Re: [Dspace-tech] [Dspace-devel] Looking for Resources - Aspect Modification and the "dim:"

[Mark Diggory]

On Thu, May 6, 2010 at 6:54 PM, Mark H. Wood  wrote:
>
> As noted by Mark Diggory, a Theme may call back into Cocoon with an
> internal request for more metadata.  I've been meaning to ask why it
> was done that way.

My assumption is that it was done because when "all" the METS is
embedded into the DRI it can slow processing, think of it as only
getting what you need.  I liken it to: The DRI is the stage, the
various METS sources are the "players", at various points in the
"play", you need to bring different players to the stage to speak
their parts.

> IIRC this was added between the final separate
> release of Manakin and its incorporation into stock DSpace 1.5.

Yes, it was a question of performance and flexibility.

> We could all do with an updated theory of operation for the later
> stages of XMLUI.

On a wild tangent... In theory, we might see a day when "METS" is
replaced in the XMLUI by something else like "FOXML", "ATOM", "RDF",
or "Place your favorite format here". Then we see that a DRI page is
really just the definition of an View over a set of resources,
resources with resolvable URI that can be gotten and presented to the
user.

Mark
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Re: [Dspace-tech] [Dspace-devel] Looking for Resources - Aspect Modification and the "dim:"

[Mark H. Wood]

If you want to change where things are placed on the final page, that
is layout, and layout is handled by XSL in the Theme stage.  Aspects
add substructures to a big XML structure (the DRI document) which
holds the nonstatic data that go into the page, and then the Theme
takes what it wants from the DRI and lays that out.  The DRI
document is entirely consumed by the Theme stage, with the interesting
bits slotted into the XHTML skeleton generated by the Theme.

As noted by Mark Diggory, a Theme may call back into Cocoon with an
internal request for more metadata.  I've been meaning to ask why it
was done that way.  IIRC this was added between the final separate
release of Manakin and its incorporation into stock DSpace 1.5.

We could all do with an updated theory of operation for the later
stages of XMLUI.

-- 
Mark H. Wood, Lead System Programmer   mw...@iupui.edu
Balance your desire for bells and whistles with the reality that only a 
little more than 2 percent of world population has broadband.
-- Ledford and Tyler, _Google Analytics 2.0_


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Re: [Dspace-tech] solr crashing dspace 1.6

[Hilton Gibson]

I use: http://psi-probe.googlecode.com/ to monitor memory usage.
Still have to get all the bells and whistles going thought.
If anybody knows of a better open source app, please let me know.


On 6 May 2010 19:27, Peter Dietz  wrote:

> With the upgrade you essentially have another webapp running, i.e. SOLR,
> which means your instance will need more memory. More for when doing a lot
> of work, and more to be permanently used i.e "permgen". When I've performed
> large batch processing (converting and importing old log files), I've bumped
> up my max memory for tomcat/java and increased the permgen. I'm not sure if
> there is something triggering solr to jump "over the edge" in your case, but
> after I've allocated more memory to java/tomcat, problems just go away.
>
> Thus for me it would be: edit /etc/init.d/tomcat6
> JAVA_OPTS="-Djava.awt.headless=true -Xmx1536M *-XX:MaxPermSize=128m*"
>
> or, however you normally set JAVA_OPTS
>
> Peter Dietz
> Systems Developer/Engineer
> Ohio State University Libraries
>
>
>
>
> On Thu, May 6, 2010 at 11:41 AM, Anderson, Charles W <
> bill.ander...@library.gatech.edu> wrote:
>
>> We're on our second attempt to upgrade from 1.5.2 to 1.6.  We have been
>> plagued with m
>> memory errors both times, and we' think we've narrowed it down to
>> something that's going
>> on in the solr webapp.  We've got solr running in it's very own Tomcat
>> instance; which has
>> helped, but hasn't completely eliminated the problems.
>>
>> Just before we crash, we're seeing lots and lots of the following in the
>> dspace log:
>>
>>org.apache.solr.common.SolrException: Internal Server Error
>>
>> Then, eventually, we start getting this:
>>
>>org.apache.commons.dbcp.SQLNestedException: Cannot get a connection,
>> pool error: Timeout waiting for idle object
>>
>> Meanwhile, over in catalina.out, we have these, which seem to correspond
>> to the solr errors in the dspace log:
>>
>>SEVERE: org.apache.solr.common.SolrException: Error opening new
>> searcher. exceeded limit of maxWarmingSearchers=2, try again later.
>>
>> And, eventually, the voice of doom:
>>
>>Exception in thread "TP-Processor550" java.lang.OutOfMemoryError:
>> PermGen space
>>
>> Has anybody else experience memory issues related to solr?
>>
>> Thanks,
>>
>> Bill
>>
>>
>>
>> Bill Anderson
>> Software Developer
>> Digital Library Development
>> Georgia Tech Library
>>
>>
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>>
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>
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Re: [Dspace-tech] Problems with Maven

[Mark Diggory]

Eija,

Are you behind a proxy? You may be able to browse the repo in your
browser, but not access it from java without proxy settings added to
you ~/.m2/settings.xml if that is the case.  Check with your system
admin.

Mark

On Wed, May 5, 2010 at 11:02 PM, Eija Airio  wrote:
> Hi,
>
> has anyone had this kind of problems: suddenly "mvn package" does not
> succeed anymore, but ends with the following messages:
>
> --
> [INFO] [resources:resources]
> [INFO] Using default encoding to copy filtered resources.
> [INFO] artifact org.dspace:dspace-api-lang: checking for updates from
> java.net
> [INFO] artifact org.dspace:dspace-api-lang: checking for updates from
> central
> [WARNING] repository metadata for: 'artifact org.dspace:dspace-api-lang'
> could not be retrieved from repository: central due to an error: Error
> transferring file
> [INFO] Repository 'central' will be blacklisted
> [INFO]
> 
> [ERROR] BUILD ERROR
> [INFO]
> 
> [INFO] Failed to resolve artifact.
>
> No versions are present in the repository for the artifact with a range
> [1.6.0.0,1.7.0.0)
>   org.dspace:dspace-api-lang:jar:null
>
> from the specified remote repositories:
>   central (http://repo1.maven.org/maven2),
>   java.net (http://download.java.net/maven/2),
>   maven.dspace.org-snapshot (http://maven.dspace.org/snapshot)
>
>
> [INFO]
> 
> [INFO] For more information, run Maven with the -e switch
> [INFO]
> 
> [INFO] Total time: 4 minutes 13 seconds
> [INFO] Finished at: Thu May 06 08:36:20 EEST 2010
> [INFO] Final Memory: 28M/51M
> [INFO]
> 
> -
>
> The same happens with DSpace 1.5.2, with dspace-api-lang [1.5.0.0,1.6.0.0).
> And yes, I am giving the command in the right directory,
> "[dspace-source]/dspace/". Is the problem in the repositories or on our
> server?
>
> - Eija
>
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Re: [Dspace-tech] [Dspace-devel] Looking for Resources - Aspect Modification and the "dim:"

[Mark Diggory]

Patrick,

You are close. Yes there is another "XML" source that is being
rendered, It is not DRI, but METS+DIM and is used as the source for
all details about the existing Community, Collection, Item when
rendering the view.

You will find out more about this source of XML by looking at some examples...

Example Item
http://demo.dspace.org/xmlui/handle/123456789/18

THE DRI representing the View
http://demo.dspace.org/xmlui/DRI/handle/123456789/18

With a referenceset representing the following item metadata...




This item appears in the following Collection(s)





THE METS+DIM representing the Item
http://demo.dspace.org/xmlui/metadata/handle/123456789/18/mets.xml

If you wish to alter the presentation of our Community, Collection or
Item views, you can override and re-implement the following
DIM-Handler templates by copying them to into your theme xslt and
altering them there.






Hope this is helpful,
Mark


On Thu, May 6, 2010 at 2:24 PM, Patrick Etienne
 wrote:
> DSpace Users / Devs -
> (Wasn't sure for which list this would be more appropriate, apologies for
> cross-posting)
>
> We're looking to move our repository's production DSpace instance from the
> JSPUI to the XMLUI. I've been working with the Manakin interface for a
> while, but have hit a bit of a stumbling block with Aspects.
> Some of the requested changes seem to be more within the realms of the
> DIM-Handler.xsl or further back within the/an aspect's java code. All of the
> resources I've found for introductions to Aspect development are either too
> high level or just very outdated. I was hoping that members of the list
> might have recommendations for resources that would help in the effort of
> customizing the interface beyond what is available through overwriting
> existing xsl templates.
> An example customization might be:
> Moving the location in which "Copyright and License" appears on Community,
> Sub-Community, Collection, and Item pages. Let's say I want to move this to
> the bottom of the page, where at the moment it appears below the level
> (community, collection, item, etc) description but above other parts of the
> page (recent submissions, etc).
> The steps I've performed so far are:
> 1) Searched through files for the string "Copyright and License" which
> pulled up the "messages.xml" file.
> 2) Found the "Copyright and License" string as having the key
> "xmlui.dri2xhtml.METS-1.0.copyright".
> 3) Searched the code for the "xmlui.dri2xhtml.METS-1.0.copyright" string,
> found within the DIM-Handler.xsl file.
> 4) Found two instances of the following template containing the
> "xmlui.dri2xhtml.METS-1.0.copyright" string:
> 
> 5) This template is not named, so cannot be called specifically from a
> parent template. This would seem to say that the rendering order of the html
> is based upon something other than directives found within the xsl
> transformations. The template is matching "dim:dim" which seems to indicate
> that there's a "secondary DRI" (for lack of a better description) whose
> elements I might want to reorder toward the goal of having these elements
> displayed in non-standard rendering order in the final html page.
> In the "structural.xsl", the prefix "dri:" is used, where in the
> DIM-Handler.xsl the prefix "dim:" is used. This seems to support the notion
> that there's another "dri-like" xml document in the cocoon chain that's
> helping to build the final output.
> Two things I'd be very interested in are:
> A) Resources I could use to read up about the "dim:" part of the pipeline.
> B) Resources that might provide insight into how to manipulate existing
> Aspects.
> I'm familiar with pre-2.2 Cocoon (before the spring/maven foundation was
> implemented) and related concepts (sitemaps, selectors, matchers,
> generators, etc).
> My educated guess is that my next step along the journey is to trace the
> Artifact Browser aspect from the sitemap through the cocoon pipeline back
> all the way to the underlying java code and just explore. Any tips, hints,
> suggestions, or resources though would be highly appreciated!
>  - Patrick E.
> ---
> Patrick K. Étienne
> Systems Analyst
> Library and Information Center
> Georgia Institute of Technology
> email: patrick.etie...@library.gatech.edu
> phone: 404.385.8121
> "Mediocre Writers Borrow; Great Writers Steal" - T.S. Eliot
>
> --
>
>
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>



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[Dspace-tech] Looking for Resources - Aspect Modification and the "dim:"

[Patrick Etienne]

DSpace Users / Devs -
(Wasn't sure for which list this would be more appropriate, apologies  
for cross-posting)


We're looking to move our repository's production DSpace instance from  
the JSPUI to the XMLUI. I've been working with the Manakin interface  
for a while, but have hit a bit of a stumbling block with Aspects.


Some of the requested changes seem to be more within the realms of the  
DIM-Handler.xsl or further back within the/an aspect's java code. All  
of the resources I've found for introductions to Aspect development  
are either too high level or just very outdated. I was hoping that  
members of the list might have recommendations for resources that  
would help in the effort of customizing the interface beyond what is  
available through overwriting existing xsl templates.


An example customization might be:
Moving the location in which "Copyright and License" appears on  
Community, Sub-Community, Collection, and Item pages. Let's say I want  
to move this to the bottom of the page, where at the moment it appears  
below the level (community, collection, item, etc) description but  
above other parts of the page (recent submissions, etc).


The steps I've performed so far are:
1) Searched through files for the string "Copyright and License" which  
pulled up the "messages.xml" file.
2) Found the "Copyright and License" string as having the key  
"xmlui.dri2xhtml.METS-1.0.copyright".
3) Searched the code for the "xmlui.dri2xhtml.METS-1.0.copyright"  
string, found within the DIM-Handler.xsl file.
4) Found two instances of the following template containing the  
"xmlui.dri2xhtml.METS-1.0.copyright" string:


5) This template is not named, so cannot be called specifically from a  
parent template. This would seem to say that the rendering order of  
the html is based upon something other than directives found within  
the xsl transformations. The template is matching "dim:dim" which  
seems to indicate that there's a "secondary DRI" (for lack of a better  
description) whose elements I might want to reorder toward the goal of  
having these elements displayed in non-standard rendering order in the  
final html page.


In the "structural.xsl", the prefix "dri:" is used, where in the DIM- 
Handler.xsl the prefix "dim:" is used. This seems to support the  
notion that there's another "dri-like" xml document in the cocoon  
chain that's helping to build the final output.


Two things I'd be very interested in are:
A) Resources I could use to read up about the "dim:" part of the  
pipeline.
B) Resources that might provide insight into how to manipulate  
existing Aspects.


I'm familiar with pre-2.2 Cocoon (before the spring/maven foundation  
was implemented) and related concepts (sitemaps, selectors, matchers,  
generators, etc).


My educated guess is that my next step along the journey is to trace  
the Artifact Browser aspect from the sitemap through the cocoon  
pipeline back all the way to the underlying java code and just  
explore. Any tips, hints, suggestions, or resources though would be  
highly appreciated!


 - Patrick E.
---
Patrick K. Étienne
Systems Analyst
Library and Information Center
Georgia Institute of Technology
email: patrick.etie...@library.gatech.edu
phone: 404.385.8121

"Mediocre Writers Borrow; Great Writers Steal" - T.S. Eliot

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Re: [Dspace-tech] How does the bitstream_format_id get set in a DSpace 1.5.1 import?

[Thornton, Susan M. (LARC-B702)[RAYTHEON TECHNICAL SERVICES COMPANY]]

Tim,

 Thanks for your comments. Your mention of the format registry made me 
think of something.  I remembered being unclear about which tables I had to 
load explicitly, for some reason, when I was implementing the two newest 
instances.  I just looked and the "fileextension" table is EMPTY in those two 
instances!  This of course would be problematic, now wouldn't it?!  :)   I'm 
not sure where in the implementation procedures this is done, but for some 
reason I missed it.  I'll just unload the fileextension table from one of the 
good instances and copy it into the two empty ones.



Thanks to all who replied to my question.  I'm pretty knowledgeable when it 
comes to DSpace, but I love having this list of folks to depend on when I'm 
stumped on something.



Sue



-Original Message-
From: Tim Donohue [mailto:tdono...@duraspace.org]
Sent: Thursday, May 06, 2010 1:20 PM
To: dspace-tech@lists.sourceforge.net; Thornton, Susan M. (LARC-B702)[RAYTHEON 
TECHNICAL SERVICES COMPANY]
Subject: Re: [Dspace-tech] How does the bitstream_format_id get set in a DSpace 
1.5.1 import?



Sue,



A few comments inline...



On 5/6/2010 11:44 AM, Thornton, Susan M. (LARC-B702)[RAYTHEON TECHNICAL

SERVICES COMPANY] wrote:

>   I just noticed in one of our DSpace instances that _all_ of the rows

> in the bitstream table have column "bitstream_format_id" set to "1" -

> Unknown. All the documents are either .pdf files or their equivalent

> .pdf.txt files (from filter-media). The strange thing is that all the

> .pdf files are in ORIGINAL bundles and all the .pdf.txt files are in

> TEXT bundles.



The ORIGINAL bundle always contains the original files (as they were

uploaded in DSpace).  The TEXT bundle always includes text-extraction

files which are auto-generated by the filter-media script.  More info on

Bundle usage can be found in the DSpace Data Model descriptions:

http://www.dspace.org/1_6_0Documentation/ch02.html#docbook-functional.html-data_model



>

> What is the proper way to set the value of "bitstream_format_id" during

> an import? Is it a field you have to include in the Contents file? Or is

> it supposed to be set programmatically in DSpace? I guess I can write a

> query to "update" the bitstream_format_id based on the document names,

> i.e., .pdf files are bitstream_format_id = "3" and .pdf.txt files should

> be "5".



DSpace will attempt to recognize File Formats automatically on

upload/ingest.  It does so in a very rudimentary way, by essentially

checking the file extension.  If the uploaded file's extension matches a

known extension in DSpace's Bitstream Format Registry, than DSpace will

assume that file is of that known format.



So, each of your ".pdf" files should have been auto-recognized as PDF

format, assuming your Bitstream Format Registry has an entry for ".pdf"

(it should, as this is a default entry -- the only way it wouldn't is if

you specifically removed it, or your Format Registry was not initialized

properly to begin with).



I'm at a loss for why this doesn't seem to be working in your DSpace

installation (as I've never seen this before).  Is there any custom

submission/ingest code that code be affecting this?   Are you ingesting

this content via a UI (XMLUI or JSPUI) or is it all ingested via

commandline (either way, DSpace should be recognizing the formats

properly -- but it could help narrow down the problem)?



- Tim
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[Dspace-tech] Error on DSIndexer run

[Stackpole, Mark]

I am plagued by Java errors. There is another one after I run DSIndexer
 

C:\dspace\bin>dsrun org.dspace.search.DSIndexer
Using DSpace installation in: C:\dspace
Exception in thread "main" java.lang.NoSuchMethodError:
org.apache.lucene.document.Document.add(Lorg/apache/lucene/document/Fiel
d;)V
at
org.dspace.search.DSIndexer.writeIndexRecord(DSIndexer.java:757)
at
org.dspace.search.DSIndexer.writeCommunityIndex(DSIndexer.java:424)
at
org.dspace.search.DSIndexer.indexAllCommunities(DSIndexer.java:368)
at org.dspace.search.DSIndexer.createIndex(DSIndexer.java:190)
at org.dspace.search.DSIndexer.main(DSIndexer.java:225)
 
I have removed all JAVA and reinstalled JDK 5
I am running Dspace 1.4.1 (the last version that worked)
Windows Server 2003

 
Mark Stackpole
Library Technologist
California Maritime Academy Library
Vallejo, CA
 

P Please consider whether it is necessary to print this email.

 
 
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Re: [Dspace-tech] solr crashing dspace 1.6

[Peter Dietz]

With the upgrade you essentially have another webapp running, i.e. SOLR,
which means your instance will need more memory. More for when doing a lot
of work, and more to be permanently used i.e "permgen". When I've performed
large batch processing (converting and importing old log files), I've bumped
up my max memory for tomcat/java and increased the permgen. I'm not sure if
there is something triggering solr to jump "over the edge" in your case, but
after I've allocated more memory to java/tomcat, problems just go away.

Thus for me it would be: edit /etc/init.d/tomcat6
JAVA_OPTS="-Djava.awt.headless=true -Xmx1536M *-XX:MaxPermSize=128m*"

or, however you normally set JAVA_OPTS

Peter Dietz
Systems Developer/Engineer
Ohio State University Libraries



On Thu, May 6, 2010 at 11:41 AM, Anderson, Charles W <
bill.ander...@library.gatech.edu> wrote:

> We're on our second attempt to upgrade from 1.5.2 to 1.6.  We have been
> plagued with m
> memory errors both times, and we' think we've narrowed it down to something
> that's going
> on in the solr webapp.  We've got solr running in it's very own Tomcat
> instance; which has
> helped, but hasn't completely eliminated the problems.
>
> Just before we crash, we're seeing lots and lots of the following in the
> dspace log:
>
>org.apache.solr.common.SolrException: Internal Server Error
>
> Then, eventually, we start getting this:
>
>org.apache.commons.dbcp.SQLNestedException: Cannot get a connection,
> pool error: Timeout waiting for idle object
>
> Meanwhile, over in catalina.out, we have these, which seem to correspond to
> the solr errors in the dspace log:
>
>SEVERE: org.apache.solr.common.SolrException: Error opening new
> searcher. exceeded limit of maxWarmingSearchers=2, try again later.
>
> And, eventually, the voice of doom:
>
>Exception in thread "TP-Processor550" java.lang.OutOfMemoryError:
> PermGen space
>
> Has anybody else experience memory issues related to solr?
>
> Thanks,
>
> Bill
>
>
>
> Bill Anderson
> Software Developer
> Digital Library Development
> Georgia Tech Library
>
>
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Re: [Dspace-tech] How does the bitstream_format_id get set in a DSpace 1.5.1 import?

[Tim Donohue]

Sue,

A few comments inline...

On 5/6/2010 11:44 AM, Thornton, Susan M. (LARC-B702)[RAYTHEON TECHNICAL 
SERVICES COMPANY] wrote:
>   I just noticed in one of our DSpace instances that _all_ of the rows
> in the bitstream table have column “bitstream_format_id” set to “1” –
> Unknown. All the documents are either .pdf files or their equivalent
> .pdf.txt files (from filter-media). The strange thing is that all the
> .pdf files are in ORIGINAL bundles and all the .pdf.txt files are in
> TEXT bundles.

The ORIGINAL bundle always contains the original files (as they were 
uploaded in DSpace).  The TEXT bundle always includes text-extraction 
files which are auto-generated by the filter-media script.  More info on 
Bundle usage can be found in the DSpace Data Model descriptions:
http://www.dspace.org/1_6_0Documentation/ch02.html#docbook-functional.html-data_model

>
> What is the proper way to set the value of “bitstream_format_id” during
> an import? Is it a field you have to include in the Contents file? Or is
> it supposed to be set programmatically in DSpace? I guess I can write a
> query to “update” the bitstream_format_id based on the document names,
> i.e., .pdf files are bitstream_format_id = “3” and .pdf.txt files should
> be “5”.

DSpace will attempt to recognize File Formats automatically on 
upload/ingest.  It does so in a very rudimentary way, by essentially 
checking the file extension.  If the uploaded file's extension matches a 
known extension in DSpace's Bitstream Format Registry, than DSpace will 
assume that file is of that known format.

So, each of your ".pdf" files should have been auto-recognized as PDF 
format, assuming your Bitstream Format Registry has an entry for ".pdf" 
(it should, as this is a default entry -- the only way it wouldn't is if 
you specifically removed it, or your Format Registry was not initialized 
properly to begin with).

I'm at a loss for why this doesn't seem to be working in your DSpace 
installation (as I've never seen this before).  Is there any custom 
submission/ingest code that code be affecting this?   Are you ingesting 
this content via a UI (XMLUI or JSPUI) or is it all ingested via 
commandline (either way, DSpace should be recognizing the formats 
properly -- but it could help narrow down the problem)?

- Tim

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Re: [Dspace-tech] How does the bitstream_format_id get set in a DSpace 1.5.1 import?

[Richard, Joel M]

Sue,

If I remember correctly (others may have more detailed info), I had to set up 
the appropriate information in the Bitstream Format Registry (In the Administer 
section) for the files that we were importing. In our case, it was MP3 files 
and adding a new entry allowed the import to automatically choose the proper 
format (based on the file extension, I presume.)

I know for certain that the "contents" file of the -import- directory does not 
like anything more than a filename in there. I know I had to go back with a SQL 
query to update the descriptions of the bitstreams because the import doesn't 
support it, but the format type was chosen automatically.

This might help, too, but isn't much different than what I mention above.

http://wiki.dspace.org/confluence/display/DSPACE/Add+a+new+format+to+the+bitstream+registry

--Joel


Joel Richard
IT Specialist, Web Services Division
Smithsonian Institution Libraries | http://www.sil.si.edu/
(202) 633-1706 | (202) 786-2861 (f) | richar...@si.edu




From: "Thornton, Susan M. (LARC-B702)[RAYTHEON TECHNICAL SERVICES COMPANY]" 

Date: Thu, 6 May 2010 12:44:15 -0400
To: "dspace-tech@lists.sourceforge.net" 
Cc: "Warren, Douglas Lewis (LARC-B7)[NCI]" 
Subject: [Dspace-tech] How does the bitstream_format_id get set in a DSpace 
1.5.1 import?

[cid:3355995558_35504712]
I just noticed in one of our DSpace instances that all of the rows in the 
bitstream table have column "bitstream_format_id" set to "1" - Unknown.  All 
the documents are either .pdf files or their equivalent .pdf.txt files (from 
filter-media).  The strange thing is that all the .pdf files are in ORIGINAL 
bundles and all the .pdf.txt files are in TEXT bundles.

 What is the proper way to set the value of "bitstream_format_id" during an 
import?  Is it a field you have to include in the Contents file?  Or is it 
supposed to be set programmatically in DSpace?  I guess I can write a query to 
"update" the bitstream_format_id based on the document names, i.e., .pdf files 
are bitstream_format_id = "3" and .pdf.txt files should be "5".

Thanks in advance,
Sue



Sue Walker-Thornton
NASA Langley Research Center
Integrated Library Systems
Developer, Application & Database Administrator
ConITS Contract ~ NCI Information Systems, Inc.
130 Research Drive
Hampton, VA  23666
Office: (757) 224-4074 ~ Mobile: (757) 506-9903 ~ Fax: (757) 224-4001
email: susan.m.thorn...@nasa.gov 


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[Dspace-tech] How does the bitstream_format_id get set in a DSpace 1.5.1 import?

[Thornton, Susan M. (LARC-B702)[RAYTHEON TECHNICAL SERVICES COMPANY]]

 I just noticed in one of our DSpace instances that all of the rows in the 
bitstream table have column "bitstream_format_id" set to "1" - Unknown.  All 
the documents are either .pdf files or their equivalent .pdf.txt files (from 
filter-media).  The strange thing is that all the .pdf files are in ORIGINAL 
bundles and all the .pdf.txt files are in TEXT bundles.

 What is the proper way to set the value of "bitstream_format_id" during an 
import?  Is it a field you have to include in the Contents file?  Or is it 
supposed to be set programmatically in DSpace?  I guess I can write a query to 
"update" the bitstream_format_id based on the document names, i.e., .pdf files 
are bitstream_format_id = "3" and .pdf.txt files should be "5".

Thanks in advance,
Sue



Sue Walker-Thornton
NASA Langley Research Center
Integrated Library Systems
Developer, Application & Database Administrator
ConITS Contract ~ NCI Information Systems, Inc.
130 Research Drive
Hampton, VA  23666
Office: (757) 224-4074 ~ Mobile: (757) 506-9903 ~ Fax: (757) 224-4001
email:  susan.m.thorn...@nasa.gov

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Re: [Dspace-tech] Email Setup Difficulties

[bryce ray]

Is it possible to set this up to not use SSL? What configuration settings do
I need to change?
When I changed the port of the mail configuration from 465 to 25 I continued
to get the same SSL problem.  I never really intended to connect to the mail
server through SSL it seems to be attempting to do so on its own or through
some configuration setting I'm not aware of.

Thanks for your help.

On Wed, May 5, 2010 at 8:32 PM, Mark H. Wood  wrote:

> Do you also have a copy of the certificate used by your cert. vendor
> to sign your server's certificate, and so on up to the selfsigned root
> CA certificate?  It looks like it is unable to build the complete trust
> path.
>
> Browsers and suchlike may come packed with big bundles of CA
> certificates that most users just blindly trust, but a JKS truststore
> is created empty -- annoying, but it's for a good reason.  Common
> practice is for a program asserting identity via certificate to
> provide the entire chain up to the root.  To do that, you need to
> install those higher-level certificates.
>
> Your CA probably has a page that provides its signing cert., as well
> as their root cert. if they use the common practice of separating the
> two functions.  (Notice I didn't say the page will be easy to find.)-:
>
> --
> Mark H. Wood, Lead System Programmer   mw...@iupui.edu
> Balance your desire for bells and whistles with the reality that only a
> little more than 2 percent of world population has broadband.
>-- Ledford and Tyler, _Google Analytics 2.0_
>
>
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[Dspace-tech] solr crashing dspace 1.6

[Anderson, Charles W]

We're on our second attempt to upgrade from 1.5.2 to 1.6.  We have been plagued 
with m
memory errors both times, and we' think we've narrowed it down to something 
that's going
on in the solr webapp.  We've got solr running in it's very own Tomcat 
instance; which has
helped, but hasn't completely eliminated the problems.  

Just before we crash, we're seeing lots and lots of the following in the dspace 
log:

org.apache.solr.common.SolrException: Internal Server Error

Then, eventually, we start getting this:

org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool 
error: Timeout waiting for idle object

Meanwhile, over in catalina.out, we have these, which seem to correspond to the 
solr errors in the dspace log:

SEVERE: org.apache.solr.common.SolrException: Error opening new searcher. 
exceeded limit of maxWarmingSearchers=2, try again later.

And, eventually, the voice of doom:

Exception in thread "TP-Processor550" java.lang.OutOfMemoryError: PermGen 
space

Has anybody else experience memory issues related to solr?

Thanks,

Bill



Bill Anderson 
Software Developer 
Digital Library Development 
Georgia Tech Library 

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Re: [Dspace-tech] Embargo setter plugin question

[Jason Fowler]

Richard,

I've been testing the setter and have run into a problem. Here's the problem:

When I select 6 months, the submission fails. The date that it tries to set is 
earlier than the date of submission. For example, if I make the submission 
today (2010-05-06), it tries to set an embargo date of 2010-04-17.

When I select a date of 1 year, the submission succeeds, but the date is wrong. 
For example, if I make the submission today (2010-05-06), it tries to set an 
embargo date of 2010-05-23.

When I select 2 years, the submission fails. The date that it tries to set is 
earlier than the date of submission. For example, if I make the submission 
today (2010-05-06), it tries to set an embargo date of 2010-04-20.

Here is what I've done.

First, I added the DayTableEmbargoSetter.java to 
[DSOURCE]/dspace-api/target/classses/org/dspace/embargo

Next, I added to dspace.cfg the following line
embargo.terms.days = 6 months:180,1 year:365,2 years:730

and I changed the embargo setter line to say
plugin.single.org.dspace.embargo.EmbargoSetter = 
org.dspace.embargo.DayTableEmbargoSetter

Then, I added to input-forms.xml

 dc
   embargo
   terms
   false
   Date of embargo duration
   dropdown
   Date when the embargo can be lifted.
   
   

and under form-value-pairs


  6 Months
  6 months


1 Year
1 year


2 Years
2 years

   

I've done all of the mvn and ant stuff correctly. Everything is in the place it 
should be. My system date is correct, and all of the other dates that get 
stored are correct.

Thanks for your help. The code looks to be very, very close. Not sure what is 
causing the inconsistency in setting dates. It could very well be something 
I've configured incorrectly. 


Jason Fowler, CA, MSLS
Archives and Special Collections Librarian
The Southern Baptist Theological Seminary
Vice President, ALABI
jfow...@sbts.edu

From: Richard Rodgers [rrodg...@mit.edu]
Sent: Tuesday, May 04, 2010 2:02 PM
To: Jason Fowler
Cc: DSpace-tech@lists.sourceforge.net
Subject: Re: [Dspace-tech] Embargo setter plugin question

Hi Jason:

Bit of an email glitch in my last reply: looks like the text became an 
attachment. But the gist is:

I sent you a setter class (source and .class file) that I haven't tested, but 
might do what you are looking for.
Let me know if you have any problems, or if the set-up description is not clear.

It's fairly general, so if it works for you, we can include it in the next 
distribution.

Thanks,

Richard R


On May 3, 2010, at 11:27 AM, Jason Fowler wrote:

> Has anyone yet developed a custom Embargo setter for 1.6 that will mimic 
> UMI's embargo terms (6 months, 1 year, 2 years). If so, would you be willing 
> to share the code?
>
> Thanks,
> Jason Fowler, CA, MSLS
> Archives and Special Collections Librarian
> The Southern Baptist Theological Seminary
> Vice President, ALABI
> jfow...@sbts.edu
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[Dspace-tech] Document Preview in DSpace

[Lewatle Phaladi]

Hi All 

 

Does anyone setup Document Preview in her/his DSpace system I have tried
lots of documents online with no success, you can sent me a web link
that you have used or document especially clear one.

 

Regards,

Lewatle

 


This communication 
is intended for the addressee only. It is confidential. If you have received 
this communication in error, please notify us immediately and destroy the 
original message. You may not copy or disseminate this communication without 
the permission of the University. Only authorized signatories are competent to 
enter into agreements on behalf of the University and recipients are thus 
advised that the content of this message may not be legally binding on the 
University and may contain the personal views and opinions of the author, which 
are not necessarily the views and opinions of The University of the 
Witwatersrand, Johannesburg. All agreements between the University and 
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Re: [Dspace-tech] More re: Embargo error on Approval

[Richard Rodgers]

Hi Richard:

Try this document for a fuller explanation. Let me know of any questions not 
addressed in it. We will try to include it in the next release.

Thanks,

Richard R
On May 5, 2010, at 6:02 PM, Jizba, Richard wrote:


I finally realized that the Embargo Setter is reading dc.embargo.terms for the 
date rather than dc.embargo.liftdate.

I’ve check our dspace.cfg file and there does not seem to be a mix-up. Nor is 
there a mix-up on the submission form.

Perhaps I don’t understand what these fields are for? What is dc.embargo.terms 
supposed to do?

Richard


_
From: Jizba, Richard
Sent: Wednesday, May 05, 2010 4:05 PM
To: 
'dspace-tech@lists.sourceforge.net'
Subject: Embargo error on Approval


Hello,

We we try to approve an item that has been submitted with an embargo date (in 
dc.embargo.liftdate) we receive the following error:

java.lang.NullPointerException

at 
org.dspace.embargo.EmbargoManager.getEmbargoDate(EmbargoManager.java:166)

Can anyone suggest how to resolve this?

We are running 1.6.

Richard Jizba

Creighton University

Omaha, NE


{\rtf1\ansi\ansicpg1252\cocoartf1038\cocoasubrtf250
{\fonttbl\f0\fswiss\fcharset0 Helvetica;\f1\fmodern\fcharset0 Courier;}
{\colortbl;\red255\green255\blue255;}
\margl1440\margr1440\vieww18820\viewh11900\viewkind0
\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\ql\qnatural\pardirnatural

\f0\fs24 \cf0 Embargo Support in DSpace 1.6\
\
i. What is an embargo?\
\
An embargo is a temporary access restriction placed on content, commencing at time of accession. It's scope or duration may vary, but the fact that it eventually expires is what distinguishes it from other content restrictions. For example, it is not unusual for content destined for DSpace to come with permanent restrictions on use or access based on license-driven or other IP-based requirements that limit access to institutionally affiliated users. Restrictions such as these are imposed and managed using standard administrative tools in DSpace, typically by attaching specific policies to Items or Collections, Bitstreams, etc.  The embargo functionally introduced in 1.6, however, includes tools to automate the imposition and removal of restrictions in managed timeframes.\
\
II.Embargo model and life-cycle\
\
Functionally, the embargo system allows you to attach 'terms'  to an item before it is placed into the repository, which express how the embargo should be applied. What do 'we mean by terms' here? They are really any expression that the system is capable of turning into (1) the time the embargo expires, and (2) a concrete set of access restrictions. Some examples:\
\
"2020-09-12"  - an absolute date (i.e. the date embargo will be lifted)\
"6 months" - a time relative to when the item is accessioned\
"forever"  - an indefinite, or open-ended embargo\
"local only until 2015" -  both a time and an exception (public has no access until 2015, local users OK immediately)\
"Nature Publishing Group standard" - look-up to a policy somewhere (typically 6 months)\
\
These terms are 'interpreted' by the embargo system to yield a specific date on which the embargo can be removed or 'lifted'., and a specific set of access policies. Obviously, some terms are easier to interpret than others (the absolute date really requires none at all), and the 'default' embargo logic understands only the most basic terms (the first and third examples above). But as we will see below, the embargo system provides you with the ability to add in your own 'interpreters' to cope with any terms expressions you wish to have. This date that is the result of the interpretation is stored with the item and the embargo system detects when that date has passed, and removes the embargo ("lifts it"), so the item bitstreams become available. Here is a more detailed life-cycle for an embargoed item:\
\
A. Terms assignment\
\
The first step in placing an embargo on an item is to attach (assign) 'terms' to it.\
If these terms are missing, no embargo will be imposed. As we will see below, terms are carried in a configurable DSpace metadata field, so assigning terms just means assigning a value to a metadata field. This can be done in a web submission user interface form, in a SWORD deposit package, a batch import, etc. - anywhere metadata is passed to DSpace. The terms are not immediately acted upon, and may be revised, corrected, removed, etc, up until the next stage of the life-cycle. Thus a submitter could enter one value, and a collection editor replace it, and only the last value will be used. Since metadata fields are multivalued, theoretically there can be multiple terms values, but in the default implementation only one is recognized.\
\
B. Terms interpretation/imposition\
\
In DSpace terminology, when an Item has exited the last of any workflow steps (or if none have been defined for it), it is said to be 'installed' into the repository. At th

Re: [Dspace-tech] Change DSpace retrospective policy

[Lewatle Phaladi]

Hi 

I got it Claudia, let me test it.
Thanks.

Regards,
Lewatle

-Original Message-
From: Claudia Jürgen [mailto:claudia.juer...@ub.tu-dortmund.de] 
Sent: 06 May 2010 09:40 AM
To: dspace-tech@lists.sourceforge.net
Subject: Re: [Dspace-tech] Change DSpace retrospective policy

Hello,

log in to your DSpace instance as admin, you'll find authorization in the 
administration navigation.

Claudia Jürgen


Am 06.05.2010 09:14, schrieb Lewatle Phaladi:
> Hi Claudia
>
> Thanks for the respond.
> I checked on DSpace interface but I don't see advanced authorization 
> management, could you please give me example path that I can use to reach 
> that?
>
> Regards,
> Lewatle
>
> -Original Message-
> From: Claudia Jürgen [mailto:claudia.juer...@ub.tu-dortmund.de]
> Sent: 06 May 2010 08:56 AM
> To: dspace-tech@lists.sourceforge.net
> Subject: Re: [Dspace-tech] Change DSpace retrospective policy
>
> Hello Lewatle,
>
> changing the DEFAULT_ITEM_READ and/or DEFAULT_BITSTREAM_READ for a collection 
> will only affect newly ingested items.
>
> In order to change authorizations for existing items you got to use the 
> advanced authorization management in the dspace admin section.
>
> Claudia Jürgen
>
>
> Am 06.05.2010 08:42, schrieb Lewatle Phaladi:
>> Hi All
>>
>>
>>
>> We had a closed policy to our items in DSpace to one community and 
>> its collections and if I change the authorizations rules to allow 
>> anonymous read it also prevents me from reading the item without 
>> logging in and it also prevents some users that were not allowed to 
>> view the item previously. I can only view files as anonymous for 
>> those that I have created recently, but all previously loaded files I 
>> can't read them as anonymous.
>>
>>
>>
>> Assistance will be appreciated as always.
>>
>>
>>
>> Regards,
>>
>> Lewatle
>>
>>
>> This 
>> communication is intended for the addressee only. It is confidential.
>> If you have received this communication in error, please notify us 
>> immediately and destroy the original message. You may not copy or 
>> disseminate this communication without the permission of the 
>> University. Only authorized signatories are competent to enter into 
>> agreements on behalf of the University and recipients are thus 
>> advised that the content of this message may not be legally binding 
>> on the University and may contain the personal views and opinions of 
>> the author, which are not necessarily the views and opinions of The 
>> University of the Witwatersrand, Johannesburg. All agreements between 
>> the University and outsiders are subject to South African Law unless 
>> the University agrees in writing to the contrary.
>>
>>
>>
>> -
>> -
>> 
>>
>>
>>
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> communication is intended for the addressee only. It is confidential. 
> If you have received this communication in error, please notify us 
> immediately and destroy the original message. You may not copy or 
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> University and may contain the personal views and opinions of the 
> author, which are not necessarily the views and opinions of The 
> University of the Witwatersrand, Johannesburg. All agreements between 
> the University and outsiders are subject to South African Law unless 
> the University agrees in writing to the contrary.
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is intended for the addressee only. It is confidential. If you have received 
this communication in error, please notify us immediately and destroy the 
original message. You may not copy or disseminate this communication without 
the permission of the University. Only authorized signatories are competent to 
enter into agreements on behalf of the University and recipients are thus 
advised that the content of this message may not be legally binding on the 
University and may contain the personal views and opinions of the author, which 
are not necessarily the views and opinions of The University of the 
Witwatersrand, Johannesburg. All agreements between the University and 
outsiders are subject to South African Law unless the University agrees in 
writing to the contrary.


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Re: [Dspace-tech] Change DSpace retrospective policy

[Claudia Jürgen]

Hello,

log in to your DSpace instance as admin, you'll find authorization in 
the administration navigation.


Claudia Jürgen


Am 06.05.2010 09:14, schrieb Lewatle Phaladi:

Hi Claudia

Thanks for the respond.
I checked on DSpace interface but I don't see advanced authorization 
management, could you please give me example path that I can use to reach that?

Regards,
Lewatle

-Original Message-
From: Claudia Jürgen [mailto:claudia.juer...@ub.tu-dortmund.de]
Sent: 06 May 2010 08:56 AM
To: dspace-tech@lists.sourceforge.net
Subject: Re: [Dspace-tech] Change DSpace retrospective policy

Hello Lewatle,

changing the DEFAULT_ITEM_READ and/or DEFAULT_BITSTREAM_READ for a collection 
will only affect newly ingested items.

In order to change authorizations for existing items you got to use the 
advanced authorization management in the dspace admin section.

Claudia Jürgen


Am 06.05.2010 08:42, schrieb Lewatle Phaladi:

Hi All



We had a closed policy to our items in DSpace to one community and its
collections and if I change the authorizations rules to allow
anonymous read it also prevents me from reading the item without
logging in and it also prevents some users that were not allowed to
view the item previously. I can only view files as anonymous for those
that I have created recently, but all previously loaded files I can't
read them as anonymous.



Assistance will be appreciated as always.



Regards,

Lewatle


This
communication is intended for the addressee only. It is confidential.
If you have received this communication in error, please notify us
immediately and destroy the original message. You may not copy or
disseminate this communication without the permission of the
University. Only authorized signatories are competent to enter into
agreements on behalf of the University and recipients are thus advised
that the content of this message may not be legally binding on the
University and may contain the personal views and opinions of the
author, which are not necessarily the views and opinions of The
University of the Witwatersrand, Johannesburg. All agreements between
the University and outsiders are subject to South African Law unless
the University agrees in writing to the contrary.



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This communication is intended for 
the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original 
message. You may not copy or disseminate this communication without the permission of the University. Only authorized signatories are competent 
to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding 
on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The 
University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the 
University agrees in writing to the contrary.


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Re: [Dspace-tech] DSpace-tech Digest, Vol 49, Issue 15: Problems with Maven

[Christof]

Dear


I also had this issue once. I solved it deleting all the directories in
my local repository (Normally this a hidden directory, called .m2,
directly under you user-home dir).

If you run 'mvn package' now, It will reisntall all needed packages,
again, in this directory.

This is strange because I still believe the problem is situated on the
remote repository.

This was also reported in:
http://www.mail-archive.com/dspace-tech@lists.sourceforge.net/msg05570.html


Yours Sincerely




Christof

Στις 06-05-2010, ημέρα Πεμ, και ώρα 06:03 +, ο/η
dspace-tech-requ...@lists.sourceforge.net έγραψε:
> Send DSpace-tech mailing list submissions to
>   dspace-tech@lists.sourceforge.net
> 
> To subscribe or unsubscribe via the World Wide Web, visit
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> or, via email, send a message with subject or body 'help' to
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> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of DSpace-tech digest..."
> 
> 
> Today's Topics:
> 
>1. Embargo error on Approval (Jizba, Richard)
>2. More re: Embargo error on Approval (Jizba, Richard)
>3. Re: More re: Embargo error on Approval (Hilton Gibson)
>4. Re: Email Setup Difficulties (Mark H. Wood)
>5. Problems with Maven (Eija Airio)
> 
> 
> --
> 
> Message: 1
> Date: Wed, 5 May 2010 16:04:46 -0500
> From: "Jizba, Richard" 
> Subject: [Dspace-tech] Embargo error on Approval
> To: dspace-tech@lists.sourceforge.net
> Message-ID:
>   
> <21ce15cd4586f94bb6c11c996aa122a90789c...@exbe02.blue.jays.creighton.edu>
>   
> Content-Type: text/plain; charset="us-ascii"
> 
> Hello,
> 
> We we try to approve an item that has been submitted with an embargo
> date (in dc.embargo.liftdate) we receive the following error:
> 
> java.lang.NullPointerException
>   at
> org.dspace.embargo.EmbargoManager.getEmbargoDate(EmbargoManager.java:166
> )
> 
> Can anyone suggest how to resolve this?
> 
> We are running 1.6.
> 
> Richard Jizba
> Creighton University
> Omaha, NE
> 
> -- next part --
> An HTML attachment was scrubbed...
> 
> --
> 
> Message: 2
> Date: Wed, 5 May 2010 17:02:27 -0500
> From: "Jizba, Richard" 
> Subject: [Dspace-tech] More re: Embargo error on Approval
> To: dspace-tech@lists.sourceforge.net
> Message-ID:
>   
> <21ce15cd4586f94bb6c11c996aa122a90789c...@exbe02.blue.jays.creighton.edu>
>   
> Content-Type: text/plain; charset="us-ascii"
> 
> I finally realized that the Embargo Setter is reading dc.embargo.terms
> for the date rather than dc.embargo.liftdate.
> 
> I've check our dspace.cfg file and there does not seem to be a mix-up.
> Nor is there a mix-up on the submission form.
> 
> Perhaps I don't understand what these fields are for? What is
> dc.embargo.terms supposed to do?
> 
> Richard
> 
> _
> From: Jizba, Richard 
> Sent: Wednesday, May 05, 2010 4:05 PM
> To: 'dspace-tech@lists.sourceforge.net'
> Subject: Embargo error on Approval
> 
> 
> Hello,
> 
> We we try to approve an item that has been submitted with an embargo
> date (in dc.embargo.liftdate) we receive the following error:
> 
> java.lang.NullPointerException
>   at
> org.dspace.embargo.EmbargoManager.getEmbargoDate(EmbargoManager.java:166
> )
> 
> Can anyone suggest how to resolve this?
> 
> We are running 1.6.
> 
> Richard Jizba
> Creighton University
> Omaha, NE
> 
> -- next part --
> An HTML attachment was scrubbed...
> 
> --
> 
> Message: 3
> Date: Thu, 6 May 2010 00:27:58 +0200
> From: Hilton Gibson 
> Subject: Re: [Dspace-tech] More re: Embargo error on Approval
> To: "Jizba, Richard" 
> Cc: dspace-tech@lists.sourceforge.net
> Message-ID:
>   
> Content-Type: text/plain; charset="utf-8"
> 
> On 6 May 2010 00:02, Jizba, Richard  wrote:
> 
> >  I finally realized that the Embargo Setter is reading dc.embargo.terms
> > for the date rather than dc.embargo.liftdate.
> >
> > I?ve check our dspace.cfg file and there does not seem to be a mix-up. Nor
> > is there a mix-up on the submission form.
> >
> > Perhaps I don?t understand what these fields are for? What is
> > dc.embargo.terms supposed to do?
> >
> > Richard
> >
> This is my take on it: http://ir.sun.ac.za/wiki/index.php/Asset_Embargo
>  
> 
> >  _
> > *From:* Jizba, Richard
> > *Sent:* Wednesday, May 05, 2010 4:05 PM
> > *To:* 'dspace-tech@lists.sourceforge.net'
> > *Subject:* Embargo error on Approval
> >
> > Hello,
> >
> > We we try to approve an item that has been submitted with an embargo date
> > (in dc.embargo.liftdate) we receive the followi

Re: [Dspace-tech] Change DSpace retrospective policy

[Lewatle Phaladi]

Hi Claudia

Thanks for the respond.
I checked on DSpace interface but I don't see advanced authorization 
management, could you please give me example path that I can use to reach that?

Regards,
Lewatle  

-Original Message-
From: Claudia Jürgen [mailto:claudia.juer...@ub.tu-dortmund.de] 
Sent: 06 May 2010 08:56 AM
To: dspace-tech@lists.sourceforge.net
Subject: Re: [Dspace-tech] Change DSpace retrospective policy

Hello Lewatle,

changing the DEFAULT_ITEM_READ and/or DEFAULT_BITSTREAM_READ for a collection 
will only affect newly ingested items.

In order to change authorizations for existing items you got to use the 
advanced authorization management in the dspace admin section.

Claudia Jürgen


Am 06.05.2010 08:42, schrieb Lewatle Phaladi:
> Hi All
>
>
>
> We had a closed policy to our items in DSpace to one community and its 
> collections and if I change the authorizations rules to allow 
> anonymous read it also prevents me from reading the item without 
> logging in and it also prevents some users that were not allowed to 
> view the item previously. I can only view files as anonymous for those 
> that I have created recently, but all previously loaded files I can't 
> read them as anonymous.
>
>
>
> Assistance will be appreciated as always.
>
>
>
> Regards,
>
> Lewatle
>
>
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