reasoner-validator 3.9.2__tar.gz → 3.9.4__tar.gz

{reasoner_validator-3.9.2 → reasoner_validator-3.9.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: reasoner-validator
-Version: 3.9.2
+Version: 3.9.4
 Summary: Validation tools for Reasoner API
 Home-page: https://github.com/NCATSTranslator
 License: MIT
@@ -23,10 +23,14 @@ Provides-Extra: web
 Requires-Dist: PyYAML (>=6.0,<7.0)
 Requires-Dist: bmt (>=1.1.2,<2.0.0)
 Requires-Dist: dictdiffer (>=0.9.0,<0.10.0)
-Requires-Dist: fastapi (>=0.68,<0.69) ; extra == "web"
+Requires-Dist: fastapi (>=0.85.0,<0.86.0) ; extra == "web"
+Requires-Dist: httpx (>=0.18.2,<0.19.0) ; extra == "web"
 Requires-Dist: jsonschema (>=4.17.3,<4.18.0)
 Requires-Dist: myst-parser (>=2.0.0,<3.0.0) ; extra == "docs"
 Requires-Dist: numpydoc (>=1.5.0,<2.0.0) ; extra == "docs"
+Requires-Dist: opentelemetry-exporter-otlp-proto-http ; extra == "web"
+Requires-Dist: opentelemetry-instrumentation-fastapi ; extra == "web"
+Requires-Dist: opentelemetry-instrumentation-httpx ; extra == "web"
 Requires-Dist: pydantic (>=1.10.11,<2.0.0)
 Requires-Dist: pytest (>=7.2.2,<8.0.0)
 Requires-Dist: pytest-cov (>=4.0.0,<5.0.0)
@@ -34,7 +38,7 @@ Requires-Dist: requests (>=2.28.1,<3.0.0)
 Requires-Dist: sphinx (>=6.2.1,<7.0.0) ; extra == "docs"
 Requires-Dist: sphinx-rtd-theme (>=1.2.2,<2.0.0) ; extra == "docs"
 Requires-Dist: urllib3 (>=1.26.15,<2.0.0)
-Requires-Dist: uvicorn (>=0.15,<0.16) ; extra == "web"
+Requires-Dist: uvicorn ; extra == "web"
 Project-URL: Bug Tracker, https://github.com/NCATSTranslator/reasoner-validator/issues
 Project-URL: Change Log, https://github.com/NCATSTranslator/reasoner-validator/blob/master/CHANGELOG.md
 Project-URL: Documentation, https://translator-reasoner-validator.readthedocs.io/en/latest/
@@ -309,6 +313,12 @@ To minimize redundancy in validation messages, messages are uniquely indexed in
 1. the (codes.yaml recorded) dot-delimited validation code path string
 2. for messages with templated parameters, by a mandatory 'identifier' field (which is expected to exist as a field in a template if such template has one or more parameterized fields)
 
+### OpenTelemetry and Jaeger
+
+The web service may be monitored for OpenTelemetry by setting an environment variable **TELEMETRY_ENDPOINT**  to a suitable trace collecting endpoint in an application like [Jaeger](https://www.jaegertracing.io/) (see also the [Translator SRI Jaeger-Demo](https://github.com/TranslatorSRI/Jaeger-demo)).
+
+**Note:** the current system Docker (Compose) design only supports OpenTemplate tracing using the internal Jaeger container and may require further refinements to enable use of an external telemetry collector.
+
 ### Running the Web Service within Docker
 
 The Reasoner Validator web service may be run inside a docker container, using Docker Compose.

{reasoner_validator-3.9.2 → reasoner_validator-3.9.4}/README.md

@@ -266,6 +266,12 @@ To minimize redundancy in validation messages, messages are uniquely indexed in
 1. the (codes.yaml recorded) dot-delimited validation code path string
 2. for messages with templated parameters, by a mandatory 'identifier' field (which is expected to exist as a field in a template if such template has one or more parameterized fields)
 
+### OpenTelemetry and Jaeger
+
+The web service may be monitored for OpenTelemetry by setting an environment variable **TELEMETRY_ENDPOINT**  to a suitable trace collecting endpoint in an application like [Jaeger](https://www.jaegertracing.io/) (see also the [Translator SRI Jaeger-Demo](https://github.com/TranslatorSRI/Jaeger-demo)).
+
+**Note:** the current system Docker (Compose) design only supports OpenTemplate tracing using the internal Jaeger container and may require further refinements to enable use of an external telemetry collector.
+
 ### Running the Web Service within Docker
 
 The Reasoner Validator web service may be run inside a docker container, using Docker Compose.

{reasoner_validator-3.9.2 → reasoner_validator-3.9.4}/docs/validation_codes_dictionary.md

@@ -380,14 +380,6 @@
 
 **Description:** Knowledge graph node must have a 'id' key with a non-empty associated value!
 
-### error.knowledge_graph.node.name.missing
-
-**Message:** Name is missing for node
-
-**Context:** identifier
-
-**Description:** Although TRAPI 1.4.0 states 'nullable: True', Translator user interface functionally requires that a non-empty 'name' property value must be specified in a knowledge graph node!
-
 ### error.knowledge_graph.node.category.missing
 
 **Message:** Category is missing for node
@@ -954,6 +946,14 @@
 
 **Description:** At least one query node is unused in the knowledge graph!
 
+### warning.knowledge_graph.node.name.missing
+
+**Message:** Name is missing for node
+
+**Context:** identifier
+
+**Description:** Although TRAPI 1.4.0 states 'nullable: True', Translator user interface functionally requires that a non-empty 'name' property value ought to be specified in a knowledge graph node!
+
 ### warning.knowledge_graph.node.category.deprecated
 
 **Message:** Node has deprecated category

{reasoner_validator-3.9.2 → reasoner_validator-3.9.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "reasoner-validator"
-version = "3.9.2"
+version = "3.9.4"
 description = "Validation tools for Reasoner API"
 authors = [
     "Richard Bruskiewich <richard.bruskiewich@delphinai.com>",
@@ -56,12 +56,22 @@ urllib3 = "^1.26.15"
 numpydoc = {version = "^1.5.0", optional = true}
 sphinx = {version = "^6.2.1", optional = true}
 myst-parser = {version = "^2.0.0", optional = true}
-fastapi = {version = "^0.68", optional = true}
-uvicorn = {version = "^0.15", optional = true}
+fastapi = {version = "^0.85.0", optional = true}
+uvicorn = {version = "*", optional = true}
 pytest-cov = {version = "^4.0.0"}
 pytest = {version = "^7.2.2"}
 sphinx-rtd-theme = {version = "^1.2.2", optional = true}
 
+# for more pre-implemented OpenTelemetry instrumentations:
+#   https://github.com/open-telemetry/opentelemetry-python-contrib/tree/main/instrumentation
+httpx = {version = "^0.18.2", optional = true}
+
+# exporting traces for jaeger
+opentelemetry-exporter-otlp-proto-http = {version = "*", optional = true}
+
+# instrumentation for fast api and httpx
+opentelemetry-instrumentation-fastapi = {version = "*", optional = true}
+opentelemetry-instrumentation-httpx = {version = "*", optional = true}
 
 [tool.poetry.urls]
 "Change Log" = "https://github.com/NCATSTranslator/reasoner-validator/blob/master/CHANGELOG.md"
@@ -69,7 +79,7 @@ sphinx-rtd-theme = {version = "^1.2.2", optional = true}
 
 [tool.poetry.extras]
 docs = ["numpydoc", "sphinx", "myst-parser", "sphinx-rtd-theme"]
-web = ["fastapi", "uvicorn"]
+web = ["fastapi", "uvicorn", "httpx", "opentelemetry-exporter-otlp-proto-http", "opentelemetry-instrumentation-fastapi", "opentelemetry-instrumentation-httpx"]
 
 [tool.coverage.run]
 source = ["reasoner_validator"]

{reasoner_validator-3.9.2 → reasoner_validator-3.9.4}/reasoner_validator/biolink/__init__.py

@@ -166,6 +166,8 @@ class BiolinkValidator(TRAPISchemaValidator, BMTWrapper):
         :param prefix: named context of the BiolinkValidator, used as a prefix in validation messages.
         :param trapi_version:  Optional[str], caller specified Biolink Model version (default: None, use TRAPI 'latest')
         :param biolink_version: Optional[str], caller specified Biolink Model version (default: None, use BMT 'latest')
+                                Note that a special biolink_version value string "suppress" disables full Biolink Model
+                                validation by the validator (i.e. limits validation to superficial validation).
         :param target_provenance: Optional[Dict[str,str]], Dictionary of context ARA and KP for provenance validation
         :param strict_validation: Optional[bool] = None, if True, some tests validate as 'error';  False, simply issues
                                   'info' message; A value of 'None' uses the default value for specific graph contexts.
@@ -328,7 +330,7 @@ class BiolinkValidator(TRAPISchemaValidator, BMTWrapper):
                 # UI team request (part of issue #35): really need names here
                 if not ("name" in slots and slots["name"]):
                     self.report(
-                        code="error.knowledge_graph.node.name.missing",
+                        code="warning.knowledge_graph.node.name.missing",
                         identifier=node_id
                     )
 

{reasoner_validator-3.9.2 → reasoner_validator-3.9.4}/reasoner_validator/codes.yaml

@@ -298,12 +298,6 @@ error:
           $context:
             - identifier
           $description: "Knowledge graph node must have a 'id' key with a non-empty associated value!"
-      name:
-        missing:
-          $message: "Name is missing for node"
-          $context:
-            - identifier
-          $description: "Although TRAPI 1.4.0 states 'nullable: True', Translator user interface functionally requires that a non-empty 'name' property value must be specified in a knowledge graph node!"
       category:
         missing:
           $message: "Category is missing for node"
@@ -744,6 +738,13 @@ warning:
           - identifier
         $description: "At least one query node is unused in the knowledge graph!"
     node:
+      name:
+        missing:
+          $message: "Name is missing for node"
+          $context:
+            - identifier
+          $description: "Although TRAPI 1.4.0 states 'nullable: True', Translator user interface functionally requires that a non-empty 'name' property value ought to be specified in a knowledge graph node!"
+
       category:
         deprecated:
           $message: "Node has deprecated category"

{reasoner_validator-3.9.2 → reasoner_validator-3.9.4}/reasoner_validator/validator.py

@@ -1,6 +1,5 @@
 from typing import Optional, List, Dict
 
-import deprecation
 from bmt import Toolkit
 
 from reasoner_validator.biolink import (
@@ -10,8 +9,7 @@ from reasoner_validator.biolink import (
 )
 
 from reasoner_validator.report import TRAPIGraphType
-from reasoner_validator.trapi import TRAPI_1_3_0_SEMVER, TRAPI_1_4_0_BETA3_SEMVER, TRAPI_1_4_0_BETA4_SEMVER, \
-    TRAPI_1_4_0_SEMVER, LATEST_TRAPI_RELEASE, LATEST_TRAPI_MAJOR_RELEASE_SEMVER
+from reasoner_validator.trapi import LATEST_TRAPI_RELEASE, LATEST_TRAPI_MAJOR_RELEASE_SEMVER
 from reasoner_validator.trapi.mapping import MappingValidator, check_node_edge_mappings
 from reasoner_validator.versioning import SemVer, SemVerError, get_latest_version
 from reasoner_validator.sri.util import get_aliases
@@ -72,6 +70,29 @@ class TRAPIResponseValidator(BiolinkValidator):
             self._is_trapi_1_4 = True
         return self._is_trapi_1_4
 
+    def sanitize_workflow(self, response: Dict) -> Dict:
+        """
+        Workflows in TRAPI Responses cannot be validated further due to missing tags and None values.
+        This method is a temporary workaround to sanitize the query for additional validation.
+
+        :param response: Dict full TRAPI Response JSON object
+        :return: Dict, response with discretionary removal of content which
+                       triggers (temporarily) unwarranted TRAPI validation failures
+        """
+        if 'workflow' in response and response['workflow']:
+            # a 'workflow' is a list of steps, which are JSON object specifications
+            workflow_steps: List[Dict] = response['workflow']
+            for step in workflow_steps:
+                if 'runner_parameters' in step and not step['runner_parameters']:
+                    self.report("warning.trapi.response.workflow.runner_parameters.missing")
+                    step.pop('runner_parameters')
+                if 'parameters' in step and not step['parameters']:
+                    # There are some workflow types that have mandatory need for 'parameters'
+                    # but this should be caught in a later schema validation step
+                    self.report("warning.trapi.response.workflow.parameters.missing")
+                    step.pop('parameters')
+        return response
+
     def check_compliance_of_trapi_response(
             self,
             response: Optional[Dict],
@@ -127,6 +148,8 @@ class TRAPIResponseValidator(BiolinkValidator):
                     self.bmt = get_biolink_model_toolkit(biolink_version=response["biolink_version"])
                     self.biolink_version = self.bmt.get_model_version()
 
+            response = self.sanitize_workflow(response)
+
             self.is_valid_trapi_query(instance=response, component="Response")
             if not self.has_critical():
 

{reasoner_validator-3.9.2 → reasoner_validator-3.9.4}/tests/test_biolink_compliance_validation.py

@@ -2466,7 +2466,7 @@ def test_validate_biolink_curie_in_qualifiers(
                     }
                 }
             },
-            "error.knowledge_graph.node.name.missing"
+            "warning.knowledge_graph.node.name.missing"
         ),
         (
             LATEST_BIOLINK_MODEL_VERSION,

{reasoner_validator-3.9.2 → reasoner_validator-3.9.4}/tests/test_response_validator.py

@@ -880,9 +880,8 @@ def test_sample_graph(edges_limit: int, number_of_nodes_returned: int, number_of
             None,
             None,
             True,
-            # removal of TRAPI Response sanitization now means
-            # that this code snippet is JSON schema invalid
-            "critical.trapi.validation"
+            # TRAPI Response workflow sanitization restored - this should pass
+            ""
         ),
         (   # Query 26 - We throw a full TRAPI JSON example here (taken directly from the
             #            TRAPI implementation guidelines...) just for fun and profit

{reasoner_validator-3.9.2 → reasoner_validator-3.9.4}/tests/test_workflows.py

@@ -8,6 +8,7 @@ from itertools import product
 from json import dumps
 
 from reasoner_validator.trapi import TRAPISchemaValidator
+from reasoner_validator.validator import TRAPIResponseValidator
 
 from tests import LATEST_TEST_RELEASES
 
@@ -78,3 +79,31 @@ def test_query_latest_trapi_workflow_properties(trapi_version: str, query: Dict)
 
     validator = TRAPISchemaValidator(trapi_version=trapi_version)
     validator.validate(query, "Query")
+
+
+SAMPLE_QUERY_3 = {
+    "message": {
+        "knowledge_graph": None,
+        "query_graph": None,
+        "results": None,
+    },
+    "log_level": None,
+    "workflow":  [
+        {
+            "id": "annotate_nodes",
+            "parameters": None,
+            "runner_parameters": None
+        },
+        {
+            "id": "lookup"
+        }
+    ]
+}
+
+
+def test_query_sanitize_response_workflow_properties():
+    """Test sanitization of flawed TRAPI Query workflow properties."""
+
+    validator = TRAPIResponseValidator()
+    response = validator.sanitize_workflow(SAMPLE_QUERY_3)
+    validator.validate(response, "Query")

{reasoner_validator-3.9.2 → reasoner_validator-3.9.4}/reasoner_validator/trapi/__init__.py

@@ -25,6 +25,25 @@ logger = logging.getLogger(__name__)
 DEFAULT_TRAPI_POST_TIMEOUT = 600.0
 
 
+TRAPI_1_3_0_SEMVER = SemVer.from_string("v1.3.0")
+TRAPI_1_3_0: str = str(TRAPI_1_3_0_SEMVER)
+TRAPI_1_4_0_BETA_SEMVER = SemVer.from_string("v1.4.0-beta")
+TRAPI_1_4_0_BETA = str(TRAPI_1_4_0_BETA_SEMVER)
+TRAPI_1_4_0_BETA2_SEMVER = SemVer.from_string("v1.4.0-beta2")
+TRAPI_1_4_0_BETA3_SEMVER = SemVer.from_string("v1.4.0-beta3")
+TRAPI_1_4_0_BETA4_SEMVER = SemVer.from_string("v1.4.0-beta4")
+TRAPI_1_4_0_SEMVER = SemVer.from_string("v1.4.0")
+TRAPI_1_4_0: str = str(TRAPI_1_4_0_SEMVER)
+TRAPI_1_4_1_SEMVER = SemVer.from_string("v1.4.1")
+TRAPI_1_4_1: str = str(TRAPI_1_4_1_SEMVER)
+TRAPI_1_4_2_SEMVER = SemVer.from_string("v1.4.2")
+TRAPI_1_4_2: str = str(TRAPI_1_4_2_SEMVER)
+LATEST_TRAPI_RELEASE_SEMVER: SemVer = TRAPI_1_4_2_SEMVER
+LATEST_TRAPI_RELEASE: str = TRAPI_1_4_2
+LATEST_TRAPI_MAJOR_RELEASE_SEMVER: SemVer = SemVer.from_string("v1.4", core_fields=['major', 'minor'])
+LATEST_TRAPI_MAJOR_RELEASE: str = str(LATEST_TRAPI_MAJOR_RELEASE_SEMVER)
+
+
 class TRAPIAccessError(RuntimeError):
     pass
 
@@ -355,22 +374,3 @@ class TRAPISchemaValidator(ValidationReporter):
         header += f" validating against TRAPI version " \
                   f"'{str(self.get_trapi_version() if self.get_trapi_version() is not None else 'Default')}'"
         return header
-
-
-TRAPI_1_3_0_SEMVER = SemVer.from_string("v1.3.0")
-TRAPI_1_3_0: str = str(TRAPI_1_3_0_SEMVER)
-TRAPI_1_4_0_BETA_SEMVER = SemVer.from_string("v1.4.0-beta")
-TRAPI_1_4_0_BETA = str(TRAPI_1_4_0_BETA_SEMVER)
-TRAPI_1_4_0_BETA2_SEMVER = SemVer.from_string("v1.4.0-beta2")
-TRAPI_1_4_0_BETA3_SEMVER = SemVer.from_string("v1.4.0-beta3")
-TRAPI_1_4_0_BETA4_SEMVER = SemVer.from_string("v1.4.0-beta4")
-TRAPI_1_4_0_SEMVER = SemVer.from_string("v1.4.0")
-TRAPI_1_4_0: str = str(TRAPI_1_4_0_SEMVER)
-TRAPI_1_4_1_SEMVER = SemVer.from_string("v1.4.1")
-TRAPI_1_4_1: str = str(TRAPI_1_4_1_SEMVER)
-TRAPI_1_4_2_SEMVER = SemVer.from_string("v1.4.2")
-TRAPI_1_4_2: str = str(TRAPI_1_4_2_SEMVER)
-LATEST_TRAPI_RELEASE_SEMVER: SemVer = TRAPI_1_4_2_SEMVER
-LATEST_TRAPI_RELEASE: str = TRAPI_1_4_2
-LATEST_TRAPI_MAJOR_RELEASE_SEMVER: SemVer = SemVer.from_string("v1.4", core_fields=['major', 'minor'])
-LATEST_TRAPI_MAJOR_RELEASE: str = str(LATEST_TRAPI_MAJOR_RELEASE_SEMVER)