- IPT - lists.gbif.org

Running IPT in Netbeans for Debugging
by Sarfaraz Ahmed Soomro 13 Jun '12

13 Jun '12

Hi I am new to IPT and I want to be able to run IPT using Netbeans and the attached Tomcat Server with Netbeans. Right now if I do Run Project in Netbeans it gives the error "Deployment error: No archive for deployment" If I do "Clean and Build Project" it would just startup the Jetty server that's bundled with IPT. Is it possible to be able to run IPT with the attached Tomcat server instance in Netbeans so I can do debugging on the code as well. Thanks, Sarfaraz

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Re: [IPT] CentOS IPT Install
by Laura Russell 05 Apr '12

05 Apr '12

Hi Tim and Burke, Yes still having issues. Tried Kyle's suggestion on Friday. Didn't work, but did cause a connection refused error in Apache. I just read Burke's suggestion below and my our IT admin here at KU just suggested the same thing. Going to recommend to Field IT. Stan Blum also indicated that he had issues with CentOS 5 and Tomcat 5 and went with fresh installs on a virtual server and Tomcat 6. Can't do a fresh system install in this situation, but might be able to update to Tomcat 6. Going to investigate the SELinux policy settings first. I'll keep the list posted as to the resolution. Thanks. 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)vertnet.org Email: larussell(a)ku.edu Google Chat: larussell(a)vertnet.org Skype: laura.anne.russell URL: http://www.vertnet.org VertNet Portals: MaNIS: http://www.manisnet.org HerpNET: http://www.herpnet.org ORNIS: http://www.ornisnet.org FishNet2: http://www.fishnet2.net From: "Burke Chih-Jen Ko [GBIF]" <bko(a)gbif.org> Date: Mon, 26 Mar 2012 11:38:55 +0200 To: Laura Russell <larussell(a)vertnet.org> Cc: "Tim Robertson [GBIF]" <trobertson(a)gbif.org> Subject: Re: [IPT] CentOS IPT Install Hi Laura, Perhaps you would also want to check the SELINUX policy settings on the CentOS box. I happened to similar situations when every setting is honoured and it turns out the SELINUX add another layer of filtering communications of the linux box. Cheers, Burke On Mar 26, 2012, at 9:10 AM, Tim Robertson [GBIF] wrote: > Hi Laura > > After our Skype session, is this still an issue? > > For the benefit of the list: We found that using the terminal the machine > could not open connections to itself on port 8080. We found this using curl > > Cheers, > Tim > > > > On Mar 23, 2012, at 5:57 PM, Laura Russell wrote: > >> I'm having difficulty with a CentOS IPT Install that I'm doing for the Field >> Museum (in Chicago, I'm remote to their server from Kansas). The Field IT >> staff enabled their Tomcat on the server. And I've deployed the IPT. >> Permissions on the iptdata folder seem to be okay as it created all the >> folders and extension files in the first step. >> >> They are running >> CentOS 5.2 >> Tomcat 5.5.23 >> Java 1.6 >> >> I'm getting the following error when trying to complete the second setup page >> on the IPT. >> >> "The Base URL does not point to an IPT installation that is accessible from >> this computer." >> >> The URL is accessible outside of the firewall. I've also tried it with the >> IP address and get the same error. >> >> I chatted with Tim Robertson a bit yesterday and I've had the Field IT staff >> check that the port is open for both incoming and outgoing connections. They >> do not think their firewall is the issue so I'm looking at other >> possibilities. >> >> I've attached the Catalina.out file and the IPT Admin and Debug logs. >> >> Any assistance is appreciated. >> >> Thanks. >> >> >> 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)vertnet.org >> Email: larussell(a)ku.edu >> Google Chat: larussell(a)vertnet.org >> Skype: laura.anne.russell >> >> URL: http://www.vertnet.org <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/> >> >> <FieldIPTerrors.zip>_______________________________________________ >> IPT mailing list >> IPT(a)lists.gbif.org >> http://lists.gbif.org/mailman/listinfo/ipt > > _______________________________________________ > IPT mailing list > IPT(a)lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt

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CentOS IPT Install
by Laura Russell 26 Mar '12

26 Mar '12

I'm having difficulty with a CentOS IPT Install that I'm doing for the Field Museum (in Chicago, I'm remote to their server from Kansas). The Field IT staff enabled their Tomcat on the server. And I've deployed the IPT. Permissions on the iptdata folder seem to be okay as it created all the folders and extension files in the first step. They are running CentOS 5.2 Tomcat 5.5.23 Java 1.6 I'm getting the following error when trying to complete the second setup page on the IPT. "The Base URL does not point to an IPT installation that is accessible from this computer." The URL is accessible outside of the firewall. I've also tried it with the IP address and get the same error. I chatted with Tim Robertson a bit yesterday and I've had the Field IT staff check that the port is open for both incoming and outgoing connections. They do not think their firewall is the issue so I'm looking at other possibilities. I've attached the Catalina.out file and the IPT Admin and Debug logs. Any assistance is appreciated. Thanks. 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)vertnet.org Email: larussell(a)ku.edu Google Chat: larussell(a)vertnet.org Skype: laura.anne.russell URL: http://www.vertnet.org VertNet Portals: MaNIS: http://www.manisnet.org HerpNET: http://www.herpnet.org ORNIS: http://www.ornisnet.org FishNet2: http://www.fishnet2.net

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All space-characters in metadata are replaced to plus-character
by Tero Mononen 10 Mar '12

10 Mar '12

Hi We have used this IPT-setup without any problems till now. System: Version 2.0.2-r3306 Apache Tomcat/6.0.24 JVM 1.6.0_29-b1 Problem: All space-characters in metadata are replaced to plus-character. For example title "foo bar car" is saved as "foo+bar+car". It affects in every text field in metadata. If I include at least one plus-char in a text value, it prevents the space replacement. For example "foo bar car+dar" is saved as it is. I think this is related to Java/Tomcat/urlencode. Do you have suggestions how to fix this problem? Best Regards, Tero Mononen -- Digitarium Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland Faculty of Science and Forestry, Joensuu Science Park Länsikatu 15 (P.O. Box 111) FI-80101 Joensuu http://www.digitarium.fi/ Tero Mononen, Analyst Programmer tero.mononen(a)uef.fi<mailto:juha.lehtonen@uef.fi> +358-50-5631788

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Running IPT under Mac OS X Server 10.6.8
by Skofic A. Milko (Bioversity - HQ) 30 Jan '12

30 Jan '12

Has anyone managed to make IPT run under Mac OS X Server 10.6.8 using the defaut installed Tomcat? In my case the installation works fine, but when I go to the site I get a bunch of errors. I am able to run the IPT with Jetty and if I made another installation of Tomcat I suspect it would also work, but that is just what I don't want to do: I would like to use the default installation. Any ideas? Running http://localhost:8080/ipt I get: type Exception report message description The server encountered an internal error () that prevented it from fulfilling this request. exception Unable to instantiate Action, org.gbif.ipt.action.portal.HomeAction, defined for '' in namespace '/'Caught Exception while registering Interceptor class org.gbif.ipt.struts2.SetupAndCancelInterceptor com.opensymphony.xwork2.DefaultActionInvocation.createAction(DefaultActionInvocation.java:318) com.opensymphony.xwork2.DefaultActionInvocation.init(DefaultActionInvocation.java:399) com.opensymphony.xwork2.DefaultActionProxy.prepare(DefaultActionProxy.java:198) org.apache.struts2.impl.StrutsActionProxy.prepare(StrutsActionProxy.java:61) org.apache.struts2.impl.StrutsActionProxyFactory.createActionProxy(StrutsActionProxyFactory.java:39) com.opensymphony.xwork2.DefaultActionProxyFactory.createActionProxy(DefaultActionProxyFactory.java:58) org.apache.struts2.dispatcher.Dispatcher.serviceAction(Dispatcher.java:475) org.apache.struts2.dispatcher.ng.ExecuteOperations.executeAction(ExecuteOperations.java:77) org.apache.struts2.dispatcher.ng.filter.StrutsPrepareAndExecuteFilter.doFilter(StrutsPrepareAndExecuteFilter.java:91) com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:66) com.google.inject.servlet.ManagedFilterPipeline.dispatch(ManagedFilterPipeline.java:118) com.google.inject.servlet.GuiceFilter.doFilter(GuiceFilter.java:113) root cause Caught Exception while registering Interceptor class org.gbif.ipt.struts2.SetupAndCancelInterceptor - interceptor - file:/Library/Tomcat/webapps/ipt/WEB-INF/classes/struts.xml:50:95 com.opensymphony.xwork2.ObjectFactory.buildInterceptor(ObjectFactory.java:213) com.google.inject.struts2.Struts2Factory.superBuildInterceptor(Struts2Factory.java:166) com.google.inject.struts2.Struts2Factory.access$200(Struts2Factory.java:45) com.google.inject.struts2.Struts2Factory$ProvidedInterceptor.inject(Struts2Factory.java:201) com.google.inject.struts2.Struts2Factory.createInjector(Struts2Factory.java:140) com.google.inject.struts2.Struts2Factory.buildBean(Struts2Factory.java:104) com.opensymphony.xwork2.ObjectFactory.buildBean(ObjectFactory.java:161) com.opensymphony.xwork2.ObjectFactory.buildBean(ObjectFactory.java:150) com.opensymphony.xwork2.ObjectFactory.buildAction(ObjectFactory.java:120) com.opensymphony.xwork2.DefaultActionInvocation.createAction(DefaultActionInvocation.java:299) com.opensymphony.xwork2.DefaultActionInvocation.init(DefaultActionInvocation.java:399) com.opensymphony.xwork2.DefaultActionProxy.prepare(DefaultActionProxy.java:198) org.apache.struts2.impl.StrutsActionProxy.prepare(StrutsActionProxy.java:61) org.apache.struts2.impl.StrutsActionProxyFactory.createActionProxy(StrutsActionProxyFactory.java:39) com.opensymphony.xwork2.DefaultActionProxyFactory.createActionProxy(DefaultActionProxyFactory.java:58) org.apache.struts2.dispatcher.Dispatcher.serviceAction(Dispatcher.java:475) org.apache.struts2.dispatcher.ng.ExecuteOperations.executeAction(ExecuteOperations.java:77) org.apache.struts2.dispatcher.ng.filter.StrutsPrepareAndExecuteFilter.doFilter(StrutsPrepareAndExecuteFilter.java:91) com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:66) com.google.inject.servlet.ManagedFilterPipeline.dispatch(ManagedFilterPipeline.java:118) com.google.inject.servlet.GuiceFilter.doFilter(GuiceFilter.java:113) root cause com.google.inject.ProvisionException: Guice provision errors: 1) Error injecting constructor, java.lang.InternalError: Can't connect to window server - not enough permissions. at org.gbif.ipt.task.Eml2Rtf.<init>(Eml2Rtf.java:75) at org.gbif.ipt.task.Eml2Rtf.class(Eml2Rtf.java:75) while locating org.gbif.ipt.task.Eml2Rtf for parameter 13 at org.gbif.ipt.service.manage.impl.ResourceManagerImpl.<init>(ResourceManagerImpl.java:127) at org.gbif.ipt.service.manage.impl.ResourceManagerImpl.class(ResourceManagerImpl.java:108) while locating org.gbif.ipt.service.manage.impl.ResourceManagerImpl while locating org.gbif.ipt.service.manage.ResourceManager for parameter 2 at org.gbif.ipt.service.admin.impl.UserAccountManagerImpl.<init>(UserAccountManagerImpl.java:65) at org.gbif.ipt.service.admin.impl.UserAccountManagerImpl.class(UserAccountManagerImpl.java:54) while locating org.gbif.ipt.service.admin.impl.UserAccountManagerImpl while locating org.gbif.ipt.service.admin.UserAccountManager for parameter 3 at org.gbif.ipt.config.ConfigManagerImpl.<init>(ConfigManagerImpl.java:64) at org.gbif.ipt.config.ConfigManagerImpl.class(ConfigManagerImpl.java:64) while locating org.gbif.ipt.config.ConfigManagerImpl while locating org.gbif.ipt.service.admin.ConfigManager for field at org.gbif.ipt.struts2.SetupAndCancelInterceptor.configManager(SetupAndCancelInterceptor.java:21) while locating org.gbif.ipt.struts2.SetupAndCancelInterceptor Caused by: java.lang.InternalError: Can't connect to window server - not enough permissions. at java.lang.ClassLoader$NativeLibrary.load(Native Method) at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1827) at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1724) at java.lang.Runtime.loadLibrary0(Runtime.java:823) at java.lang.System.loadLibrary(System.java:1045) at sun.security.action.LoadLibraryAction.run(LoadLibraryAction.java:50) at java.security.AccessController.doPrivileged(Native Method) at java.awt.Toolkit.loadLibraries(Toolkit.java:1605) at java.awt.Toolkit.<clinit>(Toolkit.java:1627) at java.awt.Color.<clinit>(Color.java:263) at org.gbif.ipt.task.Eml2Rtf.<init>(Eml2Rtf.java:77) at org.gbif.ipt.task.Eml2Rtf$$FastClassByGuice$$cad0309a.newInstance(<generated>) at com.google.inject.internal.cglib.reflect.$FastConstructor.newInstance(FastConstructor.java:40) at com.google.inject.internal.DefaultConstructionProxyFactory$1.newInstance(DefaultConstructionProxyFactory.java:60) at com.google.inject.internal.ConstructorInjector.construct(ConstructorInjector.java:85) at com.google.inject.internal.ConstructorBindingImpl$Factory.get(ConstructorBindingImpl.java:254) at com.google.inject.internal.ProviderToInternalFactoryAdapter$1.call(ProviderToInternalFactoryAdapter.java:46) at com.google.inject.internal.InjectorImpl.callInContext(InjectorImpl.java:1031) at com.google.inject.internal.ProviderToInternalFactoryAdapter.get(ProviderToInternalFactoryAdapter.java:40) at com.google.inject.Scopes$1$1.get(Scopes.java:65) at com.google.inject.internal.InternalFactoryToProviderAdapter.get(InternalFactoryToProviderAdapter.java:40) at com.google.inject.internal.SingleParameterInjector.inject(SingleParameterInjector.java:38) at com.google.inject.internal.SingleParameterInjector.getAll(SingleParameterInjector.java:62) at com.google.inject.internal.ConstructorInjector.construct(ConstructorInjector.java:84) at com.google.inject.internal.ConstructorBindingImpl$Factory.get(ConstructorBindingImpl.java:254) at com.google.inject.internal.ProviderToInternalFactoryAdapter$1.call(ProviderToInternalFactoryAdapter.java:46) at com.google.inject.internal.InjectorImpl.callInContext(InjectorImpl.java:1031) at com.google.inject.internal.ProviderToInternalFactoryAdapter.get(ProviderToInternalFactoryAdapter.java:40) at com.google.inject.Scopes$1$1.get(Scopes.java:65) at com.google.inject.internal.InternalFactoryToProviderAdapter.get(InternalFactoryToProviderAdapter.java:40) at com.google.inject.internal.InjectorImpl$3.get(InjectorImpl.java:737) at com.google.inject.internal.SingleParameterInjector.inject(SingleParameterInjector.java:38) at com.google.inject.internal.SingleParameterInjector.getAll(SingleParameterInjector.java:62) at com.google.inject.internal.ConstructorInjector.construct(ConstructorInjector.java:84) at com.google.inject.internal.ConstructorBindingImpl$Factory.get(ConstructorBindingImpl.java:254) at com.google.inject.internal.ProviderToInternalFactoryAdapter$1.call(ProviderToInternalFactoryAdapter.java:46) at com.google.inject.internal.InjectorImpl.callInContext(InjectorImpl.java:1031) at com.google.inject.internal.ProviderToInternalFactoryAdapter.get(ProviderToInternalFactoryAdapter.java:40) at com.google.inject.Scopes$1$1.get(Scopes.java:65) at com.google.inject.internal.InternalFactoryToProviderAdapter.get(InternalFactoryToProviderAdapter.java:40) at com.google.inject.internal.InjectorImpl$3.get(InjectorImpl.java:737) at com.google.inject.internal.SingleParameterInjector.inject(SingleParameterInjector.java:38) at com.google.inject.internal.SingleParameterInjector.getAll(SingleParameterInjector.java:62) at com.google.inject.internal.ConstructorInjector.construct(ConstructorInjector.java:84) at com.google.inject.internal.ConstructorBindingImpl$Factory.get(ConstructorBindingImpl.java:254) at com.google.inject.internal.ProviderToInternalFactoryAdapter$1.call(ProviderToInternalFactoryAdapter.java:46) at com.google.inject.internal.InjectorImpl.callInContext(InjectorImpl.java:1031) at com.google.inject.internal.ProviderToInternalFactoryAdapter.get(ProviderToInternalFactoryAdapter.java:40) at com.google.inject.Scopes$1$1.get(Scopes.java:65) at com.google.inject.internal.InternalFactoryToProviderAdapter.get(InternalFactoryToProviderAdapter.java:40) at com.google.inject.internal.InjectorImpl$3.get(InjectorImpl.java:737) at com.google.inject.internal.SingleFieldInjector.inject(SingleFieldInjector.java:53) at com.google.inject.internal.MembersInjectorImpl.injectMembers(MembersInjectorImpl.java:110) at com.google.inject.internal.ConstructorInjector.construct(ConstructorInjector.java:94) at com.google.inject.internal.ConstructorBindingImpl$Factory.get(ConstructorBindingImpl.java:254) at com.google.inject.internal.InjectorImpl$4$1.call(InjectorImpl.java:978) at com.google.inject.internal.InjectorImpl.callInContext(InjectorImpl.java:1024) at com.google.inject.internal.InjectorImpl$4.get(InjectorImpl.java:974) at com.google.inject.internal.InjectorImpl.getInstance(InjectorImpl.java:1013) at com.google.inject.struts2.Struts2Factory.buildBean(Struts2Factory.java:108) at com.opensymphony.xwork2.ObjectFactory.buildBean(ObjectFactory.java:161) at com.opensymphony.xwork2.ObjectFactory.buildBean(ObjectFactory.java:150) at com.opensymphony.xwork2.ObjectFactory.buildInterceptor(ObjectFactory.java:191) at com.google.inject.struts2.Struts2Factory.superBuildInterceptor(Struts2Factory.java:166) at com.google.inject.struts2.Struts2Factory.access$200(Struts2Factory.java:45) at com.google.inject.struts2.Struts2Factory$ProvidedInterceptor.inject(Struts2Factory.java:201) at com.google.inject.struts2.Struts2Factory.createInjector(Struts2Factory.java:140) at com.google.inject.struts2.Struts2Factory.buildBean(Struts2Factory.java:104) at com.opensymphony.xwork2.ObjectFactory.buildBean(ObjectFactory.java:161) at com.opensymphony.xwork2.ObjectFactory.buildBean(ObjectFactory.java:150) at com.opensymphony.xwork2.ObjectFactory.buildAction(ObjectFactory.java:120) at com.opensymphony.xwork2.DefaultActionInvocation.createAction(DefaultActionInvocation.java:299) at com.opensymphony.xwork2.DefaultActionInvocation.init(DefaultActionInvocation.java:399) at com.opensymphony.xwork2.DefaultActionProxy.prepare(DefaultActionProxy.java:198) at org.apache.struts2.impl.StrutsActionProxy.prepare(StrutsActionProxy.java:61) at org.apache.struts2.impl.StrutsActionProxyFactory.createActionProxy(StrutsActionProxyFactory.java:39) at com.opensymphony.xwork2.DefaultActionProxyFactory.createActionProxy(DefaultActionProxyFactory.java:58) at org.apache.struts2.dispatcher.Dispatcher.serviceAction(Dispatcher.java:475) 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:680) 2) Error injecting constructor, java.lang.NoClassDefFoundError: Could not initialize class java.awt.Color at org.gbif.ipt.task.Eml2Rtf.<init>(Eml2Rtf.java:75) at org.gbif.ipt.task.Eml2Rtf.class(Eml2Rtf.java:75) while locating org.gbif.ipt.task.Eml2Rtf for parameter 13 at org.gbif.ipt.service.manage.impl.ResourceManagerImpl.<init>(ResourceManagerImpl.java:127) at org.gbif.ipt.service.manage.impl.ResourceManagerImpl.class(ResourceManagerImpl.java:108) while locating org.gbif.ipt.service.manage.impl.ResourceManagerImpl while locating org.gbif.ipt.service.manage.ResourceManager for parameter 4 at org.gbif.ipt.config.ConfigManagerImpl.<init>(ConfigManagerImpl.java:64) at org.gbif.ipt.config.ConfigManagerImpl.class(ConfigManagerImpl.java:64) while locating org.gbif.ipt.config.ConfigManagerImpl while locating org.gbif.ipt.service.admin.ConfigManager for field at org.gbif.ipt.struts2.SetupAndCancelInterceptor.configManager(SetupAndCancelInterceptor.java:21) while locating org.gbif.ipt.struts2.SetupAndCancelInterceptor Caused by: java.lang.NoClassDefFoundError: Could not initialize class java.awt.Color at org.gbif.ipt.task.Eml2Rtf.<init>(Eml2Rtf.java:77) at org.gbif.ipt.task.Eml2Rtf$$FastClassByGuice$$cad0309a.newInstance(<generated>) at com.google.inject.internal.cglib.reflect.$FastConstructor.newInstance(FastConstructor.java:40) at com.google.inject.internal.DefaultConstructionProxyFactory$1.newInstance(DefaultConstructionProxyFactory.java:60) at com.google.inject.internal.ConstructorInjector.construct(ConstructorInjector.java:85) at com.google.inject.internal.ConstructorBindingImpl$Factory.get(ConstructorBindingImpl.java:254) at com.google.inject.internal.ProviderToInternalFactoryAdapter$1.call(ProviderToInternalFactoryAdapter.java:46) at com.google.inject.internal.InjectorImpl.callInContext(InjectorImpl.java:1031) at com.google.inject.internal.ProviderToInternalFactoryAdapter.get(ProviderToInternalFactoryAdapter.java:40) at com.google.inject.Scopes$1$1.get(Scopes.java:65) at com.google.inject.internal.InternalFactoryToProviderAdapter.get(InternalFactoryToProviderAdapter.java:40) at com.google.inject.internal.SingleParameterInjector.inject(SingleParameterInjector.java:38) at com.google.inject.internal.SingleParameterInjector.getAll(SingleParameterInjector.java:62) at com.google.inject.internal.ConstructorInjector.construct(ConstructorInjector.java:84) at com.google.inject.internal.ConstructorBindingImpl$Factory.get(ConstructorBindingImpl.java:254) at com.google.inject.internal.ProviderToInternalFactoryAdapter$1.call(ProviderToInternalFactoryAdapter.java:46) at com.google.inject.internal.InjectorImpl.callInContext(InjectorImpl.java:1031) at com.google.inject.internal.ProviderToInternalFactoryAdapter.get(ProviderToInternalFactoryAdapter.java:40) at com.google.inject.Scopes$1$1.get(Scopes.java:65) at com.google.inject.internal.InternalFactoryToProviderAdapter.get(InternalFactoryToProviderAdapter.java:40) at com.google.inject.internal.InjectorImpl$3.get(InjectorImpl.java:737) at com.google.inject.internal.SingleParameterInjector.inject(SingleParameterInjector.java:38) at com.google.inject.internal.SingleParameterInjector.getAll(SingleParameterInjector.java:62) at com.google.inject.internal.ConstructorInjector.construct(ConstructorInjector.java:84) at com.google.inject.internal.ConstructorBindingImpl$Factory.get(ConstructorBindingImpl.java:254) at com.google.inject.internal.ProviderToInternalFactoryAdapter$1.call(ProviderToInternalFactoryAdapter.java:46) at com.google.inject.internal.InjectorImpl.callInContext(InjectorImpl.java:1031) at com.google.inject.internal.ProviderToInternalFactoryAdapter.get(ProviderToInternalFactoryAdapter.java:40) at com.google.inject.Scopes$1$1.get(Scopes.java:65) at com.google.inject.internal.InternalFactoryToProviderAdapter.get(InternalFactoryToProviderAdapter.java:40) at com.google.inject.internal.InjectorImpl$3.get(InjectorImpl.java:737) at com.google.inject.internal.SingleFieldInjector.inject(SingleFieldInjector.java:53) at com.google.inject.internal.MembersInjectorImpl.injectMembers(MembersInjectorImpl.java:110) at com.google.inject.internal.ConstructorInjector.construct(ConstructorInjector.java:94) at com.google.inject.internal.ConstructorBindingImpl$Factory.get(ConstructorBindingImpl.java:254) at com.google.inject.internal.InjectorImpl$4$1.call(InjectorImpl.java:978) at com.google.inject.internal.InjectorImpl.callInContext(InjectorImpl.java:1024) at com.google.inject.internal.InjectorImpl$4.get(InjectorImpl.java:974) at com.google.inject.internal.InjectorImpl.getInstance(InjectorImpl.java:1013) at com.google.inject.struts2.Struts2Factory.buildBean(Struts2Factory.java:108) at com.opensymphony.xwork2.ObjectFactory.buildBean(ObjectFactory.java:161) at com.opensymphony.xwork2.ObjectFactory.buildBean(ObjectFactory.java:150) at com.opensymphony.xwork2.ObjectFactory.buildInterceptor(ObjectFactory.java:191) at com.google.inject.struts2.Struts2Factory.superBuildInterceptor(Struts2Factory.java:166) at com.google.inject.struts2.Struts2Factory.access$200(Struts2Factory.java:45) at com.google.inject.struts2.Struts2Factory$ProvidedInterceptor.inject(Struts2Factory.java:201) at com.google.inject.struts2.Struts2Factory.createInjector(Struts2Factory.java:140) at com.google.inject.struts2.Struts2Factory.buildBean(Struts2Factory.java:104) at com.opensymphony.xwork2.ObjectFactory.buildBean(ObjectFactory.java:161) at com.opensymphony.xwork2.ObjectFactory.buildBean(ObjectFactory.java:150) at com.opensymphony.xwork2.ObjectFactory.buildAction(ObjectFactory.java:120) at com.opensymphony.xwork2.DefaultActionInvocation.createAction(DefaultActionInvocation.java:299) at com.opensymphony.xwork2.DefaultActionInvocation.init(DefaultActionInvocation.java:399) at com.opensymphony.xwork2.DefaultActionProxy.prepare(DefaultActionProxy.java:198) at org.apache.struts2.impl.StrutsActionProxy.prepare(StrutsActionProxy.java:61) at org.apache.struts2.impl.StrutsActionProxyFactory.createActionProxy(StrutsActionProxyFactory.java:39) at com.opensymphony.xwork2.DefaultActionProxyFactory.createActionProxy(DefaultActionProxyFactory.java:58) at org.apache.struts2.dispatcher.Dispatcher.serviceAction(Dispatcher.java:475) 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:680) 2 errors com.google.inject.internal.InjectorImpl$4.get(InjectorImpl.java:987) com.google.inject.internal.InjectorImpl.getInstance(InjectorImpl.java:1013) com.google.inject.struts2.Struts2Factory.buildBean(Struts2Factory.java:108) com.opensymphony.xwork2.ObjectFactory.buildBean(ObjectFactory.java:161) com.opensymphony.xwork2.ObjectFactory.buildBean(ObjectFactory.java:150) com.opensymphony.xwork2.ObjectFactory.buildInterceptor(ObjectFactory.java:191) com.google.inject.struts2.Struts2Factory.superBuildInterceptor(Struts2Factory.java:166) com.google.inject.struts2.Struts2Factory.access$200(Struts2Factory.java:45) com.google.inject.struts2.Struts2Factory$ProvidedInterceptor.inject(Struts2Factory.java:201) com.google.inject.struts2.Struts2Factory.createInjector(Struts2Factory.java:140) com.google.inject.struts2.Struts2Factory.buildBean(Struts2Factory.java:104) com.opensymphony.xwork2.ObjectFactory.buildBean(ObjectFactory.java:161) com.opensymphony.xwork2.ObjectFactory.buildBean(ObjectFactory.java:150) com.opensymphony.xwork2.ObjectFactory.buildAction(ObjectFactory.java:120) com.opensymphony.xwork2.DefaultActionInvocation.createAction(DefaultActionInvocation.java:299) com.opensymphony.xwork2.DefaultActionInvocation.init(DefaultActionInvocation.java:399) com.opensymphony.xwork2.DefaultActionProxy.prepare(DefaultActionProxy.java:198) org.apache.struts2.impl.StrutsActionProxy.prepare(StrutsActionProxy.java:61) org.apache.struts2.impl.StrutsActionProxyFactory.createActionProxy(StrutsActionProxyFactory.java:39) com.opensymphony.xwork2.DefaultActionProxyFactory.createActionProxy(DefaultActionProxyFactory.java:58) org.apache.struts2.dispatcher.Dispatcher.serviceAction(Dispatcher.java:475) org.apache.struts2.dispatcher.ng.ExecuteOperations.executeAction(ExecuteOperations.java:77) org.apache.struts2.dispatcher.ng.filter.StrutsPrepareAndExecuteFilter.doFilter(StrutsPrepareAndExecuteFilter.java:91) com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:66) com.google.inject.servlet.ManagedFilterPipeline.dispatch(ManagedFilterPipeline.java:118) com.google.inject.servlet.GuiceFilter.doFilter(GuiceFilter.java:113) note The full stack trace of the root cause is available in the Apache Tomcat/6.0.32 logs. Apache Tomcat/6.0.32 Milko A. Škofič Programme Specialist, Biodiversity Informatics Project Understanding and Managing Biodiversity Programme Bioversity International - Via dei Tre Denari, 472/a - 00057 Maccarese (RM) - ITALY E-mail: m.skofic(a)cgiar.org Tel: +39 06 6118286 Fax: +39 06 61979661

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"Error Publishing Resource" message
by David Remsen (GBIF) 27 Jan '12

27 Jan '12

I have a validated DarwinCore Archive that I imported into the IPT. http://ipt.gbif.org/manage/resource.do?r=neembucu2 When I press the Publish button to publish the resource I get an error message that simply reads "Error publishing resource:" with no additional information. This file is intended to be published by Pensoft on their IPT instance which gives the same error. Any ideas? David R ---------------------------------------------------------------------------- David Remsen, Senior Programme Officer Electronic Catalog of Names of Known Organisms Global Biodiversity Information Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, Denmark Tel: +45-35321472 Fax: +45-35321480 Mobile +45 28751472 Skype: dremsen ----------------------------------------------------------------------------

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IPT 2.0.3 is available for download
by Kyle Braak (GBIF) 03 Nov '11

03 Nov '11

Dear IPT users, The GBIF Secretariat is pleased to announce that a new release of the Integrated Publishing Toolkit (IPT v2.0.3) is now available for download here. The IPT version 2.0.3 addresses 76 reported issues from the previous version, and includes translations into French and Spanish. We’d like to give special thanks to all the volunteer translators for their time and efforts: (French translators) Nicolas Noe, Louis Reymondin, and Michael Akbaraly (Spanish translators) Daniel Amariles, Angela M. Suarez, Pere Roca Ristol, Arturo H. Ariño, and Héctor Fabio Tobón R. Another special mention is owed to Peter Desmet who has spent time simplifying how to customize the style of the IPT, as explained in his article Customizing the IPT. We would like to recommend that users of previous versions update to benefit from this new functionality and bug fixing. Updating an IPT 2.0.x installation involves the following steps: 1. Replace the previous .war file with the latest edition 2. Backup the existing data directory 3. Reuse the existing data directory during setup 4. Press the “Publish all resources” button on the Administration page after initial setup is complete (this may take some time depending on the size and number of resources your IPT hosts) New users should follow the installation guidelines in the IPT User Manual that has been updated for this version. Thank you once again for all your help in testing and contributing to the IPT! With best regards, Kyle, on behalf of the IPT development team and the GBIF Secretariat

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Tomcat 7 documentation for IPT wiki
by Laura Russell 27 Oct '11

27 Oct '11

In reference to the wiki page (http://code.google.com/p/gbif-providertoolkit/wiki/IPTServerPreparation) stating that Tomcat 7 doesn't work, I'm sending a link to the screenshots I took when I installed Tomcat 7 on Win7-64 on June 14, 2011 so they can be added to the wiki if you want since Tomcat 7 does at least work in the Win7-64 configuration. http://129.237.201.204/Tomcat7_Win7-64_Screens.zip There are 17 screen shots. I think the only I did not capture was editing the tomcat-users.xml file. I used the tomcat web manager to deploy the ipt.war file. Also including a link to the Tomcat7 IPT instance if you want to take a look. This instance is my test instance that I use to demonstrate IPT to institutions that we are considering hosting on our live VertNet IPT. http://129.237.201.204:8080/ipt/ Let me know if you have any questions or need additional details. 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)vertnet.org Email: larussell(a)ku.edu Google Chat: larussell(a)vertnet.org Skype: laura.anne.russell URL: http://www.vertnet.org VertNet Portals: MaNIS: http://www.manisnet.org HerpNET: http://www.herpnet.org ORNIS: http://www.ornisnet.org FishNet2: http://www.fishnet2.net

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Looking for JAR file that is responsible for DwC-A creation.
by Aaron Low 20 Oct '11

20 Oct '11

Hi, I'm a developer working on the BDRS - http://code.google.com/p/ala-citizenscience/. I'm in the process of adding the ability to export observations of species as a darwin core archive. I've been perusing your code files at http://repository.gbif.org hoping to find a jar file that I can leverage some of the functionality of the IPT without having to run whole application. To achieve this I would like to include one (or more) of the org.gbif jars as a dependency in our maven build. Unfortunately, I can't seem to find the jar that constructs a new archive. Could someone please point me in the right direction? If the functionality I'm looking for doesn't exist, that would be great for me to know as well. Thanks for your time, Regards, Aaron Low Gaia Resources p +61 8 9227 7309 w www.gaiaresources.com.au e aaron.low(a)gaiaresources.com.au

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Fwd: RE: BushBlitz GBIF data entry
by info＠pensoft.net 06 Oct '11

06 Oct '11

A question from one of the most enthusiastic users of IPT (files are attached): At last I am writing you to say that I have sent the data for the Brueelia paper in IPT. Herewith I am sending the files generated after my submission, the zip file (dwca) with the xml and txt files, and one rtf with a summary of our project. The only concern about the this is that two of our columns were not recognized during the Darwin Core mapping, look the message: "No mapped columns The following columns of the source are not assigned to the properties of this mapping: occurrenceID, verbatimLabel." I double checked throughout the "Darwin Core Terms: A quick reference guide" and was unable to find these headings over there. Anyways, I think that our data base is small but still pretty complete and useful. If you have some idea for how to inlude these columns, it will be great. The quick class and information provide by Torsten Dikow was fundamental for this stuff be done and published in IPT. He was pretty nice and very patient with us while teaching how to handle these IPT tools. Michel P. Valim Skype me in mpvalim MSN me in mpvalim(a)hotmail.com > Date: Thu, 1 Sep 2011 12:49:23 +0300 > From: info(a)pensoft.net > To: jweckstein(a)fieldmuseum.org > CC: mpvalim(a)hotmail.com; preprint(a)pensoft.net > Subject: Re: BushBlitz GBIF data entry > > Dear Jason, > > Good to hear that. Today your final proofs will be posted, please > confirm so that the paper to be published next week. > > It makes sense to upload the data beforehand and to publish it along > with the paper as supplementary Darwin Core Archive file (with the > appropriate legend). You can easily download DwC-A once you upload the > data and fill in the metadata (or at least the most important of them). > > Then the localities in your paper will be published as data along with > the publication itself. We still have time to do that. DOI and details > can be added to the IPT after publication. > > Best regards, > Lyubo > > > > On 31.8.2011 г. 23:23 ч., Jason Weckstein wrote: > > Hi Lyubomir, > > > > Torsten Dikow just finished walking us through using IPT... so we are > > more or less ready with our files. We will just wait for the final > > paper to come out for the doi number etc. > > > > Thanks for your help with this. > > > > Sincerely, > > > > Jason > > > > On Tue, Aug 30, 2011 at 7:27 AM, info(a)pensoft.net<info(a)pensoft.net> wrote: > >> Hi Jason and Michel, > >> > >> I wonder how the trials with IPT are going? Please find attached sample > >> files created by another user, that have been successfully uploaded. > >> > >> Once uploaded, you may play with the metadata elements, with creating DwC > >> archive file from your dataset and also exporting the metadata into a "data > >> paper"manuscript (not really needed for your particular dataset). Please do > >> not hesitate to contact Teodor (preprint(a)pensoft.net) in case of questions. > >> > >> Best regards, > >> Lyubomir > > > > > > > -- > Dr Lyubomir Penev > Managing Director > Pensoft Publishers > 13a Geo Milev Street > 1111 Sofia, Bulgaria > Tel +359-2-8704281 > Fax +359-2-8704282 > www.pensoft.net > www.pensoft.net/journals/zookeys > www.pensoft.net/journals/phytokeys > info(a)pensoft.net >

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