Bypass LIMS for delivery report #3153
Merged
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
henrikstranneheim
approved these changes
Apr 19, 2024
15 tasks
…to skip-lims-report
|
|
Deployed |
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Outdated suggestions cannot be applied.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
The goal is to avoid the delivery report crashing due to samples not being present in LIMS (HTTP exception). While the report creation will still fail, it'll be possible to work around it with the
--force flag, including empty data for the application info, methods, and metrics for Rnafusion.I've also moved some methods from the report api to the analysis api since I've seen some duplication that could be introduced here: #3112
Added
Changed
How to prepare for test
uspaxaTests
Generate delivery report for a sample that's not in LIMS:
With the current master branch (exception raised and not captured, not possible to bypass generation with
--force):With this branch (generation fails gracefully, logging the missing report data.
--forceflag generates a report with empty data):Balsamicdelivery-reportRnafusiondelivery-reportMIP-DNAdelivery-reportReview
Thanks for filling in who performed the code review and the test!
This version is a
Implementation Plan