hsds writer updates

Author: jreadey

src/h5json/apps/h5tohs.py

@@ -17,10 +17,12 @@
 from h5json.hsdsstore.hsds_writer import HSDSWriter
 from h5json.h5pystore.h5py_reader import H5pyReader
 
+
 def usage():
     print(f"usage: {sys.argv[0]} [-h] [--nodata] <hdf5_file> <hsds_domain>")
     sys.exit(0)
 
+
 def main():
     no_data = False
     filename = None
@@ -59,5 +61,6 @@ def main():
 
     db.close()  # close will trigger write to HSDS
 
+
 if __name__ == "__main__":
     main()

src/h5json/h5pystore/h5py_reader.py

@@ -177,9 +177,6 @@ def open(self):
         self._id_map[self._root_id] = f
         addr = h5py.h5o.get_info(f.id).addr
         self._addr_map[addr] = self._root_id
-        #f.visititems(self.visit)
-
-        print("h5py_reader keys:", list(self.db.db.keys()))
 
         return self._root_id
 
@@ -268,7 +265,6 @@ def getAttribute(self, obj_id, name, include_data=True):
         else:
             pass  # no data
 
-        
         item['created'] = time.time()  # TBD: get attribute creation time from h5py?
         return item
 
@@ -314,7 +310,7 @@ def _getLink(self, parent, link_name):
                 item["id"] = None
             else:
                 item["id"] = self._addr_map[addr]
-            
+
         item['created'] = time.time()  # TBD: get the link creation time from h5py?
 
         return item
@@ -435,11 +431,11 @@ def _getHDF5DatasetCreationProperties(self, dset, type_class):
         return creationProps
 
     def _getDataset(self, dset):
+        """ return json representation of the given dataset """
+
         self.log.info(f"getDataset alias: [{dset.name}]")
 
         item = {"alias": dset.name}
-        print("dset:", dset)
-        print("dset type:", type(dset))
         typeid = dset.id.get_type()
         if h5py.h5t.TypeID.committed(typeid):
             type_uuid = None
@@ -479,7 +475,7 @@ def _getDataset(self, dset):
         item["cpl"] = self._getHDF5DatasetCreationProperties(dset, type_item["class"])
 
         return item
-    
+
     def _getHardLinkIds(self, parent):
         """ create any ids for hard links of the group """
 
@@ -518,21 +514,18 @@ def getObjectById(self, obj_id, include_attrs=True, include_links=True):
         if obj_id not in self._id_map:
             raise KeyError(f"{obj_id} not found")
         h5obj = self._id_map[obj_id]
-        print("h5obj:", h5obj)
-        print("h5obj.name:", h5obj.name)
-        print("h5obj type:", type(h5obj))
         if isinstance(h5obj, h5py.Group):
             self._getHardLinkIds(h5obj)
             obj_json = self._getGroup(h5obj, include_links=include_links)
         elif isinstance(h5obj, h5py.Dataset):
             obj_json = self._getDataset(h5obj)
         elif isinstance(h5obj, h5py.Datatype):
-            obj_json = self._getDataset(h5obj)
+            obj_json = self._getDatatype(h5obj)
         else:
             msg = f"unexpected object type: {type(h5obj)}"
             self.log.error(msg)
             raise TypeError(msg)
-            
+
         if include_attrs:
             attributes = self.getAttributes(obj_id)
             obj_json["attributes"] = attributes

src/h5json/h5pystore/h5py_writer.py

@@ -388,7 +388,6 @@ def updateAttributes(self, obj_id, obj):
                 continue
             self.createAttribute(obj, name, attr_json)
 
-        
     def flush(self):
         """ Write dirty items """
         if self.closed:

src/h5json/h5writer.py

@@ -67,7 +67,7 @@ def no_data(self):
     @abstractmethod
     def open(self):
         """ open storage handle, return root_id"""
-        return None
+        pass
 
     @abstractmethod
     def flush(self):