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1 package be.cropdesign.iprscan;
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2
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3 import java.io.FileNotFoundException;
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4 import java.io.FileOutputStream;
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5 import java.io.IOException;
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6 import java.util.HashMap;
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7
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8 //include POI 3.8-beta5 jars in classpath
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9 import org.apache.poi.xssf.usermodel.XSSFCell;
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10 import org.apache.poi.xssf.usermodel.XSSFRow;
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11 import org.apache.poi.xssf.usermodel.XSSFSheet;
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12 import org.apache.poi.xssf.usermodel.XSSFWorkbook;
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13
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14 /**
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15 * the .jar needs as parameters the path to the XML file with the summary tables and
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16 * the .raw file with the iprscan results.
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17 * Further the path and filename of the exported Excel file (.xlsx) is given as a parameter.
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18 * java -jar iprscan.jar -xml $XML -raw $raw -excel $excel
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19 * @author: Katrien Bernaerts and Domantas Motiejunas
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20 * @date: 21/06/2012
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21 * @affiliation: CropDesign N.V., a BASF Plant Science Company - Technologiepark 3, 9052 Zwijnaarde - Belgium
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22 */
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23 public class Main {
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24
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25 /**
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26 * @param args
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27 */
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28 public static void main(String[] args) {
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29 /*
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30 * store the arguments and their corresponding flags in a HashMap.
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31 * The availability of a HashMap with key (-flag) / value (argument) pairs makes it easier
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32 * to handle the arguments and their flags.
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33 */
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34 HashMap<String, String> arguments = new HashMap<String, String>();
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35 if (args.length == 0){
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36 System.err.println("No arguments were found at the command line.");
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37 } else {
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38 for(int i = 0; i < args.length; i++){
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39 // for the even args. args[0] is a flag, args[1] is the corresponding argument etc.
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40 if (i % 2 == 0){
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41 arguments.put(args[i], args[i+1]); // define key (-flag) - value (argument) pairs
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42 }
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43 }
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44 }
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45
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46
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47 /*
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48 * fetch the argument values for each flag in the FLAGS enumeration
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49 */
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50 String XMLFile = arguments.get(EnumFlags.XML.getFlag());
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51 String rawFile = arguments.get(EnumFlags.RAW.getFlag());
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52 String xlsxName = arguments.get(EnumFlags.EXCEL.getFlag());
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53
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54 /*
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55 * create an Excel workbook using the Apache POI library
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56 * ref: http://sanjaal.com/java/105/java-file/writing-to-excel-file-using-apache-poi/
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57 */
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58 XSSFWorkbook wb = new XSSFWorkbook();
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59 XSSFRow myRow = null;
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60 XSSFCell myCell = null;
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61
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62 /*
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63 * determine which arguments (-xml or -raw or (-xml && -raw)) were used at the command line,
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64 * and execute the methods corresponding with those arguments
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65 */
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66 if(arguments.containsKey(EnumFlags.XML.getFlag()) && arguments.containsKey(EnumFlags.RAW.getFlag())){
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67 parseXML(wb, myRow, myCell, XMLFile);
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68 parseRaw(wb, myRow, myCell, rawFile);
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69 } else if (arguments.containsKey(EnumFlags.XML.getFlag())) {
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70 parseXML(wb, myRow, myCell, XMLFile);
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71 } else if (arguments.containsKey(EnumFlags.RAW.getFlag())) {
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72 parseRaw(wb, myRow, myCell, rawFile);
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73 }
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74
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75 /*
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76 * write the parsed results to Excel
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77 */
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78 FileOutputStream fileOut;
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79 try {
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80 fileOut = new FileOutputStream(xlsxName);
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81 wb.write(fileOut);
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82 fileOut.close();
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83 } catch (FileNotFoundException fnf) {
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84 System.err.println("Filenot found: " + fnf);
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85 } catch (IOException io) {
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86 System.err.println("Input/output error: " + io);
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87 }
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88 }
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89
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90 /**
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91 * generate Excel tabsheet 2 containing the summary tables obtained by parsing the XML file
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92 */
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93 public static void parseXML(XSSFWorkbook wb, XSSFRow myRow, XSSFCell myCell, String XMLFile){
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94 XSSFSheet sheet2 = wb.createSheet("summary tables");
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95 new XMLToExcel(wb, sheet2, myRow, myCell, XMLFile);
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96 }
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97
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98 /**
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99 * generate tabsheet3: write the iprscan results in the .raw file to Excel, tabsheet "iprscan results"
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100 */
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101 public static void parseRaw(XSSFWorkbook wb, XSSFRow myRow, XSSFCell myCell, String rawFile){
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102 XSSFSheet sheet3 = wb.createSheet("iprscan results");
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103 new RawToExcel(wb, sheet3,myRow, myCell, rawFile);
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104 }
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105 }
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