VIPER
From Informatics
VIPER component of geWorkbench
This component submits the job to R to do the actual computation. The result is an expression data-like table.
code repository
- local version: as a geworkbench component
- service side: https://github.com/geworkbench-group/viper.service
The service is a string based web service. See http://docs.spring.io/spring-ws/sites/2.0/reference/html/tutorial.html
User can select to run either "local service" or "web service" from the parameter panel.
1. For the local service, the user would need to install R on the machine that he is running geWorkench on, like in SAM component.
On windows7/vista, you can install R at the default system location, then enter a writable user's directory under geworkbench Tools->Preference->R package directory. This should get viper package installed at the user's directory.
If R was installed at a custom directory on windows7/vista, then everything should work fine with "R package directory" blank in the preferences.
Removed the popup asking for annotation file when result maSet is posted to the project panel.
2. The remote version submits the job through a web service to the remote host that runs the R script.
Viper package was installed at ~cagrid/local/R/titan/viper; Viper scripts and runs were stored at ~cagrid/r/viper/;
Viper web service and index service were deployed to ~cagrid/apache-tomcat-5.5.35/webapps on afdev;
Viper web service address was returned by querying the index service;
Index web service address was added into applications.properties: "internal.indexServer.url=http://afdev.c2b2.columbia.edu:9090/index-server/services"
Server side was implemented using spring web service;
Client side was implemented using apache axis2, using existing axis2 libs in geworkbench core;
Large data transfer was supported by enabling MTOM on both client&server side, and adding "-Dsaaj.use.mimepull=true" in catalina.sh; file transfer temp files are stored at $CATALINA_HOME/temp, need manual clean-up for disk space.
Files provided from Andrea's group (R scripts and data files): //floratos20/Fileshare/For%20Zhou/Viper
Contact: Mariano
The actual R script, viper.tar,.gz, was removed from geworkbench svn repository because of license status. It is put back again.
