ERROR DbScope 2018-07-26 10:08:18,596 localhost-startStop-1 : Cannot connect to DataSource "bc2statsDataSource" defined in labkey.xml. This DataSource will not be available during this server session. org.apache.tomcat.dbcp.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (Could not create connection to database server. Attempted reconnect 3 times. Giving up.) at org.apache.tomcat.dbcp.dbcp.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:1549) at org.apache.tomcat.dbcp.dbcp.BasicDataSource.createDataSource(BasicDataSource.java:1388) at org.apache.tomcat.dbcp.dbcp.BasicDataSource.getConnection(BasicDataSource.java:1044) at org.labkey.api.data.DbScope.(DbScope.java:318) at org.labkey.api.data.DbScope.addScope(DbScope.java:1096) at org.labkey.api.data.DbScope.initializeScopes(DbScope.java:1064) at org.labkey.api.module.ModuleLoader.initializeDataSources(ModuleLoader.java:963) at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:335) at org.labkey.api.module.ModuleLoader.init(ModuleLoader.java:247) at org.apache.catalina.core.ApplicationFilterConfig.initFilter(ApplicationFilterConfig.java:279) at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:260) at org.apache.catalina.core.ApplicationFilterConfig.(ApplicationFilterConfig.java:105) at org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:4908) at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5602) at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147) at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899) at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875) at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652) at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:677) at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1962) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: java.sql.SQLNonTransientConnectionException: Could not create connection to database server. Attempted reconnect 3 times. Giving up. at com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:108) at com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:95) at com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:87) at com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:61) at com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:71) at com.mysql.cj.jdbc.ConnectionImpl.connectWithRetries(ConnectionImpl.java:932) at com.mysql.cj.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:857) at com.mysql.cj.jdbc.ConnectionImpl.(ConnectionImpl.java:444) at com.mysql.cj.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:230) at com.mysql.cj.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:226) at org.apache.tomcat.dbcp.dbcp.DriverConnectionFactory.createConnection(DriverConnectionFactory.java:38) at org.apache.tomcat.dbcp.dbcp.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:582) at org.apache.tomcat.dbcp.dbcp.BasicDataSource.validateConnectionFactory(BasicDataSource.java:1556) at org.apache.tomcat.dbcp.dbcp.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:1545) ... 24 more ERROR DatasetDefinition 2018-07-26 10:08:34,100 Module Upgrade : Likely domain project/container mismatch for urn:lsid:unibas.ch:StudyDataset.Folder-9:Participants-6e2242cf-cbbf-1031-a374-504196604ae0. Container: /home/Security Tutorial/Study, marked as project: /sciCORE Group ERROR DatasetDefinition 2018-07-26 10:08:34,100 Module Upgrade : Failed to delete orphaned dataset domain urn:lsid:unibas.ch:StudyDataset.Folder-9:Participants-6e2242cf-cbbf-1031-a374-504196604ae0 in container /home/Security Tutorial/Study org.labkey.api.exp.DomainNotFoundException: Domain Not Found: urn:lsid:unibas.ch:StudyDataset.Folder-9:Participants-6e2242cf-cbbf-1031-a374-504196604ae0 at org.labkey.api.exp.OntologyManager.deleteDomain(OntologyManager.java:918) at org.labkey.experiment.api.property.DomainImpl.delete(DomainImpl.java:320) at org.labkey.study.model.DatasetDefinition.cleanupOrphanedDatasetDomains(DatasetDefinition.java:2671) at org.labkey.study.StudyModule.startupAfterSpringConfig(StudyModule.java:448) at org.labkey.api.module.SpringModule.doStartup(SpringModule.java:121) at org.labkey.api.module.DefaultModule.startup(DefaultModule.java:250) at org.labkey.api.module.ModuleLoader.completeStartup(ModuleLoader.java:1386) at org.labkey.api.module.ModuleLoader.initiateModuleStartup(ModuleLoader.java:1328) at org.labkey.api.module.ModuleLoader.afterUpgrade(ModuleLoader.java:1488) at org.labkey.api.module.ModuleLoader.lambda$startNonCoreUpgradeAndStartup$4(ModuleLoader.java:1470) at org.labkey.api.module.ModuleLoader$$Lambda$128/1689993671.run(Unknown Source) at java.lang.Thread.run(Thread.java:745) ERROR DatasetDefinition 2018-07-26 10:08:34,114 Module Upgrade : Likely domain project/container mismatch for urn:lsid:unibas.ch:StudyDataset.Folder-9:Physical+Exam-6e2242ce-cbbf-1031-a374-504196604ae0. Container: /home/Security Tutorial/Study, marked as project: /sciCORE Group ERROR DatasetDefinition 2018-07-26 10:08:34,114 Module Upgrade : Failed to delete orphaned dataset domain urn:lsid:unibas.ch:StudyDataset.Folder-9:Physical+Exam-6e2242ce-cbbf-1031-a374-504196604ae0 in container /home/Security Tutorial/Study org.labkey.api.exp.DomainNotFoundException: Domain Not Found: urn:lsid:unibas.ch:StudyDataset.Folder-9:Physical+Exam-6e2242ce-cbbf-1031-a374-504196604ae0 at org.labkey.api.exp.OntologyManager.deleteDomain(OntologyManager.java:918) at org.labkey.experiment.api.property.DomainImpl.delete(DomainImpl.java:320) at org.labkey.study.model.DatasetDefinition.cleanupOrphanedDatasetDomains(DatasetDefinition.java:2671) at org.labkey.study.StudyModule.startupAfterSpringConfig(StudyModule.java:448) at org.labkey.api.module.SpringModule.doStartup(SpringModule.java:121) at org.labkey.api.module.DefaultModule.startup(DefaultModule.java:250) at org.labkey.api.module.ModuleLoader.completeStartup(ModuleLoader.java:1386) at org.labkey.api.module.ModuleLoader.initiateModuleStartup(ModuleLoader.java:1328) at org.labkey.api.module.ModuleLoader.afterUpgrade(ModuleLoader.java:1488) at org.labkey.api.module.ModuleLoader.lambda$startNonCoreUpgradeAndStartup$4(ModuleLoader.java:1470) at org.labkey.api.module.ModuleLoader$$Lambda$128/1689993671.run(Unknown Source) at java.lang.Thread.run(Thread.java:745)