Bug fix: Synonym Sync: Remove recapitalization of acronyms #724
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
Fixed bug where this operation was being done for -updated and -confirmed, but it should only be done for -added.
joeflack4
force-pushed
the
bugfix-syn-sync-acronym-recap
branch
from
9a5a058 to
b8c0679
Compare
joeflack4
changed the title
|
I need to come back to this. Might just want to get rid of this code here and introduce a warning elsewhere if Mondo acronyms are lowercase. |
joeflack4
changed the title
|
Can you create a ticket and explain what is happening and what the current consequences are and which of these consequences this PR fixes? Your comment: makes it sound like there is more to think through here. |
- Bug fix: I don't think we should have ever had this in the first place. I don't see that it actually fixes anything; only should cause bugs.
9 tasks
joeflack4
commented
Dec 17, 2024
joeflack4
changed the base branch from
bugfix-syn-sync-dupe-rows-684
to
develop
joeflack4
changed the base branch from
develop
to
bugfix-syn-sync-dupe-rows-684
twhetzel
approved these changes
Jan 9, 2025
joeflack4
added a commit
that referenced
this pull request
Jan 11, 2025
…tion of acronyms (#724)] * Bug: Synonym Sync: Duplicate rows #684 - Bug fix: Fixed case in which sources can have multiple synonyms which only vary by capitalization, causing duplicate rows to appear in the results. We don't consider source capitalization as authoritative, so these variations are only useful for analysis and should not show up as multiple rows to be processed. Thus, we now aggregate capitalization variations into the single column synonym_case_diff_source. - Bug fix: Address issues related to mondo capitalization variation. - Update: Ensure the following columns are now in the output and are together: synonym_case_mondo, synonym_case_diff_mondo, synonym_case_mondo_is_many, synonym_case_source, synonym_case_diff_source, synonym_case_source_is_many. Note that previously, we had removed synonym_case_mondo & synonym_case_source, opting instead for the 'diff' columns, because it was previously only valuable to show the original capitalizations if there was a difference between the two. But now that we can have multiple variations in capitalization on the same syonym, it is useful to see the original case by itself, as wel as all the variations. - Update: For synonym_case_source_is_many, ensure that all variations show up in synonym_case_source and synonym_case_diff_source columns. Note that when there are multiple capitalization variations at the source, we only need 1 row. - Update: For all synonym_case_mondo_is_many, ensure that all variations show up in the synonym_case_diff_mondo column. But leave synonym_case_mondo as it is. We need to preserve the original case for that row, since unlike the source, we will retain multiple rows in the case that Mondo has multiple capitalization variations for a single synonym. * Bug fix: Synonym Sync: Remove recapitalization of acronyms (#724) - Fixed bug where this operation was being done for -updated and -confirmed, but it should only be done for -added. - Bug fix: I don't think we should have ever had this in the first place. I don't see that it actually fixes anything; only should cause bugs.
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.
Overview
Fixed bug where this operation was being done for -updated and -confirmed, but it should only be done for -added.Removed this recapitalization.
Pre-merge checklist
Documentation
Was the documentation added/updated under
docs/?QC
Was the full pipeline run before submitting this PR using
sh run.sh make build-mondo-ingeston this branch (afterdocker pull obolibrary/odkfull:dev), and no errors occurred?New Packages
Were any new Python packages added?
Were any other non-Python packages added?
PR Review and Conversations Resolved
Has the PR been sufficiently reviewed by at least 1 team member of the Mondo Technical team and all threads resolved?