Register FIB data in ISPyB#805
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…t the end of the function, and both new and old entries are populated or updated correctly
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Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #805 +/- ##
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+ Coverage 52.20% 52.30% +0.10%
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Files 96 97 +1
Lines 10379 10436 +57
Branches 1373 1380 +7
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+ Hits 5418 5459 +41
- Misses 4677 4689 +12
- Partials 284 288 +4 🚀 New features to boost your workflow:
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… using FIB atlas data
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tieneupin
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enhancement
… needed for one function
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| # Mock the metadata returned from the image file | ||
| import murfey.workflows.fib.register_atlas |
stephen-riggs
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stephen-riggs
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This all looks like it will work, just a few queries about the structure
| if entry_point_result := entry_points( | ||
| group="murfey.workflows", name="atlas_update" | ||
| ): | ||
| (workflow,) = entry_point_result |
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Does this (and the dcg one below) need to be done here rather than sending a message to the feedback queue?
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As discussed, fully modularising this is too much effort for too little gain at the moment. However, I have rewritten this workflow so that it is triggered by the feedback_callback function instead, and can be safely acked or nacked.
| ) | ||
| visit_number = visit_name.split("-")[-1] | ||
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| # Register using thumbnail values if they are provided |
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What circumstance do you want thumbnail vs full image sizes? Could these ever get mixed up?
| .where(MurfeyDB.DataCollectionGroup.tag == imaging_site.site_name) | ||
| ).one() | ||
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| imaging_site.dcg_id = dcg_entry.id |
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Looks like you do need the dcg workflow run, this id is a bit challenging
| murfey_db=murfey_db, | ||
| ) | ||
| except Exception: | ||
| # Log error but allow workflow to proceed |
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Do you want this to proceed? If you fail would it be better to dlq the message?
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As discussed, we'll DLQ the message instead.
…nd run through the RabbitMQ feedback queue instead of being loaded directly
…ib_atlas' API endpoint
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Extends the existing FIB data registration workflow to insert a DataCollectionGroup and Atlas into ISPyB for each unique sample detected.
Currently inserts the path to the real image, as thumbnail generation logic hasn't been implemented yet.