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  1. 05 Feb, 2015 2 commits
  2. 04 Feb, 2015 2 commits
  3. 02 Feb, 2015 5 commits
  4. 31 Jan, 2015 1 commit
    • Matthieu Muffato's avatar
      Merge branch 'feature/tests_ci' · 9bdbabbf
      Matthieu Muffato authored
      Test-suite for many eHive modules (thanks kiwiroy !)
      New Hive::Utils::Test module that allows to test:
       - a runnable in standalone job mode
       - the initialisation of a pipeline
       - running a worker
      
      As part of this process, several scripts are now mainly defined in modules
      under Scripts/
      9bdbabbf
  5. 29 Jan, 2015 14 commits
  6. 28 Jan, 2015 1 commit
  7. 27 Jan, 2015 13 commits
  8. 26 Jan, 2015 1 commit
  9. 24 Jan, 2015 1 commit
    • 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