def test_enrich_pubmed_accent_duplicate(self, *_):
"""Test when two authors, Gomez C and Goméz C are both checked that they are not counted as duplicates."""
g1 = 'Gomez C'
g2 = 'Gómez C'
pmid_1, pmid_2 = pmids = [
'29324713',
'29359844',
]
get_citations_by_pmids(manager=self.manager, pmids=pmids)
time.sleep(1)
x = self.manager.get_citation_by_pmid(pmid_1)
self.assertIsNotNone(x)
self.assertEqual('Martínez-Guillén JR',
x.first.name,
msg='wrong first author name')
self.assertIn(g1, self.manager.object_cache_author)
self.assertIn(g2, self.manager.object_cache_author)
a1 = self.manager.get_author_by_name(g1)
self.assertEqual(g1, a1.name)
a2 = self.manager.get_author_by_name(g2)
self.assertEqual(g2, a2.name)
def test_enrich(self):
self.assertEqual(0, self.manager.count_citations())
get_citations_by_pmids(manager=self.manager, pmids=[self.pmid])
self.assertEqual(1, self.manager.count_citations())
c = self.manager.get_citation_by_pmid(self.pmid)
self.assertIsNotNone(c)
self.assertIsInstance(c, Citation)
self.assertEqual(CITATION_TYPE_PUBMED, c.db)
self.assertEqual(self.pmid, c.db_id)
def test_enrich(self):
pmids = get_pubmed_identifiers(self.graph)
stored_citations = self.manager.session.query(Citation).all()
self.assertEqual(0, len(stored_citations))
get_citations_by_pmids(manager=self.manager, pmids=pmids)
stored_citations = self.manager.session.query(Citation).all()
self.assertEqual(1, len(stored_citations))
def test_enrich_list_grouped(self):
pmids = [
'25818332',
'27003210',
'26438529',
'26649137',
]
get_citations_by_pmids(manager=self.manager, pmids=pmids, group_size=2)
citation = self.manager.get_citation_by_pmid('25818332')
self.assertIsNotNone(citation)
def test_enrich_list(self):
pmids = [
'25818332',
'27003210',
'26438529',
'26649137',
]
get_citations_by_pmids(manager=self.manager, pmids=pmids)
citation = self.manager.get_or_create_citation(type=CITATION_TYPE_PUBMED, reference='25818332')
self.assertIsNotNone(citation)
def test_enrich_pubmed_list(self, *_):
pmids = [
'25818332',
'27003210',
'26438529',
'26649137',
]
get_citations_by_pmids(manager=self.manager, pmids=pmids)
citation = self.manager.get_or_create_citation(
namespace=CITATION_TYPE_PUBMED, identifier='25818332')
self.assertIsNotNone(citation)
def test_accent_duplicate(self):
"""This tests when two authors, Gomez C and Goméz C are both checked that they are not counted as duplicates"""
g1 = u'Gomez C'
g2 = u'Gómez C'
pmid_1, pmid_2 = pmids = [
'29324713',
'29359844',
]
get_citations_by_pmids(manager=self.manager, pmids=pmids)
x = self.manager.get_citation_by_pmid(pmid_1)
self.assertEqual(u'Martínez-Guillén JR', x.first.name)
self.assertIn(g1, self.manager.object_cache_author)
self.assertIn(g2, self.manager.object_cache_author)
a1 = self.manager.get_author_by_name(g1)
self.assertEqual(g1, a1.name)
a2 = self.manager.get_author_by_name(g2)
self.assertEqual(g2, a2.name)
