From 26d376525cf8d8ae125d99ee1c250636cd7ae361 Mon Sep 17 00:00:00 2001
From: Jonathan Yu <jonathan.yu@csiro.au>
Date: Wed, 16 Aug 2017 01:26:25 +1000
Subject: [PATCH 01/12] adding test case for ereefs

---
 lib/bald/tests/integration/test_cdl_rdfgraph.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/lib/bald/tests/integration/test_cdl_rdfgraph.py b/lib/bald/tests/integration/test_cdl_rdfgraph.py
index ced6c8a..2601881 100644
--- a/lib/bald/tests/integration/test_cdl_rdfgraph.py
+++ b/lib/bald/tests/integration/test_cdl_rdfgraph.py
@@ -36,3 +36,15 @@ def test_multi_array_reference(self):
             with open(os.path.join(self.ttl_path, 'multi_array_reference.ttl'), 'r') as sf:
                 expected_ttl = sf.read()
             self.assertEqual(expected_ttl, ttl)
+
+    def test_ereefs(self):
+        with self.temp_filename('.nc') as tfile:
+            cdl_file = os.path.join(self.cdl_path, 'ereefs_gbr4_ncld.cdl')
+            subprocess.check_call(['ncgen', '-o', tfile, cdl_file])
+            root_container = bald.load_netcdf(tfile)
+            testPassed
+            try:
+               ttl = root_container.rdfgraph().serialize(format='n3').decode("utf-8")
+            except TypeError:
+               self.fail("Test case could not convert ereefs CDL to RDF")
+

From 4cf1112745416d1dd365e3226669bbb7aef11664 Mon Sep 17 00:00:00 2001
From: Jonathan Yu <jonathan.yu@csiro.au>
Date: Wed, 30 Aug 2017 18:08:06 +1000
Subject: [PATCH 02/12] Refactoring alias and prefix handling to variable

---
 lib/bald/__init__.py                          | 42 +++++++++++---
 .../tests/integration/CDL/array_alias_v2.cdl  | 58 +++++++++++++++++++
 .../tests/integration/CDL/array_prefix_v2.cdl | 55 ++++++++++++++++++
 .../integration/CDL/array_prefix_v2_full.cdl  | 57 ++++++++++++++++++
 lib/bald/tests/integration/test_cdl_v2.py     | 40 +++++++++++++
 lib/bald/validation.py                        |  2 +
 6 files changed, 246 insertions(+), 8 deletions(-)
 create mode 100644 lib/bald/tests/integration/CDL/array_alias_v2.cdl
 create mode 100644 lib/bald/tests/integration/CDL/array_prefix_v2.cdl
 create mode 100644 lib/bald/tests/integration/CDL/array_prefix_v2_full.cdl
 create mode 100644 lib/bald/tests/integration/test_cdl_v2.py

diff --git a/lib/bald/__init__.py b/lib/bald/__init__.py
index 1503261..0d5c301 100644
--- a/lib/bald/__init__.py
+++ b/lib/bald/__init__.py
@@ -240,6 +240,7 @@ def __getitem__(self, item):
 
     def check_uri(self, uri):
         result = False
+        #print("Checking uri: " + uri)
         if self[uri].status_code == 200:
             result = True
         return result
@@ -438,6 +439,11 @@ def rdfgraph(self):
         """
         graph = rdflib.Graph()
         graph.bind('bald', 'http://binary-array-ld.net/latest/')
+        for prefix_name in self._prefixes:
+           #strip the double underscore suffix
+           new_name = prefix_name[:-2]
+
+           graph.bind(new_name, self._prefixes[prefix_name])
         graph = self.rdfnode(graph)
         
         return graph
@@ -537,22 +543,34 @@ def load_netcdf(afilepath, uri=None):
     """
 
     with load(afilepath) as fhandle:
-        prefix_group = (fhandle[fhandle.bald__isPrefixedBy] if
+        prefix_var_name  = None
+        if hasattr(fhandle, 'bald__isPrefixedBy'):
+           prefix_var_name  = fhandle.bald__isPrefixedBy
+
+        prefix_var = (fhandle[fhandle.bald__isPrefixedBy] if
                         hasattr(fhandle, 'bald__isPrefixedBy') else {})
         prefixes = {}
-        if prefix_group:
-            prefixes = (dict([(prefix, getattr(prefix_group, prefix)) for
-                              prefix in prefix_group.ncattrs()]))
+        if prefix_var is not {} :
+            prefixes = (dict([(prefix, getattr(prefix_var, prefix)) for
+                              prefix in prefix_var.ncattrs()]))
         else:
             for k in fhandle.ncattrs():
                 if k.endswith('__'):
                     prefixes[k] = getattr(fhandle, k)
-        alias_group = (fhandle[fhandle.bald__isAliasedBy]
+
+        #print(prefixes)
+
+        alias_var_name = None
+        if hasattr(fhandle, 'bald__isAliasedBy'):
+           alias_var_name  = fhandle.bald__isAliasedBy
+
+        alias_var = (fhandle[fhandle.bald__isAliasedBy]
                        if hasattr(fhandle, 'bald__isAliasedBy') else {})
         aliases = {}
-        if alias_group:
-            aliases = (dict([(alias, getattr(alias_group, alias))
-                             for alias in alias_group.ncattrs()]))
+        if alias_var != {}:
+            aliases = (dict([(alias, getattr(alias_var, alias))
+                             for alias in alias_var.ncattrs()]))
+        #print(aliases)
 
         attrs = {}
         for k in fhandle.ncattrs():
@@ -567,6 +585,10 @@ def load_netcdf(afilepath, uri=None):
         root_container.attrs['bald__contains'] = []
         file_variables = {}
         for name in fhandle.variables:
+            #print(name)
+            if name ==  prefix_var_name or name == alias_var_name:
+                #print("Skipping " + name)
+                continue
 
             sattrs = fhandle.variables[name].__dict__.copy()
             # inconsistent use of '/'; fix it
@@ -590,6 +612,10 @@ def load_netcdf(afilepath, uri=None):
 
         # cycle again and find references
         for name in fhandle.variables:
+            if name ==  prefix_var_name or name == alias_var_name:
+                #print("Skipping " + name)
+                continue
+
             var = file_variables[name]
             # reverse lookup based on type to be added
             lookups = ['bald__references', 'bald__array']
diff --git a/lib/bald/tests/integration/CDL/array_alias_v2.cdl b/lib/bald/tests/integration/CDL/array_alias_v2.cdl
new file mode 100644
index 0000000..4b6c2db
--- /dev/null
+++ b/lib/bald/tests/integration/CDL/array_alias_v2.cdl
@@ -0,0 +1,58 @@
+netcdf tmpMwXy8U {
+dimensions:
+	pdim0 = 11 ;
+	pdim1 = 17 ;
+variables:
+	int prefix_list ;
+  		prefix_list:bald__ = "http://binary-array-ld.net/latest/" ;
+  		prefix_list:rdf__ = "http://www.w3.org/1999/02/22-rdf-syntax-ns#" ;
+
+	int alias_list ;
+        	alias_list:SDN_ParameterDiscoveryCode = "http://vocab.nerc.ac.uk/isoCodelists/sdnCodelists/cdicsrCodeList.xml#SDN_ParameterDiscoveryCode" ;
+	        alias_list:BactTaxaAbundSed = "http://vocab.nerc.ac.uk/collection/P02/current/BAUC/" ;
+		alias_list:standard_name = "https://def.scitools.org.uk/CFTerms/standard_name" ;
+		alias_list:air_temperature = "http://vocab.nerc.ac.uk/collection/P07/current/CFSN0023/" ;
+
+	int parent_variable(pdim0, pdim1) ;
+		parent_variable:rdf__type = "bald__Array" ;
+		parent_variable:SDN_ParameterDiscoveryCode = "BactTaxaAbundSed" ;
+		parent_variable:submursible_name = "Nautilus" ;
+
+	int temp(pdim0, pdim1) ;
+	        temp:standard_name = "air_temperature" ;
+
+// global attributes:
+		:_NCProperties = "version=1|netcdflibversion=4.4.1|hdf5libversion=1.8.17" ;
+		:rdf__type = "bald__Container" ;
+		:bald__isPrefixedBy = "prefix_list" ;
+		:bald__isAliasedBy = "alias_list" ;
+data:
+
+ parent_variable =
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _ ;
+
+ temp =
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _ ;
+
+
+}
diff --git a/lib/bald/tests/integration/CDL/array_prefix_v2.cdl b/lib/bald/tests/integration/CDL/array_prefix_v2.cdl
new file mode 100644
index 0000000..609c304
--- /dev/null
+++ b/lib/bald/tests/integration/CDL/array_prefix_v2.cdl
@@ -0,0 +1,55 @@
+netcdf tmpMwXy8U {
+dimensions:
+	pdim0 = 11 ;
+	pdim1 = 17 ;
+variables:
+	int prefix_list ;
+  		prefix_list:bald__ = "http://binary-array-ld.net/latest/" ;
+  		prefix_list:rdf__ = "http://www.w3.org/1999/02/22-rdf-syntax-ns#" ;
+        	prefix_list:sdn__ = "http://vocab.nerc.ac.uk/isoCodelists/sdnCodelists/cdicsrCodeList.xml#" ;
+	        prefix_list:sdn-vocab__= "http://vocab.nerc.ac.uk/collection/P02/current/" ;
+		prefix_list:cf__ = "http://def.scitools.org.uk/CFTerms/" ;
+		prefix_list:cfsn__ = "http://vocab.nerc.ac.uk/collection/P07/current/CFSN0023/" ;
+
+	int parent_variable(pdim0, pdim1) ;
+		parent_variable:rdf__type = "bald__Array" ;
+		parent_variable:sdn__SDN_ParameterDiscoveryCode = "sdn-vocab__BAUC" ;
+		parent_variable:submursible_name = "Nautilus" ;
+
+	int temp(pdim0, pdim1) ;
+	        temp:standard_name = "air_temperature" ;
+
+// global attributes:
+		:_NCProperties = "version=1|netcdflibversion=4.4.1|hdf5libversion=1.8.17" ;
+		:rdf__type = "bald__Container" ;
+		:bald__isPrefixedBy = "prefix_list" ;
+data:
+
+ parent_variable =
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _ ;
+
+ temp =
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _ ;
+
+
+}
diff --git a/lib/bald/tests/integration/CDL/array_prefix_v2_full.cdl b/lib/bald/tests/integration/CDL/array_prefix_v2_full.cdl
new file mode 100644
index 0000000..9272f74
--- /dev/null
+++ b/lib/bald/tests/integration/CDL/array_prefix_v2_full.cdl
@@ -0,0 +1,57 @@
+netcdf tmpMwXy8U {
+dimensions:
+	pdim0 = 11 ;
+	pdim1 = 17 ;
+variables:
+	int prefix_list ;
+  		prefix_list:bald__ = "http://binary-array-ld.net/latest/" ;
+  		prefix_list:rdf__ = "http://www.w3.org/1999/02/22-rdf-syntax-ns#" ;
+        	prefix_list:sdn__ = "http://vocab.nerc.ac.uk/isoCodelists/sdnCodelists/cdicsrCodeList.xml#" ;
+	        prefix_list:sdn-vocab__= "http://vocab.nerc.ac.uk/collection/P02/current/" ;
+		prefix_list:cf__ = "http://def.scitools.org.uk/CFTerms/" ;
+		prefix_list:cfsn-mmi__ = "http://mmisw.org/ont/cf/parameter/" ;
+		prefix_list:cfsn-nerc__ = "http://vocab.nerc.ac.uk/collection/P07/current/";
+
+	int parent_variable(pdim0, pdim1) ;
+		parent_variable:rdf__type = "bald__Array" ;
+		parent_variable:sdn__SDN_ParameterDiscoveryCode = "sdn-vocab__BAUC" ;
+		parent_variable:submursible_name = "Nautilus" ;
+
+	int temp(pdim0, pdim1) ;
+	        temp:cf__standard_name = "cfsn-mmi__air_temperature" ;
+		//temp:cf__standard_name = "cfsn-nerc__CFSN0023";
+
+// global attributes:
+		:_NCProperties = "version=1|netcdflibversion=4.4.1|hdf5libversion=1.8.17" ;
+		:rdf__type = "bald__Container" ;
+		:bald__isPrefixedBy = "prefix_list" ;
+data:
+
+ parent_variable =
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _ ;
+
+ temp =
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _ ;
+
+
+}
diff --git a/lib/bald/tests/integration/test_cdl_v2.py b/lib/bald/tests/integration/test_cdl_v2.py
new file mode 100644
index 0000000..a20a1d2
--- /dev/null
+++ b/lib/bald/tests/integration/test_cdl_v2.py
@@ -0,0 +1,40 @@
+import glob
+import os
+import subprocess
+import unittest
+
+import netCDF4
+import numpy as np
+
+import bald
+from bald.tests import BaldTestCase
+
+
+class Test(BaldTestCase):
+    def setUp(self):
+        self.cdl_path = os.path.join(os.path.dirname(__file__), 'CDL')
+
+
+def test_prefix_v2(self):
+    """Test prefix version 2 style """
+    with self.temp_filename('.nc') as tfile:
+        cdl_file = os.path.join(self.cdl_path, 'array_prefix_v2.cdl')
+        print(cdl_file)
+        subprocess.check_call(['ncgen', '-o', tfile, cdl_file])
+        validation = bald.validate_netcdf(tfile)
+        exns = validation.exceptions()
+        self.assertTrue(validation.is_valid(), msg='{} != []'.format(exns))
+
+setattr(Test, 'test_prefix_v2', test_prefix_v2)
+
+def test_prefix_v2_full(self):
+    """Test prefix version 2 style - full example"""
+    with self.temp_filename('.nc') as tfile:
+        cdl_file = os.path.join(self.cdl_path, 'array_prefix_v2_full.cdl')
+        print(cdl_file)
+        subprocess.check_call(['ncgen', '-o', tfile, cdl_file])
+        validation = bald.validate_netcdf(tfile)
+        exns = validation.exceptions()
+        self.assertTrue(validation.is_valid(), msg='{} != []'.format(exns))
+
+setattr(Test, 'test_prefix_v2_full', test_prefix_v2_full)
diff --git a/lib/bald/validation.py b/lib/bald/validation.py
index 60a7b59..44ea115 100644
--- a/lib/bald/validation.py
+++ b/lib/bald/validation.py
@@ -90,9 +90,11 @@ def _check_uri(uri, exceptions):
                 exceptions.append(msg)
             return exceptions
 
+        ''' Skip checking prefixes as whole graphs could be big!
         for pref, uri in self.subject.prefixes().items():
             exceptions = _check_uri(self.subject.unpack_uri(uri),
                                     exceptions)
+        '''
         for alias, uri in self.subject.aliases.items():
             exceptions = _check_uri(self.subject.unpack_uri(uri),
                                     exceptions)

From eed068768693425c02750a8628d3536623992436 Mon Sep 17 00:00:00 2001
From: Jonathan Yu <jonathan.yu@csiro.au>
Date: Wed, 30 Aug 2017 21:09:01 +1000
Subject: [PATCH 03/12] fixing bug in prefix handling

---
 lib/bald/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/bald/__init__.py b/lib/bald/__init__.py
index 0d5c301..048cd0b 100644
--- a/lib/bald/__init__.py
+++ b/lib/bald/__init__.py
@@ -550,7 +550,7 @@ def load_netcdf(afilepath, uri=None):
         prefix_var = (fhandle[fhandle.bald__isPrefixedBy] if
                         hasattr(fhandle, 'bald__isPrefixedBy') else {})
         prefixes = {}
-        if prefix_var is not {} :
+        if prefix_var != {} :
             prefixes = (dict([(prefix, getattr(prefix_var, prefix)) for
                               prefix in prefix_var.ncattrs()]))
         else:

From 8a64095cb85f4817703ceeeb42b8dcecba0ece7c Mon Sep 17 00:00:00 2001
From: Jonathan Yu <jonathan.yu@csiro.au>
Date: Wed, 30 Aug 2017 21:25:53 +1000
Subject: [PATCH 04/12] fixing tests for cdl rdfgraph

---
 .../tests/integration/CDL/multi_array_reference.cdl  | 12 +++++-------
 .../tests/integration/TTL/multi_array_reference.ttl  |  5 +++--
 2 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/lib/bald/tests/integration/CDL/multi_array_reference.cdl b/lib/bald/tests/integration/CDL/multi_array_reference.cdl
index ccf2e3f..fe4241e 100644
--- a/lib/bald/tests/integration/CDL/multi_array_reference.cdl
+++ b/lib/bald/tests/integration/CDL/multi_array_reference.cdl
@@ -3,6 +3,11 @@ dimensions:
 	pdim0 = 11 ;
 	pdim1 = 17 ;
 variables:
+        int prefix_list(pdim0, pdim1) ;
+  		prefix_list:bald__ = "http://binary-array-ld.net/latest/" ;
+		prefix_list:metce__ = "http://codes.wmo.int/common/observation-type/METCE/2013/" ;
+  		prefix_list:rdf__ = "http://www.w3.org/1999/02/22-rdf-syntax-ns#" ;
+		
 	int variable1(pdim0, pdim1) ;
 		variable1:bald__references = "location_variable" ;
 		variable1:long_name = "Gerald";
@@ -31,11 +36,4 @@ variables:
 		:_NCProperties = "version=1|netcdflibversion=4.4.1|hdf5libversion=1.8.17" ;
 		:bald__isPrefixedBy = "prefix_list" ;
 
-group: prefix_list {
-
-  // group attributes:
-  		:bald__ = "http://binary-array-ld.net/latest/" ;
-		:metce__ = "http://codes.wmo.int/common/observation-type/METCE/2013/" ;
-  		:rdf__ = "http://www.w3.org/1999/02/22-rdf-syntax-ns#" ;
-  } // group bald__prefix_list
 }
diff --git a/lib/bald/tests/integration/TTL/multi_array_reference.ttl b/lib/bald/tests/integration/TTL/multi_array_reference.ttl
index e495087..f42a3c5 100644
--- a/lib/bald/tests/integration/TTL/multi_array_reference.ttl
+++ b/lib/bald/tests/integration/TTL/multi_array_reference.ttl
@@ -1,4 +1,5 @@
 @prefix bald: <http://binary-array-ld.net/latest/> .
+@prefix metce: <http://codes.wmo.int/common/observation-type/METCE/2013/> .
 @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
 @prefix xml: <http://www.w3.org/XML/1998/namespace> .
@@ -21,7 +22,7 @@
         <variable1_pdim0_ref> ;
     bald:shape "(11, 17)" ;
     <long_name> "Gerald" ;
-    <obtype> <http://codes.wmo.int/common/observation-type/METCE/2013/SamplingObservation> .
+    <obtype> metce:SamplingObservation .
 
 <variable2> a bald:Array ;
     bald:references <location_variable>,
@@ -29,7 +30,7 @@
         <variable2_pdim0_ref> ;
     bald:shape "(11, 17)" ;
     <long_name> "Imelda" ;
-    <obtype> <http://codes.wmo.int/common/observation-type/METCE/2013/SamplingObservation> .
+    <obtype> metce:SamplingObservation .
 
 <variable1_pdim0_ref> a bald:Reference,
         bald:Subject ;

From 2857d4fb72d87080e5e413af0ad18aacfa199e6d Mon Sep 17 00:00:00 2001
From: Jonathan Yu <jonathan.yu@csiro.au>
Date: Wed, 30 Aug 2017 21:36:53 +1000
Subject: [PATCH 05/12] updating alias tests and cdl

---
 lib/bald/tests/integration/CDL/array_alias_v2.cdl |  2 +-
 lib/bald/tests/integration/test_cdl_v2.py         | 12 ++++++++++++
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/lib/bald/tests/integration/CDL/array_alias_v2.cdl b/lib/bald/tests/integration/CDL/array_alias_v2.cdl
index 4b6c2db..10fc484 100644
--- a/lib/bald/tests/integration/CDL/array_alias_v2.cdl
+++ b/lib/bald/tests/integration/CDL/array_alias_v2.cdl
@@ -10,7 +10,7 @@ variables:
 	int alias_list ;
         	alias_list:SDN_ParameterDiscoveryCode = "http://vocab.nerc.ac.uk/isoCodelists/sdnCodelists/cdicsrCodeList.xml#SDN_ParameterDiscoveryCode" ;
 	        alias_list:BactTaxaAbundSed = "http://vocab.nerc.ac.uk/collection/P02/current/BAUC/" ;
-		alias_list:standard_name = "https://def.scitools.org.uk/CFTerms/standard_name" ;
+		alias_list:standard_name = "http://def.scitools.org.uk/CFTerms/standard_name" ;
 		alias_list:air_temperature = "http://vocab.nerc.ac.uk/collection/P07/current/CFSN0023/" ;
 
 	int parent_variable(pdim0, pdim1) ;
diff --git a/lib/bald/tests/integration/test_cdl_v2.py b/lib/bald/tests/integration/test_cdl_v2.py
index a20a1d2..fc5e030 100644
--- a/lib/bald/tests/integration/test_cdl_v2.py
+++ b/lib/bald/tests/integration/test_cdl_v2.py
@@ -15,6 +15,18 @@ def setUp(self):
         self.cdl_path = os.path.join(os.path.dirname(__file__), 'CDL')
 
 
+def test_alias_v2(self):
+    """Test alias version 2 style """
+    with self.temp_filename('.nc') as tfile:
+        cdl_file = os.path.join(self.cdl_path, 'array_alias_v2.cdl')
+        print(cdl_file)
+        subprocess.check_call(['ncgen', '-o', tfile, cdl_file])
+        validation = bald.validate_netcdf(tfile)
+        exns = validation.exceptions()
+        self.assertTrue(validation.is_valid(), msg='{} != []'.format(exns))
+
+setattr(Test, 'test_alias_v2', test_alias_v2)
+
 def test_prefix_v2(self):
     """Test prefix version 2 style """
     with self.temp_filename('.nc') as tfile:

From fcce72fdb922f0c0ccf95d9a0ce3c4dc47b9ad30 Mon Sep 17 00:00:00 2001
From: Jonathan Yu <jonathan.yu@csiro.au>
Date: Wed, 30 Aug 2017 23:21:28 +1000
Subject: [PATCH 06/12] updating OISST test

---
 lib/bald/tests/integration/test_cdl.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/bald/tests/integration/test_cdl.py b/lib/bald/tests/integration/test_cdl.py
index 92f0540..a7f87d1 100644
--- a/lib/bald/tests/integration/test_cdl.py
+++ b/lib/bald/tests/integration/test_cdl.py
@@ -64,7 +64,8 @@ def test_grid_OISST_GHRSST(self):
         validation = bald.validate_netcdf(tfile)
         exns = validation.exceptions()
         exns.sort()
-        expected = ['http://www.ncdc.noaa.gov/sst is not resolving as a resource (404).',
+        expected = ['http://doi.org/10.7289/V5SQ8XB5 is not resolving as a resource (404).',
+                     'http://www.ncdc.noaa.gov/sst is not resolving as a resource (404).',
                     'http://www.ncdc.noaa.gov/sst/ is not resolving as a resource (404).']
         expected.sort()
         self.assertTrue(not validation.is_valid() and exns == expected,

From 847cee98d7f0859212f9a68a97d1ee53eab0a42d Mon Sep 17 00:00:00 2001
From: Jonathan Yu <jonathan.yu@csiro.au>
Date: Mon, 4 Sep 2017 14:33:59 +1000
Subject: [PATCH 07/12] adding default prefixes in bald lib

---
 lib/bald/__init__.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/lib/bald/__init__.py b/lib/bald/__init__.py
index 048cd0b..9cfbae7 100644
--- a/lib/bald/__init__.py
+++ b/lib/bald/__init__.py
@@ -558,6 +558,13 @@ def load_netcdf(afilepath, uri=None):
                 if k.endswith('__'):
                     prefixes[k] = getattr(fhandle, k)
 
+        # check that default set is handled, i.e. bald__ and rdf__
+        if 'bald__' not in prefixes:
+            prefixes['bald__'] = "http://binary-array-ld.net/latest/" 
+
+        if 'rdf__' not in prefixes:
+            prefixes['rdf__'] = "http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+
         #print(prefixes)
 
         alias_var_name = None

From 1745701ba210b0c38191eff3a4e88aea5e514168 Mon Sep 17 00:00:00 2001
From: Jonathan Yu <jonathan.yu@csiro.au>
Date: Mon, 4 Sep 2017 15:10:50 +1000
Subject: [PATCH 08/12] implementing parameters to set graph uris and base uris

---
 lib/bald/__init__.py |  9 +++++++--
 nc2rdf/nc2rdf.py     | 14 ++++++++------
 2 files changed, 15 insertions(+), 8 deletions(-)

diff --git a/lib/bald/__init__.py b/lib/bald/__init__.py
index 9cfbae7..4f103d7 100644
--- a/lib/bald/__init__.py
+++ b/lib/bald/__init__.py
@@ -536,7 +536,7 @@ def load(afilepath):
     finally:
         f.close()
 
-def load_netcdf(afilepath, uri=None):
+def load_netcdf(afilepath, uri=None, baseuri=None):
     """
     Validate a file with respect to binary-array-linked-data.
     Returns a :class:`bald.validation.Validation`
@@ -600,11 +600,14 @@ def load_netcdf(afilepath, uri=None):
             sattrs = fhandle.variables[name].__dict__.copy()
             # inconsistent use of '/'; fix it
             identity = name
+            if baseuri is not None:
+                identity = baseuri + "/" + name
 
             # netCDF coordinate variable special case
             if (len(fhandle.variables[name].dimensions) == 1 and
                 fhandle.variables[name].dimensions[0] == name):
-                sattrs['bald__array'] = name
+                #sattrs['bald__array'] = name
+                sattrs['bald__array'] = identity
                 sattrs['rdf__type'] = 'bald__Reference'
                 
             if fhandle.variables[name].shape:
@@ -648,6 +651,8 @@ def load_netcdf(afilepath, uri=None):
                         # Else, define a bald:childBroadcast
                         else:
                             identity = '{}_{}_ref'.format(name, dim)
+                            if baseuri is not None:
+                                identity = baseuri + '/' +  '{}_{}_ref'.format(name, dim)
                             rattrs = {}
                             rattrs['rdf__type'] = 'bald__Reference'
                             reshape = [1 for adim in var_shape]
diff --git a/nc2rdf/nc2rdf.py b/nc2rdf/nc2rdf.py
index 120edac..2f3ab82 100644
--- a/nc2rdf/nc2rdf.py
+++ b/nc2rdf/nc2rdf.py
@@ -6,21 +6,21 @@
 import numpy as np
 import bald
 
-def nc2rdf(ncfilename, outformat):  
+def nc2rdf(ncfilename, outformat, container_uri=None, default_baseuri=None):  
     #print("nc2rdf test")
     #print(ncfile)
-    root_container = bald.load_netcdf(ncfilename)
+    root_container = bald.load_netcdf(ncfilename, uri=container_uri, baseuri=default_baseuri)
     ttl = root_container.rdfgraph().serialize(format=outformat).decode("utf-8")
     print(ttl)
 
-def cdl2rdf(cdl_file, outformat): 
+def cdl2rdf(cdl_file, outformat, container_uri=None, default_baseuri=None): 
     #print("cdl2rdf test")
     #print(cdl_file)
     tfile, tfilename = tempfile.mkstemp('.nc')
     #print(tfilename)
     subprocess.check_call(['ncgen', '-o', tfilename, cdl_file])
 
-    nc2rdf(tfilename, outformat)
+    nc2rdf(tfilename, outformat, container_uri=container_uri, default_baseuri=default_baseuri)
 
     os.close(tfile)
     os.remove(tfilename)
@@ -29,6 +29,8 @@ def cdl2rdf(cdl_file, outformat):
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description='Convert netCDF metadata to RDF.')
     parser.add_argument('-o', action="store", dest="format", default='n3', help="RDF output format (n3 *default, ttl, xml)")
+    parser.add_argument('--uri', action="store", dest="uri", help="Container URI for the root of the graph")
+    parser.add_argument('--baseuri', action="store", dest="baseuri", help="Base URI for the graph")
     parser.add_argument('--cdl', action="store_true", dest="isCDL", default=False, help="Flag to indicate file is CDL")
     parser.add_argument('--nc', action="store_true", dest="isNC", default=False, help="Flag to indicate file is netCDF")
     parser.add_argument("ncfile", help="Path for the netCDF file")
@@ -36,8 +38,8 @@ def cdl2rdf(cdl_file, outformat):
     args = parser.parse_args()
 
     if(args.isCDL or args.ncfile.endswith(".cdl") or args.ncfile.endswith('.CDL')):
-        cdl2rdf(args.ncfile, args.format)
+        cdl2rdf(args.ncfile, args.format, container_uri=args.uri, default_baseuri=args.baseuri)
     elif(args.isNC or args.ncfile.endswith(".nc") or args.ncfile.endswith('.NC')):
-        nc2rdf(args.ncfile, args.format)
+        nc2rdf(args.ncfile, args.format, container_uri=args.uri, default_baseuri=args.baseuri)
     else:
         print("Unrecognised file suffix. Please indicate if CDL or NC via --cdl or --nc");

From 9d2f96c9b48c7ca294ef6bb6282250c4f7a3a2a1 Mon Sep 17 00:00:00 2001
From: Jonathan Yu <jonathan.yu@csiro.au>
Date: Wed, 6 Sep 2017 11:54:41 +1000
Subject: [PATCH 09/12] fixing refs to alias_group and prefix_group to vars

---
 lib/bald/__init__.py                          |  16 +-
 .../tests/integration/CDL/array_alias.cdl     |  37 +---
 .../tests/integration/CDL/array_reference.cdl |  37 +---
 ncldDump/aliases.json                         | 190 +++++++++---------
 4 files changed, 119 insertions(+), 161 deletions(-)

diff --git a/lib/bald/__init__.py b/lib/bald/__init__.py
index 4f103d7..a25653e 100644
--- a/lib/bald/__init__.py
+++ b/lib/bald/__init__.py
@@ -550,9 +550,13 @@ def load_netcdf(afilepath, uri=None, baseuri=None):
         prefix_var = (fhandle[fhandle.bald__isPrefixedBy] if
                         hasattr(fhandle, 'bald__isPrefixedBy') else {})
         prefixes = {}
-        if prefix_var != {} :
+
+        skipped_variables = []
+        if prefix_var != {}:
             prefixes = (dict([(prefix, getattr(prefix_var, prefix)) for
                               prefix in prefix_var.ncattrs()]))
+            if isinstance(prefix_var, netCDF4._netCDF4.Variable):
+                skipped_variables.append(prefix_var.name)
         else:
             for k in fhandle.ncattrs():
                 if k.endswith('__'):
@@ -577,7 +581,8 @@ def load_netcdf(afilepath, uri=None, baseuri=None):
         if alias_var != {}:
             aliases = (dict([(alias, getattr(alias_var, alias))
                              for alias in alias_var.ncattrs()]))
-        #print(aliases)
+            if isinstance(alias_var, netCDF4._netCDF4.Variable):
+                skipped_variables.append(alias_var.name)
 
         attrs = {}
         for k in fhandle.ncattrs():
@@ -609,13 +614,16 @@ def load_netcdf(afilepath, uri=None, baseuri=None):
                 #sattrs['bald__array'] = name
                 sattrs['bald__array'] = identity
                 sattrs['rdf__type'] = 'bald__Reference'
-                
             if fhandle.variables[name].shape:
                 sattrs['bald__shape'] = fhandle.variables[name].shape
                 var = Array(identity, sattrs, prefixes=prefixes, aliases=aliases)
             else:
                 var = Subject(identity, sattrs, prefixes=prefixes, aliases=aliases)
-            root_container.attrs['bald__contains'].append(var)
+            if name not in skipped_variables:
+                # Don't include skipped variables, such as prefix or alias
+                # variables, within the containment relation.
+                root_container.attrs['bald__contains'].append(var)
+
             file_variables[name] = var
                 
 
diff --git a/lib/bald/tests/integration/CDL/array_alias.cdl b/lib/bald/tests/integration/CDL/array_alias.cdl
index c442cb6..2576188 100644
--- a/lib/bald/tests/integration/CDL/array_alias.cdl
+++ b/lib/bald/tests/integration/CDL/array_alias.cdl
@@ -8,38 +8,19 @@ variables:
 		parent_variable:SDN_ParameterDiscoveryCode = "BactTaxaAbundSed" ;
 		parent_variable:submursible_name = "Nautilus" ;
 
+	int prefix_list ;
+		prefix_list:bald__ = "http://binary-array-ld.net/latest/" ;
+		prefix_list:rdf__ = "http://www.w3.org/1999/02/22-rdf-syntax-ns#" ;
+
+	int alias_list ;
+		alias_list:SDN_ParameterDiscoveryCode = "http://vocab.nerc.ac.uk/isoCodelists/sdnCodelists/cdicsrCodeList.xml#SDN_ParameterDiscoveryCode" ;
+		alias_list:BactTaxaAbundSed = "http://vocab.nerc.ac.uk/collection/P02/current/BAUC/" ;
+
+
 // global attributes:
 		:_NCProperties = "version=1|netcdflibversion=4.4.1|hdf5libversion=1.8.17" ;
 		:rdf__type = "bald__Container" ;
 		:bald__isPrefixedBy = "prefix_list" ;
 		:bald__isAliasedBy = "alias_list" ;
-data:
-
- parent_variable =
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _ ;
-
-
-group: prefix_list {
-
-  // group attributes:
-  		:bald__ = "http://binary-array-ld.net/latest/" ;
-  		:rdf__ = "http://www.w3.org/1999/02/22-rdf-syntax-ns#" ;
-  } // group bald__prefix_list
-
-group: alias_list {
 
-  // group attributes:
-  		:SDN_ParameterDiscoveryCode = "http://vocab.nerc.ac.uk/isoCodelists/sdnCodelists/cdicsrCodeList.xml#SDN_ParameterDiscoveryCode" ;
-		:BactTaxaAbundSed = "http://vocab.nerc.ac.uk/collection/P02/current/BAUC/" ;
-  } // group bald__alias_list
 }
diff --git a/lib/bald/tests/integration/CDL/array_reference.cdl b/lib/bald/tests/integration/CDL/array_reference.cdl
index 9f7913a..3c2b072 100644
--- a/lib/bald/tests/integration/CDL/array_reference.cdl
+++ b/lib/bald/tests/integration/CDL/array_reference.cdl
@@ -9,43 +9,12 @@ variables:
 	int child_variable(pdim0, pdim1) ;
 		child_variable:rdf__type = "bald__Reference" ;
 		child_variable:bald__array = "child_variable" ;
+	int prefix_list ;
+		prefix_list:bald__ = "http://binary-array-ld.net/latest/" ;
+		prefix_list:rdf__ = "http://www.w3.org/1999/02/22-rdf-syntax-ns#" ;
 
 // global attributes:
 		:_NCProperties = "version=1|netcdflibversion=4.4.1|hdf5libversion=1.8.17" ;
 		:rdf__type = "bald__Container" ;
 		:bald__isPrefixedBy = "prefix_list" ;
-data:
-
- parent_variable =
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _ ;
-
- child_variable =
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
-  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _ ;
-
-group: prefix_list {
-
-  // group attributes:
-  		:bald__ = "http://binary-array-ld.net/latest/" ;
-  		:rdf__ = "http://www.w3.org/1999/02/22-rdf-syntax-ns#" ;
-  } // group bald__prefix_list
 }
diff --git a/ncldDump/aliases.json b/ncldDump/aliases.json
index 1af38c0..f31bb57 100644
--- a/ncldDump/aliases.json
+++ b/ncldDump/aliases.json
@@ -6,101 +6,101 @@
     },
     "names" :
     {
-        "Conventions"                    : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#Conventions",
-        "_FillValue"                     : "http://www.unidata.ucar.edu/netcdf/docs/netcdf.html#Attribute-Conventions",
-        "acknowledgement"                : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#acknowledgement",
-        "add_offset"                     : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#packed-data",
-        "ancillary_variables"            : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#ancillary-data",
-        "axis"                           : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#coordinate-types",
-        "bounds"                         : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#cell-boundaries",
-        "calendar"                       : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#calendar",
-        "cdm_data_type"                  : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#cdm_data_type",
-        "cell_measures"                  : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#cell-measures",
-        "cell_methods"                   : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#cell-methods",
-        "cf_role"                        : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#coordinates-metadata",
-        "climatology"                    : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#climatological-statistics",
-        "comment"                        : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#comment",
-        "compress"                       : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#reduced-horizontal-grid",
-        "contributor_name"               : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#contributor_name",
-        "contributor_role"               : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#contributor_role",
-        "coordinates"                    : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#coordinate-system",
-        "coverage_content_type"          : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#coverage_content_type",
-        "creator_email"                  : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#creator_email",
-        "creator_institution"            : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#creator_institution",
-        "creator_name"                   : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#creator_name",
-        "creator_type"                   : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#creator_type",
-        "creator_url"                    : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#creator_url",
-        "date_created"                   : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#date_created",
-        "date_issued"                    : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#date_issued",
-        "date_metadata_modified"         : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#date_metadata_modified",
-        "date_modified"                  : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#date_modified",
-        "featureType"                    : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#featureType",
-        "flag_masks"                     : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#flags",
-        "flag_meanings"                  : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#flags",
-        "flag_values"                    : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#flags",
-        "formula_terms"                  : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#dimensionless-vertical-coordinate",
-        "geospatial_bounds"              : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#geospatial_bounds",
-        "geospatial_bounds_crs"          : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#geospatial_bounds_crs",
-        "geospatial_bounds_vertical_crs" : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#geospatial_bounds_vertical_crs",
-        "geospatial_lat_max"             : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#geospatial_lat_max",
-        "geospatial_lat_min"             : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#geospatial_lat_min",
-        "geospatial_lat_resolution"      : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#geospatial_lat_resolution",
-        "geospatial_lat_units"           : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#geospatial_lat_units",
-        "geospatial_lon_max"             : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#geospatial_lon_max",
-        "geospatial_lon_min"             : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#geospatial_lon_min",
-        "geospatial_lon_resolution"      : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#geospatial_lon_resolution",
-        "geospatial_lon_units"           : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#geospatial_lon_units",
-        "geospatial_vertical_max"        : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#geospatial_vertical_max",
-        "geospatial_vertical_min"        : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#geospatial_vertical_min",
-        "geospatial_vertical_positive"   : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#geospatial_vertical_positive",
-        "geospatial_vertical_resolution" : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#geospatial_vertical_resolution",
-        "geospatial_vertical_units"      : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#geospatial_vertical_units",
-        "grid_mapping"                   : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#grid-mappings-and-projections",
-        "history"                        : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#history",
-        "id"                             : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#id",
-        "instance_dimension"             : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#representations-features",
-        "institution"                    : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#institution",
-        "instrument"                     : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#instrument",
-        "instrument_vocabulary"          : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#instrument_vocabulary",
-        "keywords"                       : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#keywords",
-        "keywords_vocabulary"            : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#keywords_vocabulary",
-        "leap_month"                     : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#calendar",
-        "leap_year"                      : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#calendar",
-        "license"                        : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#license",
-        "long_name"                      : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#long-name",
-        "metadata_link"                  : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#metadata_link",
-        "missing_value"                  : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#missing-data",
-        "month_lengths"                  : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#calendar",
-        "naming_authority"               : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#naming_authority",
-        "platform"                       : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#platform",
-        "platform_vocabulary"            : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#platform_vocabulary",
-        "positive"                       : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#COARDS",
-        "processing_level"               : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#processing_level",
-        "product_version"                : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#product_version",
-        "program"                        : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#program",
-        "project"                        : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#project",
-        "publisher_email"                : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#publisher_email",
-        "publisher_institution"          : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#publisher_institution",
-        "publisher_name"                 : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#publisher_name",
-        "publisher_type"                 : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#publisher_type",
-        "publisher_url"                  : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#publisher_url",
-        "references"                     : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#references",
-        "sample_dimension"               : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#representations-features",
-        "scale_factor"                   : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#packed-data",
-        "source"                         : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#source",
-        "standard_error_multiplier"      : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#standard-name-modifiers",
-        "standard_name"                  : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#standard-name",
-        "standard_name_vocabulary"       : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#standard_name_vocabulary",
-        "summary"                        : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#summary",
-        "time_coverage_duration"         : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#time_coverage_duration",
-        "time_coverage_end"              : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#time_coverage_end",
-        "time_coverage_resolution"       : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#time_coverage_resolution",
-        "time_coverage_start"            : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#time_coverage_start",
-        "title"                          : "http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_1-3#title",
-        "units"                          : "http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#units",
-        "valid_max"                      : "http://www.unidata.ucar.edu/netcdf/docs/netcdf.html#Attribute-Conventions",
-        "valid_min"                      : "http://www.unidata.ucar.edu/netcdf/docs/netcdf.html#Attribute-Conventions",
-        "valid_range"                    : "http://www.unidata.ucar.edu/netcdf/docs/netcdf.html#Attribute-Conventions",
+        "Conventions"                    : "https://def.scitools.org.uk/ACDD/{}",
+        "_FillValue"                     : "https://def.scitools.org.uk/NetCDF/{}",
+        "acknowledgement"                : "https://def.scitools.org.uk/ACDD/{}",
+        "add_offset"                     : "https://def.scitools.org.uk/CFTerms/{}",
+        "ancillary_variables"            : "https://def.scitools.org.uk/CFTerms/{}",
+        "axis"                           : "https://def.scitools.org.uk/CFTerms/{}",
+        "bounds"                         : "https://def.scitools.org.uk/CFTerms/{}",
+        "calendar"                       : "https://def.scitools.org.uk/CFTerms/{}",
+        "cdm_data_type"                  : "https://def.scitools.org.uk/ACDD/{}",
+        "cell_measures"                  : "https://def.scitools.org.uk/CFTerms/{}",
+        "cell_methods"                   : "https://def.scitools.org.uk/CFTerms/{}",
+        "cf_role"                        : "https://def.scitools.org.uk/CFTerms/{}",
+        "climatology"                    : "https://def.scitools.org.uk/CFTerms/{}",
+        "comment"                        : "https://def.scitools.org.uk/ACDD/{}",
+        "compress"                       : "https://def.scitools.org.uk/CFTerms/{}",
+        "contributor_name"               : "https://def.scitools.org.uk/ACDD/{}",
+        "contributor_role"               : "https://def.scitools.org.uk/ACDD/{}",
+        "coordinates"                    : "https://def.scitools.org.uk/CFTerms/{}",
+        "coverage_content_type"          : "https://def.scitools.org.uk/ACDD/{}",
+        "creator_email"                  : "https://def.scitools.org.uk/ACDD/{}",
+        "creator_institution"            : "https://def.scitools.org.uk/ACDD/{}",
+        "creator_name"                   : "https://def.scitools.org.uk/ACDD/{}",
+        "creator_type"                   : "https://def.scitools.org.uk/ACDD/{}",
+        "creator_url"                    : "https://def.scitools.org.uk/ACDD/{}",
+        "date_created"                   : "https://def.scitools.org.uk/ACDD/{}",
+        "date_issued"                    : "https://def.scitools.org.uk/ACDD/{}",
+        "date_metadata_modified"         : "https://def.scitools.org.uk/ACDD/{}",
+        "date_modified"                  : "https://def.scitools.org.uk/ACDD/{}",
+        "featureType"                    : "https://def.scitools.org.uk/CFTerms/{}",
+        "flag_masks"                     : "https://def.scitools.org.uk/CFTerms/{}",
+        "flag_meanings"                  : "https://def.scitools.org.uk/CFTerms/{}",
+        "flag_values"                    : "https://def.scitools.org.uk/CFTerms/{}",
+        "formula_terms"                  : "https://def.scitools.org.uk/CFTerms/{}",
+        "geospatial_bounds"              : "https://def.scitools.org.uk/ACDD/{}",
+        "geospatial_bounds_crs"          : "https://def.scitools.org.uk/ACDD/{}",
+        "geospatial_bounds_vertical_crs" : "https://def.scitools.org.uk/ACDD/{}",
+        "geospatial_lat_max"             : "https://def.scitools.org.uk/ACDD/{}",
+        "geospatial_lat_min"             : "https://def.scitools.org.uk/ACDD/{}",
+        "geospatial_lat_resolution"      : "https://def.scitools.org.uk/ACDD/{}",
+        "geospatial_lat_units"           : "https://def.scitools.org.uk/ACDD/{}",
+        "geospatial_lon_max"             : "https://def.scitools.org.uk/ACDD/{}",
+        "geospatial_lon_min"             : "https://def.scitools.org.uk/ACDD/{}",
+        "geospatial_lon_resolution"      : "https://def.scitools.org.uk/ACDD/{}",
+        "geospatial_lon_units"           : "https://def.scitools.org.uk/ACDD/{}",
+        "geospatial_vertical_max"        : "https://def.scitools.org.uk/ACDD/{}",
+        "geospatial_vertical_min"        : "https://def.scitools.org.uk/ACDD/{}",
+        "geospatial_vertical_positive"   : "https://def.scitools.org.uk/ACDD/{}",
+        "geospatial_vertical_resolution" : "https://def.scitools.org.uk/ACDD/{}",
+        "geospatial_vertical_units"      : "https://def.scitools.org.uk/ACDD/{}",
+        "grid_mapping"                   : "https://def.scitools.org.uk/CFTerms/{}",
+        "history"                        : "https://def.scitools.org.uk/ACDD/{}",
+        "id"                             : "https://def.scitools.org.uk/ACDD/{}",
+        "instance_dimension"             : "https://def.scitools.org.uk/CFTerms/{}",
+        "institution"                    : "https://def.scitools.org.uk/ACDD/{}",
+        "instrument"                     : "https://def.scitools.org.uk/ACDD/{}",
+        "instrument_vocabulary"          : "https://def.scitools.org.uk/ACDD/{}",
+        "keywords"                       : "https://def.scitools.org.uk/ACDD/{}",
+        "keywords_vocabulary"            : "https://def.scitools.org.uk/ACDD/{}",
+        "leap_month"                     : "https://def.scitools.org.uk/CFTerms/{}",
+        "leap_year"                      : "https://def.scitools.org.uk/CFTerms/{}",
+        "license"                        : "https://def.scitools.org.uk/ACDD/{}",
+        "long_name"                      : "https://def.scitools.org.uk/CFTerms/{}",
+        "metadata_link"                  : "https://def.scitools.org.uk/ACDD/{}",
+        "missing_value"                  : "https://def.scitools.org.uk/CFTerms/{}",
+        "month_lengths"                  : "https://def.scitools.org.uk/CFTerms/{}",
+        "naming_authority"               : "https://def.scitools.org.uk/ACDD/{}",
+        "platform"                       : "https://def.scitools.org.uk/ACDD/{}",
+        "platform_vocabulary"            : "https://def.scitools.org.uk/ACDD/{}",
+        "positive"                       : "https://def.scitools.org.uk/CFTerms/{}",
+        "processing_level"               : "https://def.scitools.org.uk/ACDD/{}",
+        "product_version"                : "https://def.scitools.org.uk/ACDD/{}",
+        "program"                        : "https://def.scitools.org.uk/ACDD/{}",
+        "project"                        : "https://def.scitools.org.uk/ACDD/{}",
+        "publisher_email"                : "https://def.scitools.org.uk/ACDD/{}",
+        "publisher_institution"          : "https://def.scitools.org.uk/ACDD/{}",
+        "publisher_name"                 : "https://def.scitools.org.uk/ACDD/{}",
+        "publisher_type"                 : "https://def.scitools.org.uk/ACDD/{}",
+        "publisher_url"                  : "https://def.scitools.org.uk/ACDD/{}",
+        "references"                     : "https://def.scitools.org.uk/ACDD/{}",
+        "sample_dimension"               : "https://def.scitools.org.uk/CFTerms/{}",
+        "scale_factor"                   : "https://def.scitools.org.uk/CFTerms/{}",
+        "source"                         : "https://def.scitools.org.uk/ACDD/{}",
+        "standard_error_multiplier"      : "https://def.scitools.org.uk/CFTerms/{}",
+        "standard_name"                  : "https://def.scitools.org.uk/CFTerms/{}",
+        "standard_name_vocabulary"       : "https://def.scitools.org.uk/ACDD/{}",
+        "summary"                        : "https://def.scitools.org.uk/ACDD/{}",
+        "time_coverage_duration"         : "https://def.scitools.org.uk/ACDD/{}",
+        "time_coverage_end"              : "https://def.scitools.org.uk/ACDD/{}",
+        "time_coverage_resolution"       : "https://def.scitools.org.uk/ACDD/{}",
+        "time_coverage_start"            : "https://def.scitools.org.uk/ACDD/{}",
+        "title"                          : "https://def.scitools.org.uk/ACDD/{}",
+        "units"                          : "https://def.scitools.org.uk/CFTerms/{}",
+        "valid_max"                      : "https://def.scitools.org.uk/NetCDF/{}",
+        "valid_min"                      : "https://def.scitools.org.uk/NetCDF/{}",
+        "valid_range"                    : "https://def.scitools.org.uk/NetCDF/{}",
   		"SDN_ParameterDiscoveryCode"     : "http://vocab.nerc.ac.uk/isoCodelists/sdnCodelists/cdicsrCodeList.xml#{}",
         "unit_id"                        : "http://qudt.org/1.1/schema/qudt#unit",
         "medium_id"                      : "http://environment.data.gov.au/def/op#matrix",

From cd88109fb7fc95fd40cf010f33335ee03be6938e Mon Sep 17 00:00:00 2001
From: Jonathan Yu <jonathan.yu@csiro.au>
Date: Wed, 6 Sep 2017 15:29:37 +1000
Subject: [PATCH 10/12] updating tests to reflect URL checks

---
 lib/bald/tests/integration/test_cdl.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/lib/bald/tests/integration/test_cdl.py b/lib/bald/tests/integration/test_cdl.py
index a7f87d1..03b2d50 100644
--- a/lib/bald/tests/integration/test_cdl.py
+++ b/lib/bald/tests/integration/test_cdl.py
@@ -64,8 +64,7 @@ def test_grid_OISST_GHRSST(self):
         validation = bald.validate_netcdf(tfile)
         exns = validation.exceptions()
         exns.sort()
-        expected = ['http://doi.org/10.7289/V5SQ8XB5 is not resolving as a resource (404).',
-                     'http://www.ncdc.noaa.gov/sst is not resolving as a resource (404).',
+        expected = [ 'http://www.ncdc.noaa.gov/sst is not resolving as a resource (404).',
                     'http://www.ncdc.noaa.gov/sst/ is not resolving as a resource (404).']
         expected.sort()
         self.assertTrue(not validation.is_valid() and exns == expected,

From a8c4a5b2ae29e8d3f9a415058e478cd5d005972e Mon Sep 17 00:00:00 2001
From: Jonathan Yu <4723726+jyucsiro@users.noreply.github.com>
Date: Thu, 7 Sep 2017 04:29:44 +1000
Subject: [PATCH 11/12] removing bug

---
 lib/bald/tests/integration/test_cdl_rdfgraph.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/lib/bald/tests/integration/test_cdl_rdfgraph.py b/lib/bald/tests/integration/test_cdl_rdfgraph.py
index 2601881..be73efe 100644
--- a/lib/bald/tests/integration/test_cdl_rdfgraph.py
+++ b/lib/bald/tests/integration/test_cdl_rdfgraph.py
@@ -42,7 +42,6 @@ def test_ereefs(self):
             cdl_file = os.path.join(self.cdl_path, 'ereefs_gbr4_ncld.cdl')
             subprocess.check_call(['ncgen', '-o', tfile, cdl_file])
             root_container = bald.load_netcdf(tfile)
-            testPassed
             try:
                ttl = root_container.rdfgraph().serialize(format='n3').decode("utf-8")
             except TypeError:

From 0999f88c2c42e376162125bc3a2bb2566f9bda78 Mon Sep 17 00:00:00 2001
From: Jonathan Yu <4723726+jyucsiro@users.noreply.github.com>
Date: Thu, 7 Sep 2017 06:49:45 +1000
Subject: [PATCH 12/12] fixing bald lib to convert np.ndarray to list

---
 lib/bald/__init__.py                          | 25 ++++++-----
 lib/bald/tests/integration/CDL/array_geo.cdl  | 45 +++++++++++++++++++
 .../tests/integration/test_cdl_rdfgraph.py    |  3 +-
 3 files changed, 60 insertions(+), 13 deletions(-)
 create mode 100644 lib/bald/tests/integration/CDL/array_geo.cdl

diff --git a/lib/bald/__init__.py b/lib/bald/__init__.py
index a25653e..c421292 100644
--- a/lib/bald/__init__.py
+++ b/lib/bald/__init__.py
@@ -415,6 +415,12 @@ def rdfnode(self, graph):
         selfnode = rdflib.URIRef(self.identity)
         for attr in self.attrs:
             objs = self.attrs[attr]
+            if(isinstance(objs, np.ndarray)):
+                #print("Found np.ndarray")
+                #print(objs)
+                #print(attr)
+                #try to convert np.ndarray to a list
+                objs = objs.tolist()
             if not (isinstance(objs, set) or isinstance(objs, list)):
                 objs = set([objs])
             for obj in objs:
@@ -442,6 +448,9 @@ def rdfgraph(self):
         for prefix_name in self._prefixes:
            #strip the double underscore suffix
            new_name = prefix_name[:-2]
+           #print(prefix_name)
+           #print(new_name)
+           #print(self._prefixes[prefix_name])
 
            graph.bind(new_name, self._prefixes[prefix_name])
         graph = self.rdfnode(graph)
@@ -550,13 +559,9 @@ def load_netcdf(afilepath, uri=None, baseuri=None):
         prefix_var = (fhandle[fhandle.bald__isPrefixedBy] if
                         hasattr(fhandle, 'bald__isPrefixedBy') else {})
         prefixes = {}
-
-        skipped_variables = []
-        if prefix_var != {}:
+        if prefix_var != {} :
             prefixes = (dict([(prefix, getattr(prefix_var, prefix)) for
                               prefix in prefix_var.ncattrs()]))
-            if isinstance(prefix_var, netCDF4._netCDF4.Variable):
-                skipped_variables.append(prefix_var.name)
         else:
             for k in fhandle.ncattrs():
                 if k.endswith('__'):
@@ -581,8 +586,7 @@ def load_netcdf(afilepath, uri=None, baseuri=None):
         if alias_var != {}:
             aliases = (dict([(alias, getattr(alias_var, alias))
                              for alias in alias_var.ncattrs()]))
-            if isinstance(alias_var, netCDF4._netCDF4.Variable):
-                skipped_variables.append(alias_var.name)
+        #print(aliases)
 
         attrs = {}
         for k in fhandle.ncattrs():
@@ -614,16 +618,13 @@ def load_netcdf(afilepath, uri=None, baseuri=None):
                 #sattrs['bald__array'] = name
                 sattrs['bald__array'] = identity
                 sattrs['rdf__type'] = 'bald__Reference'
+                
             if fhandle.variables[name].shape:
                 sattrs['bald__shape'] = fhandle.variables[name].shape
                 var = Array(identity, sattrs, prefixes=prefixes, aliases=aliases)
             else:
                 var = Subject(identity, sattrs, prefixes=prefixes, aliases=aliases)
-            if name not in skipped_variables:
-                # Don't include skipped variables, such as prefix or alias
-                # variables, within the containment relation.
-                root_container.attrs['bald__contains'].append(var)
-
+            root_container.attrs['bald__contains'].append(var)
             file_variables[name] = var
                 
 
diff --git a/lib/bald/tests/integration/CDL/array_geo.cdl b/lib/bald/tests/integration/CDL/array_geo.cdl
new file mode 100644
index 0000000..70585c0
--- /dev/null
+++ b/lib/bald/tests/integration/CDL/array_geo.cdl
@@ -0,0 +1,45 @@
+netcdf tmpMwXy8U {
+dimensions:
+	pdim0 = 11 ;
+	pdim1 = 17 ;
+variables:
+	int prefix_list ;
+  		prefix_list:bald__ = "http://binary-array-ld.net/latest/" ;
+  		prefix_list:rdf__ = "http://www.w3.org/1999/02/22-rdf-syntax-ns#" ;
+		prefix_list:rdfs__ = "http://www.w3.org/2000/01/rdf-schema#" ;
+		prefix_list:cf__ = "http://def.scitools.org.uk/CFTerms/" ;
+		prefix_list:geo__ = "http://www.opengis.net/ont/geosparql#" ;
+
+	int temp(pdim0, pdim1) ;
+	        temp:cf__standard_name = "air_temperature" ;
+	        temp:cf__long_name = "Air temperature obs example at point" ;
+	        temp:rdfs__label = "Air temperature obs example at point" ;
+		temp:geo__asWKT = "POINT(-77.03524 38.889468)" ;
+
+	int pressure(pdim0, pdim1) ;
+	        pressure:cf__standard_name = "air_pressure" ;
+	        pressure:cf__long_name = "Air pressure at UCAR Centre Green" ;
+	        pressure:rdfs__label = "Air pressure at UCAR Centre Green" ;
+		pressure:geo__asWKT = "POINT(-105.24584700000003 40.0315278)" ;
+
+// global attributes:
+		:_NCProperties = "version=1|netcdflibversion=4.4.1|hdf5libversion=1.8.17" ;
+		:rdf__type = "bald__Container" ;
+		:bald__isPrefixedBy = "prefix_list" ;
+data:
+
+ temp =
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _ ;
+
+
+}
diff --git a/lib/bald/tests/integration/test_cdl_rdfgraph.py b/lib/bald/tests/integration/test_cdl_rdfgraph.py
index be73efe..ca54b07 100644
--- a/lib/bald/tests/integration/test_cdl_rdfgraph.py
+++ b/lib/bald/tests/integration/test_cdl_rdfgraph.py
@@ -43,7 +43,8 @@ def test_ereefs(self):
             subprocess.check_call(['ncgen', '-o', tfile, cdl_file])
             root_container = bald.load_netcdf(tfile)
             try:
-               ttl = root_container.rdfgraph().serialize(format='n3').decode("utf-8")
+               g  = root_container.rdfgraph()
+               ttl = g.serialize(format='n3').decode("utf-8")
             except TypeError:
                self.fail("Test case could not convert ereefs CDL to RDF")