Add author and tools details in RO-Crate #18820
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mvdbeek
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Sep 17, 2024
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Very nice. Any chance you could also add or extend tests ? 3dbe289#diff-9f3ad661ca1701467f48508ea79951efe90aa29a6d02dec3f2998d831e755bb4 contains the existing examples.
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Thanks a lot for the review and help @mvdbeek ! |
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@OliverWoolland could you review this? I think this solves many of the issues you had about the Workflow Run Crate from Galaxy |
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TO DO in a 2nd time (maybe in a later PR but I'm just putting that here to keep it in mind):
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bgruening
reviewed
Nov 1, 2024
| "name": tool_name, | ||
| "version": tool_version, | ||
| "description": tool_description, | ||
| "url": "https://toolshed.g2.bx.psu.edu", # URL if relevant |
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This is not always true. Tools could come from multiple toolsheds.
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| # Add tools used in the workflow | ||
| self._add_tools(crate) | ||
| self._add_steps(crate) |
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Workflows can have workflow inputs. Should we add them here as well? At least the types of the workflow inputs?
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Here we go again !
I am launching this PR on a bit of work I did to ameliorate the RO-Crate plugin.
I updated the
_add_worfklowfunction. I added the information on the author of the workflow:The update checks if the workflow attribute 'creator_metadata' exist. If it exists, it writes into the ro-crate the name of the creator (if there is no name it leaves a "") same for the idenifier (by default i put the ORCID maybe it's not a good Idea and if there is no Orcid it leaves a ""). If there is no 'creator_metadata' nothing is written on the creator.
I created a function
_add_toolsthat checks the different info inworkflow.stepsto add some tools details:I am not sure if I wrote that the correct way corresponding to the run crate profile (this is a bit obscure to me)
@pauldg What do you think of this ?
Thanks !!