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upload-dataset

The upload-dataset command uploads a local WEBKNOSSOS dataset to a specified WEBKNOSSOS server. It supports setting the target URL, authentication, renaming the dataset on upload, and parallel execution.

Usage

webknossos upload [OPTIONS] SOURCE

Arguments

  • SOURCE
    Path to your local WEBKNOSSOS dataset.
    Example: /path/to/local/dataset.

Options

  • --webknossos-url
    URL to the WEBKNOSSOS instance.
    Can also be provided via the WK_URL environment variable.

  • --token
    Authentication token for the WEBKNOSSOS instance (see https://webknossos.org/auth/token).
    Can also be provided via the WK_TOKEN environment variable.

  • --dataset-name
    Alternative name to rename your dataset upon upload.
    If not provided, the current dataset name is used.

  • --jobs
    Number of processes to spawn for parallel upload execution.
    Default: 5.

Environment Variables for Remote Paths

When using remote paths (e.g., HTTP or S3), configure the following environment variables:

HTTP Basic Authentication:

  • HTTP_BASIC_USER
  • HTTP_BASIC_PASSWORD

S3 Configuration:

  • S3_ENDPOINT_URL
  • AWS_ACCESS_KEY_ID
  • AWS_SECRET_ACCESS_KEY

Example Commands

Upload a dataset with default settings:

webknossos upload /path/to/local/dataset
Uploads a dataset to the WEBKNOSSOS server specified by WK_URL or to the default url https://webknossos.org.

Upload a dataset with custom configuration:

webknossos upload --webknossos-url https://webknosos.example.com --token YOUR_TOKEN --dataset-name new_name --jobs 4 /path/to/local/dataset
Uploads the dataset with a new name and uses 4 parallel processes.

Notes

  • Ensure the dataset path is accessible and contains a valid WEBKNOSSOS dataset.
  • Provide authentication details via the --token option or the WK_TOKEN environment variable.
  • The command leverages parallel processing to speed up the upload process.
  • Use --dataset-name if you wish to rename the dataset on the server.