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)