error while submitting jobs on meme tool

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navraj shrestha

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Feb 15, 2018, 11:14:44 AM2/15/18
to MEME Suite Q&A

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)

note The full stack trace of the root cause is available in the Apache Tomcat/7.0.75 logs.






Configured meme as follow. ALl test passed.
./configure --prefix=/usr/local/meme --enable-build-libxslt --enable-web=http://IP/opal2/services --enable-webservice --with-url=http://IP/meme --with-db=/usr/local/meme/meme_db

I can access happy page and looks as below. I can access opal portal

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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