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navraj shrestha

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Feb 12, 2018, 12:42:51 PM2/12/18
to MEME Suite Q&A
compile:
    [javac] Compiling 120 source files
    [javac] /usr/local/meme_4.12.0/website/src/au/edu/uq/imb/memesuite/servlet/u                       til/ComponentMotifs.java:15: error: package javax.servlet does not exist
    [javac] import javax.servlet.ServletContext;
    [javac]                     ^
    [javac] /usr/local/meme_4.12.0/website/src/au/edu/uq/imb/memesuite/servlet/u                       til/ComponentMotifs.java:16: error: package javax.servlet does not exist
    [javac] import javax.servlet.ServletException;
    [javac]                     ^
    [javac] /usr/local/meme_4.12.0/website/src/au/edu/uq/imb/memesuite/servlet/u                       til/ComponentMotifs.java:17: error: package javax.servlet.http does not exist
    [javac] import javax.servlet.http.HttpServletRequest;
    [javac]                          ^
    [javac] /usr/local/meme_4.12.0/website/src/au/edu/uq/imb/memesuite/servlet/u                       til/ComponentMotifs.java:18: error: package javax.servlet.http does not exist
    [javac] import javax.servlet.http.Part;
    [javac]                          ^
    [javac] /usr/local/meme_4.12.0/website/src/au/edu/uq/imb/memesuite/servlet/u                       til/WebUtils.java:20: error: package javax.servlet does not exist
    [javac] import javax.servlet.ServletException;
    [javac]                     ^
    [javac] /usr/local/meme_4.12.0/website/src/au/edu/uq/imb/memesuite/servlet/u                       til/WebUtils.java:21: error: package javax.servlet.http does not exist
    [javac] import javax.servlet.http.HttpServletRequest;
    [javac]                          ^
    [javac] /usr/local/meme_4.12.0/website/src/au/edu/uq/imb/memesuite/servlet/u                       til/WebUtils.java:22: error: package javax.servlet.http does not exist
    [javac] import javax.servlet.http.HttpServletResponse;
    [javac]                          ^
    [javac] /usr/local/meme_4.12.0/website/src/au/edu/uq/imb/memesuite/servlet/u                       til/WebUtils.java:23: error: package javax.servlet.http does not exist
    [javac] import javax.servlet.http.Part;
    [javac]                          ^
    [javac] /usr/local/meme_4.12.0/website/src/au/edu/uq/imb/memesuite/servlet/C                       onfigurationLoader.java:10: error: package javax.servlet does not exist
    [javac] import javax.servlet.ServletContextListener;
    [javac]                     ^
    [javac] /usr/local/meme_4.12.0/website/src/au/edu/uq/imb/memesuite/servlet/C                       onfigurationLoader.java:11: error: package javax.servlet does not exist
    [javac] import javax.servlet.ServletContextEvent;
    [javac]                     ^
    [javac] /usr/local/meme_4.12.0/website/src/au/edu/uq/imb/memesuite/servlet/C                       onfigurationLoader.java:12: error: package javax.servlet does not exist
    [javac] import javax.servlet.ServletContext;
    [javac]                     ^
    [javac] /usr/local/meme_4.12.0/website/src/au/edu/uq/imb/memesuite/servlet/C                       onfigurationLoader.java:23: error: cannot find symbol
    [javac] public class ConfigurationLoader implements ServletContextListener {
    [javac]                                             ^
    [javac]   symbol: class ServletContextListener
    [javac] /usr/local/meme_4.12.0/website/src/au/edu/uq/imb/memesuite/servlet/u                       til/PageComponent.java:6: error: package javax.servlet does not exist
    [javac] import javax.servlet.ServletException;
    [javac]                     ^
    [javac] /usr/local/meme_4.12.0/website/src/au/edu/uq/imb/memesuite/servlet/u                       til/ComponentMotifs.java:32: error: cannot find symbol
    [javac]   private ServletContext context;
    [javac]           ^
    [javac]   symbol:   class ServletContext
    [javac]   location: class ComponentMotifs
    [javac] /usr/local/meme_4.12.0/website/src/au/edu/uq/imb/memesuite/servlet/u                       til/ComponentMotifs.java:103: error: cannot find symbol
    [javac]   public ComponentMotifs(ServletContext context, HTMLTemplate info)                        throws ServletException {

CharlesEGrant

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Feb 12, 2018, 4:03:07 PM2/12/18
to MEME Suite Q&A
It looks like you are missing some required libraries in your Java SDK installation or in your Tomcat installation. Do you have Tomcat installed, and have your set your CATALINA_HOME environment variable?

Do you actually need to set up a MEME Suite web server? We don't recommend that unless you have experience working Tomcat and working with web servers.

The MEME Suite installation guide contains instructions on setting up the command line only version of MEME Suite.

navraj shrestha

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Feb 13, 2018, 7:06:54 PM2/13/18
to MEME Suite Q&A
Hi Charles, 
thanks for the reply.

yes we need to set MEME Suite web server, I was able to install it. Everything looks good however , when I submit the Job to MEME, i got following error.

HTTP Status 500 - ; nested exception is:

type Exception report

message ; nested exception is:

description The server encountered an internal error that prevented it from fulfilling this request.

exception

java.net.ConnectException: Connection refused (Connection refused)
	org.apache.axis.AxisFault.makeFault(AxisFault.java:101)
	org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:154)
	org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32)
	org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)
	org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)
	org.apache.axis.client.AxisClient.invoke(AxisClient.java:165)
	org.apache.axis.client.Call.invokeEngine(Call.java:2765)
	org.apache.axis.client.Call.invoke(Call.java:2748)
	org.apache.axis.client.Call.invoke(Call.java:2424)
	org.apache.axis.client.Call.invoke(Call.java:2347)
	org.apache.axis.client.Call.invoke(Call.java:1804)
	edu.sdsc.nbcr.opal.AppServicePortTypeSoapBindingStub.launchJob(AppServicePortTypeSoapBindingStub.java:624)
	au.edu.uq.imb.memesuite.servlet.SubmitJob.submitOpalJob(SubmitJob.java:726)
	au.edu.uq.imb.memesuite.servlet.SubmitJob.doPost(SubmitJob.java:814)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
	org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
	org.apache.catalina.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:108)

root cause

java.net.ConnectException: Connection refused (Connection refused)
	java.net.PlainSocketImpl.socketConnect(Native Method)
	java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
	java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
	java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
	java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
	java.net.Socket.connect(Socket.java:589)
	sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	java.lang.reflect.Method.invoke(Method.java:498)
	org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:153)
	org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:120)
	org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:191)
	org.apache.axis.transport.http.HTTPSender.writeToSocket(HTTPSender.java:404)
	org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:138)
	org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32)
	org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)
	org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)
	org.apache.axis.client.AxisClient.invoke(AxisClient.java:165)
	org.apache.axis.client.Call.invokeEngine(Call.java:2765)
	org.apache.axis.client.Call.invoke(Call.java:2748)
	org.apache.axis.client.Call.invoke(Call.java:2424)
	org.apache.axis.client.Call.invoke(Call.java:2347)
	org.apache.axis.client.Call.invoke(Call.java:1804)
	edu.sdsc.nbcr.opal.AppServicePortTypeSoapBindingStub.launchJob(AppServicePortTypeSoapBindingStub.java:624)
	au.edu.uq.imb.memesuite.servlet.SubmitJob.submitOpalJob(SubmitJob.java:726)
	au.edu.uq.imb.memesuite.servlet.SubmitJob.doPost(SubmitJob.java:814)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
	org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
	org.apache.catalina.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:108)

CharlesEGrant

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Feb 13, 2018, 7:33:59 PM2/13/18
to MEME Suite Q&A
It looks like Opal is not responding. Have you done troubleshooting to make sure Opal 2 is installed and running correctly? In particular have you been able to call up the "Happy Axis" page? If you don't know what I mean by the "Happy Axis" page you need to study the Opal documentation (step 9 of the Opal installation procedure in section 2.2). Note: we will provide very limited support to bring up a MEME Suite web site. We're happy to answer questions directly related to the MEME Suite tools, but the web server involves management of software outside the the MEME Suite. We simply don't have the resources to act as remote system administrators, or Tomcat and Opal trainers.

navraj shrestha

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Feb 13, 2018, 10:30:28 PM2/13/18
to MEME Suite Q&A
Opal looks good and i can access Dashboard page
Welcome to the Opal Dashboard


Opal Server Host Info

Hostname: 168.246.15.43
IP Address:168.246.15.43
Build Date:Linux usrelrhvvcl33.nafta.syngenta.org 3.10.0-693.11.6.el7.x86_64 #1 SMP Thu Dec 28 14:23:39 EST 2017 x86_64 x86_64 x86_64 GNU/Linux
Uptime:22:29:49 up 1 day, 5:24, 2 users, load average: 0.00, 0.01, 0.05
 

Opal Server Configuration

Opal Version:2.5
Data base driver:HSQL Database Engine Driver
Submission system:edu.sdsc.nbcr.opal.manager.ForkJobManager
User data lifetime:4 days




Happy Asix page looks like

Axis Happiness Page

Examining webapp configuration

Language: [en] [ja]

Needed Components

  • Found SAAJ API ( javax.xml.soap.SOAPMessage ) at an unknown location

  • Found JAX-RPC API ( javax.xml.rpc.Service ) at /usr/local/tomcat7/webapps/opal2/WEB-INF/lib/jaxrpc.jar

  • Found Apache-Axis ( org.apache.axis.transport.http.AxisServlet ) at /usr/local/tomcat7/webapps/opal2/WEB-INF/lib/axis.jar

  • Found Jakarta-Commons Discovery ( org.apache.commons.discovery.Resource ) at /usr/local/tomcat7/webapps/opal2/WEB-INF/lib/commons-discovery-0.2.jar

  • Found Jakarta-Commons Logging ( org.apache.commons.logging.Log ) at /usr/local/tomcat7/webapps/opal2/WEB-INF/lib/commons-logging-1.0.4.jar

  • Found Log4j ( org.apache.log4j.Layout ) at /usr/local/tomcat7/lib/log4j-1.2.15.jar

  • Found IBM's WSDL4Java ( com.ibm.wsdl.factory.WSDLFactoryImpl ) at /usr/local/tomcat7/webapps/opal2/WEB-INF/lib/wsdl4j-1.5.1.jar

  • Found JAXP implementation ( javax.xml.parsers.SAXParserFactory ) at an unknown location

  • Found Activation API ( javax.activation.DataHandler ) at an unknown location

Optional Components

  • Found Mail API ( javax.mail.internet.MimeMessage ) at /usr/local/tomcat7/webapps/opal2/WEB-INF/lib/javamail-1.4.3.jar

    • Warning: could not find class org.apache.xml.security.Init from file xmlsec.jar
    XML Security is not supported. 
    See http://xml.apache.org/security/

  • Found Java Secure Socket Extension ( javax.net.ssl.SSLSocketFactory ) at an unknown location

The core axis libraries are present.1 wanted optional axis librar(ies) are missing

    Note: On Tomcat 4.x and Java1.4, you may need to put libraries that contain java.* or javax.* packages into CATALINA_HOME/common/lib 
    jaxrpc.jar and saaj.jar are two such libraries.

    Note: Even if everything this page probes for is present, there is no guarantee your web service will work, because there are many configuration options that we do not check for. These tests are necessary but not sufficient

Examining Application Server

    Servlet version3.0
    XML Parsercom.sun.org.apache.xerces.internal.jaxp.SAXParserImpl
    XML ParserLocationan unknown location

Examining System Properties

    java.runtime.name=Java(TM) SE Runtime Environment
java.protocol.handler.pkgs=org.apache.axis.transport|
sun.boot.library.path=/usr/local/jdk1.8.0_161/jre/lib/amd64
java.vm.version=25.161-b12
shared.loader=
java.vm.vendor=Oracle Corporation
java.vendor.url=http://java.oracle.com/
path.separator=:
java.vm.name=Java HotSpot(TM) 64-Bit Server VM
tomcat.util.buf.StringCache.byte.enabled=true
file.encoding.pkg=sun.io
java.util.logging.config.file=/usr/local/tomcat7/conf/logging.properties
user.country=US
sun.java.launcher=SUN_STANDARD
sun.os.patch.level=unknown
java.vm.specification.name=Java Virtual Machine Specification
user.dir=/root
java.runtime.version=1.8.0_161-b12
org.apache.catalina.startup.TldConfig.jarsToSkip=tomcat7-websocket.jar
java.awt.graphicsenv=sun.awt.X11GraphicsEnvironment
java.endorsed.dirs=/usr/local/tomcat7/endorsed
os.arch=amd64
java.io.tmpdir=/usr/local/tomcat7/temp
line.separator=

java.vm.specification.vendor=Oracle Corporation
java.util.logging.manager=org.apache.juli.ClassLoaderLogManager
java.naming.factory.url.pkgs=org.apache.naming
os.name=Linux
sun.jnu.encoding=UTF-8
java.library.path=/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
tomcat.util.scan.DefaultJarScanner.jarsToSkip=bootstrap.jar,commons-daemon.jar,tomcat-juli.jar,annotations-api.jar,el-api.jar,jsp-api.jar,servlet-api.jar,websocket-api.jar,catalina.jar,catalina-ant.jar,catalina-ha.jar,catalina-tribes.jar,jasper.jar,jasper-el.jar,ecj-*.jar,tomcat-api.jar,tomcat-util.jar,tomcat-coyote.jar,tomcat-dbcp.jar,tomcat-jni.jar,tomcat-spdy.jar,tomcat-i18n-en.jar,tomcat-i18n-es.jar,tomcat-i18n-fr.jar,tomcat-i18n-ja.jar,tomcat-juli-adapters.jar,catalina-jmx-remote.jar,catalina-ws.jar,tomcat-jdbc.jar,tools.jar,commons-beanutils*.jar,commons-codec*.jar,commons-collections*.jar,commons-dbcp*.jar,commons-digester*.jar,commons-fileupload*.jar,commons-httpclient*.jar,commons-io*.jar,commons-lang*.jar,commons-logging*.jar,commons-math*.jar,commons-pool*.jar,jstl.jar,taglibs-standard-spec-*.jar,geronimo-spec-jaxrpc*.jar,wsdl4j*.jar,ant.jar,ant-junit*.jar,aspectj*.jar,jmx.jar,h2*.jar,hibernate*.jar,httpclient*.jar,jmx-tools.jar,jta*.jar,log4j.jar,log4j-1*.jar,mail*.jar,slf4j*.jar,xercesImpl.jar,xmlParserAPIs.jar,xml-apis.jar,junit.jar,junit-*.jar,hamcrest*.jar,org.hamcrest*.jar,ant-launcher.jar,cobertura-*.jar,asm-*.jar,dom4j-*.jar,icu4j-*.jar,jaxen-*.jar,jdom-*.jar,jetty-*.jar,oro-*.jar,servlet-api-*.jar,tagsoup-*.jar,xmlParserAPIs-*.jar,xom-*.jar
java.specification.name=Java Platform API Specification
java.class.version=52.0
sun.management.compiler=HotSpot 64-Bit Tiered Compilers
os.version=3.10.0-693.11.6.el7.x86_64
java.util.concurrent.ForkJoinPool.common.threadFactory=org.apache.catalina.startup.SafeForkJoinWorkerThreadFactory
user.home=/root
org.apache.catalina.startup.ContextConfig.jarsToSkip=
user.timezone=America/New_York
catalina.useNaming=true
java.awt.printerjob=sun.print.PSPrinterJob
java.specification.version=1.8
file.encoding=UTF-8
catalina.home=/usr/local/tomcat7
user.name=root
java.class.path=/usr/local/tomcat7/bin/bootstrap.jar:/usr/local/tomcat7/bin/tomcat-juli.jar
java.naming.factory.initial=org.apache.naming.java.javaURLContextFactory
package.definition=sun.,java.,org.apache.catalina.,org.apache.coyote.,org.apache.jasper.,org.apache.naming.,org.apache.tomcat.
java.vm.specification.version=1.8
sun.arch.data.model=64
java.home=/usr/local/jdk1.8.0_161/jre
sun.java.command=org.apache.catalina.startup.Bootstrap start
java.specification.vendor=Oracle Corporation
user.language=en
awt.toolkit=sun.awt.X11.XToolkit
java.vm.info=mixed mode
java.version=1.8.0_161
java.ext.dirs=/usr/local/jdk1.8.0_161/jre/lib/ext:/usr/java/packages/lib/ext
sun.boot.class.path=/usr/local/jdk1.8.0_161/jre/lib/resources.jar:/usr/local/jdk1.8.0_161/jre/lib/rt.jar:/usr/local/jdk1.8.0_161/jre/lib/sunrsasign.jar:/usr/local/jdk1.8.0_161/jre/lib/jsse.jar:/usr/local/jdk1.8.0_161/jre/lib/jce.jar:/usr/local/jdk1.8.0_161/jre/lib/charsets.jar:/usr/local/jdk1.8.0_161/jre/lib/jfr.jar:/usr/local/jdk1.8.0_161/jre/classes
java.vendor=Oracle Corporation
server.loader=
catalina.base=/usr/local/tomcat7
jdk.tls.ephemeralDHKeySize=2048
file.separator=/
java.vendor.url.bug=http://bugreport.sun.com/bugreport/
common.loader=${catalina.base}/lib,${catalina.base}/lib/*.jar,${catalina.home}/lib,${catalina.home}/lib/*.jar
sun.cpu.endian=little
sun.io.unicode.encoding=UnicodeLittle
sun.font.fontmanager=sun.awt.X11FontManager
package.access=sun.,org.apache.catalina.,org.apache.coyote.,org.apache.jasper.,org.apache.naming.resources.,org.apache.tomcat.
sun.cpu.isalist=
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