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Removing Files

🗑️ Deleting Files and Updating Metadata

When removing data files from your project, it's crucial to also update the manifest and associated metadata to maintain consistency.

1. Remove File(s) Using g3t rm

Use the g3t rm command to delete files and automatically update the manifest and metadata:

g3t rm DATA/subject-123/vcf/sample1.vcf.gz

This command performs the following actions:

  • Removes the corresponding entry from MANIFEST/.

Note

It will not:

  • Delete the specified data file.
  • Update or remove related metadata in the META/ directory.

2. Review Changes

After removing files, check the status of your project to see the staged changes:

g3t status

This will display the files marked for deletion and any updates to the manifest and metadata.

3. Update Metadata

If you need to regenerate the metadata after file deletions, use the g3t meta init command:

g3t meta init

Note

This command rebuilds the META/ directory based on the current state of the MANIFEST/, ensuring that your metadata accurately reflects the existing data files.

This command will re-create all metadata in the META/ directory.

If you have customized the metadata, you will need to manually remove the affected DocumentReference entries before running this command to avoid conflicts or inconsistencies.

4. Commit Changes

Once you've reviewed the changes, commit them to your local repository:

g3t commit -m "Removed sample1.vcf.gz and updated associated metadata"
This command records the deletion of the file and the updates to the manifest and metadata.

🚀 Pushing Updates to the Platform

After committing your changes, push them to the ACED-IDP platform to update the remote repository.

1. Push Changes

Use the g3t push command to upload your changes:

g3t push

This command performs the following actions:

  • Validates the updated manifest and metadata.
  • Uploads the changes to the remote repository.
  • Provides logs detailing the outcome of the push operation.

2. Using the --bundle and --overwrite Option

If you have previously pushed changes and want to ensure that the metadata is up-to-date, you can use the --bundle option with the g3t push command:

g3t push --bundle --overwrite

🧾 Reviewing Logs

After pushing your changes, review the logs to confirm that the operation was successful:

  • Logs are stored in the .logs/ directory.
  • Each log entry is a JSON object detailing the status of the submission (e.g., success or error).
  • Example of a successful deletion log entry:

📌 Best Practices

  • Always use g3t rm to delete files to ensure that the manifest and metadata are properly updated.
  • Use g3t meta init to regenerate metadata when necessary, especially after significant changes to your data files.
  • Utilize the --bundle option with g3t push when you need to create a cohesive, versioned set of changes for distribution or archival purposes.
  • Regularly review logs after pushing changes to confirm successful updates.

By following these steps, you can maintain a consistent and accurate state across your data, manifest, and metadata in your ACED-IDP project.