Non-destructive TRAPIResponseValidator.check_compliance_of_trapi_resp…

…onse(response) validation of TRAPI Response JSON (release 3.8.3 bug removed Message)

CHANGELOG.md

@@ -2,6 +2,10 @@
 
 The Reasoner Validator package is evolving along with progress in TRAPI and Biolink Model standards within the NCATS Biomedical Knowledge Translator.
 
+
+## 3.8.4
+- Non-destructive TRAPIResponseValidator.check_compliance_of_trapi_response(response) validation of TRAPI Response JSON (release 3.8.3 bug removed Message)
+
 ## 3.8.3
 - Fixed TRAPI release management to cache TRAPI GitHub code release and branch tags locally - in a **versions.yaml** file - to avoid Git API calling denial of service issues; Small **scripts/trapi_release.py** utility script provided to update the **versions.yaml** file, as periodically necessary.
 - YAML file management tech debt cleaned up a tiny bit. Tweaked a couple of validation codes for this reason.

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "reasoner-validator"
-version = "3.8.3"
+version = "3.8.4"
 description = "Validation tools for Reasoner API"
 authors = [
     "Richard Bruskiewich <richard.bruskiewich@delphinai.com>",
@@ -48,7 +48,7 @@ bmt = "^1.1.1"
 # since 4.18.0 appeared to break something for the
 # access and processing of JSON schemata
 jsonschema = "~4.17.3"
-
+dictdiffer = "^0.9.0"
 PyYAML = "^6.0"
 requests = "^2.28.1"
 pydantic = "^1.10.11"

reasoner_validator/validator.py

@@ -150,48 +150,55 @@ def check_compliance_of_trapi_response(
             # nothing more to validate?
             return
 
-        # here, we split the message out from the Response
-        # checking along the way whether it is empty
+        # Here, we split the TRAPI Response.Message out from the other
+        # Response components, to allow for independent TRAPI Schema
+        # validation of those non-Message components versus the Message
+        # itself (checking along the way whether the Message is empty)
         message: Optional[Dict] = response.pop('message')
-        if not message:
-            # This is valid TRAPI but reported as an error,
-            # and not interesting for further validation
-            if not self.suppress_empty_data_warnings:
-                self.report("error.trapi.response.message.empty")
-
-            # ... also, nothing more here to validate?
-            return
 
-        # we insert a stub to enable TRAPI validation
-        # of the remainder of the Response
+        # we insert a stub to enable TRAPI schema
+        # validation of the remainder of the Response
         response['message'] = {}
+        if message:
 
-        # TRAPI JSON specified versions override default versions
-        if "schema_version" in response and response["schema_version"]:
-            if self.default_trapi:
-                self.trapi_version = get_latest_version(response["schema_version"])
+            # TRAPI JSON specified versions override default versions
+            if "schema_version" in response and response["schema_version"]:
+                if self.default_trapi:
+                    self.trapi_version = get_latest_version(response["schema_version"])
 
-        if "biolink_version" in response and response["biolink_version"]:
-            if self.default_biolink:
-                self.bmt = get_biolink_model_toolkit(biolink_version=response["biolink_version"])
-                self.biolink_version = self.bmt.get_model_version()
+            if "biolink_version" in response and response["biolink_version"]:
+                if self.default_biolink:
+                    self.bmt = get_biolink_model_toolkit(biolink_version=response["biolink_version"])
+                    self.biolink_version = self.bmt.get_model_version()
 
-        response = self.sanitize_trapi_response(response)
+            response = self.sanitize_trapi_response(response)
 
-        self.is_valid_trapi_query(instance=response, component="Response")
-        if self.has_critical():
-            # we abort further processing here due to detected critical global validation errors?
-            return
+            self.is_valid_trapi_query(instance=response, component="Response")
+            if not self.has_critical():
+
+                status: Optional[str] = response['status'] if 'status' in response else None
+                if status and status not in ["OK", "Success", "QueryNotTraversable", "KPsNotAvailable"]:
+                    self.report("warning.trapi.response.status.unknown", identifier=status)
 
-        status: Optional[str] = response['status'] if 'status' in response else None
-        if status and status not in ["OK", "Success", "QueryNotTraversable", "KPsNotAvailable"]:
-            self.report("warning.trapi.response.status.unknown", identifier=status)
+                # Sequentially validate the Query Graph, Knowledge Graph then validate
+                # the Results (which rely on the validity of the other two components)
+                elif self.has_valid_query_graph(message) and \
+                        self.has_valid_knowledge_graph(message, max_kg_edges):
+                    self.has_valid_results(message, max_results)
+
+            # else:
+            #     we don't validate further if it has
+            #     critical Response level errors
+
+        else:
+            # Empty Message is valid TRAPI but reported as an error
+            # in the validation and not interesting for further validation
+            if not self.suppress_empty_data_warnings:
+                self.report("error.trapi.response.message.empty")
 
-        # Sequentially validate the Query Graph, Knowledge Graph then validate
-        # the Results (which rely on the validity of the other two components)
-        elif self.has_valid_query_graph(message) and \
-                self.has_valid_knowledge_graph(message, max_kg_edges):
-            self.has_valid_results(message, max_results)
+        # Reconstitute the original Message
+        # to the Response before returning
+        response['message'] = message
 
     @staticmethod
     def sample_results(results: List, sample_size: int = 0) -> List:

tests/test_response_validator.py

@@ -1,7 +1,7 @@
 """
 Unit tests for the generic (shared) components of the SRI Testing Framework
 """
-from typing import Tuple,  Dict
+from typing import  Dict
 from sys import stderr
 
 import logging
@@ -12,6 +12,8 @@
 
 import pytest
 
+from dictdiffer import diff
+
 from reasoner_validator.trapi import TRAPI_1_3_0, TRAPI_1_4_2
 from reasoner_validator.validator import TRAPIResponseValidator
 from reasoner_validator.report import TRAPIGraphType
@@ -431,6 +433,16 @@ def test_sanitize_trapi_query(response: Dict):
 }
 
 
+# this unit test checks that the original response object is returned verbatim
+def test_conservation_of_response_object():
+    validator: TRAPIResponseValidator = TRAPIResponseValidator()
+    input_response = deepcopy(_TEST_TRAPI_1_4_2_FULL_SAMPLE)
+    reference_response = deepcopy(_TEST_TRAPI_1_4_2_FULL_SAMPLE)
+    assert input_response == reference_response
+    validator.check_compliance_of_trapi_response(response=input_response)
+    assert not list(diff(input_response, reference_response))
+
+
 @pytest.mark.parametrize(
     "edges_limit,number_of_nodes_returned,number_of_edges_returned",
     [