Fail transparently for failed output accumulation

alphadia/outputtransform.py

@@ -27,6 +27,12 @@
 logger = logging.getLogger()
 
 
+class OutputGenerationError(Exception):
+    """Raised when an error occurs during output generation"""
+
+    pass
+
+
 def get_frag_df_generator(folder_list: list[str]):
     """Return a generator that yields a tuple of (raw_name, frag_df)
 
@@ -509,20 +515,17 @@ def build_precursor_table(
 
             if not os.path.exists(psm_path):
                 logger.warning(f"no psm file found for {raw_name}, skipping")
-                run_df = pd.DataFrame()
             else:
                 try:
                     run_df = pd.read_parquet(psm_path)
+                    psm_df_list.append(run_df)
                 except Exception as e:
                     logger.warning(f"Error reading psm file for {raw_name}")
                     logger.warning(e)
-                    run_df = pd.DataFrame()
-
-            psm_df_list.append(run_df)
 
         if len(psm_df_list) == 0:
-            logger.error("No psm files found, can't continue")
-            raise FileNotFoundError("No psm files found, can't continue")
+            logger.error("No psm files accumulated, can't continue")
+            raise OutputGenerationError("No psm files accumulated, can't continue")
 
         logger.info("Building combined output")
         psm_df = pd.concat(psm_df_list)

alphadia/planning.py

@@ -370,18 +370,13 @@ def run(
                 )
                 raise e
 
-        try:
-            base_spec_lib = SpecLibBase()
-            base_spec_lib.load_hdf(
-                os.path.join(self.output_folder, "speclib.hdf"), load_mod_seq=True
-            )
-
-            output = outputtransform.SearchPlanOutput(self.config, self.output_folder)
-            output.build(workflow_folder_list, base_spec_lib)
+        base_spec_lib = SpecLibBase()
+        base_spec_lib.load_hdf(
+            os.path.join(self.output_folder, "speclib.hdf"), load_mod_seq=True
+        )
 
-        except Exception as e:
-            logger.error(f"Output failed with error {e}", exc_info=True)
-            raise e
+        output = outputtransform.SearchPlanOutput(self.config, self.output_folder)
+        output.build(workflow_folder_list, base_spec_lib)
 
         logger.progress("=================== Search Finished ===================")