Merge pull request #195 from WengLab-InformaticsResearch/trapi15

Trapi15

Author: CaseyTa

cohd/cohd_trapi_15.py

@@ -127,7 +127,8 @@ def _check_query_input(self):
 
         # Use TRAPI Reasoner Validator to validate the query
         try:
-            validate_trapi(self._json_data, "Query")
+            # For now, bypass the TRAPI validation because reasoner_validator doesn't work with TRAPI 1.5
+            # validate_trapi(self._json_data, "Query")
             self.log('Query passed reasoner validator')
         except ValidationError as err:
             self._valid_query = False
@@ -258,6 +259,9 @@ def _interpret_query(self):
         if not input_check[0]:
             return input_check
 
+        # Check if bypass_cache is desired
+        self._bypass_cache = self._json_data.get('bypass_cache', False)
+
         # Get options that don't fit into query_graph structure from query_options
         self._query_options = self._json_data.get('query_options')
         if self._query_options is None:
@@ -942,7 +946,8 @@ def operate(self):
                                                                         domain_id=domain_id,
                                                                         concept_class_id=concept_class_id,
                                                                         ln_ratio_sign=self._association_direction,
-                                                                        confidence=self._confidence_interval)
+                                                                        confidence=self._confidence_interval,
+                                                                        bypass=self._bypass_cache)
                             if json_results:
                                 new_cohd_results.extend(json_results['results'])
                     else:
@@ -951,7 +956,8 @@ def operate(self):
                         json_results = query_cohd_mysql.query_trapi(concept_id_1=concept_1_omop_id, concept_id_2=None,
                                                                     dataset_id=self._dataset_id, domain_id=None,
                                                                     ln_ratio_sign=self._association_direction,
-                                                                    confidence=self._confidence_interval)
+                                                                    confidence=self._confidence_interval,
+                                                                    bypass=self._bypass_cache)
                         if json_results:
                             new_cohd_results.extend(json_results['results'])
 
@@ -961,7 +967,8 @@ def operate(self):
                         json_results = query_cohd_mysql.query_trapi(concept_id_1=concept_1_omop_id,
                                                                     concept_id_2=concept_2_id,
                                                                     dataset_id=self._dataset_id, domain_id=None,
-                                                                    confidence=self._confidence_interval)
+                                                                    confidence=self._confidence_interval,
+                                                                    bypass=self._bypass_cache)
                         if json_results:
                             new_cohd_results.extend(json_results['results'])
 

cohd/query_cohd_mysql.py

@@ -1453,9 +1453,13 @@ def get_total_pair_counts(dataset_id: int) -> int:
 get_total_pair_counts.total_pair_counts = None
 
 
-@cache.memoize(timeout=86400)
+def _bypass_cache(f, *args, **kwargs):
+    return kwargs.get('bypass', False)
+
+
+@cache.memoize(timeout=86400, unless=_bypass_cache)
 def query_trapi(concept_id_1, concept_id_2=None, dataset_id=None, domain_id=None, concept_class_id=None,
-                ln_ratio_sign=0, confidence=DEFAULT_CONFIDENCE):
+                ln_ratio_sign=0, confidence=DEFAULT_CONFIDENCE, bypass=False):
     """ Query for TRAPI. Performs the calculations for all association methods
 
     Parameters

cohd/trapi/reasoner_validator_ext.py

@@ -164,7 +164,7 @@ def validate_trapi_response(trapi_version, bl_version, response):
         strict_validation=None
     )
     validator.check_compliance_of_trapi_response(response)
-    vms = validator.get_messages()
+    vms = validator.get_all_messages()
 
     # Ignore certain codes
     for level, codes in codes_ignore.items():