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Add article type filtering for PubMed format generation #1163

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Copilot Oct 2, 2025
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Add PubMed article type filtering for format generation
Copilot Oct 2, 2025
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17 changes: 17 additions & 0 deletions article/choices.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,3 +15,20 @@
(DATA_STATUS_UNDEF, _("undefined")),
(DATA_STATUS_INVALID, _("invalid")),
)

# Article types eligible for PubMed format generation
# According to https://www.ncbi.nlm.nih.gov/books/NBK3828/#publisherhelp.What_types_of_articles_are
PUBMED_ARTICLE_TYPES = [
"research-article",
"review-article",
"article-commentary",
"brief-report",
"case-report",
"letter",
"rapid-communication",
"reply",
"editorial",
"correction",
"retraction",
"addendum",
]
18 changes: 10 additions & 8 deletions article/models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1200,14 +1200,16 @@ def generate_formats(cls, user, article):
)
except CrossRefConfiguration.DoesNotExist:
break
cls.generate(
user,
article,
"pubmed",
article.sps_pkg_name + ".xml",
pubmed.pipeline_pubmed,
indexed_check=False,
)
# Only generate PubMed format for eligible article types
if article.article_type in choices.PUBMED_ARTICLE_TYPES:
cls.generate(
user,
article,
"pubmed",
article.sps_pkg_name + ".xml",
pubmed.pipeline_pubmed,
indexed_check=False,
)
cls.generate(
user,
article,
Expand Down
95 changes: 94 additions & 1 deletion article/tests.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,8 @@
from django.utils.timezone import make_aware
from freezegun import freeze_time

from article.models import Article
from article import choices
from article.models import Article, ArticleFormat
from article.tasks import (
get_researcher_identifier_unnormalized,
migrate_path_xml_pid_provider_to_pid_provider,
Expand Down Expand Up @@ -120,3 +121,95 @@ def test_normalize_stored_email(self):
ResearcherIdentifier.objects.filter(identifier=email).exists(),
f"E-mail '{email}' unnormalized",
)


class PubMedArticleTypeFilteringTest(TestCase):
"""Test that PubMed format generation only happens for eligible article types"""

def setUp(self):
self.user = User.objects.create_user(username="testuser", password="testpass")

@patch("article.models.ArticleFormat.generate")
def test_pubmed_format_generated_for_research_article(self, mock_generate):
"""Test that PubMed format is generated for research-article type"""
article = Article.objects.create(
pid_v3="test-pid-1",
article_type="research-article",
sps_pkg_name="test-pkg-1",
)

ArticleFormat.generate_formats(self.user, article)

# Check that generate was called for pubmed
pubmed_calls = [
call for call in mock_generate.call_args_list if call[0][2] == "pubmed"
]
self.assertEqual(len(pubmed_calls), 1, "PubMed format should be generated")

@patch("article.models.ArticleFormat.generate")
def test_pubmed_format_not_generated_for_ineligible_type(self, mock_generate):
"""Test that PubMed format is NOT generated for ineligible article types"""
article = Article.objects.create(
pid_v3="test-pid-2",
article_type="book-review", # Not in PUBMED_ARTICLE_TYPES
sps_pkg_name="test-pkg-2",
)

ArticleFormat.generate_formats(self.user, article)

# Check that generate was NOT called for pubmed
pubmed_calls = [
call for call in mock_generate.call_args_list if call[0][2] == "pubmed"
]
self.assertEqual(
len(pubmed_calls), 0, "PubMed format should NOT be generated"
)

@patch("article.models.ArticleFormat.generate")
def test_pmc_format_always_generated(self, mock_generate):
"""Test that PMC format is always generated regardless of article type"""
# Test with ineligible type for PubMed
article = Article.objects.create(
pid_v3="test-pid-3",
article_type="book-review",
sps_pkg_name="test-pkg-3",
)

ArticleFormat.generate_formats(self.user, article)

# Check that generate was called for pmc
pmc_calls = [call for call in mock_generate.call_args_list if call[0][2] == "pmc"]
self.assertEqual(len(pmc_calls), 1, "PMC format should always be generated")

@patch("article.models.ArticleFormat.generate")
def test_pubmed_format_for_various_eligible_types(self, mock_generate):
"""Test that PubMed format is generated for various eligible article types"""
eligible_types = [
"research-article",
"review-article",
"case-report",
"editorial",
"letter",
]

for i, article_type in enumerate(eligible_types):
with self.subTest(article_type=article_type):
mock_generate.reset_mock()
article = Article.objects.create(
pid_v3=f"test-pid-eligible-{i}",
article_type=article_type,
sps_pkg_name=f"test-pkg-eligible-{i}",
)

ArticleFormat.generate_formats(self.user, article)

pubmed_calls = [
call
for call in mock_generate.call_args_list
if call[0][2] == "pubmed"
]
self.assertEqual(
len(pubmed_calls),
1,
f"PubMed format should be generated for {article_type}",
)