Re: [dspace-tech] Customization of Dspace

[Hilton Gibson]

Hi Vishal,

I have made some notes here:
http://wiki.lib.sun.ac.za/index.php/SUNScholar/Theme

Cheers

hg

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


On 11 March 2016 at 08:59,  wrote:

> Hi friends please suggest me The Customization of Dspace how can i
> customize my Dspace box as per my institutions requirements i.e Colour,Text
> formats logo etc please provide me any link /URL/Youtube video for learning
> Customization step by step procedure
> Thanks Vishal
>
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[dspace-tech] Customization of Dspace

[vishalsaxena7786]

Hi friends please suggest me The Customization of Dspace how can i 
customize my Dspace box as per my institutions requirements i.e Colour,Text 
formats logo etc please provide me any link /URL/Youtube video for learning 
Customization step by step procedure
Thanks Vishal

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[dspace-tech] Changing message.properties in new version of Dspace 5.4 src

[Gebregewergs Teklemedhin]

Dear all 


I'm using version dspace-5.4 -src-release 

how can i edit message properties to change text in jsp

please tell me the steps and commands to edit it.

 thank you.

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[dspace-tech] Re: Importing CSV file with special characters into DSpace.

[euler]

Hi Xiping,

My suggestion is to import or upload your (cleaned-up) csv file into Google 
spreadsheets. I tested your sample data and accent marks are retained (not 
100% though). See my attached screenshot. All you have to do now is to find 
and replace all the � characters. After cleaning it up, download as CSV and 
then import it back to DSpace. Take note that once you already downloaded 
it as CSV, refrain from editing it in MS Excel because in my experience, it 
will mess up your encoding again. It may seem a tedious task but I would 
rather do it this way than start all over again.

Hope this helps.

Good luck and best regards,
euler

On Friday, March 11, 2016 at 1:18:05 AM UTC+8, Xiping Liu wrote:
>
> Hello everyone, 
>
> A few months ago we started a project of cleaning up our electronic thesis 
> and dissertation records from DSpace. We exported our data from Dspace as a 
> csv file and after the cleanup we are ready to import the data back into 
> Dspace. But we noticed that some of the names (accent marks and quotes) in 
> our data are not showing correctly (I am assuming the encoding is not set 
> correctly in the very beginning after we export). But since we have already 
> done our clean up in our file, it will be really painful to go back and re 
> export the file from Dspace (so we can set the encoding correctly this 
> time) and redo all the editing. I wonder is there any way we can correct 
> the encoding after we import the data back into Dspace? Or any suggestions 
> to solve this problem? I have attached a small sample of our data. 
>
> Your help is greatly appreicated. 
>
> Xiping 
>
>
>

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Re: [dspace-tech] Re: workflow email troubleshooting

[Luiz dos Santos]

Good catch,  thanks for share!
Em 10/03/2016 16:20, "Chris Gray"  escreveu:

> We've discovered the problem.  It has nothing to do with the particular
> generator of the email but with garbage that has gotten into the email
> field of our eperson records for some of our users.
>
> We use CAS authentication and in some cases the email is getting populated
> with x:  five 'x's and the 'n's are the eperson_id.  The email
> isn't sent because the email server balks at the improper email address.
>
> Now we just have to figure out why we're getting this garbage and only for
> some users.
>
> On Thursday, March 10, 2016 at 11:07:59 AM UTC-5, Chris Gray wrote:
>>
>> In our 5.3 instance, people are not reliably receiving email notification
>> of submission rejections.  I'm at a loss to troubleshoot this problem.
>>
>> They were working previously but stopped recently.  Our campus email is a
>> complicated beasts and we are not always notified of changes, but I need
>> evidence to go to the people in charge of the email services.
>>
>> What I would like is a log of all outgoing emails but I can't find one.
>> Is there one or is there a way to turn this on?
>>
>> Other emails are going out.  Could it be a setting for that particular
>> work flow step or a particular collection?
>>
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Re: [dspace-tech] jQuery 1.6.2

[Tim Donohue]

Hi Ilja,

Yes, we'd encourage a Pull Request if you are willing. Thanks for making 
us aware of this.


- Tim

On 3/8/2016 6:55 AM, Ilja Sidoroff wrote:
At routine system scan by our IT department noticed, that mirage theme 
uses jQuery version 1.6.2, which is vulnerable to a XSS attack [1]. I 
don't know if this actually exploitable in DSpace, but anyway it seems 
that this is fixable by simple bumping the version to 1.6.4. Is it 
worth of making a pull request to fix this?


Ilja Sidoroff
Information Specialist
University of Eastern Finland, Library

[1] CVE-2011-4969 
https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2011-4969

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

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[dspace-tech] Importing CSV file with special characters into DSpace.

[Xiping Liu]

Hello everyone, 

A few months ago we started a project of cleaning up our electronic thesis 
and dissertation records from DSpace. We exported our data from Dspace as a 
csv file and after the cleanup we are ready to import the data back into 
Dspace. But we noticed that some of the names (accent marks and quotes) in 
our data are not showing correctly (I am assuming the encoding is not set 
correctly in the very beginning after we export). But since we have already 
done our clean up in our file, it will be really painful to go back and re 
export the file from Dspace (so we can set the encoding correctly this 
time) and redo all the editing. I wonder is there any way we can correct 
the encoding after we import the data back into Dspace? Or any suggestions 
to solve this problem? I have attached a small sample of our data. 

Your help is greatly appreicated. 

Xiping 


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id,collection,dc.contributor.advisor,dc.contributor.author,dc.contributor.committeeMember,dc.title,dc.description.abstract
969,10657/2,"Gustafsson, Jan-�ke",,"Ström, Anders  M||Schwartz, Robert||Webb, Paul||Wang, Yuhong",Antiproliferative and pro-­apoptotic actions of Estrogen receptor β in prostate cancer,"High Gleason grade prostate cancers are aggressive. Currently, the major target for treatment is the androgen receptor. Recent literature points towards a tumor suppressive role of estrogen receptor β (ERβ), which has a potential to be exploited as a target for novel therapeutics used for treatment of prostate cancer. 
In Chapter 2 of the thesis, we showed that ERβ-selective agonists elicited an increase in apoptosis and this was accompanied by an increase in expression of the pro-apoptotic factor PUMA. Induction of PUMA was dependent on the presence of the transcription factor FOXO3 but was independent of p53. In the ventral prostates of ERβ-/- mice, expression of FOXO3a is lower than that in WT littermates demonstrating a relationship between ERβ and FOXO3a expression found in PC3 and LNCaP cells. Furthermore, in prostate cancers of Gleason grade 4 or higher there was a marked reduction of both ERβ and FOXO3a, while both genes were well expressed in BPH sections. 
In Chapter 3 of the thesis, we investigated whether the loss of ERβ (also called as ERβ1) and/or expression of its splice variant ERβ2 affected signaling pathways involved in proliferation and bone metastasis of prostate cancer. We found repressed expression of the bone metastasis regulator Runx2 and its target gene, Slug by ERβ1. In addition, the expression of Twist1, a factor whose expression strongly correlates with high Gleason grade prostate cancer, was increased by ERβ2. In terms of cell cycle modification, of the two receptors, ERβ1, but not ERβ2, inhibited proliferation and expression of the proliferation markers Cyclin E, c-Myc, and p45Skp2. Xenograft studies using athymic nude mice confirmed the proliferative effect of ERβ2, as tumors in mice bearing PC3-ERβ2 cells were substantially larger than tumors in mice bearing PC3-control and PC3-ERβ1 cells."
482,10657/2,"Josić , Krešimir",,"Ott, William||Török, Andrew||Dabaghian, Yuri",The Interplay of Architecture and Correlated Variability in Neuronal Networks,"This much is certain: neurons are coupled, and they exhibit covariations in their output. The extent of each does not have
a single answer. Moreover, 
the strength of neuronal
correlations, in particular, has been a subject of hot debate within the neuroscience community
over the past decade, as advancing recording techniques have made available a lot of new,
sometimes seemingly conflicting, datasets. 
The impact of connectivity and the resulting correlations on the ability of animals to perform
necessary tasks is even less well understood.
In order to answer
relevant questions in these categories, novel approaches must be developed.
This work focuses  on three somewhat distinct, but inseparably coupled,
crucial avenues of research within the broader field of computational neuroscience.
First, there is a need for tools which can be applied, both by experimentalists and theorists,
to understand how networks transform their inputs. In turn, these tools will allow neuroscientists to tease apart the structure which
underlies network activity. The Generalized Thinning and Shift framework, presented in
Chapter 4, addresses this need.
Next, taking for granted a general understanding of network
architecture as well as some grasp of the behavior of its individual units, we must be able to reverse the activity to structure relationship, and 

[dspace-tech] Solr Index Failing To Build

[Scott Renton]

Fixed- the solr indexes were building (somehow) under ...tomcat/bin/solr. 
Commenting out the dataDir line in solrconfig.xml fixed it, but no idea where 
solr.data.dir was being set to this anomalous directory.

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Re: [dspace-tech] Re: No communities for a particular user

[Sean Carte]

Thanks, Claudia.

Unfortunately it doesn't appear to be that; I doubled the maxBooleanClauses
number and still get the error.

I've also tried setting maxHttpHeaderSize="8192" in the 8080 connector in
server.xml.

I took a copy of the database and am running it on a Linux machine. The
same error is logged every time I use the problematic account, but at least
the page displays.

I don't see the error when using JSP UIs, only with XML UIs.

It does seem related to solr discovery:

2016-03-10 11:15:08,892 ERROR
org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @
[user@domain
]:session_id=E71B3E57FB1FF77F883FCB38ABB3B3D7:ip_addr=10.0.36.114:Error in
Discovery
while setting up date facet range:date facet\colon; dateIssued.year
org.dspace.discovery.SearchServiceException: Error executing query
at
org.dspace.discovery.SolrServiceImpl.search(SolrServiceImpl.java:1618)
at
org.dspace.discovery.SolrServiceImpl.search(SolrServiceImpl.java:1600)
at
org.dspace.discovery.SolrServiceImpl.search(SolrServiceImpl.java:1583)


Sean

On 8 March 2016 at 19:38, Claudia Jürgen 
wrote:

> Hi Sean,
>
> just a guess, as we are not working with the xmlui, so it might not be
> relevant, but the use case it only happening  with a single user makes
> me wonder.
>
> We had a problem with the jspui after switching to 4.2 (but it persists
> in 5.4 where we are now).
> Users belonging to a special group (used in lots of workflows etc.)
> could not browse search the system.
>
> The root cause was the Rights Access Awareness which is enabled by
> default see
>
> https://wiki.duraspace.org/display/DSPACE/TechnicalFaq#TechnicalFAQ-I%27mgetting%22SolrException:BadRequest%22followedbyalongqueryora%22tooManyClauses%22Exception
>
> Might be something similar.
>
>
>
> Claudia Jürgen
>
>
>
>
>
> Am 08.03.2016 um 17:08 schrieb Sean Carte:
>
>> On 5 March 2016 at 09:35, Sean Carte  wrote:
>>
>> When a particular user logs in, the communities and collections do not
>>> display, only up to 'Select a community to browse its collections', and
>>> the
>>> following is logged:
>>>
>>> 2016-03-05 09:12:00,219 INFO
>>> org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ facets
>>> for
>>> scope, null: 3
>>> 2016-03-05 09:12:00,235 ERROR
>>> org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @
>>> [user@domain
>>> ]:session_id=2220435AEB3B8A8F6BF39A0569AA79F2:ip_addr=::1:Error
>>> in Discovery while setting up date facet range:date facet\colon;
>>> dateIssued.year
>>> org.dspace.discovery.SearchServiceException: Error executing query
>>>  at
>>> org.dspace.discovery.SolrServiceImpl.search(SolrServiceImpl.java:1618)
>>>  at
>>> org.dspace.discovery.SolrServiceImpl.search(SolrServiceImpl.java:1600)
>>>  at
>>> org.dspace.discovery.SolrServiceImpl.search(SolrServiceImpl.java:1583)
>>>  at
>>>
>>> org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer.getQueryArgs(SidebarFacetsTransformer.java:388)
>>>  at
>>>
>>> org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer.performSearch(SidebarFacetsTransformer.java:156)
>>>  at
>>>
>>> org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer.getValidity(SidebarFacetsTransformer.java:119)
>>>  at sun.reflect.GeneratedMethodAccessor110.invoke(Unknown Source)
>>>  at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown
>>> Source)
>>>  at java.lang.reflect.Method.invoke(Unknown Source)
>>>  at
>>>
>>> org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
>>>  at com.sun.proxy.$Proxy45.getValidity(Unknown Source)
>>>  at
>>>
>>> org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.getValidityForInternalPipeline(AbstractCachingProcessingPipeline.java:987)
>>> ...
>>>
>>> Other users are not affected. That is, the communities and collections
>>> display without error.
>>>
>>> Any ideas what's going on here and what I can do to rectify it?
>>>
>>> I'm using Mirage 2 on DSpace 5.4, Tomcat 8, JDK 1.8, Postgres 9.4,
>>> Windows
>>> Server 2012
>>>
>>> Sean
>>> --
>>>
>>>
>>> No ideas?
>>
>> I've tried different XML themes, but that makes no difference. If I click
>> on any of the browse links I get the 'Invalid content type' error I've
>> copied below. If I search I get no results.
>>
>> No such problems with the anonymous user, or another login.
>>
>> I've cleared the cache; that made no difference.
>>
>> The only thing I can think of doing now is deleting and recreating the
>> user. Any better ideas?
>>
>> This is the error I mentioned above:
>> Invalid content type:
>>
>> Go to UKZN ResearchSpace home 
>>
>> Please contact the site administrator if you wish to report this error. If
>> possible, please provide details about what you were doing at the time
>> this
>> error occurred.
>>
>> Contact site