Problem with deploying webapp

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Problem with deploying webapp

eadc2
Hi Devs,
I'm having problems with deploying the test malariamine webapp. I'm
running tomcat 7.0.50 and I get the following errors:

ant -v default remove-webapp release-webapp
ends with this error:

release-webapp:
[tomcat-deploy] FAIL - Failed to deploy application at context path
/malariamine

BUILD FAILED
/local/intermine_060214/intermine/imbuild/application.xml:157: FAIL -
Failed to deploy application at context path /malariamine
         at
org.apache.catalina.ant.AbstractCatalinaTask.execute(AbstractCatalina
Task.java:258)
         at org.apache.catalina.ant.DeployTask.execute(DeployTask.java:201)
         at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
         at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
         at java.lang.reflect.Method.invoke(Method.java:597)
         at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
         at org.apache.tools.ant.Task.perform(Task.java:348)
         at org.apache.tools.ant.Target.execute(Target.java:390)
         at org.apache.tools.ant.Target.performTasks(Target.java:411)
         at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
         at org.apache.tools.ant.Project.executeTarget(Project.java:1368)
         at
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
         at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
         at org.apache.tools.ant.Main.runBuild(Main.java:809)
         at org.apache.tools.ant.Main.startAnt(Main.java:217)
         at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
         at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)


Looking at the Tomcat logs shows this error:
12-Feb-2014 11:37:14 org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive
/local/intermine_060214/apache-tomcat-7.0.50/webapps/malariamine.war
12-Feb-2014 11:37:14 org.apache.tomcat.util.digester.Digester endElement
SEVERE: End event threw exception
java.lang.reflect.InvocationTargetException
     at sun.reflect.GeneratedMethodAccessor19.invoke(Unknown Source)
     at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
     at java.lang.reflect.Method.invoke(Method.java:597)
     at
org.apache.tomcat.util.IntrospectionUtils.callMethodN(IntrospectionUtils.java:911)
     at
org.apache.catalina.startup.CallMethodMultiRule.end(WebRuleSet.java:1021)
     at
org.apache.tomcat.util.digester.Digester.endElement(Digester.java:1063)
     at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:601)
     at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:1782)
     at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2938)
     at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:648)
     at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:511)
     at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:808)
     at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:737)
     at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:119)
     at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1205)
     at
com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:522)
     at org.apache.tomcat.util.digester.Digester.parse(Digester.java:1561)
     at
org.apache.catalina.startup.ContextConfig.parseWebXml(ContextConfig.java:1901)
     at
org.apache.catalina.startup.ContextConfig.webConfig(ContextConfig.java:1254)
     at
org.apache.catalina.startup.ContextConfig.configureStart(ContextConfig.java:880)
     at
org.apache.catalina.startup.ContextConfig.lifecycleEvent(ContextConfig.java:378)
     at
org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:119)
     at
org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:90)
     at
org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5343)
     at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
     at
org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
     at
org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
     at
org.apache.catalina.core.StandardHost.addChild(StandardHost.java:634)
     at
org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1074)
     at
org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:554)
     at org.apache.catalina.startup.HostConfig.check(HostConfig.java:1649)
     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
     at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
     at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
     at java.lang.reflect.Method.invoke(Method.java:597)
     at
org.apache.tomcat.util.modeler.BaseModelMBean.invoke(BaseModelMBean.java:301)
     at
com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.invoke(DefaultMBeanServerInterceptor.java:836)
     at
com.sun.jmx.mbeanserver.JmxMBeanServer.invoke(JmxMBeanServer.java:761)
     at
org.apache.catalina.manager.ManagerServlet.check(ManagerServlet.java:1447)
     at
org.apache.catalina.manager.ManagerServlet.deploy(ManagerServlet.java:679)
     at
org.apache.catalina.manager.ManagerServlet.doPut(ManagerServlet.java:437)
     at javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
     at javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
     at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
     at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
     at
org.apache.catalina.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:108)
     at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
     at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
     at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
     at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
     at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:611)
     at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
     at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)
     at
org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)
     at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
     at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:409)
     at
org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1044)
     at
org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
     at
org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:315)
     at
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
     at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
     at java.lang.Thread.run(Thread.java:662)
Caused by: java.lang.IllegalArgumentException: The servlets named
[gff3-query] and [gff3-query] are both mapped to the url-pattern
[/service/query/results/gff3] which is not permitted
     at org.apache.catalina.deploy.WebXml.addServletMapping(WebXml.java:292)
     ... 62 more
12-Feb-2014 11:37:14 org.apache.catalina.startup.ContextConfig parseWebXml
SEVERE: Parse error in application web.xml file at
jndi:/localhost/malariamine/WEB-INF/web.xml
java.lang.IllegalArgumentException: The servlets named [gff3-query] and
[gff3-query] are both mapped to the url-pattern
[/service/query/results/gff3] which is not permitted
     at
org.apache.tomcat.util.digester.Digester.createSAXException(Digester.java:2711)
     at
org.apache.tomcat.util.digester.Digester.createSAXException(Digester.java:2743)
     at
org.apache.tomcat.util.digester.Digester.endElement(Digester.java:1066)
     at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:601)
     at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:1782)
     at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2938)
     at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:648)
     at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:511)
     at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:808)
     at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:737)
     at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:119)
     at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1205)
     at
com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:522)
     at org.apache.tomcat.util.digester.Digester.parse(Digester.java:1561)
     at
org.apache.catalina.startup.ContextConfig.parseWebXml(ContextConfig.java:1901)
     at
org.apache.catalina.startup.ContextConfig.webConfig(ContextConfig.java:1254)
     at
org.apache.catalina.startup.ContextConfig.configureStart(ContextConfig.java:880)
     at
org.apache.catalina.startup.ContextConfig.lifecycleEvent(ContextConfig.java:378)
     at
org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:119)
     at
org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:90)
     at
org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5343)
     at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
     at
org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
     at
org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
     at
org.apache.catalina.core.StandardHost.addChild(StandardHost.java:634)
     at
org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1074)
     at
org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:554)
     at org.apache.catalina.startup.HostConfig.check(HostConfig.java:1649)
     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
     at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
     at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
     at java.lang.reflect.Method.invoke(Method.java:597)
     at
org.apache.tomcat.util.modeler.BaseModelMBean.invoke(BaseModelMBean.java:301)
     at
com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.invoke(DefaultMBeanServerInterceptor.java:836)
     at
com.sun.jmx.mbeanserver.JmxMBeanServer.invoke(JmxMBeanServer.java:761)
     at
org.apache.catalina.manager.ManagerServlet.check(ManagerServlet.java:1447)
     at
org.apache.catalina.manager.ManagerServlet.deploy(ManagerServlet.java:679)
     at
org.apache.catalina.manager.ManagerServlet.doPut(ManagerServlet.java:437)
     at javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
     at javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
     at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
     at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
     at
org.apache.catalina.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:108)
     at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
     at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
     at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
     at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
     at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:611)
     at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
     at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)
     at
org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)
     at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
     at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:409)
     at
org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1044)
     at
org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
     at
org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:315)
     at
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
     at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
     at java.lang.Thread.run(Thread.java:662)
Caused by: java.lang.IllegalArgumentException: The servlets named
[gff3-query] and [gff3-query] are both mapped to the url-pattern
[/service/query/results/gff3] which is not permitted
     at org.apache.catalina.deploy.WebXml.addServletMapping(WebXml.java:292)
     at sun.reflect.GeneratedMethodAccessor19.invoke(Unknown Source)
     at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
     at java.lang.reflect.Method.invoke(Method.java:597)
     at
org.apache.tomcat.util.IntrospectionUtils.callMethodN(IntrospectionUtils.java:911)
     at
org.apache.catalina.startup.CallMethodMultiRule.end(WebRuleSet.java:1021)
     at
org.apache.tomcat.util.digester.Digester.endElement(Digester.java:1063)
     ... 56 more
12-Feb-2014 11:37:14 org.apache.catalina.startup.ContextConfig parseWebXml
SEVERE: Occurred at line 231 column 19
12-Feb-2014 11:37:15 org.apache.catalina.startup.ContextConfig
configureStart
SEVERE: Marking this application unavailable due to previous error(s)
12-Feb-2014 11:37:15 org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://struts.apache.org/tags-tiles is already
defined
12-Feb-2014 11:37:15 org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://struts.apache.org/tags-html is already
defined
12-Feb-2014 11:37:15 org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://struts.apache.org/tags-logic is already
defined
12-Feb-2014 11:37:15 org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://jakarta.apache.org/taglibs/string-1.1 is
already defined
12-Feb-2014 11:37:15 org.apache.catalina.core.StandardContext startInternal
SEVERE: Error getConfigured
12-Feb-2014 11:37:15 org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/malariamine] startup failed due to previous errors

Any idea how to fix this?
Thanks,
Alastair


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problem with gene glyph in jbrowse

eadc2
Hi Devs,
I'm having difficulties getting jbrowse and intermine working together.
I've been using the malariamine test data and I've mostly got things
working except that the genes are drawn wrong - the gene name is written
repeatedly, rather than drawing boxes. My best guess is this is
something to do with parent-child relations, even though I did run the
populate_child_features post-process task. I think transcript/mRNA is
supposed to have boxes on the line as well, if so that's having the same
problem.
This can be seen at:
http://thehulk.sysbiol.cam.ac.uk:8080/malariamine/report.do?id=1000086&trail=|1000086
Help much appreciated.
Thanks,
Alastair

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Re: problem with gene glyph in jbrowse

Julie Sullivan

That URL doesn't seem to be working for me. Can you check that it's
publicly accessible?

On 18/11/14 15:14, Alastair Crisp wrote:

> Hi Devs,
> I'm having difficulties getting jbrowse and intermine working together.
> I've been using the malariamine test data and I've mostly got things
> working except that the genes are drawn wrong - the gene name is written
> repeatedly, rather than drawing boxes. My best guess is this is
> something to do with parent-child relations, even though I did run the
> populate_child_features post-process task. I think transcript/mRNA is
> supposed to have boxes on the line as well, if so that's having the same
> problem.
> This can be seen at:
> http://thehulk.sysbiol.cam.ac.uk:8080/malariamine/report.do?id=1000086&trail=|1000086
>
> Help much appreciated.
> Thanks,
> Alastair
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

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Re: problem with gene glyph in jbrowse

Alex Kalderimis-2
In reply to this post by eadc2
I discussed this issue a bit with the folks at AIP and I think that
the child-parent structure is not quite right as produced by
populate_child_features. They said they might try to improve things on
their end, but I can try and liase with them on this issue.

Alex

On Tue, Nov 18, 2014 at 03:14:41PM +0000, Alastair Crisp wrote:

> Hi Devs,
> I'm having difficulties getting jbrowse and intermine working together. I've
> been using the malariamine test data and I've mostly got things working
> except that the genes are drawn wrong - the gene name is written repeatedly,
> rather than drawing boxes. My best guess is this is something to do with
> parent-child relations, even though I did run the populate_child_features
> post-process task. I think transcript/mRNA is supposed to have boxes on the
> line as well, if so that's having the same problem.
> This can be seen at:
> http://thehulk.sysbiol.cam.ac.uk:8080/malariamine/report.do?id=1000086&trail=|1000086
> Help much appreciated.
> Thanks,
> Alastair
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

--
Alex Kalderimis
Software Developer
InterMine
Dept. of Genetics
University of Cambridge
[hidden email]

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Re: problem with gene glyph in jbrowse

eadc2
That would be great.
Thanks,
Alastair

On 18/11/2014 17:04, Alex Kalderimis wrote:

> I discussed this issue a bit with the folks at AIP and I think that
> the child-parent structure is not quite right as produced by
> populate_child_features. They said they might try to improve things on
> their end, but I can try and liase with them on this issue.
>
> Alex
>
> On Tue, Nov 18, 2014 at 03:14:41PM +0000, Alastair Crisp wrote:
>> Hi Devs,
>> I'm having difficulties getting jbrowse and intermine working together. I've
>> been using the malariamine test data and I've mostly got things working
>> except that the genes are drawn wrong - the gene name is written repeatedly,
>> rather than drawing boxes. My best guess is this is something to do with
>> parent-child relations, even though I did run the populate_child_features
>> post-process task. I think transcript/mRNA is supposed to have boxes on the
>> line as well, if so that's having the same problem.
>> This can be seen at:
>> http://thehulk.sysbiol.cam.ac.uk:8080/malariamine/report.do?id=1000086&trail=|1000086
>> Help much appreciated.
>> Thanks,
>> Alastair
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev


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