- IPT - lists.gbif.org

Questions
by Mickael Graf 29 Apr '09

29 Apr '09

Hi again, I have now a working IPT on my server. But when I register the organisation name (under Admin->Settings->Organisation) I can pick up GBIF-Sweden as Title, but I never get a password (and since yesterday I didn't get any in my mailbox). Then I cannot register my IPT (Admin->Settings->IPT instance) because I need this password (which isn't the same as the UDDI one, isn't it ?). Cheers, Mickaël -- --------------------------------- Mickaël Graf Database developper, GBIF Sweden - http://www.gbif.se tel: +46 8 5195 4045 mailto:mickael.graf@nrm.se Swedish Museum of Natural History - http://www.nrm.se Box 50007 SE-104 05 Stockholm Sweden

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Troubles with IPT
by Mickael Graf 27 Apr '09

27 Apr '09

Hi all, I downloaded and installed IPT and geoserver, and I got into troubles. I'm new to Tomcat, and this doesn't help me solving this issue. First I couldn't start geoserver. After searching the solution was to change owner (unzipping and installing defaults to root.root) and to make geoserver/data/service.xml writeable. Now I'm trying to start IPT but this doesn't work. After changing memory values, I finally get the following error message: FAIL - Application at context path /ipt could not be started The message from the logs is the following: INFO: HTMLManager: start: Starting web application at '/ipt' Resolved relative path / with servlet context : /usr/share/tomcat5/webapps/ipt/ Resolved relative path /data with servlet context : /usr/share/tomcat5/webapps/ipt/data Resolved relative path / with servlet context : /usr/share/tomcat5/webapps/ipt/ Resolved relative path /data with servlet context : /usr/share/tomcat5/webapps/ipt/data ERROR http-8080-Processor25-[/ipt].filterStart(3639) | Exception starting filter struts javax.xml.transform.TransformerFactoryConfigurationError: Provider org.apache.xalan.processor.TransformerFactoryImpl not found at javax.xml.transform.TransformerFactory.newInstance(Unknown Source) at com.opensymphony.xwork2.util.DomHelper $DOMBuilder.<clinit>(DomHelper.java:167) at com.opensymphony.xwork2.util.DomHelper.parse(DomHelper.java:115) at com.opensymphony.xwork2.config.providers.XmlConfigurationProvider.loadConfigurationFiles(XmlConfigurationProvider.java:830) at com.opensymphony.xwork2.config.providers.XmlConfigurationProvider.loadDocuments(XmlConfigurationProvider.java:131) at com.opensymphony.xwork2.config.providers.XmlConfigurationProvider.init(XmlConfigurationProvider.java:100) at com.opensymphony.xwork2.config.impl.DefaultConfiguration.reload(DefaultConfiguration.java:130) at com.opensymphony.xwork2.config.ConfigurationManager.getConfiguration(ConfigurationManager.java:52) at org.apache.struts2.dispatcher.Dispatcher.init_PreloadConfiguration(Dispatcher.java:395) at org.apache.struts2.dispatcher.Dispatcher.init(Dispatcher.java:452) at org.apache.struts2.dispatcher.FilterDispatcher.init(FilterDispatcher.java:201) at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:221) at org.apache.catalina.core.ApplicationFilterConfig.setFilterDef(ApplicationFilterConfig.java:302) at org.apache.catalina.core.ApplicationFilterConfig.<init>(ApplicationFilterConfig.java:78) at org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:3635) at org.apache.catalina.core.StandardContext.start(StandardContext.java:4222) at org.apache.catalina.manager.ManagerServlet.start(ManagerServlet.java:1176) at org.apache.catalina.manager.HTMLManagerServlet.start(HTMLManagerServlet.java:545) at org.apache.catalina.manager.HTMLManagerServlet.doGet(HTMLManagerServlet.java:105) at javax.servlet.http.HttpServlet.service(HttpServlet.java:690) 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.StandardWrapperValve.invoke(StandardWrapperValve.java:210) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:525) 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:151) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:870) 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:685) at java.lang.Thread.run(Thread.java:636) Apr 24, 2009 10:08:26 AM org.apache.catalina.core.StandardContext start SEVERE: Error filterStart Apr 24, 2009 10:08:26 AM org.apache.catalina.core.StandardContext start SEVERE: Context [/ipt] startup failed due to previous errors Apr 24, 2009 10:08:27 AM org.apache.catalina.core.ApplicationContext log INFO: HTMLManager: list: Listing contexts for virtual host 'localhost' I don't know if that means my system is missing some class/package or if it's a configuration issue. My system is Centos 5.3 Cheers, Mickaël -- --------------------------------- Mickaël Graf Database developper, GBIF Sweden - http://www.gbif.se tel: +46 8 5195 4045 mailto:mickael.graf@nrm.se Swedish Museum of Natural History - http://www.nrm.se Box 50007 SE-104 05 Stockholm Sweden

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IPT RC1 released
by "Markus Döring (GBIF)" 03 Apr '09

03 Apr '09

Dear all, we are happy to announce the first release candidate of the IPT. As usual we have an online demo, a war archive & geoserver zip for your local installation and a mac standalone version to play with on your desktop without the need to install anything more: * online demo http://ipt.gbif.org * a war archive & geoserver.zip for your own tomcat installation * a mac standalone version incl geoserver http://code.google.com/p/gbif-providertoolkit/downloads/list?can=3 There you will also find the initial version of the user manual which Arnaud Reveillon is currently working on. He will be glad about any feedback you provide to this list and suggestions on what needs more explanations. If you encounter problems, please report them as usual in the issue tracker: http://code.google.com/p/gbif-providertoolkit/issues/list We are collecting bug fixes for the next release, but will provide snapshot versions for the interested on GBIFs ftp server: ftp://ftp.gbif.org/projects/ipt/downloads/ A Version history and list of fixed bugs for the snapshot is available too: http://code.google.com/p/gbif-providertoolkit/wiki/VersionHistory best wishes, Markus

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IPT Documentation
by Arnaud Réveillon 01 Apr '09

01 Apr '09

Dear all, My name is Arnaud Réveillon and I have been appointed to write the documentation for the IPT. I am not new to the GBIF and biodiversity-related software as I worked during four years (2004-2008) for the Belgian focal point for the Convention on Biological Diversity, acting as tutor (mostly on databases, web applications, web pages editors, etc.) and as webmaster. During this period, I have been regularly in contact with members of several national GBIF nodes and am generally well aware of their work. I am not yet fully familiar with the IPT but hope to get up to speed in the next few days, with the help of the list. Please do not hesitate to let me know about your needs, the difficulties you are having with the IPT or anything that may be of interest regarding the documentation, which is scheduled to be ready on 16 April. Thank you, Arnaud Réveillon-

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IPT 1.0b.8 online
by Markus Döring (GBIF) 22 Mar '09

22 Mar '09

Dear all, a new pre relase of the IPT is available for testing. You can try it here as usual: * online demo http://ipt.gbif.org * a war archive for your own tomcat installation http://gbif-providertoolkit.googlecode.com/files/ipt-1.0b.8.war * a mac standalone version without any further dependecies ftp://ftp.gbif.org/projects/ipt/downloads/ipt-1.0b.8.dmg Many, many thanks for the valuable feedback we have received in the past weeks. There are still outstanding bugs, but the new release 1.0b. 8 fixes many of them. Work has been done to fix SQL source problems, to provide a better property mapping interface, to connect to the GBIF registry (a test registry is currently configured) and to update darwin core extensions and vocabularies for controlled terms from central sites. If you havent tried the new Flash based maps provided by Javier de la Torre, give it a go. If you encounter problems, please report them as usual in the issue tracker: http://code.google.com/p/gbif-providertoolkit/issues/list best wishes, Markus

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Re: [IPT] SQL datasource upload
by "Holetschek, Jörg" 18 Mar '09

18 Mar '09

Good idea, Tim! But no SELECT gets to the server... apparently only some preparations: SELECT @@MAX_PRECISION SET TRANSACTION ISOLATION LEVEL READ COMMITTED SET IMPLICIT_TRANSACTIONS OFF SET QUOTED_IDENTIFIER ON SET TEXTSIZE 2147483647 Cheers, Jörg -----Ursprüngliche Nachricht----- Von: Tim Robertson [mailto:trobertson@gbif.org] Gesendet: Mittwoch, 18. März 2009 11:06 An: =?ISO-8859-1?Q?=22Holetschek(a)ns.gbif.org; Holetschek, Jörg Cc: "Markus Döring (GBIF)"; ipt(a)lists.gbif.org Betreff: Re: [IPT] SQL datasource upload Hi Jörg I've looked through the code and it is not possible to switch on the SQL logging through configuration. I will change this for the next release so that the SQL is logged prior to execution for easier debug. Could you please check the SQLServer logs and report if the query reaches the DB? Cheers, Tim On 18 Mar 2009, at 10:48, Holetschek, Jörg wrote: > Hi Markus, > > I've tried to upload data from our SQL server database, after > creating one datasource and 11 mappings. > The upload takes only a second and ends up with 0 records uploaded, > even though I can't find an error in the logs... Is there something > I need to do first? > > INFO pool-1-thread-1-OccUploadTask.call(105) | Import preparation > took 78 ms > INFO pool-1-thread-1-OccUploadTask.uploadCore(225) | Starting upload > of core records for resource Desmids > INFO pool-1-thread-1-DarwinCoreManagerHibernate.removeAll(41) | > Removed 0 DarwinCores bound to resource Desmids > INFO pool-1-thread-1- > DarwinCoreManagerHibernate.flagAllAsDeleted(109) | 0 > org.gbif.provider.model.DarwinCore records of resource were flagged > as deleted. > INFO pool-1-thread-1-OccStatManagerHibernate.removeAll(41) | Removed > 0 OccStatByRegionAndTaxons bound to resource Desmids > INFO pool-1-thread-1-TreeNodeSupportHibernate.removeAll(85) | > Removed 0 taxons bound to resource Desmids > INFO pool-1-thread-1-TreeNodeSupportHibernate.removeAll(85) | > Removed 0 regions bound to resource Desmids > INFO pool-1-thread-1-AnnotationManagerHibernate.removeAll(133) | > Removed 2 annotations bound to resource Desmids > > > Cheers, > Jörg > _______________________________________________ > IPT mailing list > IPT(a)lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt >

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SQL datasource upload
by "Holetschek, Jörg" 18 Mar '09

18 Mar '09

Hi Markus, I've tried to upload data from our SQL server database, after creating one datasource and 11 mappings. The upload takes only a second and ends up with 0 records uploaded, even though I can't find an error in the logs... Is there something I need to do first? INFO pool-1-thread-1-OccUploadTask.call(105) | Import preparation took 78 ms INFO pool-1-thread-1-OccUploadTask.uploadCore(225) | Starting upload of core records for resource Desmids INFO pool-1-thread-1-DarwinCoreManagerHibernate.removeAll(41) | Removed 0 DarwinCores bound to resource Desmids INFO pool-1-thread-1-DarwinCoreManagerHibernate.flagAllAsDeleted(109) | 0 org.gbif.provider.model.DarwinCore records of resource were flagged as deleted. INFO pool-1-thread-1-OccStatManagerHibernate.removeAll(41) | Removed 0 OccStatByRegionAndTaxons bound to resource Desmids INFO pool-1-thread-1-TreeNodeSupportHibernate.removeAll(85) | Removed 0 taxons bound to resource Desmids INFO pool-1-thread-1-TreeNodeSupportHibernate.removeAll(85) | Removed 0 regions bound to resource Desmids INFO pool-1-thread-1-AnnotationManagerHibernate.removeAll(133) | Removed 2 annotations bound to resource Desmids Cheers, Jörg

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Re: [IPT] IPT 1.0b.8 online
by "Holetschek, Jörg" 18 Mar '09

18 Mar '09

Hi Markus et al, pressing the "publish" button for a data resource doesn't work like in the previous versions, I just get a never ending animation (see screenshot). Is that somehow connected to not being registered yet? Cheers, Jörg -----Ursprüngliche Nachricht----- Von: ipt-bounces(a)lists.gbif.org [mailto:ipt-bounces@lists.gbif.org]Im Auftrag von "Markus Döring (GBIF)" Gesendet: Mittwoch, 18. März 2009 09:20 An: Burke Chih-Jen Ko Cc: ipt(a)lists.gbif.org Betreff: Re: [IPT] IPT 1.0b.8 online Burke, you dont have to register,but you can if you like to try the registry integration. The registry connected is a test one until the real release, so you dont harm anyone, just go ahead and register anything you want. The functionality of the registry is still being updated, not all email notifications for example might work right now, in particular the resend password link (which you need to use an existing organisation without knowing its password). Once you have selected an existing or registered a new organisation, publishing a resource also registers it with GBIF and updates its metadata in the registry (not fully working in the current registry version). A resource therefore has 3 states: - private/draft: this is the default for new resources. Its neither registered nor should it be visible in the public portal part of the IPT - public/modified: the resource is intended to be public, its present in the IPT portal and if all goes well and your settings allow to, its also registered with GBIF. The resource metadata is modified though and differes from a) GBIFs registry metadata or b) the versioned EML document which is generated each time you press publish (actually also the geoserver WFS/WMS services have their own metadata which is out of date then too) - public/clean: same as above, but the metadata in the registry/ EML&geoserver should reflect your latest state Does this clarify the registry integration? Markus On Mar 18, 2009, at 3:59, Burke Chih-Jen Ko wrote: > Dear Markus, > > Thank GBIF team for this brilliant work! > > A question: > Now in Admin->settings->Organisation, > Must we register to test IPT? > In the publishing box, does the "private, not registered" mean the > same thing? > > Best regards, > Burke > > > Taiwan Biodiversity Information Facility, TaiBIF > Biodiversity Research Center, Academia Sinica > No. 128, Sec 2, Academia Rd., Nangang District > Taipei 115, Taiwan > Tel: +886+2+27899621 ext.220 > > _______________________________________________ IPT mailing list IPT(a)lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt

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IPT on glassfish
by Esteban Mata 17 Mar '09

17 Mar '09

Hi everybody! I was trying to deploy the ipt.war on glassfish! ... I know probably it would be easier on Tomcat but i have glassfish already installed, so I have to know if is posible to run IPT on glassfish? Could someone help me?! Thanks.

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Re: [IPT] IPT Documentation
by Mergen Patricia 17 Mar '09

17 Mar '09

Hi Arnaud First of all congratulation for your new position! In the framework of mainly the project "Central Biodiversity Information Network" to be installed in Central Africa, we are currently testing a lot with the GBIF tool including already a bit the IPT portal. For the EDIT project, there are also training materials being compiled for the moment (more for the GIS part, which is also present in form of maps in the IPT tool.) My colleague Franck is currently in Africa to do some testing, but he has internet and can answers mails from time to time. We will be happy to collaborate with you and do not hesitate to contact us to know more about the ongoing projects and compare the available docs or those in preparation in near future so that we can help each other out at best. Best regards Patricia Patricia Mergen Project Manager Biodiversity Information and Cybertaxonomy Unit Royal Museum for Central Africa Leuvensesteenweg 13 B-3080 Tervuren Phone:+ 32 2 769 56 26 Fax: + 32 2 769 56 42 E-mail: patricia.mergen(a)africamuseum.be http://www.africamuseum.be/research/cooperation -----Original Message----- From: ipt-bounces(a)lists.gbif.org [mailto:ipt-bounces@lists.gbif.org] On Behalf Of Arnaud Réveillon Sent: mardi 17 mars 2009 15:44 To: ipt(a)lists.gbif.org Subject: [IPT] IPT Documentation Dear all, My name is Arnaud Réveillon and I have been appointed to write the documentation for the IPT. I am not new to the GBIF and biodiversity-related software as I worked during four years (2004-2008) for the Belgian focal point for the Convention on Biological Diversity, acting as tutor (mostly on databases, web applications, web pages editors, etc.) and as webmaster. During this period, I have been regularly in contact with members of several national GBIF nodes and am generally well aware of their work. I am not yet fully familiar with the IPT but hope to get up to speed in the next few days, with the help of the list. Please do not hesitate to let me know about your needs, the difficulties you are having with the IPT or anything that may be of interest regarding the documentation, which is scheduled to be ready on 16 April. Thank you, Arnaud Réveillon- _______________________________________________ IPT mailing list IPT(a)lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt ########################################### This message has been scanned by ICT - Africa Museum ________________________________________ 17/3/2009 - Filtered through antispam by ICT

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