Add enable-study command and --skip-enable-study flag to cbioportalImporter.py - #178
Open
fuzhaoyuan wants to merge 1 commit into
Open
Add enable-study command and --skip-enable-study flag to cbioportalImporter.py#178fuzhaoyuan wants to merge 1 commit into
fuzhaoyuan wants to merge 1 commit into
Conversation
…porter.py - process_study_directory() gains an enable_study=True parameter guarding the final AVAILABLE status flip; default behavior is unchanged - -s import mode gains an opt-in --skip-enable-study flag to skip that flip - new enable-study command (-id/--study_ids) flips status independently, for whenever a caller decides the study is actually ready - lets a caller defer marking a study AVAILABLE until after derived tables have been rebuilt, instead of the status flip and the rebuild racing - first of two steps toward a full fix: metaImport.py doesn't use any of this yet, so its behavior is unchanged; wiring it in is a follow-up
|
I think this will need more discussion on our end. Perhaps it would be a good idea to move the status update logic into the derived table script outright, instead of trying to introduce these new commands to paper over what seems to be a product bug. |
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
2 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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Addresses #12317
Summary
process_study_directory()unconditionally marks a studyAVAILABLEas its last step, before the caller (metaImport.py) goes on to run the derived-table rebuild afterward. A newly imported study can therefore appear in listings before any derived data for it has been built.What changed
process_study_directory()gains anenable_study=Trueparameter guarding the finalAVAILABLEstatus flip; default behavior is unchanged.-simport mode gains an opt-in--skip-enable-studyflag to skip that flip.enable-studycommand (-id/--study_ids) flips status independently, for whenever a caller decides the study is actually ready — e.g. after confirming a derived-table rebuild succeeded.Not in scope
This is the first of two layers needed for a complete fix. It's opt-in: only callers that explicitly use
--skip-enable-studyandenable-studyare affected, so currentmetaImport.pycallers see no change. WiringmetaImport.pyitself to use this by default — deferringAVAILABLEuntil its own derived-table rebuild succeeds — is a follow-up fix if needed; without it, the underlying bug in #12317 is unchanged for the common case.