Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

deno validator: --filenameMode still wants dataset path and then seems to do more than just paths validation #14

Open
yarikoptic opened this issue Jun 24, 2024 · 1 comment
Labels
bug Something isn't working

Comments

@yarikoptic
Copy link
Contributor

(deno) yoh@typhon:/mnt/DATA/data/yoh/1076_spacetop$ git ls-tree -r --name-only HEAD | /home/yoh/proj/bids/bids-validator/bids-validator/./bids-validator-deno --filenameMode
A new release of Deno is available: 1.44.3 → 1.44.4 Run `deno upgrade` to install it.

Usage:   bids-validator <dataset_directory>
Version: v1.14.7-dev.0-68-g53fdba69

Description:

  This tool checks if a dataset in a given directory is compatible with the Brain Imaging Data Structure specification. To learn more about
  Brain Imaging Data Structure visit http://bids.neuroimaging.io

Options:

  -h, --help                    - Show this help.
  -V, --version                 - Show the version number for this program.
  --json                        - Output machine readable JSON
  -s, --schema          <type>  - Specify a schema version to use for validation                          (Default: "latest")
  -v, --verbose                 - Log more extensive information about issues
  --ignoreNiftiHeaders          - Disregard NIfTI header content during validation
  --debug               <type>  - Enable debug output                                                     (Default: "ERROR", Values: "NOTSET", "DEBUG", "INFO",
                                                                                                          "WARN", "ERROR", "CRITICAL")
  --filenameMode                - Enable filename checks for newline separated filenames read from stdin

  error: Missing argument(s): dataset_directory

and from the --filenameMode - Enable filename checks for newline separated filenames read from stdin it sounds like it should not require dataset path. MAy be I also misunderstood the purpose -- is this option to restrict the set of files to validate for? or operate only on file names? (@effigies mentioned that mode)

@nellh nellh added the bug Something isn't working label Jun 25, 2024
@nellh
Copy link
Member

nellh commented Jun 25, 2024

We use the filename mode to implement the OpenNeuro git hook but it does look broken in the Deno validator. It should skip reading local files and validate filenames from stdin.

@effigies effigies transferred this issue from bids-standard/legacy-validator Nov 4, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working
Projects
None yet
Development

No branches or pull requests

2 participants