fix for datasets with fillvalue

Author: jreadey

src/h5json/hdf5db.py

@@ -570,6 +570,11 @@ def getDatasetValues(self, dset_id, sel):
 
         dtype = self.getDtype(dset_json)
 
+        if "creationProperties" in dset_json:
+            cpl = dset_json["creationProperties"]
+        else:
+            cpl = {}
+
         # determine if we need to make a read request or not
         if dset_id in self._new_objects:
             fetch = False
@@ -587,7 +592,13 @@ def getDatasetValues(self, dset_id, sel):
         if fetch:
             arr = self.reader.getDatasetValues(dset_id, sel, dtype=dtype)
         else:
-            arr = np.zeros(sel.mshape, dtype=dtype)
+            if "fillValue" in cpl:
+                fillValue = cpl["fillValue"]
+                # TBD: fix for compound types
+                arr = np.zeros(sel.mshape, dtype=dtype)
+                arr[...] = fillValue
+            else:
+                arr = np.zeros(sel.mshape, dtype=dtype)
 
         if "updates" in dset_json:
             # apply any non-flushed changes that intersect the current selection

test/unit/hdf5db_test.py

@@ -526,6 +526,24 @@ def testResizableDataset(self):
 
         db.close()
 
+    def testFillValueDataset(self):
+        dtype = np.uint32
+        db = Hdf5db(app_logger=self.log)
+        root_id = db.open()
+        cpl = {"fillValue": 0xdeadbeef}
+        dset_id = db.createDataset((), dtype=dtype, cpl=cpl)
+        db.createHardLink(root_id, "dset", dset_id)
+        dset_json = db.getObjectById(dset_id)
+        self.assertTrue("creationProperties" in dset_json)
+        cpl = dset_json["creationProperties"]
+        self.assertTrue("fillValue" in cpl)
+        self.assertEqual(cpl["fillValue"], 0xdeadbeef)
+        sel_all = selections.select((), ...)
+        arr = db.getDatasetValues(dset_id, sel_all)
+        self.assertEqual(arr.dtype, dtype)
+        self.assertEqual(arr.shape, ())
+        self.assertEqual(arr[()], 0xdeadbeef)
+
 
 if __name__ == "__main__":
     # setup test files