Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix export cache spec and fix read cached spec #232

Merged
merged 2 commits into from
Nov 10, 2024
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 4 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -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)
Expand Down
7 changes: 7 additions & 0 deletions src/hdmf_zarr/backend.py
Original file line number Diff line number Diff line change
Expand Up @@ -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):
Expand Down
16 changes: 9 additions & 7 deletions src/hdmf_zarr/utils.py
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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]
Expand All @@ -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


Expand Down
Loading