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[scheduler] Even more resilient perl beanstalkd annotation worker #545

Merged
merged 51 commits into from
Jul 15, 2024
Merged

[scheduler] Even more resilient perl beanstalkd annotation worker #545

merged 51 commits into from
Jul 15, 2024

Commits on Apr 5, 2024

  1. fuck this

    @akotlar
    akotlar committed Apr 5, 2024
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Commits on Apr 25, 2024

  1. merged master

    @akotlar
    akotlar committed Apr 25, 2024
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  2. Merge branch 'master' of https://github.com/bystrogenomics/bystro

    @akotlar
    akotlar committed Apr 25, 2024
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Commits on Apr 29, 2024

  1. Merge branch 'master' of https://github.com/bystrogenomics/bystro

    @akotlar
    akotlar committed Apr 29, 2024
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Commits on May 1, 2024

  1. Merge branch 'master' of https://github.com/bystrogenomics/bystro

    @akotlar
    akotlar committed May 1, 2024
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Commits on May 3, 2024

  1. Merge branch 'master' of https://github.com/bystrogenomics/bystro

    @akotlar
    akotlar committed May 3, 2024
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Commits on May 12, 2024

  1. Merge branch 'master' of https://github.com/bystrogenomics/bystro

    @akotlar
    akotlar committed May 12, 2024
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Commits on May 17, 2024

  1. Merge branch 'master' of https://github.com/bystrogenomics/bystro

    @akotlar
    akotlar committed May 17, 2024
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Commits on May 20, 2024

  1. Merge branch 'master' of https://github.com/bystrogenomics/bystro

    @akotlar
    akotlar committed May 20, 2024
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Commits on Jun 3, 2024

  1. Merge branch 'master' of https://github.com/bystrogenomics/bystro

    @akotlar
    akotlar committed Jun 3, 2024
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Commits on Jun 7, 2024

  1. Merge branch 'master' of https://github.com/bystrogenomics/bystro

    @akotlar
    akotlar committed Jun 7, 2024
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Commits on Jun 10, 2024

  1. Merge branch 'master' of https://github.com/bystrogenomics/bystro

    @akotlar
    akotlar committed Jun 10, 2024
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Commits on Jun 14, 2024

  1. Merge branch 'master' of https://github.com/bystrogenomics/bystro

    @akotlar
    akotlar committed Jun 14, 2024
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Commits on Jun 24, 2024

  1. Merge branch 'master' of https://github.com/bystrogenomics/bystro

    @akotlar
    akotlar committed Jun 24, 2024
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Commits on Jun 27, 2024

  1. Merge branch 'master' of https://github.com/bystrogenomics/bystro

    @akotlar
    akotlar committed Jun 27, 2024
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Commits on Jul 6, 2024

  1. Merge branch 'master' of https://github.com/bystrogenomics/bystro

    @akotlar
    akotlar committed Jul 6, 2024
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Commits on Jul 8, 2024

  1. Merge branch 'master' of https://github.com/bystrogenomics/bystro

    @akotlar
    akotlar committed Jul 8, 2024
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  2. add client-side timeouts for beanstalkd operations

    @akotlar
    akotlar committed Jul 8, 2024
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Commits on Jul 9, 2024

  1. add periodic job touching

    @akotlar
    akotlar committed Jul 9, 2024
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  2. perltidy

    @akotlar
    akotlar committed Jul 9, 2024
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  3. organize outputs

    @akotlar
    akotlar committed Jul 9, 2024
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  4. clean up error reporting in handleJobFailure

    @akotlar
    akotlar committed Jul 9, 2024
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  5. cleanup

    @akotlar
    akotlar committed Jul 9, 2024
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  6. sleep between iterations of loop in bystro-server.pl

    @akotlar
    akotlar committed Jul 9, 2024
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Commits on Jul 10, 2024

  1. wip, adding better error messages and wrapping stats, touch commands … 

    …in client-side timeout
    @akotlar
    akotlar committed Jul 10, 2024
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  2. fix issues, and remove reliance on job->connect, which is no longer n… 

    …ecessary, because we properly touch() jobs
    @akotlar
    akotlar committed Jul 10, 2024
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Commits on Jul 11, 2024

  1. refactor bystro-server.pl to be more easily testable

    @akotlar
    akotlar committed Jul 11, 2024
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  2. add test for bystro-server.pl

    @akotlar
    akotlar committed Jul 11, 2024
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  3. uprev bystro veresion

    @akotlar
    akotlar committed Jul 11, 2024
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  4. remove unnecessary debug message

    @akotlar
    akotlar committed Jul 11, 2024
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  5. remove unnecessary spaces

    @akotlar
    akotlar committed Jul 11, 2024
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  6. output all debug messages to stderr

    @akotlar
    akotlar committed Jul 11, 2024
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  7. remove json::xs

    @akotlar
    akotlar committed Jul 11, 2024
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  8. fix perl test

    @akotlar
    akotlar committed Jul 11, 2024
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  9. remove unused coercions in Interface.pm

    @akotlar
    akotlar committed Jul 11, 2024
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Commits on Jul 12, 2024

  1. switch to python annotation worker

    @akotlar
    akotlar committed Jul 12, 2024
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Commits on Jul 13, 2024

  1. add lock file to Bystro annotator, to ensure multiple instances of By… 

    …stro do not run and produce outputs in the same directory
    @akotlar
    akotlar committed Jul 13, 2024
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Commits on Jul 14, 2024

  1. better file locks

    @akotlar
    akotlar committed Jul 14, 2024
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  2. Error if the annotation already completed

    @akotlar
    akotlar committed Jul 14, 2024
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  3. simplify error handling and make the double-submission explanation mo… 

    …re complete
    @akotlar
    akotlar committed Jul 14, 2024
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  4. more clarity on error

    @akotlar
    akotlar committed Jul 14, 2024
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  5. sleep between touches to reduce CPU usage

    @akotlar
    akotlar committed Jul 14, 2024
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  6. more clear error message

    @akotlar
    akotlar committed Jul 14, 2024
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  7. simplify error message

    @akotlar
    akotlar committed Jul 14, 2024
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  8. cleanup

    @akotlar
    akotlar committed Jul 14, 2024
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  9. fix mypy errors

    @akotlar
    akotlar committed Jul 14, 2024
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  10. format, and get rid of unused NotFoundError

    @akotlar
    akotlar committed Jul 14, 2024
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  11. remove unused WrappedHandlerFn

    @akotlar
    akotlar committed Jul 14, 2024
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  12. perltidy

    @akotlar
    akotlar committed Jul 14, 2024
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Commits on Jul 15, 2024

  1. more verbose logging for beanstalkd workers

    @akotlar
    akotlar committed Jul 15, 2024
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  2. log to stderr after files have been moved to the final directory

    @akotlar
    akotlar committed Jul 15, 2024
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