wiki:GIR4.1_NetKarma

Version 18 (modified by lnevers@bbn.com, 12 years ago) (diff)

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NetKarma Evaluation

This evaluation focuses on the NetKarma project software and documentation made available in March and April 2012:

  1. NetKarma GUSH Adaptor version 2.5.1 and Quick Start Guide for version 2.5.1
  2. NetKarma NS2 Adaptor Version 1.0.0, NetKarma NS2 Adaptor User Manual, and Instructions for the NetKarma Provenance Toolkit for NS2 Experiments
  3. NetKarma Cytoscape Visualization Plug-In Version 1.2.1, and NetKarma Cytoscape Visualization Plug-In Manual for Version 1.2.0

Evaluation Time Frame: April 9, 2012 -??

NetKarma Findings

NetKarma How-to

Using the 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. Karma team supplied the following:

  • NetKarma user name: karmaclient-1
  • NetKarma password: 74415909-2a04-4831-af68-8ccf87308248

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. Karma team supplied the following:

  • NetKarma user name: karmaclient-1
  • NetKarma password: 74415909-2a04-4831-af68-8ccf87308248

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

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