From 9fbaa538c4daa07a083481573c732a477f2678d9 Mon Sep 17 00:00:00 2001
From: mavaylon1 <mavaylon1@berkeley.edu>
Date: Thu, 17 Oct 2024 08:09:35 -0700
Subject: [PATCH] more tests fixed

---
 file1.zarr/.zattrs                            |   6 +
 file1.zarr/.zgroup                            |   3 +
 file1.zarr/.zmetadata                         |  64 ++++++++++
 file1.zarr/buckets/.zgroup                    |   3 +
 file1.zarr/buckets/bucket1/.zattrs            |   5 +
 file1.zarr/buckets/bucket1/.zgroup            |   3 +
 file1.zarr/buckets/bucket1/foo_holder/.zgroup |   3 +
 .../buckets/bucket1/foo_holder/foo1/.zattrs   |   7 ++
 .../buckets/bucket1/foo_holder/foo1/.zgroup   |   3 +
 .../bucket1/foo_holder/foo1/my_data/.zarray   |  20 +++
 .../bucket1/foo_holder/foo1/my_data/.zattrs   |   4 +
 .../buckets/bucket1/foo_holder/foo1/my_data/0 | Bin 0 -> 56 bytes
 file1.zarr/links/.zgroup                      |   3 +
 file1.zarr/specifications/.zgroup             |   3 +
 file1.zarr/specifications/test_core/.zgroup   |   3 +
 .../specifications/test_core/0.1.0/.zgroup    |   3 +
 .../test_core/0.1.0/namespace/.zarray         |  30 +++++
 .../test_core/0.1.0/namespace/.zattrs         |   3 +
 .../test_core/0.1.0/namespace/0               |   1 +
 .../test_core/0.1.0/test/.zarray              |  30 +++++
 .../test_core/0.1.0/test/.zattrs              |   3 +
 .../specifications/test_core/0.1.0/test/0     |   1 +
 file2.zarr/.zattrs                            |  22 ++++
 file2.zarr/.zgroup                            |   3 +
 file2.zarr/.zmetadata                         | 117 ++++++++++++++++++
 file2.zarr/buckets/.zgroup                    |   3 +
 file2.zarr/buckets/bucket1/.zattrs            |   5 +
 file2.zarr/buckets/bucket1/.zgroup            |   3 +
 file2.zarr/buckets/bucket1/foo_holder/.zgroup |   3 +
 .../buckets/bucket1/foo_holder/foo1/.zattrs   |   7 ++
 .../buckets/bucket1/foo_holder/foo1/.zgroup   |   3 +
 .../bucket1/foo_holder/foo1/my_data/.zarray   |  20 +++
 .../bucket1/foo_holder/foo1/my_data/.zattrs   |   4 +
 .../buckets/bucket1/foo_holder/foo1/my_data/0 | Bin 0 -> 56 bytes
 file2.zarr/buckets/bucket2/.zattrs            |   5 +
 file2.zarr/buckets/bucket2/.zgroup            |   3 +
 file2.zarr/buckets/bucket2/foo_holder/.zgroup |   3 +
 .../buckets/bucket2/foo_holder/foo2/.zattrs   |  14 +++
 .../buckets/bucket2/foo_holder/foo2/.zgroup   |   3 +
 file2.zarr/links/.zattrs                      |   9 ++
 file2.zarr/links/.zgroup                      |   3 +
 file2.zarr/specifications/.zgroup             |   3 +
 src/hdmf_zarr/backend.py                      |  18 +--
 test_io0.zarr/.zattrs                         |   2 +-
 test_io0.zarr/.zmetadata                      |   6 +-
 test_io0.zarr/buckets/bucket1/.zattrs         |   2 +-
 .../buckets/bucket1/foo_holder/foo1/.zattrs   |   2 +-
 test_io1.zarr/.zattrs                         |   2 +-
 test_io1.zarr/.zmetadata                      |   6 +-
 test_io1.zarr/buckets/bucket2/.zattrs         |   2 +-
 .../buckets/bucket2/foo_holder/foo2/.zattrs   |   2 +-
 test_io2.zarr/.zattrs                         |   2 +-
 test_io2.zarr/.zmetadata                      |   6 +-
 test_io2.zarr/buckets/bucket2/.zattrs         |   2 +-
 .../buckets/bucket2/foo_holder/foo2/.zattrs   |   2 +-
 tests/unit/base_tests_zarrio.py               |   8 +-
 56 files changed, 467 insertions(+), 29 deletions(-)
 create mode 100644 file1.zarr/.zattrs
 create mode 100644 file1.zarr/.zgroup
 create mode 100644 file1.zarr/.zmetadata
 create mode 100644 file1.zarr/buckets/.zgroup
 create mode 100644 file1.zarr/buckets/bucket1/.zattrs
 create mode 100644 file1.zarr/buckets/bucket1/.zgroup
 create mode 100644 file1.zarr/buckets/bucket1/foo_holder/.zgroup
 create mode 100644 file1.zarr/buckets/bucket1/foo_holder/foo1/.zattrs
 create mode 100644 file1.zarr/buckets/bucket1/foo_holder/foo1/.zgroup
 create mode 100644 file1.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zarray
 create mode 100644 file1.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zattrs
 create mode 100644 file1.zarr/buckets/bucket1/foo_holder/foo1/my_data/0
 create mode 100644 file1.zarr/links/.zgroup
 create mode 100644 file1.zarr/specifications/.zgroup
 create mode 100644 file1.zarr/specifications/test_core/.zgroup
 create mode 100644 file1.zarr/specifications/test_core/0.1.0/.zgroup
 create mode 100644 file1.zarr/specifications/test_core/0.1.0/namespace/.zarray
 create mode 100644 file1.zarr/specifications/test_core/0.1.0/namespace/.zattrs
 create mode 100644 file1.zarr/specifications/test_core/0.1.0/namespace/0
 create mode 100644 file1.zarr/specifications/test_core/0.1.0/test/.zarray
 create mode 100644 file1.zarr/specifications/test_core/0.1.0/test/.zattrs
 create mode 100644 file1.zarr/specifications/test_core/0.1.0/test/0
 create mode 100644 file2.zarr/.zattrs
 create mode 100644 file2.zarr/.zgroup
 create mode 100644 file2.zarr/.zmetadata
 create mode 100644 file2.zarr/buckets/.zgroup
 create mode 100644 file2.zarr/buckets/bucket1/.zattrs
 create mode 100644 file2.zarr/buckets/bucket1/.zgroup
 create mode 100644 file2.zarr/buckets/bucket1/foo_holder/.zgroup
 create mode 100644 file2.zarr/buckets/bucket1/foo_holder/foo1/.zattrs
 create mode 100644 file2.zarr/buckets/bucket1/foo_holder/foo1/.zgroup
 create mode 100644 file2.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zarray
 create mode 100644 file2.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zattrs
 create mode 100644 file2.zarr/buckets/bucket1/foo_holder/foo1/my_data/0
 create mode 100644 file2.zarr/buckets/bucket2/.zattrs
 create mode 100644 file2.zarr/buckets/bucket2/.zgroup
 create mode 100644 file2.zarr/buckets/bucket2/foo_holder/.zgroup
 create mode 100644 file2.zarr/buckets/bucket2/foo_holder/foo2/.zattrs
 create mode 100644 file2.zarr/buckets/bucket2/foo_holder/foo2/.zgroup
 create mode 100644 file2.zarr/links/.zattrs
 create mode 100644 file2.zarr/links/.zgroup
 create mode 100644 file2.zarr/specifications/.zgroup

diff --git a/file1.zarr/.zattrs b/file1.zarr/.zattrs
new file mode 100644
index 00000000..55b5cdc4
--- /dev/null
+++ b/file1.zarr/.zattrs
@@ -0,0 +1,6 @@
+{
+    ".specloc": "specifications",
+    "data_type": "FooFile",
+    "namespace": "test_core",
+    "object_id": "660f1c92-d141-40d2-995f-2bb46c87c017"
+}
\ No newline at end of file
diff --git a/file1.zarr/.zgroup b/file1.zarr/.zgroup
new file mode 100644
index 00000000..3b7daf22
--- /dev/null
+++ b/file1.zarr/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/file1.zarr/.zmetadata b/file1.zarr/.zmetadata
new file mode 100644
index 00000000..8322dda9
--- /dev/null
+++ b/file1.zarr/.zmetadata
@@ -0,0 +1,64 @@
+{
+    "metadata": {
+        ".zattrs": {
+            "data_type": "FooFile",
+            "namespace": "test_core",
+            "object_id": "660f1c92-d141-40d2-995f-2bb46c87c017"
+        },
+        ".zgroup": {
+            "zarr_format": 2
+        },
+        "buckets/.zgroup": {
+            "zarr_format": 2
+        },
+        "buckets/bucket1/.zattrs": {
+            "data_type": "FooBucket",
+            "namespace": "test_core",
+            "object_id": "7c5adf36-8f84-4f63-a948-75f18dade974"
+        },
+        "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": "9b3a0668-f73c-4a00-b446-38888c16e551"
+        },
+        "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/.zgroup": {
+            "zarr_format": 2
+        }
+    },
+    "zarr_consolidated_format": 1
+}
\ No newline at end of file
diff --git a/file1.zarr/buckets/.zgroup b/file1.zarr/buckets/.zgroup
new file mode 100644
index 00000000..3b7daf22
--- /dev/null
+++ b/file1.zarr/buckets/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/file1.zarr/buckets/bucket1/.zattrs b/file1.zarr/buckets/bucket1/.zattrs
new file mode 100644
index 00000000..e6bcc4fb
--- /dev/null
+++ b/file1.zarr/buckets/bucket1/.zattrs
@@ -0,0 +1,5 @@
+{
+    "data_type": "FooBucket",
+    "namespace": "test_core",
+    "object_id": "7c5adf36-8f84-4f63-a948-75f18dade974"
+}
\ No newline at end of file
diff --git a/file1.zarr/buckets/bucket1/.zgroup b/file1.zarr/buckets/bucket1/.zgroup
new file mode 100644
index 00000000..3b7daf22
--- /dev/null
+++ b/file1.zarr/buckets/bucket1/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/file1.zarr/buckets/bucket1/foo_holder/.zgroup b/file1.zarr/buckets/bucket1/foo_holder/.zgroup
new file mode 100644
index 00000000..3b7daf22
--- /dev/null
+++ b/file1.zarr/buckets/bucket1/foo_holder/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/file1.zarr/buckets/bucket1/foo_holder/foo1/.zattrs b/file1.zarr/buckets/bucket1/foo_holder/foo1/.zattrs
new file mode 100644
index 00000000..5ef83bbf
--- /dev/null
+++ b/file1.zarr/buckets/bucket1/foo_holder/foo1/.zattrs
@@ -0,0 +1,7 @@
+{
+    "attr1": "I am foo1",
+    "attr3": 3.14,
+    "data_type": "Foo",
+    "namespace": "test_core",
+    "object_id": "9b3a0668-f73c-4a00-b446-38888c16e551"
+}
\ No newline at end of file
diff --git a/file1.zarr/buckets/bucket1/foo_holder/foo1/.zgroup b/file1.zarr/buckets/bucket1/foo_holder/foo1/.zgroup
new file mode 100644
index 00000000..3b7daf22
--- /dev/null
+++ b/file1.zarr/buckets/bucket1/foo_holder/foo1/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/file1.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zarray b/file1.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zarray
new file mode 100644
index 00000000..2da665c3
--- /dev/null
+++ b/file1.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zarray
@@ -0,0 +1,20 @@
+{
+    "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
+}
\ No newline at end of file
diff --git a/file1.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zattrs b/file1.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zattrs
new file mode 100644
index 00000000..2ad81eb6
--- /dev/null
+++ b/file1.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zattrs
@@ -0,0 +1,4 @@
+{
+    "attr2": 17,
+    "zarr_dtype": "int64"
+}
\ No newline at end of file
diff --git a/file1.zarr/buckets/bucket1/foo_holder/foo1/my_data/0 b/file1.zarr/buckets/bucket1/foo_holder/foo1/my_data/0
new file mode 100644
index 0000000000000000000000000000000000000000..b049d36c50d8e8b37c8d7cd1642b52a58a34cfde
GIT binary patch
literal 56
icmZQ#H0ID?U|;}Y3m|3$Vh~`0Pz=mangvR;LTLaep#atZ

literal 0
HcmV?d00001

diff --git a/file1.zarr/links/.zgroup b/file1.zarr/links/.zgroup
new file mode 100644
index 00000000..3b7daf22
--- /dev/null
+++ b/file1.zarr/links/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/file1.zarr/specifications/.zgroup b/file1.zarr/specifications/.zgroup
new file mode 100644
index 00000000..3b7daf22
--- /dev/null
+++ b/file1.zarr/specifications/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/file1.zarr/specifications/test_core/.zgroup b/file1.zarr/specifications/test_core/.zgroup
new file mode 100644
index 00000000..3b7daf22
--- /dev/null
+++ b/file1.zarr/specifications/test_core/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/file1.zarr/specifications/test_core/0.1.0/.zgroup b/file1.zarr/specifications/test_core/0.1.0/.zgroup
new file mode 100644
index 00000000..3b7daf22
--- /dev/null
+++ b/file1.zarr/specifications/test_core/0.1.0/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/file1.zarr/specifications/test_core/0.1.0/namespace/.zarray b/file1.zarr/specifications/test_core/0.1.0/namespace/.zarray
new file mode 100644
index 00000000..7d100603
--- /dev/null
+++ b/file1.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
+}
\ No newline at end of file
diff --git a/file1.zarr/specifications/test_core/0.1.0/namespace/.zattrs b/file1.zarr/specifications/test_core/0.1.0/namespace/.zattrs
new file mode 100644
index 00000000..2592fe05
--- /dev/null
+++ b/file1.zarr/specifications/test_core/0.1.0/namespace/.zattrs
@@ -0,0 +1,3 @@
+{
+    "zarr_dtype": "scalar"
+}
\ No newline at end of file
diff --git a/file1.zarr/specifications/test_core/0.1.0/namespace/0 b/file1.zarr/specifications/test_core/0.1.0/namespace/0
new file mode 100644
index 00000000..357971a8
--- /dev/null
+++ b/file1.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]]
\ No newline at end of file
diff --git a/file1.zarr/specifications/test_core/0.1.0/test/.zarray b/file1.zarr/specifications/test_core/0.1.0/test/.zarray
new file mode 100644
index 00000000..7d100603
--- /dev/null
+++ b/file1.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
+}
\ No newline at end of file
diff --git a/file1.zarr/specifications/test_core/0.1.0/test/.zattrs b/file1.zarr/specifications/test_core/0.1.0/test/.zattrs
new file mode 100644
index 00000000..2592fe05
--- /dev/null
+++ b/file1.zarr/specifications/test_core/0.1.0/test/.zattrs
@@ -0,0 +1,3 @@
+{
+    "zarr_dtype": "scalar"
+}
\ No newline at end of file
diff --git a/file1.zarr/specifications/test_core/0.1.0/test/0 b/file1.zarr/specifications/test_core/0.1.0/test/0
new file mode 100644
index 00000000..75e3042c
--- /dev/null
+++ b/file1.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]]
\ No newline at end of file
diff --git a/file2.zarr/.zattrs b/file2.zarr/.zattrs
new file mode 100644
index 00000000..757048d7
--- /dev/null
+++ b/file2.zarr/.zattrs
@@ -0,0 +1,22 @@
+{
+    ".specloc": "specifications",
+    "data_type": "FooFile",
+    "foo_ref_attr": {
+        "value": {
+            "object_id": "2a36d892-ab46-4b0c-bd6b-31ce6533d071",
+            "path": "/buckets/bucket2/foo_holder/foo2",
+            "source": "file2.zarr",
+            "source_object_id": "660f1c92-d141-40d2-995f-2bb46c87c017"
+        },
+        "zarr_dtype": "object"
+    },
+    "namespace": "test_core",
+    "object_id": "660f1c92-d141-40d2-995f-2bb46c87c017",
+    "zarr_link": [
+        {
+            "name": "foofile_data",
+            "path": "/buckets/bucket1/foo_holder/foo1/my_data",
+            "source": "file2.zarr"
+        }
+    ]
+}
\ No newline at end of file
diff --git a/file2.zarr/.zgroup b/file2.zarr/.zgroup
new file mode 100644
index 00000000..3b7daf22
--- /dev/null
+++ b/file2.zarr/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/file2.zarr/.zmetadata b/file2.zarr/.zmetadata
new file mode 100644
index 00000000..b1c6c142
--- /dev/null
+++ b/file2.zarr/.zmetadata
@@ -0,0 +1,117 @@
+{
+    "metadata": {
+        ".zattrs": {
+            "data_type": "FooFile",
+            "foo_ref_attr": {
+                "value": {
+                    "object_id": "2a36d892-ab46-4b0c-bd6b-31ce6533d071",
+                    "path": "/buckets/bucket2/foo_holder/foo2",
+                    "source": "file2.zarr",
+                    "source_object_id": "660f1c92-d141-40d2-995f-2bb46c87c017"
+                },
+                "zarr_dtype": "object"
+            },
+            "namespace": "test_core",
+            "object_id": "660f1c92-d141-40d2-995f-2bb46c87c017",
+            "zarr_link": [
+                {
+                    "name": "foofile_data",
+                    "path": "/buckets/bucket1/foo_holder/foo1/my_data",
+                    "source": "file2.zarr"
+                }
+            ]
+        },
+        ".zgroup": {
+            "zarr_format": 2
+        },
+        "buckets/.zgroup": {
+            "zarr_format": 2
+        },
+        "buckets/bucket1/.zattrs": {
+            "data_type": "FooBucket",
+            "namespace": "test_core",
+            "object_id": "7c5adf36-8f84-4f63-a948-75f18dade974"
+        },
+        "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": "9b3a0668-f73c-4a00-b446-38888c16e551"
+        },
+        "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"
+        },
+        "buckets/bucket2/.zattrs": {
+            "data_type": "FooBucket",
+            "namespace": "test_core",
+            "object_id": "e60cc181-8b03-43d7-9c63-96a7c2b672e6"
+        },
+        "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": "2a36d892-ab46-4b0c-bd6b-31ce6533d071",
+            "zarr_link": [
+                {
+                    "name": "my_data",
+                    "path": "/buckets/bucket1/foo_holder/foo1/my_data",
+                    "source": "file2.zarr"
+                }
+            ]
+        },
+        "buckets/bucket2/foo_holder/foo2/.zgroup": {
+            "zarr_format": 2
+        },
+        "links/.zattrs": {
+            "zarr_link": [
+                {
+                    "name": "foo_link",
+                    "path": "/buckets/bucket2/foo_holder/foo2",
+                    "source": "file2.zarr"
+                }
+            ]
+        },
+        "links/.zgroup": {
+            "zarr_format": 2
+        }
+    },
+    "zarr_consolidated_format": 1
+}
\ No newline at end of file
diff --git a/file2.zarr/buckets/.zgroup b/file2.zarr/buckets/.zgroup
new file mode 100644
index 00000000..3b7daf22
--- /dev/null
+++ b/file2.zarr/buckets/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/file2.zarr/buckets/bucket1/.zattrs b/file2.zarr/buckets/bucket1/.zattrs
new file mode 100644
index 00000000..e6bcc4fb
--- /dev/null
+++ b/file2.zarr/buckets/bucket1/.zattrs
@@ -0,0 +1,5 @@
+{
+    "data_type": "FooBucket",
+    "namespace": "test_core",
+    "object_id": "7c5adf36-8f84-4f63-a948-75f18dade974"
+}
\ No newline at end of file
diff --git a/file2.zarr/buckets/bucket1/.zgroup b/file2.zarr/buckets/bucket1/.zgroup
new file mode 100644
index 00000000..3b7daf22
--- /dev/null
+++ b/file2.zarr/buckets/bucket1/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/file2.zarr/buckets/bucket1/foo_holder/.zgroup b/file2.zarr/buckets/bucket1/foo_holder/.zgroup
new file mode 100644
index 00000000..3b7daf22
--- /dev/null
+++ b/file2.zarr/buckets/bucket1/foo_holder/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/file2.zarr/buckets/bucket1/foo_holder/foo1/.zattrs b/file2.zarr/buckets/bucket1/foo_holder/foo1/.zattrs
new file mode 100644
index 00000000..5ef83bbf
--- /dev/null
+++ b/file2.zarr/buckets/bucket1/foo_holder/foo1/.zattrs
@@ -0,0 +1,7 @@
+{
+    "attr1": "I am foo1",
+    "attr3": 3.14,
+    "data_type": "Foo",
+    "namespace": "test_core",
+    "object_id": "9b3a0668-f73c-4a00-b446-38888c16e551"
+}
\ No newline at end of file
diff --git a/file2.zarr/buckets/bucket1/foo_holder/foo1/.zgroup b/file2.zarr/buckets/bucket1/foo_holder/foo1/.zgroup
new file mode 100644
index 00000000..3b7daf22
--- /dev/null
+++ b/file2.zarr/buckets/bucket1/foo_holder/foo1/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/file2.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zarray b/file2.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zarray
new file mode 100644
index 00000000..2da665c3
--- /dev/null
+++ b/file2.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zarray
@@ -0,0 +1,20 @@
+{
+    "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
+}
\ No newline at end of file
diff --git a/file2.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zattrs b/file2.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zattrs
new file mode 100644
index 00000000..2ad81eb6
--- /dev/null
+++ b/file2.zarr/buckets/bucket1/foo_holder/foo1/my_data/.zattrs
@@ -0,0 +1,4 @@
+{
+    "attr2": 17,
+    "zarr_dtype": "int64"
+}
\ No newline at end of file
diff --git a/file2.zarr/buckets/bucket1/foo_holder/foo1/my_data/0 b/file2.zarr/buckets/bucket1/foo_holder/foo1/my_data/0
new file mode 100644
index 0000000000000000000000000000000000000000..b049d36c50d8e8b37c8d7cd1642b52a58a34cfde
GIT binary patch
literal 56
icmZQ#H0ID?U|;}Y3m|3$Vh~`0Pz=mangvR;LTLaep#atZ

literal 0
HcmV?d00001

diff --git a/file2.zarr/buckets/bucket2/.zattrs b/file2.zarr/buckets/bucket2/.zattrs
new file mode 100644
index 00000000..0dfbf840
--- /dev/null
+++ b/file2.zarr/buckets/bucket2/.zattrs
@@ -0,0 +1,5 @@
+{
+    "data_type": "FooBucket",
+    "namespace": "test_core",
+    "object_id": "e60cc181-8b03-43d7-9c63-96a7c2b672e6"
+}
\ No newline at end of file
diff --git a/file2.zarr/buckets/bucket2/.zgroup b/file2.zarr/buckets/bucket2/.zgroup
new file mode 100644
index 00000000..3b7daf22
--- /dev/null
+++ b/file2.zarr/buckets/bucket2/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/file2.zarr/buckets/bucket2/foo_holder/.zgroup b/file2.zarr/buckets/bucket2/foo_holder/.zgroup
new file mode 100644
index 00000000..3b7daf22
--- /dev/null
+++ b/file2.zarr/buckets/bucket2/foo_holder/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/file2.zarr/buckets/bucket2/foo_holder/foo2/.zattrs b/file2.zarr/buckets/bucket2/foo_holder/foo2/.zattrs
new file mode 100644
index 00000000..f45aeaf2
--- /dev/null
+++ b/file2.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": "2a36d892-ab46-4b0c-bd6b-31ce6533d071",
+    "zarr_link": [
+        {
+            "name": "my_data",
+            "path": "/buckets/bucket1/foo_holder/foo1/my_data",
+            "source": "file2.zarr"
+        }
+    ]
+}
\ No newline at end of file
diff --git a/file2.zarr/buckets/bucket2/foo_holder/foo2/.zgroup b/file2.zarr/buckets/bucket2/foo_holder/foo2/.zgroup
new file mode 100644
index 00000000..3b7daf22
--- /dev/null
+++ b/file2.zarr/buckets/bucket2/foo_holder/foo2/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/file2.zarr/links/.zattrs b/file2.zarr/links/.zattrs
new file mode 100644
index 00000000..768e3287
--- /dev/null
+++ b/file2.zarr/links/.zattrs
@@ -0,0 +1,9 @@
+{
+    "zarr_link": [
+        {
+            "name": "foo_link",
+            "path": "/buckets/bucket2/foo_holder/foo2",
+            "source": "file2.zarr"
+        }
+    ]
+}
\ No newline at end of file
diff --git a/file2.zarr/links/.zgroup b/file2.zarr/links/.zgroup
new file mode 100644
index 00000000..3b7daf22
--- /dev/null
+++ b/file2.zarr/links/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/file2.zarr/specifications/.zgroup b/file2.zarr/specifications/.zgroup
new file mode 100644
index 00000000..3b7daf22
--- /dev/null
+++ b/file2.zarr/specifications/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/src/hdmf_zarr/backend.py b/src/hdmf_zarr/backend.py
index 0ba0eee0..669246b3 100644
--- a/src/hdmf_zarr/backend.py
+++ b/src/hdmf_zarr/backend.py
@@ -605,16 +605,19 @@ def write_attributes(self, **kwargs):
                         raise TypeError(str(e) + " type=" + str(type(value)) + "  data=" + str(value)) from e
             # Case 2: References
             elif isinstance(value, (Container, Builder, ReferenceBuilder)):
-                # TODO: Region References are not yet supported
-                # if isinstance(value, RegionBuilder):
-                #     type_str = 'region'
-                #     refs = self._create_ref(value.builder)
                 if isinstance(value, (ReferenceBuilder, Container, Builder)):
                     type_str = 'object'
-                    if isinstance(value, Builder):
-                        refs = self._create_ref(value, export_source)
+                    obj_filename = self.__get_store_path(obj.store)
+                    if obj_filename != export_source:
+                        if not isinstance(value, Builder):
+                            value = value.builder
+                        if value.source in (obj_filename, export_source):
+                            source = obj_filename
+                        else:
+                            source = None
                     else:
-                        refs = self._create_ref(value.builder, export_source)
+                        source = export_source
+                    refs = self._create_ref(value, source)
                 tmp = {'zarr_dtype': type_str, 'value': refs}
                 obj.attrs[key] = tmp
             # Case 3: Scalar attributes
@@ -752,6 +755,7 @@ def resolve_ref(self, zarr_ref):
             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
diff --git a/test_io0.zarr/.zattrs b/test_io0.zarr/.zattrs
index da00828f..5886527c 100644
--- a/test_io0.zarr/.zattrs
+++ b/test_io0.zarr/.zattrs
@@ -2,5 +2,5 @@
     ".specloc": "specifications",
     "data_type": "FooFile",
     "namespace": "test_core",
-    "object_id": "20283a8a-00e6-414a-8dd4-4125364c03a5"
+    "object_id": "0b75428d-4633-4b56-bb99-181980f78a36"
 }
\ No newline at end of file
diff --git a/test_io0.zarr/.zmetadata b/test_io0.zarr/.zmetadata
index 98af9637..7db53824 100644
--- a/test_io0.zarr/.zmetadata
+++ b/test_io0.zarr/.zmetadata
@@ -3,7 +3,7 @@
         ".zattrs": {
             "data_type": "FooFile",
             "namespace": "test_core",
-            "object_id": "20283a8a-00e6-414a-8dd4-4125364c03a5"
+            "object_id": "0b75428d-4633-4b56-bb99-181980f78a36"
         },
         ".zgroup": {
             "zarr_format": 2
@@ -14,7 +14,7 @@
         "buckets/bucket1/.zattrs": {
             "data_type": "FooBucket",
             "namespace": "test_core",
-            "object_id": "732346eb-b4a1-4eb6-aee1-2d64cfe8c165"
+            "object_id": "f772256b-00ee-4b8d-8939-2c143b31c6d9"
         },
         "buckets/bucket1/.zgroup": {
             "zarr_format": 2
@@ -27,7 +27,7 @@
             "attr3": 3.14,
             "data_type": "Foo",
             "namespace": "test_core",
-            "object_id": "7d47b7b1-ab86-462d-a8fc-0ae0fbf37315"
+            "object_id": "294d04fc-ba6b-49c2-8718-4e26a590932d"
         },
         "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
index 939721d3..88f4e99a 100644
--- 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": "732346eb-b4a1-4eb6-aee1-2d64cfe8c165"
+    "object_id": "f772256b-00ee-4b8d-8939-2c143b31c6d9"
 }
\ No newline at end of file
diff --git a/test_io0.zarr/buckets/bucket1/foo_holder/foo1/.zattrs b/test_io0.zarr/buckets/bucket1/foo_holder/foo1/.zattrs
index 931f98ac..625a99b6 100644
--- 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": "7d47b7b1-ab86-462d-a8fc-0ae0fbf37315"
+    "object_id": "294d04fc-ba6b-49c2-8718-4e26a590932d"
 }
\ No newline at end of file
diff --git a/test_io1.zarr/.zattrs b/test_io1.zarr/.zattrs
index d06ff75d..0fe40a70 100644
--- a/test_io1.zarr/.zattrs
+++ b/test_io1.zarr/.zattrs
@@ -2,7 +2,7 @@
     ".specloc": "specifications",
     "data_type": "FooFile",
     "namespace": "test_core",
-    "object_id": "2ad0d2b0-dd51-4c5e-84d3-e561330a4f6f",
+    "object_id": "c29b1609-23b6-4f0e-9ced-73380f4e84f5",
     "zarr_link": [
         {
             "name": "foofile_data",
diff --git a/test_io1.zarr/.zmetadata b/test_io1.zarr/.zmetadata
index c91c63fb..4e95d546 100644
--- a/test_io1.zarr/.zmetadata
+++ b/test_io1.zarr/.zmetadata
@@ -3,7 +3,7 @@
         ".zattrs": {
             "data_type": "FooFile",
             "namespace": "test_core",
-            "object_id": "2ad0d2b0-dd51-4c5e-84d3-e561330a4f6f",
+            "object_id": "c29b1609-23b6-4f0e-9ced-73380f4e84f5",
             "zarr_link": [
                 {
                     "name": "foofile_data",
@@ -21,7 +21,7 @@
         "buckets/bucket2/.zattrs": {
             "data_type": "FooBucket",
             "namespace": "test_core",
-            "object_id": "9fd11ffb-4d93-40bf-9a0e-12c1686a1a79"
+            "object_id": "d2a4ea0c-4f10-4034-8b4d-9256bbc504fe"
         },
         "buckets/bucket2/.zgroup": {
             "zarr_format": 2
@@ -34,7 +34,7 @@
             "attr3": 3.14,
             "data_type": "Foo",
             "namespace": "test_core",
-            "object_id": "432c2318-91c6-437e-81c1-e97ceecb0e18",
+            "object_id": "0bca54c6-cc60-4039-b110-544d3a106a9f",
             "zarr_link": [
                 {
                     "name": "my_data",
diff --git a/test_io1.zarr/buckets/bucket2/.zattrs b/test_io1.zarr/buckets/bucket2/.zattrs
index 39308ae4..2027080e 100644
--- a/test_io1.zarr/buckets/bucket2/.zattrs
+++ b/test_io1.zarr/buckets/bucket2/.zattrs
@@ -1,5 +1,5 @@
 {
     "data_type": "FooBucket",
     "namespace": "test_core",
-    "object_id": "9fd11ffb-4d93-40bf-9a0e-12c1686a1a79"
+    "object_id": "d2a4ea0c-4f10-4034-8b4d-9256bbc504fe"
 }
\ No newline at end of file
diff --git a/test_io1.zarr/buckets/bucket2/foo_holder/foo2/.zattrs b/test_io1.zarr/buckets/bucket2/foo_holder/foo2/.zattrs
index 3881e64f..47066196 100644
--- a/test_io1.zarr/buckets/bucket2/foo_holder/foo2/.zattrs
+++ b/test_io1.zarr/buckets/bucket2/foo_holder/foo2/.zattrs
@@ -3,7 +3,7 @@
     "attr3": 3.14,
     "data_type": "Foo",
     "namespace": "test_core",
-    "object_id": "432c2318-91c6-437e-81c1-e97ceecb0e18",
+    "object_id": "0bca54c6-cc60-4039-b110-544d3a106a9f",
     "zarr_link": [
         {
             "name": "my_data",
diff --git a/test_io2.zarr/.zattrs b/test_io2.zarr/.zattrs
index d06ff75d..0fe40a70 100644
--- a/test_io2.zarr/.zattrs
+++ b/test_io2.zarr/.zattrs
@@ -2,7 +2,7 @@
     ".specloc": "specifications",
     "data_type": "FooFile",
     "namespace": "test_core",
-    "object_id": "2ad0d2b0-dd51-4c5e-84d3-e561330a4f6f",
+    "object_id": "c29b1609-23b6-4f0e-9ced-73380f4e84f5",
     "zarr_link": [
         {
             "name": "foofile_data",
diff --git a/test_io2.zarr/.zmetadata b/test_io2.zarr/.zmetadata
index dc3fcbb3..f2f4e55a 100644
--- a/test_io2.zarr/.zmetadata
+++ b/test_io2.zarr/.zmetadata
@@ -3,7 +3,7 @@
         ".zattrs": {
             "data_type": "FooFile",
             "namespace": "test_core",
-            "object_id": "2ad0d2b0-dd51-4c5e-84d3-e561330a4f6f",
+            "object_id": "c29b1609-23b6-4f0e-9ced-73380f4e84f5",
             "zarr_link": [
                 {
                     "name": "foofile_data",
@@ -21,7 +21,7 @@
         "buckets/bucket2/.zattrs": {
             "data_type": "FooBucket",
             "namespace": "test_core",
-            "object_id": "7f8154fa-8bdb-407d-9173-3653cbb3229e"
+            "object_id": "69e2231d-601a-4163-a562-10b010583296"
         },
         "buckets/bucket2/.zgroup": {
             "zarr_format": 2
@@ -34,7 +34,7 @@
             "attr3": 3.14,
             "data_type": "Foo",
             "namespace": "test_core",
-            "object_id": "4bf361c1-b731-4f2c-8b53-22aab97d5276",
+            "object_id": "694cd193-1d6c-4244-a15b-b87c544c3a2d",
             "zarr_link": [
                 {
                     "name": "my_data",
diff --git a/test_io2.zarr/buckets/bucket2/.zattrs b/test_io2.zarr/buckets/bucket2/.zattrs
index bc0c4d6e..c36263ae 100644
--- a/test_io2.zarr/buckets/bucket2/.zattrs
+++ b/test_io2.zarr/buckets/bucket2/.zattrs
@@ -1,5 +1,5 @@
 {
     "data_type": "FooBucket",
     "namespace": "test_core",
-    "object_id": "7f8154fa-8bdb-407d-9173-3653cbb3229e"
+    "object_id": "69e2231d-601a-4163-a562-10b010583296"
 }
\ No newline at end of file
diff --git a/test_io2.zarr/buckets/bucket2/foo_holder/foo2/.zattrs b/test_io2.zarr/buckets/bucket2/foo_holder/foo2/.zattrs
index e4eef88b..b089b688 100644
--- a/test_io2.zarr/buckets/bucket2/foo_holder/foo2/.zattrs
+++ b/test_io2.zarr/buckets/bucket2/foo_holder/foo2/.zattrs
@@ -3,7 +3,7 @@
     "attr3": 3.14,
     "data_type": "Foo",
     "namespace": "test_core",
-    "object_id": "4bf361c1-b731-4f2c-8b53-22aab97d5276",
+    "object_id": "694cd193-1d6c-4244-a15b-b87c544c3a2d",
     "zarr_link": [
         {
             "name": "my_data",
diff --git a/tests/unit/base_tests_zarrio.py b/tests/unit/base_tests_zarrio.py
index d716939b..60827ca6 100644
--- a/tests/unit/base_tests_zarrio.py
+++ b/tests/unit/base_tests_zarrio.py
@@ -1331,10 +1331,10 @@ def test_append_data_export(self):
         foobucket = FooBucket('bucket1', [foo1])
         foofile = FooFile(buckets=[foobucket])
 
-        with ZarrIO(self.store_path[0], manager=get_foo_buildmanager(), mode='w') as write_io:
+        with ZarrIO("file1.zarr", manager=get_foo_buildmanager(), mode='w') as write_io:
             write_io.write(foofile)
 
-        with ZarrIO(self.store_path[0], manager=get_foo_buildmanager(), mode='r') as read_io:
+        with ZarrIO("file1.zarr", manager=get_foo_buildmanager(), mode='r') as read_io:
             read_foofile = read_io.read()
 
             # create a foo with link to existing dataset my_data, add the foo to new foobucket
@@ -1352,10 +1352,10 @@ def test_append_data_export(self):
             # also add reference from foofile to new foo2
             read_foofile.foo_ref_attr = foo2
 
-            with ZarrIO(self.store_path[1], mode='w') as export_io:
+            with ZarrIO("file2.zarr", mode='w') as export_io:
                 export_io.export(src_io=read_io, container=read_foofile)
 
-        with ZarrIO(self.store_path[1], manager=get_foo_buildmanager(), mode='r') as read_io:
+        with ZarrIO("file2.zarr", manager=get_foo_buildmanager(), mode='r') as read_io:
             read_foofile2 = read_io.read()
 
             # test new soft link to dataset in file