[Dspace-tech] Full Text Searching in DSpace 3.3

[Brett Arno]

Hello,

We recently upgraded from DSpace 1.7.2 to DSpace 3.3 and now our search
function no longer is searching full text where it was before. I can't seem
to find any configuration differences between the two versions in our setup
that should be affecting this.

We have Discovery enabled and using XMLUI. We have an Oracle backend and on
Redhat. I've refiltered all of our media and have completely reindexed the
system several times to no avail. We are also using the XPDF filters if
that makes any difference.

Any thoughts or ideas to what I could be missing?

Thanks,
Brett
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[Dspace-tech] Issue after changing title of an item

[Brett Arno]

We are experiencing a weird issue after we had changed the title of an 
item. When browsing the collection by author the item's title still 
appears as the old title, until you navigate to the actual item page. 
The correct title appears here, but also the correct title appears when 
browsing by subject, title or issue date.

This issue appears to only be affecting Firefox (tested on 4.0.1 and 
12.0). Safari and Internet Explorer are showing the correct title from 
all the browse options. I've cleared the browser cache multiple times 
and have tested on multiple systems, some which never had accessed the 
site before.

I've also run index-update to make sure everything was correct there, 
but still no change on the issue.

We are currently using 1.7.2 with the Mirage template.

Any help would be greatly appreciated.

Thanks,
Brett



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Re: [Dspace-tech] Media Filter Errors

[Brett Arno]

I think I'm starting to make some more sense of this, but maybe I'm 
missing something and could use some clarification.

Right now our assetstore is owned by the tomcat user, and the reason we 
did this was because of "could not create" errors during our submission 
process from the UI. It was originally owned by dspace or a mix of 
dspace/tomcat which we really didn't understand, so we unified it to the 
tomcat user. All was well and good until the current problem.

I'm going to take a guess that the issue is because the PDFbox/media 
filter are run by the dspace user and now that user no longer has the 
correct permissions to create the text file in the assetstore.

So the solution would be to create a method of having both dspace/tomcat 
able to write to the assetstore, which a number of options exist.

Sorry if this is just a regurgitation of everything you already said, I 
just wanted to make sure I understood the problem fully.

Thanks!
-Brett

On 4/25/12 6:00 PM, helix84 wrote:
> On Wed, Apr 25, 2012 at 23:52, Brett Arno  wrote:
>> Thanks for the helpful advice helix.
>>
>>   I do notice that our assetstore has 755 permissions set on them for the
>> tomcat user.  This may not be the correct user, but it had cleared up
>> previous issues that we were getting from the UI during the submission
>> phases. I suppose a switch to 777 would clear the issue entirely, but I'm
>> not entirely sure our IT folks would be comfortable in issuing those
>> permissions even if DSpace is the only application running on the server
>> currently.
>>
>> Right now I think our dspace and tomcat users are completely independent of
>> each other, but it's my understanding that typical installations are running
>> tomcat from the dspace user. Is this correct and is there a solution for our
>> set-up that may help our case?
> In your place I would change dspace to run under the tomcat user. Or
> chown tomcat files by the dspace user, doesn't matter. I do that and I
> never encountered this problem.
>
> Regards,
> ~~helix84


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Re: [Dspace-tech] Media Filter Errors

[Brett Arno]

Thanks for the helpful advice helix.

  I do notice that our assetstore has 755 permissions set on them for 
the tomcat user.  This may not be the correct user, but it had cleared 
up previous issues that we were getting from the UI during the 
submission phases. I suppose a switch to 777 would clear the issue 
entirely, but I'm not entirely sure our IT folks would be comfortable in 
issuing those permissions even if DSpace is the only application running 
on the server currently.

Right now I think our dspace and tomcat users are completely independent 
of each other, but it's my understanding that typical installations are 
running tomcat from the dspace user. Is this correct and is there a 
solution for our set-up that may help our case?

Thanks,
Brett

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[Dspace-tech] Media Filter Errors

[Brett Arno]

Hello All,

I'm receiving a good portion of errors when running the filter-media 
command and wondering if anyone can provide some insight.


I'm running 1.7.2 XMLUI with Mirage on a Red Hat server. Most items in 
the instance give this error:


ERROR filtering, skipping bitstream:

Item Handle: 10829/669
Bundle Name: ORIGINAL
File Size: 43066
Checksum: d302cf0378a385ff16610d63943b5368 (MD5)
Asset Store: 0
java.io.IOException: No such file or directory
java.io.IOException: No such file or directory
at java.io.UnixFileSystem.createFileExclusively(Native Method)
at java.io.File.createNewFile(File.java:900)
at edu.sdsc.grid.io.local.LocalFile.createNewFile(LocalFile.java:486)
at 
org.dspace.storage.bitstore.BitstreamStorageManager.store(BitstreamStorageManager.java:300)

at org.dspace.content.Bitstream.create(Bitstream.java:205)
at org.dspace.content.Bundle.createBitstream(Bundle.java:384)
at 
org.dspace.app.mediafilter.MediaFilterManager.processBitstream(MediaFilterManager.java:760)
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.applyFiltersAllItems(MediaFilterManager.java:414)
at 
org.dspace.app.mediafilter.MediaFilterManager.main(MediaFilterManager.java:333)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at 
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:616)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:183)

The first thing I checked was that the items files exist and can be 
accessed through the system and from my large test sample, they all had 
PDFs and all opened fine.


I've tried completely rebuilding the index to see if that may help, but 
that didn't change the results. I've tried indexing with these commands 
and none of them helped:


[dspace]/bin/dpsace index-update
[dspace]/bin/dspace index-init
[dspace]/bin/dspace index-init -r -f

We are using the PDF filter that was issued with the system and not 
using discovery.


I also noticed this error in the DSpace log:
WARN  org.apache.pdfbox.util.PDFStreamEngine @ java.io.IOException: 
Error: expected hex character and not  :32

java.io.IOException: Error: expected hex character and not  :32
at 
org.apache.fontbox.cmap.CMapParser.parseNextToken(CMapParser.java:336)

at org.apache.fontbox.cmap.CMapParser.parse(CMapParser.java:139)
at org.apache.pdfbox.pdmodel.font.PDFont.parseCmap(PDFont.java:556)
at org.apache.pdfbox.pdmodel.font.PDFont.encode(PDFont.java:390)
at 
org.apache.pdfbox.util.PDFStreamEngine.processEncodedText(PDFStreamEngine.java:386)

at org.apache.pdfbox.util.operator.ShowText.process(ShowText.java:45)
at 
org.apache.pdfbox.util.PDFStreamEngine.processOperator(PDFStreamEngine.java:567)
at 
org.apache.pdfbox.util.PDFStreamEngine.processSubStream(PDFStreamEngine.java:250)
at 
org.apache.pdfbox.util.PDFStreamEngine.processStream(PDFStreamEngine.java:208)
at 
org.apache.pdfbox.util.PDFTextStripper.processPage(PDFTextStripper.java:378)
at 
org.apache.pdfbox.util.PDFTextStripper.processPages(PDFTextStripper.java:302)
at 
org.apache.pdfbox.util.PDFTextStripper.writeText(PDFTextStripper.java:258)
at 
org.dspace.app.mediafilter.PDFFilter.getDestinationStream(PDFFilter.java:101)
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.applyFiltersAllItems(MediaFilterManager.java:414)
at 
org.dspace.app.mediafilter.MediaFilterManager.main(MediaFilterManager.java:333)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at 
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:616)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:183)


Any help would be greatly appreciated!

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Re: [Dspace-tech] About error 404

[Brett Arno]

Karol,

By default the folders you copy over to Tomcat webapps folder (or point 
Tomcat to), none are named dspace. The urls that should work are:

http://localhost:8080/xmlui  for the Manakin pages or,
http://localhost:8080/jspui   for the Java Server Pages.

Hope this helps,
Brett

On 3/7/12 3:14 PM, Karol Guzman wrote:
> I installed dspace and everything is ok but when I try to access
> http://localhost:8080/dspace appear the following error:
>
> Estado HTTP 404
> type informe de estado
> mensaje
> descripción  El recurso requerido () no está disponible
>
> Apace Tomcat/6.0.35
>
> Please, I need help
>
> Thank you
>
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Re: [Dspace-tech] Adding a static page to DSpace

[Brett Arno]

Dhanushka,

Looks like the URL you would need is https://example.com/xmlui/page/home 
 not https://example.com/xmlui/home.


-Brett

On 3/7/12 2:14 PM, Dhanushka Samarakoon wrote:

Hi,
I followed the article below to add a static page to DSpace 1.8.
https://wiki.duraspace.org/display/DSPACE/Manakin+theme+tutorial#Manakinthemetutorial-Addingstaticpages 


(Method 4)

But when I try to access the https://example.com/xmlui/home url, I'm 
getting a 'org.apache.cocoon.ResourceNotFoundException: Page cannot be 
found' error.

The example looks pretty straightforward, so what am I doing wrong here?
Thanks,
Dhanushka.


added the following code to Mirage/lib/xsl/core/page-structure.xsl
*

select="/dri:document/dri:meta/dri:pageMeta/dri:metadata[@element='title']" 
/>




 


K-REx Home Page







*






-


KREx Home


select="/dri:document/dri:meta/dri:pageMeta/dri:trail"/>






**



test="/dri:document/dri:meta/dri:pageMeta/dri:metadata[@element='alert'][@qualifier='message']">



select="/dri:document/dri:meta/dri:pageMeta/dri:metadata[@element='alert'][@qualifier='message']/node()"/>








Home Page for KREx
To add your own content to this page, edit 
webapps/xmlui/themes/dri2xhtml/structural.xsl and add your own content 
to the title, trail, and body.

  








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Re: [Dspace-tech] Java error during submission

[Brett Arno]

We had experienced this issue with our instance of DSpace and what our 
cause of the problem was mismatched permission issues within the 
assetstore folder. Our assetstore folder permissions were spread out 
between our dspace user and our tomcat user and resolved it by changing 
permissions solely to the tomcat user. However, our difference was it 
always occurred during the file upload process so your problem may be 
different, but may at least be worth taking a look at.


Hope this helps,
Brett

On 3/7/12 12:14 PM, Paul Go wrote:
On random steps of submission we're seeing a "permission denied" Java 
error. Going back a page in the browser and retrying generally 
resolves the instance but this is occurring with more frequency as 
time goes on (70% of the time, by one estimate).


We're running 1.7.1

Any help would be appreciated.

Paul Go

Systems Librarian /
Library Technology Manager
Paul V. Galvin Library
35 West 33rd Street
Chicago, IL  60616
312.567.7997
p...@iit.edu 



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Re: [Dspace-tech] Problems updating CSS files

[Brett Arno]

Hi Adam,

It appears your problem is in the Dconfig property when issuing the ant 
update command. By the sounds of it you seem to be using the literal 
[dspace] as written in the documentation. This is really a placeholder 
reference in the documentation. There are two instances of this notation 
that are very different [dspace-source] and [dspace]

[dspace-source] as probably obvious at this point is the location of 
your source files and
[dspace] which is the directory your building to.

For example in our instance when I need to run the ant update command I 
do this:

"ant -Dconfig=/data/dspace/config/dspace.cfg update"

so our [dspace] directory is /data/dspace.

Hope this helps,
Brett

On 3/5/12 1:03 PM, Adam Fullerton wrote:
> Good Day,
>
> I am walking through the suggestions I received about updating the CSS
> file for JSPUI. I have ran the following commands and I am getting
> following errors. I am probably missing the obvious but if someone
> could point it out to me I would be grateful.
>
> In the file "/build/dspace-1.7.2-src-release/dspace" I ran "mvn
> package" and it worked fine
>
> In the file 
> "/build/dspace-1.7.2-src-release/dspace/target/dspace-1.7.2-build.dir"
> I ran 'ant -Dconfig=[dspace]/config/dspace.cfg update" I also tried
> running without the brackets around dspace but got the same result as
> follows:
>
> BUILD FAILED
> /build/dpsace-.1.7.2-src-release/dspace/target/dspace1.7.2-build.dir/build.xml:62:
> Source resource does not exist:
> /build/dspace-1.7.2-src-release/dspace/target/dspace-1.7.2-build.dir/dspace/config/dspace.cfg
>
> Any ideas what I am doing wrong?
>
> Thank you
>


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Re: [Dspace-tech] Blank home page in DSpace 1.7.1 XMLUI interface

[Brett Arno]

There is definitely an error occurring in cocoon. I'm not entirely sure 
how to fix it though - but maybe just pointing it out will help some of 
the experts.


Cocoon Log:
2012-02-06 18:20:10,223 ERROR cocoon.handled  - Sitemap: error when 
calling sub-sitemap


DSpace Log:

2012-02-06 18:20:10,338 ERROR 
org.dspace.app.xmlui.cocoon.DSpaceCocoonServletFilter @ Serious Error 
Occurred Processing Request!
javax.servlet.ServletException: PWC1244: Servlet execution threw an 
exception
at 
org.apache.catalina.core.ApplicationFilterChain.servletService(ApplicationFilterChain.java:414)
at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:297)
at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:178)
at 
org.dspace.app.xmlui.cocoon.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:111)
at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:210)
at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:178)
at 
org.dspace.app.xmlui.cocoon.DSpaceCocoonServletFilter.doFilter(DSpaceCocoonServletFilter.java:246)
at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:210)
at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:178)
at 
org.apache.cocoon.servlet.multipart.MultipartFilter.doFilter(MultipartFilter.java:131)
at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:210)
at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:178)
at 
org.dspace.utils.servlet.DSpaceWebappServletFilter.doFilter(DSpaceWebappServletFilter.java:78)
at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:210)
at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:178)
at 
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:270)
at 
org.apache.catalina.core.StandardContextValve.invokeInternal(StandardContextValve.java:241)
at 
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:182)
at 
org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:571)
at 
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:160)
at 
org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:571)
at 
com.sun.webserver.connector.nsapi.NSAPIProcessor.process(NSAPIProcessor.java:149)
at 
com.sun.webserver.connector.nsapi.NSAPIConnector.service(NSAPIConnector.java:995)


On 2/6/12 6:56 PM, Peter Dietz wrote:

Hi Susan,

My initial guess is to try to append a slash to the URL. Or append a 
slash, and some random url stuff, to atleast get a 404.





Peter Dietz



On Mon, Feb 6, 2012 at 6:42 PM, Thornton, Susan M. (LARC-B702)[LITES] 
mailto:susan.m.thorn...@nasa.gov>> wrote:


Hi,

 We've been running the JSPUI version of DSpace 1.7.1 for
months now with no problems.  Recently I've been working on trying
to implement the XMLUI interface and am having big problems.  The
Maven build and ant/compile runs fine and my web server starts
successfully, but nothing displays when I enter the site url in
the browser (the page is completely blank).  I've checked my
server-log:

/[06/Feb/2012:18:18:05] info (17228): CORE1116: Sun Java System
Web Server 7.0 B12/04/2006 10:15/

/[06/Feb/2012:18:18:05] info (17229): CORE5076: Using [Java
HotSpot(TM) Server VM, Version 1.6.0_07] from [Sun Microsystems Inc.]/

/[06/Feb/2012:18:18:07] info (17229): WEB0100: Loading web module
in virtual server [ldr-dev-1.7.1-xmlui] at [/]/

/[06/Feb/2012:18:18:09] warning (17229): CORE3283: stderr:
log4j:WARN No appenders could be found for logger
(org.apache.commons.digester.Digester)./

/[06/Feb/2012:18:18:09] warning (17229): CORE3283: stderr:
log4j:WARN Please initialize the log4j system properly./

/[06/Feb/2012:18:18:13] info (17229): PWC1412: WebModule[]
ServletContext.log():Initializing Spring root WebApplicationContext/

/[06/Feb/2012:18:18:17] info (17229): PWC1412: WebModule[]
ServletContext.log():Apache Cocoon Spring Configurator v1.0.2 is
running in mode 'prod'./

/[06/Feb/2012:18:18:20] info (17229): PWC1412: WebModule[]
ServletContext.log():Cocoon: Block dispatcher was initialized
successfully./

/[06/Feb/2012:18:18:21] info (17229): HTTP3072:
http-listener-1.7.1-xmlui: http://146.165.44.232:80 ready to
accept requests/

/[06/Feb/2012:18:18:21] info (17229): CORE3274: successful server
startup/

//

And access-log:

/999.999.99.99 - - [06/Feb/2012:18:20:10 -0500] "GET / HTTP/1.1"
200 0/

I don't see any problems.

I'm attaching my dspace.log and coco

Re: [Dspace-tech] Static page 1.8.0 Patch fix, usability on 1.7.2

[Brett Arno]

Thanks Peter,

The patching process went smoothly aside from like you mentioned spacing 
issues in the structural.xsl file. After the patch was applied and I 
made the edits to our page-structure.xsl, I tried to rebuild dspace.


The build was going well until it hit this error:
[ERROR] BUILD FAILURE
[INFO] 


[INFO] Compilation failure
/dspace/svn/dspace-xmlui/dspace-xmlui-api/src/main/java/org/dspace/app/xmlui/aspect/browseArtifacts/StaticPage.java:[31,16] 
addBody(org.dspace.app.xmlui.wing.element.Body) in 
org.dspace.app.xmlui.aspect.browseArtifacts.StaticPage cannot implement 
addBody(org.dspace.app.xmlui.wing.element.Body) in 
org.dspace.app.xmlui.cocoon.DSpaceTransformer; overridden method does 
not throw org.apache.cocoon.ProcessingException


Any ideas?

-Brett

On 12/16/11 2:08 PM, Peter Dietz wrote:

Hi Brett,

Thanks for your interest in this patch. I was hoping to get more 
feedback before it went in to 1.8.1, but I could have written the 
patch sooner.


For the components that DS-1076 (Xmlui static pages) affects, it 
should work just fine with 1.7.2. So feel free to invest the time 
patching your system, it should work out. (I don't know how cleanly 
the patch will apply, i.e. line space differences, but the code will 
eventually work).


The main difference that prompted the DS-1076 improvement, was the new 
PageNotFound improvements in 1.8, so this patch is a somewhat proper 
way to do an "improper" task. Proper meaning pages in DSpace are 
created by Java, that produce DRI, improper meaning that the XSL 
hijacks the page and draws something different on the screen.


But during your testing, feel free to give feedback on how the process 
of adding a new page goes. i.e. too annoying to edit structural.xsl 
and add the title, trail, body... etc



Peter Dietz



On Fri, Dec 16, 2011 at 1:35 PM, Brett Arno <mailto:barno...@gmail.com>> wrote:


I've been following the topic of static pages and them being broken in
1.8. We are currently using 1.7.2 with Mirage and wondering if the
patch
supplied here https://jira.duraspace.org/browse/DS-1076 would be
usable
on our version?

It's my understanding that the patch is just adding a new java
file and
adding some lines to other xsl files and should not be bias based
on the
version we are using, but I'd like to know for sure before I delve
into
the process of applying the patch. My knowledge of the changes between
1.7.2 and 1.8.0 is pretty lacking, so I'm probably missing something.

Thanks,
Brett


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Microsoft is holding a special Learn Windows Azure training event for 
developers. It will provide a great way to learn Windows Azure and what it 
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[Dspace-tech] Static page 1.8.0 Patch fix, usability on 1.7.2

[Brett Arno]

I've been following the topic of static pages and them being broken in 
1.8. We are currently using 1.7.2 with Mirage and wondering if the patch 
supplied here https://jira.duraspace.org/browse/DS-1076 would be usable 
on our version?

It's my understanding that the patch is just adding a new java file and 
adding some lines to other xsl files and should not be bias based on the 
version we are using, but I'd like to know for sure before I delve into 
the process of applying the patch. My knowledge of the changes between 
1.7.2 and 1.8.0 is pretty lacking, so I'm probably missing something.

Thanks,
Brett

--
Learn Windows Azure Live!  Tuesday, Dec 13, 2011
Microsoft is holding a special Learn Windows Azure training event for 
developers. It will provide a great way to learn Windows Azure and what it 
provides. You can attend the event by watching it streamed LIVE online.  
Learn more at http://p.sf.net/sfu/ms-windowsazure
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