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How to Run a Bulk Export

Instructions

0. Prerequisite -- CLI Installation

If the new (BETA) CLI is not already installed, follow the new (BETA) CLI installation instructions to install it.

An API key will be needed to sign in to the new (BETA) CLI and run commands. This can be the exact same API key used for the Legacy CLI.

If a new API key is needed, follow the documentation for creating a user API key.

1. (Optional) Register external storage

Exporting from 'My Computer'

This step can be skipped if you are exporting data to your local computer.

If you are exporting data to an external storage device, that storage device must first be registered as an External Storage within Flywheel before the export can be started. This provides Flywheel with the necessary information about how to locate and access the storage device.

Follow the documentation explaining how to create a new "External Storage" registration in Flywheel.

2. Start the export

  1. Login using the new (BETA) CLI by running the following command:

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    fw-beta login

  2. The CLI will then prompt for the API key. Enter your API key when prompted.

  3. Start the export using the following command:

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    fw-beta export run -p <project> -s <storage>

    Where:

    • <project> is replaced with the Flywheel Hierarchy of project from which the data should be exported (e.g., fw://demo/Alzheimers)
      • Make sure to wrap this value in double-quotation marks if it contains any spaces (e.g., "fw://flywheel/Brain Tumor Progression")
    • <storage> is replaced with either:
      • The full path to where the data should be downloaded to your local machine (e.g., /Users/jdoe/Desktop/dataset1), or
      • The ID of the External Storage to which the data should be placed exported (e.g., 682e21f7487fc46c72718887).

  4. Once the export begins, the progress of the export will be displayed in the CLI output.

Tip

If you are exporting to an External Storage device, then you can exit out of this progress display by pressing Ctrl+c or by simply closing the terminal window altogether. This has no effect on the export job itself -- the export will still continue to run.

However, if you are exporting to your local computer, then the CLI process should not be terminated until all files are fully downloaded.

Next Steps

References

  1. fw-beta admin storage
  2. fw-beta export run