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package tools; |
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import tools.*; |
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import java.io.*; |
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import java.util.*; |
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import org.rosuda.JRclient.*; |
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import Jama.*; |
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|
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public class R { |
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|
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private static Rconnection c = null; |
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private static String mySqlConfString = null; |
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|
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public R(String username, String password, String connFile) { |
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|
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try { |
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c = new Rconnection(); |
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c.login(username, password); |
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mySqlConfString = readConnectionFile(connFile); |
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// treat warnings as errors |
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c.voidEval("options(warn=0)"); |
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c.voidEval("library(RMySQL);drv<-dbDriver(\"MySQL\")"); |
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} catch(RSrvException rse) { |
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System.out.println("Rserve exception: "+rse.getMessage()); |
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cleanUp(); |
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} catch(Exception e) { |
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System.out.println("Something went wrong, but it's not the Rserve: "+e.getMessage()); |
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e.printStackTrace(); |
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cleanUp(); |
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} |
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|
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} |
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|
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public double[][] simpleLinRegr(String predictorQuery, String responseQuery) { |
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|
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//predictor = intercept + slope*response |
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|
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double[][] lr = null; |
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boolean singlePredictor = true; |
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|
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try { |
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|
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c.voidEval("con<-dbConnect(drv, "+mySqlConfString+")"); |
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c.voidEval("x<-dbGetQuery(con, \""+predictorQuery+"\")"); |
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singlePredictor = c.eval("ncol(x)==1").asBool().isTRUE(); |
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|
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if (!singlePredictor) { |
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c.voidEval("discon<-dbDisconnect(con)"); |
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return lr; |
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} |
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|
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c.voidEval("x<-x[,1]"); |
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c.voidEval("rs<-dbGetQuery(con, \""+responseQuery+"\")"); |
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c.voidEval("lr.m<-matrix(0, ncol(rs), 4)"); |
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|
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c.voidEval("for (j in 1:ncol(rs)) {"+ |
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" y<-rs[,j];"+ |
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" model<-lm(y~x);"+ |
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" info<-summary(model);"+ |
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" lr.m[j,1:2]<-model$coefficients;"+ //intercept - slope |
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" lr.m[j,3]<-info$coefficients[2,4];"+ //p-value |
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" lr.m[j,4]<-sqrt(info$r.squared);"+ //r |
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"}"); |
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|
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lr = c.eval("lr.m").asDoubleMatrix(); |
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|
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c.voidEval("discon<-dbDisconnect(con)"); |
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|
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} catch(RSrvException rse) { |
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System.out.println("Rserve exception: "+rse.getMessage()); |
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cleanUp(); |
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} catch(Exception e) { |
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System.out.println("Something went wrong, but it's not the Rserve: "+e.getMessage()); |
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e.printStackTrace(); |
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cleanUp(); |
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} |
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|
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return lr; |
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|
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} |
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|
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private static void cleanUp() { |
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|
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try { |
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c.voidEval("try(discon<-dbDisconnect(con), silent = TRUE)"); |
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c.voidEval("dbUnloadDriver(drv)"); |
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} catch(RSrvException rse) { |
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System.out.println("Rserve exception: "+rse.getMessage()); |
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} finally { |
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if (c != null) { |
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c.close(); |
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} |
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} |
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} |
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|
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public void close() { |
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|
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try { |
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c.voidEval("try(discon<-dbDisconnect(con), silent = TRUE)"); |
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c.voidEval("dbUnloadDriver(drv)"); |
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} catch(RSrvException rse) { |
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System.out.println("Rserve exception: "+rse.getMessage()); |
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} finally { |
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if (c != null) { |
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c.close(); |
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} |
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} |
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} |
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|
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private static String readConnectionFile(String connFile) { |
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|
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FileReader theFile = null; |
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BufferedReader fileIn = null; |
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StringTokenizer str; |
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String item, oneLine, dummy; |
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String host = null, port = null, user = null, password = null, dbname = null; |
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|
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// list the entries in the file and decompose them |
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try { |
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File inputFile = new File(connFile); |
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theFile = new FileReader(inputFile); // open the File |
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fileIn = new BufferedReader( theFile); // open BufferedReader |
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while ((oneLine = fileIn.readLine() ) != null ) { |
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// Write the line at hand to stdout, just for testing purposes |
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// System.out.println("["+oneLine+"]"); |
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// Construct a stringTokenizer for the line that we read with : delimited |
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str = new StringTokenizer( oneLine, " ="); // true sets returnDelimiters flag |
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while ( str.hasMoreTokens()) { |
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item = str.nextToken(); |
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// System.out.println("item:"+item); |
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if( item.equals("host")) { |
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host=str.nextToken(); |
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// System.out.println("host:"+host); |
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break; |
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} // end if host |
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if( item.equals("port")) { |
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port=str.nextToken(); |
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// System.out.println("port:"+port); |
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break; |
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} // end if port |
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if( item.equals("user")) { |
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user=str.nextToken(); |
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// System.out.println("user:"+user); |
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break; |
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} // end if password |
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if( item.equals("password")) { |
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password=str.nextToken(); |
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// System.out.println("password:"+password); |
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break; |
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} // end if password |
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if( item.equals("database")) { |
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dbname=str.nextToken(); |
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// System.out.println("database:"+dbname); |
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break; |
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} // end if password |
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|
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} // next token in this line |
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} // next line in the file |
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} // end try opening the file |
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catch ( Exception e ) { System.out.println( e); } |
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|
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try { // closing the file |
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if( fileIn != null) fileIn.close(); |
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if( theFile != null) theFile.close(); |
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} catch ( Exception e ) { System.out.println( e); } |
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|
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return ("username = \""+user+"\", password = \""+password+"\", dbname = \""+dbname+"\", host = \""+host+"\", port = "+port); |
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|
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} // end class readConnectionFile |
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|
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} // end class mySQLconnect |
