Always update the tilt series length in the database after an mdoc (#307)

Author: stephen-riggs

src/murfey/client/contexts/tomo.py

@@ -835,6 +835,21 @@ def post_transfer(
                             ),
                             environment=environment,
                         )
+
+                    # Always update the tilt series length in the database after an mdoc
+                    if environment.murfey_session is not None:
+                        length_url = f"{str(environment.url.geturl())}/sessions/{environment.murfey_session}/tilt_series_length"
+                        capture_post(
+                            length_url,
+                            json={
+                                "tags": [tilt_series],
+                                "source": str(transferred_file.parent),
+                                "tilt_series_lengths": [
+                                    self._tilt_series_sizes[tilt_series]
+                                ],
+                            },
+                        )
+
         if completed_tilts and environment:
             logger.info(
                 f"The following tilt series are considered complete: {completed_tilts} "

src/murfey/server/__init__.py

@@ -2210,6 +2210,20 @@ def feedback_callback(header: dict, message: dict) -> None:
                 .where(db.AutoProcProgram.id == message["program_id"])
             ).one()
             session_id = collected_ids[0].session_id
+
+            # Find the autoprocprogram id for the alignment recipe
+            alignment_ids = murfey_db.exec(
+                select(
+                    db.DataCollection,
+                    db.ProcessingJob,
+                    db.AutoProcProgram,
+                )
+                .where(db.ProcessingJob.dc_id == db.DataCollection.id)
+                .where(db.AutoProcProgram.pj_id == db.ProcessingJob.id)
+                .where(db.DataCollection.id == collected_ids[1].id)
+                .where(db.ProcessingJob.recipe == message["em-tomo-align"])
+            ).one()
+
             relevant_tilt_and_series = murfey_db.exec(
                 select(db.Tilt, db.TiltSeries)
                 .where(db.Tilt.movie_path == message.get("movie"))
@@ -2230,7 +2244,7 @@ def feedback_callback(header: dict, message: dict) -> None:
 
                 machine_config = get_machine_config()
                 tilts = get_all_tilts(relevant_tilt_series.id)
-                ids = get_job_ids(relevant_tilt_series.id, message["program_id"])
+                ids = get_job_ids(relevant_tilt_series.id, alignment_ids[2].id)
                 preproc_params = get_tomo_preproc_params(ids.dcgid)
                 stack_file = (
                     Path(message["mrc_out"]).parents[1]

src/murfey/server/api.py

@@ -574,6 +574,25 @@ def register_tilt_series(
     db.commit()
 
 
+@router.post("/sessions/{session_id}/tilt_series_length")
+def register_tilt_series_length(
+    session_id: int,
+    tilt_series_group: TiltSeriesGroupInfo,
+    db=murfey_db,
+):
+    tilt_series_db = db.exec(
+        select(TiltSeries)
+        .where(col(TiltSeries.tag).in_(tilt_series_group.tags))
+        .where(TiltSeries.session_id == session_id)
+        .where(TiltSeries.rsync_source == tilt_series_group.source)
+    ).all()
+    for ts in tilt_series_db:
+        ts_index = tilt_series_group.tags.index(ts.tag)
+        ts.tilt_series_length = tilt_series_group.tilt_series_lengths[ts_index]
+        db.add(ts)
+    db.commit()
+
+
 @router.post("/visits/{visit_name}/{client_id}/completed_tilt_series")
 def register_completed_tilt_series(
     visit_name: str,
@@ -609,6 +628,7 @@ def register_completed_tilt_series(
                     DataCollectionGroup, DataCollection, ProcessingJob, AutoProcProgram
                 )
                 .where(DataCollectionGroup.session_id == session_id)
+                .where(DataCollectionGroup.tag == tilt_series_group.source)
                 .where(DataCollection.tag == ts.tag)
                 .where(DataCollection.dcg_id == DataCollectionGroup.id)
                 .where(ProcessingJob.dc_id == DataCollection.id)