Enhance Invenio RDM integration

[davelopez]

• Avoid erroring out when serializing file sources without credentials
• Improve the error message when trying to download files from non-public records. This might be possible in the future but there is currently no way of accessing the user credentials when fetching the files.
• Workaround for Invenio instances that use a remote or external storage backend instead of local files. Those files cannot be downloaded using the Invenio API (there is no support yet) but we can directly use the front-end download link to download them from Galaxy.

How to test the changes?

• Instructions for manual testing are as follows:

  • You can try this out with the [DataPLANT Invenio instance[(https://invenio.nfdi4plants.org/) which uses S3 as the storage backend
  • Setup your file_sources configuration:

  # file_sources_conf.yml
  - type: inveniordm
    id: invenio
    doc: Invenio RDM The turn-key research data management repository
    label: Invenio RDM DataPLANT
    url: https://invenio.nfdi4plants.org
    token: ${user.preferences['invenio|token']}
    public_name: ${user.preferences['invenio|public_name']}
    writable: true
  
  # user_preferences_extra_conf.yml
  invenio:
      description: Your Invenio RDM Account
      inputs:
          - name: token
            label: Personal Token to publish records to Invenio RDM
            type: secret
            store: vault # Requires setting up vault_config_file in your galaxy.yml
            required: False
          - name: public_name
            label: Public name to publish records (formatted as "Lastname, Firstname")
            type: text
            required: False

  • Use the Upload tool to import a file from a public record using the remote file sources.

License

• I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

[davelopez]

Thank you John!