[Dspace-tech] R: Release DSpace-CRIS v-4.1.1

2014-07-07 Thread Andrea Bollini 
Hi Alexander,I'm out-of-office these days I'm sure that Luigi will reply with information about the script need to update the pmc count.There are two script one is able to retrieve pmc/pmid identifier for items that have a doi, the other query pmc to retrieve the actual count and citation information.About the statistics you need to look to the solr log files. When you hit a researcher page do you see an insert on solr (call to the /update handler?). What if you hit an item page?AndreaInviato da Samsung Mobile Messaggio originale Da: Alexander Wong  Data:07/07/2014  06:04  (GMT+01:00) A: Pascarelli Luigi Andrea  Cc: Andrea Bollini ,dspace-tech  Oggetto: Re: Release DSpace-CRIS v-4.1.1 Dear Luigi and Andrea,I have tried to spend a few days on this stats issue but no ways out. I am wondering if there are other things I can shuffle around to get it run. My supervisors are very concerned with the statistics and I need to get it fixed asap.
I am also trying to look for pmc citation counts - I suppose it has to be triggered by a dsrun command to get all the pmc updated. Is it true?Thanks a lot again,
Alexander WongOn Wed, Jul 2, 2014 at 10:49 AM, Alexander Wong amd...@gmail.com wrote:
Dear Luigi and Andrea,Thanks for the great work. The RP refind function works pretty well at our side - I believed a minor touchup of selection box at the later time would be nice. (The select-all box is not working as expected.).

Nevertheless, I am still having solr statistics issue.I have tried to download articles, view articles, view RP and do all the things trying to trigger solr to log my stats, but still fails.

I have attached the tomcat logs for your references.Thanks  Regards,Alexander Wong

On Sun, Jun 29, 2014 at 3:08 AM, Pascarelli Luigi Andrea l.pascare...@cineca.it wrote:


  

  
  
Hi all,

we have just released DSpace-CRIS v-4.1.1. You can download the
tagged version, as usually, from git at
https://github.com/Cineca/DSpace/releases/tag/dspace-cris-4.1.1
This version resolve the issues adviced by you (the Rebind
publications feature and the NPE behaviour if a cris entities have
no name/title required metadata).
The release contains others minor fixes.
Thank you all.

Andrea



-- 

  
  
  
  
  

  

 

Luigi
  Andrea Pascarelli
  
Dipartimento Servizi e Soluzioni per
  l'Amministrazione Universitaria
  Divisione Ricerca
  Via

dei Tizii, 6 
00185 Roma, Italy 
  ph. +39 06 44486626


http://www.cineca.it
  
  

  
  

  



--
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft___
DSpace-tech mailing list
DSpace-tech@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/dspace-tech
List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette

Re: [Dspace-tech] R: Release DSpace-CRIS v-4.1.1

2014-07-07 Thread Pascarelli Luigi Andrea 
In regards to PMC, you have to build solr core for pmc (check if into 
your solr instance there is pmc core configurations). Download the csv 
file from pubmed ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/PMC-ids.csv.gz
After that try to run this script (you need a basic experience with the 
shell script and the curl tool):

split -d -l 5 file.pmc.csv split_files.
for file in `ls split_files.*`
do
curl 
'http://host:port/solr/pmc/update?update.contentType=text/csvfieldnames=,,,DOI,PMCID,PMID,,'
 
-H 'Content-type:text/csv; charset=utf-8' --data-binary @$file;
done

The script split the csv file in n files to avoid problem due to the max 
upload limit on your server and send it to your solr to ingest it. Tune 
it with your need. Good luck :-)

After that launch the main script at 
org.dspace.app.cris.pmc.script.RetrieveCitationInPMC with -x 0 
parameter, this query pmc to retrieve the actual count and citation 
informations.
After all launch org.dspace.app.cris.pmc.script.RetrievePubMedID (with 
no params) to retrieve pmc/pmid identifier for items that have a doi.

Hope this help. Let me know.

Luigi Andrea Pascarelli

Il 07/07/2014 11:50, Andrea Bollini ha scritto:
 Hi Alexander,
 I'm out-of-office these days I'm sure that Luigi will reply with information 
 about the script need to update the pmc count.
 There are two script one is able to retrieve pmc/pmid identifier for items 
 that have a doi, the other query pmc to retrieve the actual count and 
 citation information.

 About the statistics you need to look to the solr log files. When you hit a 
 researcher page do you see an insert on  solr (call to the /update handler?). 
 What if you hit an item page?

 Andrea



-- 
Cineca - Sede di Roma
via dei Tizii 6 - 00185 Roma

ph. +39 06 44486626
email: l.pascare...@cineca.it


--
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
___
DSpace-tech mailing list
DSpace-tech@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/dspace-tech
List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette

Re: [Dspace-tech] R: Release DSpace-CRIS v-4.1.1

2014-07-07 Thread Alexander Wong 
Dear Andrea,

Thanks for your help. Your active involvement in DSpace-CRIS will surely
bring the DSPACE-CRIS to the next level.

For PMC - I am now trying to follow your instruction on it.
For Stats - I have reinstall the OS from fresh and git clone again for
4.1.1.
Trigger CRIS entities will have following lines logged in dspace.log;
solr.log is kept at 0 bytes.

2014-07-08 10:33:41,362 INFO  org.dspace.browse.BrowseEngine @
anonymous:session_id=F496C193EA2B46F6ECC531D89B3A229B:ip_addr=127.0.0.1:
browse_by_item:
2014-07-08 10:33:45,998 ERROR
org.dspace.statistics.SolrLoggerUsageEventListener @
2014-07-08 10:34:08,881 WARN
 org.dspace.app.webui.cris.components.statistics.ASolrStatsConfigurerComponent
@
2014-07-08 10:34:08,969 WARN
 org.dspace.app.webui.cris.components.statistics.ASolrStatsConfigurerComponent
@

Regards,
Alexander Wong.


On Mon, Jul 7, 2014 at 8:38 PM, Pascarelli Luigi Andrea 
l.pascare...@cineca.it wrote:

 In regards to PMC, you have to build solr core for pmc (check if into your
 solr instance there is pmc core configurations). Download the csv file from
 pubmed ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/PMC-ids.csv.gz
 After that try to run this script (you need a basic experience with the
 shell script and the curl tool):

 split -d -l 5 file.pmc.csv split_files.
 for file in `ls split_files.*`
 do
 curl 'http://host:port/solr/pmc/update?update.contentType=
 text/csvfieldnames=,,,DOI,PMCID,PMID,,' -H 'Content-type:text/csv;
 charset=utf-8' --data-binary @$file;
 done

 The script split the csv file in n files to avoid problem due to the max
 upload limit on your server and send it to your solr to ingest it. Tune it
 with your need. Good luck :-)

 After that launch the main script at 
 org.dspace.app.cris.pmc.script.RetrieveCitationInPMC
 with -x 0 parameter, this query pmc to retrieve the actual count and
 citation informations.
 After all launch org.dspace.app.cris.pmc.script.RetrievePubMedID (with no
 params) to retrieve pmc/pmid identifier for items that have a doi.

 Hope this help. Let me know.

 Luigi Andrea Pascarelli

 Il 07/07/2014 11:50, Andrea Bollini ha scritto:

  Hi Alexander,
 I'm out-of-office these days I'm sure that Luigi will reply with
 information about the script need to update the pmc count.
 There are two script one is able to retrieve pmc/pmid identifier for
 items that have a doi, the other query pmc to retrieve the actual count and
 citation information.

 About the statistics you need to look to the solr log files. When you hit
 a researcher page do you see an insert on  solr (call to the /update
 handler?). What if you hit an item page?

 Andrea



 --
 Cineca - Sede di Roma
 via dei Tizii 6 - 00185 Roma

 ph. +39 06 44486626
 email: l.pascare...@cineca.it


--
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft___
DSpace-tech mailing list
DSpace-tech@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/dspace-tech
List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette