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File lists and Boutiques-based tools #831

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MontrealSergiy opened this issue Jun 27, 2019 · 1 comment
Closed

File lists and Boutiques-based tools #831

MontrealSergiy opened this issue Jun 27, 2019 · 1 comment

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@MontrealSergiy
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MontrealSergiy commented Jun 27, 2019

Intro:
CBRAIN supports import of tools in Boutiques format. Regretfully, input parameters of FIle type in Boutiques tool descriptors, are not properly supported in CBRAIN, while, I think users and tool developers could benefit from full file list support.

An example of the file list input in Boutiques format:

        {
            "id": "list",
            "value-key": "[list]",
            "list": true,
            "command-line-flag": "--list",
            "description": "Some file list. Could be e.g. the list of files with MRI data to analyze.",
            "type": "File",
            "name": "files (with MRI data_"
        },

(see https://raw.githubusercontent.com/MontrealSergiy/cbrain-plugins-eeg/bugs/cbrain_task_descriptors/filelistbug.json for full descriptor)
CBRAIN seemingly imports boutiques descriptors with file lists without any warning or error message, configuring and executing tool's task is ridden with several issues.

Steps to reproduce issues:

  1. Create boutiques with a file list input, download from above GitHub link, ( or copy one from Boutiques tests).
  2. Import boutiques into CBRAIN;
  3. Create a task and a) try to populate the input with more than one file b) run it (with one file list).

Observed: User can only supply one file per input, and, anyway, the command line will be malformed and (usually) fail

Expected: User should be able to provide multiple files and put them into file list, perhaps in the same way he can create integer or string lists

Note 1: The lists of numbers or strings are supported by CBRAIN, the problem is with file lists

Note 2: Older versions of boutiques had a few issues with file lists, which are fixed by now

@MontrealSergiy MontrealSergiy changed the title support for boutiques with file lists support for boutiques' file lists Jun 27, 2019
@MontrealSergiy MontrealSergiy changed the title support for boutiques' file lists Support for boutiques' file lists Jun 27, 2019
@MontrealSergiy MontrealSergiy changed the title Support for boutiques' file lists File lists and Boutiques-based tools Jun 27, 2019
prioux added a commit to prioux/cbrain that referenced this issue Jun 27, 2019
1- The controls channel for Bourreau has a new 'StopYourself'
   command, which is much more efficient than the old way
   of stopping the rails app using an external script.
   Fixes aces#55 .
2- The 'ibc' utility provides access to it with the 'J' command
3- Tooltips in the interface could never be positioned
   at offset_x set to 0 because 0 is falsy in javascript. Fixed.
4- We no longer ever keep a backup of database.yml on remote sites.
5- Userfiles viewers that have conditions which crash no
   longer prevent the 'show' page from rendering; instead the
   viewer is ignored and removed from the available list.
   Fixes aces#25
6- Task forms for boutiques tasks will present list
   inputs in proper order.
   Fixes aces#830
7- Support for lists for File inputs in boutiques
   Fixes aces#831
@prioux
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prioux commented Jul 2, 2019

Implemented in #832

@prioux prioux closed this as completed Jul 2, 2019
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