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New Boutiques module to validate strings used as filenames #1447

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prioux opened this issue Nov 20, 2024 · 1 comment · Fixed by #1451
Closed

New Boutiques module to validate strings used as filenames #1447

prioux opened this issue Nov 20, 2024 · 1 comment · Fixed by #1451
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@MontrealSergiy
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Boutiques Boutiques integration Enhancement User Interface

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@prioux
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prioux commented Nov 20, 2024 •
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Many tools integrated with boutiques descriptors have inputs of type 'String' that are used to provide a output path or basename for whatever files the tool is going to create. These are also used as part of the templates in the 'output' sections to tell CBRAIN what is to be saved int he database.

For exmaple, in the "inputs" section:

        {
            "description": "The name of the folder to store outputs of XCPD processing.",
            "id": "output_dir",
            "name": "output_dir",
            "optional": false,
            "type": "String",
            "value-key": "[OUTPUT_DIR]",
            "default-value": "xcpd_output"
        }

and in the "output-files" section:

        {   
            "name": "XCPD Subject Output Directory",
            "id":  "xcpd_output_dir",
            "description": "Subject level output for XCP-D",
            "optional":  false,
            "path-template": "[OUTPUT_DIR]"
        }

The prevent problems, right from the start before launching a task, we should validate them a little bit and make sure they respect the rules that CBRAIN impose for userfiles. A new custom modules need to be implemented which would be provided with the IDs of "String" inputs to check against the CBRAIN userfile naming rules, e.g.

        "cbrain:integrator_modules": {
            "BoutiquesOutputNameValidator": [ "output_dir", "other_id", "other_id_2" ]
        }
@prioux
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prioux commented Nov 20, 2024

The Ruby method to validate names is

   ok = Userfile.is_legal_filename?(name_to_check)

MontrealSergiy added a commit to MontrealSergiy/cbrain that referenced this issue Nov 26, 2024
@MontrealSergiy
Boutiques output file name verification aces#1447
609cb8d
MontrealSergiy added a commit to MontrealSergiy/cbrain that referenced this issue Nov 27, 2024
@MontrealSergiy
Minor corrections. To reduce integration experts confusion, module is…
1b62725 
… called File Name Verifier in same vein with file name matcher aces#1447
MontrealSergiy added a commit to MontrealSergiy/cbrain that referenced this issue Nov 27, 2024
@MontrealSergiy
Bourreau link for Boutiques File Name Verifier Module aces#1447
edd5514
@MontrealSergiy MontrealSergiy linked a pull request Nov 27, 2024 that will close this issue
File name verifier #1451
Merged
@MontrealSergiy MontrealSergiy mentioned this issue Nov 27, 2024
Merged
@MontrealSergiy MontrealSergiy removed a link to a pull request Dec 2, 2024
File name verifier #1451
Merged
MontrealSergiy added a commit to MontrealSergiy/cbrain that referenced this issue Dec 5, 2024
@MontrealSergiy
[bugfix] block download files of undetermined (yet) size aces#1447
982d862
MontrealSergiy added a commit to MontrealSergiy/cbrain that referenced this issue Dec 6, 2024
@MontrealSergiy
[bugfix] block download files of undetermined (yet) size. Remove redu…
851a2f2 
…ndant code aces#1447
@MontrealSergiy MontrealSergiy linked a pull request Dec 16, 2024 that will close this issue
File name verifier #1451
Merged
prioux pushed a commit that referenced this issue Jan 16, 2025
@MontrealSergiy
[bugfix] block download files of undetermined (yet) size #1447 (#1453)
2a41096
MontrealSergiy added a commit to MontrealSergiy/cbrain that referenced this issue Jan 16, 2025
@MontrealSergiy
reduce docs/comments to most essential, add empty custom property check
fad65a5 
aces#1447
MontrealSergiy added a commit to MontrealSergiy/cbrain that referenced this issue Jan 16, 2025
@MontrealSergiy
format doc json properly aces#1447
39e13fb
prioux pushed a commit that referenced this issue Jan 16, 2025
@MontrealSergiy
File name verifier (#1451)
057739d 
Boutiques output file name verification #1447
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File name verifier MontrealSergiy/cbrain
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