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Adding ereefs example with ncld annotations to a branch (#13)
* Adding ereefs example with ncld annotations
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‎lib/bald/tests/integration/CDL/ereefs-gbr4_ncld.cdl

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netcdf gbr4_1.85 {
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dimensions:
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i = 600 ;
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j = 180 ;
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k = 47 ;
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time = 50521 ;
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variables:
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double zc(k) ;
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zc:axis = "Z" ;
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zc:coordinate_type = "Z" ;
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zc:units = "m" ;
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zc:positive = "up" ;
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zc:long_name = "Z coordinate" ;
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double longitude(j, i) ;
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longitude:standard_name = "longitude" ;
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longitude:coordinate_type = "longitude" ;
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longitude:projection = "geographic" ;
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longitude:units = "degrees_east" ;
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longitude:long_name = "Longitude" ;
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double latitude(j, i) ;
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latitude:standard_name = "latitude" ;
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latitude:coordinate_type = "latitude" ;
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latitude:projection = "geographic" ;
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latitude:units = "degrees_north" ;
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latitude:long_name = "Latitude" ;
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double botz(j, i) ;
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botz:standard_name = "depth" ;
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botz:missing_value = -99. ;
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botz:positive = "down" ;
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botz:coordinates = "latitude longitude" ;
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botz:outside = "9999" ;
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botz:units = "metre" ;
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botz:long_name = "Depth of sea-bed" ;
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double time(time) ;
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time:units = "days since 1990-01-01 00:00:00 +10" ;
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time:long_name = "Time" ;
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time:standard_name = "time" ;
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time:coordinate_type = "time" ;
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time:_ChunkSizes = 1 ;
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float eta(time, j, i) ;
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eta:coordinates = "time latitude longitude" ;
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eta:units = "metre" ;
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eta:long_name = "Surface elevation" ;
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eta:standard_name = "sea_surface_height_above_sea_level" ;
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eta:valid_range = -10.f, 10.f ;
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eta:missing_value = 1.e+35f ;
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eta:positive = "up" ;
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eta:medium_id = "http://environment.data.gov.au/def/feature/ocean" ;
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eta:scaledQuantityKind_id = "http://environment.data.gov.au/def/property/sea_surface_elevation" ;
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eta:substanceOrTaxon_id = "http://environment.data.gov.au/def/feature/ocean_near_surface" ;
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eta:unit_id = "http://qudt.org/vocab/unit#Meter" ;
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eta:_ChunkSizes = 1, 180, 600 ;
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float u(time, k, j, i) ;
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u:coordinates = "time zc latitude longitude" ;
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u:units = "ms-1" ;
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u:long_name = "Eastward current" ;
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u:standard_name = "eastward_sea_water_velocity" ;
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u:vector_name = "Currents" ;
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u:vector_components = "u v" ;
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u:valid_range = -100.f, 100.f ;
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u:missing_value = 1.e+35f ;
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u:medium_id = "http://environment.data.gov.au/def/feature/ocean" ;
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u:scaledQuantityKind_id = "http://environment.data.gov.au/def/property/sea_water_velocity_eastward" ;
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u:substanceOrTaxon_id = "http://environment.data.gov.au/def/feature/ocean_current" ;
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u:unit_id = "http://qudt.org/vocab/unit#MeterPerSecond" ;
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u:_ChunkSizes = 1, 24, 90, 300 ;
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float v(time, k, j, i) ;
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v:coordinates = "time zc latitude longitude" ;
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v:units = "ms-1" ;
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v:long_name = "Northward current" ;
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v:standard_name = "northward_sea_water_velocity" ;
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v:vector_name = "Currents" ;
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v:vector_components = "u v" ;
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v:valid_range = -100.f, 100.f ;
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v:missing_value = 1.e+35f ;
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v:medium_id = "http://environment.data.gov.au/def/feature/ocean" ;
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v:scaledQuantityKind_id = "http://environment.data.gov.au/def/property/sea_water_velocity_northward" ;
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v:substanceOrTaxon_id = "http://environment.data.gov.au/def/feature/ocean_current" ;
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v:unit_id = "http://qudt.org/vocab/unit#MeterPerSecond" ;
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v:_ChunkSizes = 1, 24, 90, 300 ;
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float salt(time, k, j, i) ;
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salt:coordinates = "time zc latitude longitude" ;
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salt:units = "PSU" ;
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salt:long_name = "Salinity" ;
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salt:valid_range = 0.f, 40.f ;
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salt:missing_value = 1.e+35f ;
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salt:medium_id = "http://environment.data.gov.au/def/feature/ocean" ;
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salt:scaledQuantityKind_id = "http://environment.data.gov.au/def/property/practical_salinity" ;
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salt:substanceOrTaxon_id = "http://sweet.jpl.nasa.gov/2.2/matrWater.owl#SaltWater" ;
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salt:unit_id = "http://environment.data.gov.au/water/quality/def/unit/PSU" ;
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salt:_ChunkSizes = 1, 24, 90, 300 ;
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float temp(time, k, j, i) ;
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temp:coordinates = "time zc latitude longitude" ;
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temp:units = "degrees C" ;
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temp:long_name = "Temperature" ;
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temp:valid_range = 0.f, 40.f ;
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temp:missing_value = 1.e+35f ;
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temp:medium_id = "http://environment.data.gov.au/def/feature/ocean" ;
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temp:scaledQuantityKind_id = "http://environment.data.gov.au/def/property/sea_water_temperature" ;
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temp:substanceOrTaxon_id = "http://sweet.jpl.nasa.gov/2.2/matrWater.owl#SaltWater" ;
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temp:unit_id = "http://qudt.org/vocab/unit#DegreeCelsius" ;
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temp:_ChunkSizes = 1, 24, 90, 300 ;
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float wspeed_u(time, j, i) ;
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wspeed_u:coordinates = "time latitude longitude" ;
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wspeed_u:units = "ms-1" ;
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wspeed_u:long_name = "eastward_wind" ;
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wspeed_u:valid_range = -1000.f, 1000.f ;
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wspeed_u:missing_value = 1.e+35f ;
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wspeed_u:_ChunkSizes = 1, 180, 600 ;
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float wspeed_v(time, j, i) ;
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wspeed_v:coordinates = "time latitude longitude" ;
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wspeed_v:units = "ms-1" ;
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wspeed_v:long_name = "northward_wind" ;
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wspeed_v:valid_range = -1000.f, 1000.f ;
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wspeed_v:missing_value = 1.e+35f ;
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wspeed_v:_ChunkSizes = 1, 180, 600 ;
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// global attributes:
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:title = "GBR4 Hydro" ;
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:paramhead = "GBR 4km resolution grid" ;
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:paramfile = "in.prm" ;
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:shoc_version = "v1.1 rev(5249)" ;
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:Conventions = "CF-1.0" ;
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:Run_ID = 1.85 ;
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:hasVocab = 1 ;
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:metadata_link = "http://marlin.csiro.au/geonetwork/srv/eng/search?&uuid=72020224-f086-434a-bbe9-a222c8e5cf0d" ;
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:rdf__type = "bald__Container" ;
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:bald__isPrefixedBy = "prefix_list" ;
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:bald__isAliasedBy = "alias_list" ;
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group: prefix_list {
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// group attributes:
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:bald__ = "http://binary-array-ld.net/latest/" ;
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:rdf__ = "http://www.w3.org/1999/02/22-rdf-syntax-ns#" ;
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} // group bald__prefix_list
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group: alias_list {
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// group attributes:
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:unit_id = "http://qudt.org/1.1/schema/qudt#unit";
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:medium_id = "http://environment.data.gov.au/def/op#matrix" ;
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:scaledQuantityKind_id = "http://environment.data.gov.au/def/op#propertyKind" ;
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:substanceOrTaxon_id = "http://environment.data.gov.au/def/op#objectOfInterest" ;
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} // group bald__alias_list
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}

‎lib/bald/tests/integration/test_cdl.py

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import bald
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from bald.tests import BaldTestCase
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class Test(BaldTestCase):
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def setUp(self):
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self.cdl_path = os.path.join(os.path.dirname(__file__), 'CDL')
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print(self.cdl_path)
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def test_array_reference(self):
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with self.temp_filename('.nc') as tfile:
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cdl_file = os.path.join(self.cdl_path, 'array_reference.cdl')
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subprocess.check_call(['ncgen', '-o', tfile, cdl_file])
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validation = bald.validate_netcdf(tfile)
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exns = validation.exceptions()
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self.assertTrue(validation.is_valid(), msg='{} != []'.format(exns))
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self.assertTrue(validation.is_valid(), msg='{} != []'.format(exns))
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def test_alias(self):
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with self.temp_filename('.nc') as tfile:
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cdl_file = os.path.join(self.cdl_path, 'array_alias.cdl')
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subprocess.check_call(['ncgen', '-o', tfile, cdl_file])
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validation = bald.validate_netcdf(tfile)
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exns = validation.exceptions()
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self.assertTrue(validation.is_valid(), msg='{} != []'.format(exns))
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self.assertTrue(validation.is_valid(), msg='{} != []'.format(exns))
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def test_process_chain(self):
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with self.temp_filename('.nc') as tfile:
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cdl_file = os.path.join(self.cdl_path, 'ProcessChain0300.cdl')
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subprocess.check_call(['ncgen', '-o', tfile, cdl_file])
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validation = bald.validate_netcdf(tfile)
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exns = validation.exceptions()
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self.assertTrue(validation.is_valid(), msg='{} != []'.format(exns))
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def test_ereef(self):
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with self.temp_filename('.nc') as tfile:
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cdl_file = os.path.join(self.cdl_path, 'ereefs-gbr4_ncld.cdl')
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subprocess.check_call(['ncgen', '-o', tfile, cdl_file])
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validation = bald.validate_netcdf(tfile)
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exns = validation.exceptions()
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#self.assertTrue(validation.is_valid(), msg='{} != []'.format(exns))
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self.assertFalse(validation.is_valid(), msg='AssertionError: [\'http://qudt.org/vocab/unit#Meter is not resolving as a resource (404).\', \'http://qudt.org/vocab/unit#MeterPerSecond is not resolving as a resource (404).\', \'http://qudt.org/vocab/unit#MeterPerSecond is not resolving as a resource (404).\', \'http://qudt.org/vocab/unit#DegreeCelsius is not resolving as a resource (404).\']. Also {} != []'.format(exns))
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