Merge pull request #203 from WengLab-InformaticsResearch/mcq

Mcq

Author: CaseyTa

cohd/cohd.py

@@ -48,16 +48,44 @@ def api_cohd():
     return redirect("https://cohd.smart-api.info/", code=302)
 
 
+@app.route('/api/metadata/datasets')
+def api_metadata_datasets():
+    return query_cohd_mysql.query_db_datasets()
+
+
+@app.route('/api/metadata/domainCounts')
+def api_metadata_domainCounts():
+    dataset_id = query_cohd_mysql.get_arg_dataset_id(request.args)
+    return query_cohd_mysql.query_db_domain_counts(dataset_id)
+
+
+@app.route('/api/metadata/domainPairCounts')
+def api_metadata_domainPairCounts():
+    dataset_id = query_cohd_mysql.get_arg_dataset_id(request.args)
+    return query_cohd_mysql.query_db_domain_pair_counts(dataset_id)
+
+
+@app.route('/api/metadata/patientCount')
+def api_metadata_patientCount():
+    dataset_id = query_cohd_mysql.get_arg_dataset_id(request.args)
+    return query_cohd_mysql.query_db_patient_count(dataset_id)
+
+
 @app.route('/api/omop/findConceptIDs')
 @app.route('/api/v1/omop/findConceptIDs')
 def api_omop_reference():
-    return api_call('omop', 'findConceptIDs')
+    query = request.args.get('q')
+    dataset_id = query_cohd_mysql.get_arg_dataset_id(request.args)
+    domain_id = request.args.get('domain')
+    min_count = request.args.get('min_count')
+    return query_cohd_mysql.query_db_find_concept_ids(dataset_id, query, domain_id, min_count)
 
 
 @app.route('/api/omop/concepts')
 @app.route('/api/v1/omop/concepts')
 def api_omop_concepts():
-    return api_call('omop', 'concepts')
+    query = request.args.get('q')
+    return query_cohd_mysql.query_db_concepts(query)
 
 
 @app.route('/api/omop/conceptAncestors')
@@ -95,25 +123,6 @@ def api_omop_xrefFromOMOP():
     return api_call('omop', 'xrefFromOMOP')
 
 
-@app.route('/api/metadata/datasets')
-def api_metadata_datasets():
-    return api_call('metadata', 'datasets')
-
-
-@app.route('/api/metadata/domainCounts')
-def api_metadata_domainCounts():
-    return api_call('metadata', 'domainCounts')
-
-
-@app.route('/api/metadata/domainPairCounts')
-def api_metadata_domainPairCounts():
-    return api_call('metadata', 'domainPairCounts')
-
-
-@app.route('/api/metadata/patientCount')
-def api_metadata_patientCount():
-    return api_call('metadata', 'patientCount')
-
 
 @app.route('/api/frequencies/singleConceptFreq')
 @app.route('/api/v1/frequencies/singleConceptFreq')
@@ -160,6 +169,11 @@ def api_association_relativeFrequency():
     return api_call('association', 'relativeFrequency')
 
 
+@app.route('/api/association/mcq')
+def api_association_mcq():
+    return api_call('association', 'mcq')
+
+
 @app.route('/api/temporal/conceptAgeCounts')
 def api_temporal_conceptAgeCounts():
     return api_call('temporal', 'conceptAgeCounts')
@@ -306,7 +320,8 @@ def api_call(service=None, meta=None, query=None, version=None):
     elif service == 'association':
         if meta == 'chiSquare' or \
                 meta == 'obsExpRatio' or \
-                meta == 'relativeFrequency':
+                meta == 'relativeFrequency' or \
+                meta == 'mcq':
             result = query_cohd_mysql.query_db(service, meta, request.args)
         else:
             result = 'meta not recognized', 400

cohd/cohd_trapi.py

@@ -27,6 +27,7 @@ class TrapiStatusCode(Enum):
     UNSUPPORTED_ATTR_CONSTRAINT = 'UnsupportedAttributeConstraint'
     UNSUPPORTED_QUAL_CONSTRAINT = 'UnsupportedQualifierConstraint'
     UNSUPPORTED_SET_INTERPRETATION = 'UnsupportedSetInterpretation'
+    MISSING_MEMBER_IDS = 'MissingMemberIDs'
 
 
 class CohdTrapi(ABC):
@@ -210,6 +211,28 @@ def criteria_confidence(cohd_result, confidence, threshold=CohdTrapi.default_ln_
         return True
 
 
+def criteria_mcq_score(cohd_result, threshold=CohdTrapi.default_ln_ratio_ci_thresohld):
+    """ Checks the confidence interval of the result for significance using alpha. Only applies to observed-expected
+    frequency ratio. Returns True for all other types of results.
+
+    Parameters
+    ----------
+    cohd_result
+    confidence
+    threshold
+
+    Returns
+    -------
+    True if significant
+    """
+    if 'ln_ratio_score' in cohd_result:
+        # obsExpFreq
+        return abs(cohd_result['ln_ratio_score']) >= threshold
+    else:
+        # Missing the score to filter on
+        return False        
+
+
 mappings_domain_ontology = {
     '_DEFAULT': ['ICD9CM', 'RxNorm', 'UMLS', 'DOID', 'MONDO']
 }
@@ -318,7 +341,7 @@ def sort_cohd_results(cohd_results, sort_field='ln_ratio_ci', ascending=False):
     if cohd_results is None or len(cohd_results) == 0:
         return cohd_results
 
-    if sort_field in ['p-value', 'ln_ratio', 'relative_frequency']:
+    if sort_field in ['p-value', 'ln_ratio', 'relative_frequency', 'ln_ratio_score']:
         sort_values = [x[sort_field] for x in cohd_results]
     elif sort_field == 'ln_ratio_ci':
         sort_values = [score_cohd_result(x) for x in cohd_results]