chckpoint

docs/gallery/plot_convert_nwb_hdf5.py

@@ -100,13 +100,13 @@
 
 zf.trials.to_dataframe()[['start_time', 'stop_time', 'type', 'photo_stim_type']]
 zr.close()
-# breakpoint()
+
 ###############################################################################
 # Convert the Zarr file back to HDF5
 # ----------------------------------
 #
 # Using the same approach as above, we can now convert our Zarr file back to HDF5.
-try: # TODO: This is a temporary ignore on the convert_dtype exception. 
+try: # TODO: This is a temporary ignore on the convert_dtype exception.
     with NWBZarrIO(zarr_filename, mode='r') as read_io:  # Create Zarr IO object for read
         with NWBHDF5IO(hdf_filename, 'w') as export_io:  # Create HDF5 IO object for write
             export_io.export(src_io=read_io, write_args=dict(link_data=False))  # Export from Zarr to HDF5

src/hdmf_zarr/backend.py

@@ -247,6 +247,9 @@ def export(self, **kwargs):
                                        "link_data=True." % src_io.__class__.__name__)
 
         # write_args['export_source'] = src_io.source  # pass export_source=src_io.source to write_builder
+        # write_args['export_source'] = os.path.abspath(src_io.source) if src_io.source is not None else None
+
+
         ckwargs = kwargs.copy()
         ckwargs['write_args'] = write_args
         super().export(**ckwargs)
@@ -300,6 +303,8 @@ def get_builder_disk_path(self, **kwargs):
     def write_builder(self, **kwargs):
         """Write a builder to disk"""
         f_builder, link_data, exhaust_dci = getargs('builder', 'link_data', 'exhaust_dci', kwargs)
+        # f_builder = popargs('builder', kwargs)
+        # link_data, exhaust_dci, export_source = getargs('link_data', 'exhaust_dci', 'export_source', kwargs)
         for name, gbldr in f_builder.groups.items():
             self.write_group(parent=self.__file,
                              builder=gbldr,
@@ -310,7 +315,9 @@ def write_builder(self, **kwargs):
                                builder=dbldr,
                                link_data=link_data,
                                exhaust_dci=exhaust_dci)
-        self.write_attributes(self.__file, f_builder.attributes)
+        # for name, lbldr in f_builder.links.items():
+        #     self.write_link(self.__file, lbldr, export_source=kwargs.get("export_source"))
+        self.write_attributes(self.__file, f_builder.attributes) # the same as set_attributes in HDMF
         self.__dci_queue.exhaust_queue()  # Write all DataChunkIterators that have been queued
         self._written_builders.set_written(f_builder)
         self.logger.debug("Done writing %s '%s' to path '%s'" %
@@ -517,8 +524,13 @@ def resolve_ref(self, zarr_ref):
         else:
             source_file = str(zarr_ref['source'])
         # Resolve the path relative to the current file
+        # breakpoint()
         source_file = os.path.abspath(os.path.join(self.source, source_file))
         object_path = zarr_ref.get('path', None)
+        # if object_path == "/bucket1/bazs/baz0":
+        #     object_path = "/root/bazs/baz0"
+        # if object_path == "/bazs/baz0":
+
         # full_path = None
         # if os.path.isdir(source_file):
         #    if object_path is not None:
@@ -534,7 +546,15 @@ def resolve_ref(self, zarr_ref):
             try:
                 target_zarr_obj = target_zarr_obj[object_path]
             except Exception:
-                raise ValueError("Found bad link to object %s in file %s" % (object_path, source_file))
+            #     breakpoint()
+                try:
+                    import pathlib
+                    object_path = pathlib.Path(object_path)
+                    rel_obj_path = object_path.relative_to(*object_path.parts[:2])
+                    target_zarr_obj = target_zarr_obj[rel_obj_path]
+                except Exception:
+                    # breakpoint()
+                    raise ValueError("Found bad link to object %s in file %s" % (object_path, source_file))
         # Return the create path
         return target_name, target_zarr_obj
 
@@ -698,6 +718,7 @@ def __setup_chunked_dataset__(cls, parent, name, data, options=None):
              'doc': 'Used internally to force the data being used when we have to load the data', 'default': None},
             returns='the Zarr array that was created', rtype=Array)
     def write_dataset(self, **kwargs):  # noqa: C901
+        # breakpoint()
         parent, builder, link_data, exhaust_dci = getargs('parent', 'builder', 'link_data', 'exhaust_dci', kwargs)
         force_data = getargs('force_data', kwargs)
         if self.get_written(builder):
@@ -730,6 +751,7 @@ def write_dataset(self, **kwargs):  # noqa: C901
                 dset = parent[name]
         # When converting data between backends we may see an HDMFDataset, e.g., a H55ReferenceDataset, with references
         elif isinstance(data, HDMFDataset):
+            # breakpoint()
             # If we have a dataset of containers we need to make the references to the containers
             if len(data) > 0 and isinstance(data[0], Container):
                 ref_data = [self.__get_ref(data[i]) for i in range(len(data))]
@@ -742,6 +764,7 @@ def write_dataset(self, **kwargs):  # noqa: C901
                                               **options['io_settings'])
                 dset.attrs['zarr_dtype'] = type_str
                 dset[:] = ref_data
+                # breakpoint()
                 self._written_builders.set_written(builder)  # record that the builder has been written
             # If we have a regular dataset, then load the data and write the builder after load
             else:
@@ -752,6 +775,8 @@ def write_dataset(self, **kwargs):  # noqa: C901
                 # We can/should not update the data in the builder itself so we load the data here and instead
                 # force write_dataset when we call it recursively to use the data we loaded, rather than the
                 # dataset that is set on the builder
+                # breakpoint()
+
                 dset = self.write_dataset(parent=parent,
                                           builder=builder,
                                           link_data=link_data,
@@ -774,6 +799,7 @@ def write_dataset(self, **kwargs):  # noqa: C901
                     i = list([dts, ])
                     t = self.__resolve_dtype_helper__(i)
                     type_str.append(self.__serial_dtype__(t)[0])
+            # breakpoint()
 
             if len(refs) > 0:
                 dset = parent.require_dataset(name,
@@ -1050,7 +1076,23 @@ def get_builder(self, **kwargs): # move this to HDMFIO (define skeleton in there
         """
         zarr_obj = kwargs['zarr_obj']
         builder = self.__get_built(zarr_obj)
+        # ff = self.__built
+        # breakpoint()
+        # if zarr_obj.name == '/bazs/baz0':
+        #     breakpoint()
+        if builder is None:
+        #
+        #     breakpoint()
+            # builder = self.__temp_get_built(zarr_obj)
+            path = list(self.__built.keys())[0]
+            builder_source_path = path.replace(zarr_obj.path,'')
+
+            zarr_obj_path = zarr_obj.path
+            path = os.path.join(builder_source_path, path)
+            # breakpoint()
+            builder = self.__built.get(path, None)
         if builder is None:
+            # breakpoint()
             msg = '%s has not been built' % (zarr_obj.name)
             raise ValueError(msg)
         return builder
@@ -1064,9 +1106,23 @@ def __get_built(self, zarr_obj):
         """
         fpath = zarr_obj.store.path
         path = zarr_obj.path
+        ff = self.__built
+        # breakpoint()
         path = os.path.join(fpath, path)
         return self.__built.get(path, None)
 
+    def __temp_get_built(self, zarr_obj):
+        fpath = zarr_obj.store.path
+        path = zarr_obj.path
+        path = os.path.join('bucket1', path)
+        # breakpoint()
+        path = os.path.join(fpath, path)
+        # breakpoint()
+
+        builder_source_path = list(self.__built.keys())[0]
+        return self.__built.get(path, None)
+
+
     def __read_group(self, zarr_obj, name=None):
         ret = self.__get_built(zarr_obj)
         if ret is not None: