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  • Could not open Hibernate Session for transaction, OpenSpecimenException

    #1

    OpenSpecimen was working fine and all of the sudden got several internal errors, localhost log file I found this error, Can you assist us with this issue?

    ??? 30, 2019 9:10:28 ? org.apache.catalina.core.StandardWrapperValve invoke
    SEVERE: Servlet.service() for servlet [restApi] in context with path [/openspecimen] threw exception
    com.krishagni.catissueplus.core.common.errors.OpenSpecimenException: Could not open Hibernate Session for transaction; nested exception is org.hibernate.exception.GenericJDBCException: Could not open connection
    	at com.krishagni.catissueplus.core.common.errors.OpenSpecimenException.serverError(OpenSpecimenException.java:136)
    	at com.krishagni.catissueplus.core.common.TransactionalInterceptor.doWork(TransactionalInterceptor.java:91)
    	at com.krishagni.catissueplus.core.common.TransactionalInterceptor.ajc$inlineAccessMethod$com_krishagni_catissueplus_core_common_TransactionalInterceptor$com_krishagni_catissueplus_core_common_TransactionalInterceptor$doWork(TransactionalInterceptor.java:1)
    	at com.krishagni.catissueplus.core.common.TransactionalInterceptor.startTransaction(TransactionalInterceptor.java:64)
    	at com.krishagni.catissueplus.core.auth.services.impl.UserAuthenticationServiceImpl.validateToken(UserAuthenticationServiceImpl.java:118)
    	at com.krishagni.catissueplus.rest.filter.AuthTokenFilter.doFilter(AuthTokenFilter.java:118)
    	at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:343)
    	at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:260)
    	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
    	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
    	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
    	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
    	at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:505)
    	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
    	at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
    	at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
    	at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
    	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423)
    	at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1079)
    	at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:620)
    	at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:316)
    	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    	at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
    	at java.lang.Thread.run(Thread.java:745)
    #2

    Hi Hassan,

    From the error, it looks like the OpenSpecimen is having a problem connecting to the database server.

    Please check whether:

    1. The database is functioning normally.

    2. The database is accepting connections from the remote machine.

    3. Connections to the database can be established form the OpenSpecimen VM.

    When facing such issues it is a good idea to attach the entire OS log file, located under $OS_DATA_DIR/logs. This would help us to debug the issue faster.

    Thanks,

    #3

    the database seems to be working fine, and the catalina log prints the following

    ??? 30, 2019 9:18:09 ? org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
    SEVERE: The web application [/openspecimen] appears to have started a thread named [FileWatchdog] but has failed to stop it. This is very likely to create a memory leak.
    ??? 30, 2019 9:18:09 ? org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
    SEVERE: The web application [/openspecimen] appears to have started a thread named [Abandoned connection cleanup thread] but has failed to stop it. This is very likely to create a memory leak.
    ??? 30, 2019 9:18:09 ? org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
    SEVERE: The web application [/openspecimen] appears to have started a thread named [pool-3-thread-1] but has failed to stop it. This is very likely to create a memory leak.
    ??? 30, 2019 9:18:09 ? org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
    SEVERE: The web application [/openspecimen] appears to have started a thread named [pool-1-thread-1] but has failed to stop it. This is very likely to create a memory leak.
    ??? 30, 2019 9:18:09 ? org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
    SEVERE: The web application [/openspecimen] appears to have started a thread named [pool-1-thread-2] but has failed to stop it. This is very likely to create a memory leak.
    ??? 30, 2019 9:18:09 ? org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
    SEVERE: The web application [/openspecimen] appears to have started a thread named [pool-1-thread-3] but has failed to stop it. This is very likely to create a memory leak.
    ??? 30, 2019 9:18:09 ? org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
    SEVERE: The web application [/openspecimen] appears to have started a thread named [pool-1-thread-4] but has failed to stop it. This is very likely to create a memory leak.
    ??? 30, 2019 9:18:09 ? org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
    SEVERE: The web application [/openspecimen] appears to have started a thread named [pool-1-thread-5] but has failed to stop it. This is very likely to create a memory leak.
    ??? 30, 2019 9:18:09 ? org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
    SEVERE: The web application [/openspecimen] appears to have started a thread named [pool-2-thread-1] but has failed to stop it. This is very likely to create a memory leak.
    ??? 30, 2019 9:18:09 ? org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
    SEVERE: The web application [/openspecimen] appears to have started a thread named [pool-2-thread-2] but has failed to stop it. This is very likely to create a memory leak.
    ??? 30, 2019 9:18:09 ? org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
    SEVERE: The web application [/openspecimen] appears to have started a thread named [pool-2-thread-3] but has failed to stop it. This is very likely to create a memory leak.
    ??? 30, 2019 9:18:09 ? org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
    SEVERE: The web application [/openspecimen] appears to have started a thread named [pool-2-thread-4] but has failed to stop it. This is very likely to create a memory leak.
    ??? 30, 2019 9:18:09 ? org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
    SEVERE: The web application [/openspecimen] appears to have started a thread named [pool-2-thread-5] but has failed to stop it. This is very likely to create a memory leak.
    ??? 30, 2019 9:18:09 ? org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
    SEVERE: The web application [/openspecimen] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@f5c697b]) and a value of type [org.springframework.security.core.context.SecurityContextImpl] (value [org.springframework.security.core.context.SecurityContextImpl@ffc9143a: Authentication: org.springframework.security.authentication.UsernamePasswordAuthenticationToken@ffc9143a: Principal: com.krishagni.catissueplus.core.administrative.domain.User@35; Credentials: [PROTECTED]; Authenticated: true; Details: null; Granted Authorities: user]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
    ??? 30, 2019 9:18:09 ? org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
    SEVERE: The web application [/openspecimen] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@f5c697b]) and a value of type [org.springframework.security.core.context.SecurityContextImpl] (value [org.springframework.security.core.context.SecurityContextImpl@ffc9143a: Authentication: org.springframework.security.authentication.UsernamePasswordAuthenticationToken@ffc9143a: Principal: com.krishagni.catissueplus.core.administrative.domain.User@35; Credentials: [PROTECTED]; Authenticated: true; Details: null; Granted Authorities: user]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
    ??? 30, 2019 9:18:09 ? org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
    SEVERE: The web application [/openspecimen] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@f5c697b]) and a value of type [org.springframework.security.core.context.SecurityContextImpl] (value [org.springframework.security.core.context.SecurityContextImpl@ffc9143a: Authentication: org.springframework.security.authentication.UsernamePasswordAuthenticationToken@ffc9143a: Principal: com.krishagni.catissueplus.core.administrative.domain.User@35; Credentials: [PROTECTED]; Authenticated: true; Details: null; Granted Authorities: user]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
    ??? 30, 2019 9:18:09 ? org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
    SEVERE: The web application [/openspecimen] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@f5c697b]) and a value of type [org.springframework.security.core.context.SecurityContextImpl] (value [org.springframework.security.core.context.SecurityContextImpl@ffc9143a: Authentication: org.springframework.security.authentication.UsernamePasswordAuthenticationToken@ffc9143a: Principal: com.krishagni.catissueplus.core.administrative.domain.User@35; Credentials: [PROTECTED]; Authenticated: true; Details: null; Granted Authorities: user]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
    ??? 30, 2019 9:18:09 ? org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
    SEVERE: The web application [/openspecimen] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@f5c697b]) and a value of type [org.springframework.security.core.context.SecurityContextImpl] (value [org.springframework.security.core.context.SecurityContextImpl@ffc9143a: Authentication: org.springframework.security.authentication.UsernamePasswordAuthenticationToken@ffc9143a: Principal: com.krishagni.catissueplus.core.administrative.domain.User@35; Credentials: [PROTECTED]; Authenticated: true; Details: null; Granted Authorities: user]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
    ??? 30, 2019 9:18:09 ? org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
    SEVERE: The web application [/openspecimen] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@f5c697b]) and a value of type [org.springframework.security.core.context.SecurityContextImpl] (value [org.springframework.security.core.context.SecurityContextImpl@ffc9143a: Authentication: org.springframework.security.authentication.UsernamePasswordAuthenticationToken@ffc9143a: Principal: com.krishagni.catissueplus.core.administrative.domain.User@35; Credentials: [PROTECTED]; Authenticated: true; Details: null; Granted Authorities: user]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
    ??? 30, 2019 9:18:09 ? org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
    SEVERE: The web application [/openspecimen] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@f5c697b]) and a value of type [org.springframework.security.core.context.SecurityContextImpl] (value [org.springframework.security.core.context.SecurityContextImpl@ffc9143a: Authentication: org.springframework.security.authentication.UsernamePasswordAuthenticationToken@ffc9143a: Principal: com.krishagni.catissueplus.core.administrative.domain.User@35; Credentials: [PROTECTED]; Authenticated: true; Details: null; Granted Authorities: user]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
    ??? 30, 2019 9:18:09 ? org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
    SEVERE: The web application [/openspecimen] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@f5c697b]) and a value of type [org.springframework.security.core.context.SecurityContextImpl] (value [org.springframework.security.core.context.SecurityContextImpl@ffc9143a: Authentication: org.springframework.security.authentication.UsernamePasswordAuthenticationToken@ffc9143a: Principal: com.krishagni.catissueplus.core.administrative.domain.User@35; Credentials: [PROTECTED]; Authenticated: true; Details: null; Granted Authorities: user]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
    ??? 30, 2019 9:18:09 ? org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
    SEVERE: The web application [/openspecimen] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@f5c697b]) and a value of type [org.springframework.security.core.context.SecurityContextImpl] (value [org.springframework.security.core.context.SecurityContextImpl@95cc7c1d: Authentication: org.springframework.security.authentication.UsernamePasswordAuthenticationToken@95cc7c1d: Principal: com.krishagni.catissueplus.core.administrative.domain.User@42; Credentials: [PROTECTED]; Authenticated: true; Details: org.springframework.security.web.authentication.WebAuthenticationDetails@b364: RemoteIpAddress: 10.11.11.100; SessionId: null; Granted Authorities: user]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
    ??? 30, 2019 9:18:09 ? org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
    SEVERE: The web application [/openspecimen] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@f5c697b]) and a value of type [org.springframework.security.core.context.SecurityContextImpl] (value [org.springframework.security.core.context.SecurityContextImpl@ffc9143a: Authentication: org.springframework.security.authentication.UsernamePasswordAuthenticationToken@ffc9143a: Principal: com.krishagni.catissueplus.core.administrative.domain.User@35; Credentials: [PROTECTED]; Authenticated: true; Details: null; Granted Authorities: user]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
    May 30, 2019 12:10:30 PM org.apache.coyote.AbstractProtocol init
    SEVERE: Failed to initialize end point associated with ProtocolHandler ["http-bio-8080"]
    java.net.BindException: Address already in use: JVM_Bind <null>:8080
    	at org.apache.tomcat.util.net.JIoEndpoint.bind(JIoEndpoint.java:413)
    	at org.apache.tomcat.util.net.AbstractEndpoint.init(AbstractEndpoint.java:649)
    	at org.apache.coyote.AbstractProtocol.init(AbstractProtocol.java:434)
    	at org.apache.coyote.http11.AbstractHttp11JsseProtocol.init(AbstractHttp11JsseProtocol.java:119)
    	at org.apache.catalina.connector.Connector.initInternal(Connector.java:978)
    	at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:102)
    	at org.apache.catalina.core.StandardService.initInternal(StandardService.java:559)
    	at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:102)
    	at org.apache.catalina.core.StandardServer.initInternal(StandardServer.java:821)
    	at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:102)
    	at org.apache.catalina.startup.Catalina.load(Catalina.java:638)
    	at org.apache.catalina.startup.Catalina.load(Catalina.java:663)
    	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    	at java.lang.reflect.Method.invoke(Method.java:497)
    	at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:280)
    	at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:454)
    Caused by: java.net.BindException: Address already in use: JVM_Bind
    	at java.net.DualStackPlainSocketImpl.bind0(Native Method)
    	at java.net.DualStackPlainSocketImpl.socketBind(DualStackPlainSocketImpl.java:106)
    	at java.net.AbstractPlainSocketImpl.bind(AbstractPlainSocketImpl.java:382)
    	at java.net.PlainSocketImpl.bind(PlainSocketImpl.java:190)
    	at java.net.ServerSocket.bind(ServerSocket.java:375)
    	at java.net.ServerSocket.<init>(ServerSocket.java:237)
    	at java.net.ServerSocket.<init>(ServerSocket.java:181)
    	at org.apache.tomcat.util.net.DefaultServerSocketFactory.createSocket(DefaultServerSocketFactory.java:49)
    	at org.apache.tomcat.util.net.JIoEndpoint.bind(JIoEndpoint.java:400)
    	... 17 more
    
    May 30, 2019 12:10:30 PM org.apache.catalina.core.StandardService initInternal
    SEVERE: Failed to initialize connector [Connector[HTTP/1.1-8080]]
    org.apache.catalina.LifecycleException: Failed to initialize component [Connector[HTTP/1.1-8080]]
    	at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:106)
    	at org.apache.catalina.core.StandardService.initInternal(StandardService.java:559)
    	at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:102)
    	at org.apache.catalina.core.StandardServer.initInternal(StandardServer.java:821)
    	at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:102)
    	at org.apache.catalina.startup.Catalina.load(Catalina.java:638)
    	at org.apache.catalina.startup.Catalina.load(Catalina.java:663)
    	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    	at java.lang.reflect.Method.invoke(Method.java:497)
    	at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:280)
    	at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:454)
    Caused by: org.apache.catalina.LifecycleException: Protocol handler initialization failed
    	at org.apache.catalina.connector.Connector.initInternal(Connector.java:980)
    	at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:102)
    	... 12 more
    Caused by: java.net.BindException: Address already in use: JVM_Bind <null>:8080
    	at org.apache.tomcat.util.net.JIoEndpoint.bind(JIoEndpoint.java:413)
    	at org.apache.tomcat.util.net.AbstractEndpoint.init(AbstractEndpoint.java:649)
    	at org.apache.coyote.AbstractProtocol.init(AbstractProtocol.java:434)
    	at org.apache.coyote.http11.AbstractHttp11JsseProtocol.init(AbstractHttp11JsseProtocol.java:119)
    	at org.apache.catalina.connector.Connector.initInternal(Connector.java:978)
    	... 13 more
    Caused by: java.net.BindException: Address already in use: JVM_Bind
    	at java.net.DualStackPlainSocketImpl.bind0(Native Method)
    	at java.net.DualStackPlainSocketImpl.socketBind(DualStackPlainSocketImpl.java:106)
    	at java.net.AbstractPlainSocketImpl.bind(AbstractPlainSocketImpl.java:382)
    	at java.net.PlainSocketImpl.bind(PlainSocketImpl.java:190)
    	at java.net.ServerSocket.bind(ServerSocket.java:375)
    	at java.net.ServerSocket.<init>(ServerSocket.java:237)
    	at java.net.ServerSocket.<init>(ServerSocket.java:181)
    	at org.apache.tomcat.util.net.DefaultServerSocketFactory.createSocket(DefaultServerSocketFactory.java:49)
    	at org.apache.tomcat.util.net.JIoEndpoint.bind(JIoEndpoint.java:400)
    	... 17 more
    
    May 30, 2019 12:10:30 PM org.apache.coyote.AbstractProtocol init
    SEVERE: Failed to initialize end point associated with ProtocolHandler ["ajp-bio-8009"]
    java.net.BindException: Address already in use: JVM_Bind <null>:8009
    	at org.apache.tomcat.util.net.JIoEndpoint.bind(JIoEndpoint.java:413)
    	at org.apache.tomcat.util.net.AbstractEndpoint.init(AbstractEndpoint.java:649)
    	at org.apache.coyote.AbstractProtocol.init(AbstractProtocol.java:434)
    	at org.apache.catalina.connector.Connector.initInternal(Connector.java:978)
    	at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:102)
    	at org.apache.catalina.core.StandardService.initInternal(StandardService.java:559)
    	at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:102)
    	at org.apache.catalina.core.StandardServer.initInternal(StandardServer.java:821)
    	at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:102)
    	at org.apache.catalina.startup.Catalina.load(Catalina.java:638)
    	at org.apache.catalina.startup.Catalina.load(Catalina.java:663)
    	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    	at java.lang.reflect.Method.invoke(Method.java:497)
    	at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:280)
    	at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:454)
    Caused by: java.net.BindException: Address already in use: JVM_Bind
    	at java.net.DualStackPlainSocketImpl.bind0(Native Method)
    	at java.net.DualStackPlainSocketImpl.socketBind(DualStackPlainSocketImpl.java:106)
    	at java.net.AbstractPlainSocketImpl.bind(AbstractPlainSocketImpl.java:382)
    	at java.net.PlainSocketImpl.bind(PlainSocketImpl.java:190)
    	at java.net.ServerSocket.bind(ServerSocket.java:375)
    	at java.net.ServerSocket.<init>(ServerSocket.java:237)
    	at java.net.ServerSocket.<init>(ServerSocket.java:181)
    	at org.apache.tomcat.util.net.DefaultServerSocketFactory.createSocket(DefaultServerSocketFactory.java:49)
    	at org.apache.tomcat.util.net.JIoEndpoint.bind(JIoEndpoint.java:400)
    	... 16 more
    
    May 30, 2019 12:10:30 PM org.apache.catalina.core.StandardService initInternal
    SEVERE: Failed to initialize connector [Connector[AJP/1.3-8009]]
    org.apache.catalina.LifecycleException: Failed to initialize component [Connector[AJP/1.3-8009]]
    	at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:106)
    	at org.apache.catalina.core.StandardService.initInternal(StandardService.java:559)
    	at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:102)
    	at org.apache.catalina.core.StandardServer.initInternal(StandardServer.java:821)
    	at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:102)
    	at org.apache.catalina.startup.Catalina.load(Catalina.java:638)
    	at org.apache.catalina.startup.Catalina.load(Catalina.java:663)
    	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    	at java.lang.reflect.Method.invoke(Method.java:497)
    	at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:280)
    	at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:454)
    Caused by: org.apache.catalina.LifecycleException: Protocol handler initialization failed
    	at org.apache.catalina.connector.Connector.initInternal(Connector.java:980)
    	at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:102)
    	... 12 more
    Caused by: java.net.BindException: Address already in use: JVM_Bind <null>:8009
    	at org.apache.tomcat.util.net.JIoEndpoint.bind(JIoEndpoint.java:413)
    	at org.apache.tomcat.util.net.AbstractEndpoint.init(AbstractEndpoint.java:649)
    	at org.apache.coyote.AbstractProtocol.init(AbstractProtocol.java:434)
    	at org.apache.catalina.connector.Connector.initInternal(Connector.java:978)
    	... 13 more
    Caused by: java.net.BindException: Address already in use: JVM_Bind
    	at java.net.DualStackPlainSocketImpl.bind0(Native Method)
    	at java.net.DualStackPlainSocketImpl.socketBind(DualStackPlainSocketImpl.java:106)
    	at java.net.AbstractPlainSocketImpl.bind(AbstractPlainSocketImpl.java:382)
    	at java.net.PlainSocketImpl.bind(PlainSocketImpl.java:190)
    	at java.net.ServerSocket.bind(ServerSocket.java:375)
    	at java.net.ServerSocket.<init>(ServerSocket.java:237)
    	at java.net.ServerSocket.<init>(ServerSocket.java:181)
    	at org.apache.tomcat.util.net.DefaultServerSocketFactory.createSocket(DefaultServerSocketFactory.java:49)
    	at org.apache.tomcat.util.net.JIoEndpoint.bind(JIoEndpoint.java:400)
    	... 16 more
    #4

    Hi Hassan,

    It seems like port 8080/8009 is already in use.

    This could happen when you try to start a new instance of Tomcat without properly shutting down the older running instance. Please check whether this is the case.

    To resolve the issue please follow the below steps.

    1. Shutdown the running Tomcat service.

    2. Run ’ netstat -aon | findstr ’ command to make sure no process is running on 8080 or 8009.

    3. Once #2 is confirmed. Start the Tomcat service.

    Monitor Tomcat logs files and OpenSpecimen log files.

    Let us know how it works. If still issue continues, please share the os.log and Catalina logs with us.

    Thanks,