A few fixes for CLEM workflow (#305)

* If an XLIF file has not been seen yet then self._files_in_series[series_name] will result in a KeyError
* For the CLEM workflow, run post_transfer on every file as soon as the context has been identified
* Add determination of CLEM context without the need for a LIF
* Read XLIF using path on client machine
* If rsync_module is an empty string use data

Author: d-j-hatton

src/murfey/client/analyser.py

@@ -110,11 +110,27 @@ def _find_context(self, file_path: Path) -> bool:
 
         # CLEM workflow check
         # Look for LIF files
-        if file_path.suffix == ".lif":
+        if file_path.suffix in (".lif", ".xlif"):
             self._role = "detector"
             self._context = CLEMContext("leica", self._basepath)
             return True
 
+        if (
+            "--" in file_path.name
+            and file_path.suffix in (".tiff", ".tif")
+            and self._environment
+        ):
+            created_directories = set(
+                get_machine_config(
+                    str(self._environment.url.geturl()),
+                    demo=self._environment.demo,
+                ).get("analyse_created_directories", [])
+            )
+            if created_directories.intersection(set(file_path.parts)):
+                self._role = "detector"
+                self._context = CLEMContext("leica", self._basepath)
+                return True
+
         split_file_name = file_path.name.split("_")
         if split_file_name:
             # Files starting with "FoilHole" belong to the SPA workflow
@@ -312,6 +328,8 @@ def _analyse(self):
                                         ),
                                     }
                                 )
+                elif isinstance(self._context, CLEMContext):
+                    self.post_transfer(transferred_file)
                 elif not self._extension or self._unseen_xml:
                     self._find_extension(transferred_file)
                     if self._extension:
@@ -370,7 +388,6 @@ def _analyse(self):
                         TomographyContext,
                         SPAModularContext,
                         SPAMetadataContext,
-                        CLEMContext,
                     ),
                 ):
                     self.post_transfer(transferred_file)

src/murfey/client/contexts/clem.py

@@ -34,7 +34,7 @@ def _file_transferred_to(
     )
     return (
         Path(machine_config.get("rsync_basepath", ""))
-        / machine_config.get("rsync_module", "data")
+        / (machine_config.get("rsync_module", "data") or "data")
         / str(datetime.now().year)
         / source.name
         / file_path.relative_to(source)
@@ -143,7 +143,7 @@ def post_transfer(
                 )  # The previous 2 parent directories should be unique enough
 
                 # Extract metadata to get the expected size of the series
-                metadata = parse(file_path).getroot()
+                metadata = parse(transferred_file).getroot()
                 metadata = get_image_elements(metadata)[0]
 
                 # Get channel and dimension information
@@ -170,9 +170,8 @@ def post_transfer(
                 self._metadata_timestamp[series_name] = transferred_file.stat().st_ctime
 
             # Post message if all files for the associated series have been collected
-            if (
-                len(self._tiff_series[series_name])
-                == self._files_in_series[series_name]
+            if len(self._tiff_series[series_name]) == self._files_in_series.get(
+                series_name, 0
             ):
 
                 # Construct URL for Murfey server to communicate with