How to get jMoby

Using jMoby from CVS

The jMoby software is part of the Moby CVS repository - look for a subdirectory moby-live/Java.

Using binary distributions

There are several binary distributions, each of them focusing on some specific features. (Remember, however, that you can always get everything in one go from the CVS repository.)

Using jMoby for Maven

This is an option for those wanting to use jMoby libraries in their own Java projects.

The only thing you need to know is how to refer to the jMoby library in a Maven repository (you need to find the latest version number by browsing the given Maven repository):

<groupId>org.biomoby</groupId>
<artifactId>jmoby</artifactId>
<version>1.0.0</version>

<repository>
   <id>bio.maven.repository</id>
   <url>http://repo1.maven.org/maven2/</url>
</repository>

Latest changes are available either as a summary or in details from the CVS repository.

Using jMoby from CVS

Requirements
How to build it
What are the build targets
Where to put things
How to use it

Requirements

• Java

  Install JDK Java 1.5 or later.

• Apache Tomcat (or a similar servlet container)

  BioMoby is about Web Services - and Web Services are web applications run in a servlet container. The development of BioMoby services was mostly done by using the Apache Tomcat 5. But other container should work, as well.

• Apache Ant

  The Ant is a Java tool for building, executing and playing with Java (and perhaps other, as well) programs. jMoby, as most of any Java projects, uses it a lot.
  Please make sure that you are using Ant version 1.65 or greater.

How to build it

   ant install

   ant clean compile

   ant -projecthelp

   ant all

It also uses file build.properties (if such file exists either in this directory or in your home directory) - where you can specify your-site-specific properties. The properties - that can be set there - are described in more details in build.properties.template).

What are the build targets

There is also a graphical snapshot of our Ant tagrets (and here you can find how it was created).

Here are the common targets:

compile

It compiles all sources in the src subdirectory. If you add there a source file but it is not yet ready to be compiled put it into a directory notyet (on any level below src). It also guarantees that CLASSPATH is correctly set before compilation (including all classes created from the src and all jar files from the lib directory).

clean

It removes all generated files, including all compiled classes (but it does not remove third-party libraries from the lib directory). It is always good idea to make sure that all your changes are really compilable before you commit, by typing:

ant clean compile

docs

It generates API documentation (into docs/API) for all classes, excluding those specifically mentioned in the property excluded.documented.packages and/or excluded.documented.files.

jars

It creates several jar files (build/lib/*.jar) with all classes from src.

jar-rdfagent

It creates a jar file (build/lib/RDFagent.jar) with classes for RDF Agent sub-project.

config

It creates all run-time scripts. The templates for these scripts are in src/config and they are created in build/run. Once there they contain fully qualified paths reflecting the location of your CVS copy, so they can be used without setting any CLASSPATH.

This target is called automatically by the compile target.

all

It calls many other targets to clean, compile, generate API and to build all binary distributions.

bootstrap

This is a special target fetching the Maven library (that is needed to fetch all jMoby dependencies). It is called automatically when you call ant install.

How to use it

You do not need to be in any particular directory to use these scripts. But you need to have java on your path (the scripts are too dumb to understand JAVA_HOME environment variable).

For example, try:

   ./build/run/run-cmdline-client -help
   ./build/run/run-testing-central

   build\run\run-cmdline-client.bat -help
   build\run\run-testing-central.bat

Using jMoby from binary distributions

Servlet for host MOBY services
Graphical end-user client
Servlets producing BioMoby graphs
RDF Agent

Servlet for host MOBY services

Standalone graphical client

Servlets producing BioMoby graphs

The file is named jMoby-<date>.war. Take the latest version and put it (without unpacking it) where your servlet engine sits. For Tomcat it is here: <your-tomcat-home-directory>/webapps/. Then restart your Tomcat. It will unpack it and will create a directory webapps/jmoby. Before using it, you have to edit webapps/jmoby/WEB-INF/web.xml to reflect your local environment. Once done, start to use it (the URL depends how you edited the web.xml file).

Please report all problems, or submit features and wishes about these clients to Martin Senger.

RDF Agent

Unpack it. It creates a directory named rdfagent, go there, check the README file, and start using it.

What is the RDF Agent?

Instructions on downloading and installing the RDF Agent