migration of jira server

Question

Hi,

I have migrated the jira server from one linux to another linux. But am not able to open the JIRA server .Please help me to resolve this . Consider it as high priority . Iam pasting Log messages which is displayed in Catalina.out file

Catalina.out:

___ Plugin System Started _________________

2017-09-28 12:22:30,161 JIRA-Bootstrap INFO [c.a.jira.scheduler.JiraSchedulerLauncher] JIRA Scheduler not started: JIRA not setup yet.
2017-09-28 12:22:30,180 JIRA-Bootstrap WARN [c.a.jira.startup.JiraStartupLogger]

********************************************************************************************************************************************************************************************************
___ FAILED PLUGIN REPORT _____________________

1 plugin failed to load during JIRA startup.

'com.atlassian.jira.plugins.jira-healthcheck-plugin' - 'Atlassian JIRA - Plugins - Instance Health Plugin' failed to load.
Cannot start plugin: com.atlassian.jira.plugins.jira-healthcheck-plugin
Unresolved constraint in bundle com.atlassian.jira.plugins.jira-healthcheck-plugin [89]: Unable to resolve 89.0: missing requirement [89.0] osgi.wiring.package; (&(osgi.wiring.package=com.atlassian.support.healthcheck)(version>=2.0.11))

It was loaded from /data/apps/jira7.2.1/atlassian-jira/WEB-INF/atlassian-bundled-plugins/jira-healthcheck-plugin-2.1.14.jar

********************************************************************************************************************************************************************************************************

2017-09-28 12:22:30,181 JIRA-Bootstrap INFO [c.a.jira.startup.DefaultInstantUpgradeManager] Late startup launchers took 1s
2017-09-28 12:22:30,230 JIRA-Bootstrap INFO [c.a.jira.startup.LauncherContextListener] Memory Usage:
---------------------------------------------------------------------------------
Heap memory : Used: 198 MiB. Committed: 718 MiB. Max: 723 MiB
Non-heap memory : Used: 194 MiB. Committed: 213 MiB. Max: 1264 MiB
---------------------------------------------------------------------------------
TOTAL : Used: 392 MiB. Committed: 931 MiB. Max: 1987 MiB
---------------------------------------------------------------------------------
2017-09-28 12:22:31,082 Modification Check:thread-1 INFO [c.a.jira.startup.JiraStartupLogger]

___ Modifications ___________________________

Modified Files : jira-application.properties
Removed Files : None

2017-09-28 12:22:47,001 Timer-0 DEBUG [c.a.activeobjects.osgi.ActiveObjectsServiceFactory] getService bundle [com.atlassian.plugin.automation.automation-module]
2017-09-28 12:24:22,799 hipchat-plugin-tasks-executor-0 DEBUG [c.a.activeobjects.osgi.ActiveObjectsServiceFactory] getService bundle [com.atlassian.plugins.base-hi

Parallely below find the catalina log file message:

28-Sep-2017 12:21:50.271 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version: Apache Tomcat/8.0.33
28-Sep-2017 12:21:50.273 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Mar 18 2016 20:31:49 UTC
28-Sep-2017 12:21:50.273 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server number: 8.0.33.0
28-Sep-2017 12:21:50.273 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
28-Sep-2017 12:21:50.273 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 2.6.32-696.10.2.el6.x86_64
28-Sep-2017 12:21:50.273 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
28-Sep-2017 12:21:50.273 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /data/apps/jira7.2.1/jre
28-Sep-2017 12:21:50.273 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 1.8.0_102-b14
28-Sep-2017 12:21:50.273 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Oracle Corporation
28-Sep-2017 12:21:50.274 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /data/apps/jira7.2.1
28-Sep-2017 12:21:50.274 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /data/apps/jira7.2.1
28-Sep-2017 12:21:50.274 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/data/apps/jira7.2.1/conf/logging.properties
28-Sep-2017 12:21:50.274 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
28-Sep-2017 12:21:50.274 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xms384m
28-Sep-2017 12:21:50.274 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xmx768m
28-Sep-2017 12:21:50.275 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.awt.headless=true
28-Sep-2017 12:21:50.275 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Datlassian.standalone=JIRA
28-Sep-2017 12:21:50.275 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true
28-Sep-2017 12:21:50.282 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dmail.mime.decodeparameters=true
28-Sep-2017 12:21:50.282 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.dom4j.factory=com.atlassian.core.xml.InterningDocumentFactory
28-Sep-2017 12:21:50.282 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCDateStamps
28-Sep-2017 12:21:50.283 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:-OmitStackTraceInFastThrow
28-Sep-2017 12:21:50.283 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.endorsed.dirs=/data/apps/jira7.2.1/endorsed
28-Sep-2017 12:21:50.283 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/data/apps/jira7.2.1
28-Sep-2017 12:21:50.283 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/data/apps/jira7.2.1
28-Sep-2017 12:21:50.283 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/data/apps/jira7.2.1/temp
28-Sep-2017 12:21:50.283 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/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
28-Sep-2017 12:21:50.432 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
28-Sep-2017 12:21:50.447 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
28-Sep-2017 12:21:50.450 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 575 ms
28-Sep-2017 12:21:50.460 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service Catalina
28-Sep-2017 12:21:50.460 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.0.33
28-Sep-2017 12:21:50.472 SEVERE [Catalina-startStop-1] org.apache.catalina.startup.HostConfig.beforeStart Unable to create directory for deployment: /data/apps/jira7.2.1/conf/Catalina/localhost
28-Sep-2017 12:22:01.195 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8080"]
28-Sep-2017 12:22:01.218 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 10768 ms
28-Sep-2017 12:22:05.097 WARNING [main] org.apache.catalina.core.StandardServer.await StandardServer.await: Invalid command '' received

please try t help me as early as possibel

venugopal123 · Answer

Hi,

Thanks for the reply. Now am able to access the JIra UI in Browser. But i have mapped the jira to restored database . But its not reading the data. Its asking for application properties and database setup . Am not getting why its asking for again. I am just pasting the catalina.out log file . Please find the below details and please help to to come out of this

Catalina .out:

***********************************
___ FAILED PLUGIN REPORT _____________________

1 plugin failed to load during JIRA startup.

'com.atlassian.jira.plugins.jira-healthcheck-plugin' - 'Atlassian JIRA - Plugins - Instance Health Plugin' failed to load.
Cannot start plugin: com.atlassian.jira.plugins.jira-healthcheck-plugin
Unresolved constraint in bundle com.atlassian.jira.plugins.jira-healthcheck-plugin [89]: Unable to resolve 89.0: missing requirement [89.0] osgi.wiring.package; (&(osgi.wiring.package=com.atlassian.support.healthcheck)(version>=2.0.11))

It was loaded from /data/apps/jira7.2.1/atlassian-jira/WEB-INF/atlassian-bundled-plugins/jira-healthcheck-plugin-2.1.14.jar

********************************************************************************************************************************************************************************************************

2017-10-03 13:31:34,153 JIRA-Bootstrap INFO [c.a.jira.startup.DefaultInstantUpgradeManager] Late startup launchers took 1s
2017-10-03 13:31:34,157 JIRA-Bootstrap INFO [c.a.jira.startup.LauncherContextListener] Memory Usage:
---------------------------------------------------------------------------------
Heap memory : Used: 941 MiB. Committed: 2185 MiB. Max: 4007 MiB
Non-heap memory : Used: 203 MiB. Committed: 222 MiB. Max: 1264 MiB
---------------------------------------------------------------------------------
TOTAL : Used: 1144 MiB. Committed: 2407 MiB. Max: 5271 MiB
---------------------------------------------------------------------------------
2017-10-03 13:31:34,886 http-nio-8080-exec-19 INFO anonymous 811x3x1 1al0g13 199.63.92.5 /secure/SetupDatabase!default.jspa [c.a.j.bc.dataimport.DefaultDataImportService] Running JIRA Data Import...
2017-10-03 13:31:34,908 http-nio-8080-exec-19 INFO anonymous 811x3x1 1al0g13 199.63.92.5 /secure/SetupDatabase!default.jspa [c.a.j.bc.dataimport.DefaultDataImportService] Importing XML data...
2017-10-03 13:31:35,032 http-nio-8080-exec-19 DEBUG anonymous 811x3x1 1al0g13 199.63.92.5 /secure/SetupDatabase!default.jspa [c.a.activeobjects.osgi.ActiveObjectsServiceFactory] startCleaning
2017-10-03 13:31:35,079 http-nio-8080-exec-19 DEBUG anonymous 811x3x1 1al0g13 199.63.92.5 /secure/SetupDatabase!default.jspa [c.a.activeobjects.osgi.ActiveObjectsServiceFactory] stopCleaning
2017-10-03 13:31:35,079 http-nio-8080-exec-19 ERROR anonymous 811x3x1 1al0g13 199.63.92.5 /secure/SetupDatabase!default.jspa [c.a.j.bc.dataimport.DefaultDataImportService] Error importing data: java.lang.IllegalStateException: Could not find column 'EXCLUDE_ISSUE_DETAILS' in previously parsed query!
java.lang.IllegalStateException: Could not find column 'EXCLUDE_ISSUE_DETAILS' in previously parsed query!
at net.java.ao.schema.helper.DatabaseMetaDataReaderImpl.getFields(DatabaseMetaDataReaderImpl.java:118)
at net.java.ao.schema.ddl.SchemaReader.readFields(SchemaReader.java:126)
at net.java.ao.schema.ddl.SchemaReader.readTable(SchemaReader.java:110)
at net.java.ao.schema.ddl.SchemaReader.access$000(SchemaReader.java:62)
at net.java.ao.schema.ddl.SchemaReader$1.apply(SchemaReader.java:99)
at net.java.ao.schema.ddl.SchemaReader$1.apply(SchemaReader.java:97)
at com.google.common.collect.Iterators$8.transform(Iterators.java:799)
at com.google.common.collect.TransformedIterator.next(TransformedIterator.java:48)
at com.google.common.collect.Iterators.addAll(Iterators.java:362)
at com.google.common.collect.Lists.newArrayList(Lists.java:160)
at com.google.common.collect.Lists.newArrayList(Lists.java:144)
at net.java.ao.schema.ddl.SchemaReader.readSchema(SchemaReader.java:97)
at net.java.ao.schema.ddl.SchemaReader.readSchema(SchemaReader.java:88)
at net.java.ao.schema.ddl.SchemaReader.readSchema(SchemaReader.java:81)
at com.atlassian.activeobjects.backup.ActiveObjectsDatabaseCleaner.doCleanup(ActiveObjectsDatabaseCleaner.java:58)
at com.atlassian.activeobjects.backup.ActiveObjectsDatabaseCleaner.cleanup(ActiveObjectsDatabaseCleaner.java:45)
at com.atlassian.activeobjects.backup.ActiveObjectsBackup.clear(ActiveObjectsBackup.java:160)
at com.atlassian.jira.bc.dataimport.DefaultDataImportService.removeActiveObjects(DefaultDataImportService.java:984)
at com.atlassian.jira.bc.dataimport.DefaultDataImportService.performImport(DefaultDataImportService.java:704)
at com.atlassian.jira.bc.dataimport.DefaultDataImportService.doImport(DefaultDataImportService.java:324)
at com.atlassian.jira.startup.DatabaseInitialImporter.importInitialData(DatabaseInitialImporter.java:56)
at com.atlassian.jira.startup.DatabaseInitialImporter.importInitialData(DatabaseInitialImporter.java:48)
at com.atlassian.jira.web.action.setup.SetupDatabase.doDefault(SetupDatabase.java:141)
... 3 filtered
at java.lang.reflect.Method.invoke(Method.java:498)
at webwork.util.InjectionUtils$DefaultInjectionImpl.invoke(InjectionUtils.java:70)
at webwork.util.InjectionUtils.invoke(InjectionUtils.java:56)
... 2 filtered
at com.atlassian.jira.action.JiraActionSupport.execute(JiraActionSupport.java:63)
... 7 filtered
at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
... 56 filtered
at com.atlassian.web.servlet.plugin.request.RedirectInterceptingFilter.doFilter(RedirectInterceptingFilter.java:21)
... 58 filtered
at com.atlassian.jira.security.JiraSecurityFilter.lambda$doFilter$0(JiraSecurityFilter.java:76)
... 1 filtered
at com.atlassian.jira.security.JiraSecurityFilter.doFilter(JiraSecurityFilter.java:74)
... 36 filtered
at com.atlassian.jira.servermetrics.CorrelationIdPopulatorFilter.doFilter(CorrelationIdPopulatorFilter.java:30)
... 10 filtered
at com.atlassian.web.servlet.plugin.request.RedirectInterceptingFilter.doFilter(RedirectInterceptingFilter.java:21)
... 4 filtered
at com.atlassian.web.servlet.plugin.LocationCleanerFilter.doFilter(LocationCleanerFilter.java:36)
... 29 filtered
at com.atlassian.jira.servermetrics.MetricsCollectorFilter.doFilter(MetricsCollectorFilter.java:25)
... 27 filtered
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$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)
2017-10-03 13:31:35,093 http-nio-8080-exec-19 INFO anonymous 811x3x1 1al0g13 199.63.92.5 /secure/SetupDatabase!default.jspa [c.a.j.bc.dataimport.DefaultDataImportService] JIRA Data Import has finished.
2017-10-03 13:31:35,094 http-nio-8080-exec-19 ERROR anonymous 811x3x1 1al0g13 199.63.92.5 /secure/SetupDatabase!default.jspa [c.a.jira.startup.DatabaseInitialImporter]
2017-10-03 13:31:35,094 http-nio-8080-exec-19 ERROR anonymous 811x3x1 1al0g13 199.63.92.5 /secure/SetupDatabase!default.jspa [c.a.jira.startup.DatabaseInitialImporter] Error importing data: java.lang.IllegalStateException: Could not find column 'EXCLUDE_ISSUE_DETAILS' in previously parsed query!
2017-10-03 13:31:35,161 Modification Check:thread-1 INFO [c.a.jira.startup.JiraStartupLogger]

___ Modifications ___________________________

Modified Files : jira-application.properties
Removed Files : None

2017-10-03 13:31:51,156 Timer-0 DEBUG [c.a.activeobjects.osgi.ActiveObjectsServiceFactory] getService bundle [com.atlassian.plugin.automation.automation-module]

Andy Heinzer · Answer

The interesting error among that output is this part:

28-Sep-2017 12:21:50.472 SEVERE [Catalina-startStop-1] org.apache.catalina.startup.HostConfig.beforeStart Unable to create directory for deployment: /data/apps/jira7.2.1/conf/Catalina/localhost

That indicates to me that the user account starting the Jira process does not actually have the needed filesystem permissions to be able to create directories needed to run Jira.  I would recommend following the steps in How to fix Jira filesystem permissions in Linux in order to resolve that error.

After you complete these steps, try to restart Jira once more.  If it is not starting up, please provide an updated catalina.out.