GitLab

need that vacation ;-)

Removed single quote around a question mark in the prepare statement. Otherwise it is not considered as an argument to be passed in the execute statement later on

defined in the analysis_stats table

(was still using the original idea of setting batch_size as
constant in the RunnableDB class).  Need to deprecate that idea.

state of all jobs on the hive.  added get_analysis method to
AnalysisStates which loads the analysis for the analysis_id.  Modified
print_stats to produce a more descriptive table of stats.

needed clutches and prints them for the user with 'bsub' commands which
then the user can choose to run or modify

analyses by fetching all the control rules and checking the distributed
conditions that they are all 'DONE'

analysis objects adaptor to fetch the corresponding stats object.
Important to use correct db connection since the analysis objects may be
network distributed across multiple databases

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.