= !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 [http://groups.geni.net/geni/wiki/netKarma NetKarma] GENI project page in the [http://groups.geni.net/geni/wiki/netKarma#Software Software downloads] section: * NetKarma Version 2.5 [http://pti.iu.edu/sites/default/files/netkarma_version2.5_quick_start_guide.pdf Quick Start Guide]. * NetKarma [http://pti.iu.edu/sites/default/files/karma-adaptor-2.5.tar.gz GUSH Adaptor Version 2.5] * NetKarma [http://pti.iu.edu/sites/default/files/netkarma-gush-adaptor_v2.5_user_manual.pdf GUSH Adaptor Manual] * NetKarma [http://pti.iu.edu/sites/default/files/netkarmavisplugin-1.1.0.tar.gz Cytoscape Visualization Plug-In Version 1.1.0]. * NetKarma [http://pti.iu.edu/sites/default/files/netkarma_provenance_retrieval_and_visualization_plug-in_for_cytoscape_user_manual_v1.1.0.pdf Cytoscape Visualization Plug-In Manual]. * NetKarma [http://pti.iu.edu/sites/default/files/netkarmagmocadaptor-1.0.0.tar.gz GMOC Adaptor Version 1.0.0]. * NetKarma [http://pti.iu.edu/sites/default/files/netkarma_gmoc_adaptor_user_manual_v1.0.0.pdf GMOC Adaptor Manual]. Evaluation Time Frame: October 12, 2011 and November 01,2011. = !NetKarma Findings = Various issues were found in the initial evaluation, the feedback captured in [attachment: NetKarma-Feedback-20111012.txt]. Send additional feedback captured in [attachment: NetKarma-Feedback-20111021.txt] for which received responses in [attachment: 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 [http://gush.cs.williams.edu/trac/gush/wiki/SimpleExample 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 [http://pti.iu.edu/sites/default/files/netkarma_version2.5_quick_start_guide.pdf 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 [http://pti.iu.edu/sites/default/files/karma-adaptor-2.5.tar.gz GUSH Adaptor Version 2.5]. Found additional prerequisites for ANT, JDK and RabbitMQ server. For RabbitMQ used the instructions found the [http://www.rabbitmq.com/debian.html#apt 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.(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. -------------- {{{ #!html Email us with any questions and feedback on this page! }}}