- IPT - lists.gbif.org

IPT Workbook - try it today!
by Kyle Braak [GBIF] 11 Feb '13

11 Feb '13

Hi IPT list, I am writing to inform everybody on the list about the existence of an IPT Workbook. Originally written by Burke and I as a companion for an IPT Experts Workshop in 2011, the workbook puts together a comprehensive set of practice problems for installing, configuring, and using the IPT to publish biodiversity datasets. The problems vary in their level of difficulty, but no matter how hard the problem is, helpful hints are provided to help guide the reader through them. Never before has there been a more fun way to learn how to master the IPT! In my opinion, if you can solve the entire workbook, you can consider yourself an IPT expert. To get started, download the workbook and the required sample datasets folder. With kind regards, Kyle PS: Feedback to help improve the workbook is always welcome.

1 0

error publishing resource,
by BROSENS, Dimitri 10 Jan '13

10 Jan '13

Dear, IPT returns me an error while updating a resource. I think it s rather strange as it worked for all the updating of similar other query 's. I removed the connection to the db completely, retried and it gives me exactly the same error. I also totally removed the data and tried to update..; same error. Any ideas? Chrs, Dimi Ps: happy NY :) WARN Vocabulary URI http://rs.gbif.org/vocabulary/gbif/life_stage exists already - overwriting with new vocabulary from http://rs.gbif.org/vocabulary/gbif/life_stage.xml WARN Vocabulary URI http://rs.gbif.org/vocabulary/gbif/nomenclatural_code exists already - overwriting with new vocabulary from http://rs.gbif.org/vocabulary/gbif/nomenclatural_code.xml WARN Vocabulary URI http://rs.gbif.org/vocabulary/gbif/establishment_means/ exists already - overwriting with new vocabulary from http://rs.gbif.org/vocabulary/gbif/establishment_means.xml WARN Vocabulary URI http://iso.org/639-1 exists already - overwriting with new vocabulary from http://rs.gbif.org/vocabulary/iso/639-1.xml WARN Vocabulary URI http://dublincore.org/documents/dcmi-type-vocabulary/ exists already - overwriting with new vocabulary from http://rs.gbif.org/vocabulary/dcterms/type.xml WARN Vocabulary URI http://rs.gbif.org/vocabulary/gbif/agentRole exists already - overwriting with new vocabulary from http://rs.gbif.org/vocabulary/gbif/agent_role.xml WARN Vocabulary URI http://iso.org/639-2 exists already - overwriting with new vocabulary from http://rs.gbif.org/vocabulary/iso/639-2.xml WARN Vocabulary URI http://rs.gbif.org/vocabulary/gbif/resource_type exists already - overwriting with new vocabulary from http://rs.gbif.org/vocabulary/gbif/resource_type.xml WARN Vocabulary URI http://rs.tdwg.org/dwc/dwctype/ exists already - overwriting with new vocabulary from http://rs.gbif.org/vocabulary/dwc/basis_of_record.xml WARN Vocabulary URI http://rs.gbif.org/vocabulary/gbif/occurrence_status/ exists already - overwriting with new vocabulary from http://rs.gbif.org/vocabulary/gbif/occurrence_status.xml WARN Vocabulary URI http://rs.gbif.org/vocab/boolean/ exists already - overwriting with new vocabulary from http://rs.gbif.org/vocabulary/basic/boolean.xml WARN Vocabulary URI http://iso.org/iso3166-1/alpha2 exists already - overwriting with new vocabulary from http://rs.gbif.org/vocabulary/iso/3166-1_alpha2.xml WARN Vocabulary URI http://rs.gbif.org/vocabulary/gbif/preservation_method exists already - overwriting with new vocabulary from http://rs.gbif.org/vocabulary/gbif/preservation_method.xml WARN Vocabulary URI http://rs.gbif.org/vocabulary/gbif/rank exists already - overwriting with new vocabulary from http://rs.gbif.org/vocabulary/gbif/rank.xml WARN Vocabulary URI http://rs.gbif.org/vocab/cites/ exists already - overwriting with new vocabulary from http://rs.gbif.org/vocabulary/un/cites_appendix.xml WARN Vocabulary URI http://rs.gbif.org/vocabulary/iucn/threat_status/ exists already - overwriting with new vocabulary from http://rs.gbif.org/vocabulary/iucn/threat_status.xml WARN Vocabulary URI http://rs.gbif.org/vocabulary/gbif/sex exists already - overwriting with new vocabulary from http://rs.gbif.org/vocabulary/gbif/sex.xml ERROR Error publishing resource java.lang.NullPointerException at org.gbif.ipt.task.Eml2Rtf.addMethods(Eml2Rtf.java:547) at org.gbif.ipt.task.Eml2Rtf.writeEmlIntoRtf(Eml2Rtf.java:927) at org.gbif.ipt.service.manage.impl.ResourceManagerImpl.publishRtf(ResourceManagerImpl.java:810) at org.gbif.ipt.service.manage.impl.ResourceManagerImpl.publishMetadata(ResourceManagerImpl.java:788) at org.gbif.ipt.service.manage.impl.ResourceManagerImpl.publish(ResourceManagerImpl.java:741) at org.gbif.ipt.action.manage.OverviewAction.publish(OverviewAction.java:354) 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 com.opensymphony.xwork2.DefaultActionInvocation.invokeAction(DefaultActionInvocation.java:452) at com.opensymphony.xwork2.DefaultActionInvocation.invokeActionOnly(DefaultActionInvocation.java:291) at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:254) at com.opensymphony.xwork2.interceptor.DefaultWorkflowInterceptor.doIntercept(DefaultWorkflowInterceptor.java:176) at com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:98) at com.google.inject.struts2.Struts2Factory$ProvidedInterceptor.intercept(Struts2Factory.java:215) at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:248) at com.opensymphony.xwork2.validator.ValidationInterceptor.doIntercept(ValidationInterceptor.java:263) at org.apache.struts2.interceptor.validation.AnnotationValidationInterceptor.doIntercept(AnnotationValidationInterceptor.java:68) at com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:98) at com.google.inject.struts2.Struts2Factory$ProvidedInterceptor.intercept(Struts2Factory.java:215) at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:248) at com.opensymphony.xwork2.interceptor.ConversionErrorInterceptor.intercept(ConversionErrorInterceptor.java:133) at com.google.inject.struts2.Struts2Factory$ProvidedInterceptor.intercept(Struts2Factory.java:215) at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:248) at com.opensymphony.xwork2.interceptor.ParametersInterceptor.doIntercept(ParametersInterceptor.java:207) at com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:98) at com.google.inject.struts2.Struts2Factory$ProvidedInterceptor.intercept(Struts2Factory.java:215) at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:248) at com.opensymphony.xwork2.interceptor.ParametersInterceptor.doIntercept(ParametersInterceptor.java:207) at com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:98) at com.google.inject.struts2.Struts2Factory$ProvidedInterceptor.intercept(Struts2Factory.java:215) at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:248) at org.apache.struts2.interceptor.MultiselectInterceptor.intercept(MultiselectInterceptor.java:75) at com.google.inject.struts2.Struts2Factory$ProvidedInterceptor.intercept(Struts2Factory.java:215) at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:248) at org.apache.struts2.interceptor.CheckboxInterceptor.intercept(CheckboxInterceptor.java:94) at com.google.inject.struts2.Struts2Factory$ProvidedInterceptor.intercept(Struts2Factory.java:215) at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:248) at com.opensymphony.xwork2.interceptor.PrepareInterceptor.doIntercept(PrepareInterceptor.java:166) at com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:98) at com.google.inject.struts2.Struts2Factory$ProvidedInterceptor.intercept(Struts2Factory.java:215) at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:248) at org.apache.struts2.interceptor.ServletConfigInterceptor.intercept(ServletConfigInterceptor.java:164) at com.google.inject.struts2.Struts2Factory$ProvidedInterceptor.intercept(Struts2Factory.java:215) at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:248) at com.opensymphony.xwork2.interceptor.ExceptionMappingInterceptor.intercept(ExceptionMappingInterceptor.java:187) at com.google.inject.struts2.Struts2Factory$ProvidedInterceptor.intercept(Struts2Factory.java:215) at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:248) at com.opensymphony.xwork2.interceptor.I18nInterceptor.intercept(I18nInterceptor.java:176) at com.google.inject.struts2.Struts2Factory$ProvidedInterceptor.intercept(Struts2Factory.java:215) at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:248) at org.gbif.ipt.struts2.RedirectMessageInterceptor.doIntercept(RedirectMessageInterceptor.java:128) at com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:98) at com.google.inject.struts2.Struts2Factory$ProvidedInterceptor.intercept(Struts2Factory.java:215) at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:248) at org.gbif.ipt.struts2.RequireManagerInterceptor.intercept(RequireManagerInterceptor.java:80) at com.google.inject.struts2.Struts2Factory$ProvidedInterceptor.intercept(Struts2Factory.java:215) at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:248) at org.gbif.ipt.struts2.SetupAndCancelInterceptor.intercept(SetupAndCancelInterceptor.java:60) at com.google.inject.struts2.Struts2Factory$ProvidedInterceptor.intercept(Struts2Factory.java:215) at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:248) at org.gbif.ipt.struts2.ResourceSessionInterceptor.intercept(ResourceSessionInterceptor.java:42) at com.google.inject.struts2.Struts2Factory$ProvidedInterceptor.intercept(Struts2Factory.java:215) at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:248) at org.apache.struts2.impl.StrutsActionProxy.execute(StrutsActionProxy.java:52) at org.apache.struts2.dispatcher.Dispatcher.serviceAction(Dispatcher.java:485) at org.apache.struts2.dispatcher.ng.ExecuteOperations.executeAction(ExecuteOperations.java:77) at org.apache.struts2.dispatcher.ng.filter.StrutsPrepareAndExecuteFilter.doFilter(StrutsPrepareAndExecuteFilter.java:91) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:66) at com.google.inject.servlet.ManagedFilterPipeline.dispatch(ManagedFilterPipeline.java:118) at com.google.inject.servlet.GuiceFilter.doFilter(GuiceFilter.java:113) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:859) at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:588) at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489) at java.lang.Thread.run(Thread.java:636) ERROR Error publishing resource java.lang.NullPointerException * * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * * * Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document.

2 1

Fwd: "Species Distribution" extension for Occurrence Core in IPT
by Tim Robertson [GBIF] 27 Nov '12

27 Nov '12

Dear IPT community, Please see the request below for using the species distribution extension [1] with occurrence core [2]. This request comes from Colombia, who are setting up an IPT network in the country. I don't see any issue with this, but wanted to put this through the correct forum (this list) for any comments. Does anyone have any concerns they would like to raise? Please note, that extensions are considered immutable in concept, although we allow for minor editorial changes. Therefore this request would warrant a version increment of the distribution extension; reflected in the namespace. IPTs would therefore see 2 species distribution extensions (the second having the new version). The current version cannot be removed as datasets already exist using it, but rather would be marked as "Deprecated" in the description so new installations and updates would show this. Thanks all, Tim [1] http://rs.gbif.org/extension/gbif/1.0/distribution.xml [2] http://rs.gbif.org/core/dwc_occurrence.xml Begin forwarded message: > From: Danny Vélez [mailto:evelez@humboldt.org.co] > Sent: 21 November 2012 20:58 > To: Éamonn Ó Tuama [GBIF] > Cc: Juan Carlos Bello; Core Equipo Coordinador SIB > Subject: "Species Distribution" extension for Occurrence Core in IPT > > Dear GBIF, > > We would like to ask GBIF for open the possibility to use "Species Distribution" extension for the Occurrence Core in the IPT. Currently is it allow only for Taxon Core. > > We need it because there are several Colombian data publishers that need to use several elements included in this extension, but in the context of an occurrence dataset –not Taxon dataset- some of those elements are for example "threatStatus" and "appendixCITES. > > Is there any special procedure for this? > > All the best, > > Danny > > -- > > > > > Danny Vélez > Líder Interoperabilidad y Administración de Contenidos > > Equipo Coordinador del Sistema de Información sobre Biodiversidad de Colombia (SiB) > > GBIF Node Manager Colombia > > Instituto de Investigación de Recursos Biológicos > Alexander von Humboldt > Calle 28A No. 15-09 > PBX: (57) 1 3202767 Ext. 2112 > Bogotá, D.C., Colombia > > > > > La información aquí contenida es para uso exclusivo de la persona o entidad de destino. Está estrictamente prohibida su utilización, copia, descarga, distribución, modificación y/o reproducción total o parcial, sin el permiso expreso del Instituto Humboldt, pues su contenido puede ser de carácter confidencial y/o contener material privilegiado. Si usted recibió esta información por error, por favor contacte en forma inmediata a quien lo envió y borre este material de su computador. El Instituto Humboldt no es responsable por la información contenida en esta comunicación, el directo responsable es quien la firma o el autor de la misma. El destinatario de este mensaje debe verificar con sus protecciones que el mismo no está afectado por virus u otros defectos. El remitente no asume responsabilidad alguna por el recibo, transmisión y uso de este material. > > Antes de imprimir este mensaje, piensa si realmente necesitas hacerlo. ¡Gracias! > > >

4 3

Re: [IPT] Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder
by Barker, Katharine 24 Oct '12

24 Oct '12

Dear John, Please see our working revisions/comments/questions on the DNA/tissue extension for Darwin Core (highlighted in blue). We were able to work through the draft up through "class sample properties": https://docs.google.com/document/d/1RCgIPfu9gAPubjjbog-9vCJonvqcK1pLOaq6H8G… The document is also attached for your reference (just incase any of you are unable to access the document). Please try to respond to our questions and comments prior to our meeting tomorrow (be sure to make these changes using a different color for tracking purposes). Tomorrow we will like to 1) briefly recap our revisions on the extension so far (addressing questions and comments), 2) complete our review of the extension and 3) identify any remaining issues with DwC working with IPT (and identify if any changes in the IPT are required). Thank you for your help on this! Kind Regards, Katie From: John Wieczorek <tuco(a)berkeley.edu<mailto:tuco@berkeley.edu>> Reply-To: "tuco(a)berkeley.edu<mailto:tuco@berkeley.edu>" <tuco(a)berkeley.edu<mailto:tuco@berkeley.edu>> Date: Sunday, October 21, 2012 10:52 PM To: Gabriele Droege <g.droege(a)bgbm.org<mailto:g.droege@bgbm.org>> Cc: Katharine Barker <barkerk(a)si.edu<mailto:barkerk@si.edu>>, Paul Flemons <Paul.Flemons(a)austmus.gov.au<mailto:Paul.Flemons@austmus.gov.au>>, John Deck <jdeck(a)berkeley.edu<mailto:jdeck@berkeley.edu>>, Robert Hanner <bob.hanner(a)gmail.com<mailto:bob.hanner@gmail.com>>, Éamonn Tuama <eotuama(a)gbif.org<mailto:eotuama@gbif.org>>, Robert Robbins <rjr8222(a)gmail.com<mailto:rjr8222@gmail.com>>, "Guentsch, Anton" <a.guentsch(a)bgbm.org<mailto:a.guentsch@bgbm.org>> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder Dear all, I finished working on the Google Doc "DNA Tissue Extension Notes - TDWG 2012". Feel free to let this be a working document where comments and questions can be added. I've attached a Word Doc version for archival purposes. I added the two template extension files (DNATissueExtension.txt and DNAAmplificationExtension.txt) to the shared TDWG GGBN working group folder linked below. They are in the form they need to be submitted to GBIF to be added to their extension registry. They would both need to be updated with the term descriptions, examples, and constraints. https://drive.google.com/#folders/0BxEyFKwB7zY4WEs0WkdtUU5oVnM Cheers, John On Sun, Oct 21, 2012 at 10:38 PM, John Wieczorek <tuco(a)berkeley.edu<mailto:tuco@berkeley.edu>> wrote: Ooops ...at http://goo.gl/kGHmb. Adding touches based on the files Gabi sent. Will tell you all when finished with that and will send it as a Word doc at that time in case there are any issues with Google docs. Should be soon. Let me know if I should share to any different addresses. Cheers, John On Sun, Oct 21, 2012 at 10:34 PM, John Wieczorek <tuco(a)berkeley.edu<mailto:tuco@berkeley.edu>> wrote: That helps a lot, as it clears up some of my own misconceptions. I have shared a document where I have captured the thinking behind a couple of different ways forward with one or two extensions and an example of how the two-extension might look in the context of a Darwin Core Archive. The DNA Tissue Extension Notes Google doc can be found at On Sun, Oct 21, 2012 at 9:23 PM, "Dröge, Gabriele" <g.droege(a)bgbm.org<mailto:g.droege@bgbm.org>> wrote: Yes we do... Hi John, Thanks for getting back to us. Attached are two csv files, one with some main DNA facts and the other with associated GenBank entries und publications (2 examples with 2 GenBank entries per DNA sample). I included only UnitID/CollCode/InstCode for the related voucher specimen and I excluded the tissue facts since they are quite similar to the DNA facts and should be mapped independently. Best, Gabi -----Original Message----- From: Barker, Katharine [mailto:BarkerK@si.edu<mailto:BarkerK@si.edu>] Sent: Sunday, October 21, 2012 11:41 PM To: Paul Flemons; Dröge, Gabriele Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder Paul and Gabi, Do we have any sample data that John can use as a test case? I think he would like it today, if possible. Thanks for your help (and the team work). Katie From: John Wieczorek <tuco(a)berkeley.edu<mailto:tuco@berkeley.edu><mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu>>> Reply-To: "tuco(a)berkeley.edu<mailto:tuco@berkeley.edu><mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu>>" <tuco(a)berkeley.edu<mailto:tuco@berkeley.edu><mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu>>> Date: Sunday, October 21, 2012 12:03 PM To: Katharine Barker <barkerk(a)si.edu<mailto:barkerk@si.edu><mailto:barkerk@si.edu<mailto:barkerk@si.edu>>> Subject: Re: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core-draft reminder Hi Katie, Messages received. Will have the extension stuff ready within a few hours and hope to be able to attend remotely. One thing in the meantime. Do you have any example data that could be used as a test case to populate a core with this extension? Would like to try that with some realy data to test my assumptions. Sorry for the delay. Thanks, John On Sun, Oct 21, 2012 at 10:08 AM, Barker, Katharine <BarkerK(a)si.edu<mailto:BarkerK@si.edu><mailto:BarkerK@si.edu<mailto:BarkerK@si.edu>>> wrote: Dear John, I'm sorry that you were unable to attain a visa for China. I was really looking forward to working with you in person with the group. Paul mentioned that he had e-mailed you earlier this evening. Can you please send us the draft for the DarwinCore DNA/tissue extension as soon as possible for review during our working sessions? We have one tomorrow at 1:30 (Beijing time) and another on Tuesday at the same time. It would be really great if you could Skype into either both or one of the sessions. Thanks for your help on this. Kind Regards, Katie From: <Barker>, Katharine Barker <barkerk(a)si.edu<mailto:barkerk@si.edu><mailto:barkerk@si.edu<mailto:barkerk@si.edu>><mailto:barkerk@si.edu<mailto:barkerk@si.edu><mailto:barkerk@si.edu<mailto:barkerk@si.edu>>>> Date: Thursday, October 18, 2012 1:34 PM To: Katharine Barker <barkerk(a)si.edu<mailto:barkerk@si.edu><mailto:barkerk@si.edu<mailto:barkerk@si.edu>><mailto:barkerk@si.edu<mailto:barkerk@si.edu><mailto:barkerk@si.edu<mailto:barkerk@si.edu>>>>, 'John Deck' <jdeck(a)berkeley.edu<mailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edu>><mailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edu>>>>, Paul Flemons <Paul.Flemons(a)austmus.gov.au<mailto:Paul.Flemons@austmus.gov.au><mailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.au>><mailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.au><mailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.au>>>>, "'\"Dröge", Éamonn Tuama <eotuama(a)gbif.org<mailto:eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org>><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org>>>>, "Whitacre, Jamie" <WHITACREJ(a)si.edu<mailto:WHITACREJ@si.edu><mailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edu>><mailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edu><mailto:WHITACREJ@si.edu<mailto:WHITACREJ@si.edu>>>>, "'rjr8222(a)gmail.com<mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com>><mailto:'rjr8222(a)gmail.com<mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com>>>'" <rjr8222(a)gmail.com<mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com>><mailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com>>>>, "'a.guentsch(a)bgbm.org<mailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org>><mailto:'a.guentsch(a)bgbm.org<mailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org>>>'" <a.guentsch(a)bgbm.org<mailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org>><mailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org>>>>, "'gtuco.btuco(a)gmail.com<mailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com>><mailto:'gtuco.btuco(a)gmail.com<mailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com>>>'" <gtuco.btuco(a)gmail.com<mailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com>><mailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com>>>>, "'tuco(a)berkeley.edu<mailto:tuco@berkeley.edu><mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu>><mailto:'tuco(a)berkeley.edu<mailto:tuco@berkeley.edu><mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu>>>'" <tuco(a)berkeley.edu<mailto:tuco@berkeley.edu><mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu>><mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu><mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu>>>> Cc: "'morrison(a)cs.man.ac.uk<mailto:morrison@cs.man.ac.uk><mailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.uk>><mailto:'morrison(a)cs.man.ac.uk<mailto:morrison@cs.man.ac.uk><mailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.uk>>>'" <morrison(a)cs.man.ac.uk<mailto:morrison@cs.man.ac.uk><mailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.uk>><mailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.uk><mailto:morrison@cs.man.ac.uk<mailto:morrison@cs.man.ac.uk>>>>, "Parr, Cynthia" <parrc(a)si.edu<mailto:parrc@si.edu><mailto:parrc@si.edu<mailto:parrc@si.edu>><mailto:parrc@si.edu<mailto:parrc@si.edu><mailto:parrc@si.edu<mailto:parrc@si.edu>>>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week Dear all, This is a friendly reminder that we will be meeting next Tuesday afternoon at the TDWG 2012 Conference in order to finalize the draft DarwinCore-A DNA/tissue extension for GGBN. As you know, the immediate need for GGBN members is to publish information on tissues. This will happen through extensions to both ABCDDNA and DarwinCore-A. Here we are focused on developing the DarwinCore-A DNA/tissue extension. An update on the timeline for developing the draft DarwinCore-A DNA/tissue extension is listed below. 1) Review content requirements for DarwinCore-A DNA/tissue extension (completed, see attached required DNA and tissue elements) 2) John Weiczorek will develop the draft DarwinCore-A DNA/tissue extension (to be completed for group review prior to our break out session on Tuesday afternoon, October 23). 3) Tuesday October 23, working meeting · Questions to answer before final review of DNA/tissue extension o How do we include repeatable elements of ABCDDNA into DwC-A-DNA (References to more than one sequence record/publication are mandatory)? o How do we extend the "Basis of Record" in ABCD and DwC-A and how do we include an element similar to ABCD-"Kind of Unit" to DwC-A? o What are the remaining issues for DwC-A working with IPT? Are any changes in the IPT required? · Review and finalize draft DarwinCore-A DNA/tissue extension for posting to GBIF site. Thank you again to everyone who is involved in this project. I look forward to seeing all of you in Beijing. Kind Regards, Katie From: Barker, Katharine Sent: Friday, September 28, 2012 9:53 AM To: 'John Deck'; Paul Flemons; "Dröge, Gabriele"; eotuama(a)gbif.org<mailto:eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org>><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org>>>; Whitacre, Jamie; rjr8222(a)gmail.com<mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com>><mailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com>>>; a.guentsch(a)bgbm.org<mailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org>><mailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org>>>; gtuco.btuco(a)gmail.com<mailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com>><mailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com>>>; tuco(a)berkeley.edu<mailto:tuco@berkeley.edu><mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu>><mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu><mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu>>> Subject: RE: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week Dear all, We will be meeting this Tuesday at 1pm U.S. Eastern time over Skype in order to discuss the actions required to develop the draft proposal for the Darwin Core tissue/DNA extension. A proposal for designing, testing, and implementing the GGBN data portal is attached for your reference. Please review the timeline and action items leading up to the TDWG 2012 Conference. My Skype name is Katharine.Barker1. If possible, please forward me your skype account names prior to our meeting. Kind Regards, Katie From:jdeck88@gmail.com<mailto:From%3Ajdeck88@gmail.com><mailto:From%3Ajdeck88@gmail.com<mailto:From%253Ajdeck88@gmail.com>><mailto:jdeck88@gmail.com<mailto:jdeck88@gmail.com><mailto:jdeck88@gmail.com<mailto:jdeck88@gmail.com>>> [mailto:jdeck88@gmail.com<mailto:jdeck88@gmail.com><mailto:jdeck88@gmail.com<mailto:jdeck88@gmail.com>>] On Behalf Of John Deck Sent: Tuesday, September 25, 2012 4:04 PM To: Barker, Katharine Cc: Paul Flemons; "Dröge, Gabriele"; eotuama(a)gbif.org<mailto:eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org>><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org>>>; Whitacre, Jamie; rjr8222(a)gmail.com<mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com>><mailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com>>>; a.guentsch(a)bgbm.org<mailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org>><mailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org>>>; gtuco.btuco(a)gmail.com<mailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com>><mailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com>>>; tuco(a)berkeley.edu<mailto:tuco@berkeley.edu><mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu>><mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu><mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu>>> Subject: Re: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core//Telecon next week Here is the wrapup of the bioCollections Ontology workshop from last week at GSC14: http://biocodecommons.org/workshops/bioCollections/index.html This is relevant to these discussions since we focussed on what constitutes a "sample" and also, probably more importantly, processes that work with samples. We briefly discussed the DwC Tissue Extension and came up with a proposal for a quick-fix and a more substantial fix. The quick-fix is to create two new BasisOfRecord terms: TissueSubSample, DNAExtract (or some terms like that -- Tuco could provide more clarification on this too). Thus, theoretically we could override the dwc:Occurrence class to mean, for example, TissueSubSample the same way we do for Specimens and Observations. The bigger fix is to more fundamentally re-orient DwC around the notion of "Sample", involving adding/changing some properties although we didn't get into any specifics. P.s. I can do the 12/1/2 timeslots for that monday or tuesday but not the 11. John On Mon, Sep 24, 2012 at 12:39 PM, Barker, Katharine <BarkerK(a)si.edu<mailto:BarkerK@si.edu><mailto:BarkerK@si.edu<mailto:BarkerK@si.edu>><mailto:BarkerK@si.edu<mailto:BarkerK@si.edu><mailto:BarkerK@si.edu<mailto:BarkerK@si.edu>>>> wrote: Dear all, We will have a telecon meeting early next week in order to discuss a draft proposal for the Darwin Core tissue/DNA extension. Gabi, Paul, and I will put together a first draft for discussion to be distributed prior to the telecon. As you know, the goal is to have a working draft ready for our working group to review at the TDWG meeting in Beijing this October. These are our options for meeting next week: Monday 11am, 12pm, 1pm, 2pm US EDT Tuesday 11am, 12pm, 1pm, 2pm US EDT Please let me know if you cannot make one of these times. Thanks again to those of you who provided input last week at the GSC 14 meeting. Kind Regards, Katie From: Barker, Katharine Sent: Wednesday, September 12, 2012 10:51 AM To: 'Paul Flemons'; "Dröge, Gabriele"; eotuama(a)gbif.org<mailto:eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org>><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org><mailto:eotuama@gbif.org<mailto:eotuama@gbif.org>>>; Whitacre, Jamie; 'rjr8222(a)gmail.com<mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com>><mailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com><mailto:rjr8222@gmail.com<mailto:rjr8222@gmail.com>>>'; jdeck(a)berkeley.edu<mailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edu>><mailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edu>>>; 'a.guentsch(a)bgbm.org<mailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org>><mailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org>>>'; 'gtuco.btuco(a)gmail.com<mailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com>><mailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com><mailto:gtuco.btuco@gmail.com<mailto:gtuco.btuco@gmail.com>>>'; 'tuco(a)berkeley.edu<mailto:tuco@berkeley.edu><mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu>><mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu><mailto:tuco@berkeley.edu<mailto:tuco@berkeley.edu>>>' Subject: FW: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core Importance: High Dear all, My name is Katie Barker and I am the Global Genome Biodiversity Network Coordinator. As you know from Paul Flemons, members of the GGBN Data Standards and Data Access Task Force are trying to pull together a task group, which you are all part of, for the upcoming TDWG meeting in Beijing this October in order to address a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members. I am contacting you to schedule a meeting in late September/early October to develop a draft proposal for this extension to be completed at the upcoming TDWG meeting. Please let me know your availability for the last two weeks of September and first two weeks of October. There will be some scheduling issues, as there are task group members on the west and east coasts of the U.S., Europe and Australia. Paul Flemons (in Australia) will be in the U.S. the first week of October, so maybe we can meet in the afternoon of the 1st, anytime on the second 2nd, or in the morning of the 3rd of October over teleconference (US Eastern Daylight Time). Please let me know if any of these time slots work for you. Gabi, I believe that you and John Deck will be at the GSC 14 meeting next week. Is there any chance that you can start drawing up an outline for the proposed extension? We could review the outline during our group telecon and start drafting a proposal for review at the TDWG meeting in October. Kind Regards, Katie Task Group Members: John Weiczorek - Berkeley Éamonn O'Tuama - GBIF Jamie Whitacre - SI John Deck - Berkeley Robert Robbins - University of California, San Diego Anton Guentsch - BGBM Gabi Droege- BGBM Paul Flemons- AM From: Paul Flemons [mailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.au><mailto:Paul.Flemons@austmus.gov.au<mailto:Paul.Flemons@austmus.gov.au>>] Sent: Tuesday, August 07, 2012 2:50 AM To: tuco(a)berkley.edu<mailto:tuco@berkley.edu><mailto:tuco@berkley.edu<mailto:tuco@berkley.edu>><mailto:tuco@berkley.edu<mailto:tuco@berkley.edu><mailto:tuco@berkley.edu<mailto:tuco@berkley.edu>>>; a.guentsch(a)bgbm.org<mailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org>><mailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org><mailto:a.guentsch@bgbm.org<mailto:a.guentsch@bgbm.org>>>; j.holetschek(a)bgbm.org<mailto:j.holetschek@bgbm.org><mailto:j.holetschek@bgbm.org<mailto:j.holetschek@bgbm.org>><mailto:j.holetschek@bgbm.org<mailto:j.holetschek@bgbm.org><mailto:j.holetschek@bgbm.org<mailto:j.holetschek@bgbm.org>>>; jdeck(a)berkeley.edu<mailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edu>><mailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edu><mailto:jdeck@berkeley.edu<mailto:jdeck@berkeley.edu>>> Cc: Barker, Katharine; Éamonn Ó Tuama [GBIF]; "Dröge, Gabriele" (g.droege(a)BGBM.ORG<mailto:g.droege@BGBM.ORG><mailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.ORG>><mailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.ORG><mailto:g.droege@BGBM.ORG<mailto:g.droege@BGBM.ORG>>>) Subject: Meeting at TDWG 2012 to define a tissue/DNA extension for Darwin Core Hi all, I am on the Data Standards and Access Task Force for the Global Genome Biodiversity Network (http://ggbn.org/) which is in need of a Darwin Core extension to enable data sharing of tissues and DNA data amongst its members. To this end I am writing to you to ask if you would be interested in participating in a small working group at TDWG in Beijing this year. At this stage my plan would be to identify relevant fields for inclusion in the extension, using ABCDDNA as a reference. If sufficient progress is made then we would submit the extension for ratification by TDWG (is that how its done John?) The GGBN will use whatever comes out of the group to move towards having a suitable DwC based schema for data sharing. So please let me know if you are willing to participate in the task group and/or if there is anyone else you feel would be beneficial to have involved. How much time do you think we will need? I have been thinking that a day will be needed, so we could make that consist of either one full day or two half days. Im also thinking that during the week will be the best time for this. Thanks for your time Best Regards Paul Paul K J Flemons Manager, Collection Informatics Team Lead, Atlas of Living Australia Biodiversity Volunteer Portal<http://volunteer.ala.org.au> Biodiversity Information Standards (TDWG) Representative for Oceania Australian Museum 6 College Street Sydney NSW 2010 Australia t 61 2 9320 6343 m 0413458649 f 61 2 9320 6021 Visit: http://www.australianmuseum.net.au<http://www.australianmuseum.net.au/> Like: http://www.facebook.com/australianmuseum Follow: http://www.twitter.com/austmus Watch: http://www.youtube.com/austmus [cid:image001.png@01CDAD34.391DC790<mailto:image001.png@01CDAD34.391DC790><mailto:image001.png@01CDAD34.391DC790<mailto:image001.png@01CDAD34.391DC790>>] Inspiring the exploration of nature and cultures [cid:image002.jpg@01CDAD34.391DC790<mailto:image002.jpg@01CDAD34.391DC790><mailto:image002.jpg@01CDAD34.391DC790<mailto:image002.jpg@01CDAD34.391DC790>>] The Australian Museum. The views in this email are those of the user and do not necessarily reflect the views of the Australian Museum. The information contained in this email message and any accompanying files is or may be confidential and is for the intended recipient only. If you are not the intended recipient, any use, dissemination, reliance, forwarding, printing or copying of this email or any attached files is unauthorised. If you are not the intended recipient, please delete it and notify the sender. The Australian Museum does not guarantee the accuracy of any information contained in this e-mail or attached files. As Internet communications are not secure, the Australian Museum does not accept legal responsibility for the contents of this message or attached files. Please consider the environment before printing this email. This e-mail message has been scanned for Viruses and Content and cleared by MailMarshal. -- John Deck (541) 321-0689<tel:%28541%29%20321-0689><tel:%28541%29%20321-0689>

8 18

IPT v2.0.4 released
by Kyle Braak [GBIF] 18 Oct '12

18 Oct '12

Dear IPT users, The GBIF Secretariat is pleased to announce that a new release of the Integrated Publishing Toolkit (IPT v2.0.4) is now available for download here. Since the last version was released in November 2011, the growing user community has been actively reporting enhancement requests and minor bugs. A total of 108 issues were addressed in IPT version 2.0.4; 38 Defects, 35 Enhancements, 7 Other, 5 Patches, 18 Won't fix, 4 Duplicates, and 1 that was considered as Invalid. These are detailed in the issue tracking system. A few notable improvements to the User Interface include: Translation into Traditional Chinese Clearer setup pages aimed at preventing users from installing the IPT in the test mode unwittingly Improved user friendliness, done by adding more context help and better navigation between pages A couple of new features added in this release are: Resource migration: allows an IPT resource to replace the registration of an existing DiGIR, BioCASE, or TAPIR resource in the GBRDS [instructions] Creating a resource from an archived resource folder: allows a resource to be transferred between 2 IPTs including all its source files and mappings [instructions] As always, we’d like to give special thanks to the volunteer translators for their time and efforts: Nicolas Noé (Belgian Biodiversity Platform, Belgium) - French TaiBIF, Taiwan - Traditional Chinese Laura Roldan Gomez, Dairo Escobar, and Daniel Amariles, (Colombian Biodiversity Information System (SiB)) - Spanish Another couple of special mentions are owed to Peter Desmet and Laura Russell who provided an exceptional amount of feedback and suggestions. We highly recommend previous versions to be updated. Updating an IPT 2.0.x installation can be done in 3 simple steps: Replace the previous .war file with the latest edition Backup the existing data directory Reuse the existing data directory during setup New users should follow the installation guidelines in the IPT User Manual that has been updated for this version. A Spanish version of the IPT User Manual is also available now thanks to the volunteers from SiB. Thank you once again for using the IPT, and we hope you enjoy the latest version. With kind regards, Kyle, on behalf of the IPT development team and the GBIF Secretariat

3 2

FW: IPT Zip File Upload - Not Successful
by Palanisamy, Giri 14 Oct '12

14 Oct '12

Hi, Can you please help us solve the following issues? Derek is using the USGS IPT installation at http://bison.ornl.gov/ipt (Version 2.0.2-r3306) Thanks! Giri From: Derek Masaki The zip file upload to the IPT was not successful. I was able to zip the csv to an acceptable size and added it to the resource, however the file appears unreadable. See screen capture below [cid:part1.05060404.05000600@usgs.gov] -- From: Derek Masaki Subject: IPT Max File Size Limit Hello, Ran into this error in attempting upload of MARIS - screenshot image below. This is a 1million record dataset. The file size limit on the IPT appears to be set at 100mb. I'm going to run compression to create a zip archive as it appears that IPT may be able to handle a zip file. Is there any way to increase the file size limit? Thanks, -derek [cid:image001.png@01CDA863.F439CDB0] -- Derek Masaki U.S. Geological Survey Biological Data Manager - Core Science Analytics and Synthesis Geospatial Liaison - National Geospatial Program 310 W Kaahumanu Ave, Kahului HI 96732 Ph 808-358-2497 dmasaki(a)usgs.gov<mailto:dmasaki@usgs.gov>

3 10

Classloader leak in IPT
by Derek Broughton 01 Oct '12

01 Oct '12

I'm running IPT in Tomcat and experiencing PermGen memory errors. >From the Tomcat Manager, I can use "Find Leaks", and as suspected get: "The following web applications were stopped (reloaded, undeployed), but their classes from previous runs are still loaded in memory, thus causing a memory leak (use a profiler to confirm): /ipt" http://frankkieviet.blogspot.ca/2006/10/classloader-leaks-dreaded-permgen-s… does a pretty good job of explaining _why_ this happens. Unfortunately, I can't seem to find part two which is supposed to tell me how to go about fixing it. His blog also only deals with memory leaks on redeployment, but this is happening any time IPT is running for a while, so IPT is leaking in ordinary use, rather than just at context initialization. I'm going to try to find what's happening with a profiler, but I'm new to this... Tomcat Version 6.0.35 JVM Version Sun 1.6.0_24-b07 Linux 2.6.24-28-generic amd64 -- derek

4 6

Updating registration of vocabularies results in startup warning
by DESMET, Peter 12 Sep '12

12 Sep '12

Hi, I just updated the registration of the vocabularies on http://ipt.inbo.be, which resulted in an error I don't understand. Can anyone help? Thanks, Peter The issue is recorded at: http://code.google.com/p/gbif-providertoolkit/issues/detail?id=913 What steps will reproduce the problem? 1. Browsed to the http://ipt.inbo.be<http://ipt.inbo.be/> administration panel > Core Types and Extensions 2. Updated the registration of the 9 vocabularies 3. This resulted in an error, which reads in the log file as: WARN Updating IPT instance throught GBIF Registry WARN Vocabulary URI http://rs.gbif.org/vocabulary/gbif/agentRole exists already - overwriting with new vocabulary from http://rs.gbif.org/vocabulary/gbif/agent_role.xml WARN Cant parse local vocabulary file org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId. at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1234) at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:525) ... 4. A yellow warning is shown across the top of every page, even for not logged-in users: "IPT startup warnings, please see logs!" What version of the provider software are you using? The version should be displayed in the footer of any page. Version 2.0.3-r3672<http://code.google.com/p/gbif-providertoolkit/source/detail?r=3672> * * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * * * Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document.

1 0

JDBC Connection to MS Access
by Dan Lear 10 Sep '12

10 Sep '12

Hi, I want to connect to a MS Access database to pull-in Source Data. But get the following error: Couldnt create new external datasource connection with JDBC Class=sun.jdbc.odbc.JdbcOdbcDriver, URL=jdbc:odbc:SMSGMR, user=. Error: [unixODBC][Driver Manager]Data source name not found, and no default driver specified I have a local System DSN set up, but presumably need to bridge between ODBC and JDBC, so is this a problem that is fixed by editing jdbc.properties as detailed here: http://code.google.com/p/gbif-providertoolkit/wiki/IPT2DatabaseConnection If not, can anyone enlighten me as to how to connect to an MS Access table? Thanks Dan

1 0

Experience installing IPT on Ubuntu w/ Tomcat
by Derek Broughton 05 Aug '12

05 Aug '12

I just thought I'd share my experience installing IPT into a Tomcat (5.5 - but experience suggests 6 or 7 wouldn't have helped) installed from Ubuntu packages. In a nutshell: don't try it! Ubuntu's packages (and I imagine Debian or any Debian-based system, though I haven't confirmed that) block the normal logging available from the stock Apache versions of Tomcat. What logging there is, gets diverted to the system log (where it is both poorly formatted - no newlines - and truncated). More logging becomes available if you edit 03catalina.policy: // These permissions apply to JULI grant codeBase "file:${catalina.home}/bin/tomcat-juli.jar" { permission java.security.AllPermission; }; but in itself that isn't enough to get logging for IPT, and the IPT install fails, but is unable to log the cause of the failure (which I think is the inability to write to the log, but never managed to prove). The simple solution is to: - download Tomcat 6 from Apache (http://tomcat.apache.org/download-60.cgi - the tar.gz Binary version), - untar it anywhere (I put it in /opt), - optionally create a symbolic link from /opt/tomcat to the /opt/apache-tomcat* directory you have just created - stop your existing tomcat , - copy all .war files from /var/lib/tomcat*/webapps to the /opt/tomcat/webapps (you may want to copy the subdirectories from there too, if you have applications that store data in them) - start your new server with /opt/tomcat/bin/startup.sh (setting the environment variable JAVA_OPTS first, with any values that must be passed - for instance, our GeoServer app requires "-D GEOSERVER_DATA_DIR=/opt/geoserver/data") Don't forget to replace /etc/init.d/tomcat* with an appropriate script to start/stop the new tomcat using /opt/tomcat/bin/startup.sh & shutdown.sh -- derek broughton Pointerstop Consulting (for OBIS Canada)

2 3