17-Jan-2022 11:49:26.976 WARN [http-nio-20022-exec-54] o.s.d.i.BasicSqlService.dbRead Sql.dbRead: sql: select SS.GROUP_ID, SS.TITLE, SS.DESCRIPTION from SAKAI_SITE_GROUP SS where SS.SITE_ID = ? citationsAdmin java.sql.SQLTransientConnectionException: sakai - Connection is not available, request timed out after 51646ms. at com.zaxxer.hikari.pool.HikariPool.createTimeoutException(HikariPool.java:696) ~[HikariCP-4.0.3.jar:?] at com.zaxxer.hikari.pool.HikariPool.getConnection(HikariPool.java:197) ~[HikariCP-4.0.3.jar:?] at com.zaxxer.hikari.pool.HikariPool.getConnection(HikariPool.java:162) ~[HikariCP-4.0.3.jar:?] at com.zaxxer.hikari.HikariDataSource.getConnection(HikariDataSource.java:128) ~[HikariCP-4.0.3.jar:?] at org.sakaiproject.db.impl.BasicSqlService.borrowConnection(BasicSqlService.java:258) ~[sakai-kernel-impl-22-SNAPSHOT.jar:?] at org.sakaiproject.db.impl.BasicSqlService.dbRead(BasicSqlService.java:538) [sakai-kernel-impl-22-SNAPSHOT.jar:?] at org.sakaiproject.db.impl.BasicSqlService.dbRead(BasicSqlService.java:469) [sakai-kernel-impl-22-SNAPSHOT.jar:?] at org.sakaiproject.site.impl.DbSiteService$DbStorage.readSiteGroups(DbSiteService.java:2507) [sakai-kernel-impl-22-SNAPSHOT.jar:?] at org.sakaiproject.site.impl.BaseSite.getGroups(BaseSite.java:1030) [sakai-kernel-impl-22-SNAPSHOT.jar:?] at org.sakaiproject.site.impl.BaseSite.getGroups(BaseSite.java:1009) [sakai-kernel-impl-22-SNAPSHOT.jar:?] at org.sakaiproject.site.impl.SiteCacheSafe.notifyCacheRemove(SiteCacheSafe.java:288) [sakai-kernel-impl-22-SNAPSHOT.jar:?] at org.sakaiproject.site.impl.SiteCacheSafe.onRemoved(SiteCacheSafe.java:329) [sakai-kernel-impl-22-SNAPSHOT.jar:?] at org.sakaiproject.site.impl.SiteCacheSafe.onExpired(SiteCacheSafe.java:320) [sakai-kernel-impl-22-SNAPSHOT.jar:?] at org.sakaiproject.memory.impl.EhcacheCache.notifyElementExpired(EhcacheCache.java:344) [sakai-kernel-impl-22-SNAPSHOT.jar:?] at net.sf.ehcache.event.RegisteredEventListeners.notifyListener(RegisteredEventListeners.java:298) [ehcache-core-2.6.11.jar:?] at net.sf.ehcache.event.RegisteredEventListeners.invokeListener(RegisteredEventListeners.java:284) [ehcache-core-2.6.11.jar:?] at net.sf.ehcache.event.RegisteredEventListeners.internalNotifyElementExpiry(RegisteredEventListeners.java:216) [ehcache-core-2.6.11.jar:?] at net.sf.ehcache.event.RegisteredEventListeners.notifyElementExpiry(RegisteredEventListeners.java:194) [ehcache-core-2.6.11.jar:?] at net.sf.ehcache.Cache.notifyRemoveInternalListeners(Cache.java:2351) [ehcache-core-2.6.11.jar:?] at net.sf.ehcache.Cache.removeInternal(Cache.java:2337) [ehcache-core-2.6.11.jar:?] at net.sf.ehcache.Cache.tryRemoveImmediately(Cache.java:2117) [ehcache-core-2.6.11.jar:?] at net.sf.ehcache.Cache.searchInStoreWithStats(Cache.java:1963) [ehcache-core-2.6.11.jar:?] at net.sf.ehcache.Cache.get(Cache.java:1584) [ehcache-core-2.6.11.jar:?] at org.sakaiproject.memory.impl.EhcacheCache.get(EhcacheCache.java:84) [sakai-kernel-impl-22-SNAPSHOT.jar:?] at org.sakaiproject.site.impl.SiteCacheSafe.get(SiteCacheSafe.java:135) [sakai-kernel-impl-22-SNAPSHOT.jar:?] at org.sakaiproject.site.impl.BaseSiteService.siteExists(BaseSiteService.java:748) [sakai-kernel-impl-22-SNAPSHOT.jar:?] at org.sakaiproject.content.impl.BaseContentService.parseEntityReference(BaseContentService.java:8541) [sakai-kernel-impl-22-SNAPSHOT.jar:?] at org.sakaiproject.entity.impl.EntityManagerComponent.getEntityProducerNoDebug(EntityManagerComponent.java:463) [sakai-kernel-impl-22-SNAPSHOT.jar:?] at org.sakaiproject.entity.impl.EntityManagerComponent.getEntityProducer(EntityManagerComponent.java:329) [sakai-kernel-impl-22-SNAPSHOT.jar:?] at org.sakaiproject.entity.impl.ReferenceComponent.parse(ReferenceComponent.java:406) [sakai-kernel-impl-22-SNAPSHOT.jar:?] at org.sakaiproject.entity.impl.ReferenceComponent.(ReferenceComponent.java:89) [sakai-kernel-impl-22-SNAPSHOT.jar:?] at org.sakaiproject.entity.impl.EntityManagerComponent.newReference(EntityManagerComponent.java:261) [sakai-kernel-impl-22-SNAPSHOT.jar:?] at org.sakaiproject.citation.impl.BaseConfigurationService.exists(BaseConfigurationService.java:1606) [sakai-citations-impl-22-SNAPSHOT.jar:?] at org.sakaiproject.citation.impl.BaseConfigurationService.isConfigurationXmlAvailable(BaseConfigurationService.java:216) [sakai-citations-impl-22-SNAPSHOT.jar:?] at org.sakaiproject.citation.impl.BaseConfigurationService.librarySearchEnabled(BaseConfigurationService.java:1670) [sakai-citations-impl-22-SNAPSHOT.jar:?] at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:?] at jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:?] at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?] at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?] at org.sakaiproject.util.EditorConfiguration.enableResourceSearch(EditorConfiguration.java:94) [sakai-kernel-util-22-SNAPSHOT.jar:?] at org.sakaiproject.portal.charon.SkinnableCharonPortal.toolHeaderProperties(SkinnableCharonPortal.java:1352) [sakai-portal-impl-22-SNAPSHOT.jar:22-SNAPSHOT] at org.sakaiproject.portal.charon.SkinnableCharonPortal.startPageContext(SkinnableCharonPortal.java:1094) [sakai-portal-impl-22-SNAPSHOT.jar:22-SNAPSHOT] at org.sakaiproject.portal.charon.handlers.SiteHandler.doSite(SiteHandler.java:493) [sakai-portal-impl-22-SNAPSHOT.jar:22-SNAPSHOT] at org.sakaiproject.portal.charon.handlers.SiteHandler.doGet(SiteHandler.java:275) [sakai-portal-impl-22-SNAPSHOT.jar:22-SNAPSHOT] at org.sakaiproject.portal.charon.handlers.SiteHandler.doGet(SiteHandler.java:163) [sakai-portal-impl-22-SNAPSHOT.jar:22-SNAPSHOT] at org.sakaiproject.portal.charon.SkinnableCharonPortal.doGet(SkinnableCharonPortal.java:857) [sakai-portal-impl-22-SNAPSHOT.jar:22-SNAPSHOT] at javax.servlet.http.HttpServlet.service(HttpServlet.java:655) [servlet-api.jar:4.0.FR] at javax.servlet.http.HttpServlet.service(HttpServlet.java:764) [servlet-api.jar:4.0.FR] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:227) [catalina.jar:9.0.54] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) [catalina.jar:9.0.54] at org.sakaiproject.util.RequestFilter.doFilter(RequestFilter.java:496) [sakai-kernel-api-22-SNAPSHOT.jar:22-SNAPSHOT] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189) [catalina.jar:9.0.54] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) [catalina.jar:9.0.54] at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:53) [tomcat-websocket.jar:9.0.54] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189) [catalina.jar:9.0.54] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) [catalina.jar:9.0.54] at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:197) [catalina.jar:9.0.54] at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:97) [catalina.jar:9.0.54] at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:540) [catalina.jar:9.0.54] at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:135) [catalina.jar:9.0.54] at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:92) [catalina.jar:9.0.54] at org.apache.catalina.valves.RemoteIpValve.invoke(RemoteIpValve.java:769) [catalina.jar:9.0.54] at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:78) [catalina.jar:9.0.54] at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:357) [catalina.jar:9.0.54] at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:382) [tomcat-coyote.jar:9.0.54] at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:65) [tomcat-coyote.jar:9.0.54] at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:895) [tomcat-coyote.jar:9.0.54] at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1722) [tomcat-coyote.jar:9.0.54] at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49) [tomcat-coyote.jar:9.0.54] at org.apache.tomcat.util.threads.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1191) [tomcat-util.jar:9.0.54] at org.apache.tomcat.util.threads.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:659) [tomcat-util.jar:9.0.54] at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) [tomcat-util.jar:9.0.54] at java.lang.Thread.run(Thread.java:829) [?:?] Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure The last packet successfully received from the server was 145,841 milliseconds ago. The last packet sent successfully to the server was 145,794 milliseconds ago. at jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[?:?] at jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) ~[?:?] at jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[?:?] at java.lang.reflect.Constructor.newInstance(Constructor.java:490) ~[?:?] at com.mysql.jdbc.Util.handleNewInstance(Util.java:425) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:990) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3562) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3462) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3903) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:871) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.MysqlIO.proceedHandshakeWithPluggableAuthentication(MysqlIO.java:1714) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.MysqlIO.doHandshake(MysqlIO.java:1224) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.ConnectionImpl.coreConnect(ConnectionImpl.java:2190) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.ConnectionImpl.connectOneTryOnly(ConnectionImpl.java:2221) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2016) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.ConnectionImpl.(ConnectionImpl.java:776) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.JDBC4Connection.(JDBC4Connection.java:47) ~[mysql-connector-java-5.1.46.jar:5.1.46] at jdk.internal.reflect.GeneratedConstructorAccessor376.newInstance(Unknown Source) ~[?:?] at jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[?:?] at java.lang.reflect.Constructor.newInstance(Constructor.java:490) ~[?:?] at com.mysql.jdbc.Util.handleNewInstance(Util.java:425) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:386) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:330) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.zaxxer.hikari.util.DriverDataSource.getConnection(DriverDataSource.java:138) ~[HikariCP-4.0.3.jar:?] at com.zaxxer.hikari.pool.PoolBase.newConnection(PoolBase.java:364) ~[HikariCP-4.0.3.jar:?] at com.zaxxer.hikari.pool.PoolBase.newPoolEntry(PoolBase.java:206) ~[HikariCP-4.0.3.jar:?] at com.zaxxer.hikari.pool.HikariPool.createPoolEntry(HikariPool.java:476) ~[HikariCP-4.0.3.jar:?] at com.zaxxer.hikari.pool.HikariPool.access$100(HikariPool.java:71) ~[HikariCP-4.0.3.jar:?] at com.zaxxer.hikari.pool.HikariPool$PoolEntryCreator.call(HikariPool.java:726) ~[HikariCP-4.0.3.jar:?] at com.zaxxer.hikari.pool.HikariPool$PoolEntryCreator.call(HikariPool.java:712) ~[HikariCP-4.0.3.jar:?] at java.util.concurrent.FutureTask.run(FutureTask.java:264) ~[?:?] at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) ~[?:?] at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) ~[?:?] ... 1 more Caused by: java.io.EOFException: Can not read response from server. Expected to read 4 bytes, read 0 bytes before connection was unexpectedly lost. at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:3014) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3472) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3462) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3903) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:871) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.MysqlIO.proceedHandshakeWithPluggableAuthentication(MysqlIO.java:1714) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.MysqlIO.doHandshake(MysqlIO.java:1224) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.ConnectionImpl.coreConnect(ConnectionImpl.java:2190) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.ConnectionImpl.connectOneTryOnly(ConnectionImpl.java:2221) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2016) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.ConnectionImpl.(ConnectionImpl.java:776) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.JDBC4Connection.(JDBC4Connection.java:47) ~[mysql-connector-java-5.1.46.jar:5.1.46] at jdk.internal.reflect.GeneratedConstructorAccessor376.newInstance(Unknown Source) ~[?:?] at jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[?:?] at java.lang.reflect.Constructor.newInstance(Constructor.java:490) ~[?:?] at com.mysql.jdbc.Util.handleNewInstance(Util.java:425) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:386) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:330) ~[mysql-connector-java-5.1.46.jar:5.1.46] at com.zaxxer.hikari.util.DriverDataSource.getConnection(DriverDataSource.java:138) ~[HikariCP-4.0.3.jar:?] at com.zaxxer.hikari.pool.PoolBase.newConnection(PoolBase.java:364) ~[HikariCP-4.0.3.jar:?] at com.zaxxer.hikari.pool.PoolBase.newPoolEntry(PoolBase.java:206) ~[HikariCP-4.0.3.jar:?] at com.zaxxer.hikari.pool.HikariPool.createPoolEntry(HikariPool.java:476) ~[HikariCP-4.0.3.jar:?] at com.zaxxer.hikari.pool.HikariPool.access$100(HikariPool.java:71) ~[HikariCP-4.0.3.jar:?] at com.zaxxer.hikari.pool.HikariPool$PoolEntryCreator.call(HikariPool.java:726) ~[HikariCP-4.0.3.jar:?] at com.zaxxer.hikari.pool.HikariPool$PoolEntryCreator.call(HikariPool.java:712) ~[HikariCP-4.0.3.jar:?] at java.util.concurrent.FutureTask.run(FutureTask.java:264) ~[?:?] at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) ~[?:?] at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) ~[?:?] ... 1 more