Merge pull request #199 from WengLab-InformaticsResearch/reasoner_validator

Reasoner validator

Author: CaseyTa

cohd/cohd_trapi_15.py

@@ -41,7 +41,7 @@ class CohdTrapi150(CohdTrapi):
     edge_types_negative = ['biolink:negatively_correlated_with']
     default_negative_predicate = edge_types_negative[0]
 
-    tool_version = f'{CohdTrapi._SERVICE_NAME} 6.4.1'
+    tool_version = f'{CohdTrapi._SERVICE_NAME} 6.4.3'
     schema_version = '1.5.0'
     biolink_version = bm_version
 

cohd/trapi/reasoner_validator_ext.py

@@ -149,28 +149,27 @@ def validate_trapi_response(trapi_version, bl_version, response):
     """
     # Ignore the following codes
     codes_ignore = {
-        'warnings': [
-            'warning.response.knowledge_graph.empty',  # For TRAPI error responses, COHD uses null KG, which is allowed
-            'warning.response.results.empty',  # For TRAPI error responses, COHD uses null results, which is allowed
+        'warning': [
+            'warning.knowledge_graph.node.id.unmapped_prefix',  # False negative on SNOMEDCT
         ],
-        'errors': [
-        ]
+        'error': []
     }
 
     # Validation
     validator = TRAPIResponseValidator(
         trapi_version=trapi_version,
         biolink_version=bl_version,
-        strict_validation=None
+        strict_validation=False
     )
     validator.check_compliance_of_trapi_response(response)
-    vms = validator.get_all_messages()
+    messages = validator.get_all_messages()
+    standard_tests = messages['Validate TRAPI Response']['Standards Test']
 
     # Ignore certain codes
     for level, codes in codes_ignore.items():
-        v_messages = vms[level]
+        v_messages = standard_tests[level]
         for code in codes:
             # remove code from dictionary, no error if code not in dict
             v_messages.pop(code, None)
 
-    return vms
+    return standard_tests

notebooks/cohd_helpers/cohd_requests.py

@@ -844,10 +844,10 @@ def translator_query_100(node_1_curie, node_2_curie=None, node_2_type=None, max_
     return response, query
 
 
-def translator_query_120(node_1_curies, node_2_curies=None, node_2_categories=None, predicates=None, max_results=500,
-                         confidence_interval=None, dataset_id=3, local_oxo=True, method='obsExpRatio',
-                         min_cooccurrence=None, ontology_targets=None, biolink_only=True, threshold=None, timeout=300,
-                         query_id=True):
+def translator_query(node_1_curies, node_2_curies=None, node_2_categories=None, predicates=None, max_results=500,
+                     confidence_interval=None, dataset_id=3, local_oxo=True, method='obsExpRatio',
+                     min_cooccurrence=None, ontology_targets=None, biolink_only=True, threshold=None, timeout=300,
+                     query_id=True):
     """NCATS Translator Reasoner API. See documentation: https://github.com/NCATS-Tangerine/NCATS-ReasonerStdAPI
 
     Parameters
@@ -939,10 +939,6 @@ def translator_query_120(node_1_curies, node_2_curies=None, node_2_categories=No
     return response, query
 
 
-# TRAPI 1.3 query on COHD is currently the same as TRAPI 1.2 query
-translator_query_130 = translator_query_120
-
-
 def translator_version():
     url = f'{server}/translator/version'
     response = requests.get(url, timeout=5)

test_cohd_trapi.py

@@ -20,13 +20,13 @@
 
 # Choose which server to test
 # cr.server = 'https://dev.cohd.io/api'
-# cr.server = 'https://cohd-api.ci.transltr.io/api'
-# cr.server = 'https://cohd-api.test.transltr.io/api'  # Temporarily default to Test as Translator consrotia has only deployed TRAPI 1.4 to Test
-cr.server = 'https://cohd-api.transltr.io/api'  # Default to ITRB-Production instance
+cr.server = 'https://cohd-api.ci.transltr.io/api'
+# cr.server = 'https://cohd-api.test.transltr.io/api'  
+# cr.server = 'https://cohd-api.transltr.io/api'  
 
 # Specify what Biolink and TRAPI versions are expected by the server
-BIOLINK_VERSION = '3.5.0'
-TRAPI_VERSION = '1.4.2'
+BIOLINK_VERSION = '4.1.6'
+TRAPI_VERSION = '1.5.0'
 
 # Static instance of the Biolink Model Toolkit
 bm_toolkit = Toolkit()
@@ -37,7 +37,7 @@
 _s = namedtuple('_s', ['key', 'type'])
 
 # Proxy for main TRAPI version
-translator_query = cr.translator_query_130
+translator_query = cr.translator_query
 
 _logging_level_from_str = {logging.getLevelName(level): level for level in
                            [logging.DEBUG, logging.INFO, logging.WARNING, logging.ERROR]}
@@ -47,11 +47,11 @@ def _validate_trapi_response(response):
     vms = validate_trapi_response(TRAPI_VERSION, BIOLINK_VERSION, response)
 
     # expect no validation errors
-    assert len(vms['errors']) == 0 and len(vms['critical']) == 0, print(vms)
+    assert len(vms['error']) == 0 and len(vms['critical']) == 0, print(vms)
 
     # If there are validation warnings, display them, but don't fail
-    if len(vms['warnings']) > 0:
-        warnings.warn(str(vms['warnings']))
+    if len(vms['warning']) > 0:
+        warnings.warn(str(vms['warning']))
 
 
 def _print_trapi_log(trapi_response, print_level=logging.WARNING):
@@ -682,7 +682,7 @@ def test_translator_query_multiple_categories():
             "query_graph": {
                 "nodes": {
                     "subj": {
-                        "ids": ["UMLS:C0451709"]
+                        "ids": ["SNOMEDCT:197356006"]
                     },
                     "obj": {
                         "categories": ["biolink:DiseaseOrPhenotypicFeature"]
@@ -723,7 +723,7 @@ def test_translator_query_multiple_categories():
             "query_graph": {
                 "nodes": {
                     "subj": {
-                        "ids": ["UMLS:C0451709"]
+                        "ids": ["SNOMEDCT:197356006"]
                     },
                     "obj": {
                         "categories": ["biolink:Procedure"]
@@ -764,7 +764,7 @@ def test_translator_query_multiple_categories():
             "query_graph": {
                 "nodes": {
                     "subj": {
-                        "ids": ["UMLS:C0451709"]
+                        "ids": ["SNOMEDCT:197356006"]
                     },
                     "obj": {
                         "categories": ["biolink:DiseaseOrPhenotypicFeature", "biolink:Procedure"]
@@ -954,7 +954,7 @@ def test_translator_workflows():
             }
         },
         "workflow": [
-            {"id": "lookup"}
+            {"id": "lookup_and_score"}
         ],
         "query_options": {
             "max_results": 1