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Created with Raphaël 2.2.09Oct85432128Sep2726252120754329Aug282725242317161432131Jul25242316329Jun27262522191513111086131May30282322211817121110982123Apr1627Mar2620197124Feb23201615141031Jan208Dec29Nov2825242322211710415Oct23Sep2095125Aug181526Jul201514131286542130Jun2916151473231May2827262524232120191612111095319Apr1814131130Mar292624231817161210921Feb27Jan2120191412111065431Dec282321141326Nov26Oct22191884130Sep2826232221201614131110987432131Aug242320131211109516Jul141312230Jun2928252318171615141310326May20181714131211107654330Apr28272630Mar2624232219108427Feb2625231918171615426Jan2522161111Dec843230Nov271918216Oct1329Sep24232111Aug320Jul1327May13827Apr313Mar15Feb1215Jan9Dec30Oct2922Sep14Aug11Jul28May18Apr12Mar14Dec16Nov22May7Mar1Feb16Nov12Oct29Sep412Jun85Maybugfix: forgot to add semaphored_job_count to SQLite schema, now includedturned two unique keys into primary keys (needed by BaseAdaptor)allow the batch_size to be updated via $analysis_stats_adaptor->update($stats);removed the input_id functionality from runWorker as both redundant (standaloneJob) and probably not workingthose "return" statements would have never worked anyway, so I removed themextend the param_init() of the garbage-collected jobs to include analysis->parameters() for template substitution (still limited!)cause_of_death="" no longer used for decision making, cause_of_death IS NULL by default and FATALITY renamed UNKNOWN for clarityfetch_failed_workers() is dropped as no longer used, get_hive_current_load() cosmetically touchedEMPTY 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 joining