GitLab

bugfix: alldead mode did not set cause_of_death; now it sets it always to FATALITY (yes, there is certainly a better solution)

job_error table now holds jobs' termination messages; workers do not die when jobs die, but can be instructed to to so

adding a silent option (do not try to synchronize too much when the hive load is too high) and maximise_concurrency option (try to run as many concurrent analyses as possible instead of lots of jobs of one single analysis)

Added an optional Bio::EnsEMBL::Analysis argument to get_num_needed_workers subroutine, to only get the number of workers needed for this analysis

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.

control structure where a process/program has been made aware of the job(s)
they are responsible for controlling.  This is facilited via a job url:
   mysql://ia64e:3306/jessica_compara32b_tree/analysis_job?dbID=6065355
AnalysisJobAdptor::CreateNewJob now returns this url on job creation.
When a job is datflowed, an array of these urls is returned (one for each rule).
Jobs can now be dataflowed from a Process subclass with blocking enabled.
A job can be fetched directly with one of these URLs.
A commandline utility ehive_unblock.pl has been added to unblock a url job.
To unblock a job do:
   Bio::EnsEMBL::Hive::URLFactory->fetch($url)->update_status('READY');
This is primarily useful in asynchronous split process/parsing situations.

  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

is calculated.  If batch_size>0 use batch_size, else use avg_msec_per_job equation.

reordered where the blocking checks are done (added, deleted, moved).

a job that has been flowed into an analysis/process