Recent-submissions homepage error in DSpace 6.3

[Donna Barber]

Hi,

We’re in the process of moving from 5.6 to 6.3 with everything up and running in our development environment, except we’ve found that we’re now getting an error trying to view the recently added list from the homepage (/recent-submissions). However, it still works from the community/collection homepages.

 

Does anyone have any idea what could be the cause? We’ve stripped out our customisations and switched between Mirage and Mirage2 themes, but it’s the same. The stack trace produced when clicking on “view more” is attached.

 

Many thanks,

Donna Barber

eServices Coordinator | Kairuruku Ratonga Tāhiko

Library Access and Collections | Rōpū Tautāwhi

Phone: +64 3 369 3849 extn 93849 | Puaka - James Hight Building, Level 5, Rm 519

Learning Resources | University of Canterbury | Te Whare Wānanga o Waitaha  | Private Bag 4800 | Christchurch 8140 | New Zealand
Website: http://www.canterbury.ac.nz/library

[Tim Donohue]

Hi Donna,

I'd recommend checking that all the Database migrations ran successfully when you upgraded to 6.3.  That error seems to be returning a "null" Site object on the homepage.  The Site object is a virtual object that represents your site as a whole...it's created automatically in the database in a table named "site".  This error seems to imply that some portion of your database migration (which should have created that Site object) must have failed.

So, I'd recommend looking at your logs more closely during the upgrade....also, you should run "[dspace]/bin/dspace database info" to see if there are any migrations that your upgrade flagged as IGNORED (if so, you should run them, by running "./dspace database migrate ignored").  More info on these new database commands is at: 

https://wiki.lyrasis.org/display/DSDOC6x/Database+Utilities

Overall, it looks to me like your database upgrade didn't succeed.  It's hard to say exactly what happened without looking closer at the logs or what the "database info" command returns.  If you find an error and are not sure what is happening, feel free to forward it along to this list and hopefully someone here can help!

Tim

---

From: dspac...@googlegroups.com <dspac...@googlegroups.com> on behalf of Donna Barber <donna....@canterbury.ac.nz>
Sent: Sunday, February 16, 2020 7:27 PM
To: DSpace Technical Support <dspac...@googlegroups.com>
Subject: [dspace-tech] Recent-submissions homepage error in DSpace 6.3

 

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[Donna Barber]

Hi Tim,

 

Thanks very much for pointing us in the right direction. We think we’ve now resolved the issue by following the instructions for a post you responded to in 2015.

 

The registry update was being ignored, and when I tried to run it separately, we were getting the error:

 

Caused by: java.sql.BatchUpdateException: Batch entry 0 update public.bitstreamformatregistry set description=NULL, internal='FALSE', mimetype='application/vnd.openxmlformats-officedocument.wordprocessingml.document', short_description=NULL, support_level=-1 where bitstream_format_id=52 was aborted: ERROR: value too long for type character varying(48) 

 

Which led me to your 2015 reply to a post about the change of the bitstreamformatregistry table’s mimetype column switching from 48 to 256 characters in DSpace 1.5. We’ve been on DSpace since 1.4, so we’ve obviously been hauling this problem along for a while!

 

After altering the column character length on the 5.6 database the registry update task was initially ignored, but this time when we ran [dspace]/bin/dspace database migrate ignored, it completed successfully. We now have an entry in the site table, and the recent submissions are working – yay!

 

Hopefully there aren’t any other left-over issues that we haven’t identified, but as far as we can tell, all is well. J

 

Thanks again,
Donna

[Carl Jones]

Hi, 

We've upgraded from 1.8 to 6.3 a couple of months ago and are experiencing a similar error with the 'Recently Added' list when we try to hit the 'View more' link at the site homepage.  Tim Donohue mentioned this could be because of a missing virtual Site Object that represents our system as a whole.  We get the following Stack Trace (similar to what was reported by Donna Barber back in February of this year):

Java stacktrace: java.lang.NullPointerException at org.dspace.app.xmlui.aspect.discovery.recentSubmissions.RecentSubmissionTransformer.setMainTitle(RecentSubmissionTransformer.java:154) at org.dspace.app.xmlui.aspect.discovery.recentSubmissions.RecentSubmissionTransformer.addBody(RecentSubmissionTransformer.java:124) at org.dspace.app.xmlui.wing.AbstractWingTransformer.startElement(AbstractWingTransformer.java:234) at sun.reflect.GeneratedMethodAccessor215.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:607) at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71) at com.sun.proxy.$Proxy493.startElement(Unknown Source) at org.apache.cocoon.components.sax.XMLTeePipe.startElement(XMLTeePipe.java:87) at org.apache.cocoon.xml.AbstractXMLPipe.startElement(AbstractXMLPipe.java:94) at org.dspace.app.xmlui.wing.AbstractWingTransformer.startElement(AbstractWingTransformer.java:251) at sun.reflect.GeneratedMethodAccessor215.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:607).... 

<snip>

I followed the suggestion to run 'bin/database info' but as far as I can tell the database update checks all come back as Successful. 

I'm attaching the stack trace and database info output.

I was curious if there were any other things I might check before passing this onto our sysadmin for further investigation into what might cause a missing virtual Site object problem?

Thanks,

Carl

[Jose Blanco]

I remember having this issue, and I think it was a migration that had not run.  You can check your database to make sure you have a table named site:

=> \d site
    Table "public.site"
 Column | Type | Modifiers
--------+------+-----------
 uuid   | uuid | not null

Indexes:
    "site_pkey" PRIMARY KEY, btree (uuid)
Foreign-key constraints:
    "site_uuid_fkey" FOREIGN KEY (uuid) REFERENCES dspaceobject(uuid)

And also, In the config area take a look at this file: hibernate.cfg.xml

You should have this in the file:
        <mapping class="org.dspace.content.Site"/>

Hope this helps!

-Jose

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[Carl A Jones]

Hi Jose,

Thanks, much, for the suggestions. We’ll check those out.

Carl

[Carl Jones]

It's been a while, but following up,  what if the Site table is present but it's empty?

Carl

[Jose Blanco]

Look at this:

https://groups.google.com/g/dspace-tech/c/k33Thvse0LA/m/v2XEQeOfAQAJ

Look at what Hernan did.  I'm not sure how he created the UUID he inserted in the tables.  Perhaps you know how to create one.  I googled a bit and saw some documentation about it.

Hope this helps.

-Jose

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[Carl Jones]

Hi Jose,

Thanks for the link, looks very helpful (the table should not be empty) and I'll pass onto our sysadmin.

Carl

[Carl Jones]

Hi Jose,

That worked. Our sysadmin created the UUID and inserted into the tables as described in the earlier post. So, for whatever reason, didn't get populated as part of the 1.8 -> 6.3 upgrade process.

Thank you!

Carl