def test_missing_temporal_extent_but_start_and_end_provided_as_kwargs(self):
mmd_yaml = yaml.load(resource_string('py_mmd_tools', 'mmd_elements.yaml'), Loader=yaml.FullLoader)
nc2mmd = Nc_to_mmd('tests/data/reference_nc_missing_attrs.nc')
with self.assertRaises(AttributeError):
nc2mmd.to_mmd(time_coverage_start='1850-01-01T00:00:00Z', time_coverage_end='1950-01-01T00:00:00Z')
self.assertEqual(nc2mmd.metadata['temporal_extent']['start_date'], '1850-01-01T00:00:00Z')
self.assertEqual(nc2mmd.metadata['temporal_extent']['end_date'], '1950-01-01T00:00:00Z')
def test_missing_temporal_extent(self):
mmd_yaml = yaml.load(resource_string('py_mmd_tools', 'mmd_elements.yaml'), Loader=yaml.FullLoader)
nc2mmd = Nc_to_mmd('tests/data/reference_nc_missing_attrs.nc')
ncin = Dataset(nc2mmd.netcdf_product)
value = nc2mmd.get_temporal_extents(mmd_yaml['temporal_extent'], ncin)
self.assertEqual(value, [])
self.assertEqual(nc2mmd.missing_attributes['errors'][0], 'time_coverage_start is a required ACDD attribute')
def test_temporal_extent(self):
mmd_yaml = yaml.load(resource_string('py_mmd_tools', 'mmd_elements.yaml'), Loader=yaml.FullLoader)
nc2mmd = Nc_to_mmd('tests/data/reference_nc.nc')
ncin = Dataset(nc2mmd.netcdf_product)
value = nc2mmd.get_temporal_extents(mmd_yaml['temporal_extent'], ncin)
self.assertEqual(value[0]['start_date'], '2020-11-27T13:40:02.019817Z')
self.assertEqual(value[0]['end_date'], '2020-11-27T13:51:24.401505Z')
def test_last_metadata_update(self):
mmd_yaml = yaml.load(resource_string('py_mmd_tools', 'mmd_elements.yaml'),
Loader=yaml.FullLoader)
nc2mmd = Nc_to_mmd('tests/data/reference_nc.nc')
ncin = Dataset(nc2mmd.netcdf_product)
value = nc2mmd.get_metadata_updates(mmd_yaml['last_metadata_update'], ncin)
self.assertEqual(value['update'][0]['datetime'], '2020-11-27T14:05:56Z')
def test__to_mmd__get_correct_id_from_ncfile(self):
tested = tempfile.mkstemp()[1]
# The id attribute is a uuid
nc2mmd = Nc_to_mmd('tests/data/reference_nc.nc', output_file=tested)
nc2mmd.to_mmd()
self.assertEqual(nc2mmd.missing_attributes['warnings'][0], 'Using default value Active for metadata_status')
self.assertEqual(nc2mmd.missing_attributes['errors'], [])
def test_create_mmd_2(self):
"""ToDo: Add docstring"""
self.maxDiff = None
tested = tempfile.mkstemp()[1]
md = Nc_to_mmd(self.fail_nc, output_file=tested)
with self.assertRaises(AttributeError):
md.to_mmd()
def test_keywords_vocabulary_missing(self):
mmd_yaml = yaml.load(resource_string('py_mmd_tools', 'mmd_elements.yaml'),
Loader=yaml.FullLoader)
nc2mmd = Nc_to_mmd('tests/data/reference_nc_missing_keywords_vocab.nc')
ncin = Dataset(nc2mmd.netcdf_product)
value = nc2mmd.get_keywords(mmd_yaml['keywords'], ncin)
self.assertEqual(nc2mmd.missing_attributes['errors'][0], 'keywords_vocabulary is a required ACDD attribute')
def test_metadata_status_is_active(self):
mmd_yaml = yaml.load(resource_string('py_mmd_tools', 'mmd_elements.yaml'),
Loader=yaml.FullLoader)
nc2mmd = Nc_to_mmd('tests/data/reference_nc.nc')
ncin = Dataset(nc2mmd.netcdf_product)
value = nc2mmd.get_acdd_metadata(mmd_yaml['metadata_status'], ncin, 'metadata_status')
self.assertEqual(value, 'Active')
def test_personnel_acdd_roles_not_list(self):
"""Test that we can have multiple people in MMD personnel field"""
mmd_yaml = yaml.load(
resource_string('py_mmd_tools', 'mmd_elements.yaml'), Loader=yaml.FullLoader
)
nc2mmd = Nc_to_mmd(
'tests/data/reference_nc_attrs_multiple_and_contributor.nc',
check_only=True
)
ncin = Dataset(nc2mmd.netcdf_product)
mmd_yaml['personnel']['name']['acdd'].pop(-1)
mmd_yaml['personnel']['name']['acdd'] = mmd_yaml['personnel']['name']['acdd'][0]
mmd_yaml['personnel']['role']['acdd'].pop(-1)
mmd_yaml['personnel']['role']['acdd'] = mmd_yaml['personnel']['role']['acdd'][0]
mmd_yaml['personnel']['email'].pop('acdd_ext')
mmd_yaml['personnel']['organisation'].pop('acdd_ext')
value = nc2mmd.get_personnel(mmd_yaml['personnel'], ncin)
self.assertEqual(value[0]['name'], 'Trygve')
self.assertEqual(value[1]['name'], 'Nina')
self.assertEqual(value[0]['role'], 'Investigator')
self.assertEqual(value[1]['role'], 'Technical contact')
self.assertEqual(value[0]['email'], '*****@*****.**')
self.assertEqual(value[1]['email'], '*****@*****.**')
self.assertEqual(value[0]['organisation'], 'Norwegian Meteorological Institute')
self.assertEqual(value[1]['organisation'], 'Norwegian Meteorological Institute')
def test_create_mmd_1(self):
"""Test MMD creation from a valid netcdf file, validation
with the mmd_strict.xsd, and that some fields are as expected.
Please add new fields to test as needed..
"""
tested = tempfile.mkstemp()[1]
# md = Nc_to_mmd(self.reference_nc, output_file=tested)
md = Nc_to_mmd('tests/data/reference_nc_with_altID_multiple.nc', output_file=tested)
md.to_mmd()
xsd_obj = etree.XMLSchema(etree.parse(self.reference_xsd))
xml_doc = etree.ElementTree(file=tested)
valid = xsd_obj.validate(xml_doc)
self.assertTrue(valid)
""" Check content of the xml_doc """
# alternate_identifier
self.assertEqual(
xml_doc.getroot().find(
"{http://www.met.no/schema/mmd}alternate_identifier[@type='dummy_type']"
).text,
"dummy_id_no1"
)
self.assertEqual(
xml_doc.getroot().find(
"{http://www.met.no/schema/mmd}alternate_identifier[@type='other_type']"
).text,
"dummy_id_no2"
)
def test_alternate_identifier(self):
mmd_yaml = yaml.load(resource_string('py_mmd_tools', 'mmd_elements.yaml'),
Loader=yaml.FullLoader)
nc2mmd = Nc_to_mmd('tests/data/reference_nc.nc')
ncin = Dataset(nc2mmd.netcdf_product)
value = nc2mmd.get_acdd_metadata(mmd_yaml['alternate_identifier'], ncin, 'alternate_identifier')
self.assertEqual(value, [])
def test_spatial_repr(self):
"""ToDo: Add docstring"""
tempfile.mkstemp()[1]
nc2mmd = Nc_to_mmd('tests/data/reference_nc.nc', check_only=True)
nc2mmd.to_mmd()
spatial_repr = nc2mmd.metadata['spatial_representation']
self.assertEqual(spatial_repr, 'grid')
def test_access_constraint(self):
"""ToDo: Add docstring"""
tempfile.mkstemp()[1]
nc2mmd = Nc_to_mmd('tests/data/reference_nc.nc', check_only=True)
nc2mmd.to_mmd()
spatial_repr = nc2mmd.metadata['access_constraint']
self.assertEqual(spatial_repr, 'Open')
def test_missing_vocabulary_platform(self):
mmd_yaml = yaml.load(resource_string('py_mmd_tools', 'mmd_elements.yaml'),
Loader=yaml.FullLoader)
nc2mmd = Nc_to_mmd('tests/data/reference_nc_missing_keywords_vocab.nc')
ncin = Dataset(nc2mmd.netcdf_product)
value = nc2mmd.get_platforms(mmd_yaml['platform'], ncin)
self.assertEqual(value[0]['resource'], '')
def test_missing_geographic_extent(self):
mmd_yaml = yaml.load(resource_string('py_mmd_tools', 'mmd_elements.yaml'), Loader=yaml.FullLoader)
nc2mmd = Nc_to_mmd('tests/data/reference_nc_missing_attrs.nc')
ncin = Dataset(nc2mmd.netcdf_product)
value = nc2mmd.get_acdd_metadata(mmd_yaml['geographic_extent'], ncin, 'geographic_extent')
self.assertEqual(value['rectangle']['north'], None)
self.assertEqual(nc2mmd.missing_attributes['errors'][0], 'geospatial_lat_max is a required attribute')
def test_missing_id(self):
mmd_yaml = yaml.load(resource_string('py_mmd_tools', 'mmd_elements.yaml'), Loader=yaml.FullLoader)
# nc file is missing the id attribute
nc2mmd = Nc_to_mmd('tests/data/reference_nc_missing_keywords_vocab.nc')
ncin = Dataset(nc2mmd.netcdf_product)
value = nc2mmd.get_metadata_identifier(mmd_yaml['metadata_identifier'], ncin)
self.assertTrue(Nc_to_mmd.is_valid_uuid(value))
def test__to_mmd__error_if_accd_id_is_invalid(self):
"""Test that metadata_identifier is set to an empty string, and
that an exception is raised if the ACDD id is not a valid uuid.
"""
tested = tempfile.mkstemp()[1]
# The id attribute is not a uuid
nc2mmd = Nc_to_mmd('tests/data/reference_nc_id_not_uuid.nc', output_file=tested)
with self.assertRaises(AttributeError):
nc2mmd.to_mmd()
self.assertEqual(
nc2mmd.missing_attributes['errors'][0], (
'naming_authority is a required attribute.'
)
)
self.assertEqual(
nc2mmd.missing_attributes['errors'][1], (
'id ACDD attribute is not valid.'
)
)
self.assertEqual(nc2mmd.missing_attributes['warnings'], [])
self.assertFalse(Nc_to_mmd.is_valid_uuid(nc2mmd.metadata['metadata_identifier']))
ncin = Dataset(nc2mmd.netcdf_product)
id = ncin.getncattr('id')
self.assertNotEqual(id, nc2mmd.metadata['metadata_identifier'])
self.assertEqual(':', nc2mmd.metadata['metadata_identifier'])
def test_related_dataset(self):
nc2mmd = Nc_to_mmd('tests/data/reference_nc_id_missing.nc')
ncin = Dataset('tests/data/reference_nc_id_missing.nc')
mmd_yaml = yaml.load(resource_string('py_mmd_tools', 'mmd_elements.yaml'), Loader=yaml.FullLoader)
data = nc2mmd.get_related_dataset(mmd_yaml['related_dataset'], ncin)
self.assertEqual(data[0]['id'], 'b7cb7934-77ca-4439-812e-f560df3fe7eb')
self.assertEqual(data[0]['relation_type'], 'parent')
def test_get_data_access_dict(self):
nc2mmd = Nc_to_mmd('tests/data/reference_nc.nc')
ncin = Dataset(nc2mmd.netcdf_product)
nc2mmd.netcdf_product = 'https://thredds.met.no/thredds/dodsC/arcticdata/S2S_drift_TCD/SIDRIFT_S2S_SH/2019/07/31/' + nc2mmd.netcdf_product
data = nc2mmd.get_data_access_dict(ncin)
self.assertEqual(data[0]['type'], 'OPeNDAP')
self.assertEqual(data[1]['type'], 'HTTP')
def test_dataset_citation_missing_attrs(self):
mmd_yaml = yaml.load(resource_string('py_mmd_tools', 'mmd_elements.yaml'), Loader=yaml.FullLoader)
nc2mmd = Nc_to_mmd('tests/data/reference_nc_missing_keywords_vocab.nc')
ncin = Dataset(nc2mmd.netcdf_product)
value = nc2mmd.get_dataset_citations(mmd_yaml['dataset_citation'], ncin)
self.assertEqual(value[0]['url'], '')
self.assertEqual(value[0]['other'], '')
def test_platforms(self):
mmd_yaml = yaml.load(resource_string('py_mmd_tools', 'mmd_elements.yaml'), Loader=yaml.FullLoader)
nc2mmd = Nc_to_mmd('tests/data/reference_nc.nc')
ncin = Dataset(nc2mmd.netcdf_product)
value = nc2mmd.get_platforms(mmd_yaml['platform'], ncin)
self.assertEqual(value[0]['long_name'], 'SNPP')
self.assertEqual(value[0]['instrument']['long_name'], 'VIIRS')
def test_publication_date(self):
format = '%Y-%m-%d'
mmd_yaml = yaml.load(resource_string('py_mmd_tools', 'mmd_elements.yaml'), Loader=yaml.FullLoader)
nc2mmd = Nc_to_mmd('tests/data/reference_nc.nc')
ncin = Dataset(nc2mmd.netcdf_product)
value = nc2mmd.get_dataset_citations(mmd_yaml['dataset_citation'], ncin)
dt = datetime.datetime.strptime(value[0]['publication_date'], format)
self.assertEqual(dt, datetime.datetime(2020, 11, 27, 0, 0))
def test_create_mmd_missing_update_times(self):
mmd_yaml = yaml.load(resource_string('py_mmd_tools', 'mmd_elements.yaml'),
Loader=yaml.FullLoader)
md = Nc_to_mmd(self.fail_nc)
ncin = Dataset(md.netcdf_product)
value = md.get_metadata_updates(mmd_yaml['last_metadata_update'], ncin)
self.assertEqual(md.missing_attributes['errors'][0],
'ACDD attribute date_created or date_metadata_modified is required')
def test_keywords_multiple(self):
mmd_yaml = yaml.load(resource_string('py_mmd_tools', 'mmd_elements.yaml'), Loader=yaml.FullLoader)
nc2mmd = Nc_to_mmd('tests/data/reference_nc_attrs_multiple.nc')
ncin = Dataset(nc2mmd.netcdf_product)
value = nc2mmd.get_keywords(mmd_yaml['keywords'], ncin)
self.assertEqual(value[0]['vocabulary'], 'GCMD')
self.assertEqual(value[0]['resource'], 'https://gcmdservices.gsfc.nasa.gov/static/kms/')
self.assertEqual(value[0]['keyword'], 'Earth Science > Atmosphere > Atmospheric radiation')
def test_create_mmd_missing_abstract(self):
mmd_yaml = yaml.load(resource_string('py_mmd_tools', 'mmd_elements.yaml'),
Loader=yaml.FullLoader)
md = Nc_to_mmd(self.fail_nc)
ncin = Dataset(md.netcdf_product)
value = md.get_abstracts(mmd_yaml['abstract'], ncin)
self.assertEqual(md.missing_attributes['errors'][0],
'summary is a required ACDD attribute')
def test_iso_topic_category(self):
mmd_yaml = yaml.load(resource_string('py_mmd_tools', 'mmd_elements.yaml'), Loader=yaml.FullLoader)
nc2mmd = Nc_to_mmd('tests/data/reference_nc.nc')
ncin = Dataset(nc2mmd.netcdf_product)
value = nc2mmd.get_acdd_metadata(mmd_yaml['iso_topic_category'], ncin, 'iso_topic_category')
self.assertEqual(value[0], 'climatologyMeteorologyAtmosphere')
self.assertEqual(value[1], 'environment')
self.assertEqual(value[2], 'oceans')
def test_missing_temporal_extent_but_start_provided_as_kwarg(self):
"""ToDo: Add docstring"""
yaml.load(
resource_string('py_mmd_tools', 'mmd_elements.yaml'), Loader=yaml.FullLoader
)
nc2mmd = Nc_to_mmd('tests/data/reference_nc_missing_attrs.nc', check_only=True)
with self.assertRaises(AttributeError):
nc2mmd.to_mmd(time_coverage_start='1850-01-01T00:00:00Z')
self.assertEqual(nc2mmd.metadata['temporal_extent']['start_date'], '1850-01-01T00:00:00Z')
def test_projects(self):
"""Test getting project information from nc-file"""
mmd_yaml = yaml.load(
resource_string('py_mmd_tools', 'mmd_elements.yaml'), Loader=yaml.FullLoader
)
nc2mmd = Nc_to_mmd('tests/data/reference_nc.nc', check_only=True)
ncin = Dataset(nc2mmd.netcdf_product)
value = nc2mmd.get_projects(mmd_yaml['project'], ncin)
self.assertEqual(value[0]['long_name'], 'MET Norway core services')
def test_personnel(self):
"""Test reading of personnel from nc file into MMD"""
mmd_yaml = yaml.load(
resource_string('py_mmd_tools', 'mmd_elements.yaml'), Loader=yaml.FullLoader
)
nc2mmd = Nc_to_mmd('tests/data/reference_nc.nc', check_only=True)
ncin = Dataset(nc2mmd.netcdf_product)
value = nc2mmd.get_personnel(mmd_yaml['personnel'], ncin)
self.assertEqual(value[0]['email'], '*****@*****.**')
def test_missing_vocabulary_platform_instrument_short_name(self):
"""ToDo: Add docstring"""
mmd_yaml = yaml.load(
resource_string('py_mmd_tools', 'mmd_elements.yaml'), Loader=yaml.FullLoader
)
nc2mmd = Nc_to_mmd('tests/data/reference_nc_missing_keywords_vocab.nc', check_only=True)
ncin = Dataset(nc2mmd.netcdf_product)
value = nc2mmd.get_platforms(mmd_yaml['platform'], ncin)
self.assertEqual(value[0]['instrument']['short_name'], '')