def test_gene_criteria_types(self):
"""Test if the indexes have records"""
idx_key = "GENE_CRITERIA"
feature_type = "gene"
idx = ElasticSettings.idx(idx_key)
idx_types = CriteriaDataIntegrityUtils.get_criteria_index_types(idx_key)
gene_criterias = Criteria.get_available_criterias(feature_type)
CriteriaDataIntegrityTestUtils().test_criteria_types(idx, idx_types, gene_criterias["gene"])
CriteriaDataIntegrityTestUtils().test_criteria_mappings(idx, idx_types)
# get random doc for each type ['gene_in_region', 'cand_gene_in_region', 'cand_gene_in_study', 'is_gene_in_mhc']
idx_type = "gene_in_region"
doc_by_idx_type = ElasticUtils.get_rdm_docs(idx, idx_type, size=1)
self.assertTrue(len(doc_by_idx_type) == 1, "got back one document")
gene_in_region_doc = doc_by_idx_type[0]
# {'score': 10, 'CRO': [{'fname': '4p11', 'fid': '4p11_005'}],
# '_meta': {'_type': 'gene_in_region', '_score': 0.9997835,
# '_index': 'pydgin_imb_criteria_gene', '_id': 'ENSG00000250753'},
# 'disease_tags': ['CRO'], 'qid': 'ENSG00000250753'}
qid = getattr(gene_in_region_doc, "qid")
print(qid)
disease_tags = getattr(gene_in_region_doc, "disease_tags")
# ENSG00000248482
# ['IBD', 'UC']
# [{'fid': '5q31.1_013', 'fname': '5q31.1'}]
# [{'fid': '5q31.1_013', 'fname': '5q31.1'}]
fnotes = getattr(gene_in_region_doc, disease_tags[0])
region_id = fnotes[0]["fid"]
print(region_id)
def test_marker_criteria_types(self):
'''Test if the indexes have records'''
idx_key = 'MARKER_CRITERIA'
feature_type = 'marker'
idx = ElasticSettings.idx(idx_key)
idx_types = CriteriaDataIntegrityUtils.get_criteria_index_types(idx_key)
gene_criterias = Criteria.get_available_criterias(feature_type)
CriteriaDataIntegrityTestUtils().test_criteria_types(idx, idx_types, gene_criterias['gene'])
CriteriaDataIntegrityTestUtils().test_criteria_mappings(idx, idx_types)
# get random doc for each type ['gene_in_region', 'cand_gene_in_region', 'cand_gene_in_study', 'is_gene_in_mhc']
idx_type = 'rsq_with_index_snp'
doc_by_idx_type = ElasticUtils.get_rdm_docs(idx, idx_type, size=1)
self.assertTrue(len(doc_by_idx_type) == 1, 'got back one document')
