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extract correct dbtype and version across naming conventions

Marek Szuba requested to merge feature/division_lookup into master

Created by: magaliruffier


  • 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


Using one or more sentences, describe in detail the proposed changes. The database identification pattern has been updated to work consistently across databases used in vertebrate and invertebrates.

Use case

Describe the problem. Please provide an example representing the motivation behind the need for having these changes in place. This changes allows the script to be run across vertebrate and invertebrate database and extract the same version, for example extract 96 from homo_sapiens_core_96_38 and vitis_vinifera_core_43_96_3 Prior to that change, it would create two separate lookup databases, one of version 96 for vertebrate databases and one of version 43 for invertebrates.


If applicable, describe the advantages the changes will have. The script can be run across all divisions and store the data in a single lookup database rather than creating two separate ones.

Possible Drawbacks

If applicable, describe any possible undesirable consequence of the changes. The resulting database can be very big.


Have you added/modified unit tests to test the changes? NA The modified script was run for release 96 to create a single lookup database to be used by the joint REST server.

If so, do the tests pass/fail? NA

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

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