some tests are working

hdmf-dev · Oct 17, 2024 · 417672f · 417672f
1 parent 24ce06c
commit 417672f
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Showing 22 changed files with 163 additions and 105 deletions.
diff --git a/src/hdmf_zarr/backend.py b/src/hdmf_zarr/backend.py
@@ -744,15 +744,14 @@ def resolve_ref(self, zarr_ref):
             target_name = os.path.basename(object_path)
         else:
             target_name = ROOT_NAME
-        breakpoint()
+
         target_zarr_obj = self.__open_file_consolidated(store=source_file,
                                                         mode='r',
                                                         storage_options=self.__storage_options)
         if object_path is not None:
             try:
                 target_zarr_obj = target_zarr_obj[object_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
@@ -848,45 +847,7 @@ def write_link(self, **kwargs):
 
         self.__add_link__(parent, zarr_ref.source, zarr_ref.path, name)
         self._written_builders.set_written(builder)  # record that the builder has been written
-# @docval({'name': 'parent', 'type': Group, 'doc': 'the parent HDF5 object'},
-#             {'name': 'builder', 'type': LinkBuilder, 'doc': 'the LinkBuilder to write'},
-#             {'name': 'export_source', 'type': str,
-#              'doc': 'The source of the builders when exporting', 'default': None},
-#             returns='the Link that was created', rtype=(SoftLink, ExternalLink))
-#     def write_link(self, **kwargs):
-#         parent, builder, export_source = getargs('parent', 'builder', 'export_source', kwargs)
-#         self.logger.debug("Writing LinkBuilder '%s' to parent group '%s'" % (builder.name, parent.name))
-#         if self.get_written(builder):
-#             self.logger.debug("    LinkBuilder '%s' is already written" % builder.name)
-#             return None
-#         name = builder.name
-#         target_builder = builder.builder
-#         path = self.__get_path(target_builder)
-#         # source will indicate target_builder's location
-#         if export_source is None:
-#             write_source = builder.source
-#         else:
-#             write_source = export_source
-#
-#         parent_filename = os.path.abspath(parent.file.filename)
-#         if target_builder.source in (write_source, parent_filename):
-#             link_obj = SoftLink(path)
-#             self.logger.debug("    Creating SoftLink '%s/%s' to '%s'"
-#                               % (parent.name, name, link_obj.path))
-#         elif target_builder.source is not None:
-#             target_filename = os.path.abspath(target_builder.source)
-#             relative_path = os.path.relpath(target_filename, os.path.dirname(parent_filename))
-#             if target_builder.location is not None:
-#                 path = target_builder.location + "/" + target_builder.name
-#             link_obj = ExternalLink(relative_path, path)
-#             self.logger.debug("    Creating ExternalLink '%s/%s' to '%s://%s'"
-#                               % (parent.name, name, link_obj.filename, link_obj.path))
-#         else:
-#             msg = 'cannot create external link to %s' % path
-#             raise ValueError(msg)
-#         parent[name] = link_obj
-#         self.__set_written(builder)
-#         return link_obj
+
     @classmethod
     def __setup_chunked_dataset__(cls, parent, name, data, options=None):
         """

diff --git a/test_io0.zarr/.zattrs b/test_io0.zarr/.zattrs
@@ -2,5 +2,5 @@
     ".specloc": "specifications",
     "data_type": "FooFile",
     "namespace": "test_core",
-    "object_id": "27d9b554-421a-4cb7-8c24-66b5747b86df"
+    "object_id": "20283a8a-00e6-414a-8dd4-4125364c03a5"
 }
diff --git a/test_io0.zarr/.zmetadata b/test_io0.zarr/.zmetadata
@@ -3,7 +3,7 @@
         ".zattrs": {
             "data_type": "FooFile",
             "namespace": "test_core",
-            "object_id": "27d9b554-421a-4cb7-8c24-66b5747b86df"
+            "object_id": "20283a8a-00e6-414a-8dd4-4125364c03a5"
         },
         ".zgroup": {
             "zarr_format": 2
@@ -14,7 +14,7 @@
         "buckets/bucket1/.zattrs": {
             "data_type": "FooBucket",
             "namespace": "test_core",
-            "object_id": "464e00d7-11dd-4466-afda-def0b44bb2c9"
+            "object_id": "732346eb-b4a1-4eb6-aee1-2d64cfe8c165"
         },
         "buckets/bucket1/.zgroup": {
             "zarr_format": 2
@@ -27,7 +27,7 @@
             "attr3": 3.14,
             "data_type": "Foo",
             "namespace": "test_core",
-            "object_id": "4ad02d31-07cf-4b31-ab8b-eecca3ffb26d"
+            "object_id": "7d47b7b1-ab86-462d-a8fc-0ae0fbf37315"
         },
         "buckets/bucket1/foo_holder/foo1/.zgroup": {
             "zarr_format": 2

diff --git a/test_io0.zarr/buckets/bucket1/.zattrs b/test_io0.zarr/buckets/bucket1/.zattrs
@@ -1,5 +1,5 @@
 {
     "data_type": "FooBucket",
     "namespace": "test_core",
-    "object_id": "464e00d7-11dd-4466-afda-def0b44bb2c9"
+    "object_id": "732346eb-b4a1-4eb6-aee1-2d64cfe8c165"
 }
diff --git a/test_io0.zarr/buckets/bucket1/foo_holder/foo1/.zattrs b/test_io0.zarr/buckets/bucket1/foo_holder/foo1/.zattrs
@@ -3,5 +3,5 @@
     "attr3": 3.14,
     "data_type": "Foo",
     "namespace": "test_core",
-    "object_id": "4ad02d31-07cf-4b31-ab8b-eecca3ffb26d"
+    "object_id": "7d47b7b1-ab86-462d-a8fc-0ae0fbf37315"
 }
diff --git a/test_io1.zarr/.zattrs b/test_io1.zarr/.zattrs
@@ -2,5 +2,12 @@
     ".specloc": "specifications",
     "data_type": "FooFile",
     "namespace": "test_core",
-    "object_id": "ac0cd188-78cd-4eeb-a437-52d5ba7062e3"
+    "object_id": "2ad0d2b0-dd51-4c5e-84d3-e561330a4f6f",
+    "zarr_link": [
+        {
+            "name": "foofile_data",
+            "path": "/buckets/bucket1/foo_holder/foo1/my_data",
+            "source": "/Users/mavaylon/Research/NWB/hdmf-zarr/test_io0.zarr"
+        }
+    ]
 }
diff --git a/test_io1.zarr/.zmetadata b/test_io1.zarr/.zmetadata
@@ -3,23 +3,49 @@
         ".zattrs": {
             "data_type": "FooFile",
             "namespace": "test_core",
-            "object_id": "ac0cd188-78cd-4eeb-a437-52d5ba7062e3"
+            "object_id": "2ad0d2b0-dd51-4c5e-84d3-e561330a4f6f",
+            "zarr_link": [
+                {
+                    "name": "foofile_data",
+                    "path": "/buckets/bucket1/foo_holder/foo1/my_data",
+                    "source": "/Users/mavaylon/Research/NWB/hdmf-zarr/test_io0.zarr"
+                }
+            ]
         },
         ".zgroup": {
             "zarr_format": 2
         },
         "buckets/.zgroup": {
             "zarr_format": 2
         },
-        "links/.zattrs": {
+        "buckets/bucket2/.zattrs": {
+            "data_type": "FooBucket",
+            "namespace": "test_core",
+            "object_id": "9fd11ffb-4d93-40bf-9a0e-12c1686a1a79"
+        },
+        "buckets/bucket2/.zgroup": {
+            "zarr_format": 2
+        },
+        "buckets/bucket2/foo_holder/.zgroup": {
+            "zarr_format": 2
+        },
+        "buckets/bucket2/foo_holder/foo2/.zattrs": {
+            "attr1": "I am foo2",
+            "attr3": 3.14,
+            "data_type": "Foo",
+            "namespace": "test_core",
+            "object_id": "432c2318-91c6-437e-81c1-e97ceecb0e18",
             "zarr_link": [
                 {
-                    "name": "foo_link",
-                    "path": "/buckets/bucket1/foo_holder/foo1",
-                    "source": "test_io0.zarr"
+                    "name": "my_data",
+                    "path": "/buckets/bucket1/foo_holder/foo1/my_data",
+                    "source": "/Users/mavaylon/Research/NWB/hdmf-zarr/test_io0.zarr"
                 }
             ]
         },
+        "buckets/bucket2/foo_holder/foo2/.zgroup": {
+            "zarr_format": 2
+        },
         "links/.zgroup": {
             "zarr_format": 2
         }

diff --git a/test_io1.zarr/buckets/bucket2/.zattrs b/test_io1.zarr/buckets/bucket2/.zattrs
@@ -0,0 +1,5 @@
+{
+    "data_type": "FooBucket",
+    "namespace": "test_core",
+    "object_id": "9fd11ffb-4d93-40bf-9a0e-12c1686a1a79"
+}
diff --git a/test_io1.zarr/buckets/bucket2/.zgroup b/test_io1.zarr/buckets/bucket2/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
diff --git a/test_io1.zarr/buckets/bucket2/foo_holder/.zgroup b/test_io1.zarr/buckets/bucket2/foo_holder/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
diff --git a/test_io1.zarr/buckets/bucket2/foo_holder/foo2/.zattrs b/test_io1.zarr/buckets/bucket2/foo_holder/foo2/.zattrs
@@ -0,0 +1,14 @@
+{
+    "attr1": "I am foo2",
+    "attr3": 3.14,
+    "data_type": "Foo",
+    "namespace": "test_core",
+    "object_id": "432c2318-91c6-437e-81c1-e97ceecb0e18",
+    "zarr_link": [
+        {
+            "name": "my_data",
+            "path": "/buckets/bucket1/foo_holder/foo1/my_data",
+            "source": "/Users/mavaylon/Research/NWB/hdmf-zarr/test_io0.zarr"
+        }
+    ]
+}
diff --git a/test_io1.zarr/buckets/bucket2/foo_holder/foo2/.zgroup b/test_io1.zarr/buckets/bucket2/foo_holder/foo2/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
diff --git a/test_io1.zarr/links/.zattrs b/test_io1.zarr/links/.zattrs
diff --git a/test_io2.zarr/.zattrs b/test_io2.zarr/.zattrs
@@ -2,5 +2,12 @@
     ".specloc": "specifications",
     "data_type": "FooFile",
     "namespace": "test_core",
-    "object_id": "ac0cd188-78cd-4eeb-a437-52d5ba7062e3"
+    "object_id": "2ad0d2b0-dd51-4c5e-84d3-e561330a4f6f",
+    "zarr_link": [
+        {
+            "name": "foofile_data",
+            "path": "/buckets/bucket1/foo_holder/foo1/my_data",
+            "source": "/Users/mavaylon/Research/NWB/hdmf-zarr/test_io0.zarr"
+        }
+    ]
 }
diff --git a/test_io2.zarr/.zmetadata b/test_io2.zarr/.zmetadata
@@ -3,23 +3,49 @@
         ".zattrs": {
             "data_type": "FooFile",
             "namespace": "test_core",
-            "object_id": "ac0cd188-78cd-4eeb-a437-52d5ba7062e3"
+            "object_id": "2ad0d2b0-dd51-4c5e-84d3-e561330a4f6f",
+            "zarr_link": [
+                {
+                    "name": "foofile_data",
+                    "path": "/buckets/bucket1/foo_holder/foo1/my_data",
+                    "source": "/Users/mavaylon/Research/NWB/hdmf-zarr/test_io0.zarr"
+                }
+            ]
         },
         ".zgroup": {
             "zarr_format": 2
         },
         "buckets/.zgroup": {
             "zarr_format": 2
         },
-        "links/.zattrs": {
+        "buckets/bucket2/.zattrs": {
+            "data_type": "FooBucket",
+            "namespace": "test_core",
+            "object_id": "7f8154fa-8bdb-407d-9173-3653cbb3229e"
+        },
+        "buckets/bucket2/.zgroup": {
+            "zarr_format": 2
+        },
+        "buckets/bucket2/foo_holder/.zgroup": {
+            "zarr_format": 2
+        },
+        "buckets/bucket2/foo_holder/foo2/.zattrs": {
+            "attr1": "I am foo2",
+            "attr3": 3.14,
+            "data_type": "Foo",
+            "namespace": "test_core",
+            "object_id": "4bf361c1-b731-4f2c-8b53-22aab97d5276",
             "zarr_link": [
                 {
-                    "name": "foo_link",
-                    "path": "/buckets/bucket1/foo_holder/foo1",
-                    "source": "test_io0.zarr"
+                    "name": "my_data",
+                    "path": "/buckets/bucket1/foo_holder/foo1/my_data",
+                    "source": "/Users/mavaylon/Research/NWB/hdmf-zarr/test_io0.zarr"
                 }
             ]
         },
+        "buckets/bucket2/foo_holder/foo2/.zgroup": {
+            "zarr_format": 2
+        },
         "links/.zgroup": {
             "zarr_format": 2
         }

diff --git a/test_io2.zarr/buckets/bucket2/.zattrs b/test_io2.zarr/buckets/bucket2/.zattrs
@@ -0,0 +1,5 @@
+{
+    "data_type": "FooBucket",
+    "namespace": "test_core",
+    "object_id": "7f8154fa-8bdb-407d-9173-3653cbb3229e"
+}
diff --git a/test_io2.zarr/buckets/bucket2/.zgroup b/test_io2.zarr/buckets/bucket2/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
diff --git a/test_io2.zarr/buckets/bucket2/foo_holder/.zgroup b/test_io2.zarr/buckets/bucket2/foo_holder/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
diff --git a/test_io2.zarr/buckets/bucket2/foo_holder/foo2/.zattrs b/test_io2.zarr/buckets/bucket2/foo_holder/foo2/.zattrs
@@ -0,0 +1,14 @@
+{
+    "attr1": "I am foo2",
+    "attr3": 3.14,
+    "data_type": "Foo",
+    "namespace": "test_core",
+    "object_id": "4bf361c1-b731-4f2c-8b53-22aab97d5276",
+    "zarr_link": [
+        {
+            "name": "my_data",
+            "path": "/buckets/bucket1/foo_holder/foo1/my_data",
+            "source": "/Users/mavaylon/Research/NWB/hdmf-zarr/test_io0.zarr"
+        }
+    ]
+}
diff --git a/test_io2.zarr/buckets/bucket2/foo_holder/foo2/.zgroup b/test_io2.zarr/buckets/bucket2/foo_holder/foo2/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
diff --git a/test_io2.zarr/links/.zattrs b/test_io2.zarr/links/.zattrs