Re: [Dspace-tech] Question about tomcat 6 or 7

[Mark H. Wood]

On Thu, May 26, 2011 at 01:20:27PM -0400, George S Kozak wrote:
> I am running DSpace 1.7.1 with apache-tomcat-5.5.26 and jdk1.6.0_07.  
> Everything works fine except to the Solr Stats.   If I do a 
> http://localhost:8080/solr/statistics/admin, I get an error display and 
> clicking on the View Statistics button results in an error like
> Error using query type: 3 AND  id:431
> 
> So, I tried switching to apache-tomcat-6.0.32.  I was able now to execute the 
> http://localhost:8080/solr/statistics/admin, but if I try to view a 
> Collection or an Item, I get a
> java.lang.OutOfMemoryError: PermGen space Error
> 
> I tried apache-tomcat-7.0.14, and I got the same error.
> 
> I was using JAVA_OPTS="-server -Xms1024m -Xmx2048m -Xmn64m 
> -Dfile.encoding=UTF-8 -XX:+UseParallelGC -verbose:gc 
> -Xloggc:/dspace/dspace/log/gc.log"
> I also tried CATALINA_OPTS="-Xms256m -Xmx1028m -XX:MaxPermSize=256m"
> But neither of those helped.  I know a lot has been written about memory 
> leaks and what can be done, but I think I'm doing teh right stuff, but 
> nothhing seems to be working.

It probably depends on your OS.  On Gentoo I use something like this
(in /etc/conf.d/tomcat-6):

JAVA_OPTS="-Xmx1024M -Xms128M"
JAVA_OPTS="$JAVA_OPTS -Dfile.encoding=UTF-8"
JAVA_OPTS="$JAVA_OPTS -XX:PermSize=192M"
JAVA_OPTS="$JAVA_OPTS -XX:MaxPermSize=512M"

Adjust the actual numbers to suit your site.  Using a monitoring app
like LambdaProbe can help you dial them in.

Your JAVA_OPTS aren't addressing PermGen so they didn't help with
that.  Your CATALINA_OPTS do but I don't know what your OS does with
(or to) that when it starts up Tomcat.  (Tomcat startup tends to be an
incredible Rube Goldberg construction for some reason.)

-- 
Mark H. Wood, Lead System Programmer   mw...@iupui.edu
Asking whether markets are efficient is like asking whether people are smart.


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[Dspace-tech] Question about tomcat 6 or 7 - follow up!

[George S Kozak]

Hi...
As is always the case...after I sent out an email in final desperation, I find 
the solution!.  I had left out some of my JAVA_OPTS parameters to handle the 
java OutofMemory problem.  Sorry to bother everyone.

Here is what fixed things:
JAVA_OPTS="-server -Xms1024m -Xmx2048m -Xmn64m -Dfile.encoding=UTF-8 
-XX:+UseParallelGC -verbose:gc -Xloggc:/dspace/dspace/log/gc.log 
-XX:+HeapDumpOnOutOfMemoryError -XX:PermSize=1024m -XX:MaxPermSize=1024m 
-XX:-UseGCOverheadLimit"
George Kozak
Digital Library Specialist
Cornell University Library Information Technologies (CULIT)
501 Olin Library
Cornell University
Ithaca, NY 14853
607-255-8924


From: George S Kozak [g...@cornell.edu]
Sent: Thursday, May 26, 2011 1:20 PM
To: dspace-tech@lists.sourceforge.net
Subject: [Dspace-tech] Question about tomcat 6 or 7

Hi...

I am running DSpace 1.7.1 with apache-tomcat-5.5.26 and jdk1.6.0_07.  
Everything works fine except to the Solr Stats.   If I do a 
http://localhost:8080/solr/statistics/admin, I get an error display and 
clicking on the View Statistics button results in an error like
Error using query type: 3 AND  id:431

So, I tried switching to apache-tomcat-6.0.32.  I was able now to execute the 
http://localhost:8080/solr/statistics/admin, but if I try to view a Collection 
or an Item, I get a
java.lang.OutOfMemoryError: PermGen space Error

I tried apache-tomcat-7.0.14, and I got the same error.

I was using JAVA_OPTS="-server -Xms1024m -Xmx2048m -Xmn64m 
-Dfile.encoding=UTF-8 -XX:+UseParallelGC -verbose:gc 
-Xloggc:/dspace/dspace/log/gc.log"
I also tried CATALINA_OPTS="-Xms256m -Xmx1028m -XX:MaxPermSize=256m"
But neither of those helped.  I know a lot has been written about memory leaks 
and what can be done, but I think I'm doing teh right stuff, but nothhing seems 
to be working.
ANy idea would be appreciated.

George Kozak
Digital Library Specialist
Cornell University Library Information Technologies (CULIT)
501 Olin Library
Cornell University
Ithaca, NY 14853
607-255-8924
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[Dspace-tech] OR11 - last day to register

[Valorie Hollister]

Dear DSpace and Fedora Communities, 

Tomorrow, May 27, is the LAST DAY to register for Open Repositories 2011 on 
June 6-11, 2011.

To register: 
https://conferences.tdl.org/or/OR2011/OR2011main/schedConf/registration

To view the main conference schedule and presentations: 
https://conferences.tdl.org/or/OR2011/OR2011main/schedConf/schedule

To view the user group meeting schedule and presentations: 
https://conferences.tdl.org/or/OR2011/OR2011main/schedConf/program#DuraSpace

To view the pre-conference program information/registration (including a 
DuraCloud workshop): http://sites.tdl.org/openrepositories/or11preconference/

To join the OR11 Crowdvine: http://or11.crowdvine.com/


I'm looking forward to seeing many of you there!

Valorie Hollister
Director of Community Programs
DuraSpace
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[Dspace-tech] Question about tomcat 6 or 7

[George S Kozak]

Hi...

I am running DSpace 1.7.1 with apache-tomcat-5.5.26 and jdk1.6.0_07.  
Everything works fine except to the Solr Stats.   If I do a 
http://localhost:8080/solr/statistics/admin, I get an error display and 
clicking on the View Statistics button results in an error like
Error using query type: 3 AND  id:431

So, I tried switching to apache-tomcat-6.0.32.  I was able now to execute the 
http://localhost:8080/solr/statistics/admin, but if I try to view a Collection 
or an Item, I get a
java.lang.OutOfMemoryError: PermGen space Error

I tried apache-tomcat-7.0.14, and I got the same error.

I was using JAVA_OPTS="-server -Xms1024m -Xmx2048m -Xmn64m 
-Dfile.encoding=UTF-8 -XX:+UseParallelGC -verbose:gc 
-Xloggc:/dspace/dspace/log/gc.log"
I also tried CATALINA_OPTS="-Xms256m -Xmx1028m -XX:MaxPermSize=256m"
But neither of those helped.  I know a lot has been written about memory leaks 
and what can be done, but I think I'm doing teh right stuff, but nothhing seems 
to be working.
ANy idea would be appreciated.

George Kozak
Digital Library Specialist
Cornell University Library Information Technologies (CULIT)
501 Olin Library
Cornell University
Ithaca, NY 14853
607-255-8924
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[Dspace-tech] DSpace 1.7.1 and Firefox 4 and RSS feeds icon

[John Preston]

I'm using dspace 1.7.1 with firefox 4 and my own xmlui theme developed
under 1.6.2. When I navigate to a collection page I no longer see the
RSS feeds icon come up in the url bar. Is there any way for me to
display it explicitly via my theme .

John

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[Dspace-tech] DSpace interoperability with WSO2 framework SOA

[José Miguel Vega Guerrero]

Hi Everyone

Does anyone have the experience of integrating DSpace a Data Warehouse project 
in their institutions, for example with WSO2 framework
SOA Platform and Service Bus for integration with other document management 
systems?

Thanks!



José Miguel Vega G.

Coordinador Unidad de Gestión de Archivos Institucionales

Programa de Información Científica - CONICYT

Canadá 308, Providencia, Santiago de Chile

Fono:(56-2) 365 44 53

e-mail:

jve...@conicyt.cl

archivoconi...@conicyt.cl


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[Dspace-tech] Two harvesting questions

[Zafrin, Vika]

I've now successfully set up several collections that harvest from PubMed. It 
works!  I wonder two things, though:

- Where in the harvesting settings can I specify things like the dates 
from/until which I want to harvest?

- If my collection has an accept/reject step, is there a way to make harvested 
items completely invisible until they are accepted?  Does the answer to this 
depend on whether I'm harvesting only metadata, or also full-text files?

Many thanks,

Vika Zafrin
Institutional Repository Librarian
Boston University
+1.617.358.6370


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Re: [Dspace-tech] Repository bad gateway error

[Rui Ramos]

Hello Evans,

  Do you have Apache working on top with mod_proxy or mod_ajp or direct
access to your container ?

Chhers, Rui

-Original Message-
From: Evans, Kevin 
To: dspace-tech@lists.sourceforge.net

Cc: Leggett, Pete 
Subject: [Dspace-tech] Repository bad gateway error
Date: Thu, 26 May 2011 15:15:38 +0100

Hi

 

We are building a new Dspace Repository and we have changed the base url
for the repository in the dspace.cfg.

 

But, accessing the site we get a 400 Bad Gateway error.
https://rdms.exeter.ac.uk/repository/

We have Restarted/Rebuilt and cleared coccoon cache, but to no avail.

We are using a remote assetstore.

 

Any advice gratefully received

 

Cheers

 

Kevin

 

 

Kevin Evans

Systems Developer,
Infrastructure Systems Team,

Room 54
5th Floor, Laver Building,
University of Exeter
North Park Road,
Exeter,
EX4 4RN

01392 725573

07775027574

http://my.exeter.ac.uk

 

This email and any attachment may contain information that is
confidential, privileged, or subject to copyright, and which may be
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the addressee only. If you received this message in error, please let me
know and delete the email and any attachments immediately. The
University will not accept responsibility for the accuracy/completeness
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this message and any attachments are virus free. Any views or opinions
expressed in this message are my own and do not necessarily represent
those of the Universitydon't waste your life reading this trash and
get out and live.

 


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[Dspace-tech] Dspace CERIF-XML crosswalk

[Rui Ramos]

Hello Dspacer's

  I would like to know if someone has initiated some work in 
  crosswalk development to support the CERIF-XML schema ?

 I'l have to setup my repository exporting XML in this format, 
 can any one give me some advice on how to implement this ?

  Best Regards, Rui Ramos
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[Dspace-tech] Repository bad gateway error

[Evans, Kevin]

Hi

 

We are building a new Dspace Repository and we have changed the base url for
the repository in the dspace.cfg.

 

But, accessing the site we get a 400 Bad Gateway error.

https://rdms.exeter.ac.uk/repository/

We have Restarted/Rebuilt and cleared coccoon cache, but to no avail.

We are using a remote assetstore.

 

Any advice gratefully received

 

Cheers

 

Kevin

 

 

Kevin Evans

Systems Developer,
Infrastructure Systems Team,

Room 54
5th Floor, Laver Building,
University of Exeter
North Park Road,
Exeter,
EX4 4RN

01392 725573

07775027574

  http://my.exeter.ac.uk

 

This email and any attachment may contain information that is confidential,
privileged, or subject to copyright, and which may be exempt from disclosure
under applicable legislation. It is intended for the addressee only. If you
received this message in error, please let me know and delete the email and
any attachments immediately. The University will not accept responsibility
for the accuracy/completeness of this e-mail and its attachments. The
University cannot guarantee that this message and any attachments are virus
free. Any views or opinions expressed in this message are my own and do not
necessarily represent those of the Universitydon't waste your life
reading this trash and get out and live.

 



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Re: [Dspace-tech] Problem with ordering in browsing

[Ladislav Kulhanek]

I have solved a problem. It is hack but it works.
The problem was, then item browsing did not work correctly, when values in
bi_* tables was normalised (characters with diacritic split to two
characters - first character without diacritics and second diacritic itself)
and search results sorting did not works correctly when values in bi_* was
not normalised:)

I use my own class OrderLowerTrim.java for creating sort strings:

public class OrderLowerTrim extends AbstractTextFilterOFD {

{
filters = new TextFilter[] { new LowerCaseAndTrim() };
}

}

So strings are not normalized in db. And I modified
org.dspace.search.DSIndexer.java to ignore configuration and make sort
strings normalized. Change is on line 1166:

//String value = OrderFormat.makeSortString(dcv[0].value, dcv[0].language,
so.getType());
String value = (new OrderFormatTitle()).makeSortString(dcv[0].value,
dcv[0].language);

Sort strings are always made by OrderFormatTitle, which produce normalized
values.

Graham, thanks again for your response, it was very helpful. Can you
explain, why simply writing UTF-8 to the database tables results in very
random sorting for diacritics? I do it now in DSpace and it works.

2011/5/23 Ladislav Kulhanek 

> Thanks for responses.
>
> I created class OrderFormatLocale:
>
>  public class OrderFormatLocale extends AbstractTextFilterOFD {
>{
>filters = new TextFilter[] { new LowerCaseAndTrim(),
>   new
> LocaleOrderingFilter() };
>}
> }
>
> but sorting was then very queer. For example alphabet starts with B, A
> was after D and there was other queer things like this. So I modified
> class by removing LocaleOrderingFilter to this form:
>
> public class OrderFormatLocale extends AbstractTextFilterOFD {
>{
>filters = new TextFilter[] { new LowerCaseAndTrim()};
>}
> }
>
> Then sorting was correct in browsing ( by title, author and subjects
> too) but started to be incorrect in search results. When search
> results are sorted by title or author, string with diacritics are
> sorted to the end after all letters without diacritics.
>
> 2011/5/19 Graham Triggs :
> > Please take a look at a previous post of mine on this subject:
> >
> http://dspace.2283337.n4.nabble.com/Browse-UTF-8-and-sorting-in-1-5-tp3281449p3281450.html
> > Regards,
> > G
> >
> > On 19 May 2011 15:18, Peter Dietz  wrote:
> >>
> >> Hi Ladislav,
> >> I've noticed that our librarians here are happier with sorting when we
> use
> >> the collate of C as opposed to utf8/en_US.
> >>
> >> postgres=# create database "dspace" with owner = dspace encoding='utf8'
> >> tablespace=pg_default lc_collate = 'C' lc_ctype='en_US.UTF-8' template
> >> template0;
> >>
> >> I've add these three authors to a test collection that had some sample
> >> data in it, and it has the results you were expecting:
> >> == Author Name ==
> >> Cabanová, Zuzana
> >> Cablová, Barbora
> >> creatorlast, creatorfirst
> >> Čabla, Michael
> >>
> >>
> >>
> >> Peter Dietz
> >>
> >>
> >>
> >> On Thu, May 19, 2011 at 4:41 AM, Ladislav Kulhanek
> >>  wrote:
> >>>
> >>> Hello everybody.
> >>>
> >>> We have data in our DSpace in czech language (code "cs" in accordance
> >>> with ISO 639-1) and we have a problem with order in browsing by
> >>> author, titles and subjects (order in search results is correct).
> >>> There are letters with diacritic in czech alphabet, for example "Č"
> >>> (0x010C code in unicode). This letter should be ordered between "C"
> >>> and "D", but in DSpace it is ordered to the same place as "C". For
> >>> example we have ordered list as
> >>>
> >>> Cabanová, Zuzana
> >>> Čabla, Michael
> >>> Cablová, Barbora
> >>>
> >>> and this list should be
> >>>
> >>> Cabanová, Zuzana
> >>> Cablová, Barbora
> >>> Čabla, Michael
> >>>
> >>> And czech alphabet contains letter "Ch" (it consists from two
> >>> characters). This letter should be ordered between "h" and "i". This
> >>> letter is ordered in DSpace correctly. So it looks like DSpace order
> >>> in accordance with czech alphabet, but ignore diacritics.
> >>> We have DSpace 1.7.1, Manakin, db PostgreSQL 8.4 (database has
> >>> Collation and Ctype set as cs_CZ.UTF-8), and in tomcat connector is
> >>> URIEncoding="UTF-8". Any idea how to solve it? Thanks.
> >>>
> >>> Ladislav Kulhanek
> >>>
> >>>
> >>>
> --
> >>> What Every C/C++ and Fortran developer Should Know!
> >>> Read this article and learn how Intel has extended the reach of its
> >>> next-generation tools to help Windows* and Linux* C/C++ and Fortran
> >>> developers boost performance applications - including clusters.
> >>> http://p.sf.net/sfu/intel-dev2devmay
> >>> ___
> >>> DSpace-tech mailing list
> >>> DSpace-tech@lists.sourceforge.net
> >>> https://lists.sourceforge.net/lists/listinfo/dspace-tech
> >>
> >>
> >>
> >>
> -

Re: [Dspace-tech] DSpace submit_reject email template - add metadata

[Claudia Jürgen]

Hello Ian,

you got to customize
[dspace-source]/dspace-api/src/main/java/org/dspace/workflow/WorkflowManager.java
In the method private static void notifyOfReject(Context c, WorkflowItem 
wi, EPerson e, String reason)
you can add an argument containing the metadata.

Then you got to customize the email template
[dspace-source]/dspace/config/emails/submit_reject to process the new 
argument.

Finally you got to rebuild and redeploy your application.


Hope that helps

Claudia Jürgen




Am 26.05.2011 10:47, schrieb Wellaway, Ian:
> Hi,
>
> I'd like to add the contents of a metadata field to the submit_reject email 
> template that gets sent out if an item in the workflow gets rejected.
>
> Any ideas how I could do this?
>
> Thanks
>
> Ian
>
> 
>
> Ian Wellaway
> Senior Web Services Developer
> Academic Systems
> Exeter IT
>
> Room 909, Laver Building
> University of Exeter
> EX4 4QE
> UK
>
> tel +44 1392 722852
>
>
>
>
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>
>
>
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-- 
Claudia Juergen
Universitaetsbibliothek Dortmund
Eldorado
0231/755-4043
https://eldorado.tu-dortmund.de/

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[Dspace-tech] DSpace submit_reject email template - add metadata

[Wellaway, Ian]

Hi,

I'd like to add the contents of a metadata field to the submit_reject email 
template that gets sent out if an item in the workflow gets rejected.

Any ideas how I could do this?

Thanks

Ian



Ian Wellaway
Senior Web Services Developer
Academic Systems
Exeter IT

Room 909, Laver Building
University of Exeter
EX4 4QE
UK

tel +44 1392 722852
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[Dspace-tech] Expanded Community list in front page

[Nemiz, Elvi S.]

Dear All,

I've searched on the DSpace mailing list how to display community list in
the front page (as it appeared) when you click on the Communities &
Collections link. We are using mirage as our theme and it seems that all the
solutions that I have found were for other xmlui themes but not mirage. I
can't find the code that they're talking about and I also tried to implement
this Manakin howto:
https://wiki.duraspace.org/display/DSPACE/Add+expanding+and+collapsing+interface+to+community-list+hierarchy+%28Manakin%29,
but I think it's very hard for a newbie like me to implement this and I
wonder if how can I apply it with mirage as our theme. Please help.

Thanks in advance.

Sincerely,
Elvi S. Nemiz
Information Assistant
Library and Data Bank Services Section
Training and Information Division
SEAFDEC Aquaculture Department
Tigbauan, Iloilo
Philippines
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