Add foil hole registration with ISPyB

Author: d-j-hatton

src/murfey/client/contexts/spa.py

@@ -41,6 +41,7 @@ class FoilHole(NamedTuple):
     thumbnail_size_y: Optional[int] = None
     pixel_size: Optional[float] = None
     image: str = ""
+    diameter: Optional[float] = None
 
 
 class GridSquare(NamedTuple):
@@ -246,6 +247,7 @@ def _foil_hole_data(
         for fh_block in serialization_array[required_key]:
             pix = fh_block["b:value"]["PixelCenter"]
             stage = fh_block["b:value"]["StagePosition"]
+            diameter = fh_block["b:value"]["PixelWidthHeight"]["c:width"]
             if int(fh_block["b:key"]) == foil_hole:
                 return FoilHole(
                     id=foil_hole,
@@ -261,6 +263,7 @@ def _foil_hole_data(
                     thumbnail_size_y=None,
                     pixel_size=float(pixel_size) if image_path else None,
                     image=str(image_path),
+                    diameter=diameter,
                 )
     logger.warning(
         f"Foil hole positions could not be determined from metadata file {xml_path} for foil hole {foil_hole}"
@@ -682,6 +685,7 @@ def _position_analysis(
                         "thumbnail_size_x": fh.thumbnail_size_x,
                         "thumbnail_size_y": fh.thumbnail_size_y,
                         "pixel_size": fh.pixel_size,
+                        "diameter": fh.diameter,
                         "tag": str(source),
                         "image": str(image_path),
                     },

src/murfey/server/api/__init__.py

@@ -497,7 +497,12 @@ def register_grid_square(
             .where(DataCollectionGroup.session_id == session_id)
             .where(DataCollectionGroup.tag == grid_square_params.tag)
         ).one()
-        _transport_object.do_insert_grid_square(dcg.atlas_id, gsid, grid_square_params)
+        gs_ispyb_response = _transport_object.do_insert_grid_square(
+            dcg.atlas_id, gsid, grid_square_params
+        )
+    else:
+        # mock up response so that below still works
+        gs_ispyb_response = {"success": False, "return_value": None}
     try:
         grid_square = db.exec(
             select(GridSquare)
@@ -519,6 +524,11 @@ def register_grid_square(
         else:
             jpeg_size = (0, 0)
         grid_square = GridSquare(
+            id=(
+                gs_ispyb_response["return_value"]
+                if gs_ispyb_response["success"]
+                else None
+            ),
             name=gsid,
             session_id=session_id,
             tag=grid_square_params.tag,
@@ -569,6 +579,8 @@ def register_foil_hole(
             .one()
             .id
         )
+        if _transport_object:
+            _transport_object.do_insert_foil_hole(gsid.id, foil_hole_params)
     except NoResultFound:
         log.debug(
             f"Foil hole {sanitise(str(foil_hole_params.name))} could not be registered as grid square {sanitise(str(gs_name))} was not found"

src/murfey/server/ispyb.py

@@ -22,6 +22,7 @@
     BLSubSample,
     DataCollection,
     DataCollectionGroup,
+    FoilHole,
     GridSquare,
     ProcessingJob,
     ProcessingJobParameter,
@@ -30,7 +31,7 @@
     url,
 )
 
-from murfey.util.models import GridSquareParameters, Sample, Visit
+from murfey.util.models import FoilHoleParameters, GridSquareParameters, Sample, Visit
 
 log = logging.getLogger("murfey.server.ispyb")
 
@@ -134,6 +135,7 @@ def do_insert_grid_square(
         grid_square_id: int,
         grid_square_parameters: GridSquareParameters,
     ):
+        # need to correct height and weight by pixel ratio !!!!!
         record = GridSquare(
             atlasId=atlas_id,
             gridSquareLabel=grid_square_id,
@@ -161,6 +163,36 @@ def do_insert_grid_square(
             )
         return {"success": False, "return_value": None}
 
+    def do_insert_foil_hole(
+        self,
+        grid_square_id: int,
+        foil_hole_parameters: FoilHoleParameters,
+    ):
+        record = FoilHole(
+            gridSquareId=grid_square_id,
+            foilHoleLabel=foil_hole_parameters.name,
+            foilHoleImage=foil_hole_parameters.image,
+            pixelLocationX=foil_hole_parameters.x_location,
+            pixelLocationY=foil_hole_parameters.y_location,
+            diameter=foil_hole_parameters.diameter,
+            stageLocationX=foil_hole_parameters.x_stage_position,
+            stageLocationY=foil_hole_parameters.y_stage_position,
+            pixelSize=foil_hole_parameters.pixel_size,
+        )
+        try:
+            with Session() as db:
+                db.add(record)
+                db.commit()
+                log.info(f"Created FoilHole {record.gridSquareId}")
+                return {"success": True, "return_value": record.foilHoleId}
+        except ispyb.ISPyBException as e:
+            log.error(
+                "Inserting FoilHole entry caused exception '%s'.",
+                e,
+                exc_info=True,
+            )
+        return {"success": False, "return_value": None}
+
     def send(self, queue: str, message: dict, new_connection: bool = False):
         if self.transport:
             if not self.transport.is_connected():

src/murfey/util/models.py

@@ -293,6 +293,7 @@ class FoilHoleParameters(BaseModel):
     thumbnail_size_y: Optional[int] = None
     pixel_size: Optional[float] = None
     image: str = ""
+    diameter: Optional[float] = None
 
 
 class PostInfo(BaseModel):