GitLab

removed the input_id functionality from runWorker as both redundant (standaloneJob) and probably not working

extend the param_init() of the garbage-collected jobs to include analysis->parameters() for template substitution (still limited!)

cause_of_death="" no longer used for decision making, cause_of_death IS NULL by default and FATALITY renamed UNKNOWN for clarity

introduced semaphored_job_count, renamed unclaimed_job_count-->ready_job_count, changed reporting, fixed hive_capacity=0

moved failed_job_tolerance, max_retry_count, can_be_empty and priority columns from analysis_stats to analysis_base

bugfix: changed the order of the atomic SEMAPHORED->READY state&counter UPDATE so that it works as intended in SQLite as well

added specific defaults into analysis_stats and analysis_stats_monitor; re-ordered the fields for easier navigation

make AnalysisStats a rearrangeable EnsEMBL-style constructor, a proper store method and other preparations

retired the cmd_hive.pl script; likely not working and duplicating functionality of more flexible PipeConfig

switched Queen to become descendent of Hive::DBSQL::ObjectAdaptor and removed _generic_fetch from it

Dropped 'BLOCKED' job status and introduced 'SEMAPHORED' status that is maintained in sync with semaphore_counts; less confusing and more efficient (with new 3-part index)

record each Workers log_dir in the database; simplified the log_dir code and renamed cmdline options accordingly

allow JOIN to appear in the constraint and act wisely - so we do not need extra complicated syntax for joining