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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 - April 13, 2012

NetKarma Findings

Several Issues were discovered which include:

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 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: As suggested, also download NetKarma Adaptor user manual for instructions on building the Adaptor:

  $ wget
  $ wget
  $ 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 the ant package.

$ ant karma-adaptor
Buildfile: build.xml
    [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.
Total time: 1 second

Requested username and password for Karma-Adaptor/config/karma- 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

Modified the Karma-Adaptor/config/ file to include the new information:

# information to use RabbitMQ messaging system
# information to be used by karma adaptor-- DO NOT CHANGE

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

 $ wget
 $ 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" *

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

The karmaQueryConfig.txt and karmaVisConfig.txt used successfully can be seen at the bottom of this page.

Step 4: Upload GUSH log with NetKarma Adaptor configured in step 2.

 $ cd Karma-Adaptor 
 $ ./ -l logs/logfile-sendaria-15555-1333982537.txt
   Connecting to Server...
   Using rulefile: /home/lnevers/netkarma/Karma-Adaptor/deps/cmdline_ruleset.xml
   Creating Notifications...
   Applying dependency rules...
   Ingesting Notifications...
   Number of Notifications = 2
   Workflow Instance-ID: urn:tool:gush:d494a812-8f6e-4e59-92bd-30e45f36adb4
   Time to queue notifications for ingestion: 0.706 secs

Step 5: Start Cytoscape and use the NetKarma Provenance Retrieval Plug-in to download the provenance graph generated from the gush logfile uploaded in step 4.

  $ cd cytoscape-2.8.2
  $ ./ 
    cytoscape.CytoscapeInit[INFO]: CytoscapeInit static initialization
    cytoscape.CytoscapeInit[INFO]: Log information can now be found in the Help->Error Console menu
    cytoscape[INFO]: starting delete action
    cytoscape[INFO]: ending delete action
    cytoscape[INFO]: PreferenceAction()...
    cytoscape.actions.BookmarkAction[INFO]: BookmarkAction()...

The script brings up the Cytoscap Desktop GUI, which looks as follows:

On the Cytoscap Desktop GUI, click on the "Karma" button, which brings up the following dialog:

Note: The "Axis2" is default, must select "Rabbitmq" option

Click "OK", which brings up a dialog to enter an ID for the "Workflow Instance-ID:". Dialog looks as follows:

Click "OK", and ran into a connection refused problem... Investigating.... file needed host and port changes: Re-ran, and then paste in the ID and click OK. You will be prompted for the location where you wish to save the provenance graph, and for the name of the output graph.

Now that the graph has been retrieved, click the geni button in the Cytoscape toolbar, which brings up the Import an OPM Graph from xml file dialog:

You are then prompted for a provenance graph xml file; select the file you downloaded in the earlier step and click Open.

Once the graph is loaded various visualization fucntions can be used, following is an example that looks at the node attribute for from the provenance graph xml file:

Plugin Configuration

The file cytoscape-2.8.2/plugins/config/karmaQueryConfig.txt had the following settings:

#Properties for using Karma Query Plugin
#@author: Peng Chen (
#Information to use Axis Service and RabbitMQ messaging system
#Fri Apr 13 14:30:50 EDT 2012

The file cytoscape-2.8.2/plugins/config/karmaVisConfig.txt had the following settings:

#Properties for using Karma Query Plugin
#@author: Peng Chen (
#axis2.serviceURL: information to use Axis Service
#messaging: information to use RabbitMQ messaging system
#Fri Jul 29 15:43:35 EDT 2011

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