Initially used to manually re-run a job with runWorker.pl -job_id

and Analysis::RunnableDB superclasses

properly handle RunnableDBs that throw exceptions in the fetch_input stage.

changed INSERT syntax to be more SQL compliant

changed INSERT syntax to be more SQL compliant

changed INSERT syntax to be more SQL compliant

Set the OUTPUT_AUTOFLUSH=1 to get info immediately when in -loop mode. Also print out the time when the next loop will occur

In synchronize_AnalysisStats method, added a POSIX::ceil when setting the num_required_workers for an AnalysisStats object

used to always store a full URL

in AnalysisStatsAdaptor::fetch_by_analysis_id

modified  Bio::EnsEMBL::Analysis::stats to not do any exception catching
if  AnalysisStatsAdaptor->fetch_by_analysis_id fails there is something
very wrong and the exception should propogate out and cause the program to fail

Bio::EnsEMBL::Analysis::RunnableDB via namespace extension syntax
so that hive system can use analysis.modules that inherit from Bio::EnsEMBL::Analysis::RunnableDB

and gives the user a good overview of where processing is at.
added -analysis_stats and -worker_stats which give full statistics on all analyses
and all running workers respectfully.

'total jobs' count so one can calculate a 'progress bar'

and print_running_worker_status.

used by lsf_beekeeper to decide when it needs to do a hard resync.

to run with.  eg $worker->run($job);  This job can be pulled from database
or created on the fly.  This is to accomodate debug modes of runWorker.pl

no longer does Queen::synchronize_hive as part of autonomous loop
-sync option allows user to manually trigger a hard sync.
also removed default display of full hive status and addded option -status
which will print this full status.
Also removed adjusting needed worker count for 'pending' workers. lsf will
sometimes leave jobs in pending state for no apparent reason (new bsubed job
will run yet older pending job stays pending). Current 'pending' count also didn't
differentiate between lsf_beekeeper submited jobs and manually submitted
jobs. This pend adjustment isn't a critcal subsystem so I've removed it for
now.  If a runWorker starts (after a long pend) and there is no work left
it will die immeadiately.  I may rewrite a smarter 'pending' adjustment
in the future.

and distributed manner as it interacts with the workers over the course of its life.
When a runWorker.pl script starts and asks a queen to create a worker the queen has
a list of known analyses which are 'above the surface' where full hive analysis has
been done and the number of needed workers has been calculated. Full synch requires
joining data between the analysis, analysis_job, analysis_stats, and hive tables.
When this reached 10e7 jobs, 10e4 analyses, 10e3 workers a full hard sync took minutes
and it was clear this bit of the system wasn't scaling and wasn't going to make it
to the next order of magnitude. This occurred in the compara blastz pipeline between
mouse and rat.
Now there are some analyses 'below the surface' that have partial synchronization.
These analyses have been flagged as having 'x' new jobs (AnalysisJobAdaptor updating
analysis_stats on job insert).  If no analysis is found to asign to the newly
created worker, the queen will dip below the surface and start checking
the analyses with the highest probablity of needing the most workers.
This incremental sync is also done in Queen::get_num_needed_workers
When calculating ahead a total worker count, this routine will also dip below
the surface until the hive reaches it's current defined worker saturation.
A beekeeper is no longer a required component for the system to function.
If workers can get onto cpus the hive will run.  The beekeeper is now mainly a
user display program showing the status of the hive.  There is no longer any
central process doing work and one hive can potentially scale
beyond 10e9 jobs in graphs of 10e6 analysis nodes and 10e6 running workers.

the most time since last update are at the top of the returned list

When jobs are inserted into the analysis_job table, the analysis_stats table
for the given analysis is updated by incrementing the total_job_count,
and unclaimed_job_count and setting the status to 'LOADING'.
If the analysis is 'BLOCKED' this incremental update does not happen.
When an analysis_stats is 'BLOCKED' and then unblocked this automatically
will trigger a resync so this progress partial update is not needed.

sync unless some jobs have been loaded.

also changed default to 'LOADING' so that it can trigger a sync

than one status