Skip to content

Trigger cryoSIM processing#841

Open
tieneupin wants to merge 13 commits into
mainfrom
trigger-cryosim-processing
Open

Trigger cryoSIM processing#841
tieneupin wants to merge 13 commits into
mainfrom
trigger-cryosim-processing

Conversation

@tieneupin

@tieneupin tieneupin commented Jul 14, 2026

Copy link
Copy Markdown
Contributor

Adds more functionality to the cryoSIM workflow.

  • On the client side, Murfey will apply the cryoSIM context when it sees raw data files matching currently known criteria (raw data files have no suffix, and end with a certain set of patterns).
  • When a fluorescent data file is seen, it will submit a post to trigger data processing for the file.
  • Adds an endpoint to the backend server that will receive requests to trigger data processing from the client, and will forward the message to RabbitMQ's processing_recipe queue.
  • Updates existing tests and adds new tests to reflect the updated behaviour.

Actual diff is about +150 lines, with the rest of the diff being due to tests.

@tieneupin tieneupin added the cryo-sim Part of the cryo-SIM pipeline extension label Jul 14, 2026
@tieneupin tieneupin self-assigned this Jul 14, 2026
@tieneupin tieneupin added server Relates to the server component client Relates to the client component enhancement New feature or request labels Jul 14, 2026
Comment thread src/murfey/server/api/workflow_sim.py Fixed
@codecov

codecov Bot commented Jul 14, 2026

Copy link
Copy Markdown

Codecov Report

❌ Patch coverage is 88.67925% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 53.46%. Comparing base (c93a69c) to head (c5219b4).

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #841      +/-   ##
==========================================
+ Coverage   53.29%   53.46%   +0.16%     
==========================================
  Files         102      103       +1     
  Lines       11030    11083      +53     
  Branches     1470     1480      +10     
==========================================
+ Hits         5878     5925      +47     
- Misses       4831     4833       +2     
- Partials      321      325       +4     
🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

…nalyser should determine context using bright field files as well, whereas 'capture_post' should only be triggered on fluorescent ones
@tieneupin tieneupin marked this pull request as ready for review July 14, 2026 13:31
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

client Relates to the client component cryo-sim Part of the cryo-SIM pipeline extension enhancement New feature or request server Relates to the server component

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants