Adjust logic to CLEM workflow to support multiple registered atlases#787
Open
Adjust logic to CLEM workflow to support multiple registered atlases#787
Conversation
… reference for when updating grid squares
tieneupin
added
bug
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #787 +/- ##
=======================================
Coverage 50.72% 50.72%
=======================================
Files 96 96
Lines 10059 10060 +1
Branches 1322 1322
=======================================
+ Hits 5102 5103 +1
Misses 4690 4690
Partials 267 267 🚀 New features to boost your workflow:
|
This file contains hidden or 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
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
The CLEM workflow currently assumes that all of the datasets stored under the top level folder belong to the same grid. It currently also uses the field of view of the incoming dataset to decide if it is to be treated as an atlas image or a grid. We thus occasionally run into a situation whereby more than one datasets in a grid get registered as atlases, at which point the workflow breaks because the SQL query expects a single matching database entry or no result.
This PR updates the logic slightly so that the database query returns all matching atlas entries, sorted by insertion order, then uses the latest one to perform the ISPyB updates.