Apply 1 to 2 conversion with possible path to str problems

Author: stephen-riggs

src/murfey/server/api/prometheus.py

@@ -39,7 +39,7 @@ def increment_rsync_file_count(
         logger.error(
             f"Failed to find rsync instance for visit {sanitise(visit_name)} "
             "with the following properties: \n"
-            f"{rsyncer_info.dict()}",
+            f"{rsyncer_info.model_dump()}",
             exc_info=True,
         )
         return None

src/murfey/server/api/session_control.py

@@ -96,7 +96,7 @@ def get_current_visits(instrument_name: str, db=ispyb_db):
 
 
 class SessionInfo(BaseModel):
-    session_id: Optional[int]
+    session_id: Optional[int] = None
     session_name: str = ""
     rescale: bool = True
 

src/murfey/server/api/workflow.py

@@ -608,9 +608,9 @@ class TomoProcessFile(BaseModel):
     tag: str
     image_number: int
     pixel_size: float
-    dose_per_frame: Optional[float]
+    dose_per_frame: Optional[float] = None
     frame_count: int
-    tilt_axis: Optional[float]
+    tilt_axis: Optional[float] = None
     mc_uuid: Optional[int] = None
     voltage: float = 300
     mc_binning: int = 1

src/murfey/util/config.py

@@ -8,7 +8,7 @@
 
 import yaml
 from backports.entry_points_selectable import entry_points
-from pydantic import BaseModel, Extra, field_validator
+from pydantic import BaseModel, ConfigDict, field_validator
 from pydantic_settings import BaseSettings
 
 
@@ -94,15 +94,7 @@ class MachineConfig(BaseModel):  # type: ignore
     node_creator_queue: str = "node_creator"
     notifications_queue: str = "pato_notification"
 
-    class Config:
-        """
-        Inner class that defines this model's parsing and serialising behaviour
-        """
-
-        extra = Extra.allow
-        json_encoders = {
-            Path: str,
-        }
+    model_config = ConfigDict(extra="allow")
 
 
 def from_file(config_file_path: Path, instrument: str = "") -> dict[str, MachineConfig]:
@@ -145,10 +137,7 @@ class Security(BaseModel):
     graylog_host: str = ""
     graylog_port: Optional[int] = None
 
-    class Config:
-        json_encoders = {
-            Path: str,
-        }
+    model_config = ConfigDict()
 
     @field_validator("graylog_port")
     def check_port_present_if_host_is(

src/murfey/util/models.py

@@ -156,7 +156,7 @@ class Token(BaseModel):
 
 
 class ProcessingParametersTomo(BaseModel):
-    dose_per_frame: Optional[float]
+    dose_per_frame: Optional[float] = None
     frame_count: int
     tilt_axis: float
     gain_ref: Optional[str] = None