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Add Dataverse RDM repository integration #19367
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Dataverse RDM Repository Integration
This PR integrates Dataverse into Galaxy, mirroring the functionality developed for Invenio in PR #16381. It provides the same features tailored for Dataverse.
Terminology
The terminology used across RDM systems (like Dataverse and Invenio) and Galaxy can be confusing. The table below clarifies these differences. To reduce ambiguity, the
RDMFilesSource
base class (_rdm.py
) has been updated to use abstract terms. This description follows the abstract naming to avoid further confusion:Features
Current Limitations
Missing User Context
When downloading files from external draft containers in Dataverse, the
user_context
is not passed to the_realize_to
method of theBaseFilesSource
class. This causes authentication failures, preventing downloads. A similar issue arises when using the "Export datasets" feature to send files from Galaxy to an external draft container. These limitations currently also affect the invenio implementation.Archiving and Reimporting Histories
While exporting a history as a ZIP file to Dataverse works, the archive is automatically extracted by Dataverse and only its content is being stored. This creates an issue for Galaxy, as reimporting relies on the archive's existence. A workaround enables reimport by downloading the container as a ZIP via another API call if the original archive is not found. Note: exporting as
.tar.gz
is currently not working, as the Dataverse API returns an error (Failed to add file to dataset
). The recommended format is "RO-Crate" (ZIP) in advanced export options.For Users
You can now use all the features listed in the section "Features", which behave the same as those in the Invenio integration. UI workflows are demonstrated in the linked PR.
For Reviewers
Manual Testing Requirements
(Optional) Create a Dataverse Instance:
You may use the official demo for testing, as data is deleted once a month. Alternatively, set up a local instance using the quickstart guide.
Create a Dataverse User and API Token:
Generate a token via "Your username" → "My Data" → "API token" or directly at this URL: https://demo.dataverse.org/dataverseuser.xhtml?selectTab=apiTokenTab.
Configure the Connection:
Add this to your file_sources_conf.yml file and fill out with your data. Ideally you use a Vault to store the token but for testing purposes you could also directly provide it in the config:
Add user config:
Add a new entry in your user_preferences_extra_conf.yml to allow the user to store his required Dataverse settings:
The Add task-based history export tracking #14839 requires having Celery Task (with Redis backend) setup in your instance. So you will need something like this in your galaxy.yml:
Also ensure that redis is installed in your python environment with
pip install redis
How to test the changes?
License