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Moby Services in JAVA

Completed Tasks

Server-side

Requirements

Java

#(DONE*)Java Standard Edition (J2SE) Development Kit (JDK) 5.0 Update 6 *
https://sdlc2d.sun.com/ECom/EComActionServlet;jsessionid=CB9B1AD7B234BEA9BA89E3BD36D61105

    1. After installation, set the environment variable JAVA_HOME to the installed path.
    2. Make sure that java, javac and javadoc are found in your command PATH.
      #(DONE)Java Standard Edition (J2SE) Runtime Environment (JRE) 5.0 Update 6
      #(DONE)Eclipse SDK 3.1.2: development platform
    3. Eclipse 1.3 (http://www.eclipse.org/downloads/ )

Web Server Environment

  1. (DONE) Apache 1.3.34: HTTP server
    1. If you do a new installation, you should prefer at least the 2.0 branch (most current release is 2.0.59). The Apache site recommends the 2.2 version which is quite new and I have no experience with that. Both versions are available at the same URL as given above.
  2. (DONE)Apache Tomcat 5.5.16: servlet container
    http://archive.apache.org/dist/tomcat/tomcat-5/v5.5.16/
    • Start tomcat on **..**.67 : su - tomcat -c /usr/local/tomcat5/bin/startup.sh
    • Shutdown tomcat on **..**.67 : su - tomcat -c /usr/local/tomcat5/bin/shutdown.sh
  1. (DONE)mod_jk 1.2.15: Tomcat-Apache plug-in
    1. http://archive.apache.org/dist/tomcat/tomcat-connectors/jk/binaries/win32/ Rename file mod_jk-apache-2.x.xx.so to mod_jk.so, and place under directory \path\to\Apache2\modules
  2. (DONE)Axis 1.3: SOAP implementation

Perl

see http://bioinfo.mpiz-koeln.mpg.de/araws/documentation/help/perl-services/requirements/

  1. (DONE) install Perl 5.8.8 (note: stable production releases are even numbers, e.g., 5.8.whatever is stable, 5.9.whatever is not). Downloaded perl into ~root/ann_installs/perl and followed the directions.
  2. (DONE) write simple test script (~aloraine/src/pt.pl) with import statements to check for dependencies.
  3. install dependencies using command cpan -i modulename
    *Note:* I can't figure out how to keep wiki from interpreting double colons as non-format characters. Interpret spaces in module names below as double-colons
    1. LWP UserAgent (DONE)
    2. MIME Parser (DONE)
    3. SOAP MIME (DONE)
    4. Test More (DONE)
    5. Text Shellwords (DONE)
    6. XML Parser
    7. libxml2 (DONE - v. 2.6.28 April 07) - needed to install afresh because no header file available in /usr/header, which is needed to build XML perl tools below
    8. XML LibXML (DONE - v. 1.62)
    9. XML LibXML Common (DONE)
    10. XML XPath (DONE)
    11. SOAP Lite (DONE - v. 0.60, as recommended)

To-Do

Axis

  • Write a simple calculator app and deploy it as a service.

Useful Resources

  1. https://biomoby.tigr.org/wiki/index.php/Main_Page#Guides
  2. http://johnturner.com/howto/apache2-tomcat4127-jk-rh9-howto.html

Axis

  1. http://www.herongyang.com/ws/soap_java_2.html

Useful Commands

  • java org.apache.axis.wsdl.WSDL2Java -o ./server -dSession -Strue -s -B -p server.genemodel VinService.wsdl
  • java org.apache.axis.wsdl.WSDL2Java -o ./client -v -B -pclient.genemodel VinService.wsdl
  • java org.apache.axis.client.AdminClient -p 80 undeploy.wsdd
  • java org.apache.axis.client.AdminClient -p 80 deploy.wsdd
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