This project is mirrored from https://:*****@github.com/Ensembl/ensembl-hive.git. Pull mirroring updated .
  1. 11 Aug, 2010 1 commit
  2. 16 Jul, 2010 1 commit
  3. 12 Jul, 2010 1 commit
  4. 25 Jun, 2010 1 commit
  5. 26 Mar, 2010 1 commit
  6. 11 Jan, 2010 1 commit
  7. 11 Dec, 2009 2 commits
  8. 03 Dec, 2009 1 commit
  9. 24 Sep, 2009 2 commits
  10. 23 Sep, 2009 1 commit
  11. 14 Aug, 2008 1 commit
  12. 28 May, 2008 1 commit
  13. 16 Nov, 2006 1 commit
  14. 14 Mar, 2006 1 commit
  15. 06 Mar, 2006 1 commit
  16. 22 Nov, 2005 1 commit
    • Jessica Severin's avatar
      removed a residual (pre autocalc of batchsize from runtime statistics) · bd83c1eb
      Jessica Severin authored
      design element in Worker::batch_size
      - old design: setting the batch_size for a worker changed the batch_size for
        all workers by updating the analysis_stats.batch_size of the corresponding
        analysis. Although this code was never triggered in the current system, it
        could have caused potential problems for future developers.
      Now setting the batch_size explicitly for a worker only effects the
      batch_size for that Worker instance. If it has not been set, the Worker pulls
      the batch_size from the analysis_stats record and optionally autocalcs from
      avg_msec_per_job if the batch_size<=0.
      bd83c1eb
  17. 07 Nov, 2005 1 commit
  18. 14 Oct, 2005 1 commit
  19. 01 Oct, 2005 1 commit
    • Jessica Severin's avatar
      Improved system for running specific jobs. System now properly runs · f971d01f
      Jessica Severin authored
      jobs that were created outside the database.  Also added ability to not
      write (doesn't execute write_output or dataflow jobs).  Improved logic so
      that if a job is specified, but something is wrong that the worker fails
      rather than reverting to autonomous behaviour mode.
      Fully tested by running a complete homology production test.
      f971d01f
  20. 22 Sep, 2005 1 commit
  21. 09 Aug, 2005 1 commit
  22. 13 Jun, 2005 1 commit
    • Jessica Severin's avatar
      - moved worker/process code related to persistant /tmp/worker_## directory · c8c45241
      Jessica Severin authored
        into the Worker object (and out of the Process)
      - added Process::worker method so that running processes can talk to the
        worker that is currently running itself.
      - modified system so that if a process subclass uses Process::dataflow_output_id
        on branch_code 1, it will turn off the automatic of flowing of the input_job
        out on branch_code 1.  This will make coding much cleaner so that processes
        no longer need to modifiy the input_id of the input_job
      - added method Process::autoflow_inputjob which toggles this autoflow behaviour
        if a subclass would like to modify this directly
      - auto_dataflow now happens right after the Process::write_output stage
      c8c45241
  23. 04 Mar, 2005 2 commits
  24. 03 Mar, 2005 2 commits
    • Jessica Severin's avatar
      changed the way the output_dir is created. The hive_id is split so that · 1a3fce82
      Jessica Severin authored
      each digit becomes a directory with a final directory created with the full hive_id
      hive_id=1234 => <base_dir>/1/2/3/4/hive_id_1234/
      hive_id=12   => <base_dir>/1/2/hive_id_12/
      this should distribute the output directories
      1a3fce82
    • Jessica Severin's avatar
      created Bio::EnsEMBL::Hive::Process as a processing module superclass alternative · 55cd98de
      Jessica Severin authored
      to RunnableDB to allow full benefit of dataflow graph capabilities.
      - Removed from Extension.pm branch_code, analysis_job_id, reset_job extensions to
        RunnableDB (no longer trying to shoe-horn hive 'extra' functions into them)
      - Bio::EnsEMBL::Hive::Process mirrors some of the RunnableDB interface
        (new, analysis, fetch_input, run, write_output)
        but uses a new job interface (input_job, dataflow_output_id) instead of
        input_id (but provides convenience method $self->input_id which redirects to
        $self->input_job->input_id to simplify porting)
      - Changed Worker to only use hive 'extended' function if the processing module
        isa(Bio::EnsEMBL::Hive::Process).  Also allows all RunnableDB modules to
        still be used (or any object which implements a minimal 'RunnableDB interface')
        (new, input_id, db, fetch_input, run, write_output)
      55cd98de
  25. 23 Feb, 2005 1 commit
  26. 21 Feb, 2005 1 commit
    • Jessica Severin's avatar
      YAHRF (Yet Another Hive ReFactor).....chapter 1 · 7675c31c
      Jessica Severin authored
      needed to better manage the hive system's load on the database housing all
      the hive related tables (in case the database is overloaded by multiple users).
      Added analysis_stats.sync_lock column (and correspondly in Object and Adaptor)
      Added Queen::safe_synchronize_AnalysisStats method which wraps over the
        synchronize_AnalysisStats method and does various checks and locks to ensure
        that only one worker is trying to do a 'synchronize' on a given analysis at
        any given moment.
      Cleaned up API between Queen/Worker so that worker only talks directly to the
        Queen, rather than getting the underlying database adaptor.
      Added analysis_job columns runtime_msec, query_count to provide more data on
        how the jobs hammer a database (queries/sec).
      7675c31c
  27. 17 Feb, 2005 1 commit
  28. 16 Feb, 2005 1 commit
  29. 10 Feb, 2005 1 commit
  30. 04 Feb, 2005 1 commit
    • Jessica Severin's avatar
      new calculation of avg_msec_per_job · d3ab594d
      Jessica Severin authored
      better debug system to allow worker to control analysis debug level
      new batch_size method will use avg_msec_per_job to calculate batch_size on the fly
        if analysis_stat.batch_size==0
      d3ab594d
  31. 13 Jan, 2005 1 commit
  32. 12 Jan, 2005 1 commit
  33. 24 Nov, 2004 1 commit
  34. 17 Nov, 2004 1 commit
  35. 16 Nov, 2004 1 commit
  36. 04 Nov, 2004 1 commit