Merge pull request #1 from ACCESS-NRI/add-more-variables-live-cmoriser

Add Ocean variables to the ACCESS-Live CMORiser

doc/quickstart/find_data.rst

@@ -615,12 +615,12 @@ Key                  Description                            Default value if not
 ``modeling_realm``   Realm attribute include `atm`, `ice`   No default (needs to be 
                      and `oce`                              specified in extra facets or
                                                             recipe if default DRS is used)
-```special_attr``    A special attribute in the filename    No default
+``frequency_attribute``    A special attribute in the filename    No default
                      `ACCESS-ESM` raw data, it's related to 
                      frquency of raw data
 ``sub_dataset``      Part of the ACCESS-ESM raw dataset     No default
                      root, need to specify if you want to
-                     use the cmoriser                                                                       
+                     use the cmoriser                                                              
 ==================== ====================================== =================================
 
 .. _data-retrieval:

esmvalcore/cmor/_fixes/access/_base_fix.py

@@ -2,6 +2,8 @@
 
 import logging
 
+import numpy as np
+
 from iris.cube import CubeList
 
 from esmvalcore.cmor._fixes.native_datasets import NativeDatasetFix
@@ -27,3 +29,37 @@ def get_cubes_from_multivar(self, cubes):
         for name in name_list:
             data_list.append(self.get_cube(cubes, name))
         return CubeList(data_list)
+
+    def fix_ocean_dim_coords(self, cube):
+        """Fix dim coords of ocean variables"""
+        cube.dim_coords[-2].points = np.array([int(i) for i in range(300)])
+        cube.dim_coords[-2].standard_name = None
+        cube.dim_coords[-2].var_name = 'j'
+        cube.dim_coords[-2].long_name = 'cell index along second dimension'
+        cube.dim_coords[-2].attributes = None
+
+        cube.dim_coords[-1].points = np.array([int(i) for i in range(360)])
+        cube.dim_coords[-1].standard_name = None
+        cube.dim_coords[-1].var_name = 'i'
+        cube.dim_coords[-1].long_name = 'cell index along first dimension'
+        cube.dim_coords[-1].attributes = None
+
+    def fix_ocean_aux_coords(self, cube):
+        """Fix aux coords of ocean variables"""
+        temp_points=[]
+        for i in cube.aux_coords[-1].points:
+            temp_points.append([j + 360 for j in i if j < 0]+[j for j in i if j >= 0])
+        cube.aux_coords[-1].points = np.array(temp_points)
+        cube.aux_coords[-1].standard_name = 'longitude'
+        cube.aux_coords[-1].long_name = 'longitude'
+        cube.aux_coords[-1].var_name = 'longitude'
+        cube.aux_coords[-1].attributes = None
+
+        temp_points=[]
+        for i in cube.aux_coords[-2].points:
+            temp_points.append([j.astype(np.float64) for j in i])
+        cube.aux_coords[-2].points = np.array(temp_points)
+        cube.aux_coords[-2].standard_name = 'latitude'
+        cube.aux_coords[-2].long_name = 'latitude'
+        cube.aux_coords[-2].var_name = 'latitude'
+        cube.aux_coords[-2].attributes = None

esmvalcore/cmor/_fixes/access/access_esm1_5.py

@@ -5,6 +5,8 @@
 
 from ._base_fix import AccessFix
 
+from cf_units import Unit
+
 logger = logging.getLogger(__name__)
 
 
@@ -125,3 +127,65 @@ def fix_height_value(self, cube):
         """Fix height value to make it comparable to other dataset."""
         if cube.coord('height').points[0] != 2:
             cube.coord('height').points = [2]
+
+class Tos(AccessFix):
+    """Fixes for Tos"""
+
+    def fix_metadata(self, cubes):
+        """Fix metadata.
+
+        Parameters
+        ----------
+        cubes : iris.cube.CubeList
+            Input cubes.
+
+        Returns
+        -------
+        iris.cube.CubeList
+        """
+
+        cube = self.get_cube(cubes)
+
+        self.fix_ocean_dim_coords(cube)
+        self.fix_ocean_aux_coords(cube)
+
+        return CubeList([cube])
+
+
+class So(AccessFix):
+    """FIxes for So"""
+
+    def fix_metadata(self, cubes):
+        """Fix metadata.
+
+        Parameters
+        ----------
+        cubes : iris.cube.CubeList
+            Input cubes.
+
+        Returns
+        -------
+        iris.cube.CubeList
+        """
+
+        cube = self.get_cube(cubes)
+
+        self.fix_ocean_dim_coords(cube)
+        self.fix_ocean_aux_coords(cube)
+        self.fix_depth_metadata(cube)
+        self.fix_so_units(cube)
+
+        return CubeList([cube])
+
+    def fix_depth_metadata(self, cube):
+        """fix depth metadata"""
+        cube.dim_coords[1].standard_name = 'depth'
+        cube.dim_coords[1].long_name = 'ocean depth coordinate'
+        cube.dim_coords[1].var_name = 'lev'
+        cube.dim_coords[1].attributes = {'positive':'down'}  
+
+    def fix_so_units(self, cube):
+        """fix units of so"""
+        cube.attributes.pop('invalid_units')
+        cube.units=Unit(0.001)     
+

esmvalcore/config-developer.yml

@@ -200,8 +200,11 @@ ACCESS:
   input_dir:
     default:
       - '{dataset}/{sub_dataset}/{exp}/{modeling_realm}/netCDF'
+      - '{dataset}/{sub_dataset}/{exp}/{modeling_realm}/'
   input_file:
-    default: '{sub_dataset}.{special_attr}-*.nc'
+    default: 
+    - '{sub_dataset}.{frequency_attribute}-2000*.nc'
+    - 'ocean_{frequency_attribute}.nc-2000*'
   output_file: '{project}_{dataset}_{mip}_{exp}_{institute}_{sub_dataset}_{special_attr}_{short_name}'
   cmor_type: 'CMIP6'
   cmor_default_table_prefix: 'CMIP6_'

esmvalcore/config/extra_facets/access-mappings.yml

@@ -7,6 +7,7 @@
 ACCESS-ESM1-5:
 
   '*':
+  # atm
 
     tas:
       raw_name: fld_s03i236
@@ -66,3 +67,121 @@ ACCESS-ESM1-5:
         - fld_s01i201 
       modeling_realm: atm
 
+    clivi:
+      raw_name: fld_s30i406
+      modeling_realm: atm
+
+    evspsbl:
+      raw_name: fld_s03i223
+      modeling_realm: atm
+
+    hfls:
+      raw_name: fld_s03i234
+      modeling_realm: atm
+
+    hfss:
+      raw_name: fld_s03i217
+      modeling_realm: atm
+
+    hur:
+      raw_name: fld_s30i206
+      modeling_realm: atm
+
+    hurs:
+      raw_name: fld_s03i245
+      modeling_realm: atm
+
+    huss:
+      raw_name: fld_s03i237
+      modeling_realm: atm
+
+    prsn:
+      raw_name: fld_s05i215
+      modeling_realm: atm
+
+    rldscs:
+      raw_name: fld_s02i208
+      modeling_realm: atm
+
+    rsdt:
+      raw_name: fld_s01i207
+      modeling_realm: atm
+
+    rsuscs:
+      raw_name: fld_s01i211
+      modeling_realm: atm
+
+    rsut:
+      raw_name: fld_s01i208
+      modeling_realm: atm
+
+    rsutcs:
+      raw_name: fld_s01i209
+      modeling_realm: atm
+
+    sci:
+      raw_name: fld_s05i270
+      modeling_realm: atm
+
+    sfcWind:
+      raw_name: fld_s03i230
+      modeling_realm: atm
+
+    sfcWindmax:
+      raw_name: fld_s03i227_max
+      modeling_realm: atm
+
+    tauu:
+      raw_name: fld_s03i460
+      modeling_realm: atm
+
+    tauv:
+      raw_name: fld_s03i461
+      modeling_realm: atm
+
+    ts:
+      raw_name: fld_s00i024
+      modeling_realm: atm
+
+    ua:
+      raw_name: fld_s30i201
+      modeling_realm: atm
+
+    uas:
+      raw_name: fld_s03i209
+      modeling_realm: atm
+
+    va:
+      raw_name: fld_s30i202
+      modeling_realm: atm
+
+    vas:
+      raw_name: fld_s03i210
+      modeling_realm: atm
+
+    wap:
+      raw_name: fld_s30i208
+      modeling_realm: atm
+
+    zg:
+      raw_name: fld_s30i207
+      modeling_realm: atm
+
+    rls:
+      raw_name: fld_s02i201
+      modeling_realm: atm
+
+    rss:
+      raw_name: fld_s01i201
+      modeling_realm: atm
+
+    # ocean
+
+    tos:
+      raw_name: sst
+      modeling_realm: ocn
+
+    so:
+      raw_name: salt
+      modeling_realm: ocn
+