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Added URL posts to register CLEM workflow files #357

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Added URL posts to register CLEM workflow files #357

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tieneupin
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  • Additionally, fixed minor bugs found in code after last minor update.

@tieneupin tieneupin added enhancement New feature or request server Relates to the server component client Relates to the client component cryo-clem Part of the cryo-CLEM pipeline extension labels Oct 2, 2024
@tieneupin tieneupin self-assigned this Oct 2, 2024
github-advanced-security[bot]
github-advanced-security bot found potential problems Oct 2, 2024
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src/murfey/client/contexts/clem.py
Comment on lines +422 to +426
def register_tiff_file(
self,
tiff_file: Path,
environment: MurfeyInstanceEnvironment,
):

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Code scanning / CodeQL

Explicit returns mixed with implicit (fall through) returns Note

Mixing implicit and explicit returns may indicate an error as implicit returns always return None.
src/murfey/client/contexts/clem.py
Comment on lines +449 to +453
def process_tiff_series(
self,
tiff_dataset: dict,
environment: MurfeyInstanceEnvironment,
):

Check notice

Code scanning / CodeQL

Explicit returns mixed with implicit (fall through) returns Note

Mixing implicit and explicit returns may indicate an error as implicit returns always return None.
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codecov bot commented Oct 2, 2024 •
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Codecov Report

Attention: Patch coverage is 9.78261% with 83 lines in your changes missing coverage. Please review.

Project coverage is 28.98%. Comparing base (0fa51e3) to head (bbd3e29).

Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #357      +/-   ##
==========================================
- Coverage   29.12%   28.98%   -0.14%     
==========================================
  Files          70       70              
  Lines        9481     9540      +59     
  Branches     1747     1756       +9     
==========================================
+ Hits         2761     2765       +4     
- Misses       6618     6673      +55     
  Partials      102      102

@tieneupin
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tieneupin commented Oct 3, 2024 •
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Validation checks:

  • register_lif_file request post works
  • process_lif_file request post works
  • register_tiff_file request post works
  • process_tiff_dataset request post works

The cluster submission ones are too challenging for me to test at present, but both registration functions work when I construct the URL and post it via requests.post().

@tieneupin
Used Path object to resolve file path in 'validate_and_sanitise'; add…
bbd3e29 
…ed additional 'raise Exception' to catch unexpected ones when loading rsync_basepath
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@d-j-hatton d-j-hatton Awaiting requested review from d-j-hatton

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