Re: [Dspace-tech] CAS for DSpace 5.1 XMLUI (Mirage 2)

[Àlex Magaz Graça]

El 22/04/15 a les 21:14, Graham Faulkner ha escrit:
 Hi there,

 We are trying to set up CAS authentication for a DSpace 5.1 instance
 running XMLUI (Mirage 2).

 I have taken some cues from this GitHub pull request
 (https://github.com/DSpace/DSpace/pull/804) and from a custom CAS
 implementation from our DS 3.1 instance.  We have installed a
 certificate and can view things via https on port 8443.

 However, upon performing the CAS login and returning to the website, we
 encounter this error: “HTTP Status 500 -
 javax.net.ssl.SSLProtocolException: handshake alert: unrecognized_name”

 Doing some Googling, it seems like this is an issue with the newer JVM,
 and that we need to disable SNI, by setting this flag:
 “-Djsse.enableSNIExtension=false”. (e.g.
 https://wiki.jasig.org/display/CASUM/SSL+Troubleshooting+and+Reference+Guide)


 I added it to JAVA_OPTS value in the /dspace-source/dspace/bin/dspace
 file, and rebuilt everything.  However, I’m still encountering the error
 when attempting a CAS login.

 Has anyone successfully got CAS working with DSpace 5.1, XMLUI (Mirage
 2), or have pointers in the right direction?

 Cheers,

 Graham

 -

 Graham Faulkner

 Web Developer / Programmer

 Digital Initiatives, Library

 University of Waterloo

 Waterloo, Ontario N2L 3G1 CANADA

 519-888-4567 x32461

 graham.faulk...@uwaterloo.ca mailto:graham.faulk...@uwaterloo.ca



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Hi Graham,

I'm not sure this will solve the problem, but I'd say you should set JAVA_OPTS 
for Tomcat instead. For example, if you are using Ubuntu, you can set it in 
/etc/default/tomcat7.

Cheers,
Àlex

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[Dspace-tech] Are embargoes through SWORD possible with the new system?

[Àlex Magaz Graça]

Hi,

Currently we are submitting embargoed items through SWORD to a DSpace 
4.3 with the old embargo system. If I understand it correctly, it works 
because DSpace finds the embargo terms field which is used to set the 
embargo.

I was looking into switching to the new embargo system, but it no longer 
uses a metadata field. So, is there any way to submit an embargoed item 
through SWORD with the new system?

Thanks,
Àlex

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Re: [Dspace-tech] managing dspace and tomcat log files

[Àlex Magaz Graça]

El 06/04/15 a les 22:19, Hilton Gibson ha escrit:
 Hi Chris

 1. Check the log clean-up here:
 http://wiki.lib.sun.ac.za/index.php/SUNScholar/Daily_Admin/4.X#Sample_crontab
 2. Check the daily restart that also cleans out the tomcat logs here:
 http://wiki.lib.sun.ac.za/index.php/SUNScholar/Restart_DSpace

 Cheers

 hg

 *Hilton Gibson*
 Ubuntu Linux 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

 On 6 April 2015 at 20:20, Chris Gray cpg...@uwaterloo.ca
 mailto:cpg...@uwaterloo.ca wrote:

 We have an instance of 3.1 (scheduled to be replaced by 5.1
 eventually)
 where the log files for dspace and tomcat keep overflowing the file
 system.

 Is there any place that documents best practices for rolling over
 these
 files and keeping disk usage reasonable?  Both tomcat and dspace are
 deployed in the /home/dspace directory.  The server is RHEL 6.6.

 One problem is that catalina.out seems to grow without bounds.  It is
 currently ~30GB.  Shouldn't it be truncated when the daily log is
 broken
 off?

 Chris Gray
 Systems Analyst
 519-888-4567, ext. 35764
 cpg...@uwaterloo.ca mailto:cpg...@uwaterloo.ca
 University of Waterloo


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Hi,

You can further reduce the logs generated by Tomcat by doing the following:

- Disable localhost_access_log by commenting this entry in Tomcat's
server.xml:

!--
Valve className=org.apache.catalina.valves.AccessLogValve
 directory=logs
 prefix=localhost_access_log. suffix=.txt
 pattern=%h %l %u %t quot;%rquot; %s %b /
--

- Disable manager, host-manager and ConsoleHandler leaving Tomcat's
logging.properties like this:
 handlers = 1catalina.org.apache.juli.FileHandler, 
2localhost.org.apache.juli.FileHandler
   .handlers = 1catalina.org.apache.juli.FileHandler

   
   # Handler specific properties.
   # Describes specific configuration info for Handlers.
   

   1catalina.org.apache.juli.FileHandler.level = FINE 
1catalina.org.apache.juli.FileHandler.directory = ${catalina.base}/logs
   1catalina.org.apache.juli.FileHandler.prefix = catalina.

   2localhost.org.apache.juli.FileHandler.level = WARNING
   2localhost.org.apache.juli.FileHandler.directory = ${catalina.base}/logs
   2localhost.org.apache.juli.FileHandler.prefix = localhost.

   
   # Facility specific properties.
   # Provides extra control for each logger.
   

   org.apache.catalina.core.ContainerBase.[Catalina].[localhost].level = 
INFO
 
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].handlers = 
2localhost.org.apache.juli.FileHandler


Before disabling these logs ensure you really don't need them.

Cheers,
Àlex

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Re: [Dspace-tech] Expand communities collections by default in Mirage 2

[Àlex Magaz Graça]

El 23/03/15 a les 07:41, euler ha escrit:
 In Mirage 2, the communities and collections were collapsed by default. My
 boss wanted to expand these by default since we only have a few communities
 and collections in our repository. Can anybody help me on how to achieve
 this? Thanks in advance.

 -euler



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Hi euler,

You have to remove the hidden class from this line:

https://github.com/DSpace/DSpace/blob/master/dspace-xmlui-mirage2/src/main/webapp/xsl/preprocess/communitylist.xsl#L116

I'd also remove the toggle buttons to avoid them behaving in an unexpected way:

https://github.com/DSpace/DSpace/blob/master/dspace-xmlui-mirage2/src/main/webapp/xsl/aspect/artifactbrowser/community-list.xsl#L110

Cheers,
Àlex

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Re: [Dspace-tech] IntelliJ IDEA + tomcat7 + XMLUI + Mac = Eexception

[Àlex Magaz Graça]

El 19/03/15 a les 23:13, Monika C. Mevenkamp ha escrit:
 I have a working XMLUI code base - aka if I go the normal route of mvn
 package; ant updatelocalhost:8080/xmlui gives me the expected home
 page.

 I followed the written instructions on the wiki explaining how to do the
 developer integration
 https://wiki.duraspace.org/display/DSPACE/IDE+Integration+-+DSpace+and+IDEA.

 I did discover Bram’s youtube after the fact - some nice ideas there -
 so I added a link to the wiki page. The Youtube has a comment about the
 same NullPointerException that I have. So here a few more specifics

 I defined a Run/Debug configuration for tomcat with two Deployment wars:
 xmlui.war and sol.war.   To make tomcat come up I had to do the funny
 link from /usr/local/Cellar/tomcat/7.0.54/libexec/bin/${dspace.dir} to
 my installation directory. When I start a debug session I see that the
 process comes up as follows:

 /Library/Java/JavaVirtualMachines/jdk1.7.0_45.jdk/Contents/Home/bin/java
 -Djava.util.logging.config.file=/Users/monikam/Library/Caches/IntelliJIdea14/tomcat/Unnamed_dspace-parent/conf/logging.properties

 -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
 -agentlib:jdwp=transport=dt_socket,address=127.0.0.1:51692,suspend=y,server=n

 -Dcom.sun.management.jmxremote= -Dcom.sun.management.jmxremote.port=1099
 -Dcom.sun.management.jmxremote.ssl=false
 -Dcom.sun.management.jmxremote.authenticate=false
 -Djava.rmi.server.hostname=127.0.0.1
 -Djava.endorsed.dirs=/usr/local/Cellar/tomcat/7.0.54/libexec/endorsed
 -classpath
 /usr/local/Cellar/tomcat/7.0.54/libexec/bin/bootstrap.jar:/usr/local/Cellar/tomcat/7.0.54/libexec/bin/tomcat-juli.jar

 -Dcatalina.base=/Users/monikam/Library/Caches/IntelliJIdea14/tomcat/Unnamed_dspace-parent

 -Dcatalina.home=/usr/local/Cellar/tomcat/7.0.54/libexec
 -Djava.io.tmpdir=/usr/local/Cellar/tomcat/7.0.54/libexec/temp
 org.apache.catalina.startup.Bootstrap start

 I can set breakpoints in the code and all that - which is a big
 improvement over adding traces and recompiling, redeploying. But when I
 visit localhost:8080  I get an exception , which I do not get when going
 the mvn/ant route. So there is something wrong in the way IDEAS puts
 things together. I went and compares the xmlui  webapp directories
 generated by mvn/ant versus IDEA - but nothing stuck out. I am attaching
 the diffs in case somebody wants to look.

 I should probably also mention - this is dspace 5, with a few config
 changes, running with a database that mentions all sorts of bitstreams
 that do not exist in the local assetstore. This is ugly - I know - but
 it does not explain the difference in behaviour - since we are talking
 about the same code and configs put together slightly differently.


 I am sure this is a small something somewhere - but what and where ?

 Monika



 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @
 java.lang.NullPointerException
  at
 org.dspace.discovery.SearchUtils.getDiscoveryConfiguration(SearchUtils.java:51)
  at
 org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer.getQueryArgs(SidebarFacetsTransformer.java:317)
  at
 org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer.performSearch(SidebarFacetsTransformer.java:156)
  at
 org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer.getValidity(SidebarFacetsTransformer.java:119)
  at sun.reflect.GeneratedMethodAccessor40.invoke(Unknown Source)
  at
 sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  at java.lang.reflect.Method.invoke(Method.java:606)
  at
 org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
  at com.sun.proxy.$Proxy25.getValidity(Unknown Source)
  at
 org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.getValidityForInternalPipeline(AbstractCachingProcessingPipeline.java:987)
  at
 org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.setupValidities(AbstractCachingProcessingPipeline.java:482)
  at
 org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.setupPipeline(AbstractCachingProcessingPipeline.java:720)
  at
 org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.preparePipeline(AbstractProcessingPipeline.java:466)
  at
 org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.prepareInternal(AbstractProcessingPipeline.java:480)
  at sun.reflect.GeneratedMethodAccessor85.invoke(Unknown Source)
  at
 sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  at java.lang.reflect.Method.invoke(Method.java:606)
  at
 org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
  at com.sun.proxy.$Proxy20.prepareInternal(Unknown Source)
  at
 

Re: [Dspace-tech] Reinstate a group of items that has previously been withdrawn with Batch Metadata Editing Tool

[Àlex Magaz Graça]

El 26/02/15 a les 12:13, Àlex Magaz Graça ha escrit:
 El 26/02/15 a les 10:12, BARRERA BARRERA, Carlos ha escrit:
  Hello,
 
  We are tring to reinstate a group of items that has previously been
  withdrawn with Batch Metadata Editing Tool:
 
  [dspace]/bin/dspace metadata-import -f metadata.csv
 
  heading row:
  id,collection,action
 
  item rows:
  28801,1,reinstate
  26223,1,reinstate
 
  performing 'actions' on items, but throws the next error:
 
  Bad metadata declaration in row 1: id;collection;action
 
  Does anyone use this tool or know another way to make it?
 
  We look forward to your reply.
 
  Thank you,
 
  *Carles Barrera Barrera*
  /Programador/
 
  Unitat d'Aplicacions Corporatives
  Servei d'Informàtica
 
  Plaça de la Mercè, 10-12 | 08002 Barcelona
  [Tel.] (+34) 93 542 16 93[Fax.] (+34) 93 542 21 45
  carles.barr...@upf.edu  mailto:carles.barr...@upf.edu
  http://www.upf.edu/bibtic/
 
  Universitat Pompeu Fabra, Barcelona
 
 
 
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 Hello Carlos,

 You must remove the first row with the headers for it to work.

 Cheers,
 Àlex

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Forget it. My mind got mixed with PostgreSQL...

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Re: [Dspace-tech] Use AND logic search instead of OR

[Àlex Magaz Graça]

El 11/02/15 a les 22:20, Xerio Cheri ha escrit:
 Hi Tim,

 Thanks so much. Sorry for not mentioning the DSpace version, we're using
 v. 4.1, so Discovery is the enabled engine. I'll tell the staff how it
 works and how to force the AND logic. Thanks again!

 2015-02-11 21:16 GMT+00:00 Tim Donohue tdono...@duraspace.org
 mailto:tdono...@duraspace.org:

 Hi,

 What version of DSpace are you using?

 The most recent versions of DSpace (4.x and 5.x) both use Discovery
 (based on Solr) for searching. This means they actually perform
 weighted/relevancy searches.

 So, if you search on multiple words, items which have both words
 (essentially an AND) will appear at the top of the search results.

 More info on Discovery is at
 https://wiki.duraspace.org/__display/DSDOC5x/Discovery
 https://wiki.duraspace.org/display/DSDOC5x/Discovery

 Discovery has existed in DSpace since DSpace 1.7, but it was
 disabled by default for some time. Starting in DSpace 4, it is the
 default search and browse engine for DSpace. If you are not yet
 using Discovery, you may wish to consider enabling it as it sounds
 like it may meet your needs.

 If you are using Discovery, you actually can force a boolean AND
 by simply entering two words with AND. For example:
   * test AND document -  would only return items that have both
 test and document
   * test document - would return all items that have either test
 or document but the ones that have *both* would appear at the top
 of the results.

 Good luck!

 - Tim


 On 2/11/2015 2:42 PM, Xerio Cheri wrote:

 Hi,

 It has been proposed by our staff to change the way DSpace searches
 terms on XMLUI. By default, it uses OR logic, so if more than
 one term
 is entered, any of them will be matched. Is there a simple way
 to change
 that behavior so if more than one word is entered in the search
 box only
 items that have ALL of them will be displayed?

 Thank you


 
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Hi Xerio,

If you prefer having less results when performing a search, you can 
still change the behaviour. You just have to change the value of this 
option in dspace/solr/search/conf/schema.xml to AND:

solrQueryParser defaultOperator=OR/

Cheers,
Àlex

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Re: [Dspace-tech] dspace 3.1 oai adding namespace to dcterms

[Àlex Magaz Graça]

El 21/11/14 a les 13:53, Lars Möller ha escrit:

 hello,

 we are using dspace 3 and the DSpace OAI-PMH Data Provider.
 i created an ese exporter to use the europeana namesapce.
 starting with

 europeana:record
 xmlns:europeana=http://www.europeana.eu/schemas/ese/xmlns:dcterms=http://purl.org/dc/terms/xmlns:doc=http://www.lyncode.com/xoaixmlns:dc=http://purl.org/dc/elements/1.1/;

 in the ese.xml i have the fields e.g.:
dc:title xmlns:dc=http://purl.org/dc/elements/1.1/;
 europeana:dataProvider xmlns:europeana=http://europeana.eu/terms;


 out puts:

 dc:title

 europeana:provider  xmlns:europeana=http://europeana.eu/terms;


 so the schema in dc:title got lost.

 is there a way to bring the schema back to the dc and dcterm fields?

 best
 lars moeller







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Hi Lars,

I think you're affected by this bug:

https://jira.duraspace.org/browse/DS-1959

Cheers,
Àlex

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[Dspace-tech] Duplicate log configuration for Solr?

[Àlex Magaz Graça]

Hi,

While adjusting the logging configuration (DSpace 4.1) I've noticed Solr 
logs seem to be configured in two places: log4j.properties [1] and 
log4j-solr.properties. If this is intended, what is the difference?

[1] 
https://github.com/DSpace/DSpace/blob/master/dspace/config/log4j.properties#L104

Thanks,
Àlex

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Re: [Dspace-tech] [DSpace] DS-1905: add emailAdr commandline parameter to dspace checker-emailer command (#489)

[Àlex Magaz Graça]

El 09/10/14 a les 21:46, Monika Mevenkamp ha escrit:
 I have trouble getting a clean PR together. Here is what I tried

 I started with my branch
 https://github.com/akinom/DSpace/commits/DS-1905-checker-emailer
 which is based on 1.8_x - sighh we are way behind

 git checkout DS-1905-checker-emailer
 https://github.com/akinom/DSpace/commits/DS-1905-checker-emailer
 git rebase -s recursive -X theirs upstream/master

 I interpret that the --theirs option favors the changes from upstream

 This produces lots of conflicts of the  'deleted in upstream - left file
 on file system'.
 For some reason rebase gets all upset about pom.xml files and not about
 all the other files that moved.

 I did
  rm offender-file
  git rm offender-file
 whenever that happened

 A couple cases there were complaints that a file was 'modified by both'

 so I tried with
 git revert HEAD  -- offender-file
 git checkout --theirs -- offender-file

 and whenever conflicts went away I did   rebase --continue


 I ended up with something that shows files differing that should really
 not be part of this.

 Before I go ahead and try to cherry-pick -  is there some git feature I
 should know/try ?

 Monika

 https://github.com/akinom/DSpace/commits/DS-1905-checker-emailer
 On 10/7/14, 4:24 PM, Hardy Pottinger wrote:
 
  Hi, the DSpace 5.0 release team is reviewing feature pull requests for
  possible inclusion for DSpace 5.0, and we see that this PR is not yet
  complete. We'd like to ask if you foresee being able to complete this
  work in progress by October 14? If there's anything we can do to help,
  please don't hesitate to ask. Thanks!
 
  —
  Reply to this email directly or view it on GitHub
  https://github.com/DSpace/DSpace/pull/489#issuecomment-58254765.
 

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Hi Monika,

I think in these cases it's better to do something like this to avoid
these conflicts:

git checkout  DS-1905-checker-emailer
git rebase --onto master 1234^

where 1234 would be the id of the first commit you made in 
DS-1905-checker-emailer. This way you avoid the commits that modify the 
pom.xml. Not sure about -s and -X parameters.

Cheers,
Àlex

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[Dspace-tech] Customising Mirage 2 from Netbeans

[Àlex Magaz Graça]

Hello,

With Mirage I used to modify the files under 
[dspace-src]/dspace-xmlui/src/main/webapp/themes/Mirage/ (I didn't use 
overlays) while running the project DSpace XML-UI (Manakin) from 
Netbeans (8.0). This way I could see the changes in XSLs and CSSs just 
by reloading the page from the browser.

I was wondering if it is still possible to do the same with Mirage 2, 
because if it is, I haven't been able to figure out the way. In case it 
is not possible, what would you recommend to speed up the testing of 
changes?

Thanks,
Àlex

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Re: [Dspace-tech] Mirage2 to installed Dspace

[Àlex Magaz Graça]

El 25/09/14 a les 09:58, Ahmed Maher ha escrit:
 Hi all ,

 Is there is  away to add Mirage2 theme to my installed Dspace4 ?

 thanks


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Hi Ahmed,

I don't know if there is a port somewhere, but I just applied the pull requests 
[1][2] to 4.1. I can share it in GitHub, if you want.

[1] https://github.com/DSpace/DSpace/pull/587
[2] https://github.com/DSpace/DSpace/pull/616

Cheers,
Àlex

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[Dspace-tech] Problems trying to deposit through SWORD

[Àlex Magaz Graça]

Hi,

I've been trying to deposit through SWORD (both with versions 1 and 2) 
but it either fails or does it incorrectly. Fetching the servicedocument 
and depositing a file to an item work though.

With SWORD v1:

curl -i --data-binary @dspace-sword/example/example.zip -H 
Content-Disposition: filename=test1.zip -H Content-Type: 
application/zip -H X-Packaging: 
http://purl.org/net/sword-types/METSDSpaceSIP; -H X-No-Op: false -H 
X-Verbose: true --user user:pass http://1.2.3.4/sword/deposit/12345/2

It gives me this error:

  WARN  org.dspace.content.packager.METSManifest @ Got no bitstream 
ADMID, file@ID=sword-mets-file-3
  [...]
  ERROR org.dspace.sword.SWORDMETSIngester @ caught exception:
  org.dspace.content.packager.PackageValidationException: Invalid METS 
Manifest: file element without ID attribute.
  at 
org.dspace.content.packager.AbstractMETSIngester.addBitstreams(AbstractMETSIngester.java:850)
  at 
org.dspace.content.packager.AbstractMETSIngester.ingestObject(AbstractMETSIngester.java:500)
  at 
org.dspace.content.packager.AbstractMETSIngester.ingest(AbstractMETSIngester.java:234)
  at 
org.dspace.sword.SWORDMETSIngester.ingest(SWORDMETSIngester.java:93)
  at 
org.dspace.sword.CollectionDepositor.doDeposit(CollectionDepositor.java:111)
  [...]


Actually, the file element has an ID attribute, what the code is really 
checking for is the ADMID attribute, which I've confirmed it is missing.

With SWORD v2:

curl -i --data-binary @dspace-sword/example/example.zip -H 
Content-Disposition: filename=test1.zip -H Content-Type: 
application/zip -H X-Packaging: 
http://purl.org/net/sword/package/METSDSpaceSIP; -H X-No-Op: false -H 
X-Verbose: true --user user:pass 
http://1.2.3.4/swordv2/collection/12345/2

The deposit doesn't fail, but the zip doesn't get unpacked either. An 
item is created with no metadata from the METS file. It just contains a 
bitstream with the name test1.zip, which corresponds to example.zip.

In the logs I see this warning:

WARN  org.dspace.core.PluginManager @ Cannot find named plugin for 
interface=org.dspace.sword2.SwordContentIngester, name=application/zip

It seems like it is using the Content-Type header instead of 
X-Packaging. So if set the value of the Content-Type header of the 
previous command to Content-Type: 
http://purl.org/net/sword/package/METSDSpaceSIP;, I get this error:

  [...]
  WARN  org.dspace.content.packager.METSManifest @ Got no bitstream 
ADMID, file@ID=sword-mets-file-3
  INFO  org.dspace.content.Bitstream @ 
sword:session_id=0:update_bitstream:bitstream_id=18
  ERROR org.dspace.sword2.SwordMETSContentIngester @ caught exception:
  org.dspace.content.packager.PackageValidationException: Invalid METS 
Manifest: file element without ID attribute.
  at 
org.dspace.content.packager.AbstractMETSIngester.addBitstreams(AbstractMETSIngester.java:850)
  at 
org.dspace.content.packager.AbstractMETSIngester.replaceObject(AbstractMETSIngester.java:660)
  at 
org.dspace.content.packager.AbstractMETSIngester.replace(AbstractMETSIngester.java:1187)
  at 
org.dspace.sword2.SwordMETSContentIngester.ingestToCollection(SwordMETSContentIngester.java:108)
  at 
org.dspace.sword2.AbstractSwordContentIngester.ingest(AbstractSwordContentIngester.java:45)
  at 
org.dspace.sword2.SwordMETSContentIngester.ingest(SwordMETSContentIngester.java:44)
  at 
org.dspace.sword2.CollectionDepositManagerDSpace.createNewFromBinary(CollectionDepositManagerDSpace.java:229)
  [...]

If I try to deposit from another repository with the SWORD client 
functionality, it also fails with the ID attribute error, although in 
this case the ADMID attribute is present in the file element.

I've made all these tests with DSpace 4 (master) test machine without 
any customisation apart from the install directories in 
build.properties. Nevertheless, I get the same results with demo.dspace.org.

Any idea of what am I doing wrong?

Thanks,
Àlex

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Re: [Dspace-tech] Some properties not expanded in dspace.cfg

[Àlex Magaz Graça]

El 25/11/13 15:38, Mark H. Wood ha escrit:
 On Mon, Nov 25, 2013 at 03:03:04PM +0100, Àlex Magaz Graça wrote:
 At least since DSpace 1.7, I've been noticing that some properties in
 dspace.cfg are not expanded after running ant update. For example,
 dspace.dir value is not expanded in log.init.config option.

 Does that cause a problem?  This expansion should be happening at
 runtime, if unexpanded variables still exist in dspace.cfg.  Whenever
 some bit of code asks for a configuration variable, its value is
 examined for unexpanded variables and edited accordingly.


Ah! I didn't know they were expanded at runtime. I don't think I've had 
any problem with this, but as there are always problems when testing, I 
always have the doubt and end up fixing it by hand, just to be sure.

Thanks,
Àlex


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[Dspace-tech] Some properties not expanded in dspace.cfg

[Àlex Magaz Graça]

Hi,

At least since DSpace 1.7, I've been noticing that some properties in 
dspace.cfg are not expanded after running ant update. For example, 
dspace.dir value is not expanded in log.init.config option.

I thought it had something to do with my setup (Ant version or 
whatever), but now, after looking at the issue, I don't see anything wrong.

I've seen in the prepare_configs target (in Ant's build.xml) how all 
configuration files but dspace.cfg are copied with a filter chain that 
expands the properties. So I've tried changing this line:

  copy file=${config} tofile=config-temp/dspace.cfg 
preservelastmodified=true /

with this:

copy file=${config} tofile=config-temp/dspace.cfg 
preservelastmodified=true 
 filterchain
  expandproperties /
 /filterchain
/copy

Afeter this change the properties are expanded correctly.

I build (mvn package) DSpace 4 from one machine with these versions:

OpenJDK 1.7.0_25
Maven 2.2.1

and deploy (ant update) in another machine with these versions:

OpenJDK 1.7.0_45
Ant 1.9.2

Any idea of what I am doing wrong?

Thanks,
Àlex

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Re: [Dspace-tech] How do I add a static block to the sidebar ?

[Àlex Magaz Graça]

El dia dt 19 nov 2013 05:22:02 CET, Patrick Rynhart va escriure:
 Hi,

 I'm running DSpace 3.2 using XMLUI.

 I would like to add a new block to the sidebar, i.e. a block similiar
 to the default Search DSpace, Browse, My Account, and Discover.

 The new block will contain only external links, so it doesn't really
 need to be integrated into DSpace, just displayed somehow. i.e.

 Box Title = Links
 =
 * Link1
 * Link2
 

 Attached is a screenshot of what I'm wanting (which I've mocked up
 using Firebug).

 If you could please let me know a simple / minimal way to achieve this
 that would be great.

 Thank you,

 Patrick Rynhart





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Hi Patrick,

I'm not sure you can add the block in the position you want. I think 
you'll have to put it either at the end or just before the RSS feeds 
block.

To do so, just put the block code into the dri:options template in the 
file 
dspace-xmlui/src/main/webapp/themes/Mirage/lib/xsl/core/navigation.xsl. 
Change Mirage with your theme name.

Cheers,
Àlex

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Re: [Dspace-tech] Harvesting error

[Àlex Magaz Graça]

El dia dc 13 nov 2013 12:20:23 CET, Daniel Deogratus va escriure:
 Hello,

 i was trying to Harvest on Dspace and i have the following error,
 anyone who have an Idea Should Help me Please

 Regards.

 ///


 Collection 1 failed on harvest:

 Date:   11/13/13 10:15 AM
 Status Flag:3

 Handle collision: attempted to re-assign handle '2164/266' to an
 incoming harvested item 'oai:aura.abdn.ac.uk:2164/2312
 http://aura.abdn.ac.uk:2164/2312
 '.

 Exception:
 org.dspace.harvest.OAIHarvester$HarvestingException: Handle collision:
 attempted to re-assign handle '2164/266' to an incoming harvested item
 'oai:aura.abdn.ac.uk:2164/2312 http://aura.abdn.ac.uk:2164/2312'.
 at
 org.dspace.harvest.OAIHarvester.processRecord(OAIHarvester.java:535)
 at
 org.dspace.harvest.OAIHarvester.runHarvest(OAIHarvester.java:362)
 at
 org.dspace.app.xmlui.aspect.administrative.FlowContainerUtils.processRunCollectionHarvest(FlowContainerUtils.java:275)
 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 at
 sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 at
 sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 at java.lang.reflect.Method.invoke(Method.java:597)
 at org.mozilla.javascript.MemberBox.invoke(MemberBox.java:155)
 at
 org.mozilla.javascript.NativeJavaMethod.call(NativeJavaMethod.java:243)
 at
 org.mozilla.javascript.Interpreter.interpretLoop(Interpreter.java:3237)
 at
 org.mozilla.javascript.Interpreter.interpret(Interpreter.java:2394)
 at
 org.mozilla.javascript.InterpretedFunction.call(InterpretedFunction.java:162)
 at
 org.mozilla.javascript.ContextFactory.doTopCall(ContextFactory.java:393)
 at
 org.mozilla.javascript.ScriptRuntime.doTopCall(ScriptRuntime.java:2834)
 at
 org.mozilla.javascript.InterpretedFunction.call(InterpretedFunction.java:160)
 at org.mozilla.javascript.Context.call(Context.java:538)
 at
 org.mozilla.javascript.ScriptableObject.callMethod(ScriptableObject.java:1833)
 at
 org.mozilla.javascript.ScriptableObject.callMethod(ScriptableObject.java:1803)
 at
 org.apache.cocoon.components.flow.javascript.fom.FOM_JavaScriptInterpreter.handleContinuation(FOM_JavaScriptInterpreter.java:698)
 at
 org.apache.cocoon.components.treeprocessor.sitemap.CallFunctionNode.invoke(CallFunctionNode.java:94)
 at
 org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:55)
 at
 org.apache.cocoon.components.treeprocessor.sitemap.MatchNode.invoke(MatchNode.java:87)
 at
 org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:55)
 at
 org.apache.cocoon.components.treeprocessor.sitemap.MatchNode.invoke(MatchNode.java:87)
 at
 org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:78)
 at
 org.apache.cocoon.components.treeprocessor.sitemap.SelectNode.invoke(SelectNode.java:82)
 at
 org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:78)
 at
 org.apache.cocoon.components.treeprocessor.sitemap.PipelineNode.invoke(PipelineNode.java:143)
 at
 org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:78)
 at
 org.apache.cocoon.components.treeprocessor.sitemap.PipelinesNode.invoke(PipelinesNode.java:81)
 at
 org.apache.cocoon.components.treeprocessor.ConcreteTreeProcessor.process(ConcreteTreeProcessor.java:239)
 at
 org.apache.cocoon.components.treeprocessor.ConcreteTreeProcessor.buildPipeline(ConcreteTreeProcessor.java:186)
 at
 org.apache.cocoon.components.treeprocessor.TreeProcessor.buildPipeline(TreeProcessor.java:260)
 at
 org.apache.cocoon.components.treeprocessor.sitemap.MountNode.invoke(MountNode.java:107)
 at
 org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:78)
 at
 org.apache.cocoon.components.treeprocessor.sitemap.SelectNode.invoke(SelectNode.java:87)
 at
 org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:55)
 at
 org.apache.cocoon.components.treeprocessor.sitemap.MatchNode.invoke(MatchNode.java:87)
 at
 org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:78)
 at
 org.apache.cocoon.components.treeprocessor.sitemap.PipelineNode.invoke(PipelineNode.java:143)
 at
 

Re: [Dspace-tech] Disable discovery facets in homepage

[Àlex Magaz Graça]

El dia dl 04 nov 2013 16:55:10 CET, RUIZ MORENO, ROBERT va escriure:

Hi everyone,

I'm using DSpace 3.1 XMLUI.

I need to hide the Discovery Facets shown, but only in the homepage.
Any approach or code to do this?

Thanks in advance
Robert


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Hi Robert,

We've also disabled the facets in the home page, so I'm attaching a 
patch with the changes. I'm not sure this is the best way to do so, but 
it works :)


Cheers,
Àlex
diff --git a/dspace-xmlui/src/main/webapp/themes/dri2xhtml-alt/core/navigation.xsl b/dspace-xmlui/src/main/webapp/themes/dri2xhtml-alt/core/navigation.xsl
index 022d6ca..f08c634 100644
--- a/dspace-xmlui/src/main/webapp/themes/dri2xhtml-alt/core/navigation.xsl
+++ b/dspace-xmlui/src/main/webapp/themes/dri2xhtml-alt/core/navigation.xsl
@@ -119,6 +119,22 @@
 /div
 /xsl:template
 
+!-- Disable Discovery facets on the home page --
+xsl:template match=dri:options/dri:list[@id='aspect.discovery.Navigation.list.discovery'] priority=5
+xsl:if test=/dri:document/dri:meta/dri:pageMeta/dri:metadata[@element='request' and @qualifier='URI'] != ''
+!-- Copied from the next rule (dri:options/dri:list[dri:list]). --
+xsl:apply-templates select=dri:head/
+div
+xsl:call-template name=standardAttributes
+xsl:with-param name=classds-option-set/xsl:with-param
+/xsl:call-template
+ul class=ds-options-list
+xsl:apply-templates select=*[not(name()='head')] mode=nested/
+/ul
+/div
+/xsl:if
+/xsl:template
+
 
 !-- The template that applies to lists directly under the options tag that have other lists underneath
 them. Each list underneath the matched one becomes an option-set and is handled by the appropriate
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Re: [Dspace-tech] Export to RefWorks button

[Àlex Magaz Graça]

El dia dj 18 jul 2013 20:07:44 CEST, Javier Távara va escriure:

Does anyone know how to implement an option to export items to
RefWorks? I have seen this in many repositories like this
http://demo.openrepository.com/demo/handle/2384/238591

I'm using DSpace 3.1 and XMLUI.

Thank you so much.


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Hi Javier,

Assuming you have already applied the patch for JSPUI [1], you just 
have to apply the attached patch. Then change example.com with your 
DSpace host name and add the image /images/refworks-export.png to 
your theme.


Cheers,
Àlex

[1] 
http://dspace.2283337.n4.nabble.com/Refworks-on-Dspace-tp3285733p3285734.html
=== modified file 'dspace/modules/xmlui/src/main/webapp/themes/UdL/lib/xsl/aspect/artifactbrowser/item-view.xsl'
--- dspace/modules/xmlui/src/main/webapp/themes/UdL/lib/xsl/aspect/artifactbrowser/item-view.xsl	2011-06-02 07:31:19 +
+++ dspace/modules/xmlui/src/main/webapp/themes/UdL/lib/xsl/aspect/artifactbrowser/item-view.xsl	2011-06-17 11:13:51 +
@@ -73,6 +73,7 @@
 !-- Generate the Creative Commons license information from the file section (DSpace deposit license hidden by default)--
 xsl:apply-templates select=./mets:fileSec/mets:fileGrp[@USE='CC-LICENSE']/
 
+xsl:call-template name=refworks-link /
 /xsl:template
 
 
@@ -481,4 +482,16 @@
 
 /xsl:template
 
+xsl:template name=refworks-link
+xsl:variable name=handle select=substring-after(/mets:METS/@OBJID, '/handle/') /
+xsl:variable name=url-parameter select=concat(
+'http://example.com/jspui/refworks-export?handle=',
+$handle) /
+p
+a href=http://www.refworks.com/express/ExpressImport.asp?filter=Refworks%20Tagged%20Formatamp;vendor=MINDS%40UWamp;url={$url-parameter}; target=RefWorksMain
+img src={concat($theme-path, '/images/refworks-export.png')} alt=Refworks Export /
+/a
+/p
+/xsl:template
+
 /xsl:stylesheet

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Re: [Dspace-tech] XPDF Thumbnail Creation

[Àlex Magaz Graça]

El dia dc 24 jul 2013 10:55:41 CEST, RENTON Scott va escriure:
 Hi folks

 I'm trying to generate PDF thumbnails for a repository, and I have followed 
 the instructions at 
 https://wiki.duraspace.org/display/DSDOC18/Configuration#Configuration-XPDFFilter

 I've built on a Mac, incorporating the java advanced imaging jars, and 
 uploaded, including the XPDF tools to a Linux box. The error I get from 
 media-filter is as follows:

 ERROR filtering, skipping bitstream:

 Item Handle: 123456789/8545
 Bundle Name: ORIGINAL
 File Size: 13249898
 Checksum: b0152697cf45c5a396a5f85f21df1979 (MD5)
 Asset Store: 0
 java.io.IOException: Unknown failure while transforming file to preview: no 
 image produced.
 java.io.IOException: Unknown failure while transforming file to preview: no 
 image produced.
 at 
 org.dspace.app.mediafilter.XPDF2Thumbnail.getDestinationStream(XPDF2Thumbnail.java:274)
 at 
 org.dspace.app.mediafilter.MediaFilterManager.processBitstream(MediaFilterManager.java:737)
 at 
 org.dspace.app.mediafilter.MediaFilterManager.filterBitstream(MediaFilterManager.java:561)
 at 
 org.dspace.app.mediafilter.MediaFilterManager.filterItem(MediaFilterManager.java:511)
 at 
 org.dspace.app.mediafilter.MediaFilterManager.applyFiltersItem(MediaFilterManager.java:479)
 at 
 org.dspace.app.mediafilter.MediaFilterManager.main(MediaFilterManager.java:353)
 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 at 
 sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 at 
 sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 at java.lang.reflect.Method.invoke(Method.java:597)
 at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:183)
 Updating search index:

 It looks as though, in XPDF2Thumbnail.java, I am ok up to the call to

 source = ImageIO.read(outf);

 as the previous logs say

 2013-07-23 16:28:13,932 DEBUG org.dspace.app.mediafilter.XPDF2Thumbnail @ 
 DPI: pdfinfo method got dpi=72 for max dim=792 (points, 1/72)
 2013-07-23 16:28:13,933 DEBUG org.dspace.app.mediafilter.XPDF2Thumbnail @ 
 Running xpdf command: [/u01/dspace/dspace/bin/xpdf/pdftoppm, -q, -f, 1, -l, 
 1, -r, 72, /tmp/DSfilt7452068847272888953.pdf, 
 /tmp/prevu8069855567105058459out]
 2013-07-23 16:28:14,065 DEBUG org.dspace.app.mediafilter.XPDF2Thumbnail @ 
 PDFTOPPM output is: /tmp/prevu8069855567105058459out-01.ppm, exists=true

 Source is null coming out of ImageIO. Just wondering if anyone knows enough 
 about the class to give me any pointers as to why the transform should fail.

 Thanks very much- I can give more information if it will help!
 Scott




Hi Scott,

I had the same problem some days ago. It happened because I forgot the 
-Pxpdf-mediafilter-support when running Maven. As a consequence the 
ImageIO JARs weren't included and the read() call returned null. Check 
for the following JARs in [dspace]/lib/ in case they are missing for 
some reason:

jai_core-1.1.2_01.jar
jai_imageio-1.0_01.jar

Cheers,
Àlex

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Re: [Dspace-tech] Error choosing CC License, in Catalan

[Àlex Magaz Graça]

Al 25/10/12 10:53, En/na RUIZ MORENO, ROBERT ha escrit:

Hi everyone,

we use DSpace 1.7.1 with XMLUI interface.

Our instance of DSpace has 3 languages available: Spanish, English  Catalan

If we start a submission in Catalan language, when we arrive to CC
License Step and clic on button that moves to CC page, it moves to:


*URL: http://creativecommons.org/license/*


  Server Error

*An error occurred. See the error logs for more information. (Turn debug
on to display exception reports here) *


The strange thing is, if we do the submission while navigating in
Spanish or English, the CC License Step redirects correctly and all
works fine.

In our logs don't appear any error or warning message.

Any help?

Thanks in advance.
Robert




Hi Robert,

There are some bugs in 1.7 that may be the source of your problem. I 
guess you already applied this one: 
https://jira.duraspace.org/browse/DS-1090.


Another problem I found some time ago was that If the button that sends 
the user to the Creative Commons web page to select the license contains 
accented characters, DSpace generates a wrong POST URL
which ends up with a server error in Creative Commons web. It's already 
fixed in 1.8, but you may want to fix it by just removing accents from 
the string, like in the patch attached.


Cheers,
Àlex
=== modified file dspace/modules/xmlui/src/main/webapp/i18n/messages_ca.xml
--- dspace/modules/xmlui/src/main/webapp/i18n/messages_ca.xml	2011-09-07 07:39:30 +
+++ dspace/modules/xmlui/src/main/webapp/i18n/messages_ca.xml	2011-10-05 07:52:43 +
@@ -363,7 +363,7 @@
   message key=xmlui.Submission.submit.CCLicenseStep.licenseLlicència/message
   message key=xmlui.Submission.submit.CCLicenseStep.no_licenseno heu seleccionat cap llicència Creative Commons/message
   message key=xmlui.Submission.submit.CCLicenseStep.submit_removeElimina aquesta llicència Creative Commons/message
-  message key=xmlui.Submission.submit.CCLicenseStep.submit_to_creative_commonsVés al lloc web de Creative Commons per seleccionar una llicència/message
+  message key=xmlui.Submission.submit.CCLicenseStep.submit_to_creative_commonsVes al lloc web de Creative Commons per seleccionar una llicencia/message
   message key=xmlui.Submission.submit.CompletedStep.go_submissionVés a la pàgina d'enviaments./message
   message key=xmlui.Submission.submit.CompletedStep.headEnviament conclòs/message
   message key=xmlui.Submission.submit.CompletedStep.info1Ara el vostre enviament seguirà el procés de revisió d'aquesta col·lecció. Quan el vostre enviament haja sigut incorporat a la col·lecció, o si hi ha algun problema amb l'enviament, rebreu una notificació per correu electrònic. També podeu comprovar l'estat del vostre enviament consultant la vostra pàgina d'enviaments./message
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[Dspace-tech] Collections at the root level

[Àlex Magaz Graça]

Hi,

I have some repositories for which the most sensible communities and 
collections structure has collections at the root level (i.e. they are 
not inside a (sub)community). The problem is DSpace only allows to 
create communities at the root level. I usually workaround the problem 
by creating a single root community with all the content, but it's not a 
very convincing solution.

Is there a reason for this limitation? Does someone know of a better 
workaround?

Thanks,
Àlex

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