Handle case where variable data not provided or is None

Author: mhidas

ncwriter/schema.py

@@ -38,7 +38,8 @@
             "items": {"type": "string", "pattern": NAME_PATTERN}
         },
         "type": {"type": "string"},
-        "attributes": ATTRIBUTES_SCHEMA
+        "attributes": ATTRIBUTES_SCHEMA,
+        "data": {"type": ["null", "array"]}
     },
     "additionalProperties": False
 }

ncwriter/template.py

@@ -407,7 +407,10 @@ def createVariables(self, **kwargs):
                     varname, datatype, dimensions=dimensions, **var_c_opts)
 
             # add variable values
-            ncvar[:] = var['data']
+            if 'data' not in var:
+                raise ValueError('No data specified for variable {varname}'.format(varname=varname))
+            if var['data'] is not None:
+                ncvar[:] = var['data']
 
             # add variable attributes
             if var.get('attributes'):

test_ncwriter/test_schema.py

@@ -32,12 +32,14 @@ def test_validate_variables(self):
         validate_variables({'X': {'type': 'float32'}})
         validate_variables({'X': {'dimensions': []}})
         validate_variables({'X': {'attributes': {'name': 'X'}}})
+        validate_variables({'X': {'data': None}})
         validate_variables({'X': {'dimensions': ['X'], 'type': 'float32'}})
         validate_variables({
             'X': {
                 'dimensions': ['X'],
                 'type': 'float32',
-                'attributes': {'name': 'X', 'count': 1}
+                'attributes': {'name': 'X', 'count': 1},
+                'data': [42]
             }
         })
 
@@ -51,6 +53,8 @@ def test_validate_variables(self):
             validate_variables({'X': {'type': 'float32', 'something': 'else'}})
         with self.assertRaises(ValidationError):
             validate_variables({'X': {'type': 'float32', 'attributes': 'none'}})
+        with self.assertRaises(ValidationError):
+            validate_variables({'X': {'data': 100}})
 
     def test_validate_attributes(self):
         validate_attributes({})

test_ncwriter/test_template.py

@@ -140,6 +140,21 @@ def test_create_empty_file(self):
         template.to_netcdf(self.temp_nc_file)
         dataset = Dataset(self.temp_nc_file)
 
+    def test_create_empty_variable(self):
+        template = DatasetTemplate(dimensions={'X': 10})
+        template.variables['X'] = {'dimensions': ['X'], 'type': 'float32'}
+        self.assertRaises(ValueError, template.to_netcdf, self.temp_nc_file)  # not providing 'data' is an error
+
+        del self._temp_nc_file  # Get a new temp file
+        template.variables['X']['data'] = None  # This is ok, it's a shortcut for all fill values
+        template.to_netcdf(self.temp_nc_file)
+
+        dataset = Dataset(self.temp_nc_file)
+        dataset.set_auto_mask(True)
+        dsx = dataset.variables['X']
+        self.assertIsInstance(dsx[:], np.ma.MaskedArray)
+        self.assertTrue(dsx[:].mask.all())
+
     def test_create_file(self):
         template = DatasetTemplate.from_json(TEMPLATE_JSON)
         template.variables['TIME']['data'] = self.values10
@@ -184,6 +199,7 @@ def test_fill_values(self):
         template.to_netcdf(self.temp_nc_file)
 
         dataset = Dataset(self.temp_nc_file)
+        dataset.set_auto_mask(True)
         dsx = dataset.variables['X']
         self.assertEqual(-999., dsx._FillValue)
         self.assertIsInstance(dsx[:], np.ma.MaskedArray)