Upgrade to Dspace 5.5 causes error when accessing e-person

[Tom Avino]

I just upgraded from 3.3 to 5.5.  Everything seems to work fine with the exception of adding, modifying, or anything to do with e-persons.

I get the following error in my log.

2016-05-23 12:46:00,994 WARN  org.dspace.app.webui.servlet.InternalErrorServlet @ :session_id=8BF240B6BB6E818B5130008A9D01FF8F:internal_error:-- URL Was: https://ldr-d.larc.nasa.gov/tools/eperson-list?multiple=false

-- Method: GET

-- Parameters were:

-- multiple: "false"

java.lang.NullPointerException

at org.dspace.eperson.EPerson.findAll(EPerson.java:523)

at org.dspace.app.webui.servlet.admin.EPersonListServlet.doDSGet(EPersonListServlet.java:91)

at org.dspace.app.webui.servlet.DSpaceServlet.processRequest(DSpaceServlet.java:119)

at org.dspace.app.webui.servlet.DSpaceServlet.doGet(DSpaceServlet.java:67)

at javax.servlet.http.HttpServlet.service(HttpServlet.java:624)

at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)

at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)

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:505)

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:957)

at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)

at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423)

at org.apache.coyote.ajp.AjpProcessor.process(AjpProcessor.java:190)

at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:620)

at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:316)

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)

2016-05-23 12:46:00,996 WARN  org.dspace.app.webui.util.UIUtil @ Unable to send email alert

java.lang.NullPointerException

at org.dspace.storage.rdbms.DatabaseManager.queryTable(DatabaseManager.java:230)

at org.dspace.content.DSpaceObject$MetadataCache.retrieveMetadata(DSpaceObject.java:1330)

at org.dspace.content.DSpaceObject$MetadataCache.get(DSpaceObject.java:1265)

at org.dspace.content.DSpaceObject.getMetadata(DSpaceObject.java:676)

at org.dspace.content.DSpaceObject.getMetadata(DSpaceObject.java:585)

at org.dspace.content.DSpaceObject.getMetadataFirstValue(DSpaceObject.java:653)

at org.dspace.eperson.EPerson.getFirstName(EPerson.java:772)

at org.dspace.eperson.EPerson.getFullName(EPerson.java:748)

at org.dspace.app.webui.util.UIUtil.sendAlert(UIUtil.java:419)

at org.dspace.app.webui.servlet.InternalErrorServlet.doGet(InternalErrorServlet.java:54)

at javax.servlet.http.HttpServlet.service(HttpServlet.java:624)

at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)

at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:748)

at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:488)

at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:411)

at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:338)

at org.apache.catalina.core.StandardHostValve.custom(StandardHostValve.java:476)

at org.apache.catalina.core.StandardHostValve.throwable(StandardHostValve.java:420)

at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:208)

at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)

at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:957)

at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)

at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423)

at org.apache.coyote.ajp.AjpProcessor.process(AjpProcessor.java:190)

at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:620)

at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:316)

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)

[Claudia Jürgen]

Hello Tom,

have you run update-sequences prior to doing the database migrate see 10.b
https://wiki.duraspace.org/display/DSDOC5x/Upgrading+DSpace

There has been issues:
https://jira.duraspace.org/browse/DS-2558
resolved with https://jira.duraspace.org/browse/DS-2480

Hope this helps

Claudia Jürgen

-- 
Claudia Juergen
Eldorado

Technische Universität Dortmund
Universitätsbibliothek
Vogelpothsweg 76
44227 Dortmund

Tel.: +49 231-755 40 43
Fax: +49 231-755 40 32
claudia...@tu-dortmund.de
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[ORIOL OLIVÉ COMADIRA]

Hi Tom,

 

I think that you must to upgrade your schemes before upgrading the database.

 

bin/dspace registry-loader -metadata config/registries/dcterms-types.xml
bin/dspace registry-loader -metadata config/registries/eperson-types.xml
bin/dspace registry-loader -metadata config/registries/sword-metadata.xml
bin/dspace registry-loader -metadata config/registries/workflow-types.xml

 

Warning about that: DSpace upgrades the database when you start tomcat server...

 

 

Good luck!

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[Tom Avino]

I have gone through the documentation of 5.5 upgrade and there is no reference to run these.  Are there others that are not in the documentation that I need to run??

This seems pretty major to not be listed in the instructions

When does the database get upgraded?  Can I run the script manually?  I thought the postgres database upgrade script gets run when dspace is started for the first time.

How can I run the below scripts before the database upgrade, if the upgrade happens when I start Tomcat, which I need to do to run the scripts below?

[Tim Donohue]

Hi Tom,

Based on the error, it seems like the new "eperson" metadata registry wasn't created properly when you upgraded.  You can (manually) create it by running:

bin/dspace registry-loader -metadata config/registries/eperson-types.xml

To clarify, all of these new registry updates should have occurred *automatically* when you upgraded to 5.5.  All of the scripts that Oriol listed should be automatically triggered as part of the upgrade process.  However, it sounds like something may have failed (or was interrupted) during your upgrade and these new metadata fields were *not* successfully created.

You may wish to manually run each of those scripts listed (just in case another failed to run as well).  They can be run manually, and only require the database to be started up. It is safe to run them *after* your upgrade, assuming everything else ran properly.  You can also check the status of your database upgrades by running:

bin/dspace database info

(If the rest of the upgrade succeeded, you should see a state of "Success" next to each upgrade step listed in the output table.)

The reason these scripts are not listed in the documentation is that they are supposed to run automatically. It's hard to say why they failed to run during your upgrade (my guess is an error may have been thrown in your logs that would give more information).

As for your question about the database upgrade process: As of DSpace 5, the database will auto-upgrade the first time you startup Tomcat.  However, if you still want to upgrade your database manually, you can trigger the upgrade manually (prior to starting Tomcat) by simply running "bin/dspace database migrate".  This information is all listed in the 5.x documentation under step 10:
https://wiki.duraspace.org/display/DSDOC5x/Upgrading+DSpace

Good luck,

Tim

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

[ORIOL OLIVÉ COMADIRA]

Hi Tim and Tom,

 

In my case, I had errors with e-person and merge problems with bitstream name, collection/community title, bundle name and item name.

 

I upgraded from 1.8 to 5.2... I don't know if it can affect, but the upgrade failed me 3 times...

 

 

Good luck Tom

[Claudia Jürgen]

Hi Tom,

> In my case, I had errors with e-person and merge problems with bitstream name, collection/community title, bundle name and item name.

In DSpace 5 metadata for all DSpace Objects was introduced see
https://wiki.duraspace.org/display/DSPACE/Metadata+for+all+DSpace+objects
So these elements are now in metadatavalue rather than the e-person,
bitstream, collection ... tables

Seems as if your step to DSpace 5.0 did might not have worked properly.
Had you any migration errors at this point?

Hope this helps

Claudia Jürgen


>

> I upgraded from 1.8 to 5.2... I don't know if it can affect, but the upgrade failed me 3 times...
>
>

> Good luck Tom [*THUMBS UP*]

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