Merged recent changes from 'main' branch

tieneupin · tieneupin · commit 07ca21541e7b · 2025-03-26T18:05:35.000Z
diff --git a/.bumpclient.toml b/.bumpclient.toml
@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "0.17.4"
+current_version = "0.17.5"
 commit = true
 tag = false
 
diff --git a/.bumpversion.toml b/.bumpversion.toml
@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "0.17.4"
+current_version = "0.17.5"
 commit = true
 tag = true
 
diff --git a/Helm/Chart.yaml b/Helm/Chart.yaml
@@ -1,7 +1,7 @@
 apiVersion: v1
 name: murfey-services
 description: Umbrella Helm chart for deploying the servers and daemons needed to enable Murfey to transfer and process data
-version: 0.17.4
+version: 0.17.5
 dependencies:
   - name: murfey-instrument-server-clem
   - name: murfey-instrument-server-tem
diff --git a/Helm/charts/murfey-instrument-server-clem/Chart.yaml b/Helm/charts/murfey-instrument-server-clem/Chart.yaml
@@ -1,4 +1,4 @@
 apiVersion: v1
 name: murfey-instrument-server-clem
 description: Helm chart for deploying a Murfey instrument server, which executes orders to detect, modify, and transfer files on the instrument PC, and notifies the backend server about transferred files
-version: 0.17.4
+version: 0.17.5
diff --git a/Helm/charts/murfey-rsync/Chart.yaml b/Helm/charts/murfey-rsync/Chart.yaml
@@ -1,4 +1,4 @@
 apiVersion: v1
 name: murfey-rsync
 description: Helm chart for deploying an rsync daemon, which is responsible for executing the transfer of files from the client storage directory to the server storage system
-version: 0.17.4
+version: 0.17.5
diff --git a/Helm/charts/murfey-server/Chart.yaml b/Helm/charts/murfey-server/Chart.yaml
@@ -1,4 +1,4 @@
 apiVersion: v1
 name: murfey-server
 description: Helm chart for deploying a Murfey backend server, which is responsible for orchestrating the data transfer and processing workflow between the client PC and the storage system
-version: 0.17.4
+version: 0.17.5
diff --git a/pyproject.toml b/pyproject.toml
@@ -7,7 +7,7 @@ requires = [
 
 [project]
 name = "murfey"
-version = "0.17.4"
+version = "0.17.5"
 description = "Client-Server architecture hauling Cryo-EM data"
 readme = "README.md"
 keywords = [
diff --git a/src/murfey/__init__.py b/src/murfey/__init__.py
@@ -1,4 +1,4 @@
 from __future__ import annotations
 
-__version__ = "0.17.4"
-__supported_client_version__ = "0.17.4"
+__version__ = "0.17.5"
+__supported_client_version__ = "0.17.5"
diff --git a/src/murfey/client/contexts/spa_metadata.py b/src/murfey/client/contexts/spa_metadata.py
@@ -271,20 +271,8 @@ def post_transfer(
                     transferred_file,
                     int(gs_name),
                 )
-                metadata_source_as_str = (
-                    "/".join(source.parts[:-2])
-                    + f"/{environment.visit}/"
-                    + source.parts[-2]
-                )
-                metadata_source = Path(
-                    metadata_source_as_str[1:]
-                    if metadata_source_as_str.startswith("//")
-                    else metadata_source_as_str
-                )
                 image_path = (
-                    _file_transferred_to(
-                        environment, metadata_source, Path(gs_info.image)
-                    )
+                    _file_transferred_to(environment, source, Path(gs_info.image))
                     if gs_info.image
                     else ""
                 )
diff --git a/src/murfey/client/customlogging.py b/src/murfey/client/customlogging.py
@@ -20,7 +20,10 @@ def prepare(self, record):
         self.format(record)
         record_dict = record.__dict__
         record_dict["type"] = "log"
-        return json.dumps(record_dict)
+        try:
+            return json.dumps(record_dict)
+        except TypeError:
+            return json.dumps({str(k): str(v) for k, v in record_dict.items})
 
     def emit(self, record):
         try:
diff --git a/src/murfey/instrument_server/api.py b/src/murfey/instrument_server/api.py
@@ -241,6 +241,10 @@ def register_processing_parameters(
     for k, v in proc_param_block.params.dict().items():
         if v is not None:
             data_collection_parameters[proc_param_block.label][k] = v
+    if controllers.get(session_id):
+        controllers[session_id].data_collection_parameters.update(
+            data_collection_parameters[proc_param_block.label]
+        )
     return {"success": True}
 
 
diff --git a/src/murfey/server/api/processing_parameters.py b/src/murfey/server/api/processing_parameters.py
@@ -0,0 +1,63 @@
+from logging import getLogger
+from typing import Optional
+
+from fastapi import APIRouter, Depends
+from pydantic import BaseModel
+from sqlmodel import Session, select
+
+from murfey.server.api.auth import MurfeySessionID, validate_token
+from murfey.server.murfey_db import murfey_db
+from murfey.util.db import SessionProcessingParameters
+
+logger = getLogger("murfey.server.api.processing_parameters")
+
+router = APIRouter(dependencies=[Depends(validate_token)])
+
+
+class EditableSessionProcessingParameters(BaseModel):
+    gain_ref: str = ""
+    dose_per_frame: Optional[float] = None
+    eer_fractionation_file: str = ""
+    symmetry: str = ""
+
+
+@router.get("/sessions/{session_id}/session_processing_parameters")
+def get_session_processing_parameters(
+    session_id: MurfeySessionID, db: Session = murfey_db
+) -> EditableSessionProcessingParameters:
+    proc_params = db.exec(
+        select(SessionProcessingParameters).where(
+            SessionProcessingParameters.session_id == session_id
+        )
+    ).one()
+    return EditableSessionProcessingParameters(
+        gain_ref=proc_params.gain_ref,
+        dose_per_frame=proc_params.dose_per_frame,
+        eer_fractionation_file=proc_params.eer_fractionation_file,
+        symmetry=proc_params.symmetry,
+    )
+
+
+@router.post("/sessions/{session_id}/session_processing_parameters")
+def set_session_processing_parameters(
+    session_id: MurfeySessionID,
+    edited_parameters: EditableSessionProcessingParameters,
+    db: Session = murfey_db,
+) -> EditableSessionProcessingParameters:
+    proc_params = db.exec(
+        select(SessionProcessingParameters).where(
+            SessionProcessingParameters.session_id == session_id
+        )
+    ).one()
+    proc_params.gain_ref = edited_parameters.gain_ref or proc_params.gain_ref
+    proc_params.dose_per_frame = (
+        edited_parameters.dose_per_frame or proc_params.dose_per_frame
+    )
+    proc_params.eer_fractionation_file = (
+        edited_parameters.eer_fractionation_file or proc_params.eer_fractionation_file
+    )
+    proc_params.symmetry = edited_parameters.symmetry or proc_params.symmetry
+    db.add(proc_params)
+    db.commit()
+    db.close()
+    return edited_parameters
diff --git a/src/murfey/server/demo_api.py b/src/murfey/server/demo_api.py
@@ -28,7 +28,6 @@
     _flush_grid_square_records,
     _flush_tomography_preprocessing,
     _murfey_id,
-    _register_picked_particles_use_diameter,
     feedback_callback,
     get_hostname,
     get_microscope,
@@ -91,6 +90,7 @@
 )
 from murfey.util.processing_params import default_spa_parameters
 from murfey.util.state import global_state
+from murfey.workflows.spa.picking import _register_picked_particles_use_diameter
 
 log = logging.getLogger("murfey.server.demo_api")
 
diff --git a/src/murfey/server/main.py b/src/murfey/server/main.py
@@ -17,6 +17,7 @@
 import murfey.server.api.display
 import murfey.server.api.hub
 import murfey.server.api.instrument
+import murfey.server.api.processing_parameters
 import murfey.server.api.spa
 import murfey.server.websocket
 import murfey.util.models
@@ -74,6 +75,7 @@ class Settings(BaseSettings):
 app.include_router(murfey.server.api.display.router)
 app.include_router(murfey.server.api.instrument.router)
 app.include_router(murfey.server.api.hub.router)
+app.include_router(murfey.server.api.processing_parameters.router)
 app.include_router(murfey.server.websocket.ws)
 
 # Search external packages for additional routers to include in Murfey
