This project is mirrored from https://:*****@github.com/Ensembl/ensembl-hive.git. Pull mirroring updated .
  1. 29 Jan, 2015 11 commits
  2. 27 Jan, 2015 11 commits
  3. 26 Jan, 2015 1 commit
  4. 24 Jan, 2015 3 commits
    • Matthieu Muffato's avatar
      Merge branch 'master' into feature/tests_ci · aee2e800
      Matthieu Muffato authored
      * master: (21 commits)
        bugfix: record job_id, role_id and worker_id of the job that deadlocked when checking in
        logging of deadlocks via callback
        interface_change: protected_prepare_execute() takes all sql-related parameters as first argument
        wait for random time with increasing upper boundary
        log deadlocks and retries in log_message
        grab_jobs_for_role now uses PPE instead of bare do()
        PPE now returns a value
        capture all "dies" during worker->run() and try to record them in log_message
        bugfix: specialization failures should not be considered critical
        bugfix: the claimed batch was not released
        MySQL and PostgreSQL have a maximum length for database names
        Added 'meadow_user' to Worker object+schema which is now routinely recorded. Also renamed 'host' to 'meadow_host' for consistency
        Allow script-based schema patches that can use API in addition to pure SQL-based patches
        Updated the copyright to 1999-2015
        don't mix missing and incomplete options in the report
        No references to "self_burial" any more as the concept is gon
        Test that it is defined, not logically true
        cause_of_death can be undefined here (for local meadows, for instance)
        Backported the recent changes from Ensembl's DBConnection
        Numbers are returned as real numbers, not strings;
        ...
      
      Conflicts:
      	modules/Bio/EnsEMBL/Hive/Queen.pm
      	modules/Bio/EnsEMBL/Hive/Worker.pm
      aee2e800
    • Matthieu Muffato's avatar
      standaloneJob core code is now defined in a module · 9110b1b1
      Matthieu Muffato authored
      The function can thus be called from both the usual script
      standaloneJob.pl and the test interface
      9110b1b1
    • Matthieu Muffato's avatar
      init_pipeline core code is now defined in a module · 0acb92c2
      Matthieu Muffato authored
      The function can thus be called from both the usual script init_pipeline.pl
      and the test interface
      0acb92c2
  5. 20 Jan, 2015 3 commits
  6. 19 Jan, 2015 4 commits
  7. 16 Jan, 2015 6 commits
  8. 15 Jan, 2015 1 commit
    • Matthieu Muffato's avatar
      bugfix: the claimed batch was not released · d9f1b05b
      Matthieu Muffato authored
      The problem was when a worker is contaminated and has to die: remainings jobs
      of the batch were not released.
      We now have an explicit list of all the cause_of_death that could happen through
      a batch, and for which we should free the jobs
      d9f1b05b