• 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
Extensions.pm 6.39 KB