Errors in jobs:
2016-10-06 14:41:01 [244478ea5b01dbb5fb34b0a9] mw1169 wikidatawiki 1.28.0-wmf.20 exception ERROR: [244478ea5b01dbb5fb34b0a9] /rpc/RunJobs.php?wiki=wikidatawiki&type=refreshLinks&maxtime=30&maxmem=300M Wikibase\DataModel\Entity\EntityIdParsingException from line 54 of /srv/mediawiki/php-1.28.0-wmf.20/extensions/Wikidata/vendor/wikibase/data-model/src/Entity/DispatchingEntityIdParser.php: The serialization "Q10000000000" is not recognized by the configured id builders {"exception_id":"244478ea5b01dbb5fb34b0a9"} [Exception Wikibase\DataModel\Entity\EntityIdParsingException] (/srv/mediawiki/php-1.28.0-wmf.20/extensions/Wikidata/vendor/wikibase/data-model/src/Entity/DispatchingEntityIdParser.php:54) The serialization "Q10000000000" is not recognized by the configured id builders #0 /srv/mediawiki/php-1.28.0-wmf.20/extensions/Wikidata/extensions/Wikibase/client/includes/Usage/Sql/EntityUsageTable.php(202): Wikibase\DataModel\Entity\DispatchingEntityIdParser->parse(string) #1 /srv/mediawiki/php-1.28.0-wmf.20/extensions/Wikidata/extensions/Wikibase/client/includes/Usage/Sql/EntityUsageTable.php(179): Wikibase\Client\Usage\Sql\EntityUsageTable->convertRowsToUsages(ResultWrapper) #2 /srv/mediawiki/php-1.28.0-wmf.20/extensions/Wikidata/extensions/Wikibase/client/includes/Usage/Sql/SqlUsageTracker.php(179): Wikibase\Client\Usage\Sql\EntityUsageTable->queryUsages(integer) #3 /srv/mediawiki/php-1.28.0-wmf.20/extensions/Wikidata/extensions/Wikibase/client/includes/Store/UsageUpdater.php(107): Wikibase\Client\Usage\Sql\SqlUsageTracker->replaceUsedEntities(integer, array) #4 /srv/mediawiki/php-1.28.0-wmf.20/extensions/Wikidata/extensions/Wikibase/client/includes/Hooks/DataUpdateHookHandlers.php(139): Wikibase\Client\Store\UsageUpdater->replaceUsagesForPage(integer, array) #5 /srv/mediawiki/php-1.28.0-wmf.20/extensions/Wikidata/extensions/Wikibase/client/includes/Hooks/DataUpdateHookHandlers.php(63): Wikibase\Client\Hooks\DataUpdateHookHandlers->doLinksUpdateComplete(LinksUpdate) #6 /srv/mediawiki/php-1.28.0-wmf.20/includes/Hooks.php(195): Wikibase\Client\Hooks\DataUpdateHookHandlers::onLinksUpdateComplete(LinksUpdate) #7 /srv/mediawiki/php-1.28.0-wmf.20/includes/deferred/LinksUpdate.php(179): Hooks::run(string, array) #8 /srv/mediawiki/php-1.28.0-wmf.20/includes/libs/rdbms/database/Database.php(2593): Closure$LinksUpdate::doUpdate(integer) #9 /srv/mediawiki/php-1.28.0-wmf.20/includes/libs/rdbms/loadbalancer/LoadBalancer.php(1133): Database->runOnTransactionIdleCallbacks(integer) #10 /srv/mediawiki/php-1.28.0-wmf.20/includes/libs/rdbms/loadbalancer/LoadBalancer.php(1357): Closure$LoadBalancer::runMasterPostTrxCallbacks(DatabaseMysqli) #11 /srv/mediawiki/php-1.28.0-wmf.20/includes/libs/rdbms/loadbalancer/LoadBalancer.php(1142): LoadBalancer->forEachOpenMasterConnection(Closure$LoadBalancer::runMasterPostTrxCallbacks;929355047) #12 /srv/mediawiki/php-1.28.0-wmf.20/includes/libs/rdbms/lbfactory/LBFactory.php(312): LoadBalancer->runMasterPostTrxCallbacks(integer) #13 /srv/mediawiki/php-1.28.0-wmf.20/includes/libs/rdbms/lbfactory/LBFactoryMulti.php(407): Closure$LBFactory::commitMasterChanges(LoadBalancer) #14 /srv/mediawiki/php-1.28.0-wmf.20/includes/libs/rdbms/lbfactory/LBFactory.php(314): LBFactoryMulti->forEachLB(Closure$LBFactory::commitMasterChanges;1602246427) #15 /srv/mediawiki/php-1.28.0-wmf.20/includes/jobqueue/JobRunner.php(526): LBFactory->commitMasterChanges(string) #16 /srv/mediawiki/php-1.28.0-wmf.20/includes/jobqueue/JobRunner.php(276): JobRunner->commitMasterChanges(LBFactoryMulti, RefreshLinksJob, string) #17 /srv/mediawiki/php-1.28.0-wmf.20/includes/jobqueue/JobRunner.php(184): JobRunner->executeJob(RefreshLinksJob, LBFactoryMulti, BufferingStatsdDataFactory, integer) #18 /srv/mediawiki/rpc/RunJobs.php(47): JobRunner->run(array) #19 {main}
The problem here is that the wbc_entity_usage table contains entity ids which are (no longer) valid. These can be identified by querying SELECT * FROM wbc_entity_usage WHERE LENGTH(eu_entity_id) > 10 AND REPLACE(REPLACE(eu_entity_id, 'Q', ''), 'P', '') > 2147483647;. EntityUsageTable is not able to purge these given it can't even construct entity id objects for them.
I suggest deleting these row manually (by primary key, given the above query is a little expensive). We could also look at making EntityUsageTable just purge rows it can't turn into entity ids.