Resolution of Issue 106 plus general update of dependencies

README.md

@@ -154,7 +154,7 @@ The request body consists of JSON data structure with two top level tag:
 
 ### Running the Web Service Directly
 
-First install the web-specific dependencies, if not already done (e.g. by **`--all-extras`** above):
+First, install the web-specific dependencies, if not already done:
 
 ```bash
 poetry install --with web
@@ -286,7 +286,7 @@ To stop the service:
 docker-compose down
 ```
 
-Of course, the above docker-compose commands may be customized by the user to suit their needs. Note that the docker implementation assumes the use of uvicorn
+Of course, the user may customize the above docker-compose commands to suit their needs. Note that the docker implementation assumes the use of uvicorn
 
 ## Change Log
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "reasoner-validator"
-version = "5.0.0"
+version = "5.0.1"
 description = "Validation tools for Reasoner API"
 authors = [
     "Richard Bruskiewich <[email protected]>",
@@ -40,9 +40,10 @@ include = [
 ]
 
 [tool.poetry.dependencies]
-python = ">=3.9,<3.13"
-bmt = "^1.4.5"
-bioregistry = "^0.12.33"
+python = ">=3.10,<3.13"
+bmt = "==1.4.6"
+biolink-model = "^4.3.6"
+bioregistry = "^0.12.46"
 jsonschema = "^4.24.0"
 dictdiffer = "^0.9.0"
 PyYAML = "^6.0"
@@ -57,9 +58,9 @@ poetry-core = "^2.1.3"
 
 [tool.poetry.group.dev.dependencies]
 setuptools = "^78.1.1"
-pytest = "^7.4.4"
-pytest-cov = "^4.1.0"
-pytest-asyncio = "^0.23.3"
+pytest = "^8.4.1"
+pytest-cov = "^7.0.0"
+pytest-asyncio = "^1.3.0"
 
 [tool.poetry.group.docs.dependencies]
 numpydoc = "^1.5.0"

reasoner_validator/biolink/__init__.py

@@ -4,10 +4,12 @@
 from typing import Optional, Any, Dict, List, Tuple
 from numbers import Number
 from functools import lru_cache
+from importlib.resources import files
 import re
 from urllib.error import HTTPError
 from pprint import PrettyPrinter
 
+from linkml_runtime.utils.schemaview import SchemaView
 
 from bmt import Toolkit, utils
 from linkml_runtime.linkml_model import ClassDefinition, Element
@@ -63,8 +65,9 @@ def get_reference(curie: str) -> Optional[str]:
     return reference
 
 
-def _get_biolink_model_schema(biolink_version: Optional[str] = None) -> Optional[str]:
-    # Get Biolink Model Schema
+@lru_cache(maxsize=3)
+def get_biolink_schema(biolink_version: Optional[str] = None) -> SchemaView:
+    """Get cached Biolink schema, loading it if not already cached."""
     if biolink_version:
         try:
             svm = SemVer.from_string(biolink_version)
@@ -84,49 +87,46 @@ def _get_biolink_model_schema(biolink_version: Optional[str] = None) -> Optional
             biolink_version = "v" + str(svm)
         else:
             biolink_version = str(svm)
-        schema = f"https://raw.githubusercontent.com/biolink/biolink-model/{biolink_version}/biolink-model.yaml"
-        return schema
+
+        schema_view = SchemaView(f"https://raw.githubusercontent.com/biolink/biolink-model/{biolink_version}/biolink-model.yaml")
+        logger.debug("Successfully loaded user-specified Biolink schema from URL")
+        return schema_view
     else:
-        return None
+        # Try to load from the local Biolink Model package
+        # from the locally installed distribution
+        try:
+            schema_path = files("biolink_model.schema").joinpath("biolink_model.yaml")
+            schema_view = SchemaView(str(schema_path))
+            logger.debug("Successfully loaded locally-specified Biolink schema from local file")
+            return schema_view
+        except Exception as e:
+            logger.warning(f"Failed to load local Biolink schema: {e}")
+            # Fallback to loading from official URL
+            schema_view = SchemaView("https://w3id.org/biolink/biolink-model.yaml")
+            logger.debug("Successfully loaded current release Biolink schema from URL")
+            return schema_view
 
 
-# At any given time, only a modest number of Biolink Model versions
-# are expected to be active targets for SRI Test validations?
-@lru_cache(maxsize=3)
-def get_biolink_model_toolkit(biolink_version: Optional[str] = None) -> Toolkit:
-    """
-    Return Biolink Model Toolkit corresponding to specified version of the model (Default: current 'latest' version).
+def get_current_biolink_version(biolink_version: Optional[str] = None) -> str:
+    return get_biolink_schema(biolink_version).schema.version
 
-    :param biolink_version: Optional[str], caller specified Biolink Model version (default: None)
-    :type biolink_version: Optional[str] or None
-    :return: Biolink Model Toolkit.
-    :rtype: Toolkit
 
-    """
-    if biolink_version:
-        # If errors occur while instantiating non-default Toolkit;
-        # then log the error but just use default as a workaround?
-        try:
-            biolink_schema = _get_biolink_model_schema(biolink_version=biolink_version)
-            bmt = Toolkit(biolink_schema)
-            return bmt
-        except (TypeError, HTTPError) as ex:
-            logger.error(str(ex))
-
-    # 'latest' default Biolink Model
-    # version of given Toolkit returned
-    return Toolkit()
+@lru_cache(maxsize=3)
+def get_biolink_model_toolkit(biolink_version: Optional[str] = None) -> Toolkit:
+    """Get a Biolink Model Toolkit configured with the expected project Biolink Model schema."""
+    return Toolkit(schema=get_biolink_schema(biolink_version).schema)
 
 
 class BMTWrapper:
     def __init__(self, biolink_version: Optional[str] = None):
         self.bmt: Optional[Toolkit] = None
         self.default_biolink: bool = False
         if biolink_version != "suppress":
-            # Here, the Biolink Model version is validated, and the relevant Toolkit pulled.
+            # Here, the Biolink Model version is validated,
+            # and the relevant Toolkit pulled.
             if biolink_version is None:
                 self.default_biolink = True
-            self.bmt = get_biolink_model_toolkit(biolink_version=biolink_version)
+            self.bmt = get_biolink_model_toolkit(biolink_version)
             self.biolink_version = self.bmt.get_model_version()
         else:
             self.biolink_version = "suppress"
@@ -205,14 +205,14 @@ def __init__(
     ):
         """
         Biolink Validator constructor.
-        :param default_test: Optional[str] =  None, initial default test context of the BiolinkValidator messages
-        :param default_target: Optional[str] =  None, initial default target context of the BiolinkValidator,
+        :param default_test: Optional[str] = None, initial default test context of the BiolinkValidator messages
+        :param default_target: Optional[str] = None, initial default target context of the BiolinkValidator,
                                                 also 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 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.
 

reasoner_validator/report.py

@@ -52,12 +52,9 @@ def label(self) -> str:
 class ValidationReporter:
     """
     General wrapper for managing validation status messages: information, warnings, errors and 'critical' (errors).
-    The TRAPI version and Biolink Model versions are also tracked for convenience at this abstract level
+    The TRAPI version and Biolink Model versions are also tracked for convenience at this abstract level,
     although their application is within specific pertinent subclasses.
     """
-
-    # Default major version resolves to latest TRAPI OpenAPI release,
-    # specifically 1.3.0, as of September 1st, 2022
     DEFAULT_TRAPI_VERSION = "1"
 
     def __init__(
@@ -67,11 +64,11 @@ def __init__(
             strict_validation: Optional[bool] = None
     ):
         """
-        :param default_test: Optional[str] =  None, initial default test context of the Validator messages
+        :param default_test: Optional[str] = None, initial default test context of the Validator messages
                              Default "global" if not provided.
-        :param default_target: Optional[str] =  None, initial default target context of the Validator,
+        :param default_target: Optional[str] = None, initial default target context of the Validator,
                                also used as a prefix in validation messages. Default "global" if not provided.
-        :param strict_validation: Optional[bool] = None, if True, some tests validate as 'error';  False, simply issues
+        :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.
         """
         self.default_test: str = default_test if default_test else "Test"
@@ -112,7 +109,7 @@ def get_default_target(self) -> str:
     def is_strict_validation(self, graph_type: TRAPIGraphType, ignore_graph_type: bool = False) -> bool:
         """
         Predicate to test if strict validation is to be applied. If the internal
-        'strict_validation' flag is not set (i.e. None), then graph_type is
+        'strict_validation' flag is not set (i.e., None), then graph_type is
         to resolve strictness based on TRAPI graph type context.
 
         :param graph_type: TRAPIGraphType, type of TRAPI graph component being validated
@@ -632,8 +629,8 @@ def report_header(self, title: Optional[str] = "", compact_format: bool = True)
         :param title: Optional[str], if the title is None, then only the 'reasoner-validator' version is printed out
                       in the header. If the title is an empty string (the default), then 'Validation Report' used.
         :param compact_format: bool, whether to print the header in compact format (default: True).
-                               Extra line feeds are otherwise provided to provide space around header
-                               and control characters are output to underline the header.
+                               Extra line feeds are otherwise provided to provide space around the header.
+                               Control characters are also output to underline the header.
         :return: str, generated header.
         """
         header: str = ""
@@ -657,7 +654,7 @@ def report_header(self, title: Optional[str] = "", compact_format: bool = True)
         try:
             # This only works if the reasoner-validator
             # is locally installed as a package into the environment
-            version = f" version '{metadata.version('reasoner-validator')}'"
+            version = f"version '{metadata.version('reasoner-validator')}'"
         except metadata.PackageNotFoundError:
             #
             version = ""

reasoner_validator/trapi/__init__.py

@@ -235,11 +235,11 @@ def __init__(
     ):
         """
         TRAPI Validator constructor.
-        :param default_test: Optional[str] =  None, initial default test context of the TRAPISchemaValidator messages
-        :param default_target: Optional[str] =  None, initial default target context of the TRAPISchemaValidator,
-                                                also used as a prefix in validation messages.
-        :param trapi_version: str, version of component to validate against
-        :param strict_validation: Optional[bool] = None, if True, some tests validate as 'error';  False, simply issues
+        :param default_test: Optional[str] = None, initial default test context of the TRAPISchemaValidator messages
+        :param default_target: Optional[str] = None, initial default target context of the TRAPISchemaValidator,
+                                            also used as a prefix in validation messages.
+        :param trapi_version: Str, version of the component to validate against
+        :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.
 
         """

reasoner_validator/versioning.py

@@ -258,7 +258,7 @@ def get_latest_version(release_tag: Optional[str]) -> Optional[str]:
     """
     Return the latest TRAPI version corresponding to the release tag given.
     Note that if the release tag looks like a YAML file, then it is assumed
-    to be a direct schema specification. If a Git branch name in the schema
+    to be a direct schema specification. If a Git branch name is in the schema
     repository, the branch name is also passed on.
 
     :param release_tag: (possibly partial) SemVer string, Git branch name,

scripts/trapi_validator.py

@@ -154,7 +154,7 @@ async def direct_trapi_request(
                     print(f"Submitting TRAPI Response file to endpoint '{endpoint}'")
 
             # Make the TRAPI call to the Case targeted
-            # endpoint with specified TRAPI request
+            # endpoint with a specified TRAPI request
             result = await call_trapi(endpoint, trapi_request)
 
             # Was the web service (HTTP) call successful?
@@ -308,6 +308,7 @@ def main():
 
     # Retrieve the TRAPI JSON Response result to be validated
     if args.endpoint:
+        # Response directly retrieved from a target endpoint
         if args.local_request:
             # The internal TRAPI call is a coroutine
             # from which the results in a global variable
@@ -328,18 +329,21 @@ def main():
 
     elif args.arax_id:
         retrieve_arax_result(args.arax_id)
-    
+
     elif args.ars_response_id:
         if isfile(args.ars_response_id):
             # The response identifier can just be a local file...
             with open(args.ars_response_id) as infile:
                 trapi_response = json.load(infile)
         else:
-            # ... unless, it is an ARS PK
+            # ... unless it is an ARS PK
             retrieve_ars_result(response_id=args.ars_response_id, verbose=args.verbose)
 
     else:
-        print("Need to specify either an --endpoint/--local_request or a --response_id input argument to proceed!")
+        print(
+            "Need to specify either an --endpoint plus --local_request, "
+            "--arax_id or --ars_response_id input argument to proceed!"
+        )
 
     if not trapi_response:
         print("TRAPI Response JSON is unavailable for validation?")
@@ -348,9 +352,8 @@ def main():
     # OK, we have something to validate here...
     validator.check_compliance_of_trapi_response(response=trapi_response)
 
-    # Print out the outcome of the main validation of the TRAPI Response
+    # Print out the outcome of the TRAPI Response main validation
     validation_report(validator, args)
 
-
 if __name__ == "__main__":
     main()