def metamap_dataset(self, ncdataset):
with app.app_context():
# gets a metamap document of this service using wicken
beliefs = IOOSNCCheck.beliefs()
ncnamespaces = {'nc': pb_namespaces['ncml']}
doc = NetCDFDogma('nc',
beliefs,
ncdataset,
namespaces=ncnamespaces)
# now make a map out of this
# @TODO wicken should make this easier
m_names, m_units = ['Variable Names*', 'Variable Units*']
metamap = {}
for k in beliefs:
try:
metamap[k] = getattr(doc, doc._fixup_belief(k)[0])
except Exception as e:
app.logger.exception("Problem setting belief (%s)", k)
metamap[m_names] = [
] # Override the Wicken return to preserve the order
metamap[m_units] = [
] # Override the Wicken return to preserve the order
# Wicken doesn't preserve the order between the names and the units,
# so what you wind up with is two lists that can't be related, but we
# want to keep the relationship between the name and the units
for k in ncdataset.variables.iterkeys():
var_name = k
standard_name = getattr(ncdataset.variables[k],
'standard_name', '')
units = getattr(ncdataset.variables[k], 'units', '')
# Only map metadata where we have all three
if var_name and standard_name and units:
metamap[m_names].append('%s (%s)' %
(var_name, standard_name))
metamap[m_units].append(units)
return metamap
def get_pair(self, nc_dataset):
'''
Return a pairwise object for the dataset
'''
if isinstance(nc_dataset, basestring):
nc_dataset = Dataset(nc_dataset, 'r')
self.addCleanup(nc_dataset.close)
dogma = NetCDFDogma('nc', self.cf.beliefs(), nc_dataset)
pair = DSPair(nc_dataset, dogma)
return pair
def metamap_dataset(self, ncdataset):
with app.app_context():
# gets a metamap document of this service using wicken
beliefs = IOOSNCCheck.beliefs()
ncnamespaces = {'nc': pb_namespaces['ncml']}
doc = NetCDFDogma('nc', beliefs, ncdataset,
namespaces=ncnamespaces)
# now make a map out of this
# @TODO wicken should make this easier
m_names, m_units = ['Variable Names*', 'Variable Units*']
metamap = {}
for k in beliefs:
try:
metamap[k] = getattr(doc, doc._fixup_belief(k)[0])
except Exception:
app.logger.exception("Problem setting belief (%s)", k)
# Override the Wicken return to preserve the order
metamap[m_names] = []
# Override the Wicken return to preserve the order
metamap[m_units] = []
# Wicken doesn't preserve the order between the names and the units,
# so what you wind up with is two lists that can't be related, but we
# want to keep the relationship between the name and the units
for k in ncdataset.variables.iterkeys():
var_name = k
standard_name = getattr(
ncdataset.variables[k], 'standard_name', '')
units = getattr(ncdataset.variables[k], 'units', '')
# Only map metadata where we have all three
if var_name and standard_name and units:
metamap[m_names].append('%s (%s)' %
(var_name, standard_name))
metamap[m_units].append(units)
return metamap
def metamap_dataset(self, ncdataset):
with app.app_context():
# gets a metamap document of this service using wicken
beliefs = IOOSNCCheck.beliefs()
ncnamespaces = {'nc':pb_namespaces['ncml']}
doc = NetCDFDogma('nc', beliefs, ncdataset, namespaces=ncnamespaces)
# now make a map out of this
# @TODO wicken should make this easier
metamap = {}
for k in beliefs:
try:
metamap[k] = getattr(doc, doc._fixup_belief(k)[0])
except Exception as e:
print k, e
return metamap
def load_datapair(self, ds):
# allow ncml as well as nc prefixes
namespaces = pb_namespaces.copy()
namespaces['nc'] = namespaces['ncml']
namespaces['ncml'] = namespaces['ncml']
data_object = NetCDFDogma('ds',
self.beliefs(),
ds,
namespaces=namespaces)
return DSPair(ds, data_object)
# typically loaded from a file - a modified version of the IOOS Asset_SOS_MAP spread sheet for example
'service_provider_institution':
"""/ncml:netcdf/ncml:attribute[@name='institution']/@value""",
'data_conventions':
"""/ncml:netcdf/ncml:attribute[@name='institution']/@value""",
'latitude_units':
"""/ncml:netcdf/ncml:variable[@name='latitude']/ncml:attribute[@name='units']/@value""",
'does_not_exist':
"""/ncml:netcdf/ncml:attribute[@name='does_not_exist']/@value"""
}
#read a file
ds = Dataset('test_ncs/result_surface.nc', 'a')
data_object = NetCDFDogma('NetcdfCF', cf_metadata_beliefs, ds)
data_object.__class__.__name__
data_object.service_provider_institution
data_object.data_conventions
data_object.latitude_units
# will return empty
data_object.does_not_exist
data_object.service_provider_institution = 'David Stuebe'
data_object.data_conventions = 'CF-3.14159'
data_object.latitude_units = 'degrees a little bit west of north'
# will fail - can't make a new attribute element (yet?)
data_object.does_not_exist = 'foobar'
cf_metadata_beliefs = {
# A map of what you call the metadata property to an xpath expression for it in some convention/encoding
# typically loaded from a file - a modified version of the IOOS Asset_SOS_MAP spread sheet for example
'service_provider_institution':"""/ncml:netcdf/ncml:attribute[@name='institution']/@value""",
'data_conventions':"""/ncml:netcdf/ncml:attribute[@name='institution']/@value""",
'latitude_units':"""/ncml:netcdf/ncml:variable[@name='latitude']/ncml:attribute[@name='units']/@value""",
'does_not_exist':"""/ncml:netcdf/ncml:attribute[@name='does_not_exist']/@value"""
}
#read a file
ds = Dataset('test_ncs/result_surface.nc','a')
data_object = NetCDFDogma('NetcdfCF',cf_metadata_beliefs,ds)
data_object.__class__.__name__
data_object.service_provider_institution
data_object.data_conventions
data_object.latitude_units
# will return empty
data_object.does_not_exist
data_object.service_provider_institution = 'David Stuebe'
data_object.data_conventions = 'CF-3.14159'
data_object.latitude_units = 'degrees a little bit west of north'
