Add db components from ispyb for processing outputs (#706)

Currently just adds all the ispyb tables into the murfey database. Separating out the databases was too hard as sqlmodel does not support subclassing, and splitting files causes a circular import.

---------

Co-authored-by: Dan Hatton <daniel.hatton@diamond.ac.uk>

Author: stephen-riggs

src/murfey/cli/create_db.py

@@ -7,7 +7,6 @@ def run():
     parser = argparse.ArgumentParser(
         description="Generate the necessary tables for the Murfey database"
     )
-
     parser.add_argument(
         "--no-clear",
         dest="clear",
@@ -22,4 +21,5 @@ def run():
 
     if args.clear:
         clear(url())
+
     setup(url())

src/murfey/server/api/workflow.py

@@ -479,6 +479,7 @@ async def request_spa_preprocessing(
             db.add(feedback_params)
         movie = Movie(
             murfey_id=murfey_ids[0],
+            data_collection_id=detached_ids[1],
             path=proc_file.path,
             image_number=proc_file.image_number,
             tag=proc_file.tag,
@@ -731,6 +732,17 @@ async def request_tomography_preprocessing(
                 0
             ].eer_fractionation_file
 
+        movie = Movie(
+            murfey_id=murfey_ids[0],
+            data_collection_id=dcid,
+            path=proc_file.path,
+            image_number=proc_file.image_number,
+            tag=proc_file.tag,
+        )
+        db.add(movie)
+        db.commit()
+        db.close()
+
         zocalo_message: dict = {
             "recipes": [recipe_name],
             "parameters": {

src/murfey/server/feedback.py

@@ -1429,6 +1429,7 @@ def _flush_tomography_preprocessing(message: dict, _db):
             p.parent.mkdir(parents=True)
         movie = db.Movie(
             murfey_id=murfey_ids[0],
+            data_collection_id=detached_ids[1],
             path=f.file_path,
             image_number=f.image_number,
             tag=f.tag,
@@ -1818,8 +1819,8 @@ def _save_bfactor(message: dict, _db):
                         "ispyb_command": "insert_particle_classification"
                     },
                     "program_id": message["program_id"],
-                    "bfactor_fit_intercept": str(bfactor_fitting[1]),
-                    "bfactor_fit_linear": str(bfactor_fitting[0]),
+                    "bfactor_fit_intercept": str(float(bfactor_fitting[1])),
+                    "bfactor_fit_linear": str(float(bfactor_fitting[0])),
                 },
                 new_connection=True,
             )