Merge branch 'add_rt_length_to_output' into add_rt_length_to_output_II

alphadia/workflow/base.py

@@ -92,7 +92,6 @@ def load(
         )
 
         self._dia_data = raw_file_manager.get_dia_data_object(dia_data_path)
-        raw_file_manager.calc_stats(self._dia_data)
         raw_file_manager.save()
 
         self.reporter.log_event("loading_data", {"progress": 1})

alphadia/workflow/manager.py

@@ -55,6 +55,7 @@ def __init__(
         self.reporter = reporting.LogBackend() if reporter is None else reporter
 
         if load_from_file:
+            # Note: be careful not to overwrite loaded values by initializing them in child classes after calling super().__init__()
             self.load()
 
     @property

alphadia/workflow/managers/raw_file_manager.py

@@ -20,8 +20,9 @@ def __init__(
         load_from_file: bool = False,
         **kwargs,
     ):
-        """Contains and updates timing information for the portions of the workflow."""
-        self.stats = {}  # needs to be before super().__init__ to avoid overwriting when loading
+        """Handles raw file loading and contains information on the raw file."""
+        self.stats = {}  # needs to be before super().__init__ to avoid overwriting loaded values
+
         super().__init__(path=path, load_from_file=load_from_file, **kwargs)
 
         self._config: Config = config
@@ -52,7 +53,7 @@ def get_dia_data_object(
 
         is_wsl = self._config["general"]["wsl"]
         if is_wsl:
-            # copy file to /tmp # TODO why is that?
+            # copy file to /tmp # TODO check if WSL support can be dropped
             import shutil
 
             tmp_path = "/tmp"
@@ -106,9 +107,15 @@ def get_dia_data_object(
         if is_wsl:
             os.remove(tmp_dia_data_path)
 
+        self._calc_stats(dia_data)
+
+        self._log_stats()
+
         return dia_data
 
-    def calc_stats(self, dia_data: bruker.TimsTOFTranspose | alpharaw_wrapper.AlphaRaw):
+    def _calc_stats(
+        self, dia_data: bruker.TimsTOFTranspose | alpharaw_wrapper.AlphaRaw
+    ):
         """Calculate statistics from the DIA data."""
         rt_values = dia_data.rt_values
         cycle = dia_data.cycle
@@ -132,8 +139,6 @@ def calc_stats(self, dia_data: bruker.TimsTOFTranspose | alpharaw_wrapper.AlphaR
 
         self.stats = stats
 
-        self._log_stats()
-
     def _log_stats(self):
         """Log the statistics calculated from the DIA data."""
         rt_duration_min = self.stats["rt_duration_sec"] / 60