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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 <l.r.westerhof@uu.nl>
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 <l.r.westerhof@uu.nl>
(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)
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 <claravox@users.noreply.github.com> Co-authored-by: Sirjan <s.kaur@uu.nl>
(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 <l.r.westerhof@uu.nl>
Co-authored-by: Lazlo Westerhof <l.r.westerhof@uu.nl>
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.
If a vault resource has been configured, use it when copying data from a research collection to the vault collection. Also use configuration for number of threads when copying data.
Add sanity checks for source and destination paths when copying data to the vault so that users can't make the vault module copy data in an unintended way by manipulating vault metadata. This also makes this part of the system more robust against unexpected inputs. (Backport to Yoda 1.9.x)
Update the SRAM logo parameter to use a BASE64 encoded image rather than a URL. This is needed because of a breaking change in the SRAM API: SURFscz/SBS#1604 See https://sram.surf.nl/apidocs/#/Organisation/post_api_collaborations_v1 for information on the current version of the API.
When importing groups from a CSV file in the group manager, the portal did not show any role changes, which made it look like role changes were not processed. This fix ensures that users can see any role changes that are made as a result of an import with the update flag enabled.
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