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Allow nwbinspector CLI to accept URLs #559

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merged 4 commits into from
Feb 20, 2025
Merged

Allow nwbinspector CLI to accept URLs #559

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6d8bf07
add tests for inspect_url
stephprince Jan 30, 2025
4d6a482
update CHANGELOG
stephprince Jan 30, 2025
48d29b9
Merge branch 'dev' into fix-inspect-url
stephprince Feb 20, 2025
e6f99ff
move test to cli test file
stephprince Feb 20, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -5,6 +5,7 @@

### Fixes
* Fix wrongly triggered compression check [#552](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/552)
* Fixed URL inspection using the CLI [#559](https://github.com/NeurodataWithoutBorders/nwbinspector/issues/559)

## Improvements
* Added a section for describing the issues with negative timestamps in `TimeSeries` [#545](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/545)
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2 changes: 1 addition & 1 deletion src/nwbinspector/_nwbinspector_cli.py
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Expand Up @@ -160,7 +160,7 @@ def _nwbinspector_cli(
show_progress_bar=show_progress_bar,
)
# Scan a single NWB file in a Dandiset
elif stream and ":" in path:
elif stream and ":" in path and not path_is_url:
dandiset_id, dandi_file_path = path.split(":")
dandiset_version = version_id

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14 changes: 14 additions & 0 deletions tests/streaming_cli_tests.py
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Expand Up @@ -120,3 +120,17 @@ def test_dandiset_streaming_cli_with_version_saved_report(tmpdir: py.path.local)
expected_report_length = 38
report_end = report_start + expected_report_length
assert test_report[report_start:report_end] == expected_report[14:]


@pytest.mark.skipif(not STREAMING_TESTS_ENABLED, reason=DISABLED_STREAMING_TESTS_REASON or "")
def test_inspect_url_cli(tmp_path):
"""Test that the CLI correctly handles inspecting a URL."""
url = "https://dandiarchive.s3.amazonaws.com/blobs/11e/c89/11ec8933-1456-4942-922b-94e5878bb991"
console_output_file = tmp_path / "url_console_output.txt"

os.system(f"nwbinspector {url} " "--skip-validate " f"> {console_output_file}")

# Read and check the contents of the console output file
with open(console_output_file, "r") as file:
output = file.read()
assert "Subject species is missing." in output
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