Register FIB milling progress#815
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…hat can be run through the 'feedback_callback' function
… database entries
…, and added a new table to record a Murfey-side copy of ISPyB's 'MillingStep' table
…c 'None' for the 'status' field
* GridSquare ID needs to be passed in when creating a new ISPyB record * Need to check if MillingStep update on ISPyB was successful before updating the corresponding Murfey record * Get site number from Pydantic model instead of working it out from first priciples again
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Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #815 +/- ##
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+ Coverage 52.39% 52.98% +0.59%
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Files 97 98 +1
Lines 10461 10684 +223
Branches 1381 1405 +24
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+ Hits 5481 5661 +180
- Misses 4691 4727 +36
- Partials 289 296 +7 🚀 New features to boost your workflow:
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…ead, since the 'MillingStepNameId' requires a DB query
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…o' master dictionary; added test function to check the early exit cases
stephen-riggs
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Jun 12, 2026
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Too big to review thoroughly but the general workflow looks fine
| "Received the following FIB metadata for registration:\n" | ||
| f"{json.dumps(site_info.model_dump(exclude_none=True), indent=2, default=str)}" | ||
| ) | ||
| except Exception: |
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There's several bare Except clauses in the run function which would be better excepting specific things
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Adds new database tables + relationships and workflow functions to support the registration and tracking of the FIB milling process. The AutoTEM metadata read by Murfey will now be registered in ISPyB's new
MillingSteptable, and a local Murfey copy will be created so that Murfey can propagate updates to existing rows.As part of this PR, the ISPyB schema and Python package versions have been bumped to make use of the newly introduced
MillingSteptable.The diff looks huge, but +540 of those lines are due to tests.