Internal System Error on dspace 5.2

[Emmanuel Wilson]

Hello all,

i am facing internal system error while soing metadata-import. Now even i cannot create a new collection or edit the existing item.

Please see the error log:

 1st error
2016-07-29 10:02:41,878 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL create Error -
org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "webapp_pkey"
  Detail: Key (webapp_id)=(12) already exists.
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2103)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1836)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:257)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:512)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:388)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:273)
    at org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:96)
    at org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:96)
    at org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:96)
    at org.dspace.storage.rdbms.DatabaseManager.doInsertPostgres(DatabaseManager.java:1743)
    at org.dspace.storage.rdbms.DatabaseManager.insert(DatabaseManager.java:711)
    at org.dspace.storage.rdbms.DatabaseManager.create(DatabaseManager.java:476)
    at org.dspace.app.util.AbstractDSpaceWebapp.register(AbstractDSpaceWebapp.java:80)
    at org.dspace.app.util.DSpaceContextListener.contextInitialized(DSpaceContextListener.java:128)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5027)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5525)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1575)
    at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1565)
    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)

2nd error
2016-07-29 10:30:52,482 WARN  org.dspace.app.webui.servlet.DSpaceServlet @ dspace@localhost:session_id=C7C8E09E87658CA1D659C4C0C5255EB0:ip_addr=0:0:0:0:0:0:0:1:database_error:org.postgresql.util.PSQLException\colon; ERROR\colon; duplicate key value violates unique constraint "metadatavalue_pkey"
  Detail\colon; Key (metadata_value_id)=(125069) already exists.
org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "metadatavalue_pkey"
  Detail: Key (metadata_value_id)=(125069) already exists.
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2103)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1836)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:257)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:512)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:388)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:273)
    at org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:96)
    at org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:96)
    at org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:96)
    at org.dspace.storage.rdbms.DatabaseManager.doInsertPostgres(DatabaseManager.java:1743)
    at org.dspace.storage.rdbms.DatabaseManager.insert(DatabaseManager.java:711)
    at org.dspace.content.MetadataValue.create(MetadataValue.java:293)
    at org.dspace.content.DSpaceObject.updateMetadata(DSpaceObject.java:256)
    at org.dspace.content.Bitstream.update(Bitstream.java:502)
    at org.dspace.app.webui.servlet.admin.EditItemServlet.processUpdateItem(EditItemServlet.java:752)
    at org.dspace.app.webui.servlet.admin.EditItemServlet.doDSPost(EditItemServlet.java:231)
    at org.dspace.app.webui.servlet.DSpaceServlet.processRequest(DSpaceServlet.java:115)
    at org.dspace.app.webui.servlet.DSpaceServlet.doPost(DSpaceServlet.java:73)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:646)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
    at org.dspace.app.webui.filter.RegisteredOnlyFilter.doFilter(RegisteredOnlyFilter.java:66)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
    at org.dspace.utils.servlet.DSpaceWebappServletFilter.doFilter(DSpaceWebappServletFilter.java:78)
    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:503)
    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:421)
    at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1070)
    at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:611)
    at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:316)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
    at java.lang.Thread.run(Thread.java:745)

[Tim Donohue]

Hi Emmanuel,

Based on both errors, it sounds like some of your database sequences need to be updated (that's usually the cause of a "duplicate key" error). 

Sometimes the underlying sequences that DSpace uses to create new content in the database can end up needing "re-syncing". This doesn't happen frequently though, but can occur especially after restoring data from a backup or restoring content via AIPs (or some other rare scenarios).

In any case, it should be easily fixable by simply running the provided "[dspace]/etc/[db-type]/update-sequences.sql" script on your database.

For example, if you are using PostgreSQL, you'd run something like this:

psql -U [database-user] -f [dspace]/etc/postgres/update-sequences.sql [database-name]

If your DSpace [database-user] and [database-name] are both named "dspace" (which is often the case), then run this:

psql -U dspace -f [dspace]/etc/postgres/update-sequences.sql dspace

This "update-sequences.sql" script is not harmful, and can be run while Tomcat is still running.

- Tim

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-- 
Tim Donohue
Technical Lead for DSpace & DSpaceDirect
DuraSpace.org | DSpace.org | DSpaceDirect.org

[Emmanuel Wilson]

Thank You so much Tim and tech team....that was exactly i am looking for. I found the previous backup file works fine now even new database also with this script.

Thanks again.

--

Emmanuel Wilson

Kerala Forest Research Institute 
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