| 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(); |
| } |
| |
| } |
| } |