Remove references to role

Author: stephen-riggs

src/murfey/client/analyser.py

@@ -57,7 +57,6 @@ def __init__(
         self._limited = limited
         self._experiment_type = ""
         self._acquisition_software = ""
-        self._role = ""
         self._extension: str = ""
         self._unseen_xml: list = []
         self._context: Context | None = None
@@ -126,14 +125,12 @@ def _find_context(self, file_path: Path) -> bool:
         in the Context classes themselves.
         """
         if "atlas" in file_path.parts:
-            self._role = "detector"
             self._context = SPAMetadataContext("epu", self._basepath)
             return True
 
         # CLEM workflow checks
         # Look for LIF and XLIF files
         if file_path.suffix in (".lif", ".xlif"):
-            self._role = "detector"
             self._context = CLEMContext("leica", self._basepath)
             return True
         # Look for TIFF files associated with CLEM workflow
@@ -152,7 +149,6 @@ def _find_context(self, file_path: Path) -> bool:
                 ).get("analyse_created_directories", [])
             )
             if created_directories.intersection(set(file_path.parts)):
-                self._role = "detector"
                 self._context = CLEMContext("leica", self._basepath)
                 return True
 
@@ -181,9 +177,6 @@ def _find_context(self, file_path: Path) -> bool:
                         else SPAContext("epu", self._basepath)
                     )
                 self.parameters_model = ProcessingParametersSPA
-                # Assign it the detector attribute if not already present
-                if not self._role:
-                    self._role = "detector"
                 return True
 
             # Files starting with "Position" belong to the standard tomography workflow
@@ -198,9 +191,6 @@ def _find_context(self, file_path: Path) -> bool:
                     logger.info("Acquisition software: tomo")
                     self._context = TomographyContext("tomo", self._basepath)
                     self.parameters_model = PreprocessingParametersTomo
-                # Assign role if not already present
-                if not self._role:
-                    self._role = "detector"
                 return True
 
             # Files with these suffixes belong to the serial EM tomography workflow
@@ -225,16 +215,14 @@ def _find_context(self, file_path: Path) -> bool:
                     return False
                 self._context = TomographyContext("serialem", self._basepath)
                 self.parameters_model = PreprocessingParametersTomo
-                if not self._role:
-                    self._role = "detector"
                 return True
         return False
 
     def post_transfer(self, transferred_file: Path):
         try:
             if self._context:
                 self._context.post_transfer(
-                    transferred_file, role=self._role, environment=self._environment
+                    transferred_file, environment=self._environment
                 )
         except Exception as e:
             logger.error(f"An exception was encountered post transfer: {e}")
@@ -292,19 +280,17 @@ def _analyse(self):
                         self.queue.task_done()
                         continue
                     elif self._extension:
-                        logger.info(f"Context found successfully: {self._role}")
+                        logger.info(
+                            f"Context found successfully for {transferred_file}"
+                        )
                         try:
                             self._context.post_first_transfer(
                                 transferred_file,
-                                role=self._role,
                                 environment=self._environment,
                             )
                         except Exception as e:
                             logger.error(f"Exception encountered: {e}")
-                        if (
-                            self._role == "detector"
-                            and "atlas" not in transferred_file.parts
-                        ):
+                        if "atlas" not in transferred_file.parts:
                             if not dc_metadata:
                                 try:
                                     dc_metadata = self._context.gather_metadata(
@@ -360,20 +346,16 @@ def _analyse(self):
                     self._find_extension(transferred_file)
                     if self._extension:
                         logger.info(
-                            f"Context found successfully: {self._role}, {transferred_file}"
+                            f"Extension found successfully for {transferred_file}"
                         )
                         try:
                             self._context.post_first_transfer(
                                 transferred_file,
-                                role=self._role,
                                 environment=self._environment,
                             )
                         except Exception as e:
                             logger.error(f"Exception encountered: {e}")
-                        if (
-                            self._role == "detector"
-                            and "atlas" not in transferred_file.parts
-                        ):
+                        if "atlas" not in transferred_file.parts:
                             if not dc_metadata:
                                 try:
                                     dc_metadata = self._context.gather_metadata(

src/murfey/client/context.py

@@ -40,14 +40,14 @@ def __init__(self, name: str, acquisition_software: str):
         self._acquisition_software = acquisition_software
         self.name = name
 
-    def post_transfer(self, transferred_file: Path, role: str = "", **kwargs):
+    def post_transfer(self, transferred_file: Path, **kwargs):
         # Search external packages for additional hooks to include in Murfey
         for h in entry_points(group="murfey.post_transfer_hooks"):
             if h.name == self.name:
-                h.load()(transferred_file, role=role, **kwargs)
+                h.load()(transferred_file, **kwargs)
 
-    def post_first_transfer(self, transferred_file: Path, role: str = "", **kwargs):
-        self.post_transfer(transferred_file, role=role, **kwargs)
+    def post_first_transfer(self, transferred_file: Path, **kwargs):
+        self.post_transfer(transferred_file, **kwargs)
 
     def gather_metadata(
         self, metadata_file: Path, environment: MurfeyInstanceEnvironment | None = None

src/murfey/client/contexts/clem.py

@@ -101,14 +101,11 @@ def __init__(self, acquisition_software: str, basepath: Path):
     def post_transfer(
         self,
         transferred_file: Path,
-        role: str = "",
         environment: Optional[MurfeyInstanceEnvironment] = None,
         **kwargs,
     ) -> bool:
 
-        super().post_transfer(
-            transferred_file, role=role, environment=environment, **kwargs
-        )
+        super().post_transfer(transferred_file, environment=environment, **kwargs)
 
         # Process files generated by "auto-save" acquisition mode
         # These include TIF/TIFF and XLIF files

src/murfey/client/contexts/fib.py

@@ -44,13 +44,10 @@ def __init__(self, acquisition_software: str, basepath: Path):
     def post_transfer(
         self,
         transferred_file: Path,
-        role: str = "",
         environment: MurfeyInstanceEnvironment | None = None,
         **kwargs,
     ):
-        super().post_transfer(
-            transferred_file, role=role, environment=environment, **kwargs
-        )
+        super().post_transfer(transferred_file, environment=environment, **kwargs)
         if self._acquisition_software == "autotem":
             parts = transferred_file.parts
             if "DCImages" in parts and transferred_file.suffix == ".png":