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Releases: NCATSTranslator/reasoner-validator

ID Prefix mapping bug fix, silencing of workflow spec null values, plus some tech debt clean-up

10 Jan 03:34
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  • pydantic updated to 1.10.13
  • Small clean-up of trapi_validator.py CLI help text
  • gitignore JSON files in scripts subfolder to allow local validation of said JSON files without committing them to the repo
  • silenced warnings about missing workflow schema defined 'parameters' and 'runner_parameters' (workflow schema allows these to be null but...) - but keeping the validation codes in the codes.yaml (for now)
  • fixed subtle bug with id prefix mapping validation

node name error to warning; workflow sanitization restored

26 Sep 05:49
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  • Demote 'knowledge_graph.node.name.missing' validation error into a warning.
  • Restore TRAPI 'workflow' sanitization to fix null 'parameters' or 'runner_parameters', pending future repairs to the workflow schema (i.e. 'nullable: true' directives?)

v3.9.3

19 Sep 23:01
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  • Added (optional) OpenTelemetry functionality for web service.

fix dangling nodes validation

12 Sep 23:49
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  • demoted dangling nodes 'error' down to 'warning' message, annotated with the list of missing nodes as the identifier

v3.9.1

11 Sep 19:47
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  • Upgrade to Biolink Model Toolkit 1.1.2
  • Removed all residual references to 'sanitize_trapi_response()' (warning: validation with pre-release versions of TRAPI 1.4 earlier than 1.4.2 may trigger some funny false positive validation messages)
  • BiolinkValidator.PREDICATE_INCLUSIONS added (just with "biolink:interacts_with") to bypass 'mixin' Biolink Model validation error (pending full community review of the 'mixin' status of this predicate); unit tests modified to suit
  • plus a small internal DRY refactor in test suit with respect to LATEST_BIOLINK_MODEL_VERSION

Detect uniformative, dangling and nameless nodes

04 Sep 21:11
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  • Detect missing knowledge_graph names (resolves part of issue#35)
  • detection of uninformative QNodes (resolve issue#14)
  • Dangling ("unused") nodes detection is fully implemented (complements "edge nodes not in nodes list" detection already in place); resolves issue#74

Minor patch to validation messages for qualifiers and attributes

01 Sep 19:39
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  • 'attribute_type_id' term which are Biolink (node) 'category' or (edge) 'predicate' terms generate a specific warning (not just a 'not an association slot' warning)
  • Knowledge graph edge qualifiers qualifier "value unresolved" validation error demoted to a warning

Additional patch to qualifier value validation of 'empty' values

21 Aug 19:30
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"error.knowledge_graph.edge.attribute.value.empty" should not now be triggered by numeric zeros

Attribute value validation patch

18 Aug 02:30
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  • 'False' attribute values now properly handled; all other 'empty' values will continue to trigger an error message

Validation quality patch

17 Aug 05:52
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  • Add additional JSON element path context to "critical.trapi.validation" validation messages
  • Remove TRAPI Response JSON sanitization, since TRAPI 1.4.2 is now the 'latest' and desired validation standard