Upgrade to TRAPI 1.3

[gaurav]

Here are a list of changes from TRAPI 1.2 to TRAPI 1.3 as recorded in the Changelog:

• Check any other changes recorded in GitHub but not summarized above.
• Misc documentation fixes
• Clarification on expectations for /meta_knowledge_graph for KPs and ARAs NCATSTranslator/ReasonerAPI@e2ed87a
  • Improve MetaKnowledgeGraphServiceTest tests #562
• Add support for Qualifiers in KGs and queries https://github.com/NCATSTranslator/ReasonerAPI/pull/330/files
  • Currently in progress in Update TRAPI model to 1.3 #559
• Added NodeBinding.Attributes
  • Currently in progress in Update TRAPI model to 1.3 #559
• Permit unlimited recursion of attributes NCATSTranslator/ReasonerAPI@6ec8ea2
  • Currently in progress in Update TRAPI model to 1.3 #559
• 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
  • Currently in progress in Update TRAPI model to 1.3 #559

Currently in progress:

• Add NodeBinding.query_id property. Optional but a substantial change to current practice NCATSTranslator/ReasonerAPI@dc6e864
  • Currently in progress in Add query_id to NodeBinding #563
• Ensure that CAM-KP-API responds correctly to unsupported constraints #565
  • Currently in review in Check for unsupported constraints #566

The following issues will take too long to implement, so I think we should leave them as TRAPI 1.3 conformance bug until release:

• Clarification on previously-agreed handling of QNode and QEdge additional properties NCATSTranslator/ReasonerAPI@85fefd4
  • Currently in progress in Test for unrecognized properties on QNode and QEdge #560

The following issues are not essential for implementing TRAPI 1.3, and so will not be implemented as part of this issue:

• Add support for Creative Mode #561
• Add test_data_location in x-trapi #556

We don't need to implement the following changes:

• Clarified meaning of batch_size_limit NCATSTranslator/ReasonerAPI@ad3c16a
  • We don't know what the maximum length of any single QNode.ids list should be, so we should probably leave this attribute unset for now and set it later if/when we discover what our limit.
• Clarification on how to properly to specify KP "allowlist"s and "denylist"s via constraints NCATSTranslator/ReasonerAPI@82218fc
  • Not necessary in this release; will be developed later as part of Add support for attribute constraints #567
• Add === operator to Constraint NCATSTranslator/ReasonerAPI@875112b
  • Since we don't have any code for supporting constraints, we don't need to change anything here 😁

This issue covers investigating whether any of these changes are relevant to CAM-KP-API and tracks tickets to apply the relevant fixes. I propose the following syntax:

• Add bullet points underneath each point with any notes on changes required. Ideally, this would either be an explanation of why this issue doesn't affect CAM-KP-API or a link to the issue where the necessary change is made.
• Check off a change once it has been fully dealt with.

[gaurav]

We've deployed CAM-KP-API v0.2 with TRAPI 1.3 to ITRB and updated on https://arax.ncats.io/?smartapi=1. PR #563 still needs to be reviewed, but if anything is wrong with that, I'll make fixes and deploy v0.2.1. Closing.