- IPT - lists.gbif.org

Re: [IPT] [ZooKeys] GBIF IPT
by Tim Robertson 29 Jan '10

29 Jan '10

Dear Ivailo Sorry for the delay in replying but I have been away. I get a timeout when I try and reach http://85.130.9.84:8080/ipt/index.html - is it running? I believe what you are seeing relates to a critical bug that is now fixed, but I would like to try and find a workaround for your issue. Please can you send all future questions to the ipt(a)lists.gbif.org to make sure that you get the best and quickest response? Best wishes, Tim On Jan 6, 2010, at 9:32 AM, Ivailo Stoyanov wrote: > Dear Tim, > > I need to upload another dataset into the ZooKeys IPT (http://85.130.9.84:8080/ipt/index.html > ), but after entering the basic metadata for a new "Occurence > Resource" I get the following errors and can not proceed: > > = > = > = > = > = > = > = > = > = > = > = > = > ====================================================================== > > Yikes! > > javax.servlet.ServletException: could not insert: > [org.gbif.provider.model.OccurrenceResource] > at > net.sf.ehcache.constructs.web.filter.Filter.logThrowable(Filter.java: > 152) > at net.sf.ehcache.constructs.web.filter.Filter.doFilter(Filter.java: > 97) > at > org > .apache > .catalina > .core > .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: > 215) > at > org > .apache > .catalina > .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) > at > org > .appfuse > .webapp.filter.LocaleFilter.doFilterInternal(LocaleFilter.java:74) > at > org > .springframework > .web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java: > 76) > at > org > .apache > .catalina > .core > .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: > 215) > at > org > .apache > .catalina > .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) > at > org > .springframework > .orm > .hibernate3 > .support > .OpenSessionInViewFilter > .doFilterInternal(OpenSessionInViewFilter.java:198) > at > org > .springframework > .web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java: > 76) > at > org > .apache > .catalina > .core > .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: > 215) > at > org > .apache > .catalina > .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) > at org.springframework.security.util.FilterChainProxy > $VirtualFilterChain.doFilter(FilterChainProxy.java:359) > at org.springframework.security.intercept.web.FilterSecurityInterceptor.invoke > (FilterSecurityInterceptor.java:109) > at org.springframework.security.intercept.web.FilterSecurityInterceptor.doFilter > (FilterSecurityInterceptor.java:83) > at org.springframework.security.util.FilterChainProxy > $VirtualFilterChain.doFilter(FilterChainProxy.java:371) > at > org > .springframework > .security > .ui > .ExceptionTranslationFilter > .doFilterHttp(ExceptionTranslationFilter.java:101) > at > org > .springframework > .security.ui.SpringSecurityFilter.doFilter(SpringSecurityFilter.java: > 53) > at org.springframework.security.util.FilterChainProxy > $VirtualFilterChain.doFilter(FilterChainProxy.java:371) > at > org > .springframework > .security > .providers > .anonymous > .AnonymousProcessingFilter > .doFilterHttp(AnonymousProcessingFilter.java:105) > at > org > .springframework > .security.ui.SpringSecurityFilter.doFilter(SpringSecurityFilter.java: > 53) > at org.springframework.security.util.FilterChainProxy > $VirtualFilterChain.doFilter(FilterChainProxy.java:371) > at > org > .springframework > .security > .ui > .rememberme > .RememberMeProcessingFilter > .doFilterHttp(RememberMeProcessingFilter.java:116) > at > org > .springframework > .security.ui.SpringSecurityFilter.doFilter(SpringSecurityFilter.java: > 53) > at org.springframework.security.util.FilterChainProxy > $VirtualFilterChain.doFilter(FilterChainProxy.java:371) > at > org > .springframework > .security > .wrapper > .SecurityContextHolderAwareRequestFilter > .doFilterHttp(SecurityContextHolderAwareRequestFilter.java:91) > at > org > .springframework > .security.ui.SpringSecurityFilter.doFilter(SpringSecurityFilter.java: > 53) > at org.springframework.security.util.FilterChainProxy > $VirtualFilterChain.doFilter(FilterChainProxy.java:371) > at > org > .springframework > .security > .ui > .basicauth > .BasicProcessingFilter.doFilterHttp(BasicProcessingFilter.java:172) > at > org > .springframework > .security.ui.SpringSecurityFilter.doFilter(SpringSecurityFilter.java: > 53) > at org.springframework.security.util.FilterChainProxy > $VirtualFilterChain.doFilter(FilterChainProxy.java:371) > at > org > .springframework > .security > .ui > .AbstractProcessingFilter.doFilterHttp(AbstractProcessingFilter.java: > 268) > at > org > .springframework > .security.ui.SpringSecurityFilter.doFilter(SpringSecurityFilter.java: > 53) > at org.springframework.security.util.FilterChainProxy > $VirtualFilterChain.doFilter(FilterChainProxy.java:371) > at > org > .springframework > .security.ui.logout.LogoutFilter.doFilterHttp(LogoutFilter.java:87) > at > org > .springframework > .security.ui.SpringSecurityFilter.doFilter(SpringSecurityFilter.java: > 53) > at org.springframework.security.util.FilterChainProxy > $VirtualFilterChain.doFilter(FilterChainProxy.java:371) > at > org > .springframework > .security > .ui > .SessionFixationProtectionFilter > .doFilterHttp(SessionFixationProtectionFilter.java:61) > at > org > .springframework > .security.ui.SpringSecurityFilter.doFilter(SpringSecurityFilter.java: > 53) > at org.springframework.security.util.FilterChainProxy > $VirtualFilterChain.doFilter(FilterChainProxy.java:371) > at > org > .springframework > .security > .context > .HttpSessionContextIntegrationFilter > .doFilterHttp(HttpSessionContextIntegrationFilter.java:235) > at > org > .springframework > .security.ui.SpringSecurityFilter.doFilter(SpringSecurityFilter.java: > 53) > at org.springframework.security.util.FilterChainProxy > $VirtualFilterChain.doFilter(FilterChainProxy.java:371) > at > org > .springframework > .security.util.FilterChainProxy.doFilter(FilterChainProxy.java:174) > at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate > (DelegatingFilterProxy.java:236) > at > org > .springframework > .web > .filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:167) > at > org > .apache > .catalina > .core > .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: > 215) > at > org > .apache > .catalina > .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) > at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal > (CharacterEncodingFilter.java:96) > at > org > .springframework > .web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java: > 76) > at > org > .apache > .catalina > .core > .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: > 215) > at > org > .apache > .catalina > .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) > at > org > .apache > .catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java: > 213) > at > org > .apache > .catalina.core.StandardContextValve.invoke(StandardContextValve.java: > 172) > at > org > .apache > .catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) > at > org > .apache > .catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) > at > org > .apache > .catalina.core.StandardEngineValve.invoke(StandardEngineValve.java: > 108) > at > org > .apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java: > 174) > at > org > .apache.coyote.http11.Http11Processor.process(Http11Processor.java: > 875) > at org.apache.coyote.http11.Http11BaseProtocol > $Http11ConnectionHandler.processConnection(Http11BaseProtocol.java: > 665) > at > org > .apache > .tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java: > 528) > at > org > .apache > .tomcat > .util > .net > .LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) > at org.apache.tomcat.util.threads.ThreadPool > $ControlRunnable.run(ThreadPool.java:689) > at java.lang.Thread.run(Unknown Source) > > = > = > = > = > = > = > = > = > = > = > = > = > ====================================================================== > > What can I do now in order to reach the upload interface? > > Best wishes for the New Year, > Ivailo > -- > I. Stoyanov > Editorial Secretary > > ZOOKEYS -- http://pensoftonline.net/zookeys > BIORISK -- http://pensoftonline.net/biorisk >

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Re: [IPT] Set of short presentations about IPT
by Alberto González-Talaván (GBIF) 28 Jan '10

28 Jan '10

Dear friends from the IPT list, I have received two sets of IPT presentations (Chinese by Elie Yueh-Chih Chen and French by Franck Theeten) that are now available in the GBIF Community Site for everybody's use. My thanks to Elie and Franck for that! <http://elggtest.gbif.org/pg/pages/view/3872/> http://elggtest.gbif.org/pg/pages/view/3872/ This location is an interim solution while the Resources Section of the GBIF Online Resource Centre for Training is being developed. The page is public so everybody should be able to access it. To those who volunteered to produce the presentations in other languages: if you are short in time, I would suggest that you focus on the presentations 1 (introduction) and 4 (user interface), which are the most useful ones to present the IPT to general audiences, data publishers and data users. The IPT is ready for translation of its interface now! We will contact you back soon on this regard to proceed with the translation process in a coordinated manner. This will surely be a big step for the deployment of the tool all over the world! Cheers Alberto ---------- Dutch - André Heughebaert; German - Jörg Holetschek; Italian - Antonella Linguanti; Portuguese - Pedro Correa; Spanish - Silvia Lusa & Aurelio Sanabria. ---------- Alberto GONZÁLEZ TALAVÁN Training Officer Global Biodiversity Information Facility Secretariat Universitetsparken 15 DK-2100 Copenhagen, Denmark email: <mailto:atalavan@gbif.org> atalavan(a)gbif.org web: <http://www.gbif.org/> http://www.gbif.org/ T: +45 35 32 14 83 F: +45 35 32 14 80 From: Alberto González-Talaván (GBIF) [mailto:atalavan@gbif.org] Sent: Wednesday, November 11, 2009 5:23 PM To: 'ipt(a)lists.gbif.org' Subject: RE: [IPT] Set of short presentations about IPT Dear friends, Sorry for not getting back to some of you about the translations of the short presentations on the IPT that I requested last month. After a nice period of holidays I am again ready to continue with this issue :) I have received the following proposals up to now: Chinese - Elie Yueh-Chih Chen; Dutch - André Heughebaert; French - André Heughebaert and Franck Theeten; German - Jörg Holetschek; Italian - Antonella Linguanti; Portuguese - Pedro Correa; First, I would like to thank you all for your enthusiastic response! Please proceed with the translations as you own time allows and send them back to me when you are finished. We will make sure they have the widest spread possible. For those who are still thinking about volunteering, I would like to encourage you to do so (What about my Spanish-speaking colleagues!?). The more people involved the less we will have to face individually, and all the group will be benefited. We are trying to improve the accessibility to some of the IPT promotional and training materials. We will get back to you soon on that regard. The Training CD derived from the IPT workshop is also about to be published in the GBIF website... and more news to come! I look forward to hearing from you soon! Alberto ---------- Alberto GONZÁLEZ TALAVÁN Training Officer Global Biodiversity Information Facility Secretariat Universitetsparken 15 DK-2100 Copenhagen, Denmark email: <mailto:atalavan@gbif.org> atalavan(a)gbif.org web: http://www.gbif.org/ T: +45 35 32 14 83 F: +45 35 32 14 80 From: Alberto González-Talaván (GBIF) [mailto:atalavan@gbif.org] Sent: Tuesday, October 13, 2009 5:47 PM To: ipt(a)lists.gbif.org Subject: [IPT] Set of short presentations about IPT Dear friends of the IPT list, During the last meeting of the GBIF Governing Board we had a 1,5 hours session on the IPT addressed to GBIF Node Managers (those in charge of coordinating the biodiversity information networks that form GBIF). We tried to keep this session basic in the technical level, but informative for anyone who is evaluating the IPT as an alternative for biodiversity data publishing. I would like to share with you the presentations displayed during that season. I hope you can use them in future IPT promotional activities. There are 6 very short presentations, that could be easily merged into a single one if needed. The original presentations are in English. Does anyone volunteer to translate them into other languages and share them with the community? If you are interested drop me an email and we will coordinate the efforts! The presentations are hosted in the GBIF Community Site, that is still in its closed alpha testing phase. Once the open beta testing starts, I trust we will used it also for interactions regarding the IPT. I will inform the list when this happens. With best regards Alberto 1.- Introduction: http://elggtest.gbif.org/pg/file/atalavan/read/2400/ipt-training-introducti… 2.- Basic requirements to have an IPT installation http://elggtest.gbif.org/pg/file/atalavan/read/2407/ipt-training-basic-requ… 3.- IPT Data Interfaces http://elggtest.gbif.org/pg/file/atalavan/read/2414/ipt-training-data-inter… 4.- IPT User Interface http://elggtest.gbif.org/pg/file/atalavan/read/2421/ipt-training-user-inter… 5.- Customisation and internationalisation of the GBIF IPT http://elggtest.gbif.org/pg/file/atalavan/read/2428/ipt-training-customisat… 6.- Extensions http://elggtest.gbif.org/pg/file/atalavan/read/2435/ipt-training-extensions ---------- Alberto GONZÁLEZ TALAVÁN Training Officer Global Biodiversity Information Facility Secretariat Universitetsparken 15 DK-2100 Copenhagen, Denmark email: <mailto:atalavan@gbif.org> atalavan(a)gbif.org web: http://www.gbif.org/ T: +45 35 32 14 83 F: +45 35 32 14 80

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Improvements for the IPT documentation
by Arnaud Réveillon 15 Dec '09

15 Dec '09

Dear all, I am at last going to start working on the IPT documentation again, first to fix issues that may be present in the current version (available on the wiki) then to add some new sections. I would like to ask you, as users of the IPT, to help me find out what needs to be done to improve the documentation. First, could you let me know of any issues you have or have had with it? As it has not been modified since its first release, I am convinced there are things to be clarified, improvements to be made, errors to be fixed, etc., and I would like users to let me know about them. Second, could you also let me know of any improvements, any new sections or any new features you would like to see added to the documentation. We will review these requests and decide whether or not they should be included in future releases of the documentation. Thank you, Arnaud Réveillon-

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IPT training opportunity in Ghana
by Alberto González-Talaván (GBIF) 14 Dec '09

14 Dec '09

Dear friends from the IPT list, George Owusu-Afriyie from GhanaBIF (GBIF Ghana, http://www2.ug.edu.gh/ghanabif/) is seeking IPT experts to help them with a training event for 12 institutions within the country. The event will be held in English, in Ghana (probably Accra). The dates are not set and will have to be arranged between the organisers and the potential trainers. This activity will very likely include the installation of a national IPT instance for the GhanaBIF. As previously announced, the participation of the trainers in this activity (= travel + accommodation + per diem) is eligible for financial support from the GBIF distributed helpdesk grants. If you are interested in collaborating with GhanaBIF, please contact me or George directly in his email address: georgeoa AT 4u.com.gh. Thanks in advance Alberto ---------- Alberto GONZÁLEZ TALAVÁN Training Officer Global Biodiversity Information Facility Secretariat Universitetsparken 15 DK-2100 Copenhagen, Denmark email: <mailto:atalavan@gbif.org> atalavan(a)gbif.org web: http://www.gbif.org/ T: +45 35 32 14 83 F: +45 35 32 14 80

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Re: [IPT] IPT multiple source files
by "Markus Döring (GBIF)" 08 Dec '09

08 Dec '09

Hannu, I am afraid the current version doesnt allow to map multiple sources files to "the core". The darwin core archive format allows for this, but we havent implemented that in the IPT yet. It is a missing feature that has been reported to me before, so I have added a feature request to the code site: http://code.google.com/p/gbif-providertoolkit/issues/detail?id=249 anyone supporting this request please star the issue or comment on it! Markus On Dec 8, 2009, at 11:30, Andrea Hahn (GBIF Helpdesk) wrote: > Hi Markus, > > Would you be able to answer Hannu's first question, regarding multiple source files? I am not sure I completely understand the scenario, but I could imagine (as he is a user of the old "GBIF portal toolkit") that he is trying to upload one dataset from multiple source files. In the toolkit, those could just be glued together after upload. Is there provision for this in the IPT, or should the whole resource be coming as one file? > > Many thanks! > Andrea > > From: Hannu Saarenmaa [mailto:hannu.saarenmaa@helsinki.fi] > Sent: Tuesday, December 08, 2009 10:25 AM > To: GBIF Helpdesk > Cc: Mikko Koho; Nina M Laurenne > Subject: IPT multiple source files > > Hello > > We have just successfully published our first dataset from IPT! > > However, there are two Source Files, and only the first one was exported to the cache. There seems to be no way to add mapping for the other to Darwin Core, only to extensions. Both files can be seen in the pulldown menu Add New Mapping. What to do? > > Furthermore, why did I get 5 emails like below, all at the same minute. Why? > > Hannu > > -------- Original Message -------- > Subject: > GBIF: New UDDI Registration for the resource 'Hymenoptera Collection of the Finnish Museum of Natural History' > Date: > Tue, 8 Dec 2009 10:12:11 +0100 (CET) > From: > registry(a)gbif.org > To: > hannu.saarenmaa(a)helsinki.fi > CC: > helpdesk(a)gbif.org > > > Dear Hannu Saarenmaa: > > A new resource has been registered under your organisation 'Finnish Museum of Natural History' to the GBIF UDDI registry, with the following information: > > - Resource Name: Hymenoptera Collection of the Finnish Museum of Natural History > - Description: This resource contains Hymenoptera data from the collection of the Finnish Museum of Natural History. It also contains field observation data gathered by scientists. > - Primary Contact Type: administrative > - Primary Contact Name: Juho Paukkunen > - Primary Contact Email: juho.paukkunen(a)helsinki.fi > If you think this registration is erroneous or would just want to request further information on the registration process, please contact GBIF's Help Desk (helpdesk(a)gbif.org) > > - GBIF (Global Biodiversity Information Facility) > http://www.gbif.org > helpdesk(a)gbif.org > > > > -- > Hannu Saarenmaa > Senior Curator (yli-intendentti) > Finnish Museum of Natural History > P.O. Box 17 (P.Rautatiekatu 13) > FIN-00014 University of Helsinki > > hannu.saarenmaa(a)helsinki.fi > Telephone +358-9-191-28688 > Mobile +358-50-3102689 > http://www.gbif.fi/

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Re: [IPT] Question sur l'IPT
by "Markus Döring (GBIF)" 08 Dec '09

08 Dec '09

Mélianie, if you use the IPT as a hosted service and not in a local network there are several things to consider: a) it is unlikely that your system admin will open the database ports to the internet. Therefore you will only be able to upload text files into the IPT which you will need to export from the original provider database. The other option you have is to host a copy of the original database as it is in their original database system at GBIF france. This way the IPT can read locally from the DB. But it requires you to host a variety of systems and people to dump their entire database. I would think the ttext file approach is more likely - but maybe a mixed approach would work too. b) in any case the IPT always reads in an entire dataset, even if only few records have changed. There are some technical and some usability reasons for this c) the current IPT needs to be linked to a single organisation, so the resource metadata will always point to this single organisation. This is obviously not suited for hosting datasets from across the country. We plan to release a new version 1.1 at the end of march to address this, which is specifically targeted at an hosted environment. Markus On Dec 8, 2009, at 9:12, Mélianie Raymond (GBIF) wrote: > Dear Tim, Andrea and Marcus, > > I'm forwarding you a question from Delphine Gasc from GBIF France concerning > the IPT. She has asked me to help translate the question so here goes: > > GBIF France is planning to install a public IPT installation to test the > scenario in which different users could connect their data via a central IPT > installation. They are starting with a 'test' data provider who has asked > them a question regarding database updates. If they have already connected > their database to the central IPT installation and then update it, do they > need to send the whole updated database to GBIF France (and GBIF France will > then do the replacement) or should they just send the new data points (and > then GBIF France should just add these)? What is accepted by the IPT? > > Would any of you be able to help clarify this? Or point us in the right > direction? > > Thanks! > > Mélianie > > > --------------------------------------- > Mélianie Raymond > Programme Assistant for Nodes > GBIF Secretariat > Universitetsparken 15 > DK-2100 Copenhagen, Denmark > Tel.: +45 35 32 14 96 / Fax: +45 35 32 14 80 > E-mail: mraymond(a)gbif.org > URL: www.gbif.org > > > > > > -----Original Message----- > From: Delphine Gasc [mailto:gasc@gbif.fr] > Sent: Monday, December 07, 2009 4:58 PM > To: Melianie Raymond (GBIF) > Subject: Question sur l'IPT > > Bonjour Mélianie, > > J'espère que le temps n'est pas trop mauvais à Copenhague. > Le retour de Madagascar s'est bien passé? > > J'ai une question concernant l'IPT, et je ne sais pas trop à qui la > poser (ni comment la poser en anglais) donc je fais appel à toi. > > Nous envisageons d'installer un IPT public au GBIF France afin de tester > l'IPT en situation réelle pour connecter des bases françaises. Le > fournisseur qui nous servira de test demande comment se passeront les > mises à jour : devra-t-il nous renvoyer toute sa base mise à jour (et > donc on fera du remplacement), ou bien simplement les nouveaux > enregistrements (et on fera de l'ajout). > Je ne sais pas ce qui est accepté par l'IPT. > > Peux-tu te renseigner là-dessus pour moi s'il te plait? > > Bonne fin de journée > Delphine > > >

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IPT and 32 bit vs 64 bit servers
by Russell, Laura 04 Dec '09

04 Dec '09

Is there any issue with running IPT on a 64 bit Fedora virtual machine? (We've also tried on 64 bit Ubuntu and Centos virtual machines as well) I seem to remember something about this from IPT training, but I don't have any notes on it. Or maybe I'm missing something else. Geoserver starts up, but not IPT. Pasted IPT content from the log file below. In the mean time, going back to configuring a 32 bit to see if we can get that one working. Thanks for the help. Laura Log File for IPT content: catalina.out Dec 3, 2009 3:40:00 PM org.apache.catalina.startup.HostConfig deployWAR INFO: Deploying web application archive ipt.war Resolved relative path / with servlet context : /usr/share/tomcat5/webapps/ipt/ Resolved relative path /data with servlet context : /usr/share/tomcat5/webapps/ipt/data Resolved relative path / with servlet context : /usr/share/tomcat5/webapps/ipt/ Resolved relative path /data with servlet context : /usr/share/tomcat5/webapps/ipt/data ERROR main-[/ipt].filterStart(3639) | Exception starting filter struts javax.xml.transform.TransformerFactoryConfigurationError: Provider org.apache.xalan.processor.TransformerFactoryImpl not found at javax.xml.transform.TransformerFactory.newInstance(TransformerFactory.java:120) at com.opensymphony.xwork2.util.DomHelper$DOMBuilder.<clinit>(DomHelper.java:167) at com.opensymphony.xwork2.util.DomHelper.parse(DomHelper.java:115) at com.opensymphony.xwork2.config.providers.XmlConfigurationProvider.loadConfigurationFiles(XmlConfigurationProvider.java:830) at com.opensymphony.xwork2.config.providers.XmlConfigurationProvider.loadDocuments(XmlConfigurationProvider.java:131) at com.opensymphony.xwork2.config.providers.XmlConfigurationProvider.init(XmlConfigurationProvider.java:100) at com.opensymphony.xwork2.config.impl.DefaultConfiguration.reload(DefaultConfiguration.java:130) at com.opensymphony.xwork2.config.ConfigurationManager.getConfiguration(ConfigurationManager.java:52) at org.apache.struts2.dispatcher.Dispatcher.init_PreloadConfiguration(Dispatcher.java:395) at org.apache.struts2.dispatcher.Dispatcher.init(Dispatcher.java:452) at org.apache.struts2.dispatcher.FilterDispatcher.init(FilterDispatcher.java:201) at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:221) at org.apache.catalina.core.ApplicationFilterConfig.setFilterDef(ApplicationFilterConfig.java:302) at org.apache.catalina.core.ApplicationFilterConfig.<init>(ApplicationFilterConfig.java:78) at org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:3635) at org.apache.catalina.core.StandardContext.start(StandardContext.java:4222) at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760) at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:740) at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:544) at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:831) at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:720) at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:490) at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1150) at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:311) at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1022) at org.apache.catalina.core.StandardHost.start(StandardHost.java:736) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1014) at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443) at org.apache.catalina.core.StandardService.start(StandardService.java:448) at org.apache.catalina.core.StandardServer.start(StandardServer.java:700) at org.apache.catalina.startup.Catalina.start(Catalina.java:552) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295) at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433) Dec 3, 2009 3:40:05 PM org.apache.catalina.core.StandardContext start SEVERE: Error filterStart Dec 3, 2009 3:40:05 PM org.apache.catalina.core.StandardContext start SEVERE: Context [/ipt] startup failed due to previous errors Dec 3, 2009 3:40:06 PM org.apache.catalina.loader.WebappClassLoader loadClass INFO: Illegal access: this web application instance has been stopped already. Could not load org.apache.log4j.helpers.NullEnumeration. The eventual following stack trace is caused by an error thrown for debugging purposes as well as to attempt to terminate the thread which caused the illegal access, and has no functional impact. java.lang.IllegalStateException at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1272) at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1232) at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:332) at org.apache.log4j.Category.getAllAppenders(Category.java:410) at org.apache.velocity.runtime.log.SimpleLog4JLogSystem.shutdown(SimpleLog4JLogSystem.java:162) at org.apache.velocity.runtime.log.SimpleLog4JLogSystem.finalize(SimpleLog4JLogSystem.java:156) at java.lang.ref.Finalizer.invokeFinalizeMethod(Native Method) at java.lang.ref.Finalizer.runFinalizer(Finalizer.java:101) at java.lang.ref.Finalizer.access$100(Finalizer.java:32) at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:178) Laura Russell VertNet Programmer Biodiversity Institute University of Kansas Dyche Hall 1345 Jayhawk Blvd., Room 606 Lawrence, KS 66045 Phone: 785.864.4681 Fax: 785.864.5335 Email: larussell(a)ku.edu URL: http://www.vertnet.org VertNet Portals: MaNIS: http://www.manisnet.org <http://www.manisnet.org/> HerpNET: http://www.herpnet.org <http://www.herpnet.org/> ORNIS: http://www.ornisnet.org <http://www.ornisnet.org/> FishNet2: http://www.fishnet2.net <http://www.fishnet2.net/>

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Re: [IPT] Help for Dag
by "Markus Döring (GBIF)" 30 Nov '09

30 Nov '09

Dag, I have started a short wiki page for details on the IPT TAPIR implementation for everyone interested. Please feel invited to update it with anything you think is missing. http://code.google.com/p/gbif-providertoolkit/wiki/TapirImplementation Markus On Nov 30, 2009, at 9:45 AM, Dag Terje Filip Endresen wrote: > Hi Tim, > > This is absolutely NOT urgent! > > I was only playing around... > We are working on an EU application including a work-package for the > upgrade of the European distributed data network (ECPGR EURISCO). > The wiki page was meant as a reply to questions from the work- > package coordinator. One important objective besides harvesting > distributed genebank datasets - is to break crop based subsets out > from the EURISCO dataset (EURISCO being the central European portal/ > index). Crop based subsets for the crop specific sub-portals. > > I have started to play with the TapirLink toolkit: > http://www.nordgen.org/epgris3/wiki/index.php/TAPIR_DataInterface > > First I started only with the example Tapir Output Models from the > TDWG site. Running these I get an error that the FullScientificName > (ABCD) or the ScientificName (DwC) is not mapped. Running an > inventory on this term give me good results - so there must be > something with the output models I did not do correct when adopting > the examples :-) > > I was planning to use the IPT for the genebanks, but started to play > with the TapirLink TAPIR interface just to get more understanding of > how the TAPIR protocol works... > > Cheers > Dag > > From: Tim Robertson [mailto:trobertson@gbif.org] > To: Dag Terje Filip Endresen [mailto:dag.endresen@nordgen.org] > Cc: Markus Döring [mailto:mdoering@gbif.org] > Sent: Mon, 30 Nov 2009 09:16:20 +0100 > Subject: Re: Help for Dag > > Hi Dag, > > The output model in the IPT is a fixed one based on the star schema. > Could you please provide some more information (and perhaps a URL to > your IPT if it is public) so that Markus and I can help? > > Thanks > Tim > > > On Nov 28, 2009, at 9:28 AM, Samy Gaiji (GBIF) wrote: > > > Dag: "Do you know the TAPIR output models...? I started to play with > > them a little today, but so far I did not get an output model I > > like. Using the examples there are taxon terms I did not map from > > the NordGen providers making errors messages." > > > > Could you please provide him some clarifications? > > > > Best regards > > > > ____________________________________________________________ > > > > Samy Gaiji > > Head of Informatics > > Global Biodiversity Information Facility Secretariat (GBIF) > > Universitetsparken 15, 2100 Copenhagen Ø, Denmark > > http://www.gbif.org > > sgaiji(a)gbif.org > > Phone: +45 35 32 14 85 (Direct) +45 35 32 14 70 (Office) > > Fax: +45 35 32 14 80 > > Skype: sgaiji > > ____________________________________________________________ > > > > "It is not the strongest of the species that survives, nor the most > > intelligent that survives. It is the one that is the most adaptable > > to change." > > Charles Darwin > > > > > > > > > > >

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Feedback for the IPT from NODES
by Dag Terje Filip Endresen 27 Nov '09

27 Nov '09

Dear all, During the previous NODES meeting at GB16 in October, the NODES meeting asked for a development process for the GBIF toolkits. The NODES wanted to develop requirements and request features as input to the GBIF secretariat and other developers for the toolkits. Mihail of DanBIF have helped us to start a group for this purpose at the new GBIF community site. http://elggtest.gbif.org/pg/groups/2678/gbif-tools-advisory-groups/ Here you will find a discussion page for the IPT, HIT and the NPT toolkit as well as for the GBRDS. Feedback to this group is of course welcome also from participants outside of the NODES community. We will share important feedback and suggestions back to this IPT mailing list. With this email I would like to share the IPT feature request from NODES regarding the possibility to group users and datasets at the local IPT installation. Some NODES have asked for the possibility to create a subgroup with users allowed to add datasets to only this group. And a group administrator with permissions to add new users only to this subgroup. There have also been feedback that at least two levels for the subgroups would be valuable (institution top group and department/collection sub group). http://elggtest.gbif.org/pg/pages/view/3959/ best regards Dag Endresen

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GBIF GB informed about new IPT resources and opportunities
by Alberto González-Talaván (GBIF) 23 Nov '09

23 Nov '09

Dear members of the IPT list, Just wanted to send an update about a couple of IPT-related issues: the release of the IPT Training CD and the financial support available for IPT helpdesk and training activities. The GBIF Governing Board has already been informed about this. The message sent to them is pasted below. If any of you with experience on the IPT wants to join the Experts Network on IPT Helpdesk and Training, please let me know and I will send you an invitation to join the group in the GBIF Community Test Site. With best regards Alberto -------------- Dear Members of the GBIF Governing Board: A training CD, based on materials from the Helpdesk <http://www.gbif.org/participation/training/events/training-event-details/?e ventid=70> Experts Workshop on the GBIF Integrated Publishing Toolkit (IPT) has just been released. This CD is a compilation of presentations, promotional materials, technical documents, videos and online resources about the GBIF IPT. It represents a complete set of materials for those willing to collaborate in the deployment and dissemination of this recently released biodiversity data publishing tool. The CD image is available in the training resources section of the GBIF website: http://www.gbif.org/participation/training/resources/gbif-training-cds/ As a result of the above mentioned training event, an Experts Network on IPT Helpdesk and Training has been created. Those interested in having an IPT instance running but lack the technical capacity needed can request technical support from the group, or from the expert who they have a the closest affinity to (geographically, in language, work area, etc). Financial support is available from the GBIF Distributed Helpdesk System if travelling on-site is required for the helpdesk or training activities. Please contract Andrea Hahn (ahahn(a)gbif.org) or Alberto González-Talaván (atalavan(a)gbif.org) if you want to apply for this financial support. We look forward your proposals and feedback on IPT implementation, promotional and training activities. With best regards Alberto PS: This information is also available as a news item in the GBIF website: http://www.gbif.org/communications/news-and-events/showsingle/article/gbif-i pt-new-resources-and-opportunities/ --- Members of the Experts Network on IPT Helpdesk and Training: · Akbaraly, <http://www.gbif.org/communications/directory-of-contacts/contact-details/?I D=1931> Michael (France, Europe) · Akpona, <http://www.gbif.org/communications/directory-of-contacts/contact-details/?I D=1921> Adéloui Hugues (Benin, Africa) · Chen, <http://www.gbif.org/communications/directory-of-contacts/contact-details/?I D=1932> Elie (Chinese Taipei, Asia) · Daly, <http://www.gbif.org/communications/directory-of-contacts/contact-details/?I D=62> Brenda (South Africa, Africa) · Desmet, <http://www.gbif.org/communications/directory-of-contacts/contact-details/?I D=1887> Peter (Canada, North America) · <http://www.gbif.org/communications/directory-of-contacts/contact-details/?I D=74> Endresen, Dag Terje Filip (Sweden, Europe) · Graf <http://www.gbif.org/communications/directory-of-contacts/contact-details/?I D=635> , Mickaël (Sweden, Europe) · <http://www.gbif.org/communications/directory-of-contacts/contact-details/?I D=1922> Haefeli, Inés Amalia (Argentina, Latin America) · Holetschek, <http://www.gbif.org/communications/directory-of-contacts/contact-details/?I D=724> Jörg (Germany, Europe) · Jinbo, <http://www.gbif.org/communications/directory-of-contacts/contact-details/?I D=797> Utsugi (Japan, Asia) · Kim, <http://www.gbif.org/communications/directory-of-contacts/contact-details/?I D=1979> DaeHwan (Rep. of Korea, Asia) · Lange, <http://www.gbif.org/communications/directory-of-contacts/contact-details/?I D=906> Christian (Denmark, Europe) · Lusa, <http://www.gbif.org/communications/directory-of-contacts/contact-details/?I D=960> Silvia (Spain, Europe) · <http://www.gbif.org/communications/directory-of-contacts/contact-details/?I D=1920> Moreno Vargas, Diego Alexander (Colombia, Latin America) · Noé, <http://www.gbif.org/communications/directory-of-contacts/contact-details/?I D=1924> Nicolas (Belgium, Europe) · <http://www.gbif.org/communications/directory-of-contacts/contact-details/?I D=1942> Pîzzigatti Correa, Pedro Luiz (Brazil, Latin America) · <http://www.gbif.org/communications/directory-of-contacts/contact-details/?I D=1938> Rasoamanana, Mbolatiana Toky (Madagascar, Africa) · Russell, <http://www.gbif.org/communications/directory-of-contacts/contact-details/?I D=1912> Laura (USA, North America) · <http://www.gbif.org/communications/directory-of-contacts/contact-details/?I D=1929> Sanabria Rodríguez, Aurelio (Costa Rica, Latin America) · <http://www.gbif.org/communications/directory-of-contacts/contact-details/?I D=1923> Sotillo Enriquez, Arelys (Cuba, Latin America) · Theeten, <http://www.gbif.org/communications/directory-of-contacts/contact-details/?I D=1790> Franck (Belgium, Europe) ---------- Alberto GONZÁLEZ TALAVÁN Training Officer Global Biodiversity Information Facility Secretariat Universitetsparken 15 DK-2100 Copenhagen, Denmark email: atalavan(a)gbif.org web: http://www.gbif.org/ T: +45 35 32 14 83 F: +45 35 32 14 80

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