[dspace-tech] DSpace Developer Show And Tell - Meeting Video Posted + Next Session has been Scheduled

[Terry Brady]

We had a great turnout for our first DSpace Developer Show and Tell Meeting
.
15 people attended.  A video of the session is posted here:
https://youtu.be/exi-4xwUwns.

Our next meeting will be on Mar 27 from 1500-1630 UTC.

   - See
   
https://wiki.duraspace.org/display/DSPACE/Janitor+and+DSpace%2C+DSpace+Development+on+Codenvy+-+Mar+27%2C+2018+at+1500+UTC

Terry

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Terry Brady
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Georgetown University Library Information Technology
https://github.com/terrywbrady/info
425-298-5498 (Seattle, WA)

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Re: [dspace-tech] customizin dspace: delete search browse in all community

[Michael Plate]

Hi Damian,

Am 26.02.2018 um 23:57 schrieb Damian:
> 
> I'm trying to delete (or not visualize) the search engine that appears
> in all communities (in the main page of the community, not in lateral
> navigation bar, attached image to identify) I can not find the file that
> generates it. can anybody help me ? Thank you very much

assuming you use XMLUI and Mirage2 you can modify CSS or XSL...

When modifying XSL, go to the Tomcat-Webroot and then

xmlui/themes/Mirage2/xsl/core

I can't find the correct place currently, but adding this




at the top of navigation.xsl (after the  )
deletes the search bar there.

CU

Michael

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Description: S/MIME Cryptographic Signature

Re: [dspace-tech] Sherpa-romeo configuring

[Bollini Andrea]

Sherpa-Romeo appears only when you have an ISSN in the submission, do you have 
it? are you using an item metadata to store the ISSN or are you using the 
journal entity as authority?

The sherpa.xml spring file define how the issn is found in the submission item

https://github.com/4Science/DSpace/blob/dspace-5_x_x-cris/dspace/config/spring/api/sherpa.xml

the default looks for a standard item metadata but you can use this class

https://github.com/4Science/DSpace/blob/dspace-5_x_x-cris/dspace-cris/api/src/main/java/org/dspace/app/cris/sherpa/submit/CrisISSNExtractor.java

to lookup for virtual metadata (i.e. metadata of the journal entity linked by 
the item)

Hope this help,
Andrea

Il 27/02/2018 16:25, gonzalo perl ha scritto:

Hello everybody

I am trying to configuring Sherpa integration in dspace-cris jspui. I have 
uncommented the dspace.cfg line and have changed the value to true


webui.submission.sherparomeo-policy-enabled = true


and i have add my apy-key


sherpa.romeo.apikey =
#

But in the submission process, i can not see the sherpa api into dspace-cris.

¿Any idea?

Regards
Gonzalo



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[dspace-tech] Re: Problemas para generar indices

[Facundo Adorno]

¿Podrías poner el stacktrace del error completo? Gracias. 

El martes, 27 de febrero de 2018, 10:11:33 (UTC-3), Jose Miguel Ravasi 
escribió:
>
> Hola a todos
> Estoy trabajando con Dspace 6.2 y tengo algunas dificultades, si alguno me 
> puede echar una mano lo voy a agradecer.
> La configuración de mi equipo es la siguiente:
>
>- Ubuntu 16.04 LTS server
>- java 1.8.0_151
>- Tomcat 8.5.24
>- Maven 3.5.2
>- Ant 1.9.10
>- Git 2.7.4
>- Postgresql 9.5
>- Dspace 6.2
>
> Todo parece marchar bien, tengo cargados 70 items que mude desde la 
> version Dspace 4.2
>
> Digo que todo parece marchar bien pues con el servidor encendido, desde 
> una computadora en red puedo acceder ip:8080/xmlui
>
> Veo las colecciones y puedo entrar a los items logueandome con mi cuenta
>
>
> El problema es que no puedo generar los indices, (Autor, materia)
>
>
> desde la terminal del servidor ejecute ./dspace index-discovery  y me 
> devuelve error del Solr
>
>
> No logro descubrir cual es el problema.
>
> Desde ya muchas gracias
>
>
> José Miguel Ravasi
>
> Biblioteca Fac. Ingeniería
>
> Universidad Nacional de Mar del Plata
>
>
>
>
>

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Re: [dspace-tech] Re: Notes on PostgreSQL connection pooling with a Tomcat JNDI resource

[Tom Desair]

Some other useful configuration options you can use in combination with the
"removeAbandoned='true'" setting:

   - abandonWhenPercentageFull: Only start cleaning up abandoned
   connections if the pool is used for more than X %.
   - jdbcInterceptors="ResetAbandonedTimer": Make sure the "abondoned"
   timer is reset every time there is activity on a connection

https://tomcat.apache.org/tomcat-7.0-doc/jdbc-pool.html#Tomcat_JDBC_Enhanced_Attributes

@Alan, can you check if any of these indexes improves the performance of
that query:
https://github.com/DSpace/DSpace/pull/1791/files#diff-5244ef3f861b63643134797c3866e16a
?



[image: logo] Tom Desair
250-B Suite 3A, Lucius Gordon Drive, West Henrietta, NY 14586
Gaston Geenslaan 14, Leuven 3001, Belgium
www.atmire.com


2018-02-27 14:48 GMT+01:00 Alan Orth :

> Hello,
>
> *The JDBC pool parameter removeAbandoned='true' absolutely solves the idle
> in transaction issue*.
>
> However! In the past two weeks since I enabled it, I notice that we don't
> have any "idle in transaction" connections in pg_stat_activity anymore—and
> only a handful of active connections at any given time. The default timeout
> is to prune "abandoned" connections after 60 seconds, which doesn't seem to
> be a problem except on the XMLUI submissions page. One user with many
> (thousands?) of submissions says this page is very slow and experiences
> "Socket closed" errors eventually. This is presumably PostgreSQL killing
> his connection. I've tried increasing this to 90 and even 180 seconds, but
> it doesn't help. What is happening on the /submissions page?
>
> Anyways, as an experiment, this morning I turned off the
> removeAbandoned='true' setting on the JDBC pool and within a few hours
> DSpace was down and there were 200 "idle in transaction" connections again.
> *sigh* For what it's worth, pg_stat_activity shows 100 "idle in
> transaction" connections running the following query:
>
> SELECT * FROM resourcepolicy WHERE resource_type_id= $1 AND resource_id=
> $2 AND action_id= $3
>
> I'm hoping for some insight on what this query is, and about the XMLUI
> submissions page being slow! Again, we're running DSpace 5.5, PostgreSQL
> 9.5.11, and XMLUI with ~70,000 items.
>
> Thanks,
>
> On Sat, Feb 10, 2018 at 5:13 PM Alan Orth  wrote:
>
>> Tim,
>>
>> Any idea why DSpace thinks those connections are busy when PostgreSQL
>> itself reports them as idle?
>>
>> In order to try to understand the traffic that is coming in I wrote a
>> Munin plugin[0] that uses JMX to monitor the number of active sessions in
>> DSpace applications (REST doesn't appear to create sessions). From that
>> it's clear that we have quite a lot of traffic sometimes, with nearly 1500
>> active sessions sometimes (see attached)! We aggressively add bot user
>> agents to Tomcat's Crawler Session Manager Valve so all of these bots like
>> Google, Bing, and Baidu that browse from fifty IP addresses concurrently
>> get lumped into one JSESSIONID.
>>
>> In any case I've adjusted my JDBC pool parameters to include the
>> parameters removeAbandoned='true' and testOnReturn='true' in addition to
>> those Mark and I were using earlier in this thread. Things are calm on the
>> site the last few days but let's see what happens during the week. We're in
>> the process of upgrading from 5.5 to 5.8, which will include some database
>> fixes, but I'm definitely looking forward to moving our repository to
>> DSpace 6.x to take advantage of the Hibernate work.
>>
>> [0] https://github.com/ilri/rmg-ansible-public/blob/master/
>> roles/munin/files/jmx_dspace_sessions
>>
>> Cheers,
>>
>> On Thu, Feb 8, 2018 at 7:26 PM Tim Donohue 
>> wrote:
>>
>>> Hi Alan,
>>>
>>> We do occasionally find areas of DSpace that fail to properly close
>>> database connections or otherwise clean up after themselves.  So, it's not
>>> unheard of for database leaks to be found and then fixed.  Obviously
>>> though, if we were aware of a specific leak in XMLUI, we'd get it fixed.
>>>
>>> I do know that significant work at the database layer went into DSpace 6
>>> (with the move to Hibernate)... and I've heard reports (from a few folks)
>>> that these sorts of issues are less frequent in DSpace 6.x.  (As I have
>>> heard of other large sites that said they had to restart DSpace every once
>>> in a while prior to 6.x, but are not seeing the same issues with 6.x.  I've
>>> not seen this behavior myself, but it's very possible that it is
>>> encountered more with highly active and/or larger sites)
>>>
>>> That unfortunately doesn't solve the issues you are seeing though.  Is
>>> your site extremely active (in terms of concurrent users)?  Are you perhaps
>>> having a lot of bad behaving spiders that are hitting your site and
>>> possibly using up database connections?  250 connections in the pool sounds
>>> like plenty, but it obviously may be dependent on how many concurre

Re: [dspace-tech] foreignkey-constraint community2community_child_comm_id_fkey

[Tim Donohue]

Hi Stefan & All,

Thanks for logging this as a bug.  I'm not sure myself what the solution is
yet, but if others are encountering this situation and/or have found a
solution, please do let us know on the new bug ticket (that Stefan created)
at: https://jira.duraspace.org/browse/DS-3856

- Tim

On Fri, Feb 23, 2018 at 5:38 AM Stefan Fritzsche <
stefan.fritzs...@tu-dresden.de> wrote:

> Dear Members,
>
> on November 22,2017 Mr. Paul Warner already mentioned the error "dspace
> 6.1 delete community foreignkey-constraint
> community2community_child_comm_id_fkey" on this list. This error also
> occurs during our installation. Since we have implemented a lot of our
> own developments in DSpace, the behavior was examined on a new standard
> installation of version 6.3. We could observe the same restraint as on
> our adapted installation.
>
> The error occurs under the following conditions:
>   - Community has  a parent
>   - the administrator group of this community is created
>
> Mr. Paul Warner solved the problem by a manual intervention in the DB.
> Are there already other solutions for this bug?
>
> Regards,
> Stefan
>
> --
> Stefan Fritzsche
> Fachinformatiker/digitale Archivierung
>
> Technische Universität Dresden
> Zentrum für Informationsdienste und Hochleistungsrechnen
> Abt: Operative Prozesse und Systeme
> 01062 Dresden
>
> Tel.: +49 351 463-33212 <+49%20351%2046333212>
> E-Mail: stefan.fritzs...@tu-dresden.de
>
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Technical Lead for DSpace & DSpaceDirect
DuraSpace.org | DSpace.org | DSpaceDirect.org

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[dspace-tech] Sherpa-romeo configuring

[gonzalo perl]

Hello everybody

I am trying to configuring Sherpa integration in dspace-cris jspui. I have 
uncommented the dspace.cfg line and have changed the value to true


webui.submission.sherparomeo-policy-enabled = true


and i have add my apy-key


sherpa.romeo.apikey =
#

But in the submission process, i can not see the sherpa api into 
dspace-cris.

¿Any idea?

Regards
Gonzalo


 

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[dspace-tech] Fwd: Feb 27 16:00UTC-17:30UTC DSpace Developer Show and Tell - DSpace on AWS and Janitor and DSpace

[Terry Brady]

For all developers who are interested in joining, here is a reminder for
the meeting starting at 16:00UTC / 11AM ET.

https://wiki.duraspace.org/display/DSPACE/DSpace+on+AWS%
2C+Janitor+and+DSpace+-+Feb+27%2C+2018+at+1600UTC

-- Forwarded message --
From: Terry Brady 
Date: Sat, Feb 24, 2018 at 6:35 PM
Subject: Feb 27 16:00UTC-17:30UTC DSpace Developer Show and Tell - DSpace
on AWS and Janitor and DSpace
To: DSpace Technical Support , DSpace
Community , DSpace Committers <
dspace-com...@googlegroups.com>


The first DSpace Developer Show and Tell meeting will be held on Tues 2/27
at 16:00 UTC (11AM ET).   The meeting will be held in the DSpace meeting
room on Zoom:  https://duraspace.zoom.us/my/dspace.


   - Tim Donohue (DuraSpace) will present on Basic deployment of DSpace in
   AWS (Amazon Web Services)
   - Patrick Trottier (Laurentian University) will present on Developing
   DSpace with Janitor 


Information about the meeting in located here:

   - https://wiki.duraspace.org/display/DSPACE/DSpace+on+AWS%
   2C+Janitor+and+DSpace+-+Feb+27%2C+2018+at+1600UTC
   


We hope to make the Developer Show and Tell into a regular meeting series
to discuss developer tools and processes.  If you have ideas for future
topics, please register them here:

   - https://wiki.duraspace.org/display/DSPACE/DSpace+
   Developer+Show+and+Tell+Meetings
   



Terry

-- 
Terry Brady
Applications Programmer Analyst
Georgetown University Library Information Technology
https://github.com/terrywbrady/info
425-298-5498 <(425)%20298-5498> (Seattle, WA)



-- 
Terry Brady
Applications Programmer Analyst
Georgetown University Library Information Technology
https://github.com/terrywbrady/info
425-298-5498 (Seattle, WA)

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Re: [dspace-tech] Re: Notes on PostgreSQL connection pooling with a Tomcat JNDI resource

[Alan Orth]

Hello,

*The JDBC pool parameter removeAbandoned='true' absolutely solves the idle
in transaction issue*.

However! In the past two weeks since I enabled it, I notice that we don't
have any "idle in transaction" connections in pg_stat_activity anymore—and
only a handful of active connections at any given time. The default timeout
is to prune "abandoned" connections after 60 seconds, which doesn't seem to
be a problem except on the XMLUI submissions page. One user with many
(thousands?) of submissions says this page is very slow and experiences
"Socket closed" errors eventually. This is presumably PostgreSQL killing
his connection. I've tried increasing this to 90 and even 180 seconds, but
it doesn't help. What is happening on the /submissions page?

Anyways, as an experiment, this morning I turned off the
removeAbandoned='true' setting on the JDBC pool and within a few hours
DSpace was down and there were 200 "idle in transaction" connections again.
*sigh* For what it's worth, pg_stat_activity shows 100 "idle in
transaction" connections running the following query:

SELECT * FROM resourcepolicy WHERE resource_type_id= $1 AND resource_id= $2
AND action_id= $3

I'm hoping for some insight on what this query is, and about the XMLUI
submissions page being slow! Again, we're running DSpace 5.5, PostgreSQL
9.5.11, and XMLUI with ~70,000 items.

Thanks,

On Sat, Feb 10, 2018 at 5:13 PM Alan Orth  wrote:

> Tim,
>
> Any idea why DSpace thinks those connections are busy when PostgreSQL
> itself reports them as idle?
>
> In order to try to understand the traffic that is coming in I wrote a
> Munin plugin[0] that uses JMX to monitor the number of active sessions in
> DSpace applications (REST doesn't appear to create sessions). From that
> it's clear that we have quite a lot of traffic sometimes, with nearly 1500
> active sessions sometimes (see attached)! We aggressively add bot user
> agents to Tomcat's Crawler Session Manager Valve so all of these bots like
> Google, Bing, and Baidu that browse from fifty IP addresses concurrently
> get lumped into one JSESSIONID.
>
> In any case I've adjusted my JDBC pool parameters to include the
> parameters removeAbandoned='true' and testOnReturn='true' in addition to
> those Mark and I were using earlier in this thread. Things are calm on the
> site the last few days but let's see what happens during the week. We're in
> the process of upgrading from 5.5 to 5.8, which will include some database
> fixes, but I'm definitely looking forward to moving our repository to
> DSpace 6.x to take advantage of the Hibernate work.
>
> [0]
> https://github.com/ilri/rmg-ansible-public/blob/master/roles/munin/files/jmx_dspace_sessions
>
> Cheers,
>
> On Thu, Feb 8, 2018 at 7:26 PM Tim Donohue  wrote:
>
>> Hi Alan,
>>
>> We do occasionally find areas of DSpace that fail to properly close
>> database connections or otherwise clean up after themselves.  So, it's not
>> unheard of for database leaks to be found and then fixed.  Obviously
>> though, if we were aware of a specific leak in XMLUI, we'd get it fixed.
>>
>> I do know that significant work at the database layer went into DSpace 6
>> (with the move to Hibernate)... and I've heard reports (from a few folks)
>> that these sorts of issues are less frequent in DSpace 6.x.  (As I have
>> heard of other large sites that said they had to restart DSpace every once
>> in a while prior to 6.x, but are not seeing the same issues with 6.x.  I've
>> not seen this behavior myself, but it's very possible that it is
>> encountered more with highly active and/or larger sites)
>>
>> That unfortunately doesn't solve the issues you are seeing though.  Is
>> your site extremely active (in terms of concurrent users)?  Are you perhaps
>> having a lot of bad behaving spiders that are hitting your site and
>> possibly using up database connections?  250 connections in the pool sounds
>> like plenty, but it obviously may be dependent on how many concurrent hits
>> you are seeing.
>>
>> In searching around, I also came across some older (circa 2010) notes on
>> our wiki at
>> https://wiki.duraspace.org/display/DSPACE/Idle+In+Transaction+Problem
>>  It doesn't provide any exact solutions though, but it shows that you are
>> not alone (I'm not sure I'd recommend killing "idle in transaction"
>> processes though, as that wiki page suggests).  Also here's more info from
>> Postgres on what "idle in transaction" means:
>> https://www.postgresql.org/docs/9.2/static/monitoring-ps.html (it also
>> suggests that looking at pg_locks system view might provide info on what
>> transactions are still open, etc).
>>
>> So, I don't have any answers here, but maybe these will provide you with
>> clues or inspiration to dig in a bit further.  Please do let us know what
>> you find, and feel free to post back with any clues or breadcrumbs you
>> discover along the way.
>>
>> - Tim
>>
>> On Wed, Feb 7, 2018 at 5:07 PM Alan Orth  wrote:
>>
>>> Is there some kind of database transacti

[dspace-tech] Problemas para generar indices

[Jose Miguel Ravasi]

Hola a todos
Estoy trabajando con Dspace 6.2 y tengo algunas dificultades, si alguno me 
puede echar una mano lo voy a agradecer.
La configuración de mi equipo es la siguiente:

   - Ubuntu 16.04 LTS server
   - java 1.8.0_151
   - Tomcat 8.5.24
   - Maven 3.5.2
   - Ant 1.9.10
   - Git 2.7.4
   - Postgresql 9.5
   - Dspace 6.2

Todo parece marchar bien, tengo cargados 70 items que mude desde la version 
Dspace 4.2

Digo que todo parece marchar bien pues con el servidor encendido, desde una 
computadora en red puedo acceder ip:8080/xmlui

Veo las colecciones y puedo entrar a los items logueandome con mi cuenta


El problema es que no puedo generar los indices, (Autor, materia)


desde la terminal del servidor ejecute ./dspace index-discovery  y me 
devuelve error del Solr


No logro descubrir cual es el problema.

Desde ya muchas gracias


José Miguel Ravasi

Biblioteca Fac. Ingeniería

Universidad Nacional de Mar del Plata




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Re: [dspace-tech] Icon next to authorities names

[Bollini Andrea]

Yes, this is an easy but danger solution.
You will need to deal with this customization everywhere, in the OAI-PMH, REST, 
indexing, etc.
moreover, if you need to update an author because he leaves your institution 
(i.e. become a former researcher) you will need to update all the items where 
it is listed with the risk to keep some inconsistency.
The institutional role is a metadata of the person not a metadata of the item, 
so you need a separate entity where such information can be stored, this is the 
approach used by DSpace-CRIS.
Andrea


Il 23/02/2018 16:08, Alan Orth ha scritto:
Hugo,

The sky is really the limit regarding the possibility for customization based 
on the text fields and XSL transformations, but you're absolutely right: it 
feels a bit dirty to me to store other information in the dc.contributor.author 
field other than the author name!

Cheers,

On Fri, Feb 23, 2018 at 3:15 PM Hugo Carlos 
mailto:hugo.car...@ufabc.edu.br>> wrote:
Hello Alan! Thanks for your answer!
If this configuration works only under an spefic theme, i think maybe it is not 
a good practice to use this "institutional tag" as part of the dc.contributor 
content. I was imagining this icon somehow as another field under the authority 
control.

Thanks!

_
Hugo da Silva Carlos
Bibliotecário
Universidade Federal do ABC
55+ (11) 4996-7934

2018-02-22 17:07 GMT-03:00 Alan Orth 
mailto:alan.o...@gmail.com>>:
Hello, Hugo.

This is just simple configuration of the Mirage 2 XMLUI theme using XSLT. The 
metadata stored in dc.contributor.author includes a piece of text like 
"[UNIFESP]" so you can use an XSL test like "if" or "choose" and apply certain 
HTML to the the theme conditionally. Pretty easy!

Cheers,

On Mon, Feb 19, 2018 at 10:09 PM Bollini Andrea 
mailto:andrea.boll...@4science.it>> wrote:
Hi Hugo,
this looks like a local customisation. A similar feature that is likely what 
you have seen widely is available out of box in dspace-cris
https://wiki.duraspace.org/display/DSPACECRIS/DSpace-CRIS+Home
as example here
http://ira.lib.polyu.edu.hk

You can set eventually different icons (or no icon) for
- current researchers (blue in the above example)
- former researchers (gray above)
- external researchers (no icon)
it can be easily extended to different categories for instance role based (phd 
students, associate professors, etc.)

Hope this help,
Andrea




Inviato da smartphone Samsung Galaxy.
 Messaggio originale 
Da: Hugo Carlos mailto:hugobciuf...@gmail.com>>
Data: 19/02/18 19:24 (GMT+01:00)
A: DSpace Technical Support 
mailto:dspace-tech@googlegroups.com>>
Oggetto: [dspace-tech] Icon next to authorities names

Hello! Guys, I have seen that some repositories have an icon of the 
researcher's institution next to their name in the DSpace.

How to achieve this? I saw several repositories have this interesting visual 
resource that facilitates identification of which author belongs to the 
institution, according to the example below. However, unfortunately I do not 
even know the name of this feature to search google correctly. Could anyone 
help?

Example:

[https://lh3.googleusercontent.com/-3agDKSfonyk/Wor7W7wO7dI/A34/ekz_BAWkus86-GNDX3UPgW8AKk9A94XpACLcBGAs/s1600/author%2Bcom%2Bicone.jpg]









[https://lh3.googleusercontent.com/-lj1eUbP9juI/Wor7aNRePoI/A38/KArtZ-h_aikPPq_rtlBjfYgBsIx_MautgCLcBGAs/s1600/author%2Bcom%2Bicone2.jpg]















== in portuguese: 

Olá! Pessoal, tenho visto que alguns repositórios possuem um ícone da 
instituição do pesquisador ao lado do seu nome no Dspace.

Como conseguir isso? Vi vários repositórios terem esse interessante recurso 
visual que facilita identificação de qual o autor pertencente a instituição, 
conforme exemplo abaixo. Porem, infelizmente não sei nem ao menos o nome desse 
recurso para buscar no google corretamente. Alguém poderia ajudar?
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