- IPT - lists.gbif.org

Re: [IPT] IPT-lite in Google code?
by Dag Terje Filip Endresen 19 Mar '10

19 Mar '10

Hi Hanna, The DEMO site for IPT LITE is at: http://ipt-lite.gbif.org/index.html There is an OLD compile of the IPT LITE from the Google Code site (September 15, 2009) http://gbif-providertoolkit.googlecode.com/files/gbif-ipt-lite-1.0RC2.war I did not test this LITE version myself. But I expect that this LITE version is much less demanding regarding memory. The LITE will only provide a tool to generate the Darwin Core text Archive (DwC-A) and not provide the visual display of your datasets. See also the Google Code Issue 254: Revive IPT lite to be build via war overlay based on the regular IPT. "IPT lite is a stripped down IPT that does share 99% of IPT code base, but removes the entire portal, webservices and even the database storing dwc records. It is only meant for creating dwc archives as efficient as possible and authoring metadata about the resource. Good for large datasets and a hosting environment." http://code.google.com/p/gbif-providertoolkit/issues/detail?id=254 I believe that you will build a recent version of the IPT LITE together with the standard IPT if you download the source code (SVN checkout) and build this with for example Maven. BUT it is probably much easier for you to download the GBIF IPT LITE 1.0 RC2 to start testing this version of the toolkit... The Darwin Core Google Code project includes a Darwin Core Archive (DwC-A) reader (dwc-archive-1.0.jar, dwca-reader-1.0.jar). I am not sure how (if at all) these relates to the IPT LITE. But perhaps worthwhile to test as well? http://code.google.com/p/darwincore/downloads/list I have no hands-on experiences with the LITE version so I copy my reply to the IPT mailing list to see if we can catch any remarks for others more experienced with this LITE version. Cheers Dag Terje _____ From: Hanna Koivula [mailto:hanna.koivula@helsinki.fi] To: dag.endresen(a)nordgen.org Sent: Fri, 19 Mar 2010 12:48:26 +0100 Subject: IPT-lite in Google code? Hi Dag! It was nice to meet you in Alikante! I’ll try to get some pics from the Castillo to the community site… You mentioned that you have commented how to make IPT Lite on the Google code platform. Can you guide me where to find that? I think our developers would love to try that out, since our Metacat installation is not proceeding and they need to get the metadata out in public somehow… Best wishes, Hanna ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~* Hanna Koivula Data Manager Finnish Museum of Natural History 000014 Helsinki University http://www.fmnh.helsinki.fi/english/ tel. +358 50 4154850 ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*

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Short presentations about the IPT available in Portuguese
by Alberto González-Talaván (GBIF) 18 Mar '10

18 Mar '10

Dear Friends from the IPT list, Thanks to Pedro Corrêa, André Quintela Bertuzzi, Bruno Vannucci and Paulo Pessoa from the University of São Paulo (Brazil) we have now available the set of 6 short presentations about the IPT available also in Portuguese! The presentations are available in the IPT resources page of the "GBIF IPT helpdesk and training experts" group of the GBIF Community Site. For those of you who are not members of the group, please consider creating an account in the GBIF Community Site and joining the group and give a hand in the deployment of the tool around the world ;-) http://community.gbif.org/pg/pages/view/3872/ So now Chinese, Dutch, English, French, Portuguese and Spanish are the languages in which these presentations are available! This is really impressive and I cannot but thank again to all of you who have collaborated in this! The person who initially offered to make the translation into German is quite busy at the moment, so if any other German speaker wants to collaborate translating some (or all) of the translations, please drop me a line! With best regards Alberto ---------- Alberto GONZÁLEZ TALAVÁN Training Officer Global Biodiversity Information Facility Secretariat Universitetsparken 15 DK-2100 Copenhagen, Denmark email: <mailto:atalavan@gbif.org> atalavan(a)gbif.org web: <http://www.gbif.org/> http://www.gbif.org/ T: +45 35 32 14 83 F: +45 35 32 14 80

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Short presentations about the IPT available in Spanish
by Alberto González-Talaván (GBIF) 03 Mar '10

03 Mar '10

Dear Friends, Thanks to Silvia Lusa from GBIF Spain and Aurelio Sanabria from GBIF Costa Rica we have now available the set of 6 short presentations about the IPT available in Spanish! The presentations, as usual, are available in the IPT resources page of the "GBIF IPT helpdesk and training experts" group of the GBIF Community Site: http://community.gbif.org/pg/pages/view/3872/ As you can see, we have now these presentations available in Chinese, Dutch, English, French and Spanish! Thanks to all of you who have collaborated in this common effort! Those of you who have experience using the GBIF IPT and think that you can help/train others to overcome their problems with the tool, please consider joining that group of the GBIF Community Site (http://community.gbif.org/) Please contact me if you find any difficulties in the process. With best regards Alberto ---------- Alberto GONZÁLEZ TALAVÁN Training Officer Global Biodiversity Information Facility Secretariat Universitetsparken 15 DK-2100 Copenhagen, Denmark email: <mailto:atalavan@gbif.org> atalavan(a)gbif.org web: http://www.gbif.org/ T: +45 35 32 14 83 F: +45 35 32 14 80

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IPT short presentations available in Dutch
by Alberto González-Talaván (GBIF) 01 Mar '10

01 Mar '10

Dear friends of the IPT list, The short presentations about the GBIF IPT are now available also in Dutch thanks to the work done by our colleagues Andre Heughebaert and Dimitri Brosens from the Belgian Biodiversity Platform (www.bebif.be) They are available in the resources page of the 'IPT helpdesk and training experts' group of the GBIF Community site: http://community.gbif.org/pg/pages/view/3872/ Our sincere thanks to Andre and Dimitri for making this available for the group! Alberto ---------- Alberto GONZÁLEZ TALAVÁN Training Officer Global Biodiversity Information Facility Secretariat Universitetsparken 15 DK-2100 Copenhagen, Denmark email: <mailto:atalavan@gbif.org> atalavan(a)gbif.org web: http://www.gbif.org/ T: +45 35 32 14 83 F: +45 35 32 14 80

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FW: What does Yikes mean
by Andrea Hahn (GBIF) 18 Feb '10

18 Feb '10

Dear GBIF IPT contributors, Hannu is getting stuck with a "Yikes" issue (original email below). I am aware of the issue outlined in the IPT FAQ at http://code.google.com/p/gbif-providertoolkit/wiki/FAQ, and have pointed Hannu at it. Do you have any additional comment or advice that might help to fix this? Many thanks in advance, Andrea --------------------------------------------------------------- Andrea Hahn (ahahn(a)gbif.org) Data Portal Manager Global Biodiversity Information Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, Denmark Tel: +45-35321491 Fax: +45-35321480 URL: <http://www.gbif.org> http://www.gbif.org --------------------------------------------------------------- -----Original Message----- From: Hannu Saarenmaa [mailto:hannu.saarenmaa@helsinki.fi] Sent: Thursday, February 18, 2010 4:40 PM To: GBIF Helpdesk Subject: What does Yikes mean Our IPT has become unusable. Even simple things like upload of new file and click on Mappings->Edit (dump below) give this kind of trail. We are not Java and Tomcat experts, so we need help. Does this dump tell you something? Hannu Yikes! javax.servlet.ServletException: Filter execution threw an exception at net.sf.ehcache.constructs.web.filter.Filter.logThrowable(Filter.java:152) at net.sf.ehcache.constructs.web.filter.Filter.doFilter(Filter.java:97) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applicati onFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilter Chain.java:188) at org.appfuse.webapp.filter.LocaleFilter.doFilterInternal(LocaleFilter.java: 74) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerReques tFilter.java:76) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applicati onFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilter Chain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilte rInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerReques tFilter.java:76) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applicati onFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilter Chain.java:188) at org.springframework.security.util.FilterChainProxy$VirtualFilterChain.doFi lter(FilterChainProxy.java:359) at org.springframework.security.intercept.web.FilterSecurityInterceptor.invok e(FilterSecurityInterceptor.java:109) at org.springframework.security.intercept.web.FilterSecurityInterceptor.doFil ter(FilterSecurityInterceptor.java:83) at org.springframework.security.util.FilterChainProxy$VirtualFilterChain.doFi lter(FilterChainProxy.java:371) at org.springframework.security.ui.ExceptionTranslationFilter.doFilterHttp(Ex ceptionTranslationFilter.java:101) at org.springframework.security.ui.SpringSecurityFilter.doFilter(SpringSecuri tyFilter.java:53) at org.springframework.security.util.FilterChainProxy$VirtualFilterChain.doFi lter(FilterChainProxy.java:371) at org.springframework.security.providers.anonymous.AnonymousProcessingFilter .doFilterHttp(AnonymousProcessingFilter.java:105) at org.springframework.security.ui.SpringSecurityFilter.doFilter(SpringSecuri tyFilter.java:53) at org.springframework.security.util.FilterChainProxy$VirtualFilterChain.doFi lter(FilterChainProxy.java:371) at org.springframework.security.ui.rememberme.RememberMeProcessingFilter.doFi lterHttp(RememberMeProcessingFilter.java:116) at org.springframework.security.ui.SpringSecurityFilter.doFilter(SpringSecuri tyFilter.java:53) at org.springframework.security.util.FilterChainProxy$VirtualFilterChain.doFi lter(FilterChainProxy.java:371) at org.springframework.security.wrapper.SecurityContextHolderAwareRequestFilt er.doFilterHttp(SecurityContextHolderAwareRequestFilter.java:91) at org.springframework.security.ui.SpringSecurityFilter.doFilter(SpringSecuri tyFilter.java:53) at org.springframework.security.util.FilterChainProxy$VirtualFilterChain.doFi lter(FilterChainProxy.java:371) at org.springframework.security.ui.basicauth.BasicProcessingFilter.doFilterHt tp(BasicProcessingFilter.java:172) at org.springframework.security.ui.SpringSecurityFilter.doFilter(SpringSecuri tyFilter.java:53) at org.springframework.security.util.FilterChainProxy$VirtualFilterChain.doFi lter(FilterChainProxy.java:371) at org.springframework.security.ui.AbstractProcessingFilter.doFilterHttp(Abst ractProcessingFilter.java:268) at org.springframework.security.ui.SpringSecurityFilter.doFilter(SpringSecuri tyFilter.java:53) at org.springframework.security.util.FilterChainProxy$VirtualFilterChain.doFi lter(FilterChainProxy.java:371) at org.springframework.security.ui.logout.LogoutFilter.doFilterHttp(LogoutFil ter.java:87) at org.springframework.security.ui.SpringSecurityFilter.doFilter(SpringSecuri tyFilter.java:53) at org.springframework.security.util.FilterChainProxy$VirtualFilterChain.doFi lter(FilterChainProxy.java:371) at org.springframework.security.ui.SessionFixationProtectionFilter.doFilterHt tp(SessionFixationProtectionFilter.java:61) at org.springframework.security.ui.SpringSecurityFilter.doFilter(SpringSecuri tyFilter.java:53) at org.springframework.security.util.FilterChainProxy$VirtualFilterChain.doFi lter(FilterChainProxy.java:371) at org.springframework.security.context.HttpSessionContextIntegrationFilter.d oFilterHttp(HttpSessionContextIntegrationFilter.java:235) at org.springframework.security.ui.SpringSecurityFilter.doFilter(SpringSecuri tyFilter.java:53) at org.springframework.security.util.FilterChainProxy$VirtualFilterChain.doFi lter(FilterChainProxy.java:371) at org.springframework.security.util.FilterChainProxy.doFilter(FilterChainPro xy.java:174) at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(Delega tingFilterProxy.java:236) at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFi lterProxy.java:167) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applicati onFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilter Chain.java:188) at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(Ch aracterEncodingFilter.java:96) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerReques tFilter.java:76) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applicati onFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilter Chain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve. java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve. java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:1 27) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:1 17) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.ja va:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174 ) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:873) at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.proces sConnection(Http11BaseProtocol.java:665) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.j ava:528) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollower WorkerThread.java:81) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.j ava:689) at java.lang.Thread.run(Thread.java:619) -- Hannu Saarenmaa Head of Unit for Biodiversity Informatics (yli-intendentti, lajitietotiimi) Finnish Museum of Natural History P.O. Box 17 (P.Rautatiekatu 13) FIN-00014 University of Helsinki hannu.saarenmaa(a)helsinki.fi Telephone +358-9-191-28688 Mobile +358-50-3102689 http://www.gbif.fi/

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FW: indexing of "Marchantiophyta/Hepatics/Liverworts of Russian Fennoscandia"
by Andrea Hahn (GBIF) 18 Feb '10

18 Feb '10

Dear IPT specialists, Could you help with advice on system requirements for running the IPT on Linux? Please see the original email below. Many thanks in advance, Andrea --------------------------------------------------------------- Andrea Hahn (ahahn(a)gbif.org) Data Portal Manager Global Biodiversity Information Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, Denmark Tel: +45-35321491 Fax: +45-35321480 URL: http://www.gbif.org --------------------------------------------------------------- From: Hannu Saarenmaa [mailto:hannu.saarenmaa@helsinki.fi] Sent: Thursday, February 18, 2010 9:42 AM To: GBIF Helpdesk; Ciprian Marius Vizitiu Cc: portal(a)livelink.gbif.org; Dare Talvitie; 'Mikko Koho'; Tommi Koskinen Subject: Re: indexing of "Marchantiophyta/Hepatics/Liverworts of Russian Fennoscandia" Andrea & Co. I am fixing this, but cannot "Import" the data anymore. The IPT gets stuck. There seems to be some kind of timeout, as I get "Done" when it is not done. We have to restart tomcat all the time. The log shows out-of-memory errors. We have now increased tomcat memory to 1.5 GB, and AJP Connector to connectionTimeout="5000", but still cannot figure this out. This is a Linux machine that is also doing other things. Can you give me indication of what kind of hardware the IPT should normally run on Linux? Hannu

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New IPT release (RC3) now available for download
by Aaron Steele 16 Feb '10

16 Feb '10

The latest IPT release (RC3) is now available for download and testing! http://gbif-providertoolkit.googlecode.com/files/ipt-1.0-RC3.war This release depends on the updated GeoServer IPT plugin which is bundled here: http://gbif-providertoolkit.googlecode.com/files/ipt-geoserver-1.0-RC3.zip New features include internationalization support, Darwin Core updates that reflect the latest ratified standard, and several bug fixes. Note that we are still unable to reproduce the delete bug (http://code.google.com/p/gbif-providertoolkit/issues/detail?id=155) and we are actively looking for testers who can reproduce this issue (or discover new issues) before the IPT version 1 release. As always, please submit issues here: http://code.google.com/p/gbif-providertoolkit/issues/entry Thanks! The GBIF IPT Team

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FW: IPT Finland
by Andrea Hahn (GBIF) 08 Feb '10

08 Feb '10

Dear list members, dear Aaron, Do you have any advice for Hannu (forwarded message below)? Many thanks, Andrea --------------------------------------------------------------- Andrea Hahn (ahahn(a)gbif.org) Data Portal Manager Global Biodiversity Information Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, Denmark Tel: +45-35321491 Fax: +45-35321480 URL: http://www.gbif.org --------------------------------------------------------------- -----Original Message----- From: Hannu Saarenmaa [mailto:hannu.saarenmaa@helsinki.fi] Sent: Saturday, February 06, 2010 9:25 AM To: helpdesk(a)gbif.org Subject: IPT Finland We have updated the metadata of Mosses from Russian Carelia, including the name. I wonder what is the meaning of pushing again the registrer-button. Will the metadata be updated at registry? Do I have to recreate the cache if I modify only metadata? Question: On home page the system shows the creator of the resource as "Modifier". Not the user who last modified it. Can that somehow be fixed. -- Hannu Saarenmaa Senior Curator (yli-intendetti) Finnish Museum of Natural History P.O. Box 17 (P.Rautatiekatu 13) FIN-00014 University of Helsinki hannu.saarenmaa(a)helsinki.fi Telephone +358-9-191-28688 Mobile +358-50-3102689 http://www.gbif.fi/

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set JAVA_OPTS="-Djava.awt.headless=true" for launchd to start geoserver
by Burke Chih-Jen Ko 01 Feb '10

01 Feb '10

Hello list members, For people who runs Mac OS X to host Tomcat container and wants to automatically start up with "launchd", in order to startup geoserver successfully, it is suggested that you set EnvironmentVariable as <key>EnvironmentVariables</key> <dict> <key>CATALINA_HOME</key> <string>/Library/Tomcat</string> <key>JAVA_OPTS</key> <string>-Djava.awt.headless=true</string> </dict> by adding "-Djava.awt.headless=true" to JAVA_OPTS in a launchd plist file. I try to describe what I experienced below. Please feel free to correct me as I am a newbie to jsp and Tomcat. I found this when recently I installed IPT-RC3 and the accompanying geoserver, it was strange that the geoserver couldn't successfully startup after I launched Tomcat by using Server Admin on Mac OS X Server 10.6 and 10.5, while IPT started up ok. But if I started Tomcat by bin/start.sh, geoserver would launch ok with a process called org.apache.catalina.startup.Bootstrap on the Dock. Later I tried testing with a separate installation of Tomcat (in addition to the Apple shipped version). By using the plist described in this book page: http://books.google.com/books?id=vJttHyVF0SUC&lpg=PA32&ots=i_9xrTuSd1&dq=ma… (Tomcat: The Definitive Guide, O'Reilly, p.33) geoserver was started up ok if I "sudo launchctl load" the plist in the Terminal, but failed to start up after I reboot the OS. After some googling I understood the org.apache.catalina.startup.Bootstrap process is relevant to the launching of geoserver while logged in. So specifying JAVA_OPTS="-Djava.awt.headless=true" prevents the need to invoke the bootstrap process at the GUI front, which is usually not ready during the booting process. What I didn't test, but I think it'll work, is that the variable can also be specified in the catalina.sh, which is called by launch daemon. Hope this could be helpful. Burke Taiwan Biodiversity Information Facility, TaiBIF Biodiversity Research Center, Academia Sinica 128 Sec 2, Academia Rd., Nangang District Taipei 115, Taiwan Tel: +886 2 27899621 ext. 220

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Fwd: [ZooKeys] GBIF IPT
by Tim Robertson (GBIF) 30 Jan '10

30 Jan '10

Dear list, Please see below. Tim > From: Ivailo Stoyanov <istoyanov(a)pensoftonline.net> > Date: January 29, 2010 5:02:13 PM GMT+01:00 > To: Tim Robertson <trobertson(a)gbif.org> > Subject: Re: [ZooKeys] GBIF IPT > Thanks, Tim, for the help. > > I have imported the data, but when I tried to update the metadata > with a new title and description I get the following error: > > ==================================================== > Data Access Failure > > Hibernate flushing: Could not execute JDBC batch update; > uncategorized SQLException for SQL [update resource set created=?, > creator_fk=?, geo_coverage_max_latitude=?, > geo_coverage_max_longitude=?, geo_coverage_min_latitude=?, > geo_coverage_min_longitude=?, guid=?, meta_contact_email=?, > meta_contact_name=?, meta_description=?, meta_link=?, > meta_location_latitude=?, meta_location_longitude=?, meta_title=?, > meta_uddi_id=?, modified=?, modifier_fk=?, status=?, type=?, > jdbc_driver_class=?, jdbc_password=?, jdbc_url=?, jdbc_user=?, > last_upload_event_fk=?, num_accepted=?, num_classes=?, > num_families=?, num_genera=?, num_kingdoms=?, num_orders=?, > num_phyla=?, num_species=?, num_synonyms=?, num_taxa=?, > num_terminal_taxa=?, bbox_max_latitude=?, bbox_max_longitude=?, > bbox_min_latitude=?, bbox_min_longitude=?, feature_hash=?, > num_countries=?, num_regions=?, num_terminal_regions=?, > rec_with_altitude=?, rec_with_coordinates=?, rec_with_country=?, > rec_with_date=? where id=?]; SQL state [90005]; error code [90005]; > Value too long for column META_TITLE: 'Western Palaearctic > Ectoedemia (Zimmermannia) Hering and Ectoedemia Busck s. str. > (Lepidoptera: Nepticulidae): five new species... [90005-104]; nested > exception is org.h2.jdbc.JdbcSQLException: Value too long for column > META_TITLE: 'Western Palaearctic Ectoedemia (Zimmermannia) Hering > and Ectoedemia Busck s. str. (Lepidoptera: Nepticulidae): five new > species... [90005-104] > ==================================================== > > Could you help with this? > > All the best, > Ivailo > -- > I. Stoyanov > Editorial Secretary > > ZOOKEYS -- http://pensoftonline.net/zookeys > BIORISK -- http://pensoftonline.net/biorisk

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