[Dspace-tech] error messages when submitting to dspace

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Sandy De Groote

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Aug 25, 2015, 11:33:05 AM8/25/15

to dspac...@lists.sourceforge.net

We are getting many internal error messages when submitting to dspace?
We typically get
them at two places: 1. uploading the file or 2. the final page when we
click on "I grant the license." Also, we are unable to
upload anything to one of our communities. We get an error on
the final page almost every time.

Can anyone point us in the right direction to fix this? I tried looking
at the documentation but I couldn't get to the right release. (We are
not using the latest version of dspace - we are using the one before 1.5)
Sandy

--
Sandy De Groote, MLIS, AHIP sgr...@uic.edu
Assistant Health Sciences Librarian and Associate Professor
Visiting Digital Publishing Librarian
309-671-8494
UIC Library of the Health Sciences-Peoria
PO Box 1649, Peoria IL 61656

felipe Melero

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Aug 25, 2015, 11:33:06 AM8/25/15

to dspac...@lists.sourceforge.net

Could you please put the stack trace of dspace.log?
regards,
Felipe

Sandy De Groote escribió:

Claudia Jürgen

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Aug 25, 2015, 11:33:07 AM8/25/15

to Sandy De Groote, dspac...@lists.sourceforge.net

Hi Sandy,

could you provide more information (stack trace).

Just a guess. Got the tomcat user the proper rights - i.e. does [dspace]
your dspace intallation directory belongs to the user tomcat (assuming
this is your servlet container) is running as?

Claudia Jürgen

Sandy De Groote schrieb:

Sandy De Groote

unread,

Aug 25, 2015, 11:33:09 AM8/25/15

to Claudia Jürgen, dspac...@lists.sourceforge.net

Claudia,
Thanks for any help you can provide!

Jan 20, 2009 8:30:13 AM org.apache.catalina.core.StandardWrapperValve invoke
WARNING: Servlet.service() for servlet submit threw exception
java.io.IOException: No such file or directory
at java.io.UnixFileSystem.createFileExclusively(Native Method)
at java.io.File.createNewFile(File.java:850)
at edu.sdsc.grid.io.local.LocalFile.createNewFile(LocalFile.java:486)
at
org.dspace.storage.bitstore.BitstreamStorageManager.store(BitstreamStorageManager.java:332)
at org.dspace.content.Bitstream.create(Bitstream.java:184)
at org.dspace.content.Bundle.createBitstream(Bundle.java:362)
at org.dspace.content.Item.createSingleBitstream(Item.java:1185)
at org.dspace.content.Item.licenseGranted(Item.java:1265)
at
org.dspace.app.webui.servlet.SubmitServlet.processLicense(SubmitServlet.java:1615)
at
org.dspace.app.webui.servlet.SubmitServlet.doDSPost(SubmitServlet.java:424)
at
org.dspace.app.webui.servlet.DSpaceServlet.processRequest(DSpaceServlet.java:147)
at
org.dspace.app.webui.servlet.DSpaceServlet.doPost(DSpaceServlet.java:105)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:709)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at
org.dspace.app.webui.filter.RegisteredOnlyFilter.doFilter(RegisteredOnlyFilter.java:98)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)
at
org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:541)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869)
at
org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:664)
at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)
at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80)
at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)
at java.lang.Thread.run(Thread.java:595)
Jan 20, 2009 8:44:05 AM org.apache.catalina.core.StandardWrapperValve invoke
WARNING: Servlet.service() for servlet submit threw exception
java.io.IOException: No such file or directory
at java.io.UnixFileSystem.createFileExclusively(Native Method)
at java.io.File.createNewFile(File.java:850)
at edu.sdsc.grid.io.local.LocalFile.createNewFile(LocalFile.java:486)
at
org.dspace.storage.bitstore.BitstreamStorageManager.store(BitstreamStorageManager.java:332)
at org.dspace.content.Bitstream.create(Bitstream.java:184)
at org.dspace.content.Bundle.createBitstream(Bundle.java:362)
at org.dspace.content.Item.createSingleBitstream(Item.java:1185)
at org.dspace.content.Item.licenseGranted(Item.java:1265)
at
org.dspace.app.webui.servlet.SubmitServlet.processLicense(SubmitServlet.java:1615)
at
org.dspace.app.webui.servlet.SubmitServlet.doDSPost(SubmitServlet.java:424)
at
org.dspace.app.webui.servlet.DSpaceServlet.processRequest(DSpaceServlet.java:147)
at
org.dspace.app.webui.servlet.DSpaceServlet.doPost(DSpaceServlet.java:105)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:709)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at
org.dspace.app.webui.filter.RegisteredOnlyFilter.doFilter(RegisteredOnlyFilter.java:98)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)
at
org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:541)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869)
at
org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:664)
at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)
at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80)
at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)
at java.lang.Thread.run(Thread.java:595)
Jan 20, 2009 9:43:15 PM org.apache.catalina.core.StandardWrapperValve invoke
SEVERE: Servlet.service() for servlet handle threw exception
java.lang.OutOfMemoryError: Java heap space
Jan 20, 2009 9:43:15 PM org.apache.catalina.core.ApplicationDispatcher
invoke
SEVERE: Servlet.service() for servlet internal-error threw exception
java.lang.ClassCastException: java.lang.OutOfMemoryError
at
org.dspace.app.webui.servlet.InternalErrorServlet.doGet(InternalErrorServlet.java:86)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:689)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at
org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:672)
at
org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:465)
at
org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:398)
at
org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301)
at
org.apache.catalina.core.StandardHostValve.custom(StandardHostValve.java:363)
at
org.apache.catalina.core.StandardHostValve.throwable(StandardHostValve.java:212)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:134)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)
at
org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:541)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869)
at
org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:664)
at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)
at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80)
at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)
at java.lang.Thread.run(Thread.java:595)
Jan 20, 2009 9:43:15 PM org.apache.catalina.core.StandardHostValve custom
SEVERE: Exception Processing
ErrorPage[exceptionType=java.lang.Exception, location=/internal-error]
java.lang.ClassCastException: java.lang.OutOfMemoryError
at
org.dspace.app.webui.servlet.InternalErrorServlet.doGet(InternalErrorServlet.java:86)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:689)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at
org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:672)
at
org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:465)
at
org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:398)
at
org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301)
at
org.apache.catalina.core.StandardHostValve.custom(StandardHostValve.java:363)
at
org.apache.catalina.core.StandardHostValve.throwable(StandardHostValve.java:212)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:134)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)
at
org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:541)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869)
at
org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:664)
at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)
at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80)
at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)
at java.lang.Thread.run(Thread.java:595)

Claudia Jürgen

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Aug 25, 2015, 11:33:11 AM8/25/15

to Sandy De Groote, dspac...@lists.sourceforge.net

Hi Sandy,

seems to be the problem mentioned below, an authorization one.

Your tomcat user needs the authorization to write to
[dspace]/assetstore.

In the installation instructions it is recommended to run tomcat as the
dspace user which owns the [dspace] directory.

Claudia

Sandy De Groote schrieb:

Diggory Mark

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Aug 25, 2015, 11:33:20 AM8/25/15

to Claudia Jürgen, dspac...@lists.sourceforge.net, Sandy De Groote

Yes, filesystem permissions in the assetstore would cause both to
fail. But also look at your filesystem quota as well to make sure
there is disk space.

On Jan 22, 2009, at 9:32 AM, Claudia Jürgen wrote:

> Hi Sandy,
>

>> $ControlRunnable.run(ThreadPool.java:684)
>>
>> at java.lang.Thread.run(Thread.java:595)
>>
>>
>>
>>
>> Claudia Jürgen wrote:
>>> Hi Sandy,
>>>
>>> could you provide more information (stack trace).
>>>
>>> Just a guess. Got the tomcat user the proper rights - i.e. does
>>> [dspace] your dspace intallation directory belongs to the user
>>> tomcat
>>> (assuming this is your servlet container) is running as?
>>>
>>> Claudia Jürgen
>>>
>>>
>>>
>>> Sandy De Groote schrieb:
>>>> We are getting many internal error messages when submitting to
>>>> dspace? We typically get
>>>> them at two places: 1. uploading the file or 2. the final page
>>>> when we
>>>> click on "I grant the license." Also, we are unable to
>>>> upload anything to one of our communities. We get an error on
>>>> the final page almost every time.
>>>>
>>>> Can anyone point us in the right direction to fix this? I tried
>>>> looking at the documentation but I couldn't get to the right
>>>> release. (We are not using the latest version of dspace - we are
>>>> using the one before 1.5)
>>>> Sandy
>>>>
>>
>

> ------------------------------------------------------------------------------
> This SF.net email is sponsored by:
> SourcForge Community
> SourceForge wants to tell your story.
> http://p.sf.net/sfu/sf-spreadtheword
> _______________________________________________
> DSpace-tech mailing list
> DSpac...@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/dspace-tech

~~~~~~~~~~~~~
Mark R. Diggory
http://purl.org/net/mdiggory/homepage

Sandy De Groote

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Aug 25, 2015, 11:33:41 AM8/25/15

to Diggory Mark, dspac...@lists.sourceforge.net, Claudia Jürgen

Unfortunately non of these suggestions seems to be the problem. Any
other suggestions?
thanks.

Diggory Mark wrote:
> Yes, filesystem permissions in the assetstore would cause both to
> fail. But also look at your filesystem quota as well to make sure
> there is disk space.
>
> On Jan 22, 2009, at 9:32 AM, Claudia Jürgen wrote:
>
>> Hi Sandy,
>>
>> seems to be the problem mentioned below, an authorization one.
>>
>> Your tomcat user needs the authorization to write to
>> [dspace]/assetstore.
>>
>> In the installation instructions it is recommended to run tomcat as the
>> dspace user which owns the [dspace] directory.
>>
>> Claudia
>>
>>
>>
>> Sandy De Groote schrieb:
>>> Claudia,
>>> Thanks for any help you can provide!
>>>
>>>
>>>
>>> Jan 20, 2009 8:30:13 AM org.apache.catalina.core.StandardWrapperValve
>>> invoke
>>> WARNING: Servlet.service() for servlet submit threw exception
>>> java.io.IOException: No such file or directory
>>> at java.io.UnixFileSystem.createFileExclusively(Native Method)
>>> at java.io.File.createNewFile(File.java:850)
>>> at
>>> edu.sdsc.grid.io.local.LocalFile.createNewFile(LocalFile.java:486)
>>> at

>>> org.dspace.storage.bitstore.BitstreamStorageManager.store(BitstreamStorageManager.java:332)

>>>
>>>
>>> at org.dspace.content.Bitstream.create(Bitstream.java:184)
>>> at org.dspace.content.Bundle.createBitstream(Bundle.java:362)
>>> at org.dspace.content.Item.createSingleBitstream(Item.java:1185)
>>> at org.dspace.content.Item.licenseGranted(Item.java:1265)
>>> at

>>> org.dspace.app.webui.servlet.SubmitServlet.processLicense(SubmitServlet.java:1615)
>>>
>>>
>>> at
>>> org.dspace.app.webui.servlet.SubmitServlet.doDSPost(SubmitServlet.java:424)
>>>
>>> at
>>> org.dspace.app.webui.servlet.DSpaceServlet.processRequest(DSpaceServlet.java:147)
>>>
>>>
>>> at

>>> org.dspace.app.webui.servlet.DSpaceServlet.doPost(DSpaceServlet.java:105)

>>>
>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:709)
>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
>>> at

>>> org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)

>>>
>>>
>>> at java.lang.Thread.run(Thread.java:595)
>>> Jan 20, 2009 8:44:05 AM org.apache.catalina.core.StandardWrapperValve
>>> invoke
>>> WARNING: Servlet.service() for servlet submit threw exception
>>> java.io.IOException: No such file or directory
>>> at java.io.UnixFileSystem.createFileExclusively(Native Method)
>>> at java.io.File.createNewFile(File.java:850)
>>> at
>>> edu.sdsc.grid.io.local.LocalFile.createNewFile(LocalFile.java:486)
>>> at

>>> org.dspace.storage.bitstore.BitstreamStorageManager.store(BitstreamStorageManager.java:332)

>>> org.dspace.app.webui.servlet.DSpaceServlet.doPost(DSpaceServlet.java:105)

>>>
>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:709)
>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
>>> at

>>> org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)

>>>
>>>
>>> at java.lang.Thread.run(Thread.java:595)
>>> Jan 20, 2009 9:43:15 PM org.apache.catalina.core.StandardWrapperValve
>>> invoke
>>> SEVERE: Servlet.service() for servlet handle threw exception
>>> java.lang.OutOfMemoryError: Java heap space
>>> Jan 20, 2009 9:43:15 PM org.apache.catalina.core.ApplicationDispatcher
>>> invoke
>>> SEVERE: Servlet.service() for servlet internal-error threw exception
>>> java.lang.ClassCastException: java.lang.OutOfMemoryError
>>> at

>>> org.dspace.app.webui.servlet.InternalErrorServlet.doGet(InternalErrorServlet.java:86)

>>>
>>>
>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:689)
>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
>>> at

>>> org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)

>>>
>>>
>>> at java.lang.Thread.run(Thread.java:595)
>>> Jan 20, 2009 9:43:15 PM org.apache.catalina.core.StandardHostValve
>>> custom
>>> SEVERE: Exception Processing

>>> ErrorPage[exceptionType=java.lang.Exception, location=/internal-error]
>>> java.lang.ClassCastException: java.lang.OutOfMemoryError
>>> at

>>> org.dspace.app.webui.servlet.InternalErrorServlet.doGet(InternalErrorServlet.java:86)

>>>
>>>
>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:689)
>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
>>> at

>>> org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)

Diggory Mark

unread,

Aug 25, 2015, 11:33:42 AM8/25/15

to Sandy De Groote, dspac...@lists.sourceforge.net, Claudia Jürgen

Can you go into you assetstore directory and create files via the
commandline as your tomcat user? Likewise verify that you are testing
with your webapplication servers permissions more specifically, if
your application server can't create files in the directory, you will
get this sort of error.

Mark

>>>> org
>>>> .dspace
>>>> .storage
>>>> .bitstore

>>>> .util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)

>>>>
>>>> at
>>>> org
>>>> .apache
>>>> .tomcat
>>>> .util
>>>> .net
>>>> .LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:
>>>> 80)
>>>>
>>>> at
>>>> org.apache.tomcat.util.threads.ThreadPool

>>>> $ControlRunnable.run(ThreadPool.java:684)
>>>>
>>>> at java.lang.Thread.run(Thread.java:595)
>>>> Jan 20, 2009 8:44:05 AM
>>>> org.apache.catalina.core.StandardWrapperValve
>>>> invoke
>>>> WARNING: Servlet.service() for servlet submit threw exception
>>>> java.io.IOException: No such file or directory
>>>> at java.io.UnixFileSystem.createFileExclusively(Native Method)
>>>> at java.io.File.createNewFile(File.java:850)
>>>> at
>>>> edu.sdsc.grid.io.local.LocalFile.createNewFile(LocalFile.java:486)
>>>> at

>>>> org
>>>> .dspace
>>>> .storage
>>>> .bitstore

>>>> .util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)

>>>> $ControlRunnable.run(ThreadPool.java:684)
>>>>
>>>> at java.lang.Thread.run(Thread.java:595)
>>>> Jan 20, 2009 9:43:15 PM
>>>> org.apache.catalina.core.StandardWrapperValve
>>>> invoke
>>>> SEVERE: Servlet.service() for servlet handle threw exception
>>>> java.lang.OutOfMemoryError: Java heap space
>>>> Jan 20, 2009 9:43:15 PM
>>>> org.apache.catalina.core.ApplicationDispatcher
>>>> invoke
>>>> SEVERE: Servlet.service() for servlet internal-error threw
>>>> exception
>>>> java.lang.ClassCastException: java.lang.OutOfMemoryError
>>>> at
>>>> org
>>>> .dspace
>>>> .app
>>>> .webui
>>>> .servlet.InternalErrorServlet.doGet(InternalErrorServlet.java:86)
>>>>
>>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:689)
>>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
>>>> at

>>>> .util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)

>>>> ErrorPage[exceptionType=java.lang.Exception, location=/internal-
>>>> error]
>>>> java.lang.ClassCastException: java.lang.OutOfMemoryError
>>>> at
>>>> org
>>>> .dspace
>>>> .app
>>>> .webui

>>>> .servlet.InternalErrorServlet.doGet(InternalErrorServlet.java:86)
>>>>
>>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:689)
>>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
>>>> at

>>>> .util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)

Brian Freels-Stendel

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Aug 25, 2015, 11:33:43 AM8/25/15

to dspac...@lists.sourceforge.net

FWIW, we see the same upload and license errors on a regular, but not
quite common, basis. Particular accounts seem to be affected
intermittently. If the submitter tries again, though, the second
attempt is nearly always successful. We find the same errors in our log
files.

Our tomcat runs as 'tomcat', but dspace and tomcat users belong to each
others' groups, so they should both be able to write to all relevant
directories.

I don't have any information to add except that it happens to us, too.

Brian Freels-Stendel
University of New Mexico

>>> On 1/23/2009 at 2:00 PM, in message <497A2FDE...@uic.edu>,
Sandy De Groote

org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcherj
> ava:672)
>>>>
>>>>
>>>> at
>>>>
>
org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDisp
> atcher.java:465)
>>>>
>>>>
>>>> at
>>>>
>
org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatche
> r.java:398)
>>>>
>>>>
>>>> at
>>>>
>
org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.

> java:301)
>>>>
>>>>
>>>> at
>>>>
>
org.apache.catalina.core.StandardHostValve.custom(StandardHostValve.java:363)

>
>>>>
>>>>
>>>> at
>>>>
>
org.apache.catalina.core.StandardHostValve.throwable(StandardHostValve.java:2
> 12)
>>>>
>>>>
>>>> at
>>>>
>
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:134)

>
>>>>
>>>>
>>>> at
>>>>
>
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)

>
>>>>
>>>>
>>>> at
>>>>
org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:541)

>>>>
>>>> at
>>>>
>
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:
> 107)
>>>>
>>>>
>>>> at
>>>>
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)

>>>>
>>>> at
>>>>
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869)

>>>>
>>>> at
>>>>
>
org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processCo

> nnection(Http11BaseProtocol.java:664)
>>>>
>>>>
>>>> at
>>>>
>
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java
> :527)
>>>>
>>>>
>>>> at
>>>>
>
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWor

> kerThread.java:80)
>>>>
>>>>
>>>> at
>>>>
>
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java
> :684)
>>>>
>>>>
>>>> at java.lang.Thread.run(Thread.java:595)
>>>> Jan 20, 2009 9:43:15 PM org.apache.catalina.core.StandardHostValve

>>>> custom
>>>> SEVERE: Exception Processing
>>>> ErrorPage[exceptionType=java.lang.Exception,
location=/internal-error]
>>>> java.lang.ClassCastException: java.lang.OutOfMemoryError
>>>> at
>>>>
>
org.dspace.app.webui.servlet.InternalErrorServlet.doGet(InternalErrorServlet.

> java:86)
>>>>
>>>>
>>>> at
javax.servlet.http.HttpServlet.service(HttpServlet.java:689)
>>>> at
javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
>>>> at
>>>>
>
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationF
> ilterChain.java:252)
>>>>
>>>>
>>>> at
>>>>
>
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterCha
> in.java:173)
>>>>
>>>>
>>>> at
>>>>
>

Diggory Mark

unread,

Aug 25, 2015, 11:33:44 AM8/25/15

to Brian Freels-Stendel, dspac...@lists.sourceforge.net

On Jan 23, 2009, at 2:31 PM, Brian Freels-Stendel wrote:

> FWIW, we see the same upload and license errors on a regular, but not
> quite common, basis. Particular accounts seem to be affected
> intermittently. If the submitter tries again, though, the second
> attempt is nearly always successful. We find the same errors in our
> log
> files.

Just a speculation (from my own experience) that may be "frequently
active submission accounts" rather that specific accounts.

> Our tomcat runs as 'tomcat', but dspace and tomcat users belong to
> each
> others' groups, so they should both be able to write to all relevant
> directories.

This may not always be the case if your group permissions are not
maintained (via a stickybit) on the assetstore directory when new
directories are created in it. We have the same permissions setup
while I was working at MIT, you need to make sure to have "group"
permissions set to write on the directories, there is a chance that
they can get "stripped" if you run any CLI dspace scripts with the
umask set wrong. Likewise, if the startup script for your tomcat
forces you to a more secure umask while running, you cannot get tomcat
not to write the group write permission on any file it creates.

I ultimately setup a cron job that scanned the assetstore periodically
checking for and correcting errant permissions bits.

I ultimately have come to the conclusion that trying to run the CLI
apps and the tomcat with separate user accounts on linux is an arduous
thing to deal with, especially with debian rooted "start-stop-deamon"
based scripts having forced umask security embedded in them stopping
the group and world permissions from being write. f you can run under
the same user... you'll rather save your sys admin some torture. But
hey, now we're really digging in the dark...

-Mark

> org
> .dspace
> .app.webui.servlet.SubmitServlet.processLicense(SubmitServlet.java:
>> 1615)
>>>>>
>>>>>
>>>>> at
>>>>>
> org
> .dspace.app.webui.servlet.SubmitServlet.doDSPost(SubmitServlet.java:
> 424)
>
>>>>>
>>>>> at
>>>>>
>>
> org
> .dspace
> .app.webui.servlet.DSpaceServlet.processRequest(DSpaceServlet.java:

>> 147)
>>>>>
>>>>>
>>>>> at
>>>>>
> org.dspace.app.webui.servlet.DSpaceServlet.doPost(DSpaceServlet.java:
> 105)
>
>>>>>
>>>>> at
> javax.servlet.http.HttpServlet.service(HttpServlet.java:709)
>>>>> at
> javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
>>>>> at
>>>>>
>>
> org
> .apache
> .catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationF
>> ilterChain.java:252)
>>>>>
>>>>>

>>>>> at
>>>>>
>>
> org
> .apache
> .catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterCha
>> in.java:173)
>>>>>
>>>>>
>>>>> at
>>>>>
>>
> org
> .dspace
> .app.webui.filter.RegisteredOnlyFilter.doFilter(RegisteredOnlyFilte
>> r.java:98)
>>>>>
>>>>>
>>>>> at
>>>>>
>>
> org
> .apache
> .catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationF
>> ilterChain.java:202)
>>>>>
>>>>>
>>>>> at
>>>>>
>>
> org
> .apache
> .catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterCha
>> in.java:173)
>>>>>
>>>>>
>>>>> at
>>>>>
>>
> org

> .catalina.core.StandardHostValve.invoke(StandardHostValve.java:126)
>
>>
>>>>>
>>>>>
>>>>> at
>>>>>
>>
> org.apache.catalina.valves.ErrorReportValve.i
> nvoke(ErrorReportValve.java:105)
>
>>
>>>>>
>>>>>
>>>>> at
>>>>>
> org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:
> 541)
>
>>>>>
>>>>> at
>>>>>
>>

> org
> .apache
> .catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:
>> 107)
>>>>>
>>>>>
>>>>> at
>>>>>
> org
> .apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:
> 148)
>
>>>>>
>>>>> at
>>>>>
> org
> .apache.coyote.http11.Http11Processor.process(Http11Processor.java:
> 869)
>
>>>>>
>>>>> at
>>>>>
>>
> org.apache.coyote.http11.Http11BaseProtocol
> $Http11ConnectionHandler.processCo

>> nnection(Http11BaseProtocol.java:664)

>>>>>
>>>>>
>>>>> at
>>>>>
>>
> org
> .apache
> .tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java
>> :527)
>>>>>
>>>>>
>>>>> at
>>>>>
>>
> org
> .apache
> .tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWor
>> kerThread.java:80)
>>>>>
>>>>>
>>>>> at
>>>>>
>>
> org.apache.tomcat.util.threads.ThreadPool
> $ControlRunnable.run(ThreadPool.java

>> :684)
>>>>>
>>>>>
>>>>> at java.lang.Thread.run(Thread.java:595)
>>>>> Jan 20, 2009 8:44:05 AM
> org.apache.catalina.core.StandardWrapperValve
>>>>> invoke
>>>>> WARNING: Servlet.service() for servlet submit threw exception
>>>>> java.io.IOException: No such file or directory
>>>>> at java.io.UnixFileSystem.createFileExclusively(Native Method)
>>>>> at java.io.File.createNewFile(File.java:850)
>>>>> at
>>>>>
> edu.sdsc.grid.io.local.LocalFile.createNewFile(LocalFile.java:486)
>>>>> at
>>>>>
>>
> org
> .dspace
> .storage.bitstore.BitstreamStorageManager.store(BitstreamStorageMan

>> ager.java:332)
>>>>>
>>>>>
>>>>> at org.dspace.content.Bitstream.create(Bitstream.java:184)
>>>>> at org.dspace.content.Bundle.createBitstream(Bundle.java:362)
>>>>> at
> org.dspace.content.Item.createSingleBitstream(Item.java:1185)
>>>>> at org.dspace.content.Item.licenseGranted(Item.java:1265)
>>>>> at
>>>>>
>>

> .apache
> .catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.jav
>> a:213)
>>>>>
>>>>>
>>>>> at
>>>>>
>>
> org
> .apache
> .catalina.core.StandardContextValve.invoke(StandardContextValve.jav
>> a:178)
>>>>>
>>>>>
>>>>> at
>>>>>
>>
> org
> .apache
> .catalina.core.StandardHostValve.invoke(StandardHostValve.java:126)
>
>>
>>>>>
>>>>>
>>>>> at
>>>>>
>>
> org
> .apache

> .catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)
>
>>
>>>>>
>>>>>
>>>>> at
>>>>>
> org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:
> 541)
>
>>>>>
>>>>> at
>>>>>
>>

> org
> .apache
> .catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:
>> 107)
>>>>>
>>>>>
>>>>> at
>>>>>
> org
> .apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:
> 148)
>
>>>>>
>>>>> at
>>>>>
> org
> .apache.coyote.http11.Http11Processor.process(Http11Processor.java:
> 869)
>
>>>>>
>>>>> at
>>>>>
>
>>
> org.apache.coyote.http11.Http11BaseProtocol
> $Http11ConnectionHandler.processCo

>> nnection(Http11BaseProtocol.java:664)

>>>>> at
>>>>>
>>
> org
> .apache
> .catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterCha
>> in.java:173)
>>>>>
>>>>>
>>>>> at
>>>>>
>>
> org

> .apache
> .catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcherj
>> ava:672)
>>>>>
>>>>>
>>>>> at
>>>>>
>>
> org
> .apache
> .catalina.core.ApplicationDispatcher.processRequest(ApplicationDisp

>> nnection(Http11BaseProtocol.java:664)

>> :684)
>>>>>
>>>>>
>>>>> at java.lang.Thread.run(Thread.java:595)
>>>>> Jan 20, 2009 9:43:15 PM org.apache.catalina.core.StandardHostValve
>
>>>>> custom
>>>>> SEVERE: Exception Processing
>>>>> ErrorPage[exceptionType=java.lang.Exception,
> location=/internal-error]
>>>>> java.lang.ClassCastException: java.lang.OutOfMemoryError
>>>>> at
>>>>>
>>
> org
> .dspace
> .app.webui.servlet.InternalErrorServlet.doGet(InternalErrorServlet.

>> java:86)
>>>>>
>>>>>
>>>>> at
> javax.servlet.http.HttpServlet.service(HttpServlet.java:689)
>>>>> at
> javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
>>>>> at
>>>>>
>>
> org
> .apache
> .catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationF
>> ilterChain.java:252)
>>>>>
>>>>>

>>>>> at
>>>>>
>>
> org
> .apache
> .catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterCha
>> in.java:173)
>>>>>
>>>>>
>>>>> at
>>>>>
>>
> org

>> nnection(Http11BaseProtocol.java:664)

Van Ly

unread,

Aug 25, 2015, 11:33:47 AM8/25/15

to sgr...@uic.edu, dspac...@lists.sourceforge.net

You may have run out of inodes before disk blocks, try

df -i

--
Van Ly : University of Sydney Library

Diggory Mark

unread,

Aug 25, 2015, 11:33:48 AM8/25/15

to Van Ly, dspac...@lists.sourceforge.net, sgr...@uic.edu

Yes, good catch. We've encountered that in the past as well.

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