Merge branch 'dev' into s3test

hdmf-dev · Jul 19, 2024 · 6221c20 · 6221c20
2 parents 35d8bbf + 626341c
commit 6221c20
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # HDMF-ZARR Changelog
 
+## 0.9.0 (Upcoming)
+### Enhancements
+* NWBZarrIO load_namespaces=True by default. @mavaylon1 [#204](https://github.com/hdmf-dev/hdmf-zarr/pull/204)
+
 ## 0.8.0 (June 4, 2024)
 ### Bug Fixes
 * Fixed bug when opening a file in with `mode=r+`. The file will open without using the consolidated metadata. @mavaylon1 [#182](https://github.com/hdmf-dev/hdmf-zarr/issues/182)

diff --git a/src/hdmf_zarr/backend.py b/src/hdmf_zarr/backend.py
@@ -197,13 +197,17 @@ def is_remote(self):
             {'name': 'path',
              'type': (str, *SUPPORTED_ZARR_STORES),
              'doc': 'the path to the Zarr file or a supported Zarr store'},
-            {'name': 'namespaces', 'type': list, 'doc': 'the namespaces to load', 'default': None})
-    def load_namespaces(cls, namespace_catalog, path, namespaces=None):
+            {'name': 'storage_options', 'type': dict,
+             'doc': 'Zarr storage options to read remote folders',
+             'default': None},
+            {'name': 'namespaces', 'type': list, 'doc': 'the namespaces to load', 'default': None}
+            )
+    def load_namespaces(cls, namespace_catalog, path, storage_options, namespaces=None):
         '''
         Load cached namespaces from a file.
         '''
         # TODO: how to use storage_options here?
-        f = zarr.open(path, mode='r')
+        f = zarr.open(path, mode='r', storage_options=storage_options)
         if SPEC_LOC_ATTR not in f.attrs:
             msg = "No cached namespaces found in %s" % path
             warnings.warn(msg)

diff --git a/src/hdmf_zarr/nwb.py b/src/hdmf_zarr/nwb.py
@@ -22,25 +22,22 @@ class NWBZarrIO(ZarrIO):
         @docval(*get_docval(ZarrIO.__init__),
                 {'name': 'load_namespaces', 'type': bool,
                  'doc': 'whether or not to load cached namespaces from given path - not applicable in write mode',
-                 'default': False},
+                 'default': True},
                 {'name': 'extensions', 'type': (str, TypeMap, list),
                  'doc': 'a path to a namespace, a TypeMap, or a list consisting paths  to namespaces and TypeMaps',
                  'default': None})
         def __init__(self, **kwargs):
             path, mode, manager, extensions, load_namespaces, synchronizer, storage_options = \
                 popargs('path', 'mode', 'manager', 'extensions',
                         'load_namespaces', 'synchronizer', 'storage_options', kwargs)
-            if load_namespaces:
-                if manager is not None:
-                    warn("loading namespaces from file - ignoring 'manager'")
-                if extensions is not None:
-                    warn("loading namespaces from file - ignoring 'extensions' argument")
-                # namespaces are not loaded when creating an NWBZarrIO object in write mode
-                if 'w' in mode or mode == 'x':
-                    raise ValueError("cannot load namespaces from file when writing to it")
 
+            io_modes_that_create_file = ['w', 'w-', 'x']
+            if mode in io_modes_that_create_file or manager is not None or extensions is not None:
+                load_namespaces = False
+
+            if load_namespaces:
                 tm = get_type_map()
-                super(NWBZarrIO, self).load_namespaces(tm, path)
+                super(NWBZarrIO, self).load_namespaces(tm, path, storage_options)
                 manager = BuildManager(tm)
             else:
                 if manager is not None and extensions is not None: