Contents of this directory


build.xml - This is the main build file for this software.

antfiles/ - This directory contains files related to the build process
of this project.

licenses/ - This directory contains licenses of software that is distributed
with the Tropix source. Licenses for software pulled in via ivy are not in this 
directory.


projects/ - This directory contains the various projects required to
build various facets of this software.

eclipse/ - Holds various eclipse settings that can be loaded to apply Tropix
specific settings to eclipse, such as Tropix coding guidelines.

skeleton/ - Contains a skeleton project structure that should be copied when
creating a new Tropix subproject.

tools/ - External tools used in the build and deploy process of Tropix.
  finddugs-***/ - This is a tool for static error checking of Java projects.
    It is used by the 'findbugs' ant task available in various subprojects of 
    Tropix.
  checkstyle-all-***.jar - This jar file contains the checkstyle ant task which
    is used to verify Tropix style guidelines are being followed.
  tomcat.zip - Contains a clean distribution of the Apache Tomcat servlet container. This
    is used in the TIPServices subproject to build war files.
  ws-core.zip - Contains a clean distribution of Globus core with the appropriate caGrid patches.
    This is used in the TIPServices subproject to build war files.

Building "TINT" - 

Building TINT requires that a valid Java 5+ JDK and Ant 1.7+ be installed and properly configured.

A Java 5+ JDK can be obtained from the following URL: http://java.sun.com/javase/downloads/index.jsp.

Ant 1.7 can be obtained from the following URL: http://ant.apache.org/bindownload.cgi. Ant 1.6.X contains
memory leaks that will almost certainly prevent Tropix from compiling and should not be used to compile 
Tropix.

At least two environment variables should be set before building Tropix. 

GLOBUS_LOCATION - This should point to a Globus core distribution as distributed by 
caGrid, that is ws-core-4.0.3-enum. The distribution is distributed with the tropix source
and can be found in the tools directory.

--- OPTIONAL -----

Certain build tasks such recreating or resyncing caGrid services (not usually necessary) also
require caGrid to be installed along with the Spring and Jobs extensions. After this is setup the environment
variable CAGRID_LOCATION should be configured to point at your caGrid installation.

For information on installing caGrid 1.2, please see http://cagrid.org/display/downloads/caGrid+1.2+Installation+Quickstart.
Once caGrid 1.2 is installed you can obtain the Spring extension from the caGrid incubator project.
The incubator project must be checked out of svn from the url https://gforge.nci.nih.gov/svnroot/grid-incubation/trunk/grid-incubation.
Once you have obtained the project it should be built by running the ant task 'all' from the projects main directory.
The Spring extension can then be installed by executing the ant task 'installIntroduceExtensions' from the projects/interfaces
directory. The Jobs extensions can be installed by first building this Tropix distribution 
and then running the installIntroduceExtensions ant task from the TropixJobQueue project.

------------------

Before building any war deployments, the whole project should be
compiled. This can done by running the publish ant task from the
directory containing this file.

The war file for the TINT web gui can then be created by executing
the war task from the project `projects/TropixWebGui`. This file will 
be placed at `projects/TropixWebGui/build/tropix.war`.

The war file for each analytic service can be created by executing the
appropriate ant task in the project `projects/TIPsServices`. These war
files will be placed in the directory
`projects/TIPsServices/build/wars`.  The available ant tasks are
build-war-X where X can be any of the following:
sequest,xtandem,omssa,scaffold,rawextract,itraqquantitation,bowtie.

Eclipse -

For Tropix to appear without errors in eclipse all dependencies need
to be resolved and generated code needs to be created. Executing the
publish task from the directory containing this file should accomplish
this task. 


For Developers -

Testing - 
  Testing should performed with TestNG. Test which break into the following
categories should specified as belonging to a group with the stated name.

-- Unit Tests --

Simple Unit Tests (group - unit):
  These are simple tests which aim to test at most one class. These tests should
not have dependencies external to the project.
  
Linux Unit Tests (group - linux):
  These are unit tests which may only be performed on linux machines, because they
target external OS resources.
  
-- Integration Tests Not Requiring External Resources --  
  
Spring Integration Tests (group - spring) :  
  
Persistence Integration Tests (group - persistence) :  
  
-- Integration Tests Required External Resources --
  
Integration (group - integration) :  
  These tests must be performed against specific grid resources or Tropix configuration
files. For tests only target grid resources (Proxies, CDS, GridFTP), these resources 
should be loaded from ~/.tropix/test, and which resources are required to be placed in 
that directory should be documented.

Deployment (group - deployment) :
  These tests verify the operation of installed components, such as grid services that
have been stood up.