Trigger cryoSIM processing#841
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…g jobs to RabbitMQ
…ed by the CryoSIM workflow
…mit them for processing
tieneupin
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Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #841 +/- ##
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+ Coverage 53.29% 53.47% +0.18%
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Files 102 103 +1
Lines 11030 11071 +41
Branches 1470 1476 +6
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+ Hits 5878 5920 +42
Misses 4831 4831
+ Partials 321 320 -1 🚀 New features to boost your workflow:
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…nalyser should determine context using bright field files as well, whereas 'capture_post' should only be triggered on fluorescent ones
stephen-riggs
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stephen-riggs
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No issues I can see, but questions about code duplication and return values
| logger = logging.getLogger("murfey.client.contexts.sim") | ||
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| def _get_source(file_path: Path, environment: MurfeyInstanceEnvironment) -> Path | None: |
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You might be able to use the _get_source in the context.py as that should have the same behaviour. Looks like some contexts use that and some don't
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You're right. This would be a good opportunity to make sure that the shared get_source works across workflows. I'll switch to it and test it for the SIM workflow.
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| def _file_transferred_to( |
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Same here, _file_transferred_to exists in the parent context.py with the same behaviour
| source: Path, | ||
| file_path: Path, | ||
| rsync_basepath: Path, | ||
| ) -> Path | None: |
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How would this return None?
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This might have been oversight on my part back when I was learning how to set up the function for the CLEM workflow. I'll switch over to using the shared file_transferred_to function.
| file_path=transferred_file, | ||
| rsync_basepath=Path(self._machine_config.get("rsync_basepath", "")), | ||
| ) | ||
| if destination_file is None: |
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Same as above, what situation would the destination_file be None?
…ions, and updated cryoSIM tests to reflect this
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Thanks for the quick review and helpful comments. I've taken your suggestions on board, and switched to using the shared A future housekeeping-related PR would involve revisiting the other context files developed and switching them to using the shared |
3 participants
Adds more functionality to the cryoSIM workflow.
processing_recipequeue. The actual submission of the message will be deferred until the processing recipe and service have been set up.Actual diff is about +170 lines, with the rest of the diff being due to tests.