Merge branch 'dev' into rly-patch-1

CHANGELOG.md

@@ -1,11 +1,15 @@
 # HDMF-ZARR Changelog
 
 ## 1.0.0 (Upcoming)
+
 ### Enhancements
 * Added support for Pathlib paths. @mavaylon1 [#212](https://github.com/hdmf-dev/hdmf-zarr/pull/212)
 * Updated packages used for testing and readthedocs configuration. @mavaylon1, @rly [#214](https://github.com/hdmf-dev/hdmf-zarr/pull/214)
 * Add `force_overwite` parameter for `ZarrIO.__init__` to allow overwriting an existing file or directory. @oruebel [#229](https://github.com/hdmf-dev/hdmf-zarr/pull/229)
 
+### Bug Fixes
+* Fix reading of cached specs and caching of specs during export. @rly [#232](https://github.com/hdmf-dev/hdmf-zarr/pull/232)
+
 ## 0.9.0 (September 16, 2024)
 ### Enhancements
 * Added support for appending a dataset of references. @mavaylon1 [#203](https://github.com/hdmf-dev/hdmf-zarr/pull/203)

docs/source/installation.rst

@@ -32,7 +32,6 @@ in a Conda environment. Normally we don't need to install ``hdmf`` directly, but
 
     conda create --name hdmf-zarr-test python=3.9
     conda activate hdmf-zarr-test
-    conda install h5py
 
     git clone --recurse-submodules https://github.com/hdmf-dev/hdmf.git
     cd hdmf

src/hdmf_zarr/backend.py

@@ -399,6 +399,13 @@ def export(self, **kwargs):
             ckwargs['clear_cache'] = True
         super().export(**ckwargs)
         if cache_spec:
+            # add any namespaces from the src_io that have not yet been loaded
+            for namespace in src_io.manager.namespace_catalog.namespaces:
+                if namespace not in self.manager.namespace_catalog.namespaces:
+                    self.manager.namespace_catalog.add_namespace(
+                        name=namespace,
+                        namespace=src_io.manager.namespace_catalog.get_namespace(namespace)
+                    )
             self.__cache_spec()
 
     def get_written(self, builder, check_on_disk=False):

src/hdmf_zarr/utils.py

@@ -5,6 +5,7 @@
 import math
 import json
 import logging
+import os
 from collections import deque
 from collections.abc import Iterable
 from typing import Optional, Union, Literal, Tuple, Dict, Any
@@ -373,12 +374,12 @@ class ZarrSpecReader(SpecReader):
     Class to read format specs from Zarr
     """
 
-    @docval({'name': 'group', 'type': Group, 'doc': 'the Zarr file to read specs from'},
-            {'name': 'source', 'type': str, 'doc': 'the path spec files are relative to', 'default': '.'})
+    @docval({'name': 'group', 'type': Group, 'doc': 'the Zarr file to read specs from'})
     def __init__(self, **kwargs):
-        self.__group, source = getargs('group', 'source', kwargs)
-        super_kwargs = {'source': source}
-        super(ZarrSpecReader, self).__init__(**super_kwargs)
+        self.__group = getargs('group', kwargs)
+        source = "%s:%s" % (os.path.abspath(self.__group.store.path), self.__group.name)
+        super().__init__(source=source)
+        self.__cache = None
 
     def __read(self, path):
         s = self.__group[path][0]
@@ -391,8 +392,9 @@ def read_spec(self, spec_path):
 
     def read_namespace(self, ns_path):
         """Read a namespace from the given path"""
-        ret = self.__read(ns_path)
-        ret = ret['namespaces']
+        if self.__cache is None:
+            self.__cache = self.__read(ns_path)
+        ret = self.__cache['namespaces']
         return ret