May 2014 - ALA-Portal - lists.gbif.org

DwC-A loading problems
by Daniel Lins 27 Jun '14

27 Jun '14

Hi Nick and Dave, We are having some problems in Biocache during the upload of DwC-A files. As shown below, after run the method "au.org.ala.util.DwCALoader", our system returns the error message "Exception in thread "main" org.gbif.dwc.text.UnkownDelimitersException: Unable to detect field delimiter" I accomplished tests using DwC-A files with tab-delimited text files and comma-delimited text files. In both cases the error generated was the same. What causes these problems? (** CSV Loader works great) *tab-delimited file test* poliusp@poliusp-VirtualBox:~/dev/biocache$ s*udo java -cp .:biocache.jar au.org.ala.util.DwCALoader dr7 -l /data/collectory/upload/1398658607824/2f676abc-4503-489e-8f0c-fcb6e1bc554b.zip* 2014-04-28 01:44:02,837 INFO : [ConfigModule] - Loading configuration from /data/biocache/config/biocache-config.properties 2014-04-28 01:44:03,090 INFO : [ConfigModule] - Initialise SOLR 2014-04-28 01:44:03,103 INFO : [ConfigModule] - Initialise name matching indexes 2014-04-28 01:44:03,605 INFO : [ConfigModule] - Initialise persistence manager 2014-04-28 01:44:03,606 INFO : [ConfigModule] - Configure complete Loading archive /data/collectory /upload/1398658607824/2f676abc-4503-489e-8f0c-fcb6e1bc554b.zip for resource dr7 with unique terms List(dwc:occurrenceID) stripping spaces false incremental false testing false *Exception in thread "main" org.gbif.dwc.text.UnkownDelimitersException: Unable to detect field delimiter* at org.gbif.file.CSVReaderFactory.buildArchiveFile( CSVReaderFactory.java:129) at org.gbif.file.CSVReaderFactory.build(CSVReaderFactory.java:46) at org.gbif.dwc.text.ArchiveFactory.readFileHeaders( ArchiveFactory.java:344) at org.gbif.dwc.text.ArchiveFactory.openArchive(ArchiveFactory.java: 289) at au.org.ala.util.DwCALoader.loadArchive(DwCALoader.scala:129) at au.org.ala.util.DwCALoader.loadLocal(DwCALoader.scala:106) at au.org.ala.util.DwCALoader$.main(DwCALoader.scala:52) at au.org.ala.util.DwCALoader.main(DwCALoader.scala) *comma-delimited file test* poliusp@poliusp-VirtualBox:~/dev/biocache$ *sudo java -cp .:biocache.jar au.org.ala.util.DwCALoader dr7 -l ./dwca-teste3.zip* 2014-04-28 01:56:04,683 INFO : [ConfigModule] - Loading configuration from /data/biocache/config/biocache-config.properties 2014-04-28 01:56:04,940 INFO : [ConfigModule] - Initialise SOLR 2014-04-28 01:56:04,951 INFO : [ConfigModule] - Initialise name matching indexes 2014-04-28 01:56:05,437 INFO : [ConfigModule] - Initialise persistence manager 2014-04-28 01:56:05,438 INFO : [ConfigModule] - Configure complete Loading archive ./dwca-teste3.zip for resource dr7 with unique terms List( dwc:occurrenceID) stripping spaces false incremental false testing false *Exception in thread "main" org.gbif.dwc.text.UnkownDelimitersException: Unable to detect field delimiter* at org.gbif.file.CSVReaderFactory.buildArchiveFile( CSVReaderFactory.java:129) at org.gbif.file.CSVReaderFactory.build(CSVReaderFactory.java:46) at org.gbif.dwc.text.ArchiveFactory.readFileHeaders( ArchiveFactory.java:344) at org.gbif.dwc.text.ArchiveFactory.openArchive(ArchiveFactory.java: 289) at au.org.ala.util.DwCALoader.loadArchive(DwCALoader.scala:129) at au.org.ala.util.DwCALoader.loadLocal(DwCALoader.scala:106) at au.org.ala.util.DwCALoader$.main(DwCALoader.scala:52) at au.org.ala.util.DwCALoader.main(DwCALoader.scala) Thanks! Regards. -- Daniel Lins da Silva (Mobile) 55 11 96144-4050 Research Center on Biodiversity and Computing (Biocomp) University of Sao Paulo, Brazil daniellins(a)usp.br daniel.lins(a)gmail.com

3 18

ala-geo-spatial
by Paulo André 02 Jun '14

02 Jun '14

Hi We've deployed ala-geo-spatial project. We've found 2 issues: - No WebApplicationContext found: no ContextLoaderListener registered? - Invocation of method 'reloadCache' on target class [class au.org.ala.spatial.data.FacetCacheImpl] failed java.lang.IllegalArgumentException: [null/search/grouped/facets] is not a valid HTTP URL Have you ever seen this issues? BR Paulo 18:29:16.705 [main] ERROR org.zkoss.zk.ui.util.Configuration - Failed to invoke class org.zkoss.spring.init.SecurityWebAppInit java.lang.IllegalStateException: No WebApplicationContext found: no ContextLoaderListener registered? at org.springframework.web.context.support.WebApplicationContextUtils.getRequiredWebApplicationContext(WebApplicationContextUtils.java:84) at org.zkoss.spring.init.SecurityWebAppInit.init(SecurityWebAppInit.java:47) at org.zkoss.zk.ui.util.Configuration.invokeWebAppInits(Configuration.java:733) at org.zkoss.zk.ui.impl.AbstractWebApp.init(AbstractWebApp.java:204) at org.zkoss.zk.ui.http.SimpleWebApp.init(SimpleWebApp.java:58) at org.zkoss.zk.ui.http.WebManager.<init>(WebManager.java:228) at org.zkoss.zk.ui.http.HttpSessionListener23.contextInitialized(HttpSessionListener23.java:140) at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4206) at org.apache.catalina.core.StandardContext.start(StandardContext.java:4705) at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:799) at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:779) at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:601) at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:675) at org.apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:601) at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:502) at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1317) at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:324) at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:142) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1065) at org.apache.catalina.core.StandardHost.start(StandardHost.java:840) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1057) at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:463) at org.apache.catalina.core.StandardService.start(StandardService.java:525) at org.apache.catalina.core.StandardServer.start(StandardServer.java:754) at org.apache.catalina.startup.Catalina.start(Catalina.java:595) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) 2014-05-22 18:29:21,980 ERROR [pool-2-thread-1] (MethodInvokingRunnable.java:68) - Invocation of method 'reloadCache' on target class [class au.org.ala.spatial.data.FacetCacheImpl] failed java.lang.IllegalArgumentException: [null/search/grouped/facets] is not a valid HTTP URL at org.springframework.web.util.UriUtils.encodeHttpUrl(UriUtils.java:245) at org.springframework.web.client.RestTemplate$HttpUrlTemplate.encodeUri(RestTemplate.java:651) at org.springframework.web.util.UriTemplate.expand(UriTemplate.java:140) at org.springframework.web.client.RestTemplate.execute(RestTemplate.java:400) at org.springframework.web.client.RestTemplate.getForObject(RestTemplate.java:199) at au.org.ala.spatial.data.FacetCacheImpl.reloadCache(FacetCacheImpl.java:59) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.springframework.util.MethodInvoker.invoke(MethodInvoker.java:273) at org.springframework.scheduling.support.MethodInvokingRunnable.run(MethodInvokingRunnable.java:65) at org.springframework.scheduling.support.DelegatingErrorHandlingRunnable.run(DelegatingErrorHandlingRunnable.java:51) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:304) at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:178) at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:744) 2014-05-22 18:29:21,991 ERROR [pool-2-thread-1] (MethodInvokingRunnable.java:68) - Invocation of method 'reloadCache' on target class [class au.org.ala.spatial.data.SpeciesListUtil] failed java.lang.NullPointerException at java.lang.StringBuilder.<init>(StringBuilder.java:109) at au.org.ala.spatial.data.SpeciesListUtil.getLists(SpeciesListUtil.java:70) at au.org.ala.spatial.data.SpeciesListUtil.getNumberOfPublicSpeciesLists(SpeciesListUtil.java:61) at au.org.ala.spatial.data.SpeciesListUtil.reloadCache(SpeciesListUtil.java:40) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.springframework.util.MethodInvoker.invoke(MethodInvoker.java:273) at org.springframework.scheduling.support.MethodInvokingRunnable.run(MethodInvokingRunnable.java:65) at org.springframework.scheduling.support.DelegatingErrorHandlingRunnable.run(DelegatingErrorHandlingRunnable.java:51) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:304) at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:178) at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:744)

4 5

Installation page updated
by Burke Chih-Jen Ko [GBIF] 29 May '14

29 May '14

Dear list members, (Sorry for cross-posting.) I would like to let you know that we've just updated these two pages on the wiki: 1. Essential tools and environment configurations: http://dev.gbif.org/wiki/display/ALA/01+Essential+tools+and+environment+con… 2. Installation: http://dev.gbif.org/wiki/display/ALA/02+Installation We are able to install the ALA portal demo by following these steps. Any suggestions on improving the documentation are highly appreciated! Cheers, Burke

4 5

Smooth installation and some issues
by Burke Chih-Jen Ko [GBIF] 26 May '14

26 May '14

Hi all, Words cannot describe how impressed I am to be able to get the ALA site up and running locally in 24 hours with Vagrant and Ansible as a freshman to these technologies - well done ALA devs! I found some issues during the installation and I've filed them as issues in Jira: http://dev.gbif.org/issues/browse/ALA-31 http://dev.gbif.org/issues/browse/ALA-32 http://dev.gbif.org/issues/browse/ALA-33 http://dev.gbif.org/issues/browse/ALA-34 I think ALA-33 is the critical one to address earlier. I'll keep the list posted about the progress of the documentation. Again thanks for your great work! Burke Informatics Liaison GBIF Secretariat Tel: +45 35 32 15 11 Fax: +45 32 32 14 80 Mobile: +45 24 66 88 80 E-mail: bko(a)gbif.org Skype: burkeker http://community.gbif.org/pg/profile/burkeker

4 4

Taxon Profile
by Allan Koch 22 May '14

22 May '14

Hi colleagues, We have an issues related taxons names in Biocache. Natasha did an adaptation in Namematching for we genarate an Taxon Names Index based on a DwC-A. This worked perferctly!!! But, I guess that the names added in the Taxon Names Index have to be added in the Taxon Profile database (Cassandra) too. I'm right? If yes, there is another way to add names in Taxon Profile beyond to insert records manually in Cassandra database? Thanks, Allan Koch Veiga Núcleo de Pesquisa em Biodiversidade e Computação - BioComp Laboratório de Automação Agrícola - LAA Depto. de Engenharia de Computação e Sistemas Digitais - PCS Engenharia Elétrica - Escola Politécnica da USP Celular: +55 11 8401-2277 Email: allan.kv(a)usp.br "*Stay hungry, stay foolish.*" Stewart Brand

2 2

Problems with Process Function (Biocache-Store)
by Daniel Lins 09 May '14

09 May '14

Hi David, We are configuring a new test server (with CentOS) and we having a problem never seen before in our other ALA instances. We are loading the data in the Biocache-Store correctly (These data are saved in the Cassandra database), but the processing function doesn't works.The delete-resource didn't works too. In both cases, no error messages are shown (see the screens). https://www.dropbox.com/s/oorsagr529n2qan/ScreensCentOS.zip I thought it was something related to taxon files, but we repeat the configuration steps and this error remained. Do you have any suggestions to solve this problem? Regards, Daniel Lins da Silva (Mobile) 55 11 96144-4050 Research Center on Biodiversity and Computing (Biocomp) University of Sao Paulo, Brazil daniellins(a)usp.br daniel.lins(a)gmail.com

2 1

bie-webapp2 - url search
by Paulo André 08 May '14

08 May '14

Hi We've deployed bie-webapp2 project. But the search does not able to find path resource "/ws". Ex.: http://localhost:8080/bie-webapp2/ws/search.json?q=lala&start=0&pageSize=10…<http://localhost:8080/biocache-service/ws> Error Failed calling web service. class java.io.FileNotFoundException http://localhost:8080/bie-webapp2/ws/search.json?q=lala&start=0&pageSize=10… http://localhost:8080/bie-webapp2/ws/search.json?q=lala&start=0&pageSize=10… . We are using svn version 4309. Is url search correct? []'s Paulo

1 0

ala-cas - svn version 4248 - Cannot construct org.apache.maven.plugin.war.util.WebappStructure as it does not have a no-args constructor
by Paulo André 08 May '14

08 May '14

Hi We've run mvn package for ala-cas (svn version 4248) and we've caught this issue: "Cannot construct org.apache.maven.plugin.war.util.WebappStructure as it does not have a no-args constructor". Have you ever had this issue? BR Paulo [ERROR] FATAL ERROR [INFO] ------------------------------------------------------------------------ [INFO] Cannot construct org.apache.maven.plugin.war.util.WebappStructure as it does not have a no-args constructor ---- Debugging information ---- message : Cannot construct org.apache.maven.plugin.war.util.WebappStructure as it does not have a no-args constructor cause-exception : com.thoughtworks.xstream.converters.reflection.ObjectAccessException cause-message : Cannot construct org.apache.maven.plugin.war.util.WebappStructure as it does not have a no-args constructor class : org.apache.maven.plugin.war.util.WebappStructure required-type : org.apache.maven.plugin.war.util.WebappStructure path : /webapp-structure line number : 1 ------------------------------- [INFO] ------------------------------------------------------------------------ [INFO] Trace com.thoughtworks.xstream.converters.ConversionException: Cannot construct org.apache.maven.plugin.war.util.WebappStructure as it does not have a no-args constructor ---- Debugging information ---- message : Cannot construct org.apache.maven.plugin.war.util.WebappStructure as it does not have a no-args constructor cause-exception : com.thoughtworks.xstream.converters.reflection.ObjectAccessException cause-message : Cannot construct org.apache.maven.plugin.war.util.WebappStructure as it does not have a no-args constructor class : org.apache.maven.plugin.war.util.WebappStructure required-type : org.apache.maven.plugin.war.util.WebappStructure path : /webapp-structure line number : 1 ------------------------------- at com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:63) at com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:45) at com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:46) at com.thoughtworks.xstream.core.TreeUnmarshaller.start(TreeUnmarshaller.java:117) at com.thoughtworks.xstream.core.ReferenceByXPathMarshallingStrategy.unmarshal(ReferenceByXPathMarshallingStrategy.java:29) at com.thoughtworks.xstream.XStream.unmarshal(XStream.java:846) at com.thoughtworks.xstream.XStream.unmarshal(XStream.java:833) at com.thoughtworks.xstream.XStream.fromXML(XStream.java:781) at org.apache.maven.plugin.war.util.WebappStructureSerializer.fromXml(WebappStructureSerializer.java:73) at org.apache.maven.plugin.war.AbstractWarMojo.buildWebapp(AbstractWarMojo.java:404) at org.apache.maven.plugin.war.AbstractWarMojo.buildExplodedWebapp(AbstractWarMojo.java:375) at org.apache.maven.plugin.war.WarMojo.performPackaging(WarMojo.java:181) at org.apache.maven.plugin.war.WarMojo.execute(WarMojo.java:143) at org.apache.maven.plugin.DefaultPluginManager.executeMojo(DefaultPluginManager.java:490) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoals(DefaultLifecycleExecutor.java:694) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoalWithLifecycle(DefaultLifecycleExecutor.java:556) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoal(DefaultLifecycleExecutor.java:535) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoalAndHandleFailures(DefaultLifecycleExecutor.java:387) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeTaskSegments(DefaultLifecycleExecutor.java:348) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.execute(DefaultLifecycleExecutor.java:180) at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:328) at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:138) at org.apache.maven.cli.MavenCli.main(MavenCli.java:362) at org.apache.maven.cli.compat.CompatibleMain.main(CompatibleMain.java:60) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.codehaus.classworlds.Launcher.launchEnhanced(Launcher.java:315) at org.codehaus.classworlds.Launcher.launch(Launcher.java:255) at org.codehaus.classworlds.Launcher.mainWithExitCode(Launcher.java:430) at org.codehaus.classworlds.Launcher.main(Launcher.java:375) Caused by: com.thoughtworks.xstream.converters.reflection.ObjectAccessException: Cannot construct org.apache.maven.plugin.war.util.WebappStructure as it does not have a no-args constructor at com.thoughtworks.xstream.converters.reflection.PureJavaReflectionProvider.newInstance(PureJavaReflectionProvider.java:59) at com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.instantiateNewInstance(AbstractReflectionConverter.java:257) at com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshal(AbstractReflectionConverter.java:124) at com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:56) ... 31 more [INFO] ------------------------------------------------------------------------ [INFO] Total time: 23 seconds [INFO] Finished at: Thu May 08 16:24:37 BRT 2014 [INFO] Final Memory: 20M/89M [INFO] ------------------------------------------------------------------------

1 1

biocache-service - not deployed
by Paulo André 06 May '14

06 May '14

Hi We've deployed biocache-service (svn version 4428) on tomcat 6. But biocache-service does not enable for request. We're seen a issue on log (catalina.out): SEVERE: The web application [/biocache-service] appears to have started a thread named [AsyncAppender-Dispatcher-Thread-3] but has failed to stop it. This is very likely to create a memory leak. Have you ever had this issue? BR Paulo

2 2