GitLab

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/

Only redefine locally methods in Bio::EnsEMBL::Hive::Process (to allow the later implementation of runWorker to use them)

* 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

The function can thus be called from both the usual script
standaloneJob.pl and the test interface

The function can thus be called from both the usual script init_pipeline.pl
and the test interface