Database problem at startup after updating from 5.5 to 6

[Sébastien Nadeau]

I followed the upgrade path decumented at https://wiki.duraspace.org/display/DSDOC6x/Upgrading+DSpace

Essentially, the update went well, I have a couple of problems having the maven build to work perfectly, but after a few tries got it to compile successfully.

I went to run the ant build with update and test database as targets and then started Tomcat. That's when DSpace complains about the database and won't start the jspui webapp. here's the result of ant target test-database:

test_database:

     [java] 2016-12-09 14:24:45,264 WARN  org.dspace.services.email.EmailServiceImpl @ Couldn't get an email session from environment:  Need to specify class name in environment or system property, or as an applet parameter, or in an application resource file:  java.naming.factory.initial

     [java] Attempting to connect to database

     [java] Connected successfully!

     [java] Database Type: oracle

     [java] Database URL: jdbc:oracle:thin:@//localhost:1521/xe

     [java] Database Schema: DSPACE

     [java] Database Username: DSPACE

     [java] Database Software: Oracle version Oracle Database 11g Express Edition Release 11.2.0.2.0 - 64bit Production

     [java] Database Driver: Oracle JDBC driver version 11.2.0.4.0

     [java] 2016-12-09 14:24:45,842 WARN  org.dspace.services.sessions.SessionRequestServiceImpl @ Request interceptor (org.dspace.services.events.SystemEventService$EventRequestInterceptor@5a277d08) failed to execute on end (request-675-1481311485558): null

BUILD SUCCESSFUL

Total time: 4 seconds

There seems to be a warning in there, but I don't know what's wrong. And when starting Tomcat 8.0.28:

java.lang.ExceptionInInitializerError

at org.dspace.app.util.AbstractDSpaceWebapp.register(AbstractDSpaceWebapp.java:74)

at org.dspace.app.util.DSpaceWebappListener.contextInitialized(DSpaceWebappListener.java:31)

at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4738)

at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5181)

at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)

at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:725)

at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:701)

at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:717)

at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:586)

at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1780)

at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)

at java.util.concurrent.FutureTask.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

at java.lang.Thread.run(Thread.java:745)

Caused by: java.lang.NullPointerException

at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:547)

at org.dspace.core.Context.<clinit>(Context.java:94)

... 15 more

The webapp fails to start and I can't figure out why since I can perfectly connect to my Oracle XE database using Toad using the same config as DSpace. Here's the content of the schema_version table:

installed_rank,version,description,type,script,checksum,installed_by,installed_on,execution_time,success

1,1,<< Flyway Init >>,BASELINE,<< Flyway Init >>,,DSPACE,2015/10/13 08:56:16,071000,0,1

2,1.2,Initial DSpace 1.2 Oracle database schema,SQL,V1.2__Initial_DSpace_1.2_Oracle_database_schema.sql,-127558648,DSPACE,2015/10/13 08:56:17,068000,737,1

3,1.3,Upgrade to DSpace 1.3 schema,SQL,V1.3__Upgrade_to_DSpace_1.3_schema.sql,711674715,DSPACE,2015/10/13 08:56:17,179000,99,1

4,1.3.9,Drop constraint for DSpace 1 4 schema,JDBC,org.dspace.storage.rdbms.migration.V1_3_9__Drop_constraint_for_DSpace_1_4_schema,-1,DSPACE,2015/10/13 08:56:17,251000,61,1

5,1.4,Upgrade to DSpace 1.4 schema,SQL,V1.4__Upgrade_to_DSpace_1.4_schema.sql,291561119,DSPACE,2015/10/13 08:56:17,798000,532,1

6,1.4.2,Upgrade to DSpace 1.4.2 schema,SQL,V1.4.2__Upgrade_to_DSpace_1.4.2_schema.sql,-1161287423,DSPACE,2015/10/13 08:56:18,263000,453,1

7,1.5,Upgrade to DSpace 1.5 schema,SQL,V1.5__Upgrade_to_DSpace_1.5_schema.sql,1802146540,DSPACE,2015/10/13 08:56:18,929000,658,1

8,1.5.9,Drop constraint for DSpace 1 6 schema,JDBC,org.dspace.storage.rdbms.migration.V1_5_9__Drop_constraint_for_DSpace_1_6_schema,-1,DSPACE,2015/10/13 08:56:18,988000,43,1

9,1.6,Upgrade to DSpace 1.6 schema,SQL,V1.6__Upgrade_to_DSpace_1.6_schema.sql,-648817059,DSPACE,2015/10/13 08:56:19,099000,98,1

10,1.7,Upgrade to DSpace 1.7 schema,SQL,V1.7__Upgrade_to_DSpace_1.7_schema.sql,-589640641,DSPACE,2015/10/13 08:56:19,119000,8,1

11,1.8,Upgrade to DSpace 1.8 schema,SQL,V1.8__Upgrade_to_DSpace_1.8_schema.sql,-171791117,DSPACE,2015/10/13 08:56:19,142000,13,1

12,3.0,Upgrade to DSpace 3.x schema,SQL,V3.0__Upgrade_to_DSpace_3.x_schema.sql,-1909953848,DSPACE,2015/10/13 08:56:19,251000,83,1

13,4.0,Upgrade to DSpace 4.x schema,SQL,V4.0__Upgrade_to_DSpace_4.x_schema.sql,1369713442,DSPACE,2015/10/13 08:56:19,333000,66,1

14,5.0.2014.08.08,DS-1945 Helpdesk Request a Copy,SQL,V5.0_2014.08.08__DS-1945_Helpdesk_Request_a_Copy.sql,-1654867497,DSPACE,2015/10/13 08:56:19,361000,10,1

15,5.0.2014.09.25,DS 1582 Metadata For All Objects drop constraint,JDBC,org.dspace.storage.rdbms.migration.V5_0_2014_09_25__DS_1582_Metadata_For_All_Objects_drop_constraint,-1,DSPACE,2015/10/13 08:56:19,380000,9,1

16,5.0.2014.09.26,DS-1582 Metadata For All Objects,SQL,V5.0_2014.09.26__DS-1582_Metadata_For_All_Objects.sql,-380178133,DSPACE,2015/10/13 08:56:19,777000,386,1

17,5.6.2016.08.23,DS-3097,SQL,V5.6_2016.08.23__DS-3097.sql,-709455653,DSPACE,2016/12/07 15:36:35,175000,20,1

18,6.0.2015.03.06,DS 2701 Dso Uuid Migration,JDBC,org.dspace.storage.rdbms.migration.V6_0_2015_03_06__DS_2701_Dso_Uuid_Migration,-1,DSPACE,2016/12/07 15:36:35,301000,119,1

19,6.0.2015.03.07,DS-2701 Hibernate migration,SQL,V6.0_2015.03.07__DS-2701_Hibernate_migration.sql,113344134,DSPACE,2016/12/07 15:36:37,165000,1856,1

20,6.0.2015.08.31,DS 2701 Hibernate Workflow Migration,JDBC,org.dspace.storage.rdbms.migration.V6_0_2015_08_31__DS_2701_Hibernate_Workflow_Migration,-1,DSPACE,2016/12/07 15:36:37,269000,98,1

21,6.0.2016.01.03,DS-3024,SQL,V6.0_2016.01.03__DS-3024.sql,257838196,DSPACE,2016/12/07 15:36:37,337000,63,1

22,6.0.2016.01.26,DS 2188 Remove DBMS Browse Tables,JDBC,org.dspace.storage.rdbms.migration.V6_0_2016_01_26__DS_2188_Remove_DBMS_Browse_Tables,-1,DSPACE,2016/12/07 15:36:37,411000,68,1

23,6.0.2016.02.25,DS-3004-slow-searching-as-admin,SQL,V6.0_2016.02.25__DS-3004-slow-searching-as-admin.sql,1891362624,DSPACE,2016/12/07 15:36:37,428000,12,1

24,6.0.2016.04.01,DS-1955 Increase embargo reason,SQL,V6.0_2016.04.01__DS-1955_Increase_embargo_reason.sql,1151216187,DSPACE,2016/12/07 15:36:37,466000,32,1

25,6.0.2016.04.04,DS-3086-OAI-Performance-fix,SQL,V6.0_2016.04.04__DS-3086-OAI-Performance-fix.sql,-1176994537,DSPACE,2016/12/07 15:36:37,565000,94,1

26,6.0.2016.04.14,DS-3125-fix-bundle-bitstream-delete-rights,SQL,V6.0_2016.04.14__DS-3125-fix-bundle-bitstream-delete-rights.sql,1999534659,DSPACE,2016/12/07 15:36:37,576000,6,1

27,6.0.2016.05.10,DS-3168-fix-requestitem item id column,SQL,V6.0_2016.05.10__DS-3168-fix-requestitem_item_id_column.sql,-997233444,DSPACE,2016/12/07 15:36:37,627000,46,1

28,6.0.2016.07.21,DS-2775,SQL,V6.0_2016.07.21__DS-2775.sql,-1759785522,DSPACE,2016/12/07 15:36:37,662000,30,1

29,6.0.2016.07.26,DS-3277 fix handle assignment,SQL,V6.0_2016.07.26__DS-3277_fix_handle_assignment.sql,-206807667,DSPACE,2016/12/07 15:36:37,680000,13,1

30,6.0.2016.08.23,DS-3097,SQL,V6.0_2016.08.23__DS-3097.sql,1063873081,DSPACE,2016/12/07 15:36:37,700000,15,1

Hope someone can help me troubleshoot this show stopper or give me a hint at what to look next.

Thank you,

Sébastien Nadeau

Université Laval

Quebec City, Canada

[Sébastien Nadeau]

I solved my own problem by upgrading the database at the command line and commenting out lines 92 to 99 in org.dspace.core.Context.java. Webapp jspui starts correctly and DSpace 6 is running.