Re: [dspace-tech] StartSubmissionLookupStep

[emilio lorenzo]

Hi

In XMLUI exists the functionality of importing items via online services 
as Crossref https://wiki.duraspace.org/pages/viewpage.action?pageId=68064788


You can provide a DOI in the first step of submissions and the metadata 
is retrieved from Crossref.  Similar services with pubmed or other 
online services...


BEst



El 20/03/2019 a las 3:19, Gary Browne escribió:


Hi all,

Currently on JSPUI DSpace 4, soon to be on XMLUI DSpace 6.

We are interested in the DOI lookup facility for submissions. There is 
this statement in the documentation ( 
https://wiki.duraspace.org/display/DSDOC6x/Submission+User+Interface#SubmissionUserInterface-ConfiguringStartSubmissionLookupStep 
):


*UI compatibility*

The new step is available *only for JSP UI*. Nonetheless, if you run 
both UIs and want the JSP UI benefit of the new step you can configure 
it as processing class also for XML as it degrades gracefully to the 
standard SelectCollectionStep logic


Am I right in concluding that this functionality is only available for 
JSPUI? If so, is there anything similar for the XMLUI?


Thanks,
Gary

Gary Browne | Technical Manager, Developments
Online Services
University of Sydney Library
THE UNIVERSITY OF SYDNEY
Level 1, Fisher Library F03, The University of Sydney NSW 2006
T +61 2 9351 5946 | M +61 405 647 868
E gary.bro...@sydney.edu.au 



The University of Sydney Camperdown campus stands on land of the 
Gadigal peoples of the Eora nation.


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<>

[dspace-tech] StartSubmissionLookupStep

[Gary Browne]

Hi all,

Currently on JSPUI DSpace 4, soon to be on XMLUI DSpace 6.

We are interested in the DOI lookup facility for submissions. There is this 
statement in the documentation ( 
https://wiki.duraspace.org/display/DSDOC6x/Submission+User+Interface#SubmissionUserInterface-ConfiguringStartSubmissionLookupStep
 ):


UI compatibility

The new step is available only for JSP UI. Nonetheless, if you run both UIs and 
want the JSP UI benefit of the new step you can configure it as processing 
class also for XML as it degrades gracefully to the standard 
SelectCollectionStep logic

Am I right in concluding that this functionality is only available for JSPUI? 
If so, is there anything similar for the XMLUI?

Thanks,
Gary



Gary Browne | Technical Manager, Developments
Online Services
University of Sydney Library
THE UNIVERSITY OF SYDNEY
Level 1, Fisher Library F03, The University of Sydney NSW 2006
T +61 2 9351 5946 | M +61 405 647 868
E 
gary.bro...@sydney.edu.au
The University of Sydney Camperdown campus stands on land of the Gadigal 
peoples of the Eora nation.

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Re: [dspace-tech] dspace after fresh_install error

[Tim Donohue]

Hello Paulo,

Unfortunately, there's no enough information in this message to provide you
help.  It sounds like it might be a Tomcat issue (if you are using Tomcat),
or perhaps even a local firewall issue.

You may want to look closer at your DSpace and Tomcat logs to see if more
information is provided there. Here's a guide for finding errors in logs:
https://wiki.duraspace.org/display/DSPACE/Troubleshoot+an+error

If you find a more descriptive error in your logs and cannot figure it out,
feel free to send it to this list (along with the version of DSpace you are
running, and the version of Tomcat, and Java).

Tim

On Tue, Mar 19, 2019 at 1:08 PM Paulo Jobim  wrote:

> I am getting an error after fresh_install on a linux server
> when I try to access xmlii on the site I get:
> The origin server did not find a current representation for the target
> resource or is not willing to disclose that one exists.
> thanks
>
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-- 

Tim Donohue
Technical Lead for DSpace & DSpaceDirect
DuraSpace.org | DSpace.org | DSpaceDirect.org

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Re: [dspace-tech] Re: Strategies for granting anonymous, uni-affiliated users access to the submission form via Shibboleth

[Tim Donohue]

Hi Gabe,

The pieces you'd need on the DSpace-side seem do-able (assuming I'm
understanding your use case properly)

First, you'd need to setup DSpace to use Shibboleth:
https://wiki.duraspace.org/display/DSDOC6x/Authentication+Plugins#AuthenticationPlugins-ShibbolethAuthentication


Second, you'd need to ensure that there's a DSpace Group that all (or some)
of you Shibboleth users are being "mapped" into. You'd need to setup some
form of "Role Based Groups".  They are described in the documentation
above, and the configuration is in this section of the
"authentication-shibboleth.cfg" file:
https://github.com/DSpace/DSpace/blob/dspace-6_x/dspace/config/modules/authentication-shibboleth.cfg#L149

So, for example, using Role Based Groups, you can configure DSpace to look
for anyone who logs into Shibboleth *and* is a member of the "Faculty"
Shibboleth group to be automatically added into a DSpace group named
"Faculty-members" (this group can be named anything).

Once you have all of the above setup, then anyone who logs into DSpace via
Shibboleth should automatically be added to a specific group (only for the
remainder of their logged in session).

Third, you'd add that DSpace group (e.g. "Faculty-members") as a Submitter
rights to a specific Collection in your DSpace.

At this point, you'd likely want to perform some tests. Have a user (who is
a member of the Shibboleth group you mapped) login, and see if they
immediately have submit rights to that Collection.
If they do, then, you just need to provide a direct link to the Submission
form for that Collection (which should be the Collection URL with "/submit"
appended on the end).

In the end, the process should look something like this:
1) User clicks on the Collection submit link, which should look like
https://[url-to-dspace]/handle/[collection-handle]/submit
2) User will be prompted to login via Shibboleth.
3) After logging in, the user will be sent into the submission process for
that Collection in DSpace.
4) If the user cancels the submission, or walks away, they may have to log
back into DSpace (again with their Shibboleth login) to restart the
submission.  But, otherwise, this process should work.

Hopefully that gives you some clues on how to proceed. If you need more
ideas or run into problems, let us know on this list.

Tim


On Tue, Mar 19, 2019 at 9:23 AM  wrote:

> Does anyone have any leads on this?
>
> On Wednesday, March 6, 2019 at 4:18:00 PM UTC-5, tuf0...@temple.edu wrote:
>>
>> Group-
>>
>> At my University we'd like to take users directly from a Shibboleth
>> authentication screen to the first page of the Submission User Interface
>> (pictured in screenshot).  We'd also like to, if possible:
>>
>> --Do this for three separate submission forms, one leading to a 'data'
>> community, one for an 'articles' community, and a third for an 'ETD'
>> community.
>> --Be able to put a 'Submit to our IR!' link on outside webpages.  This
>> will take users to a Shib authentication page, then directly to the
>> Submission user interface
>>
>> What are some workable strategies for doing all this?  Thank you so much
>> for your help!!
>>
>> In other words, we want them to go directly from the Shib login screen to
>> here:
>>
>> [image: Screen Shot 2019-03-06 at 4.10.41 PM.png]
>> Thanks!
>> -Gabe
>>
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-- 

Tim Donohue
Technical Lead for DSpace & DSpaceDirect
DuraSpace.org | DSpace.org | DSpaceDirect.org

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Re: [dspace-tech] DSpace 4 error when select submit item from user profile action "Start a New Submission"

[Tim Donohue]

Hello,

Unfortunately, there's not enough information provided about the error to
give an accurate answer.  I'd recommend looking at your DSpace logs to
locate the full error stack, as it will likely detail exactly *which*
document or object is "Not Found".  The error message you saw from the user
interface doesn't provide that information by default.

Here's a guide for finding errors in logs:
https://wiki.duraspace.org/display/DSPACE/Troubleshoot+an+error

Once you find the error, send the error stack to this mailing list, and
hopefully someone here can help you.

Tim

On Mon, Mar 18, 2019 at 3:53 AM  wrote:

> I added this configuration in Dspace 4 to send me directly to the
> submission form when I select to send Item within a collection:
> item-submission.xml:
>
> 
> 
>
>
> 
>
>
> 
>  "traditional" />
> 
>
>
> 
>
> 
>  
> org.dspace.submit.step.SelectCollectionStep
> 
> 
> org.dspace.app.webui.submit.step.JSPSelectCollectionStep
> 
> org.dspace.app.xmlui.aspect.submission.submit.SelectCollectionStep
> 
> false
> 
>
>
> 
> 
>
>
> 
> submit.progressbar.complete
> org.dspace.submit.step.CompleteStep
> 
> 
> org.dspace.app.webui.submit.step.JSPCompleteStep
> false
> 
>
>
> 
> 
> Sample
> org.dspace.submit.step.SampleStep
> 
> org.dspace.app.webui.submit.step.JSPSampleStep
> 
> true
> 
> 
>
>
> 
>
>
> 
> 
>
>
> 
> 
>
>
> 
> 
> 
> org.dspace.submit.step.SkipInitialQuestionsStep
> 
>
>
> 
>
>
> 
> 
> 
> submit.progressbar.describe
> org.dspace.submit.step.DescribeStep
> 
> 
> org.dspace.app.webui.submit.step.JSPDescribeStep
> 
> org.dspace.app.xmlui.aspect.submission.submit.DescribeStep
> true
> 
>
>
> 
>
>
> 
> 
> submit.progressbar.upload
> org.dspace.submit.step.UploadStep
> 
> 
> org.dspace.app.webui.submit.step.JSPUploadStep
> 
> org.dspace.app.xmlui.aspect.submission.submit.UploadStep
> true
> 
>
>
>
>
> 
>
>
> 
> 
>
>
> 
> 
> 
>
>
> 
> 
>
> 
>
>
> 
>
>
> 
>
> When i try to submit a Item within a collection works good, open the
> submit form and send the item to the correct collection. But when i go to
> my profile "My Dspace" page and click in the button "Start a New
> Submission" it gives me the error:
>
> [image: 2019-03-15-154024_1920x1080_scrot.png]
>
> Any ideas? Thanks in advance 
>
> --
> All messages to this mailing list should adhere to the DuraSpace Code of
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-- 

Tim Donohue
Technical Lead for DSpace & DSpaceDirect
DuraSpace.org | DSpace.org | DSpaceDirect.org

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Re: [dspace-tech] Problem with filter-media script.

[Kev Evans]

Thanks, 

I'll look into it. In the meantime the script used over 99% CPU and crashed the 
site.

 I have increased memory to over 4gb so I can't see where the problem is caused.

Kev

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[dspace-tech] dspace after fresh_install error

[Paulo Jobim]

I am getting an error after fresh_install on a linux server
when I try to access xmlii on the site I get:
The origin server did not find a current representation for the target 
resource or is not willing to disclose that one exists.
thanks

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[dspace-tech] dc.dc.description.abstract not being exported/imported in OAI-

[Admire Mutsikiwa]

I have created a collection that harvest harvests its content from an 
external source and it harvest only metadata. I have discovered that it is 
not harvesting the abstract,dc.dc.description.abstract . I want the 
abstract to be harvested. Either it is not being exported, I do not have an 
idear. The following dc metadata fields are being harvested. ( I have 
removed the actual values for the metadata
c.creator 

dc.date 2018-09-19T07:18:25Z 
dc.date 2018-09-19T07:18:25Z 
dc.date 1963-01 
dc.date.accessioned 2019-03-19T15:58:22Z 
dc.date.available 2019-03-19T15:58:22Z 
dc.identifier 

dc.identifier http://hdl.handle.net/10646/3648 
dc.identifier.uri 

dc.description.provenance Made available in DSpace on 2019-03-19T15:58:22Z 
(GMT). No. of bitstreams: 0 en 
dc.description.provenance Item created via OAI harvest from source: 
http://ir.uz.ac.zw/oai/request on 2019-03-19T15:58:22Z (GMT). Item's OAI 
Record identifier: oai:ir.uz.ac.zw:10646/3648 en 
dc.language en_ZW 
dc.publisher 

dc.subject 

dc.subject 

dc.subject 

dc.title 

dc.type

I will appreciate any pointers
Article   


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[dspace-tech] CNRI Handle not resolving

[Admire Mutsikiwa]

Hi 
My CNRI handle is not resolving.  A netstat -tnlp is giving 
tcp0  0 127.0.0.1:8005  0.0.0.0:*   
LISTEN  2408/java   
tcp0  0 0.0.0.0:80  0.0.0.0:*   
LISTEN  2408/java   
tcp6   0  0 10.12.1.13:8000 :::*
LISTEN  3977/java   
tcp6   0  0 10.12.1.13:2641 :::*
LISTEN  3977/java 

I can access http://ir.uz.ac.zw:8000 and when I put in a handle e.g  
10646/3515, it is resolving. I can also telnet port  2641 on my server 
ir.uz.ac.zw from  https://www.adminkit.net/telnet.aspx, which means the 
port is open. However, if I attempt to access 
http://hdl.handle.net/10646/3515, it is giving me an error, 
on accessing the  $HOME/handle-server/error.log. I am been greeted with 

"2019/03/19 07:16:44 CAT" 25 Started new run.
Saving global values to: /home/dspace/.handle/root_info
"2019/03/19 07:16:45 CAT" 50 unspecified max_handlers count, using default: 
200
"2019/03/19 07:16:45 CAT" 50 unspecified max_handlers count, using default: 
200
"2019/03/19 07:16:45 CAT" 50 unspecified max_handlers count, using default: 
200
"2019/03/19 07:22:36 CAT" 75 class net.handle.server.HdlTcpRequestHandler: 
Exception processing request: HandleException (INTERNAL_ERROR) Unknown 
opCode in message: 0


Any pointers will be greatly appreciated.


Regards,

Admire Mutsikiwa

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Re: [dspace-tech] Problem with filter-media script.

[MALMQUIST Hrafn]

Hi Kev


There have been issues with the "old" Wordfilter and PoiWordfilter is set to 
replace it.

see: https://github.com/DSpace/DSpace/pull/2266



Alternatively you can skip items by listing item handle/s in the command, after 
the -s option. I.e.


./dspace filter-media -s 10023/597, 10023/594


Hrafn


From: dspace-tech@googlegroups.com  on behalf of 
Kev Evans 
Sent: 19 March 2019 15:37:41
To: DSpace Technical Support
Subject: [dspace-tech] Problem with filter-media script.

Hi,

I am having continuing problems with the /bin scripts in particular 
filter-media.

I have just put a DSpace 6.3 XMLUI Repository into production. Prior to go live 
this script would run without problem with the snapshot of data in the Postgres 
DB.

I have turned off all ImageMajick filters and relying in the original filters. 
I have also deleted the cocoon cache files too.

It repeatedly hangs on one particular file. Is it possible to skip this file or 
force the script to run.

Help Please

Kevin





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The University of Edinburgh is a charitable body, registered in Scotland, with 
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[dspace-tech] Re: Solr lock obtained timeout

[Mark H. Wood]

On Tuesday, March 19, 2019 at 11:35:47 AM UTC-4, Alan Orth wrote:
>
> Dear list,
>
> In the last few months we've been having issues with Solr throwing "Error 
> creating core" errors one out of every two times we start Tomcat. This 
> results in our statistics from previous years being inaccessible. For 
> example, from the Solr log yesterday:
>
> 2019-03-18 12:32:39,799 ERROR org.apache.solr.core.CoreContainer @ Error 
> creating core [statistics-2018]: Error opening new searcher 
> ... 
> Caused by: org.apache.solr.common.SolrException: Error opening new 
> searcher 
> at 
> org.apache.solr.core.SolrCore.openNewSearcher(SolrCore.java:1565) 
> at org.apache.solr.core.SolrCore.getSearcher(SolrCore.java:1677) 
> at org.apache.solr.core.SolrCore.(SolrCore.java:845) 
> ... 31 more 
> Caused by: org.apache.lucene.store.LockObtainFailedException: Lock obtain 
> timed out: NativeFSLock@/dspace/solr/statistics-2018/data/index/write.lock
>
> Some old Stack Overflow posts recommend setting Solr's address space to 
> unlimited (ulimit -v unlimited), but the issue still occurs seemingly 
> randomly for us.
>


I think that raising ulimit would only help if Tomcat's JVM memory settings 
add up to more than the OS was configured to give the process.  Those 
recommendations may have been for stand-alone Solr running in its own Jetty 
instance.

 

> Now I usually just try to restart Tomcat again, or sometimes I shut it 
> down cleanly, delete all the Solr write locks, and then start Tomcat back 
> up. It's starting to feel a bit superstitious... maybe I should try to kill 
> a chicken.
>
 

> We are running DSpace 5.8 with Tomcat 7.0.93 on Ubuntu 16.04. We upgraded 
> from DSpace 5.5 in late 2018 and 2019 was the first year that the yearly 
> stats-util sharding completed successfully (fixed in DSpace 5.7). I believe 
> our problems are related to the existence of these shards. It feels like 
> there is some kind of *race condition* because it only every so often and 
> it's not always the same core that Solr is refusing to create. Sometimes 
> it's statistics-2018, statistics-2015, etc.
>


So, sometimes Solr doesn't remove all of its locks when shut down.  Does it 
log ([DSpace]log/solr*.log) anything interesting at shutdown? does Tomcat?

 

> On this note, is there any reason we are still using Solr 4.10.2 with 
> DSpace 5.x and 6.x? The Solr project issued two bug fix releases in that 
> series—4.10.3 and 4.10.4—and there are about fifty bug fixes in those 
> releases, some of which address memory leaks and shard handling. See the 
> change logs for 4.10.3¹ and 4.10.4². As an experiment I just bumped the 
> version to 4.10.3 in my test environment and DSpace starts up... so that's 
> a good sign. I will do more testing of ingests, indexing, etc and report 
> back.
>
>

I think the reason is that nobody went looking for newer releases.  Your 
experiment is definitely worth trying, and your results will be interesting.

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[dspace-tech] Problem with filter-media script.

[Kev Evans]

Hi, 

I am having continuing problems with the /bin scripts in particular 
filter-media. 

I have just put a DSpace 6.3 XMLUI Repository into production. Prior to go 
live this script would run without problem with the snapshot of data in the 
Postgres DB.

I have turned off all ImageMajick filters and relying in the original 
filters. I have also deleted the cocoon cache files too. 

It repeatedly hangs on one particular file. Is it possible to skip this 
file or force the script to run.

Help Please

Kevin




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[dspace-tech] Solr lock obtained timeout

[Alan Orth]

Dear list,

In the last few months we've been having issues with Solr throwing "Error
creating core" errors one out of every two times we start Tomcat. This
results in our statistics from previous years being inaccessible. For
example, from the Solr log yesterday:

2019-03-18 12:32:39,799 ERROR org.apache.solr.core.CoreContainer @ Error
creating core [statistics-2018]: Error opening new searcher
...
Caused by: org.apache.solr.common.SolrException: Error opening new searcher
at
org.apache.solr.core.SolrCore.openNewSearcher(SolrCore.java:1565)
at org.apache.solr.core.SolrCore.getSearcher(SolrCore.java:1677)
at org.apache.solr.core.SolrCore.(SolrCore.java:845)
... 31 more
Caused by: org.apache.lucene.store.LockObtainFailedException: Lock obtain
timed out: NativeFSLock@/dspace/solr/statistics-2018/data/index/write.lock

Some old Stack Overflow posts recommend setting Solr's address space to
unlimited (ulimit -v unlimited), but the issue still occurs seemingly
randomly for us. Now I usually just try to restart Tomcat again, or
sometimes I shut it down cleanly, delete all the Solr write locks, and then
start Tomcat back up. It's starting to feel a bit superstitious... maybe I
should try to kill a chicken.

We are running DSpace 5.8 with Tomcat 7.0.93 on Ubuntu 16.04. We upgraded
from DSpace 5.5 in late 2018 and 2019 was the first year that the yearly
stats-util sharding completed successfully (fixed in DSpace 5.7). I believe
our problems are related to the existence of these shards. It feels like
there is some kind of *race condition* because it only every so often and
it's not always the same core that Solr is refusing to create. Sometimes
it's statistics-2018, statistics-2015, etc.

On this note, is there any reason we are still using Solr 4.10.2 with
DSpace 5.x and 6.x? The Solr project issued two bug fix releases in that
series—4.10.3 and 4.10.4—and there are about fifty bug fixes in those
releases, some of which address memory leaks and shard handling. See the
change logs for 4.10.3¹ and 4.10.4². As an experiment I just bumped the
version to 4.10.3 in my test environment and DSpace starts up... so that's
a good sign. I will do more testing of ingests, indexing, etc and report
back.

Thank you and regards,

¹ https://archive.apache.org/dist/lucene/solr/4.10.3/changes/Changes.html
² https://archive.apache.org/dist/lucene/solr/4.10.4/changes/Changes.html
-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch
"In heaven all the interesting people are missing." ―Friedrich Nietzsche

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Re: [dspace-tech] Re: How to update the Solr index

[Mark H. Wood]

On Monday, March 18, 2019 at 2:34:45 PM UTC-4, Terry Brady wrote:
>
> The index-discovery command updates the "search" repository in Solr.  It 
> does not update the "statistics" repo.
>
> For efficiency purposes, there is a commit delay for statistics records.  
> The usage statistics are not real time.  There is a delay of a few minutes 
> before the results are visible.
>
> On Mon, Mar 18, 2019 at 8:54 AM Ashim Kapoor  
> wrote:
>
>> Hi,
>>
>> Can someone please answer my query?
>>
>> Best,
>> Ashim
>>
>>
>> On Mon, 18 Mar 2019 at 16:02, Ashim Kapoor  
>> wrote:
>>
>>> Hello,
>>>
>>> Simply after waiting for some time the new query it shows up in the 
>>> Statistics.
>>>
>>> May I ask, is there a delay between doing index-discovery and the 
>>> corresponding display  of new search terms in the XMLUI ?
>>>
>>> Best,
>>> Ashim
>>>
>>> On Mon, 18 Mar 2019 at 15:37, Ashim Kapoor  
>>> wrote:
>>>
 Dear all,

 I have installed the solr webapp for DSPACE 6 on Debian 9.  I did some 
 searches in XMLUI  and then I did [dspace]/bin/dspace index-discovery and 
 I 
 could see statistics for queries made by me by clicking on View Search 
 Statistics( after logging in to XMLUI )  .

 After this I did some new queries and again I did [dspace]/bin/dspace 
 index-discovery. But this time my new queries are not being reflected in 
 the statistics.

 Can someone please help me? 

>>>
>

Coincidentally, there has been very recent discussion of changing this 
time-out, and of what sort of interval would be best.  To commit every view 
event instantly would probably be excessive at a busy site, creating a good 
deal of load on Solr.  But some have questioned whether the current 
15-minute interval is too long.  Prompt updating of usage statistics is 
probably a bigger issue for those who develop, test, and run DSpace than 
for the typical user, but there may be a better trade-off point.

The time-out is set in [DSpace]solr/statistics/conf/solrconfig.xml.  Look 
for   The current setting is 900 000 
milliseconds.  You could try setting a lower value and restarting Solr.  Of 
course I recommend trying this on a test instance first.  I have no 
experience from which to suggest any particular value.

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[dspace-tech] Re: Strategies for granting anonymous, uni-affiliated users access to the submission form via Shibboleth

[tuf04742]

Does anyone have any leads on this?  

On Wednesday, March 6, 2019 at 4:18:00 PM UTC-5, tuf0...@temple.edu wrote:
>
> Group-  
>
> At my University we'd like to take users directly from a Shibboleth 
> authentication screen to the first page of the Submission User Interface 
> (pictured in screenshot).  We'd also like to, if possible:
>
> --Do this for three separate submission forms, one leading to a 'data' 
> community, one for an 'articles' community, and a third for an 'ETD' 
> community.  
> --Be able to put a 'Submit to our IR!' link on outside webpages.  This 
> will take users to a Shib authentication page, then directly to the 
> Submission user interface
>
> What are some workable strategies for doing all this?  Thank you so much 
> for your help!!
>
> In other words, we want them to go directly from the Shib login screen to 
> here:  
>
> [image: Screen Shot 2019-03-06 at 4.10.41 PM.png]
> Thanks!
> -Gabe
>

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