Add Tool-Centric APIs to the Tool Shed 2.0

[jmchilton]

Adds the following backend enhancements to galaxy-tool-util...

• Brings in model layer from structured tool state work to describe tool inputs.
• Reworks citation handling for proper separation of parsing into galaxy.tool_util.parser.
• Implement a variety of Pydantic models to describe tool outputs.

... and brings those together to add two new APIs to the Tool Shed 2.0 designed for reasoning about tools outside of Galaxy.

• /api/tools/{trs_tool_id}/version/{version} returns a parsed version of various information from the ToolSource abstraction that is de-coupled from XML and not dependent on Galaxy's Tool classes. The model for this information is:

class ParsedTool(BaseModel):
    id: str
    version: Optional[str]
    name: str
    description: Optional[str]
    inputs: List[ToolParameterT]
    outputs: List[ToolOutput]
    citations: List[Citation]
    license: Optional[str]
    profile: Optional[str]
    edam_operations: List[str]
    edam_topics: List[str]
    xrefs: List[XrefDict]
    help: Optional[str]

• /api/tools/{trs_tool_id}/version/{version}/parameter_request_schema returns a JSON schema that can be used to validate a tool inputs according to the API that will be added with the Galaxy internals portion of the structured tool state PR Structured tool state #17393. This is generated from the metadata model that is exposed via the other API as the inputs field.

This is better than the last attempt #18470 for a variety of reasons - the tool state work has advanced and repeat min and max instance counts are now represented by the schema as are section elements, the tool shed API is much richer and more harmonious (modeling inputs and outputs together should allow for full workflow validation by external tooling, including citations, xrefs, and help in the API should enhance our ability to provide information about tools from sources such the IDE plugin), the caching has been reworked to be more future facing and gracefully handle model changes, and finally this version exposes stock tools as well.

How to test the changes?

(Select all options that apply)

• I've included appropriate automated tests.

License

• I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

[mvdbeek]

Looks great, just some minor comments in line. Can't wait to play with this.

[hexylena]

(Just want to say this is fantastic to see, it'll let me throw away a repository where I collect this data from live servers as the old TS doesn't expose it and I need this metadata. happy day. Thank you @jmchilton!!)

[mvdbeek]

Looks great, let's deploy it. Can you regenerate the conflicting schema ?

[mvdbeek]

This is so awesome, thanks a lot @jmchilton! This will enable so many cool things for a long time to come!

[galaxyproject-sentryintegration]

Suspect Issues

This pull request was deployed and Sentry observed the following issues:

• ‼️ ValueError: too many values to unpack (expected 3) /api/tools/{tool_id}/versions/{tool_version} View Issue
• ‼️ AttributeError: 'NoneType' object has no attribute 'installable_revisions' /api/tools/{tool_id}/versions/{tool_version} View Issue
• ‼️ AttributeError: 'object' object has no attribute 'app' /api/tools/{tool_id}/versions/{tool_version} View Issue
• ‼️ ValidationError: 1 validation error for Citation https://127.0.0.1:9009/repository/display_tool View Issue
• ‼️ AssertionError https://127.0.0.1:9009/repository/display_tool View Issue

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