Merge pull request #83 from kmuehlbauer/handle-not-implemented

when getting object by address do not fully instantiate when iterating

Author: davidhassell

pyfive/dataobjects.py

@@ -675,7 +675,12 @@ def get_id_storage_params(self):
         version, dims, layout_class, property_offset = (
             self._get_data_message_properties(msg_offset))
         return msg_offset, layout_class, property_offset
-    
+
+    @property
+    def is_group(self):
+        """ True when DataObjects points to a group, False for a dataset. """
+        return len(self.find_msg_type(GROUP_INFO_MSG_TYPE)) > 0
+
     @property
     def is_dataset(self):
         """ True when DataObjects points to a dataset, False for a group. """

pyfive/high_level.py

@@ -50,7 +50,7 @@ def __len__(self):
         return len(self._links)
 
     def _dereference(self, ref):
-        """ Deference a Reference object. """
+        """ Dereference a Reference object. """
         if not ref:
             raise ValueError('cannot deference null reference')
         obj = self.file._get_object_by_address(ref.address_of_reference)
@@ -217,8 +217,19 @@ def _get_object_by_address(self, obj_addr):
         """ Return the object pointed to by a given address. """
         if self._dataobjects.offset == obj_addr:
             return self
-        return self.visititems(
-            lambda x, y: y if y._dataobjects.offset == obj_addr else None)
+        
+        queue = deque([(self.name.rstrip('/'), self)])
+        while queue:
+            base, grp = queue.popleft()
+            for name, link_addr in grp._links.items():
+                full_path = f"{base}/{name}" if base else f"/{name}"
+                # check address without instantiating
+                if link_addr == obj_addr:
+                    # return instantiated object
+                    return grp[name]
+                # descend only if it's a subgroup (need to instantiate minimally)
+                if DataObjects(self.file._fh, link_addr).is_group:
+                    queue.append((full_path, grp[name]))
 
     def close(self):
         """ Close the file. """

tests/test_h5netcdf.py

@@ -57,4 +57,21 @@ def test_file_contents():
             print('Attempting to compare ',x)
             print(h5file[x])
             print(p5file[x])
-            raise
+            raise
+
+    # check dereferencing
+    ref1 = p5file["foo"].attrs["DIMENSION_LIST"][0][-1]
+    assert p5file["x"].id == p5file[ref1].id
+    assert str(p5file["x"][:]) == str(p5file[ref1][:])
+
+    ref2 = p5file["subgroup/subvar"].attrs["DIMENSION_LIST"][0][-1]
+    assert p5file["x"].id == p5file[ref2].id
+    assert str(p5file["x"][:]) == str(p5file[ref2][:])
+
+    assert p5file[ref1].id == p5file[ref2].id
+    assert str(p5file[ref1][:]) == str(p5file[ref2][:])
+
+    ref3 = p5file["subgroup/y_var"].attrs["DIMENSION_LIST"][0][-1]
+    assert p5file["subgroup/y"].id == p5file[ref3].id
+    assert str(p5file["subgroup/y"][:]) == str(p5file[ref3][:])
+    assert p5file["y"].id != p5file[ref3].id