wiki:GIR3.2_NetKarma

Version 20 (modified by lnevers@bbn.com, 8 years ago) (diff)

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NetKarma Evaluation

The GENI Provenance Registry NetKarma version 2.5 was evaluated for this effort. This NetKarma version introduces the Provenance Adaptor for GUSH and the Provenance Visualization plug-in for Cytoscape. The software evaluated was downloaded from the NetKarma GENI project page in the Software downloads section:

Evaluation Time Frame: October 12, 2011 and November 01,2011.

NetKarma Findings

Various issues were found in the initial evaluation, the feedback captured in NetKarma-Feedback-20111012.txt. Send additional feedback captured in NetKarma-Feedback-20111021.txt for which received responses in NetKarma-response-20111028.txt. Updated versions were made available for the Quick Start Guide, the NetKarma Gush Adapter Manual, and the tarball for the NetKarma Adaptor (for changes in the README file).

Ran into an issue with rulefile not being correct version. The issue was that the generic rulefile that is installed as the default for the NetKarma adapter is designed for the logs GUSH generates when experiments are configured using XML. The logs GUSH generates based on shell commands are somewhat different and required additional changes in the files delivered. Due to the previous switched to gush logs that captured the results of a simple experiment,like the one described at the Gush simple experiment example page. After initial investigation into using the GMOC Adaptor found that this is an administrative service that is run by the NetKarma folks only, because of issues of controlled access to the Karma server on a GMOC machine. The GMOC adaptor is not intended for users to either build or run themselves. Stopped evaluation of GMOC Adaptor.

NetKarma How-to

Using the instructions in the NetKarma Version 2.5 Quick Start Guide, proceeded to download the only prerequisite tool the third-party Cytoscape visualization tool, which is available at: http://www.cytoscape.org. The download is one file a script named Cytoscape_2_8_2_unix.sh. Ran the Cytoscape script which brings up an installation wizard.. need to capture here.

NetKarma Gush Adaptor How-to

Proceeded to unpack the NetKarma GUSH Adaptor Version 2.5. Found additional prerequisites for ANT, JDK and RabbitMQ server. For RabbitMQ used the instructions found the Debian APT repository page.

 $ tar xvzf karma-adaptor-2.5.tar.gz 
 $ cd Karma-Adaptor

As instructed modified the adaptor_stdenvs.cfg file to set the ADAPTOR_HOME and the JAVA_HOME variables. File looks as follows:

#
# Copyright 2007 The Trustees of Indiana University
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# -----------------------------------------------------------------
#
# Project:  Karma-adaptor
# File:  adaptor_stdenvs.cfg
# Description:  config-file for the shell-scripts
# -----------------------------------------------------------------
export ADAPTOR_HOME=/home/netkarma/rc2/Karma-Adaptor
export JAVA_HOME=/usr/local/jdk1.6.0_03
export JAVA_HOME=/usr/lib/jvm/java-6-openjdk

export CLASSPATH=$ADAPTOR_HOME/lib/commons-cli-1.1.jar:$ADAPTOR_HOME/lib/commons-collections-3.2.1.jar:$ADAPTOR_HOME/lib/netk
arma-adaptor-types.jar:$ADAPTOR_HOME/lib/opm-core-1.1.1.jar:$ADAPTOR_HOME/lib/commons-io-1.2.jar:$ADAPTOR_HOME/lib/opm-elmo-1
.1.1.jar:$ADAPTOR_HOME/lib/commons-logging-1.1.1.jar:$ADAPTOR_HOME/lib/rabbitmq-client.jar:$ADAPTOR_HOME/lib/karma-messaging.
jar:$ADAPTOR_HOME/lib/xbean.jar:$ADAPTOR_HOME/lib/karma-types.jar:$ADAPTOR_HOME/bin

Build the Karma adaptor:

$ ant karma-adaptor 
Buildfile: build.xml

clean:

compile:
    [mkdir] Created dir: /home/lnevers/netkarma/rc2/Karma-Adaptor/bin
    [javac] Compiling 15 source files to /home/lnevers/netkarma/rc2/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: 2 seconds

Once the adaptor was built tried to run the provenance collector to upload a gush log:

$ ./provenance_collector.sh gush-logs/logfile-sendaria-15555-1301929239.txt
Connecting to Server...
Creating Notifications...
Invalid rulefile, use the correct version of the rulefile!

Looking into the rulefile problem.

After re-installing the Gush Karma Adaptor, problem no longer occurred and was able to get the logs partially processed:

Uploading Gush logs started by command line:
==============================
$ ./provenance_collector.sh logfile-sendaria-15555.txt
Connecting to Server...
Creating Notifications...
doMapping.................
doMapping.................
Exception in thread "main" java.lang.NullPointerException
        at java.lang.String.<init>(String.java:164)
        at edu.indiana.d2i.adaptor.RuleApplier.checkDependencies(Unknown Source)
        at edu.indiana.d2i.adaptor.RuleApplier.createNotificationData(Unknown Source)
        at edu.indiana.d2i.adaptor.RuleApplier.saveNotificationData(Unknown Source)
        at edu.indiana.d2i.adaptor.LogParser.parseRuleFile(Unknown Source)
        at edu.indiana.d2i.adaptor.client.KarmaAdaptor.main(Unknown Source)

Waiting on feedback for the above failure.

NetKarma GMOC Adaptor How-to

Unpacked the package and compiled, note ant and JDK are prerequisites:

$ tar xvzf netkarmagmocadaptor-1.0.0.tar.gz
$ cd GMOCAdaptor/
$ ant create.jar
Buildfile: build.xml

init:

wsdl2java:
     [java] Retrieving document at '/home/lnevers/netkarma/rc3/GMOCAdaptor/config/KarmaService.wsdl'.
     [java] Retrieving schema at 'karma_query_schema.xsd', relative to 'file:/home/lnevers/netkarma/rc3/GMOCAdaptor/config/KarmaService.wsdl'.
     [java] Retrieving schema at 'rdf.xsd', relative to 'file:/home/lnevers/netkarma/rc3/GMOCAdaptor/config/karma_query_schema.xsd'.
     [java] Retrieving schema at 'karma_ingest_type_schema.xsd', relative to 'file:/home/lnevers/netkarma/rc3/GMOCAdaptor/config/karma_query_schema.xsd'.
     [java] Retrieving schema at 'opm.1_1.xsd', relative to 'file:/home/lnevers/netkarma/rc3/GMOCAdaptor/config/karma_query_schema.xsd'.
     [java] Retrieving schema at 'karma_ingest_type_schema.xsd', relative to 'file:/home/lnevers/netkarma/rc3/GMOCAdaptor/config/KarmaService.wsdl'.
     [java] log4j:WARN No appenders could be found for logger (org.apache.axis2.description.WSDL11ToAllAxisServicesBuilder).
     [java] log4j:WARN Please initialize the log4j system properly.

jar:
    [javac] Compiling 624 source files to /home/lnevers/netkarma/rc3/GMOCAdaptor/client_gen/classes
    [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.
      [jar] Building jar: /home/lnevers/netkarma/rc3/GMOCAdaptor/dist/lib/client-stub-types.jar

create.compile:

create.jar:

BUILD SUCCESSFUL
Total time: 10 seconds

In order to configure the GMOC Adaptor the file GMOC_config.txt has to be updated to define several parameters, following is the GMOC_config.txt as delivered:

#Properties for using GMOCAdaptor
#@author: Peng Chen (chenpeng@indiana.edu)
#Mon Jul 11 16:44:26 EDT 2011
url=URL of Mysql database
url_options=URL options for using SSL
dbName=name of GMOC database
driver=Mysql JDBC driver class
userName=username for logging into GMOC database
password=password for logging into GMOC database
serviceURL=URL of Karma axis2 webservice

Requested account for access to http://gmoc.grnoc.iu.edu/ by sending email request to globalnoc@iu.edu because GMOC account information is needed to configure the adaptor.

At this point found out that the GMOC Adaptor found that this is an administrative service that is run by the NetKarma folks only that is not intended for users because of access to the Karma server on a GMOC machine. Stopped evaluation of GMOC Adaptor.


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