some support for groups

test_io0.zarr/.zattrs

@@ -2,5 +2,5 @@
     ".specloc": "specifications",
     "data_type": "FooFile",
     "namespace": "test_core",
-    "object_id": "9b13a8b3-2851-451f-baf9-873182f8a674"
+    "object_id": "27d9b554-421a-4cb7-8c24-66b5747b86df"
 }

test_io0.zarr/.zmetadata

@@ -3,7 +3,7 @@
         ".zattrs": {
             "data_type": "FooFile",
             "namespace": "test_core",
-            "object_id": "9b13a8b3-2851-451f-baf9-873182f8a674"
+            "object_id": "27d9b554-421a-4cb7-8c24-66b5747b86df"
         },
         ".zgroup": {
             "zarr_format": 2
@@ -14,7 +14,7 @@
         "buckets/bucket1/.zattrs": {
             "data_type": "FooBucket",
             "namespace": "test_core",
-            "object_id": "67435668-7f5b-4c98-9200-65840eca9958"
+            "object_id": "464e00d7-11dd-4466-afda-def0b44bb2c9"
         },
         "buckets/bucket1/.zgroup": {
             "zarr_format": 2
@@ -27,7 +27,7 @@
             "attr3": 3.14,
             "data_type": "Foo",
             "namespace": "test_core",
-            "object_id": "a6d08cb5-1eee-437f-bdac-99dffb93ceea"
+            "object_id": "4ad02d31-07cf-4b31-ab8b-eecca3ffb26d"
         },
         "buckets/bucket1/foo_holder/foo1/.zgroup": {
             "zarr_format": 2
@@ -56,15 +56,6 @@
             "attr2": 17,
             "zarr_dtype": "int64"
         },
-        "links/.zattrs": {
-            "zarr_link": [
-                {
-                    "name": "foo_link",
-                    "path": "/buckets/bucket1/foo_holder/foo1",
-                    "source": "test_io0.zarr"
-                }
-            ]
-        },
         "links/.zgroup": {
             "zarr_format": 2
         }

test_io0.zarr/buckets/bucket1/.zattrs

@@ -1,5 +1,5 @@
 {
     "data_type": "FooBucket",
     "namespace": "test_core",
-    "object_id": "67435668-7f5b-4c98-9200-65840eca9958"
+    "object_id": "464e00d7-11dd-4466-afda-def0b44bb2c9"
 }

test_io0.zarr/buckets/bucket1/foo_holder/foo1/.zattrs

@@ -3,5 +3,5 @@
     "attr3": 3.14,
     "data_type": "Foo",
     "namespace": "test_core",
-    "object_id": "a6d08cb5-1eee-437f-bdac-99dffb93ceea"
+    "object_id": "4ad02d31-07cf-4b31-ab8b-eecca3ffb26d"
 }

test_io1.zarr/.zattrs

@@ -2,5 +2,5 @@
     ".specloc": "specifications",
     "data_type": "FooFile",
     "namespace": "test_core",
-    "object_id": "9b13a8b3-2851-451f-baf9-873182f8a674"
+    "object_id": "ac0cd188-78cd-4eeb-a437-52d5ba7062e3"
 }

test_io1.zarr/.zmetadata

@@ -3,59 +3,14 @@
         ".zattrs": {
             "data_type": "FooFile",
             "namespace": "test_core",
-            "object_id": "9b13a8b3-2851-451f-baf9-873182f8a674"
+            "object_id": "ac0cd188-78cd-4eeb-a437-52d5ba7062e3"
         },
         ".zgroup": {
             "zarr_format": 2
         },
         "buckets/.zgroup": {
             "zarr_format": 2
         },
-        "buckets/bucket1/.zattrs": {
-            "data_type": "FooBucket",
-            "namespace": "test_core",
-            "object_id": "67435668-7f5b-4c98-9200-65840eca9958"
-        },
-        "buckets/bucket1/.zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/bucket1/foo_holder/.zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/bucket1/foo_holder/foo1/.zattrs": {
-            "attr1": "I am foo1",
-            "attr3": 3.14,
-            "data_type": "Foo",
-            "namespace": "test_core",
-            "object_id": "a6d08cb5-1eee-437f-bdac-99dffb93ceea"
-        },
-        "buckets/bucket1/foo_holder/foo1/.zgroup": {
-            "zarr_format": 2
-        },
-        "buckets/bucket1/foo_holder/foo1/my_data/.zarray": {
-            "chunks": [
-                5
-            ],
-            "compressor": {
-                "blocksize": 0,
-                "clevel": 5,
-                "cname": "lz4",
-                "id": "blosc",
-                "shuffle": 1
-            },
-            "dtype": "<i8",
-            "fill_value": 0,
-            "filters": null,
-            "order": "C",
-            "shape": [
-                5
-            ],
-            "zarr_format": 2
-        },
-        "buckets/bucket1/foo_holder/foo1/my_data/.zattrs": {
-            "attr2": 17,
-            "zarr_dtype": "int64"
-        },
         "links/.zattrs": {
             "zarr_link": [
                 {

test_io1.zarr/specifications/test_core/0.1.0/namespace/.zarray

@@ -0,0 +1,30 @@
+{
+    "chunks": [
+        1
+    ],
+    "compressor": null,
+    "dtype": "|O",
+    "fill_value": 0,
+    "filters": [
+        {
+            "allow_nan": true,
+            "check_circular": true,
+            "encoding": "utf-8",
+            "ensure_ascii": true,
+            "id": "json2",
+            "indent": null,
+            "separators": [
+                ",",
+                ":"
+            ],
+            "skipkeys": false,
+            "sort_keys": true,
+            "strict": true
+        }
+    ],
+    "order": "C",
+    "shape": [
+        1
+    ],
+    "zarr_format": 2
+}

test_io1.zarr/specifications/test_core/0.1.0/namespace/.zattrs

@@ -0,0 +1,3 @@
+{
+    "zarr_dtype": "scalar"
+}

test_io1.zarr/specifications/test_core/0.1.0/namespace/0

@@ -0,0 +1 @@
+["{\"namespaces\":[{\"doc\":\"a test namespace\",\"schema\":[{\"source\":\"test\"}],\"name\":\"test_core\",\"version\":\"0.1.0\"}]}","|O",[1]]

test_io1.zarr/specifications/test_core/0.1.0/test/.zarray

@@ -0,0 +1,30 @@
+{
+    "chunks": [
+        1
+    ],
+    "compressor": null,
+    "dtype": "|O",
+    "fill_value": 0,
+    "filters": [
+        {
+            "allow_nan": true,
+            "check_circular": true,
+            "encoding": "utf-8",
+            "ensure_ascii": true,
+            "id": "json2",
+            "indent": null,
+            "separators": [
+                ",",
+                ":"
+            ],
+            "skipkeys": false,
+            "sort_keys": true,
+            "strict": true
+        }
+    ],
+    "order": "C",
+    "shape": [
+        1
+    ],
+    "zarr_format": 2
+}

test_io1.zarr/specifications/test_core/0.1.0/test/.zattrs

@@ -0,0 +1,3 @@
+{
+    "zarr_dtype": "scalar"
+}

test_io1.zarr/specifications/test_core/0.1.0/test/0

@@ -0,0 +1 @@
+["{\"groups\":[{\"datasets\":[{\"dtype\":\"int\",\"doc\":\"an example dataset\",\"name\":\"my_data\",\"attributes\":[{\"doc\":\"an example integer attribute\",\"name\":\"attr2\",\"dtype\":\"int\"}]}],\"doc\":\"A test group specification with a data type\",\"data_type_def\":\"Foo\",\"attributes\":[{\"doc\":\"an example string attribute\",\"name\":\"attr1\",\"dtype\":\"text\"},{\"doc\":\"an example float attribute\",\"name\":\"attr3\",\"dtype\":\"float\"}]},{\"groups\":[{\"groups\":[{\"doc\":\"the Foos in this bucket\",\"quantity\":\"*\",\"data_type_inc\":\"Foo\"}],\"doc\":\"A subgroup for Foos\",\"name\":\"foo_holder\"}],\"doc\":\"A test group specification for a data type containing data type\",\"data_type_def\":\"FooBucket\"},{\"groups\":[{\"groups\":[{\"doc\":\"One or more FooBuckets\",\"quantity\":\"*\",\"data_type_inc\":\"FooBucket\"}],\"doc\":\"Holds the FooBuckets\",\"name\":\"buckets\"},{\"links\":[{\"doc\":\"Foo link\",\"name\":\"foo_link\",\"target_type\":\"Foo\",\"quantity\":\"?\"}],\"doc\":\"Foo link group\",\"name\":\"links\"}],\"datasets\":[{\"dtype\":\"int\",\"doc\":\"Foo data\",\"name\":\"foofile_data\",\"quantity\":\"?\"}],\"doc\":\"A file of Foos contained in FooBuckets\",\"data_type_def\":\"FooFile\",\"attributes\":[{\"doc\":\"Foo ref attr\",\"name\":\"foo_ref_attr\",\"required\":false,\"dtype\":{\"target_type\":\"Foo\",\"reftype\":\"object\"}}]}]}","|O",[1]]

test_io2.zarr/.zattrs

@@ -2,5 +2,5 @@
     ".specloc": "specifications",
     "data_type": "FooFile",
     "namespace": "test_core",
-    "object_id": "6442cffd-1d1b-4015-b515-8069153279f8"
+    "object_id": "ac0cd188-78cd-4eeb-a437-52d5ba7062e3"
 }

test_io2.zarr/.zmetadata

@@ -3,7 +3,7 @@
         ".zattrs": {
             "data_type": "FooFile",
             "namespace": "test_core",
-            "object_id": "6442cffd-1d1b-4015-b515-8069153279f8"
+            "object_id": "ac0cd188-78cd-4eeb-a437-52d5ba7062e3"
         },
         ".zgroup": {
             "zarr_format": 2

tests/unit/base_tests_zarrio.py

@@ -1125,10 +1125,10 @@ def test_soft_link_group(self):
 
         with ZarrIO("test_io0.zarr", manager=get_foo_buildmanager(), mode='r') as read_io:
             with ZarrIO("test_io1.zarr", mode='w') as export_io:
-                export_io.export(src_io=read_io,
-                                 write_args=dict(link_data=False))
+                export_io.export(src_io=read_io)
         with ZarrIO("test_io1.zarr", manager=get_foo_buildmanager(), mode='r') as read_io:
             read_foofile2 = read_io.read()
+            # breakpoint()
             # make sure the linked group is within the same file
             self.assertEqual(read_foofile2.foo_link.container_source, "test_io1.zarr")
             # zarr_linkspec1 = zarr.open(self.store_path[0])['links'].attrs.asdict()['zarr_link'][0]
@@ -1164,7 +1164,7 @@ def test_external_link_group(self):
         with ZarrIO("test_io2.zarr", manager=get_foo_buildmanager(), mode='r') as read_io:
             read_foofile2 = read_io.read()
             # make sure the linked group is read from the first file
-            self.assertEqual(read_foofile2.foo_link.container_source, '/Users/mavaylon/Research/NWB/hdmf-zarr/test_io0.zarr')
+            self.assertEqual(read_foofile2.foo_link.container_source, 'test_io0.zarr')
 
 
     def test_external_link_dataset(self):