static and some test

src/hdmf_zarr/backend.py

@@ -448,16 +448,17 @@ def consolidate_metadata(self, store):
         """
         zarr.consolidate_metadata(store, metadata_key='.zmetadata')
 
-    def __get_store_path(self, zarr_object):
+    @staticmethod
+    def __get_store_path(store):
         """
         Method to retrieve the path from the Zarr storage.
         ConsolidatedMetadataStore wraps around other Zarr Store objects, requiring a check to
         retrieve the path.
         """
-        if isinstance(zarr_object.store, zarr.storage.ConsolidatedMetadataStore):
-            fpath = zarr_object.store.store.path
+        if isinstance(store, zarr.storage.ConsolidatedMetadataStore):
+            fpath = store.store.path
         else:
-            fpath = zarr_object.store.path
+            fpath = store.path
 
         return fpath
 
@@ -627,7 +628,8 @@ def __get_path(self, builder):
             path = "%s%s" % (delim, delim.join(reversed(names)))
         return path
 
-    def get_zarr_paths(self, zarr_object):
+    @staticmethod
+    def get_zarr_paths(zarr_object):
         """
         For a Zarr object find 1) the path to the main zarr file it is in and 2) the path to the object within the file
         :param zarr_object: Object for which we are looking up the path
@@ -637,7 +639,7 @@ def get_zarr_paths(self, zarr_object):
         # In Zarr the path is a combination of the path of the store and the path of the object. So we first need to
         # merge those two paths, then remove the path of the file, add the missing leading "/" and then compute the
         # directory name to get the path of the parent
-        fpath = self.__get_store_path(zarr_object)
+        fpath = ZarrIO._ZarrIO__get_store_path(zarr_object.store)
         fullpath = os.path.normpath(os.path.join(fpath, zarr_object.path)).replace("\\", "/")
         # To determine the filepath we now iterate over the path and check if the .zgroup object exists at
         # a level, indicating that we are still within the Zarr file. The first level we hit where the parent
@@ -651,14 +653,15 @@ def get_zarr_paths(self, zarr_object):
         # return the result
         return filepath, objectpath
 
-    def get_zarr_parent_path(self, zarr_object):
+    @staticmethod
+    def get_zarr_parent_path(zarr_object):
         """
         Get the location of the parent of a zarr_object within the file
         :param zarr_object: Object for which we are looking up the path
         :type zarr_object: Zarr Group or Array
         :return: String with the path
         """
-        filepath, objectpath = self.get_zarr_paths(zarr_object)
+        filepath, objectpath = ZarrIO.get_zarr_paths(zarr_object)
         parentpath = os.path.dirname(objectpath)
         return parentpath
 
@@ -948,7 +951,7 @@ def write_dataset(self, **kwargs):  # noqa: C901
         if isinstance(data, Array):
             # copy the dataset
             if link_data:
-                path = self.__get_store_path(data)
+                path = self.__get_store_path(data.store)
                 self.__add_link__(parent, path, data.name, name)
                 linked = True
                 dset = None
@@ -1266,7 +1269,7 @@ def read_builder(self):
 
     def __set_built(self, zarr_obj, builder):
         # fpath = zarr_obj.store.path
-        fpath = self.__get_store_path(zarr_obj)
+        fpath = self.__get_store_path(zarr_obj.store)
         path = zarr_obj.path
         path = os.path.join(fpath, path)
         self.__built.setdefault(path, builder)
@@ -1307,7 +1310,7 @@ def __get_built(self, zarr_obj):
         :return: Builder in the self.__built cache or None
         """
 
-        fpath = self.__get_store_path(zarr_obj)
+        fpath = self.__get_store_path(zarr_obj.store)
         path = zarr_obj.path
         path = os.path.join(fpath, path)
         return self.__built.get(path, None)
@@ -1323,7 +1326,7 @@ def __read_group(self, zarr_obj, name=None):
         # Create the GroupBuilder
         attributes = self.__read_attrs(zarr_obj)
         ret = GroupBuilder(name=name, source=self.source, attributes=attributes)
-        ret.location = self.get_zarr_parent_path(zarr_obj)
+        ret.location = ZarrIO.get_zarr_parent_path(zarr_obj)
 
         # read sub groups
         for sub_name, sub_group in zarr_obj.groups():
@@ -1418,7 +1421,7 @@ def __read_dataset(self, zarr_obj, name):
         if name is None:
             name = str(os.path.basename(zarr_obj.name))
         ret = DatasetBuilder(name, **kwargs)  # create builder object for dataset
-        ret.location = self.get_zarr_parent_path(zarr_obj)
+        ret.location = ZarrIO.get_zarr_parent_path(zarr_obj)
         self._written_builders.set_written(ret)  # record that the builder has been written
         self.__set_built(zarr_obj, ret)
         return ret

tests/unit/example.zarr/.zattrs

@@ -0,0 +1,12 @@
+{
+    ".specloc": "specifications",
+    "colnames": [
+        "first_name",
+        "last_name",
+        "phone_number"
+    ],
+    "data_type": "DynamicTable",
+    "description": "a table containing data/metadata about users, one user per row",
+    "namespace": "hdmf-common",
+    "object_id": "ea83daef-37db-4b95-af84-6f5d840423f6"
+}

tests/unit/example.zarr/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

tests/unit/example.zarr/first_name/.zarray

@@ -0,0 +1,24 @@
+{
+    "chunks": [
+        2
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "|O",
+    "fill_value": 0,
+    "filters": [
+        {
+            "id": "vlen-utf8"
+        }
+    ],
+    "order": "C",
+    "shape": [
+        2
+    ],
+    "zarr_format": 2
+}

tests/unit/example.zarr/first_name/.zattrs

@@ -0,0 +1,7 @@
+{
+    "data_type": "VectorData",
+    "description": "the first name of the user",
+    "namespace": "hdmf-common",
+    "object_id": "cdbf89b5-00bd-44e5-a350-2b4ba549dc3c",
+    "zarr_dtype": "str"
+}

tests/unit/example.zarr/id/.zarray

@@ -0,0 +1,20 @@
+{
+    "chunks": [
+        2
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "<i8",
+    "fill_value": 0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        2
+    ],
+    "zarr_format": 2
+}

tests/unit/example.zarr/id/.zattrs

@@ -0,0 +1,6 @@
+{
+    "data_type": "ElementIdentifiers",
+    "namespace": "hdmf-common",
+    "object_id": "6b8eebde-6762-43da-8d0c-885f3aef95dc",
+    "zarr_dtype": "int64"
+}

tests/unit/example.zarr/last_name/.zarray

@@ -0,0 +1,24 @@
+{
+    "chunks": [
+        2
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "|O",
+    "fill_value": 0,
+    "filters": [
+        {
+            "id": "vlen-utf8"
+        }
+    ],
+    "order": "C",
+    "shape": [
+        2
+    ],
+    "zarr_format": 2
+}

tests/unit/example.zarr/last_name/.zattrs

@@ -0,0 +1,7 @@
+{
+    "data_type": "VectorData",
+    "description": "the last name of the user",
+    "namespace": "hdmf-common",
+    "object_id": "ff302d07-62c1-4e84-b50a-75f4d8586e88",
+    "zarr_dtype": "str"
+}

tests/unit/example.zarr/phone_number/.zarray

@@ -0,0 +1,24 @@
+{
+    "chunks": [
+        3
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "|O",
+    "fill_value": 0,
+    "filters": [
+        {
+            "id": "vlen-utf8"
+        }
+    ],
+    "order": "C",
+    "shape": [
+        3
+    ],
+    "zarr_format": 2
+}

tests/unit/example.zarr/phone_number/.zattrs

@@ -0,0 +1,7 @@
+{
+    "data_type": "VectorData",
+    "description": "the phone number of the user",
+    "namespace": "hdmf-common",
+    "object_id": "a3ef9627-dd8a-4715-a144-afe6b62c400a",
+    "zarr_dtype": "str"
+}

tests/unit/example.zarr/phone_number_index/.zarray

@@ -0,0 +1,20 @@
+{
+    "chunks": [
+        2
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "|u1",
+    "fill_value": 0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        2
+    ],
+    "zarr_format": 2
+}

tests/unit/example.zarr/phone_number_index/.zattrs

@@ -0,0 +1,16 @@
+{
+    "data_type": "VectorIndex",
+    "description": "Index for VectorData 'phone_number'",
+    "namespace": "hdmf-common",
+    "object_id": "fbf1016a-f086-4d9a-9660-eb2c84a5e36c",
+    "target": {
+        "value": {
+            "object_id": null,
+            "path": "/phone_number",
+            "source": ".",
+            "source_object_id": "ea83daef-37db-4b95-af84-6f5d840423f6"
+        },
+        "zarr_dtype": "object"
+    },
+    "zarr_dtype": "uint8"
+}

tests/unit/example.zarr/specifications/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

tests/unit/example.zarr/specifications/hdmf-common/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

tests/unit/example.zarr/specifications/hdmf-common/1.8.0/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

tests/unit/example.zarr/specifications/hdmf-common/1.8.0/base/.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
+}

tests/unit/example.zarr/specifications/hdmf-common/1.8.0/base/.zattrs

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

tests/unit/example.zarr/specifications/hdmf-common/1.8.0/base/0

@@ -0,0 +1 @@
+["{\"datasets\":[{\"doc\":\"An abstract data type for a dataset.\",\"data_type_def\":\"Data\"}],\"groups\":[{\"doc\":\"An abstract data type for a group storing collections of data and metadata. Base type for all data and metadata containers.\",\"data_type_def\":\"Container\"},{\"groups\":[{\"doc\":\"Container objects held within this SimpleMultiContainer.\",\"quantity\":\"*\",\"data_type_inc\":\"Container\"}],\"datasets\":[{\"doc\":\"Data objects held within this SimpleMultiContainer.\",\"quantity\":\"*\",\"data_type_inc\":\"Data\"}],\"doc\":\"A simple Container for holding onto multiple containers.\",\"data_type_inc\":\"Container\",\"data_type_def\":\"SimpleMultiContainer\"}]}","|O",[1]]

tests/unit/example.zarr/specifications/hdmf-common/1.8.0/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
+}

tests/unit/example.zarr/specifications/hdmf-common/1.8.0/namespace/.zattrs

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

tests/unit/example.zarr/specifications/hdmf-common/1.8.0/namespace/0

@@ -0,0 +1 @@
+["{\"namespaces\":[{\"doc\":\"Common data structures provided by HDMF\",\"schema\":[{\"source\":\"base\"},{\"source\":\"table\"},{\"source\":\"sparse\"}],\"name\":\"hdmf-common\",\"full_name\":\"HDMF Common\",\"version\":\"1.8.0\",\"author\":[\"Andrew Tritt\",\"Oliver Ruebel\",\"Ryan Ly\",\"Ben Dichter\"],\"contact\":[\"[email protected]\",\"[email protected]\",\"[email protected]\",\"[email protected]\"]}]}","|O",[1]]