TRAPIResponseValidator.check_compliance_of_trapi_response(response) bug fix

• Non-destructive TRAPIResponseValidator.check_compliance_of_trapi_response(response) validation of TRAPI Response JSON (release 3.8.3 bug removed Message)

Caching Github TRAPI project releases and branches to avoid issue git Github API denial of service

• 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.
• Added DEVELOPER_NOTES.md to guide uniform project release management (especially, of the esoteric bits of the project like TRAPI release and validation code updates)

Fixed source trail - global reporting bug plus some small enhancements

• Removed check_trapi_validity() standalone API method to enforce a two-step process of instantiating a TRAPISchemaValidator instance then calling its is_valid_trapi_query() method.
• Spurious leading newline removed from TRAPI and Biolink Model validation version reporting log messages
• Fixed insidious edge source validation message reporting bug which masked all but the first of edges with a specified validation error
• Minor tweak to validation codes definitions to reduce duplication in reporting output or clarity of definition
• Fixed (and extended some) unit test cases related to all of the above.

Generally more informative validator output for some messages (plus some)

• Generally repaired validation 'sources' ('source_trail') context recording to cover all applicable validation message cases (especially, edge 'qualifier' validation); tested with unit tests
• TRAPIGraphType class moved up the class/module hierarchy, alongside ValidatorReporter; strict_validation as Optional[bool] wrapped in the is_strict_validation() method which uses graph_type to decide on None default strictness (based on graph type)
• TRAPI and Biolink Model versions resolved now only reported in logger.info, not stderr
• only preset target_provenance in validator reporter constructors, not the various method signatures
• add 'categories' into edge context labels for reports (long lists of categories may be challenging here but ...)

Refactor of class hiearchy with changed imports

Formal release of changes that evolved over recent 3.7.* releases, with improved documentation (and some tech debt remediation)

• Internal class hierarchy restructured for logical clarity in recent releases, formally highlighted in this release
• Most visible TRAPIResponseValidator class (previously) moved from the reasoner_validator.__init__.py package module, into its own reasoner_validator.validator module
• Some documentation repair

Enhanced qualifier validation plus TRAPI Response schema/biolink version management

• TRAPI qualifier validation enhanced by use of biolink:Association subclass slot_usage driven constraints (leveraging novel Biolink Model Toolkit 1.1.1 methods)
• Validation made TRAPI Response (TRAPI) schema_version and biolink_version aware, taking precedence over default (non-overridden) values of these version parameters.

Patch mainly to fix abstract category warning, issue #92

• Added TRAPI Response schema version and biolink version validation warning codes
• Warning about 'biolink:BiologicalCategory' and 'biolink:InformationContentEntity' are not issued if these categories are parent categories of concrete category instances specified in the 'categories' list

Parse semi-colon delimited infores curies as valid (in RetrievalSource objects)

Resolves issue #89

Future proof some attribute_type_id's

Adding special override list for some attribute_type_id terms as exceptions to stop error messages. This will apply to terms scheduled for implementation in a near term future Biolink Model release, but not yet out the door (but implemented proactively by early adopters within the Translator consortium). The initial list of such terms are the pre-Biolink Model version 3.5.0 terms biolink:knowledge_level and biolink:agent_type.

Small patch - see below

• biolink:InformationContentEntity added to exceptions only triggering a 'warning', not an 'error' validation message.
• Publish the reasoner-validator version to the validation report dump(s)