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[ENH] Add -u flag to dataget instruction #435

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[ENH] Add -u flag to dataget instruction #435

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@surchs surchs commented Jan 11, 2025 •
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This will help ensure dataget runs as the
current user

Changes proposed in this pull request:

NOTE: If this pull request is to be released, the release label must be applied once the review process is done to avoid the local and remote from going out of sync as a consequence of the bump version workflow run

Checklist

This section is for the PR reviewer

  • PR has an interpretable title with a prefix ([ENH], [FIX], [REF], [TST], [CI], [MNT], [INF], [MODEL], [DOC]) (see our Contributing Guidelines for more info)
  • PR has a label for the release changelog or skip-release (to be applied by maintainers only)
  • PR links to GitHub issue with mention Closes #XXXX
  • Tests pass
  • Checks pass
  • If the PR changes the participant-level and/or the dataset-level result file, the query-tool-results files in the neurobagel_examples repo have been regenerated

For new features:

  • Tests have been added

For bug fixes:

  • There is at least one test that would fail under the original bug conditions.

Summary by Sourcery

Enhancements:

  • Ensure downloaded data is owned by the current user.

@surchs
[ENH] Add -u flag to dataget instruction
2f6fe43 
This will help ensure dataget runs as the
current user
@sourcery-ai Sourcery AI
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sourcery-ai bot commented Jan 11, 2025 •
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Reviewer's Guide by Sourcery

This pull request adds the -u flag to the docker run command used by the dataget instruction. This flag sets the user and group ID of the container to match the current user, ensuring that downloaded files are owned by the current user and not root. This change addresses permission issues that could arise when running dataget as a non-root user.

Sequence diagram for dataget command execution with user permissions

sequenceDiagram
    participant User as User
    participant Docker as Docker Container
    participant FS as File System

    User->>Docker: Run dataget with -u $(id -u):$(id -g)
    Note over Docker: Container runs with user's UID/GID
    Docker->>FS: Create output directory
    Docker->>FS: Download and write data
    Note over FS: Files owned by user's UID/GID
    FS-->>User: Access downloaded files with correct permissions
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File-Level Changes

Change Details Files
Added the -u flag to the docker run command to ensure the container runs with the user's UID/GID.
  • Added -u $(id -u):$(id -g) to the docker run command.
  • Added an explanation to the help text about the -u flag and its purpose to clarify the change for users.
  • Updated the path to the query results file in the docker run command from neurobagel-query-results-with-URIs.tsv to neurobagel-query-results.tsv
 src/components/GetDataDialog.tsx

Assessment against linked issues

Issue Objective Addressed Explanation
#431 Include -u flag to change user to current user in the docker run command ✅
#431 Update the docker run command to use the correct input file name ✅
#431 Add a note explaining the purpose of the -u flag ✅

Possibly linked issues

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netlify bot commented Jan 11, 2025 •
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@surchs surchs mentioned this pull request Jan 11, 2025
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@surchs surchs added the pr-documentation Change that only affects user documentation label Jan 11, 2025
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Update code snippet for dataget
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