GitLab

cosmetic: not sure if we need this module to be around. The only purpose it currently serves is to muddy the waters when it comes to documentation.

removed rearrange() and throw() from AnalysisJobAdaptor by removing the unused CreateNewJob() method

Storable->new() now performs setting of all parameters without the use of rearrange (NB: change of call format!)

core-independent version of DBAdaptor. new() clean from URLFactory and self-reference, but still plays nice with optional Registry

fix: HiveGeneric_conf needs to declare that it in fact uses Registry (this could move into EnsemblGeneric_conf together with ApiVersion)

removed dependency on Core's DBSQL::BaseAdaptor and Storable by introducing own lightweight Hive::Storable

cosmetic: added deprecated message to CreateNewJob() and some documentation to store_jobs_and_adjust_counters()

store_jobs_and_adjust_counters() now also deals with semaphore_count corrections. It is now the preferred job-creation interface.

bugfix: no hope for other DBD drivers to support detection of auto-incrementing fields => use our inernal fixed rule

bugfix: stop printing overflow-related debug output to STDOUT; interface with overflow adaptor simplified

bugfix: substituting --password for --pass to pacify mysql 5.5.34+ that no longer recognizes options by their prefix

drop fetch_all_by_from_analysis_id_and_branch_code() method and rely on AUTOLOADed BaseAdaptor's methods instead

If greedy disoriented Workers overshoot analysis_capacity|hive_capacity, make sure they respecialize after the first batch

Individual Worker's specialization is now routed through Scheduler's main subroutine, to enforce more checks