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TranslatorSRI / SRI_testing

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Upgrade SRI Testing harness to accept and adequately validate TRAPI 1.3 #41

Closed RichardBruskiewich closed 2 years ago

RichardBruskiewich commented 2 years ago

See https://github.com/NCATSTranslator/ReasonerAPI/tree/1.3

In particular, see the change log in https://github.com/NCATSTranslator/ReasonerAPI/pull/340

RichardBruskiewich commented 2 years ago

SRI Testing currently simply relies directly on the reasoner-validator module which itself just relies on the jsonschema module validation of the TRAPI schema.

It would appear that the current iteration of TRAPI 1.3 (as of this date, 25-8-2022) has problematic validation. For example, the following error trace is thrown for the infores:sri-reference-kg based on the current 1.3.0 TRAPI: 

FAILED     [ 58%][{'node_bindings': {'a': [{'id': 'MGI:1928401', 'query_id': None, 'attributes': None}], 'b': [{'id': 'GO:0035371', 'query_id': None, 'attributes': None, 'qnode_id': 'GO:0035371'}]}, 'edge_bindings': {'ab': [{'id': 'uuid:3aed51ea-d0a0-11ec-b00f-0242ac110002', 'attributes': None}]}, 'score': None},

 ...] is not of type 'object'

Failed validating 'type' in schema:
    {'additionalProperties': True,
     'components': {'schemas': {'AsyncQuery': {'additionalProperties': True,
                                               'description': 'The AsyncQuery class is effectively the same as the Query class but it requires a callback property.',
                                               'properties': {'callback': {'description': 'Upon completion, this server ...'
                                                                           'format': 'uri',
                                                                           'pattern': '^https?://',
                                                                           'type': 'string'},
                                                              'log_level': {'oneOf': [{'allOf': [{'$ref': '#/components/schemas/LogLevel'}],
                                                                                       'description': 'The least critical level of logs to return'},
                                                                                      {'type': 'null'}]},
                                                              'message': {'$ref': '#/components/schemas/Message',
                                                                          'description': 'The query Message is a serialization ...},
etc.
RichardBruskiewich commented 2 years ago

The back end reasoner-validator jsonschema validation is now patched to validate 1.3.0 with commit https://github.com/NCATSTranslator/reasoner-validator/commit/d566566f3389703d73f18cfef7908b16df2689d6 (but some TRAPI 1.4.0 remedial work needed in the future).