Simplify exception handling - concentrate them in the decorator

.vscode/launch.json

@@ -376,7 +376,11 @@
             //"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250903_20250903/20250903T202626/202509032026_202509032030.nc4", "--no_cleanup"]
             // Fails in nudge_positions, maybe bad GPS data?
             //"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250911T073640/202509110736_202509120809.nc4", "--no_cleanup"]
-            "args": ["-v", "1", "--auv_name", "brizo", "--start", "20250901T000000", "--end", "20251001T000000", "--noinput", "--num_cores", "1", "--no_cleanup"]
+            // Raises InvalidCombinedFile error
+            //"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250916_20250922/20250921T001456/202509210014_202509221430.nc4", "--no_cleanup"]
+            // A depth coordinate was not found for instrument navigation in
+            //"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250903_20250903/20250903T175939/202509031759_202509032026.nc4", "--no_cleanup"]
+            "args": ["-v", "1", "--auv_name", "brizo", "--start", "20250901T000000", "--end", "20251001T000000", "--no_cleanup"]
         },
 
     ]

src/data/process.py

@@ -106,6 +106,8 @@ def wrapper(self, log_file: str):
             return func(self, log_file)
         except (TestMission, FailedMission, EOFError) as e:
             self.logger.info(str(e))
+        except (FileNotFoundError, InvalidCalFile, InvalidCombinedFile, InvalidAlignFile) as e:
+            self.logger.warning(str(e))
         except Exception:
             # Catch all other exceptions and log full traceback
             self.logger.exception("Exception occurred while processing %s", log_file)
@@ -525,9 +527,8 @@ def calibrate(self, mission: str) -> None:
         try:
             netcdf_dir = cal_netcdf.process_logs()
             cal_netcdf.write_netcdf(netcdf_dir)
-        except (FileNotFoundError, EOFError) as e:
-            cal_netcdf.logger.error("%s %s", mission, e)  # noqa: TRY400
-        cal_netcdf.logger.removeHandler(self.log_handler)
+        finally:
+            cal_netcdf.logger.removeHandler(self.log_handler)
 
     def align(self, mission: str = "", log_file: str = "") -> None:
         self.logger.info("Alignment steps for %s", mission or log_file)
@@ -548,15 +549,6 @@ def align(self, mission: str = "", log_file: str = "") -> None:
             else:
                 netcdf_dir = align_netcdf.process_cal()
                 align_netcdf.write_combined_netcdf(netcdf_dir)
-        except (FileNotFoundError, EOFError) as e:
-            align_netcdf.logger.error("%s %s", mission or log_file, e)  # noqa: TRY400
-            error_message = f"{mission or log_file} {e}"
-            raise InvalidCalFile(error_message) from e
-        except Exception:
-            align_netcdf.logger.exception(
-                "Exception occurred during alignment of %s", mission or log_file
-            )
-            raise
         finally:
             align_netcdf.logger.removeHandler(self.log_handler)
 
@@ -611,13 +603,6 @@ def resample(self, mission: str = "", log_file: str = "") -> None:
             subprocess.run([wget_path, dap_file_str, "-O", nc_file_str], check=True)  # noqa: S603
         try:
             resamp.resample_align_file(nc_file)
-        except (FileNotFoundError, InvalidAlignFile) as e:
-            self.logger.error("%s %s", nc_file, e)  # noqa: TRY400
-        except Exception:
-            resamp.logger.exception(
-                "Exception occurred during resampling of %s", mission or log_file
-            )
-            raise
         finally:
             resamp.logger.removeHandler(self.log_handler)
 
@@ -1001,9 +986,6 @@ def extract(self, log_file: str) -> None:
             extract.logger.info("Downloading %s", url)
             input_file = extract.download_with_pooch(url, output_dir)
             return extract.extract_groups_to_files_netcdf4(input_file)
-        except Exception:
-            extract.logger.exception("Exception occurred during extraction of %s", log_file)
-            raise
         finally:
             extract.logger.removeHandler(self.log_handler)
 
@@ -1025,9 +1007,6 @@ def combine(self, log_file: str) -> None:
         try:
             combine.combine_groups()
             combine.write_netcdf()
-        except Exception:
-            combine.logger.exception("Exception occurred during combine of %s", log_file)
-            raise
         finally:
             combine.logger.removeHandler(self.log_handler)
 

src/data/resample.py

@@ -1807,7 +1807,7 @@ def resample_align_file(  # noqa: C901, PLR0912, PLR0915, PLR0913
                 # 'seabird25p' if needed for i2map missions. Early LRAUV missions
                 # had only CTD_NeilBrown instruments, later ones had CTD_Seabird.
                 pitch_corrected_instr = self._get_pitch_corrected_instrument()
-                if pitch_corrected_instr in instrs_to_pad:
+                if pitch_corrected_instr == "seabird25p" and pitch_corrected_instr in instrs_to_pad:
                     # Use navigation if seabird25p failed to record
                     # data all the way to the end of the mission
                     pitch_corrected_instr = "navigation"