= !NetKarma Evaluation =

This evaluation focuses on the NetKarma project software and documentation made available in March and April 2012:
 1. [http://d2i.indiana.edu/sites/default/files/karma-adaptor-2.5.1.tar.gz NetKarma GUSH Adaptor version 2.5.1] and [http://d2i.indiana.edu/sites/default/files/netkarma_version2.5.1_quick_start_guide.pdf Quick Start Guide for version 2.5.1]  
 2. [http://d2i.indiana.edu/sites/default/files/ns2adaptor.tar NetKarma NS2 Adaptor Version 1.0.0], [http://d2i.indiana.edu/sites/default/files/netkarma_ns2_adaptor_user_manual_v1.0.0.pdf NetKarma NS2 Adaptor User Manual], and [http://d2i.indiana.edu/sites/default/files/instructions_for_the_netkarma_provenance_toolkit_for_ns2_experiments.pdf Instructions for the NetKarma Provenance Toolkit for NS2 Experiments]  
 3. [http://d2i.indiana.edu/sites/default/files/netkarma_visualization_plugin-1.2.1.tar.gz NetKarma Cytoscape Visualization Plug-In Version 1.2.1], and [http://d2i.indiana.edu/sites/default/files/karmavisualizationusermanual-1.2.0.pdf NetKarma Cytoscape Visualization Plug-In Manual for Version 1.2.0]

Evaluation Time Frame: April 9, 2012 -??

= !NetKarma Findings =

= !NetKarma How-to =


Using the [http://d2i.indiana.edu/sites/default/files/netkarma_version2.5.1_quick_start_guide.pdf Quick Start Guide for version 2.5.1]  followed to install the Cytoscape visualization tool, the NetKarma Adaptor, and the NetKarma plug-ins for Cytoscape.

Quick Start Guide provides 5 steps to follow for installation which are captured below:

'''Step 1:''' Download and install the current version (2.8.1 or later) of the third-party Cytoscape visualization tool from http://www.cytoscape.org. Downloaded Cytoscape version 2.8.2 and installed it.

'''Step 2:''' Download, build, and configure version 2.5.1 of the NetKarma Adaptor available at: http://d2i.indiana.edu/sites/default/files/karma-adaptor-2.5.1.tar.gz.  As suggested, also download NetKarma Adaptor user manual for instructions on building the Adaptor:
{{{
  $ wget http://d2i.indiana.edu/sites/default/files/netkarma-gush-adaptor_v2.5_user_manual.pdf
  $ wget http://d2i.indiana.edu/sites/default/files/karma-adaptor-2.5.1.tar.gz
  $ tar xvzf karma-adaptor-2.5.1.tar.gz
  $ cd  Karma-adaptor
}}}

Set environment variable in adaptor_stdenvs.cfg file:

{{{
export ADAPTOR_HOME=/home/lnevers/netkarma/Karma-Adaptor
export JAVA_HOME=/usr/lib/jvm/java-6-openjdk
}}}

Had to install ant package. Need to configure "Karma-Adaptor/config/karma-adaptor.properties" not sure how to fill values yet." Built the adaptor:
{{{
$ ant karma-adaptor
Buildfile: build.xml

clean:

compile:
    [mkdir] Created dir: /home/lnevers/netkarma/Karma-Adaptor/bin
    [javac] Compiling 15 source files to /home/lnevers/netkarma/Karma-Adaptor/bin
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.

karma-adaptor:

BUILD SUCCESSFUL
Total time: 1 second
}}}

Requested username and password for Karma-Adaptor/config/karma- adaptor.properties file.
Attempts to use pre-existing guest account results in authentication failure.

'''Step 3:''' Download the NetKarma Cytoscape Version 1.2.1 Plug-ins available at:

{{{
 $ wget http://d2i.indiana.edu/sites/default/files/netkarma_visualization_plugin-1.2.1.tar.gz
 $ tar xvzf netkarma_visualization_plugin-1.2.1.tar.gz 
 $ cp visualization/Karma_query/KarmaRetrieval.jar cytoscape-2.8.2/plugins/.
 $ cp visualization/Karma_query/lib/* cytoscape-2.8.2/plugins/.
 $ cp visualization/OPM_visualization/KarmaGraph.jar cytoscape-2.8.2/plugins/.
 $ cp visualization/OPM_visualization/lib/* cytoscape-2.8.2/plugins/.
 $ mkdir cytoscape-2.8.2/plugins/config
 $ cp visualization/Karma_query/config/* cytoscape-2.8.2/plugins/config/.
 $ cp visualization/OPM_visualization/config/* cytoscape-2.8.2/plugins/config/.
 $ cd cytoscape-2.8.2/plugins/config/
 $ egrep "username|password" *
   karmaQueryConfig.txt:messaging.username=guest
   karmaQueryConfig.txt:messaging.password=8bfabfb5-5416-4ddf-8b8c-efc29285906f
   karmaVisConfig.txt:messaging.username=guest
   karmaVisConfig.txt:messaging.password=guest

}}}

As instructed, requested password for cytoscape-2.8.2/plugins/config files karmaQueryConfig.txt and karmaVisConfig.txt. 
It seem the enclosed guest accounts are not to be used. 

TO DO:

{{{

  $ wget http://d2i.indiana.edu/sites/default/files/ns2adaptor.tar
  $ wget http://d2i.indiana.edu/sites/default/files/netkarma_visualization_plugin-1.2.1.tar.gz
}}}