Standardise contexts (#844)

* Switched FIBContext to using the shared '_get_source' and '_file_transferred_to' functions
* Switched CLEMContext to using the shared '_get_source' and '_file_transferred_to' functions
* Streamlined conditionals in the CLEMContext
* Switched CLEMContext 'post_transfer' function to return 'None'
* Added tests for the CLEMContext

Author: tieneupin

src/murfey/client/contexts/clem.py

@@ -10,42 +10,14 @@
 
 from defusedxml.ElementTree import parse
 
-from murfey.client.context import Context
+from murfey.client.context import Context, _file_transferred_to, _get_source
 from murfey.client.instance_environment import MurfeyInstanceEnvironment
 from murfey.util.client import capture_post
 
 # Create logger object
 logger = logging.getLogger("murfey.client.contexts.clem")
 
 
-def _file_transferred_to(
-    environment: MurfeyInstanceEnvironment,
-    source: Path,
-    file_path: Path,
-    rsync_basepath: Path,
-):
-    """
-    Returns the Path of the transferred file on the DLS file system.
-    """
-    # Construct destination path
-    base_destination = rsync_basepath / Path(environment.default_destinations[source])
-    # Add visit number to the path if it's not present in default destination
-    if environment.visit not in environment.default_destinations[source]:
-        base_destination = base_destination / environment.visit
-    destination = base_destination / file_path.relative_to(source)
-    return destination
-
-
-def _get_source(file_path: Path, environment: MurfeyInstanceEnvironment):
-    """
-    Returns the Path of the file on the client PC.
-    """
-    for s in environment.sources:
-        if file_path.is_relative_to(s):
-            return s
-    return None
-
-
 def _get_image_elements(root: ET.Element) -> list[ET.Element]:
     """
     Searches the XML metadata recursively to find the nodes tagged as "Element" that
@@ -100,25 +72,23 @@ def post_transfer(
         transferred_file: Path,
         environment: MurfeyInstanceEnvironment | None = None,
         **kwargs,
-    ) -> bool:
+    ):
         super().post_transfer(transferred_file, environment=environment, **kwargs)
 
+        # Early exit if environment was not set
+        if not environment:
+            logger.warning("No environment was set")
+            return None
+
         # Process files generated by "auto-save" acquisition mode
         # These include TIF/TIFF and XLIF files
         if transferred_file.suffix in (".tif", ".tiff", ".xlif"):
             logger.debug(f"File extension {transferred_file.suffix!r} detected")
-
-            # Type checking to satisfy MyPy
-            if not environment:
-                logger.warning("No environment passed in")
-                return False
-
             # Location of the file on the client PC
             source = _get_source(transferred_file, environment)
-            # Type checking to satisfy MyPy
             if not source:
                 logger.warning(f"No source found for file {transferred_file}")
-                return False
+                return None
 
             # Get the file Path at the destination
             destination_file = _file_transferred_to(
@@ -127,18 +97,13 @@ def post_transfer(
                 file_path=transferred_file,
                 rsync_basepath=Path(self._machine_config.get("rsync_basepath", "")),
             )
-            if not destination_file:
-                logger.warning(
-                    f"File {transferred_file.name!r} not found on the storage system"
-                )
-                return False
 
             # Skip processing of binned "_pmd" image series
             if "_pmd_" in transferred_file.stem:
                 logger.debug(
                     f"File {transferred_file.name!r} belongs to the '_pmd_' series of binned images; skipping processing"
                 )
-                return True
+                return None
 
             # Process TIF/TIFF files
             if transferred_file.suffix in (".tif", ".tiff"):
@@ -150,7 +115,7 @@ def post_transfer(
                     logger.warning(
                         f"File {transferred_file.name!r} is likely not part of the CLEM workflow"
                     )
-                    return False
+                    return None
                 logger.debug(
                     f"File {transferred_file.name!r} is part of a TIFF image series"
                 )
@@ -179,21 +144,21 @@ def post_transfer(
                 )
 
             # Process XLIF files
-            if transferred_file.suffix == ".xlif":
+            elif transferred_file.suffix == ".xlif":
                 # Skip processing of "_histo" histogram XLIF files
                 if transferred_file.stem.endswith("_histo"):
                     logger.debug(
                         f"File {transferred_file.name!r} contains histogram metadata; skipping processing"
                     )
-                    return True
+                    return None
 
                 # Skip processing of "IOManagerConfiguation.xlif" files
                 #   YES, the 'Configuation' typo IS part of the file name
                 if "IOManagerConfiguation" in transferred_file.stem:
                     logger.debug(
                         f"File {transferred_file.name!r} is a Leica configuration file; skipping processing"
                     )
-                    return True
+                    return None
 
                 logger.debug(
                     f"File {transferred_file.name!r} contains metadata for an image series"
@@ -242,12 +207,10 @@ def post_transfer(
             # .get(series_name, 0) returns 0 if no associated key is found
             if not len(self._tiff_series.get(series_name, [])):
                 logger.debug(f"TIFF series {series_name!r} not yet loaded")
-                return True
             elif self._files_in_series.get(series_name, 0) == 0:
                 logger.debug(
                     f"Metadata for TIFF series {series_name!r} not yet processed"
                 )
-                return True
             elif len(
                 self._tiff_series.get(series_name, [])
             ) >= self._files_in_series.get(series_name, 0):
@@ -261,10 +224,8 @@ def post_transfer(
                     "tiff_files": self._tiff_series[series_name][0:1],
                     "series_metadata": self._series_metadata[series_name],
                 }
-                post_result = self.process_tiff_series(tiff_dataset, environment)
-                if post_result is False:
-                    return False
-                logger.info(f"Started preprocessing of TIFF series {series_name!r}")
+                if self.process_tiff_series(tiff_dataset, environment):
+                    logger.info(f"Started preprocessing of TIFF series {series_name!r}")
 
                 # Clean up memory after posting
                 del self._tiff_series[series_name]
@@ -274,18 +235,12 @@ def post_transfer(
                 logger.debug(f"TIFF series {series_name!r} is still being processed")
 
         # Process LIF files
-        if transferred_file.suffix == ".lif":
-            # Type checking to satisfy MyPy
-            if not environment:
-                logger.warning("No environment passed in")
-                return False
-
+        elif transferred_file.suffix == ".lif":
             # Location of the file on the client PC
             source = _get_source(transferred_file, environment)
-            # Type checking to satisfy MyPy
             if not source:
                 logger.warning(f"No source found for file {transferred_file}")
-                return False
+                return None
 
             logger.debug(
                 f"File {transferred_file.name!r} is a valid LIF file; starting processing"
@@ -298,20 +253,13 @@ def post_transfer(
                 file_path=transferred_file,
                 rsync_basepath=Path(self._machine_config.get("rsync_basepath", "")),
             )
-            if not destination_file:
-                logger.warning(
-                    f"File {transferred_file.name!r} not found on the storage system"
-                )
-                return False
 
             # Post URL to trigger job and convert LIF file into image stacks
-            post_result = self.process_lif_file(destination_file, environment)
-            if post_result is False:
-                return False
-            logger.info(f"Started preprocessing of {destination_file.name!r}")
+            if self.process_lif_file(destination_file, environment):
+                logger.info(f"Started preprocessing of {destination_file.name!r}")
 
         # Function has completed as expected
-        return True
+        return None
 
     def process_lif_file(
         self,

src/murfey/client/contexts/fib.py

@@ -7,7 +7,7 @@
 from pathlib import Path
 from typing import Callable, Type, TypeVar, cast
 
-from murfey.client.context import Context
+from murfey.client.context import Context, _file_transferred_to, _get_source
 from murfey.client.instance_environment import MurfeyInstanceEnvironment
 from murfey.util.client import capture_post
 from murfey.util.fib import get_slot_number, number_from_name
@@ -200,34 +200,6 @@ def _get_project_name(file_path: Path):
         return None
 
 
-def _get_source(file_path: Path, environment: MurfeyInstanceEnvironment) -> Path | None:
-    """
-    Returns the Path of the file on the client PC.
-    """
-    for s in environment.sources:
-        if file_path.is_relative_to(s):
-            return s
-    return None
-
-
-def _file_transferred_to(
-    environment: MurfeyInstanceEnvironment,
-    source: Path,
-    file_path: Path,
-    rsync_basepath: Path,
-) -> Path | None:
-    """
-    Returns the Path of the transferred file on the DLS file system.
-    """
-    # Construct destination path
-    base_destination = rsync_basepath / Path(environment.default_destinations[source])
-    # Add visit number to the path if it's not present in default destination
-    if environment.visit not in environment.default_destinations[source]:
-        base_destination = base_destination / environment.visit
-    destination = base_destination / file_path.relative_to(source)
-    return destination
-
-
 @dataclass
 class FIBImage:
     images: list[Path] = field(default_factory=list)
@@ -338,11 +310,6 @@ def post_transfer(
                     file_path=transferred_file,
                     rsync_basepath=Path(self._machine_config.get("rsync_basepath", "")),
                 )
-                if destination_file is None:
-                    logger.warning(
-                        f"Could not find destination file path for {transferred_file.name!r}"
-                    )
-                    return None
 
                 # Register image in database
                 self._register_atlas(destination_file, environment)
@@ -599,11 +566,6 @@ def _make_drift_correction_gif(
                 file_path=file,
                 rsync_basepath=Path(self._machine_config.get("rsync_basepath", "")),
             )
-            if destination_file is None:
-                logger.warning(
-                    f"Could not find destination file path for {file.name!r}"
-                )
-                return
         else:
             destination_file = file