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Mock pubmed 557 #567

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merged 5 commits into from
Aug 30, 2024
Merged

Mock pubmed 557 #567

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f0b765f
Mocked one test, mock seems to apply to others. #557
knirirr Aug 20, 2024
a0adc99
Mocked tests and fixed test_isatools_utils #557
knirirr Aug 27, 2024
fc63569
Merge branch 'develop' into mock_pubmed_557
knirirr Aug 27, 2024
7467ffb
Removed tests not needed due to mocking. #557
knirirr Aug 27, 2024
0b4afe6
Fix ols test.
knirirr Aug 30, 2024
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47 changes: 25 additions & 22 deletions tests/utils/test_isatools_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
from io import StringIO
from jsonschema.exceptions import ValidationError

from unittest.mock import Mock

from isatools import isajson
from isatools import isatab
Expand Down Expand Up @@ -82,11 +83,12 @@ def test_get_ontology(self):
ontology_source = ols.get_ols_ontology('efo')
self.assertIsInstance(ontology_source, OntologySource)
self.assertEqual(ontology_source.name, 'efo')
self.assertIn("https://www.ebi.ac.uk/ols", ontology_source.file)
self.assertIn("/api/ontologies/efo?lang=en", ontology_source.file)
self.assertIsInstance(ontology_source.version, str)
self.assertEqual(
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@knirirr I recall that we coded it this way with @terazus to guard against version change, ( which makes the assumption that the service would keep the pattern and can not be guaranteed)

ontology_source.description, 'Experimental Factor Ontology')
ontology_source.file,
'https://www.ebi.ac.uk/ols4/api/ontologies/efo?lang=en')
self.assertIsInstance(ontology_source.version, str)
self.assertEqual(ontology_source.description, 'Experimental Factor Ontology')


def test_search_for_term(self):
ontology_source = ols.get_ols_ontology('efo')
Expand Down Expand Up @@ -167,17 +169,22 @@ def test_create_isatab_archive_filter_on_transcription_profiling(self):


class TestPubMedIDUtil(unittest.TestCase):
return_values = {
'doi': 'abc123',
'authors': ['A', 'B'],
'year': 1912,
'journal': 'shipping news',
'title': 'surprise'
}

def test_get_pubmed_article(self):
J = pubmed.get_pubmed_article('25520553')
self.assertEqual(J['doi'], '10.4137/CIN.S13895')
self.assertEqual(J['authors'], ['Johnson D', 'Connor AJ', 'McKeever S',
'Wang Z', 'Deisboeck TS', 'Quaiser T',
'Shochat E'])
self.assertEqual(J['year'], '2014')
self.assertEqual(J['journal'], 'Cancer Inform')
self.assertEqual(
J['title'], 'Semantically linking in silico cancer models.')
pubmed.get_pubmed_article = Mock(return_value = self.return_values)
j = pubmed.get_pubmed_article('25520553')
self.assertEqual(j['doi'], self.return_values['doi'])
self.assertEqual(j['authors'], self.return_values['authors'])
self.assertEqual(j['year'], self.return_values['year'])
self.assertEqual(j['journal'], self.return_values['journal'])
self.assertEqual(j['title'], self.return_values['title'])

J1 = pubmed.get_pubmed_article('890406')
self.assertEqual(J1['doi'], '')
Expand All @@ -192,20 +199,16 @@ def test_get_pubmed_article(self):
self.assertEqual(J4['doi'], "")

def test_set_pubmed_article(self):
pubmed.get_pubmed_article = Mock(return_value=self.return_values)
p = Publication(pubmed_id='25520553')
prs = Person(first_name="bob")
pubmed.set_pubmed_article(p)
self.assertEqual(p.doi, '10.4137/CIN.S13895')
self.assertEqual(p.author_list, 'Johnson D, Connor AJ, McKeever S, '
'Wang Z, Deisboeck TS, Quaiser T, '
'Shochat E')
self.assertEqual(p.title, 'Semantically linking in silico cancer models.')
self.assertEqual(p.doi, self.return_values['doi'])
self.assertEqual(p.author_list, ", ".join(self.return_values['authors']))
self.assertEqual(p.title, self.return_values['title'])
self.assertIsInstance(p.comments[0], Comment)
self.assertEqual(p.comments[0].name, 'Journal')
self.assertEqual(p.comments[0].value, 'Cancer Inform')
with self.assertRaises(Exception) as context:
pubmed.set_pubmed_article(prs)
self.assertTrue("Can only set PubMed details on a Publication object" in context.exception)
self.assertEqual(p.comments[0].value, self.return_values['journal'])


class TestIsaTabFixer(unittest.TestCase):
Expand Down
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