update for h5py NULL_SPACE feature - cf h5py issue #279

Author: jreadey

h5json/hdf5db.py

@@ -814,7 +814,10 @@ def getNullRegionReference(self):
 
     def getShapeItemByDsetObj(self, obj):
         item = {}
-        if len(obj.shape) == 0:
+        if obj.shape is None:
+            # new with h5py 2.6, null space datasets will return None for shape
+            item['class'] = 'H5S_NULL'
+        elif len(obj.shape) == 0:
             # check to see if this is a null space vs a scalar dataset we'll do
             # this by seeing if an exception is raised when reading the dataset
             # h5py issue https://github.com/h5py/h5py/issues/279 will provide a
@@ -846,7 +849,7 @@ def getShapeItemByDsetObj(self, obj):
 
     def getShapeItemByAttrObj(self, obj):
         item = {}
-        if obj.get_storage_size() == 0:
+        if obj.shape is None or obj.get_storage_size() == 0:
             # If storage size is 0, assume this is a null space obj
             # See: h5py issue https://github.com/h5py/h5py/issues/279
             item['class'] = 'H5S_NULL'
@@ -2100,6 +2103,10 @@ def getDatasetValuesByUuid(self, obj_uuid, slices=Ellipsis, format="json"):
             self.log.info(msg)
             raise IOError(errno.EINVAL, msg)
 
+        if dset.shape is None:
+            # null space dataset (with h5py 2.6.0)
+            return None   
+               
         rank = len(dset.shape)
 
         if rank == 0:

test/unit/hdf5dbTest.py

@@ -507,14 +507,37 @@ def testCreateCommittedCompoundTypeDataset(self):
 
 
     def testReadZeroDimDataset(self):
-         filepath = getFile('zerodim.h5', 'readzerodeimdataset.h5')
-         d111_values = None
-         d112_values = None
-         with Hdf5db(filepath, app_logger=self.log) as db:
+        filepath = getFile('zerodim.h5', 'readzerodeimdataset.h5')
+              
+        with Hdf5db(filepath, app_logger=self.log) as db:
             dsetUuid = db.getUUIDByPath('/dset')
             self.assertEqual(len(dsetUuid), UUID_LEN)
             dset_value = db.getDatasetValuesByUuid(dsetUuid)
             self.assertEqual(dset_value, 42)
+            
+            
+    def testReadNullSpaceDataset(self):
+        filepath = getFile('null_space_dset.h5', 'readnullspacedataset.h5')
+         
+        with Hdf5db(filepath, app_logger=self.log) as db:
+            dsetUuid = db.getUUIDByPath('/DS1')
+            self.assertEqual(len(dsetUuid), UUID_LEN)
+            obj = db.getDatasetObjByUuid(dsetUuid)
+            shape_item = db.getShapeItemByDsetObj(obj)
+            self.assertTrue('class' in shape_item)
+            self.assertEqual(shape_item['class'], 'H5S_NULL')
+            
+    def testReadNullSpaceAttribute(self):
+        filepath = getFile('null_space_attr.h5', 'readnullspaceattr.h5')
+         
+        with Hdf5db(filepath, app_logger=self.log) as db:
+            rootUuid = db.getUUIDByPath('/')
+            self.assertEqual(len(rootUuid), UUID_LEN)
+            item = db.getAttributeItem("groups", rootUuid, "attr1") 
+            self.assertTrue('shape' in item)
+            shape_item = item['shape']
+            self.assertTrue('class' in shape_item)
+            self.assertEqual(shape_item['class'], 'H5S_NULL')
 
     def testReadAttribute(self):
         # getAttributeItemByUuid