ChangeLog.md

Change Log TRAPI 1.4.0 (2023-06-23) -> 1.5.0 (2023-05-26)

https://github.com/NCATSTranslator/ReasonerAPI/compare/v1.4.0...1.5

• Add x-trapi pathfinderquery: true/false https://github.com/NCATSTranslator/ReasonerAPI/pull/487/files

• Add x-trapi multicuriequery: true/false https://github.com/NCATSTranslator/ReasonerAPI/pull/488/files

• Fix minor syntax errors https://github.com/NCATSTranslator/ReasonerAPI/pull/485/files

• Update knowledge_level_agent_type_specification.md https://github.com/NCATSTranslator/ReasonerAPI/pull/486/files

• Add QNode.member_ids https://github.com/NCATSTranslator/ReasonerAPI/pull/481/files

• Change workflow schema to https and version 1.3.5 https://github.com/NCATSTranslator/ReasonerAPI/commit/aeddb4323ed9fd5aead5986c5e5ffbab167e6524 https://github.com/NCATSTranslator/ReasonerAPI/commit/1fdd0351c8edfb59d8fcf52dfe387f5547f1fc27 https://github.com/NCATSTranslator/ReasonerAPI/commit/6c4215a92a5895cdb9062124700a5c84b5e1c249

• Revert OneOf to additionalProperties (TRAPI 1.4.2 correction) https://github.com/NCATSTranslator/ReasonerAPI/commit/795b13836bde2042687cbd7927f10e6dbee923e1 https://github.com/NCATSTranslator/ReasonerAPI/commit/98077dd71f6c582ff71ac32719c708c118132245

• Make Query.message a oneOf $ref and nullable false https://github.com/NCATSTranslator/ReasonerAPI/commit/1f9a9828a1dbeb146bb34de9b8bda2277895b985

• Fix ambiguiities in Response https://github.com/NCATSTranslator/ReasonerAPI/commit/55ccfdfa9a9988a1f271dd28708c9ade0fc347bf

• convert to oneOf with - https://github.com/NCATSTranslator/ReasonerAPI/commit/505ddb954310eab37d58d37be881006751dda5e2

• Fix EdgeBinding and AuxGraph https://github.com/NCATSTranslator/ReasonerAPI/commit/91cd63b174b81d6d7629ae478f0a8d4eb4bd60ec

• Insert missing dashes at lines 267 and 320 https://github.com/NCATSTranslator/ReasonerAPI/commit/c17fe1be1dbc131800cfab444a7b739b8b75a3cc https://github.com/NCATSTranslator/ReasonerAPI/commit/ffb2fedf1a8788e75714e9f140afee936feba060

• Make attributes required with minItems 0 https://github.com/NCATSTranslator/ReasonerAPI/commit/e5f52be4f47391e8f3496dcfc538c0764a5824b3

• Make Query.message a oneOf $ref and nullable false https://github.com/NCATSTranslator/ReasonerAPI/commit/cc2b67d1c5f93dd62c934080c11607a2e15c5100

• Fix EdgeBinding and AuxGraph https://github.com/NCATSTranslator/ReasonerAPI/commit/6d5bfdb7cff85a216df3830fce36a63db22976d3

• Set_interpretation and is_set changes https://github.com/NCATSTranslator/ReasonerAPI/pull/475/files

• Add bypass_cache https://github.com/NCATSTranslator/ReasonerAPI/pull/473/files Implementation note: bypass_cache MUST be passed down to downstream queries: ARS -> ARAs -> KP2 -> NodeNorm

• Clarify minItems 1 for Attributes https://github.com/NCATSTranslator/ReasonerAPI/pull/472/files

• Clarify NodeBinding https://github.com/NCATSTranslator/ReasonerAPI/pull/468/files

• Make Message.Results minItems 0 https://github.com/NCATSTranslator/ReasonerAPI/pull/464/files

• Make logs minItems: 1 https://github.com/NCATSTranslator/ReasonerAPI/pull/466/files

• Clarify Result Not yet merged. Abrar checking on a potential snag https://github.com/NCATSTranslator/ReasonerAPI/pull/467/files

Documentation updates:

• Update retrieval_provenance_specification https://github.com/NCATSTranslator/ReasonerAPI/commit/78dafcf07f33dc0511e8a18c7f801fd68226d73e https://github.com/NCATSTranslator/ReasonerAPI/commit/4d3e457b7e46425548cf855562127e67de2757e5

• Update supporting_publications_specification https://github.com/NCATSTranslator/ReasonerAPI/commit/b856d79c4df1fe2dbba937ddb339019958cb1150

Minor updates during the beta phase:

• Pending

Change Log TRAPI 1.3 (2022-09-01) -> 1.4-beta (2023-03-23)

https://github.com/NCATSTranslator/ReasonerAPI/compare/v1.3.0...1.4

• Edge.predicate switched to nullable false and made required, Edge.subject and Edge.object switched to nullable false https://github.com/NCATSTranslator/ReasonerAPI/pull/377/files

• External workflow schema updated from version 1.0.0 to version 1.3.2 https://github.com/NCATSTranslator/ReasonerAPI/pull/365/files

• Node.categories clarified that they SHOULD be Biolink Model categories and MUST NOT be of type 'abstract' or 'mixin'. 'deprecated' categories SHOULD also be avoided. https://github.com/NCATSTranslator/ReasonerAPI/pull/383/files

• In MetaKnowledgeGraph component, added MetaEdge.qualifiers as list of new MetaQualifier types https://github.com/NCATSTranslator/ReasonerAPI/pull/387/files

• Add /async_query_status/{job_id} endpoint https://github.com/NCATSTranslator/ReasonerAPI/pull/395/files

• Constrain Qualifier.qualifier_type_id to be a biolink CURIE https://github.com/NCATSTranslator/ReasonerAPI/pull/391/files

• Encoding extra supporting graph information in TRAPI This is a complex breaking change that moves Result.edge_bindings into Result.analyses which link to AuxiliaryGraph objects https://github.com/NCATSTranslator/ReasonerAPI/pull/389/files

• Enhance encoding of EPC retrieval sources by adding Edge.sources as list of RetrievalSource items (required, minItems: 1) https://github.com/NCATSTranslator/ReasonerAPI/pull/393/files

• Switch all cases of "allOf" to "oneOf" to be compatible with actual schema semantics and TRAPI (JSONSchema) validation https://github.com/NCATSTranslator/ReasonerAPI/pull/403/files

• New properties Response.schema_version and Response.biolink_version to aid in TRAPI (JSONSchema) validation https://github.com/NCATSTranslator/ReasonerAPI/pull/405/files

Minor updates during the beta phase:

• Everyone should be tagging at 1.4.0: https://github.com/NCATSTranslator/ReasonerAPI/pull/419/files

• Change RetrievalSource.resource and upstream_resources to RetrievalSource.resource_id and upstream_resource_ids for consistency: https://github.com/NCATSTranslator/ReasonerAPI/pull/418/files

• Change Analysis.reasoner_id to Analysis.resource_id

• Version v1.4.0-beta2 was corrupted somehow and should not be used. It is replaced by v1.4.0-beta3

Change Log TRAPI 1.2 -> 1.3

https://github.com/NCATSTranslator/ReasonerAPI/compare/v1.2.0...1.3

• Add test_data_location in x-trapi https://github.com/NCATSTranslator/ReasonerAPI/pull/339/files

• Add flag for knowledge_type flag for Creative Mode https://github.com/NCATSTranslator/ReasonerAPI/pull/331/files

• Add support for Qualifiers in KGs and queries https://github.com/NCATSTranslator/ReasonerAPI/pull/330/files

• Add knowledge_types support to /meta_knowledge_graph https://github.com/NCATSTranslator/ReasonerAPI/pull/333/files

• Add === operator to Constraint https://github.com/NCATSTranslator/ReasonerAPI/commit/875112b7a349c9f8e89bb5660725af5c895c9a24

• Clarified meaning of batch_size_limit https://github.com/NCATSTranslator/ReasonerAPI/commit/ad3c16a3ecc085cc041b0ebbeeb7f0803e054fd0

• Misc documentation fixes

• Add NodeBinding.query_id property. Optional but a substantial change to current practice https://github.com/NCATSTranslator/ReasonerAPI/commit/dc6e864af5e498f7e420318b16be7d4a2f9a03ef

• Clarification on expectations for /meta_knowledge_graph for KPs and ARAs https://github.com/NCATSTranslator/ReasonerAPI/commit/e2ed87aa4f02dac55dcbd8eac7e190b8c188fbdd

• Permit unlimited recursion of attributes https://github.com/NCATSTranslator/ReasonerAPI/commit/6ec8ea28f3262ac163803622017bb651a4adac33

• Added NodeBinding.Attributes

• Clarification on how to properly to specify KP "allowlist"s and "denylist"s via constraints https://github.com/NCATSTranslator/ReasonerAPI/commit/82218fc86be74755ec1ffa9b8679eac0075df364

• Clarification on previously-agreed handling of QNode and QEdge additional properties https://github.com/NCATSTranslator/ReasonerAPI/commit/85fefd44925652a5b2e9648fef1d6c70c5099ea9

Change Log TRAPI 1.1 -> 1.2

• /predicates endpoint is REMOVED https://github.com/NCATSTranslator/ReasonerAPI/pull/261/files

• Removed all 'relation' properties in Edge, QEdge, MetaEdge

• /meta_knowledge_graph allows optional attributes[] property (encouraged but not required) https://github.com/NCATSTranslator/ReasonerAPI/pull/259/files

• Add support for workflow and operations v1.0.0 (encouraged but not yet required) https://github.com/NCATSTranslator/ReasonerAPI/pull/262/files

• /asyncquery endpoint added (recommended but not required) https://github.com/NCATSTranslator/ReasonerAPI/pull/255/files https://github.com/NCATSTranslator/ReasonerAPI/pull/263/files

• Add result.score (highly encouraged but not required) https://github.com/NCATSTranslator/ReasonerAPI/pull/247/files

• /meta_knowledge_graph should only include specific relationships, not ancestor-inferred relationships (policy clarification)

• Add one level of subattributes to Attribute https://github.com/NCATSTranslator/ReasonerAPI/pull/268/files

• Add attributes[] to EdgeBinding to complement Edge and Node https://github.com/NCATSTranslator/ReasonerAPI/pull/269/files

• QNode.constraints and QEdge.constraints no longer nullable. Now use empty list as default instead of null https://github.com/NCATSTranslator/ReasonerAPI/pull/286/files

Change Log TRAPI 1.0 -> 1.1

• Many changes to "info" template at top. Please refresh to the latest template
• info.version is now your API version not TRAPI version
• x-trapi now contains the official TRAPI version
• x-translator now contains mandatory metadata
• Remove tag "reasoner". Add tag "trapi"
• /predicates endpoint is marked deprecated
• New /meta_knowledge_graph endpoint replaces /predicates endpoint. Note that counts are optional as defined in extended schema
• log_level property in Query specifies desired logging level in Response
• QNode.id pluralized to ids and changed from CURIE or array of CURIEs to just array of CURIEs with array length > 0
• QNode.category pluralized to categories and changed from BiolinkEntity or array of BiolinkEntitys to just array of BiolinkEntitys with array length > 0
• QNode.predicate pluralized to predicates and changed from BiolinkPredicate or array of BiolinkPredicates to just array of BiolinkPredicates with array length > 0
• Attribute class extended and properties renamed
• QNode.constraints and QEdge.constraints as array of Constraint added