Retrieve all studies returned by querying the archives

p-j-smith commented 1 week ago

Description

Fixes #522

if querying an archive returns multiple studies, retrieve all studies into Orthanc Raw
don't delete resources for studies in Orthanc Raw (previously only the most recently updated resources was kept). This sometimes leads to a report being kept and the corresponding imaging study (that we want to export) being deleted
in the Orthanc Anon plugin, retrieve all resources from Orthanc Raw for a given StudyUID
in the Orthanc Anon plugin, download the study bytes directly from Orthanc Raw before anonymising

Type of change

Please delete options accordingly to the description.

[ ] Bug fix (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)
[ ] This change requires a documentation update

Suggested Checklist

[ ] I have performed a self-review of my own code.
[ ] I have made corresponding changes to the documentation.
[ ] My changes generate no new warnings.
[ ] I have commented my code, particularly in hard-to-understand areas.
[ ] I have passed on my local host device. (see further details at the CONTRIBUTING document)
[ ] Make sure your branch is up-to-date with main branch. See CONTRIBUTING for a general example to syncronise your branch with the main branch.
[ ] I have requested review to this PR.
[ ] I have addressed and marked as resolved all the review comments in my PR.
[ ] Finally, I have selected squash and merge

codecov[bot] commented 1 week ago

Codecov Report

Attention: Patch coverage is 83.33333% with 5 lines in your changes missing coverage. Please review.

Project coverage is 80.09%. Comparing base (a51995b) to head (8d22259). Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
pixl_imaging/src/pixl_imaging/_orthanc.py	50.00%	4 Missing :warning:
pixl_imaging/src/pixl_imaging/_processing.py	95.45%	1 Missing :warning:

:exclamation: There is a different number of reports uploaded between BASE (a51995b) and HEAD (8d22259). Click for more details.

HEAD has 1 upload less than BASE
| Flag | BASE (a51995b) | HEAD (8d22259) | |------|------|------| ||8|7|

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #523 +/- ## ========================================== - Coverage 87.13% 80.09% -7.05% ========================================== Files 76 74 -2 Lines 3460 3421 -39 ========================================== - Hits 3015 2740 -275 - Misses 445 681 +236 ```

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p-j-smith commented 1 week ago

thanks for the reviews! I've ran this on the test instance and we're now getting all the studies through, and using threads in the anon plugin means we're not blocking the main thread anymore

SAFEHR-data / PIXL