- IPT - lists.gbif.org

found a bit...
by Fabian Haas 11 Nov '09

11 Nov '09

thats what is says now: Resource Complete import took 255216 ms * IPT * 11-Nov-2009 10:34:02 * close somehow it imported/chache 9000 datasets while the excel sheet has something short of 400 Best -- ********************************************************** fhaas(a)icipe.org, Extension -2052 The African Insect Taxonomy Toolkit AITT http://taxonomy.icipe.org Dr. Fabian Haas Insect Taxonomist and ABS Specialist ICIPE - African Insect Science for Food and Health Duduville Campus, Kasarani P.O. Box 30772 - 00100 N A I R O B I Kenya Telephone No. +254 (0)20 8632000 Fax No. +254 (0)20 8632001 Cell Phone +254 (0)728 132868 This position is supported by CIM, the Centre for International Migration www.cimonline.de

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IPT crashes
by Nicolas Noé 10 Nov '09

10 Nov '09

Hi, Our IPT instance (1.0 RC2) just started crash whenever I click on the "Explore" button, with following java exception, does anyone have an idea about how we could track this ? javax.servlet.ServletException: r.recTotal is undefined. 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$VirtualFilterChain.doFilter(FilterChainProxy.java:371) at org.springframework.security.util.FilterChainProxy.doFilter(FilterChainProxy.java:174) at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:236) at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:167) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:96) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:174) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:874) at org.apache.coyote.http11.Http11BaseProtocol$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(Thread.java:595) A user also reported the following NullPointerException, but I'm not sure about what he was doing at the time : java.lang.NullPointerException at org.apache.struts2.views.jsp.ComponentTagSupport.doStartTag(ComponentTagSupport.java:50) at org.apache.jsp._403_jsp._jspx_meth_s_005ftext_005f0(_403_jsp.java:177) at org.apache.jsp._403_jsp._jspx_meth_c_005fset_005f1(_403_jsp.java:150) at org.apache.jsp._403_jsp._jspService(_403_jsp.java:96) at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98) at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:331) at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:329) at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265) at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679) at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:463) at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:399) at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301) at org.apache.catalina.core.StandardHostValve.custom(StandardHostValve.java:364) at org.apache.catalina.core.StandardHostValve.status(StandardHostValve.java:285) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:137) 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:874) 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(Thread.java:595) Thanks again i will try to find precise ways to reproduct these errors, because our IPT instance is very unstable at the moment ! Have a nice day ! Nicolas -- Nicolas Noé (IT software engineer) Belgian Biodiversity Platform <http://www.biodiversity.be> ULB, Campus de la Plaine, CP 257, B-1050 Brussels Tel:+32 2 650 5752 Fax: +32 2 650 5124

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Generation of GUIDs in IPT
by Steve Baskauf 05 Nov '09

05 Nov '09

I am attempting to educate myself about IPT and to do so have read the User Manual and looked at the website. In the May 2009 version of the manual on p.35 it says that a GUID for the record is optional but will be generated automatically if not mapped. I have been unable to find details about how this works. What I am curious about is: 1. What type of GUID is generated (LSID, http uri, or something else)? 2. If it is either an LSID or http uri based on the format of an LSID, what is the authority? gbif.org ? 3. If it is either an LSID or http uri based on the format of an LSID, how is the namespace determined? Is this assigned by GBIF or negotiated during the process of setting up the IPT instance? I'm assuming that the identifier part of the LSID (if it is LSID-related) is the source ID provided by the user. Thanks, Steve Baskauf -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: VU Station B 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 343-6707 http://bioimages.vanderbilt.edu

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darwin core archive meta.xml validator
by "Markus Döring (GBIF)" 10 Oct '09

10 Oct '09

Dear all, I wanted to share my little servlet that validates a meta.xml descriptor for darwin core archives. This is a simple xml file that provides the information about the layout of text data files, mainly which column represents which darwin core term. People often want to handcraft darwin core archives as it is so simple to dump data straight from a database into text files. This tool helps to make sure that the descriptor, which usually is a static write-it- once file, is valid without knowing how to use oxygen or other xml tools. http://ecat-ws.gbif.org/dwca-validator/ regards, Markus

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Some questions from developer from China
by 许哲平 09 Oct '09

09 Oct '09

Dear Sir: The Chinese Virtual Herbarium (CVH) is an on-line portal allowing access to herbarium specimen information and other botanical knowledge(online from 2006). CVH is a collaboration among more than 20 major herbaria in China with the aim of creating comprehensive and sustainable access to scholarly resources about China’s plant biodiversity. From last year, we have made our new effort to develop a newer and more powerful CVH system. We have taken following computer techniques: Ajax: Jquery,XML,json Database: Mysql Language: PHP, Java Data Standards: LSID, Darwin Core, IPTC, GIS: Google Map & Google Earth, GBIF IPT(in the future) DEMO PAGE: Beta Homepage of Chinese Virtual Herbarium: http://beta.cvh.org.cn/cms/ ,the current Homepage is : http://www.cvh.org.cn Name LSID: http://beta.cvh.org.cn/lsid/index.php?lsid=urn:lsid:cvh.org.cn:names:cnpc_1… Specimen LSID: http://beta.cvh.org.cn/groups/hgas/specimen.php?lsid=urn:lsid:cvh.org.cn:sp… Data Partner: http://beta.cvh.org.cn/groups/hgas/lsid.php?lsid=urn:lsid:cvh.org.cn:names:… Google Earth Plugin for Plant Photo In China: http://beta.cvh.org.cn/cms/cn/node/57 You are welcome to make some comments and feedback about our work. And, as we will want to take GBIF IPT in our future work. So we wonder how to (or can we) join the develop group or is the code in Google Code(http://code.google.com/p/gbif-providertoolkit/) the latest code? Regards, Xu Zheping Ph.D. Director Assistant of Center for Documentation and Information, Institute of Botany, the Chinese Academy of Sciences, Haidian,B eijing P. R. of China, 100093

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resource identifier on the IPT instance page?
by Wm.A.Stafford 30 Sep '09

30 Sep '09

The 'Resource Identifier' contains the text "Not registered with GBIF". Does this mean that my organization is really not registered after finally making it past the Organization page? If so, is there a way to tell why registration failed? Second question. What does the point given by lat/lon represent? The location of the organization? Thanks, -=bill

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Can't get past the Organization page
by Wm.A.Stafford 30 Sep '09

30 Sep '09

I probably am doing something really stupid but I seem to be stuck on the Organization page. When I select the title of my organization all fields but 'organization password' pre-fill. If I select 'resend password' I get: org.springframework.mail.MailSendException: Mail server connection failed; nested exception is javax.mail.MessagingException: Unknown SMTP host: aaa.gbif.org; nested exception is: java.net.UnknownHostException: aaa.gbif.org org.springframework.mail.javamail.JavaMailSenderImpl.doSend(JavaMailSenderImpl.java:419) So the GBIF email address is not configured correctly. I probably missed a step in the setup. Where is this done? Thanks, -=bill

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Organization password
by Wm.A.Stafford 29 Sep '09

29 Sep '09

How do I find out what the Organization password is? Thanks, -=bill

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IPT Contributors Group
by Aaron Steele 12 Sep '09

12 Sep '09

We wanted to announce a new group for people to discuss IPT development stuff (e.g. design, building, submitting patches) called IPT Contributors: http://groups.google.com/group/gbif-ipt-contributors Anyone can join, and even if you don't submit code, your participation is a valuable contribution.

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Re: [IPT] IPT Production installations, Extensions
by Holetschek, Jörg 04 Sep '09

04 Sep '09

Hi Markus, same here... coordinates are correct for the Berlin installation! http://de.mirror.gbif.org/ipt/occDetail.html?guid=19e5f679-7ac6-45f3-9f8c-b… Cheers from Berlin, Jörg -----Ursprüngliche Nachricht----- Von: Dag Terje Filip Endresen [mailto:dag.endresen@nordgen.org] Gesendet: Donnerstag, 3. September 2009 14:41 An: "Markus Döring (GBIF)"; Holetschek, Jörg Cc: Tim Robertson; gbif-ipt-contributors(a)googlegroups.com Betreff: Re: AW: AW: AW: AW: AW: AW: [IPT] IPT Production installations, Extensions Hi Markus, Great! I replaced the file occurence.ftl for the NordGen IPT, and the coordinates are now correctly displayed on Windows XP (in Parallels) with both Google Chrome and Internet Explorer (v6). These two browsers displayed the wrong location earlier. I attach a screenshoot before and after replacing the occurrence.ftl file. http://ipt.nordgen.org/ipt/occ/aef6f23f-99c4-47ea-b994-7f58129a0f29 Cheers Dag Terje _____ From: "Markus Döring (GBIF)" [mailto:mdoering@gbif.org] To: Jörg Holetschek [mailto:j.holetschek@bgbm.org] Cc: Tim Robertson [mailto:trobertson@gbif.org], Dag Terje Filip Endresen [mailto:dag.endresen@nordgen.org], gbif-ipt-contributors(a)googlegroups.com Sent: Thu, 03 Sep 2009 14:07:32 +0200 Subject: Re: AW: AW: AW: AW: AW: AW: [IPT] IPT Production installations, Extensions Ahh, here we go! This might be the famous locale setting again. It doesnt seem to understand the doubles cause they use dots instead of commas or vice versa and treats them as integers. I am pretty sure thats why. Let me check... So it seems I had fixed that in the admin settings, but apparently not on the record detail. Can you try and see that if on browsers where the points are wrong the IPT location given in the admin ipt configuration is still correct and not rounded? Attached is a new version of the template for the record detail, can you try to replace the following with the attached file and see if that removes the problem? WEB-INF/pages/portal/occ/occurrence.ftl I have also committed the change to SVN already, ipt-lite is not affected as it doesnt have the built in portal. Markus

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