GitLab

Bio::EnsEMBL::DBSQL::DBAdaptor to match symetry with core,pipeline,compara
This means I can remove all 'hive' adaptors from compara now and the
URLFactory now returns by default a Hive::DBSQL::DBAdaptor.
This also means I can make my graph configuring runnableDBs really
adaptible to run on both Pipeline and Hive systems by doing
if($self->db->isa('Bio::EnsEMBL::Pipeline::DBAdaptor')) {...}
if($self->db->isa('Bio::EnsEMBL::Hive::DBAdaptor')) {...}

'living' workers in the hive. Also changed the way adaptors are held
to avoid any problems of the type of DBAdaptor used to create the queen

this logic into the Queen

and summarizes it's state via analysis_stats.

URL's to specify analysis objects from mysql databases distributed
across a network.  AnalysisJobAdaptor was switched to create jobs with
a cless method that gets the db connection from the analysis object that
is passed.  Thus the system now exists in a distributed state.
The dataflow rule also implements branching via the branch_code.
SimpleRule will be deprecated.

workers) and added methods for reseting jobs for a lost worker.
$queen->register_worker_death($worker) without a defined cause_of_death
will register worker as a FATALITY and reset its unfinished jobs.

the analysis table/object.  New object class and tables includes a good
guess of what kind of stats I'll need for the Queen to monitor a hive
Also cleaned up some bugs caused by the extraction from compara.