def test_get_criteria_details(self):
config = IniParser().read_ini(MY_INI_FILE)
idx = ElasticSettings.idx('MARKER_CRITERIA')
available_criterias = MarkerCriteria.get_available_criterias(config=config)['marker']
idx_type = ','.join(available_criterias)
doc_by_idx_type = ElasticUtils.get_rdm_docs(idx, idx_type, size=1)
self.assertTrue(len(doc_by_idx_type) == 1)
feature_id = getattr(doc_by_idx_type[0], 'qid')
criteria_details = MarkerCriteria.get_criteria_details(feature_id, config=config)
hits = criteria_details['hits']
first_hit = hits[0]
_type = first_hit['_type']
_index = first_hit['_index']
_id = first_hit['_id']
_source = first_hit['_source']
disease_tag = _source['disease_tags'][0]
self.assertTrue(feature_id, _id)
self.assertIn(_type, idx_type)
self.assertTrue(idx, _index)
self.assertIn(disease_tag, list(_source.keys()))
fdetails = _source[disease_tag][0]
self.assertIn('fid', fdetails.keys())
self.assertIn('fname', fdetails.keys())
def test_get_disease_tags(self):
config = IniParser().read_ini(MY_INI_FILE)
idx = ElasticSettings.idx('MARKER_CRITERIA')
available_criterias = MarkerCriteria.get_available_criterias(config=config)['marker']
idx_type = ','.join(available_criterias)
doc_by_idx_type = ElasticUtils.get_rdm_docs(idx, idx_type, size=1)
self.assertTrue(len(doc_by_idx_type) == 1)
feature_id = getattr(doc_by_idx_type[0], 'qid')
disease_docs = MarkerCriteria.get_disease_tags(feature_id)
self.assertIsNotNone(disease_docs, 'got back result docs')
disease_tags = [getattr(disease_doc, 'code') for disease_doc in disease_docs]
self.assertIsNotNone(disease_tags, "got back disease tags")