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Updated RO-Crate metadata for Galaxy workflow. #100
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,69 +1,77 @@ | ||
| { | ||
| "@context": [ | ||
| "https://w3id.org/ro/crate/1.1/context", | ||
| { "runsOn": "https://w3id.org/ro/terms/test#runsOn" } | ||
| ], | ||
| "@graph": [ | ||
| "@context": "https://w3id.org/ro/crate/1.2/context", | ||
| "@graph": [ | ||
| { | ||
| "@id": "./", | ||
| "@type": ["Dataset"], | ||
| "name": "Galaxy Example Workflow", | ||
| "description": "This is an example of a workflow using the Galaxy platform.", | ||
| "license": { | ||
| "@id": "https://spdx.org/licenses/GPL-3.0" | ||
| }, | ||
| "datePublished": "2025-05-06T14:35:47+00:00", | ||
| "mainEntity": { | ||
| "@id": "workflow/galaxy_workflow.ga" | ||
| }, | ||
| "hasPart": [ | ||
| { | ||
| "@id": "./", | ||
| "@type": "Dataset", | ||
| "name": "Galaxy Example Workflow", | ||
| "description": "This is an example of a workflow using the Galaxy platform.", | ||
| "license": "GNU General Public License v3.0", | ||
| "datePublished": "2025-05-06T14:35:47+00:00", | ||
| "mainEntity" : { "@id": "#workflow" }, | ||
| "runsOn" : { "@id": "#destination" }, | ||
| "hasPart": [ | ||
| { "@id": "#workflow" }, | ||
| { "@id": "#textfile" }, | ||
| { "@id": "#destination" } | ||
| ] | ||
| "@id": "workflow/galaxy_workflow.ga" | ||
| }, | ||
| { | ||
| "@id": "ro-crate-metadata.json", | ||
| "@type": "CreativeWork", | ||
| "about": { | ||
| "@id": "./" | ||
| }, | ||
| "conformsTo": { | ||
| "@id": "https://w3id.org/ro/crate/1.1" | ||
| } | ||
| }, | ||
| { | ||
| "@id": "#workflow", | ||
| "@type": [ | ||
| "File", | ||
| "SoftwareSourceCode", | ||
| "ComputationalWorkflow" | ||
| ], | ||
| "name": "Example galaxy workflow", | ||
| "programmingLanguage": { | ||
| "@id": "https://w3id.org/workflowhub/workflow-ro-crate#galaxy" | ||
| }, | ||
| "url": "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" | ||
| }, | ||
| { | ||
| "@id": "https://w3id.org/workflowhub/workflow-ro-crate#galaxy", | ||
| "@type": "ComputerLanguage", | ||
| "identifier": { | ||
| "@id": "https://galaxyproject.org/" | ||
| }, | ||
| "name": "Galaxy", | ||
| "url": { | ||
| "@id": "https://galaxyproject.org/" | ||
| } | ||
| }, | ||
| { | ||
| "@id": "#textfile", | ||
| "@type": "File", | ||
| "name": "simpletext_input", | ||
| "url": "https://example-files.online-convert.com/document/txt/example.txt", | ||
| "encodingFormat": "text/txt" | ||
| }, | ||
| { | ||
| "@id": "#destination", | ||
| "@type" : "Service", | ||
| "url": "https://usegalaxy.eu/" | ||
| "@id": "inputs/example.txt" | ||
| } | ||
| ] | ||
| ] | ||
| }, | ||
| { | ||
| "@id": "ro-crate-metadata.json", | ||
| "@type": "CreativeWork", | ||
| "about": { | ||
| "@id": "./" | ||
| }, | ||
| "conformsTo": { | ||
| "@id": "https://w3id.org/ro/crate/1.2" | ||
| } | ||
| }, | ||
| { | ||
| "@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" | ||
| } | ||
| }, | ||
| { | ||
| "@id": "inputs/example.txt", | ||
| "@type": "File", | ||
| "name": "simpletext_input", | ||
| "encodingFormat": "text/plain", | ||
| "contentUrl": "https://example-files.online-convert.com/document/txt/example.txt" | ||
| }, | ||
| { | ||
| "@id": "https://w3id.org/workflowhub/workflow-ro-crate#galaxy", | ||
| "@type": "ComputerLanguage", | ||
| "name": "Galaxy", | ||
| "identifier": { | ||
| "@id": "https://galaxyproject.org/" | ||
| }, | ||
| "url": { | ||
| "@id": "https://galaxyproject.org/" | ||
| } | ||
| }, | ||
| { | ||
| "@id": "#destination", | ||
| "@type": "Service", | ||
| "name": "Galaxy Europe", | ||
| "description": "Galaxy workflow execution service", | ||
| "url": { | ||
| "@id": "https://usegalaxy.eu/" | ||
| } | ||
| } | ||
| ] | ||
| } | ||
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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.
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Indeed. It is not a minor issue. We need to think how to link it while still being compliant and interoperable.
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One way is to use softwareRequirements from the spec for ComputationalWorkflow which seems to allow for
runtime environmentswhich would be something like:There was a problem hiding this comment.
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@andrejcermak For semantic diff you can use json diff tools like https://jsoncompare.com/