Updated RO-Crate metadata for Galaxy workflow.

[recap]

Updates:

• License is resolvable URI
• Misuse of # for Data Entities; # is for files that do not exist yet like outputs
• url -> contentUrl
• Correct MIME types
• Remove runsOn does not seem to be part of RO-Crate which might break interoperability?
• Service incorrectly in hasPart; hasPart is for Data Entities; Service is contextual.

[andrejcermak]

Could you please reformat the json so it is apparent what the removed and added lines are?

[micafer]

Maybe it is a minor problem, but this element is "orphaned"; it is not linked with any other entity.
This is why, in the previous version, we had the "runsOn" field; maybe it wasn't the best solution, but it links the "destination" with the main entity.

[recap]

Indeed. It is not a minor issue. We need to think how to link it while still being compliant and interoperable.

[recap]

One way is to use softwareRequirements from the spec for ComputationalWorkflow which seems to allow for runtime environments which would be something like:

{
  "@id": "workflow/galaxy_workflow.ga",
  "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
  "name": "Example Galaxy workflow",
  "description": "Example Galaxy workflow reversing a text file.",
  "programmingLanguage": {
    "@id": "https://w3id.org/workflowhub/workflow-ro-crate#galaxy"
  },
  "encodingFormat": "application/json",
  "contentUrl": "https://dockstore.org/api/ga4gh/trs/v2/tools/%23workflow%2Fgithub.com%2Flaitanawe%2Fismb2024%2Fgalaxy_example/versions/main/PLAIN_GALAXY/descriptor//Galaxy-Workflow-reverse_file_galaxy_workflow.ga",
  "softwareRequirements": {
    "@id": "#destination"
  }
}

[recap]

@andrejcermak For semantic diff you can use json diff tools like https://jsoncompare.com/

[andrejcermak]

hi @recap I am currently working on a major change for the whole ROCrate approach, including compliance with the ROCrate standards. I will include your comments from the top of this thread and we can then discuss it.