[CodyCBakerPhD]

Summary

Carries dandi/s3-log-extraction#320 down to the DANDI plugin. dandis3logextraction extract <s3_root> --mode remote --inventory … --cache … --check reports whether any log files are pending extraction, then exits without extracting.

• It returns before any extraction setup and stops at the first log file not yet extracted. It writes no records and no temporary directory.
• It exits 3 when something is pending and 0 when nothing is, matching the upstream flag. 1 stays an error, such as corrupted records, so a script can tell the two apart. One short line is printed either way.
• It goes through DandiRemoteS3LogAccessExtractor.has_unprocessed_s3_urls. The records files are named after the extractor class (DandiRemoteS3LogAccessExtractor_s3-url-processing-end.txt), so the upstream CLI would read the wrong records for the DANDI cache.
• An earlier revision added a standalone pending command instead. It was removed without an alias.

This is for the host-side cron check in brain-bbqs-runners/dandi-usage-runner#11, so the daily extraction workflow only runs when there is something to extract.

• Version bumped to 1.6.2. Changelog and README updated.
• The upstream pin is raised to s3_log_extraction>=1.14.1, the release that shipped --check and has_unprocessed_s3_urls. The 1.11.11 this PR first pinned was never published.

Upstream 1.14.1 compatibility

1.14.1 also carries the breaking changes of dandi/s3-log-extraction#321. The plugin only reads excluded addresses through config.get_excluded_ips(), which is still public, so nothing here breaks.

One behavior gap is out of scope for this PR. Upstream 1.14.1 now drops excluded IPs at extraction by passing EXCLUDED_IPS to its awk script. The DANDI extractor uses its own _dandi_extraction.awk, which does not read that variable, so DANDI extraction keeps their records. The DANDI summaries still leave them out.

Testing

• New tests/test_extract_check.py (marked ai_generated) checks output and exit codes against DANDI-named records. It also checks that no temporary directory is left behind and that the records are unchanged.
• I ran the suite locally against the published s3-log-extraction==1.14.1, with gawk. 123 passed and 1 failed. The failure is test_dandi_summaries.py::test_dandiset_summaries, which needs api.dandiarchive.org, and this container's proxy refuses it (403). pre-commit run --all-files passes.

🤖 Generated with Claude Code

https://claude.ai/code/session_019NGBLufw1kq2iy4LNeWs89

[CodyCBakerPhD]

CI on this PR is expected to fail at install time: it requires s3_log_extraction>=1.11.11, which only exists once dandi/s3-log-extraction#320 is merged and released to PyPI. Re-running CI after that release should go green. This is not worked around here.

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Generated by Claude Code

[codecov]

Codecov Report

❌ Patch coverage is 68.75000% with 5 lines in your changes missing coverage. Please review.
✅ Project coverage is 85.15%. Comparing base (2e2fd34) to head (9552a48).

Files with missing lines	Patch %	Lines
..._s3_log_extraction/_command_line_interface/_cli.py	68.75%	5 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##             main     #107       +/-   ##
===========================================
+ Coverage   67.05%   85.15%   +18.09%     
===========================================
  Files           4        9        +5     
  Lines         170      660      +490     
===========================================
+ Hits          114      562      +448     
- Misses         56       98       +42     

Flag	Coverage Δ
unittests	85.15% <68.75%> (+18.09%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
..._s3_log_extraction/_command_line_interface/_cli.py	62.30% <68.75%> (-0.86%)	⬇️

... and 6 files with indirect coverage changes

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