Add Zenodo integration

[davelopez]

Requires #18028

This PR adds a new Zenodo file source plugin based on Invenio to make the integration a bit more obvious.

This also uses new schemes for Invenio (invenio://) and Zenodo (zenodo://) file sources as they should have been from the beginning... The previous gxfiles:// scheme in the case of existing exports will still work as expected.

How to test the changes?

(Select all options that apply)

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:
  • Set enable_celery_tasks to true in your galaxy.yml config file.
  • Add to your file_sources_conf.yml

      - type: zenodo
        id: zenodo
        doc: Zenodo is a general-purpose open-access repository developed under the European OpenAIRE program and operated by CERN. It allows researchers to deposit data sets, research software, reports, and any other research-related digital artifacts. For each submission, a persistent digital object identifier (DOI) is minted, which makes the stored items easily citeable.
        label: Zenodo
        url: https://sandbox.zenodo.org # To use the real Zenodo instance replace with https://zenodo.org
        token: ${user.user_vault.read_secret('preferences/zenodo/token')}
        # token: ${user.preferences['zenodo|token']} # Alternatively use this for retrieving the token from user preferences instead of the Vault
        public_name: ${user.preferences['zenodo|public_name']}
        writable: true

  • Add to your user_preferences_extra_conf.yml

        zenodo:
                description: Your Zenodo Integration Settings
                inputs:
                    - name: token
                      label: Personal Access Token used to create draft records and to upload files. You can manage your tokens at https://zenodo.org/account/settings/applications/
                      type: secret
                      store: vault # Requires setting up vault_config_file in your galaxy.yml
                      required: False
                    - name: public_name
                      label: Creator name to associate with new records (formatted as "Last name, First name"). If left blank "Anonymous Galaxy User" will be used. You can always change this by editing your record directly.
                      type: text
                      required: False

  • Try to export a history

License

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

[davelopez]

API test failure unrelated and fixed in #18026

[jmchilton]

This is so ridiculously cool.

[bgruening]

Thanks for the rebase @davelopez!