Merge tripal_biodb module into tripal module
laceysanderson opened this issue · 3 comments
We want to move the new tripal_biodb module into the tripal directory. This module is a core requirement of tripal_chado moving forward and also generic enough to aid integration with other PostgreSQL-based schemas. As such it makes sense for the two to be merged for easier installation of Tripal and better integration with the new functionality.
The above-mentioned PR moves all the query-specific BioDB code to Tripal DBX in the core Tripal module. It also adds a lot of documentation both in the classes themselves as well as in readthedocs.
All automated testing from the original BioDB is moved into core Tripal and passes on Drupal 9.1.x, 9.2.x and 9.3.x (our current target version).
It is still failing on 9.4.x due to Drupals automated table prefixing. I believe there is a change somewhere in Drupal core related to table prefixing but have yet to find the specific problem.
We are merging anyway as there are a number of fixes to the API that are needed for other goals in Tripal 4.
Note to self: I believe the problem is somewhere in TripalDbxSchema::findTables and TripalDbxSchema::queryTableInformation and their interaction with the Drupal api.
You can now find the new documentation for this API on readthedocs at Extending Tripal > Biological Data Storage > Tripal DBX: Generic cross-database support for Drupal. There is also a lot of added documentation to the classes which you can find at tripal/src/TripalDBX.
Closing as Tripal DBX is in core now + the other issue mentioned is split out into another issue.