1 | /* |
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2 | * To change this license header, choose License Headers in Project Properties. |
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3 | * To change this template file, choose Tools | Templates |
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4 | * and open the template in the editor. |
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5 | */ |
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6 | |
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7 | package org.biohackathon.SPARQLBuilder.OWL; |
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8 | |
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9 | import java.io.*; |
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10 | import java.util.*; |
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11 | |
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12 | /** |
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13 | * |
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14 | * @author atsuko |
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15 | */ |
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16 | |
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17 | public class QueryPathGenerator { |
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18 | private String sparqlEndpoint = null; |
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19 | private RDFSchemaAnalyzerFactory factory = null; |
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20 | private RDFSchemaAnalyzer analyzer = null; |
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21 | private OWLClassGraph graph; |
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22 | private boolean askcheck; |
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23 | |
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24 | private static final String CDIR = "cdata"; |
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25 | |
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26 | public static void main(String[] args){ |
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27 | QueryPathGenerator qpg = new QueryPathGenerator(); |
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28 | //String[] elist = qpg.getFactory().getEndpointURIList(); |
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29 | List<String> elist = new LinkedList<String>(); |
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30 | File file0 = new File("eplist.txt"); |
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31 | try{ |
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32 | BufferedReader br = new BufferedReader(new FileReader(file0)); |
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33 | String buf = null; |
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34 | while( (buf = br.readLine()) != null){ |
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35 | elist.add(buf); |
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36 | } |
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37 | }catch(IOException e){ |
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38 | System.err.println(e); |
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39 | } |
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40 | |
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41 | ListIterator<String> eit = elist.listIterator(); |
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42 | int i = 0; |
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43 | while(eit.hasNext()){ |
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44 | String ep = eit.next(); |
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45 | qpg.setSPARQLendpoint(ep); |
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46 | qpg.graph = new OWLClassGraph(qpg.analyzer); |
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47 | SClass[] classes = qpg.getClasses(null); |
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48 | File file1 = new File("path".concat(Integer.toString(i)).concat(".txt")); |
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49 | File file2 = new File("ptable".concat(Integer.toString(i)).concat(".txt")); |
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50 | try{ |
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51 | BufferedWriter bw1 = new BufferedWriter(new FileWriter(file1)); |
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52 | BufferedWriter bw2 = new BufferedWriter(new FileWriter(file2)); |
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53 | String jsonstr = "["; |
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54 | int m = 0; |
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55 | for ( int j = 0 ; j < classes.length; j ++ ){ |
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56 | SClass start = classes[j]; |
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57 | for ( int k = j + 1 ; k < classes.length; k++ ){ |
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58 | SClass end = classes[k]; |
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59 | Path[] paths = qpg.getPaths(start.getClassURI(), end.getClassURI(), false); |
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60 | for( int l = 0; l < paths.length; l++ ){ |
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61 | if ( paths[l] == null ){ |
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62 | continue; |
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63 | } |
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64 | if (m > 0 ){ |
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65 | jsonstr += ","; |
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66 | } |
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67 | double cost = paths[l].computeCost(); |
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68 | bw2.write(Double.toString(cost)); |
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69 | bw2.write(","); |
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70 | bw2.write(Boolean.toString(EndpointAccess.checkPath(paths[l], ep))); |
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71 | bw2.newLine(); |
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72 | jsonstr += paths[i].toJSONString3(classes); |
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73 | m++; |
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74 | } |
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75 | } |
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76 | } |
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77 | jsonstr += "]"; |
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78 | bw1.write(jsonstr); |
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79 | bw1.newLine(); |
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80 | |
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81 | bw1.close(); |
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82 | bw2.close(); |
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83 | }catch(IOException e){ |
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84 | System.err.println(e); |
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85 | } |
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86 | i++; |
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87 | } |
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88 | } |
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89 | |
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90 | public QueryPathGenerator(){ |
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91 | factory = new RDFSchemaAnalyzerFactory(CDIR); |
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92 | } |
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93 | |
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94 | public QueryPathGenerator(String sparqlEndpoint){ |
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95 | factory = new RDFSchemaAnalyzerFactory(CDIR); |
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96 | setSPARQLendpoint(sparqlEndpoint); |
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97 | } |
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98 | |
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99 | public void setOWLClassGraph(String startClass){ |
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100 | //graph = new OWLClassGraph(analyzer, sparqlEndpoint, startClass, askcheck); |
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101 | graph = new OWLClassGraph(analyzer, sparqlEndpoint, startClass, true); |
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102 | } |
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103 | |
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104 | public SClass[] getClasses(String keyword){ |
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105 | String[] keywords = null; |
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106 | if ( keyword != null ){ |
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107 | if ( keyword.length() != 0 ){ |
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108 | keywords = new String[1]; |
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109 | keywords[0] = keyword; |
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110 | } |
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111 | } |
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112 | try { |
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113 | return analyzer.getOWLClasses(null, keywords, null, true); |
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114 | }catch(Exception e){ |
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115 | System.err.println(e); |
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116 | return null; |
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117 | } |
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118 | } |
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119 | |
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120 | public Path[] getPaths(String startClass, String endClass, boolean askcheck){ |
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121 | if ( graph == null ){ |
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122 | //System.err.println("Class graph is null."); |
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123 | setOWLClassGraph(startClass); |
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124 | } |
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125 | graph.askcheck = askcheck; |
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126 | return graph.getPaths(startClass, endClass); |
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127 | } |
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128 | |
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129 | public void setSPARQLendpoint(String sparqlEndpoint){ |
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130 | this.sparqlEndpoint = sparqlEndpoint; |
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131 | setAnalyzer(); |
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132 | } |
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133 | |
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134 | public RDFSchemaAnalyzerFactory getFactory(){ |
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135 | return factory; |
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136 | } |
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137 | |
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138 | private void setAnalyzer(){ |
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139 | try { |
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140 | analyzer = factory.create(sparqlEndpoint); |
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141 | } catch (Exception e) { |
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142 | System.err.println(e); |
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143 | } |
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144 | } |
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145 | |
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146 | public static String getClassLabelfromList(String classURI, SClass[] classes){ |
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147 | if ( classURI == null ){ |
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148 | return ""; |
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149 | } |
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150 | SClass sclass = null; |
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151 | for ( int i = 0 ; i < classes.length; i++ ){ |
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152 | if ( classURI.equals(classes[i].getClassURI()) ){ |
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153 | return getClassLabelfromClass(classes[i]); |
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154 | } |
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155 | } |
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156 | return ""; |
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157 | } |
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158 | |
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159 | public static String getClassLabelfromClass(SClass sclass){ |
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160 | Label[] labels = sclass.getLabels(); |
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161 | for ( int i = 0 ; i < labels.length; i++ ){ |
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162 | if ( labels[i].getLanguage() == null ){ |
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163 | return labels[i].getLabel(); |
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164 | }else if ( labels[i].getLanguage().equals("en") ){ |
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165 | return labels[i].getLabel(); |
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166 | } |
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167 | } |
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168 | String[] url = sclass.getClassURI().split("/"); |
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169 | String tmplabel = url[url.length-1]; |
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170 | String[] tmplabel2 = tmplabel.split("#"); |
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171 | String label = tmplabel2[tmplabel2.length-1]; |
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172 | return label; |
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173 | } |
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174 | |
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175 | public OWLClassGraph getOWLClassGraph(){ |
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176 | /*if ( graph == null ){ |
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177 | graph = new OWLClassGraph(analyzer); |
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178 | }*/ |
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179 | return graph; |
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180 | } |
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181 | } |
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