populate_metadata.py: add batches to write_to_omero (rebased onto metadata53)#5220
Closed
atarkowska wants to merge 10 commits intoome:metadata53from
atarkowska:rebased/metadata53/populate-batches
Closed
populate_metadata.py: add batches to write_to_omero (rebased onto metadata53)#5220atarkowska wants to merge 10 commits intoome:metadata53from atarkowska:rebased/metadata53/populate-batches
atarkowska wants to merge 10 commits intoome:metadata53from
atarkowska:rebased/metadata53/populate-batches
Conversation
For extremely large screens (idr0016), both adding map annotations as well as deleting them lead to either PG errors or Ice.MessageSizeMax exceptions. Now both are done in batches of 1000.
The list of map annotations and file annotations have duplicates which cause secondary deletes to fail.
Member
Author
|
--rebased-from #4754 |
This was referenced Apr 4, 2017
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
3 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
This is the same as gh-4754 but rebased onto metadata53.
What this PR does
The new
QueryContextimplementations inpopulate_metadata.pywere not batching in theirwrite_to_omeromethods. For very large screens (e.g. idr0016):BulkToMapAnnotationContexttends to hit MESSAGESIZEMAX limits andDeleteMapAnnotationContexthitsCaused by: java.io.IOException: Tried to send an out-of-range integer as a 2-byte value: 109734Now both are done in batches of 1000.
Note: projections are also causing issues so batching is being added to invocations of
projectionas well.Testing this PR
test/integration/metadata/test_populate.py.Related reading
cc: @eleanorwilliams