core/org.eclipse.stem.utility/src/org/eclipse/stem/utility/generators/InfectorInoculatorGenerator.java - stem/org.eclipse.stem - Git at Google

 package org.eclipse.stem.utility.generators;

 /*******************************************************************************
  * Copyright (c) 2009 IBM Corporation and others.
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
  * which accompanies this distribution, and is available at
  * http://www.eclipse.org/legal/epl-v10.html
  *
  * Contributors:
  *     IBM Corporation - initial API and implementation
  *******************************************************************************/

 import java.io.BufferedReader;
 import java.io.FileInputStream;
 import java.io.FileWriter;
 import java.io.InputStreamReader;
 import java.util.ArrayList;
 import java.util.StringTokenizer;

 /**
  * The file imports an infectious log file (param1), a population log file (param 2)
  * and using the specified disease name (param3) it generates infector and inoculator XML file
  * that can be imported into a scenario to initialize it to the initial log file
  * state
  */
 public class InfectorInoculatorGenerator {

 	/**
 	 * NLS Prefix for Infector name
 	 */
 	public static String infectorPrefix = Messages.getString("Inoculator.1"); //$NON-NLS-1$

 	/**
 	 * NLS Prefix for Inoculator name
 	 */
 	public static String inoculatorPrefix = Messages.getString("Inoculator.2"); //$NON-NLS-1$

 	/**
 	 *
 	 * @param args
 	 */
 	@SuppressWarnings("nls")
 	public static void main(String [] args) {
 		if(args.length < 6) {
 			System.err.println("Usage: InfectorInoculatorGenerator <I file> <R file> <P file> <disease name> <project name> <default I% (optional)> <scale R fraction (optional)>"); //$NON-NLS-1$
 			System.exit(-1);
 		}

 		String diseaseName = args[3];
 		String projectName = args[4];

 		boolean useDefault = false;
 		double iperc = 0.0;
 		double rscale = 1.0;

 		if(args.length >5) {
 			useDefault = true;
 			iperc = Double.parseDouble(args[5]);
 		}
 		if(args.length > 6) {
 			useDefault = true;
 			rscale = Double.parseDouble(args[6]);
 		}

 		ArrayList<String>locations = new ArrayList<String>();
 		ArrayList<Double>infectious = new ArrayList<Double>();
 		ArrayList<Double>recovered = new ArrayList<Double>();
 		ArrayList<Double>population = new ArrayList<Double>();

 		try {
 			 // Read infectious file
 			 FileInputStream ifile = new FileInputStream(args[0]);
 		     BufferedReader ireader = new BufferedReader(new InputStreamReader(ifile));
 		     String header = null;
 		     header=ireader.readLine();
 		     if(header == null) {
 		    	 System.err.println("Error, "+args[0]+" file is empty!");  //$NON-NLS-1$//$NON-NLS-2$
 		    	 System.exit(-2);
 		     }
 		     StringTokenizer st = new StringTokenizer(header, ","); //$NON-NLS-1$
 		     int column = 0;
 		     while(st.hasMoreTokens()) {
 		    	 String val = st.nextToken();
 		    	 if(column < 2) {++column;continue;}
 		    	 locations.add(val.trim());
 		    	 ++column;
 		     }

 		    String data = null;
 		    data=ireader.readLine();
 		    if(data == null) {
 		    	 System.err.println("Error, "+args[0]+" file has no data!");  //$NON-NLS-1$//$NON-NLS-2$
 		    	 System.exit(-2);
 		     }

 		    st = new StringTokenizer(data, ","); //$NON-NLS-1$
 		    column = 0;
 			while (st.hasMoreTokens()) {
 				String val = st.nextToken().trim();
 				if(column < 2) {++column;continue;} // skip iteration, time
 				infectious.add(Double.parseDouble(val));
 			    ++ column;
 		    } // read tokens

 		    ireader.close();

 		    // Read recovered file
 		    ifile = new FileInputStream(args[1]);
 		    ireader = new BufferedReader(new InputStreamReader(ifile));
 		    header = null;
 		    header=ireader.readLine();
 		    if(header == null) {
 		     System.err.println("Error, "+args[1]+" file is empty!"); //$NON-NLS-1$//$NON-NLS-2$
 		     System.exit(-2);
 		    }

 		    data = null;
 		    data=ireader.readLine();
 		    if(data == null) {
 		    	 System.err.println("Error, "+args[1]+" file has no data!"); //$NON-NLS-1$//$NON-NLS-2$
 		    	 System.exit(-2);
 		     }

 		    st = new StringTokenizer(data, ","); //$NON-NLS-1$
 		    column = 0;
 			while (st.hasMoreTokens()) {
 				String val = st.nextToken().trim();
 				if(column < 2) {++column;continue;} // skip iteration, time
 				recovered.add(Double.parseDouble(val));
 			    ++ column;
 		    } // read tokens

 		    ireader.close();

 		    // Read population file
 		    ifile = new FileInputStream(args[2]);
 		    ireader = new BufferedReader(new InputStreamReader(ifile));
 		    header = null;
 		    header=ireader.readLine();
 		    if(header == null) {
 		     System.err.println("Error, "+args[2]+" file is empty!"); //$NON-NLS-1$//$NON-NLS-2$
 		     System.exit(-2);
 		    }

 		    data = null;
 		    data=ireader.readLine();
 		    if(data == null) {
 		    	 System.err.println("Error, "+args[2]+" file has no data!"); //$NON-NLS-1$//$NON-NLS-2$
 		    	 System.exit(-2);
 		     }

 		    st = new StringTokenizer(data, ","); //$NON-NLS-1$
 		    column = 0;
 			while (st.hasMoreTokens()) {
 				String val = st.nextToken().trim();
 				if(column < 2) {++column;continue;} // skip iteration, time
 				population.add(Double.parseDouble(val));
 			    ++ column;
 		    } // read tokens

 		    ireader.close();


 		    int index = 0;
 		    // Write
 		    for(String location:locations) {
 		    	String infectorfilename = infectorPrefix+index;
 		    	String inoculatorfilename = inoculatorPrefix+index;
 		    	FileWriter infectorfw = new FileWriter(infectorfilename+".standard");
 		    	FileWriter inoculatorfw = new FileWriter(inoculatorfilename+".standard");

 		    	double infd = infectious.get(index);
 		    	if(infd == 0.0 && useDefault) {
 		    		infd = population.get(index)*iperc/100.0;
 		    	}

 		    	infectorfw.write("<?xml version=\"1.0\" encoding=\"ASCII\"?>\n");
 		    	infectorfw.write("<org.eclipse.stem.diseasemodels.standard:SIInfector xmi:version=\"2.0\" xmlns:xmi=\"http://www.omg.org/XMI\" xmlns:org.eclipse.stem.diseasemodels.standard=\"http:///org/eclipse/stem/diseasemodels/standard.ecore\" ");
 		    	infectorfw.write(" uRI=\"platform:/resource/"+projectName+"/decorators/"+infectorfilename+".standard\" typeURI=\"stemtype://org.eclipse.stem/identifiable83\" ");
 		    	infectorfw.write(" diseaseName=\""+diseaseName+"\" targetISOKey=\""+location+"\" populationIdentifier=\"human\" infectiousCount=\""+infd+"\">\n");
 		    	infectorfw.write(" <dublinCore title=\"Infect "+infd+" &quot;human&quot; population members with the disease &quot;"+diseaseName+"&quot; at the location &quot;"+location+"&quot;.\" identifier=\"platform:/resource/"+projectName+"/decorators/"+infectorfilename+".standard\" description=\"Infect "+infd+" &quot;human&quot; population members with the disease &quot;"+diseaseName+"&quot; at the location &quot;"+location+"&quot; (CH-GN).\" creator=\"generated\" format=\"http:///org/eclipse/stem/diseasemodels/standard.ecore\" type=\"stemtype://org.eclipse.stem/identifiable83\" created=\"2008-12-17\"/>\n");
 		    	infectorfw.write("</org.eclipse.stem.diseasemodels.standard:SIInfector>\n");
 		    	infectorfw.flush();
 		    	infectorfw.close();

 		    	double inoculatedPercentage = 100.0*recovered.get(index)/population.get(index);
 		    	inoculatedPercentage = inoculatedPercentage * rscale;
 		    	UtilLogger.logInformation("r_scale:"+rscale);

 		    	inoculatorfw.write("<?xml version=\"1.0\" encoding=\"ASCII\"?>\n");
 		    	inoculatorfw.write("<org.eclipse.stem.diseasemodels.standard:SIRInoculator xmi:version=\"2.0\" xmlns:xmi=\"http://www.omg.org/XMI\" xmlns:org.eclipse.stem.diseasemodels.standard=\"http:///org/eclipse/stem/diseasemodels/standard.ecore\" ");
 		    	inoculatorfw.write(" uRI=\"platform:/resource/"+projectName+"/decorators/"+inoculatorfilename+".standard\" typeURI=\"stemtype://org.eclipse.stem/identifiable9\" ");
 		    	inoculatorfw.write(" diseaseName=\""+diseaseName+"\" targetISOKey=\""+location+"\" populationIdentifier=\"human\" infectiousCount=\"0\" inoculatedPercentage=\""+inoculatedPercentage+"\">\n");
 		    	inoculatorfw.write(" <dublinCore title=\"Inoculate "+inoculatedPercentage+" &quot;human&quot; percent of population against the disease &quot;"+diseaseName+"&quot; at the location &quot;"+location+"&quot;.\" identifier=\"platform:/resource/"+projectName+"/decorators/"+inoculatorfilename+".standard\" description=\"Inoculate "+inoculatedPercentage+" &quot;human&quot; percent of population against the disease &quot;"+diseaseName+"&quot; at the location &quot;"+location+"&quot; .\" creator=\"generated\" format=\"http:///org/eclipse/stem/diseasemodels/standard.ecore\" type=\"stemtype://org.eclipse.stem/identifiable9\" created=\"2008-12-17\"/>\n");
 		    	inoculatorfw.write("</org.eclipse.stem.diseasemodels.standard:SIRInoculator>\n");
 		    	inoculatorfw.flush();
 		    	inoculatorfw.close();


 		    	++index;
 		    }
 		} catch(Exception e) {
 			e.printStackTrace();
 		}

 	}
 }
	package org.eclipse.stem.utility.generators;

	/*******************************************************************************
	* Copyright (c) 2009 IBM Corporation and others.
	* All rights reserved. This program and the accompanying materials
	* are made available under the terms of the Eclipse Public License v1.0
	* which accompanies this distribution, and is available at
	* http://www.eclipse.org/legal/epl-v10.html
	*
	* Contributors:
	* IBM Corporation - initial API and implementation
	*******************************************************************************/

	import java.io.BufferedReader;
	import java.io.FileInputStream;
	import java.io.FileWriter;
	import java.io.InputStreamReader;
	import java.util.ArrayList;
	import java.util.StringTokenizer;

	/**
	* The file imports an infectious log file (param1), a population log file (param 2)
	* and using the specified disease name (param3) it generates infector and inoculator XML file
	* that can be imported into a scenario to initialize it to the initial log file
	* state
	*/
	public class InfectorInoculatorGenerator {

	/**
	* NLS Prefix for Infector name
	*/
	public static String infectorPrefix = Messages.getString("Inoculator.1"); //$NON-NLS-1$

	/**
	* NLS Prefix for Inoculator name
	*/
	public static String inoculatorPrefix = Messages.getString("Inoculator.2"); //$NON-NLS-1$

	/**
	*
	* @param args
	*/
	@SuppressWarnings("nls")
	public static void main(String [] args) {
	if(args.length < 6) {
	System.err.println("Usage: InfectorInoculatorGenerator <I file> <R file> <P file> <disease name> <project name> <default I% (optional)> <scale R fraction (optional)>"); //$NON-NLS-1$
	System.exit(-1);
	}

	String diseaseName = args[3];
	String projectName = args[4];

	boolean useDefault = false;
	double iperc = 0.0;
	double rscale = 1.0;

	if(args.length >5) {
	useDefault = true;
	iperc = Double.parseDouble(args[5]);
	}
	if(args.length > 6) {
	useDefault = true;
	rscale = Double.parseDouble(args[6]);
	}

	ArrayList<String>locations = new ArrayList<String>();
	ArrayList<Double>infectious = new ArrayList<Double>();
	ArrayList<Double>recovered = new ArrayList<Double>();
	ArrayList<Double>population = new ArrayList<Double>();

	try {
	// Read infectious file
	FileInputStream ifile = new FileInputStream(args[0]);
	BufferedReader ireader = new BufferedReader(new InputStreamReader(ifile));
	String header = null;
	header=ireader.readLine();
	if(header == null) {
	System.err.println("Error, "+args[0]+" file is empty!"); //$NON-NLS-1$//$NON-NLS-2$
	System.exit(-2);
	}
	StringTokenizer st = new StringTokenizer(header, ","); //$NON-NLS-1$
	int column = 0;
	while(st.hasMoreTokens()) {
	String val = st.nextToken();
	if(column < 2) {++column;continue;}
	locations.add(val.trim());
	++column;
	}

	String data = null;
	data=ireader.readLine();
	if(data == null) {
	System.err.println("Error, "+args[0]+" file has no data!"); //$NON-NLS-1$//$NON-NLS-2$
	System.exit(-2);
	}

	st = new StringTokenizer(data, ","); //$NON-NLS-1$
	column = 0;
	while (st.hasMoreTokens()) {
	String val = st.nextToken().trim();
	if(column < 2) {++column;continue;} // skip iteration, time
	infectious.add(Double.parseDouble(val));
	++ column;
	} // read tokens

	ireader.close();

	// Read recovered file
	ifile = new FileInputStream(args[1]);
	ireader = new BufferedReader(new InputStreamReader(ifile));
	header = null;
	header=ireader.readLine();
	if(header == null) {
	System.err.println("Error, "+args[1]+" file is empty!"); //$NON-NLS-1$//$NON-NLS-2$
	System.exit(-2);
	}

	data = null;
	data=ireader.readLine();
	if(data == null) {
	System.err.println("Error, "+args[1]+" file has no data!"); //$NON-NLS-1$//$NON-NLS-2$
	System.exit(-2);
	}

	st = new StringTokenizer(data, ","); //$NON-NLS-1$
	column = 0;
	while (st.hasMoreTokens()) {
	String val = st.nextToken().trim();
	if(column < 2) {++column;continue;} // skip iteration, time
	recovered.add(Double.parseDouble(val));
	++ column;
	} // read tokens

	ireader.close();

	// Read population file
	ifile = new FileInputStream(args[2]);
	ireader = new BufferedReader(new InputStreamReader(ifile));
	header = null;
	header=ireader.readLine();
	if(header == null) {
	System.err.println("Error, "+args[2]+" file is empty!"); //$NON-NLS-1$//$NON-NLS-2$
	System.exit(-2);
	}

	data = null;
	data=ireader.readLine();
	if(data == null) {
	System.err.println("Error, "+args[2]+" file has no data!"); //$NON-NLS-1$//$NON-NLS-2$
	System.exit(-2);
	}

	st = new StringTokenizer(data, ","); //$NON-NLS-1$
	column = 0;
	while (st.hasMoreTokens()) {
	String val = st.nextToken().trim();
	if(column < 2) {++column;continue;} // skip iteration, time
	population.add(Double.parseDouble(val));
	++ column;
	} // read tokens

	ireader.close();


	int index = 0;
	// Write
	for(String location:locations) {
	String infectorfilename = infectorPrefix+index;
	String inoculatorfilename = inoculatorPrefix+index;
	FileWriter infectorfw = new FileWriter(infectorfilename+".standard");
	FileWriter inoculatorfw = new FileWriter(inoculatorfilename+".standard");

	double infd = infectious.get(index);
	if(infd == 0.0 && useDefault) {
	infd = population.get(index)*iperc/100.0;
	}

	infectorfw.write("<?xml version=\"1.0\" encoding=\"ASCII\"?>\n");
	infectorfw.write("<org.eclipse.stem.diseasemodels.standard:SIInfector xmi:version=\"2.0\" xmlns:xmi=\"http://www.omg.org/XMI\" xmlns:org.eclipse.stem.diseasemodels.standard=\"http:///org/eclipse/stem/diseasemodels/standard.ecore\" ");
	infectorfw.write(" uRI=\"platform:/resource/"+projectName+"/decorators/"+infectorfilename+".standard\" typeURI=\"stemtype://org.eclipse.stem/identifiable83\" ");
	infectorfw.write(" diseaseName=\""+diseaseName+"\" targetISOKey=\""+location+"\" populationIdentifier=\"human\" infectiousCount=\""+infd+"\">\n");
	infectorfw.write(" <dublinCore title=\"Infect "+infd+" "human" population members with the disease ""+diseaseName+"" at the location ""+location+"".\" identifier=\"platform:/resource/"+projectName+"/decorators/"+infectorfilename+".standard\" description=\"Infect "+infd+" "human" population members with the disease ""+diseaseName+"" at the location ""+location+"" (CH-GN).\" creator=\"generated\" format=\"http:///org/eclipse/stem/diseasemodels/standard.ecore\" type=\"stemtype://org.eclipse.stem/identifiable83\" created=\"2008-12-17\"/>\n");
	infectorfw.write("</org.eclipse.stem.diseasemodels.standard:SIInfector>\n");
	infectorfw.flush();
	infectorfw.close();

	double inoculatedPercentage = 100.0*recovered.get(index)/population.get(index);
	inoculatedPercentage = inoculatedPercentage * rscale;
	UtilLogger.logInformation("r_scale:"+rscale);

	inoculatorfw.write("<?xml version=\"1.0\" encoding=\"ASCII\"?>\n");
	inoculatorfw.write("<org.eclipse.stem.diseasemodels.standard:SIRInoculator xmi:version=\"2.0\" xmlns:xmi=\"http://www.omg.org/XMI\" xmlns:org.eclipse.stem.diseasemodels.standard=\"http:///org/eclipse/stem/diseasemodels/standard.ecore\" ");
	inoculatorfw.write(" uRI=\"platform:/resource/"+projectName+"/decorators/"+inoculatorfilename+".standard\" typeURI=\"stemtype://org.eclipse.stem/identifiable9\" ");
	inoculatorfw.write(" diseaseName=\""+diseaseName+"\" targetISOKey=\""+location+"\" populationIdentifier=\"human\" infectiousCount=\"0\" inoculatedPercentage=\""+inoculatedPercentage+"\">\n");
	inoculatorfw.write(" <dublinCore title=\"Inoculate "+inoculatedPercentage+" "human" percent of population against the disease ""+diseaseName+"" at the location ""+location+"".\" identifier=\"platform:/resource/"+projectName+"/decorators/"+inoculatorfilename+".standard\" description=\"Inoculate "+inoculatedPercentage+" "human" percent of population against the disease ""+diseaseName+"" at the location ""+location+"" .\" creator=\"generated\" format=\"http:///org/eclipse/stem/diseasemodels/standard.ecore\" type=\"stemtype://org.eclipse.stem/identifiable9\" created=\"2008-12-17\"/>\n");
	inoculatorfw.write("</org.eclipse.stem.diseasemodels.standard:SIRInoculator>\n");
	inoculatorfw.flush();
	inoculatorfw.close();


	++index;
	}
	} catch(Exception e) {
	e.printStackTrace();
	}

	}
	}