Silence "converting a masked element to nan" warning

api/app/database/user_info_model.py

@@ -1,13 +1,11 @@
-"""Alert database model."""
+"""UserInfo database model."""
 import datetime
-import json
 import logging
 
 from sqlalchemy import JSON, TIMESTAMP, Column, DateTime, Identity, Integer, String
 from sqlalchemy.ext.declarative import DeclarativeMeta, declarative_base
 from sqlalchemy.sql.sqltypes import Boolean
 
-logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
 Base = declarative_base()

api/app/main.py

@@ -30,7 +30,11 @@
 from .geotiff_from_stac_api import get_geotiff
 from .models import AlertsModel, StatsModel, UserInfoPydanticModel
 
-logging.basicConfig(level=logging.DEBUG)
+logging.basicConfig(
+    format="%(asctime)s %(levelname)-8s %(message)s",
+    level=logging.DEBUG,
+    datefmt="%Y-%m-%d %H:%M:%S",
+)
 logger = logging.getLogger(__name__)
 
 # silence boto3 logging to avoid spamming the logs

api/app/utils.py

@@ -1,3 +1,5 @@
+import logging
+
 import requests
 from fastapi import HTTPException
 
@@ -12,3 +14,27 @@ def forward_http_error(resp: requests.Response, excluded_codes: list[int]) -> No
         obj = resp.json()
         detail = obj.get("detail", "Unknown error")
         raise HTTPException(status_code=resp.status_code, detail=detail)
+
+
+class WarningsFilter(logging.Filter):
+    """Custom logging filter for warnings."""
+
+    def __init__(self):
+        super().__init__()
+        self.max_warnings = 1
+        self.warning_count = 0
+
+    def filter(self, record):
+        if (
+            self.warning_count >= self.max_warnings
+            and record.levelno == logging.WARNING
+            and "converting a masked element to nan" in record.getMessage()
+        ):
+            return True
+        if (
+            record.levelno == logging.WARNING
+            and "converting a masked element to nan" in record.getMessage()
+        ):
+            self.warning_count += 1
+
+        return False

api/app/zonal_stats.py

@@ -1,5 +1,6 @@
 """Calulate zonal statistics and return a json or a geojson."""
 import logging
+import warnings
 from collections import defaultdict
 from datetime import datetime
 from json import dump, load
@@ -20,6 +21,7 @@
 )
 from app.raster_utils import calculate_pixel_area, gdal_calc, reproj_match
 from app.timer import timed
+from app.utils import WarningsFilter
 from app.validation import VALID_OPERATORS
 from fastapi import HTTPException
 from rasterio.warp import Resampling
@@ -29,6 +31,9 @@
 
 logger = logging.getLogger(__name__)
 
+# Add custom filter to silence 'converting a masked element to nan' warnings
+logger.addFilter(WarningsFilter())
+
 
 DEFAULT_STATS = ["min", "max", "mean", "median", "sum", "std", "nodata", "count"]