- IPT - lists.gbif.org

Non-Latin characters support in IPT
by David Remsen (GBIF) 23 Nov '09

23 Nov '09

Can someone clarify if non-Latin character sets are supported in the IPT and if not, what would it take to support them. In haste from GBIF Asian Nodes meeting David Remsen

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Re: [IPT] Set of short presentations about IPT
by Alberto González-Talaván (GBIF) 13 Nov '09

13 Nov '09

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/> 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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Login page missing in French installation
by John R. WIECZOREK 13 Nov '09

13 Nov '09

We think it would be extremely helpful from the development standpoint to remove Appfuse from IPT. It has taken about a week to figure out the of not seeing the login page as Michael Akbaraly discovered and reported. It turns out, after some three-way troubleshooting this morning, that the Login screen invokes appfuse for authentication and can't read the struts properties. This results in a blank login page (no source either) whenever the system language is not english. Michael changed his Ubuntu system language setting to english and ran the application and it worked fine. Supporting evidence comes when running revision 1646 in an english environment. Run the IPT, select the flag for France and the interface changes to French (except for the version in the footer - different manifestation of the same problem?). Select the "Connexion" button - the login page does appear, but using only the default properties (it appears all in English, including the version).

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Set of short presentations about IPT
by Alberto González-Talaván (GBIF) 11 Nov '09

11 Nov '09

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-introductio n 2.- Basic requirements to have an IPT installation http://elggtest.gbif.org/pg/file/atalavan/read/2407/ipt-training-basic-requi rements 3.- IPT Data Interfaces http://elggtest.gbif.org/pg/file/atalavan/read/2414/ipt-training-data-interf aces 4.- IPT User Interface http://elggtest.gbif.org/pg/file/atalavan/read/2421/ipt-training-user-interf ace 5.- Customisation and internationalisation of the GBIF IPT http://elggtest.gbif.org/pg/file/atalavan/read/2428/ipt-training-customisati on-and-internationalisation 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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Fwd: found a bit...
by Tim Robertson 11 Nov '09

11 Nov '09

Dear Fabian, Is your IPT available on the internet? If so could you please provide a URL and I will take a look. If not, could you please select "explore", choose your dataset and then select "webservices & resources" and send me the zip file downloaded when you select the "data archive"? Many thanks, Tim On Nov 11, 2009, at 8:47 AM, Fabian Haas wrote: > 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 > _______________________________________________ > IPT mailing list > IPT(a)lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt >

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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 09 Nov '09

09 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 04 Nov '09

04 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)" 09 Oct '09

09 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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