def test_fetch_metadata_from_dois_no_paper(self, monkeypatch):
"""
If no paper created, expect None
"""
monkeypatch.setattr(Paper, 'create_by_doi', lambda x: None)
monkeypatch.setattr(CrossRef, 'fetch_batch', lambda x: [None])
o = OrcidPaperSource()
papers = list(o.fetch_metadata_from_dois('spam', 'ham', ['any_doi']))
assert len(papers) == 1
assert papers[0] is None
def fetch_crossref_profile(request, django_db_setup, django_db_blocker, get_researcher_by_name):
with django_db_blocker.unblock():
call_command('loaddata', 'test_dump.json')
self = request.cls
self.i = Institution.objects.get(name='ENS')
self.d = Department.objects.get(name='Chemistry dept')
self.r2 = get_researcher_by_name('Ludovic', 'Jullien')
self.r3 = get_researcher_by_name('Antoine', 'Amarilli')
cr_api = OrcidPaperSource()
cr_api.fetch_and_save(request.cls.r3)
def fetch_crossref_profile(request, django_db_setup, django_db_blocker):
with django_db_blocker.unblock():
call_command('loaddata', 'test_dump.json')
self = request.cls
self.i = Institution.objects.get(name='ENS')
self.d = Department.objects.get(name='Chemistry dept')
self.r2 = get_researcher_by_name('Ludovic', 'Jullien')
self.r3 = get_researcher_by_name('Antoine', 'Amarilli')
cr_api = OrcidPaperSource()
cr_api.fetch_and_save(request.cls.r3)
def test_enhance_paper_orcid_oai_exists(self, researcher_lesot):
"""
If source exists, nothing must happen
"""
doi = '10.1016/j.ijar.2017.06.011'
p = Paper.create_by_doi(doi)
o = OrcidPaperSource()
ref_name = (researcher_lesot.name.first, researcher_lesot.name.last)
p = o._enhance_paper(p, ref_name, researcher_lesot.orcid)
# Lesot is now a researcher of the paper
assert p.authors_list[1]['researcher_id'] == researcher_lesot.pk
# There must be a second OaiRecord
p.cache_oairecords() # Cache is not up to date
assert len(p.oairecords) == 2
def test_unmerge_orcid_nones(self):
# First, fetch a few DOIs
dois = [
"10.1075/aicr.90.09ngo",
"10.1075/aicr.90.04wad",
]
for doi in dois:
Paper.create_by_doi(doi)
# Then, fetch an ORCID profile with a buggy version of the ORCID interface, which incorrectly merges papers together
with patch.object(OrcidPaperSource,
'_oai_id_for_doi') as mock_identifier:
mock_identifier.return_value = "https://pub.orcid.org/v2.1/0000-0002-1909-134X/work/None"
profile = OrcidProfileStub('0000-0002-1909-134X',
instance='orcid.org')
trung = Researcher.get_or_create_by_orcid('0000-0002-1909-134X',
profile=profile)
OrcidPaperSource().fetch_and_save(trung, profile=profile)
# The two papers are incorrectly merged!
papers = [Paper.get_by_doi(doi) for doi in dois]
self.assertEqual(papers[0], papers[1])
# We unmerge them
unmerge_orcid_nones()
# The two papers are now distinct
papers = [Paper.get_by_doi(doi) for doi in dois]
self.assertTrue(papers[0] != papers[1])
def test_fetch_metadata_from_dois(self, researcher_lesot):
"""
Fetch metadata from doi
"""
dois = ['10.1016/j.ijar.2017.06.011']
o = OrcidPaperSource()
ref_name = (researcher_lesot.name.first, researcher_lesot.name.last)
papers = list(
o.fetch_metadata_from_dois(ref_name, researcher_lesot.orcid, dois))
assert len(papers) == 1
p = papers[0]
# Lesot is now a researcher of the paper
assert p.authors_list[1]['researcher_id'] == researcher_lesot.pk
# There must be a second OaiRecord
p.cache_oairecords() # Cache is not up to date
assert len(p.oairecords) == 2
def fetch_everything_for_researcher(pk):
sources = [
('orcid', OrcidPaperSource(max_results=1000)),
]
r = Researcher.objects.get(pk=pk)
# If it is the first time we fetch this researcher
# if r.stats is None:
# make sure publications already known are also considered
update_researcher_task(r, 'clustering')
try:
for key, source in sources:
update_researcher_task(r, key)
source.fetch_and_save(r)
update_researcher_task(r, None)
except MetadataSourceException as e:
raise e
finally:
r = Researcher.objects.get(pk=pk)
update_researcher_task(r, 'stats')
r.update_stats()
r.harvester = None
update_researcher_task(r, None)
def fetch_everything_for_researcher(pk):
orcid_paper_source = OrcidPaperSource(max_results=1000)
r = Researcher.objects.get(pk=pk)
# If it is the first time we fetch this researcher
# if r.stats is None:
# make sure publications already known are also considered
update_researcher_task(r, 'orcid')
try:
orcid_paper_source.link_existing_papers(r)
orcid_paper_source.fetch_and_save(r)
update_researcher_task(r, None)
except MetadataSourceException as e:
raise e
finally:
r = Researcher.objects.get(pk=pk)
update_researcher_task(r, 'stats')
r.update_stats()
r.harvester = None
update_researcher_task(r, None)
def setUpClass(self):
super(OrcidIntegrationTest, self).setUpClass()
self.source = OrcidPaperSource()
class OrcidIntegrationTest(PaperSourceTest):
@classmethod
def setUpClass(self):
super(OrcidIntegrationTest, self).setUpClass()
self.source = OrcidPaperSource()
def check_papers(self, papers):
p = Paper.objects.get(
title='From Natural Language to RDF Graphs with Pregroups')
p.check_authors()
author = p.authors[0]
self.assertEqual(author.orcid, self.r4.orcid)
p = Paper.objects.get(
title='Complexity of Grammar Induction for Quantum Types')
p.check_authors()
author = p.authors[0]
self.assertEqual(author.orcid, self.r4.orcid)
def test_previously_present_papers_are_attributed(self):
# Fetch papers from a researcher
pablo = Researcher.get_or_create_by_orcid('0000-0002-6293-3231')
self.source.fetch_and_save(pablo)
p = Paper.objects.get(oairecord__doi='10.1007/978-3-642-25516-8_1')
self.assertEqual(p.authors[2].orcid, pablo.orcid)
# Now fetch a coauthor of him
antoine = Researcher.get_or_create_by_orcid('0000-0002-7977-4441')
self.source.fetch_and_save(antoine)
# This paper should be attributed to both ORCID ids
p = Paper.objects.get(oairecord__doi='10.1007/978-3-642-25516-8_1')
self.assertEqual(p.authors[0].orcid, antoine.orcid)
self.assertEqual(p.authors[2].orcid, pablo.orcid)
def test_fetch_dois(self):
pboesu = Researcher.get_or_create_by_orcid('0000-0001-6723-6833')
self.source.fetch_and_save(pboesu)
doi = '10.3354/meps09890'
p = Paper.get_by_doi(doi)
dois_in_paper = [r.doi for r in p.oairecords]
self.assertTrue(doi in dois_in_paper)
def test_orcid_affiliation(self):
# this used to raise an error.
# a more focused test might be preferable (focused on the said
# paper)
papers = list(self.source.fetch_orcid_records('0000-0002-9658-1473'))
self.assertTrue(len(papers) > 30)
def test_bibtex_fallback(self):
papers = list(self.source.fetch_orcid_records('0000-0002-1900-3901'))
titles = [paper.title for paper in papers]
self.assertTrue(
'Company-Coq: Taking Proof General one step closer to a real IDE'
in titles)
def test_import_with_crossref_error(self):
stergios = Researcher.get_or_create_by_orcid('0000-0001-9232-4042')
self.source.fetch_and_save(stergios)
p = Paper.objects.get(oairecord__doi='10.1016/j.metabol.2017.10.007')
# crossref claims that the ORCID should be associated to author 2
# but it should actually be associated to author 0
self.assertEqual(p.authors[0].orcid, '0000-0001-9232-4042')
self.assertEqual(p.authors[2].orcid, None)
self.assertEqual(p.authors[0].researcher_id, stergios.id)
self.assertEqual(p.authors[2].researcher_id, None)
class OrcidIntegrationTest(PaperSourceTest):
def setUp(self):
super(OrcidIntegrationTest, self).setUp()
self.source = OrcidPaperSource()
def test_fetch(self):
profile = OrcidProfileStub('0000-0002-8612-8827', instance='orcid.org')
papers = list(
self.source.fetch_papers(self.researcher, profile=profile))
for paper in papers:
paper = Paper.from_bare(paper)
self.assertTrue(len(papers) > 1)
self.check_papers(papers)
def check_papers(self, papers):
p = Paper.objects.get(
title='From Natural Language to RDF Graphs with Pregroups')
p.check_authors()
author = p.authors[0]
self.assertEqual(author.orcid, self.r4.orcid)
p = Paper.objects.get(
title='Complexity of Grammar Induction for Quantum Types')
p.check_authors()
author = p.authors[0]
self.assertEqual(author.orcid, self.r4.orcid)
def test_previously_present_papers_are_attributed(self):
# Fetch papers from a researcher
profile_pablo = OrcidProfileStub('0000-0002-6293-3231',
instance='orcid.org')
pablo = Researcher.get_or_create_by_orcid('0000-0002-6293-3231',
profile=profile_pablo)
self.source.fetch_and_save(pablo, profile=profile_pablo)
p = Paper.objects.get(oairecord__doi='10.1007/978-3-642-25516-8_1')
self.assertEqual(p.authors[2].orcid, pablo.orcid)
# Now fetch a coauthor of him
profile_antoine = OrcidProfileStub('0000-0002-7977-4441',
instance='orcid.org')
antoine = Researcher.get_or_create_by_orcid('0000-0002-7977-4441',
profile=profile_antoine)
self.source.fetch_and_save(antoine, profile=profile_antoine)
# This paper should be attributed to both ORCID ids
p = Paper.objects.get(oairecord__doi='10.1007/978-3-642-25516-8_1')
self.assertEqual(p.authors[0].orcid, antoine.orcid)
self.assertEqual(p.authors[2].orcid, pablo.orcid)
def test_fetch_dois(self):
profile = OrcidProfileStub('0000-0001-6723-6833', instance='orcid.org')
pboesu = Researcher.get_or_create_by_orcid('0000-0001-6723-6833',
profile=profile)
self.source.fetch_and_save(pboesu, profile=profile)
doi = '10.3354/meps09890'
p = Paper.get_by_doi(doi)
dois_in_paper = [r.doi for r in p.oairecords]
self.assertTrue(doi in dois_in_paper)
def test_orcid_affiliation(self):
# this used to raise an error.
# a more focused test might be preferable (focused on the said
# paper)
papers = list(
self.source.fetch_orcid_records(
'0000-0002-9658-1473',
OrcidProfileStub('0000-0002-9658-1473')))
self.assertTrue(len(papers) > 30)
def test_bibtex_fallback(self):
papers = list(
self.source.fetch_orcid_records(
'0000-0002-1900-3901',
profile=OrcidProfileStub('0000-0002-1900-3901')))
titles = [paper.title for paper in papers]
self.assertTrue(
'Company-Coq: Taking Proof General one step closer to a real IDE'
in titles)
def test_import_with_crossref_error(self):
profile = OrcidProfileStub('0000-0001-9232-4042', instance='orcid.org')
stergios = Researcher.get_or_create_by_orcid('0000-0001-9232-4042',
profile=profile)
self.source.fetch_and_save(stergios, profile=profile)
p = Paper.objects.get(oairecord__doi='10.1016/j.metabol.2017.10.007')
# crossref claims that the ORCID should be associated to author 2
# but it should actually be associated to author 0
self.assertEqual(p.authors[0].orcid, '0000-0001-9232-4042')
self.assertEqual(p.authors[2].orcid, None)
self.assertEqual(p.authors[0].researcher_id, stergios.id)
self.assertEqual(p.authors[2].researcher_id, None)
def test_bibtex_not_ignored(self):
profile = OrcidProfileStub('0000-0003-2888-1770', instance='orcid.org')
adrien = Researcher.get_or_create_by_orcid('0000-0003-2888-1770',
profile=profile)
self.source.fetch_and_save(adrien, profile=profile)
p1 = Paper.objects.get(title='A Fuzzy Take on Graded Beliefs')
p2 = Paper.objects.get(title='Information quality and uncertainty')
self.assertTrue(p1 != p2)
def test_link_existing_papers(self):
# Fetch papers from a researcher
profile_pablo = OrcidProfileStub('0000-0002-6293-3231',
instance='orcid.org')
pablo = Researcher.get_or_create_by_orcid('0000-0002-6293-3231',
profile=profile_pablo)
self.source.fetch_and_save(pablo, profile=profile_pablo)
papers = list(pablo.papers)
nb_papers = len(papers)
self.assertEqual(nb_papers, 9)
# Remove the researcher_ids from the papers
for paper in papers:
for author in paper.authors_list:
if author.get('researcher_id') == pablo.id:
del author['researcher_id']
paper.save()
# Now the profile has no papers anymore
self.assertEqual(pablo.papers.count(), 0)
# Let's fix that!
self.source.link_existing_papers(pablo)
# Now it's fine!!
self.assertEqual(Researcher.objects.get(id=pablo.id).papers.count(), 9)
def setUp(self):
super(OrcidIntegrationTest, self).setUp()
self.source = OrcidPaperSource()
class OrcidIntegrationTest(PaperSourceTest):
def setUp(self):
super(OrcidIntegrationTest, self).setUp()
self.source = OrcidPaperSource()
def test_fetch(self):
profile = OrcidProfileStub('0000-0002-8612-8827', instance='orcid.org')
papers = list(self.source.fetch_papers(self.researcher, profile=profile))
for paper in papers:
paper = Paper.from_bare(paper)
self.assertTrue(len(papers) > 1)
self.check_papers(papers)
def check_papers(self, papers):
p = Paper.objects.get(
title='From Natural Language to RDF Graphs with Pregroups')
p.check_authors()
author = p.authors[0]
self.assertEqual(author.orcid, self.r4.orcid)
p = Paper.objects.get(
title='Complexity of Grammar Induction for Quantum Types')
p.check_authors()
author = p.authors[0]
self.assertEqual(author.orcid, self.r4.orcid)
def test_previously_present_papers_are_attributed(self):
# Fetch papers from a researcher
profile_pablo = OrcidProfileStub('0000-0002-6293-3231', instance='orcid.org')
pablo = Researcher.get_or_create_by_orcid('0000-0002-6293-3231',
profile=profile_pablo)
self.source.fetch_and_save(pablo, profile=profile_pablo)
p = Paper.objects.get(oairecord__doi='10.1007/978-3-642-25516-8_1')
self.assertEqual(p.authors[2].orcid, pablo.orcid)
# Now fetch a coauthor of him
profile_antoine = OrcidProfileStub('0000-0002-7977-4441', instance='orcid.org')
antoine = Researcher.get_or_create_by_orcid('0000-0002-7977-4441',
profile=profile_antoine)
self.source.fetch_and_save(antoine, profile=profile_antoine)
# This paper should be attributed to both ORCID ids
p = Paper.objects.get(oairecord__doi='10.1007/978-3-642-25516-8_1')
self.assertEqual(p.authors[0].orcid, antoine.orcid)
self.assertEqual(p.authors[2].orcid, pablo.orcid)
def test_fetch_dois(self):
profile = OrcidProfileStub('0000-0001-6723-6833', instance='orcid.org')
pboesu = Researcher.get_or_create_by_orcid('0000-0001-6723-6833',
profile=profile)
self.source.fetch_and_save(pboesu, profile=profile)
doi = '10.3354/meps09890'
p = Paper.get_by_doi(doi)
dois_in_paper = [r.doi for r in p.oairecords]
self.assertTrue(doi in dois_in_paper)
def test_orcid_affiliation(self):
# this used to raise an error.
# a more focused test might be preferable (focused on the said
# paper)
papers = list(self.source.fetch_orcid_records('0000-0002-9658-1473',
OrcidProfileStub('0000-0002-9658-1473')))
self.assertTrue(len(papers) > 30)
def test_bibtex_fallback(self):
papers = list(self.source.fetch_orcid_records('0000-0002-1900-3901',
profile=OrcidProfileStub('0000-0002-1900-3901')))
titles = [paper.title for paper in papers]
self.assertTrue('Company-Coq: Taking Proof General one step closer to a real IDE' in titles)
def test_import_with_crossref_error(self):
profile = OrcidProfileStub('0000-0001-9232-4042', instance='orcid.org')
stergios = Researcher.get_or_create_by_orcid('0000-0001-9232-4042',
profile=profile)
self.source.fetch_and_save(stergios, profile=profile)
p = Paper.objects.get(oairecord__doi='10.1016/j.metabol.2017.10.007')
# crossref claims that the ORCID should be associated to author 2
# but it should actually be associated to author 0
self.assertEqual(p.authors[0].orcid, '0000-0001-9232-4042')
self.assertEqual(p.authors[2].orcid, None)
self.assertEqual(p.authors[0].researcher_id, stergios.id)
self.assertEqual(p.authors[2].researcher_id, None)
def test_bibtex_not_ignored(self):
profile = OrcidProfileStub('0000-0003-2888-1770', instance='orcid.org')
adrien = Researcher.get_or_create_by_orcid('0000-0003-2888-1770', profile=profile)
self.source.fetch_and_save(adrien, profile=profile)
p1 = Paper.objects.get(title='A Fuzzy Take on Graded Beliefs')
p2 = Paper.objects.get(title='Information quality and uncertainty')
self.assertTrue(p1 != p2)
def setUp(self):
self.source = OrcidPaperSource()
self.researcher = self.r4
def setUpClass(self):
super(StatisticsTest, self).setUpClass()
cr_api = OrcidPaperSource()
cr_api.fetch_and_save(self.r3)