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Use paths instead of io in pynwb.validate call #425

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merged 5 commits into from
Dec 19, 2023
Merged

Use paths instead of io in pynwb.validate call #425

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565e0bb
Update nwbinspector.py
rly Dec 19, 2023
361d573
Update CHANGELOG.md
rly Dec 19, 2023
c958cfe
Update nwbinspector.py
rly Dec 19, 2023
813b407
Fix pynwb.validate call
rly Dec 19, 2023
984adcc
Make tests pass on pynwb 2.1.0
rly Dec 19, 2023
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,10 @@

* Added `check_rate_is_not_zero` for ensuring non-zero rate value of `TimeSeries` that has more than one frame. [#389](https://github.com/NeurodataWithoutBorders/nwbinspector/issues/389)

### Fixes

* Use cached extension namespaces when calling pynwb validate instead of just the core namespace. [#425](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/425)

# v0.4.30

### Fixes
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24 changes: 22 additions & 2 deletions src/nwbinspector/nwbinspector.py
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Expand Up @@ -13,6 +13,7 @@
from warnings import filterwarnings, warn
from distutils.util import strtobool
from collections import defaultdict
from packaging.version import Version

import click
import pynwb
Expand All @@ -29,7 +30,14 @@
)
from .register_checks import InspectorMessage, Importance
from .tools import get_s3_urls_and_dandi_paths
from .utils import FilePathType, PathType, OptionalListOfStrings, robust_s3_read, calculate_number_of_cpu
from .utils import (
FilePathType,
PathType,
OptionalListOfStrings,
robust_s3_read,
calculate_number_of_cpu,
get_package_version,
)
from nwbinspector import __version__

INTERNAL_CONFIGS = dict(dandi=Path(__file__).parent / "internal_configs" / "dandi.inspector_config.yaml")
Expand Down Expand Up @@ -550,8 +558,20 @@ def inspect_nwbfile(
filterwarnings(action="ignore", message="No cached namespaces found in .*")
filterwarnings(action="ignore", message="Ignoring cached namespace .*")

if not skip_validate and get_package_version("pynwb") >= Version("2.2.0"):
validation_error_list, _ = pynwb.validate(paths=[nwbfile_path], driver=driver)
for validation_namespace_errors in validation_error_list:
for validation_error in validation_namespace_errors:
yield InspectorMessage(
message=validation_error.reason,
importance=Importance.PYNWB_VALIDATION,
check_function_name=validation_error.name,
location=validation_error.location,
file_path=nwbfile_path,
)

with pynwb.NWBHDF5IO(path=nwbfile_path, mode="r", load_namespaces=True, driver=driver) as io:
if not skip_validate:
if not skip_validate and get_package_version("pynwb") < Version("2.2.0"):
validation_errors = pynwb.validate(io=io)
for validation_error in validation_errors:
yield InspectorMessage(
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