Xref fixes #679
Merged
Xref fixes #679
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Description
Fixes for some xref bugs that were discovered in the 112 run.
Use case
There was a bug in parsing UniProt gene names that was discovered in the recent 112 xref run which didn't include the colon ":" character in the regex used.
Another bug that was found was related to populating the xref intermediate DBs where data was being copied over from the central DB. The way the data was copied was by creating a .sql file with the insert statements. However, when running the pipeline for multiple species at once (normal process), they were all rewriting the same sql file over and over again which lead to some of the intermediate DBs having no data. The added fix removed this copying of the central DB data altogether, as there already exists a file that has this data (populate_metadata.sql) which is created when the central DB is created. Instead, the preparse flag value was added into this metadata filename in order to handle multiple runs of the pipeline (maybe with different preparse flags).
Benefits
No rewriting of the same file for no reason, no corrupted intermediate DBs, and no wrong UniProt gene names.
Possible Drawbacks
None
Testing
Have you added/modified unit tests to test the changes?
If so, do the tests pass/fail?
Have you run the entire test suite and no regression was detected?