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Document somewhere the special cbrain flag for Boutiques descriptors #1128

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prioux opened this issue Jun 9, 2021 · 6 comments · May be fixed by #1378
Open

Document somewhere the special cbrain flag for Boutiques descriptors #1128

prioux opened this issue Jun 9, 2021 · 6 comments · May be fixed by #1378
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@prioux
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prioux commented Jun 9, 2021

The CBRAIN Boutiques integrator supports a set of special flags in the "custom" field of the descriptor.

Document them all somewhere?

At the top of my head:

"custom": {
  "cbrain:author": "descriptor author",
  "cbrain:inherits-from-class": "ClassName",
  "cbrain:can-submit-new-tasks": truefalse,
  "cbrain:ignore-exit-status": truefalse,
  "cbrain:ignore_outputs": [id, id, id],
  "cbrain:save_back_inputs": [id, id, id],
  "cbrain:readonly-input-files": truefalse,
  "cbrain:alters-input-files": truefalse
}
@MontrealSergiy
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MontrealSergiy commented Aug 23, 2022

Also code bases (templates) contain cbrain:alters-input-files

I see also

  • cbrain:boutiques_bosh_exec_mode
  • cbrain:walltime-estimate
  • also multiple cbrain:integrator_modules

Could go somewhere into developer's wiki, readme of cbrain-neuro-plugins or cbrain.ca. Also I believe @natacha-beck had a wiki on boutiques integration, not sure why it did not get into the main wiki.

Update, checked today

@natacha-beck
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@MontrealSergiy here is the page you are refering: https://github.com/natacha-beck/cbrain-wiki/wiki/Tasks-Integration-With-Boutiques

It was document about old Boutiques integration. We should at least have documentation about both way to integrate Boutiques (in cbrain_task_descriptors and in boutiques_descriptors).

@MontrealSergiy
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actually there is a designated CBRAIN Boutiques wiki section now, is it a good place for it?
https://github.com/aces/cbrain/wiki/Tool-integration-with-Boutiques-or-Scientific-tool-integration-in-CBRAIN

@MontrealSergiy
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@MontrealSergiy MontrealSergiy self-assigned this Jan 17, 2024
@prioux
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prioux commented Jan 18, 2024

I want this documentation to be part of the codebase.

I am not sure which file is more appropriate, but given we have a library for loading and accessing Boutiques descriptor files, maybe we should put it there.

A larger comment block should enumerate them all in a table. Then we could have a nice new set of accessor methods for each of the special flags, something like

# Return the CBRAIN author of the descripto from the custom field
#    "custom": { "cbrain:author": "Name of person" }
def custom_cbrain_author
   self.custom['cbain:author']
end

This would also allow us to handle gracefully the inconsistencies we have in these custom sections (e.g. some descriptors have cbrain:author as a string, some as an array of strings).

@prioux
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prioux commented Jan 18, 2024

Once the methods are all nicely created, we can modify the integration code to use these methods instead of trying to directly access the custom structure.

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