fixing bald lib to convert np.ndarray to list

Author: jyucsiro

lib/bald/__init__.py

@@ -414,6 +414,12 @@ 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:
@@ -583,16 +589,13 @@ def load_netcdf(afilepath, uri=None):
                 fhandle.variables[name].dimensions[0] == name):
                 sattrs['bald__array'] = name
                 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
 
 

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 =
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
+  _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _ ;
+
+
+}

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)
+            try:
+               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")
+