def test_get_criteria_details(self):
config = IniParser().read_ini(MY_INI_FILE)
idx = ElasticSettings.idx('GENE_CRITERIA')
available_criterias = GeneCriteria.get_available_criterias(config=config)['gene']
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) > 0)
feature_id = getattr(doc_by_idx_type[0], 'qid')
criteria_details = GeneCriteria.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_available_criterias(self):
config = IniParser().read_ini(MY_INI_FILE)
available_criterias = GeneCriteria.get_available_criterias(config=config)
expected_dict = {'gene': ['cand_gene_in_study', 'gene_in_region', 'is_gene_in_mhc', 'cand_gene_in_region']}
self.assertIsNotNone(available_criterias, 'Criterias as not none')
self.assertIn('cand_gene_in_study', available_criterias['gene'])
self.assertEqual(available_criterias.keys(), expected_dict.keys(), 'Dic keys equal')
def get_random_feature_id(self):
config = IniParser().read_ini(MY_INI_FILE)
idx = ElasticSettings.idx('GENE_CRITERIA')
available_criterias = GeneCriteria.get_available_criterias(config=config)['gene']
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) > 0)
feature_id = getattr(doc_by_idx_type[0], 'qid')
return feature_id
