[us-commits] [ehb54/us3lims_common] d7e6bf: fix: sha commit update

Fri Jul 10 11:46:46 MDT 2026

  Branch: refs/heads/780-request-pbs-gfac-cleanup
  Home:   https://github.com/ehb54/us3lims_common
  Commit: d7e6bf08f525197b266920787c3d969398b09b10
      https://github.com/ehb54/us3lims_common/commit/d7e6bf08f525197b266920787c3d969398b09b10
  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: 3f0fbf730f024188579702b09bc22cf574ca7248
      https://github.com/ehb54/us3lims_common/commit/3f0fbf730f024188579702b09bc22cf574ca7248
  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 #19 from ehb54/902-update-bump-pr-sha-us3lims_common

Fix SHA commit update

  Commit: b2febe50a398d26dd8aad44be9607bcec7e4f54a
      https://github.com/ehb54/us3lims_common/commit/b2febe50a398d26dd8aad44be9607bcec7e4f54a
  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: 2257f349a7f87f57990c1a9e6fa79f25257682e3
      https://github.com/ehb54/us3lims_common/commit/2257f349a7f87f57990c1a9e6fa79f25257682e3
  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 #20 from ehb54/bump-to-v4.1.0

Bump to v4.1.0

  Commit: a6f9e2ef5a75d86857bb1a34acafa0e6573a7b62
      https://github.com/ehb54/us3lims_common/commit/a6f9e2ef5a75d86857bb1a34acafa0e6573a7b62
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-20 (Sat, 20 Jun 2026)

  Changed paths:
    M class/submit_local.php
    M global_config.php.template

  Log Message:
  -----------
  Validate sbatch submission status before recording a gfacID

submit_job() never checked the exit status of the sbatch/qsub exec()
call, and parsed the job ID positionally from the first output line
assuming it was always "Submitted batch job <N>". Under scheduler
load, sbatch can instead fail with e.g. "sbatch: error: Batch job
submission failed: Socket timed out on send/recv operation" - the
positional parse of that line happens to land on the literal word
"job", which then got stored as gfacID and tracked through the rest
of the pipeline as if a real job existed, eventually surfacing much
later and opaquely as "Failed data fetch" during cleanup.

Validate the sbatch output against /^Submitted batch job\s+(\d+)/
and check exec()'s exit status before accepting a job ID. Retry the
submission with exponential backoff on failure (configurable via
$global_sbatch_submit_retries / $global_sbatch_submit_retry_wait_seconds
in global_config.php, overridable per-cluster), since this class of
failure is transient and load-related. If all retries are exhausted,
update_db() now marks the request SUBMIT_TIMEOUT with the real error
instead of recording an empty/bogus gfacID and launching a jobmonitor
to watch a job that was never submitted.

Fixes ehb54/ultrascan-tickets#915

  Commit: 847e5742c9b159e56f1b3bbc82d72546fe9ec7a2
      https://github.com/ehb54/us3lims_common/commit/847e5742c9b159e56f1b3bbc82d72546fe9ec7a2
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-20 (Sat, 20 Jun 2026)

  Changed paths:
    M class/submit_local.php

  Log Message:
  -----------
  Extract mark_autoflow_submit_failed() to remove duplication

The submission-failure handling in update_db() inlined the same
connect/query/error/close pattern already used by the rest of the
function. Pull it into a small dedicated method instead.

  Commit: 65ff7461ff08cfb95bbb820e7270133bc9672a2a
      https://github.com/ehb54/us3lims_common/commit/65ff7461ff08cfb95bbb820e7270133bc9672a2a
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-20 (Sat, 20 Jun 2026)

  Changed paths:
    M class/submit_local.php

  Log Message:
  -----------
  Mark mark_autoflow_submit_failed() as private

Fixes the SonarCloud-flagged missing visibility modifier (php:S1784).

  Commit: 07777995aaccb65764ffb804c55ae5e29c8c6369
      https://github.com/ehb54/us3lims_common/commit/07777995aaccb65764ffb804c55ae5e29c8c6369
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-20 (Sat, 20 Jun 2026)

  Changed paths:

  Log Message:
  -----------
  Retrigger SonarCloud analysis after fixing cpd.exclusions setting

  Commit: ed4504fe59fb16de017293bf2a1168bcc884dee1
      https://github.com/ehb54/us3lims_common/commit/ed4504fe59fb16de017293bf2a1168bcc884dee1
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-20 (Sat, 20 Jun 2026)

  Changed paths:
    M class/submit_local.php

  Log Message:
  -----------
  Reduce submit_job() cognitive complexity, fix method naming

Extract the sbatch/qsub retry loop and result-parsing logic out of
submit_job() into two small private helpers (attemptSubmit(),
parseSubmitResult()), addressing SonarCloud's flagged Cognitive
Complexity (29 vs 15 allowed). No behavior change, just relocated
code.

Also rename mark_autoflow_submit_failed() to markAutoflowSubmitFailed()
to satisfy the PHP method naming convention rule (php:S100).

  Commit: 367f2e89e377f413ebb2c4c5a3baef1074ee3646
      https://github.com/ehb54/us3lims_common/commit/367f2e89e377f413ebb2c4c5a3baef1074ee3646
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-20 (Sat, 20 Jun 2026)

  Changed paths:
    M class/submit_local.php
    M global_config.php.template

  Log Message:
  -----------
  Merge pull request #21 from ehb54/ehb54-issue-915

Validate sbatch submission status before recording a gfacID

  Commit: 651d220f49c593fb9a5d43d699e8ac1797b0818b
      https://github.com/ehb54/us3lims_common/commit/651d220f49c593fb9a5d43d699e8ac1797b0818b
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-24 (Wed, 24 Jun 2026)

  Changed paths:
    M class/submit_local.php

  Log Message:
  -----------
  Reset $output between sbatch retry attempts in attemptSubmit()

PHP's exec() appends to $output rather than replacing it. Since $output
was only initialized once before the retry loop added in PR #21,
parseSubmitResult()'s check of $output[0] (used to extract the slurm job
ID) stayed permanently stuck on the first attempt's output for the rest
of the retries, even after a later attempt genuinely succeeded.

Confirmed live via us3lims_dbutils' uslims_autoflow_test.php
--fake-sbatch fail-once: after a deliberately-failed first attempt,
attempts 2-4 each succeeded for real (three separate, duplicate jobs
submitted to the actual cluster) but were still misjudged as failures,
so the whole submission ended up reported FAILED with one of the
duplicate real jobs left running with no LIMS record of it.

Fixes ehb54/ultrascan-tickets#931

  Commit: 2a60c1339566ae809b747a57f9810040eaa2b306
      https://github.com/ehb54/us3lims_common/commit/2a60c1339566ae809b747a57f9810040eaa2b306
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-24 (Wed, 24 Jun 2026)

  Changed paths:
    M class/submit_local.php

  Log Message:
  -----------
  Merge pull request #22 from ehb54/ehb54-issue-931

Reset $output between sbatch retry attempts in attemptSubmit()

  Commit: ded16d851d2f1334891c40665ef8ed01a005d92d
      https://github.com/ehb54/us3lims_common/commit/ded16d851d2f1334891c40665ef8ed01a005d92d
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-07-03 (Fri, 03 Jul 2026)

  Changed paths:
    M VERSION

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

  Commit: 4e25de4a189a80e74e25cde0e799e908ba9c0abf
      https://github.com/ehb54/us3lims_common/commit/4e25de4a189a80e74e25cde0e799e908ba9c0abf
  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 #23 from ehb54/bump-to-v4.2.0-dev

Bump to v4.2.0-dev

  Commit: a20741d7a949cc83a15dd33374cde79aad159779
      https://github.com/ehb54/us3lims_common/commit/a20741d7a949cc83a15dd33374cde79aad159779
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-05 (Sun, 05 Jul 2026)

  Changed paths:
    M class/submit_slurm.php
    M global_config.php.template

  Log Message:
  -----------
  Port sbatch retry/backoff and validation from submit_local.php (#915/#931)

submit_local.php is being removed in favor of submit_slurm.php's SSH+Slurm
path, but origin/main independently hardened submit_local.php's submit_job()
against transient sbatch failures (exit-status validation, --parsable
output validation, exponential-backoff retry, SUBMIT_TIMEOUT on exhausted
retries) to fix tickets #915 and #931. Port that behavior into
submit_slurm.php before it becomes the only submission path, via a new
runExec() seam so the retry logic is unit-testable without a real cluster.

  Commit: 8eabb9204c9029705ac2341cb980b3d2125a6407
      https://github.com/ehb54/us3lims_common/commit/8eabb9204c9029705ac2341cb980b3d2125a6407
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-05 (Sun, 05 Jul 2026)

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

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/main' into 780-request-pbs-gfac-cleanup

# Conflicts:
#	class/submit_local.php

  Commit: 360369d24f15b6773737d956e5618bd54f142160
      https://github.com/ehb54/us3lims_common/commit/360369d24f15b6773737d956e5618bd54f142160
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M global_config.php.template

  Log Message:
  -----------
  fix: set max queue/run time to 0 so jobs aren't ended early.

Compare: https://github.com/ehb54/us3lims_common/compare/cf287c5a9797...360369d24f15

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