[Dspace-tech] new install: internal system error

[Eric Luhrs]

Hello,
I have DSpace v1.4.1 running on RHEL4 with Tomcat5, Ant 1.6, and JDK
1.5. When I start Tomcat and go to http://localhost:8080/dspace,
everything looks fine. The page loads, and even though I have yet to
add any content, the links all seem to work. However, when I attempt
to search, I receive an internal system error. Everything also looks
fine when I login to http://localhost:8080/dspace/dspace-admin. I can
successfully edit E-people, Groups, add Bitstream Formats, and edit
News and Default License text. However, I receive the same internal
system error when I attempt to create a community. The form loads
fine, but I get the error when I attempt to submit it. I don't have
all that much experience with java apps, so I'm having trouble tracing
the error reported in dspace.log to the actual problem.
Attempts to search and create communities both give the same error:
"java.io.IOException: Permission denied". I've looked in various log
files, but can't pinpoint the source of this permission problem. I am
including both search and create community errors from dspace.log in
case someone on this list has any suggestions for me. Thanks in
advance for whatever help you can provide.

Eric Luhrs
Digital Initiatives Librarian
Lafayette College

--

2007-01-12 02:37:25,262 WARN
org.dspace.app.webui.servlet.InternalErrorServlet @
:session_id=2F35C8E1AF2ABF523EA91EE52F6839AA:internal_error:-- URL
Was: http://ds2.lafayette.edu:8080/dspace/simple-search?query=test+search&submit=Go
-- Method: GET
-- Parameters were:
-- submit: "Go"
-- query: "test search"

java.io.IOException: Permission denied
at java.io.UnixFileSystem.createFileExclusively(Native Method)
at java.io.File.createNewFile(File.java:876)
at org.apache.lucene.store.FSDirectory$1.obtain(FSDirectory.java:363)
at org.apache.lucene.store.Lock.obtain(Lock.java:51)
at org.apache.lucene.index.IndexReader.getCurrentVersion(IndexReader.java:235)
at org.apache.lucene.index.IndexReader.getCurrentVersion(IndexReader.java:214)
at org.apache.lucene.index.IndexReader.getCurrentVersion(IndexReader.java:200)
at org.dspace.search.DSQuery.getSearcher(DSQuery.java:401)
at org.dspace.search.DSQuery.doQuery(DSQuery.java:138)
at org.dspace.app.webui.servlet.SimpleSearchServlet.doDSGet(SimpleSearchServlet.java:208)
at org.dspace.app.webui.servlet.DSpaceServlet.processRequest(DSpaceServlet.java:151)
at org.dspace.app.webui.servlet.DSpaceServlet.doGet(DSpaceServlet.java:99)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:689)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:868)
at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:663)
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:797)




2007-01-12 02:36:37,635 INFO org.dspace.content.Community @
luh...@lafayette.edu:session_id=2F35C8E1AF2ABF523EA91EE52F6839AA:ip_addr=139.147.234.131:create_community:community_id=8,handle=123456789/8
2007-01-12 02:36:37,661 INFO org.dspace.content.Community @
luh...@lafayette.edu:session_id=2F35C8E1AF2ABF523EA91EE52F6839AA:ip_addr=139.147.234.131:update_community:community_id=8
2007-01-12 02:36:37,694 WARN
org.dspace.app.webui.servlet.InternalErrorServlet @
:session_id=2F35C8E1AF2ABF523EA91EE52F6839AA:internal_error:-- URL
Was: http://ds2.lafayette.edu:8080/dspace/dspace-admin/edit-communities
-- Method: POST
-- Parameters were:
-- create: "true"
-- name: "test name"
-- short_description: "dest description"
-- submit: "Create"
-- parent_community_id: "-1"
-- action: "7"
-- copyright_text: "test copyright"
-- introductory_text: "test introduction"
-- side_bar_text: "dest sidebar"

java.io.IOException: Permission denied
at java.io.UnixFileSystem.createFileExclusively(Native Method)
at java.io.File.createNewFile(File.java:876)
at org.apache.lucene.store.FSDirectory$1.obtain(FSDirectory.java:363)
at org.apache.lucene.store.Lock.obtain(Lock.java:51)
at org.apache.lucene.store.Lock$With.run(Lock.java:98)
at org.apache.lucene.index.IndexReader.open(IndexReader.java:141)
at org.apache.lucene.index.IndexReader.open(IndexReader.java:125)
at org.dspace.search.DSIndexer.unIndexContent(DSIndexer.java:141)
at org.dspace.search.DSIndexer.unIndexContent(DSIndexer.java:134)
at org.dspace.search.DSIndexer.reIndexContent(DSIndexer.java:175)
at org.dspace.content.Community.update(Community.java:441)
at org.dspace.app.webui.servlet.admin.EditCommunitiesServlet.processConfirmEditCommunity(EditCommunitiesServlet.java:410)
at org.dspace.app.webui.servlet.admin.EditCommunitiesServlet.doDSPost(EditCommunitiesServlet.java:230)
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.AdminOnlyFilter.doFilter(AdminOnlyFilter.java:103)
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.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:868)
at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:663)
at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)
at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80)
at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)
at java.lang.Thread.run(Thread.java:797)

[James Rutherford]

> java.io.IOException: Permission denied
> at java.io.UnixFileSystem.createFileExclusively(Native Method)
> at java.io.File.createNewFile(File.java:876)

looks like you forgot to set the correct permissions on your [dspace]
directory. the installation documentation details what they should be.

jim.

[Eric Luhrs]

Thanks for your suggestions. I looked again and didn't see exact
permission settings listed in the documentation, but I changed
[dspace] and [dspace]\assetstore to permissions to 775. I still get
the Internal System Error message, but the errors in dspace.log have
changed slightly. I also tried 777 permissions as a test, but
received the same results. New log messages are included below.

Eric

--

2007-01-12 03:20:12,610 WARN
org.dspace.app.webui.servlet.InternalErrorServlet @
:session_id=95960DF6D7521B50385AE37ADC2E8516:internal_error:-- URL Was:
http://ds2.lafayette.edu:8080/dspace/simple-search?query=test&submit=Go

-- Method: GET
-- Parameters were:
-- submit: "Go"
-- query: "test"

2007-01-12 03:20:17,269 INFO
org.dspace.app.webui.servlet.CommunityListServlet @
luh...@lafayette.edu:session_id=95960DF6D7521B50385AE37ADC2E8516:ip_addr=139.147.234.131:view_community_list:
2007-01-12 03:20:22,262 INFO org.dspace.content.Community @
luh...@lafayette.edu:session_id=95960DF6D7521B50385AE37ADC2E8516:ip_addr=139.147.234.131:create_community:community_id=13,han$
2007-01-12 03:20:22,278 INFO org.dspace.content.Community @
luh...@lafayette.edu:session_id=95960DF6D7521B50385AE37ADC2E8516:ip_addr=139.147.234.131:update_community:community_id=13
2007-01-12 03:20:22,308 WARN
org.dspace.app.webui.servlet.InternalErrorServlet @
:session_id=95960DF6D7521B50385AE37ADC2E8516:internal_error:-- URL Was:

http://ds2.lafayette.edu:8080/dspace/dspace-admin/edit-communities
-- Method: POST
-- Parameters were:
-- create: "true"
-- name: "test"

-- short_description: ""

-- submit: "Create"
-- parent_community_id: "-1"
-- action: "7"
-- copyright_text: ""

-- introductory_text: ""
-- side_bar_text: ""

java.io.IOException: Permission denied
at java.io.UnixFileSystem.createFileExclusively(Native Method)
at java.io.File.createNewFile(File.java:876)
at org.apache.lucene.store.FSDirectory$1.obtain(FSDirectory.java:363)
at org.apache.lucene.store.Lock.obtain(Lock.java:51)
at org.apache.lucene.store.Lock$With.run(Lock.java:98)
at org.apache.lucene.index.IndexReader.open(IndexReader.java:141)
at org.apache.lucene.index.IndexReader.open(IndexReader.java:125)
at org.dspace.search.DSIndexer.unIndexContent(DSIndexer.java:141)
at org.dspace.search.DSIndexer.unIndexContent(DSIndexer.java:134)
at org.dspace.search.DSIndexer.reIndexContent(DSIndexer.java:175)
at org.dspace.content.Community.update(Community.java:441)

at org.dspace.app.webui.servlet.admin.EditCommunitiesServlet.processConfirmEditCommunity(EditCommunitiesServlet.java:$

[Eric Luhrs]

Thanks again to those who replied to my help request. I eventually
solved the problem While the [dspace] and [dspace]\assetstore dirs
were okay, I finally figured out that tomcat (running as user dspace)
wasn't able to write to one of the files here:

/var/cache/tomcat5/work/Catalina/localhost

I'm not sure specifically which file was causing the permission denied
error, but running "chown -R dspace:dspace /var/cache/tomcat5" solved
the problem.

Eric Luhrs