February 2011 - IPT - lists.gbif.org

digir/tapirlink useful features ... Howto in IPT?
by Herbario SANT 17 Feb '11

17 Feb '11

Thanks for your answer Markus. What I am trying to figure out is the best way to reconfigure an IPT when for some reason the server stops working (we buy a new computer, we migrate from/to windows to/from linux, or something alike). How to restore everything fastly and safely? I used to keep copies of some xml files when using digir/tapirlink, and this was a reasonably easy task to do. But what about IPT? One more question regarding digir/tapirlink versus IPT: It was possible to launch direct xml queries to them, so I could construct a web server to show inventories or specific searches of an specific data provider. How can I do this with IPT? I haven't looked in detail but I guess the only way to get data from IPT is downloading full datasets Nobody else has requested this feature? Would it be possible to have something like this built in IPT, without reducing IPT performance a lot? (even with a different technic but similar client interface services): http://tapirlink.berkeley.edu/tapir_client.php http://algae.manoa.hawaii.edu/database/lib/tapirlink/www/tapir_client.php Thanks for your answers David -- David García San León Herbario SANT Facultade de Farmacia - Laboratorio de Botánica Universidade de Santiago de Compostela 15782 - Galicia (Spain) http://www.usc.es/herbario Tel. +34 881815022 Fax +34 981594912

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IPT v2.0 is ready
by Oliver Meyn 17 Feb '11

17 Feb '11

Dear IPT users, The GBIF Secretariat are pleased to announce that following three rounds of formal testing, a stable release of the Integrated Publishing Toolkit Version 2.0 (IPT v2.0) is now available for download from http://code.google.com/p/gbif-providertoolkit/. The IPT v2.0 enables simple biodiversity data publishing to the internet according to global standards. We would like to encourage early adopters to install/upgrade this latest release, particularly if you have an existing IPT installation. Updated information about this version of the IPT and instructions on how to join the IPT mailing lists is available on the GBIF Website: http://www.gbif.org/informatics/infrastructure/publishing/. In addition: - The live user manual can be found online [http://code.google.com/p/gbif-providertoolkit/wiki/IPT2ManualNotes?tm=6] All users are invited to contribute and update this manual. We will soon start a process to ensure that versions are available in some of the major languages. - We kindly ask those of you that will install and use this new version to report any issues on the project site [http://code.google.com/p/gbif-providertoolkit/issues/list] and address questions to the IPT-users mailing list [http://lists.gbif.org/mailman/listinfo/ipt] - The project roadmap outlining the technical developments of the software [http://code.google.com/p/gbif-providertoolkit/wiki/Roadmap] will provide a schedule of any minor version releases planned for the future. This new version of the IPT will be officially launched in October 2011 at the 18th GBIF Governing Board Meeting in Buenos Aires, Argentina. The GBIF Secretariat will work closely with the Nodes Strategy Group and key IPT users to ensure that a comprehensive uptake plan is ready for the IPT v2.0 launch. This plan will include a technology transition guide, a training programme, final user manuals and technical documentation, an expert network and a distributed helpdesk. Thank you once again for all your help in testing and contributing to the IPT! With best regards, Oliver, on behalf of the IPT development team and the GBIF Secretariat -- Oliver Meyn Software Developer Global Biodiversity Information Facility (GBIF) +45 35 32 15 12 http://www.gbif.org

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IPT Linux configuration
by Deependra Tandukar 04 Feb '11

04 Feb '11

Hello, Please let me know the requirement/configuration for IPT in linux - space, dependent packages, memory, etc. Best regards, [cid:image001.jpg@01CBC4AD.A3A7CAA0]<http://www.icimod.org/> Deependra Tandukar Knowledge Management and Web Specialist, Knowledge Management International Centre for Integrated Mountain Development GPO Box 3226, Khumaltar, Lalitpur, Kathmandu, Nepal. Tel +977-1-5003222 Ext 154 Fax +977-1-5003277 Web www.icimod.org<http://www.icimod.org/> Connect to ICIMOD: [cid:image002.jpg@01CBC4AD.A3A7CAA0] <http://www.facebook.com/icimod> [cid:image003.jpg@01CBC4AD.A3A7CAA0] <http://www.twitter.com/icimod> [cid:image004.jpg@01CBC4AD.A3A7CAA0] <http://www.youtube.com/icimod> [cid:image005.jpg@01CBC4AD.A3A7CAA0] <http://www.icimod.org/enews>

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GBIF registration options // Validate
by Aurelio Sanabria 03 Feb '11

03 Feb '11

Hello, I'm trying to change the data provider from DiGIR to IPT. Because I need to shut down the machine hosting the DiGIR data provider (it's almost dying). The problem comes when I try to validate the URL, in the "GBIF registration options" page. The current IPT instance can be accessed using this URL http://lucina.inbio.ac.cr/ipt/ Anyone knows if I'm missing something? PS: The error the IPT instance its giving me: "Validation failed! Please check your internet connection. If connected, check the Base URL and the Proxy URL (if needed on this server)." -- Regards, Aurelio Sanabria http://informatics.inbio.ac.cr/

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Data resource publishing problems. (Oracle database)
by Aurelio Sanabria 02 Feb '11

02 Feb '11

Hello there, I'm trying to install the IPT RC3 acording to the instruction on the web page of the project and everything goes well until I try to publish the resource. It return the next error: (see attachment screenshot.1.png) ------------------------------------------------------------------------------------------------------------------- Feb 1, 2011 8:55:38 AM Failed. Fatal error! Continue to resource overview. Log Messages Archive generation started for resource cr-inbio 8:55:38 AM Start writing data file for Darwin Core Occurrence 8:55:38 AM Exception org.gbif.ipt.task.GenerateDwca.dumpData(GenerateDwca.java:423) org.gbif.ipt.task.GenerateDwca.addDataFile(GenerateDwca.java:140) org.gbif.ipt.task.GenerateDwca.createDataFiles(GenerateDwca.java:260) org.gbif.ipt.task.GenerateDwca.call(GenerateDwca.java:205) org.gbif.ipt.task.GenerateDwca.call(GenerateDwca.java:37) java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) java.util.concurrent.FutureTask.run(FutureTask.java:138) java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) java.lang.Thread.run(Thread.java:619) ------------------------------------------------------------------------------------------------------------------- If I check the errors it shows this: ------------------------------------------------------------------------------------------------------------------- ERROR 01-Feb-2011 08:51:46 java.sql.SQLException: Invalid argument(s) in call: setFetchSize ERROR 01-Feb-2011 08:51:46 Fatal DwC-A Generator Error org.gbif.ipt.service.SourceException: Cant build iterator for source biodiversidaddecostarica :Invalid argument(s) in call: setFetchSize at org.gbif.ipt.service.manage.impl.SourceManagerImpl.rowIterator(SourceManagerImpl.java:572) at org.gbif.ipt.task.GenerateDwca.dumpData(GenerateDwca.java:346) at org.gbif.ipt.task.GenerateDwca.addDataFile(GenerateDwca.java:140) at org.gbif.ipt.task.GenerateDwca.createDataFiles(GenerateDwca.java:260) at org.gbif.ipt.task.GenerateDwca.call(GenerateDwca.java:205) at org.gbif.ipt.task.GenerateDwca.call(GenerateDwca.java:37) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:619) ERROR 01-Feb-2011 08:51:46 Process for resource cr-inbio aborted due to error: org.gbif.ipt.task.GeneratorException: java.lang.NullPointerException ERROR 01-Feb-2011 08:55:38 java.sql.SQLException: Invalid argument(s) in call: setFetchSize ERROR 01-Feb-2011 08:55:38 Fatal DwC-A Generator Error org.gbif.ipt.service.SourceException: Cant build iterator for source biodiversidaddecostarica :Invalid argument(s) in call: setFetchSize at org.gbif.ipt.service.manage.impl.SourceManagerImpl.rowIterator(SourceManagerImpl.java:572) at org.gbif.ipt.task.GenerateDwca.dumpData(GenerateDwca.java:346) at org.gbif.ipt.task.GenerateDwca.addDataFile(GenerateDwca.java:140) at org.gbif.ipt.task.GenerateDwca.createDataFiles(GenerateDwca.java:260) at org.gbif.ipt.task.GenerateDwca.call(GenerateDwca.java:205) at org.gbif.ipt.task.GenerateDwca.call(GenerateDwca.java:37) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:619) ERROR 01-Feb-2011 08:55:38 Process for resource cr-inbio aborted due to error: org.gbif.ipt.task.GeneratorException: java.lang.NullPointerException ------------------------------------------------------------------------------------------------------------------- I have been searching if its a problem in my database (by the way its an oracle 9i) and found this[0] The question is, is there a way to bypass this problem? should I add this as a bug? in the project site? [0] http://opensource.atlassian.com/projects/hibernate/browse/HHH-682 -- Saludos, Aurelio Sanabria http://informatics.inbio.ac.cr/

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NOT production use versus GBIF registration & organisations in IPT
by Herbario SANT 01 Feb '11

01 Feb '11

On Fri, Jan 7, 2011 at 10:48 PM, Tim Robertson <trobertson(a)gbif.org> wrote: > As we are approaching the 2.0 General Availability release, RC3 allows > users to configure the IPT to register against the GBIF live registry > and register and publish data to the GBIF network. On a new > installation, after the data directory is selected, you may choose > “production use”, which will ensure the IPT communicates with the LIVE > GBIF registry. Once selected, this cannot be altered so please be > vigilant in your selection. If your intention is to test and > evaluate, please do not select production installation. My intention is to test and evaluate. Sorry if this has an obvious answer but just to be safe I prefer to ask before. I am following these instructions here: http://code.google.com/p/gbif-providertoolkit/wiki/IPT2ManualNotes#IPT_setu… I have chosen "NOT production use". Beyond that point, the Quick Reference Guide says: "Click on the button labeled 'Continue' to open the IPT Administration page (...) Before adding data resources to the IPT, the administrator must (...) set the GBIF registration options, and associate the IPT with an organisation. The Organisations button is disabled by default until the GBIF registration options have been set". As I am just testing the software, my question is: in a "NOT production" installation, can I safely test all the steps above? Is it possible to set the GBIF registration options and associate to an organisation in "not production mode"? Is there a live GBIF registry plus another "test GBIF registry" for "not production" IPT installations? In this case I suppose there is no problem in using a server address/port which is not the same I will use when going into a production server. Right? Thanks in advance for your answers David -- David García San León Herbario SANT Universidade de Santiago de Compostela (Spain)

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