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Created with Raphaël 2.2.04Oct32128Sep2726252120754329Aug282725242317161432131Jul25242316329Jun27262522191513111086131May30282322211817121110982123Apr1627Mar2620197124Feb23201615141031Jan208Dec29Nov2825242322211710415Oct23Sep2095125Aug181526Jul201514131286542130Jun2916151473231May2827262524232120191612111095319Apr1814131130Mar292624231817161210921Feb27Jan2120191412111065431Dec282321141326Nov26Oct22191884130Sep2826232221201614131110987432131Aug242320131211109516Jul141312230Jun2928252318171615141310326May20181714131211107654330Apr28272630Mar2624232219108427Feb2625231918171615426Jan2522161111Dec843230Nov271918216Oct1329Sep24232111Aug320Jul1327May13827Apr313Mar15Feb1215Jan9Dec30Oct2922Sep14Aug11Jul28May18Apr12Mar14Dec16Nov22May7Mar1Feb16Nov12Oct29Sep412Jun85May22Mar1715146EMPTY state added and definitions of READY and WORKING made more intuitivebugfix: a typointroduced semaphored_job_count, renamed unclaimed_job_count-->ready_job_count, changed reporting, fixed hive_capacity=0common denominator for schedule_workers and specialize_new_workerFetching data via AnalysisAdaptor allows to print logic_names of failed analysesprint stats if could not create worker anyway, but do not sync in the end (too cryptic)renamed -input_job_id to -prev_job_id to be in sync with other namesupdated schema diagramsmoved failed_job_tolerance, max_retry_count, can_be_empty and priority columns from analysis_stats to analysis_basebugfix: do not forget PRE_- and POST_CLEANUP statesbugfix: changed the order of the atomic SEMAPHORED->READY state&counter UPDATE so that it works as intended in SQLite as welladded a fake default to last_update field (required by stricter MySQL setup of Vega)added specific defaults into analysis_stats and analysis_stats_monitor; re-ordered the fields for easier navigationbugfix: fetch_by_dbID should work now (thanks to ChuangKee and Miguel)bugfix: primary_key_constraint now works (thanks to Miguel!)bugfix: typo fixed, thanks to Miguel for pointing out!make AnalysisStats a rearrangeable EnsEMBL-style constructor, a proper store method and other preparationssimplification of DYNAMIC hive_capacity update coderetired the cmd_hive.pl script; likely not working and duplicating functionality of more flexible PipeConfigbugfix: also release jobs that were in PRE_CLEANUP or POST_CLEANUP statesswitched Queen to become descendent of Hive::DBSQL::ObjectAdaptor and removed _generic_fetch from itrearranged Worker's storable getters/setters, introduced and used a proper rearranging new() methodWorker doesnt really need its own reference to db (can go via adaptor)bugfix: GROUP BY now includes a proper prefix of the indexDropped 'BLOCKED' job status and introduced 'SEMAPHORED' status that is maintained in sync with semaphore_counts; less confusing and more efficient (with new 3-part index)record each Workers log_dir in the database; simplified the log_dir code and renamed cmdline options accordinglymoved resource_class_id from analysis_stats and analysis_stats_monitor to analysis_basefetch_all never seems to be executed for these adaptorsbugfix: better parsing of the LSF-job-nameoptimization: worker should not sync analyses it is not ready to runreplaced internal rc_id by rc_name in the Meadow code and in most of the Scheduler; needs testingallow JOIN to appear in the constraint and act wisely - so we do not need extra complicated syntax for joiningnot ready yet to scrap the "Runnable" support(patch offered by Matthieu) Allow the Job to kill the Worker even on succecssUpdated the list of eHive tablesthese methods are already defined in the parent classtrimmed the commented-out 'use' statementsslimmed down the Extensions module a bit (valuable code already moved into Hive::Analysis)substituted the overloaded legacy 'analysis' table by a slimmer 'analysis_base'actually switch to using rc_name in the workers commandline