feat: ingest motion-corrected micrograph image paths (#309)#311
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vredchenko wants to merge 1 commit into
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feat: ingest motion-corrected micrograph image paths (#309)#311vredchenko wants to merge 1 commit into
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Persist the motion-corrected image artefacts cryoem-services produces so the micrograph leaf can be served (ADR 0021). This is the ingestion half; the serving endpoint is #308. - add nullable micrograph.motion_corrected_image_path and motion_corrected_snapshot_path columns (Alembic migration, no backfill) - extend MotionCorrectionCompletedRequest and MotionCorrectionCompleteBody additively with both optional paths (backward-compatible) - thread the paths through publish_motion_correction_completed and persist whichever are present in handle_motion_correction_complete The two paths arrive via the existing motion_correction/completed contract; callers that omit them are unaffected.
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Closes #309. Implements the ingestion half of ADR 0021 (smartem-devtools PR #232): persist the motion-corrected micrograph image paths so the leaf image can be served. The serving endpoint is #308 (gated behind this); the cryoem-services adapter that supplies the paths is #310 (external).
What
The scientifically meaningful micrograph image is the motion-corrected artefact cryoem-services already produces (a 2D
.mrcand a downscaled.jpegsnapshot) — not the storedhigh_res_path(raw multi-GB movie stack; 3D-array encode failure + OOM). Those paths arrive through SmartEM's existingPOST /micrographs/{uuid}/motion_correction/completedcontract, which this PR extends additively.d5e6f7a8b9c0— adds two nullable columns tomicrograph:motion_corrected_image_path,motion_corrected_snapshot_path. No backfill; existing/dump rows stay null.MotionCorrectionCompletedRequest(HTTP) andMotionCorrectionCompleteBody(RabbitMQ body) each gain both fields as optional (nullable, defaultNone). Callers that omit them are unaffected — backward-compatible.publish_motion_correction_completedthreads the two paths into the event; the endpoint forwards them from the payload;handle_motion_correction_completepersists whichever paths are present onto the micrograph row (previously it touched only statistics andupdated_at).Verification
downgrade -1drops them; re-upgrade +--autogeneratereports no drift (model matches migration).test_processing_feedback_endpoints.py+test_consumer_async_handlers.pypass (2 new cases: paths forwarded through the endpoint, paths persisted by the consumer).Notes
total_motion/average_motion(the data the motion-correction event carries together).micrograph_imageendpoint (feat(api): serve motion-corrected micrograph preview image (ADR 0021) #308) returns 404 — correct behaviour. A release is warranted once feat(api): serve motion-corrected micrograph preview image (ADR 0021) #308 lands (new endpoint + migration + contract fields).