Tolerate problems with dorado mission 2006.338.11.

.vscode/launch.json

@@ -207,7 +207,8 @@
             //"args": ["--auv_name", "dorado", "--mission", "2025.316.02", "-v", "1"],
             //"args": ["-v", "1", "--log_file", "pontus/missionlogs/2025/20250604_20250616/20250608T020852/202506080209_202506081934.nc4"],
             //"args": ["-v", "1", "--log_file", "ahi/missionlogs/2025/20250414_20250418/20250414T205440/202504142054_202504150400.nc4"],
-            "args": ["--auv_name", "dorado", "--mission", "2022.201.00", "-v", "1"],
+            //"args": ["--auv_name", "dorado", "--mission", "2022.201.00", "-v", "1"],
+            "args": ["--auv_name", "dorado", "--mission", "2006.338.11", "-v", "1"],
         },
         {
             "name": "5.0 - archive.py",
@@ -232,7 +233,8 @@
             //"args": ["-v", "1", "--auv_name", "dorado", "--mission", "2023.192.01", "--local"],
             //"args": ["-v", "2", "--auv_name", "dorado", "--mission", "2016.270.00"],
             //"args": ["-v", "1", "--auv_name", "dorado", "--mission", "2022.201.00"],
-            "args": ["-v", "1", "--log_file", "pontus/missionlogs/2024/20240715_20240725/20240723T023501/202407230235_202407232319.nc4"],
+            //"args": ["-v", "1", "--log_file", "pontus/missionlogs/2024/20240715_20240725/20240723T023501/202407230235_202407232319.nc4"],
+            "args": ["-v", "1", "--auv_name", "dorado", "--mission", "2006.338.11"],
         },
         {
             "name": "7.0 - email.py",
@@ -344,7 +346,9 @@
             // File "/src/data/resample.py", line 587, in save_coordinates f"{self.ds[f'{pitch_corrected_instr}_depth'].attrs['comment']}"
             //"args": ["-v", "1", "--mission", "2003.164.02", "--noinput", "--no_cleanup" ],
             // File "/src/data/calibrate.py", line 698, in global_metadata f"{self.nudge_total_minutes:.1f} minutes nudged toward GPS fixes."
-            "args": ["-v", "1", "--mission", "2003.191.00", "--noinput", "--no_cleanup" ],
+            //"args": ["-v", "1", "--mission", "2003.191.00", "--noinput", "--no_cleanup" ],
+            //   File "/src/data/resample.py", line 736,  IndexError: index -1 is out of bounds for axis 0 with size 0
+            "args": ["-v", "1", "--mission", "2006.338.11", "--noinput", "--no_cleanup" ],
 
         },
         {

src/data/create_products.py

@@ -375,7 +375,14 @@ def _grid_dims(self) -> tuple:
         # distnav = cumsum(sqrt(dxFix.^2 + dyFix.^2));	% in m
         # dists = distnav / 1000; 	% in km
 
-        utm_zone = int(31 + (self.ds.cf["longitude"].mean() // 6))
+        try:
+            utm_zone = int(31 + (self.ds.cf["longitude"].mean() // 6))
+        except ValueError:
+            self.logger.warning(
+                "Cannot compute mean longitude for UTM zone calculation, "
+                "longitude data may be empty or contain NaNs",
+            )
+            return None, None, None
         MAX_LONGITUDE_VALUES = 400
         n_subsample = 200 if len(self.ds.cf["longitude"].to_numpy()) > MAX_LONGITUDE_VALUES else 1
         lon_sub_intrp = np.interp(
@@ -1139,7 +1146,9 @@ def plot_2column(self) -> str:  # noqa: C901, PLR0912, PLR0915
         self._open_ds()
 
         idist, iz, distnav = self._grid_dims()
-        scfac = max(idist) / max(iz)  # noqa: F841
+        if idist is None or iz is None or distnav is None:
+            self.logger.warning("Skipping plot_2column due to missing gridding dimensions")
+            return None
 
         fig, ax = plt.subplots(nrows=5, ncols=2, figsize=(18, 10))
         plt.subplots_adjust(hspace=0.15, wspace=0.01, left=0.05, right=1.01, top=0.96, bottom=0.06)
@@ -1242,7 +1251,7 @@ def plot_2column(self) -> str:  # noqa: C901, PLR0912, PLR0915
         self.logger.info("Saved 2column plot to %s", output_file)
         return str(output_file)
 
-    def plot_biolume(self) -> str:
+    def plot_biolume(self) -> str:  # noqa: C901
         """Create bioluminescence plot showing raw signal and proxy variables"""
         # Skip plotting in pytest environment - too many prerequisites for CI
         if "pytest" in sys.modules:
@@ -1258,6 +1267,10 @@ def plot_biolume(self) -> str:
             return None
 
         idist, iz, distnav = self._grid_dims()
+        if idist is None or iz is None or distnav is None:
+            self.logger.warning("Skipping plot_biolume due to missing gridding dimensions")
+            return None
+
         profile_bottoms = self._profile_bottoms(distnav)
 
         # Create figure with subplots for biolume variables

src/data/resample.py

@@ -108,6 +108,12 @@ def _build_global_metadata(self) -> None:
         # Skip dynamic metadata during testing to ensure reproducible results
         if "pytest" in sys.modules:
             return {}
+        if self.resampled_nc.time.size == 0:
+            self.logger.warning(
+                "No time data available to build global metadata",
+            )
+            return {}
+
         # Try to get actual host name, fall back to container name
         actual_hostname = os.getenv("HOST_NAME", gethostname())
         repo = git.Repo(search_parent_directories=True)
@@ -724,6 +730,11 @@ def _find_lat_lon_variables(self) -> tuple[str, str]:
         return lat_var, lon_var
 
     def add_profile(self, depth_threshold: float) -> None:
+        if len(self.resampled_nc["depth"]) == 0:
+            self.logger.warning(
+                "No depth data available to compute profile numbers",
+            )
+            return
         # Find depth vertices value using scipy's find_peaks algorithm
         options = {"prominence": 10, "width": 30}
         peaks_pos, _ = signal.find_peaks(self.resampled_nc["depth"], **options)