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fix: add sleep rule before start #1311

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merged 12 commits into from
Jan 29, 2024
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@mathiasbio mathiasbio commented Nov 1, 2023

This PR:

BREAK GLASS IN CASE OF KEY_ERROR EMERGENCY

This PR is an ugly solution to the key_error issue (#1300) we sometimes see when a rule finishes before all the jobs have been submitted. It simply adds a 5 minute sleep rule before the actual workflow starts.

If we see this error appearing during verification and validation we can merge this.

image

After 5 minutes downstream rules begin:
image

Added:

  • Sleep 300 seconds before starting analysis

Tests run:

  • TGA T+N case unitedbeagle is running successfully
  • TGA T+N case unitedbeagle finished successfully

Review and tests:

  • Tests pass
  • Code review
  • New code is executed and covered by tests, and test approve

@mathiasbio mathiasbio changed the base branch from master to develop November 1, 2023 14:21
@mathiasbio mathiasbio self-assigned this Nov 1, 2023
@mathiasbio mathiasbio marked this pull request as ready for review November 1, 2023 14:22
@mathiasbio mathiasbio requested a review from a team as a code owner November 1, 2023 14:22
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sonarqubecloud bot commented Nov 1, 2023

SonarCloud Quality Gate failed.    Quality Gate failed

Bug C 7 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 17 Code Smells

No Coverage information No Coverage information
0.4% 0.4% Duplication

idea Catch issues before they fail your Quality Gate with our IDE extension sonarlint SonarLint

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codecov bot commented Nov 1, 2023

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (ae1788a) 99.44% compared to head (17e55fd) 99.44%.

Additional details and impacted files
@@           Coverage Diff           @@
##           master    #1311   +/-   ##
=======================================
  Coverage   99.44%   99.44%           
=======================================
  Files          39       39           
  Lines        1974     1975    +1     
=======================================
+ Hits         1963     1964    +1     
  Misses         11       11           
Flag Coverage Δ
unittests 99.44% <100.00%> (+<0.01%) ⬆️

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@mathiasbio mathiasbio changed the base branch from develop to release_v13.0.0 January 15, 2024 13:04
@ivadym ivadym linked an issue Jan 18, 2024 that may be closed by this pull request
Base automatically changed from release_v13.0.0 to master January 19, 2024 15:28
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👍

CHANGELOG.rst Outdated Show resolved Hide resolved
BALSAMIC/workflows/PON.smk Outdated Show resolved Hide resolved
BALSAMIC/snakemake_rules/misc/sleep.rule Outdated Show resolved Hide resolved
CHANGELOG.rst Outdated

Added:
^^^^^^
* Sleep rule before start to fix key_error https://github.com/Clinical-Genomics/BALSAMIC/pull/1310
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Suggested change
* Sleep rule before start to fix key_error https://github.com/Clinical-Genomics/BALSAMIC/pull/1310
* Sleep rule before start to fix key_error https://github.com/Clinical-Genomics/BALSAMIC/pull/1311

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Quality Gate Passed Quality Gate passed

Kudos, no new issues were introduced!

0 New issues
0 Security Hotspots
No data about Coverage
0.0% Duplication on New Code

See analysis details on SonarCloud

@ivadym ivadym mentioned this pull request Jan 29, 2024
7 tasks
@ivadym ivadym changed the base branch from master to release_v13.0.1 January 29, 2024 13:35
@ivadym ivadym merged commit 458aa45 into release_v13.0.1 Jan 29, 2024
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@ivadym ivadym deleted the add_sleep_rule_before_start branch January 29, 2024 13:49
@ivadym ivadym mentioned this pull request Jan 29, 2024
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Successfully merging this pull request may close these issues.

Intermittent KeyError Disrupts Slurm Job Submissions
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