February 2010 - IPT - lists.gbif.org

FW: What does Yikes mean
by Andrea Hahn (GBIF) 19 Feb '10

19 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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