From 164afeb1c91e064485dec701b429a9d190d29605 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 12 Jan 2026 21:48:12 +0000 Subject: [PATCH 1/8] Initial plan From 9a3b732df54f2f3d7efac3346c14995f4ffa3b76 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 12 Jan 2026 21:55:58 +0000 Subject: [PATCH 2/8] Add cross-reference table for treebase-servlet.xml pages vs documentation Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com> --- doc/PAGE_CROSS_REFERENCE.md | 224 ++++++++++++++++++++++++++++++++++++ doc/README.md | 5 + 2 files changed, 229 insertions(+) create mode 100644 doc/PAGE_CROSS_REFERENCE.md diff --git a/doc/PAGE_CROSS_REFERENCE.md b/doc/PAGE_CROSS_REFERENCE.md new file mode 100644 index 000000000..d528e0156 --- /dev/null +++ b/doc/PAGE_CROSS_REFERENCE.md @@ -0,0 +1,224 @@ +# Cross-Reference: treebase-servlet.xml Pages Not in Documentation + +This table lists all URL mappings from `treebase-servlet.xml` that are NOT mentioned in any markdown documentation file in the repository. + +**Analysis Date:** 2026-01-12 + +**Summary:** +- Total URL mappings in treebase-servlet.xml: 138 +- Documented URLs: 8 +- Undocumented URLs: 130 + +--- + +## Public Pages + +| URL | Controller | Description | +|-----|------------|-------------| +| `/contact.html` | filenameController | Contact information page | +| `/dataMan.html` | filenameController | Data management page | +| `/help.html` | helpController | Help page | +| `/journal.html` | filenameController | Journal information page | +| `/login.html` | filenameController | User login page | +| `/partnership.html` | filenameController | Partnership information page | +| `/people.html` | filenameController | People/contributors page | +| `/register.html` | registerUserController | User registration page | +| `/resetPassword.html` | resetPasswordController | Password reset page | +| `/passwordForm.html` | passwordFormController | Password form page | +| `/submitTutorial.html` | filenameController | Submission tutorial page | +| `/technology.html` | filenameController | Technology stack page | +| `/urlAPI.html` | filenameController | URL API documentation page | +| `/accessviolation.html` | filenameController | Access violation error page | + +## Search Section + +| URL | Controller | Description | +|-----|------------|-------------| +| `/searchForm.html` | searchFormController | Search form page | +| `/searchResult.html` | filenameController | Search results page | +| `/searchStudy.html` | searchStudyController | Search study page | +| `/searchStudyList.html` | listSearchStudyController | Search study list | +| `/study-query.html` | updateStudyQueryController | Study query form | +| `/search/classificationSearch.html` | classificationSearchController | Classification search | +| `/search/matrixSearch.html` | matrixSearchController | Matrix search | +| `/search/studySearch.html` | studySearchController | Study search | +| `/search/taxonSearch.html` | taxonSearchController | Taxon search | +| `/search/treeSearch.html` | treeSearchController | Tree search | +| `/search/treeTopSearch.html` | treeTopSearchController | Tree topology search | +| `/search/summary.html` | summaryController | Search summary | +| `/search/matrixRowList.html` | listMatrixRowController | Matrix row list | +| `/search/taxonList.html` | listTaxaSearchController | Taxon list | +| `/search/downloadAMatrix.html` | downloadAMatrixController | Download matrix | +| `/search/downloadANexusFile.html` | downloadANexusFileController | Download NEXUS file | +| `/search/downloadANexusRCTFile.html` | downloadANexusRCTFileController | Download NEXUS RCT file | +| `/search/downloadAStudy.html` | downloadAStudyController | Download study | +| `/search/downloadATree.html` | downloadATreeController | Download tree | +| `/search/downloadATreeBlock.html` | downloadATreeBlockController | Download tree block | +| `/search/downloadAnAnalysisStep.html` | downloadAnAnalysisStepController | Download analysis step | +| `/search/searchResultsAsRDF.rdf` | searchResultsAsRDFController | Search results as RDF | + +## Search Study Detail Pages + +| URL | Controller | Description | +|-----|------------|-------------| +| `/search/study/analyses.html` | searchSummaryController | Study analyses view | +| `/search/study/analysis.html` | searchSummaryController | Analysis detail view | +| `/search/study/anyObjectAsRDF.rdf` | anyObjectAsRDFController | RDF export for any object | +| `/search/study/matrices.html` | searchSummaryController | Study matrices view | +| `/search/study/matrix.html` | searchSummaryController | Matrix detail view | +| `/search/study/rowSegments.html` | searchSummaryController | Row segments view | +| `/search/study/rowSegmentsTSV.html` | downloadRowSegmentDataController | Row segments TSV download | +| `/search/study/summary.html` | searchSummaryController | Study summary view | +| `/search/study/taxa.html` | searchSummaryController | Study taxa view | +| `/search/study/tree.html` | searchMapToPhyloWidgetController | Tree viewer | +| `/search/study/treeBlock.html` | searchMapToPhyloWidgetController | Tree block viewer | +| `/search/study/treeBlocks.html` | searchSummaryController | Tree blocks list | +| `/search/study/trees.html` | searchSummaryController | Trees list | + +## PhyloWS API Endpoints + +These PhyloWS endpoints ARE documented in [API.md](API.md): +- `/phylows/study/**` - Study web service +- `/phylows/taxon/**` - Taxon web service +- `/phylows/tree/**` - Tree web service + +These PhyloWS endpoints are NOT documented: + +| URL | Controller | Description | +|-----|------------|-------------| +| `/phylows/classification/**` | phyloWSClassificationController | Classification web service | +| `/phylows/matrix/**` | phyloWSMatrixController | Matrix web service | + +## Admin Section + +| URL | Controller | Description | +|-----|------------|-------------| +| `/admin/adminDeletingUserStepOne.html` | adminDeletingUserStepOneController | Delete user - step 1 | +| `/admin/adminDeletingUserStepTwo.html` | adminDeletingUserStepTwoController | Delete user - step 2 | +| `/admin/adminMergingPersons.html` | adminMergingPersonsController | Merge person records | +| `/admin/adminMergingUsers.html` | adminMergingUsersController | Merge user accounts | +| `/admin/adminSelectPersons.html` | adminSelectPersonsController | Select persons for admin action | +| `/admin/adminSelectUsers.html` | adminSelectUsersController | Select users for admin action | +| `/admin/adminUpdatingUserInfo.html` | adminUpdatingUserInfoController | Update user information | +| `/admin/administrationPage.html` | filenameController | Main administration page | +| `/admin/changeStudyStatus.html` | changeStudyStatusController | Change study status | +| `/admin/messageToAdminAfterAction.html` | filenameController | Admin action confirmation | +| `/admin/overrideUserProfile.html` | adminOverridingUserFormController | Override user profile | +| `/admin/personList.html` | filenameController | List persons | +| `/admin/readyStateStudies.html` | changeStudyStatusController | Ready state studies list | +| `/admin/searchBySubmissionID.html` | searchBySubmissionIDController | Search by submission ID | +| `/admin/selectStudies.html` | selectStudiesController | Select studies for admin action | +| `/admin/userList.html` | filenameController | List users | +| `/admin/userManagement.html` | userManagementController | User management | + +## User Submission Section + +| URL | Controller | Description | +|-----|------------|-------------| +| `/user/addAnalyzedData.html` | addAnalyzedDataController | Add analyzed data to study | +| `/user/addAuthor.html` | addAuthorController | Add author to citation | +| `/user/analyses.html` | summaryController | View study analyses | +| `/user/analysisDisplay.html` | displayAnalysisController | Display analysis details | +| `/user/analysisForm.html` | analysisFormController | Edit analysis form | +| `/user/analysisList.html` | listAnalysisController | List analyses | +| `/user/analysisStepForm.html` | analysisStepFormController | Edit analysis step | +| `/user/analysisStepList.html` | listAnalysisStepController | List analysis steps | +| `/user/analyzedDataForm.html` | analyzedDataFormController | Edit analyzed data | +| `/user/analyzedDataList.html` | listAnalyzedDataController | List analyzed data | +| `/user/authorForm.html` | authorFormController | Edit author form | +| `/user/authorList.html` | authorFormController | List authors | +| `/user/authorSearchForm.html` | authorSearchFormController | Search for authors | +| `/user/citationForm.html` | citationFormController | Edit citation form | +| `/user/deleteAMatrix.html` | deleteAMatrixController | Delete a matrix | +| `/user/deleteARowSegment.html` | deleteARowSegmentController | Delete a row segment | +| `/user/deleteATree.html` | deleteATreeController | Delete a tree | +| `/user/deleteATreeBlock.html` | deleteATreeBlockController | Delete a tree block | +| `/user/deleteStudy.html` | deleteStudyController | Delete a study | +| `/user/directMapToPhyloWidget.html` | directMapToPhyloWidgetController | Direct map to tree viewer | +| `/user/directToPhyloWidget.html` | directToPhyloWidgetController | Direct to tree viewer | +| `/user/displaySubmissionMenu.html` | displaySubmissionMenuController | Submission menu | +| `/user/downloadAMatrix.html` | downloadAMatrixController | Download matrix | +| `/user/downloadANexusFile.html` | downloadANexusFileController | Download NEXUS file | +| `/user/downloadANexusRCTFile.html` | downloadANexusRCTFileController | Download NEXUS RCT file | +| `/user/downloadATree.html` | downloadATreeController | Download tree | +| `/user/downloadATreeBlock.html` | downloadATreeBlockController | Download tree block | +| `/user/editSetTaxonLabel.html` | editSetTaxonLabelController | Edit taxon label set | +| `/user/editTaxonLabel.html` | editTaxonLabelController | Edit taxon label | +| `/user/editorForm.html` | editorFormController | Edit editor form | +| `/user/exportRowSegmentData.html` | exportRowSegmentDataController | Export row segment data | +| `/user/exportRowSegmentTemplate.html` | exportRowSegmentTemplateController | Export row segment template | +| `/user/matrixList.html` | listMatrixController | List matrices | +| `/user/matrixRowList.html` | listMatrixRowController | List matrix rows | +| `/user/matrixRowSegmentForm.html` | matrixRowSegmentFormController | Edit matrix row segment | +| `/user/matrixRowSegmentList.html` | listMatrixRowSegmentController | List matrix row segments | +| `/user/nexusFiles.html` | nexusFilesController | View NEXUS files | +| `/user/processUser.html` | processUserController | Process user action | +| `/user/readOnlyListTree.html` | readOnlyListTreeController | Read-only tree list | +| `/user/readyState.html` | readyStateController | Change ready state | +| `/user/rowSegmentDataTable.html` | rowSegmentDataTableController | Row segment data table | +| `/user/studyForm.html` | studyFormController | Edit study form | +| `/user/submissionList.html` | listSubmissionController | List submissions | +| `/user/submissionMain.html` | filenameController | Submission main page | +| `/user/summary.html` | summaryController | Submission summary | +| `/user/taxaList.html` | listTaxaController | List taxa | +| `/user/treeBlockList.html` | listTreeBlockController | List tree blocks | +| `/user/treeList.html` | listTreeController | List trees | +| `/user/treeParser.html` | treeParserController | Tree parser | +| `/user/treeParserResult.html` | treeParserResultController | Tree parser results | +| `/user/updateProfile.html` | userFormController | Update user profile | +| `/user/uploadFile.html` | uploadFileController | Upload file | +| `/user/uploadFileSummary.html` | uploadFileSummaryController | Upload file summary | +| `/user/uploadRowSegmentData.html` | uploadRowSegmentDataController | Upload row segment data | +| `/user/viewAllRowSegmentData.html` | viewAllRowSegmentDataController | View all row segment data | +| `/user/viewXML.html` | filenameController | View XML | + +## Other Pages + +| URL | Controller | Description | +|-----|------------|-------------| +| `/appletInteraction.html` | appletInteractionController | Applet interaction handler | +| `/feed.xml` | rssFeedController | RSS feed (alternate) | +| `/json/submissionIsland.html` | submissionToJsonController | JSON submission data | +| `/rss.xml` | rssFeedController | RSS feed | +| `/sitemap.xml` | siteMapController | XML sitemap for SEO | +| `/test/testParser.html` | treeParserController | Test parser (development) | + +--- + +## Documented URLs (8 total) + +The following URLs from `treebase-servlet.xml` ARE mentioned in the markdown documentation: + +| URL | Documented In | +|-----|---------------| +| `/about.html` | README.md | +| `/home.html` | Various docs | +| `/phylows/study/**` | API.md | +| `/phylows/taxon/**` | API.md | +| `/phylows/tree/**` | API.md | +| `/reference.html` | Various docs | +| `/search/` | Various docs | +| `/top/**` | OAI-PMH.md | + +--- + +## Notes + +1. **filenameController** - These pages use the `ShortPathUrlFilenameViewController` which maps URLs directly to JSP files without custom controller logic. + +2. **PhyloWS API** - The API.md documentation covers the study, taxon, and tree endpoints but not the classification and matrix endpoints. + +3. **Admin Section** - All admin pages are undocumented. These are internal administrative tools. + +4. **User Section** - All user submission pages are undocumented. These are internal user workflow pages. + +5. **Search Section** - All search pages are undocumented except for the general `/search/` path mention. + +--- + +## Recommendations + +1. **Document PhyloWS endpoints** - Add `/phylows/classification/**` and `/phylows/matrix/**` to API.md +2. **Create User Guide** - Document the user submission workflow pages +3. **Create Admin Guide** - Document administrative functionality +4. **Add Search Documentation** - Document the various search interfaces and their capabilities diff --git a/doc/README.md b/doc/README.md index 554ce3976..b32428224 100644 --- a/doc/README.md +++ b/doc/README.md @@ -7,6 +7,10 @@ This directory contains the organized documentation for TreeBASE. - **[API.md](API.md)** - PhyloWS web service API documentation - **[OAI-PMH.md](OAI-PMH.md)** - OAI-PMH metadata harvesting interface documentation +## Page Reference + +- **[PAGE_CROSS_REFERENCE.md](PAGE_CROSS_REFERENCE.md)** - Cross-reference of treebase-servlet.xml URL mappings and documentation coverage + ## Directory Structure ### [development/](development/) @@ -36,6 +40,7 @@ Historical documentation that is no longer relevant for current deployments: - **Use the PhyloWS API** → [API.md](API.md) - **Use the OAI-PMH interface** → [OAI-PMH.md](OAI-PMH.md) +- **See all web pages** → [PAGE_CROSS_REFERENCE.md](PAGE_CROSS_REFERENCE.md) - **Build TreeBASE from source** → [development/BUILDING.md](development/BUILDING.md) - **Deploy TreeBASE to a server** → [development/DEPLOYING.md](development/DEPLOYING.md) - **Understand DWR integration** → [technical-notes/DWR.md](technical-notes/DWR.md) From f192288ef5f045059c53b4d82f0983406ad15ba0 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 12 Jan 2026 22:03:54 +0000 Subject: [PATCH 3/8] Fix cross-reference to analyze v3 user story docs instead of all markdown files Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com> --- doc/PAGE_CROSS_REFERENCE.md | 312 +++++++++++++++++------------------- doc/README.md | 4 +- 2 files changed, 148 insertions(+), 168 deletions(-) diff --git a/doc/PAGE_CROSS_REFERENCE.md b/doc/PAGE_CROSS_REFERENCE.md index d528e0156..c84ef8d1f 100644 --- a/doc/PAGE_CROSS_REFERENCE.md +++ b/doc/PAGE_CROSS_REFERENCE.md @@ -1,224 +1,204 @@ -# Cross-Reference: treebase-servlet.xml Pages Not in Documentation +# Cross-Reference: treebase-servlet.xml Pages vs v3 User Story Documentation -This table lists all URL mappings from `treebase-servlet.xml` that are NOT mentioned in any markdown documentation file in the repository. +This document cross-references the URL mappings in `treebase-servlet.xml` against the pages documented in the v3 UI/UX user story markdown files (`doc/v3/*.md`). **Analysis Date:** 2026-01-12 +**Source Documents:** +- `treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml` +- `doc/v3/user-story-01-search.md` +- `doc/v3/user-story-02-account.md` +- `doc/v3/user-story-03-submission.md` +- `doc/v3/user-story-04-review.md` +- `doc/v3/user-story-05-admin.md` +- `doc/v3/user-story-06-technical.md` +- `doc/v3/user-story-07-governance.md` + **Summary:** - Total URL mappings in treebase-servlet.xml: 138 -- Documented URLs: 8 -- Undocumented URLs: 130 +- Pages accounted for in user stories: 99 +- Pages NOT in user stories: 40 --- -## Public Pages +## Pages NOT in User Story Documentation -| URL | Controller | Description | -|-----|------------|-------------| -| `/contact.html` | filenameController | Contact information page | -| `/dataMan.html` | filenameController | Data management page | -| `/help.html` | helpController | Help page | -| `/journal.html` | filenameController | Journal information page | -| `/login.html` | filenameController | User login page | -| `/partnership.html` | filenameController | Partnership information page | -| `/people.html` | filenameController | People/contributors page | -| `/register.html` | registerUserController | User registration page | -| `/resetPassword.html` | resetPasswordController | Password reset page | -| `/passwordForm.html` | passwordFormController | Password form page | -| `/submitTutorial.html` | filenameController | Submission tutorial page | -| `/technology.html` | filenameController | Technology stack page | -| `/urlAPI.html` | filenameController | URL API documentation page | -| `/accessviolation.html` | filenameController | Access violation error page | +The following pages from `treebase-servlet.xml` are NOT mentioned in any "Pages to Account For" section of the v3 user story documents: -## Search Section +### Public/Utility Pages | URL | Controller | Description | |-----|------------|-------------| -| `/searchForm.html` | searchFormController | Search form page | -| `/searchResult.html` | filenameController | Search results page | -| `/searchStudy.html` | searchStudyController | Search study page | -| `/searchStudyList.html` | listSearchStudyController | Search study list | -| `/study-query.html` | updateStudyQueryController | Study query form | -| `/search/classificationSearch.html` | classificationSearchController | Classification search | -| `/search/matrixSearch.html` | matrixSearchController | Matrix search | -| `/search/studySearch.html` | studySearchController | Study search | -| `/search/taxonSearch.html` | taxonSearchController | Taxon search | -| `/search/treeSearch.html` | treeSearchController | Tree search | -| `/search/treeTopSearch.html` | treeTopSearchController | Tree topology search | -| `/search/summary.html` | summaryController | Search summary | -| `/search/matrixRowList.html` | listMatrixRowController | Matrix row list | -| `/search/taxonList.html` | listTaxaSearchController | Taxon list | -| `/search/downloadAMatrix.html` | downloadAMatrixController | Download matrix | -| `/search/downloadANexusFile.html` | downloadANexusFileController | Download NEXUS file | -| `/search/downloadANexusRCTFile.html` | downloadANexusRCTFileController | Download NEXUS RCT file | -| `/search/downloadAStudy.html` | downloadAStudyController | Download study | -| `/search/downloadATree.html` | downloadATreeController | Download tree | -| `/search/downloadATreeBlock.html` | downloadATreeBlockController | Download tree block | -| `/search/downloadAnAnalysisStep.html` | downloadAnAnalysisStepController | Download analysis step | -| `/search/searchResultsAsRDF.rdf` | searchResultsAsRDFController | Search results as RDF | +| `/accessviolation.html` | filenameController | Access violation error page | +| `/login.html` | filenameController | Login page (note: `/login.jsp` is documented instead) | -## Search Study Detail Pages +### RSS and Feed Pages | URL | Controller | Description | |-----|------------|-------------| -| `/search/study/analyses.html` | searchSummaryController | Study analyses view | -| `/search/study/analysis.html` | searchSummaryController | Analysis detail view | -| `/search/study/anyObjectAsRDF.rdf` | anyObjectAsRDFController | RDF export for any object | -| `/search/study/matrices.html` | searchSummaryController | Study matrices view | -| `/search/study/matrix.html` | searchSummaryController | Matrix detail view | -| `/search/study/rowSegments.html` | searchSummaryController | Row segments view | -| `/search/study/rowSegmentsTSV.html` | downloadRowSegmentDataController | Row segments TSV download | -| `/search/study/summary.html` | searchSummaryController | Study summary view | -| `/search/study/taxa.html` | searchSummaryController | Study taxa view | -| `/search/study/tree.html` | searchMapToPhyloWidgetController | Tree viewer | -| `/search/study/treeBlock.html` | searchMapToPhyloWidgetController | Tree block viewer | -| `/search/study/treeBlocks.html` | searchSummaryController | Tree blocks list | -| `/search/study/trees.html` | searchSummaryController | Trees list | - -## PhyloWS API Endpoints - -These PhyloWS endpoints ARE documented in [API.md](API.md): -- `/phylows/study/**` - Study web service -- `/phylows/taxon/**` - Taxon web service -- `/phylows/tree/**` - Tree web service - -These PhyloWS endpoints are NOT documented: +| `/feed.xml` | rssFeedController | RSS feed (alternate URL) | +| `/rss.xml` | rssFeedController | RSS feed | + +### Legacy Search Pages | URL | Controller | Description | |-----|------------|-------------| -| `/phylows/classification/**` | phyloWSClassificationController | Classification web service | -| `/phylows/matrix/**` | phyloWSMatrixController | Matrix web service | +| `/search/` | studySearchController | Search root redirect | +| `/searchForm.html` | searchFormController | Legacy search form | +| `/searchResult.html` | filenameController | Legacy search results | +| `/searchStudy.html` | searchStudyController | Legacy study search | +| `/searchStudyList.html` | listSearchStudyController | Legacy study search list | +| `/study-query.html` | updateStudyQueryController | Study query form | -## Admin Section +### Search Download/Export Pages | URL | Controller | Description | |-----|------------|-------------| -| `/admin/adminDeletingUserStepOne.html` | adminDeletingUserStepOneController | Delete user - step 1 | -| `/admin/adminDeletingUserStepTwo.html` | adminDeletingUserStepTwoController | Delete user - step 2 | -| `/admin/adminMergingPersons.html` | adminMergingPersonsController | Merge person records | -| `/admin/adminMergingUsers.html` | adminMergingUsersController | Merge user accounts | -| `/admin/adminSelectPersons.html` | adminSelectPersonsController | Select persons for admin action | -| `/admin/adminSelectUsers.html` | adminSelectUsersController | Select users for admin action | -| `/admin/adminUpdatingUserInfo.html` | adminUpdatingUserInfoController | Update user information | -| `/admin/administrationPage.html` | filenameController | Main administration page | -| `/admin/changeStudyStatus.html` | changeStudyStatusController | Change study status | -| `/admin/messageToAdminAfterAction.html` | filenameController | Admin action confirmation | -| `/admin/overrideUserProfile.html` | adminOverridingUserFormController | Override user profile | -| `/admin/personList.html` | filenameController | List persons | -| `/admin/readyStateStudies.html` | changeStudyStatusController | Ready state studies list | -| `/admin/searchBySubmissionID.html` | searchBySubmissionIDController | Search by submission ID | -| `/admin/selectStudies.html` | selectStudiesController | Select studies for admin action | -| `/admin/userList.html` | filenameController | List users | -| `/admin/userManagement.html` | userManagementController | User management | - -## User Submission Section +| `/search/downloadANexusRCTFile.html` | downloadANexusRCTFileController | Download reconstructed NEXUS file | +| `/search/downloadAStudy.html` | downloadAStudyController | Download entire study | +| `/search/downloadATreeBlock.html` | downloadATreeBlockController | Download tree block | +| `/search/downloadAnAnalysisStep.html` | downloadAnAnalysisStepController | Download analysis step data | +| `/search/matrixRowList.html` | listMatrixRowController | Matrix row list view | +| `/search/searchResultsAsRDF.rdf` | searchResultsAsRDFController | Search results as RDF | +| `/search/summary.html` | summaryController | Search summary page | +| `/search/taxonList.html` | listTaxaSearchController | Taxon list view | + +### User Submission Pages | URL | Controller | Description | |-----|------------|-------------| -| `/user/addAnalyzedData.html` | addAnalyzedDataController | Add analyzed data to study | -| `/user/addAuthor.html` | addAuthorController | Add author to citation | -| `/user/analyses.html` | summaryController | View study analyses | -| `/user/analysisDisplay.html` | displayAnalysisController | Display analysis details | -| `/user/analysisForm.html` | analysisFormController | Edit analysis form | -| `/user/analysisList.html` | listAnalysisController | List analyses | -| `/user/analysisStepForm.html` | analysisStepFormController | Edit analysis step | -| `/user/analysisStepList.html` | listAnalysisStepController | List analysis steps | -| `/user/analyzedDataForm.html` | analyzedDataFormController | Edit analyzed data | -| `/user/analyzedDataList.html` | listAnalyzedDataController | List analyzed data | -| `/user/authorForm.html` | authorFormController | Edit author form | -| `/user/authorList.html` | authorFormController | List authors | -| `/user/authorSearchForm.html` | authorSearchFormController | Search for authors | -| `/user/citationForm.html` | citationFormController | Edit citation form | -| `/user/deleteAMatrix.html` | deleteAMatrixController | Delete a matrix | -| `/user/deleteARowSegment.html` | deleteARowSegmentController | Delete a row segment | -| `/user/deleteATree.html` | deleteATreeController | Delete a tree | -| `/user/deleteATreeBlock.html` | deleteATreeBlockController | Delete a tree block | -| `/user/deleteStudy.html` | deleteStudyController | Delete a study | -| `/user/directMapToPhyloWidget.html` | directMapToPhyloWidgetController | Direct map to tree viewer | -| `/user/directToPhyloWidget.html` | directToPhyloWidgetController | Direct to tree viewer | -| `/user/displaySubmissionMenu.html` | displaySubmissionMenuController | Submission menu | -| `/user/downloadAMatrix.html` | downloadAMatrixController | Download matrix | -| `/user/downloadANexusFile.html` | downloadANexusFileController | Download NEXUS file | -| `/user/downloadANexusRCTFile.html` | downloadANexusRCTFileController | Download NEXUS RCT file | -| `/user/downloadATree.html` | downloadATreeController | Download tree | -| `/user/downloadATreeBlock.html` | downloadATreeBlockController | Download tree block | -| `/user/editSetTaxonLabel.html` | editSetTaxonLabelController | Edit taxon label set | -| `/user/editTaxonLabel.html` | editTaxonLabelController | Edit taxon label | -| `/user/editorForm.html` | editorFormController | Edit editor form | +| `/user/analyses.html` | summaryController | Study analyses (duplicate of analysisDisplay) | +| `/user/authorForm.html` | authorFormController | Author edit form | +| `/user/authorList.html` | authorFormController | Author list | +| `/user/deleteARowSegment.html` | deleteARowSegmentController | Delete row segment | +| `/user/directToPhyloWidget.html` | directToPhyloWidgetController | Direct PhyloWidget link (alternate) | +| `/user/displaySubmissionMenu.html` | displaySubmissionMenuController | Submission menu display | +| `/user/downloadANexusRCTFile.html` | downloadANexusRCTFileController | Download reconstructed NEXUS | +| `/user/editorForm.html` | editorFormController | Editor edit form | | `/user/exportRowSegmentData.html` | exportRowSegmentDataController | Export row segment data | | `/user/exportRowSegmentTemplate.html` | exportRowSegmentTemplateController | Export row segment template | -| `/user/matrixList.html` | listMatrixController | List matrices | -| `/user/matrixRowList.html` | listMatrixRowController | List matrix rows | -| `/user/matrixRowSegmentForm.html` | matrixRowSegmentFormController | Edit matrix row segment | -| `/user/matrixRowSegmentList.html` | listMatrixRowSegmentController | List matrix row segments | +| `/user/matrixRowSegmentForm.html` | matrixRowSegmentFormController | Matrix row segment form | | `/user/nexusFiles.html` | nexusFilesController | View NEXUS files | -| `/user/processUser.html` | processUserController | Process user action | | `/user/readOnlyListTree.html` | readOnlyListTreeController | Read-only tree list | -| `/user/readyState.html` | readyStateController | Change ready state | | `/user/rowSegmentDataTable.html` | rowSegmentDataTableController | Row segment data table | -| `/user/studyForm.html` | studyFormController | Edit study form | -| `/user/submissionList.html` | listSubmissionController | List submissions | | `/user/submissionMain.html` | filenameController | Submission main page | -| `/user/summary.html` | summaryController | Submission summary | -| `/user/taxaList.html` | listTaxaController | List taxa | -| `/user/treeBlockList.html` | listTreeBlockController | List tree blocks | -| `/user/treeList.html` | listTreeController | List trees | | `/user/treeParser.html` | treeParserController | Tree parser | | `/user/treeParserResult.html` | treeParserResultController | Tree parser results | -| `/user/updateProfile.html` | userFormController | Update user profile | -| `/user/uploadFile.html` | uploadFileController | Upload file | -| `/user/uploadFileSummary.html` | uploadFileSummaryController | Upload file summary | | `/user/uploadRowSegmentData.html` | uploadRowSegmentDataController | Upload row segment data | -| `/user/viewAllRowSegmentData.html` | viewAllRowSegmentDataController | View all row segment data | -| `/user/viewXML.html` | filenameController | View XML | +| `/user/viewXML.html` | filenameController | View XML output | -## Other Pages +### Development/Test Pages | URL | Controller | Description | |-----|------------|-------------| -| `/appletInteraction.html` | appletInteractionController | Applet interaction handler | -| `/feed.xml` | rssFeedController | RSS feed (alternate) | -| `/json/submissionIsland.html` | submissionToJsonController | JSON submission data | -| `/rss.xml` | rssFeedController | RSS feed | -| `/sitemap.xml` | siteMapController | XML sitemap for SEO | | `/test/testParser.html` | treeParserController | Test parser (development) | ---- +### JSON/API Pages -## Documented URLs (8 total) +| URL | Controller | Description | +|-----|------------|-------------| +| `/json/submissionIsland.html` | submissionToJsonController | Submission JSON data | +| `/appletInteraction.html` | appletInteractionController | Applet interaction handler | -The following URLs from `treebase-servlet.xml` ARE mentioned in the markdown documentation: +--- -| URL | Documented In | -|-----|---------------| -| `/about.html` | README.md | -| `/home.html` | Various docs | -| `/phylows/study/**` | API.md | -| `/phylows/taxon/**` | API.md | -| `/phylows/tree/**` | API.md | -| `/reference.html` | Various docs | -| `/search/` | Various docs | -| `/top/**` | OAI-PMH.md | +## Pages Accounted For in User Stories + +The following pages from `treebase-servlet.xml` ARE documented in the v3 user story "Pages to Account For" sections: + +### User Story 01: Search (25 pages) +- `/search/studySearch.html`, `/search/matrixSearch.html`, `/search/treeSearch.html` +- `/search/taxonSearch.html`, `/search/treeTopSearch.html`, `/search/classificationSearch.html` +- `/search/study/summary.html`, `/search/study/matrices.html`, `/search/study/trees.html` +- `/search/study/taxa.html`, `/search/study/analyses.html`, `/search/study/analysis.html` +- `/search/study/matrix.html`, `/search/study/tree.html`, `/search/study/treeBlock.html` +- `/search/study/treeBlocks.html`, `/search/study/rowSegments.html`, `/search/study/rowSegmentsTSV.html` +- `/search/study/anyObjectAsRDF.rdf`, `/search/downloadATree.html`, `/search/downloadAMatrix.html` +- `/search/downloadANexusFile.html`, `/phylows/study/**`, `/phylows/matrix/**` +- `/phylows/tree/**`, `/phylows/taxon/**` + +### User Story 02: Account (17 pages) +- `/register.html`, `/passwordForm.html`, `/resetPassword.html` +- `/user/updateProfile.html`, `/user/processUser.html`, `/user/submissionList.html` +- `/admin/adminSelectUsers.html`, `/admin/userList.html`, `/admin/overrideUserProfile.html` +- `/admin/adminUpdatingUserInfo.html`, `/admin/adminDeletingUserStepOne.html` +- `/admin/adminDeletingUserStepTwo.html`, `/admin/adminMergingUsers.html`, `/admin/userManagement.html` + +### User Story 03: Submission (35 pages) +- `/user/submissionList.html`, `/user/studyForm.html`, `/user/summary.html` +- `/user/citationForm.html`, `/user/authorSearchForm.html`, `/user/addAuthor.html` +- `/user/uploadFile.html`, `/user/uploadFileSummary.html`, `/user/treeBlockList.html` +- `/user/treeList.html`, `/user/directMapToPhyloWidget.html`, `/user/deleteATree.html` +- `/user/deleteATreeBlock.html`, `/user/matrixList.html`, `/user/matrixRowList.html` +- `/user/matrixRowSegmentList.html`, `/user/viewAllRowSegmentData.html`, `/user/deleteAMatrix.html` +- `/user/taxaList.html`, `/user/editTaxonLabel.html`, `/user/editSetTaxonLabel.html` +- `/user/analysisList.html`, `/user/analysisDisplay.html`, `/user/analysisForm.html` +- `/user/analysisStepList.html`, `/user/analysisStepForm.html`, `/user/analyzedDataList.html` +- `/user/analyzedDataForm.html`, `/user/addAnalyzedData.html`, `/user/readyState.html` +- `/user/deleteStudy.html`, `/submitTutorial.html`, `/user/downloadATree.html` +- `/user/downloadATreeBlock.html`, `/user/downloadAMatrix.html`, `/user/downloadANexusFile.html` + +### User Story 04: Review (8 pages) +- `/search/study/summary.html`, `/search/study/trees.html`, `/search/study/tree.html` +- `/search/study/matrices.html`, `/search/study/matrix.html`, `/search/study/taxa.html` +- `/search/study/analyses.html`, `/search/study/analysis.html` + +### User Story 05: Administration (17 pages) +- `/admin/administrationPage.html`, `/admin/userManagement.html`, `/admin/readyStateStudies.html` +- `/admin/searchBySubmissionID.html`, `/admin/selectStudies.html`, `/admin/changeStudyStatus.html` +- `/admin/adminSelectUsers.html`, `/admin/userList.html`, `/admin/adminUpdatingUserInfo.html` +- `/admin/overrideUserProfile.html`, `/admin/adminDeletingUserStepOne.html` +- `/admin/adminDeletingUserStepTwo.html`, `/admin/adminMergingUsers.html` +- `/admin/adminSelectPersons.html`, `/admin/personList.html`, `/admin/adminMergingPersons.html` +- `/admin/messageToAdminAfterAction.html` + +### User Story 06: Technical (12 pages) +- `/urlAPI.html`, `/technology.html`, `/about.html`, `/contact.html` +- `/submitTutorial.html`, `/help.html`, `/sitemap.xml` +- `/phylows/study/**`, `/phylows/tree/**`, `/phylows/matrix/**` +- `/phylows/taxon/**`, `/phylows/classification/**`, `/top/**` + +### User Story 07: Governance (11 pages) +- `/home.html`, `/about.html`, `/people.html`, `/partnership.html` +- `/reference.html`, `/technology.html`, `/submitTutorial.html` +- `/urlAPI.html`, `/dataMan.html`, `/journal.html`, `/contact.html` --- -## Notes +## Recommendations -1. **filenameController** - These pages use the `ShortPathUrlFilenameViewController` which maps URLs directly to JSP files without custom controller logic. +### Pages to Consider Adding to User Stories -2. **PhyloWS API** - The API.md documentation covers the study, taxon, and tree endpoints but not the classification and matrix endpoints. +1. **RSS Feeds** (`/feed.xml`, `/rss.xml`) - Consider adding to User Story 06 (Technical) as these are programmatic access points -3. **Admin Section** - All admin pages are undocumented. These are internal administrative tools. +2. **Legacy Search Pages** - May need documentation in User Story 01 if they are still active, or marked for deprecation -4. **User Section** - All user submission pages are undocumented. These are internal user workflow pages. +3. **Row Segment Operations** - Several row segment pages are not documented: + - `/user/rowSegmentDataTable.html` + - `/user/uploadRowSegmentData.html` + - `/user/exportRowSegmentData.html` + - `/user/deleteARowSegment.html` + - These should be added to User Story 03 (Submission) -5. **Search Section** - All search pages are undocumented except for the general `/search/` path mention. +4. **Tree Parser** (`/user/treeParser.html`, `/user/treeParserResult.html`) - Consider adding to User Story 03 + +5. **Download Pages** - Some download endpoints are missing: + - `/search/downloadAStudy.html` + - `/search/downloadATreeBlock.html` + - `/search/downloadAnAnalysisStep.html` + - `/search/downloadANexusRCTFile.html` + - These should be added to User Story 01 (Search) + +6. **JSON/API Endpoints** (`/json/submissionIsland.html`) - Consider adding to User Story 06 (Technical) --- -## Recommendations +## Notes + +1. **Duplicate URLs**: Some URLs appear in multiple user stories (e.g., `/user/submissionList.html` appears in both User Story 02 and 03). This is expected as pages serve multiple workflows. + +2. **Static JSP vs Controller**: Pages using `filenameController` map directly to JSP files without custom controller logic. + +3. **PhyloWS Wildcards**: Endpoints like `/phylows/study/**` cover multiple sub-paths for the REST API. -1. **Document PhyloWS endpoints** - Add `/phylows/classification/**` and `/phylows/matrix/**` to API.md -2. **Create User Guide** - Document the user submission workflow pages -3. **Create Admin Guide** - Document administrative functionality -4. **Add Search Documentation** - Document the various search interfaces and their capabilities +4. **login.jsp vs login.html**: The user stories reference `/login.jsp` but the servlet maps `/login.html` - this may be a routing inconsistency to investigate. diff --git a/doc/README.md b/doc/README.md index b32428224..e888a259b 100644 --- a/doc/README.md +++ b/doc/README.md @@ -9,7 +9,7 @@ This directory contains the organized documentation for TreeBASE. ## Page Reference -- **[PAGE_CROSS_REFERENCE.md](PAGE_CROSS_REFERENCE.md)** - Cross-reference of treebase-servlet.xml URL mappings and documentation coverage +- **[PAGE_CROSS_REFERENCE.md](PAGE_CROSS_REFERENCE.md)** - Cross-reference of treebase-servlet.xml URL mappings vs v3 user story documentation (identifies pages not yet covered in UI/UX user stories) ## Directory Structure @@ -40,7 +40,7 @@ Historical documentation that is no longer relevant for current deployments: - **Use the PhyloWS API** → [API.md](API.md) - **Use the OAI-PMH interface** → [OAI-PMH.md](OAI-PMH.md) -- **See all web pages** → [PAGE_CROSS_REFERENCE.md](PAGE_CROSS_REFERENCE.md) +- **See pages not in user stories** → [PAGE_CROSS_REFERENCE.md](PAGE_CROSS_REFERENCE.md) - **Build TreeBASE from source** → [development/BUILDING.md](development/BUILDING.md) - **Deploy TreeBASE to a server** → [development/DEPLOYING.md](development/DEPLOYING.md) - **Understand DWR integration** → [technical-notes/DWR.md](technical-notes/DWR.md) From 1f2d1967703521ccba37d757f72c9beb6f446d23 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 12 Jan 2026 22:08:25 +0000 Subject: [PATCH 4/8] Clarify alternative search URL patterns in cross-reference doc Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com> --- doc/PAGE_CROSS_REFERENCE.md | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/doc/PAGE_CROSS_REFERENCE.md b/doc/PAGE_CROSS_REFERENCE.md index c84ef8d1f..244c5aee9 100644 --- a/doc/PAGE_CROSS_REFERENCE.md +++ b/doc/PAGE_CROSS_REFERENCE.md @@ -39,15 +39,17 @@ The following pages from `treebase-servlet.xml` are NOT mentioned in any "Pages | `/feed.xml` | rssFeedController | RSS feed (alternate URL) | | `/rss.xml` | rssFeedController | RSS feed | -### Legacy Search Pages +### Alternative Search URL Patterns + +These are search-related URLs that use different URL patterns than those documented in User Story 01 (which documents `/search/studySearch.html`, etc.): | URL | Controller | Description | |-----|------------|-------------| | `/search/` | studySearchController | Search root redirect | -| `/searchForm.html` | searchFormController | Legacy search form | -| `/searchResult.html` | filenameController | Legacy search results | -| `/searchStudy.html` | searchStudyController | Legacy study search | -| `/searchStudyList.html` | listSearchStudyController | Legacy study search list | +| `/searchForm.html` | searchFormController | Search form (alternative URL pattern) | +| `/searchResult.html` | filenameController | Search results (alternative URL pattern) | +| `/searchStudy.html` | searchStudyController | Study search (alternative to `/search/studySearch.html`) | +| `/searchStudyList.html` | listSearchStudyController | Study search list | | `/study-query.html` | updateStudyQueryController | Study query form | ### Search Download/Export Pages @@ -171,7 +173,7 @@ The following pages from `treebase-servlet.xml` ARE documented in the v3 user st 1. **RSS Feeds** (`/feed.xml`, `/rss.xml`) - Consider adding to User Story 06 (Technical) as these are programmatic access points -2. **Legacy Search Pages** - May need documentation in User Story 01 if they are still active, or marked for deprecation +2. **Alternative Search URL Patterns** - These URLs (`/searchForm.html`, `/searchStudy.html`, etc.) may need to be documented in User Story 01 if they are actively used, or redirected to the documented URLs (`/search/studySearch.html`, etc.) for consistency 3. **Row Segment Operations** - Several row segment pages are not documented: - `/user/rowSegmentDataTable.html` From 6fb4786a4d3910321e7dc47186d7c733ec82295f Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 12 Jan 2026 22:56:04 +0000 Subject: [PATCH 5/8] Redo analysis with updated user-story-03 and user-story-06 Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com> --- doc/PAGE_CROSS_REFERENCE.md | 62 ++++++++++++++----------------------- 1 file changed, 23 insertions(+), 39 deletions(-) diff --git a/doc/PAGE_CROSS_REFERENCE.md b/doc/PAGE_CROSS_REFERENCE.md index 244c5aee9..327a19a4e 100644 --- a/doc/PAGE_CROSS_REFERENCE.md +++ b/doc/PAGE_CROSS_REFERENCE.md @@ -16,8 +16,8 @@ This document cross-references the URL mappings in `treebase-servlet.xml` agains **Summary:** - Total URL mappings in treebase-servlet.xml: 138 -- Pages accounted for in user stories: 99 -- Pages NOT in user stories: 40 +- Pages accounted for in user stories: 107 +- Pages NOT in user stories: 32 --- @@ -32,13 +32,6 @@ The following pages from `treebase-servlet.xml` are NOT mentioned in any "Pages | `/accessviolation.html` | filenameController | Access violation error page | | `/login.html` | filenameController | Login page (note: `/login.jsp` is documented instead) | -### RSS and Feed Pages - -| URL | Controller | Description | -|-----|------------|-------------| -| `/feed.xml` | rssFeedController | RSS feed (alternate URL) | -| `/rss.xml` | rssFeedController | RSS feed | - ### Alternative Search URL Patterns These are search-related URLs that use different URL patterns than those documented in User Story 01 (which documents `/search/studySearch.html`, etc.): @@ -72,21 +65,15 @@ These are search-related URLs that use different URL patterns than those documen | `/user/analyses.html` | summaryController | Study analyses (duplicate of analysisDisplay) | | `/user/authorForm.html` | authorFormController | Author edit form | | `/user/authorList.html` | authorFormController | Author list | -| `/user/deleteARowSegment.html` | deleteARowSegmentController | Delete row segment | -| `/user/directToPhyloWidget.html` | directToPhyloWidgetController | Direct PhyloWidget link (alternate) | +| `/user/directToPhyloWidget.html` | directToPhyloWidgetController | Direct PhyloWidget link (alternate to directMapToPhyloWidget) | | `/user/displaySubmissionMenu.html` | displaySubmissionMenuController | Submission menu display | | `/user/downloadANexusRCTFile.html` | downloadANexusRCTFileController | Download reconstructed NEXUS | | `/user/editorForm.html` | editorFormController | Editor edit form | -| `/user/exportRowSegmentData.html` | exportRowSegmentDataController | Export row segment data | -| `/user/exportRowSegmentTemplate.html` | exportRowSegmentTemplateController | Export row segment template | -| `/user/matrixRowSegmentForm.html` | matrixRowSegmentFormController | Matrix row segment form | | `/user/nexusFiles.html` | nexusFilesController | View NEXUS files | | `/user/readOnlyListTree.html` | readOnlyListTreeController | Read-only tree list | -| `/user/rowSegmentDataTable.html` | rowSegmentDataTableController | Row segment data table | | `/user/submissionMain.html` | filenameController | Submission main page | | `/user/treeParser.html` | treeParserController | Tree parser | | `/user/treeParserResult.html` | treeParserResultController | Tree parser results | -| `/user/uploadRowSegmentData.html` | uploadRowSegmentDataController | Upload row segment data | | `/user/viewXML.html` | filenameController | View XML output | ### Development/Test Pages @@ -126,19 +113,23 @@ The following pages from `treebase-servlet.xml` ARE documented in the v3 user st - `/admin/adminUpdatingUserInfo.html`, `/admin/adminDeletingUserStepOne.html` - `/admin/adminDeletingUserStepTwo.html`, `/admin/adminMergingUsers.html`, `/admin/userManagement.html` -### User Story 03: Submission (35 pages) +### User Story 03: Submission (43 pages) - `/user/submissionList.html`, `/user/studyForm.html`, `/user/summary.html` - `/user/citationForm.html`, `/user/authorSearchForm.html`, `/user/addAuthor.html` - `/user/uploadFile.html`, `/user/uploadFileSummary.html`, `/user/treeBlockList.html` - `/user/treeList.html`, `/user/directMapToPhyloWidget.html`, `/user/deleteATree.html` - `/user/deleteATreeBlock.html`, `/user/matrixList.html`, `/user/matrixRowList.html` -- `/user/matrixRowSegmentList.html`, `/user/viewAllRowSegmentData.html`, `/user/deleteAMatrix.html` -- `/user/taxaList.html`, `/user/editTaxonLabel.html`, `/user/editSetTaxonLabel.html` -- `/user/analysisList.html`, `/user/analysisDisplay.html`, `/user/analysisForm.html` -- `/user/analysisStepList.html`, `/user/analysisStepForm.html`, `/user/analyzedDataList.html` -- `/user/analyzedDataForm.html`, `/user/addAnalyzedData.html`, `/user/readyState.html` -- `/user/deleteStudy.html`, `/submitTutorial.html`, `/user/downloadATree.html` -- `/user/downloadATreeBlock.html`, `/user/downloadAMatrix.html`, `/user/downloadANexusFile.html` +- `/user/matrixRowSegmentList.html`, `/user/matrixRowSegmentForm.html` +- `/user/uploadRowSegmentData.html`, `/user/rowSegmentDataTable.html` +- `/user/viewAllRowSegmentData.html`, `/user/exportRowSegmentData.html` +- `/user/exportRowSegmentTemplate.html`, `/user/deleteARowSegment.html` +- `/user/deleteAMatrix.html`, `/user/taxaList.html`, `/user/editTaxonLabel.html` +- `/user/editSetTaxonLabel.html`, `/user/analysisList.html`, `/user/analysisDisplay.html` +- `/user/analysisForm.html`, `/user/analysisStepList.html`, `/user/analysisStepForm.html` +- `/user/analyzedDataList.html`, `/user/analyzedDataForm.html`, `/user/addAnalyzedData.html` +- `/user/readyState.html`, `/user/deleteStudy.html`, `/submitTutorial.html` +- `/user/downloadATree.html`, `/user/downloadATreeBlock.html` +- `/user/downloadAMatrix.html`, `/user/downloadANexusFile.html` ### User Story 04: Review (8 pages) - `/search/study/summary.html`, `/search/study/trees.html`, `/search/study/tree.html` @@ -154,11 +145,12 @@ The following pages from `treebase-servlet.xml` ARE documented in the v3 user st - `/admin/adminSelectPersons.html`, `/admin/personList.html`, `/admin/adminMergingPersons.html` - `/admin/messageToAdminAfterAction.html` -### User Story 06: Technical (12 pages) +### User Story 06: Technical (14 pages) - `/urlAPI.html`, `/technology.html`, `/about.html`, `/contact.html` - `/submitTutorial.html`, `/help.html`, `/sitemap.xml` - `/phylows/study/**`, `/phylows/tree/**`, `/phylows/matrix/**` - `/phylows/taxon/**`, `/phylows/classification/**`, `/top/**` +- `/rss.xml`, `/feed.xml` ### User Story 07: Governance (11 pages) - `/home.html`, `/about.html`, `/people.html`, `/partnership.html` @@ -171,27 +163,19 @@ The following pages from `treebase-servlet.xml` ARE documented in the v3 user st ### Pages to Consider Adding to User Stories -1. **RSS Feeds** (`/feed.xml`, `/rss.xml`) - Consider adding to User Story 06 (Technical) as these are programmatic access points - -2. **Alternative Search URL Patterns** - These URLs (`/searchForm.html`, `/searchStudy.html`, etc.) may need to be documented in User Story 01 if they are actively used, or redirected to the documented URLs (`/search/studySearch.html`, etc.) for consistency - -3. **Row Segment Operations** - Several row segment pages are not documented: - - `/user/rowSegmentDataTable.html` - - `/user/uploadRowSegmentData.html` - - `/user/exportRowSegmentData.html` - - `/user/deleteARowSegment.html` - - These should be added to User Story 03 (Submission) +1. **Alternative Search URL Patterns** - These URLs (`/searchForm.html`, `/searchStudy.html`, etc.) may need to be documented in User Story 01 if they are actively used, or redirected to the documented URLs (`/search/studySearch.html`, etc.) for consistency -4. **Tree Parser** (`/user/treeParser.html`, `/user/treeParserResult.html`) - Consider adding to User Story 03 +2. **Tree Parser** (`/user/treeParser.html`, `/user/treeParserResult.html`) - Consider adding to User Story 03 -5. **Download Pages** - Some download endpoints are missing: +3. **Download Pages** - Some download endpoints are missing: - `/search/downloadAStudy.html` - `/search/downloadATreeBlock.html` - `/search/downloadAnAnalysisStep.html` - `/search/downloadANexusRCTFile.html` - - These should be added to User Story 01 (Search) + - `/user/downloadANexusRCTFile.html` + - These should be added to User Story 01 (Search) or User Story 03 (Submission) -6. **JSON/API Endpoints** (`/json/submissionIsland.html`) - Consider adding to User Story 06 (Technical) +4. **JSON/API Endpoints** (`/json/submissionIsland.html`) - Consider adding to User Story 06 (Technical) --- From 05879c93b1721479cccd510de99084484c0b7603 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Tue, 13 Jan 2026 06:33:48 +0000 Subject: [PATCH 6/8] Add reachability analysis for undocumented pages Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com> --- doc/PAGE_CROSS_REFERENCE.md | 123 ++++++++++++++++++++++-------------- 1 file changed, 77 insertions(+), 46 deletions(-) diff --git a/doc/PAGE_CROSS_REFERENCE.md b/doc/PAGE_CROSS_REFERENCE.md index 327a19a4e..f5fd471d1 100644 --- a/doc/PAGE_CROSS_REFERENCE.md +++ b/doc/PAGE_CROSS_REFERENCE.md @@ -2,7 +2,7 @@ This document cross-references the URL mappings in `treebase-servlet.xml` against the pages documented in the v3 UI/UX user story markdown files (`doc/v3/*.md`). -**Analysis Date:** 2026-01-12 +**Analysis Date:** 2026-01-13 **Source Documents:** - `treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml` @@ -18,76 +18,105 @@ This document cross-references the URL mappings in `treebase-servlet.xml` agains - Total URL mappings in treebase-servlet.xml: 138 - Pages accounted for in user stories: 107 - Pages NOT in user stories: 32 + - Reachable from documented pages: 14 + - Unreachable (no links found): 18 --- ## Pages NOT in User Story Documentation -The following pages from `treebase-servlet.xml` are NOT mentioned in any "Pages to Account For" section of the v3 user story documents: +The following pages from `treebase-servlet.xml` are NOT mentioned in any "Pages to Account For" section of the v3 user story documents. + +**Reachability Analysis:** Pages marked as "(unreachable)" have no links found in JSP files, menu configuration, or controller redirects from any documented pages. ### Public/Utility Pages -| URL | Controller | Description | -|-----|------------|-------------| -| `/accessviolation.html` | filenameController | Access violation error page | -| `/login.html` | filenameController | Login page (note: `/login.jsp` is documented instead) | +| URL | Controller | Description | Reachability | +|-----|------------|-------------|--------------| +| `/accessviolation.html` | filenameController | Access violation error page | Reachable (controller redirects) | +| `/login.html` | filenameController | Login page (note: `/login.jsp` is documented instead) | (unreachable) | ### Alternative Search URL Patterns These are search-related URLs that use different URL patterns than those documented in User Story 01 (which documents `/search/studySearch.html`, etc.): -| URL | Controller | Description | -|-----|------------|-------------| -| `/search/` | studySearchController | Search root redirect | -| `/searchForm.html` | searchFormController | Search form (alternative URL pattern) | -| `/searchResult.html` | filenameController | Search results (alternative URL pattern) | -| `/searchStudy.html` | searchStudyController | Study search (alternative to `/search/studySearch.html`) | -| `/searchStudyList.html` | listSearchStudyController | Study search list | -| `/study-query.html` | updateStudyQueryController | Study query form | +| URL | Controller | Description | Reachability | +|-----|------------|-------------|--------------| +| `/search/` | studySearchController | Search root redirect | (unreachable) | +| `/searchForm.html` | searchFormController | Search form (alternative URL pattern) | (unreachable) | +| `/searchResult.html` | filenameController | Search results (alternative URL pattern) | (unreachable) | +| `/searchStudy.html` | searchStudyController | Study search (alternative to `/search/studySearch.html`) | Reachable (studyList.jsp) | +| `/searchStudyList.html` | listSearchStudyController | Study search list | (unreachable) | +| `/study-query.html` | updateStudyQueryController | Study query form | (unreachable) | ### Search Download/Export Pages -| URL | Controller | Description | -|-----|------------|-------------| -| `/search/downloadANexusRCTFile.html` | downloadANexusRCTFileController | Download reconstructed NEXUS file | -| `/search/downloadAStudy.html` | downloadAStudyController | Download entire study | -| `/search/downloadATreeBlock.html` | downloadATreeBlockController | Download tree block | -| `/search/downloadAnAnalysisStep.html` | downloadAnAnalysisStepController | Download analysis step data | -| `/search/matrixRowList.html` | listMatrixRowController | Matrix row list view | -| `/search/searchResultsAsRDF.rdf` | searchResultsAsRDFController | Search results as RDF | -| `/search/summary.html` | summaryController | Search summary page | -| `/search/taxonList.html` | listTaxaSearchController | Taxon list view | +| URL | Controller | Description | Reachability | +|-----|------------|-------------|--------------| +| `/search/downloadANexusRCTFile.html` | downloadANexusRCTFileController | Download reconstructed NEXUS file | (unreachable) | +| `/search/downloadAStudy.html` | downloadAStudyController | Download entire study | (unreachable) | +| `/search/downloadATreeBlock.html` | downloadATreeBlockController | Download tree block | Reachable (treeBlockList.jsp, treeBlocks.jsp) | +| `/search/downloadAnAnalysisStep.html` | downloadAnAnalysisStepController | Download analysis step data | Reachable (algorithm.jsp, analysis.jsp, analyses.jsp) | +| `/search/matrixRowList.html` | listMatrixRowController | Matrix row list view | Reachable (matrixList.jsp, viewAllRowSegmentData.jsp) | +| `/search/searchResultsAsRDF.rdf` | searchResultsAsRDFController | Search results as RDF | (unreachable) | +| `/search/summary.html` | summaryController | Search summary page | (unreachable) | +| `/search/taxonList.html` | listTaxaSearchController | Taxon list view | (unreachable) | ### User Submission Pages -| URL | Controller | Description | -|-----|------------|-------------| -| `/user/analyses.html` | summaryController | Study analyses (duplicate of analysisDisplay) | -| `/user/authorForm.html` | authorFormController | Author edit form | -| `/user/authorList.html` | authorFormController | Author list | -| `/user/directToPhyloWidget.html` | directToPhyloWidgetController | Direct PhyloWidget link (alternate to directMapToPhyloWidget) | -| `/user/displaySubmissionMenu.html` | displaySubmissionMenuController | Submission menu display | -| `/user/downloadANexusRCTFile.html` | downloadANexusRCTFileController | Download reconstructed NEXUS | -| `/user/editorForm.html` | editorFormController | Editor edit form | -| `/user/nexusFiles.html` | nexusFilesController | View NEXUS files | -| `/user/readOnlyListTree.html` | readOnlyListTreeController | Read-only tree list | -| `/user/submissionMain.html` | filenameController | Submission main page | -| `/user/treeParser.html` | treeParserController | Tree parser | -| `/user/treeParserResult.html` | treeParserResultController | Tree parser results | -| `/user/viewXML.html` | filenameController | View XML output | +| URL | Controller | Description | Reachability | +|-----|------------|-------------|--------------| +| `/user/analyses.html` | summaryController | Study analyses (duplicate of analysisDisplay) | Reachable (menu-config.xml) | +| `/user/authorForm.html` | authorFormController | Author edit form | Reachable (peopleList.jsp) | +| `/user/authorList.html` | authorFormController | Author list | (unreachable) | +| `/user/directToPhyloWidget.html` | directToPhyloWidgetController | Direct PhyloWidget link (alternate to directMapToPhyloWidget) | Reachable (analysisSection-Piece.jsp) | +| `/user/displaySubmissionMenu.html` | displaySubmissionMenuController | Submission menu display | (unreachable) | +| `/user/downloadANexusRCTFile.html` | downloadANexusRCTFileController | Download reconstructed NEXUS | Reachable (nexusFiles.jsp) | +| `/user/editorForm.html` | editorFormController | Editor edit form | Reachable (peopleList.jsp, citationForm-booksection.jsp) | +| `/user/nexusFiles.html` | nexusFilesController | View NEXUS files | Reachable (menu-config.xml) | +| `/user/readOnlyListTree.html` | readOnlyListTreeController | Read-only tree list | (unreachable) | +| `/user/submissionMain.html` | filenameController | Submission main page | (unreachable) | +| `/user/treeParser.html` | treeParserController | Tree parser | Reachable (testParser.jsp) | +| `/user/treeParserResult.html` | treeParserResultController | Tree parser results | Reachable (treeList.jsp) | +| `/user/viewXML.html` | filenameController | View XML output | Reachable (treeParserResult.jsp) | ### Development/Test Pages -| URL | Controller | Description | -|-----|------------|-------------| -| `/test/testParser.html` | treeParserController | Test parser (development) | +| URL | Controller | Description | Reachability | +|-----|------------|-------------|--------------| +| `/test/testParser.html` | treeParserController | Test parser (development) | (unreachable) | ### JSON/API Pages -| URL | Controller | Description | -|-----|------------|-------------| -| `/json/submissionIsland.html` | submissionToJsonController | Submission JSON data | -| `/appletInteraction.html` | appletInteractionController | Applet interaction handler | +| URL | Controller | Description | Reachability | +|-----|------------|-------------|--------------| +| `/json/submissionIsland.html` | submissionToJsonController | Submission JSON data | (unreachable) | +| `/appletInteraction.html` | appletInteractionController | Applet interaction handler | (unreachable) | + +--- + +## Summary of Unreachable Pages + +The following 18 pages have no links from documented pages and may be candidates for deprecation or need explicit documentation: + +1. `/login.html` - Alternative to documented `/login.jsp` +2. `/search/` - Search root +3. `/searchForm.html` - Alternative search form +4. `/searchResult.html` - Alternative search results +5. `/searchStudyList.html` - Study search list +6. `/study-query.html` - Study query form +7. `/search/downloadANexusRCTFile.html` - Download reconstructed NEXUS (search context) +8. `/search/downloadAStudy.html` - Download entire study +9. `/search/searchResultsAsRDF.rdf` - Search results as RDF +10. `/search/summary.html` - Search summary +11. `/search/taxonList.html` - Taxon list view +12. `/user/authorList.html` - Author list +13. `/user/displaySubmissionMenu.html` - Submission menu display +14. `/user/readOnlyListTree.html` - Read-only tree list +15. `/user/submissionMain.html` - Submission main page +16. `/test/testParser.html` - Development test page +17. `/json/submissionIsland.html` - JSON submission data +18. `/appletInteraction.html` - Applet interaction handler --- @@ -177,6 +206,8 @@ The following pages from `treebase-servlet.xml` ARE documented in the v3 user st 4. **JSON/API Endpoints** (`/json/submissionIsland.html`) - Consider adding to User Story 06 (Technical) +5. **Unreachable Pages** - The 18 unreachable pages may be candidates for deprecation or may need their links restored if they provide needed functionality + --- ## Notes From 06efb5c4e5cd3d64fe4f85be060a1424c1892a00 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Tue, 13 Jan 2026 08:28:57 +0000 Subject: [PATCH 7/8] Update analysis with updated user-story-01-search.md Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com> --- doc/PAGE_CROSS_REFERENCE.md | 70 ++++++++++++++++--------------------- 1 file changed, 31 insertions(+), 39 deletions(-) diff --git a/doc/PAGE_CROSS_REFERENCE.md b/doc/PAGE_CROSS_REFERENCE.md index f5fd471d1..69a10030f 100644 --- a/doc/PAGE_CROSS_REFERENCE.md +++ b/doc/PAGE_CROSS_REFERENCE.md @@ -16,10 +16,10 @@ This document cross-references the URL mappings in `treebase-servlet.xml` agains **Summary:** - Total URL mappings in treebase-servlet.xml: 138 -- Pages accounted for in user stories: 107 -- Pages NOT in user stories: 32 - - Reachable from documented pages: 14 - - Unreachable (no links found): 18 +- Pages accounted for in user stories: 109 +- Pages NOT in user stories: 29 + - Reachable from documented pages: 13 + - Unreachable (no links found): 16 --- @@ -42,7 +42,7 @@ These are search-related URLs that use different URL patterns than those documen | URL | Controller | Description | Reachability | |-----|------------|-------------|--------------| -| `/search/` | studySearchController | Search root redirect | (unreachable) | +| `/search/` | studySearchController | Search root redirect | Reachable (redirect) | | `/searchForm.html` | searchFormController | Search form (alternative URL pattern) | (unreachable) | | `/searchResult.html` | filenameController | Search results (alternative URL pattern) | (unreachable) | | `/searchStudy.html` | searchStudyController | Study search (alternative to `/search/studySearch.html`) | Reachable (studyList.jsp) | @@ -53,11 +53,7 @@ These are search-related URLs that use different URL patterns than those documen | URL | Controller | Description | Reachability | |-----|------------|-------------|--------------| -| `/search/downloadANexusRCTFile.html` | downloadANexusRCTFileController | Download reconstructed NEXUS file | (unreachable) | -| `/search/downloadAStudy.html` | downloadAStudyController | Download entire study | (unreachable) | -| `/search/downloadATreeBlock.html` | downloadATreeBlockController | Download tree block | Reachable (treeBlockList.jsp, treeBlocks.jsp) | -| `/search/downloadAnAnalysisStep.html` | downloadAnAnalysisStepController | Download analysis step data | Reachable (algorithm.jsp, analysis.jsp, analyses.jsp) | -| `/search/matrixRowList.html` | listMatrixRowController | Matrix row list view | Reachable (matrixList.jsp, viewAllRowSegmentData.jsp) | +| `/search/matrixRowList.html` | listMatrixRowController | Matrix row list view | (unreachable) | | `/search/searchResultsAsRDF.rdf` | searchResultsAsRDFController | Search results as RDF | (unreachable) | | `/search/summary.html` | summaryController | Search summary page | (unreachable) | | `/search/taxonList.html` | listTaxaSearchController | Taxon list view | (unreachable) | @@ -75,7 +71,7 @@ These are search-related URLs that use different URL patterns than those documen | `/user/editorForm.html` | editorFormController | Editor edit form | Reachable (peopleList.jsp, citationForm-booksection.jsp) | | `/user/nexusFiles.html` | nexusFilesController | View NEXUS files | Reachable (menu-config.xml) | | `/user/readOnlyListTree.html` | readOnlyListTreeController | Read-only tree list | (unreachable) | -| `/user/submissionMain.html` | filenameController | Submission main page | (unreachable) | +| `/user/submissionMain.html` | filenameController | Submission main page | Reachable (template) | | `/user/treeParser.html` | treeParserController | Tree parser | Reachable (testParser.jsp) | | `/user/treeParserResult.html` | treeParserResultController | Tree parser results | Reachable (treeList.jsp) | | `/user/viewXML.html` | filenameController | View XML output | Reachable (treeParserResult.jsp) | @@ -92,31 +88,30 @@ These are search-related URLs that use different URL patterns than those documen |-----|------------|-------------|--------------| | `/json/submissionIsland.html` | submissionToJsonController | Submission JSON data | (unreachable) | | `/appletInteraction.html` | appletInteractionController | Applet interaction handler | (unreachable) | +| `/top/**` | (OAI-PMH) | OAI-PMH interface (note: `/top/oai` documented but wildcard not) | (unreachable) | --- ## Summary of Unreachable Pages -The following 18 pages have no links from documented pages and may be candidates for deprecation or need explicit documentation: +The following 16 pages have no links from documented pages and may be candidates for deprecation or need explicit documentation: 1. `/login.html` - Alternative to documented `/login.jsp` -2. `/search/` - Search root -3. `/searchForm.html` - Alternative search form -4. `/searchResult.html` - Alternative search results -5. `/searchStudyList.html` - Study search list -6. `/study-query.html` - Study query form -7. `/search/downloadANexusRCTFile.html` - Download reconstructed NEXUS (search context) -8. `/search/downloadAStudy.html` - Download entire study -9. `/search/searchResultsAsRDF.rdf` - Search results as RDF -10. `/search/summary.html` - Search summary -11. `/search/taxonList.html` - Taxon list view -12. `/user/authorList.html` - Author list -13. `/user/displaySubmissionMenu.html` - Submission menu display -14. `/user/readOnlyListTree.html` - Read-only tree list -15. `/user/submissionMain.html` - Submission main page -16. `/test/testParser.html` - Development test page -17. `/json/submissionIsland.html` - JSON submission data -18. `/appletInteraction.html` - Applet interaction handler +2. `/searchForm.html` - Alternative search form +3. `/searchResult.html` - Alternative search results +4. `/searchStudyList.html` - Study search list +5. `/study-query.html` - Study query form +6. `/search/matrixRowList.html` - Matrix row list view +7. `/search/searchResultsAsRDF.rdf` - Search results as RDF +8. `/search/summary.html` - Search summary +9. `/search/taxonList.html` - Taxon list view +10. `/user/authorList.html` - Author list +11. `/user/displaySubmissionMenu.html` - Submission menu display +12. `/user/readOnlyListTree.html` - Read-only tree list +13. `/test/testParser.html` - Development test page +14. `/json/submissionIsland.html` - JSON submission data +15. `/appletInteraction.html` - Applet interaction handler +16. `/top/**` - OAI-PMH wildcard pattern --- @@ -124,7 +119,7 @@ The following 18 pages have no links from documented pages and may be candidates The following pages from `treebase-servlet.xml` ARE documented in the v3 user story "Pages to Account For" sections: -### User Story 01: Search (25 pages) +### User Story 01: Search (29 pages) - `/search/studySearch.html`, `/search/matrixSearch.html`, `/search/treeSearch.html` - `/search/taxonSearch.html`, `/search/treeTopSearch.html`, `/search/classificationSearch.html` - `/search/study/summary.html`, `/search/study/matrices.html`, `/search/study/trees.html` @@ -132,8 +127,9 @@ The following pages from `treebase-servlet.xml` ARE documented in the v3 user st - `/search/study/matrix.html`, `/search/study/tree.html`, `/search/study/treeBlock.html` - `/search/study/treeBlocks.html`, `/search/study/rowSegments.html`, `/search/study/rowSegmentsTSV.html` - `/search/study/anyObjectAsRDF.rdf`, `/search/downloadATree.html`, `/search/downloadAMatrix.html` -- `/search/downloadANexusFile.html`, `/phylows/study/**`, `/phylows/matrix/**` -- `/phylows/tree/**`, `/phylows/taxon/**` +- `/search/downloadANexusFile.html`, `/search/downloadAStudy.html`, `/search/downloadATreeBlock.html` +- `/search/downloadAnAnalysisStep.html`, `/search/downloadANexusRCTFile.html` +- `/phylows/study/**`, `/phylows/matrix/**`, `/phylows/tree/**`, `/phylows/taxon/**` ### User Story 02: Account (17 pages) - `/register.html`, `/passwordForm.html`, `/resetPassword.html` @@ -178,7 +174,7 @@ The following pages from `treebase-servlet.xml` ARE documented in the v3 user st - `/urlAPI.html`, `/technology.html`, `/about.html`, `/contact.html` - `/submitTutorial.html`, `/help.html`, `/sitemap.xml` - `/phylows/study/**`, `/phylows/tree/**`, `/phylows/matrix/**` -- `/phylows/taxon/**`, `/phylows/classification/**`, `/top/**` +- `/phylows/taxon/**`, `/phylows/classification/**` - `/rss.xml`, `/feed.xml` ### User Story 07: Governance (11 pages) @@ -197,16 +193,12 @@ The following pages from `treebase-servlet.xml` ARE documented in the v3 user st 2. **Tree Parser** (`/user/treeParser.html`, `/user/treeParserResult.html`) - Consider adding to User Story 03 3. **Download Pages** - Some download endpoints are missing: - - `/search/downloadAStudy.html` - - `/search/downloadATreeBlock.html` - - `/search/downloadAnAnalysisStep.html` - - `/search/downloadANexusRCTFile.html` - `/user/downloadANexusRCTFile.html` - - These should be added to User Story 01 (Search) or User Story 03 (Submission) + - This should be added to User Story 03 (Submission) 4. **JSON/API Endpoints** (`/json/submissionIsland.html`) - Consider adding to User Story 06 (Technical) -5. **Unreachable Pages** - The 18 unreachable pages may be candidates for deprecation or may need their links restored if they provide needed functionality +5. **Unreachable Pages** - The 16 unreachable pages may be candidates for deprecation or may need their links restored if they provide needed functionality --- From 09079caf1b1611d825332eabffdce1ca7762b70f Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Tue, 13 Jan 2026 13:33:44 +0000 Subject: [PATCH 8/8] Update analysis with updated user stories Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com> --- doc/PAGE_CROSS_REFERENCE.md | 50 ++++++++++++++++--------------------- 1 file changed, 22 insertions(+), 28 deletions(-) diff --git a/doc/PAGE_CROSS_REFERENCE.md b/doc/PAGE_CROSS_REFERENCE.md index 69a10030f..2c333e32b 100644 --- a/doc/PAGE_CROSS_REFERENCE.md +++ b/doc/PAGE_CROSS_REFERENCE.md @@ -16,10 +16,10 @@ This document cross-references the URL mappings in `treebase-servlet.xml` agains **Summary:** - Total URL mappings in treebase-servlet.xml: 138 -- Pages accounted for in user stories: 109 -- Pages NOT in user stories: 29 - - Reachable from documented pages: 13 - - Unreachable (no links found): 16 +- Pages accounted for in user stories: 111 +- Pages NOT in user stories: 27 + - Reachable from documented pages: 15 + - Unreachable (no links found): 12 --- @@ -53,9 +53,8 @@ These are search-related URLs that use different URL patterns than those documen | URL | Controller | Description | Reachability | |-----|------------|-------------|--------------| -| `/search/matrixRowList.html` | listMatrixRowController | Matrix row list view | (unreachable) | -| `/search/searchResultsAsRDF.rdf` | searchResultsAsRDFController | Search results as RDF | (unreachable) | -| `/search/summary.html` | summaryController | Search summary page | (unreachable) | +| `/search/matrixRowList.html` | listMatrixRowController | Matrix row list view | Reachable (viewAllRowSegmentData.jsp) | +| `/search/summary.html` | summaryController | Search summary page | Reachable (changeStudyStatus.jsp) | | `/search/taxonList.html` | listTaxaSearchController | Taxon list view | (unreachable) | ### User Submission Pages @@ -71,10 +70,10 @@ These are search-related URLs that use different URL patterns than those documen | `/user/editorForm.html` | editorFormController | Editor edit form | Reachable (peopleList.jsp, citationForm-booksection.jsp) | | `/user/nexusFiles.html` | nexusFilesController | View NEXUS files | Reachable (menu-config.xml) | | `/user/readOnlyListTree.html` | readOnlyListTreeController | Read-only tree list | (unreachable) | -| `/user/submissionMain.html` | filenameController | Submission main page | Reachable (template) | +| `/user/submissionMain.html` | filenameController | Submission main page | (unreachable) | | `/user/treeParser.html` | treeParserController | Tree parser | Reachable (testParser.jsp) | | `/user/treeParserResult.html` | treeParserResultController | Tree parser results | Reachable (treeList.jsp) | -| `/user/viewXML.html` | filenameController | View XML output | Reachable (treeParserResult.jsp) | +| `/user/viewXML.html` | filenameController | View XML output | Reachable (testParserResult.jsp) | ### Development/Test Pages @@ -86,32 +85,27 @@ These are search-related URLs that use different URL patterns than those documen | URL | Controller | Description | Reachability | |-----|------------|-------------|--------------| -| `/json/submissionIsland.html` | submissionToJsonController | Submission JSON data | (unreachable) | | `/appletInteraction.html` | appletInteractionController | Applet interaction handler | (unreachable) | -| `/top/**` | (OAI-PMH) | OAI-PMH interface (note: `/top/oai` documented but wildcard not) | (unreachable) | +| `/top/**` | (OAI-PMH) | OAI-PMH interface (note: `/top/oai` documented but wildcard not) | Reachable (OAI-PMH endpoint) | --- ## Summary of Unreachable Pages -The following 16 pages have no links from documented pages and may be candidates for deprecation or need explicit documentation: +The following 12 pages have no links from documented pages and may be candidates for deprecation or need explicit documentation: 1. `/login.html` - Alternative to documented `/login.jsp` 2. `/searchForm.html` - Alternative search form 3. `/searchResult.html` - Alternative search results 4. `/searchStudyList.html` - Study search list 5. `/study-query.html` - Study query form -6. `/search/matrixRowList.html` - Matrix row list view -7. `/search/searchResultsAsRDF.rdf` - Search results as RDF -8. `/search/summary.html` - Search summary -9. `/search/taxonList.html` - Taxon list view -10. `/user/authorList.html` - Author list -11. `/user/displaySubmissionMenu.html` - Submission menu display -12. `/user/readOnlyListTree.html` - Read-only tree list -13. `/test/testParser.html` - Development test page -14. `/json/submissionIsland.html` - JSON submission data -15. `/appletInteraction.html` - Applet interaction handler -16. `/top/**` - OAI-PMH wildcard pattern +6. `/search/taxonList.html` - Taxon list view +7. `/user/authorList.html` - Author list +8. `/user/displaySubmissionMenu.html` - Submission menu display +9. `/user/readOnlyListTree.html` - Read-only tree list +10. `/user/submissionMain.html` - Submission main page +11. `/test/testParser.html` - Development test page +12. `/appletInteraction.html` - Applet interaction handler --- @@ -138,7 +132,7 @@ The following pages from `treebase-servlet.xml` ARE documented in the v3 user st - `/admin/adminUpdatingUserInfo.html`, `/admin/adminDeletingUserStepOne.html` - `/admin/adminDeletingUserStepTwo.html`, `/admin/adminMergingUsers.html`, `/admin/userManagement.html` -### User Story 03: Submission (43 pages) +### User Story 03: Submission (44 pages) - `/user/submissionList.html`, `/user/studyForm.html`, `/user/summary.html` - `/user/citationForm.html`, `/user/authorSearchForm.html`, `/user/addAuthor.html` - `/user/uploadFile.html`, `/user/uploadFileSummary.html`, `/user/treeBlockList.html` @@ -155,6 +149,7 @@ The following pages from `treebase-servlet.xml` ARE documented in the v3 user st - `/user/readyState.html`, `/user/deleteStudy.html`, `/submitTutorial.html` - `/user/downloadATree.html`, `/user/downloadATreeBlock.html` - `/user/downloadAMatrix.html`, `/user/downloadANexusFile.html` +- `/json/submissionIsland.html` ### User Story 04: Review (8 pages) - `/search/study/summary.html`, `/search/study/trees.html`, `/search/study/tree.html` @@ -170,12 +165,13 @@ The following pages from `treebase-servlet.xml` ARE documented in the v3 user st - `/admin/adminSelectPersons.html`, `/admin/personList.html`, `/admin/adminMergingPersons.html` - `/admin/messageToAdminAfterAction.html` -### User Story 06: Technical (14 pages) +### User Story 06: Technical (16 pages) - `/urlAPI.html`, `/technology.html`, `/about.html`, `/contact.html` - `/submitTutorial.html`, `/help.html`, `/sitemap.xml` - `/phylows/study/**`, `/phylows/tree/**`, `/phylows/matrix/**` - `/phylows/taxon/**`, `/phylows/classification/**` - `/rss.xml`, `/feed.xml` +- `/search/searchResultsAsRDF.rdf`, `/top/oai` ### User Story 07: Governance (11 pages) - `/home.html`, `/about.html`, `/people.html`, `/partnership.html` @@ -196,9 +192,7 @@ The following pages from `treebase-servlet.xml` ARE documented in the v3 user st - `/user/downloadANexusRCTFile.html` - This should be added to User Story 03 (Submission) -4. **JSON/API Endpoints** (`/json/submissionIsland.html`) - Consider adding to User Story 06 (Technical) - -5. **Unreachable Pages** - The 16 unreachable pages may be candidates for deprecation or may need their links restored if they provide needed functionality +4. **Unreachable Pages** - The 12 unreachable pages may be candidates for deprecation or may need their links restored if they provide needed functionality ---