Version 21 (modified by 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:
- NetKarma GUSH Adaptor version 2.5.1 and Quick Start Guide for version 2.5.1
- NetKarma NS2 Adaptor Version 1.0.0, NetKarma NS2 Adaptor User Manual, and Instructions for the NetKarma Provenance Toolkit for NS2 Experiments
- 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:
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:
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:
$ 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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