Ro crate validator

[AbbyGavin]

Adding validation to uploaded RO crates. This uses a python based validator: https://github.com/crs4/rocrate-validator. Currently this doesn't have version 1.3 validation, though they have an issue for it crs4/rocrate-validator#179. It doesn't support version 1.0 crates, so we first check if the crate contains an ro-crate-metadata.json file. If it doesn't, we pass through to the existing validation since version 1.0 crates use an ro-crate-metadata.jsonld file instead.

Fixes #1191.

[Copilot]

Pull request overview

This PR introduces RO-Crate validation during workflow RO-Crate uploads by invoking a Python-based validator before attempting to parse/extract the crate, and updates tests to reflect the new validation/error behavior.

Changes:

• Add a Python script (script/validate-ro-crate.py) to run RO-Crate validation and print validation issues.
• Invoke the validator from WorkflowCrateExtractor only when the crate includes ro-crate-metadata.json (i.e., not RO-Crate 1.0 .jsonld crates).
• Update test expectations (including normalized source_link_url with a trailing slash and new validation error messaging).

Reviewed changes

Copilot reviewed 4 out of 10 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
app/forms/workflow_crate_extractor.rb	Adds conditional pre-parse RO-Crate validation via an external Python validator.
script/validate-ro-crate.py	New validator runner script that prints validation issues for the Ruby layer to surface.
requirements.txt	Adds the validator dependency and updates cwltool version.
test/functional/workflows_controller_test.rb	Updates expectations for the new validation error output.
test/integration/api/git_workflow_ro_crate_api_test.rb	Updates expectations for source_link_url normalization (trailing slash).

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[fbacall]

On hold for now - Investigating some performance issues of the validator library on crates with large numbers of entities