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')) {...}

when ALL of their conditions are 'DONE')

'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

added method fetch_by_needed_workers for queen to determine new worker
types

so the base adaptor will be a compara DBAdaptor which inherits from the
core DBAdaptor

directory if one isn't specified

a machine.  Very rough and not fully functional.

this logic into the Queen

and summarizes it's state via analysis_stats.

are bound to analysis rather than being distinct

setter analysis share the same adaptor (same database) then use the
logic_name as the url rather than a full url.

added default values of 1 to batch_size and hive_capacity

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.

Should output into a file and register as a analysis_job_file.

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.