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Created with Raphaël 2.2.027Jan26242322201916151312987522Dec1918418Nov171514131110754329Oct27252421201716151310763130Sep2926252423221918842128Aug12418Jul169843130Jun27171311105423May222120191615141398230Apr292524231611109432128Mar272625242120181713121110713Feb111076431Jan30282724221714138719Dec16121194327Nov2521191812116525Oct241582127Sep262523222119161311109use job breakout_label as more legibleImplementation of runWorkerOnly redefine locally methods in Bio::EnsEMBL::Hive::Process (to allow the later implementation of runWorker to use them)init_pipeline now returns $hive_dbaThe hive_driver should not be hardcodedUse isa_ok()Fixup the last merge of masterMerge branch 'master' into feature/tests_cistandaloneJob core code is now defined in a moduleinit_pipeline core code is now defined in a moduleoptimization: avoid calling count_running_workers twice per Scheduler iterationstart using meadow_user for querying the LSFadded autoloaded counting in groups; removed some undefined value warningsbugfix: record job_id, role_id and worker_id of the job that deadlocked when checking inlogging of deadlocks via callbackinterface_change: protected_prepare_execute() takes all sql-related parameters as first argumentwait for random time with increasing upper boundarylog deadlocks and retries in log_messagegrab_jobs_for_role now uses PPE instead of bare do()PPE now returns a valuecapture all "dies" during worker->run() and try to record them in log_messagepulled in the "non-critical specialization failures" bugfix from upstreampulled in the "non-critical specialization failures" bugfix from upstreampulled in the "non-critical specialization failures" bugfix from upstreampulled in the "non-critical specialization failures" bugfix from upstreambugfix: specialization failures should not be considered criticalbugfix: the claimed batch was not releasedMySQL and PostgreSQL have a maximum length for database namesAdded 'meadow_user' to Worker object+schema which is now routinely recorded. Also renamed 'host' to 'meadow_host' for consistencysql_schema_63_s…sql_schema_63_startAllow script-based schema patches that can use API in addition to pure SQL-based patchesCheck that all the events have been raisedfixup: msgThe import is tested laterNew test function for init_pipeline (replaces Hive::Config)New argument to test the dataflow and warning events raised by the runnableApiarist is not needed any more because we have a way of testing runnablesTest data moved to its own file + use the test-standaloneJob methodNew method to test a Runnable in standaloneJob modeRemoved the unused import path t/libMoved more things to Hive::Utils::Test