Resulting catilina.out

gistfile1.txt

09-Jul-2015 16:30:55.745 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version:        Apache Tomcat/8.0.24
09-Jul-2015 16:30:55.746 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built:          Jul 1 2015 20:19:55 UTC
09-Jul-2015 16:30:55.746 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server number:         8.0.24.0
09-Jul-2015 16:30:55.746 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name:               Linux
09-Jul-2015 16:30:55.746 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version:            3.13.0-55-generic
09-Jul-2015 16:30:55.746 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture:          amd64
09-Jul-2015 16:30:55.747 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home:             /usr/lib/jvm/java-7-openjdk-amd64/jre
09-Jul-2015 16:30:55.747 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version:           1.7.0_79-b14
09-Jul-2015 16:30:55.747 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor:            Oracle Corporation
09-Jul-2015 16:30:55.747 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE:         /home/joncrall/code/Wildbook/apache-tomcat-8.0.24
09-Jul-2015 16:30:55.747 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME:         /home/joncrall/code/Wildbook/apache-tomcat-8.0.24
09-Jul-2015 16:30:55.747 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/home/joncrall/code/Wildbook/apache-tomcat-8.0.24/conf/logging.properties
09-Jul-2015 16:30:55.747 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
09-Jul-2015 16:30:55.747 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.endorsed.dirs=/home/joncrall/code/Wildbook/apache-tomcat-8.0.24/endorsed
09-Jul-2015 16:30:55.747 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/home/joncrall/code/Wildbook/apache-tomcat-8.0.24
09-Jul-2015 16:30:55.747 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/home/joncrall/code/Wildbook/apache-tomcat-8.0.24
09-Jul-2015 16:30:55.747 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/home/joncrall/code/Wildbook/apache-tomcat-8.0.24/temp
09-Jul-2015 16:30:55.747 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/local/cuda-6.0/lib64::/usr/local/cuda/lib64:/usr/local/lib:/usr/local/cuda/lib64:/usr/local/lib:/usr/java/packages/lib/amd64:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib
09-Jul-2015 16:30:55.820 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
09-Jul-2015 16:30:55.834 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
09-Jul-2015 16:30:55.836 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["ajp-nio-8009"]
09-Jul-2015 16:30:55.837 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
09-Jul-2015 16:30:55.838 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 413 ms
09-Jul-2015 16:30:55.856 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service Catalina
09-Jul-2015 16:30:55.856 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.0.24
09-Jul-2015 16:30:55.880 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deploying web application archive /home/joncrall/code/Wildbook/apache-tomcat-8.0.24/webapps/wildbook-5.3.0-RELEASE.war
09-Jul-2015 16:30:58.654 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
16:30:58,701 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.groovy]
16:30:58,701 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
16:30:58,701 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/home/joncrall/code/Wildbook/apache-tomcat-8.0.24/webapps/wildbook-5.3.0-RELEASE/WEB-INF/classes/logback.xml]
16:30:58,775 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - debug attribute not set
16:30:58,776 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - About to instantiate appender of type [ch.qos.logback.core.FileAppender]
16:30:58,778 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - Naming appender as [SUBMISSIONFILE]
16:30:58,810 |-WARN in ch.qos.logback.core.FileAppender[SUBMISSIONFILE] - This appender no longer admits a layout as a sub-component, set an encoder instead.
16:30:58,810 |-WARN in ch.qos.logback.core.FileAppender[SUBMISSIONFILE] - To ensure compatibility, wrapping your layout in LayoutWrappingEncoder.
16:30:58,810 |-WARN in ch.qos.logback.core.FileAppender[SUBMISSIONFILE] - See also http://logback.qos.ch/codes.html#layoutInsteadOfEncoder for details
16:30:58,810 |-INFO in ch.qos.logback.core.FileAppender[SUBMISSIONFILE] - File property is set to [./webapps/ROOT/logs/encounter-submission.htm]
16:30:58,813 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - About to instantiate appender of type [ch.qos.logback.core.FileAppender]
16:30:58,813 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - Naming appender as [ENCOUNTERDELETEFILE]
16:30:58,814 |-WARN in ch.qos.logback.core.FileAppender[ENCOUNTERDELETEFILE] - This appender no longer admits a layout as a sub-component, set an encoder instead.
16:30:58,814 |-WARN in ch.qos.logback.core.FileAppender[ENCOUNTERDELETEFILE] - To ensure compatibility, wrapping your layout in LayoutWrappingEncoder.
16:30:58,814 |-WARN in ch.qos.logback.core.FileAppender[ENCOUNTERDELETEFILE] - See also http://logback.qos.ch/codes.html#layoutInsteadOfEncoder for details
16:30:58,814 |-INFO in ch.qos.logback.core.FileAppender[ENCOUNTERDELETEFILE] - File property is set to [./webapps/ROOT/logs/encounter-delete.htm]
16:30:58,814 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - About to instantiate appender of type [ch.qos.logback.core.FileAppender]
16:30:58,814 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - Naming appender as [USERFILE]
16:30:58,814 |-WARN in ch.qos.logback.core.FileAppender[USERFILE] - This appender no longer admits a layout as a sub-component, set an encoder instead.
16:30:58,814 |-WARN in ch.qos.logback.core.FileAppender[USERFILE] - To ensure compatibility, wrapping your layout in LayoutWrappingEncoder.
16:30:58,814 |-WARN in ch.qos.logback.core.FileAppender[USERFILE] - See also http://logback.qos.ch/codes.html#layoutInsteadOfEncoder for details
16:30:58,814 |-INFO in ch.qos.logback.core.FileAppender[USERFILE] - File property is set to [./webapps/ROOT/logs/user-access.htm]
16:30:58,814 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - About to instantiate appender of type [ch.qos.logback.core.FileAppender]
16:30:58,814 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - Naming appender as [FILE]
16:30:58,815 |-WARN in ch.qos.logback.core.FileAppender[FILE] - This appender no longer admits a layout as a sub-component, set an encoder instead.
16:30:58,815 |-WARN in ch.qos.logback.core.FileAppender[FILE] - To ensure compatibility, wrapping your layout in LayoutWrappingEncoder.
16:30:58,815 |-WARN in ch.qos.logback.core.FileAppender[FILE] - See also http://logback.qos.ch/codes.html#layoutInsteadOfEncoder for details
16:30:58,815 |-INFO in ch.qos.logback.core.FileAppender[FILE] - File property is set to [./webapps/ROOT/logs/logback-debug.htm]
16:30:58,815 |-INFO in ch.qos.logback.classic.joran.action.LoggerAction - Setting level of logger [org.ecocean.servlet.SubmitAction] to INFO
16:30:58,815 |-INFO in ch.qos.logback.core.joran.action.AppenderRefAction - Attaching appender named [SUBMISSIONFILE] to Logger[org.ecocean.servlet.SubmitAction]
16:30:58,815 |-INFO in ch.qos.logback.classic.joran.action.LoggerAction - Setting level of logger [org.ecocean.servlet.EncounterDelete] to INFO
16:30:58,815 |-INFO in ch.qos.logback.core.joran.action.AppenderRefAction - Attaching appender named [ENCOUNTERDELETEFILE] to Logger[org.ecocean.servlet.EncounterDelete]
16:30:58,816 |-INFO in ch.qos.logback.classic.joran.action.LoggerAction - Setting level of logger [org.apache.jsp.welcome_jsp] to INFO
16:30:58,816 |-INFO in ch.qos.logback.core.joran.action.AppenderRefAction - Attaching appender named [USERFILE] to Logger[org.apache.jsp.welcome_jsp]
16:30:58,816 |-INFO in ch.qos.logback.classic.joran.action.LoggerAction - Setting level of logger [org.apache.jsp.logout_jsp] to INFO
16:30:58,816 |-INFO in ch.qos.logback.core.joran.action.AppenderRefAction - Attaching appender named [USERFILE] to Logger[org.apache.jsp.logout_jsp]
16:30:58,816 |-INFO in ch.qos.logback.classic.joran.action.RootLoggerAction - Setting level of ROOT logger to DEBUG
16:30:58,816 |-INFO in ch.qos.logback.core.joran.action.AppenderRefAction - Attaching appender named [FILE] to Logger[ROOT]
16:30:58,816 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@59079e59 - Registering current configuration as safe fallback point

09-Jul-2015 16:30:58.938 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive /home/joncrall/code/Wildbook/apache-tomcat-8.0.24/webapps/wildbook-5.3.0-RELEASE.war has finished in 3,058 ms
09-Jul-2015 16:30:58.938 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory /home/joncrall/code/Wildbook/apache-tomcat-8.0.24/webapps/docs
09-Jul-2015 16:30:58.951 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory /home/joncrall/code/Wildbook/apache-tomcat-8.0.24/webapps/docs has finished in 12 ms
09-Jul-2015 16:30:58.951 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory /home/joncrall/code/Wildbook/apache-tomcat-8.0.24/webapps/ROOT
09-Jul-2015 16:30:58.965 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory /home/joncrall/code/Wildbook/apache-tomcat-8.0.24/webapps/ROOT has finished in 14 ms
09-Jul-2015 16:30:58.965 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory /home/joncrall/code/Wildbook/apache-tomcat-8.0.24/webapps/manager
09-Jul-2015 16:30:58.988 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory /home/joncrall/code/Wildbook/apache-tomcat-8.0.24/webapps/manager has finished in 23 ms
09-Jul-2015 16:30:58.988 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory /home/joncrall/code/Wildbook/apache-tomcat-8.0.24/webapps/host-manager
09-Jul-2015 16:30:59.004 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory /home/joncrall/code/Wildbook/apache-tomcat-8.0.24/webapps/host-manager has finished in 16 ms
09-Jul-2015 16:30:59.004 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory /home/joncrall/code/Wildbook/apache-tomcat-8.0.24/webapps/examples
09-Jul-2015 16:30:59.132 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory /home/joncrall/code/Wildbook/apache-tomcat-8.0.24/webapps/examples has finished in 128 ms
09-Jul-2015 16:30:59.135 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8080"]
09-Jul-2015 16:30:59.138 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["ajp-nio-8009"]
09-Jul-2015 16:30:59.139 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 3301 ms
Creating tomcat user account...
Creating tomcat roles...
Creating tomcat user account...
reading file??? /home/joncrall/code/Wildbook/apache-tomcat-8.0.24/webapps/wildbook-5.3.0-RELEASE/WEB-INF/classes/apiaccess.xml
[class org.ecocean.Encounter] roles for user '': []
{sex=deny, location=deny}
[class org.ecocean.MarkedIndividual] roles for user '': []
{}
[class org.ecocean.SinglePhotoVideo] roles for user '': []
{}
09-Jul-2015 16:31:09.135 INFO [localhost-startStop-2] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory /home/joncrall/code/Wildbook/apache-tomcat-8.0.24/webapps/webapps
09-Jul-2015 16:31:09.168 INFO [localhost-startStop-2] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory /home/joncrall/code/Wildbook/apache-tomcat-8.0.24/webapps/webapps has finished in 34 ms
09-Jul-2015 16:31:09.168 INFO [localhost-startStop-2] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory /home/joncrall/code/Wildbook/apache-tomcat-8.0.24/webapps/shepherd_derby_database
09-Jul-2015 16:31:09.188 INFO [localhost-startStop-2] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory /home/joncrall/code/Wildbook/apache-tomcat-8.0.24/webapps/shepherd_derby_database has finished in 20 ms
reading file??? /home/joncrall/code/Wildbook/apache-tomcat-8.0.24/webapps/wildbook-5.3.0-RELEASE/WEB-INF/classes/apiaccess.xml
[class org.ecocean.Encounter] roles for user '': []
{sex=deny, location=deny}
[class org.ecocean.MarkedIndividual] roles for user '': []
{}
[class org.ecocean.SinglePhotoVideo] roles for user '': []
{}
Starting LoginUser servlet...