= !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 - April 13, 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. 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

'''Step 4:''' Upload GUSH log with NetKarma Adaptor configured in step 2.
{{{
 $ cd Karma-Adaptor 
 $ ./provenance_collector.sh -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.sh 
    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 cytoscape.sh script brings up the ''Cytoscap Desktop'' GUI, which looks as follows:

[[Image(netkarma-1.jpg)]]

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''

[[Image(netkarma-2.jpg)]]

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

[[Image(netkarma-3.jpg)]]

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.

[[Image(netkarma-4.jpg)]]

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:

[[Image(netkarma-5.jpg)]]
 
You are then prompted for a provenance graph xml file; select the file you downloaded in the earlier step and click Open.

[[Image(netkarma-6.jpg)]]

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:

[[Image(netkarma-7.jpg)]]