Preparing release 4.1.9 which temporarily removes 'biolink:treats'-dr…

…iven validation of "biolink:support_graphs", as per CQS team discussions

CHANGELOG.md

@@ -2,10 +2,14 @@
 
 The Reasoner Validator package is evolving along with progress in TRAPI and Biolink Model standards within the NCATS Biomedical Knowledge Translator.
 
+## 4.1.9
+
+- temporarily removed **`biolink:treats`** predicate validation check for **`biolink:supporting_graphs`** attribute value, pending community-wide implementation of the recently specified 'treats' predicate knowledge graph annotation standards.
+
 ## 4.1.8
 
 - BMT update to 1.4.1 (with default Biolink Model 4.2.1)
-- implemented rudimentary **`biolink:treats`** predicate validation check for **`biolink:supporting_graph`** attribute value.
+- implemented rudimentary **`biolink:treats`** predicate validation check for **`biolink:supporting_graphs`** attribute value.
 
 ## 4.1.7
 

DEVELOPER_NOTES.md

@@ -28,12 +28,12 @@ Steps to properly issue a new project release:
 2. If the **codes.yaml** were revised, regenerated the associate code documentation by running the **reasoner_validator/validation_codes.py** module as a script from the CLI.
 3. Run the unit test suite to ensure that nothing fails. Iterate to fix failures (in the code or in terms of revised unit tests to reflect fresh code designs)
 4. Document release changes in the **CHANGELOG.md**
-5. Update the **`[Tool Poetry]version =`** field in the **pyprojects.yaml**, e.g. "4.1.8"
+5. Update the **`[Tool Poetry]version =`** field in the **pyprojects.yaml**, e.g. "4.1.9"
 6. Run **`poetry update`** (preferably within  **`poetry shell`**)
 7. The project pip **requirements.txt** file snapshot of dependencies should also be updated at this point (type **`$ poetry export --output requirements.txt`**, assuming that the [proper poetry export plugin is installed](https://python-poetry.org/docs/pre-commit-hooks#poetry-export)). This may facilitate module deployment within environments that prefer to use pip rather than poetry to manage their deployments. 
 8. Commit or pull request merge all files (including the **poetry.lock** file) to **master**
-9. Add the equivalent Git **tag** to **master**. This should be the Semantic Version string from step 4 with an added 'v' prefix, i.e. "v4.1.8". 
+9. Add the equivalent Git **tag** to **master**. This should be the Semantic Version string from step 4 with an added 'v' prefix, i.e. "v4.1.9". 
 10. Push **master** to remote.
 11. Check if Git Actions for testing and documentation complete successfully.
-12. Create the release using the same release tag, i.e. "v4.1.8". 
-13. Check if Git Action for package deployment is successful and check if the new version (i.e. "4.1.8") is now visible on **[pypy.org](https://pypi.org/search/?q=reasoner-validator)**
+12. Create the release using the same release tag, i.e. "v4.1.9". 
+13. Check if Git Action for package deployment is successful and check if the new version (i.e. "4.1.9") is now visible on **[pypy.org](https://pypi.org/search/?q=reasoner-validator)**

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "reasoner-validator"
-version = "4.1.8"
+version = "4.1.9"
 description = "Validation tools for Reasoner API"
 authors = [
     "Richard Bruskiewich <[email protected]>",

reasoner_validator/biolink/__init__.py

@@ -785,8 +785,9 @@ def validate_attributes(
             found_knowledge_level = False
             found_agent_type = False
 
-            # Track presence of 'support_graph' for some predicates (e.g. 'treats')
-            found_support_graph = False
+            # TODO: Defer tracking of the presence of 'biolink:support_graphs'
+            #       for specified predicates like 'treats' or its descendants
+            # found_support_graphs = False
 
             for attribute in attributes:
 
@@ -926,9 +927,10 @@ def validate_attributes(
                                                                         infores == kp_source:
                                                                     found_kp_knowledge_source = True
 
-                                                # Check for 'support_graph'
-                                                if attribute_type_id == "biolink:support_graph":
-                                                    found_support_graph = False
+                                                # TODO: Defer tracking of the presence of 'biolink:support_graphs'
+                                                #       for specified predicates like 'treats' or its descendants
+                                                # if attribute_type_id == "biolink:support_graphs":
+                                                #     found_support_graphs = False
 
                                                 # We expect at this point that, if 'attribute_type_id' is a
                                                 # 'knowledge_level' or 'agent_type', then the value is a scalar
@@ -1008,13 +1010,14 @@ def validate_attributes(
                             identifier=edge_id
                         )
 
-                #
-                predicate = edge['predicate'] if 'predicate' in edge else None
-                if self.is_treats(predicate) and not found_support_graph:
-                    self.report(
-                        code="warning.knowledge_graph.edge.treats.support_graph.missing",
-                        identifier=edge_id
-                    )
+                # TODO: Defer tracking of the presence of 'biolink:support_graphs'
+                #       for specified predicates like 'treats' or its descendants
+                # predicate = edge['predicate'] if 'predicate' in edge else None
+                # if self.is_treats(predicate) and not found_support_graphs:
+                #     self.report(
+                #         code="warning.knowledge_graph.edge.treats.support_graph.missing",
+                #         identifier=edge_id
+                #     )
 
         return source_trail  # may be 'None' if the required attributes are missing