documentation:software:webapi:r_service_bus_setup_guide
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| - | ~~NOTOC~~ | ||
| - | =====R Service Bus Setup Guide ===== | ||
| - | ---- | ||
| - | |||
| - | This is a new feature and as such is not as stable as some other parts of the OHDSI technology stack. Please ask questions on the forums if you have any issues establishing your environment so we can improve the level of support we provide here in the documentation. | ||
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| - | |||
| - | ==== Installation Steps ==== | ||
| - | |||
| - | |||
| - | * Install R | ||
| - | |||
| - | |||
| - | ==== Required R Packages==== | ||
| - | RSB requires additional the following R Packages be loaded into your R environment | ||
| - | |||
| - | install.packages("XML") | ||
| - | install.packages("RJSONIO") | ||
| - | install.packages(c("properties", "RSBXml", "RSBJson"), repos = "http://repos.openanalytics.eu", type = "source") | ||
| - | install.packages(c("rj", "rj.gd"), repos="http://download.walware.de/rj-2.0") | ||
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| - | |||
| - | * Deploy R Service Bus WAR | ||
| - | |||
| - | Test RSB deployment status: | ||
| - | http://webserver/rsb/api/rest/system/health/check | ||
| - | |||
| - | * Deploy RPooli WAR | ||
| - | * requires R_HOME environment variable | ||
| - | |||
| - | The poolconfig.properties and rconfig.properties files are typically found in the WEB-INF subdirectory of the rpooli installation. For example: | ||
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| - | C:\Program Files\Apache Software Foundation\Tomcat 8.0\webapps\rpooli\WEB-INF | ||
| - | |||
| - | ==== Sample poolconfig.properties ==== | ||
| - | |||
| - | max_wait.millis=3000 | ||
| - | min_idle.millis=600000 | ||
| - | max_total.count=20 | ||
| - | eviction_timeout.millis=1800000 | ||
| - | max_idle.count=10 | ||
| - | min_idle.count=5 | ||
| - | max_usage.count=100 | ||
| - | |||
| - | |||
| - | ==== Sample rconfig.properties==== | ||
| - | |||
| - | de.walware.rj.rpkg.path=C\:\\R\\Packages | ||
| - | r_home.path=C\:\\Program Files\\R\\R-3.3.1 | ||
| - | r_startup.snippet=library(RSBXml)\r\nlibrary(RSBJson)\r\nlibrary(OhdsiServiceWrapper)\r\noptions('fftempdir' = 'C:/FFTemp') | ||
| - | debug_verbose.enabled=true | ||
| - | debug_console.enabled=false | ||
| - | node_cmd.args= | ||
| - | startstop_timeout.millis=30000 | ||
| - | |||
| - | |||
| - | ==== Enabling CORS access to RPooli ==== | ||
| - | To enable CORS on Tomcat add the following section to the RPooli web.xml | ||
| - | |||
| - | |||
| - | <filter> | ||
| - | <filter-name>CorsFilter</filter-name> | ||
| - | <filter-class>org.apache.catalina.filters.CorsFilter</filter-class> | ||
| - | </filter> | ||
| - | <filter-mapping> | ||
| - | <filter-name>CorsFilter</filter-name> | ||
| - | <url-pattern>/*</url-pattern> | ||
| - | </filter-mapping> | ||
| - | |||
| - | |||
| - | ==== Sending a Job to your R Pool ==== | ||
| - | Sending a job to the RSB Rest Job endpoint is a POST to the following endpoint: | ||
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| - | http://webserver/rsb/api/rest/jobs | ||
| - | |||
| - | The Job message format is as follows: | ||
| - | |||
| - | |||
| - | { | ||
| - | "RFunction":"paste", | ||
| - | "a": 1, | ||
| - | "b" : 2 | ||
| - | } | ||
| - | |||
| - | wherein the RFunction attribute contains the function that will be the target of an R call to do.call and the remaining named attributes will be passed as a named list of parameters to the RFunction. | ||
| - | |||
| - | |||
| - | ==== Debugging an Installation ==== | ||
| - | |||
| - | Make sure R is up to date and all the necessary R packages have been installed. | ||
| - | Start by checking your container log file, for example if you are running in Tomcat, check the Tomcat log for errors. | ||
| - | |||
| - | ==== R Logging ==== | ||
| - | |||
| - | Logs generated by R processing can be found within the container's log directory. Typically something like | ||
| - | |||
| - | C:\Program Files\Apache Software Foundation\Tomcat 8.0\temp\rpooli-1474396212594 | ||
| - | |||
| - | You will find a directory for each node within your R Pool with individual output log files. | ||
documentation/software/webapi/r_service_bus_setup_guide.1474399118.txt.gz ยท Last modified: 2016/09/20 19:18 by frank_defalco
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