Yoda 1.9.5 [draft] #533
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Yoda 1.9.5 [draft] #533
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By default, when calling the integration test rule, we run all tests. This adds an option to run a single test, or all tests with a particular prefix (e.g. "util.collection.*").
(backport to Yoda 1.9) Co-authored-by: Lazlo Westerhof <[email protected]>
In the script for transforming publication metadata to support base DOIs, adjust the query condition for selecting the zone of a collection. Selecting on USER_ZONE does not reliably return all data package collections in the zone. We need to either check the zone of the collection itself, or check the beginning of the collection name to select its zone.
The log messages for copying ACLs did not match the actions that the system was performing.
In the schema transformation code, ignore ACLs of non-existent users when copying ACLs from a parent. This is needed because iRODS keeps ACLs referring to deleted users / groups around in the database (see irods/irods#7778).
This also includes a script for manually updating provenance logs.
Add basic integration tests for meta.get_latest_vault_metadata_path
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Co-authored-by: Lazlo Westerhof <[email protected]>
(backport to Yoda 1.9)
Added errors='replace' parameter in decode function to replace invalid UTF-8 sequences in file.
(backport to Yoda 1.9)
The revision creation job used to stop with a failure when a data object scheduled for revision creation could no longer be found on the resource where the revision creation job was looking for it. This can happen e.g. after a resource tree change. The revision creation job now logs an error message and continues with processing the next data object scheduled for revision creation, so that one such error can't stop the entire revision creation process. This also extracts the function to gather data object properties to util.data_object and covers it with integration tests, so that this function can be re-used in other parts of the ruleset.
Add optional parameter to the update-publications rule so that it updates only a single publication, rather than all publications on the system. This is useful when troubleshooting an issue with a single publication.
Get baseDOIMinted from the previous version, use Python get rather than try except
The job for revision creation now removes revision creation AVUs from data objects in trash. This makes it easier to monitor the number of data objects waiting for revision creation.
The metadata schema transformation code from default-2 to default-3 transformed ORCID-IDs and Researcher IDs, but not Scopus IDs and ISNI IDs. Because of this, metadata files with the default-2 schema containing Scopus or ISNI IDs can usually not be converted automatically to default-3. Solution: Add a transformation function that handles transformation of an ISNI and Scopus ID that consists of a series of digits (with optional spaces) to the format that is specified in the default-3 schema
Problem When modifying groups with a CSV, I use groups that are already created (to add users for example) . I check the “Allow updates” button and “Process CSV”. I then get an error for existing groups even though the users have been added Solution When import groups using a CSV file, now the user can be informed with a simple, but useful descriptive message of the actions taken: A message may consist of 1 or more of the following phrases: Group '<group_name>' created. Group '<group_name>' already exists. Users added (<no_users_added>). Users removed (<no_users_removed>).
(Backport to Yoda 1.9) Co-authored-by: claravox <[email protected]> Co-authored-by: Sirjan <[email protected]>
(Backport to Yoda 1.9)
Configure API/integration tests to run on the Yoda 1.9 container images for Yoda 1.9.x RC versions.
Co-authored-by: Lazlo Westerhof <[email protected]>
Co-authored-by: Lazlo Westerhof <[email protected]>
Upgrade UU microservices to v1.2.0 for testing the release candidate version of Yoda 1.9.5, since it works with a different microservices version than we currently have in the Docker image.
On API test failures, print more information for troubleshooting purposes: - CI: On failures, print web server error logs and portal access log for troubleshooting on portal level. - API tests: if tests are unable to get a CSRF token, print the user that the error occurred with and the response from the web server for troubleshooting purposes. (version for Yoda 1.9)
Install any new portal dependencies in CI. These may be needed for the API tests.
We always run them with Python 3
Use Python 3.8 instead of distribution default Python 3.6, because Python 3.6 has different (incompatible) arguments for the subprocess module.
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This PR is currently a draft. It's not yet ready for review and merging.