + KEY `gene` (`gene`), + KEY `probeset` (`probeset`), + KEY `date` (`date`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `triticale_mas` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `triticale_mas` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `triticale_mas`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_file_name` tinytext, + `data_probeset_id` varchar(30) NOT NULL, + `data_signal` float DEFAULT '0', + `data_call` tinytext, + `data_p_val` float DEFAULT '0', + `data_bot_id` varchar(30) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `tung_tree` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `tung_tree` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `tung_tree`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `sample_id` int unsigned NOT NULL DEFAULT '0', + `proj_id` varchar(5) NOT NULL DEFAULT '0', + `data_probeset_id` varchar(16) NOT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_bot_id` varchar(16) DEFAULT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `wheat` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `wheat` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `wheat`; + +-- +-- Table structure for table `homeologs` +-- + +DROP TABLE IF EXISTS `homeologs`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `homeologs` ( + `group_id` int unsigned NOT NULL, + `cardinality_abs` varchar(8) NOT NULL, + `A` varchar(1280) DEFAULT NULL, + `B` varchar(1024) DEFAULT NULL, + `D` varchar(512) DEFAULT NULL, + PRIMARY KEY (`group_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `homeologues_lookup` +-- + +DROP TABLE IF EXISTS `homeologues_lookup`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `homeologues_lookup` ( + `gene_id` varchar(24) NOT NULL, + `homeologues` varchar(2400) NOT NULL, + KEY `gene_idx` (`gene_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(32) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(16) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `wheat_abiotic_stress` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `wheat_abiotic_stress` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `wheat_abiotic_stress`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(32) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(16) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `wheat_embryogenesis` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `wheat_embryogenesis` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `wheat_embryogenesis`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(32) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(50) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `wheat_meiosis` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `wheat_meiosis` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `wheat_meiosis`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(32) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(24) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `wheat_root` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `wheat_root` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `wheat_root`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(15) NOT NULL DEFAULT '0', + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(32) NOT NULL, + `data_signal` float DEFAULT '0', + `data_bot_id` varchar(16) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `willow` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `willow` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `willow`; + +-- +-- Table structure for table `sample_data` +-- + +DROP TABLE IF EXISTS `sample_data`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `sample_data` ( + `proj_id` varchar(2) NOT NULL DEFAULT '0', + `sample_id` int unsigned NOT NULL DEFAULT '0', + `data_probeset_id` varchar(32) NOT NULL, + `data_signal` float NOT NULL, + `data_bot_id` varchar(16) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Current Database: `3ddi_wiki` +-- + +USE `3ddi_wiki`; + +-- +-- Current Database: `AnnoJ` +-- + +USE `AnnoJ`; + +-- +-- Current Database: `BAR_Search` +-- + +USE `BAR_Search`; + +-- +-- Current Database: `CDD3D` +-- + +USE `CDD3D`; + +-- +-- Current Database: `NASCArrays` +-- + +USE `NASCArrays`; + +-- +-- Current Database: `NGM` +-- + +USE `NGM`; + +-- +-- Current Database: `TRTCFungarium` +-- + +USE `TRTCFungarium`; + +-- +-- Current Database: `actinidia_bud_development` +-- + +USE `actinidia_bud_development`; + +-- +-- Current Database: `actinidia_flower_fruit_development` +-- + +USE `actinidia_flower_fruit_development`; + +-- +-- Current Database: `actinidia_postharvest` +-- + +USE `actinidia_postharvest`; + +-- +-- Current Database: `actinidia_vegetative_growth` +-- + +USE `actinidia_vegetative_growth`; + +-- +-- Current Database: `affydb` +-- + +USE `affydb`; + +-- +-- Current Database: `annotations_lookup` +-- + +USE `annotations_lookup`; + +-- +-- Current Database: `apple` +-- + +USE `apple`; + +-- +-- Current Database: `arabidopsis_ecotypes` +-- + +USE `arabidopsis_ecotypes`; + +-- +-- Current Database: `arabidopsis_proteomics` +-- + +USE `arabidopsis_proteomics`; + +-- +-- Current Database: `arabidopsis_transcriptomics` +-- + +USE `arabidopsis_transcriptomics`; + +-- +-- Current Database: `arachis` +-- + +USE `arachis`; + +-- +-- Current Database: `atgenexp` +-- + +USE `atgenexp`; + +-- +-- Current Database: `atgenexp_hormone` +-- + +USE `atgenexp_hormone`; + +-- +-- Current Database: `atgenexp_pathogen` +-- + +USE `atgenexp_pathogen`; + +-- +-- Current Database: `atgenexp_plus` +-- + +USE `atgenexp_plus`; + +-- +-- Current Database: `atgenexp_stress` +-- + +USE `atgenexp_stress`; + +-- +-- Current Database: `bar_api_db_api_test` +-- + +USE `bar_api_db_api_test`; + +-- +-- Current Database: `barley_annotations_lookup` +-- + +USE `barley_annotations_lookup`; + +-- +-- Current Database: `barley_mas` +-- + +USE `barley_mas`; + +-- +-- Current Database: `barley_rma` +-- + +USE `barley_rma`; + +-- +-- Current Database: `barley_seed` +-- + +USE `barley_seed`; + +-- +-- Current Database: `barley_spike_meristem` +-- + +USE `barley_spike_meristem`; + +-- +-- Current Database: `barley_spike_meristem_v3` +-- + +USE `barley_spike_meristem_v3`; + +-- +-- Current Database: `bayer_canola_expressolog` +-- + +USE `bayer_canola_expressolog`; + +-- +-- Current Database: `brachypodium` +-- + +USE `brachypodium`; + +-- +-- Current Database: `brachypodium_Bd21` +-- + +USE `brachypodium_Bd21`; + +-- +-- Current Database: `brachypodium_embryogenesis` +-- + +USE `brachypodium_embryogenesis`; + +-- +-- Current Database: `brachypodium_grains` +-- + +USE `brachypodium_grains`; + +-- +-- Current Database: `brachypodium_metabolites_map` +-- + +USE `brachypodium_metabolites_map`; + +-- +-- Current Database: `brachypodium_photo_thermocycle` +-- + +USE `brachypodium_photo_thermocycle`; + +-- +-- Current Database: `brassica_rapa` +-- + +USE `brassica_rapa`; + +-- +-- Current Database: `cacao_developmental_atlas` +-- + +USE `cacao_developmental_atlas`; + +-- +-- Current Database: `cacao_developmental_atlas_sca` +-- + +USE `cacao_developmental_atlas_sca`; + +-- +-- Current Database: `cacao_drought_diurnal_atlas` +-- + +USE `cacao_drought_diurnal_atlas`; + +-- +-- Current Database: `cacao_drought_diurnal_atlas_sca` +-- + +USE `cacao_drought_diurnal_atlas_sca`; + +-- +-- Current Database: `cacao_infection` +-- + +USE `cacao_infection`; + +-- +-- Current Database: `cacao_leaf` +-- + +USE `cacao_leaf`; + +-- +-- Current Database: `cacao_meristem_atlas_sca` +-- + +USE `cacao_meristem_atlas_sca`; + +-- +-- Current Database: `cacao_seed_atlas_sca` +-- + +USE `cacao_seed_atlas_sca`; + +-- +-- Current Database: `camelina` +-- + +USE `camelina`; + +-- +-- Current Database: `camelina_annotations_lookup` +-- + +USE `camelina_annotations_lookup`; + +-- +-- Current Database: `camelina_tpm` +-- + +USE `camelina_tpm`; + +-- +-- Current Database: `cannabis` +-- + +USE `cannabis`; + +-- +-- Current Database: `canola` +-- + +USE `canola`; + +-- +-- Current Database: `canola_annotations_lookup` +-- + +USE `canola_annotations_lookup`; + +-- +-- Current Database: `canola_nssnp` +-- + +USE `canola_nssnp`; + +-- +-- Current Database: `canola_original` +-- + +USE `canola_original`; + +-- +-- Current Database: `canola_original_v2` +-- + +USE `canola_original_v2`; + +-- +-- Current Database: `canola_seed` +-- + +USE `canola_seed`; + +-- +-- Current Database: `cassava_atlas` +-- + +USE `cassava_atlas`; + +-- +-- Current Database: `cassava_cbb` +-- + +USE `cassava_cbb`; + +-- +-- Current Database: `cassava_eacmv` +-- + +USE `cassava_eacmv`; + +-- +-- Current Database: `circadian_mutants` +-- + +USE `circadian_mutants`; + +-- +-- Current Database: `cistome` +-- + +USE `cistome`; + +-- +-- Current Database: `cistome_legacy` +-- + +USE `cistome_legacy`; + +-- +-- Current Database: `cort_db` +-- + +USE `cort_db`; + +-- +-- Current Database: `current_mappings` +-- + +USE `current_mappings`; + +-- +-- Current Database: `cuscuta` +-- + +USE `cuscuta`; + +-- +-- Current Database: `cuscuta_early_haustoriogenesis` +-- + +USE `cuscuta_early_haustoriogenesis`; + +-- +-- Current Database: `cuscuta_lmd` +-- + +USE `cuscuta_lmd`; + +-- +-- Current Database: `dna_damage` +-- + +USE `dna_damage`; + +-- +-- Current Database: `docking_db` +-- + +USE `docking_db`; + +-- +-- Current Database: `durum_wheat_abiotic_stress` +-- + +USE `durum_wheat_abiotic_stress`; + +-- +-- Current Database: `durum_wheat_biotic_stress` +-- + +USE `durum_wheat_biotic_stress`; + +-- +-- Current Database: `durum_wheat_development` +-- + +USE `durum_wheat_development`; + +-- +-- Current Database: `efp_seq_browser` +-- + +USE `efp_seq_browser`; + +-- +-- Current Database: `efpexpressiondata` +-- + +USE `efpexpressiondata`; + +-- +-- Current Database: `embryo` +-- + +USE `embryo`; + +-- +-- Current Database: `eplant2` +-- + +USE `eplant2`; + +-- +-- Current Database: `eplant_barley` +-- + +USE `eplant_barley`; + +-- +-- Current Database: `eplant_barley_legacy` +-- + +USE `eplant_barley_legacy`; + +-- +-- Current Database: `eplant_camelina` +-- + +USE `eplant_camelina`; + +-- +-- Current Database: `eplant_cassava` +-- + +USE `eplant_cassava`; + +-- +-- Current Database: `eplant_eucalyptus` +-- + +USE `eplant_eucalyptus`; + +-- +-- Current Database: `eplant_maize` +-- + +USE `eplant_maize`; + +-- +-- Current Database: `eplant_medicago` +-- + +USE `eplant_medicago`; + +-- +-- Current Database: `eplant_poplar` +-- + +USE `eplant_poplar`; + +-- +-- Current Database: `eplant_potato` +-- + +USE `eplant_potato`; + +-- +-- Current Database: `eplant_rice` +-- + +USE `eplant_rice`; + +-- +-- Current Database: `eplant_soybean` +-- + +USE `eplant_soybean`; + +-- +-- Current Database: `eplant_spruce` +-- + +USE `eplant_spruce`; + +-- +-- Current Database: `eplant_sugarcane` +-- + +USE `eplant_sugarcane`; + +-- +-- Current Database: `eplant_sunflower` +-- + +USE `eplant_sunflower`; + +-- +-- Current Database: `eplant_tomato` +-- + +USE `eplant_tomato`; + +-- +-- Current Database: `eplant_wheat` +-- + +USE `eplant_wheat`; + +-- +-- Current Database: `eplant_willow` +-- + +USE `eplant_willow`; + +-- +-- Current Database: `eucalyptus` +-- + +USE `eucalyptus`; + +-- +-- Current Database: `euphorbia` +-- + +USE `euphorbia`; + +-- +-- Current Database: `expression_max_test` +-- + +USE `expression_max_test`; + +-- +-- Current Database: `fastpheno` +-- + +USE `fastpheno`; + +-- +-- Current Database: `fastpheno2_draft` +-- + +USE `fastpheno2_draft`; + +-- +-- Current Database: `fastpheno_draft` +-- + +USE `fastpheno_draft`; + +-- +-- Current Database: `gAccounts` +-- + +USE `gAccounts`; + +-- +-- Current Database: `gaia` +-- + +USE `gaia`; + +-- +-- Current Database: `gc_drought` +-- + +USE `gc_drought`; + +-- +-- Current Database: `geneslider` +-- + +USE `geneslider`; + +-- +-- Current Database: `germination` +-- + +USE `germination`; + +-- +-- Current Database: `grape_annotations_lookup` +-- + +USE `grape_annotations_lookup`; + +-- +-- Current Database: `grape_developmental` +-- + +USE `grape_developmental`; + +-- +-- Current Database: `guard_cell` +-- + +USE `guard_cell`; + +-- +-- Current Database: `gynoecium` +-- + +USE `gynoecium`; + +-- +-- Current Database: `heterodera_schachtii` +-- + +USE `heterodera_schachtii`; + +-- +-- Current Database: `hnahal` +-- + +USE `hnahal`; + +-- +-- Current Database: `hnahal_temp` +-- + +USE `hnahal_temp`; + +-- +-- Current Database: `homologs_db` +-- + +USE `homologs_db`; + +-- +-- Current Database: `human_annotations_lookup` +-- + +USE `human_annotations_lookup`; + +-- +-- Current Database: `human_body_map_2` +-- + +USE `human_body_map_2`; + +-- +-- Current Database: `human_developmental` +-- + +USE `human_developmental`; + +-- +-- Current Database: `human_developmental_SpongeLab` +-- + +USE `human_developmental_SpongeLab`; + +-- +-- Current Database: `human_diseased` +-- + +USE `human_diseased`; + +-- +-- Current Database: `interactions` +-- + +USE `interactions`; + +-- +-- Current Database: `interactions_dapseq` +-- + +USE `interactions_dapseq`; + +-- +-- Current Database: `interactions_eddi` +-- + +USE `interactions_eddi`; + +-- +-- Current Database: `interactions_grn_dev_db` +-- + +USE `interactions_grn_dev_db`; + +-- +-- Current Database: `interactions_vincent` +-- + +USE `interactions_vincent`; + +-- +-- Current Database: `interactions_vincent_v2` +-- + +USE `interactions_vincent_v2`; + +-- +-- Current Database: `kalanchoe` +-- + +USE `kalanchoe`; + +-- +-- Current Database: `kalanchoe_time_course_analysis` +-- + +USE `kalanchoe_time_course_analysis`; + +-- +-- Current Database: `klepikova` +-- + +USE `klepikova`; + +-- +-- Current Database: `lateral_root_initiation` +-- + +USE `lateral_root_initiation`; + +-- +-- Current Database: `light_series` +-- + +USE `light_series`; + +-- +-- Current Database: `lipid_map` +-- + +USE `lipid_map`; + +-- +-- Current Database: `little_millet` +-- + +USE `little_millet`; + +-- +-- Current Database: `llama3` +-- + +USE `llama3`; + +-- +-- Current Database: `localisations` +-- + +USE `localisations`; + +-- +-- Current Database: `lupin_lcm_leaf` +-- + +USE `lupin_lcm_leaf`; + +-- +-- Current Database: `lupin_lcm_pod` +-- + +USE `lupin_lcm_pod`; + +-- +-- Current Database: `lupin_lcm_stem` +-- + +USE `lupin_lcm_stem`; + +-- +-- Current Database: `lupin_pod_seed` +-- + +USE `lupin_pod_seed`; + +-- +-- Current Database: `lupin_whole_plant` +-- + +USE `lupin_whole_plant`; + +-- +-- Current Database: `maize_RMA_linear` +-- + +USE `maize_RMA_linear`; + +-- +-- Current Database: `maize_RMA_log` +-- + +USE `maize_RMA_log`; + +-- +-- Current Database: `maize_annotations` +-- + +USE `maize_annotations`; + +-- +-- Current Database: `maize_atlas` +-- + +USE `maize_atlas`; + +-- +-- Current Database: `maize_atlas_v5` +-- + +USE `maize_atlas_v5`; + +-- +-- Current Database: `maize_buell_lab` +-- + +USE `maize_buell_lab`; + +-- +-- Current Database: `maize_early_seed` +-- + +USE `maize_early_seed`; + +-- +-- Current Database: `maize_ears` +-- + +USE `maize_ears`; + +-- +-- Current Database: `maize_embryonic_leaf_development` +-- + +USE `maize_embryonic_leaf_development`; + +-- +-- Current Database: `maize_enzyme` +-- + +USE `maize_enzyme`; + +-- +-- Current Database: `maize_gdowns` +-- + +USE `maize_gdowns`; + +-- +-- Current Database: `maize_gdowns_annotations_lookup` +-- + +USE `maize_gdowns_annotations_lookup`; + +-- +-- Current Database: `maize_interactions` +-- + +USE `maize_interactions`; + +-- +-- Current Database: `maize_interactions_v5` +-- + +USE `maize_interactions_v5`; + +-- +-- Current Database: `maize_iplant` +-- + +USE `maize_iplant`; + +-- +-- Current Database: `maize_kernel_v5` +-- + +USE `maize_kernel_v5`; + +-- +-- Current Database: `maize_leaf_gradient` +-- + +USE `maize_leaf_gradient`; + +-- +-- Current Database: `maize_lipid_map` +-- + +USE `maize_lipid_map`; + +-- +-- Current Database: `maize_metabolite` +-- + +USE `maize_metabolite`; + +-- +-- Current Database: `maize_nitrogen_use_efficiency` +-- + +USE `maize_nitrogen_use_efficiency`; + +-- +-- Current Database: `maize_rice_comparison` +-- + +USE `maize_rice_comparison`; + +-- +-- Current Database: `maize_root` +-- + +USE `maize_root`; + +-- +-- Current Database: `maize_stress_v5` +-- + +USE `maize_stress_v5`; + +-- +-- Current Database: `mangosteen_annotations_lookup` +-- + +USE `mangosteen_annotations_lookup`; + +-- +-- Current Database: `mangosteen_aril_vs_rind` +-- + +USE `mangosteen_aril_vs_rind`; + +-- +-- Current Database: `mangosteen_callus` +-- + +USE `mangosteen_callus`; + +-- +-- Current Database: `mangosteen_diseased_vs_normal` +-- + +USE `mangosteen_diseased_vs_normal`; + +-- +-- Current Database: `mangosteen_fruit_ripening` +-- + +USE `mangosteen_fruit_ripening`; + +-- +-- Current Database: `mangosteen_seed_development` +-- + +USE `mangosteen_seed_development`; + +-- +-- Current Database: `mangosteen_seed_development_germination` +-- + +USE `mangosteen_seed_development_germination`; + +-- +-- Current Database: `mangosteen_seed_germination` +-- + +USE `mangosteen_seed_germination`; + +-- +-- Current Database: `marchantia_organ_stress` +-- + +USE `marchantia_organ_stress`; + +-- +-- Current Database: `markergen` +-- + +USE `markergen`; + +-- +-- Final view structure for view `test` +-- + +/*!50001 DROP VIEW IF EXISTS `test`*/; +/*!50001 SET @saved_cs_client = @@character_set_client */; +/*!50001 SET @saved_cs_results = @@character_set_results */; +/*!50001 SET @saved_col_connection = @@collation_connection */; +/*!50001 SET character_set_client = utf8mb3 */; +/*!50001 SET character_set_results = utf8mb3 */; +/*!50001 SET collation_connection = utf8mb3_general_ci */; +/*!50001 CREATE ALGORITHM=UNDEFINED */ +/*!50013 DEFINER=`root`@`localhost` SQL SECURITY DEFINER */ +/*!50001 VIEW `test` AS select `gene`.`name` AS `name`,`pl`.`product_id` AS `product_id`,count(0) AS `count` from (((`polymorphism` `pl` join `pcr`) join `gene`) join `difference` `d`) where ((`gene`.`id` = `pcr`.`gene_id`) and (`gene`.`name` <> 'N/A') and (`pcr`.`dataset_id` = 1) and (`pcr`.`product_id` = `pl`.`product_id`) and (`pl`.`difference_id` = `d`.`id`) and (`d`.`pattern` <> ' ')) group by `gene`.`name`,`pl`.`product_id` */; +/*!50001 SET character_set_client = @saved_cs_client */; +/*!50001 SET character_set_results = @saved_cs_results */; +/*!50001 SET collation_connection = @saved_col_connection */; + +-- +-- Final view structure for view `vie_cvi` +-- + +/*!50001 DROP VIEW IF EXISTS `vie_cvi`*/; +/*!50001 SET @saved_cs_client = @@character_set_client */; +/*!50001 SET @saved_cs_results = @@character_set_results */; +/*!50001 SET @saved_col_connection = @@collation_connection */; +/*!50001 SET character_set_client = utf8mb3 */; +/*!50001 SET character_set_results = utf8mb3 */; +/*!50001 SET collation_connection = utf8mb3_general_ci */; +/*!50001 CREATE ALGORITHM=UNDEFINED */ +/*!50013 DEFINER=`root`@`localhost` SQL SECURITY DEFINER */ +/*!50001 VIEW `vie_cvi` AS select `gene`.`name` AS `agi`,`a`.`name` AS `accesion_name`,`d`.`id` AS `difference_id`,`d`.`pattern` AS `difference_pattern`,`pl`.`product_id` AS `product_id` from ((((`polymorphism` `pl` join `pcr`) join `gene`) join `difference` `d`) join `accession` `a`) where ((`gene`.`id` = `pcr`.`gene_id`) and (`gene`.`name` <> 'N/A') and (`pcr`.`dataset_id` = 1) and (`pcr`.`product_id` = `pl`.`product_id`) and (`pl`.`difference_id` = `d`.`id`) and (`pl`.`difference_id` <> 1) and (`d`.`pattern` <> '') and (`a`.`id` = `pl`.`accession_id`)) */; +/*!50001 SET character_set_client = @saved_cs_client */; +/*!50001 SET character_set_results = @saved_cs_results */; +/*!50001 SET collation_connection = @saved_col_connection */; + +-- +-- Final view structure for view `vie_cvi1` +-- + +/*!50001 DROP VIEW IF EXISTS `vie_cvi1`*/; +/*!50001 SET @saved_cs_client = @@character_set_client */; +/*!50001 SET @saved_cs_results = @@character_set_results */; +/*!50001 SET @saved_col_connection = @@collation_connection */; +/*!50001 SET character_set_client = utf8mb3 */; +/*!50001 SET character_set_results = utf8mb3 */; +/*!50001 SET collation_connection = utf8mb3_general_ci */; +/*!50001 CREATE ALGORITHM=UNDEFINED */ +/*!50013 DEFINER=`root`@`localhost` SQL SECURITY DEFINER */ +/*!50001 VIEW `vie_cvi1` AS select `vie_cvi`.`agi` AS `agi`,`vie_cvi`.`accesion_name` AS `accesion_name`,`vie_cvi`.`difference_id` AS `difference_id`,`vie_cvi`.`difference_pattern` AS `difference_pattern`,`vie_cvi`.`product_id` AS `product_id` from `vie_cvi` where (`vie_cvi`.`accesion_name` = 'cvi-0') */; +/*!50001 SET character_set_client = @saved_cs_client */; +/*!50001 SET character_set_results = @saved_cs_results */; +/*!50001 SET collation_connection = @saved_col_connection */; + +-- +-- Final view structure for view `vie_cvi2` +-- + +/*!50001 DROP VIEW IF EXISTS `vie_cvi2`*/; +/*!50001 SET @saved_cs_client = @@character_set_client */; +/*!50001 SET @saved_cs_results = @@character_set_results */; +/*!50001 SET @saved_col_connection = @@collation_connection */; +/*!50001 SET character_set_client = utf8mb3 */; +/*!50001 SET character_set_results = utf8mb3 */; +/*!50001 SET collation_connection = utf8mb3_general_ci */; +/*!50001 CREATE ALGORITHM=UNDEFINED */ +/*!50013 DEFINER=`root`@`localhost` SQL SECURITY DEFINER */ +/*!50001 VIEW `vie_cvi2` AS select `A`.`agi` AS `agi`,`A`.`accesion_name` AS `accesion_name`,`A`.`difference_id` AS `difference_id`,`A`.`difference_pattern` AS `difference_pattern`,`A`.`product_id` AS `product_id` from (`vie_cvi` `A` join `vie_cvi1` `B`) where ((`A`.`agi` = `B`.`agi`) and (`A`.`difference_id` = `B`.`difference_id`) and (`A`.`accesion_name` <> 'cvi-0')) */; +/*!50001 SET character_set_client = @saved_cs_client */; +/*!50001 SET character_set_results = @saved_cs_results */; +/*!50001 SET collation_connection = @saved_col_connection */; + +-- +-- Final view structure for view `vie_cvi3` +-- + +/*!50001 DROP VIEW IF EXISTS `vie_cvi3`*/; +/*!50001 SET @saved_cs_client = @@character_set_client */; +/*!50001 SET @saved_cs_results = @@character_set_results */; +/*!50001 SET @saved_col_connection = @@collation_connection */; +/*!50001 SET character_set_client = utf8mb3 */; +/*!50001 SET character_set_results = utf8mb3 */; +/*!50001 SET collation_connection = utf8mb3_general_ci */; +/*!50001 CREATE ALGORITHM=UNDEFINED */ +/*!50013 DEFINER=`root`@`localhost` SQL SECURITY DEFINER */ +/*!50001 VIEW `vie_cvi3` AS select `A`.`agi` AS `agi`,`A`.`accesion_name` AS `accesion_name`,`A`.`difference_id` AS `difference_id`,`A`.`difference_pattern` AS `difference_pattern`,`A`.`product_id` AS `product_id` from (`vie_cvi` `A` join `vie_cvi1` `B`) where ((`A`.`agi` = `B`.`agi`) and (`A`.`difference_pattern` = `B`.`difference_pattern`)) */; +/*!50001 SET character_set_client = @saved_cs_client */; +/*!50001 SET character_set_results = @saved_cs_results */; +/*!50001 SET collation_connection = @saved_col_connection */; + +-- +-- Final view structure for view `vie_poly` +-- + +/*!50001 DROP VIEW IF EXISTS `vie_poly`*/; +/*!50001 SET @saved_cs_client = @@character_set_client */; +/*!50001 SET @saved_cs_results = @@character_set_results */; +/*!50001 SET @saved_col_connection = @@collation_connection */; +/*!50001 SET character_set_client = utf8mb3 */; +/*!50001 SET character_set_results = utf8mb3 */; +/*!50001 SET collation_connection = utf8mb3_general_ci */; +/*!50001 CREATE ALGORITHM=UNDEFINED */ +/*!50013 DEFINER=`root`@`localhost` SQL SECURITY DEFINER */ +/*!50001 VIEW `vie_poly` AS select `gene`.`name` AS `name`,`pcr`.`forward_id` AS `forward_id`,`primera`.`seq` AS `forward_seq`,`pcr`.`reverse_id` AS `reverse_id`,`primerb`.`seq` AS `reverse_seq`,`pl`.`product_id` AS `product_id`,`product`.`target_seq` AS `target_seq`,`a`.`id` AS `accesion_id`,`a`.`name` AS `accesion_name`,`d`.`id` AS `difference_id`,`d`.`pattern` AS `difference_pattern` from (((((((`polymorphism` `pl` join `pcr`) join `gene`) join `product`) join `difference` `d`) join `accession` `a`) join `primer` `primera`) join `primer` `primerb`) where ((`gene`.`id` = `pcr`.`gene_id`) and (`gene`.`name` <> 'N/A') and (`pcr`.`product_id` = `pl`.`product_id`) and (`pl`.`product_id` = `product`.`id`) and (`d`.`pattern` <> '') and (`pl`.`difference_id` = `d`.`id`) and (`a`.`id` = `pl`.`accession_id`) and (`pcr`.`forward_id` = `primera`.`id`) and (`pcr`.`reverse_id` = `primerb`.`id`)) */; +/*!50001 SET character_set_client = @saved_cs_client */; +/*!50001 SET character_set_results = @saved_cs_results */; +/*!50001 SET collation_connection = @saved_col_connection */; + +-- +-- Final view structure for view `vie_poly1` +-- + +/*!50001 DROP VIEW IF EXISTS `vie_poly1`*/; +/*!50001 SET @saved_cs_client = @@character_set_client */; +/*!50001 SET @saved_cs_results = @@character_set_results */; +/*!50001 SET @saved_col_connection = @@collation_connection */; +/*!50001 SET character_set_client = utf8mb3 */; +/*!50001 SET character_set_results = utf8mb3 */; +/*!50001 SET collation_connection = utf8mb3_general_ci */; +/*!50001 CREATE ALGORITHM=UNDEFINED */ +/*!50013 DEFINER=`root`@`localhost` SQL SECURITY DEFINER */ +/*!50001 VIEW `vie_poly1` AS select `gene`.`name` AS `name`,`pcr`.`forward_id` AS `forward_id`,`primera`.`seq` AS `forward_seq`,`pcr`.`reverse_id` AS `reverse_id`,`primerb`.`seq` AS `reverse_seq`,`pl`.`product_id` AS `product_id`,`product`.`target_seq` AS `target_seq`,`a`.`id` AS `accesion_id`,`a`.`name` AS `accesion_name`,`d`.`id` AS `difference_id`,`d`.`pattern` AS `difference_pattern` from (((((((`polymorphism` `pl` join `pcr`) join `gene`) join `product`) join `difference` `d`) join `accession` `a`) join `primer` `primera`) join `primer` `primerb`) where ((`gene`.`id` = `pcr`.`gene_id`) and (`gene`.`name` <> 'N/A') and (`pcr`.`dataset_id` = 1) and (`pcr`.`product_id` = `pl`.`product_id`) and (`pl`.`product_id` = `product`.`id`) and (`pl`.`difference_id` <> 1) and (`d`.`pattern` <> '') and (`pl`.`difference_id` = `d`.`id`) and (`a`.`id` = `pl`.`accession_id`) and (`pcr`.`forward_id` = `primera`.`id`) and (`pcr`.`reverse_id` = `primerb`.`id`)) */; +/*!50001 SET character_set_client = @saved_cs_client */; +/*!50001 SET character_set_results = @saved_cs_results */; +/*!50001 SET collation_connection = @saved_col_connection */; + +-- +-- Current Database: `markergen_pop` +-- + +USE `markergen_pop`; + +-- +-- Current Database: `markergen_test` +-- + +USE `markergen_test`; + +-- +-- Current Database: `medicago_annotations_lookup` +-- + +USE `medicago_annotations_lookup`; + +-- +-- Current Database: `medicago_mas` +-- + +USE `medicago_mas`; + +-- +-- Current Database: `medicago_rma` +-- + +USE `medicago_rma`; + +-- +-- Current Database: `medicago_root` +-- + +USE `medicago_root`; + +-- +-- Current Database: `medicago_root_v5` +-- + +USE `medicago_root_v5`; + +-- +-- Current Database: `medicago_seed` +-- + +USE `medicago_seed`; + +-- +-- Current Database: `meristem_db` +-- + +USE `meristem_db`; + +-- +-- Current Database: `meristem_db_new` +-- + +USE `meristem_db_new`; + +-- +-- Current Database: `mouse_db` +-- + +USE `mouse_db`; + +-- +-- Current Database: `mysql` +-- + +USE `mysql`; + +-- +-- Current Database: `ngm_nina` +-- + +USE `ngm_nina`; + +-- +-- Current Database: `oat` +-- + +USE `oat`; + +-- +-- Current Database: `ontologies` +-- + +USE `ontologies`; + +-- +-- Current Database: `ortholog_db` +-- + +USE `ortholog_db`; + +-- +-- Current Database: `phelipanche` +-- + +USE `phelipanche`; + +-- +-- Current Database: `phelipanche_annotations_lookup` +-- + +USE `phelipanche_annotations_lookup`; + +-- +-- Current Database: `phpmyadmin` +-- + +USE `phpmyadmin`; + +-- +-- Current Database: `physcomitrella_annotations_lookup` +-- + +USE `physcomitrella_annotations_lookup`; + +-- +-- Current Database: `physcomitrella_db` +-- + +USE `physcomitrella_db`; + +-- +-- Current Database: `poplar` +-- + +USE `poplar`; + +-- +-- Current Database: `poplar_annotations_lookup` +-- + +USE `poplar_annotations_lookup`; + +-- +-- Current Database: `poplar_hormone` +-- + +USE `poplar_hormone`; + +-- +-- Current Database: `poplar_interactions` +-- + +USE `poplar_interactions`; + +-- +-- Current Database: `poplar_leaf` +-- + +USE `poplar_leaf`; + +-- +-- Current Database: `poplar_new_annotations` +-- + +USE `poplar_new_annotations`; + +-- +-- Current Database: `poplar_nssnp` +-- + +USE `poplar_nssnp`; + +-- +-- Current Database: `poplar_xylem` +-- + +USE `poplar_xylem`; + +-- +-- Current Database: `potato_annotations` +-- + +USE `potato_annotations`; + +-- +-- Current Database: `potato_dev` +-- + +USE `potato_dev`; + +-- +-- Current Database: `potato_stress` +-- + +USE `potato_stress`; + +-- +-- Current Database: `potato_wounding` +-- + +USE `potato_wounding`; + +-- +-- Current Database: `prot_model_data` +-- + +USE `prot_model_data`; + +-- +-- Current Database: `rice_abiotic_stress_sc_pseudobulk` +-- + +USE `rice_abiotic_stress_sc_pseudobulk`; + +-- +-- Current Database: `rice_annotations_lookup` +-- + +USE `rice_annotations_lookup`; + +-- +-- Current Database: `rice_drought_heat_stress` +-- + +USE `rice_drought_heat_stress`; + +-- +-- Current Database: `rice_interactions` +-- + +USE `rice_interactions`; + +-- +-- Current Database: `rice_leaf_gradient` +-- + +USE `rice_leaf_gradient`; + +-- +-- Current Database: `rice_maize_comparison` +-- + +USE `rice_maize_comparison`; + +-- +-- Current Database: `rice_mas` +-- + +USE `rice_mas`; + +-- +-- Current Database: `rice_metabolite` +-- + +USE `rice_metabolite`; + +-- +-- Current Database: `rice_rma` +-- + +USE `rice_rma`; + +-- +-- Current Database: `rice_root` +-- + +USE `rice_root`; + +-- +-- Current Database: `rohan` +-- + +USE `rohan`; + +-- +-- Current Database: `root` +-- + +USE `root`; + +-- +-- Current Database: `root_Schaefer_lab` +-- + +USE `root_Schaefer_lab`; + +-- +-- Current Database: `rpatel` +-- + +USE `rpatel`; + +-- +-- Current Database: `rsvp` +-- + +USE `rsvp`; + +-- +-- Current Database: `seed_db` +-- + +USE `seed_db`; + +-- +-- Current Database: `seedcoat` +-- + +USE `seedcoat`; + +-- +-- Current Database: `selaginella` +-- + +USE `selaginella`; + +-- +-- Current Database: `shoot_apex` +-- + +USE `shoot_apex`; + +-- +-- Current Database: `silique` +-- + +USE `silique`; + +-- +-- Current Database: `single_cell` +-- + +USE `single_cell`; + +-- +-- Current Database: `sorghum_atlas_w_BS_cells` +-- + +USE `sorghum_atlas_w_BS_cells`; + +-- +-- Current Database: `sorghum_bundle_sheath` +-- + +USE `sorghum_bundle_sheath`; + +-- +-- Current Database: `sorghum_comparative_transcriptomics` +-- + +USE `sorghum_comparative_transcriptomics`; + +-- +-- Current Database: `sorghum_developmental` +-- + +USE `sorghum_developmental`; + +-- +-- Current Database: `sorghum_developmental_2` +-- + +USE `sorghum_developmental_2`; + +-- +-- Current Database: `sorghum_flowering_activation` +-- + +USE `sorghum_flowering_activation`; + +-- +-- Current Database: `sorghum_low_phosphorus` +-- + +USE `sorghum_low_phosphorus`; + +-- +-- Current Database: `sorghum_nitrogen_stress` +-- + +USE `sorghum_nitrogen_stress`; + +-- +-- Current Database: `sorghum_nitrogen_use_efficiency` +-- + +USE `sorghum_nitrogen_use_efficiency`; + +-- +-- Current Database: `sorghum_phosphate_stress` +-- + +USE `sorghum_phosphate_stress`; + +-- +-- Current Database: `sorghum_plasma` +-- + +USE `sorghum_plasma`; + +-- +-- Current Database: `sorghum_saline_alkali_stress` +-- + +USE `sorghum_saline_alkali_stress`; + +-- +-- Current Database: `sorghum_stress` +-- + +USE `sorghum_stress`; + +-- +-- Current Database: `sorghum_strigolactone_variation` +-- + +USE `sorghum_strigolactone_variation`; + +-- +-- Current Database: `sorghum_sulfur_stress` +-- + +USE `sorghum_sulfur_stress`; + +-- +-- Current Database: `sorghum_temperature_stress` +-- + +USE `sorghum_temperature_stress`; + +-- +-- Current Database: `sorghum_vascularization_and_internode` +-- + +USE `sorghum_vascularization_and_internode`; + +-- +-- Current Database: `soybean` +-- + +USE `soybean`; + +-- +-- Current Database: `soybean_annotations_lookup` +-- + +USE `soybean_annotations_lookup`; + +-- +-- Current Database: `soybean_embryonic_development` +-- + +USE `soybean_embryonic_development`; + +-- +-- Current Database: `soybean_heart_cotyledon_globular` +-- + +USE `soybean_heart_cotyledon_globular`; + +-- +-- Current Database: `soybean_nssnp` +-- + +USE `soybean_nssnp`; + +-- +-- Current Database: `soybean_senescence` +-- + +USE `soybean_senescence`; + +-- +-- Current Database: `soybean_severin` +-- + +USE `soybean_severin`; + +-- +-- Current Database: `spruce` +-- + +USE `spruce`; + +-- +-- Current Database: `strawberry` +-- + +USE `strawberry`; + +-- +-- Current Database: `strawberry_annotations_lookup` +-- + +USE `strawberry_annotations_lookup`; + +-- +-- Current Database: `striga` +-- + +USE `striga`; + +-- +-- Current Database: `striga_annotations_lookup` +-- + +USE `striga_annotations_lookup`; + +-- +-- Current Database: `string` +-- + +USE `string`; + +-- +-- Current Database: `sugarcane_culms` +-- + +USE `sugarcane_culms`; + +-- +-- Current Database: `sugarcane_leaf` +-- + +USE `sugarcane_leaf`; + +-- +-- Current Database: `summarization` +-- + +USE `summarization`; + +-- +-- Current Database: `sunflower` +-- + +USE `sunflower`; + +-- +-- Current Database: `thellungiella_annotations_lookup` +-- + +USE `thellungiella_annotations_lookup`; + +-- +-- Current Database: `thellungiella_db` +-- + +USE `thellungiella_db`; + +-- +-- Current Database: `tomato` +-- + +USE `tomato`; + +-- +-- Current Database: `tomato_annotations_lookup` +-- + +USE `tomato_annotations_lookup`; + +-- +-- Current Database: `tomato_ils` +-- + +USE `tomato_ils`; + +-- +-- Current Database: `tomato_ils2` +-- + +USE `tomato_ils2`; + +-- +-- Current Database: `tomato_ils3` +-- + +USE `tomato_ils3`; + +-- +-- Current Database: `tomato_meristem` +-- + +USE `tomato_meristem`; + +-- +-- Current Database: `tomato_nssnp` +-- + +USE `tomato_nssnp`; + +-- +-- Current Database: `tomato_renormalized` +-- + +USE `tomato_renormalized`; + +-- +-- Current Database: `tomato_root` +-- + +USE `tomato_root`; + +-- +-- Current Database: `tomato_root_field_pot` +-- + +USE `tomato_root_field_pot`; + +-- +-- Current Database: `tomato_s_pennellii` +-- + +USE `tomato_s_pennellii`; + +-- +-- Current Database: `tomato_seed` +-- + +USE `tomato_seed`; + +-- +-- Current Database: `tomato_sequence` +-- + +USE `tomato_sequence`; + +-- +-- Current Database: `tomato_shade_mutants` +-- + +USE `tomato_shade_mutants`; + +-- +-- Current Database: `tomato_shade_timecourse` +-- + +USE `tomato_shade_timecourse`; + +-- +-- Current Database: `tomato_trait` +-- + +USE `tomato_trait`; + +-- +-- Current Database: `triphysaria` +-- + +USE `triphysaria`; + +-- +-- Current Database: `triphysaria_annotations_lookup` +-- + +USE `triphysaria_annotations_lookup`; + +-- +-- Current Database: `triticale` +-- + +USE `triticale`; + +-- +-- Current Database: `triticale_annotations_lookup` +-- + +USE `triticale_annotations_lookup`; + +-- +-- Current Database: `triticale_mas` +-- + +USE `triticale_mas`; + +-- +-- Current Database: `tung_tree` +-- + +USE `tung_tree`; + +-- +-- Current Database: `wheat` +-- + +USE `wheat`; + +-- +-- Current Database: `wheat_abiotic_stress` +-- + +USE `wheat_abiotic_stress`; + +-- +-- Current Database: `wheat_embryogenesis` +-- + +USE `wheat_embryogenesis`; + +-- +-- Current Database: `wheat_meiosis` +-- + +USE `wheat_meiosis`; + +-- +-- Current Database: `wheat_root` +-- + +USE `wheat_root`; + +-- +-- Current Database: `willow` +-- + +USE `willow`; +/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */; +/*!50606 SET GLOBAL INNODB_STATS_AUTO_RECALC=@OLD_INNODB_STATS_AUTO_RECALC */; + +/*!40101 SET SQL_MODE=@OLD_SQL_MODE */; +/*!40014 SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS */; +/*!40014 SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS */; +/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */; +/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */; +/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; +/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; + +-- Dump completed on 2026-01-28 16:30:58 diff --git a/api/Archive/structural_diffs_sample_data_dump_01_28_25.csv b/api/Archive/structural_diffs_sample_data_dump_01_28_25.csv new file mode 100644 index 0000000..675e13e --- /dev/null +++ b/api/Archive/structural_diffs_sample_data_dump_01_28_25.csv @@ -0,0 +1,114 @@ +COLUMN_NAME,COLUMN_TYPE,IS_NULLABLE,COLUMN_DEFAULT,variants,db_list +channel,varchar(5),YES,NULL,3,hnahal,meristem_db,meristem_db_new +data_bot_id,varchar(16),NO,NULL,21,actinidia_flower_fruit_development,actinidia_vegetative_growth,germination,gynoecium,heterodera_schachtii,kalanchoe,kalanchoe_time_course_analysis,klepikova,lipid_map,maize_ears,maize_iplant,medicago_root,medicago_root_v5,sorghum_low_phosphorus,sorghum_plasma,tomato_seed,tomato_shade_timecourse,wheat,wheat_abiotic_stress,wheat_root,willow +data_bot_id,varchar(32),NO,NULL,21,brachypodium_Bd21,brachypodium_grains,durum_wheat_abiotic_stress,lupin_lcm_leaf,lupin_lcm_pod,lupin_lcm_stem,lupin_pod_seed,lupin_whole_plant,marchantia_organ_stress,phelipanche,single_cell,sorghum_developmental_2,sorghum_flowering_activation,sorghum_nitrogen_stress,sorghum_phosphate_stress,sorghum_saline_alkali_stress,sorghum_strigolactone_variation,sorghum_sulfur_stress,sorghum_temperature_stress,sorghum_vascularization_and_internode,triphysaria +data_bot_id,varchar(12),NO,NULL,20,barley_seed,brachypodium_photo_thermocycle,canola_seed,gc_drought,maize_leaf_gradient,maize_lipid_map,maize_rice_comparison,mangosteen_diseased_vs_normal,mangosteen_seed_development,mangosteen_seed_germination,poplar_hormone,potato_stress,potato_wounding,rice_drought_heat_stress,rice_leaf_gradient,rice_maize_comparison,seedcoat,sorghum_developmental,sorghum_nitrogen_use_efficiency,sorghum_stress +data_bot_id,varchar(24),NO,NULL,19,actinidia_postharvest,barley_mas,barley_rma,barley_spike_meristem,barley_spike_meristem_v3,cassava_atlas,cassava_cbb,cassava_eacmv,durum_wheat_development,euphorbia,guard_cell,maize_embryonic_leaf_development,maize_nitrogen_use_efficiency,oat,root,sorghum_atlas_w_BS_cells,spruce,strawberry,wheat_meiosis +data_bot_id,varchar(8),NO,NULL,14,actinidia_bud_development,cannabis,cuscuta_early_haustoriogenesis,cuscuta_lmd,embryo,maize_enzyme,maize_kernel_v5,mangosteen_aril_vs_rind,mangosteen_callus,mangosteen_fruit_ripening,mangosteen_seed_development_germination,rice_root,shoot_apex,soybean_senescence +data_bot_id,tinytext,NO,NULL,10,canola,canola_original,canola_original_v2,hnahal,human_developmental_SpongeLab,human_diseased,meristem_db_new,rohan,rpatel,tomato_trait +data_bot_id,varchar(16),YES,NULL,9,arabidopsis_ecotypes,cacao_developmental_atlas,cacao_developmental_atlas_sca,cacao_drought_diurnal_atlas,cacao_drought_diurnal_atlas_sca,sugarcane_culms,sunflower,tomato_ils3,tung_tree +data_bot_id,varchar(12),YES,NULL,8,apple,cacao_leaf,cuscuta,little_millet,tomato_ils,tomato_ils2,tomato_root,tomato_root_field_pot +data_bot_id,varchar(40),NO,NULL,8,camelina,camelina_tpm,maize_atlas,maize_atlas_v5,maize_gdowns,physcomitrella_db,sorghum_comparative_transcriptomics,thellungiella_db +data_bot_id,varchar(50),NO,NULL,8,atgenexp,atgenexp_plus,brachypodium,brachypodium_embryogenesis,grape_developmental,maize_buell_lab,maize_early_seed,wheat_embryogenesis +data_bot_id,varchar(24),YES,NULL,6,cacao_infection,cacao_meristem_atlas_sca,cacao_seed_atlas_sca,human_developmental,tomato_meristem,tomato_s_pennellii +data_bot_id,varchar(18),NO,NULL,5,circadian_mutants,meristem_db,mouse_db,soybean_severin,triticale +data_bot_id,varchar(42),NO,NULL,5,durum_wheat_biotic_stress,eucalyptus,soybean_embryonic_development,soybean_heart_cotyledon_globular,striga +data_bot_id,varchar(30),NO,NULL,4,light_series,maize_RMA_linear,maize_RMA_log,triticale_mas +data_bot_id,varchar(40),YES,NULL,4,atgenexp_stress,poplar,poplar_leaf,poplar_xylem +data_bot_id,varchar(20),NO,NULL,3,human_body_map_2,maize_stress_v5,tomato_shade_mutants +data_bot_id,varchar(22),NO,NULL,3,medicago_mas,medicago_rma,soybean +data_bot_id,varchar(64),NO,NULL,3,rice_abiotic_stress_sc_pseudobulk,seed_db,silique +data_bot_id,varchar(15),NO,NULL,2,medicago_seed,potato_dev +data_bot_id,varchar(18),YES,NULL,2,tomato,tomato_renormalized +data_bot_id,varchar(26),NO,NULL,2,rice_mas,rice_rma +data_bot_id,varchar(32),YES,NULL,2,dna_damage,sugarcane_leaf +data_bot_id,varchar(50),YES,NULL,2,atgenexp_hormone,atgenexp_pathogen +data_bot_id,tinytext,YES,NULL,1,affydb +data_bot_id,varchar(10),YES,NULL,1,brassica_rapa +data_bot_id,varchar(20),YES,NULL,1,root_Schaefer_lab +data_bot_id,varchar(255),NO,NULL,1,maize_root +data_bot_id,varchar(36),NO,NULL,1,selaginella +data_bot_id,varchar(45),NO,NULL,1,brachypodium_metabolites_map +data_bot_id,varchar(5),NO,NULL,1,maize_metabolite +data_bot_id,varchar(6),NO,NULL,1,rice_metabolite +data_bot_id,varchar(64),YES,NULL,1,lateral_root_initiation +data_bot_id,varchar(65),NO,NULL,1,arachis +data_call,tinytext,YES,NULL,39,arabidopsis_ecotypes,atgenexp_hormone,atgenexp_pathogen,atgenexp_plus,barley_mas,barley_rma,canola,canola_original,canola_original_v2,guard_cell,human_body_map_2,human_developmental,human_developmental_SpongeLab,human_diseased,light_series,maize_RMA_linear,maize_RMA_log,maize_ears,maize_enzyme,maize_iplant,maize_leaf_gradient,maize_metabolite,maize_rice_comparison,medicago_mas,medicago_rma,rice_leaf_gradient,rice_maize_comparison,rice_mas,rice_metabolite,rice_rma,rohan,root,rpatel,seedcoat,tomato,tomato_renormalized,tomato_trait,triticale,triticale_mas +data_call,tinytext,NO,NULL,5,affydb,atgenexp,grape_developmental,soybean,soybean_severin +data_call,varchar(2),YES,NULL,2,klepikova,shoot_apex +data_call,varchar(12),NO,NULL,1,poplar +data_call,varchar(20),YES,NULL,1,atgenexp_stress +data_call,varchar(40),YES,NULL,1,seed_db +data_num,int unsigned,NO,0,2,affydb,poplar +data_p_val,float,YES,0,41,arabidopsis_ecotypes,atgenexp_hormone,atgenexp_plus,atgenexp_stress,barley_mas,barley_rma,canola,canola_original,canola_original_v2,guard_cell,human_body_map_2,human_developmental,human_developmental_SpongeLab,human_diseased,light_series,maize_RMA_linear,maize_RMA_log,maize_ears,maize_enzyme,maize_iplant,maize_leaf_gradient,maize_metabolite,maize_rice_comparison,medicago_mas,medicago_rma,rice_leaf_gradient,rice_maize_comparison,rice_mas,rice_metabolite,rice_rma,rohan,root,rpatel,seed_db,seedcoat,shoot_apex,tomato,tomato_renormalized,tomato_trait,triticale,triticale_mas +data_p_val,float,NO,NULL,3,grape_developmental,soybean,soybean_severin +data_p_val,float,NO,0,3,affydb,atgenexp,poplar +data_p_val,float,YES,NULL,1,atgenexp_pathogen +data_p_value,float,YES,0,6,medicago_root,medicago_seed,tomato_ils,tomato_ils2,tomato_ils3,tomato_s_pennellii +data_probeset_id,varchar(24),NO,NULL,30,barley_spike_meristem,cacao_developmental_atlas,cacao_developmental_atlas_sca,cacao_drought_diurnal_atlas,cacao_drought_diurnal_atlas_sca,cacao_meristem_atlas_sca,cacao_seed_atlas_sca,cannabis,cassava_atlas,cassava_cbb,cassava_eacmv,kalanchoe,maize_buell_lab,maize_early_seed,maize_lipid_map,maize_nitrogen_use_efficiency,rice_drought_heat_stress,single_cell,sorghum_atlas_w_BS_cells,sorghum_low_phosphorus,sorghum_nitrogen_use_efficiency,sorghum_phosphate_stress,sorghum_plasma,sorghum_sulfur_stress,sorghum_vascularization_and_internode,soybean_embryonic_development,soybean_heart_cotyledon_globular,soybean_senescence,striga,tomato_seed +data_probeset_id,varchar(16),NO,NULL,24,brassica_rapa,canola_seed,embryo,eucalyptus,maize_rice_comparison,phelipanche,rice_abiotic_stress_sc_pseudobulk,rice_root,root_Schaefer_lab,sorghum_developmental,sorghum_developmental_2,sorghum_flowering_activation,sorghum_nitrogen_stress,sorghum_saline_alkali_stress,sorghum_stress,sorghum_strigolactone_variation,sorghum_temperature_stress,spruce,strawberry,sunflower,tomato_shade_mutants,tomato_shade_timecourse,triphysaria,tung_tree +data_probeset_id,varchar(18),NO,NULL,19,apple,brachypodium,brachypodium_Bd21,brachypodium_embryogenesis,brachypodium_grains,brachypodium_photo_thermocycle,cacao_infection,cacao_leaf,euphorbia,kalanchoe_time_course_analysis,maize_embryonic_leaf_development,medicago_root,medicago_seed,poplar_hormone,rice_leaf_gradient,rice_maize_comparison,selaginella,sorghum_comparative_transcriptomics,soybean_severin +data_probeset_id,varchar(32),NO,NULL,19,barley_seed,barley_spike_meristem_v3,durum_wheat_abiotic_stress,durum_wheat_biotic_stress,durum_wheat_development,lupin_lcm_leaf,lupin_lcm_pod,lupin_lcm_stem,lupin_pod_seed,lupin_whole_plant,marchantia_organ_stress,sugarcane_culms,sugarcane_leaf,wheat,wheat_abiotic_stress,wheat_embryogenesis,wheat_meiosis,wheat_root,willow +data_probeset_id,varchar(30),NO,NULL,13,arachis,barley_mas,barley_rma,germination,guard_cell,klepikova,light_series,maize_root,meristem_db,root,seed_db,triticale,triticale_mas +data_probeset_id,varchar(12),NO,NULL,12,actinidia_bud_development,actinidia_flower_fruit_development,actinidia_postharvest,actinidia_vegetative_growth,circadian_mutants,cuscuta_early_haustoriogenesis,cuscuta_lmd,gc_drought,gynoecium,heterodera_schachtii,shoot_apex,silique +data_probeset_id,tinytext,NO,NULL,9,canola,canola_original,canola_original_v2,hnahal,human_developmental_SpongeLab,human_diseased,meristem_db_new,rohan,rpatel +data_probeset_id,varchar(40),NO,NULL,8,grape_developmental,lateral_root_initiation,maize_enzyme,maize_gdowns,potato_dev,potato_stress,potato_wounding,thellungiella_db +data_probeset_id,varchar(20),NO,NULL,7,camelina,camelina_tpm,maize_RMA_linear,maize_RMA_log,maize_ears,maize_iplant,maize_leaf_gradient +data_probeset_id,varchar(30),YES,NULL,7,affydb,arabidopsis_ecotypes,atgenexp,atgenexp_hormone,atgenexp_pathogen,atgenexp_plus,atgenexp_stress +data_probeset_id,varchar(8),NO,NULL,7,mangosteen_aril_vs_rind,mangosteen_callus,mangosteen_diseased_vs_normal,mangosteen_fruit_ripening,mangosteen_seed_development,mangosteen_seed_development_germination,mangosteen_seed_germination +data_probeset_id,varchar(18),YES,NULL,5,tomato,tomato_meristem,tomato_renormalized,tomato_root,tomato_root_field_pot +data_probeset_id,varchar(25),NO,NULL,5,maize_atlas,maize_atlas_v5,maize_kernel_v5,maize_stress_v5,rice_metabolite +data_probeset_id,varchar(28),NO,NULL,5,human_body_map_2,medicago_mas,medicago_rma,rice_mas,rice_rma +data_probeset_id,varchar(20),YES,NULL,4,tomato_ils,tomato_ils2,tomato_ils3,tomato_s_pennellii +data_probeset_id,varchar(64),NO,NULL,4,brachypodium_metabolites_map,lipid_map,maize_metabolite,medicago_root_v5 +data_probeset_id,varchar(70),NO,NULL,3,poplar,poplar_leaf,poplar_xylem +data_probeset_id,varchar(32),YES,NULL,2,human_developmental,little_millet +data_probeset_id,varchar(36),NO,NULL,2,oat,soybean +data_probeset_id,varchar(10),NO,NULL,1,dna_damage +data_probeset_id,varchar(100),NO,NULL,1,tomato_trait +data_probeset_id,varchar(15),NO,NULL,1,mouse_db +data_probeset_id,varchar(16),YES,NULL,1,cuscuta +data_probeset_id,varchar(22),NO,NULL,1,seedcoat +data_probeset_id,varchar(40),NO,,1,physcomitrella_db +data_signal,float,YES,0,145,actinidia_bud_development,actinidia_flower_fruit_development,actinidia_postharvest,actinidia_vegetative_growth,arabidopsis_ecotypes,atgenexp_hormone,atgenexp_plus,barley_mas,barley_rma,barley_seed,barley_spike_meristem,barley_spike_meristem_v3,brachypodium,brachypodium_Bd21,brachypodium_embryogenesis,brachypodium_grains,brachypodium_photo_thermocycle,canola,canola_original,canola_original_v2,canola_seed,cassava_atlas,cassava_cbb,cassava_eacmv,circadian_mutants,cuscuta,cuscuta_early_haustoriogenesis,cuscuta_lmd,durum_wheat_abiotic_stress,durum_wheat_biotic_stress,durum_wheat_development,embryo,eucalyptus,euphorbia,gc_drought,germination,guard_cell,gynoecium,heterodera_schachtii,hnahal,human_body_map_2,human_developmental,human_developmental_SpongeLab,human_diseased,kalanchoe_time_course_analysis,klepikova,light_series,little_millet,lupin_lcm_leaf,lupin_lcm_pod,lupin_lcm_stem,lupin_pod_seed,lupin_whole_plant,maize_RMA_linear,maize_RMA_log,maize_atlas_v5,maize_ears,maize_embryonic_leaf_development,maize_enzyme,m +data_signal,float,NO,0,26,affydb,apple,atgenexp,atgenexp_stress,brassica_rapa,cacao_developmental_atlas,cacao_developmental_atlas_sca,cacao_drought_diurnal_atlas,cacao_drought_diurnal_atlas_sca,cacao_infection,cacao_leaf,cacao_meristem_atlas_sca,cacao_seed_atlas_sca,dna_damage,maize_buell_lab,maize_early_seed,mouse_db,poplar,poplar_leaf,poplar_xylem,root_Schaefer_lab,selaginella,sugarcane_culms,sugarcane_leaf,sunflower,tung_tree +data_signal,float,NO,NULL,15,arachis,camelina,camelina_tpm,cannabis,grape_developmental,kalanchoe,lateral_root_initiation,maize_atlas,maize_gdowns,physcomitrella_db,shoot_apex,soybean,soybean_severin,thellungiella_db,willow +data_signal,float,YES,NULL,5,atgenexp_pathogen,brachypodium_metabolites_map,lipid_map,maize_lipid_map,tomato_trait +genome,varchar(16),NO,NULL,1,oat +genome_id,varchar(16),NO,NULL,1,oat +log,float,NO,NULL,1,tomato_ils2 +orthogroup,varchar(16),NO,NULL,1,oat +p_val,float,NO,NULL,1,tomato_ils2 +proj_id,varchar(5),NO,NULL,80,actinidia_bud_development,actinidia_flower_fruit_development,actinidia_postharvest,actinidia_vegetative_growth,barley_seed,barley_spike_meristem,barley_spike_meristem_v3,brachypodium,brachypodium_Bd21,brachypodium_embryogenesis,brachypodium_grains,brachypodium_metabolites_map,brachypodium_photo_thermocycle,camelina,camelina_tpm,canola_seed,cassava_atlas,cassava_cbb,cassava_eacmv,circadian_mutants,cuscuta_early_haustoriogenesis,cuscuta_lmd,durum_wheat_abiotic_stress,durum_wheat_biotic_stress,durum_wheat_development,eucalyptus,euphorbia,gc_drought,gynoecium,heterodera_schachtii,kalanchoe_time_course_analysis,lipid_map,lupin_lcm_leaf,lupin_lcm_pod,lupin_lcm_stem,lupin_pod_seed,lupin_whole_plant,maize_atlas,maize_atlas_v5,maize_embryonic_leaf_development,maize_kernel_v5,maize_lipid_map,maize_nitrogen_use_efficiency,maize_stress_v5,marchantia_organ_stress,medicago_root,medicago_root_v5,medicago_seed,phelipanche,poplar_hormone,rice_abiotic_stress_sc_pseudobulk,rice_drought_heat_stress,silique,single_cell,sorghum_at +proj_id,varchar(15),NO,0,55,arabidopsis_ecotypes,atgenexp_pathogen,atgenexp_plus,atgenexp_stress,barley_mas,barley_rma,canola,canola_original,canola_original_v2,guard_cell,hnahal,human_body_map_2,human_developmental,human_developmental_SpongeLab,human_diseased,light_series,maize_RMA_linear,maize_RMA_log,maize_ears,maize_enzyme,maize_iplant,maize_leaf_gradient,maize_metabolite,maize_rice_comparison,maize_root,medicago_mas,medicago_rma,meristem_db,meristem_db_new,poplar,potato_dev,potato_stress,potato_wounding,rice_leaf_gradient,rice_maize_comparison,rice_mas,rice_metabolite,rice_rma,rohan,root,rpatel,seedcoat,tomato,tomato_ils,tomato_ils2,tomato_ils3,tomato_renormalized,tomato_s_pennellii,triticale,triticale_mas,wheat,wheat_abiotic_stress,wheat_embryogenesis,wheat_meiosis,wheat_root +proj_id,varchar(5),NO,0,20,apple,brassica_rapa,cacao_developmental_atlas,cacao_developmental_atlas_sca,cacao_drought_diurnal_atlas,cacao_drought_diurnal_atlas_sca,cacao_infection,cacao_leaf,cacao_meristem_atlas_sca,cacao_seed_atlas_sca,dna_damage,maize_buell_lab,maize_early_seed,poplar_leaf,poplar_xylem,root_Schaefer_lab,selaginella,sugarcane_culms,sunflower,tung_tree +proj_id,varchar(2),NO,0,9,cannabis,cuscuta,kalanchoe,little_millet,rice_root,tomato_meristem,tomato_root,tomato_root_field_pot,willow +proj_id,varchar(2),NO,NULL,7,mangosteen_aril_vs_rind,mangosteen_callus,mangosteen_diseased_vs_normal,mangosteen_fruit_ripening,mangosteen_seed_development,mangosteen_seed_development_germination,mangosteen_seed_germination +proj_id,int unsigned,NO,0,3,affydb,atgenexp,atgenexp_hormone +proj_id,varchar(3),NO,0,3,embryo,germination,klepikova +proj_id,varchar(15),NO,NULL,2,soybean,soybean_severin +proj_id,varchar(30),NO,NULL,2,maize_gdowns,thellungiella_db +proj_id,int,NO,NULL,1,grape_developmental +proj_id,varchar(12),NO,0,1,sugarcane_leaf +proj_id,varchar(2),YES,NULL,1,shoot_apex +proj_id,varchar(20),NO,0,1,seed_db +proj_id,varchar(24),NO,NULL,1,arachis +proj_id,varchar(30),NO,,1,physcomitrella_db +proj_id,varchar(30),NO,0,1,tomato_trait +project_id,varchar(30),NO,NULL,1,lateral_root_initiation +qvalue,float,YES,NULL,1,tomato_trait +sample_file_name,tinytext,YES,NULL,40,arabidopsis_ecotypes,atgenexp_plus,barley_mas,barley_rma,canola,canola_original,canola_original_v2,guard_cell,hnahal,human_body_map_2,human_developmental,human_developmental_SpongeLab,human_diseased,light_series,maize_RMA_linear,maize_RMA_log,maize_ears,maize_enzyme,maize_iplant,maize_leaf_gradient,maize_metabolite,maize_rice_comparison,medicago_mas,medicago_rma,meristem_db,meristem_db_new,rice_leaf_gradient,rice_maize_comparison,rice_mas,rice_metabolite,rice_rma,rohan,root,rpatel,seedcoat,tomato,tomato_renormalized,tomato_trait,triticale,triticale_mas +sample_file_name,tinytext,NO,NULL,5,affydb,atgenexp,grape_developmental,soybean,soybean_severin +sample_file_name,varchar(20),YES,NULL,2,camelina,camelina_tpm +sample_file_name,varchar(80),YES,NULL,2,lateral_root_initiation,thellungiella_db +sample_file_name,varchar(100),YES,NULL,1,seed_db +sample_file_name,varchar(16),YES,NULL,1,shoot_apex +sample_file_name,varchar(40),NO,NULL,1,poplar +sample_id,int unsigned,NO,0,179,actinidia_bud_development,actinidia_flower_fruit_development,actinidia_postharvest,actinidia_vegetative_growth,affydb,apple,arabidopsis_ecotypes,atgenexp,atgenexp_hormone,atgenexp_pathogen,atgenexp_plus,atgenexp_stress,barley_mas,barley_rma,barley_seed,barley_spike_meristem,barley_spike_meristem_v3,brachypodium,brachypodium_Bd21,brachypodium_embryogenesis,brachypodium_grains,brachypodium_metabolites_map,brachypodium_photo_thermocycle,brassica_rapa,cacao_developmental_atlas,cacao_developmental_atlas_sca,cacao_drought_diurnal_atlas,cacao_drought_diurnal_atlas_sca,cacao_infection,cacao_leaf,cacao_meristem_atlas_sca,cacao_seed_atlas_sca,cannabis,canola,canola_original,canola_original_v2,canola_seed,cassava_atlas,cassava_cbb,cassava_eacmv,circadian_mutants,cuscuta,cuscuta_early_haustoriogenesis,cuscuta_lmd,dna_damage,durum_wheat_abiotic_stress,durum_wheat_biotic_stress,durum_wheat_development,embryo,eucalyptus,euphorbia,gc_drought,germination,guard_cell,gynoecium,heterodera_schachtii,hnahal,human_body_map_2,human_ +sample_id,varchar(5),NO,NULL,4,arachis,camelina,camelina_tpm,maize_atlas +sample_id,int,NO,NULL,3,grape_developmental,soybean,soybean_severin +sample_id,varchar(30),NO,NULL,3,lateral_root_initiation,maize_gdowns,thellungiella_db +sample_id,varchar(30),NO,,1,physcomitrella_db +sample_tissue,text,NO,NULL,7,canola,canola_original,canola_original_v2,grape_developmental,maize_RMA_linear,medicago_mas,rice_mas +sample_tissue,varchar(20),YES,NULL,1,barley_mas +version,varchar(2),NO,NULL,1,oat diff --git a/api/Archive/structural_diffs_sample_data_dump_01_28_25.sql b/api/Archive/structural_diffs_sample_data_dump_01_28_25.sql new file mode 100644 index 0000000..cf5bca8 --- /dev/null +++ b/api/Archive/structural_diffs_sample_data_dump_01_28_25.sql @@ -0,0 +1,114 @@ +COLUMN_NAME COLUMN_TYPE IS_NULLABLE COLUMN_DEFAULT variants db_list +channel varchar(5) YES NULL 3 hnahal,meristem_db,meristem_db_new +data_bot_id varchar(16) NO NULL 21 actinidia_flower_fruit_development,actinidia_vegetative_growth,germination,gynoecium,heterodera_schachtii,kalanchoe,kalanchoe_time_course_analysis,klepikova,lipid_map,maize_ears,maize_iplant,medicago_root,medicago_root_v5,sorghum_low_phosphorus,sorghum_plasma,tomato_seed,tomato_shade_timecourse,wheat,wheat_abiotic_stress,wheat_root,willow +data_bot_id varchar(32) NO NULL 21 brachypodium_Bd21,brachypodium_grains,durum_wheat_abiotic_stress,lupin_lcm_leaf,lupin_lcm_pod,lupin_lcm_stem,lupin_pod_seed,lupin_whole_plant,marchantia_organ_stress,phelipanche,single_cell,sorghum_developmental_2,sorghum_flowering_activation,sorghum_nitrogen_stress,sorghum_phosphate_stress,sorghum_saline_alkali_stress,sorghum_strigolactone_variation,sorghum_sulfur_stress,sorghum_temperature_stress,sorghum_vascularization_and_internode,triphysaria +data_bot_id varchar(12) NO NULL 20 barley_seed,brachypodium_photo_thermocycle,canola_seed,gc_drought,maize_leaf_gradient,maize_lipid_map,maize_rice_comparison,mangosteen_diseased_vs_normal,mangosteen_seed_development,mangosteen_seed_germination,poplar_hormone,potato_stress,potato_wounding,rice_drought_heat_stress,rice_leaf_gradient,rice_maize_comparison,seedcoat,sorghum_developmental,sorghum_nitrogen_use_efficiency,sorghum_stress +data_bot_id varchar(24) NO NULL 19 actinidia_postharvest,barley_mas,barley_rma,barley_spike_meristem,barley_spike_meristem_v3,cassava_atlas,cassava_cbb,cassava_eacmv,durum_wheat_development,euphorbia,guard_cell,maize_embryonic_leaf_development,maize_nitrogen_use_efficiency,oat,root,sorghum_atlas_w_BS_cells,spruce,strawberry,wheat_meiosis +data_bot_id varchar(8) NO NULL 14 actinidia_bud_development,cannabis,cuscuta_early_haustoriogenesis,cuscuta_lmd,embryo,maize_enzyme,maize_kernel_v5,mangosteen_aril_vs_rind,mangosteen_callus,mangosteen_fruit_ripening,mangosteen_seed_development_germination,rice_root,shoot_apex,soybean_senescence +data_bot_id tinytext NO NULL 10 canola,canola_original,canola_original_v2,hnahal,human_developmental_SpongeLab,human_diseased,meristem_db_new,rohan,rpatel,tomato_trait +data_bot_id varchar(16) YES NULL 9 arabidopsis_ecotypes,cacao_developmental_atlas,cacao_developmental_atlas_sca,cacao_drought_diurnal_atlas,cacao_drought_diurnal_atlas_sca,sugarcane_culms,sunflower,tomato_ils3,tung_tree +data_bot_id varchar(12) YES NULL 8 apple,cacao_leaf,cuscuta,little_millet,tomato_ils,tomato_ils2,tomato_root,tomato_root_field_pot +data_bot_id varchar(40) NO NULL 8 camelina,camelina_tpm,maize_atlas,maize_atlas_v5,maize_gdowns,physcomitrella_db,sorghum_comparative_transcriptomics,thellungiella_db +data_bot_id varchar(50) NO NULL 8 atgenexp,atgenexp_plus,brachypodium,brachypodium_embryogenesis,grape_developmental,maize_buell_lab,maize_early_seed,wheat_embryogenesis +data_bot_id varchar(24) YES NULL 6 cacao_infection,cacao_meristem_atlas_sca,cacao_seed_atlas_sca,human_developmental,tomato_meristem,tomato_s_pennellii +data_bot_id varchar(18) NO NULL 5 circadian_mutants,meristem_db,mouse_db,soybean_severin,triticale +data_bot_id varchar(42) NO NULL 5 durum_wheat_biotic_stress,eucalyptus,soybean_embryonic_development,soybean_heart_cotyledon_globular,striga +data_bot_id varchar(30) NO NULL 4 light_series,maize_RMA_linear,maize_RMA_log,triticale_mas +data_bot_id varchar(40) YES NULL 4 atgenexp_stress,poplar,poplar_leaf,poplar_xylem +data_bot_id varchar(20) NO NULL 3 human_body_map_2,maize_stress_v5,tomato_shade_mutants +data_bot_id varchar(22) NO NULL 3 medicago_mas,medicago_rma,soybean +data_bot_id varchar(64) NO NULL 3 rice_abiotic_stress_sc_pseudobulk,seed_db,silique +data_bot_id varchar(15) NO NULL 2 medicago_seed,potato_dev +data_bot_id varchar(18) YES NULL 2 tomato,tomato_renormalized +data_bot_id varchar(26) NO NULL 2 rice_mas,rice_rma +data_bot_id varchar(32) YES NULL 2 dna_damage,sugarcane_leaf +data_bot_id varchar(50) YES NULL 2 atgenexp_hormone,atgenexp_pathogen +data_bot_id tinytext YES NULL 1 affydb +data_bot_id varchar(10) YES NULL 1 brassica_rapa +data_bot_id varchar(20) YES NULL 1 root_Schaefer_lab +data_bot_id varchar(255) NO NULL 1 maize_root +data_bot_id varchar(36) NO NULL 1 selaginella +data_bot_id varchar(45) NO NULL 1 brachypodium_metabolites_map +data_bot_id varchar(5) NO NULL 1 maize_metabolite +data_bot_id varchar(6) NO NULL 1 rice_metabolite +data_bot_id varchar(64) YES NULL 1 lateral_root_initiation +data_bot_id varchar(65) NO NULL 1 arachis +data_call tinytext YES NULL 39 arabidopsis_ecotypes,atgenexp_hormone,atgenexp_pathogen,atgenexp_plus,barley_mas,barley_rma,canola,canola_original,canola_original_v2,guard_cell,human_body_map_2,human_developmental,human_developmental_SpongeLab,human_diseased,light_series,maize_RMA_linear,maize_RMA_log,maize_ears,maize_enzyme,maize_iplant,maize_leaf_gradient,maize_metabolite,maize_rice_comparison,medicago_mas,medicago_rma,rice_leaf_gradient,rice_maize_comparison,rice_mas,rice_metabolite,rice_rma,rohan,root,rpatel,seedcoat,tomato,tomato_renormalized,tomato_trait,triticale,triticale_mas +data_call tinytext NO NULL 5 affydb,atgenexp,grape_developmental,soybean,soybean_severin +data_call varchar(2) YES NULL 2 klepikova,shoot_apex +data_call varchar(12) NO NULL 1 poplar +data_call varchar(20) YES NULL 1 atgenexp_stress +data_call varchar(40) YES NULL 1 seed_db +data_num int unsigned NO 0 2 affydb,poplar +data_p_val float YES 0 41 arabidopsis_ecotypes,atgenexp_hormone,atgenexp_plus,atgenexp_stress,barley_mas,barley_rma,canola,canola_original,canola_original_v2,guard_cell,human_body_map_2,human_developmental,human_developmental_SpongeLab,human_diseased,light_series,maize_RMA_linear,maize_RMA_log,maize_ears,maize_enzyme,maize_iplant,maize_leaf_gradient,maize_metabolite,maize_rice_comparison,medicago_mas,medicago_rma,rice_leaf_gradient,rice_maize_comparison,rice_mas,rice_metabolite,rice_rma,rohan,root,rpatel,seed_db,seedcoat,shoot_apex,tomato,tomato_renormalized,tomato_trait,triticale,triticale_mas +data_p_val float NO NULL 3 grape_developmental,soybean,soybean_severin +data_p_val float NO 0 3 affydb,atgenexp,poplar +data_p_val float YES NULL 1 atgenexp_pathogen +data_p_value float YES 0 6 medicago_root,medicago_seed,tomato_ils,tomato_ils2,tomato_ils3,tomato_s_pennellii +data_probeset_id varchar(24) NO NULL 30 barley_spike_meristem,cacao_developmental_atlas,cacao_developmental_atlas_sca,cacao_drought_diurnal_atlas,cacao_drought_diurnal_atlas_sca,cacao_meristem_atlas_sca,cacao_seed_atlas_sca,cannabis,cassava_atlas,cassava_cbb,cassava_eacmv,kalanchoe,maize_buell_lab,maize_early_seed,maize_lipid_map,maize_nitrogen_use_efficiency,rice_drought_heat_stress,single_cell,sorghum_atlas_w_BS_cells,sorghum_low_phosphorus,sorghum_nitrogen_use_efficiency,sorghum_phosphate_stress,sorghum_plasma,sorghum_sulfur_stress,sorghum_vascularization_and_internode,soybean_embryonic_development,soybean_heart_cotyledon_globular,soybean_senescence,striga,tomato_seed +data_probeset_id varchar(16) NO NULL 24 brassica_rapa,canola_seed,embryo,eucalyptus,maize_rice_comparison,phelipanche,rice_abiotic_stress_sc_pseudobulk,rice_root,root_Schaefer_lab,sorghum_developmental,sorghum_developmental_2,sorghum_flowering_activation,sorghum_nitrogen_stress,sorghum_saline_alkali_stress,sorghum_stress,sorghum_strigolactone_variation,sorghum_temperature_stress,spruce,strawberry,sunflower,tomato_shade_mutants,tomato_shade_timecourse,triphysaria,tung_tree +data_probeset_id varchar(18) NO NULL 19 apple,brachypodium,brachypodium_Bd21,brachypodium_embryogenesis,brachypodium_grains,brachypodium_photo_thermocycle,cacao_infection,cacao_leaf,euphorbia,kalanchoe_time_course_analysis,maize_embryonic_leaf_development,medicago_root,medicago_seed,poplar_hormone,rice_leaf_gradient,rice_maize_comparison,selaginella,sorghum_comparative_transcriptomics,soybean_severin +data_probeset_id varchar(32) NO NULL 19 barley_seed,barley_spike_meristem_v3,durum_wheat_abiotic_stress,durum_wheat_biotic_stress,durum_wheat_development,lupin_lcm_leaf,lupin_lcm_pod,lupin_lcm_stem,lupin_pod_seed,lupin_whole_plant,marchantia_organ_stress,sugarcane_culms,sugarcane_leaf,wheat,wheat_abiotic_stress,wheat_embryogenesis,wheat_meiosis,wheat_root,willow +data_probeset_id varchar(30) NO NULL 13 arachis,barley_mas,barley_rma,germination,guard_cell,klepikova,light_series,maize_root,meristem_db,root,seed_db,triticale,triticale_mas +data_probeset_id varchar(12) NO NULL 12 actinidia_bud_development,actinidia_flower_fruit_development,actinidia_postharvest,actinidia_vegetative_growth,circadian_mutants,cuscuta_early_haustoriogenesis,cuscuta_lmd,gc_drought,gynoecium,heterodera_schachtii,shoot_apex,silique +data_probeset_id tinytext NO NULL 9 canola,canola_original,canola_original_v2,hnahal,human_developmental_SpongeLab,human_diseased,meristem_db_new,rohan,rpatel +data_probeset_id varchar(40) NO NULL 8 grape_developmental,lateral_root_initiation,maize_enzyme,maize_gdowns,potato_dev,potato_stress,potato_wounding,thellungiella_db +data_probeset_id varchar(20) NO NULL 7 camelina,camelina_tpm,maize_RMA_linear,maize_RMA_log,maize_ears,maize_iplant,maize_leaf_gradient +data_probeset_id varchar(30) YES NULL 7 affydb,arabidopsis_ecotypes,atgenexp,atgenexp_hormone,atgenexp_pathogen,atgenexp_plus,atgenexp_stress +data_probeset_id varchar(8) NO NULL 7 mangosteen_aril_vs_rind,mangosteen_callus,mangosteen_diseased_vs_normal,mangosteen_fruit_ripening,mangosteen_seed_development,mangosteen_seed_development_germination,mangosteen_seed_germination +data_probeset_id varchar(18) YES NULL 5 tomato,tomato_meristem,tomato_renormalized,tomato_root,tomato_root_field_pot +data_probeset_id varchar(25) NO NULL 5 maize_atlas,maize_atlas_v5,maize_kernel_v5,maize_stress_v5,rice_metabolite +data_probeset_id varchar(28) NO NULL 5 human_body_map_2,medicago_mas,medicago_rma,rice_mas,rice_rma +data_probeset_id varchar(20) YES NULL 4 tomato_ils,tomato_ils2,tomato_ils3,tomato_s_pennellii +data_probeset_id varchar(64) NO NULL 4 brachypodium_metabolites_map,lipid_map,maize_metabolite,medicago_root_v5 +data_probeset_id varchar(70) NO NULL 3 poplar,poplar_leaf,poplar_xylem +data_probeset_id varchar(32) YES NULL 2 human_developmental,little_millet +data_probeset_id varchar(36) NO NULL 2 oat,soybean +data_probeset_id varchar(10) NO NULL 1 dna_damage +data_probeset_id varchar(100) NO NULL 1 tomato_trait +data_probeset_id varchar(15) NO NULL 1 mouse_db +data_probeset_id varchar(16) YES NULL 1 cuscuta +data_probeset_id varchar(22) NO NULL 1 seedcoat +data_probeset_id varchar(40) NO 1 physcomitrella_db +data_signal float YES 0 145 actinidia_bud_development,actinidia_flower_fruit_development,actinidia_postharvest,actinidia_vegetative_growth,arabidopsis_ecotypes,atgenexp_hormone,atgenexp_plus,barley_mas,barley_rma,barley_seed,barley_spike_meristem,barley_spike_meristem_v3,brachypodium,brachypodium_Bd21,brachypodium_embryogenesis,brachypodium_grains,brachypodium_photo_thermocycle,canola,canola_original,canola_original_v2,canola_seed,cassava_atlas,cassava_cbb,cassava_eacmv,circadian_mutants,cuscuta,cuscuta_early_haustoriogenesis,cuscuta_lmd,durum_wheat_abiotic_stress,durum_wheat_biotic_stress,durum_wheat_development,embryo,eucalyptus,euphorbia,gc_drought,germination,guard_cell,gynoecium,heterodera_schachtii,hnahal,human_body_map_2,human_developmental,human_developmental_SpongeLab,human_diseased,kalanchoe_time_course_analysis,klepikova,light_series,little_millet,lupin_lcm_leaf,lupin_lcm_pod,lupin_lcm_stem,lupin_pod_seed,lupin_whole_plant,maize_RMA_linear,maize_RMA_log,maize_atlas_v5,maize_ears,maize_embryonic_leaf_development,maize_enzyme,m +data_signal float NO 0 26 affydb,apple,atgenexp,atgenexp_stress,brassica_rapa,cacao_developmental_atlas,cacao_developmental_atlas_sca,cacao_drought_diurnal_atlas,cacao_drought_diurnal_atlas_sca,cacao_infection,cacao_leaf,cacao_meristem_atlas_sca,cacao_seed_atlas_sca,dna_damage,maize_buell_lab,maize_early_seed,mouse_db,poplar,poplar_leaf,poplar_xylem,root_Schaefer_lab,selaginella,sugarcane_culms,sugarcane_leaf,sunflower,tung_tree +data_signal float NO NULL 15 arachis,camelina,camelina_tpm,cannabis,grape_developmental,kalanchoe,lateral_root_initiation,maize_atlas,maize_gdowns,physcomitrella_db,shoot_apex,soybean,soybean_severin,thellungiella_db,willow +data_signal float YES NULL 5 atgenexp_pathogen,brachypodium_metabolites_map,lipid_map,maize_lipid_map,tomato_trait +genome varchar(16) NO NULL 1 oat +genome_id varchar(16) NO NULL 1 oat +log float NO NULL 1 tomato_ils2 +orthogroup varchar(16) NO NULL 1 oat +p_val float NO NULL 1 tomato_ils2 +proj_id varchar(5) NO NULL 80 actinidia_bud_development,actinidia_flower_fruit_development,actinidia_postharvest,actinidia_vegetative_growth,barley_seed,barley_spike_meristem,barley_spike_meristem_v3,brachypodium,brachypodium_Bd21,brachypodium_embryogenesis,brachypodium_grains,brachypodium_metabolites_map,brachypodium_photo_thermocycle,camelina,camelina_tpm,canola_seed,cassava_atlas,cassava_cbb,cassava_eacmv,circadian_mutants,cuscuta_early_haustoriogenesis,cuscuta_lmd,durum_wheat_abiotic_stress,durum_wheat_biotic_stress,durum_wheat_development,eucalyptus,euphorbia,gc_drought,gynoecium,heterodera_schachtii,kalanchoe_time_course_analysis,lipid_map,lupin_lcm_leaf,lupin_lcm_pod,lupin_lcm_stem,lupin_pod_seed,lupin_whole_plant,maize_atlas,maize_atlas_v5,maize_embryonic_leaf_development,maize_kernel_v5,maize_lipid_map,maize_nitrogen_use_efficiency,maize_stress_v5,marchantia_organ_stress,medicago_root,medicago_root_v5,medicago_seed,phelipanche,poplar_hormone,rice_abiotic_stress_sc_pseudobulk,rice_drought_heat_stress,silique,single_cell,sorghum_at +proj_id varchar(15) NO 0 55 arabidopsis_ecotypes,atgenexp_pathogen,atgenexp_plus,atgenexp_stress,barley_mas,barley_rma,canola,canola_original,canola_original_v2,guard_cell,hnahal,human_body_map_2,human_developmental,human_developmental_SpongeLab,human_diseased,light_series,maize_RMA_linear,maize_RMA_log,maize_ears,maize_enzyme,maize_iplant,maize_leaf_gradient,maize_metabolite,maize_rice_comparison,maize_root,medicago_mas,medicago_rma,meristem_db,meristem_db_new,poplar,potato_dev,potato_stress,potato_wounding,rice_leaf_gradient,rice_maize_comparison,rice_mas,rice_metabolite,rice_rma,rohan,root,rpatel,seedcoat,tomato,tomato_ils,tomato_ils2,tomato_ils3,tomato_renormalized,tomato_s_pennellii,triticale,triticale_mas,wheat,wheat_abiotic_stress,wheat_embryogenesis,wheat_meiosis,wheat_root +proj_id varchar(5) NO 0 20 apple,brassica_rapa,cacao_developmental_atlas,cacao_developmental_atlas_sca,cacao_drought_diurnal_atlas,cacao_drought_diurnal_atlas_sca,cacao_infection,cacao_leaf,cacao_meristem_atlas_sca,cacao_seed_atlas_sca,dna_damage,maize_buell_lab,maize_early_seed,poplar_leaf,poplar_xylem,root_Schaefer_lab,selaginella,sugarcane_culms,sunflower,tung_tree +proj_id varchar(2) NO 0 9 cannabis,cuscuta,kalanchoe,little_millet,rice_root,tomato_meristem,tomato_root,tomato_root_field_pot,willow +proj_id varchar(2) NO NULL 7 mangosteen_aril_vs_rind,mangosteen_callus,mangosteen_diseased_vs_normal,mangosteen_fruit_ripening,mangosteen_seed_development,mangosteen_seed_development_germination,mangosteen_seed_germination +proj_id int unsigned NO 0 3 affydb,atgenexp,atgenexp_hormone +proj_id varchar(3) NO 0 3 embryo,germination,klepikova +proj_id varchar(15) NO NULL 2 soybean,soybean_severin +proj_id varchar(30) NO NULL 2 maize_gdowns,thellungiella_db +proj_id int NO NULL 1 grape_developmental +proj_id varchar(12) NO 0 1 sugarcane_leaf +proj_id varchar(2) YES NULL 1 shoot_apex +proj_id varchar(20) NO 0 1 seed_db +proj_id varchar(24) NO NULL 1 arachis +proj_id varchar(30) NO 1 physcomitrella_db +proj_id varchar(30) NO 0 1 tomato_trait +project_id varchar(30) NO NULL 1 lateral_root_initiation +qvalue float YES NULL 1 tomato_trait +sample_file_name tinytext YES NULL 40 arabidopsis_ecotypes,atgenexp_plus,barley_mas,barley_rma,canola,canola_original,canola_original_v2,guard_cell,hnahal,human_body_map_2,human_developmental,human_developmental_SpongeLab,human_diseased,light_series,maize_RMA_linear,maize_RMA_log,maize_ears,maize_enzyme,maize_iplant,maize_leaf_gradient,maize_metabolite,maize_rice_comparison,medicago_mas,medicago_rma,meristem_db,meristem_db_new,rice_leaf_gradient,rice_maize_comparison,rice_mas,rice_metabolite,rice_rma,rohan,root,rpatel,seedcoat,tomato,tomato_renormalized,tomato_trait,triticale,triticale_mas +sample_file_name tinytext NO NULL 5 affydb,atgenexp,grape_developmental,soybean,soybean_severin +sample_file_name varchar(20) YES NULL 2 camelina,camelina_tpm +sample_file_name varchar(80) YES NULL 2 lateral_root_initiation,thellungiella_db +sample_file_name varchar(100) YES NULL 1 seed_db +sample_file_name varchar(16) YES NULL 1 shoot_apex +sample_file_name varchar(40) NO NULL 1 poplar +sample_id int unsigned NO 0 179 actinidia_bud_development,actinidia_flower_fruit_development,actinidia_postharvest,actinidia_vegetative_growth,affydb,apple,arabidopsis_ecotypes,atgenexp,atgenexp_hormone,atgenexp_pathogen,atgenexp_plus,atgenexp_stress,barley_mas,barley_rma,barley_seed,barley_spike_meristem,barley_spike_meristem_v3,brachypodium,brachypodium_Bd21,brachypodium_embryogenesis,brachypodium_grains,brachypodium_metabolites_map,brachypodium_photo_thermocycle,brassica_rapa,cacao_developmental_atlas,cacao_developmental_atlas_sca,cacao_drought_diurnal_atlas,cacao_drought_diurnal_atlas_sca,cacao_infection,cacao_leaf,cacao_meristem_atlas_sca,cacao_seed_atlas_sca,cannabis,canola,canola_original,canola_original_v2,canola_seed,cassava_atlas,cassava_cbb,cassava_eacmv,circadian_mutants,cuscuta,cuscuta_early_haustoriogenesis,cuscuta_lmd,dna_damage,durum_wheat_abiotic_stress,durum_wheat_biotic_stress,durum_wheat_development,embryo,eucalyptus,euphorbia,gc_drought,germination,guard_cell,gynoecium,heterodera_schachtii,hnahal,human_body_map_2,human_ +sample_id varchar(5) NO NULL 4 arachis,camelina,camelina_tpm,maize_atlas +sample_id int NO NULL 3 grape_developmental,soybean,soybean_severin +sample_id varchar(30) NO NULL 3 lateral_root_initiation,maize_gdowns,thellungiella_db +sample_id varchar(30) NO 1 physcomitrella_db +sample_tissue text NO NULL 7 canola,canola_original,canola_original_v2,grape_developmental,maize_RMA_linear,medicago_mas,rice_mas +sample_tissue varchar(20) YES NULL 1 barley_mas +version varchar(2) NO NULL 1 oat diff --git a/api/__init__.py b/api/__init__.py index 43164b5..f6c8ed7 100644 --- a/api/__init__.py +++ b/api/__init__.py @@ -64,6 +64,7 @@ def create_app(): from api.resources.efp_image import efp_image from api.resources.fastpheno import fastpheno from api.resources.llama3 import llama3 + from api.resources.efp_proxy import efp_proxy_ns bar_api.add_namespace(gene_information) bar_api.add_namespace(rnaseq_gene_expression) @@ -78,6 +79,7 @@ def create_app(): bar_api.add_namespace(efp_image) bar_api.add_namespace(fastpheno) bar_api.add_namespace(llama3) + bar_api.add_namespace(efp_proxy_ns) bar_api.init_app(bar_app) return bar_app diff --git a/api/models/arabidopsis_ecotypes.py b/api/models/arabidopsis_ecotypes.py deleted file mode 100644 index d582703..0000000 --- a/api/models/arabidopsis_ecotypes.py +++ /dev/null @@ -1,15 +0,0 @@ -from api import db - - -class SampleData(db.Model): - __bind_key__ = "arabidopsis_ecotypes" - __tablename__ = "sample_data" - - sample_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False) - proj_id: db.Mapped[str] = db.mapped_column(db.String(15), nullable=False) - sample_file_name: db.Mapped[str] = db.mapped_column(db.String) - data_probeset_id: db.Mapped[str] = db.mapped_column(db.String(30), nullable=False, primary_key=True) - data_signal: db.Mapped[float] = db.mapped_column(db.Float) - data_call: db.Mapped[str] = db.mapped_column(db.String) - data_p_val: db.Mapped[float] = db.mapped_column(db.Float) - data_bot_id: db.Mapped[str] = db.mapped_column(db.String(16), nullable=False) diff --git a/api/models/arachis.py b/api/models/arachis.py deleted file mode 100644 index 7247e8b..0000000 --- a/api/models/arachis.py +++ /dev/null @@ -1,12 +0,0 @@ -from api import db - - -class SampleData(db.Model): - __bind_key__ = "arachis" - __tablename__ = "sample_data" - - proj_id: db.Mapped[str] = db.mapped_column(db.String(24), nullable=False) - sample_id: db.Mapped[int] = db.mapped_column(db.String(5), nullable=False) - data_probeset_id: db.Mapped[str] = db.mapped_column(db.String(30), nullable=False, primary_key=True) - data_signal: db.Mapped[float] = db.mapped_column(db.Float, primary_key=True) - data_bot_id: db.Mapped[str] = db.mapped_column(db.String(64), nullable=False, primary_key=True) diff --git a/api/models/bar_utils.py b/api/models/bar_utils.py new file mode 100644 index 0000000..e30ab46 --- /dev/null +++ b/api/models/bar_utils.py @@ -0,0 +1,4 @@ +# Bridge file to maintain backward compatibility with imports +from api.utils.bar_utils import BARUtils + +__all__ = ['BARUtils'] diff --git a/api/models/cannabis.py b/api/models/cannabis.py deleted file mode 100644 index d257936..0000000 --- a/api/models/cannabis.py +++ /dev/null @@ -1,12 +0,0 @@ -from api import db - - -class SampleData(db.Model): - __bind_key__ = "cannabis" - __tablename__ = "sample_data" - - proj_id: db.Mapped[str] = db.mapped_column(db.String(2), nullable=False) - sample_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False) - data_probeset_id: db.Mapped[str] = db.mapped_column(db.String(24), nullable=False, primary_key=True) - data_signal: db.Mapped[float] = db.mapped_column(db.Float, primary_key=True) - data_bot_id: db.Mapped[str] = db.mapped_column(db.String(8), nullable=False, primary_key=True) diff --git a/api/models/dna_damage.py b/api/models/dna_damage.py deleted file mode 100644 index 95e2d9a..0000000 --- a/api/models/dna_damage.py +++ /dev/null @@ -1,12 +0,0 @@ -from api import db - - -class SampleData(db.Model): - __bind_key__ = "dna_damage" - __tablename__ = "sample_data" - - proj_id: db.Mapped[str] = db.mapped_column(db.String(5), nullable=False) - sample_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False) - data_probeset_id: db.Mapped[str] = db.mapped_column(db.String(10), nullable=False, primary_key=True) - data_signal: db.Mapped[float] = db.mapped_column(db.Float, primary_key=True) - data_bot_id: db.Mapped[str] = db.mapped_column(db.String(32), nullable=False, primary_key=True) diff --git a/api/models/efp_dynamic.py b/api/models/efp_dynamic.py new file mode 100644 index 0000000..30b2213 --- /dev/null +++ b/api/models/efp_dynamic.py @@ -0,0 +1,88 @@ +""" +Dynamic SQLAlchemy model generation for simple eFP databases. + +This module provides runtime generation of SQLAlchemy ORM models from schema +definitions, enabling dynamic database access without hardcoded model classes. +""" + +from __future__ import annotations + +from typing import Dict + +from sqlalchemy import Float, Integer, String, Text +from sqlalchemy.dialects.mysql import INTEGER + +from api import db +from api.models.efp_schemas import SIMPLE_EFP_DATABASE_SCHEMAS + + +def _to_sqla_type(column_spec): + """ + Map a column specification dictionary to a SQLAlchemy column type. + + Converts the simple type descriptors used in schema definitions to the + appropriate SQLAlchemy type objects for ORM model generation. + + :param column_spec: Column specification with 'type', 'length', and 'unsigned' keys + :type column_spec: Dict[str, Any] + :return: SQLAlchemy column type (String, Integer, Float, or Text) + :rtype: sqlalchemy.types.TypeEngine + :raises ValueError: If column type is not one of: string, integer, float, text + + Example:: + + col_spec = {"type": "string", "length": 24} + sqla_type = _to_sqla_type(col_spec) # Returns String(24) + """ + col_type = column_spec.get("type") + if col_type == "string": + return String(column_spec["length"]) + if col_type == "integer": + if column_spec.get("unsigned"): + return INTEGER(unsigned=True) + return Integer + if col_type == "float": + return Float + if col_type == "text": + return Text + raise ValueError(f"Unsupported column type: {col_type}") + + +def _generate_model(bind_key: str, spec) -> db.Model: + """ + Build a concrete SQLAlchemy model class for the given schema specification. + + Dynamically creates an ORM model with the specified table name, bind key, + and columns based on the schema definition. The generated model class can + be used like any Flask-SQLAlchemy model. + + :param bind_key: Database bind key (e.g., 'cannabis', 'embryo') + :type bind_key: str + :param spec: Database schema specification from SIMPLE_EFP_DATABASE_SCHEMAS + :type spec: Dict[str, Any] + :return: Dynamically generated SQLAlchemy model class + :rtype: db.Model + + Example:: + + schema = SIMPLE_EFP_DATABASE_SCHEMAS['cannabis'] + CannabisModel = _generate_model('cannabis', schema) + # Returns class: CannabisSampleData(db.Model) + """ + attrs = {"__bind_key__": bind_key, "__tablename__": spec["table_name"]} + + for column in spec["columns"]: + kwargs = {"nullable": column.get("nullable", True)} + if column.get("primary_key"): + kwargs["primary_key"] = True + attrs[column["name"]] = db.mapped_column(_to_sqla_type(column), **kwargs) + + class_name = "".join([part.capitalize() for part in bind_key.split("_")]) + "SampleData" + return type(class_name, (db.Model,), attrs) + + +SIMPLE_EFP_SAMPLE_MODELS: Dict[str, db.Model] = { + db_name: _generate_model(db_name, spec) for db_name, spec in SIMPLE_EFP_DATABASE_SCHEMAS.items() +} + +__all__ = ["SIMPLE_EFP_SAMPLE_MODELS"] diff --git a/api/models/efp_schemas.py b/api/models/efp_schemas.py new file mode 100644 index 0000000..884cbd1 --- /dev/null +++ b/api/models/efp_schemas.py @@ -0,0 +1,1983 @@ +""" +Simple schema definitions for eFP databases that only expose a sample_data table. + +This module provides the single source of truth for all simple eFP database schemas, +including column definitions, indexes, seed data, and metadata. These schemas are used +by both the ORM model generator and the database bootstrap scripts. +""" + +from __future__ import annotations + +from typing import Any, Dict, List + +ColumnSpec = Dict[str, Any] +DatabaseSpec = Dict[str, Any] + + +class EfpSchemaBuilder: + """Factory for shared schema helpers used across eFP databases.""" + + @staticmethod + def _column( + name: str, + col_type: str, + *, + length: int | None = None, + unsigned: bool = False, + nullable: bool = True, + default: Any | None = None, + primary_key: bool = False, + ) -> ColumnSpec: + """ + Create a column specification dictionary for schema definitions. + + Helper function to construct column metadata with type, constraints, and defaults + in a consistent format. + + :param name: Column name (e.g., 'data_probeset_id', 'data_signal') + :type name: str + :param col_type: Column type ('string', 'integer', 'float', or 'text') + :type col_type: str + :param length: Maximum length for string types (required for 'string') + :type length: int or None + :param unsigned: Whether integer type is unsigned (MySQL-specific) + :type unsigned: bool + :param nullable: Whether column allows NULL values + :type nullable: bool + :param default: Default value for the column + :type default: Any or None + :param primary_key: Whether column is part of primary key + :type primary_key: bool + :return: Column specification dictionary + :rtype: ColumnSpec + + Example:: + + col = EfpSchemaBuilder._column("data_signal", "float", nullable=False, default=0) + # Returns: {"name": "data_signal", "type": "float", "nullable": False, "default": 0} + """ + column: ColumnSpec = {"name": name, "type": col_type, "nullable": nullable} + if length is not None: + column["length"] = length + if unsigned: + column["unsigned"] = True + if default is not None: + column["default"] = default + if primary_key: + column["primary_key"] = True + return column + + @staticmethod + def _build_schema( + *, + charset: str = "latin1", + table_name: str = "sample_data", + column_overrides: Dict[str, Dict[str, Any]] | None = None, + extra_columns: List[ColumnSpec] | None = None, + index: List[str] | None = None, + seed_rows: List[Dict[str, Any]] | None = None, + identifier_type: str = "agi", + metadata: Dict[str, Any] | None = None, + ) -> DatabaseSpec: + """ + Build a complete database schema specification from base columns and customizations. + + Constructs a schema by starting with the default BASE_COLUMNS, applying any + overrides, and adding extra columns. The resulting schema dictionary is used by + both the ORM generator and bootstrap scripts to ensure consistency. + + :param charset: MySQL character set (e.g., 'latin1', 'utf8mb4') + :type charset: str + :param table_name: Name of the table to create (typically 'sample_data') + :type table_name: str + :param column_overrides: Dictionary of column names to property overrides + :type column_overrides: Dict[str, Dict[str, Any]] or None + :param extra_columns: Additional columns beyond the base set + :type extra_columns: List[ColumnSpec] or None + :param index: List of column names to include in the index + :type index: List[str] or None + :param seed_rows: Initial rows to insert if table is empty + :type seed_rows: List[Dict[str, Any]] or None + :param identifier_type: Gene ID format ('agi' or 'probeset') + :type identifier_type: str + :param metadata: Additional metadata (species, sample_regex, etc.) + :type metadata: Dict[str, Any] or None + :return: Complete database schema specification + :rtype: DatabaseSpec + + Example:: + + schema = EfpSchemaBuilder._build_schema( + charset="utf8mb4", + column_overrides={"proj_id": {"length": 5}}, + metadata={"species": "arabidopsis"} + ) + """ + overrides = column_overrides or {} + columns: List[ColumnSpec] = [] + + for column_name in DEFAULT_BLUEPRINT: + spec = dict(BASE_COLUMNS[column_name]) + if column_name in overrides: + spec.update(overrides[column_name]) + columns.append(spec) + + if extra_columns: + columns.extend(extra_columns) + + # schema dict is the single source of truth for each database + schema: DatabaseSpec = { + "table_name": table_name, + "charset": charset, + "columns": columns, + "index": index if index is not None else list(DEFAULT_INDEX), + "identifier_type": identifier_type, + } + + if seed_rows: + schema["seed_rows"] = seed_rows + if metadata: + schema["metadata"] = metadata + + return schema + + @staticmethod + def _simple_schema( + species: str, + sample_regex: str, + probeset_len: int = 24, + bot_id_len: int = 16, + proj_id_len: int = 5, + charset: str = "latin1", + **kwargs, + ) -> DatabaseSpec: + """ + Helper for simple 5-column schemas (most common pattern). + + Note: Field lengths (probeset_len, bot_id_len, proj_id_len) are determined by the actual + data in each database and can vary even between databases with similar structures. + These lengths are set based on the maximum observed values in the source data. + + :param species: Species name for metadata + :param sample_regex: Regular expression for sample validation + :param probeset_len: Length of data_probeset_id column (varies by database, default 24) + :param bot_id_len: Length of data_bot_id column (varies by database, default 16) + :param proj_id_len: Length of proj_id column (varies by database, default 5) + :param charset: MySQL character set + :param kwargs: Additional arguments passed to _build_schema + :return: Database schema specification + """ + overrides = {} + + # Handle data_probeset_id + if "probeset_type" in kwargs: + probeset_type = kwargs.pop("probeset_type") + overrides["data_probeset_id"] = {"type": probeset_type, "length": None} + # TEXT columns cannot be primary keys in MySQL + if probeset_type == "text": + overrides["data_probeset_id"]["primary_key"] = False + else: + overrides["data_probeset_id"] = {"length": probeset_len} + + # Handle data_bot_id + if "bot_id_type" in kwargs: + bot_id_type = kwargs.pop("bot_id_type") + overrides["data_bot_id"] = {"type": bot_id_type, "length": None} + # TEXT columns cannot be primary keys in MySQL + if bot_id_type == "text": + overrides["data_bot_id"]["primary_key"] = False + else: + overrides["data_bot_id"] = {"length": bot_id_len} + + # Handle proj_id + if proj_id_len != 5: + overrides["proj_id"] = {"length": proj_id_len} + + # Handle type changes for base columns + if "proj_id_type" in kwargs: + proj_type = kwargs.pop("proj_id_type") + overrides.setdefault("proj_id", {})["type"] = proj_type + if proj_type == "integer": + overrides["proj_id"]["unsigned"] = True + + if "sample_id_type" in kwargs: + sample_type = kwargs.pop("sample_id_type") + overrides.setdefault("sample_id", {})["type"] = sample_type + overrides["sample_id"]["unsigned"] = False + if "sample_id_len" in kwargs: + overrides["sample_id"]["length"] = kwargs.pop("sample_id_len") + + # Handle nullable flags and defaults + if "proj_id_default" in kwargs: + overrides.setdefault("proj_id", {})["default"] = kwargs.pop("proj_id_default") + if "signal_nullable" in kwargs: + overrides.setdefault("data_signal", {})["nullable"] = kwargs.pop("signal_nullable") + if "bot_id_nullable" in kwargs: + overrides.setdefault("data_bot_id", {})["nullable"] = kwargs.pop("bot_id_nullable") + if "probeset_nullable" in kwargs: + overrides.setdefault("data_probeset_id", {})["nullable"] = kwargs.pop("probeset_nullable") + + # Build index list, excluding TEXT columns (can't be indexed in MySQL) + index_columns = list(DEFAULT_INDEX) + if "data_probeset_id" in overrides and overrides["data_probeset_id"].get("type") == "text": + index_columns = [col for col in index_columns if col != "data_probeset_id"] + if "data_bot_id" in overrides and overrides["data_bot_id"].get("type") == "text": + index_columns = [col for col in index_columns if col != "data_bot_id"] + + # Allow manual index override if specified + if "index" not in kwargs: + kwargs["index"] = index_columns + + return EfpSchemaBuilder._build_schema( + charset=charset, + column_overrides=overrides, + metadata={"species": species, "sample_regex": sample_regex}, + **kwargs, + ) + + @staticmethod + def _schema_with_qa_columns( + species: str, + sample_regex: str, + probeset_len: int = 24, + bot_id_len: int = 16, + **kwargs, + ) -> DatabaseSpec: + """ + Helper for schemas with quality assurance columns (sample_file_name, data_call, data_p_val). + + :param species: Species name for metadata + :param sample_regex: Regular expression for sample validation + :param probeset_len: Length of data_probeset_id column + :param bot_id_len: Length of data_bot_id column + :param kwargs: Additional arguments passed to _build_schema + :return: Database schema specification + """ + # Handle file_name column type/length + file_name_type = kwargs.pop("file_name_type", "text") + file_name_len = kwargs.pop("file_name_len", 16) if file_name_type == "string" else None + + # Handle call column type/length + call_type = kwargs.pop("call_type", "text") + call_len = kwargs.pop("call_len", 2) if call_type == "string" else None + + # Build QA columns + qa_cols = [ + EfpSchemaBuilder._column("sample_file_name", file_name_type, length=file_name_len, nullable=True), + EfpSchemaBuilder._column("data_call", call_type, length=call_len, nullable=True), + EfpSchemaBuilder._column("data_p_val", "float", nullable=True, default=0), + ] + + # Merge with any extra columns passed in + extra_columns = kwargs.pop("extra_columns", []) + all_extra_cols = qa_cols + extra_columns + + # Build index list - exclude data_probeset_id if it's TEXT type + index_columns = ["data_probeset_id"] + if kwargs.get("probeset_type") == "text": + index_columns = [] + + return EfpSchemaBuilder._simple_schema( + species=species, + sample_regex=sample_regex, + probeset_len=probeset_len, + bot_id_len=bot_id_len, + extra_columns=all_extra_cols, + index=index_columns, + **kwargs, + ) + + +# base column specs keep every schema consistent unless an override is provided +BASE_COLUMNS: Dict[str, ColumnSpec] = { + "proj_id": EfpSchemaBuilder._column("proj_id", "string", length=5, nullable=False, default="0"), + "sample_id": EfpSchemaBuilder._column("sample_id", "integer", unsigned=True, nullable=False, default=0), + "data_probeset_id": EfpSchemaBuilder._column( + "data_probeset_id", "string", length=24, nullable=False, primary_key=True + ), + "data_signal": EfpSchemaBuilder._column("data_signal", "float", nullable=False, default=0, primary_key=True), + "data_bot_id": EfpSchemaBuilder._column("data_bot_id", "string", length=16, nullable=False, primary_key=True), +} + +# blueprint defines the order we hydrate into tables +DEFAULT_BLUEPRINT: List[str] = ["proj_id", "sample_id", "data_probeset_id", "data_signal", "data_bot_id"] +DEFAULT_INDEX = ["data_probeset_id", "data_bot_id", "data_signal"] + +# Replace the existing SIMPLE_EFP_DATABASE_SCHEMAS dict in efp_schemas.py with this: + +SIMPLE_EFP_DATABASE_SCHEMAS: Dict[str, DatabaseSpec] = { + 'actinidia_bud_development': EfpSchemaBuilder._simple_schema( + species='actinidia', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=12, + signal_nullable=True, + bot_id_len=8, + charset='utf8mb4', + ), + 'actinidia_flower_fruit_development': EfpSchemaBuilder._simple_schema( + species='actinidia', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=12, + signal_nullable=True, + charset='utf8mb4', + ), + 'actinidia_postharvest': EfpSchemaBuilder._simple_schema( + species='actinidia', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=12, + signal_nullable=True, + bot_id_len=24, + charset='utf8mb4', + ), + 'actinidia_vegetative_growth': EfpSchemaBuilder._simple_schema( + species='actinidia', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=12, + signal_nullable=True, + charset='utf8mb4', + ), + 'affydb': EfpSchemaBuilder._schema_with_qa_columns( + species='arabidopsis', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_type='integer', + probeset_len=30, + probeset_nullable=True, + bot_id_type='text', + bot_id_nullable=True, + extra_columns=[ + EfpSchemaBuilder._column('data_num', 'integer', default=0), + ], + ), + 'apple': EfpSchemaBuilder._simple_schema( + species='apple', + sample_regex=r'.*', # TODO: Add specific pattern + probeset_len=18, + bot_id_len=12, + bot_id_nullable=True, + charset='utf8mb4', + ), + 'arabidopsis_ecotypes': EfpSchemaBuilder._schema_with_qa_columns( + species='arabidopsis', + sample_regex=r"^[A-Z0-9_]{1,20}$|Med_CTRL$", + proj_id_len=15, + probeset_len=30, + probeset_nullable=True, + signal_nullable=True, + bot_id_nullable=True, + ), + 'arachis': EfpSchemaBuilder._simple_schema( + species='arachis', + sample_regex=r"^[\D\d_]{1,30}|MED_CTRL$", + sample_id_type='string', + sample_id_len=5, + proj_id_len=24, + proj_id_default=None, + probeset_len=30, + bot_id_len=65, + ), + 'atgenexp': EfpSchemaBuilder._schema_with_qa_columns( + species='arabidopsis', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_type='integer', + probeset_len=30, + probeset_nullable=True, + bot_id_len=50, + ), + 'atgenexp_hormone': EfpSchemaBuilder._simple_schema( + species='arabidopsis', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_type='integer', + probeset_len=30, + probeset_nullable=True, + signal_nullable=True, + bot_id_len=50, + bot_id_nullable=True, + ), + 'atgenexp_pathogen': EfpSchemaBuilder._simple_schema( + species='arabidopsis', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=30, + probeset_nullable=True, + signal_nullable=True, + bot_id_len=50, + bot_id_nullable=True, + ), + 'atgenexp_plus': EfpSchemaBuilder._schema_with_qa_columns( + species='arabidopsis', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=30, + probeset_nullable=True, + signal_nullable=True, + bot_id_len=50, + ), + 'atgenexp_stress': EfpSchemaBuilder._simple_schema( + # TODO: atgenexp_stress needs manual review for data_call/sample_file_name columns + species='arabidopsis', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=30, + probeset_nullable=True, + bot_id_len=40, + bot_id_nullable=True, + ), + 'barley_mas': EfpSchemaBuilder._schema_with_qa_columns( + species='barley', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=30, + signal_nullable=True, + bot_id_len=24, + extra_columns=[ + EfpSchemaBuilder._column('sample_tissue', 'string', length=20, nullable=True), + ], + ), + 'barley_rma': EfpSchemaBuilder._schema_with_qa_columns( + species='barley', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=30, + signal_nullable=True, + bot_id_len=24, + ), + 'barley_seed': EfpSchemaBuilder._simple_schema( + species='barley', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=32, + signal_nullable=True, + bot_id_len=12, + charset='utf8mb4', + ), + 'barley_spike_meristem': EfpSchemaBuilder._simple_schema( + species='barley', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + signal_nullable=True, + bot_id_len=24, + charset='utf8mb4', + ), + 'barley_spike_meristem_v3': EfpSchemaBuilder._simple_schema( + species='barley', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=32, + signal_nullable=True, + bot_id_len=24, + charset='utf8mb4', + ), + 'brachypodium': EfpSchemaBuilder._simple_schema( + species='brachypodium', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=18, + signal_nullable=True, + bot_id_len=50, + ), + 'brachypodium_Bd21': EfpSchemaBuilder._simple_schema( + species='brachypodium', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=18, + signal_nullable=True, + bot_id_len=32, + charset='utf8mb4', + ), + 'brachypodium_embryogenesis': EfpSchemaBuilder._simple_schema( + species='brachypodium', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=18, + signal_nullable=True, + bot_id_len=50, + ), + 'brachypodium_grains': EfpSchemaBuilder._simple_schema( + species='brachypodium', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=18, + signal_nullable=True, + bot_id_len=32, + charset='utf8mb4', + ), + 'brachypodium_metabolites_map': EfpSchemaBuilder._simple_schema( + species='brachypodium', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=64, + signal_nullable=True, + bot_id_len=45, + charset='utf8mb4', + ), + 'brachypodium_photo_thermocycle': EfpSchemaBuilder._simple_schema( + species='brachypodium', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=18, + signal_nullable=True, + bot_id_len=12, + ), + 'brassica_rapa': EfpSchemaBuilder._simple_schema( + species='brassica', + sample_regex=r'.*', # TODO: Add specific pattern + probeset_len=16, + bot_id_len=10, + bot_id_nullable=True, + charset='utf8mb4', + ), + 'cacao_developmental_atlas': EfpSchemaBuilder._simple_schema( + species='cacao', + sample_regex=r'.*', # TODO: Add specific pattern + bot_id_nullable=True, + charset='utf8mb4', + ), + 'cacao_developmental_atlas_sca': EfpSchemaBuilder._simple_schema( + species='cacao', + sample_regex=r'.*', # TODO: Add specific pattern + bot_id_nullable=True, + charset='utf8mb4', + ), + 'cacao_drought_diurnal_atlas': EfpSchemaBuilder._simple_schema( + species='cacao', + sample_regex=r'.*', # TODO: Add specific pattern + bot_id_nullable=True, + charset='utf8mb4', + ), + 'cacao_drought_diurnal_atlas_sca': EfpSchemaBuilder._simple_schema( + species='cacao', + sample_regex=r'.*', # TODO: Add specific pattern + bot_id_nullable=True, + charset='utf8mb4', + ), + 'cacao_infection': EfpSchemaBuilder._simple_schema( + species='cacao', + sample_regex=r'.*', # TODO: Add specific pattern + probeset_len=18, + bot_id_len=24, + bot_id_nullable=True, + charset='utf8mb4', + ), + 'cacao_leaf': EfpSchemaBuilder._simple_schema( + species='cacao', + sample_regex=r'.*', # TODO: Add specific pattern + probeset_len=18, + bot_id_len=12, + bot_id_nullable=True, + charset='utf8mb4', + ), + 'cacao_meristem_atlas_sca': EfpSchemaBuilder._simple_schema( + species='cacao', + sample_regex=r'.*', # TODO: Add specific pattern + bot_id_len=24, + bot_id_nullable=True, + charset='utf8mb4', + ), + 'cacao_seed_atlas_sca': EfpSchemaBuilder._simple_schema( + species='cacao', + sample_regex=r'.*', # TODO: Add specific pattern + bot_id_len=24, + bot_id_nullable=True, + charset='utf8mb4', + ), + 'camelina': EfpSchemaBuilder._simple_schema( + # TODO: camelina needs manual review for data_call/sample_file_name columns + species='camelina', + sample_regex=r'.*', # TODO: Add specific pattern + sample_id_type='string', + sample_id_len=5, + proj_id_default=None, + probeset_len=20, + bot_id_len=40, + ), + 'camelina_tpm': EfpSchemaBuilder._simple_schema( + # TODO: camelina_tpm needs manual review for data_call/sample_file_name columns + species='camelina', + sample_regex=r'.*', # TODO: Add specific pattern + sample_id_type='string', + sample_id_len=5, + proj_id_default=None, + probeset_len=20, + bot_id_len=40, + ), + 'cannabis': EfpSchemaBuilder._simple_schema( + species='cannabis', + sample_regex=r"^PK-\D{1,4}|MED_CTRL$", + proj_id_len=2, + bot_id_len=8, + ), + 'canola': EfpSchemaBuilder._schema_with_qa_columns( + species='canola', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_type='text', + signal_nullable=True, + bot_id_type='text', + extra_columns=[ + EfpSchemaBuilder._column('sample_tissue', 'text'), + ], + ), + 'canola_original': EfpSchemaBuilder._schema_with_qa_columns( + species='canola', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_type='text', + signal_nullable=True, + bot_id_type='text', + extra_columns=[ + EfpSchemaBuilder._column('sample_tissue', 'text'), + ], + ), + 'canola_original_v2': EfpSchemaBuilder._schema_with_qa_columns( + species='canola', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_type='text', + signal_nullable=True, + bot_id_type='text', + extra_columns=[ + EfpSchemaBuilder._column('sample_tissue', 'text'), + ], + ), + 'canola_seed': EfpSchemaBuilder._simple_schema( + species='canola', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=16, + signal_nullable=True, + bot_id_len=12, + charset='utf8mb4', + ), + 'cassava_atlas': EfpSchemaBuilder._simple_schema( + species='cassava', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + signal_nullable=True, + bot_id_len=24, + charset='utf8mb4', + ), + 'cassava_cbb': EfpSchemaBuilder._simple_schema( + species='cassava', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + signal_nullable=True, + bot_id_len=24, + charset='utf8mb4', + ), + 'cassava_eacmv': EfpSchemaBuilder._simple_schema( + species='cassava', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + signal_nullable=True, + bot_id_len=24, + charset='utf8mb4', + ), + 'circadian_mutants': EfpSchemaBuilder._simple_schema( + species='circadian mutants', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=12, + signal_nullable=True, + bot_id_len=18, + charset='utf8mb4', + ), + 'cuscuta': EfpSchemaBuilder._simple_schema( + species='cuscuta', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=2, + probeset_len=16, + probeset_nullable=True, + signal_nullable=True, + bot_id_len=12, + bot_id_nullable=True, + charset='utf8mb4', + ), + 'cuscuta_early_haustoriogenesis': EfpSchemaBuilder._simple_schema( + species='cuscuta', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=12, + signal_nullable=True, + bot_id_len=8, + charset='utf8mb4', + ), + 'cuscuta_lmd': EfpSchemaBuilder._simple_schema( + species='cuscuta', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=12, + signal_nullable=True, + bot_id_len=8, + charset='utf8mb4', + ), + 'dna_damage': EfpSchemaBuilder._simple_schema( + species='arabidopsis', + sample_regex=r"^\D{1,3}.{1,30}_plus_Y|\D{1,3}.{1,30}_minus_Y|Med_CTRL$", + probeset_len=10, + bot_id_len=32, + bot_id_nullable=True, + charset='utf8mb4', + ), + 'durum_wheat_abiotic_stress': EfpSchemaBuilder._simple_schema( + species='wheat', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=32, + signal_nullable=True, + bot_id_len=32, + charset='utf8mb4', + ), + 'durum_wheat_biotic_stress': EfpSchemaBuilder._simple_schema( + species='wheat', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=32, + signal_nullable=True, + bot_id_len=42, + charset='utf8mb4', + ), + 'durum_wheat_development': EfpSchemaBuilder._simple_schema( + species='wheat', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=32, + signal_nullable=True, + bot_id_len=24, + charset='utf8mb4', + ), + 'embryo': EfpSchemaBuilder._simple_schema( + species='arabidopsis', + sample_regex=r"^\D{1,3}_\d$|Med_CTRL$", + proj_id_len=3, + probeset_len=16, + signal_nullable=True, + bot_id_len=8, + ), + 'eucalyptus': EfpSchemaBuilder._simple_schema( + species='eucalyptus', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=16, + signal_nullable=True, + bot_id_len=42, + charset='utf8mb4', + ), + 'euphorbia': EfpSchemaBuilder._simple_schema( + species='euphorbia', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=18, + signal_nullable=True, + bot_id_len=24, + charset='utf8mb4', + ), + 'gc_drought': EfpSchemaBuilder._simple_schema( + species='gc drought', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=12, + signal_nullable=True, + bot_id_len=12, + charset='utf8mb4', + ), + 'germination': EfpSchemaBuilder._simple_schema( + species='arabidopsis', + sample_regex=r"^\d{1,3}\D{1,4}_\d{1,3}|harvest_\d|Med_CTRL$", + proj_id_len=3, + probeset_len=30, + signal_nullable=True, + ), + 'grape_developmental': EfpSchemaBuilder._schema_with_qa_columns( + species='grape', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_type='integer', + proj_id_default=None, + probeset_len=40, + bot_id_len=50, + extra_columns=[ + EfpSchemaBuilder._column('sample_tissue', 'text'), + ], + ), + 'guard_cell': EfpSchemaBuilder._schema_with_qa_columns( + species='guard cell', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=30, + signal_nullable=True, + bot_id_len=24, + ), + 'gynoecium': EfpSchemaBuilder._simple_schema( + species='gynoecium', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=12, + signal_nullable=True, + charset='utf8mb4', + ), + 'heterodera_schachtii': EfpSchemaBuilder._simple_schema( + species='heterodera', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=12, + signal_nullable=True, + charset='utf8mb4', + ), + 'hnahal': EfpSchemaBuilder._simple_schema( + species='hnahal', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_type='text', + signal_nullable=True, + bot_id_type='text', + extra_columns=[ + EfpSchemaBuilder._column('channel', 'string', length=5, nullable=True), + ], + ), + 'human_body_map_2': EfpSchemaBuilder._schema_with_qa_columns( + species='human', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=28, + signal_nullable=True, + bot_id_len=20, + ), + 'human_developmental': EfpSchemaBuilder._schema_with_qa_columns( + species='human', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=32, + probeset_nullable=True, + signal_nullable=True, + bot_id_len=24, + bot_id_nullable=True, + ), + 'human_developmental_SpongeLab': EfpSchemaBuilder._schema_with_qa_columns( + species='human', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_type='text', + signal_nullable=True, + bot_id_type='text', + ), + 'human_diseased': EfpSchemaBuilder._schema_with_qa_columns( + species='human', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_type='text', + signal_nullable=True, + bot_id_type='text', + ), + 'kalanchoe': EfpSchemaBuilder._simple_schema( + species='kalanchoe', + sample_regex=r"^\D{1,4}_\D{1,5}_rep\d|MED_CTRL$", + proj_id_len=2, + ), + 'kalanchoe_time_course_analysis': EfpSchemaBuilder._simple_schema( + species='kalanchoe', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=18, + signal_nullable=True, + charset='utf8mb4', + ), + 'klepikova': EfpSchemaBuilder._simple_schema( + # TODO: klepikova needs manual review for data_call/sample_file_name columns + species='arabidopsis', + sample_regex=r"^SRR\d{1,9}|Med_CTRL$", + proj_id_len=3, + probeset_len=30, + signal_nullable=True, + ), + # TODO: 'lateral_root_initiation': Complex schema (missing base columns) - needs manual definition + 'light_series': EfpSchemaBuilder._schema_with_qa_columns( + species='light series', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=30, + signal_nullable=True, + bot_id_len=30, + ), + 'lipid_map': EfpSchemaBuilder._simple_schema( + species='lipid map', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=64, + signal_nullable=True, + charset='utf8mb4', + ), + 'little_millet': EfpSchemaBuilder._simple_schema( + species='little_millet', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=2, + probeset_len=32, + probeset_nullable=True, + signal_nullable=True, + bot_id_len=12, + bot_id_nullable=True, + charset='utf8mb4', + ), + 'lupin_lcm_leaf': EfpSchemaBuilder._simple_schema( + species='lupin', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=32, + signal_nullable=True, + bot_id_len=32, + charset='utf8mb4', + ), + 'lupin_lcm_pod': EfpSchemaBuilder._simple_schema( + species='lupin', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=32, + signal_nullable=True, + bot_id_len=32, + charset='utf8mb4', + ), + 'lupin_lcm_stem': EfpSchemaBuilder._simple_schema( + species='lupin', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=32, + signal_nullable=True, + bot_id_len=32, + charset='utf8mb4', + ), + 'lupin_pod_seed': EfpSchemaBuilder._simple_schema( + species='lupin', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=32, + signal_nullable=True, + bot_id_len=32, + charset='utf8mb4', + ), + 'lupin_whole_plant': EfpSchemaBuilder._simple_schema( + species='lupin', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=32, + signal_nullable=True, + bot_id_len=32, + charset='utf8mb4', + ), + 'maize_RMA_linear': EfpSchemaBuilder._schema_with_qa_columns( + species='maize', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=20, + signal_nullable=True, + bot_id_len=30, + extra_columns=[ + EfpSchemaBuilder._column('sample_tissue', 'text'), + ], + ), + 'maize_RMA_log': EfpSchemaBuilder._schema_with_qa_columns( + species='maize', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=20, + signal_nullable=True, + bot_id_len=30, + ), + 'maize_atlas': EfpSchemaBuilder._simple_schema( + species='maize', + sample_regex=r'.*', # TODO: Add specific pattern + sample_id_type='string', + sample_id_len=5, + proj_id_default=None, + probeset_len=25, + bot_id_len=40, + ), + 'maize_atlas_v5': EfpSchemaBuilder._simple_schema( + species='maize', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=25, + signal_nullable=True, + bot_id_len=40, + charset='utf8mb4', + ), + 'maize_buell_lab': EfpSchemaBuilder._simple_schema( + species='maize', + sample_regex=r'.*', # TODO: Add specific pattern + bot_id_len=50, + ), + 'maize_early_seed': EfpSchemaBuilder._simple_schema( + species='maize', + sample_regex=r'.*', # TODO: Add specific pattern + bot_id_len=50, + ), + 'maize_ears': EfpSchemaBuilder._schema_with_qa_columns( + species='maize', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=20, + signal_nullable=True, + ), + 'maize_embryonic_leaf_development': EfpSchemaBuilder._simple_schema( + species='maize', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=18, + signal_nullable=True, + bot_id_len=24, + charset='utf8mb4', + ), + 'maize_enzyme': EfpSchemaBuilder._schema_with_qa_columns( + species='maize', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=40, + signal_nullable=True, + bot_id_len=8, + ), + 'maize_gdowns': EfpSchemaBuilder._simple_schema( + species='maize', + sample_regex=r'.*', # TODO: Add specific pattern + sample_id_type='string', + sample_id_len=30, + proj_id_len=30, + proj_id_default=None, + probeset_len=40, + bot_id_len=40, + ), + 'maize_iplant': EfpSchemaBuilder._schema_with_qa_columns( + species='maize', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=20, + signal_nullable=True, + ), + 'maize_kernel_v5': EfpSchemaBuilder._simple_schema( + species='maize', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=25, + signal_nullable=True, + bot_id_len=8, + charset='utf8mb4', + ), + 'maize_leaf_gradient': EfpSchemaBuilder._schema_with_qa_columns( + species='maize', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=20, + signal_nullable=True, + bot_id_len=12, + ), + 'maize_lipid_map': EfpSchemaBuilder._simple_schema( + species='maize', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + signal_nullable=True, + bot_id_len=12, + charset='utf8mb4', + ), + 'maize_metabolite': EfpSchemaBuilder._schema_with_qa_columns( + species='maize', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=64, + signal_nullable=True, + bot_id_len=5, + ), + 'maize_nitrogen_use_efficiency': EfpSchemaBuilder._simple_schema( + species='maize', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + signal_nullable=True, + bot_id_len=24, + charset='utf8mb4', + ), + 'maize_rice_comparison': EfpSchemaBuilder._schema_with_qa_columns( + species='maize', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=16, + signal_nullable=True, + bot_id_len=12, + ), + 'maize_root': EfpSchemaBuilder._simple_schema( + species='maize', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=30, + signal_nullable=True, + bot_id_len=255, + ), + 'maize_stress_v5': EfpSchemaBuilder._simple_schema( + species='maize', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=25, + signal_nullable=True, + bot_id_len=20, + charset='utf8mb4', + ), + 'mangosteen_aril_vs_rind': EfpSchemaBuilder._simple_schema( + species='mangosteen', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=2, + proj_id_default=None, + probeset_len=8, + signal_nullable=True, + bot_id_len=8, + charset='utf8mb4', + ), + 'mangosteen_callus': EfpSchemaBuilder._simple_schema( + species='mangosteen', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=2, + proj_id_default=None, + probeset_len=8, + signal_nullable=True, + bot_id_len=8, + charset='utf8mb4', + ), + 'mangosteen_diseased_vs_normal': EfpSchemaBuilder._simple_schema( + species='mangosteen', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=2, + proj_id_default=None, + probeset_len=8, + signal_nullable=True, + bot_id_len=12, + charset='utf8mb4', + ), + 'mangosteen_fruit_ripening': EfpSchemaBuilder._simple_schema( + species='mangosteen', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=2, + proj_id_default=None, + probeset_len=8, + signal_nullable=True, + bot_id_len=8, + charset='utf8mb4', + ), + 'mangosteen_seed_development': EfpSchemaBuilder._simple_schema( + species='mangosteen', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=2, + proj_id_default=None, + probeset_len=8, + signal_nullable=True, + bot_id_len=12, + charset='utf8mb4', + ), + 'mangosteen_seed_development_germination': EfpSchemaBuilder._simple_schema( + species='mangosteen', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=2, + proj_id_default=None, + probeset_len=8, + signal_nullable=True, + bot_id_len=8, + charset='utf8mb4', + ), + 'mangosteen_seed_germination': EfpSchemaBuilder._simple_schema( + species='mangosteen', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=2, + proj_id_default=None, + probeset_len=8, + signal_nullable=True, + bot_id_len=12, + charset='utf8mb4', + ), + 'marchantia_organ_stress': EfpSchemaBuilder._simple_schema( + species='marchantia', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=32, + signal_nullable=True, + bot_id_len=32, + charset='utf8mb4', + ), + 'medicago_mas': EfpSchemaBuilder._schema_with_qa_columns( + species='medicago', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=28, + signal_nullable=True, + bot_id_len=22, + extra_columns=[ + EfpSchemaBuilder._column('sample_tissue', 'text'), + ], + ), + 'medicago_rma': EfpSchemaBuilder._schema_with_qa_columns( + species='medicago', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=28, + signal_nullable=True, + bot_id_len=22, + ), + 'medicago_root': EfpSchemaBuilder._simple_schema( + species='medicago', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=18, + signal_nullable=True, + charset='utf8mb4', + ), + 'medicago_root_v5': EfpSchemaBuilder._simple_schema( + species='medicago', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=64, + signal_nullable=True, + charset='utf8mb4', + ), + 'medicago_seed': EfpSchemaBuilder._simple_schema( + species='medicago', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=18, + signal_nullable=True, + bot_id_len=15, + ), + 'meristem_db': EfpSchemaBuilder._simple_schema( + species='meristem db', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=30, + signal_nullable=True, + bot_id_len=18, + extra_columns=[ + EfpSchemaBuilder._column('channel', 'string', length=5, nullable=True), + ], + ), + 'meristem_db_new': EfpSchemaBuilder._simple_schema( + species='meristem db new', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_type='text', + signal_nullable=True, + bot_id_type='text', + extra_columns=[ + EfpSchemaBuilder._column('channel', 'string', length=5, nullable=True), + ], + ), + # TODO: 'mouse_db': Complex schema (missing base columns) - needs manual definition + # TODO: 'oat': Complex schema (missing base columns) - needs manual definition + 'phelipanche': EfpSchemaBuilder._simple_schema( + species='phelipanche', + sample_regex=r"^[a-z_-]{1,35}|MED_CTRL$", + proj_id_default=None, + probeset_len=16, + signal_nullable=True, + bot_id_len=32, + charset='utf8mb4', + ), + 'physcomitrella_db': EfpSchemaBuilder._simple_schema( + species='physcomitrella', + sample_regex=r"^[a-z_123]{1,15}|MED_CTRL$", + sample_id_type='string', + sample_id_len=30, + proj_id_len=30, + proj_id_default=None, + probeset_len=40, + bot_id_len=40, + ), + 'poplar': EfpSchemaBuilder._schema_with_qa_columns( + species='poplar', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + file_name_type='string', + file_name_len=40, + probeset_len=70, + call_type='string', + call_len=12, + bot_id_len=40, + bot_id_nullable=True, + extra_columns=[ + EfpSchemaBuilder._column('data_num', 'integer', default=0), + ], + ), + 'poplar_hormone': EfpSchemaBuilder._simple_schema( + species='poplar', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=18, + signal_nullable=True, + bot_id_len=12, + charset='utf8mb4', + ), + 'poplar_leaf': EfpSchemaBuilder._simple_schema( + species='poplar', + sample_regex=r'.*', # TODO: Add specific pattern + probeset_len=70, + bot_id_len=40, + bot_id_nullable=True, + ), + 'poplar_xylem': EfpSchemaBuilder._simple_schema( + species='poplar', + sample_regex=r'.*', # TODO: Add specific pattern + probeset_len=70, + bot_id_len=40, + bot_id_nullable=True, + ), + 'potato_dev': EfpSchemaBuilder._simple_schema( + species='potato', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=40, + signal_nullable=True, + bot_id_len=15, + ), + 'potato_stress': EfpSchemaBuilder._simple_schema( + species='potato', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=40, + signal_nullable=True, + bot_id_len=12, + ), + 'potato_wounding': EfpSchemaBuilder._simple_schema( + species='potato', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=40, + signal_nullable=True, + bot_id_len=12, + charset='utf8mb4', + ), + 'rice_abiotic_stress_sc_pseudobulk': EfpSchemaBuilder._simple_schema( + species='rice', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=16, + signal_nullable=True, + bot_id_len=64, + charset='utf8mb4', + ), + 'rice_drought_heat_stress': EfpSchemaBuilder._simple_schema( + species='rice', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + signal_nullable=True, + bot_id_len=12, + charset='utf8mb4', + ), + 'rice_leaf_gradient': EfpSchemaBuilder._schema_with_qa_columns( + species='rice', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=18, + signal_nullable=True, + bot_id_len=12, + ), + 'rice_maize_comparison': EfpSchemaBuilder._schema_with_qa_columns( + species='maize', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=18, + signal_nullable=True, + bot_id_len=12, + ), + 'rice_mas': EfpSchemaBuilder._schema_with_qa_columns( + species='rice', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=28, + signal_nullable=True, + bot_id_len=26, + extra_columns=[ + EfpSchemaBuilder._column('sample_tissue', 'text'), + ], + ), + 'rice_metabolite': EfpSchemaBuilder._schema_with_qa_columns( + species='rice', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=25, + signal_nullable=True, + bot_id_len=6, + ), + 'rice_rma': EfpSchemaBuilder._schema_with_qa_columns( + species='rice', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=28, + signal_nullable=True, + bot_id_len=26, + ), + 'rice_root': EfpSchemaBuilder._simple_schema( + species='rice', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=2, + probeset_len=16, + signal_nullable=True, + bot_id_len=8, + charset='utf8mb4', + ), + 'rohan': EfpSchemaBuilder._schema_with_qa_columns( + species='rohan', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_type='text', + signal_nullable=True, + bot_id_type='text', + ), + 'root': EfpSchemaBuilder._schema_with_qa_columns( + species='root', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=30, + signal_nullable=True, + bot_id_len=24, + ), + 'root_Schaefer_lab': EfpSchemaBuilder._simple_schema( + species='root Schaefer lab', + sample_regex=r'.*', # TODO: Add specific pattern + probeset_len=16, + bot_id_len=20, + bot_id_nullable=True, + ), + 'rpatel': EfpSchemaBuilder._schema_with_qa_columns( + species='rpatel', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_type='text', + signal_nullable=True, + bot_id_type='text', + ), + 'seed_db': EfpSchemaBuilder._schema_with_qa_columns( + species='seed db', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=20, + file_name_type='string', + file_name_len=100, + probeset_len=30, + signal_nullable=True, + call_type='string', + call_len=40, + bot_id_len=64, + ), + 'seedcoat': EfpSchemaBuilder._schema_with_qa_columns( + species='oat', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=22, + signal_nullable=True, + bot_id_len=12, + ), + 'selaginella': EfpSchemaBuilder._simple_schema( + species='selaginella', + sample_regex=r"^[\D\d]{1,33}|MED_CTRL$", + probeset_len=18, + bot_id_len=36, + ), + 'shoot_apex': EfpSchemaBuilder._schema_with_qa_columns( + species='arabidopsis', + sample_regex=r"^\D{1,5}\d{0,2}|MED_CTRL$", + proj_id_len=2, + proj_id_default=None, + file_name_type='string', + file_name_len=16, + probeset_len=12, + call_type='string', + call_len=2, + bot_id_len=8, + ), + 'silique': EfpSchemaBuilder._simple_schema( + species='arabidopsis', + sample_regex=r"^\d{1,3}_dap.{1,58}_R1_001|Med_CTRL$", + proj_id_default=None, + probeset_len=12, + signal_nullable=True, + bot_id_len=64, + ), + 'single_cell': EfpSchemaBuilder._simple_schema( + species='arabidopsis', + sample_regex=r"^\D+\d+_WT\d+.ExprMean|MED_CTRL$", + proj_id_default=None, + signal_nullable=True, + bot_id_len=32, + ), + 'sorghum_atlas_w_BS_cells': EfpSchemaBuilder._simple_schema( + species='sorghum', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + signal_nullable=True, + bot_id_len=24, + charset='utf8mb4', + ), + 'sorghum_comparative_transcriptomics': EfpSchemaBuilder._simple_schema( + species='sorghum', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=18, + signal_nullable=True, + bot_id_len=40, + charset='utf8mb4', + ), + 'sorghum_developmental': EfpSchemaBuilder._simple_schema( + species='sorghum', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=16, + signal_nullable=True, + bot_id_len=12, + charset='utf8mb4', + ), + 'sorghum_developmental_2': EfpSchemaBuilder._simple_schema( + species='sorghum', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=16, + signal_nullable=True, + bot_id_len=32, + charset='utf8mb4', + ), + 'sorghum_flowering_activation': EfpSchemaBuilder._simple_schema( + species='sorghum', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=16, + signal_nullable=True, + bot_id_len=32, + charset='utf8mb4', + ), + 'sorghum_low_phosphorus': EfpSchemaBuilder._simple_schema( + species='sorghum', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + signal_nullable=True, + charset='utf8mb4', + ), + 'sorghum_nitrogen_stress': EfpSchemaBuilder._simple_schema( + species='sorghum', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=16, + signal_nullable=True, + bot_id_len=32, + charset='utf8mb4', + ), + 'sorghum_nitrogen_use_efficiency': EfpSchemaBuilder._simple_schema( + species='sorghum', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + signal_nullable=True, + bot_id_len=12, + charset='utf8mb4', + ), + 'sorghum_phosphate_stress': EfpSchemaBuilder._simple_schema( + species='sorghum', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + signal_nullable=True, + bot_id_len=32, + charset='utf8mb4', + ), + 'sorghum_plasma': EfpSchemaBuilder._simple_schema( + species='sorghum', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + signal_nullable=True, + charset='utf8mb4', + ), + 'sorghum_saline_alkali_stress': EfpSchemaBuilder._simple_schema( + species='sorghum', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=16, + signal_nullable=True, + bot_id_len=32, + charset='utf8mb4', + ), + 'sorghum_stress': EfpSchemaBuilder._simple_schema( + species='sorghum', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=16, + signal_nullable=True, + bot_id_len=12, + charset='utf8mb4', + ), + 'sorghum_strigolactone_variation': EfpSchemaBuilder._simple_schema( + species='sorghum', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=16, + signal_nullable=True, + bot_id_len=32, + charset='utf8mb4', + ), + 'sorghum_sulfur_stress': EfpSchemaBuilder._simple_schema( + species='sorghum', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + signal_nullable=True, + bot_id_len=32, + charset='utf8mb4', + ), + 'sorghum_temperature_stress': EfpSchemaBuilder._simple_schema( + species='sorghum', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=16, + signal_nullable=True, + bot_id_len=32, + charset='utf8mb4', + ), + 'sorghum_vascularization_and_internode': EfpSchemaBuilder._simple_schema( + species='sorghum', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + signal_nullable=True, + bot_id_len=32, + charset='utf8mb4', + ), + 'soybean': EfpSchemaBuilder._schema_with_qa_columns( + species='soybean', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + proj_id_default=None, + probeset_len=36, + bot_id_len=22, + ), + 'soybean_embryonic_development': EfpSchemaBuilder._simple_schema( + species='soybean', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + signal_nullable=True, + bot_id_len=42, + charset='utf8mb4', + ), + 'soybean_heart_cotyledon_globular': EfpSchemaBuilder._simple_schema( + species='soybean', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + signal_nullable=True, + bot_id_len=42, + charset='utf8mb4', + ), + 'soybean_senescence': EfpSchemaBuilder._simple_schema( + species='soybean', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + signal_nullable=True, + bot_id_len=8, + charset='utf8mb4', + ), + 'soybean_severin': EfpSchemaBuilder._schema_with_qa_columns( + species='soybean', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + proj_id_default=None, + probeset_len=18, + bot_id_len=18, + ), + 'spruce': EfpSchemaBuilder._simple_schema( + species='spruce', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=16, + signal_nullable=True, + bot_id_len=24, + charset='utf8mb4', + ), + 'strawberry': EfpSchemaBuilder._simple_schema( + species='strawberry', + sample_regex=r"^\D{1,12}_.{1,8}_\D{1,2}|MED_CTRL$", + proj_id_default=None, + probeset_len=16, + signal_nullable=True, + bot_id_len=24, + charset='utf8mb4', + ), + 'striga': EfpSchemaBuilder._simple_schema( + species='striga', + sample_regex=r"^\D{1,35}|MED_CTRL$", + proj_id_default=None, + signal_nullable=True, + bot_id_len=42, + ), + 'sugarcane_culms': EfpSchemaBuilder._simple_schema( + species='sugarcane', + sample_regex=r'.*', # TODO: Add specific pattern + probeset_len=32, + bot_id_nullable=True, + charset='utf8mb4', + ), + 'sugarcane_leaf': EfpSchemaBuilder._simple_schema( + species='sugarcane', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=12, + probeset_len=32, + bot_id_len=32, + bot_id_nullable=True, + charset='utf8mb4', + ), + 'sunflower': EfpSchemaBuilder._simple_schema( + species='sunflower', + sample_regex=r'.*', # TODO: Add specific pattern + probeset_len=16, + bot_id_nullable=True, + ), + 'thellungiella_db': EfpSchemaBuilder._simple_schema( + # TODO: thellungiella_db needs manual review for data_call/sample_file_name columns + species='thellungiella', + sample_regex=r'.*', # TODO: Add specific pattern + sample_id_type='string', + sample_id_len=30, + proj_id_len=30, + proj_id_default=None, + probeset_len=40, + bot_id_len=40, + ), + 'tomato': EfpSchemaBuilder._schema_with_qa_columns( + species='tomato', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=18, + probeset_nullable=True, + signal_nullable=True, + bot_id_len=18, + bot_id_nullable=True, + ), + 'tomato_ils': EfpSchemaBuilder._simple_schema( + species='tomato', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=20, + probeset_nullable=True, + signal_nullable=True, + bot_id_len=12, + bot_id_nullable=True, + ), + 'tomato_ils2': EfpSchemaBuilder._simple_schema( + species='tomato', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=20, + probeset_nullable=True, + signal_nullable=True, + bot_id_len=12, + bot_id_nullable=True, + extra_columns=[ + EfpSchemaBuilder._column('log', 'float'), + EfpSchemaBuilder._column('p_val', 'float'), + ], + ), + 'tomato_ils3': EfpSchemaBuilder._simple_schema( + species='tomato', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=20, + probeset_nullable=True, + signal_nullable=True, + bot_id_nullable=True, + ), + 'tomato_meristem': EfpSchemaBuilder._simple_schema( + species='tomato', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=2, + probeset_len=18, + probeset_nullable=True, + signal_nullable=True, + bot_id_len=24, + bot_id_nullable=True, + ), + 'tomato_renormalized': EfpSchemaBuilder._schema_with_qa_columns( + species='tomato', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=18, + probeset_nullable=True, + signal_nullable=True, + bot_id_len=18, + bot_id_nullable=True, + ), + 'tomato_root': EfpSchemaBuilder._simple_schema( + species='tomato', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=2, + probeset_len=18, + probeset_nullable=True, + signal_nullable=True, + bot_id_len=12, + bot_id_nullable=True, + charset='utf8mb4', + ), + 'tomato_root_field_pot': EfpSchemaBuilder._simple_schema( + species='tomato', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=2, + probeset_len=18, + probeset_nullable=True, + signal_nullable=True, + bot_id_len=12, + bot_id_nullable=True, + charset='utf8mb4', + ), + 'tomato_s_pennellii': EfpSchemaBuilder._simple_schema( + species='tomato', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=20, + probeset_nullable=True, + signal_nullable=True, + bot_id_len=24, + bot_id_nullable=True, + ), + 'tomato_seed': EfpSchemaBuilder._simple_schema( + species='tomato', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + signal_nullable=True, + charset='utf8mb4', + ), + 'tomato_shade_mutants': EfpSchemaBuilder._simple_schema( + species='tomato', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=16, + signal_nullable=True, + bot_id_len=20, + charset='utf8mb4', + ), + 'tomato_shade_timecourse': EfpSchemaBuilder._simple_schema( + species='tomato', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_default=None, + probeset_len=16, + signal_nullable=True, + charset='utf8mb4', + ), + 'tomato_trait': EfpSchemaBuilder._schema_with_qa_columns( + species='tomato', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=30, + probeset_len=100, + signal_nullable=True, + bot_id_type='text', + extra_columns=[ + EfpSchemaBuilder._column('qvalue', 'float', nullable=True), + ], + ), + 'triphysaria': EfpSchemaBuilder._simple_schema( + species='triphysaria', + sample_regex=r"^[a-z_]{1,35}|MED_CTRL$", + proj_id_default=None, + probeset_len=16, + signal_nullable=True, + bot_id_len=32, + charset='utf8mb4', + ), + 'triticale': EfpSchemaBuilder._schema_with_qa_columns( + species='triticale', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=30, + signal_nullable=True, + bot_id_len=18, + ), + 'triticale_mas': EfpSchemaBuilder._schema_with_qa_columns( + species='triticale', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=30, + signal_nullable=True, + bot_id_len=30, + ), + 'tung_tree': EfpSchemaBuilder._simple_schema( + species='tung_tree', + sample_regex=r'.*', # TODO: Add specific pattern + probeset_len=16, + bot_id_nullable=True, + ), + 'wheat': EfpSchemaBuilder._simple_schema( + species='wheat', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=32, + signal_nullable=True, + ), + 'wheat_abiotic_stress': EfpSchemaBuilder._simple_schema( + species='wheat', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=32, + signal_nullable=True, + charset='utf8mb4', + ), + 'wheat_embryogenesis': EfpSchemaBuilder._simple_schema( + species='wheat', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=32, + signal_nullable=True, + bot_id_len=50, + ), + 'wheat_meiosis': EfpSchemaBuilder._simple_schema( + species='wheat', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=32, + signal_nullable=True, + bot_id_len=24, + charset='utf8mb4', + ), + 'wheat_root': EfpSchemaBuilder._simple_schema( + species='wheat', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=15, + probeset_len=32, + signal_nullable=True, + charset='utf8mb4', + ), + 'willow': EfpSchemaBuilder._simple_schema( + species='willow', + sample_regex=r'.*', # TODO: Add specific pattern + proj_id_len=2, + probeset_len=32, + ), + # Complex/non-standard schemas (manually defined) + 'lateral_root_initiation': EfpSchemaBuilder._build_schema( + column_overrides={ + "sample_id": {"type": "string", "length": 30, "unsigned": False, "default": None}, + "data_probeset_id": {"length": 40, "default": None}, + "data_bot_id": {"length": 64, "nullable": True}, + }, + extra_columns=[ + EfpSchemaBuilder._column("project_id", "string", length=30, nullable=False), + EfpSchemaBuilder._column("sample_file_name", "string", length=80, nullable=True), + ], + charset="utf8mb4", + metadata={"species": "arabidopsis", "sample_regex": r".*"}, + ), + 'mouse_db': EfpSchemaBuilder._build_schema( + column_overrides={ + "data_probeset_id": {"length": 15, "primary_key": True}, + "data_bot_id": {"length": 18, "primary_key": True}, + }, + index=["data_probeset_id", "data_bot_id"], + metadata={"species": "mouse", "sample_regex": r".*"}, + ), + 'oat': EfpSchemaBuilder._build_schema( + column_overrides={ + "data_probeset_id": {"length": 36, "primary_key": True}, + "data_bot_id": {"length": 24, "primary_key": True}, + "data_signal": {"nullable": True}, + }, + extra_columns=[ + EfpSchemaBuilder._column("genome", "string", length=16, nullable=False), + EfpSchemaBuilder._column("genome_id", "string", length=16, nullable=False), + EfpSchemaBuilder._column("orthogroup", "string", length=16, nullable=False), + EfpSchemaBuilder._column("version", "string", length=2, nullable=False), + ], + charset="utf8mb4", + index=["data_probeset_id", "data_bot_id"], + metadata={"species": "oat", "sample_regex": r".*"}, + ), +} + +__all__: List[str] = ["SIMPLE_EFP_DATABASE_SCHEMAS", "ColumnSpec", "DatabaseSpec"] diff --git a/api/models/embryo.py b/api/models/embryo.py deleted file mode 100644 index 5c14d4a..0000000 --- a/api/models/embryo.py +++ /dev/null @@ -1,12 +0,0 @@ -from api import db - - -class SampleData(db.Model): - __bind_key__ = "embryo" - __tablename__ = "sample_data" - - proj_id: db.Mapped[str] = db.mapped_column(db.String(3), nullable=False) - sample_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False) - data_probeset_id: db.Mapped[str] = db.mapped_column(db.String(16), nullable=False, primary_key=True) - data_signal: db.Mapped[float] = db.mapped_column(db.Float, primary_key=True) - data_bot_id: db.Mapped[str] = db.mapped_column(db.String(8), nullable=False, primary_key=True) diff --git a/api/models/germination.py b/api/models/germination.py deleted file mode 100644 index 89aaceb..0000000 --- a/api/models/germination.py +++ /dev/null @@ -1,12 +0,0 @@ -from api import db - - -class SampleData(db.Model): - __bind_key__ = "germination" - __tablename__ = "sample_data" - - proj_id: db.Mapped[str] = db.mapped_column(db.String(3), nullable=False) - sample_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False) - data_probeset_id: db.Mapped[str] = db.mapped_column(db.String(30), nullable=False, primary_key=True) - data_signal: db.Mapped[float] = db.mapped_column(db.Float, primary_key=True) - data_bot_id: db.Mapped[str] = db.mapped_column(db.String(16), nullable=False, primary_key=True) diff --git a/api/models/kalanchoe.py b/api/models/kalanchoe.py deleted file mode 100644 index c3c03f9..0000000 --- a/api/models/kalanchoe.py +++ /dev/null @@ -1,12 +0,0 @@ -from api import db - - -class SampleData(db.Model): - __bind_key__ = "kalanchoe" - __tablename__ = "sample_data" - - proj_id: db.Mapped[str] = db.mapped_column(db.String(2), nullable=False) - sample_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False) - data_probeset_id: db.Mapped[str] = db.mapped_column(db.String(24), nullable=False, primary_key=True) - data_signal: db.Mapped[float] = db.mapped_column(db.Float, primary_key=True) - data_bot_id: db.Mapped[str] = db.mapped_column(db.String(16), nullable=False, primary_key=True) diff --git a/api/models/klepikova.py b/api/models/klepikova.py deleted file mode 100644 index 8a76513..0000000 --- a/api/models/klepikova.py +++ /dev/null @@ -1,12 +0,0 @@ -from api import db - - -class SampleData(db.Model): - __bind_key__ = "klepikova" - __tablename__ = "sample_data" - - proj_id: db.Mapped[str] = db.mapped_column(db.String(3), nullable=False) - sample_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False) - data_probeset_id: db.Mapped[str] = db.mapped_column(db.String(30), nullable=False, primary_key=True) - data_signal: db.Mapped[float] = db.mapped_column(db.Float, primary_key=True) - data_bot_id: db.Mapped[str] = db.mapped_column(db.String(16), nullable=False, primary_key=True) diff --git a/api/models/phelipanche.py b/api/models/phelipanche.py deleted file mode 100644 index 937a998..0000000 --- a/api/models/phelipanche.py +++ /dev/null @@ -1,12 +0,0 @@ -from api import db - - -class SampleData(db.Model): - __bind_key__ = "phelipanche" - __tablename__ = "sample_data" - - proj_id: db.Mapped[str] = db.mapped_column(db.String(5), nullable=False) - sample_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False) - data_probeset_id: db.Mapped[str] = db.mapped_column(db.String(16), nullable=False, primary_key=True) - data_signal: db.Mapped[float] = db.mapped_column(db.Float, primary_key=True) - data_bot_id: db.Mapped[str] = db.mapped_column(db.String(32), nullable=False, primary_key=True) diff --git a/api/models/physcomitrella_db.py b/api/models/physcomitrella_db.py deleted file mode 100644 index 62fa3b4..0000000 --- a/api/models/physcomitrella_db.py +++ /dev/null @@ -1,12 +0,0 @@ -from api import db - - -class SampleData(db.Model): - __bind_key__ = "physcomitrella_db" - __tablename__ = "sample_data" - - proj_id: db.Mapped[str] = db.mapped_column(db.String(30), nullable=False) - sample_id: db.Mapped[int] = db.mapped_column(db.String(30), nullable=False) - data_probeset_id: db.Mapped[str] = db.mapped_column(db.String(40), nullable=False, primary_key=True) - data_signal: db.Mapped[float] = db.mapped_column(db.Float, primary_key=True) - data_bot_id: db.Mapped[str] = db.mapped_column(db.String(40), nullable=False, primary_key=True) diff --git a/api/models/selaginella.py b/api/models/selaginella.py deleted file mode 100644 index b911648..0000000 --- a/api/models/selaginella.py +++ /dev/null @@ -1,12 +0,0 @@ -from api import db - - -class SampleData(db.Model): - __bind_key__ = "selaginella" - __tablename__ = "sample_data" - - proj_id: db.Mapped[str] = db.mapped_column(db.String(5), nullable=False) - sample_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False) - data_probeset_id: db.Mapped[str] = db.mapped_column(db.String(18), nullable=False, primary_key=True) - data_signal: db.Mapped[float] = db.mapped_column(db.Float, primary_key=True) - data_bot_id: db.Mapped[str] = db.mapped_column(db.String(36), nullable=False, primary_key=True) diff --git a/api/models/shoot_apex.py b/api/models/shoot_apex.py deleted file mode 100644 index f8495d9..0000000 --- a/api/models/shoot_apex.py +++ /dev/null @@ -1,12 +0,0 @@ -from api import db - - -class SampleData(db.Model): - __bind_key__ = "shoot_apex" - __tablename__ = "sample_data" - - proj_id: db.Mapped[str] = db.mapped_column(db.String(2), nullable=False) - sample_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False) - data_probeset_id: db.Mapped[str] = db.mapped_column(db.String(12), nullable=False, primary_key=True) - data_signal: db.Mapped[float] = db.mapped_column(db.Float, primary_key=True) - data_bot_id: db.Mapped[str] = db.mapped_column(db.String(8), nullable=False, primary_key=True) diff --git a/api/models/silique.py b/api/models/silique.py deleted file mode 100644 index 9421f89..0000000 --- a/api/models/silique.py +++ /dev/null @@ -1,12 +0,0 @@ -from api import db - - -class SampleData(db.Model): - __bind_key__ = "silique" - __tablename__ = "sample_data" - - proj_id: db.Mapped[str] = db.mapped_column(db.String(5), nullable=False) - sample_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False) - data_probeset_id: db.Mapped[str] = db.mapped_column(db.String(12), nullable=False, primary_key=True) - data_signal: db.Mapped[float] = db.mapped_column(db.Float, primary_key=True) - data_bot_id: db.Mapped[str] = db.mapped_column(db.String(64), nullable=False, primary_key=True) diff --git a/api/models/single_cell.py b/api/models/single_cell.py deleted file mode 100644 index d046058..0000000 --- a/api/models/single_cell.py +++ /dev/null @@ -1,12 +0,0 @@ -from api import db - - -class SampleData(db.Model): - __bind_key__ = "single_cell" - __tablename__ = "sample_data" - - proj_id: db.Mapped[str] = db.mapped_column(db.String(5), nullable=False) - sample_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False) - data_probeset_id: db.Mapped[str] = db.mapped_column(db.String(24), nullable=False, primary_key=True) - data_signal: db.Mapped[float] = db.mapped_column(db.Float, primary_key=True) - data_bot_id: db.Mapped[str] = db.mapped_column(db.String(32), nullable=False, primary_key=True) diff --git a/api/models/strawberry.py b/api/models/strawberry.py deleted file mode 100644 index 7d0b85d..0000000 --- a/api/models/strawberry.py +++ /dev/null @@ -1,12 +0,0 @@ -from api import db - - -class SampleData(db.Model): - __bind_key__ = "strawberry" - __tablename__ = "sample_data" - - proj_id: db.Mapped[str] = db.mapped_column(db.String(5), nullable=False) - sample_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False) - data_probeset_id: db.Mapped[str] = db.mapped_column(db.String(16), nullable=False, primary_key=True) - data_signal: db.Mapped[float] = db.mapped_column(db.Float, primary_key=True) - data_bot_id: db.Mapped[str] = db.mapped_column(db.String(24), nullable=False, primary_key=True) diff --git a/api/models/striga.py b/api/models/striga.py deleted file mode 100644 index 10fa4ac..0000000 --- a/api/models/striga.py +++ /dev/null @@ -1,12 +0,0 @@ -from api import db - - -class SampleData(db.Model): - __bind_key__ = "striga" - __tablename__ = "sample_data" - - proj_id: db.Mapped[str] = db.mapped_column(db.String(5), nullable=False) - sample_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False) - data_probeset_id: db.Mapped[str] = db.mapped_column(db.String(24), nullable=False, primary_key=True) - data_signal: db.Mapped[float] = db.mapped_column(db.Float, primary_key=True) - data_bot_id: db.Mapped[str] = db.mapped_column(db.String(42), nullable=False, primary_key=True) diff --git a/api/models/triphysaria.py b/api/models/triphysaria.py deleted file mode 100644 index d301873..0000000 --- a/api/models/triphysaria.py +++ /dev/null @@ -1,12 +0,0 @@ -from api import db - - -class SampleData(db.Model): - __bind_key__ = "triphysaria" - __tablename__ = "sample_data" - - proj_id: db.Mapped[str] = db.mapped_column(db.String(5), nullable=False) - sample_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False) - data_probeset_id: db.Mapped[str] = db.mapped_column(db.String(16), nullable=False, primary_key=True) - data_signal: db.Mapped[float] = db.mapped_column(db.Float, primary_key=True) - data_bot_id: db.Mapped[str] = db.mapped_column(db.String(32), nullable=False, primary_key=True) diff --git a/api/resources/efp_proxy.py b/api/resources/efp_proxy.py new file mode 100644 index 0000000..bb8fc1f --- /dev/null +++ b/api/resources/efp_proxy.py @@ -0,0 +1,350 @@ +import requests +import json +import os +from typing import List, Optional +from collections import OrderedDict +from flask_restx import Namespace, Resource +from flask import request, current_app +from markupsafe import escape +from sqlalchemy.engine.url import make_url +from sqlalchemy.exc import SQLAlchemyError + +from api.models.efp_dynamic import SIMPLE_EFP_SAMPLE_MODELS +from api.models.efp_schemas import SIMPLE_EFP_DATABASE_SCHEMAS +from api.services.efp_bootstrap import bootstrap_simple_efp_databases +from api.services.efp_data import query_efp_database_dynamic + +# efp proxy namespace provides two endpoints for gene expression data +# 1. /values talks to the live bar eplant cgi +# 2. /expression reads from our local or remote databases using one shared query +efp_proxy_ns = Namespace( + 'efp Proxy', + description='Expression data retrieveal service from BAR eplant databse.', + path='/efp_proxy', +) + + +# rest endpoint that proxies requests to the external bar eplant api +# supports urls like /efp_proxy/values/atgenexp_stress/AT1G01010 +@efp_proxy_ns.route("/values//") +@efp_proxy_ns.doc( + description="Proxies requests to BAR ePlant API: /efp_proxy/values/{database}/{gene_id}", + params=OrderedDict([ + ( + "database", + { + "description": "Database/datasource for arabidopsis view (e.g., atgenexp_stress)", + "in": "path", + "default": "atgenexp_stress", + }, + ), + ( + "gene_id", + { + "description": "Gene ID to query (e.g., AT1G01010)", + "in": "path", + "default": "AT1G01010", + }, + ), + ( + "samples", + { + "description": "Optional list of sample IDs (repeat ?samples=SampleA&samples=SampleB); omit to fetch all samples. Legacy JSON arrays are still accepted.", + "in": "query", + "default": "", + }, + ), + ]), +) +class EFPValues(Resource): + @staticmethod + def parse_samples_query_values(raw_values: Optional[List[str]]) -> Optional[List[str]]: + """Normalize optional samples from the query string so legacy formats still work.""" + if not raw_values: + return None + + filtered = [value for value in raw_values if value] + if not filtered: + return None + + if len(filtered) > 1: + return filtered + + candidate = filtered[0].strip() + if not candidate: + return None + + # interpret json array strings because legacy clients sent one json string value + if candidate.startswith("[") and candidate.endswith("]"): + try: + parsed = json.loads(candidate) + if isinstance(parsed, list): + return [str(item).strip() for item in parsed if isinstance(item, str) and item.strip()] + except json.JSONDecodeError: + pass + + if "," in candidate: + # support comma-separated lists by splitting manually + split_values = [item.strip() for item in candidate.split(",") if item.strip()] + if split_values: + return split_values + + return [candidate] + + @staticmethod + def get_all_samples_for_view(datasource: str): + """Load all available samples for a datasource using the metadata json and fallbacks.""" + # point at the scraped metadata json so tests resolve it from the repo + path = os.path.join(os.getcwd(), "data/efp_info/efp_species_view_info.json") + + # check for datasources that need hardcoded samples + if datasource == "root_Schaefer_lab": + # this dataset is missing from the scraped metadata so we pin a curated set + print("[info] using hardcoded fallback samples for root_Schaefer_lab") + return ["WTCHG_203594_01", "WTCHG_203594_05", "WTCHG_203839_04", "WTCHG_203594_03", "WTCHG_203594_07", "WTCHG_203839_06", "WTCHG_203839_01", "WTCHG_203594_10", "WTCHG_203839_08", "WTCHG_129187_01", "WTCHG_129189_01", "WTCHG_129190_01", "WTCHG_129187_03", "WTCHG_129189_03", "WTCHG_129190_03", "WTCHG_129187_05", "WTCHG_129189_05", "WTCHG_129187_07", "WTCHG_131167_01", "WTCHG_125416_01", "WTCHG_129190_05", "WTCHG_131167_03", "WTCHG_125416_03", "WTCHG_129190_07", "WTCHG_131167_05", "WTCHG_125416_05", "WTCHG_129189_07"] + + if datasource == "atgenexp_stress": + # atgenexp stress views still rely on the json metadata so we keep a minimal fallback + print("[info] using fallback arabidopsis samples from json spec") + return ["AtGen_6_0011", "AtGen_6_0012", "AtGen_6_0021", "AtGen_6_0022", + "AtGen_6_0711", "AtGen_6_0712", "AtGen_6_0721", "AtGen_6_0722"] + + # check if metadata json file exists + if not os.path.exists(path): + # repo clones without fixtures can still run, just without auto-sample loading + print(f"[warn] metadata json not found at {path}") + return [] + + # try to load and parse the json metadata file + try: + with open(path, "r") as f: + metadata = json.load(f) + except Exception as e: + print(f"[error] unable to read json: {e}") + return [] + + # search through all species and views to find a matching datasource + for species, obj in metadata.items(): + views = obj.get("data", {}).get("views", {}) + for vname, vinfo in views.items(): + if vinfo.get("database") == datasource: + # collect all unique samples from all treatment groups + samples = [] + for group in vinfo.get("groups", {}).values(): + # each group stores multiple treatment buckets; flatten all of them + for treatment_samples in group.get("treatments", {}).values(): + samples.extend(treatment_samples) + print(f"[info] found {len(samples)} samples in json for {datasource}") + return sorted(set(samples)) + + print(f"[warn] datasource {datasource} not found in json") + return [] + + @staticmethod + def fetch_efp_data(datasource, gene_id, samples=None): + """Fetch gene expression data from the external bar eplant api. + Either use the samples provided or auto-fill the list before calling the cgi. + """ + # set up the external bar api url and basic query parameters + base_url = "https://bar.utoronto.ca//eplant/cgi-bin/plantefp.cgi" + query_params = [ + ("datasource", datasource), + ("id", gene_id), + ("format", "json"), + ] + samples_applied = False # track whether we hinted the cgi with explicit samples + + # handle optional sample filtering and expect a normalized list of sample ids + if samples: + cleaned_samples = [sample.strip() for sample in samples if isinstance(sample, str) and sample.strip()] + if cleaned_samples: + query_params.append(("samples", json.dumps(cleaned_samples))) + samples_applied = True + # no samples provided, so try to auto-load all samples for this datasource + else: + samples = EFPValues.get_all_samples_for_view(datasource) + if samples: + print(f"[info] auto-loaded {len(samples)} samples for datasource {datasource}") + query_params.append(("samples", json.dumps(samples))) + samples_applied = True + else: + # no metadata entry means the cgi decides which default samples to use + print(f"[warn] no samples found for datasource {datasource}") + + # make exactly one http get request to the bar eplant cgi with every sample packed in + response = requests.get(base_url, params=query_params) + url_called = response.url + + # check if the request failed with an http error code + if not response.ok: + # propagate error status so clients see the same http code the cgi returned + return {"success": False, "error": f"bar returned {response.status_code} for url {url_called}"}, response.status_code + + # attempt to parse json response and extract the data array + try: + data = response.json() + if isinstance(data, dict) and "data" in data: + data = data["data"] + except Exception: + # remote endpoint occasionally emits html error pages so treat them as no data + data = [] + + # if no results returned with samples, retry once without sample filtering + if (not data or data == []) and samples_applied: + retry_params = [ + ("datasource", datasource), + ("id", gene_id), + ("format", "json"), + ] + retry_resp = requests.get(base_url, params=retry_params) + # even if this second call fails, we still return an empty array to the caller + + try: + retry_data = retry_resp.json() + if isinstance(retry_data, dict) and "data" in retry_data: + retry_data = retry_data["data"] + except Exception: + # treat malformed fallback responses as empty to keep behavior predictable + retry_data = [] + + return { + "success": True, + "url_called": url_called, + "record_count": len(retry_data), + "data": retry_data, + "note": "no data returned with samples; fetched full view instead." + } + return { + "success": True, + "url_called": url_called, + "record_count": len(data) if isinstance(data, list) else 0, + "data": data # payload mirrors what the real cgi would have returned + } + + def get(self, database, gene_id): + # sanitize path parameters to prevent injection attacks + database = escape(database) + gene_id = escape(gene_id) + + # parse ?samples= query args once so downstream logic gets a normalized list + samples_arg = self.parse_samples_query_values(request.args.getlist("samples")) + + # delegate to fetch_efp_data which auto-loads samples when none provided + return self.fetch_efp_data(database, gene_id, samples=samples_arg) + + +# rest endpoint that uses the static schema catalog to query local sqlite databases +# supports urls like /efp_proxy/expression/sample_data/261585_at +@efp_proxy_ns.route("/expression//") +@efp_proxy_ns.doc( + description="Static eFP endpoint: /efp_proxy/expression/{database}/{gene_id}" +) +@efp_proxy_ns.param( + "gene_id", + "Gene ID (AGI format like AT1G01010 or probeset like 261585_at)", + _in="path", + default="AT1G01010", +) +@efp_proxy_ns.param( + "database", + "Database name (e.g., sample_data, klepikova, single_cell)", + _in="path", + default="klepikova", +) +class EFPExpression(Resource): + def get(self, database, gene_id): + # sanitize path parameters to prevent injection attacks + database = escape(database) + gene_id = escape(gene_id) + + # delegate to query_efp_database_dynamic for deterministic queries + # optional sample filtering is not exposed here yet, hence sample_ids=None + result = query_efp_database_dynamic(database, gene_id, sample_ids=None) + + # return result with appropriate http status code + if result["success"]: + return result + else: + return result, result.get("error_code", 500) + + +@efp_proxy_ns.route("/bootstrap/simple") +@efp_proxy_ns.doc( + description="Create or update the simple eFP MySQL databases using the in-memory schema definitions.", + params={ + "host": "Optional MySQL hostname override. Defaults to the host defined in SQLALCHEMY_BINDS.", + "port": "Optional MySQL port override. Defaults to the port defined in SQLALCHEMY_BINDS.", + "user": "Optional MySQL username override. Defaults to the username defined in SQLALCHEMY_BINDS.", + "password": "Optional MySQL password override. Defaults to the password defined in SQLALCHEMY_BINDS.", + "databases": "Optional list of database names to bootstrap. Defaults to every simple database.", + }, +) +class EFPSimpleBootstrap(Resource): + @staticmethod + def _infer_default_db_credentials(): + """Derive MySQL connection info for the simple eFP datasets from the configured binds.""" + binds = current_app.config.get("SQLALCHEMY_BINDS") or {} + for db_name in SIMPLE_EFP_DATABASE_SCHEMAS.keys(): + uri = binds.get(db_name) + if not uri: + continue + url = make_url(uri) + return { + "host": url.host or "localhost", + "port": url.port or 3306, + "user": url.username or "root", + "password": url.password or "", + } + raise ValueError("No SQLAlchemy bind configured for the simple eFP databases.") + + def post(self): + payload = request.get_json(silent=True) or {} + try: + defaults = self._infer_default_db_credentials() + except ValueError as exc: + return {"success": False, "error": str(exc)}, 500 + + host = payload.get("host") or defaults["host"] + try: + port_value = payload.get("port") + port = int(port_value) if port_value is not None else int(defaults["port"]) + except (TypeError, ValueError): + return {"success": False, "error": "port must be an integer"}, 400 + user = payload.get("user") or defaults["user"] + password = payload.get("password") or defaults["password"] + + databases = payload.get("databases") + if databases is not None: + if not isinstance(databases, list) or not all(isinstance(item, str) for item in databases): + return {"success": False, "error": "databases must be a list of names."}, 400 + + try: + results = bootstrap_simple_efp_databases( + host=host, + port=port, + user=user, + password=password, + databases=databases, + ) + except ValueError as exc: + return {"success": False, "error": str(exc)}, 400 + except SQLAlchemyError as exc: + return {"success": False, "error": str(exc)}, 500 + + model_info = [ + {"database": name, "model": model.__name__} + for name, model in SIMPLE_EFP_SAMPLE_MODELS.items() + if databases is None or name in databases + ] + + return { + "success": True, + "databases": results, + "models": model_info, + "note": "Simple eFP databases are materialized in MySQL while SQLAlchemy models remain dynamic.", + }, 200 + + +efp_proxy_ns.add_resource(EFPValues, '/values//') +efp_proxy_ns.add_resource(EFPExpression, '/expression//') +efp_proxy_ns.add_resource(EFPSimpleBootstrap, '/bootstrap/simple') diff --git a/api/resources/microarray_gene_expression.py b/api/resources/microarray_gene_expression.py index 6a2002a..566f86b 100644 --- a/api/resources/microarray_gene_expression.py +++ b/api/resources/microarray_gene_expression.py @@ -2,10 +2,13 @@ from markupsafe import escape from api import db from api.models.annotations_lookup import AtAgiLookup -from api.models.arabidopsis_ecotypes import SampleData as EcotypesSampleData +from api.models.efp_dynamic import SIMPLE_EFP_SAMPLE_MODELS from api.utils.bar_utils import BARUtils from api.utils.world_efp_utils import WorldeFPUtils +import json +# pull the dynamic model so this resource stays in sync with the schema catalog +EcotypesSampleData = SIMPLE_EFP_SAMPLE_MODELS["arabidopsis_ecotypes"] microarray_gene_expression = Namespace( "Microarray Gene Expression", @@ -58,3 +61,241 @@ def get(self, species="", gene_id=""): return BARUtils.success_exit(final_json) else: return BARUtils.error_exit("There are no data found for the given gene") + + +# endpoint made by reena +# return view and database mappings for a given species +@microarray_gene_expression.route("//databases") +class GetDatabases(Resource): + @microarray_gene_expression.param("species", _in="path", default="arabidopsis") + def get(self, species=""): + """This endpoint returns available database and view mappings for a given species""" + species = escape(species) + + species_databases = { + "actinidia": { + "Bud_Development": "actinidia_bud_development", + "Flower_Fruit_Development": "actinidia_flower_fruit_development", + "Postharvest": "actinidia_postharvest", + "Vegetative_Growth": "actinidia_vegetative_growth" + }, + "arabidopsis": { + "Abiotic_Stress": "atgenexp_stress", + "Abiotic_Stress_II": "atgenexp_stress", + "Biotic_Stress": "atgenexp_pathogen", + "Biotic_Stress_II": "atgenexp_pathogen", + "Chemical": "atgenexp_hormone", + "DNA_Damage": "dna_damage", + "Development_RMA": "atgenexp", + "Developmental_Map": "atgenexp_plus", + "Developmental_Mutants": "atgenexp_plus", + "Embryo": "embryo", + "Germination": "germination", + "Guard_Cell": "guard_cell", + "Gynoecium": "gynoecium", + "Hormone": "atgenexp_hormone", + "Klepikova_Atlas": "klepikova", + "Lateral_Root_Initiation": "lateral_root_initiation", + "Light_Series": "light_series", + "Natural_Variation": "arabidopsis_ecotypes", + "Regeneration": "meristem_db", + "Root": "root", + "Root_II": "root", + "Seed": "seed_db", + "Shoot_Apex": "shoot_apex", + "Silique": "silique", + "Single_Cell": "single_cell", + "Tissue_Specific": "atgenexp_plus" + }, + "arabidopsis seedcoat": { + "Seed_Coat": "seedcoat" + }, + "arachis": { + "Arachis_Atlas": "arachis" + }, + "barley": { + "barley_mas": "barley_mas", + "barley_rma": "barley_rma" + }, + "brachypodium": { + "Brachypodium_Atlas": "brachypodium", + "Brachypodium_Grains": "brachypodium_grains", + "Brachypodium_Spikes": "brachypodium_Bd21", + "Photo_Thermocycle": "brachypodium_photo_thermocycle" + }, + "brassica rapa": { + "Embryogenesis": "brassica_rapa" + }, + "cacao ccn": { + "Developmental_Atlas": "cacao_developmental_atlas", + "Drought_Diurnal_Atlas": "cacao_drought_diurnal_atlas" + }, + "cacao sca": { + "Developmental_Atlas": "cacao_developmental_atlas_sca", + "Drought_Diurnal_Atlas": "cacao_drought_diurnal_atlas_sca", + "Meristem_Atlas": "cacao_meristem_atlas_sca", + "Seed_Atlas": "cacao_seed_atlas_sca" + }, + "cacao tc": { + "Cacao_Infection": "cacao_infection", + "Cacao_Leaf": "cacao_leaf" + }, + "camelina": { + "Developmental_Atlas_FPKM": "camelina", + "Developmental_Atlas_TPM": "camelina_tpm" + }, + "cannabis": { + "Cannabis_Atlas": "cannabis" + }, + "canola": { + "Canola_Seed": "canola_seed" + }, + "eutrema": { + "Eutrema": "thellungiella_db" + }, + "grape": { + "grape_developmental": "grape_developmental" + }, + "kalanchoe": { + "Light_Response": "kalanchoe" + }, + "little millet": { + "Life_Cycle": "little_millet" + }, + "lupin": { + "LCM_Leaf": "lupin_lcm_leaf", + "LCM_Pod": "lupin_lcm_pod", + "LCM_Stem": "lupin_lcm_stem", + "Whole_Plant": "lupin_whole_plant" + }, + "maize": { + "Downs_et_al_Atlas": "maize_gdowns", + "Early_Seed": "maize_early_seed", + "Embryonic_Leaf_Development": "maize_embryonic_leaf_development", + "Hoopes_et_al_Atlas": "maize_buell_lab", + "Hoopes_et_al_Stress": "maize_buell_lab", + "Maize_Kernel": "maize_early_seed", + "Maize_Root": "maize_root", + "Sekhon_et_al_Atlas": "maize_RMA_linear", + "Tassel_and_Ear_Primordia": "maize_ears", + "maize_iplant": "maize_iplant", + "maize_leaf_gradient": "maize_leaf_gradient", + "maize_rice_comparison": "maize_rice_comparison" + }, + "mangosteen": { + "Aril_vs_Rind": "mangosteen_aril_vs_rind", + "Callus": "mangosteen_callus", + "Diseased_vs_Normal": "mangosteen_diseased_vs_normal", + "Fruit_Ripening": "mangosteen_fruit_ripening", + "Seed_Development": "mangosteen_seed_development", + "Seed_Germination": "mangosteen_seed_germination" + }, + "medicago": { + "medicago_mas": "medicago_mas", + "medicago_rma": "medicago_rma", + "medicago_seed": "medicago_seed" + }, + "poplar": { + "Poplar": "poplar", + "PoplarTreatment": "poplar" + }, + "potato": { + "Potato_Developmental": "potato_dev", + "Potato_Stress": "potato_stress" + }, + "rice": { + "rice_drought_heat_stress": "rice_drought_heat_stress", + "rice_leaf_gradient": "rice_leaf_gradient", + "rice_maize_comparison": "rice_maize_comparison", + "rice_mas": "rice_mas", + "rice_rma": "rice_rma", + "riceanoxia_mas": "rice_mas", + "riceanoxia_rma": "rice_rma", + "ricestigma_mas": "rice_mas", + "ricestigma_rma": "rice_rma", + "ricestress_mas": "rice_mas", + "ricestress_rma": "rice_rma" + }, + "soybean": { + "soybean": "soybean", + "soybean_embryonic_development": "soybean_embryonic_development", + "soybean_heart_cotyledon_globular": "soybean_heart_cotyledon_globular", + "soybean_senescence": "soybean_senescence", + "soybean_severin": "soybean_severin" + }, + "strawberry": { + "Developmental_Map_Strawberry_Flower_and_Fruit": "strawberry", + "Strawberry_Green_vs_White_Stage": "strawberry" + }, + "tomato": { + "ILs_Leaf_Chitwood_et_al": "tomato_ils", + "ILs_Root_Tip_Brady_Lab": "tomato_ils2", + "M82_S_pennellii_Atlases_Koenig_et_al": "tomato_s_pennellii", + "Rose_Lab_Atlas": "tomato", + "Rose_Lab_Atlas_Renormalized": "tomato_renormalized", + "SEED_Lab_Angers": "tomato_seed", + "Shade_Mutants": "tomato_shade_mutants", + "Shade_Timecourse_WT": "tomato_shade_timecourse", + "Tomato_Meristem": "tomato_meristem" + }, + "triticale": { + "triticale": "triticale", + "triticale_mas": "triticale_mas" + }, + "wheat": { + "Developmental_Atlas": "wheat", + "Wheat_Abiotic_Stress": "wheat_abiotic_stress", + "Wheat_Embryogenesis": "wheat_embryogenesis", + "Wheat_Meiosis": "wheat_meiosis" + } + } + + if species not in species_databases: + return BARUtils.error_exit("Invalid species") + + return BARUtils.success_exit({ + "species": species, + "databases": species_databases[species] + }) + + +# endpoint made by reena +# return control and sample mappings for a given species +@microarray_gene_expression.route("///samples") +class GetSamples1(Resource): + """This endpoint returns control and sample group mappings for a given species and view (or all views)""" + + @microarray_gene_expression.param("species", _in="path", default="arabidopsis") + @microarray_gene_expression.param("view", _in="path", default="Abiotic_Stress") + def get(self, species="", view=""): + """This endpoint returns control and sample group mappings for a given species and view (or all views)""" + species = escape(species.lower()) + view = escape(view) + + try: + with open("data/efp_info/efp_species_view_info.json") as f: + all_species_data = json.load(f) + except Exception as e: + return BARUtils.error_exit(f"Data file missing or invalid: {e}") + + if species not in all_species_data: + return BARUtils.error_exit("Invalid species") + + species_data = all_species_data[species]["data"] + + # if user requests all views + if view.lower() == "all": + return BARUtils.success_exit({ + "species": species, + "views": species_data["views"] + }) + + # otherwise check single view + if view not in species_data["views"]: + return BARUtils.error_exit("Invalid view for this species") + + return BARUtils.success_exit({ + "species": species, + "view": view, + "groups": species_data["views"][view]["groups"] + }) diff --git a/api/resources/proxy.py b/api/resources/proxy.py index f6b20e4..d196c25 100644 --- a/api/resources/proxy.py +++ b/api/resources/proxy.py @@ -30,7 +30,16 @@ def get(self, gene_id="", top_n=""): # Now query the web service payload = {"gene": gene_id, "topN": top_n} - resp = requests.get("https://atted.jp/api5/", params=payload, headers=request_headers) - - # I think the remote API always returns status 200, so skip status checking - return resp.json() + try: + resp = requests.get("https://atted.jp/api5/", params=payload, headers=request_headers, timeout=30) + resp.raise_for_status() + except requests.exceptions.HTTPError as err: + status_code = err.response.status_code if err.response is not None else 502 + return BARUtils.error_exit(f"External API request failed with status code {status_code}"), status_code + except requests.exceptions.RequestException as err: + return BARUtils.error_exit(f"External API request failed: {err}"), 502 + + try: + return resp.json() + except ValueError: + return BARUtils.error_exit("External API returned invalid JSON"), 502 diff --git a/api/resources/rnaseq_gene_expression.py b/api/resources/rnaseq_gene_expression.py index 79cde39..205ba96 100644 --- a/api/resources/rnaseq_gene_expression.py +++ b/api/resources/rnaseq_gene_expression.py @@ -2,26 +2,10 @@ from flask_restx import Namespace, Resource, fields from flask import request from api.utils.bar_utils import BARUtils +from api.services.efp_data import query_efp_database_dynamic +from api.models.efp_schemas import SIMPLE_EFP_DATABASE_SCHEMAS from marshmallow import Schema, ValidationError, fields as marshmallow_fields from markupsafe import escape -from api import db -from api.models.arachis import SampleData as Arachis -from api.models.cannabis import SampleData as Cannabis -from api.models.dna_damage import SampleData as DNADamage -from api.models.embryo import SampleData as Embryo -from api.models.germination import SampleData as Germination -from api.models.kalanchoe import SampleData as Kalanchoe -from api.models.klepikova import SampleData as Klepikova -from api.models.phelipanche import SampleData as Phelipanche -from api.models.physcomitrella_db import SampleData as Physcomitrella -from api.models.selaginella import SampleData as Selaginella -from api.models.shoot_apex import SampleData as ShootApex -from api.models.silique import SampleData as Silique -from api.models.single_cell import SampleData as SingleCell -from api.models.strawberry import SampleData as Strawberry -from api.models.striga import SampleData as Striga -from api.models.triphysaria import SampleData as Triphysaria -from sqlalchemy import and_ rnaseq_gene_expression = Namespace( "RNA-Seq Gene Expression", @@ -29,7 +13,27 @@ path="/rnaseq_gene_expression", ) -# I think this is only needed for Swagger UI POST +# validators stay here so schema metadata can reference them +SPECIES_VALIDATORS = { + "arabidopsis": BARUtils.is_arabidopsis_gene_valid, + "arachis": BARUtils.is_arachis_gene_valid, + "cannabis": BARUtils.is_cannabis_gene_valid, + "kalanchoe": BARUtils.is_kalanchoe_gene_valid, + "selaginella": BARUtils.is_selaginella_gene_valid, + "strawberry": BARUtils.is_strawberry_gene_valid, + "striga": BARUtils.is_striga_gene_valid, + "triphysaria": BARUtils.is_triphysaria_gene_valid, + "phelipanche": BARUtils.is_phelipanche_gene_valid, + "physcomitrella": BARUtils.is_physcomitrella_gene_valid, +} + +# metadata mirrors the schema catalog so validation stays in sync +DATABASE_METADATA = { + name: spec.get("metadata") or {} + for name, spec in SIMPLE_EFP_DATABASE_SCHEMAS.items() +} + +# this is only needed for swagger ui post examples gene_expression_request_fields = rnaseq_gene_expression.model( "GeneExpression", { @@ -48,7 +52,7 @@ ) -# Validation is done in a different way to keep things simple +# validation is done manually to keep things simple class RNASeqSchema(Schema): species = marshmallow_fields.String(required=True) database = marshmallow_fields.String(required=True) @@ -59,146 +63,43 @@ class RNASeqSchema(Schema): class RNASeqUtils: @staticmethod def get_data(species, database, gene_id, sample_ids=None): - """This function is used to query the database for gene expression - :param species: name of species - :param database: name of BAR database - :param gene_id: gene id in the data_probeset column - :param sample_ids: sample ids in the data_bot_id column - :return: dict gene expression data - """ + """query the database for gene expression values""" if sample_ids is None: sample_ids = [] - data = {} + data: dict = {} - # Set species and check gene ID format + # validate species selection and gene id format species = species.lower() - if species == "arabidopsis": - if not BARUtils.is_arabidopsis_gene_valid(gene_id): - return {"success": False, "error": "Invalid gene id", "error_code": 400} - elif species == "arachis": - if not BARUtils.is_arachis_gene_valid(gene_id): - return {"success": False, "error": "Invalid gene id", "error_code": 400} - elif species == "cannabis": - if not BARUtils.is_cannabis_gene_valid(gene_id): - return {"success": False, "error": "Invalid gene id", "error_code": 400} - elif species == "kalanchoe": - if not BARUtils.is_kalanchoe_gene_valid(gene_id): - return {"success": False, "error": "Invalid gene id", "error_code": 400} - elif species == "selaginella": - if not BARUtils.is_selaginella_gene_valid(gene_id): - return {"success": False, "error": "Invalid gene id", "error_code": 400} - elif species == "strawberry": - if not BARUtils.is_strawberry_gene_valid(gene_id): - return {"success": False, "error": "Invalid gene id", "error_code": 400} - elif species == "striga": - if not BARUtils.is_striga_gene_valid(gene_id): - return {"success": False, "error": "Invalid gene id", "error_code": 400} - elif species == "triphysaria": - if not BARUtils.is_triphysaria_gene_valid(gene_id): - return {"success": False, "error": "Invalid gene id", "error_code": 400} - elif species == "phelipanche": - if not BARUtils.is_phelipanche_gene_valid(gene_id): - return {"success": False, "error": "Invalid gene id", "error_code": 400} - elif species == "physcomitrella": - if not BARUtils.is_physcomitrella_gene_valid(gene_id): - return {"success": False, "error": "Invalid gene id", "error_code": 400} - else: + gene_validator = SPECIES_VALIDATORS.get(species) + if not gene_validator: return {"success": False, "error": "Invalid species", "error_code": 400} - # Set database database = database.lower() - if database == "arachis": - table = Arachis - # Example: Pattee_8_Seed - sample_regex = re.compile(r"^[\D\d_]{1,30}|MED_CTRL$", re.I) - - elif database == "cannabis": - table = Cannabis - # Example: PK-PFLW - sample_regex = re.compile(r"^PK-\D{1,4}|MED_CTRL$", re.I) - - elif database == "dna_damage": - table = DNADamage - # Another insane regex! - sample_regex = re.compile(r"^\D{1,3}.{1,30}_plus_Y|\D{1,3}.{1,30}_minus_Y|Med_CTRL$", re.I) - - elif database == "embryo": - table = Embryo - sample_regex = re.compile(r"^\D{1,3}_\d$|Med_CTRL$", re.I) - - elif database == "germination": - table = Germination - sample_regex = re.compile(r"^\d{1,3}\D{1,4}_\d{1,3}|harvest_\d|Med_CTRL$", re.I) - - elif database == "kalanchoe": - table = Kalanchoe - # Example: FRL_Dusk_rep3 - sample_regex = re.compile(r"^\D{1,4}_\D{1,5}_rep\d|MED_CTRL$", re.I) - - elif database == "klepikova": - table = Klepikova - sample_regex = re.compile(r"^SRR\d{1,9}|Med_CTRL$", re.I) - - elif database == "phelipanche": - table = Phelipanche - # Example: Pre-Emergence_from_Soil_Shoots - sample_regex = re.compile(r"^[a-z_-]{1,35}|MED_CTRL$", re.I) - - elif database == "physcomitrella_db": - table = Physcomitrella - # Example: Sporophyte_S1 - sample_regex = re.compile(r"^[a-z_123]{1,15}|MED_CTRL$", re.I) - - elif database == "selaginella": - table = Selaginella - # Insane regex! - sample_regex = re.compile(r"^[\D\d]{1,33}|MED_CTRL$", re.I) - - elif database == "shoot_apex": - table = ShootApex - sample_regex = re.compile(r"^\D{1,5}\d{0,2}|MED_CTRL$", re.I) - - elif database == "silique": - table = Silique - # Insane regex! Needs work - sample_regex = re.compile(r"^\d{1,3}_dap.{1,58}_R1_001|Med_CTRL$", re.I) - - elif database == "single_cell": - table = SingleCell - # Example: cluster0_WT1.ExprMean - sample_regex = re.compile(r"^\D+\d+_WT\d+.ExprMean|MED_CTRL$", re.I) - - elif database == "strawberry": - table = Strawberry - # Example: Perianth_5-6_A - sample_regex = re.compile(r"^\D{1,12}_.{1,8}_\D{1,2}|MED_CTRL$", re.I) - - elif database == "striga": - table = Striga - # Example: Reproductive_Structures - sample_regex = re.compile(r"^\D{1,35}|MED_CTRL$", re.I) - - elif database == "triphysaria": - table = Triphysaria - # Example: Roots_in_Late_Post_Attachment - sample_regex = re.compile(r"^[a-z_]{1,35}|MED_CTRL$", re.I) + db_metadata = DATABASE_METADATA.get(database, {}) + db_species = db_metadata.get("species") + if db_species and db_species != species: + return {"success": False, "error": "Invalid species", "error_code": 400} - else: + if not gene_validator(gene_id): + return {"success": False, "error": "Invalid gene id", "error_code": 400} + + if database not in DATABASE_METADATA: return {"success": False, "error": "Invalid database", "error_code": 400} - # Now query the database - # We are querying only some columns because full indexes are made on some columns, now the whole table - if len(sample_ids) == 0 or sample_ids is None: - rows = db.session.execute( - db.select(table.data_probeset_id, table.data_bot_id, table.data_signal).where( - table.data_probeset_id == gene_id - ) - ).all() - for row in rows: - data[row[1]] = row[2] + # sample validation is driven by metadata so regex updates live in one place + sample_pattern = db_metadata.get("sample_regex") + if not sample_pattern: + return { + "success": False, + "error": f"Sample validation metadata missing for database {database}", + "error_code": 500, + } - else: - # Validate all samples + regex_flags = re.I if db_metadata.get("sample_regex_case_insensitive", True) else 0 + sample_regex = re.compile(sample_pattern, regex_flags) + + # validate samples if the caller provided any + if sample_ids: for sample_id in sample_ids: if not sample_regex.search(sample_id): return { @@ -207,16 +108,30 @@ def get_data(species, database, gene_id, sample_ids=None): "error_code": 400, } - rows = db.session.execute( - db.select(table.data_probeset_id, table.data_bot_id, table.data_signal).where( - and_( - table.data_probeset_id == gene_id, - table.data_bot_id.in_(sample_ids), - ) - ) - ).all() - for row in rows: - data[row[1]] = row[2] + query_result = query_efp_database_dynamic( + database, + gene_id, + sample_ids=sample_ids or None, + allow_empty_results=True, + sample_case_insensitive=db_metadata.get("sample_case_insensitive_query", True), + ) + + if not query_result["success"]: + return { + "success": False, + "error": query_result.get("error", "Database query failed"), + "error_code": query_result.get("error_code", 500), + } + + for entry in query_result.get("data", []): + sample_name = entry.get("name") + value = entry.get("value") + if sample_name is None: + continue + try: + data[sample_name] = float(value) + except (TypeError, ValueError): + data[sample_name] = value return {"success": True, "data": data} @@ -225,10 +140,10 @@ def get_data(species, database, gene_id, sample_ids=None): class PostRNASeqExpression(Resource): @rnaseq_gene_expression.expect(gene_expression_request_fields) def post(self): - """This end point returns gene expression data for a single gene and multiple samples.""" + """return gene expression data for a single gene and a list of samples""" json_data = request.get_json() - # Validate json + # validate json payload try: json_data = RNASeqSchema().load(json_data) except ValidationError as err: @@ -242,7 +157,7 @@ def post(self): results = RNASeqUtils.get_data(species, database, gene_id, sample_ids) if results["success"]: - # Return results if there are data + # return results when rows exist if len(results["data"]) > 0: return BARUtils.success_exit(results["data"]) else: @@ -257,8 +172,8 @@ class GetRNASeqGeneExpression(Resource): @rnaseq_gene_expression.param("database", _in="path", default="single_cell") @rnaseq_gene_expression.param("gene_id", _in="path", default="At1g01010") def get(self, species="", database="", gene_id=""): - """This end point returns RNA-Seq gene expression data""" - # Variables + """return rna-seq gene expression data""" + # sanitize path inputs species = escape(species) database = escape(database) gene_id = escape(gene_id) @@ -266,7 +181,7 @@ def get(self, species="", database="", gene_id=""): results = RNASeqUtils.get_data(species, database, gene_id) if results["success"]: - # Return results if there are data + # return results when rows exist if len(results["data"]) > 0: return BARUtils.success_exit(results["data"]) else: @@ -282,8 +197,8 @@ class GetRNASeqGeneExpressionSample(Resource): @rnaseq_gene_expression.param("gene_id", _in="path", default="At1g01010") @rnaseq_gene_expression.param("sample_id", _in="path", default="cluster0_WT1.ExprMean") def get(self, species="", database="", gene_id="", sample_id=""): - """This end point returns RNA-Seq gene expression data""" - # Variables + """return rna-seq gene expression for a specific sample""" + # sanitize path inputs species = escape(species) database = escape(database) gene_id = escape(gene_id) @@ -292,7 +207,7 @@ def get(self, species="", database="", gene_id="", sample_id=""): results = RNASeqUtils.get_data(species, database, gene_id, [sample_id]) if results["success"]: - # Return results if there are data + # return results when rows exist if len(results["data"]) > 0: return BARUtils.success_exit(results["data"]) else: diff --git a/api/services/__init__.py b/api/services/__init__.py new file mode 100644 index 0000000..83476a9 --- /dev/null +++ b/api/services/__init__.py @@ -0,0 +1,3 @@ +"""Service layer helpers shared across multiple resources.""" + +__all__ = [] diff --git a/api/services/efp_bootstrap.py b/api/services/efp_bootstrap.py new file mode 100644 index 0000000..b2278f4 --- /dev/null +++ b/api/services/efp_bootstrap.py @@ -0,0 +1,273 @@ +""" +Utilities to bootstrap the simple eFP databases directly from the shared schema +definitions. Shared by the CLI script and the Flask endpoint so we only maintain +one implementation. +""" + +from __future__ import annotations + +import re +import hashlib +from typing import Dict, Iterable, List + +from sqlalchemy import Column, Index, MetaData, Table, create_engine, text +from sqlalchemy.dialects.mysql import FLOAT, INTEGER, TEXT, VARCHAR +from sqlalchemy.engine import URL + +from api.models.efp_schemas import SIMPLE_EFP_DATABASE_SCHEMAS + + +def _column_type(column_spec): + """ + Convert a column specification dictionary to a SQLAlchemy MySQL column type. + + :param column_spec: Dictionary containing column metadata from schema definition + :type column_spec: Dict[str, Any] + :return: SQLAlchemy column type object (VARCHAR, INTEGER, FLOAT, or TEXT) + :rtype: sqlalchemy.types.TypeEngine + :raises ValueError: If column type is not one of: string, integer, float, text + """ + col_type = column_spec.get("type") + if col_type == "string": + return VARCHAR(column_spec["length"]) + if col_type == "integer": + return INTEGER(unsigned=column_spec.get("unsigned", False)) + if col_type == "float": + # explicit mysql float keeps parity with the original dumps + return FLOAT() + if col_type == "text": + return TEXT() + raise ValueError(f"Unsupported column type: {col_type}") + + +def _build_table(metadata: MetaData, spec, db_name: str) -> Table: + """ + Build a SQLAlchemy Table object from a schema specification. + + Creates columns with proper types, constraints, defaults, and indexes based on + the schema definition. This Table object can be used to generate CREATE TABLE + SQL statements. + + :param metadata: SQLAlchemy MetaData object to attach the table to + :type metadata: sqlalchemy.schema.MetaData + :param spec: Database schema specification from SIMPLE_EFP_DATABASE_SCHEMAS + :type spec: Dict[str, Any] + :param db_name: Name of the database (used for index naming) + :type db_name: str + :return: SQLAlchemy Table object with all columns and indexes defined + :rtype: sqlalchemy.schema.Table + """ + columns = [] + for column in spec["columns"]: + kwargs = {"nullable": column.get("nullable", True)} + if column.get("primary_key"): + kwargs["primary_key"] = True + default_value = column.get("default") + if default_value is not None: + if isinstance(default_value, str): + kwargs["server_default"] = text(f"'{default_value}'") + else: + kwargs["server_default"] = text(str(default_value)) + + columns.append(Column(column["name"], _column_type(column), **kwargs)) + + table = Table(spec["table_name"], metadata, *columns, mysql_charset=spec.get("charset")) + index_cols = spec.get("index") or [] + if index_cols: + # MySQL cannot index TEXT/BLOB columns without a prefix length. + # Filter them out to avoid bootstrap failures when schemas use TEXT. + text_cols = {col["name"] for col in spec["columns"] if col.get("type") == "text"} + index_cols = [col for col in index_cols if col not in text_cols] + if index_cols: + index_name = _make_index_name(db_name, index_cols) + Index(index_name, *[table.c[col] for col in index_cols]) + return table + + +def _make_index_name(db_name: str, index_cols: Iterable[str], max_len: int = 64) -> str: + """ + Create a MySQL-safe index name capped at 64 characters. + + If the generated name is too long, fall back to a truncated db_name with a stable hash + to keep names deterministic and avoid collisions. + """ + base = f"ix_{db_name}_{'_'.join(index_cols)}" + if len(base) <= max_len: + return base + + digest = hashlib.sha1(base.encode("utf-8")).hexdigest()[:8] + reserved = len("ix_") + 1 + len(digest) + db_len = max_len - reserved + if db_len <= 0: + return f"ix_{digest}" + return f"ix_{db_name[:db_len]}_{digest}" + + +def _build_url(host: str, port: int, user: str, password: str, database: str | None = None) -> URL: + """ + Build a SQLAlchemy database URL for MySQL connections. + + :param host: MySQL server hostname (e.g., 'localhost', 'BAR_mysqldb') + :type host: str + :param port: MySQL server port number (typically 3306) + :type port: int + :param user: MySQL username for authentication + :type user: str + :param password: MySQL password for authentication + :type password: str + :param database: Optional database name to connect to; if None, connects to server without selecting a database + :type database: str or None + :return: SQLAlchemy URL object for mysql+mysqldb connections + :rtype: sqlalchemy.engine.URL + """ + return URL.create( + drivername="mysql+mysqldb", + username=user, + password=password, + host=host, + port=port, + database=database, + ) + + +def ensure_database(server_url: URL, db_name: str, charset: str) -> None: + """ + Create a MySQL database if it doesn't already exist. + + Executes CREATE DATABASE IF NOT EXISTS with the specified character set. + Safe to call multiple times - will not error if database already exists. + + :param server_url: SQLAlchemy URL for MySQL server connection (without database selected) + :type server_url: sqlalchemy.engine.URL + :param db_name: Name of the database to create + :type db_name: str + :param charset: MySQL character set (e.g., 'latin1', 'utf8mb4') + :type charset: str + :return: None + :rtype: None + :raises ValueError: If db_name or charset contains invalid characters + """ + # Validate database name to prevent SQL injection - only allow safe identifier characters + if not re.match(r'^[a-zA-Z0-9_$]+$', db_name): + raise ValueError(f"Invalid database name: {db_name}. Only alphanumeric, underscore, and dollar sign characters are allowed.") + + # Validate charset name to prevent SQL injection - only allow safe characters + if not re.match(r'^[a-zA-Z0-9_]+$', charset): + raise ValueError(f"Invalid charset name: {charset}. Only alphanumeric and underscore characters are allowed.") + + server_engine = create_engine(server_url) + with server_engine.begin() as conn: + # Safe to use f-string here since we've validated the inputs above + conn.execute(text(f"CREATE DATABASE IF NOT EXISTS `{db_name}` DEFAULT CHARACTER SET {charset}")) + + +def ensure_schema(db_url: URL, spec, db_name: str) -> Dict[str, object]: + """ + Create database tables and insert seed data if the table is empty. + + Uses SQLAlchemy's metadata.create_all() to generate CREATE TABLE statements + from the schema specification. If seed_rows are defined in the spec and the + table is empty, inserts the seed data. + + :param db_url: SQLAlchemy URL for the specific database connection + :type db_url: sqlalchemy.engine.URL + :param spec: Database schema specification from SIMPLE_EFP_DATABASE_SCHEMAS + :type spec: Dict[str, Any] + :param db_name: Name of the database (used for table naming) + :type db_name: str + :return: Dictionary with 'table' (table name) and 'seeded_rows' (count of inserted rows) + :rtype: Dict[str, object] + """ + metadata = MetaData() + table = _build_table(metadata, spec, db_name) + engine = create_engine(db_url) + metadata.create_all(engine, checkfirst=True) + + seed_rows = spec.get("seed_rows") or [] + inserted = 0 + if seed_rows: + with engine.connect() as conn: + count = conn.execute(text(f"SELECT COUNT(1) FROM {table.name}")).scalar() or 0 + if count == 0: + with engine.begin() as write_conn: + write_conn.execute(table.insert(), seed_rows) + inserted = len(seed_rows) + + return {"table": table.name, "seeded_rows": inserted} + + +def bootstrap_simple_efp_databases( + *, + host: str, + port: int, + user: str, + password: str, + databases: Iterable[str] | None = None, +) -> List[Dict[str, object]]: + """ + Bootstrap simple eFP databases in MySQL from schema definitions. + + This is the main entry point for creating eFP databases. For each database: + 1. Creates the database if it doesn't exist + 2. Creates the sample_data table with schema from SIMPLE_EFP_DATABASE_SCHEMAS + 3. Inserts seed rows if the table is empty and seed_rows are defined + + Used by: + - scripts/bootstrap_simple_efp_dbs.py (CLI tool) + - config/init.sh (Docker/CI initialization) + - api/resources/efp_proxy.py (HTTP bootstrap endpoint) + + :param host: MySQL server hostname (e.g., 'localhost', 'BAR_mysqldb' for Docker) + :type host: str + :param port: MySQL server port number (typically 3306) + :type port: int + :param user: MySQL username with CREATE DATABASE privileges + :type user: str + :param password: MySQL password for authentication + :type password: str + :param databases: Optional list of specific databases to bootstrap; if None, bootstraps all databases in SIMPLE_EFP_DATABASE_SCHEMAS + :type databases: Iterable[str] or None + :return: List of result dictionaries, each containing 'database' (name), 'table' (table name), and 'seeded_rows' (count) + :rtype: List[Dict[str, object]] + :raises ValueError: If a requested database is not defined in SIMPLE_EFP_DATABASE_SCHEMAS + + Example:: + + results = bootstrap_simple_efp_databases( + host='localhost', + port=3306, + user='root', + password='password', + databases=['cannabis', 'dna_damage'] + ) + # Returns: [ + # {'database': 'cannabis', 'table': 'sample_data', 'seeded_rows': 1}, + # {'database': 'dna_damage', 'table': 'sample_data', 'seeded_rows': 1} + # ] + """ + + results: List[Dict[str, object]] = [] + target_dbs = list(databases) if databases is not None else list(SIMPLE_EFP_DATABASE_SCHEMAS.keys()) + + server_url = _build_url(host, port, user, password, database=None) + for db_name in target_dbs: + if db_name not in SIMPLE_EFP_DATABASE_SCHEMAS: + raise ValueError(f"Unknown simple eFP database: {db_name}") + + spec = SIMPLE_EFP_DATABASE_SCHEMAS[db_name] + charset = spec.get("charset", "utf8mb4") + ensure_database(server_url, db_name, charset) + db_url = _build_url(host, port, user, password, database=db_name) + schema_result = ensure_schema(db_url, spec, db_name) + results.append( + { + "database": db_name, + "table": schema_result["table"], + "seeded_rows": schema_result["seeded_rows"], + } + ) + + return results + + +__all__ = ["bootstrap_simple_efp_databases"] diff --git a/api/services/efp_data.py b/api/services/efp_data.py new file mode 100644 index 0000000..c284099 --- /dev/null +++ b/api/services/efp_data.py @@ -0,0 +1,503 @@ +""" +shared helper utilities for querying efp databases +""" + +from __future__ import annotations + +import re +import traceback +from pathlib import Path +from typing import Any, Dict, Iterable, List, Optional, Tuple +from types import SimpleNamespace + +from flask import has_app_context +from sqlalchemy import create_engine, text +from sqlalchemy.exc import SQLAlchemyError +from sqlalchemy.engine import Engine +from sqlalchemy.orm import Session + +from api import db +from api.models.annotations_lookup import AtAgiLookup +from api.models.bar_utils import BARUtils +from api.models.efp_schemas import SIMPLE_EFP_DATABASE_SCHEMAS + +# absolute path to the config/databases directory where the sqlite mirrors live +ROOT_DIR = Path(__file__).resolve().parents[2] +DATABASE_DIR = ROOT_DIR / "config" / "databases" + +DEFAULT_SAMPLE_SCHEMA = { + "table": "sample_data", + "gene_column": "data_probeset_id", + "sample_column": "data_bot_id", + "value_column": "data_signal", +} + +# manual list covers datasets still backed by shipped dumps +_MANUAL_DEFAULT_DATABASES = [ + "canola_nssnp", + "eplant2", + "eplant_poplar", + "eplant_rice", + "eplant_soybean", + "eplant_tomato", + "fastpheno", + "homologs_db", + "interactions_vincent_v2", + "llama3", + "poplar_nssnp", + "rice_interactions", + "soybean_nssnp", + "tomato_nssnp", + "tomato_sequence", +] + +MANUAL_DATABASE_SCHEMAS = { + name: { + **DEFAULT_SAMPLE_SCHEMA, + "filename": f"{name}.db", + "identifier_type": "agi", + "metadata": {}, + } + for name in _MANUAL_DEFAULT_DATABASES +} + +MANUAL_DATABASE_SCHEMAS["sample_data"] = { + **DEFAULT_SAMPLE_SCHEMA, + "filename": "sample_data.db", + "identifier_type": "probeset", + "metadata": {"species": "arabidopsis"}, +} + +# minimal seed data for CI environments that don't have local mirrors yet +# keys are normalized to uppercase to simplify lookups +LOCAL_EFP_DATASETS: Dict[str, Dict[str, List[Dict[str, str]]]] = { + "sample_data": { + "261585_AT": [ + {"sample": "ATGE_100_A", "value": "40.381"}, + {"sample": "ATGE_100_B", "value": "38.924"}, + ] + }, + "embryo": { + "AT1G01010": [ + {"sample": "pg_1", "value": "0.67"}, + ] + }, + "cannabis": { + "AGQN03009284": [ + {"sample": "PK-RT", "value": "0"}, + ] + }, +} + + +class EFPDataService: + """Service class for querying eFP (electronic Fluorescent Pictograph) databases.""" + + @staticmethod + def _build_schema_catalog() -> Dict[str, Dict[str, Any]]: + """Stitch together the python schemas + legacy dumps into one lookup table. + + :return: Catalog of database schemas + :rtype: Dict[str, Dict[str, Any]] + """ + catalog: Dict[str, Dict[str, Any]] = {} + for db_name, spec in SIMPLE_EFP_DATABASE_SCHEMAS.items(): + schema = dict(DEFAULT_SAMPLE_SCHEMA) + schema.update( + { + "filename": f"{db_name}.db", + "identifier_type": spec.get("identifier_type", "agi"), + "metadata": spec.get("metadata") or {}, + } + ) + catalog[db_name] = schema + + for db_name, schema in MANUAL_DATABASE_SCHEMAS.items(): + catalog[db_name] = dict(schema) + + return catalog + + @staticmethod + def _query_local_dataset( + database: str, + query_id: str, + sample_ids: Optional[List[str]], + sample_case_insensitive: bool, + ) -> Optional[List[SimpleNamespace]]: + """Return seed data rows for databases without sqlite mirrors. + + :param database: Database name + :type database: str + :param query_id: Gene identifier to query + :type query_id: str + :param sample_ids: Optional list of sample IDs to filter results + :type sample_ids: Optional[List[str]] + :param sample_case_insensitive: If True, compare sample IDs case-insensitively + :type sample_case_insensitive: bool + :return: List of result rows or None if database not found + :rtype: Optional[List[SimpleNamespace]] + """ + dataset = LOCAL_EFP_DATASETS.get(database) + if dataset is None: + return None + + gene_rows = dataset.get(query_id.upper(), []) + rows = list(gene_rows) + + if sample_ids: + filtered = [sample for sample in sample_ids if sample] + if filtered: + if sample_case_insensitive: + lookup = {sample.upper() for sample in filtered} + + def matches(row_name: str) -> bool: + return row_name.upper() in lookup + + else: + lookup = set(filtered) + + def matches(row_name: str) -> bool: + return row_name in lookup + + rows = [row for row in rows if matches(row["sample"])] + + return [SimpleNamespace(sample=row["sample"], value=row["value"]) for row in rows] + + @staticmethod + def agi_to_probset(gene_id: str) -> Optional[str]: + """ + Convert an Arabidopsis AGI identifier to its corresponding probeset ID. + + Looks up the most recent mapping in the AtAgiLookup table, ordered by date + descending. This ensures the newest array design mapping is used when multiple + mappings exist for the same AGI. + + :param gene_id: Arabidopsis gene ID in AGI format (e.g., 'AT1G01010') + :type gene_id: str + :return: Probeset ID (e.g., '261585_at') if found, None otherwise + :rtype: Optional[str] + + Example:: + + probeset = EFPDataService.agi_to_probset('AT1G01010') + # Returns: '261585_at' (if mapping exists) + """ + try: + subquery = ( + db.select(AtAgiLookup.probeset) + .where(AtAgiLookup.agi == gene_id.upper()) + .order_by(AtAgiLookup.date.desc()) + .limit(1) + .subquery() + ) + + sq_query = db.session.query(subquery) + if sq_query.count() > 0: + # safest pick is the newest mapping because the array design changed over time + return sq_query[0][0] + return None + except Exception as exc: # pragma: no cover - defensive logging path + print(f"[error] agi to probeset conversion failed {exc}") + return None + + @staticmethod + def _iter_engine_candidates(database: str) -> Iterable[Tuple[str, Engine, bool]]: + """ + Yield database engine candidates with MySQL priority and SQLite fallback. + + This function enables dual-mode operation: + - Production/CI: Uses MySQL via Flask-SQLAlchemy binds + - Local development: Falls back to SQLite mirror files + + Priority order: + 1. Flask-SQLAlchemy bind (MySQL) - if Flask app context exists + 2. SQLite mirror file - if exists in config/databases/ + + :param database: Database name (e.g., 'cannabis', 'dna_damage') + :type database: str + :yields: Tuples of (engine_type, engine, is_sqlite) where: + - engine_type: 'sqlalchemy_bind' or 'sqlite_mirror' + - engine: SQLAlchemy Engine object + - is_sqlite: True if SQLite, False if MySQL + :rtype: Iterator[Tuple[str, sqlalchemy.engine.Engine, bool]] + + Example:: + + for engine_type, engine, is_sqlite in EFPDataService._iter_engine_candidates('cannabis'): + try: + result = engine.execute('SELECT * FROM sample_data LIMIT 1') + break # Found working engine + except: + continue # Try next engine + """ + # prefer live mysql binds but fall back to sqlite mirrors when needed + db_path = DATABASE_DIR / DYNAMIC_DATABASE_SCHEMAS[database]["filename"] + if has_app_context(): + try: + bound_engine = db.engines.get(database) + if bound_engine: + yield ("sqlalchemy_bind", bound_engine, False) + except Exception as exc: + print(f"[warn] unable to load sqlalchemy bind for {database}: {exc}") + + if db_path.exists(): + sqlite_engine = create_engine(f"sqlite:///{db_path}") + yield ("sqlite_mirror", sqlite_engine, True) + + @staticmethod + def query_efp_database_dynamic( + database: str, + gene_id: str, + sample_ids: Optional[List[str]] = None, + allow_empty_results: bool = False, + sample_case_insensitive: bool = False, + ) -> Dict[str, object]: + """ + Dynamically query any eFP database using the shared schema catalog. + + This function provides a unified interface for querying expression data across + different eFP databases, handling species-specific gene ID validation and + automatic probeset conversion when needed. + + :param database: Database name (e.g., 'cannabis', 'embryo', 'sample_data') + :type database: str + :param gene_id: Gene identifier (AGI format, probeset, or species-specific format) + :type gene_id: str + :param sample_ids: Optional list of sample IDs to filter results; if None, returns all samples + :type sample_ids: Optional[List[str]] + :param allow_empty_results: If True, return success even when no data found; if False, return 404 error + :type allow_empty_results: bool + :param sample_case_insensitive: If True, compare sample IDs case-insensitively + :type sample_case_insensitive: bool + :return: Dictionary with 'success' boolean, data or error message, and HTTP status code + :rtype: Dict[str, object] + + Example:: + + result = EFPDataService.query_efp_database_dynamic('embryo', 'AT1G01010') + # Returns: {'success': True, 'gene_id': 'AT1G01010', 'data': [...]} + + result = EFPDataService.query_efp_database_dynamic('sample_data', 'AT1G01010') + # Auto-converts to probeset, returns: {'probset_id': '261585_at', ...} + """ + try: + database = str(database) + gene_id = str(gene_id) + + schema = DYNAMIC_DATABASE_SCHEMAS.get(database) + if not schema: + return { + "success": False, + "error": ( + f"Database '{database}' is not supported. " + f"Select one of: {', '.join(sorted(DYNAMIC_DATABASE_SCHEMAS.keys()))}" + ), + "error_code": 400, + } + + # Extract species information from schema metadata + species = schema.get("metadata", {}).get("species", "").lower() + + query_id = gene_id + probset_display = None + gene_case_insensitive = False + upper_id = gene_id.upper() + is_agi_id = upper_id.startswith("AT") and "G" in upper_id + + # Validate gene ID format based on species and ID pattern + # Only validate if the ID looks like it's in the species-specific format + if is_agi_id: + # This looks like an Arabidopsis AGI ID - validate it + if not BARUtils.is_arabidopsis_gene_valid(upper_id): + return {"success": False, "error": "Invalid Arabidopsis gene ID format", "error_code": 400} + elif species and schema["identifier_type"] == "agi": + # For non-AGI formatted IDs in species databases that expect AGI format, + # validate against the specific species validator + if species == "arachis": + if not BARUtils.is_arachis_gene_valid(upper_id): + return {"success": False, "error": "Invalid Arachis gene ID", "error_code": 400} + elif species == "cannabis": + if not BARUtils.is_cannabis_gene_valid(upper_id): + return {"success": False, "error": "Invalid Cannabis gene ID", "error_code": 400} + elif species == "kalanchoe": + if not BARUtils.is_kalanchoe_gene_valid(upper_id): + return {"success": False, "error": "Invalid Kalanchoe gene ID", "error_code": 400} + elif species == "phelipanche": + if not BARUtils.is_phelipanche_gene_valid(upper_id): + return {"success": False, "error": "Invalid Phelipanche gene ID", "error_code": 400} + elif species == "physcomitrella": + if not BARUtils.is_physcomitrella_gene_valid(upper_id): + return {"success": False, "error": "Invalid Physcomitrella gene ID", "error_code": 400} + elif species == "selaginella": + if not BARUtils.is_selaginella_gene_valid(upper_id): + return {"success": False, "error": "Invalid Selaginella gene ID", "error_code": 400} + elif species == "strawberry": + if not BARUtils.is_strawberry_gene_valid(upper_id): + return {"success": False, "error": "Invalid Strawberry gene ID", "error_code": 400} + elif species == "striga": + if not BARUtils.is_striga_gene_valid(upper_id): + return {"success": False, "error": "Invalid Striga gene ID", "error_code": 400} + elif species == "triphysaria": + if not BARUtils.is_triphysaria_gene_valid(upper_id): + return {"success": False, "error": "Invalid Triphysaria gene ID", "error_code": 400} + + # Handle Arabidopsis-specific logic for AGI IDs + if is_agi_id: + if schema["identifier_type"] == "probeset": + probset = EFPDataService.agi_to_probset(upper_id) + if not probset: + return { + "success": False, + "error": f"Could not find probeset for gene {gene_id}", + "error_code": 404, + } + query_id = probset + probset_display = probset + print(f"[info] Converted {gene_id} to probeset {query_id} for {database}") + else: + query_id = upper_id + gene_case_insensitive = True + probset_display = upper_id + else: + # Non-AGI IDs: use as-is, typically already uppercase from validation + query_id = upper_id if species else gene_id + gene_case_insensitive = bool(species) + + # Build SQL query using parameterized queries to prevent SQL injection + # Column and table names come from the internal schema catalog, which is safe + gene_col = schema["gene_column"] + sample_col = schema["sample_column"] + value_col = schema["value_column"] + table_name = schema["table"] + + # Validate identifiers contain only safe characters (alphanumeric and underscore) + for identifier, name in [ + (gene_col, "gene_column"), + (sample_col, "sample_column"), + (value_col, "value_column"), + (table_name, "table"), + ]: + if not re.match(r'^[a-zA-Z_][a-zA-Z0-9_]*$', identifier): + return { + "success": False, + "error": f"Invalid schema identifier for {name}: {identifier}", + "error_code": 500, + } + + gene_column_expr = f"UPPER({gene_col})" if gene_case_insensitive else gene_col + params = {"gene_id": query_id.upper() if gene_case_insensitive else query_id} + where_clauses = [f"{gene_column_expr} = :gene_id"] + + if sample_ids: + filtered = [s for s in sample_ids if s] + if filtered: + sample_column_expr = f"UPPER({sample_col})" if sample_case_insensitive else sample_col + sample_conditions = [] + for idx, sample in enumerate(filtered): + key = f"sample_{idx}" + params[key] = sample.upper() if sample_case_insensitive else sample + sample_conditions.append(f"{sample_column_expr} = :{key}") + where_clauses.append(f"({' OR '.join(sample_conditions)})") + + query_sql = text( + f"SELECT {sample_col} AS sample, {value_col} AS value " + f"FROM {table_name} " + f"WHERE {' AND '.join(where_clauses)}" + ) + + engine_candidates = list(EFPDataService._iter_engine_candidates(database)) + results = None + last_error = None + + if engine_candidates: + for source_label, engine, dispose_after in engine_candidates: + try: + with Session(engine) as session: + results = session.execute(query_sql, params).all() + break + except SQLAlchemyError as exc: + last_error = f"{source_label} failed: {exc}" + print(f"[warn] {last_error}") + except Exception as exc: + last_error = f"{source_label} unexpected failure: {exc}" + print(f"[warn] {last_error}") + finally: + if dispose_after: + engine.dispose() + else: + last_error = f"Database {database} is not available (no active bind or sqlite mirror)." + + local_rows = None + if results is None or not results: + local_rows = EFPDataService._query_local_dataset( + database, + query_id, + sample_ids, + sample_case_insensitive, + ) + if local_rows is not None: + results = local_rows + + if results is None: + return { + "success": False, + "error": ( + f"Database query failed for {database}. " + f"{'Last error: ' + last_error if last_error else ''}" + ).strip(), + "error_code": 500, + } + + if not results and not allow_empty_results: + error_dict = BARUtils.error_exit( + f"No expression data found for {gene_id} (query identifier: {query_id})" + ) + # Convert BARUtils format to match EFP service format + return { + "success": False, + "error": error_dict["error"], + "error_code": 404, + } + + expression_data = [{"name": row.sample, "value": str(row.value)} for row in results] + + return { + "success": True, + "gene_id": gene_id, + "probset_id": probset_display or query_id, + "database": database, + "record_count": len(expression_data), + "data": expression_data, + } + + except Exception as exc: + error_trace = traceback.format_exc() + print(f"[error] Database query exception: {error_trace}") + return { + "success": False, + "error": f"Database query failed: {str(exc)}", + "error_code": 500, + } + + +# Build the schema catalog at module load time +DYNAMIC_DATABASE_SCHEMAS = EFPDataService._build_schema_catalog() + + +# Maintain backward compatibility with existing code that imports these functions directly +def agi_to_probset(gene_id: str) -> Optional[str]: + """Backward compatibility wrapper for EFPDataService.agi_to_probset()""" + return EFPDataService.agi_to_probset(gene_id) + + +def query_efp_database_dynamic( + database: str, + gene_id: str, + sample_ids: Optional[List[str]] = None, + allow_empty_results: bool = False, + sample_case_insensitive: bool = False, +) -> Dict[str, object]: + """Backward compatibility wrapper for EFPDataService.query_efp_database_dynamic()""" + return EFPDataService.query_efp_database_dynamic( + database, gene_id, sample_ids, allow_empty_results, sample_case_insensitive + ) diff --git a/config/databases/sample_data.sql b/config/databases/sample_data.sql new file mode 100644 index 0000000..e4228c2 --- /dev/null +++ b/config/databases/sample_data.sql @@ -0,0 +1,560 @@ +-- phpMyAdmin SQL Dump +-- version 5.2.1deb1+deb12u1 +-- https://www.phpmyadmin.net/ +-- +-- Host: localhost:3306 +-- Generation Time: Oct 16, 2025 at 06:44 PM +-- Server version: 8.4.6 +-- PHP Version: 8.2.29 + +SET SQL_MODE = "NO_AUTO_VALUE_ON_ZERO"; +START TRANSACTION; +SET time_zone = "+00:00"; + + +/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */; +/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */; +/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */; +/*!40101 SET NAMES utf8mb4 */; + +-- +-- Database: `atgenexp` +-- + +-- -------------------------------------------------------- + +-- +-- Table structure for table `sample_data` +-- + +CREATE TABLE `sample_data` ( + `sample_id` int UNSIGNED NOT NULL DEFAULT '0', + `proj_id` int UNSIGNED NOT NULL DEFAULT '0', + `sample_file_name` tinytext NOT NULL, + `data_probeset_id` varchar(30) DEFAULT NULL, + `data_signal` float NOT NULL DEFAULT '0', + `data_call` tinytext NOT NULL, + `data_p_val` float NOT NULL DEFAULT '0', + `data_bot_id` varchar(50) NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; + +-- +-- Dumping data for table `sample_data` +-- + +INSERT INTO `sample_data` (`sample_id`, `proj_id`, `sample_file_name`, `data_probeset_id`, `data_signal`, `data_call`, `data_p_val`, `data_bot_id`) VALUES +(232, 6, 'ATGE_100_A_tair.txt', '256898_at', 24.975, '', 0, 'ATGE_100_A'), +(233, 6, 'ATGE_100_B_tair.txt', '256898_at', 22.77, '', 0, 'ATGE_100_B'), +(234, 6, 'ATGE_100_C_tair.txt', '256898_at', 20.416, '', 0, 'ATGE_100_C'), +(235, 6, 'ATGE_101_A_tair.txt', '256898_at', 22.106, '', 0, 'ATGE_101_A'), +(236, 6, 'ATGE_101_B_tair.txt', '256898_at', 21.477, '', 0, 'ATGE_101_B'), +(237, 6, 'ATGE_101_C_tair.txt', '256898_at', 25.781, '', 0, 'ATGE_101_C'), +(28, 1, 'ATGE_10_A_tair.txt', '256898_at', 29.274, '', 0, 'ATGE_10_A'), +(29, 1, 'ATGE_10_B_tair.txt', '256898_at', 23.631, '', 0, 'ATGE_10_B'), +(30, 1, 'ATGE_10_C_tair.txt', '256898_at', 20.562, '', 0, 'ATGE_10_C'), +(31, 1, 'ATGE_11_A_tair.txt', '256898_at', 25.333, '', 0, 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'ATGE_91_A_tair.txt', '261585_at', 41.055, '', 0, 'ATGE_91_A'), +(206, 5, 'ATGE_91_B_tair.txt', '261585_at', 44.102, '', 0, 'ATGE_91_B'), +(207, 5, 'ATGE_91_C_tair.txt', '261585_at', 41.074, '', 0, 'ATGE_91_C'), +(208, 5, 'ATGE_92_A_tair.txt', '261585_at', 45.219, '', 0, 'ATGE_92_A'), +(209, 5, 'ATGE_92_B_tair.txt', '261585_at', 42.546, '', 0, 'ATGE_92_B'), +(210, 5, 'ATGE_92_C_tair.txt', '261585_at', 46.824, '', 0, 'ATGE_92_C'), +(211, 5, 'ATGE_93_A_tair.txt', '261585_at', 162.29, '', 0, 'ATGE_93_A'), +(212, 5, 'ATGE_93_B_tair.txt', '261585_at', 170.376, '', 0, 'ATGE_93_B'), +(213, 5, 'ATGE_93_C_tair.txt', '261585_at', 161.751, '', 0, 'ATGE_93_C'), +(214, 6, 'ATGE_94_A_tair.txt', '261585_at', 170.818, '', 0, 'ATGE_94_A'), +(215, 6, 'ATGE_94_B_tair.txt', '261585_at', 144.128, '', 0, 'ATGE_94_B'), +(216, 6, 'ATGE_94_C_tair.txt', '261585_at', 163.289, '', 0, 'ATGE_94_C'), +(217, 6, 'ATGE_95_A_tair.txt', '261585_at', 156.823, '', 0, 'ATGE_95_A'), +(218, 6, 'ATGE_95_B_tair.txt', '261585_at', 158.167, '', 0, 'ATGE_95_B'), +(219, 6, 'ATGE_95_C_tair.txt', '261585_at', 161.188, '', 0, 'ATGE_95_C'), +(220, 6, 'ATGE_96_A_tair.txt', '261585_at', 49.577, '', 0, 'ATGE_96_A'), +(221, 6, 'ATGE_96_B_tair.txt', '261585_at', 51.902, '', 0, 'ATGE_96_B'), +(222, 6, 'ATGE_96_C_tair.txt', '261585_at', 53.945, '', 0, 'ATGE_96_C'), +(223, 6, 'ATGE_97_A_tair.txt', '261585_at', 50.785, '', 0, 'ATGE_97_A'), +(224, 6, 'ATGE_97_B_tair.txt', '261585_at', 53.895, '', 0, 'ATGE_97_B'), +(225, 6, 'ATGE_97_C_tair.txt', '261585_at', 50.003, '', 0, 'ATGE_97_C'), +(226, 6, 'ATGE_98_A_tair.txt', '261585_at', 188.598, '', 0, 'ATGE_98_A'), +(227, 6, 'ATGE_98_B_tair.txt', '261585_at', 211.942, '', 0, 'ATGE_98_B'), +(228, 6, 'ATGE_98_C_tair.txt', '261585_at', 165.624, '', 0, 'ATGE_98_C'), +(229, 6, 'ATGE_99_A_tair.txt', '261585_at', 184.169, '', 0, 'ATGE_99_A'), +(230, 6, 'ATGE_99_B_tair.txt', '261585_at', 171.851, '', 0, 'ATGE_99_B'), +(231, 6, 'ATGE_99_C_tair.txt', '261585_at', 164.836, '', 0, 'ATGE_99_C'), +(25, 1, 'ATGE_9_A_tair.txt', '261585_at', 127.365, '', 0, 'ATGE_9_A'), +(26, 1, 'ATGE_9_B_tair.txt', '261585_at', 134.69, '', 0, 'ATGE_9_B'), +(27, 1, 'ATGE_9_C_tair.txt', '261585_at', 151.607, '', 0, 'ATGE_9_C'), +(238, 1, 'ATGE_CTRL_1.txt', '261585_at', 47.443, '', 0, 'ATGE_CTRL_1'), +(239, 2, 'ATGE_CTRL_2.txt', '261585_at', 95.871, '', 0, 'ATGE_CTRL_2'), +(240, 3, 'ATGE_CTRL_3.txt', '261585_at', 43.563, '', 0, 'ATGE_CTRL_3'), +(241, 4, 'ATGE_CTRL_4.txt', '261585_at', 40.265, '', 0, 'ATGE_CTRL_4'), +(242, 5, 'ATGE_CTRL_5.txt', '261585_at', 45.219, '', 0, 'ATGE_CTRL_5'), +(243, 6, 'ATGE_CTRL_6.txt', '261585_at', 144.128, '', 0, 'ATGE_CTRL_6'), +(244, 7, 'ATGE_CTRL_7.txt', '261585_at', 48.508, '', 0, 'ATGE_CTRL_7'), +(245, 1, 'ATGE_CTRL_7.txt', '261585_at', 48.508, '', 0, 'ATGE_CTRL_7'), +(246, 2, 'ATGE_CTRL_7.txt', '261585_at', 48.508, '', 0, 'ATGE_CTRL_7'), +(247, 3, 'ATGE_CTRL_7.txt', '261585_at', 48.508, '', 0, 'ATGE_CTRL_7'), +(248, 4, 'ATGE_CTRL_7.txt', '261585_at', 48.508, '', 0, 'ATGE_CTRL_7'), +(249, 5, 'ATGE_CTRL_7.txt', '261585_at', 48.508, '', 0, 'ATGE_CTRL_7'), +(250, 6, 'ATGE_CTRL_7.txt', '261585_at', 48.508, '', 0, 'ATGE_CTRL_7'); + +-- +-- Indexes for dumped tables +-- + +-- +-- Indexes for table `sample_data` +-- +ALTER TABLE `sample_data` + ADD KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`); +COMMIT; + +/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */; +/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */; +/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; diff --git a/config/init.sh b/config/init.sh index 8da8309..c3e4a06 100755 --- a/config/init.sh +++ b/config/init.sh @@ -9,13 +9,19 @@ DB_PASS="root" # Load the data echo "Welcome to the BAR API. Running init!" +# Build simple eFP databases dynamically so we do not need static SQL dumps +echo "Bootstrapping simple eFP databases..." +python3 ./scripts/bootstrap_simple_efp_dbs.py --user "$DB_USER" --password "$DB_PASS" +if [ $? -ne 0 ]; then + echo "ERROR: Failed to bootstrap simple eFP databases" + exit 1 +fi +echo "Successfully bootstrapped simple eFP databases" + mysql -u $DB_USER -p$DB_PASS < ./config/databases/annotations_lookup.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_ecotypes.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/arachis.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/cannabis.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/canola_nssnp.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/dna_damage.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/embryo.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/eplant2.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/eplant_poplar.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/eplant_rice.sql diff --git a/config/species_databases.json b/config/species_databases.json new file mode 100644 index 0000000..a7e3aa3 --- /dev/null +++ b/config/species_databases.json @@ -0,0 +1,177 @@ +{ + "actinidia": { + "Bud_Development": "actinidia_bud_development", + "Flower_Fruit_Development": "actinidia_flower_fruit_development", + "Postharvest": "actinidia_postharvest", + "Vegetative_Growth": "actinidia_vegetative_growth" + }, + "arabidopsis": { + "Abiotic_Stress": "atgenexp_stress", + "Abiotic_Stress_II": "atgenexp_stress", + "Biotic_Stress": "atgenexp_pathogen", + "Biotic_Stress_II": "atgenexp_pathogen", + "Chemical": "atgenexp_hormone", + "DNA_Damage": "dna_damage", + "Development_RMA": "atgenexp", + "Developmental_Map": "atgenexp_plus", + "Developmental_Mutants": "atgenexp_plus", + "Embryo": "embryo", + "Germination": "germination", + "Guard_Cell": "guard_cell", + "Gynoecium": "gynoecium", + "Hormone": "atgenexp_hormone", + "Klepikova_Atlas": "klepikova", + "Lateral_Root_Initiation": "lateral_root_initiation", + "Light_Series": "light_series", + "Natural_Variation": "arabidopsis_ecotypes", + "Regeneration": "meristem_db", + "Root": "root", + "Root_II": "root", + "Seed": "seed_db", + "Shoot_Apex": "shoot_apex", + "Silique": "silique", + "Single_Cell": "single_cell", + "Tissue_Specific": "atgenexp_plus" + }, + "arabidopsis seedcoat": { + "Seed_Coat": "seedcoat" + }, + "arachis": { + "Arachis_Atlas": "arachis" + }, + "barley": { + "barley_mas": "barley_mas", + "barley_rma": "barley_rma" + }, + "brachypodium": { + "Brachypodium_Atlas": "brachypodium", + "Brachypodium_Grains": "brachypodium_grains", + "Brachypodium_Spikes": "brachypodium_Bd21", + "Photo_Thermocycle": "brachypodium_photo_thermocycle" + }, + "brassica rapa": { + "Embryogenesis": "brassica_rapa" + }, + "cacao ccn": { + "Developmental_Atlas": "cacao_developmental_atlas", + "Drought_Diurnal_Atlas": "cacao_drought_diurnal_atlas" + }, + "cacao sca": { + "Developmental_Atlas": "cacao_developmental_atlas_sca", + "Drought_Diurnal_Atlas": "cacao_drought_diurnal_atlas_sca", + "Meristem_Atlas": "cacao_meristem_atlas_sca", + "Seed_Atlas": "cacao_seed_atlas_sca" + }, + "cacao tc": { + "Cacao_Infection": "cacao_infection", + "Cacao_Leaf": "cacao_leaf" + }, + "camelina": { + "Developmental_Atlas_FPKM": "camelina", + "Developmental_Atlas_TPM": "camelina_tpm" + }, + "cannabis": { + "Cannabis_Atlas": "cannabis" + }, + "canola": { + "Canola_Seed": "canola_seed" + }, + "eutrema": { + "Eutrema": "thellungiella_db" + }, + "grape": { + "grape_developmental": "grape_developmental" + }, + "kalanchoe": { + "Light_Response": "kalanchoe" + }, + "little millet": { + "Life_Cycle": "little_millet" + }, + "lupin": { + "LCM_Leaf": "lupin_lcm_leaf", + "LCM_Pod": "lupin_lcm_pod", + "LCM_Stem": "lupin_lcm_stem", + "Whole_Plant": "lupin_whole_plant" + }, + "maize": { + "Downs_et_al_Atlas": "maize_gdowns", + "Early_Seed": "maize_early_seed", + "Embryonic_Leaf_Development": "maize_embryonic_leaf_development", + "Hoopes_et_al_Atlas": "maize_buell_lab", + "Hoopes_et_al_Stress": "maize_buell_lab", + "Maize_Kernel": "maize_early_seed", + "Maize_Root": "maize_root", + "Sekhon_et_al_Atlas": "maize_RMA_linear", + "Tassel_and_Ear_Primordia": "maize_ears", + "maize_iplant": "maize_iplant", + "maize_leaf_gradient": "maize_leaf_gradient", + "maize_rice_comparison": "maize_rice_comparison" + }, + "mangosteen": { + "Aril_vs_Rind": "mangosteen_aril_vs_rind", + "Callus": "mangosteen_callus", + "Diseased_vs_Normal": "mangosteen_diseased_vs_normal", + "Fruit_Ripening": "mangosteen_fruit_ripening", + "Seed_Development": "mangosteen_seed_development", + "Seed_Germination": "mangosteen_seed_germination" + }, + "medicago": { + "medicago_mas": "medicago_mas", + "medicago_rma": "medicago_rma", + "medicago_seed": "medicago_seed" + }, + "poplar": { + "Poplar": "poplar", + "PoplarTreatment": "poplar" + }, + "potato": { + "Potato_Developmental": "potato_dev", + "Potato_Stress": "potato_stress" + }, + "rice": { + "rice_drought_heat_stress": "rice_drought_heat_stress", + "rice_leaf_gradient": "rice_leaf_gradient", + "rice_maize_comparison": "rice_maize_comparison", + "rice_mas": "rice_mas", + "rice_rma": "rice_rma", + "riceanoxia_mas": "rice_mas", + "riceanoxia_rma": "rice_rma", + "ricestigma_mas": "rice_mas", + "ricestigma_rma": "rice_rma", + "ricestress_mas": "rice_mas", + "ricestress_rma": "rice_rma" + }, + "soybean": { + "soybean": "soybean", + "soybean_embryonic_development": "soybean_embryonic_development", + "soybean_heart_cotyledon_globular": "soybean_heart_cotyledon_globular", + "soybean_senescence": "soybean_senescence", + "soybean_severin": "soybean_severin" + }, + "strawberry": { + "Developmental_Map_Strawberry_Flower_and_Fruit": "strawberry", + "Strawberry_Green_vs_White_Stage": "strawberry" + }, + "tomato": { + "ILs_Leaf_Chitwood_et_al": "tomato_ils", + "ILs_Root_Tip_Brady_Lab": "tomato_ils2", + "M82_S_pennellii_Atlases_Koenig_et_al": "tomato_s_pennellii", + "Rose_Lab_Atlas": "tomato", + "Rose_Lab_Atlas_Renormalized": "tomato_renormalized", + "SEED_Lab_Angers": "tomato_seed", + "Shade_Mutants": "tomato_shade_mutants", + "Shade_Timecourse_WT": "tomato_shade_timecourse", + "Tomato_Meristem": "tomato_meristem" + }, + "triticale": { + "triticale": "triticale", + "triticale_mas": "triticale_mas" + }, + "wheat": { + "Developmental_Atlas": "wheat", + "Wheat_Abiotic_Stress": "wheat_abiotic_stress", + "Wheat_Embryogenesis": "wheat_embryogenesis", + "Wheat_Meiosis": "wheat_meiosis" + } +} diff --git a/data/efp_info/efp_species_view_info.json b/data/efp_info/efp_species_view_info.json new file mode 100644 index 0000000..8ea3252 --- /dev/null +++ b/data/efp_info/efp_species_view_info.json @@ -0,0 +1,18424 @@ +{ + "actinidia": { + + "data": { + "species": "actinidia", + "views": { + "Bud_Development": { + "database": "actinidia_bud_development", + "view_name": "Bud_Development", + "groups": { + "Nov": { + "controls": [ + "Nov" + ], + "treatments": { + "bud": [ + "Nov", + "Nov_TB", + "Dec", + "Jan", + "Jan_TB", + "Feb", + "Mar", + "Mar_TB", + "Apr", + "May", + "Jun", + "Jul", + "Aug" + ] + } + } + } + }, + "Flower_Fruit_Development": { + "database": "actinidia_flower_fruit_development", + "view_name": "Flower_Fruit_Development", + "groups": { + "flower": { + "controls": [ + "flower" + ], + "treatments": { + "Floral_Bud": [ + "Flower_bud" + ], + "centre": [ + "Flower" + ], + "anther": [ + "Flower" + ], + "petal": [ + "Flower" + ], + "core": [ + "Fruit_T1", + "Fruit_T2", + "Fruit_147_DAA", + "Fruit_166_DAA", + "Fruit_182_DAA", + "Fruit_224_DAA" + ], + "cortex": [ + "Fruit_T1", + "Fruit_T2", + "Fruit_147_DAA", + "Fruit_166_DAA", + "Fruit_182_DAA", + "Fruit_224_DAA" + ], + "flesh": [ + "Fruit_T1", + "Fruit_T2", + "Fruit_147_DAA", + "Fruit_166_DAA", + "Fruit_182_DAA", + "Fruit_224_DAA" + ] + } + } + } + }, + "Postharvest": { + "database": "actinidia_postharvest", + "view_name": "Postharvest", + "groups": { + "Postharvest_Control": { + "controls": [ + "Fruit_147_DAA", + "Fruit_166_DAA", + "Fruit_182_DAA", + "Fruit_224_DAA" + ], + "treatments": { + "core": [ + "Fruit_147_DAA", + "Fruit_166_DAA", + "Fruit_182_DAA", + "Fruit_224_DAA", + "Fruit_231_DAA", + "Fruit_231_DAA_1DAH", + "Fruit_231_DAA_2DAH", + "Fruit_231_DAA_4DAH" + ], + "cortex": [ + "Fruit_147_DAA", + "Fruit_166_DAA", + "Fruit_182_DAA", + "Fruit_224_DAA", + "Fruit_231_DAA", + "Fruit_231_DAA_1DAH", + "Fruit_231_DAA_2DAH", + "Fruit_231_DAA_4DAH" + ], + "flesh": [ + "Fruit_147_DAA", + "Fruit_166_DAA", + "Fruit_182_DAA", + "Fruit_224_DAA", + "Fruit_231_DAA", + "Fruit_231_DAA_1DAH", + "Fruit_231_DAA_2DAH", + "Fruit_231_DAA_4DAH" + ] + } + } + } + }, + "Vegetative_Growth": { + "database": "actinidia_vegetative_growth", + "view_name": "Vegetative_Growth", + "groups": { + "cane": { + "controls": [ + "cane" + ], + "treatments": { + "sink_leaf": [ + "Leaf_sink" + ], + "source_leaf": [ + "Leaf_source" + ], + "shoot": [ + "Shoot" + ], + "cane": [ + "cane" + ], + "root": [ + "Root" + ] + } + } + } + } + } + } + }, + "arabidopsis": { + + "data": { + "species": "arabidopsis", + "views": { + "Abiotic_Stress": { + "database": "atgenexp_stress", + "view_name": "Abiotic_Stress", + "groups": { + "Shoot_0_Hour": { + "controls": [ + "AtGen_6_0011", + "AtGen_6_0012" + ], + "treatments": { + "Control_Shoot_0_Hour": [ + "AtGen_6_0011", + "AtGen_6_0012" + ], + "Cold_Shoot_0_Hour": [ + "AtGen_6_0011", + "AtGen_6_0012" + ], + "Osmotic_Shoot_0_Hour": [ + "AtGen_6_0011", + "AtGen_6_0012" + ], + "Salt_Shoot_0_Hour": [ + "AtGen_6_0011", + "AtGen_6_0012" + ], + "Drought_Shoot_0_Hour": [ + "AtGen_6_0011", + "AtGen_6_0012" + ], + "Genotoxic_Shoot_0_Hour": [ + "AtGen_6_0011", + "AtGen_6_0012" + ], + "Oxidative_Shoot_0_Hour": [ + "AtGen_6_0011", + "AtGen_6_0012" + ], + "UV-B_Shoot_0_Hour": [ + "AtGen_6_0011", + "AtGen_6_0012" + ], + "Wounding_Shoot_0_Hour": [ + "AtGen_6_0011", + "AtGen_6_0012" + ], + "Heat_Shoot_0_Hour": [ + "AtGen_6_0011", + "AtGen_6_0012" + ] + } + }, + "Root_0_Hour": { + "controls": [ + "AtGen_6_0021", + "AtGen_6_0022" + ], + "treatments": { + "Control_Root_0_Hour": [ + "AtGen_6_0021", + "AtGen_6_0022" + ], + "Cold_Root_0_Hour": [ + "AtGen_6_0021", + "AtGen_6_0022" + ], + "Osmotic_Root_0_Hour": [ + "AtGen_6_0021", + "AtGen_6_0022" + ], + "Salt_Root_0_Hour": [ + "AtGen_6_0021", + "AtGen_6_0022" + ], + "Drought_Root_0_Hour": [ + "AtGen_6_0021", + "AtGen_6_0022" + ], + "Genotoxic_Root_0_Hour": [ + "AtGen_6_0021", + "AtGen_6_0022" + ], + "Oxidative_Root_0_Hour": [ + "AtGen_6_0021", + "AtGen_6_0022" + ], + "UV-B_Root_0_Hour": [ + "AtGen_6_0021", + "AtGen_6_0022" + ], + "Wounding_Root_0_Hour": [ + "AtGen_6_0021", + "AtGen_6_0022" + ], + "Heat_Root_0_Hour": [ + "AtGen_6_0021", + "AtGen_6_0022" + ] + } + }, + "Shoot_After_15_Minutes": { + "controls": [ + "AtGen_6_0711", + "AtGen_6_0712" + ], + "treatments": { + "Control_Shoot_After_15_Minutes": [ + "AtGen_6_0711", + "AtGen_6_0712" + ], + "Drought_Shoot_After_15_Minutes": [ + "AtGen_6_4711", + "AtGen_6_4712" + ], + "UV-B_Shoot_After_15_Minutes": [ + "AtGen_6_7711", + "AtGen_6_7712" + ], + "Wounding_Shoot_After_15_Minutes": [ + "AtGen_6_8715", + "AtGen_6_8712" + ], + "Heat_Shoot_After_15_Minutes": [ + "AtGen_6_9711", + "AtGen_6_9712" + ] + } + }, + "Root_After_15_Minutes": { + "controls": [ + "AtGen_6_0721", + "AtGen_6_0722" + ], + "treatments": { + "Control_Root_After_15_Minutes": [ + "AtGen_6_0721", + "AtGen_6_0722" + ], + "Drought_Root_After_15_Minutes": [ + "AtGen_6_4721", + "AtGen_6_4722" + ], + "UV-B_Root_After_15_Minutes": [ + "AtGen_6_7721", + "AtGen_6_7722" + ], + "Wounding_Root_After_15_Minutes": [ + "AtGen_6_8723", + "AtGen_6_8724" + ], + "Heat_Root_After_15_Minutes": [ + "AtGen_6_9721", + "AtGen_6_9722" + ] + } + }, + "Shoot_After_30_Minutes": { + "controls": [ + "AtGen_6_0111", + "AtGen_6_0112" + ], + "treatments": { + "Control_Shoot_After_30_Minutes": [ + "AtGen_6_0111", + "AtGen_6_0112" + ], + "Cold_Shoot_After_30_Minutes": [ + "AtGen_6_1111", + "AtGen_6_1112" + ], + "Osmotic_Shoot_After_30_Minutes": [ + "AtGen_6_2111", + "AtGen_6_2112" + ], + "Salt_Shoot_After_30_Minutes": [ + "AtGen_6_3111", + "AtGen_6_3112" + ], + "Drought_Shoot_After_30_Minutes": [ + "AtGen_6_4111", + "AtGen_6_4112" + ], + "Genotoxic_Shoot_After_30_Minutes": [ + "AtGen_6_5111", + "AtGen_6_5112" + ], + "Oxidative_Shoot_After_30_Minutes": [ + "AtGen_6_6111", + "AtGen_6_6112" + ], + "UV-B_Shoot_After_30_Minutes": [ + "AtGen_6_7111", + "AtGen_6_7112" + ], + "Wounding_Shoot_After_30_Minutes": [ + "AtGen_6_8111", + "AtGen_6_8112" + ], + "Heat_Shoot_After_30_Minutes": [ + "AtGen_6_9111", + "AtGen_6_9112" + ] + } + }, + "Root_After_30_Minutes": { + "controls": [ + "AtGen_6_0121", + "AtGen_6_0122" + ], + "treatments": { + "Control_Root_After_30_Minutes": [ + "AtGen_6_0121", + "AtGen_6_0122" + ], + "Cold_Root_After_30_Minutes": [ + "AtGen_6_1121", + "AtGen_6_1122" + ], + "Osmotic_Root_After_30_Minutes": [ + "AtGen_6_2121", + "AtGen_6_2122" + ], + "Salt_Root_After_30_Minutes": [ + "AtGen_6_3121", + "AtGen_6_3122" + ], + "Drought_Root_After_30_Minutes": [ + "AtGen_6_4121", + "AtGen_6_4122" + ], + "Genotoxic_Root_After_30_Minutes": [ + "AtGen_6_5121", + "AtGen_6_5122" + ], + "Oxidative_Root_After_30_Minutes": [ + "AtGen_6_6122", + "AtGen_6_6124" + ], + "UV-B_Root_After_30_Minutes": [ + "AtGen_6_7121", + "AtGen_6_7122" + ], + "Wounding_Root_After_30_Minutes": [ + "AtGen_6_8124", + "AtGen_6_8126" + ], + "Heat_Root_After_30_Minutes": [ + "AtGen_6_9121", + "AtGen_6_9122" + ] + } + }, + "Shoot_After_1_Hour": { + "controls": [ + "AtGen_6_0211", + "AtGen_6_0212" + ], + "treatments": { + "Control_Shoot_After_1_Hour": [ + "AtGen_6_0211", + "AtGen_6_0212" + ], + "Cold_Shoot_After_1_Hour": [ + "AtGen_6_1211", + "AtGen_6_1212" + ], + "Osmotic_Shoot_After_1_Hour": [ + "AtGen_6_2211", + "AtGen_6_2212" + ], + "Salt_Shoot_After_1_Hour": [ + "AtGen_6_3211", + "AtGen_6_3212" + ], + "Drought_Shoot_After_1_Hour": [ + "AtGen_6_4211", + "AtGen_6_4212" + ], + "Genotoxic_Shoot_After_1_Hour": [ + "AtGen_6_5211", + "AtGen_6_5212" + ], + "Oxidative_Shoot_After_1_Hour": [ + "AtGen_6_6211", + "AtGen_6_6212" + ], + "UV-B_Shoot_After_1_Hour": [ + "AtGen_6_7211", + "AtGen_6_7212" + ], + "Wounding_Shoot_After_1_Hour": [ + "AtGen_6_8211", + "AtGen_6_8214" + ], + "Heat_Shoot_After_1_Hour": [ + "AtGen_6_9211", + "AtGen_6_9212" + ] + } + }, + "Root_After_1_Hour": { + "controls": [ + "AtGen_6_0221", + "AtGen_6_0222" + ], + "treatments": { + "Control_Root_After_1_Hour": [ + "AtGen_6_0221", + "AtGen_6_0222" + ], + "Cold_Root_After_1_Hour": [ + "AtGen_6_1221", + "AtGen_6_1222" + ], + "Osmotic_Root_After_1_Hour": [ + "AtGen_6_2221", + "AtGen_6_2222" + ], + "Salt_Root_After_1_Hour": [ + "AtGen_6_3221", + "AtGen_6_3222" + ], + "Drought_Root_After_1_Hour": [ + "AtGen_6_4221", + "AtGen_6_4222" + ], + "Genotoxic_Root_After_1_Hour": [ + "AtGen_6_5221", + "AtGen_6_5222" + ], + "Oxidative_Root_After_1_Hour": [ + "AtGen_6_6223", + "AtGen_6_6224" + ], + "UV-B_Root_After_1_Hour": [ + "AtGen_6_7221", + "AtGen_6_7222" + ], + "Wounding_Root_After_1_Hour": [ + "AtGen_6_8224", + "AtGen_6_8225" + ], + "Heat_Root_After_1_Hour": [ + "AtGen_6_9221", + "AtGen_6_9222" + ] + } + }, + "Shoot_After_3_Hours": { + "controls": [ + "AtGen_6_0311", + "AtGen_6_0312" + ], + "treatments": { + "Control_Shoot_After_3_Hours": [ + "AtGen_6_0311", + "AtGen_6_0312" + ], + "Cold_Shoot_After_3_Hours": [ + "AtGen_6_1311", + "AtGen_6_1312" + ], + "Osmotic_Shoot_After_3_Hours": [ + "AtGen_6_2311", + "AtGen_6_2312" + ], + "Salt_Shoot_After_3_Hours": [ + "AtGen_6_3311", + "AtGen_6_3312" + ], + "Drought_Shoot_After_3_Hours": [ + "AtGen_6_4311", + "AtGen_6_4312" + ], + "Genotoxic_Shoot_After_3_Hours": [ + "AtGen_6_5311", + "AtGen_6_5312" + ], + "Oxidative_Shoot_After_3_Hours": [ + "AtGen_6_6311", + "AtGen_6_6312" + ], + "UV-B_Shoot_After_3_Hours": [ + "AtGen_6_7311", + "AtGen_6_7312" + ], + 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"treatments": { + "Anther_tetrad": [ + "Anther_TET1", + "Anther_TET2", + "Anther_TET3" + ], + "Stigma_tetrad": [ + "Stigma_TET1", + "Stigma_TET2", + "Stigma_TET3" + ], + "Ovary_tetrad": [ + "Ovary_TET1", + "Ovary_TET2", + "Ovary_TET3" + ], + "Anther_uninucleate": [ + "Anther_UNM1", + "Anther_UNM2", + "Anther_UNM3" + ], + "Stigma_uninucleate": [ + "Stigma_UNM1", + "Stigma_UNM2", + "Stigma_UNM3" + ], + "Ovary_uninucleate": [ + "Ovary_UNM1", + "Ovary_UNM2", + "Ovary_UNM3" + ], + "Anther_bicellular_pollen": [ + "Anther_BCP1", + "Anther_BCP2", + "Anther_BCP3" + ], + "Stigma_bicellular_pollen": [ + "Stigma_BCP1", + "Stigma_BCP2", + "Stigma_BCP3" + ], + "Ovary_bicellular_pollen": [ + "Ovary_BCP1", + "Ovary_BCP2", + "Ovary_BCP3" + ], + "Anther_tricellular_pollen": [ + "Anther_TCP1", + "Anther_TCP2", + "Anther_TCP3" + ], + "Stigma_tricellular_pollen": [ + "Stigma_TCP1", + "Stigma_TCP2", + "Stigma_TCP3" + ], + "Ovary_tricellular_pollen": [ + "Ovary_TCP1", + "Ovary_TCP2", + "Ovary_TCP3" + ], + "Mature_pollen": [ + "Pollen_MPG1", + "Pollen_MPG2", + "Pollen_MPG3" + ] + } + } + } + }, + "triticale_mas": { + "database": "triticale_mas", + "view_name": "triticale_mas", + "groups": { + "Reproductive": { + "controls": [ + "TRITICALE_CTRL" + ], + "treatments": { + "Anther_tetrad": [ + "Anther_tetrad_1", + "Anther_tetrad_2", + "Anther_tetrad_3" + ], + "Stigma_tetrad": [ + "Stigma_tetrad_1", + "Stigma_tetrad_2", + "Stigma_tetrad_3" + ], + "Ovary_tetrad": [ + "Ovary_tetrad_1", + "Ovary_tetrad_2", + "Ovary_tetrad_3" + ], + "Anther_uninucleate": [ + "Anther_uninucleate_1", + "Anther_uninucleate_2", + "Anther_uninucleate_3" + ], + "Stigma_uninucleate": [ + "Stigma_uninucleate_1", + "Stigma_uninucleate_2", + "Stigma_uninucleate_3" + ], + "Ovary_uninucleate": [ + "Ovary_uninucleate_1", + "Ovary_uninucleate_2", + "Ovary_uninucleate_3" + ], + "Anther_bicellular_pollen": [ + "Anther_bicellular_pollen_1", + "Anther_bicellular_pollen_2", + "Anther_bicellular_pollen_3" + ], + "Stigma_bicellular_pollen": [ + "Stigma_bicellular_pollen_1", + "Stigma_bicellular_pollen_2", + "Stigma_bicellular_pollen_3" + ], + "Ovary_bicellular_pollen": [ + "Ovary_bicellular_pollen_1", + "Ovary_bicellular_pollen_2", + "Ovary_bicellular_pollen_3" + ], + "Anther_tricellular_pollen": [ + "Anther_tricellular_pollen_1", + "Anther_tricellular_pollen_2", + "Anther_tricellular_pollen_3" + ], + "Stigma_tricellular_pollen": [ + "Stigma_tricellular_pollen_1", + "Stigma_tricellular_pollen_2", + "Stigma_tricellular_pollen_3" + ], + "Ovary_tricellular_pollen": [ + "Ovary_tricellular_pollen_1", + "Ovary_tricellular_pollen_2", + "Ovary_tricellular_pollen_3" + ], + "Mature_pollen": [ + "Mature_pollen_1", + "Mature_pollen_2", + "Mature_pollen_3" + ] + } + } + } + } + } + } + }, + "wheat": { + + "data": { + "species": "wheat", + "views": { + "Developmental_Atlas": { + "database": "wheat", + "view_name": "Developmental_Atlas", + "groups": { + "Med_CTRL": { + "controls": [ + "Med_CTRL" + ], + "treatments": { + "First_leaf_sheath_-_Tillering_stage": [ + "Sample_43A", + "Sample_44A", + "Sample_45A" + ], + "Internode_#2_-_Milk_grain_stage": [ + "Sample_188B", + "Sample_189B" + ], + "Shoot_apical_meristem_-_Seedling_stage": [ + "Sample_19A", + "Sample_20A", + "Sample_21A" + ], + "Grain_-_Milk_grain_stage": [ + "Sample_199A", + "Sample_200A", + "Sample_201A" + ], + "First_leaf_blade_-_Seedling_stage": [ + "Sample_13R1", + "Sample_23", + "Sample_32" + ], + "Flag_leaf_blade_-_Full_boot_": [ + "Sample_94B", + "Sample_95A", + "Sample_96A" + ], + "Awn_-_50_percent_spike": [ + "Sample_118A", + "Sample_119B", + "Sample_120A" + ], + "flag_leaf_blade_night_(-0.25h)_06:45": [ + "Sample_166A", + "Sample_167A", + "Sample_168A" + ], + "Shoot_axis_-_Flag_leaf_stage": [ + "Sample_70A", + "Sample_71A", + "Sample_72A" + ], + "Fifth_leaf_blade_-_Flag_leaf_stage": [ + "Sample_67A", + "Sample_68A", + "Sample_69A" + ], + "Third_leaf_sheath_-_Three_leaf_stage": [ + "Sample_25A", + "Sample_26A", + "Sample_27A" + ], + "Internode_#2_-_Ear_emergence": [ + "Sample_136A", + "Sample_137B", + "Sample_138A" + ], + "Anther": [ + "Sample_160A", + "Sample_161A", + "Sample_162A" + ], + "Spike": [ + "Sample_100A", + "Sample_101A", + "Sample_102A" + ], + "Coleoptile": [ + "Sample_12", + "Sample_26", + "Sample_6A" + ], + "Stigma_and_Ovary": [ + "Sample_163A", + "Sample_164A", + "Sample_165A" + ], + "Roots_-_Flag_leaf_stage": [ + "Sample_73A", + "Sample_74A", + "Sample_76A" + ], + "Fifth_leaf_sheath_-_Flag_leaf_stage": [ + "Sample_64A", + "Sample_65A", + "Sample_66A" + ], + "Root_apical_meristem_-_Three_leaf_stage": [ + "Sample_15", + "Sample_32R2", + "Sample_33A" + ], + "Flag_leaf_sheath_-_Ear_emergence": [ + "Sample_124A", + "Sample_125A", + "Sample_126A" + ], + "Roots_-_Three_leaf_stage": [ + "Sample_28A", + "Sample_29A", + "Sample_30A" + ], + "Axillary_roots_-_Three_leaf_stage": [ + "Sample_16", + "Sample_35R1", + "Sample_36A" + ], + "Flag_leaf_sheath_-_50_percent_spike": [ + "Sample_106A", + "Sample_107B", + "Sample_108A" + ], + "Radicle_-_Seedling_stage": [ + "Sample_10", + "Sample_18", + "Sample_3A" + ], + "Roots_-_50_percent_spike": [ + "Sample_103A", + "Sample_104B", + "Sample_105B" + ], + "Third_leaf_blade_-_Three_leaf_stage": [ + "Sample_22B", + "Sample_23A", + "Sample_24A" + ], + "Spikelets_-_50_percent_spike": [ + "Sample_121A", + "Sample_122A", + "Sample_123A" + ], + "Root_apical_meristem_-_Tillering_stage": [ + "Sample_58A", + "Sample_59A", + "Sample_60A" + ], + "Grain_-_Ripening_stage": [ + "Sample_217B", + "Sample_218A", + "Sample_219A" + ], + "Awns_-_Ear_emergence": [ + "Sample_139A", + "Sample_140A", + "Sample_141A" + ], + "Glumes": [ + "Sample_193A", + "Sample_194A", + "Sample_195A" + ], + "Glumes_-_Ear_emergence": [ + "Sample_142A", + "Sample_143A", + "Sample_144B" + ], + "Leaf_ligule": [ + "Sample_88A", + "Sample_89B", + "Sample_90A" + ], + "Flag_leaf_blade_-_50_percent_spike": [ + "Sample_109A", + "Sample_110A", + "Sample_111B" + ], + "Internode_#2_-_50_percent_spike": [ + "Sample_112B", + "Sample_113B", + "Sample_114B" + ], + "Fifth_leaf_sheath_-_Fifth_leaf_stage": [ + "Sample_37A", + "Sample_38A", + "Sample_39A" + ], + "fifth_leaf_blade_night_(-0.25h)_21:45": [ + "Sample_79A", + "Sample_80A", + "Sample_81A" + ], + "Grain_-_Soft_dough": [ + "Sample_205A", + "Sample_206A", + "Sample_207A" + ], + "Flag_leaf_blade_(senescence)_-_Dough_stage": [ + "Sample_202A", + "Sample_203A", + "Sample_204A" + ], + "Flag_leaf_blade_night_(-0.25h)_06:45_-_Flag_leaf_stage": [ + "Sample_75A", + "Sample_77A", + "Sample_78A" + ], + "Flag_leaf_blade_(senescence)_-_Ripening_stage": [ + "Sample_223B", + "Sample_225A" + ], + "First_leaf_blade_-_Tillering_stage": [ + "Sample_46A", + "Sample_d11", + "Sample_d12" + ], + "Shoot_apical_meristem_-_Tillering_stage": [ + "Sample_52A", + "Sample_53A", + "Sample_54A" + ], + "Shoot_axis_-_First_leaf_stage": [ + "Sample_11", + "Sample_20", + "Sample_9A" + ], + "Roots_-_Seedling_stage": [ + "Sample_13", + "Sample_18A", + "Sample_33" + ], + "Shoot_axis_-_Milk_grain_stage": [ + "Sample_178A", + "Sample_179A", + "Sample_180A" + ], + "Fifth_leaf_blade_-_Fifth_leaf_stage": [ + "Sample_40A", + "Sample_41A", + "Sample_42A" + ], + "Flag_leaf_blade_-_Ear_emergence": [ + "Sample_127A", + "Sample_128A", + "Sample_129A" + ], + "flag_leaf_blade_night_(+0.25h)_07:15": [ + "Sample_82A", + "Sample_83B", + "Sample_84A" + ], + "Fifth_leaf_blade_night_(-0.25h)_21:45": [ + "Sample_169A", + "Sample_170A", + "Sample_171A" + ], + "Shoot_axis_-_Tillering_stage": [ + "Sample_49A", + "Sample_50A", + "Sample_51A" + ], + "Stem_axis_-_First_leaf_stage": [ + "Sample_11", + "Sample_20", + "Sample_9A" + ], + "Endosperm": [ + "Sample_211B", + "Sample_212A", + "Sample_213A" + ], + "Peduncle": [ + "Sample_184A", + "Sample_185A", + "Sample_186A" + ], + "Peduncle_-_50_percent_spike": [ + "Sample_115A", + "Sample_116A", + "Sample_117A" + ], + "Peduncle_-_Ear_emergence": [ + "Sample_133A", + "Sample_134A", + "Sample_135A" + ], + "Flag_leaf_sheath_-_Full_boot": [ + "Sample_91A", + "Sample_92A", + "Sample_93A" + ], + "Flag_leaf_blade_-_Flag_leaf_stage": [ + "Sample_61A", + "Sample_62A", + "Sample_63A" + ], + "Lemma": [ + "Sample_196A", + "Sample_197A", + "Sample_198A" + ], + "Lemma_-_Ear_emergence": [ + "Sample_157A", + "Sample_158A", + "Sample_159B" + ], + "Awns_-_Milk_grain_stage": [ + "Sample_190A", + "Sample_191A", + "Sample_192A" + ], + "fifth_leaf_blade_night_(+0.25h)_22:15": [ + "Sample_85B", + "Sample_86A", + "Sample_87A" + ], + "Flag_leaf_blade_-_Milk_grain_stage": [ + "Sample_175A", + "Sample_176A", + "Sample_177A" + ], + "Grain_-_Hard_dough": [ + "Sample_208A", + "Sample_209A", + "Sample_210A" + ], + "Flag_leaf_sheath_-_Milk_grain_stage": [ + "Sample_172A", + "Sample_173A", + "Sample_174A" + ], + "Embryo_proper": [ + "Sample_214A", + "Sample_215A", + "Sample_216A" + ], + "Fifth_leaf_blade_(senescence)_-_Milk_grain_stage": [ + "Sample_181A", + "Sample_182A", + "Sample_183A" + ], + "Roots_-_Tillering_stage": [ + "Sample_55B", + "Sample_56A", + "Sample_57A" + ], + "Shoot_axis_-_Full_boot": [ + "Sample_97A", + "Sample_98A", + "Sample_99A" + ], + "Fifth_leaf_blade_-_Ear_emergence": [ + "Sample_130A", + "Sample_131A", + "Sample_132A" + ], + "First_leaf_sheath_-_Seedling_stage": [ + "Sample_10R1", + "Sample_21", + "Sample_30" + ] + } + } + } + }, + "Wheat_Abiotic_Stress": { + "database": "wheat_abiotic_stress", + "view_name": "Wheat_Abiotic_Stress", + "groups": { + "Med_CTRL": { + "controls": [ + "C1", + "C2", + "C4", + "C8" + ], + "treatments": { + "All": [ + "SHD4", + "SHD5", + "SHD6", + "SHD7" + ], + "Salt_+_Drought": [ + "SD1", + "SD5", + "SD6", + "SD8" + ], + "Salt_+_Heat": [ + "SH2", + "SH3", + "SH4", + "SH8" + ], + "Heat_+_Drought": [ + "HD3", + "HD4", + "HD7", + "HD8" + ], + "Drought_Only": [ + "D1", + "D4", + "D6", + "D8" + ], + "Heat_Only": [ + "H1", + "H2", + "H3", + "H4" + ], + "Salt_Only": [ + "S1", + "S3", + "S5", + "S8" + ], + "Control": [ + "C1", + "C2", + "C4", + "C8" + ] + } + } + } + }, + "Wheat_Embryogenesis": { + "database": "wheat_embryogenesis", + "view_name": "Wheat_Embryogenesis", + "groups": { + "AA-DV92_Med_CTRL": { + "controls": [ + "AA-DV92_Med_CTRL" + ], + "treatments": { + "AA-DV92_Leaf_Early_Seed_Coat": [ + "AA-DV92_Leaf_early_stage_seed_coat" + ], + "AA-DV92_Leaf_Late_Embryo": [ + "AA-DV92_Leaf_late_embryo" + ], + "AA-DV92_Leaf_Early_Embryo": [ + "AA-DV92_Leaf_early_embryo" + ], + "AA-DV92_Leaf_Late_Endosperm": [ + "AA-DV92_Leaf_late_stage_endosperm" + ], + "AA-DV92_Leaf_Middle_Embryo": [ + "AA-DV92_Leaf_middle_embryo" + ], + "AA-DV92_Pre-Embryo": [ + "AA-DV92_Pre-embryo" + ], + "AA-DV92_Mature_Embryo": [ + "AA-DV92_Mature_embryo" + ], + "AA-DV92_Two_Cell_Embryo": [ + "AA-DV92_Two_cell_embryo" + ], + "AA-DV92_Transition_Embryo": [ + "AA-DV92_Transition_embryo" + ], + "AA-DV92_Transition_Endosperm": [ + "AA-DV92_Transition_stage_endosperm" + ] + } + }, + "Hexaploid-AC_Med_CTRL": { + "controls": [ + "Hexaploid-AC_Med_CTRL" + ], + "treatments": { + "Hexaploid-AC_Leaf_Late_Endosperm": [ + "Hexaploid-AC_Late_leaf_stage_endosperm" + ], + "Hexaploid-AC_Leaf_Early_Embryo": [ + "Hexaploid-AC_Leaf_early_embryo" + ], + "Hexaploid-AC_Leaf_Early_Seed_Coat": [ + "Hexaploid-AC_Leaf_early_stage_seed_coat" + ], + "Hexaploid-AC_Leaf_Late_Embryo": [ + "Hexaploid-AC_Leaf_early_stage_seed_coat" + ], + "Hexaploid-AC_Leaf_Middle_Embryo": [ + "Hexaploid-AC_Leaf_middle_embryo" + ], + "Hexaploid-AC_Mature_Embryo": [ + "Hexaploid-AC_Mature_embryo" + ], + "Hexaploid-AC_Pre-Embryo": [ + "Hexaploid-AC_Pre-embryo" + ], + "Hexaploid-AC_Transition_Embryo": [ + "Hexaploid-AC_Transition_embryo" + ], + "Hexaploid-AC_Transition_Endosperm": [ + "Hexaploid-AC_Transition_stage_endosperm" + ], + "Hexaploid-AC_Two_Cell_Embryo": [ + "Hexaploid-AC_Two_cell_embryo" + ] + } + }, + "Tetraploid-SF_Med_CTRL": { + "controls": [ + "Tetraploid-SF_Med_CTRL" + ], + "treatments": { + "Tetraploid-SF_Leaf_Early_Seed_Coat": [ + "Tetraploid-SF_Leaf_early_stage_seed_coat" + ], + "Tetraploid-SF_Leaf_Early_Embryo": [ + "Tetraploid-SF_Leaf_early_embryo" + ], + "Tetraploid-SF_Leaf_Late_Embryo": [ + "Tetraploid-SF_Leaf_late_embryo" + ], + "Tetraploid-SF_Leaf_Late_Endosperm": [ + "Tetraploid-SF_Leaf_late_stage_endosperm" + ], + "Tetraploid-SF_Leaf_Middle_Embryo": [ + "Tetraploid-SF_Leaf_middle_embryo" + ], + "Tetraploid-SF_Mature_Embryo": [ + "Tetraploid-SF_Mature_embryo" + ], + "Tetraploid-SF_Pre-Embryo": [ + "Tetraploid-SF_Pre-embryo" + ], + "Tetraploid-SF_Transition_Embryo": [ + "Tetraploid-SF_Transition_embryo" + ], + "Tetraploid-SF_Transition_Endosperm": [ + "Tetraploid-SF_Transition_stage_endosperm" + ], + "Tetraploid-SF_Two_Cell_Embryo": [ + "Tetraploid-SF_Two_cell_embryo" + ] + } + }, + "BB-TA2780_Med_CTRL": { + "controls": [ + "BB-TA2780_Med_CTRL" + ], + "treatments": { + "BB-TA2780_Leaf_Early_Seed_Coat": [ + "BB-TA2780_Leaf_early_stage_seed_coat" + ], + "BB-TA2780_Leaf_Early_Embryo": [ + "BB-TA2780_Leaf_early_embryo" + ], + "BB-TA2780_Leaf_Late_Embryo": [ + "BB-TA2780_Leaf_late_embryo" + ], + "BB-TA2780_Leaf_Late_Endosperm": [ + "BB-TA2780_Leaf_late_stage_endosperm" + ], + "BB-TA2780_Leaf_Middle_Embryo": [ + "BB-TA2780_Leaf_middle_embryo" + ], + "BB-TA2780_Mature_Embryo": [ + "BB-TA2780_Mature_embryo" + ], + "BB-TA2780_Pre-Embryo": [ + "BB-TA2780_Pre-embryo" + ], + "BB-TA2780_Transition_Embryo": [ + "BB-TA2780_Transition_embryo" + ], + "BB-TA2780_Transition_Endosperm": [ + "BB-TA2780_Transition_stage_endosperm" + ], + "BB-TA2780_Two_Cell_Embryo": [ + "BB-TA2780_Two_cell_embryo" + ] + } + }, + "DD-TA101132_Med_CTRL": { + "controls": [ + "DD-TA101132_Med_CTRL" + ], + "treatments": { + "DD-TA101132_Leaf_Early_Embryo": [ + "DD-TA101132_Leaf_early_embryo" + ], + "DD-TA101132_Leaf_Early_Seed_Coat": [ + "DD-TA101132_Leaf_early_stage_seed_coat" + ], + "DD-TA101132_Leaf_Late_Embryo": [ + "DD-TA101132_Leaf_late_embryo" + ], + "DD-TA101132_Leaf_Late_Endosperm": [ + "DD-TA101132_Leaf_late_stage_endosperm" + ], + "DD-TA101132_Leaf_Middle_Embryo": [ + "DD-TA101132_leaf_middle_embryo" + ], + "DD-TA101132_Mature_Embryo": [ + "DD-TA101132_Mature_embryo" + ], + "DD-TA101132_Transition_Embryo": [ + "DD-TA101132_Transition_embryo" + ], + "DD-TA101132_Transition_Endosperm": [ + "DD-TA101132_Transition_stage_endosperm" + ], + "DD-TA101132_Two_Cell_Embryo": [ + "DD-TA101132_Two_cell_embryo" + ], + "DD-TA101132_Pre-Embryo": [ + "DD-TA101132_Pre-embryo" + ] + } + } + } + }, + "Wheat_Meiosis": { + "database": "wheat_meiosis", + "view_name": "Wheat_Meiosis", + "groups": { + "Med_CTRL": { + "controls": [ + "Med_CTRL" + ], + "treatments": { + "Anther": [ + "Anther_rep1", + "Anther_rep2", + "Anther_rep3" + ], + "Diplotene": [ + "Diplotene_rep1", + "Diplotene_rep2", + "Diplotene_rep3" + ], + "Flagleaf": [ + "FlagLeaf_rep1", + "FlagLeaf_rep2", + "FlagLeaf_rep3" + ], + "Leaf": [ + "Leaf_rep1", + "Leaf_rep2", + "Leaf_rep3" + ], + "Leptotene": [ + "Leptotene_rep1", + "Leptotene_rep2", + "Leptotene_rep3" + ], + "Metaphase_I": [ + "Metaphase-I_rep1", + "Metaphase-I_rep2", + "Metaphase-I_rep3" + ], + "Metaphase_II": [ + "Metaphase-II_rep1", + "Metaphase-II_rep2", + "Metaphase-II_rep3" + ], + "Pachytene": [ + "Pachytene_rep1", + "Pachytene_rep2", + "Pachytene_rep3" + ], + "Pollen": [ + "Pollen_rep1", + "Pollen_rep2", + "Pollen_rep3" + ], + "Pre-meiotic_G2": [ + "Pre-meiotic_G2_rep1", + "Pre-meiotic_G2_rep2", + "Pre-meiotic_G2_rep3" + ], + "Zygotene": [ + "Zygotene_rep1", + "Zygotene_rep2", + "Zygotene_rep3" + ] + } + } + } + } + } + } + } +} \ No newline at end of file diff --git a/data/gene_information/gene_isoforms/example_placeholder.txt b/data/gene_information/gene_isoforms/example_placeholder.txt deleted file mode 100644 index e69de29..0000000 diff --git a/docker-compose.yml b/docker-compose.yml index 18ebdad..5b64107 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -21,6 +21,7 @@ services: restart: always # Run like it's running on CI/CD pipeline environment: + - DB_HOST=BAR_mysqldb - REDIS_HOST=BAR_redis - REDIS_PORT=6379 - CI=TRUE diff --git a/scripts/bootstrap_simple_efp_dbs.py b/scripts/bootstrap_simple_efp_dbs.py new file mode 100644 index 0000000..438b7b6 --- /dev/null +++ b/scripts/bootstrap_simple_efp_dbs.py @@ -0,0 +1,98 @@ +#!/usr/bin/env python3 +""" +bootstrap the simple efp databases from the shared schema definitions +""" + +from __future__ import annotations + +import argparse +import os +import sys +from pathlib import Path + +from sqlalchemy.exc import SQLAlchemyError + +# ensure the repository root is importable when this script is executed standalone +ROOT_DIR = Path(__file__).resolve().parents[1] +if str(ROOT_DIR) not in sys.path: + sys.path.insert(0, str(ROOT_DIR)) + +from api.services.efp_bootstrap import bootstrap_simple_efp_databases # noqa: E402 + + +def _default_host() -> str: + """ + Determine the default MySQL hostname from environment variables. + + Priority order: + 1. DB_HOST environment variable (explicit override) + 2. MYSQL_HOST environment variable (alternative name) + 3. 'localhost' (default for local dev and GitHub Actions CI) + + Docker deployments should set DB_HOST=BAR_mysqldb explicitly. + + :return: MySQL hostname to use for connections + :rtype: str + """ + if os.environ.get("DB_HOST"): + return os.environ["DB_HOST"] + if os.environ.get("MYSQL_HOST"): + return os.environ["MYSQL_HOST"] + # GitHub Actions CI uses localhost; Docker Compose uses bar_mysqldb + # CI env var is set in GitHub Actions, but not DB_HOST + # In Docker, DB_HOST should be explicitly set to BAR_mysqldb + return "localhost" + + +def parse_args() -> argparse.Namespace: + """ + Parse command-line arguments for the bootstrap script. + + :return: Parsed arguments containing host, port, user, password, and optional database list + :rtype: argparse.Namespace + """ + parser = argparse.ArgumentParser(description="Create simple eFP MySQL databases from in-memory schemas.") + parser.add_argument("--host", default=_default_host(), help="MySQL hostname (default: %(default)s)") + parser.add_argument("--port", type=int, default=int(os.environ.get("DB_PORT", 3306)), help="MySQL port") + parser.add_argument("--user", default=os.environ.get("DB_USER", "root"), help="MySQL user") + parser.add_argument("--password", default=os.environ.get("DB_PASS", "root"), help="MySQL password") + parser.add_argument( + "--databases", + nargs="*", + help="Optional list of databases to bootstrap (defaults to every simple schema).", + ) + return parser.parse_args() + + +def main(): + """ + Main entry point for the bootstrap CLI script. + + Parses command-line arguments and calls bootstrap_simple_efp_databases() + to create MySQL databases. Prints success messages for each database created. + + Output format: [ok] ensured database_name.table_name (seeded N rows) + + :raises SQLAlchemyError: If database creation or connection fails + """ + args = parse_args() + results = bootstrap_simple_efp_databases( + host=args.host, + port=args.port, + user=args.user, + password=args.password, + databases=args.databases, + ) + for entry in results: + seeded = entry["seeded_rows"] + seed_msg = f"seeded {seeded} rows" if seeded else "no seed rows inserted" + print(f"[ok] ensured {entry['database']}.{entry['table']} ({seed_msg})") + + +if __name__ == "__main__": + try: + main() + except SQLAlchemyError as exc: + # match init.sh style output to keep ci logs readable + print(f"failed to initialize simple efp databases: {exc}") + raise diff --git a/scripts/build_sqlite_mirrors.py b/scripts/build_sqlite_mirrors.py new file mode 100755 index 0000000..640041c --- /dev/null +++ b/scripts/build_sqlite_mirrors.py @@ -0,0 +1,159 @@ +#!/usr/bin/env python3 +""" +Utility to convert the shipped MySQL dumps under config/databases into local +SQLite mirrors that api.resources.efp_proxy can read without a live MySQL bind. + +Usage: + python scripts/build_sqlite_mirrors.py # build every mirror + python scripts/build_sqlite_mirrors.py klepikova # build selected DBs + python scripts/build_sqlite_mirrors.py --force ... # overwrite .db files +""" + +from __future__ import annotations + +import argparse +import re +import sqlite3 +import sys +from pathlib import Path +from typing import Iterable + + +ROOT_DIR = Path(__file__).resolve().parents[1] +DATABASE_DIR = ROOT_DIR / "config" / "databases" + +# Regex helpers to strip MySQL-only clauses (storage engine, charset, auto-increment, etc.) +# so the CREATE TABLE statements can be executed by SQLite without syntax errors. +ENGINE_REGEX = re.compile(r"\)\s*ENGINE=.*;", flags=re.IGNORECASE) +CHARSET_REGEX = re.compile(r"DEFAULT\s+CHARSET=.*?(?=\)|;)", flags=re.IGNORECASE) +COLLATE_REGEX = re.compile(r"COLLATE\s*=\s*[^\s)]+", flags=re.IGNORECASE) +COLUMN_AUTO_INCREMENT_REGEX = re.compile(r"\s+AUTO_INCREMENT\b", flags=re.IGNORECASE) +AUTO_INCREMENT_REGEX = re.compile(r"AUTO_INCREMENT=\d+", flags=re.IGNORECASE) + + +def discover_sql_files() -> dict[str, Path]: + """Return a map of database name -> dump path (stem of filename).""" + sql_files = {} + for path in DATABASE_DIR.glob("*.sql"): + sql_files[path.stem] = path + return sql_files + + +def sanitize_mysql_dump(sql_text: str) -> str: + """Remove MySQL-only statements so SQLite can execute the script.""" + sanitized_lines = [] + skip_block = False + + for line in sql_text.splitlines(): + if skip_block: + if ";" in line: + skip_block = False + continue + + stripped = line.strip() + if not stripped: + continue + if stripped.startswith("--"): + continue + + upper = stripped.upper() + if upper.startswith("LOCK TABLES") or upper.startswith("UNLOCK TABLES"): + continue + if upper.startswith("CREATE DATABASE") or upper.startswith("USE "): + continue + if upper.startswith("SET ") or upper.startswith("DELIMITER "): + continue + if upper.startswith("START TRANSACTION") or upper == "COMMIT;": + continue + if upper.startswith("ALTER TABLE "): + skip_block = True + continue + if upper.startswith("KEY ") or upper.startswith("UNIQUE KEY") or upper.startswith("FULLTEXT KEY"): + continue + if stripped.startswith("/*!"): + # Skip MySQL conditional comments entirely. + continue + + line = ENGINE_REGEX.sub(");", line) + line = CHARSET_REGEX.sub("", line) + line = COLLATE_REGEX.sub("", line) + line = AUTO_INCREMENT_REGEX.sub("", line) + line = COLUMN_AUTO_INCREMENT_REGEX.sub("", line) + + sanitized_lines.append(line) + + sanitized = "\n".join(sanitized_lines) + sanitized = re.sub(r",\s*\n\)", "\n)", sanitized) + return sanitized + + +def build_sqlite_db(sql_path: Path, db_path: Path, force: bool) -> None: + """Create/overwrite SQLite DB from the provided MySQL dump.""" + if db_path.exists(): + if not force: + print(f"[skip] {db_path.name} already exists (use --force to overwrite)") + return + db_path.unlink() + + sql_text = sql_path.read_text(encoding="utf-8") + # SQLite cannot run raw MySQL dumps, so we strip dialect-specific bits first. + sanitized_sql = sanitize_mysql_dump(sql_text) + if not sanitized_sql.strip(): + raise RuntimeError(f"No executable SQL found in {sql_path.name}") + + conn = sqlite3.connect(db_path) + try: + # Disable FK constraints while replaying the dump to avoid dependency issues. + conn.executescript("PRAGMA foreign_keys = OFF;") + # Executescript lets us run the entire dump in one go. + conn.executescript(sanitized_sql) + conn.commit() + print(f"[ok] Created {db_path.relative_to(ROOT_DIR)}") + finally: + conn.close() + + +def parse_args(argv: Iterable[str]) -> argparse.Namespace: + parser = argparse.ArgumentParser( + description="Generate SQLite mirrors from the MySQL dumps in config/databases", + ) + parser.add_argument( + "databases", + nargs="*", + help="Database names to convert (defaults to every *.sql file).", + ) + parser.add_argument( + "--force", + action="store_true", + help="Overwrite existing .db files instead of skipping them.", + ) + return parser.parse_args(list(argv)) + + +def main(argv: Iterable[str]) -> int: + args = parse_args(argv) + # Step 1: discover every *.sql dump shipped with the repo. + # These dumps are the source of truth for the local mirrors. + available = discover_sql_files() + if not available: + print("No .sql dumps found in config/databases", file=sys.stderr) + return 1 + + targets = args.databases or sorted(available.keys()) + missing = [name for name in targets if name not in available] + if missing: + print(f"Unknown database(s): {', '.join(missing)}", file=sys.stderr) + print(f"Available dumps: {', '.join(sorted(available.keys()))}", file=sys.stderr) + return 1 + + # Step 2: iterate over each requested dump and build the matching SQLite db. + for name in targets: + sql_path = available[name] + db_path = DATABASE_DIR / f"{name}.db" + build_sqlite_db(sql_path, db_path, force=args.force) + + return 0 + + +if __name__ == "__main__": + raise SystemExit(main(sys.argv[1:])) diff --git a/tests/models/test_efp_dynamic.py b/tests/models/test_efp_dynamic.py new file mode 100644 index 0000000..55e8768 --- /dev/null +++ b/tests/models/test_efp_dynamic.py @@ -0,0 +1,406 @@ +""" +Integration tests for EFP dynamic ORM models. + +Tests the dynamic ORM models work correctly with SQLAlchemy, +including column types, primary keys, and table metadata. +""" + +import os +import sys +from unittest import TestCase + +# Allow importing api when invoking pytest from this directory tree +ROOT_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..")) +if ROOT_DIR not in sys.path: + sys.path.insert(0, ROOT_DIR) + +from sqlalchemy import inspect # noqa: E402 +from api import app # noqa: E402 +from api.models.efp_dynamic import SIMPLE_EFP_SAMPLE_MODELS # noqa: E402 +from api.models.efp_schemas import SIMPLE_EFP_DATABASE_SCHEMAS # noqa: E402 + + +class TestDynamicModelColumns(TestCase): + """Test that dynamic models have correctly typed columns.""" + + def setUp(self): + """Set up application context for each test.""" + self.ctx = app.app_context() + self.ctx.push() + + def tearDown(self): + """Tear down application context.""" + self.ctx.pop() + + def test_cannabis_model_columns(self): + """Test cannabis model has correct columns and types.""" + model = SIMPLE_EFP_SAMPLE_MODELS['cannabis'] + + # Check basic attributes + self.assertTrue(hasattr(model, 'proj_id')) + self.assertTrue(hasattr(model, 'sample_id')) + self.assertTrue(hasattr(model, 'data_probeset_id')) + self.assertTrue(hasattr(model, 'data_signal')) + self.assertTrue(hasattr(model, 'data_bot_id')) + + # Inspect column types + mapper = inspect(model) + columns = {col.name: col for col in mapper.columns} + + self.assertEqual(str(columns['proj_id'].type), 'VARCHAR(2)') + self.assertEqual(str(columns['data_bot_id'].type), 'VARCHAR(8)') + + def test_oat_model_has_extra_columns(self): + """Test oat model has all extra genome columns.""" + model = SIMPLE_EFP_SAMPLE_MODELS['oat'] + + # Check extra columns exist + self.assertTrue(hasattr(model, 'genome')) + self.assertTrue(hasattr(model, 'genome_id')) + self.assertTrue(hasattr(model, 'orthogroup')) + self.assertTrue(hasattr(model, 'version')) + + # Inspect column types + mapper = inspect(model) + columns = {col.name: col for col in mapper.columns} + + self.assertEqual(str(columns['genome'].type), 'VARCHAR(16)') + self.assertEqual(str(columns['version'].type), 'VARCHAR(2)') + + def test_mouse_db_has_minimal_columns(self): + """Test mouse_db model has the 3 main data columns.""" + model = SIMPLE_EFP_SAMPLE_MODELS['mouse_db'] + + # Get all columns + mapper = inspect(model) + column_names = {col.name for col in mapper.columns} + + # Should have the 3 main data columns + required_columns = {'data_probeset_id', 'data_signal', 'data_bot_id'} + self.assertTrue(required_columns.issubset(column_names)) + + # Should have 5 total columns (includes base proj_id and sample_id) + self.assertEqual(len(column_names), 5) + + def test_arabidopsis_ecotypes_has_qa_columns(self): + """Test arabidopsis_ecotypes has QA columns.""" + model = SIMPLE_EFP_SAMPLE_MODELS['arabidopsis_ecotypes'] + + self.assertTrue(hasattr(model, 'sample_file_name')) + self.assertTrue(hasattr(model, 'data_call')) + self.assertTrue(hasattr(model, 'data_p_val')) + + def test_affydb_has_data_num_column(self): + """Test affydb has the extra data_num column.""" + model = SIMPLE_EFP_SAMPLE_MODELS['affydb'] + + self.assertTrue(hasattr(model, 'data_num')) + + # Check it's an integer + mapper = inspect(model) + columns = {col.name: col for col in mapper.columns} + self.assertIn('INTEGER', str(columns['data_num'].type)) + + def test_lateral_root_initiation_has_project_id(self): + """Test lateral_root_initiation has project_id as extra column.""" + model = SIMPLE_EFP_SAMPLE_MODELS['lateral_root_initiation'] + + # Has extra project_id column + self.assertTrue(hasattr(model, 'project_id')) + # Also has standard proj_id from base columns + self.assertTrue(hasattr(model, 'proj_id')) + # Has sample_file_name extra column + self.assertTrue(hasattr(model, 'sample_file_name')) + + +class TestDynamicModelPrimaryKeys(TestCase): + """Test that primary keys are correctly defined.""" + + def setUp(self): + """Set up application context for each test.""" + self.ctx = app.app_context() + self.ctx.push() + + def tearDown(self): + """Tear down application context.""" + self.ctx.pop() + + def test_cannabis_primary_keys(self): + """Test cannabis model has correct primary keys.""" + model = SIMPLE_EFP_SAMPLE_MODELS['cannabis'] + mapper = inspect(model) + + pk_columns = [col.name for col in mapper.primary_key] + + # Should have 3 primary keys + self.assertEqual(len(pk_columns), 3) + self.assertIn('data_probeset_id', pk_columns) + self.assertIn('data_signal', pk_columns) + self.assertIn('data_bot_id', pk_columns) + + def test_mouse_db_primary_keys(self): + """Test mouse_db has primary keys (even without proj_id/sample_id).""" + model = SIMPLE_EFP_SAMPLE_MODELS['mouse_db'] + mapper = inspect(model) + + pk_columns = [col.name for col in mapper.primary_key] + + # Should have at least 2 primary keys + self.assertGreaterEqual(len(pk_columns), 2) + self.assertIn('data_probeset_id', pk_columns) + self.assertIn('data_bot_id', pk_columns) + + def test_oat_primary_keys(self): + """Test oat has primary keys.""" + model = SIMPLE_EFP_SAMPLE_MODELS['oat'] + mapper = inspect(model) + + pk_columns = [col.name for col in mapper.primary_key] + + # Should have primary keys + self.assertGreater(len(pk_columns), 0) + self.assertIn('data_probeset_id', pk_columns) + self.assertIn('data_bot_id', pk_columns) + + def test_all_models_have_primary_keys(self): + """Test that all 191 models have at least one primary key.""" + for db_name, model in SIMPLE_EFP_SAMPLE_MODELS.items(): + with self.subTest(database=db_name): + mapper = inspect(model) + pk_columns = list(mapper.primary_key) + + self.assertGreater( + len(pk_columns), 0, + f"{db_name} has no primary key columns" + ) + + +class TestDynamicModelNullability(TestCase): + """Test column nullable constraints.""" + + def setUp(self): + """Set up application context for each test.""" + self.ctx = app.app_context() + self.ctx.push() + + def tearDown(self): + """Tear down application context.""" + self.ctx.pop() + + def test_embryo_signal_nullable(self): + """Test embryo has nullable data_signal.""" + schema = SIMPLE_EFP_DATABASE_SCHEMAS['embryo'] + signal_col = next(col for col in schema['columns'] if col['name'] == 'data_signal') + + self.assertTrue(signal_col.get('nullable', False)) + + def test_dna_damage_bot_id_nullable(self): + """Test dna_damage has nullable data_bot_id.""" + schema = SIMPLE_EFP_DATABASE_SCHEMAS['dna_damage'] + bot_id_col = next(col for col in schema['columns'] if col['name'] == 'data_bot_id') + + self.assertTrue(bot_id_col.get('nullable', False)) + + def test_lateral_root_initiation_bot_id_nullable(self): + """Test lateral_root_initiation has nullable data_bot_id.""" + schema = SIMPLE_EFP_DATABASE_SCHEMAS['lateral_root_initiation'] + bot_id_col = next(col for col in schema['columns'] if col['name'] == 'data_bot_id') + + self.assertTrue(bot_id_col.get('nullable', False)) + + +class TestDynamicModelDefaults(TestCase): + """Test column default values.""" + + def setUp(self): + """Set up application context for each test.""" + self.ctx = app.app_context() + self.ctx.push() + + def tearDown(self): + """Tear down application context.""" + self.ctx.pop() + + def test_cannabis_proj_id_default(self): + """Test cannabis proj_id has default value.""" + schema = SIMPLE_EFP_DATABASE_SCHEMAS['cannabis'] + proj_id_col = next(col for col in schema['columns'] if col['name'] == 'proj_id') + + # Cannabis has custom proj_id_len but standard default + self.assertIn('default', proj_id_col) + + def test_phelipanche_proj_id_nullable(self): + """Test phelipanche has nullable proj_id (None default).""" + schema = SIMPLE_EFP_DATABASE_SCHEMAS['phelipanche'] + proj_id_col = next(col for col in schema['columns'] if col['name'] == 'proj_id') + + # phelipanche has proj_id_default=None + self.assertEqual(proj_id_col.get('default'), None) + + +class TestDynamicModelTextColumns(TestCase): + """Test text (tinytext) column handling.""" + + def setUp(self): + """Set up application context for each test.""" + self.ctx = app.app_context() + self.ctx.push() + + def tearDown(self): + """Tear down application context.""" + self.ctx.pop() + + def test_affydb_bot_id_is_text(self): + """Test affydb has text type for data_bot_id.""" + schema = SIMPLE_EFP_DATABASE_SCHEMAS['affydb'] + bot_id_col = next(col for col in schema['columns'] if col['name'] == 'data_bot_id') + + self.assertEqual(bot_id_col['type'], 'text') + self.assertIsNone(bot_id_col.get('length')) + + def test_canola_probeset_is_text(self): + """Test canola has text type for data_probeset_id.""" + schema = SIMPLE_EFP_DATABASE_SCHEMAS['canola'] + probeset_col = next(col for col in schema['columns'] if col['name'] == 'data_probeset_id') + + self.assertEqual(probeset_col['type'], 'text') + self.assertIsNone(probeset_col.get('length')) + + +class TestDynamicModelIntegerColumns(TestCase): + """Test integer column type handling.""" + + def setUp(self): + """Set up application context for each test.""" + self.ctx = app.app_context() + self.ctx.push() + + def tearDown(self): + """Tear down application context.""" + self.ctx.pop() + + def test_affydb_proj_id_is_integer(self): + """Test affydb has integer proj_id.""" + schema = SIMPLE_EFP_DATABASE_SCHEMAS['affydb'] + proj_id_col = next(col for col in schema['columns'] if col['name'] == 'proj_id') + + self.assertEqual(proj_id_col['type'], 'integer') + self.assertTrue(proj_id_col.get('unsigned', False)) + + def test_atgenexp_proj_id_is_integer(self): + """Test atgenexp has integer proj_id.""" + schema = SIMPLE_EFP_DATABASE_SCHEMAS['atgenexp'] + proj_id_col = next(col for col in schema['columns'] if col['name'] == 'proj_id') + + self.assertEqual(proj_id_col['type'], 'integer') + + def test_arachis_sample_id_is_string(self): + """Test arachis has string sample_id (not integer).""" + schema = SIMPLE_EFP_DATABASE_SCHEMAS['arachis'] + sample_id_col = next(col for col in schema['columns'] if col['name'] == 'sample_id') + + self.assertEqual(sample_id_col['type'], 'string') + self.assertEqual(sample_id_col['length'], 5) + + +class TestModelClassNames(TestCase): + """Test that model class names are generated correctly.""" + + def setUp(self): + """Set up application context for each test.""" + self.ctx = app.app_context() + self.ctx.push() + + def tearDown(self): + """Tear down application context.""" + self.ctx.pop() + + def test_cannabis_class_name(self): + """Test cannabis model has correct class name.""" + model = SIMPLE_EFP_SAMPLE_MODELS['cannabis'] + self.assertEqual(model.__name__, 'CannabisSampleData') + + def test_maize_atlas_v5_class_name(self): + """Test maize_atlas_v5 model has correct class name.""" + model = SIMPLE_EFP_SAMPLE_MODELS['maize_atlas_v5'] + self.assertEqual(model.__name__, 'MaizeAtlasV5SampleData') + + def test_lateral_root_initiation_class_name(self): + """Test lateral_root_initiation model has correct class name.""" + model = SIMPLE_EFP_SAMPLE_MODELS['lateral_root_initiation'] + self.assertEqual(model.__name__, 'LateralRootInitiationSampleData') + + +class TestSampleDatabases(TestCase): + """Test a representative sample of databases from different categories.""" + + def setUp(self): + """Set up application context for each test.""" + self.ctx = app.app_context() + self.ctx.push() + + def tearDown(self): + """Tear down application context.""" + self.ctx.pop() + + def test_arabidopsis_databases(self): + """Test all arabidopsis-related databases load.""" + arabidopsis_dbs = [ + 'arabidopsis_ecotypes', 'embryo', 'germination', + 'dna_damage', 'single_cell', 'silique' + ] + + for db_name in arabidopsis_dbs: + with self.subTest(database=db_name): + self.assertIn(db_name, SIMPLE_EFP_SAMPLE_MODELS) + model = SIMPLE_EFP_SAMPLE_MODELS[db_name] + self.assertIsNotNone(model) + + def test_cereal_databases(self): + """Test cereal crop databases (wheat, barley, rice, maize, sorghum, oat).""" + cereal_dbs = [ + 'wheat', 'barley_seed', 'rice_root', + 'maize_atlas_v5', 'sorghum_atlas_w_BS_cells', 'oat' + ] + + for db_name in cereal_dbs: + with self.subTest(database=db_name): + self.assertIn(db_name, SIMPLE_EFP_SAMPLE_MODELS) + model = SIMPLE_EFP_SAMPLE_MODELS[db_name] + self.assertIsNotNone(model) + + def test_legume_databases(self): + """Test legume databases (soybean, medicago, lupin).""" + legume_dbs = [ + 'soybean_senescence', 'medicago_root', + 'lupin_whole_plant', 'arachis' + ] + + for db_name in legume_dbs: + with self.subTest(database=db_name): + self.assertIn(db_name, SIMPLE_EFP_SAMPLE_MODELS) + model = SIMPLE_EFP_SAMPLE_MODELS[db_name] + self.assertIsNotNone(model) + + def test_tree_databases(self): + """Test tree/woody plant databases (poplar, spruce, eucalyptus).""" + tree_dbs = ['poplar_hormone', 'spruce', 'eucalyptus', 'willow'] + + for db_name in tree_dbs: + with self.subTest(database=db_name): + self.assertIn(db_name, SIMPLE_EFP_SAMPLE_MODELS) + model = SIMPLE_EFP_SAMPLE_MODELS[db_name] + self.assertIsNotNone(model) + + def test_tropical_crop_databases(self): + """Test tropical crop databases (cacao, cassava, mangosteen).""" + tropical_dbs = [ + 'cacao_developmental_atlas', 'cassava_atlas', + 'mangosteen_fruit_ripening' + ] + + for db_name in tropical_dbs: + with self.subTest(database=db_name): + self.assertIn(db_name, SIMPLE_EFP_SAMPLE_MODELS) + model = SIMPLE_EFP_SAMPLE_MODELS[db_name] + self.assertIsNotNone(model) diff --git a/tests/models/test_efp_schemas.py b/tests/models/test_efp_schemas.py new file mode 100644 index 0000000..47ae930 --- /dev/null +++ b/tests/models/test_efp_schemas.py @@ -0,0 +1,472 @@ +""" +Comprehensive tests for EFP database schemas and dynamic ORM generation. + +Tests all 191 EFP databases to ensure: +1. Schema definitions are valid +2. Dynamic ORM models generate correctly +3. Column types and constraints are properly configured +4. Complex schemas (lateral_root_initiation, mouse_db, oat) work correctly +""" + +import os +import sys +from unittest import TestCase + +# Allow importing api when invoking pytest from this directory tree +ROOT_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..")) +if ROOT_DIR not in sys.path: + sys.path.insert(0, ROOT_DIR) + +from api import app # noqa: E402 +from api.models.efp_schemas import SIMPLE_EFP_DATABASE_SCHEMAS, EfpSchemaBuilder # noqa: E402 +from api.models.efp_dynamic import SIMPLE_EFP_SAMPLE_MODELS # noqa: E402 + + +class TestEfpSchemaDefinitions(TestCase): + """Test all 191 EFP database schema definitions.""" + + def test_all_191_databases_loaded(self): + """Verify all 191 databases from CSV are loaded.""" + self.assertEqual( + len(SIMPLE_EFP_DATABASE_SCHEMAS), + 191, + f"Expected 191 databases, found {len(SIMPLE_EFP_DATABASE_SCHEMAS)}" + ) + + def test_all_schemas_have_required_keys(self): + """Every schema must have table_name, charset, columns, index, and metadata.""" + required_keys = {'table_name', 'charset', 'columns', 'index', 'metadata'} + + for db_name, schema in SIMPLE_EFP_DATABASE_SCHEMAS.items(): + with self.subTest(database=db_name): + missing_keys = required_keys - set(schema.keys()) + self.assertEqual( + len(missing_keys), 0, + f"{db_name} missing required keys: {missing_keys}" + ) + + def test_all_schemas_have_metadata(self): + """Every schema must have species and sample_regex metadata.""" + for db_name, schema in SIMPLE_EFP_DATABASE_SCHEMAS.items(): + with self.subTest(database=db_name): + metadata = schema.get('metadata', {}) + self.assertIn('species', metadata, f"{db_name} missing species metadata") + self.assertIn('sample_regex', metadata, f"{db_name} missing sample_regex metadata") + + def test_all_schemas_have_base_columns(self): + """Most databases should have the 5 base columns (except mouse_db which has only 3).""" + base_column_names = {'proj_id', 'sample_id', 'data_probeset_id', 'data_signal', 'data_bot_id'} + + for db_name, schema in SIMPLE_EFP_DATABASE_SCHEMAS.items(): + with self.subTest(database=db_name): + column_names = {col['name'] for col in schema['columns']} + + # mouse_db is special - only has 3 columns + if db_name == 'mouse_db': + expected = {'data_probeset_id', 'data_signal', 'data_bot_id'} + self.assertTrue( + expected.issubset(column_names), + f"{db_name} missing expected columns. Has: {column_names}" + ) + # lateral_root_initiation has project_id instead of proj_id + elif db_name == 'lateral_root_initiation': + expected = {'sample_id', 'data_probeset_id', 'data_signal', 'data_bot_id', 'project_id'} + self.assertTrue( + expected.issubset(column_names), + f"{db_name} missing expected columns. Has: {column_names}" + ) + else: + # Standard databases should have all 5 base columns + self.assertTrue( + base_column_names.issubset(column_names), + f"{db_name} missing base columns. Has: {column_names}" + ) + + def test_column_types_are_valid(self): + """All column types must be one of: string, integer, float, text.""" + valid_types = {'string', 'integer', 'float', 'text'} + + for db_name, schema in SIMPLE_EFP_DATABASE_SCHEMAS.items(): + for column in schema['columns']: + with self.subTest(database=db_name, column=column['name']): + col_type = column.get('type') + self.assertIn( + col_type, valid_types, + f"{db_name}.{column['name']} has invalid type: {col_type}" + ) + + def test_string_columns_have_length(self): + """String columns must have a length specified.""" + for db_name, schema in SIMPLE_EFP_DATABASE_SCHEMAS.items(): + for column in schema['columns']: + with self.subTest(database=db_name, column=column['name']): + if column.get('type') == 'string': + self.assertIn( + 'length', column, + f"{db_name}.{column['name']} is string but missing length" + ) + self.assertIsInstance( + column['length'], int, + f"{db_name}.{column['name']} length must be int" + ) + self.assertGreater( + column['length'], 0, + f"{db_name}.{column['name']} length must be > 0" + ) + + def test_text_columns_have_no_length(self): + """Text columns should not have a length.""" + for db_name, schema in SIMPLE_EFP_DATABASE_SCHEMAS.items(): + for column in schema['columns']: + with self.subTest(database=db_name, column=column['name']): + if column.get('type') == 'text': + length = column.get('length') + self.assertIsNone( + length, + f"{db_name}.{column['name']} is text but has length={length}" + ) + + def test_charset_is_valid(self): + """Charset must be either latin1 or utf8mb4.""" + valid_charsets = {'latin1', 'utf8mb4'} + + for db_name, schema in SIMPLE_EFP_DATABASE_SCHEMAS.items(): + with self.subTest(database=db_name): + charset = schema.get('charset') + self.assertIn( + charset, valid_charsets, + f"{db_name} has invalid charset: {charset}" + ) + + def test_known_databases_have_correct_species(self): + """Verify species metadata for known databases.""" + known_species = { + 'cannabis': 'cannabis', + 'embryo': 'arabidopsis', + 'wheat': 'wheat', + 'maize_atlas_v5': 'maize', + 'rice_root': 'rice', + 'sorghum_atlas_w_BS_cells': 'sorghum', + 'oat': 'oat', + 'mouse_db': 'mouse', + } + + for db_name, expected_species in known_species.items(): + with self.subTest(database=db_name): + schema = SIMPLE_EFP_DATABASE_SCHEMAS.get(db_name) + self.assertIsNotNone(schema, f"{db_name} not found in schemas") + actual_species = schema['metadata']['species'] + self.assertEqual( + actual_species, expected_species, + f"{db_name} has species={actual_species}, expected {expected_species}" + ) + + def test_primary_keys_are_defined(self): + """Each schema should have at least one primary key column.""" + for db_name, schema in SIMPLE_EFP_DATABASE_SCHEMAS.items(): + with self.subTest(database=db_name): + pk_columns = [col['name'] for col in schema['columns'] if col.get('primary_key')] + self.assertGreater( + len(pk_columns), 0, + f"{db_name} has no primary key columns" + ) + + +class TestDynamicOrmGeneration(TestCase): + """Test dynamic ORM model generation for all databases.""" + + def setUp(self): + """Set up application context for each test.""" + self.ctx = app.app_context() + self.ctx.push() + + def tearDown(self): + """Tear down application context.""" + self.ctx.pop() + + def test_all_191_models_generated(self): + """Verify all 191 dynamic ORM models are generated.""" + self.assertEqual( + len(SIMPLE_EFP_SAMPLE_MODELS), + 191, + f"Expected 191 ORM models, found {len(SIMPLE_EFP_SAMPLE_MODELS)}" + ) + + def test_model_names_match_database_names(self): + """ORM model keys should match schema keys.""" + schema_names = set(SIMPLE_EFP_DATABASE_SCHEMAS.keys()) + model_names = set(SIMPLE_EFP_SAMPLE_MODELS.keys()) + + self.assertEqual( + schema_names, model_names, + f"Mismatch between schemas and models. Missing: {schema_names - model_names}" + ) + + def test_all_models_have_tablename(self): + """Every model must have __tablename__ attribute.""" + for db_name, model in SIMPLE_EFP_SAMPLE_MODELS.items(): + with self.subTest(database=db_name): + self.assertTrue( + hasattr(model, '__tablename__'), + f"{db_name} model missing __tablename__" + ) + self.assertEqual( + model.__tablename__, 'sample_data', + f"{db_name} has wrong table name" + ) + + def test_all_models_have_bind_key(self): + """Every model must have __bind_key__ matching the database name.""" + for db_name, model in SIMPLE_EFP_SAMPLE_MODELS.items(): + with self.subTest(database=db_name): + self.assertTrue( + hasattr(model, '__bind_key__'), + f"{db_name} model missing __bind_key__" + ) + self.assertEqual( + model.__bind_key__, db_name, + f"{db_name} has wrong bind_key" + ) + + def test_models_have_correct_column_count(self): + """Models should have the same number of columns as their schema.""" + for db_name, model in SIMPLE_EFP_SAMPLE_MODELS.items(): + with self.subTest(database=db_name): + schema = SIMPLE_EFP_DATABASE_SCHEMAS[db_name] + expected_cols = len(schema['columns']) + + # Count actual columns (excluding internal attributes) + actual_cols = len([ + attr for attr in dir(model) + if not attr.startswith('_') and + hasattr(getattr(model, attr), 'type') + ]) + + self.assertEqual( + actual_cols, expected_cols, + f"{db_name} model has {actual_cols} columns, schema has {expected_cols}" + ) + + def test_known_models_have_expected_columns(self): + """Verify specific models have their expected columns.""" + test_cases = { + 'cannabis': ['proj_id', 'sample_id', 'data_probeset_id', 'data_signal', 'data_bot_id'], + 'oat': ['proj_id', 'sample_id', 'data_probeset_id', 'data_signal', 'data_bot_id', + 'genome', 'genome_id', 'orthogroup', 'version'], + 'mouse_db': ['data_probeset_id', 'data_signal', 'data_bot_id'], + } + + for db_name, expected_columns in test_cases.items(): + with self.subTest(database=db_name): + model = SIMPLE_EFP_SAMPLE_MODELS[db_name] + for col_name in expected_columns: + self.assertTrue( + hasattr(model, col_name), + f"{db_name} model missing column: {col_name}" + ) + + +class TestComplexSchemas(TestCase): + """Test the 3 complex/non-standard schemas.""" + + def test_lateral_root_initiation_has_project_id(self): + """lateral_root_initiation has both project_id and sample_file_name as extra columns.""" + schema = SIMPLE_EFP_DATABASE_SCHEMAS['lateral_root_initiation'] + column_names = {col['name'] for col in schema['columns']} + + # Has the extra project_id column + self.assertIn('project_id', column_names) + # Also has standard proj_id from base columns + self.assertIn('proj_id', column_names) + # Has sample_file_name extra column + self.assertIn('sample_file_name', column_names) + + def test_lateral_root_initiation_has_string_sample_id(self): + """lateral_root_initiation has string sample_id instead of integer.""" + schema = SIMPLE_EFP_DATABASE_SCHEMAS['lateral_root_initiation'] + sample_id_col = next(col for col in schema['columns'] if col['name'] == 'sample_id') + + self.assertEqual(sample_id_col['type'], 'string') + self.assertEqual(sample_id_col['length'], 30) + + def test_mouse_db_has_minimal_columns(self): + """mouse_db has the 3 main data columns (still includes base proj_id/sample_id from template).""" + schema = SIMPLE_EFP_DATABASE_SCHEMAS['mouse_db'] + column_names = {col['name'] for col in schema['columns']} + + # Has the 3 data columns + self.assertIn('data_probeset_id', column_names) + self.assertIn('data_signal', column_names) + self.assertIn('data_bot_id', column_names) + + # Should have 5 columns total (includes base proj_id and sample_id) + self.assertEqual(len(column_names), 5) + + def test_oat_has_extra_genome_columns(self): + """oat has 4 extra columns: genome, genome_id, orthogroup, version.""" + schema = SIMPLE_EFP_DATABASE_SCHEMAS['oat'] + column_names = {col['name'] for col in schema['columns']} + + extra_columns = {'genome', 'genome_id', 'orthogroup', 'version'} + self.assertTrue( + extra_columns.issubset(column_names), + "oat missing expected extra columns" + ) + + def test_oat_has_utf8mb4_charset(self): + """oat uses utf8mb4 charset.""" + schema = SIMPLE_EFP_DATABASE_SCHEMAS['oat'] + self.assertEqual(schema['charset'], 'utf8mb4') + + +class TestSchemaBuilderHelpers(TestCase): + """Test the schema builder helper methods.""" + + def test_simple_schema_creates_valid_schema(self): + """_simple_schema helper should create a valid schema structure.""" + schema = EfpSchemaBuilder._simple_schema( + species='test_species', + sample_regex=r'.*', + probeset_len=24, + bot_id_len=16, + ) + + self.assertIn('table_name', schema) + self.assertIn('columns', schema) + self.assertIn('metadata', schema) + self.assertEqual(schema['metadata']['species'], 'test_species') + + def test_schema_with_qa_columns_adds_three_columns(self): + """_schema_with_qa_columns should add sample_file_name, data_call, data_p_val.""" + schema = EfpSchemaBuilder._schema_with_qa_columns( + species='test_species', + sample_regex=r'.*', + ) + + column_names = {col['name'] for col in schema['columns']} + qa_columns = {'sample_file_name', 'data_call', 'data_p_val'} + + self.assertTrue( + qa_columns.issubset(column_names), + "QA schema missing QA columns" + ) + + def test_build_schema_handles_extra_columns(self): + """_build_schema should properly merge extra columns.""" + extra_cols = [ + EfpSchemaBuilder._column('test_col', 'string', length=10) + ] + + schema = EfpSchemaBuilder._build_schema( + extra_columns=extra_cols, + metadata={'species': 'test', 'sample_regex': r'.*'} + ) + + column_names = {col['name'] for col in schema['columns']} + self.assertIn('test_col', column_names) + + +class TestDatabaseCategoryDistribution(TestCase): + """Test distribution of databases by species and type.""" + + def test_species_distribution(self): + """Verify we have databases for expected species.""" + species_counts = {} + for schema in SIMPLE_EFP_DATABASE_SCHEMAS.values(): + species = schema['metadata']['species'] + species_counts[species] = species_counts.get(species, 0) + 1 + + # Check we have major species covered + major_species = ['arabidopsis', 'maize', 'wheat', 'rice', 'sorghum'] + for species in major_species: + with self.subTest(species=species): + self.assertIn( + species, species_counts, + f"No databases found for {species}" + ) + self.assertGreater( + species_counts[species], 0, + f"Expected databases for {species}" + ) + + def test_charset_distribution(self): + """Verify charset distribution (should have both latin1 and utf8mb4).""" + charset_counts = {} + for schema in SIMPLE_EFP_DATABASE_SCHEMAS.values(): + charset = schema['charset'] + charset_counts[charset] = charset_counts.get(charset, 0) + 1 + + # Should have both charsets + self.assertIn('latin1', charset_counts) + self.assertIn('utf8mb4', charset_counts) + + # utf8mb4 should be more common (126 databases) + self.assertGreater( + charset_counts['utf8mb4'], 100, + f"Expected ~126 utf8mb4 databases, found {charset_counts['utf8mb4']}" + ) + + def test_qa_column_distribution(self): + """Verify we have databases with and without QA columns.""" + with_qa = 0 + without_qa = 0 + + for schema in SIMPLE_EFP_DATABASE_SCHEMAS.values(): + column_names = {col['name'] for col in schema['columns']} + if 'sample_file_name' in column_names: + with_qa += 1 + else: + without_qa += 1 + + # Should have both types + self.assertGreater(with_qa, 0, "No databases with QA columns found") + self.assertGreater(without_qa, 0, "No databases without QA columns found") + + # Most should be without QA columns + self.assertGreater(without_qa, with_qa, "Expected more non-QA databases") + + +class TestVarcharLengths(TestCase): + """Test that varchar lengths are within expected ranges.""" + + def test_data_bot_id_max_length(self): + """data_bot_id varchar should not exceed 255.""" + for db_name, schema in SIMPLE_EFP_DATABASE_SCHEMAS.items(): + bot_id_col = next( + (col for col in schema['columns'] if col['name'] == 'data_bot_id'), + None + ) + if bot_id_col and bot_id_col['type'] == 'string': + with self.subTest(database=db_name): + self.assertLessEqual( + bot_id_col['length'], 255, + f"{db_name}.data_bot_id length exceeds 255" + ) + + def test_data_probeset_id_max_length(self): + """data_probeset_id varchar should not exceed 100.""" + for db_name, schema in SIMPLE_EFP_DATABASE_SCHEMAS.items(): + probeset_col = next( + (col for col in schema['columns'] if col['name'] == 'data_probeset_id'), + None + ) + if probeset_col and probeset_col['type'] == 'string': + with self.subTest(database=db_name): + self.assertLessEqual( + probeset_col['length'], 100, + f"{db_name}.data_probeset_id length exceeds 100" + ) + + def test_proj_id_max_length(self): + """proj_id varchar should not exceed 30.""" + for db_name, schema in SIMPLE_EFP_DATABASE_SCHEMAS.items(): + proj_id_col = next( + (col for col in schema['columns'] if col['name'] == 'proj_id'), + None + ) + if proj_id_col and proj_id_col['type'] == 'string': + with self.subTest(database=db_name): + self.assertLessEqual( + proj_id_col['length'], 30, + f"{db_name}.proj_id length exceeds 30" + ) diff --git a/tests/resources/test_proxy.py b/tests/resources/test_proxy.py index aca80e5..b6814a1 100644 --- a/tests/resources/test_proxy.py +++ b/tests/resources/test_proxy.py @@ -1,6 +1,9 @@ from api import app from json import load from unittest import TestCase +from unittest.mock import MagicMock, patch + +import requests class TestIntegrations(TestCase): @@ -12,23 +15,48 @@ def test_get_atted_api5(self): :return: """ # Valid data - response = self.app_client.get("/proxy/atted_api5/At1g01010/5") - # Note: pytest is running from project root. So path is relative to project root with open("tests/data/get_atted_api5.json") as json_file: expected = load(json_file) - self.assertEqual(response.json, expected) - # Invalid gene - response = self.app_client.get("/proxy/atted_api5/At1g0101x/5") - expected = {"wasSuccessful": False, "error": "Invalid gene id"} - self.assertEqual(response.json, expected) + mock_success = MagicMock() + mock_success.status_code = 200 + mock_success.json.return_value = expected + mock_success.raise_for_status.return_value = None - # If no data, the service should return this response - response = self.app_client.get("/proxy/atted_api5/At1g01011/5") - expected = {"error": "No gene ID specified.", "status_code": 400} - self.assertEqual(response.json, expected) + mock_no_data = MagicMock() + mock_no_data.status_code = 200 + mock_no_data.json.return_value = {"error": "No gene ID specified.", "status_code": 400} + mock_no_data.raise_for_status.return_value = None + + with patch("api.resources.proxy.requests.get", side_effect=[mock_success, mock_no_data]): + response = self.app_client.get("/proxy/atted_api5/At1g01010/5") + + self.assertEqual(response.json, expected) + + # Invalid gene + response = self.app_client.get("/proxy/atted_api5/At1g0101x/5") + expected = {"wasSuccessful": False, "error": "Invalid gene id"} + self.assertEqual(response.json, expected) + + # If no data, the service should return this response + response = self.app_client.get("/proxy/atted_api5/At1g01011/5") + expected = {"error": "No gene ID specified.", "status_code": 400} + self.assertEqual(response.json, expected) + + # Invalid topN count + response = self.app_client.get("proxy/atted_api5/At1g01010/9999999999999999999") + expected = {"wasSuccessful": False, "error": "Invalid count"} + self.assertEqual(response.json, expected) + + def test_get_atted_api5_handles_external_error(self): + failure_response = MagicMock() + failure_response.status_code = 403 + http_error = requests.exceptions.HTTPError(response=failure_response) + failure_response.raise_for_status.side_effect = http_error + + with patch("api.resources.proxy.requests.get", return_value=failure_response): + response = self.app_client.get("/proxy/atted_api5/At1g01010/5") - # Invalid topN count - response = self.app_client.get("proxy/atted_api5/At1g01010/9999999999999999999") - expected = {"wasSuccessful": False, "error": "Invalid count"} + expected = {"wasSuccessful": False, "error": "External API request failed with status code 403"} + self.assertEqual(response.status_code, 403) self.assertEqual(response.json, expected) diff --git a/tests/services/test_efp_data.py b/tests/services/test_efp_data.py new file mode 100644 index 0000000..3133324 --- /dev/null +++ b/tests/services/test_efp_data.py @@ -0,0 +1,112 @@ +import os +import sys +from datetime import date +from unittest import TestCase + +# allow importing api when invoking pytest from this directory tree +ROOT_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..")) +if ROOT_DIR not in sys.path: + sys.path.insert(0, ROOT_DIR) + +from api import app, db # noqa: E402 +from api.models.annotations_lookup import AtAgiLookup # noqa: E402 +from api.services.efp_data import query_efp_database_dynamic # noqa: E402 + + +class TestDynamicEfpData(TestCase): + """unit tests for the shared efp query helper in api/services/efp_data.py""" + + def setUp(self): + # each test needs an application context so flask-sqlalchemy can look up binds + self.ctx = app.app_context() + self.ctx.push() + + def tearDown(self): + self.ctx.pop() + + def test_embryo_query_is_case_insensitive(self): + """lower-case agi ids still return the embryo sample row""" + result = query_efp_database_dynamic("embryo", "at1g01010", allow_empty_results=False) + self.assertTrue(result["success"]) + self.assertEqual(result["record_count"], 1) + self.assertEqual(result["data"][0]["name"], "pg_1") + self.assertEqual(result["data"][0]["value"], "0.67") + + def test_sample_filter_handles_case(self): + """sample filters compare case-insensitively when the flag is set""" + result = query_efp_database_dynamic( + "shoot_apex", + "AT1G01010", + sample_ids=["ufo"], + allow_empty_results=False, + sample_case_insensitive=True, + ) + self.assertTrue(result["success"]) + self.assertEqual(result["record_count"], 1) + self.assertEqual(result["data"][0]["name"], "UFO") + self.assertEqual(result["data"][0]["value"], "1.61714") + + def test_invalid_database(self): + """an unsupported database name should trigger a 400 error""" + result = query_efp_database_dynamic("not_a_db", "AT1G01010") + self.assertFalse(result["success"]) + self.assertEqual(result["error_code"], 400) + + def test_invalid_gene_format(self): + """malformed agi ids are rejected before hitting the database""" + result = query_efp_database_dynamic("embryo", "AT1G0101X") + self.assertFalse(result["success"]) + self.assertEqual(result["error_code"], 400) + self.assertIn("Invalid Arabidopsis gene ID format", result["error"]) + + def test_sample_data_agi_is_converted_to_probeset(self): + """sample_data requires probesets, so agi ids should be converted automatically""" + mapping_date = date(2020, 1, 1) + db.session.query(AtAgiLookup).filter_by( + probeset="261585_at", agi="AT1G01010", date=mapping_date + ).delete() + db.session.add( + AtAgiLookup( + probeset="261585_at", + agi="AT1G01010", + date=mapping_date, + ) + ) + db.session.commit() + result = None + try: + result = query_efp_database_dynamic("sample_data", "At1g01010", allow_empty_results=False) + finally: + db.session.query(AtAgiLookup).filter_by( + probeset="261585_at", agi="AT1G01010", date=mapping_date + ).delete() + db.session.commit() + + self.assertTrue(result["success"]) + self.assertEqual(result["probset_id"], "261585_at") + self.assertGreater(result["record_count"], 0) + sample_lookup = {row["name"]: row["value"] for row in result["data"]} + self.assertEqual(sample_lookup["ATGE_100_A"], "40.381") + + def test_sample_data_filter_returns_case_insensitive_matches(self): + """sample_data filters should honor case-insensitive flag just like other datasets""" + result = query_efp_database_dynamic( + "sample_data", + "261585_at", + sample_ids=["atge_100_a", "ATGE_100_B"], + allow_empty_results=False, + sample_case_insensitive=True, + ) + self.assertTrue(result["success"]) + self.assertEqual(result["record_count"], 2) + names = sorted(row["name"] for row in result["data"]) + self.assertEqual(names, ["ATGE_100_A", "ATGE_100_B"]) + + def test_sample_data_empty_results_allowed(self): + """allow_empty_results should return success even when filters exclude everything""" + result = query_efp_database_dynamic( + "sample_data", "256898_at", sample_ids=["DOES_NOT_EXIST"], allow_empty_results=True + ) + self.assertTrue(result["success"]) + self.assertEqual(result["record_count"], 0) + self.assertEqual(result["data"], [])