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Propose handling of prefixes in global attrs #104

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Propose handling of prefixes in global attrs #104

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4883288
Propose handling of prefixes in global attrs
jyucsiro Jun 7, 2022
329e93a
only process global attrs if isPrefixedBy is not set
jyucsiro Jun 30, 2022
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14 changes: 14 additions & 0 deletions lib/bald/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -829,6 +829,15 @@ def _prefixes_and_aliases(fhandle, identity, alias_dict, prefix_contexts, cache)
prefix in prefix_group.ncattrs() if prefix.endswith('__')]))
if isinstance(prefix_group, netCDF4._netCDF4.Variable):
skipped_variables.append(prefix_var.name)

#add prefixes defined in global attributes
#note: this will overwrite any in prefix_list
#only process global attrs if bald__isPrefixedBy is not set
if not hasattr(fhandle, 'bald__isPrefixedBy'):
for k in fhandle.ncattrs():
if k.endswith('__'):
prefixes[k] = getattr(fhandle, k)

# else:
# for k in fhandle.ncattrs():
# if k.endswith('__'):
Expand Down Expand Up @@ -1222,6 +1231,11 @@ def load_netcdf(afilepath, baseuri=None, alias_dict=None, prefix_contexts=None,
for k in fhandle.ncattrs():
attrs[k] = getattr(fhandle, k)

#remove any prefixes in global attributes so that it isn't in the output graph container
for p in prefixes:
if p in attrs:
attrs.pop(p)

root_container = Container(baseuri, baseuri, '', attrs, prefixes=prefixes,
aliases=aliases, alias_graph=aliasgraph,
file_resource=True, file_locator=file_locator)
Expand Down
130 changes: 130 additions & 0 deletions lib/bald/tests/integration/CDL/ereefs_gbr4_ncld_global_prefixes.cdl
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Original file line number Diff line number Diff line change
@@ -0,0 +1,130 @@
netcdf gbr4_1.85 {
dimensions:
i = 600 ;
j = 180 ;
k = 47 ;
time = 5 ;
variables:
double zc(k) ;
zc:axis = "Z" ;
zc:coordinate_type = "Z" ;
zc:units = "m" ;
zc:positive = "up" ;
zc:long_name = "Z coordinate" ;
double longitude(j, i) ;
longitude:standard_name = "longitude" ;
longitude:coordinate_type = "longitude" ;
longitude:projection = "geographic" ;
longitude:units = "degrees_east" ;
longitude:long_name = "Longitude" ;
double latitude(j, i) ;
latitude:standard_name = "latitude" ;
latitude:coordinate_type = "latitude" ;
latitude:projection = "geographic" ;
latitude:units = "degrees_north" ;
latitude:long_name = "Latitude" ;
double botz(j, i) ;
botz:standard_name = "depth" ;
botz:missing_value = -99. ;
botz:positive = "down" ;
botz:coordinates = "latitude longitude" ;
botz:outside = "9999" ;
botz:units = "metre" ;
botz:long_name = "Depth of sea-bed" ;
double time(time) ;
time:units = "days since 1990-01-01 00:00:00 +10" ;
time:long_name = "Time" ;
time:standard_name = "time" ;
time:coordinate_type = "time" ;
time:_ChunkSizes = 1 ;
float eta(time, j, i) ;
eta:coordinates = "time latitude longitude" ;
eta:units = "metre" ;
eta:long_name = "Surface elevation" ;
eta:standard_name = "sea_surface_height_above_sea_level" ;
eta:valid_range = -10.f, 10.f ;
eta:missing_value = 1.e+35f ;
eta:positive = "up" ;
eta:medium_id = "http://environment.data.gov.au/def/feature/ocean" ;
eta:scaledQuantityKind_id = "http://environment.data.gov.au/def/property/sea_surface_elevation" ;
eta:substanceOrTaxon_id = "http://environment.data.gov.au/def/feature/ocean_near_surface" ;
eta:unit_id = "http://qudt.org/vocab/unit#Meter" ;
eta:_ChunkSizes = 1, 180, 600 ;
float u(time, k, j, i) ;
u:coordinates = "time zc latitude longitude" ;
u:units = "ms-1" ;
u:long_name = "Eastward current" ;
u:standard_name = "eastward_sea_water_velocity" ;
u:vector_name = "Currents" ;
u:vector_components = "u v" ;
u:valid_range = -100.f, 100.f ;
u:missing_value = 1.e+35f ;
u:medium_id = "http://environment.data.gov.au/def/feature/ocean" ;
u:scaledQuantityKind_id = "http://environment.data.gov.au/def/property/sea_water_velocity_eastward" ;
u:substanceOrTaxon_id = "http://environment.data.gov.au/def/feature/ocean_current" ;
u:unit_id = "http://qudt.org/vocab/unit#MeterPerSecond" ;
u:_ChunkSizes = 1, 24, 90, 300 ;
float v(time, k, j, i) ;
v:coordinates = "time zc latitude longitude" ;
v:units = "ms-1" ;
v:long_name = "Northward current" ;
v:standard_name = "northward_sea_water_velocity" ;
v:vector_name = "Currents" ;
v:vector_components = "u v" ;
v:valid_range = -100.f, 100.f ;
v:missing_value = 1.e+35f ;
v:medium_id = "http://environment.data.gov.au/def/feature/ocean" ;
v:scaledQuantityKind_id = "http://environment.data.gov.au/def/property/sea_water_velocity_northward" ;
v:substanceOrTaxon_id = "http://environment.data.gov.au/def/feature/ocean_current" ;
v:unit_id = "http://qudt.org/vocab/unit#MeterPerSecond" ;
v:_ChunkSizes = 1, 24, 90, 300 ;
float salt(time, k, j, i) ;
salt:coordinates = "time zc latitude longitude" ;
salt:units = "PSU" ;
salt:long_name = "Salinity" ;
salt:missing_value = 1.e+35f ;
salt:medium_id = "http://environment.data.gov.au/def/feature/ocean" ;
salt:scaledQuantityKind_id = "http://environment.data.gov.au/def/property/practical_salinity" ;
salt:substanceOrTaxon_id = "http://sweet.jpl.nasa.gov/2.2/matrWater.owl#SaltWater" ;
salt:unit_id = "http://environment.data.gov.au/water/quality/def/unit/PSU" ;
salt:_ChunkSizes = 1, 24, 90, 300 ;
float temp(time, k, j, i) ;
temp:coordinates = "time zc latitude longitude" ;
temp:units = "degrees C" ;
temp:long_name = "Temperature" ;
temp:valid_range = -3.f, 40.f ;
temp:missing_value = 1.e+35f ;
temp:medium_id = "http://environment.data.gov.au/def/feature/ocean" ;
temp:scaledQuantityKind_id = "http://environment.data.gov.au/def/property/sea_water_temperature" ;
temp:substanceOrTaxon_id = "http://sweet.jpl.nasa.gov/2.2/matrWater.owl#SaltWater" ;
temp:unit_id = "http://qudt.org/vocab/unit#DegreeCelsius" ;
temp:_ChunkSizes = 1, 24, 90, 300 ;
float wspeed_u(time, j, i) ;
wspeed_u:coordinates = "time latitude longitude" ;
wspeed_u:units = "ms-1" ;
wspeed_u:long_name = "eastward_wind" ;
wspeed_u:valid_range = -1000.f, 1000.f ;
wspeed_u:missing_value = 1.e+35f ;
wspeed_u:_ChunkSizes = 1, 180, 600 ;
float wspeed_v(time, j, i) ;
wspeed_v:coordinates = "time latitude longitude" ;
wspeed_v:units = "ms-1" ;
wspeed_v:long_name = "northward_wind" ;
wspeed_v:valid_range = -1000.f, 1000.f ;
wspeed_v:missing_value = 1.e+35f ;
wspeed_v:_ChunkSizes = 1, 180, 600 ;

// global attributes:
:title = "GBR4 Hydro" ;
:paramhead = "GBR 4km resolution grid" ;
:paramfile = "in.prm" ;
:shoc_version = "v1.1 rev(5249)" ;
:Conventions = "CF-1.0" ;
:Run_ID = 1.85 ;
:hasVocab = 1 ;
:metadata_link = "http://marlin.csiro.au/geonetwork/srv/eng/search?&uuid=72020224-f086-434a-bbe9-a222c8e5cf0d" ;
:bald__ = "https://www.opengis.net/def/binary-array-ld/" ;
:rdf__ = "http://www.w3.org/1999/02/22-rdf-syntax-ns#" ;


}