def test_get_criteria_details(self):
config = IniParser().read_ini(MY_INI_FILE)
idx = ElasticSettings.idx('REGION_CRITERIA')
available_criterias = RegionCriteria.get_available_criterias(config=config)['region']
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 = RegionCriteria.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_is_region_for_disease(self):
config = IniParser().read_ini(MY_INI_FILE)
criteria_results = RegionCriteria.is_region_for_disease(self.region_region1, config=config, result_container={})
expected_dict = {'1p36.32_002': {'IBD': [{'fid': 'IBD', 'fname': 'IBD'}],
'PSC': [{'fid': 'PSC', 'fname': 'PSC'}],
'CEL': [{'fid': 'CEL', 'fname': 'CEL'}],
'RA': [{'fid': 'RA', 'fname': 'RA'}],
'UC': [{'fid': 'UC', 'fname': 'UC'}],
'ATD': [{'fid': 'ATD', 'fname': 'ATD'}],
'MS': [{'fid': 'MS', 'fname': 'MS'}]}}
self.assertEqual(criteria_results, expected_dict, 'Got result dict for is_region_for_disease as expected')
def test_is_region_in_mhc(self):
config = IniParser().read_ini(MY_INI_FILE)
criteria_results = RegionCriteria.is_region_in_mhc(self.region_region1, config=config, result_container={})
# should be tagged to all the diseases
expected_dict = {'1p36.32_002': {'NAR': [{'fname': 'NAR', 'fid': 'NAR'}],
'ATD': [{'fname': 'ATD', 'fid': 'ATD'}],
'PSC': [{'fname': 'PSC', 'fid': 'PSC'}],
'IBD': [{'fname': 'IBD', 'fid': 'IBD'}], 'AA': [{'fname': 'AA', 'fid': 'AA'}],
'JIA': [{'fname': 'JIA', 'fid': 'JIA'}],
'RA': [{'fname': 'RA', 'fid': 'RA'}], 'SLE': [{'fname': 'SLE', 'fid': 'SLE'}],
'SSC': [{'fname': 'SSC', 'fid': 'SSC'}],
'VIT': [{'fname': 'VIT', 'fid': 'VIT'}], 'AS': [{'fname': 'AS', 'fid': 'AS'}],
'UC': [{'fname': 'UC', 'fid': 'UC'}],
'CRO': [{'fname': 'CRO', 'fid': 'CRO'}],
'SJO': [{'fname': 'SJO', 'fid': 'SJO'}],
'MS': [{'fname': 'MS', 'fid': 'MS'}],
'PSO': [{'fname': 'PSO', 'fid': 'PSO'}],
'T1D': [{'fname': 'T1D', 'fid': 'T1D'}],
'PBC': [{'fname': 'PBC', 'fid': 'PBC'}],
'IGE': [{'fid': 'IGE', 'fname': 'IGE'}],
'CEL': [{'fname': 'CEL', 'fid': 'CEL'}]}}
self.assertEqual(criteria_results, expected_dict, 'Got result dict for is_region_in_mhc as expected')
def criteria_details(request):
''' Get criteria details for a given region ID. '''
feature_id = request.POST.get('feature_id')
criteria_details = RegionCriteria.get_criteria_details(feature_id)
return JsonResponse(criteria_details)
def criteria_disease_tags(cls, request, qids):
''' Get criteria disease tags for a given ensembl ID for all criterias. '''
criteria_disease_tags = RegionCriteria.get_all_criteria_disease_tags(qids)
return criteria_disease_tags