Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Refactor project path resolvers in CohortExtractor #1957

Merged
merged 18 commits into from
Oct 10, 2024
Merged

Conversation

rkm
Copy link
Member

@rkm rkm commented Oct 4, 2024

Proposed Changes

  • DefaultProjectPathResolver has been renamed to StudySeriesOriginalFilenameProjectPathResolver
  • Undo handling UIDs with leading dot (Fix/cohort extractor output paths #1506) as this was causing difficulties with path lookups elsewhere
  • Add StudySeriesSOPProjectPathResolver which generates filenames using SOPInstanceUID instead of the original file name. This is now the default path resolver
  • Disallow null Study/Series/SOPInstanceUID values, which should never occur in practice

Types of changes

  • Bugfix (non-breaking change which fixes an issue)
  • New Feature (non-breaking change which adds functionality)
  • Breaking Change (fix or feature that would cause existing functionality to not work as expected)
  • Documentation-Only Update (if none of the other choices apply)
    • In this case, ensure that the message of the head commit from the source branch is prefixed with [skip ci]

Checklist

By opening this PR, I confirm that I have:

  • Reviewed the contributing guidelines for this repository
  • Ensured that the PR branch is in sync with the target branch (i.e. it is automatically merge-able)
  • Updated any relevant API documentation
  • Created or updated any tests if relevant
  • Created a news file
    • NOTE: This must include any changes to any of the following files: default.yaml, any of the RabbitMQ server configurations, GlobalOptions.cs
  • Listed myself in the CONTRIBUTORS file 🚀
  • Requested a review by the @SMI/Reviewers team

Issues

@rkm rkm changed the title Feature/path resolvers Refactor project path resolvers in CohortExtractor Oct 4, 2024
Copy link

codecov bot commented Oct 7, 2024

Codecov Report

Attention: Patch coverage is 82.60870% with 8 lines in your changes missing coverage. Please review.

Project coverage is 64.81%. Comparing base (f547cf4) to head (7f6d1ae).
Report is 18 commits behind head on main.

Files with missing lines Patch % Lines
...ProjectPathResolvers/ProjectPathResolverFactory.cs 42.85% 3 Missing and 1 partial ⚠️
...ohortExtractor/RequestFulfillers/QueryToExecute.cs 66.66% 0 Missing and 4 partials ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #1957      +/-   ##
==========================================
- Coverage   64.82%   64.81%   -0.01%     
==========================================
  Files         181      183       +2     
  Lines        6538     6554      +16     
  Branches      963      963              
==========================================
+ Hits         4238     4248      +10     
- Misses       2017     2020       +3     
- Partials      283      286       +3     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@rkm rkm marked this pull request as ready for review October 10, 2024 13:18
@rkm rkm requested a review from a team October 10, 2024 13:18
@rkm rkm merged commit 83dc691 into main Oct 10, 2024
19 checks passed
@jas88 jas88 deleted the feature/path-resolvers branch October 10, 2024 13:35
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

Use SOPInstanceUID to generate anon file path instead of original filename
2 participants