[us-commits] [ehb54/us3lims_gridctl] 9299e8: fix: sha commit update

Sat Jul 18 13:49:29 MDT 2026

  Branch: refs/heads/780-request-pbs-gfac-cleanup
  Home:   https://github.com/ehb54/us3lims_gridctl
  Commit: 9299e856f36d6b086ae0a508a7c9b7447c5c0d5f
      https://github.com/ehb54/us3lims_gridctl/commit/9299e856f36d6b086ae0a508a7c9b7447c5c0d5f
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-06-16 (Tue, 16 Jun 2026)

  Changed paths:
    M .github/workflows/bump-version.yml

  Log Message:
  -----------
  fix: sha commit update

  Commit: 65f411d468ae31e9a7dfa74a8969d609c4aa50b9
      https://github.com/ehb54/us3lims_gridctl/commit/65f411d468ae31e9a7dfa74a8969d609c4aa50b9
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    M .github/workflows/bump-version.yml

  Log Message:
  -----------
  Merge pull request #24 from ehb54/900-update-bump-pr-sha-us3lims_gridctl

Fix SHA commit update

  Commit: cf43a7500425d7a2057e708eb198a34abeae95f9
      https://github.com/ehb54/us3lims_gridctl/commit/cf43a7500425d7a2057e708eb198a34abeae95f9
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    A VERSION

  Log Message:
  -----------
  Bump version to 4.1.0

  Commit: c96169aa306b38ddf8516d25b1bb3341047be050
      https://github.com/ehb54/us3lims_gridctl/commit/c96169aa306b38ddf8516d25b1bb3341047be050
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    A VERSION

  Log Message:
  -----------
  Merge pull request #25 from ehb54/bump-to-v4.1.0

Bump to v4.1.0

  Commit: 2843ec5521e3abaca87929751db9d635958a789e
      https://github.com/ehb54/us3lims_gridctl/commit/2843ec5521e3abaca87929751db9d635958a789e
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-20 (Sat, 20 Jun 2026)

  Changed paths:
    M cleanup.php
    M jobmonitor/cleanup.php

  Log Message:
  -----------
  Fix race condition causing intermittent "Failed data fetch"

The analysis-results.tar scp had no retry, and the only wait/backoff
loop polled for stderr's arrival, not the tar itself. If the remote
job finished writing stderr before closing the tar, the tar fetch
silently failed and was never retried, leaving gfac.analysis.tarfile
empty even though the job succeeded.

Add a retry to the tar scp matching stdout/stderr, and a dedicated
backoff loop that re-checks for and re-fetches the tar before giving
up. Applied identically to cleanup.php and jobmonitor/cleanup.php.

Fixes ehb54/ultrascan-tickets#914

  Commit: 299622e1aa03a28eb4bc2874245e56e64cce1aa5
      https://github.com/ehb54/us3lims_gridctl/commit/299622e1aa03a28eb4bc2874245e56e64cce1aa5
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-20 (Sat, 20 Jun 2026)

  Changed paths:
    M cleanup.php
    M jobmonitor/cleanup.php

  Log Message:
  -----------
  Add curly braces around single-statement if blocks (SonarCloud)

  Commit: 31337ffaf7aec158264331b22425837f3697d050
      https://github.com/ehb54/us3lims_gridctl/commit/31337ffaf7aec158264331b22425837f3697d050
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-20 (Sat, 20 Jun 2026)

  Changed paths:
    M cleanup.php
    M jobmonitor/cleanup.php

  Log Message:
  -----------
  Merge pull request #26 from ehb54/ehb54-issue-914

Fix race condition causing intermittent "Failed data fetch"

  Commit: 7314df59df76c69f5b7650b1f79273e98c855fdc
      https://github.com/ehb54/us3lims_gridctl/commit/7314df59df76c69f5b7650b1f79273e98c855fdc
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-22 (Mon, 22 Jun 2026)

  Changed paths:
    M submitone.php

  Log Message:
  -----------
  Detect job submission failures in submitone.php's CLI error checks

The included web pages (2DSA_1.php/2DSA_2.php, PCSA_1.php/PCSA_2.php,
etc.) never push job submission failures into $cli_errors themselves
- they only echo an ERROR: line into the dumped output. As a result,
submitone.php's check_cli_errors() saw an empty array and proceeded
as if the submission had succeeded, even when it hadn't (e.g. the
sbatch failure case fixed in ehb54/us3lims_common#21).

Add check_cli_errors_in_dump(), which scans the dump file for any
ERROR: line and folds it into $cli_errors, called right before
check_cli_errors() after both the PCSA and 2DSA job-type includes.

This doesn't change GMP/autoflow's own failure detection, which
already polls autoflowAnalysis.status directly - it only gives
submitone.php its own immediate signal that a submission it just ran
failed.

Fixes ehb54/ultrascan-tickets#917

  Commit: 5d00d5db8381168ffca0014e20c8e48ce3d7402a
      https://github.com/ehb54/us3lims_gridctl/commit/5d00d5db8381168ffca0014e20c8e48ce3d7402a
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-22 (Mon, 22 Jun 2026)

  Changed paths:
    M submitone.php

  Log Message:
  -----------
  Merge pull request #27 from ehb54/ehb54-issue-917

Detect job submission failures in submitone.php's CLI error checks

  Commit: 9cb26506131078dc3676ef1d4f163f6853e1a892
      https://github.com/ehb54/us3lims_gridctl/commit/9cb26506131078dc3676ef1d4f163f6853e1a892
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M VERSION

  Log Message:
  -----------
  Bump version to 4.2.0-dev

  Commit: b0acd2f3bb3a3897b2534094cccc427450087213
      https://github.com/ehb54/us3lims_gridctl/commit/b0acd2f3bb3a3897b2534094cccc427450087213
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M VERSION

  Log Message:
  -----------
  Merge pull request #29 from ehb54/bump-to-v4.2.0-dev

Bump to v4.2.0-dev

  Commit: c50e86c1a89d96fa8bf2522f1420f903090a8974
      https://github.com/ehb54/us3lims_gridctl/commit/c50e86c1a89d96fa8bf2522f1420f903090a8974
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-16 (Thu, 16 Jul 2026)

  Changed paths:
    M jobmonitor/cleanup.php
    M jobmonitor/cleanup_gfac.php
    M jobmonitor/gridctl.php

  Log Message:
  -----------
  jobmonitor: finalize COMPLETE jobs without relying on UDP 'Finished'

check_job()'s COMPLETE case exited the per-job monitor even when
gfac_cleanup() returned 0 ("not yet finalizable, retry later"), which
orphaned the job until a manual uslims_jobs.php --restart. Separately, the
finalize fallback compared time() to strtotime(queue_messages.time), so a
timezone/clock skew (observed ~7h at zentriforce) made the delta negative
and the fallback never fired.

- check_job() COMPLETE case now retries (returns false, keeps polling) when
  complete() returns 0; stops on 1 (finalized) or -1 (terminal).
- cleanup()/complete() propagate the gfac_cleanup()/aira_cleanup() result;
  contract: -1 terminal, 0 retry, 1 finalized.
- gfac_cleanup() times the finalize grace on the jobmonitor's own epoch clock
  via a per-job marker file ($lock_dir/complete_seen), immune to tz/clock
  skew, with a hard ceiling. Grace/ceiling read from
  $global_complete_grace_seconds / $global_complete_max_seconds (default
  600 / 21600) when defined.

Refs ehb54/ultrascan-tickets#969

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>

  Commit: 060dbce49b93f5858119c2c584693a55cdec320a
      https://github.com/ehb54/us3lims_gridctl/commit/060dbce49b93f5858119c2c584693a55cdec320a
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-16 (Thu, 16 Jul 2026)

  Changed paths:
    M jobmonitor/cleanup.php
    M jobmonitor/cleanup_gfac.php
    M jobmonitor/gridctl.php

  Log Message:
  -----------
  address SonarCloud: drop return() parens, brace single-statement ifs

Clears 7 of the 8 new-code smells on PR #30:
- S6600: return( expr ) -> return expr (new returns only)
- S121: added braces to the new single-statement if bodies

The remaining S1142 (cleanup() has 5 returns) is accepted separately.

Refs ehb54/ultrascan-tickets#969

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>

  Commit: fdb69dc880499d8d05e439355288d06eafedb212
      https://github.com/ehb54/us3lims_gridctl/commit/fdb69dc880499d8d05e439355288d06eafedb212
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-17 (Fri, 17 Jul 2026)

  Changed paths:
    M jobmonitor/cleanup.php
    M jobmonitor/cleanup_gfac.php
    M jobmonitor/gridctl.php

  Log Message:
  -----------
  Merge pull request #30 from ehb54/ehb54-issue-969

jobmonitor: finalize COMPLETE jobs robustly (issue #969)

  Commit: eb0c70fc5589445468d5c18a8a51278d6067ad08
      https://github.com/ehb54/us3lims_gridctl/commit/eb0c70fc5589445468d5c18a8a51278d6067ad08
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-18 (Sat, 18 Jul 2026)

  Changed paths:
    M .github/workflows/bump-version.yml
    A VERSION
    M gridctl.php
    A jobmonitor/cleanup.php
    M jobmonitor/cleanup_job.php
    M jobmonitor/gridctl.php
    M jobmonitor/jobmonitor.php
    M submitone.php

  Log Message:
  -----------
  Merge origin/main: COMPLETE-finalize retry, submission-failure detection, and race-condition fixes (issues 969/917/914)

  Commit: a75cdf8991db6b8d09e9ff5e7b0e5899f4985e06
      https://github.com/ehb54/us3lims_gridctl/commit/a75cdf8991db6b8d09e9ff5e7b0e5899f4985e06
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-18 (Sat, 18 Jul 2026)

  Changed paths:
    M gridctl.php
    M jobmonitor/cleanup.php
    M jobmonitor/gridctl.php

  Log Message:
  -----------
  Finish config-driven cluster migration and remove remaining dead Airavata code in gridctl/cleanup paths

Compare: https://github.com/ehb54/us3lims_gridctl/compare/5afda25367d1...a75cdf8991db

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