Bleh

Author: manishvenu

regional_mom6/validate.py

@@ -0,0 +1,108 @@
+"""
+MOM6 requires NetCDF files to be in a very specific format to pass validation, including fill value and missing value attributes. This module is designed to accept input files and warn users of potential issues with their files
+If you can, leave proof in the form of the exact lines of Fortran code where this is required!
+
+"""
+
+from pathlib import Path
+import xarray as xr
+from .utils import setup_logger
+
+logger = setup_logger(__name__)
+
+
+def get_file(file: Path | xr.Dataset):
+    """accept a filepath or xarray dataset and return the xarray dataset"""
+    if type(file) == xr.Dataset:
+        return file
+    else:
+        return xr.open_dataset(file)
+
+
+def check(condition, warning):
+    condition or logger.warn(warning)
+
+
+# Individual validation rule functions
+def _check_fill_value(da: xr.DataArray):
+    """Check that fill values are set correctly"""
+    check("_FillValue" in da.attrs, f"{var_name} does not have a FillValue attribute")
+
+    check(
+        not np.isnan(da.attrs["_FillValue"]),
+        f"Fill Value for variable {var_name} is NaN (normally not wanted)",
+    )
+
+
+def _check_coordinates(ds: xr.Dataset, var_name: str):
+    """Check that missing values are set correctly"""
+
+    assert var_name in ds
+    check(
+        "coordinates" in ds[var_name].attrs,
+        f"{var_name} does not have a coordinates attribute",
+    )
+
+    coordinates = ds[var_name].attrs["coordinates"]
+    coordinates = coordinates.strip(" ")
+    for coord in coordinates:
+        check(coord in ds, f"Coordinate {coord} for variable {var_name} does not exist")
+
+
+def _check_required_dimensions(da: xr.DataArray, surface=False):
+    """Check that required dimensions exist"""
+    if not surface:
+        check(len(da.dims) == 4, f"Variable {da.name} does not have 4 dimensions")
+    else:
+        check(
+            len(da.dims) == 3, f"Surface Variable {da.name} does not have 3 dimensions"
+        )
+
+
+def validate_obc_file(
+    file: Path | xr.Dataset, variable_names: list, encoding_dict={}, surface_var="eta"
+):
+    """Validate boundary condition file specifically (requires additional segment number validation)"""
+    ds = get_file(file)
+
+    # Check individual data variable specifications (nothing that starts with dz)
+    print(
+        "This function identifies variables by if they have the word 'segment' in the name and don't start with nz,dz,lon,lat."
+    )
+
+    for var in variable_names:
+
+        # check variable name format
+        check(
+            ends_with_3_digits(var),
+            f"Variable {var} does not end with a 3 digit number. OBC file variables must end with a number",
+        )
+        check(
+            "segment" in var,
+            f"Variable {var} does not end with a 3 digit number. OBC file variables must end with a number",
+        )
+
+        # Add encodings
+        if var in encoding_dict:
+            for key, value in encoding_dict[var].item():
+                ds[var].attrs[key] = value
+
+        # Check if there is a non-NaN fill value
+        _check_fill_value(ds[var])
+
+        # check coordinates
+        _check_coordinates(ds, var_name=var)
+
+        # Check the correct number of dimensions
+        _check_required_dimensions(ds[var], surface=(var == surface_var))  # just two
+
+        # Check for thickness variable
+        if var != surface_var:
+            check(
+                f"dz_{var}" in ds,
+                f"Cannot find thickness variable for var {var}, it should be of the form dz_{var}",
+            )
+
+
+def ends_with_3_digits(s: str) -> bool:
+    return bool(re.search(r"\d{3}$", s))