Skip to content

ENSCORESW-2827: minimal test on xref config validity

Marek Szuba requested to merge feature/xref_test into master

Created by: magaliruffier

Requirements

  • Filling out the template is required. Any pull request that does not include enough information to be reviewed in a timely manner may be closed at the maintainers' discretion;
  • Review the contributing guidelines for this repository; remember in particular:
    • do not modify code without testing for regression
    • provide simple unit tests to test the changes
    • if you change the schema you must patch the test databases as well, see Updating the schema
    • the PR must not fail unit testing

Description

Using one or more sentences, describe in detail the proposed changes. The xref_config.ini file is large and messy. Additionally, a small change in the configuration can have dire consequences on the results of the xref pipeline update. This change aims to provide a basic test on the syntax of the configuration and that there is available configuration for any source mentioned.

Use case

Describe the problem. Please provide an example representing the motivation behind the need for having these changes in place. If a source is removed but is referenced somewhere else in the configuration file, the generation of the metadata sql file is interrupted. This is not captured within the eHive pipeline but will cause downstream consequences, in particular missing data and species.

Benefits

If applicable, describe the advantages the changes will have. Avoid breaking the xref pipeline for a misformatted configuration.

Possible Drawbacks

If applicable, describe any possible undesirable consequence of the changes.

Testing

Have you added/modified unit tests to test the changes? This is a new test unit

If so, do the tests pass/fail? The test passes

Have you run the entire test suite and no regression was detected? Yes

Merge request reports