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Fix support for pynwb v3 which has changed API slightly #1584

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merged 1 commit into from
Mar 3, 2025
+9 −3
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Fix support for pynwb v3 which has changed API slightly #1584

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4 changes: 3 additions & 1 deletion dandi/pynwb_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -352,7 +352,9 @@
path = str(path) # Might come in as pathlib's PATH
errors: list[ValidationResult] = []
try:
if Version(pynwb.__version__) >= Version(
if Version(pynwb.__version__) >= Version("3.0.0"):
error_outputs = pynwb.validate(path=path)
elif Version(pynwb.__version__) >= Version(

Check warning on line 357 in dandi/pynwb_utils.py

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dandi/pynwb_utils.py#L357 

Added line #L357 was not covered by tests
"2.2.0"
): # Use cached namespace feature
# argument get_cached_namespaces is True by default
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2 changes: 1 addition & 1 deletion dandi/tests/fixtures.py
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Expand Up @@ -767,7 +767,7 @@ def _create_nwb_files(video_list: list[tuple[Path, Path]]) -> Path:
sex="M",
description="lab mouse ",
)
device = Device(f"imaging_device_{i}")
device = Device(name=f"imaging_device_{i}")
name = f"{vid_1.stem}_{i}"
nwbfile = NWBFile(
f"{name}{i}",
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6 changes: 5 additions & 1 deletion dandi/tests/test_files.py
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Expand Up @@ -379,7 +379,11 @@ def test_validate_bogus(tmp_path):
# but that would be too rigid to test. Let's just see that we have expected errors
assert any(
e.message.startswith(
("Unable to open file", "Unable to synchronously open file")
(
"Unable to open file",
"Unable to synchronously open file",
"Could not find an IO to read the file",
)
)
for e in errors
)
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