[dspace-tech] Dspace-CRIS Deduplication: the merge tool error

[Yen-Tang Chen]

Dear all

I test to Deduplication function in the Dspace-CRIS-5.6.1 that I start two 
same submission. 
I use Compare function => error
(Deduplicationt_he merge tool.png)
(Deduplicationt_he merge tool_001.png)

I don't know what the problem is error
I'm missing a step?


dspace.log message

2016-12-09 10:35:01,275 WARN  
org.dspace.app.webui.servlet.InternalErrorServlet @ 
:session_id=C848406B638AC7632F36A10836B1E809:internal_error:-- URL Was: 
http://140.112.113.49:8080/jspui/tools/duplicate
-- Method: POST
-- Parameters were:
-- mergeByUser: "false"
-- submittargetchoice: "Compare"
-- itemstomerge: "62"
-- target: "61"
-- rule: "0"
-- scope: "0"
-- signatureType: "null"

java.lang.ArrayIndexOutOfBoundsException: 3
at 
org.dspace.content.DSpaceObject.getMetadataByMetadataString(DSpaceObject.java:635)
at 
org.dspace.content.DSpaceObject.getMetadataValueInDCFormat(DSpaceObject.java:1403)
at 
org.dspace.content.DSpaceObject$$FastClassByCGLIB$$5da9b798.invoke()
at net.sf.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204)
at 
org.springframework.aop.framework.Cglib2AopProxy$CglibMethodInvocation.invokeJoinpoint(Cglib2AopProxy.java:689)
at 
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at 
org.dspace.app.cris.integration.CrisItemWrapper.invoke(CrisItemWrapper.java:107)
at 
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at 
org.springframework.aop.framework.Cglib2AopProxy$DynamicAdvisedInterceptor.intercept(Cglib2AopProxy.java:622)
at 
org.dspace.content.Item$$EnhancerByCGLIB$$d63e1dbd.getMetadataValueInDCFormat()
at 
org.dspace.app.webui.cris.servlet.DuplicateCheckerServlet.loadTarget(DuplicateCheckerServlet.java:891)
at 
org.dspace.app.webui.cris.servlet.DuplicateCheckerServlet.doDSPost(DuplicateCheckerServlet.java:520)
at 
org.dspace.app.webui.servlet.DSpaceServlet.processRequest(DSpaceServlet.java:115)
at 
org.dspace.app.webui.servlet.DSpaceServlet.doPost(DSpaceServlet.java:73)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:648)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:292)
at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
at 
org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240)
at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
at 
org.dspace.app.webui.filter.RegisteredOnlyFilter.doFilter(RegisteredOnlyFilter.java:66)
at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240)
at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
at 
org.dspace.utils.servlet.DSpaceWebappServletFilter.doFilter(DSpaceWebappServletFilter.java:78)
at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240)
at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
at 
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:212)
at 
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106)
at 
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
at 
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:141)
at 
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)
at 
org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:616)
at 
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88)
at 
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:528)
at 
org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1100)
at 
org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:687)
at 
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1520)
at 
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1476)
at 
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at 
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at 
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:745)




Sincerely yours, Yen-Tang Chen

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[dspace-tech] Re: Running Jetty as different user, problems uploading file

[David Brian Holt]

OK, I changed the user that runs Jetty (by editing the jetty script in the 
init.d directory and changing the JETTY_USER to "postgres", the same user I 
created when I installed).  Now I'm getting a different error when I upload.




Any suggestions?

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[dspace-tech] xmlui.bitstream.mods / xmlui.bitstream.mets

[Terry Brady]

Re-posting with a meaningful subject line

On Thursday, December 8, 2016 at 1:17:55 PM UTC-8, Terry Brady wrote:
>
> The XMLUI Configuration Reference Page on the Wiki 
> 
>  mentions 
> 2 settings.
>
>- xmlui.bitstream.mods
>- xmlui.bitstream.mets
>
> How does a DSpace instance behave when these settings are in use?
>
> Do you know of examples where these settings are active?
>
> Thanks, Terry
>
> -- 
> Terry Brady
> Applications Programmer Analyst
> Georgetown University Library Information Technology
> http://georgetown-university-libraries.github.io/ 
> 
> 425-298-5498 (Seattle, WA)
>

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[dspace-tech] Re: the dspce is not running

[Null Null]

help me?

18 Kasım 2016 Cuma 16:44:08 UTC+3 tarihinde Null Null yazdı:
>
> hi.
> I did the installation. I did not get any errors. The anchors are not 
> working now. 
>
> error
>
> FAIL - Application at context path /jspui could not be started
>
>  
> 
>
> FAIL - Application at context path /xmlui could not be started
>
>

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Re: [dspace-tech] Git Rebase Issue

[Terry Brady]

Ivan,

Thanks for the instructions.  I have added them to my git cheat sheet.

I am not sure why my original rebase created this error.  I am glad to see
that I was able to repair 3 of my 4 branches.

I concur with Hardy that it could be useful to have a set of useful git
recipes on the DSpace wiki.

Terry

On Thu, Dec 8, 2016 at 6:02 AM, Hardy Pottinger 
wrote:

> Helix84, that is a fantastic write-up! Would you consider adding a version
> of it to the DSpace wiki in the section about how to use Git? I have always
> wondered what might have happened when I have seen thousands of commits not
> my own show up in a pull request. So far the only thing I've found to work
> in this situation is to "take a Mulligan" and re-do the branch (either
> manually, or via a "cherry-pluck" (warning, not an actual command, just a
> descriptive word, coined by Peter Dietz). This poster [1] has been helpful
> to me. But, I feel better knowing that someone can explain what *probably*
> went wrong, and that there *are* commands you can run to *put it right*
> without resorting to the Mulligan.
>
> Thanks!
>
> --Hardy
>
> [1] http://justinhileman.info/article/git-pretty/git-pretty.pdf
>
> On Thu, Dec 8, 2016 at 3:03 AM, helix84  wrote:
>
>> The last command should have been just:
>>
>> git push terrywbrady ds3282 --force
>>
>>
>> Regards,
>> ~~helix84
>>
>> Compulsory reading: DSpace Mailing List Etiquette
>> https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
>>
>> --
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>>
>
>


-- 
Terry Brady
Applications Programmer Analyst
Georgetown University Library Information Technology
http://georgetown-university-libraries.github.io/

425-298-5498 (Seattle, WA)

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[dspace-tech] Re: [dspace-community] Mirage 2 not working after upgrading to DSpace 6.0

[Pedro Amorim]

Hello Yongming,

Check this topic on DSpace Tech:
https://groups.google.com/forum/#!searchin/dspace-tech/pedro$20amorim%7Csort:relevance/dspace-tech/2qQvNL2KOB8/0HxajN6zAQAJ

You should use maven 3.3.9.
Also, check the build process on the Mirage 2 Local Customizations
component, the overall DSpace build might be successfull but actually fail
at Mirage 2. In my case, bower wasnt being installed correctly and Î had to
create the directories manually.

Good luck,

Pedro Amorim

2016-12-08 13:52 GMT-01:00 Wang, Yongming :

> Dear all,
>
> I have just upgraded our DSpace 5.1 to 6.0.
>
> In DSpace 5.1 we used jspui. In 6.1 we decide to use xmlui.  I followed
> the upgrade/install instruction to include and enable Mirage 2 by the
> following steps:
>
> 1. edit /local/home/dspace/dspace-6.0-release/dspace/config/xmlui.xconf
> change
> 
> to
> 
>
> 2. [dspace-source]/dspace]$ mvn -U clean package -Dmirage2.on=true
>
> The build process is success without any error.
>
> But when I access the homepage of our DSpace, the Mirage 2 is obviously
> not displaying right. It looked like the template is somehow broken. And I
> saw this message on the screen:
>
> "JavaScript is disabled for your browser. Some features of this site may
> not work without it."
>
> My browser's javascript IS enabled!
>
>
> Does anyone know what the reason is and how to solve this issue?
>
>
> Thank you very much.
>
>
>
>
> Yongming
>
>
>
> --
> Yongming Wang
> Systems Librarian/Associate Professor
> The College of New Jersey
> tel: 609-771-3337 <(609)%20771-3337>
> email: wan...@tcnj.edu
>
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Re: [dspace-tech] Re: Question about DSpace code and version control of local mods

[Luiz dos Santos]

Thank you Tom!

Luiz Claudio Santos
http://luizclaudiosantos.me/

On Thu, Dec 8, 2016 at 9:11 AM, Mark Wood  wrote:

> We used to keep our local DSpace in SVN alongside a copy of stock code, to
> make it easy to keep our mod.s updated.  Some time ago we switched to git,
> and now keep local DSpace and stock in a local instance of GitHub
> Enterprise.  I find SCM tools to be much easier to work with than the
> overlay stuff.
>
> --
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Re: [dspace-tech] Question about DSpace code and version control of local mods

[George Kozak]

Thank you, everyone for your suggestions and comments!
George Kozak
Cornell University

On Wed, Dec 7, 2016 at 5:15 PM, Luiz dos Santos  wrote:

> Sure, let me reformulate my question, what is the difference between the
> build configuration in the "development version" and "release version", for
> example, I got that the configuration of the maven "license-maven-plugin"
> is different in the pom.xml is different, it makes sense, because in the
> end of the day the files are not there, in the release version, so there is
> less to check, but I wonder where else there is a difference (maybe
> assembly plugin)?
>
> Sorry George, out of topic, but I am curious about it, and I guess your
> question was already answered, right?
>
> Thanks
> Luiz Claudio Santos
> http://luizclaudiosantos.me/
>
> On Wed, Dec 7, 2016 at 4:38 PM, Tom Desair  wrote:
>
>> No you cannot just delete them. You have to start from the correct format.
>>
>> DSpace is always released under two formats: a "release-src" archive that
>> contains the full DSpace source as it can be found on Github and a
>> "release" archive that only contains the configuration files and some
>> folders where you can put Java customisations. The "release" version will
>> download the (compiled) DSpace source code at build time from Maven.
>>
>> The example repository uses this "release" version. For DSpace 6, you can
>> download that version here https://github.com/DSpace
>> /DSpace/releases/download/dspace-6.0/dspace-6.0-release.tar.gz (
>> https://github.com/DSpace/DSpace/releases/tag/dspace-6.0)
>>
>>
>> [image: logo] Tom Desair
>> 250-B Suite 3A, Lucius Gordon Drive, West Henrietta, NY 14586
>> Esperantolaan 4, Heverlee 3001, Belgium
>> www.atmire.com
>> 
>>
>>
>> 2016-12-07 21:31 GMT+01:00 Luiz dos Santos :
>>
>>> Hi Tom,
>>>
>>>   One question, the repository that you add the link there are some
>>> folders missing, such as dspace-jspui, dspace-api, dspace-oai... How did
>>> you do that? Just delete it? Do you add these as dependencies somewhere
>>> else?
>>>
>>> Thanks in advance
>>> Luiz Claudio Santos
>>> http://luizclaudiosantos.me/
>>>
>>> On Wed, Dec 7, 2016 at 3:19 PM, Tom Desair 
>>> wrote:
>>>
 Hi all,

 The general approach we use, is to download the release version of
 DSpace (note: note the src-release version) which is very small and push
 this to a Git repository. Then we save all our customisations in the
 relevant module directory. This process is described here:
 https://wiki.duraspace.org/display/DSDOC5x/Advanced+Customisation

 An open source example of a highly customised DSpace using this
 technique can be found here: https://github.com/milie
 uinfo/dspace54-atmire/tree/java-DEV

 Best regards,
 Tom


 [image: logo] Tom Desair
 250-B Suite 3A, Lucius Gordon Drive, West Henrietta, NY 14586
 Esperantolaan 4, Heverlee 3001, Belgium
 www.atmire.com
 

 2016-12-07 20:45 GMT+01:00 Alan Orth :

> Hi, George.
>
> You should absolutely be using a git-based workflow. First, git is fun
> and cool and much better in every way than CVS/SVN, but it's also the
> official version control of the DSpace project itself since about 2014
> or so. This is important for cherry-picking patches, rebasing your
> local changes on top of upstream point releases, etc.
>
> Second, GitHub is great. We forked DSpace's DSpace repository there
> and I cherry-pick commits from their branch from time to time, as well
> as rebase on their point releases as I mentioned above. Even though
> I'm basically the only technical one doing DSpace on our team, I make
> *extensive* use of GitHub other features like issues, pull requests,
> and wikis. For example, when a user reports a bug or feature, I create
> an issue to track it, then when I get time to address it I make a pull
> request to my institution's repository from my personal repository.
>
> Here's our repo, where all of our code is (~25 Mirage 2 themes, custom
> input forms, etc):
>
> https://github.com/ilri/DSpace
>
> On Wed, Dec 7, 2016 at 9:34 PM, Luiz dos Santos 
> wrote:
> > Hi,
> >
> >  We have code in github and svn. The svn is old version that
> Atmire
> > folks are updating now. Soon, it's gonna github only, most of the
> code of
> > the code is in a maven repository, as a jar files, only the local
> changes
> > and config file are in the github repository. The developers have
> their own
> > maven profile in the main pom.xml, it helps a lot.
> >
> > Luiz Claudio 

[dspace-tech] Re: SAF and Metadata Export Ordering

[Mark Wood]

It's probably ordered by whatever the DBMS finds convenient.  In that case 
it may not even be consistently ordered as items are added to a 
collection.  A relational query doesn't guarantee any particular order; the 
DBMS is free to arrange and re-arrange its own storage in 
implementation-dependent ways.  I imagine that nobody ever thought of a 
reason to pay the cost of sorting by adding ORDER BY to the query that 
produces the stream of items.

Are you asking out of sheer curiosity, or have you discovered a way in 
which the order of exports can be significant?

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[dspace-tech] Re: Question about DSpace code and version control of local mods

[Mark Wood]

We used to keep our local DSpace in SVN alongside a copy of stock code, to 
make it easy to keep our mod.s updated.  Some time ago we switched to git, 
and now keep local DSpace and stock in a local instance of GitHub 
Enterprise.  I find SCM tools to be much easier to work with than the 
overlay stuff.

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[dspace-tech] Re: Tomcat 8 versus Tomcat 7

[Mark Wood]

On my development box I'm currently using Tomcat 8.0 with 5x and 6.  We're 
still on 7.0 in production (5x) but I want to move to 8 when I can find the 
time.

The only issue I can recall is that Tomcat 8's classloader setup is much 
more finicky, and that collides with the way I like to deploy webapp.s.  I 
inject a ready-made database connection pool via JNDI, and if I'm not 
careful to delete the database driver JAR from each DSpace webapp. then 8 
will complain that it can't find the driver (because there's one in 
Tomcat's own classloader, which supplies the pool, and another in the 
webapp's classloader, and they aren't the same 'Class'es even though they 
are loaded from identical files).  I reckon that most sites won't have that 
problem.  When I have some time, I mean to create an option to leave the 
database driver JAR out of the webapps during assembly.

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Re: [dspace-tech] E-Prints to Dspace conversion (URGENT)

[Hilton Gibson]

Hi Divya,

Here are the interoperability options:
http://wiki.lib.sun.ac.za/index.php/SUNScholar/Interoperability

Cheers

hg

*Hilton Gibson*
Stellenbosch University Library
*http://orcid.org/-0002-2992-208X
*


On 8 December 2016 at 13:10, Divya Batra  wrote:

> Dear All,
>
> Dspace uses PostgreSQL for database.
>
> We were earlier using Eprints which uses MySQL database.
> We are now shifting to Dspace as document repository.
>
> I want to ask that is there any way we can convert MySQL database to
> PostgreSQL directly so that we can easily import the data as our database
> has more than 4000 records and it will be very time consuming to do
> individual data entry for all the records.
>
> Hoping for a solution.
>
> Thanks & Regards
> Divya
>
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Re: [dspace-tech] E-Prints to Dspace conversion (URGENT)

[helix84]

It doesn't work that way at all. It's apples and oranges.

Since you indicated it's urgent and you don't even know how to start,
I suggest you contact one of the commercial service providers who can
surely help you:

http://www.dspace.org/service-providers


Regards,
~~helix84

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


On Thu, Dec 8, 2016 at 12:10 PM, Divya Batra  wrote:
> Dear All,
>
> Dspace uses PostgreSQL for database.
>
> We were earlier using Eprints which uses MySQL database.
> We are now shifting to Dspace as document repository.
>
> I want to ask that is there any way we can convert MySQL database to
> PostgreSQL directly so that we can easily import the data as our database
> has more than 4000 records and it will be very time consuming to do
> individual data entry for all the records.
>
> Hoping for a solution.
>
> Thanks & Regards
> Divya
>
> --
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> "DSpace Technical Support" group.
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[dspace-tech] RE: Installing DSpace 6.0 without git : Maven build error

[Devaux Cédric]

Thanks.
(This error occured when installing DSpace 6.0 from Source Release : 
dspace-6.0-src-release.zip, I haven't tested from Binary Release : 
dspace-6.0-release.zip)

Regards,
Cedric


De : Terry Brady [mailto:tw...@georgetown.edu]
Envoyé : mercredi 7 décembre 2016 21:12
À : DSpace Technical Support
Cc : Devaux Cédric
Objet : Re: Installing DSpace 6.0 without git : Maven build error

A ticket has been created in the DSpace proejct to track this issue.

https://jira.duraspace.org/browse/DS-3418

On Monday, December 5, 2016 at 6:39:40 AM UTC-8, Devaux Cédric wrote:
Hello,

When installing DSpace 6.0 ( default theme, not Mirage 2 theme), an error has 
occurred at the step "7.Build the Installation Package : mvn clean package" 
because git is not installed  :
[ERROR] Failed to execute goal 
org.codehaus.mojo:buildnumber-maven-plugin:1.4:create (default) on project 
dspace-api: Cannot get the revision information from the scm repository :
[ERROR] Exception while executing SCM command. Error while executing command. 
Error while executing process. Cannot run program "git"

This error disappears if I remove from [dspace-source]dspace-api\pom.xml, the 
lines about buildnumber-maven-plugin (...) and the installation of 
DSpace 6.0 seems OK.
I haven't investigate the consequences of the removal.
So, Git has to be installed for Dspace 6.0  (XMLUI and JSPUI default theme) or 
buildnumber-maven-plugin has to be removed from pom?

Regards,
Cedric

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Re: [dspace-tech] Git Rebase Issue

[helix84]

The last command should have been just:

git push terrywbrady ds3282 --force


Regards,
~~helix84

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

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Re: [dspace-tech] Git Rebase Issue

[helix84]

The problem is that the same changeset is there twice (commit with the
same content). What the diff doesn't exactly show you why that is. If
you want to see that, take a look at the DAG using a tool like gitk or
gitg or what have you. You'll see that each of them is on a different
branch and when you merged them, one of them became a no-op.

There are two possible approches how to fix it (result is the same),
cherry-pick or rebase:

git checkout master
git pull upstream master

git checkout -b ds3282-new

git cherry-pick a7ffd60
git push terrywbrady ds3282-new:ds3282 --force

or

git checkout --track terrywbrady/ds3282
git rebase -i master

pick a7ffd60 Fix js error for filters with dashes
drop ecf6f42 Fix js error for filters with dashes

git push terrywbrady ds3282-new:ds3282 --force


Regards,
~~helix84

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

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Re: [dspace-tech] Embargoed bitstreams can be accessed

[Tom Desair]

Hi Gary,

This bug has been reported here https://jira.duraspace.org/browse/DS-3097
and is fixed in more recent DSpace versions.

It is important to realise that resource policies have to be defined on
item level and on bitstream level. When downloading a bitstream, only the
resource policies on the bitstream level are checked. Configuring an
embargo on item level does not automatically apply it to all bitstreams. In
this example (XMLUI) the item is embargoed but the bitstream is not:
[image: Inline afbeelding 1]

Best regards,
Tom


[image: logo] Tom Desair
250-B Suite 3A, Lucius Gordon Drive, West Henrietta, NY 14586
Esperantolaan 4, Heverlee 3001, Belgium
www.atmire.com


2016-12-08 4:54 GMT+01:00 Gary Browne :

> Hi all,
>
> Using:
>
> DSpace JSPUI v 4.1
> RHEL 6
> Tomcat 7
> Apache 2.2
>
> Bitstreams of items that are embargoed can be accessed by obtaining the
> link (either from source HTML or right-clicking the bitstream link). Is
> there something wrong with our DSpace setup or is does embargo not limit
> bitstream-level access?
>
> I tried removing all resource policies from a sample embargoed item but I
> was still able to access it.
>
> Thanks,
> Gary
>
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