Help Please Mark  2014-12-24 05:48
Status: Closed
 
I am trying to install labkey server on:
ubuntu 14, tomcat7, postgresql and I get the following error

Can someone help me find why I get this error please?



500: Unexpected server error
A failure occurred during LabKey Server startup.

java.lang.RuntimeException: org.springframework.jdbc.BadSqlGrammarException: ExecutingSelector; bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: relation "core.Containers" does not exist
  Position: 15
       at org.labkey.api.data.SchemaTableInfoCache$SchemaTableLoader.load(SchemaTableInfoCache.java:91)
       at org.labkey.api.data.SchemaTableInfoCache$SchemaTableLoader.load(SchemaTableInfoCache.java:77)
       at org.labkey.api.cache.BlockingCache.get(BlockingCache.java:139)
       at org.labkey.api.cache.BlockingCache.get(BlockingCache.java:81)
       at org.labkey.api.data.SchemaTableInfoCache.get(SchemaTableInfoCache.java:44)
       at org.labkey.api.data.DbScope.getTable(DbScope.java:794)
       at org.labkey.api.data.DbSchema.getTable(DbSchema.java:497)
       at org.labkey.api.data.CoreSchema.getTableInfoSqlScripts(CoreSchema.java:82)
       at org.labkey.api.data.SqlScriptManager$CoreSqlScriptManager.getTableInfoSqlScripts(SqlScriptManager.java:328)
       at org.labkey.api.data.SqlScriptManager.insert(SqlScriptManager.java:262)
       at org.labkey.api.data.SqlScriptManager.runScript(SqlScriptManager.java:217)
       at org.labkey.api.data.SqlScriptRunner.runScripts(SqlScriptRunner.java:82)
       at org.labkey.api.module.DefaultModule.versionUpdate(DefaultModule.java:353)
       at org.labkey.api.module.ModuleUpgrader.upgrade(ModuleUpgrader.java:59)
       at org.labkey.api.module.ModuleLoader.upgradeCoreModule(ModuleLoader.java:943)
       at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:352)
       at org.labkey.api.module.ModuleLoader.init(ModuleLoader.java:255)
       at org.apache.catalina.core.ApplicationFilterConfig.initFilter(ApplicationFilterConfig.java:279)
       at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:260)
       at org.apache.catalina.core.ApplicationFilterConfig.<init>(ApplicationFilterConfig.java:105)
       at org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:4809)
       at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5485)
       at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
       at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
       at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
       at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:632)
       at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:670)
       at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1839)
       at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
       at java.util.concurrent.FutureTask.run(FutureTask.java:262)
       at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
       at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
       at java.lang.Thread.run(Thread.java:745)
Caused by: org.springframework.jdbc.BadSqlGrammarException: ExecutingSelector; bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: relation "core.Containers" does not exist
  Position: 15
       at org.springframework.jdbc.support.SQLErrorCodeSQLExceptionTranslator.translate(SQLErrorCodeSQLExceptionTranslator.java:276)
       at org.labkey.api.data.ExceptionFramework$1.translate(ExceptionFramework.java:37)
       at org.labkey.api.data.ExceptionFramework$1.translate(ExceptionFramework.java:31)
       at org.labkey.api.data.SqlExecutingSelector$ExecutingResultSetFactory.handleSqlException(SqlExecutingSelector.java:443)
       at org.labkey.api.data.BaseSelector.handleResultSet(BaseSelector.java:263)
       at org.labkey.api.data.BaseSelector.getObject(BaseSelector.java:163)
       at org.labkey.api.data.BaseSelector.getObject(BaseSelector.java:158)
       at org.labkey.api.data.ContainerManager.getForPath(ContainerManager.java:870)
       at org.labkey.api.data.ContainerManager.getForPath(ContainerManager.java:855)
       at org.labkey.api.data.ContainerManager.getRoot(ContainerManager.java:909)
       at org.labkey.api.settings.AbstractSettingsGroup.lookupStringValue(AbstractSettingsGroup.java:56)
       at org.labkey.api.settings.AppPropsImpl.getServerGUID(AppPropsImpl.java:390)
       at org.labkey.api.util.MothershipReport.addServerSessionParams(MothershipReport.java:281)
       at org.labkey.api.util.ExceptionUtil.reportExceptionToMothership(ExceptionUtil.java:351)
       at org.labkey.api.util.ExceptionUtil.logExceptionToMothership(ExceptionUtil.java:324)
       at org.labkey.api.util.ExceptionUtil.logExceptionToMothership(ExceptionUtil.java:281)
       at org.labkey.core.dialect.PostgreSql84Dialect$PostgreSQLColumnMetaDataReader.getDomainScale(PostgreSql84Dialect.java:1525)
       at org.labkey.core.dialect.PostgreSql84Dialect$PostgreSQLColumnMetaDataReader.getScale(PostgreSql84Dialect.java:1506)
       at org.labkey.api.data.ColumnInfo.createFromDatabaseMetaData(ColumnInfo.java:1468)
       at org.labkey.api.data.SchemaColumnMetaData.loadColumnsFromMetaData(SchemaColumnMetaData.java:227)
       at org.labkey.api.data.SchemaColumnMetaData.loadFromMetaData(SchemaColumnMetaData.java:182)
       at org.labkey.api.data.SchemaColumnMetaData.<init>(SchemaColumnMetaData.java:73)
       at org.labkey.api.data.SchemaTableInfo.getColumnMetaData(SchemaTableInfo.java:404)
       at org.labkey.api.data.SchemaTableInfo.getColumn(SchemaTableInfo.java:379)
       at org.labkey.api.data.SchemaTableInfo.getContainerFieldKey(SchemaTableInfo.java:1053)
       at org.labkey.api.data.SchemaTableInfo.getContainerContext(SchemaTableInfo.java:1044)
       at org.labkey.api.data.SchemaTableInfo.afterConstruct(SchemaTableInfo.java:141)
       at org.labkey.api.data.DbSchema.loadTable(DbSchema.java:361)
       at org.labkey.api.data.SchemaTableInfoCache$SchemaTableLoader.load(SchemaTableInfoCache.java:87)
       ... 32 more
Caused by: org.postgresql.util.PSQLException: ERROR: relation "core.Containers" does not exist
  Position: 15
       at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2198)
       at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1927)
       at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
       at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:561)
       at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:405)
       at org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:285)
       at org.labkey.api.data.dialect.StatementWrapper.executeQuery(StatementWrapper.java:916)
       at org.labkey.api.data.SqlExecutingSelector$ExecutingResultSetFactory.executeQuery(SqlExecutingSelector.java:374)
       at org.labkey.api.data.SqlExecutingSelector$ExecutingResultSetFactory.getResultSet(SqlExecutingSelector.java:324)
       at org.labkey.api.data.BaseSelector.handleResultSet(BaseSelector.java:249)
       ... 56 more
 
 
Brian Connolly responded:  2014-12-24 08:18
Mark,
I am sorry to hear you are having a problem. Can you provide a little more information about what is occurring?

1. What version of PostgreSQL are you running on the server?

2. Did you install PostgreSQL and Tomcat using the package manager or from the binary distribution/source?

3. Is the user PostgreSQL user account (ie the credentials you put in the labkey.xml file) have super-user privileges on PostgreSQL. If not, how was the labkey directory created?

4. Can you attach the log file, labkey.log, to your response? You can find the log file in the "TOMCAT_INSTALL_DIR/logs" directory if you installed TOMCAT from source or in "/var/log/tomcat7" directory if you installed TOMCAT using the package manager.

Thank you,

Brian
 
Mark responded:  2014-12-24 09:36
Hi Brian

Thank you for reply and helping.
1.
PostgreSQL 9.3.5
2.
"sudo apt-get install"
3.
Yes postgresql has super-user prilviledge
4.
attached labkey log files

Thanks again
 
Brian Connolly responded:  2014-12-24 10:14
Mark,

This is an error I have not seen before. If you look inside the "labkey" database do you see any tables created?

Also, are you using Oracle's JAVA to run TOMCAT or are you using the default version of JAVA which is openJDK. For LabKey Server you must use Oracle's JAVA.

Thank you,

Brian
 
Mark responded:  2014-12-24 11:10
Hi Brian

No tables gets created in the newly created "labkey" database

Yes I am using JAVA_HOME=/usr/lib/jvm/java-7-oracle

Any other pointers would be grateful

Thanks again
 
Brian Connolly responded:  2014-12-24 12:10
Mark,

We normally recommend installing Tomcat using the binary distribution instead of using the version shipped with the Ubuntu. See https://www.labkey.org/wiki/home/Documentation/page.view?name=installComponents.

If you would like to keep using the version of Tomcat installed via the package manager, I recommend verifying that all the files shipped with the LabKey distribution are located in the correct place. See https://www.labkey.org/wiki/home/Documentation/page.view?name=configTomcat.

Especially important if verifying that step #1 is complete. For your installation, where did you place these files?



Also can you review your PostgreSQL server logs to see if there are any errors in the log file.


Brian
 
Mark responded:  2014-12-24 15:39
Thanks Brian

I went over the steps you suggested and indeed it clears up the problem that I was seeing.

Thanks again and apologizes for the inconvenience