- IPT - lists.gbif.org

Data resource publishing problems. (Oracle database)
by Aurelio Sanabria 03 Feb '11

03 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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data dir
by Deependra Tandukar 25 Jan '11

25 Jan '11

Thanks Burke and Tim for you quick response - it is working now. What is the good practice of path for saving the data dir and how do I give permission for IPT? Best regards, [cid:image001.jpg@01CBBC76.A3F052F0] 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>

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installation error
by Deependra Tandukar 25 Jan '11

25 Jan '11

Hello, please have a look - I am getting following error while trying to install, please suggest what is wrong here. HTTP Status 404 - /ipt.war ________________________________ type Status report message /ipt.war description The requested resource (/ipt.war) is not available. ________________________________ Apache Tomcat/6.0.20 Best regards, [cid:image001.jpg@01CBBC63.94C31C30] 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>

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IPT status update
by Oliver Meyn (GBIF) 21 Jan '11

21 Jan '11

Dear IPT testers, Thank you once again for all your contributions. During testing at DanBIF over the last few days, some issues relating to changing the Base URL were uncovered, which the development team are addressing now. The issues list stands at 4 remaining issues, 2 of which relate to the Base URL change, one a minor issue in the metadata authoring and one relates to the character encoding in organisation names. Could I kindly request that all testers make as much effort as possible during the coming days, and report any issues they face that make the IPT unusable, to help assess whether the IPT is ready to be released? The more feedback we get the more confident we'll be that the release is stable. Thanks very much, Oliver, on behaf of the IPT development team -- Oliver Meyn Software Developer Global Biodiversity Information Facility (GBIF) +45 35 32 15 12 http://www.gbif.org

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Re: [IPT] IPT post from mukul.kapur@gmail.com requires approval
by Tim Robertson (GBIF) 08 Jan '11

08 Jan '11

Dear Mukul, Thank you also from me for your interest in the IPT, and your offer to contribute. The IPT has recently undergone a huge refactoring effort recently, with the latest IPT 2.0 in the trunk/gbif-ipt directory. It is this codebase that we are all working towards. We have just announced 2.0RC3 and are shortly going to release version 2.0GA, but following this there is likely to be some exciting new developments on the IPT during 2011. I think it could be a great time to be involved; The IPT development team is widespread (Colombia, US, Denmark, Germany and I am in Kiribati currently and there are active testers in Sweden, France, Argentina, Italy, Australia, Korea, Taiwan, Madagascar, India etc etc) - we anticipate worldwide installations. Like Markus says, and similar to the way Apache runs open source projects, the best way to get into the project would be to indicate that you are working on an issue, and then submit a patch (eclipse right click, create patch) which will be verified by a developer before being applied to the truck. I would suggest doing a couple of very small ones, before tackling something more sizable - there are things like setting eclipse to use the correct coding conventions (http://rs.gbif.org ) that need to be respected, and with appropriate JUnit coverage where applicable before code will be accepted. After a few contributions, you would then become a committer. There are some issues in there to build some good unit test coverages - this could be a good place to learn the code, which will make a great addition to the continued stability of the software, especially as the development team expands. Best wishes and thank you for your interest Tim On Jan 9, 2011, at 6:33 AM, Markus Döring (GBIF) wrote: > Dear Mukul, > as the IPT is an open source project we always welcome > contributions. Before you dive into the codebase though be aware > that we use struts2, google guice instead of spring and only a very > slim persistency layer around XStream using xml files. > > Issues targeted at the next 2.0.1 release might be candidates to > work on: > http://code.google.com/p/gbif-providertoolkit/issues/list?q=milestone=Relea… > > If you are interested in working on any of these issues please drop > us a line. > As a start please send us patches before we will make you a committer. > > Developer documentation is on its way, but as a start we have this > FAQ and some more wiki pages: > http://code.google.com/p/gbif-providertoolkit/wiki/DeveloperFAQ > > Thanks for getting in touch, > > Markus > > > -- > Markus Döring > Senior Developer ECAT > GBIF Secretariat > mdoering(a)gbif.org > > > On Jan 8, 2011, at 15:59, ipt-owner(a)lists.gbif.org wrote: > >> As list administrator, your authorization is requested for the >> following mailing list posting: >> >> List: IPT(a)lists.gbif.org >> From: mukul.kapur(a)gmail.com >> Subject: Fwd: Enquiry for volunteer contribution to gbif project >> Reason: Post by non-member to a members-only list >> >> At your convenience, visit: >> >> http://lists.gbif.org/mailman/admindb/ipt >> >> to approve or deny the request. >> >> From: Mukul Kapur <mukul.kapur(a)gmail.com> >> Date: January 8, 2011 15:59:45 GMT+01:00 >> To: ipt(a)lists.gbif.org >> Subject: Fwd: Enquiry for volunteer contribution to gbif project >> >> >> >> Hi >> >> I am a junior software developer from New Delhi India. >> >> I was looking for some hands on experience on Struts/Spring/ >> Hibernate framework . >> >> I wished to enquire whether the gbif project is currently looking >> for any volunteer developers.. >> >> Looking forward to hearing from you.. >> >> Thanks and Regards >> >> Mukul >> >> >> >> >> >> >> From: ipt-request(a)lists.gbif.org >> Subject: confirm cd6bce1f1071cc4a876301519cc087bd7e7a791a >> >> >> If you reply to this message, keeping the Subject: header intact, >> Mailman will discard the held message. Do this if the message is >> spam. If you reply to this message and include an Approved: header >> with the list password in it, the message will be approved for >> posting >> to the list. The Approved: header can also appear in the first line >> of the body of the reply. >> > > > > > > > > > > >

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Fwd: Enquiry for volunteer contribution to gbif project
by Mukul Kapur 08 Jan '11

08 Jan '11

Hi I am a junior software developer from New Delhi India. I was looking for some hands on experience on Struts framework . I wished to enquire whether the gbif project is currently looking for any volunteer developers.. Looking forward to hearing from you.. Thanks and Regards Mukul

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IPT 2.0RC3 available for download
by Tim Robertson 07 Jan '11

07 Jan '11

Dear all, The IPT development team are happy to announce that the IPT 2.0 release candidate 3 (IPT 2.0RC3) is now available for download and testing from http://code.google.com/p/gbif-providertoolkit/downloads/list Thank you once again to everyone who has reported bugs and proposed enhancements during the testing phase. Since the IPT 2.0RC2 was released some further 36 issues have been reported and addressed (http://tinyurl.com/2dev7uu ), with a total of 159 issues now fixed since testing commenced – well done to everyone involved! 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. The expectation is that the 2.0 General Availability release (2.0GA) will be offered in week 3, 2011, but this will not be done without the agreement from the testing community. During that week, we will call a vote on the mailing list, to ask if anyone believes the IPT is not yet ready to use for publishing data through GBIF so please consider this during your testing. Following 2.0GA we will continue to provide corrective fixes, and will initiate discussions on the future direction and functionality of the product. The IPT roadmap planning is primarily based on the issues reported on http://code.google.com/p/gbif-providertoolkit/issues/list Thank you once again for all your contributions and we welcome all suggestions on how we can improve the process. Kind regards, Tim, on behalf of the IPT development team

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IPT-2.0RC2: no .jsp files
by Bruce Wilson 16 Dec '10

16 Dec '10

I must be doing something wrong in the installation of the itp-2.0RC2.war file. Here is what I did: 1. Download ipt-2.0RC2.war into the .../tomcat 6.0/webapps folder (in a Windows Server 2003 system) 2. Wait for the directories to be built out: only webapps/itp-2.0RC2/WEB-INF was created. No index.jsp showed up. 3. Go to http://science.uvu.edu:8080/itp-2.0RC2/ and get only an apache 404 error message. So is this a problem in the installer not having all the files it needs, or should I have named it itp.war to put the new .jar files into the existing ipt-1.0RC3 installation (which I renamed to just /ipt/)? I guess a third option exists, should I just not try to test and wait for the GA release? References: http://science.uvu.edu:8080/ipt/ current 1.0RC3 installation, not completed, unpublished, but mostly running http://science.uvu.edu:8080/ipt-2.0RC2/ the 404 error message. Directory structure created: ../tomcat 6.0/webapps/ipt-2.0RC2/WEB-INF/classes (contains one .properties file) ../tomcat 6.0/webapps/ipt-2.0RC2/WEB-INF/lib (contains 11.3 MB in 35 .jar files) Bruce Wilson Department of Chemistry | Mail Stop 179 | UVU | 800 W University Parkway, Orem UT 84058 (801)863-7138 | bruce.wilson(a)uvu.edu | http://science.uvu.edu/wilson

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IPT 2.0RC2 available for download
by Tim Robertson (GBIF) 15 Dec '10

15 Dec '10

Dear all, The IPT development team are happy to announce that the IPT 2.0 release candidate 2 (IPT 2.0RC2) is now available for download and testing from http://code.google.com/p/gbif-providertoolkit/downloads/list Thank you once again to everyone who has reported bugs and proposed enhancements during the testing phase. Since the IPT 2.0RC1 was released some 43 issues have been reported and addressed (http://tinyurl.com/2g9jzjo) In particular the following critical issues have been worked on, and any assistance in testing them would be greatly appreciated. - IPT operation on windows environments - Performance in connection of the IPT to databases (PostGRES, MySQL, Oracle, MSSql) - We particularly seek assistance testing connections to Oracle and MSSql The IPT will not be released until the testing community confirms that the product is suitably robust to do so. At this stage, we anticipate releasing 2.0RC3 during week 1, 2011 which will allow users to register against the live GBIF registry, with the expectation that a final 2.0 General Availability release (2.0GA) will be offered in week 3, 2011. However, this depends on the outcome of further tests. Our roadmap planning is based on the issues on http://code.google.com/p/gbif-providertoolkit/issues/list Thank you once again for all your contributions and as always, we welcome suggestions on how we can improve the process. Kind regards, Tim, on behalf of the IPT development team

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