updating capability to check if files exist before overwriting.

python/ctsm/site_and_regional/base_case.py

@@ -18,6 +18,7 @@
 import xarray as xr
 
 # -- import local classes for this script
+from ctsm.utils import abort
 from ctsm.git_utils import get_ctsm_git_short_hash
 
 USRDAT_DIR = "CLM_USRDAT_DIR"
@@ -46,6 +47,9 @@ class BaseCase:
         flag for creating DATM files
     create_user_mods
         flag for creating a user_mods directory
+    overwrite : bool
+        flag for overwriting if the file already exists
+
     Methods
     -------
     create_1d_coord(filename, lon_varname , lat_varname,x_dim , y_dim )
@@ -56,7 +60,7 @@ class BaseCase:
     """
 
     def __init__(self, create_domain, create_surfdata, create_landuse, create_datm,
-                 create_user_mods):
+                 create_user_mods, overwrite):
         """
         Initializes BaseCase with the given arguments.
 
@@ -72,12 +76,15 @@ def __init__(self, create_domain, create_surfdata, create_landuse, create_datm,
             Flag for creating datm files a region/single point
         create_user_mods : bool
             Flag for creating user mods directories and files for running CTSM
+        overwrite : bool
+            flag for overwriting if the file already exists
         """
         self.create_domain = create_domain
         self.create_surfdata = create_surfdata
         self.create_landuse = create_landuse
         self.create_datm = create_datm
         self.create_user_mods = create_user_mods
+        self.overwrite = overwrite
 
     def __str__(self):
         """
@@ -108,9 +115,10 @@ def create_1d_coord(filename, lon_varname, lat_varname, x_dim, y_dim):
             f_out (xarray Dataset): Xarray Dataset with 1-d coords
 
         """
-        logger.debug("Open file: %s", filename)
 
-        if os.path.exists:
+        if os.path.exists(filename):
+            logger.debug("Open file: %s", filename)
+
             f_in = xr.open_dataset(filename)
         else:
             err_msg = "File not found : " + filename
@@ -184,3 +192,27 @@ def write_to_file(text, file):
         Writes text to a file, surrounding text with \n characters
         """
         file.write("\n{}\n".format(text))
+
+    def write_to_netcdf (self, xr_ds, nc_fname):
+        """
+        Writes a netcdf file if
+            - the file does not exist.
+            or
+            - overwrite flag is chosen.
+
+        Args:
+            xr_ds : Xarray Dataset
+                The xarray dataset that we are write out to netcdf file.
+            nc_fname : str
+                Netcdf file name
+        Raises:
+            Error and aborts the code if the file exists and --overwrite is not used.
+        """
+        if not os.path.exists(nc_fname) or self.overwrite:
+            # mode 'w' overwrites file
+            xr_ds.to_netcdf(path=nc_fname, mode="w", format="NETCDF3_64BIT")
+        else:
+            err_msg = ("File "+nc_fname+ " already exists."+
+                       "\n Either remove the file or use --overwrite to overwrite the existing files.")
+            abort (err_msg)
+

python/ctsm/site_and_regional/regional_case.py

@@ -43,6 +43,9 @@ class RegionalCase(BaseCase):
         flag for creating DATM files
     create_user_mods : bool
         flag for creating user mods files and folders
+    overwrite : bool
+        flag for over-writing files if they already exist
+
 
     Methods
     -------
@@ -75,12 +78,13 @@ def __init__(
             create_datm,
             create_user_mods,
             out_dir,
+            overwrite,
     ):
         """
         Initializes RegionalCase with the given arguments.
         """
         super().__init__(create_domain, create_surfdata, create_landuse, create_datm,
-                         create_user_mods)
+                         create_user_mods, overwrite)
         self.lat1 = lat1
         self.lat2 = lat2
         self.lon1 = lon1
@@ -129,7 +133,7 @@ def create_domain_at_reg(self, indir, file):
 
         # mode 'w' overwrites file
         wfile = os.path.join(self.out_dir, fdomain_out)
-        f_out.to_netcdf(path=wfile, mode="w", format='NETCDF3_64BIT')
+        self.write_to_netcdf (f_out, wfile)
         logger.info("Successfully created file (fdomain_out) %s", wfile)
         f_in.close()
         f_out.close()
@@ -163,7 +167,7 @@ def create_surfdata_at_reg(self, indir, file, user_mods_dir):
 
         # mode 'w' overwrites file
         wfile = os.path.join(self.out_dir, fsurf_out)
-        f_out.to_netcdf(path=wfile, mode="w", format='NETCDF3_64BIT')
+        self.write_to_netcdf (f_out, wfile)
         logger.info("created file (fsurf_out) %s", wfile)
         f_in.close()
         f_out.close()
@@ -205,7 +209,7 @@ def create_landuse_at_reg(self, indir, file, user_mods_dir):
 
         # mode 'w' overwrites file
         wfile = os.path.join(self.out_dir, fluse_out)
-        f_out.to_netcdf(path=wfile, mode="w", format='NETCDF3_64BIT')
+        self.write_to_netcdf (f_out, wfile)
         logger.info("Successfully created file (fluse_out) %s", wfile)
         f_in.close()
         f_out.close()

python/ctsm/site_and_regional/single_point_case.py

@@ -61,6 +61,8 @@ class SinglePointCase(BaseCase):
         flag for creating datasets using uniform snowpack
     saturation_excess : bool
         flag for making dataset using saturation excess
+    overwrite : bool
+        flag for over-writing files if they already exist
 
     Methods
     -------
@@ -107,9 +109,10 @@ def __init__(
             uni_snow,
             cap_saturation,
             out_dir,
+            overwrite,
     ):
         super().__init__(create_domain, create_surfdata, create_landuse, create_datm,
-                         create_user_mods)
+                         create_user_mods, overwrite)
         self.plat = plat
         self.plon = plon
         self.site_name = site_name
@@ -310,7 +313,7 @@ def create_domain_at_point(self, indir, file):
         f_out.attrs["Created_from"] = fdomain_in
 
         wfile = os.path.join(self.out_dir, fdomain_out)
-        f_out.to_netcdf(path=wfile, mode="w", format="NETCDF3_64BIT")
+        self.write_to_netcdf (f_out, wfile)
         logger.info("Successfully created file (fdomain_out) %s", wfile)
         f_in.close()
         f_out.close()
@@ -354,8 +357,7 @@ def create_landuse_at_point(self, indir, file, user_mods_dir):
         f_out.attrs["Created_from"] = fluse_in
 
         wfile = os.path.join(self.out_dir, fluse_out)
-        # mode 'w' overwrites file
-        f_out.to_netcdf(path=wfile, mode="w", format="NETCDF3_64BIT")
+        self.write_to_netcdf (f_out, wfile)
         logger.info("Successfully created file (fluse_out), %s", wfile)
         f_in.close()
         f_out.close()
@@ -469,9 +471,9 @@ def create_surfdata_at_point(self, indir, file, user_mods_dir):
         # update attributes
         self.update_metadata(f_out)
         f_out.attrs["Created_from"] = fsurf_in
-        # mode 'w' overwrites file
+
         wfile = os.path.join(self.out_dir, fsurf_out)
-        f_out.to_netcdf(path=wfile, mode="w", format="NETCDF3_64BIT")
+        self.write_to_netcdf (f_out, wfile)
         logger.info("Successfully created file (fsurf_out) %s", wfile)
         f_in.close()
         f_out.close()
@@ -510,9 +512,8 @@ def create_datmdomain_at_point(self, datm_tuple: DatmFiles):
         self.update_metadata(f_out)
         f_out.attrs["Created_from"] = fdatmdomain_in
 
-        # mode 'w' overwrites file
         wfile = os.path.join(self.out_dir, fdatmdomain_out)
-        f_out.to_netcdf(path=wfile, mode="w", format = 'NETCDF3_64BIT')
+        self.write_to_netcdf (f_out, wfile)
         logger.info("Successfully created file (fdatmdomain_out) : %s", wfile)
         f_in.close()
         f_out.close()
@@ -537,8 +538,7 @@ def extract_datm_at(self, file_in, file_out):
         self.update_metadata(f_out)
         f_out.attrs["Created_from"] = file_in
 
-        # mode 'w' overwrites file
-        f_out.to_netcdf(path=file_out, mode="w")
+        self.write_to_netcdf (f_out, file_out)
         logger.info("Successfully created file : %s", file_out)
         f_in.close()
         f_out.close()

python/ctsm/subset_data.py

@@ -308,6 +308,12 @@ def get_parser():
             type=str,
             default="",
         )
+        subparser.add_argument(
+            "--overwrite",
+            help="Flag to overwrite if the files already exists.",
+            action="store_true",
+            dest="overwrite",
+        )
         add_logging_args(subparser)
 
     # -- print help for both subparsers
@@ -440,6 +446,7 @@ def subset_point(args, file_dict: dict):
         uni_snow = args.uni_snow,
         cap_saturation = args.cap_saturation,
         out_dir = args.out_dir,
+        overwrite = args.overwrite,
     )
 
     logger.debug(single_point)
@@ -496,6 +503,7 @@ def subset_region(args, file_dict: dict):
         create_datm = args.create_datm,
         create_user_mods = args.create_user_mods,
         out_dir = args.out_dir,
+        overwrite = args.overwrite,
     )
 
     logger.debug(region)