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iris-r-gateway-template

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iris-r-gateway-template

This repository is a template for using the new R gateway for IRIS 2021.1.

The architecture of this template is as follows:

It is composed of three containers, with one for:

IRIS
R and RServe
A Java Gateway

Iris and the R server will discuss through the java gateway.

These first two containers are bound to the data/ local folder, and so have access to the same data:

abalone.csv

This file is loaded as a table in IRIS :

Test.Data

The R container also has access to the r/ folder, and in it is the following script:

test.R

getMode <- function(x) {
  l <- unique(x)
  l[which.max(tabulate(match(x, l)))]
}
getLength <- function(x) {

length(x)

}
createHistJPG <- function(data, dir, label) {

dir2 = paste(dir, "/hist.jpeg", sep="")

jpeg(file = dir2)

hist(data, xlab=label)

dev.off()

}
createHistPNG <- function(data, dir, label) {

dir2 = paste(dir, "/hist.png", sep="")

png(file = dir2)

hist(data, xlab=label)

dev.off()

}
createHistPDF <- function(data, dir, label) {

dir2 = paste(dir, "/hist.pdf", sep="")

pdf(file = dir2)

hist(data, xlab=label)

dev.off()

}

Run this template

git clone https://github.com/grongierisc/iris-r-gateway-template

then :

docker compose up

Play with this template

Run the following ObjectScript commands

Run random R expression

do ##class(Demo.RGateway).RunEval()

output :

"R version 3.4.4 (2018-03-15)"

code :

ClassMethod RunEval() As %Status
{
	// Get a gateway instance
    set gateway = ##class(%Net.Remote.Gateway).%New()
    set tSC = gateway.%Connect(..#JGWHOST, ..#JGWPORT)
	if $$$ISERR(tSC) quit
	// Bind the gateway to the Rserve

set c = ##class(%Net.Remote.Object).%ClassMethod(.gateway,"com.intersystems.rgateway.Helper","createRConnection", ..#RHOST, ..#RPORT)
	// Run a random R command

zw c.eval("R.version$version.string").asString()
<span class="pl-k">do</span>:<span class="pl-v">c</span>'=<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span> <span class="pl-v">c</span>.<span class="pl-e">close</span>()
<span class="pl-k">do</span>:<span class="pl-v">gateway</span>'=<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span> <span class="pl-v">gateway</span>.<span class="pl-e">%Disconnect</span>()
<span class="pl-k">quit</span>

}

Run R expression from IRIS SQL

do ##class(Demo.RGateway).FromSQLOnIris()

output :

"mean = 0.5239920995930093"
"median = 0.545"

code :

ClassMethod FromSQLOnIris()
{
    set gateway = ##class(%Net.Remote.Gateway).%New()
    set tSC = gateway.%Connect("r",55554)
	if $$$ISERR(tSC) quit
<span class="pl-k">set</span> <span class="pl-v">c</span> = <span class="pl-k">##class</span>(<span class="pl-en">%Net.Remote.Object</span>).<span class="pl-e">%ClassMethod</span>(.<span class="pl-e">gateway</span>,<span class="pl-s"><span class="pl-pds">"</span>com.intersystems.rgateway.Helper<span class="pl-pds">"</span></span>,<span class="pl-s"><span class="pl-pds">"</span>createRConnection<span class="pl-pds">"</span></span>)

	// SQL Query

set q = "select length from Test.Data"

set resultSet = ##class(%SQL.Statement).%ExecDirect( , .q)
	// Prepare R vector

do c.eval("l = c()")

while resultSet.%Next() {

		 // Append resultSet to the R vector

do c.assign("x", ##class(%Net.Remote.Object).%New(gateway, "org.rosuda.REngine.REXPDouble", resultSet.Length))

do c.eval("l = append(l, c(x))")

}
	// Produce mean from R

zw "mean = " _c.eval("mean(l)").asString()
	// Produce median from R

zw "median = "_c.eval("median(l)").asString()
<span class="pl-k">do</span>:<span class="pl-v">c</span>'=<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span> <span class="pl-v">c</span>.<span class="pl-e">close</span>()
<span class="pl-k">do</span>:<span class="pl-v">gateway</span>'=<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span> <span class="pl-v">gateway</span>.<span class="pl-e">%Disconnect</span>()
<span class="pl-k">quit</span>

}

Run R Script and plot

do ##class(Demo.RGateway).FromCSVOnRServe()

output :

"mean = 0.5239920995930093"
"median = 0.545"
"mode = 0.55"
"plot produced in /tmp/data/hist.png"
"plot produced in /tmp/data/hist.jpeg"
"plot produced in /tmp/data/hist.pdf"

code :

ClassMethod FromCSVOnRServe()
{
    set gateway = ##class(%Net.Remote.Gateway).%New()
    set tSC = gateway.%Connect(..#JGWHOST, ..#JGWPORT)
	if $$$ISERR(tSC) quit
<span class="pl-k">set</span> <span class="pl-v">c</span> = <span class="pl-k">##class</span>(<span class="pl-en">%Net.Remote.Object</span>).<span class="pl-e">%ClassMethod</span>(.<span class="pl-e">gateway</span>,<span class="pl-s"><span class="pl-pds">"</span>com.intersystems.rgateway.Helper<span class="pl-pds">"</span></span>,<span class="pl-s"><span class="pl-pds">"</span>createRConnection<span class="pl-pds">"</span></span>, ..#RHOST, ..#RPORT)

	// Read a file from R

	// assign an R variable for the data file 

set filename = "/tmp/data/abalone.csv"

do c.assign("filename", filename)

	// Read the file from the R server

do c.eval("data = read.csv(filename)")
<span class="pl-k">zw</span> <span class="pl-s"><span class="pl-pds">"</span>mean = <span class="pl-pds">"</span></span>_<span class="pl-v">c</span>.<span class="pl-e">eval</span>(<span class="pl-s"><span class="pl-pds">"</span>mean(data$Length)<span class="pl-pds">"</span></span>).<span class="pl-e">asString</span>()
<span class="pl-k">zw</span> <span class="pl-s"><span class="pl-pds">"</span>median = <span class="pl-pds">"</span></span>_<span class="pl-v">c</span>.<span class="pl-e">eval</span>(<span class="pl-s"><span class="pl-pds">"</span>median(data$Length)<span class="pl-pds">"</span></span>).<span class="pl-e">asString</span>()

	// Call function from R script

	// assign an R variable for the script file 

do c.assign("rFile", "/tmp/r/src/test.R")

do c.eval("source(rFile)")
<span class="pl-k">zw</span> <span class="pl-s"><span class="pl-pds">"</span>mode = <span class="pl-pds">"</span></span>_<span class="pl-v">c</span>.<span class="pl-e">eval</span>(<span class="pl-s"><span class="pl-pds">"</span>getMode(data$Length)<span class="pl-pds">"</span></span>).<span class="pl-e">asString</span>()

	// Plot graphs

	// assign a directory to save files

do c.assign("dir", "/tmp/data")

	// produce plot PNG

do c.eval("createHistPNG(data$Rings, dir, ""Rings"")")

zw "plot produced in /tmp/data/hist.png"

	// produce plot JPG

do c.eval("createHistJPG(data$Rings, dir, ""Rings"")")

zw "plot produced in /tmp/data/hist.jpeg"

	// produce plot PDF

do c.eval("createHistPDF(data$Rings, dir, ""Rings"")")

zw "plot produced in /tmp/data/hist.pdf"
<span class="pl-k">do</span>:<span class="pl-v">c</span>'=<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span> <span class="pl-v">c</span>.<span class="pl-e">close</span>()
<span class="pl-k">do</span>:<span class="pl-v">gateway</span>'=<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span> <span class="pl-v">gateway</span>.<span class="pl-e">%Disconnect</span>()
<span class="pl-k">quit</span>

}

Another R Gateway

You can have a look at this R Gateway for IRIS :

https://github.com/intersystems-community/RGateway

This one doesn't use the java gateway and use a direct connection between IRIS and R Server.

Exemple :

Set c = ##class(R.RConnection).%New() // Create a R client
Set x = ##class(R.REXPDouble).%New(3.0) // A single double value
Do c.assign("x", x) // Assign the value to R variable x
Do c.eval("y<-sqrt(x)") // Evaluate R script
Set y = c.get("y") // Get the value of R variable y
Write y.toJSON().%ToJSON()

Robert Cemper26 September 2021

an excellent 6* template

this is an example package you should really consume
a clear description with graphic explains what is happening
3 Docker containers are built and act together smootly
tests work as described and results (including graphic + pdf) are created
nothing is missing, nothing requires intervention
a real pleasure to use it

Rating

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iris-r-gateway-template

What's new in this version

iris-r-gateway-template

Run this template

Play with this template

Run random R expression

Run R expression from IRIS SQL

Run R Script and plot

Another R Gateway

Tag version: 1.0.0

Released: 2021-06-17 13:56:41