sheepdog-exporter 🐑🐑

Export metadata from the DCP!

First, download your credentials from the DCP Web interface.

Then, install sheepdog exporter: pip install sheepdog-exporter.

You can now find programs to export using: sheepdog-exporter!

Once you've found a program and project you want to export, use: sheepdog-exporter my_program my_project. This will create a JSON file in the current directory with all of the relevant metadata!

You can change the output path, path to your credentials, or the DCP URL using arguments:

sheepdog-exporter program project --dcp-url my-url --credentials path/to/credentials --output-path /path/to/write/output

The resulting JSON has the form:

{
  "data_objects": [{DataObject},...],
  "metadata": {
        metadata_type: [{metadata_value}], ...
  }
}

Metadata types that are expected to have files associated with them will have an object_id that matches an object_id in the data object manifest.

Development

• A simple test demonstrates usage of the Exporter class in test.

Using the Python API

The exporter is available for reuse from your Python code, instantiate it with the location of the credentials.json and the location of the DCP instance you would like to export from:

from sheepdog_exporter import Exporter
exporter = Exporter('path/to/credentials', 'https://dcp.bionimbus.org')
my_export = exporter.export('topmed', 'public')

Other convenience methods are available for listing programs and projects: .get_projects() and .get_programs().

See sheepdog_exporter.py for more.

Releases

Releases are made on the creation of a new tag. Versioning follows semantic versioning practices. Any breaking changes to the API should result in a change in the major version.

To change the release maintainer, edit the travis.yml to remove the pypi release details. Then follow the directions on encrypting your PyPi credentials using Travis CLI.

Issues

• Provenance to the original JSON schemas are lost. #9
  • It has not been tested if JSON dumps can be used as sheepdog input.
• Some functions in the exporter are unused.
• Print messages cannot be easily suppressed. #12
• Errors in converting data from DCP are not always relayed properly to the CLI. #11