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articles: fixes import with existing doi
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Signed-off-by: Pamfilos Fokianos <[email protected]>
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@pamfilos
pamfilos committed Dec 10, 2024
1 parent 808091e commit ed80b8e
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Showing 2 changed files with 192 additions and 6 deletions.
175 changes: 175 additions & 0 deletions scoap3/articles/tests/test_article_views.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@

from scoap3.articles.models import Article
from scoap3.articles.util import parse_string_to_date_object
from scoap3.authors.models import Author
from scoap3.misc.models import PublicationInfo

pytestmark = pytest.mark.django_db
Expand Down Expand Up @@ -447,6 +448,180 @@ def test_create_update_from_workflow_without_journal_year(
)
assert article_with_updated_publication_date.volume_year == "2024"

def test_articles_from_workflows_duplicates(self, client, user):
client.force_login(user)
data = {
"license": [
{
"url": "http://creativecommons.org/licenses/by/4.0/",
"license": "CC-BY-4.0",
}
],
"copyright": [{"statement": "The Author"}],
"_oai": {
"updated": "2023-10-31T08:21:45Z",
"id": "oai:repo.scoap3.org:81204",
"sets": ["APPB"],
},
"dois": [{"value": "10.5506/APhysPolB.54.10-A3"}],
"_files": [
{
"checksum": "md5:2ff0ee8af466b72271926bcfed748017",
"filetype": "pdf",
"bucket": "e8c24dab-4bf6-403d-848a-fdafe0b62042",
"version_id": "9bdb249d-4805-4faa-b784-41b8a599ca74",
"key": "10.5506/APhysPolB.54.10-A3.pdf",
"size": 505407,
},
{
"checksum": "md5:b215d3b2e0697ac47c98c90f8c5a51f7",
"filetype": "pdfa",
"bucket": "e8c24dab-4bf6-403d-848a-fdafe0b62042",
"version_id": "69e24af7-3785-472b-80cc-948ff155e406",
"key": "10.5506/APhysPolB.54.10-A3.pdfa",
"size": 977378,
},
],
"record_creation_date": "2023-10-31T08:20:22.109303",
"authors": [
{
"affiliations": [
{
"country": "Colombia",
"value": "Universidad Nacional de Colombia, Bogot\u00e1, Colombia",
}
],
"full_name": "De Sanctis, M.",
}
],
"titles": [
{
"title": "The Effective QCD Running Coupling Constant and a Dirac Model for the Charmonium Spectrum"
}
],
"arxiv_eprints": [{"categories": ["hep-ph"], "value": "2310.16258"}],
"publication_info": [
{
"page_end": "13",
"journal_title": "Acta Physica Polonica B",
"material": "article",
"journal_volume": "54",
"year": 2023,
"page_start": "A3.1",
"journal_issue": "10",
}
],
"$schema": "http://repo.scoap3.org/schemas/hep.json",
"abstracts": [
{
"value": 'The QCD <span class="it">effective charge</span> extracted from the experimental data is used to construct the vector interaction of a Dirac relativistic model for the charmonium spectrum. The process required to fit the spectrum is discussed and the relationship with a previous study of the vector interaction is analyzed.' # noqa: E501
}
],
"imprints": [
{"date": "2023-10-31", "publisher": "Jagiellonian University"}
],
"acquisition_source": {
"date": "2023-10-31T08:20:22.109321",
"source": "Jagiellonian University",
"method": "scroap3_push",
},
}
response = client.post(
reverse("api:article-workflow-import-list"),
data,
content_type="application/json",
)
assert response.status_code == status.HTTP_200_OK

response2 = client.post(
reverse("api:article-workflow-import-list"),
data,
content_type="application/json",
)
assert response2.status_code == status.HTTP_200_OK

article_id = response.data["id"]
article = Article.objects.get(id=article_id)
assert (
article.title
== "The Effective QCD Running Coupling Constant and a Dirac Model for the Charmonium Spectrum"
)

data2 = data.copy()
data["titles"][0]["title"] = "New title"
data["dois"].append({"value": "10.5506/APhysPolB.54.10-A5"})
data["authors"] = [
{
"affiliations": [
{
"country": "Colombia",
"value": "Universidad Nacional de Colombia, Bogot\u00e1, Colombia",
}
],
"full_name": "De Sanctis, M.",
},
{
"affiliations": [
{
"country": "Brazil",
"value": "Universidad Nacional de Brazil, Sao\u00e1, Brazil",
}
],
"full_name": "Authorius, M.",
},
]
response = client.post(
reverse("api:article-workflow-import-list"),
data,
content_type="application/json",
)
assert response.status_code == status.HTTP_200_OK

all_authors = Author.objects.all()
assert len(all_authors) == 2

data2["authors"] = [
{
"affiliations": [
{
"country": "Colombia",
"value": "Universidad Nacional de Colombia, Bogot\u00e1, Colombia",
}
],
"full_name": "De Sanccctis, M.",
},
{
"affiliations": [
{
"country": "Brazil",
"value": "Universidad Nacional de Brazil, Sao\u00e1, Brazil",
}
],
"full_name": "Authorius, M.",
},
]
response = client.post(
reverse("api:article-workflow-import-list"),
data2,
content_type="application/json",
)
assert response.status_code == status.HTTP_200_OK

all_authors = Author.objects.all()
assert len(all_authors) == 2

article_id = response.data["id"]
article = Article.objects.get(id=article_id)
expected_dois = [
doi.identifier_value
for doi in article.article_identifiers.filter(identifier_type="DOI").all()
]

assert article.title == "New title"
assert len(expected_dois) == 2
assert "10.5506/APhysPolB.54.10-A5" in expected_dois
assert "10.5506/APhysPolB.54.10-A3" in expected_dois


class TestArticleIdentifierViewSet:
def test_get_article_identifier(self, client):
Expand Down
23 changes: 17 additions & 6 deletions scoap3/tasks.py
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Original file line number Diff line number Diff line change
Expand Up @@ -82,12 +82,11 @@ def _create_licenses(data):
return licenses


def _create_article(data, licenses):
def _create_article(data):
article_data = {
"title": data["titles"][0].get("title"),
"subtitle": data["titles"][0].get("subtitle", ""),
}

try:
article_data["abstract"] = data["abstracts"][0].get("value", "")
except (KeyError, IndexError):
Expand Down Expand Up @@ -133,11 +132,16 @@ def _create_article(data, licenses):
if publication_date:
article_data["publication_date"] = publication_date
article.__dict__.update(**article_data)
if len(data.get("authors", [])) > 0:
article.authors.all().delete()

# else create new
else:
article_data["publication_date"] = publication_date
article = Article.objects.create(**article_data)
article._created_at = data.get("_created") or data.get("record_creation_date")

licenses = _create_licenses(data["license"])
article.related_licenses.set(licenses)
article.save()
return article
Expand Down Expand Up @@ -374,9 +378,17 @@ def _create_affiliation(data, authors):
return affiliations


def get_articles_by_doi(dois):
articles = Article.objects.filter(
article_identifiers__identifier_type="DOI",
article_identifiers__identifier_value__in=dois,
).distinct()

return articles


def import_to_scoap3(data, migrate_files):
licenses = _create_licenses(data["license"])
article = _create_article(data, licenses)
article = _create_article(data)
if migrate_files:
_create_article_file(data, article)
_create_article_identifier(data, article)
Expand All @@ -393,8 +405,7 @@ def import_to_scoap3(data, migrate_files):


def update_affiliations(data):
licenses = _create_licenses(data["license"])
article = _create_article(data, licenses)
article = _create_article(data)
authors = _create_author(data, article)
_create_affiliation(data, authors)

Expand Down

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