date:20130522

Hi,

I am getting the below error while I am doing keyword search in Collections and 
Communities of dspace. I am a newbie and please help me out:

2013-05-22 12:18:37,064 INFO  org.dspace.app.webui.servlet.CommunityListServlet 
@ 
anonymous:session_id=3A68B48FDB6F78295600FECEE2757233:ip_addr=10.10.100.1:view_community_list:
2013-05-22 12:18:39,803 INFO  org.dspace.app.webui.servlet.DSpaceServlet @ 
anonymous:session_id=3A68B48FDB6F78295600FECEE2757233:ip_addr=10.10.100.1:view_collection:collection_id=17
2013-05-22 12:18:39,803 INFO  org.dspace.browse.BrowseEngine @ 
anonymous:session_id=3A68B48FDB6F78295600FECEE2757233:ip_addr=10.10.100.1:browse_mini:
2013-05-22 12:18:45,504 WARN  org.dspace.app.webui.servlet.InternalErrorServlet 
@ :session_id=3A68B48FDB6F78295600FECEE2757233:internal_error:-- URL Was: 
http://ir.niist.res.in:8080/jspui/simple-search?query=biodiesel
-- Method: GET
-- Parameters were:
-- query: biodiesel

java.io.IOException: read past EOF
at 
org.apache.lucene.store.BufferedIndexInput.refill(BufferedIndexInput.java:146)
at 
org.apache.lucene.store.BufferedIndexInput.readByte(BufferedIndexInput.java:38)
at org.apache.lucene.store.IndexInput.readInt(IndexInput.java:66)
at org.apache.lucene.index.SegmentInfos$2.doBody(SegmentInfos.java:357)
at 
org.apache.lucene.index.SegmentInfos$FindSegmentsFile.run(SegmentInfos.java:636)
at 
org.apache.lucene.index.SegmentInfos.readCurrentVersion(SegmentInfos.java:349)
at 
org.apache.lucene.index.IndexReader.getCurrentVersion(IndexReader.java:350)
at 
org.apache.lucene.index.IndexReader.getCurrentVersion(IndexReader.java:334)
at 
org.apache.lucene.index.IndexReader.getCurrentVersion(IndexReader.java:319)
at org.dspace.search.DSQuery.getSearcher(DSQuery.java:482)
at org.dspace.search.DSQuery.doQuery(DSQuery.java:148)
at 
org.dspace.app.webui.servlet.SimpleSearchServlet.doDSGet(SimpleSearchServlet.java:242)
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:617)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at 
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
at 
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
at 
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
at 
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
at 
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
at 
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:293)
at 
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:859)
at 
org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:602)
at 
org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)
at java.lang.Thread.run(Thread.java:679)


Is it something related to permission issues in any files/folder in the 
backend? I am running Dspace 1.5.2 in Ubuntu 12.04


Regards,

Ribin Jones S.B 
IT LAB, Knowledge Resource Centre 
CSIR - NIIST (National Institute for Interdisciplinary Science and Technology), 
Govt. of India 
Pappanamcode, Thiruvananthapuram - 695019 
Kerala, India 
www.niist.res.in 
Mob: +91 9895226242 


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Re: [Dspace-tech] Internal server error while doing keyword search

On Wed, May 22, 2013 at 8:59 AM,  ribin.jo...@niist.res.in wrote:
 java.io.IOException: read past EOF
 at 
 org.apache.lucene.store.BufferedIndexInput.refill(BufferedIndexInput.java:146)
 at 
 org.apache.lucene.store.BufferedIndexInput.readByte(BufferedIndexInput.java:38)

Hi Ribin,

it seems like this issue in Lucene:
https://issues.apache.org/jira/browse/LUCENE-2729

 Is it something related to permission issues in any files/folder in the 
 backend? I am running Dspace 1.5.2 in Ubuntu 12.04

Probably not, but it never hurts to run
chown -R [dspace-user]:[dspace-group] [dspace]/search

It seems your lucene index has become corrupted for some reason. It's
no big deal, it can be easily recreated. Stop Tomcat and run
[dspace]/bin/dspace index-init -r -v

This can take a while but the error should go away after you start
Tomcat. If the error ever occurs again, don't hesitate to contact us
and we'll try to investigate further.


Regards,
~~helix84

Compulsory reading: DSpace Mailing List Etiquette
https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette

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Re: [Dspace-tech] tomcat shutdown automatically

On Wed, May 22, 2013 at 5:36 AM, Ady Wahyudi Paundu ad...@unhas.ac.id wrote:
 also along the line there is suggestion from Peter Dietz to use
 [dspace]/bin/dspace update-discovery-index -o
 should i use that too?

Yes, it's recommended to run it periodically. Probably daily,
depending on how frequently you update/insert new content.


Regards,
~~helix84

Compulsory reading: DSpace Mailing List Etiquette
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Re: [Dspace-tech] best practice for scheduled maintenance or optimization process

Perhaps this will help:
http://wiki.lib.sun.ac.za/index.php/SUNScholar/Daily_Admin



On 22 May 2013 06:00, Ady Wahyudi Paundu ad...@unhas.ac.id wrote:

 Hi,
 can anybody give suggestion on a best practice for scheduled maintenance
 or optimization process?

 i'm running 3.1 and this is my current dspace-user crontab:
 0  1 * * * /usr/local/dspace/bin/dspace generate-sitemaps
 0  2 * * * /usr/local/dspace/bin/dspace itemcounter
 0  3 * * * /usr/local/dspace/bin/dspace stats-util --optimize
 30 1 1 1 * /usr/local/dspace/bin/dspace stats-util --shard-solr-index

 and this is my postgres crontab:
 0 4 * * * vacuumdb --analyze dspace3  /dev/null 21

 Best regards,
 AdyWP

 
 Powered by PTIK UNHAS ~ http://unhas.ac.id/



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Re: [Dspace-tech] Change the default background color of Mirage Header

Perhaps these links will help.

http://wiki.lib.sun.ac.za/index.php/SUNScholar/Theme/Page_Structure
http://wiki.lib.sun.ac.za/index.php/SUNScholar/Theme/Page_Content

Cheers

hg


On 21 May 2013 19:17, Henry Agbodza henry_agbo...@libr.ug.edu.gh wrote:

 Thanks for the quick response. I have solved it now. The login link at the
 header section still has a white colour.
 How do i change that?
 Thanks.

 On Tue, 05/21/2013 04:33 PM, helix84 heli...@centrum.sk wrote:

 On Tue, May 21, 2013 at 6:20 PM, Henry Agbodza
 henry_agbo...@libr.ug.edu.gh wrote:
  Can someone direct me as to how i can change the default background
 color of
  Mirage theme Header.

 Header background:

 https://github.com/DSpace/DSpace/blob/master/dspace-xmlui/src/main/webapp/themes/Mirage/lib/css/style.css#L48
 Breadcrumb trail:

 https://github.com/DSpace/DSpace/blob/master/dspace-xmlui/src/main/webapp/themes/Mirage/lib/css/style.css#L90


 Regards,
 ~~helix84

 Compulsory reading: DSpace Mailing List Etiquette
 https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette



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-- 
*Hilton Gibson*
Systems Administrator
JS Gericke Library
Room 1025C
Stellenbosch University
Private Bag X5036
Stellenbosch
7599
South Africa

Tel: +27 21 808 4100 | Cell: +27 84 646 4758
http://library.sun.ac.za
http://scholar.sun.ac.za
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Re: [Dspace-tech] Internal server error while doing keyword search

I am new to this whole thing...Could you pls be specific on solving this issue?

Regards,

Ribin Jones S.B 
IT LAB, Knowledge Resource Centre 
CSIR - NIIST (National Institute for Interdisciplinary Science and Technology), 
Govt. of India 
Pappanamcode, Thiruvananthapuram - 695019 
Kerala, India 
www.niist.res.in 
Mob: +91 9895226242 

- Original Message -
From: helix84 heli...@centrum.sk
To: ribin jones ribin.jo...@niist.res.in
Cc: dspace-tech DSpace-tech@lists.sourceforge.net
Sent: Wednesday, May 22, 2013 1:02:32 PM
Subject: Re: [Dspace-tech] Internal server error while doing keyword search

On Wed, May 22, 2013 at 8:59 AM,  ribin.jo...@niist.res.in wrote:
 java.io.IOException: read past EOF
 at 
 org.apache.lucene.store.BufferedIndexInput.refill(BufferedIndexInput.java:146)
 at 
 org.apache.lucene.store.BufferedIndexInput.readByte(BufferedIndexInput.java:38)

Hi Ribin,

it seems like this issue in Lucene:
https://issues.apache.org/jira/browse/LUCENE-2729

 Is it something related to permission issues in any files/folder in the 
 backend? I am running Dspace 1.5.2 in Ubuntu 12.04

Probably not, but it never hurts to run
chown -R [dspace-user]:[dspace-group] [dspace]/search

It seems your lucene index has become corrupted for some reason. It's
no big deal, it can be easily recreated. Stop Tomcat and run
[dspace]/bin/dspace index-init -r -v

This can take a while but the error should go away after you start
Tomcat. If the error ever occurs again, don't hesitate to contact us
and we'll try to investigate further.


Regards,
~~helix84

Compulsory reading: DSpace Mailing List Etiquette
https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette

--
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Re: [Dspace-tech] Internal server error while doing keyword search

Stop Tomcat and run the following command (replace [dspace] with your
DSpace installation directory):

[dspace]/bin/dspace index-init -r -v

Then start Tomcat.


Regards,
~~helix84

Compulsory reading: DSpace Mailing List Etiquette
https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette

--
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Re: [Dspace-tech] Internal server error while doing keyword search

That means that the error is also triggered when indexing, not just
when querying the index. Try this to fix the index structure:

java -cp /home/dspace/lib/lucene-core-3.5.0.jar
-ea:org.apache.lucene... org.apache.lucene.index.CheckIndex
/home/dspace/search -fix

This assumes DSpace 3. If you're using an older version, lucene-core
version may also be different.


Regards,
~~helix84

Compulsory reading: DSpace Mailing List Etiquette
https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette

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Re: [Dspace-tech] Internal server error while doing keyword search

I get the below error:

root@itlab:/home/dspace/log# java -cp 
/home/dspace/lib/lucene-core-2.3.0.jar-ea:org.apache.lucene... 
org.apache.lucene.index.CheckIndex /home/dspace/search/ -fix
Exception in thread main java.lang.NoClassDefFoundError: 
org/apache/lucene/index/CheckIndex
Caused by: java.lang.ClassNotFoundException: org.apache.lucene.index.CheckIndex
at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
Could not find the main class: org.apache.lucene.index.CheckIndex. Program will 
exit.

Our Dspace is version 1.5.2 and lucene 2.3 ...Pls chk whether the syntax of the 
command I have given above is correct.

Regards,

Ribin Jones S.B 
Scientist 
IT LAB, Knowledge Resource Centre 
CSIR - NIIST (National Institute for Interdisciplinary Science and Technology), 
Govt. of India 
Pappanamcode, Thiruvananthapuram - 695019 
Kerala, India 
www.niist.res.in 
Mob: +91 9895226242 

- Original Message -
From: helix84 heli...@centrum.sk
To: ribin jones ribin.jo...@niist.res.in
Cc: dspace-tech DSpace-tech@lists.sourceforge.net
Sent: Wednesday, May 22, 2013 2:14:20 PM
Subject: Re: [Dspace-tech] Internal server error while doing keyword search

That means that the error is also triggered when indexing, not just
when querying the index. Try this to fix the index structure:

java -cp /home/dspace/lib/lucene-core-3.5.0.jar
-ea:org.apache.lucene... org.apache.lucene.index.CheckIndex
/home/dspace/search -fix

This assumes DSpace 3. If you're using an older version, lucene-core
version may also be different.


Regards,
~~helix84

Compulsory reading: DSpace Mailing List Etiquette
https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette

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Re: [Dspace-tech] Internal server error while doing keyword search

On Wed, May 22, 2013 at 10:54 AM,  ribin.jo...@niist.res.in wrote:
 root@itlab:/home/dspace/log# java -cp
/home/dspace/lib/lucene-core-2.3.0.jar-ea:org.apache.lucene...
org.apache.lucene.index.CheckIndex /home/dspace/search/ -fix

There should be a space before -ea. Here's the full command for you:

java -cp /home/dspace/lib/lucene-core-2.3.0.jar -ea:org.apache.lucene...
org.apache.lucene.index.CheckIndex /home/dspace/search/ -fix


Regards,
~~helix84

Compulsory reading: DSpace Mailing List Etiquette
https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
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[Dspace-tech] help

2013-05-22 Thread Krassen Stefanov


- Original Message -
From: dspace-tech-requ...@lists.sourceforge.net
To: dspace-tech@lists.sourceforge.net
Sent: Wed, 22 May 2013 11:23:02 +0300 (EEST)
Subject: DSpace-tech Digest, Vol 85, Issue 89

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Today's Topics:

   1. Re: Internal server error while doing keyword search
  (ribin.jo...@niist.res.in)


--

Message: 1
Date: Wed, 22 May 2013 13:53:30 +0530 (IST)
From: ribin.jo...@niist.res.in
Subject: Re: [Dspace-tech] Internal server error while doing keyword
search
To: heli...@centrum.sk
Cc: dspace-tech DSpace-tech@lists.sourceforge.net
Message-ID: 1876174955.48071.1369211010934.JavaMail.root@primary
Content-Type: text/plain; charset=utf-8

I get the below while doing that:

root@itlab:/home/dspace/bin# /home/dspace/bin/index-init -r -v
Creating browse index
Creating search index
Exception in thread main java.io.IOException: read past EOF
at 
org.apache.lucene.store.BufferedIndexInput.refill(BufferedIndexInput.   
 
java:146)
at 
org.apache.lucene.store.BufferedIndexInput.readByte(BufferedIndexInpu   
 
t.java:38)
at org.apache.lucene.store.IndexInput.readInt(IndexInput.java:66)
at org.apache.lucene.index.SegmentInfos.read(SegmentInfos.java:207)
at 
org.apache.lucene.index.IndexFileDeleter.init(IndexFileDeleter.java   
 
:168)
at org.apache.lucene.index.IndexWriter.init(IndexWriter.java:722)
at org.apache.lucene.index.IndexWriter.init(IndexWriter.java:452)
at org.dspace.search.DSIndexer.openIndex(DSIndexer.java:778)
at org.dspace.search.DSIndexer.createIndex(DSIndexer.java:422)
at org.dspace.search.DSIndexer.main(DSIndexer.java:536)


Below  is the log when I again try keyword searching. I still don't get any 
search results..(see the attached screenshot)

2013-05-22 13:50:31,782 ERROR org.dspace.search.DSQuery @ Unable to use 
speficied sort option: type/relevance
2013-05-22 13:50:31,783 INFO  org.dspace.app.webui.servlet.SimpleSearchServlet 
@ 
anonymous:session_id=5E0432E316E66A9CCD5C65D9D1A99660:ip_addr=10.10.100.1:search:collection_id=17,query=biodiesel,results=(0,0,0)


Ribin Jones S.B 
IT LAB, Knowledge Resource Centre 
CSIR - NIIST (National Institute for Interdisciplinary Science and Technology), 
Govt. of India 
Pappanamcode, Thiruvananthapuram - 695019 
Kerala, India 
www.niist.res.in 
Mob: +91 9895226242 

- Original Message -
From: helix84 heli...@centrum.sk
To: ribin jones ribin.jo...@niist.res.in
Cc: dspace-tech DSpace-tech@lists.sourceforge.net
Sent: Wednesday, May 22, 2013 1:39:47 PM
Subject: Re: [Dspace-tech] Internal server error while doing keyword search

Stop Tomcat and run the following command (replace [dspace] with your
DSpace installation directory):

[dspace]/bin/dspace index-init -r -v

Then start Tomcat.


Regards,
~~helix84

Compulsory reading: DSpace Mailing List Etiquette
https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
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Re: [Dspace-tech] Change the default background color of Mirage Header

2013-05-22 Thread Henry Agbodza

Thanks a lot.

On Tue, 05/21/2013 08:11 PM, helix84 heli...@centrum.sk wrote:
 On Tue, May 21, 2013 at 7:17 PM, Henry Agbodza
  target=_blankhenry_agbo...@libr.ug.edu.gh wrote:
  Thanks for the quick response. I have solved it now. The login link at the
  header section still has a white colour.
  How do i change that?
 
 https://github.com/DSpace/DSpace/blob/master/dspace-xmlui/src/main/webapp/themes/Mirage/lib/css/style.css#L86
 
 
 Regards,
 ~~helix84
 
 Compulsory reading: DSpace Mailing List Etiquette
 https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
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Re: [Dspace-tech] Internal server error while doing keyword search

Did that...It says:

root@itlab:/home/dspace/log# java -cp /home/dspace/lib/lucene-core-2.3.0.jar 
-ea:org.apache.lucene... org.apache.lucene.index.CheckIndex 
/home/dspace/search/ -fix

Opening index @ /home/dspace/search/

Segments file=segments_x4 numSegments=0 version=FORMAT_SHARED_DOC_STORE [Lucene 
2.3]
No problems were detected with this index.

But still my keyword searching problem exists.

Regards,

Ribin Jones S.B 
Scientist 
IT LAB, Knowledge Resource Centre 
CSIR - NIIST (National Institute for Interdisciplinary Science and Technology), 
Govt. of India 
Pappanamcode, Thiruvananthapuram - 695019 
Kerala, India 
www.niist.res.in 
Mob: +91 9895226242 

- Original Message -
From: helix84 heli...@centrum.sk
To: ribin jones ribin.jo...@niist.res.in
Cc: dspace-tech DSpace-tech@lists.sourceforge.net
Sent: Wednesday, May 22, 2013 2:32:01 PM
Subject: Re: [Dspace-tech] Internal server error while doing keyword search


On Wed, May 22, 2013 at 10:54 AM,  ribin.jo...@niist.res.in  wrote: 
 root@itlab:/home/dspace/log# java -cp 
 /home/dspace/lib/lucene-core-2.3.0.jar-ea:org.apache.lucene... 
 org.apache.lucene.index.CheckIndex /home/dspace/search/ -fix 

There should be a space before -ea. Here's the full command for you: 


java -cp /home/dspace/lib/lucene-core-2.3.0.jar -ea:org.apache.lucene... 
org.apache.lucene.index.CheckIndex /home/dspace/search/ -fix 



Regards, 
~~helix84 

Compulsory reading: DSpace Mailing List Etiquette 
https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette 


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Re: [Dspace-tech] Internal server error while doing keyword search

Ok. To be clear you are using Ubuntu 12.04 with DSpace 1.5.2 and want the
XMLUI to be the default.

If so, please review: http://wiki.lib.sun.ac.za/index.php/SUNScholar/Dspace

The wiki guide is a step-by-step procedure for the installation and setup
of an institutional repository, based Ubuntu 12.04 LTS and DSpace 1.8.2.

It has been used quite extensively and a PDF version is available from
here: http://hdl.handle.net/10019.1/79321

All these materials are free to use and distribute as you please,

Cheers

hg



On 22 May 2013 10:03, ribin.jo...@niist.res.in wrote:

 I am new to this whole thing...Could you pls be specific on solving this
 issue?

 Regards,

 Ribin Jones S.B
 IT LAB, Knowledge Resource Centre
 CSIR - NIIST (National Institute for Interdisciplinary Science and
 Technology), Govt. of India
 Pappanamcode, Thiruvananthapuram - 695019
 Kerala, India
 www.niist.res.in
 Mob: +91 9895226242

 - Original Message -
 From: helix84 heli...@centrum.sk
 To: ribin jones ribin.jo...@niist.res.in
 Cc: dspace-tech DSpace-tech@lists.sourceforge.net
 Sent: Wednesday, May 22, 2013 1:02:32 PM
 Subject: Re: [Dspace-tech] Internal server error while doing keyword search

 On Wed, May 22, 2013 at 8:59 AM,  ribin.jo...@niist.res.in wrote:
  java.io.IOException: read past EOF
  at
 org.apache.lucene.store.BufferedIndexInput.refill(BufferedIndexInput.java:146)
  at
 org.apache.lucene.store.BufferedIndexInput.readByte(BufferedIndexInput.java:38)

 Hi Ribin,

 it seems like this issue in Lucene:
 https://issues.apache.org/jira/browse/LUCENE-2729

  Is it something related to permission issues in any files/folder in the
 backend? I am running Dspace 1.5.2 in Ubuntu 12.04

 Probably not, but it never hurts to run
 chown -R [dspace-user]:[dspace-group] [dspace]/search

 It seems your lucene index has become corrupted for some reason. It's
 no big deal, it can be easily recreated. Stop Tomcat and run
 [dspace]/bin/dspace index-init -r -v

 This can take a while but the error should go away after you start
 Tomcat. If the error ever occurs again, don't hesitate to contact us
 and we'll try to investigate further.


 Regards,
 ~~helix84

 Compulsory reading: DSpace Mailing List Etiquette
 https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette


 --
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Re: [Dspace-tech] Internal server error while doing keyword search

OK, try this:

1) stop Tomcat
2) mv /home/dspace/search /home/dspace/search.bak
3) mkdir /home/dspace/search
4) /home/dspace/bin/dspace index-init -r -v
5) start Tomcat


Regards,
~~helix84

Compulsory reading: DSpace Mailing List Etiquette
https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette

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Re: [Dspace-tech] Internal server error while doing keyword search

Hi,

I had a working dspace and suddenly it stopped working..I am trying to fix it.

Ribin Jones S.B 
Scientist 
IT LAB, Knowledge Resource Centre 
CSIR - NIIST (National Institute for Interdisciplinary Science and Technology), 
Govt. of India 
Pappanamcode, Thiruvananthapuram - 695019 
Kerala, India 
www.niist.res.in 
Mob: +91 9895226242 

- Original Message -
From: Hilton Gibson hilton.gib...@gmail.com
To: ribin jones ribin.jo...@niist.res.in
Cc: Ivan Masár heli...@centrum.sk, dspace-tech 
DSpace-tech@lists.sourceforge.net
Sent: Wednesday, May 22, 2013 2:42:23 PM
Subject: Re: [Dspace-tech] Internal server error while doing keyword search


Ok. To be clear you are using Ubuntu 12.04 with DSpace 1.5.2 and want the XMLUI 
to be the default. 


If so, please review: http://wiki.lib.sun.ac.za/index.php/SUNScholar/Dspace 


The wiki guide is a step-by-step procedure for the installation and setup of an 
institutional repository, based Ubuntu 12.04 LTS and DSpace 1.8.2. 


It has been used quite extensively and a PDF version is available from here: 
http://hdl.handle.net/10019.1/79321 


All these materials are free to use and distribute as you please, 


Cheers 


hg 





On 22 May 2013 10:03,  ribin.jo...@niist.res.in  wrote: 


I am new to this whole thing...Could you pls be specific on solving this issue? 

Regards, 

Ribin Jones S.B 
IT LAB, Knowledge Resource Centre 
CSIR - NIIST (National Institute for Interdisciplinary Science and Technology), 
Govt. of India 
Pappanamcode, Thiruvananthapuram - 695019 
Kerala, India 
www.niist.res.in 
Mob: +91 9895226242 

- Original Message - 
From: helix84  heli...@centrum.sk  
To: ribin jones  ribin.jo...@niist.res.in  
Cc: dspace-tech  DSpace-tech@lists.sourceforge.net  
Sent: Wednesday, May 22, 2013 1:02:32 PM 
Subject: Re: [Dspace-tech] Internal server error while doing keyword search 

On Wed, May 22, 2013 at 8:59 AM,  ribin.jo...@niist.res.in  wrote: 
 java.io.IOException: read past EOF 
 at 
 org.apache.lucene.store.BufferedIndexInput.refill(BufferedIndexInput.java:146)
  
 at 
 org.apache.lucene.store.BufferedIndexInput.readByte(BufferedIndexInput.java:38)
  

Hi Ribin, 

it seems like this issue in Lucene: 
https://issues.apache.org/jira/browse/LUCENE-2729 

 Is it something related to permission issues in any files/folder in the 
 backend? I am running Dspace 1.5.2 in Ubuntu 12.04 

Probably not, but it never hurts to run 
chown -R [dspace-user]:[dspace-group] [dspace]/search 

It seems your lucene index has become corrupted for some reason. It's 
no big deal, it can be easily recreated. Stop Tomcat and run 
[dspace]/bin/dspace index-init -r -v 

This can take a while but the error should go away after you start 
Tomcat. If the error ever occurs again, don't hesitate to contact us 
and we'll try to investigate further. 


Regards, 
~~helix84 

Compulsory reading: DSpace Mailing List Etiquette 
https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette 

-- 
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Systems Administrator 
JS Gericke Library 
Room 1025C 
Stellenbosch University 
Private Bag X5036 
Stellenbosch 
7599 
South Africa 


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Re: [Dspace-tech] Change the default background color of Mirage Header

2013-05-22 Thread Henry Agbodza

Thanks Hilton.

On Wed, 05/22/2013 07:43 AM, Hilton Gibson hilton.gib...@gmail.com wrote:
Perhaps these links will help.
http://wiki.lib.sun.ac.za/index.php/SUNScholar/Theme/Page_Structure

http://wiki.lib.sun.ac.za/index.php/SUNScholar/Theme/Page_Content

Cheers

On 21 May 2013 19:17, Henry Agbodza henry_agbo...@libr.ug.edu.gh wrote:

Thanks for the quick response. I have solved it now. The login link at the
header section still has a white colour.

How do i change that?
Thanks.

On Tue, 05/21/2013 04:33 PM, helix84 heli...@centrum.sk wrote:

On Tue, May 21, 2013 at 6:20 PM, Henry Agbodza
henry_agbo...@libr.ug.edu.gh wrote:
Can someone direct me as to how i can change the default background color of

Mirage theme Header.

Header background:
https://github.com/DSpace/DSpace/blob/master/dspace-xmlui/src/main/webapp/themes/Mirage/lib/css/style.css#L48

Breadcrumb trail:
https://github.com/DSpace/DSpace/blob/master/dspace-xmlui/src/main/webapp/themes/Mirage/lib/css/style.css#L90

Regards,
~~helix84

Compulsory reading: DSpace Mailing List Etiquette
https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette

Try New Relic Now We'll Send You this Cool Shirt

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7599South Africa
Tel: +27 21 808 4100 | Cell: +27 84 646
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Re: [Dspace-tech] view item only shows collection name



Hi Mr. Phiri,
1) yes, i did reindexing (i think i did), by execute [dspace]/bin/ 
dspace index-init


2) well, i dont think that is the case, since my 1.7 system also use 
http://repository.unhas.ac.id and it went just ok
i use direction from here 
http://rspproject.wordpress.com/2011/03/22/running-dspace-on-a-root-url/  for 
that feature


Best Regards,
AdyWP

On 05/22/2013 01:42 PM, Lighton Phiri wrote:

It looks as though the problem is with the way you configured your
repository base URL; items can be accessed when you include xmlui
context path.

http://repository.unhas.ac.id/xmlui

Lighton Phiri
http://lightonphiri.org


On 22 May 2013 07:20, Lighton Phirilighton.ph...@gmail.com  wrote:
   

How were these items ingested into the DSpace 3.1 instance? If you
migrated from a 1.7 instance, did you re-index?

Lighton Phiri
http://lightonphiri.org


On 22 May 2013 04:57, Ady Wahyudi Paunduad...@unhas.ac.id  wrote:
 

Hi all,

i'm running a 3.1 with xmlui-mirage, This system has running for just 4 days
now.
I just realise now that if i click an item (as guest or an identified user
or as an admin) the 'View Item' page only shows:

This item appears in the following Collection(s)

Skripsi (S1) [932]

nothing more,
as in my previous dspace version (1.7 xmlui-manakin) it shows several
metadata such as title, author, abstract, ... even its bitstream file.

what have i done wrong?

best regards,
adywp


   
   




 
Powered by PTIK UNHAS ~ http://unhas.ac.id/


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Re: [Dspace-tech] Internal server error while doing keyword search

Great...It worked!!!

Thanks very much. :)

Ribin Jones S.B 
Scientist 
IT LAB, Knowledge Resource Centre 
CSIR - NIIST (National Institute for Interdisciplinary Science and Technology), 
Govt. of India 
Pappanamcode, Thiruvananthapuram - 695019 
Kerala, India 
www.niist.res.in 
Mob: +91 9895226242 

- Original Message -
From: helix84 heli...@centrum.sk
To: ribin jones ribin.jo...@niist.res.in
Cc: dspace-tech DSpace-tech@lists.sourceforge.net
Sent: Wednesday, May 22, 2013 2:46:21 PM
Subject: Re: [Dspace-tech] Internal server error while doing keyword search

OK, try this:

1) stop Tomcat
2) mv /home/dspace/search /home/dspace/search.bak
3) mkdir /home/dspace/search
4) /home/dspace/bin/dspace index-init -r -v
5) start Tomcat


Regards,
~~helix84

Compulsory reading: DSpace Mailing List Etiquette
https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette

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[Dspace-tech] Error generated after clicking on feedback

2013-05-22 Thread Henry Agbodza

I had this error after clicking on the Feedback link.
I'm using Dspace 3.1 and the mirage theme.
java.lang.StringIndexOutOfBoundsException:
  String index out of range: -1

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Re: [Dspace-tech] tomcat shutdown automatically

2013-05-22 Thread Pottinger, Hardy J.

Hi, there is no need to apply that patch to the version of DSpace you are 
running, it is already in there. I am sadly still unfamiliar with Discovery, 
but I would expect there to also be a need to regularly optimize the Discovery 
Solr index.

--Hardy

Sent from my iPad

On May 21, 2013, at 10:54 PM, Ady Wahyudi Paundu 
ad...@unhas.ac.idmailto:ad...@unhas.ac.id wrote:


Thank you Mr. Pottinger,
i have now added a new crontab line: [dspace]/bin/dspace stats-util --optimize

my next question, right now i'm running DS-3.1, should i patch it using patch 
from here: https://jira.duraspace.org/browse/DS-615 or not?

also along the line there is suggestion from Peter Dietz to use 
[dspace]/bin/dspace update-discovery-index -o
should i use that too?

for your kind attention i thank you...

Best Regards,
adywp


On 05/22/2013 11:10 AM, Pottinger, Hardy J. wrote:
Hi, I think you may not be optimizing your Solr index, which is recommended 
practice. See this thread 
http://dspace.2283337.n4.nabble.com/Documentation-and-changes-for-DS-615-td3675851.html

--Hardy


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Re: [Dspace-tech] view item only shows collection name

You can also use this guide for setting up a clean URL:
http://wiki.lib.sun.ac.za/index.php/SUNScholar/Install_Dspace/S08



On 22 May 2013 11:10, Ady Wahyudi Paundu ad...@unhas.ac.id wrote:

 **

 Hi Mr. Phiri,
 1) yes, i did reindexing (i think i did), by execute [dspace]/bin/ dspace
 index-init

 2) well, i dont think that is the case, since my 1.7 system also use
 http://repository.unhas.ac.id and it went just ok
 i use direction from here
 http://rspproject.wordpress.com/2011/03/22/running-dspace-on-a-root-url/
 for that feature

 Best Regards,
 AdyWP

 On 05/22/2013 01:42 PM, Lighton Phiri wrote:

 It looks as though the problem is with the way you configured your
 repository base URL; items can be accessed when you include xmlui
 context path.
 http://repository.unhas.ac.id/xmlui

 Lighton Phirihttp://lightonphiri.org


 On 22 May 2013 07:20, Lighton Phiri lighton.ph...@gmail.com 
 lighton.ph...@gmail.com wrote:


  How were these items ingested into the DSpace 3.1 instance? If you
 migrated from a 1.7 instance, did you re-index?

 Lighton Phirihttp://lightonphiri.org


 On 22 May 2013 04:57, Ady Wahyudi Paundu ad...@unhas.ac.id 
 ad...@unhas.ac.id wrote:


  Hi all,

 i'm running a 3.1 with xmlui-mirage, This system has running for just 4 days
 now.
 I just realise now that if i click an item (as guest or an identified user
 or as an admin) the 'View Item' page only shows:

 This item appears in the following Collection(s)

 Skripsi (S1) [932]

 nothing more,
 as in my previous dspace version (1.7 xmlui-manakin) it shows several
 metadata such as title, author, abstract, ... even its bitstream file.

 what have i done wrong?

 best regards,
 adywp







 --
 Try New Relic Now  We'll Send You this Cool Shirt
 New Relic is the only SaaS-based application performance monitoring service
 that delivers powerful full stack analytics. Optimize and monitor your
 browser, app,  servers with just a few lines of code. Try New Relic
 and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_may
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Re: [Dspace-tech] What are the possible data format export options in Dspace?

2013-05-22 Thread Evans, Kev

Hi Helix84

This looks just what me need.

I notice there is a GUI option. When enabled what should I expect to see? Is it 
in the context menu? Or a specific uri?

Cheers

Kevin

-Original Message-
From: ivan.ma...@gmail.com [mailto:ivan.ma...@gmail.com] On Behalf Of helix84
Sent: 21 May 2013 16:36
To: Evans, Kev
Cc: dspace-tech@lists.sourceforge.net
Subject: Re: [Dspace-tech] What are the possible data format export options in 
Dspace?

On Tue, May 21, 2013 at 4:47 PM, Evans, Kev kevin.ev...@exeter.ac.uk wrote:
 What are the possible data format export options in DSpace?

 Are Repository Administrators/Curators  able to easily extract 
 information that can be used  to check compliance levels with funder 
 open access policies.

 For example, I'd like to be able to get the following list:

 Author, Title, Date of publication, Funder, Rights etc. exported into Excel?

Hi Kevin,

there are in fact many options how to export data from DSpace. Most prominently 
OAI which lets you define many metadata formats, but also some package-like 
formats as described in the System Administration section [1].

Since you're interested in export of particlar metadata fields into Excel, I'd 
recommend you to use the Batch Metadata Editing Tool, which can export a CSV 
[2] with all the metadata of a specified site/community/collection/item.

[1] https://wiki.duraspace.org/display/DSDOC3x/DSpace+3.x+Documentation
[2] https://wiki.duraspace.org/display/DSDOC3x/Batch+Metadata+Editing


Regards,
~~helix84

Compulsory reading: DSpace Mailing List Etiquette 
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Re: [Dspace-tech] What are the possible data format export options in Dspace?

On Wed, May 22, 2013 at 3:03 PM, Evans, Kev kevin.ev...@exeter.ac.uk wrote:
 I notice there is a GUI option. When enabled what should I expect to see? Is 
 it in the context menu? Or a specific uri?

That means you can also do it from web UI. if you log in as admin in
XMLUI, you can find it un der Administrative - Import Metadata. But
when called from web UI, it is subject to the limit set here:

https://github.com/DSpace/DSpace/blob/dspace-3.1/dspace/config/modules/bulkedit.cfg#L19


Regards,
~~helix84

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[Dspace-tech] Submission in collection

2013-05-22 Thread Luis Rojas C. (CATIE)

Hi all, i need to submit ítems directly in the communities in DSpace 3.1. Is 
that posible, because i can submit only in the collections.
Thanks for your support

Luis

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Re: [Dspace-tech] Submission in collection

2013-05-22 Thread Lighton Phiri

Hello,

Unfortunately not, however, Helix proposed a possible solution here
[1] --I am yet to try this out.

[1] 
http://dspace.2283337.n4.nabble.com/Item-Submission-in-Community-tp4659141p4659144.html


Lighton Phiri
http://lightonphiri.org


On 22 May 2013 22:41, Luis Rojas C. (CATIE) luisro...@catie.ac.cr wrote:
 Hi all, i need to submit ítems directly in the communities in DSpace 3.1. Is
 that posible, because i can submit only in the collections.

 Thanks for your support



 Luis









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Re: [Dspace-tech] Submission in collection

2013-05-22 Thread Luis Rojas C. (CATIE)

Hi Lighton, thanks for your response. Hoe i créate a invisible comunity?

Luis

-Mensaje original-
De: Lighton Phiri [mailto:lighton.ph...@gmail.com] 
Enviado el: miércoles, 22 de mayo de 2013 3:13 
Para: Luis Rojas C. (CATIE)
CC: dspace-tech@lists.sourceforge.net
Asunto: Re: [Dspace-tech] Submission in collection

Hello,

Unfortunately not, however, Helix proposed a possible solution here [1] --I am 
yet to try this out.

[1] 
http://dspace.2283337.n4.nabble.com/Item-Submission-in-Community-tp4659141p4659144.html


Lighton Phiri
http://lightonphiri.org


On 22 May 2013 22:41, Luis Rojas C. (CATIE) luisro...@catie.ac.cr wrote:
 Hi all, i need to submit ítems directly in the communities in DSpace 
 3.1. Is that posible, because i can submit only in the collections.

 Thanks for your support



 Luis









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[Dspace-tech] iRODS support in DSpace

2013-05-22 Thread Harish Maringanti

We are thinking about supporting big datasets via dspace and the option of
iRODS came up as that is supported in the computer science department here.
I found this reference to dspace on irods website -
https://www.irods.org/index.php/DSpace but couldn't tell if that code ever
made it to dspace.

I saw some SRB options in dspace.cfg but no reference to irods. Has anyone
integrated irods with dspace ?

-Harish

-
Harish Maringanti
ITS Coordinator
Kansas State University Libraries
785.532.3261
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Re: [Dspace-tech] Submission in collection

On Wed, May 22, 2013 at 11:44 PM, Luis Rojas C. (CATIE) 
luisro...@catie.ac.cr wrote:
 Hi Lighton, thanks for your response. Hoe i créate a invisible comunity?

You don't. You just don't display it. Here's a very rough example (where
you would replace comm with coll).

Here's how you hide the community list from the front page:


  xsl:template name=hide_homepage_community-list
match=dri:div[@id='aspect.artifactbrowser.CommunityBrowser.div.comunity-browser']
  /xsl:template


Here's how you display the number of items (strength) in a community
(assuming you're using Discovery):


xsl:template name=community-count-85 match=dri:div[@id='comm85']
b
xsl:text [/xsl:text
xsl:value-of
select=document('http://localhost:8080/solr/search/select/?q=location.comm:85+AND+search.resourcetype:2amp;version=2.2amp;start=0amp;rows=0amp;indent=onamp;facet=true')/response/result[@numFound]/@numFound/
xsl:text]/xsl:text
/b
/xsl:template


With that template ready, you simply add this static list of communities
(or, in your case, top-level collections) to [dspace]/config/news-xmlui.xml

div id=file.news.div.news n=news
rend=primaryheadi18n:textxyz.intro.head/i18n:text/headpi18n:textxyz.intro.p.1/i18n:text/plist
  itemxref 
target=http://example.com/handle/123456789/1;i18n:textxyz.intro.li.1/i18n:text/xrefdiv
id=comm86/div/item
  itemxref 
target=http://example.com/handle/123456789/2;i18n:textxyz.intro.li.2/i18n:text/xrefdiv
id=comm88/div/item
  itemxref 
target=http://example.com/handle/123456789/3;i18n:textxyz.intro.li.3/i18n:text/xrefdiv
id=comm85/div/item/listpi18n:textxyz.intro.p.2/i18n:text/p/div


This should be enough to get you started.


Regards,
~~helix84

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Re: [Dspace-tech] iRODS support in DSpace

On Wed, May 22, 2013 at 11:40 PM, Harish Maringanti har...@k-state.edu wrote:
 We are thinking about supporting big datasets via dspace and the option of 
 iRODS came up as that is supported in the computer science department here. I 
 found this reference to dspace on irods website - 
 https://www.irods.org/index.php/DSpace but couldn't tell if that code ever 
 made it to dspace.

 I saw some SRB options in dspace.cfg but no reference to irods. Has anyone 
 integrated irods with dspace ?

Yes, SRB has been a part of DSpace for a long time.
But iRODS has never been officially proposed, there's nothing in our
issue tracker:

https://jira.duraspace.org/secure/IssueNavigator.jspa?reset=truejqlQuery=project+%3D+DS+AND+%28summary+~+iRODS+OR+description+~+iRODS+OR+comment+~+iRODS%29

If you're interested in picking it up and submitting it to DSpace (so
that it would be integrated in the next released version), you should
create such feature request in our Jira:

https://jira.duraspace.org/browse/DS

And creating a GitHub pull request against our latest code (master
branch) in GitHub:

https://github.com/DSpace/DSpace

Since hardly anyone has access to an iRODS infrastructure, I think an
exception could be made with regards to the required amount of testing
a feature must get before being accepted as long as it works for you
and is not specific for your institution.

The obvious benefit for you from submitting the feature to DSpace as
opposed to maintaining it as a local customization would be that after
it's accepted, you don't have to maintain that custom code locally
(starting from your upgrade to the version of DSpace that would
contain it).

Regards,
~~helix84

Compulsory reading: DSpace Mailing List Etiquette
https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette

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Re: [Dspace-tech] iRODS support in DSpace

To give more details on the procedure, you should first take a look at
how the customization changed the BitstreamStorageManager class
compared to how that class looked at that time. So you need to look at
the diff of these two contemporary files:

https://github.com/DSpace/DSpace/commit/9ae95a94e79e80eeda99280857b4516734b4135d#dspace-api/src/main/java/org/dspace/storage/bitstore/BitstreamStorageManager.java

https://www.irods.org/dspace/BitstreamStorageManager.java

And port those differences to the file as it looks today:

https://github.com/DSpace/DSpace/blob/master/dspace-api/src/main/java/org/dspace/storage/bitstore/BitstreamStorageManager.java

In addition, the wiki page mentions adding the jargon.jar library as a
dependency. You would do that here:

https://github.com/DSpace/DSpace/blob/master/pom.xml#L443

The dspace.cfg changes are pretty clear.

That's the development part. Then you need to make sure it works in
your environment. Then I can help with the administrative part (GitHub
and Jira) of filing the feature request.

Regards,
~~helix84

Compulsory reading: DSpace Mailing List Etiquette
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Re: [Dspace-tech] iRODS support in DSpace

You may also want to get in touch with Lucas Gilbert who developed the
iRODS code for DSpace. Optionally to help with forward-porting it,
definitely to help testing it once it's forward-ported.


Regards,
~~helix84

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Re: [Dspace-tech] tomcat shutdown automatically


Thank you Mr. Pottinger and Helix,
its been one day without automatic shutdown big improvement :)

Best regards
AdyWP

On 05/22/2013 03:35 PM, helix84 wrote:
 On Wed, May 22, 2013 at 5:36 AM, Ady Wahyudi Paunduad...@unhas.ac.id  wrote:

 also along the line there is suggestion from Peter Dietz to use
 [dspace]/bin/dspace update-discovery-index -o
 should i use that too?
  
 Yes, it's recommended to run it periodically. Probably daily,
 depending on how frequently you update/insert new content.


 Regards,
 ~~helix84

 Compulsory reading: DSpace Mailing List Etiquette
 https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette




 
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Re: [Dspace-tech] best practice for scheduled maintenance or optimization process



Thank you Mr. Gibson,
now i'm using that cron script

Best Regards,
AdyWP

On 05/22/2013 03:40 PM, Hilton Gibson wrote:
Perhaps this will help: 
http://wiki.lib.sun.ac.za/index.php/SUNScholar/Daily_Admin




On 22 May 2013 06:00, Ady Wahyudi Paundu ad...@unhas.ac.id 
mailto:ad...@unhas.ac.id wrote:


Hi,
can anybody give suggestion on a best practice for scheduled
maintenance
or optimization process?

i'm running 3.1 and this is my current dspace-user crontab:
0  1 * * * /usr/local/dspace/bin/dspace generate-sitemaps
0  2 * * * /usr/local/dspace/bin/dspace itemcounter
0  3 * * * /usr/local/dspace/bin/dspace stats-util --optimize
30 1 1 1 * /usr/local/dspace/bin/dspace stats-util --shard-solr-index

and this is my postgres crontab:
0 4 * * * vacuumdb --analyze dspace3  /dev/null 21

Best regards,
AdyWP


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Re: [Dspace-tech] view item only shows collection name