I am writing a Java code where in I am trying to get the data from PostgreSQL and doing simple computation on it(calculating median). First I am loading the RPostgreSQL library from Java code itself and then loading the driver and establishing the connection between R and PostgreSQL through Java. But when I am trying to fire a query command(which is used to get query from PostgreSQL to R) through Java then I am getting error as:
NOTE:THIS ERROR IS RESOLVED.PLEASE LOOK BELOW FOR CURRENT ERROR(Script File Error)
org.rosuda.REngine.REngineException: eval failed, request status: R parser: syntax error
org.rosuda.REngine.Rserve.RConnection.parseAndEval(RConnection.java:454)
org.rosuda.REngine.REngine.parseAndEval(REngine.java:108)
Rtemp.main(Rtemp.java:40)
sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
java.lang.reflect.Method.invoke(Method.java:483)
com.intellij.rt.execution.application.AppMain.main(AppMain.java:120)
My current code is :
import org.rosuda.REngine.REXP;
import org.rosuda.REngine.Rserve.*;
public class Rtemp {
public static void main(String[] args) throws Exception {
RConnection c = null;
try {
c = new RConnection();
//Loading RPostgreSQL library
REXP x = c.eval("library(RPostgreSQL)");
//Loading PostgreSQL driver
REXP drv = c.eval("dbDriver(\"PostgreSQL\")");
// Establishing connection
REXP r = c.parseAndEval("try(\"dbConnect(drv, host='localhost', port='5432',dbname='r1', user='postgres', password='pwd')\",silent=TRUE)");
if (r.inherits("try-error")) System.err.println("Error: "+r.asString());
else System.out.println("Success eval 1");
REXP rs = c.parseAndEval("try(dbSendQuery(r,\"select colmn1 from host_brnd345633456_table1 limit 10 \"), silent=TRUE)");
if (rs.inherits("try-error")) System.err.println("Error: "+rs.asString());
else System.out.println("Success eval 2");
REXP ftch = c.parseAndEval("try(ftch(rs,n=-1),silent=TRUE)");
if (ftch.inherits("try-error")) System.err.println("Error: "+ftch.asString());
else System.out.println("Success eval 3");
REXP res = c.parseAndEval("try(median(ftch$colmn1),silent=TRUE)");
if (res.inherits("try-error")) System.err.println("Error: "+res.asString());
else {
System.out.println("Success eval 4");
System.out.println(res.asDouble());
}
#The line 58 error mentioned below in the error section is coming at this line
System.out.println(res.asDouble());
//System.out.println(x.asString());
System.out.println("Library loaded successfully");
} catch(Exception e) {
e.printStackTrace();
} finally {
if ( c != null )
try {
c.close();
}
}
}
}
I don't think that there is any problem with Rserve connection as for simple code like displaying version of R it is getting executed correctly.
Also there is no problem with the syntax of writing commands for R to PostgreSQL part like the dbSendQuery() or similar as when I using them directly from within R they are working perfectly fine. So, the problem that I think is in writing the same in Java(corresponding syntax for Java).
UPDATE 1: ERROR 2 (THIS ERROR IS RESOLVED)
After taking suggestion from @ on_the_shores_of_linux_sea I have modified my code a bit but now a different error is coming as:
Success eval 1
Error: Error in is(object, Cl) :
error in evaluating the argument 'conn' in selecting a method for function 'dbSendQuery': Error: object 'r' not found
Error: Error in is(object, Cl) :
error in evaluating the argument 'res' in selecting a method for function 'fetch': Error: object 'rs' not found
Error: Error in median(ftch$t31001400) : object 'ftch' not found
org.rosuda.REngine.REXPMismatchException: attempt to access org.rosuda.REngine.REXPString as double
at org.rosuda.REngine.REXP.asDoubles(REXP.java:77)
at org.rosuda.REngine.REXP.asDouble(REXP.java:103)
at Rtemp.main(Rtemp.java:58)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:483)
at com.intellij.rt.execution.application.AppMain.main(AppMain.java:120)
Process finished with exit code 0
I am not able to figure out why the error is and how to resolve it
SECONDARY QUESTION: This a secondary question as I also want to know that is it possible that I can write the R queries or statements in a file(a special R format file or any other format file) and then make Java read the file and push the R commands into R so as to execute them?
UPDATE 2: SCRIPT FILE ERROR
The method 1 mentioned by @on_the_shores_of_linux_sea below is working fine now. I am also trying to do through method 2 but having some difficulties in managing script through Java. The Java code that I am using is:
public class Java_RScript {
public static void main(String[] args) throws Exception {
RConnection c = null;
try {
c = new RConnection();
c.parseAndEval("try(source("script.R"),silent=TRUE)");
REXP res = c.parseAndEval("try(\"do_operation()\", silent=TRUE)");
System.out.println("Success:" + res.asDouble());
} catch (Exception e) {
e.printStackTrace();
} finally {
if (c != null) {
try {
c.close();
} finally {
}
}
}
}
}
The error on output console that is getting printed is as:
org.rosuda.REngine.REXPMismatchException: attempt to access org.rosuda.REngine.REXPString as double
My script file syntax is:
do_operation <- function()
{
drv <- dbDriver("PostgreSQL")
r <- dbConnect(drv, host='localhost', port='1234',dbname='db', user='user1', password='pswd')
rs <-dbSendQuery(r,"select colmn1 from hostess_table limit 10")
ftch <- fetch(rs,n=-1)
res <- median(ftch$colmn1)
return(res)
}
I am not sure whether the error is in script file or my Java syntax.