1 | /** |
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2 | * |
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3 | */ |
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4 | package de.mpiwg.itgroup.annotations.neo4j; |
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5 | |
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6 | import java.util.ArrayList; |
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7 | import java.util.Calendar; |
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8 | import java.util.List; |
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9 | |
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10 | import org.apache.log4j.Logger; |
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11 | import org.neo4j.graphdb.Direction; |
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12 | import org.neo4j.graphdb.GraphDatabaseService; |
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13 | import org.neo4j.graphdb.Node; |
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14 | import org.neo4j.graphdb.Relationship; |
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15 | import org.neo4j.graphdb.RelationshipType; |
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16 | import org.neo4j.graphdb.Transaction; |
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17 | import org.neo4j.graphdb.index.Index; |
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18 | import org.neo4j.graphdb.index.IndexHits; |
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19 | |
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20 | import de.mpiwg.itgroup.annotations.Actor; |
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21 | import de.mpiwg.itgroup.annotations.Annotation; |
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22 | import de.mpiwg.itgroup.annotations.Annotation.FragmentTypes; |
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23 | import de.mpiwg.itgroup.annotations.Group; |
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24 | import de.mpiwg.itgroup.annotations.Person; |
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25 | |
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26 | /** |
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27 | * @author casties |
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28 | * |
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29 | */ |
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30 | public class AnnotationStore { |
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31 | |
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32 | protected static Logger logger = Logger.getLogger(AnnotationStore.class); |
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33 | |
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34 | protected GraphDatabaseService graphDb; |
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35 | |
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36 | public static enum NodeTypes { |
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37 | ANNOTATION, PERSON, TARGET |
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38 | } |
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39 | |
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40 | protected List<Index<Node>> nodeIndexes; |
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41 | |
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42 | public static enum RelationTypes implements RelationshipType { |
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43 | ANNOTATES, CREATED, PERMITS_ADMIN, PERMITS_DELETE, PERMITS_UPDATE, PERMITS_READ |
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44 | } |
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45 | |
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46 | public static String ANNOTATION_URI_BASE = "http://entities.mpiwg-berlin.mpg.de/annotations/"; |
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47 | |
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48 | public AnnotationStore(GraphDatabaseService graphDb) { |
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49 | super(); |
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50 | this.graphDb = graphDb; |
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51 | nodeIndexes = new ArrayList<Index<Node>>(3); |
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52 | // List.set(enum.ordinal(), val) seems not to work. |
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53 | nodeIndexes.add(NodeTypes.ANNOTATION.ordinal(), graphDb.index().forNodes("annotations")); |
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54 | nodeIndexes.add(NodeTypes.PERSON.ordinal(), graphDb.index().forNodes("persons")); |
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55 | nodeIndexes.add(NodeTypes.TARGET.ordinal(), graphDb.index().forNodes("targets")); |
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56 | } |
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57 | |
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58 | protected Index<Node> getNodeIndex(NodeTypes type) { |
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59 | return nodeIndexes.get(type.ordinal()); |
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60 | } |
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61 | |
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62 | /** |
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63 | * Returns the Annotation with the given id. |
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64 | * |
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65 | * @param id |
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66 | * @return |
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67 | */ |
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68 | public Annotation getAnnotationById(String id) { |
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69 | Node annotNode = getNodeIndex(NodeTypes.ANNOTATION).get("id", id).getSingle(); |
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70 | Annotation annot = createAnnotationFromNode(annotNode); |
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71 | return annot; |
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72 | } |
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73 | |
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74 | /** |
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75 | * Returns an Annotation object from an annotation-Node. |
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76 | * |
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77 | * @param annotNode |
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78 | * @return |
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79 | */ |
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80 | public Annotation createAnnotationFromNode(Node annotNode) { |
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81 | Annotation annot = new Annotation(); |
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82 | annot.setUri((String) annotNode.getProperty("id", null)); |
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83 | annot.setBodyText((String) annotNode.getProperty("bodyText", null)); |
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84 | annot.setBodyUri((String) annotNode.getProperty("bodyUri", null)); |
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85 | // get annotation target from relation |
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86 | Relationship targetRel = getRelation(annotNode, RelationTypes.ANNOTATES, null); |
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87 | if (targetRel != null) { |
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88 | Node target = targetRel.getEndNode(); |
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89 | annot.setTargetBaseUri((String) target.getProperty("uri", null)); |
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90 | } else { |
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91 | logger.error("annotation " + annotNode + " has no target node!"); |
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92 | } |
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93 | annot.setTargetFragment((String) annotNode.getProperty("targetFragment", null)); |
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94 | String ft = (String) annotNode.getProperty("fragmentType", null); |
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95 | if (ft != null) { |
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96 | annot.setFragmentType(FragmentTypes.valueOf(ft)); |
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97 | } |
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98 | // get creator from relation |
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99 | Relationship creatorRel = getRelation(annotNode, RelationTypes.CREATED, null); |
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100 | if (creatorRel != null) { |
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101 | Node creatorNode = creatorRel.getStartNode(); |
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102 | Actor creator = createActorFromNode(creatorNode); |
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103 | annot.setCreator(creator); |
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104 | } else { |
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105 | logger.error("annotation " + annotNode + " has no creator node!"); |
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106 | } |
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107 | // get creation date |
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108 | annot.setCreated((String) annotNode.getProperty("created", null)); |
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109 | // get permissions |
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110 | Relationship adminRel = getRelation(annotNode, RelationTypes.PERMITS_ADMIN, null); |
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111 | if (adminRel != null) { |
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112 | Node adminNode = adminRel.getEndNode(); |
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113 | Actor admin = createActorFromNode(adminNode); |
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114 | annot.setAdminPermission(admin); |
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115 | } |
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116 | Relationship deleteRel = getRelation(annotNode, RelationTypes.PERMITS_DELETE, null); |
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117 | if (deleteRel != null) { |
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118 | Node deleteNode = deleteRel.getEndNode(); |
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119 | Actor delete = createActorFromNode(deleteNode); |
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120 | annot.setDeletePermission(delete); |
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121 | } |
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122 | Relationship updateRel = getRelation(annotNode, RelationTypes.PERMITS_UPDATE, null); |
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123 | if (updateRel != null) { |
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124 | Node updateNode = updateRel.getEndNode(); |
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125 | Actor update = createActorFromNode(updateNode); |
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126 | annot.setUpdatePermission(update); |
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127 | } |
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128 | Relationship readRel = getRelation(annotNode, RelationTypes.PERMITS_READ, null); |
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129 | if (readRel != null) { |
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130 | Node readNode = readRel.getEndNode(); |
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131 | Actor read = createActorFromNode(readNode); |
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132 | annot.setReadPermission(read); |
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133 | } |
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134 | |
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135 | return annot; |
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136 | } |
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137 | |
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138 | /** |
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139 | * Returns an Actor object from a node. |
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140 | * |
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141 | * @param actorNode |
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142 | * @return |
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143 | */ |
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144 | protected Actor createActorFromNode(Node actorNode) { |
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145 | String uri = (String) actorNode.getProperty("uri", null); |
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146 | String name = (String) actorNode.getProperty("name", null); |
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147 | String type = (String) actorNode.getProperty("TYPE", null); |
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148 | if (type != null && type.equals("PERSON")) { |
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149 | return new Person(uri, name); |
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150 | } else if (type != null && type.equals("GROUP")) { |
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151 | return new Group(uri, name); |
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152 | } |
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153 | return null; |
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154 | } |
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155 | |
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156 | /** |
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157 | * Store a new annotation in the store or update an existing one. Returns |
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158 | * the stored annotation. |
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159 | * |
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160 | * @param annot |
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161 | * @return |
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162 | */ |
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163 | public Annotation storeAnnotation(Annotation annot) { |
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164 | Node annotNode = null; |
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165 | Transaction tx = graphDb.beginTx(); |
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166 | try { |
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167 | /* |
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168 | * create or get the annotation |
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169 | */ |
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170 | String id = annot.getUri(); |
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171 | if (id == null) { |
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172 | id = createRessourceURI("annot:"); |
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173 | } |
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174 | annotNode = getOrCreateAnnotationNode(id); |
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175 | |
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176 | /* |
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177 | * the annotation body |
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178 | */ |
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179 | String bodyText = annot.getBodyText(); |
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180 | if (bodyText != null) { |
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181 | annotNode.setProperty("bodyText", bodyText); |
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182 | } |
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183 | String bodyUri = annot.getBodyUri(); |
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184 | if (bodyUri != null) { |
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185 | annotNode.setProperty("bodyUri", bodyUri); |
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186 | } |
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187 | |
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188 | /* |
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189 | * the annotation target |
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190 | */ |
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191 | String targetBaseUri = annot.getTargetBaseUri(); |
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192 | if (targetBaseUri != null) { |
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193 | Node target = getOrCreateTargetNode(targetBaseUri); |
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194 | getOrCreateRelation(annotNode, RelationTypes.ANNOTATES, target); |
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195 | } |
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196 | |
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197 | /* |
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198 | * The fragment part of the annotation target. |
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199 | */ |
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200 | String targetFragment = annot.getTargetFragment(); |
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201 | FragmentTypes fragmentType = annot.getFragmentType(); |
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202 | if (targetFragment != null) { |
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203 | annotNode.setProperty("targetFragment", targetFragment); |
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204 | annotNode.setProperty("fragmentType", fragmentType.name()); |
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205 | } |
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206 | |
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207 | /* |
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208 | * The creator of this annotation. |
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209 | */ |
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210 | Actor creator = annot.getCreator(); |
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211 | if (creator != null) { |
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212 | Node creatorNode = getOrCreatePersonNode(creator); |
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213 | getOrCreateRelation(creatorNode, RelationTypes.CREATED, annotNode); |
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214 | } |
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215 | |
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216 | /* |
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217 | * The creation date of this annotation. |
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218 | */ |
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219 | String created = annot.getCreated(); |
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220 | if (created != null) { |
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221 | annotNode.setProperty("created", created); |
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222 | } |
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223 | |
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224 | /* |
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225 | * Permissions for this annotation. |
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226 | */ |
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227 | setPermissionRelation(annotNode, RelationTypes.PERMITS_ADMIN, annot.getAdminPermission()); |
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228 | setPermissionRelation(annotNode, RelationTypes.PERMITS_DELETE, annot.getDeletePermission()); |
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229 | setPermissionRelation(annotNode, RelationTypes.PERMITS_UPDATE, annot.getUpdatePermission()); |
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230 | setPermissionRelation(annotNode, RelationTypes.PERMITS_READ, annot.getReadPermission()); |
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231 | |
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232 | tx.success(); |
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233 | } finally { |
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234 | tx.finish(); |
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235 | } |
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236 | |
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237 | // re-read and return annotation |
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238 | Annotation storedAnnot = createAnnotationFromNode(annotNode); |
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239 | return storedAnnot; |
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240 | } |
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241 | |
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242 | /** |
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243 | * Deletes the annotation with the given id. |
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244 | * |
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245 | * @param id |
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246 | */ |
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247 | public void deleteById(String id) { |
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248 | Node annotNode = getNodeIndex(NodeTypes.ANNOTATION).get("id", id).getSingle(); |
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249 | if (annotNode != null) { |
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250 | // delete related objects |
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251 | Transaction tx = graphDb.beginTx(); |
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252 | try { |
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253 | for (Relationship rel : annotNode.getRelationships()) { |
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254 | // delete relation and the related node if it has no other |
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255 | // relations |
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256 | Node other = rel.getOtherNode(annotNode); |
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257 | rel.delete(); |
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258 | if (!other.hasRelationship()) { |
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259 | deleteNode(other); |
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260 | } |
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261 | } |
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262 | if (!annotNode.hasRelationship()) { |
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263 | deleteNode(annotNode); |
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264 | } else { |
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265 | logger.error("deleteById: unable to delete: Node still has relations."); |
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266 | } |
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267 | tx.success(); |
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268 | } finally { |
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269 | tx.finish(); |
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270 | } |
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271 | } |
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272 | } |
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273 | |
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274 | /** |
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275 | * Returns all annotations with the given uri and/or user. |
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276 | * |
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277 | * @param uri |
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278 | * @param userUri |
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279 | * @param limit |
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280 | * @param offset |
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281 | * @return |
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282 | */ |
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283 | public List<Annotation> searchByUriUser(String targetUri, String userUri, String limit, String offset) { |
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284 | List<Annotation> annotations = new ArrayList<Annotation>(); |
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285 | if (targetUri != null) { |
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286 | // there should be only one |
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287 | Node target = getNodeIndex(NodeTypes.TARGET).get("uri", targetUri).getSingle(); |
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288 | if (target != null) { |
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289 | Iterable<Relationship> relations = target.getRelationships(RelationTypes.ANNOTATES); |
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290 | for (Relationship relation : relations) { |
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291 | Node ann = relation.getStartNode(); |
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292 | if (ann.getProperty("TYPE", "").equals("ANNOTATION")) { |
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293 | Annotation annot = createAnnotationFromNode(ann); |
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294 | annotations.add(annot); |
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295 | } else { |
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296 | logger.error("ANNOTATES relation does not start with ANNOTATION: " + ann); |
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297 | } |
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298 | } |
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299 | } |
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300 | } |
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301 | if (userUri != null) { |
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302 | // there should be only one |
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303 | Node person = getNodeIndex(NodeTypes.PERSON).get("uri", userUri).getSingle(); |
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304 | if (person != null) { |
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305 | Iterable<Relationship> relations = person.getRelationships(RelationTypes.CREATED); |
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306 | for (Relationship relation : relations) { |
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307 | Node ann = relation.getEndNode(); |
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308 | if (ann.getProperty("TYPE", "").equals("ANNOTATION")) { |
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309 | Annotation annot = createAnnotationFromNode(ann); |
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310 | annotations.add(annot); |
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311 | } else { |
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312 | logger.error("CREATED relation does not end with ANNOTATION: " + ann); |
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313 | } |
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314 | } |
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315 | } |
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316 | } |
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317 | return annotations; |
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318 | } |
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319 | |
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320 | protected Relationship getOrCreateRelation(Node start, RelationshipType type, Node end) { |
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321 | if (start.hasRelationship()) { |
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322 | // there are relations |
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323 | Iterable<Relationship> rels = start.getRelationships(type, Direction.OUTGOING); |
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324 | for (Relationship rel : rels) { |
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325 | if (rel.getEndNode().equals(end)) { |
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326 | // relation exists |
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327 | return rel; |
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328 | } |
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329 | } |
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330 | } |
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331 | // create new one |
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332 | Relationship rel; |
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333 | Transaction tx = graphDb.beginTx(); |
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334 | try { |
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335 | rel = start.createRelationshipTo(end, type); |
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336 | tx.success(); |
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337 | } finally { |
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338 | tx.finish(); |
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339 | } |
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340 | return rel; |
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341 | } |
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342 | |
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343 | protected Node getOrCreateAnnotationNode(String id) { |
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344 | Index<Node> idx = getNodeIndex(NodeTypes.ANNOTATION); |
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345 | IndexHits<Node> annotations = idx.get("id", id); |
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346 | Node annotation = annotations.getSingle(); |
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347 | if (annotation == null) { |
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348 | // does not exist yet |
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349 | Transaction tx = graphDb.beginTx(); |
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350 | try { |
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351 | annotation = graphDb.createNode(); |
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352 | annotation.setProperty("TYPE", NodeTypes.ANNOTATION.name()); |
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353 | annotation.setProperty("id", id); |
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354 | idx.add(annotation, "id", id); |
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355 | tx.success(); |
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356 | } finally { |
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357 | tx.finish(); |
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358 | } |
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359 | } |
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360 | return annotation; |
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361 | } |
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362 | |
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363 | protected Node getOrCreateTargetNode(String uri) { |
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364 | Index<Node> idx = getNodeIndex(NodeTypes.TARGET); |
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365 | IndexHits<Node> targets = idx.get("uri", uri); |
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366 | Node target = targets.getSingle(); |
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367 | if (target == null) { |
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368 | // does not exist yet |
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369 | Transaction tx = graphDb.beginTx(); |
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370 | try { |
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371 | target = graphDb.createNode(); |
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372 | target.setProperty("TYPE", NodeTypes.TARGET.name()); |
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373 | target.setProperty("uri", uri); |
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374 | idx.add(target, "uri", uri); |
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375 | tx.success(); |
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376 | } finally { |
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377 | tx.finish(); |
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378 | } |
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379 | } |
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380 | return target; |
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381 | } |
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382 | |
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383 | protected Node getOrCreatePersonNode(Actor actor) { |
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384 | // Person is identified by URI |
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385 | String uri = actor.getUriString(); |
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386 | String name = actor.getName(); |
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387 | Index<Node> idx = getNodeIndex(NodeTypes.PERSON); |
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388 | IndexHits<Node> persons = idx.get("uri", uri); |
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389 | Node person = persons.getSingle(); |
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390 | if (person == null) { |
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391 | // does not exist yet |
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392 | Transaction tx = graphDb.beginTx(); |
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393 | try { |
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394 | person = graphDb.createNode(); |
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395 | person.setProperty("TYPE", NodeTypes.PERSON.name()); |
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396 | person.setProperty("uri", uri); |
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397 | idx.add(person, "uri", uri); |
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398 | if (name != null) { |
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399 | person.setProperty("name", name); |
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400 | } |
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401 | tx.success(); |
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402 | } finally { |
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403 | tx.finish(); |
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404 | } |
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405 | } |
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406 | return person; |
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407 | } |
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408 | |
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409 | /** |
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410 | * Create or update permissions relations for an annotation. |
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411 | * |
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412 | * @param annotNode |
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413 | * @param type |
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414 | * @param annot |
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415 | */ |
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416 | protected void setPermissionRelation(Node annotNode, RelationTypes type, Actor actor) { |
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417 | Node newActorNode = null; |
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418 | if (actor != null) { |
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419 | newActorNode = getOrCreatePersonNode(actor); |
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420 | } |
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421 | Relationship rel = getRelation(annotNode, type, null); |
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422 | if (rel != null) { |
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423 | // relation exists |
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424 | Node oldActorNode = rel.getEndNode(); |
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425 | if (!oldActorNode.equals(newActorNode)) { |
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426 | // new admin is different |
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427 | rel.delete(); |
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428 | if (newActorNode != null) { |
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429 | rel = getOrCreateRelation(annotNode, type, newActorNode); |
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430 | } |
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431 | } |
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432 | } else { |
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433 | // no relation yet |
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434 | if (newActorNode != null) { |
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435 | rel = getOrCreateRelation(annotNode, type, newActorNode); |
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436 | } |
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437 | } |
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438 | } |
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439 | |
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440 | /** |
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441 | * Unindexes and deletes given Node if it has no relations. |
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442 | * |
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443 | * @param node |
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444 | */ |
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445 | protected void deleteNode(Node node) { |
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446 | Transaction tx = graphDb.beginTx(); |
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447 | try { |
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448 | if (node.hasRelationship()) { |
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449 | logger.error("deleteNode: unable to delete: Node still has relations."); |
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450 | } else { |
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451 | String ts = (String) node.getProperty("TYPE", null); |
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452 | try { |
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453 | NodeTypes type = NodeTypes.valueOf(ts); |
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454 | getNodeIndex(type).remove(node); |
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455 | } catch (Exception e) { |
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456 | logger.error("deleteNode: unable to get TYPE of node: " + node); |
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457 | } |
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458 | node.delete(); |
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459 | } |
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460 | tx.success(); |
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461 | } finally { |
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462 | tx.finish(); |
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463 | } |
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464 | } |
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465 | |
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466 | protected Relationship getRelation(Node start, RelationTypes type, Direction direction) { |
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467 | Iterable<Relationship> rels; |
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468 | if (direction == null) { |
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469 | // ignore direction |
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470 | rels = start.getRelationships(type); |
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471 | } else { |
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472 | rels = start.getRelationships(type, direction); |
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473 | } |
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474 | for (Relationship rel : rels) { |
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475 | return rel; |
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476 | } |
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477 | return null; |
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478 | } |
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479 | |
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480 | /** |
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481 | * Erzeuge eine urn aus der aktuellen Zeit in millis |
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482 | * |
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483 | * @return |
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484 | */ |
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485 | private String createRessourceURI(String prefix) { |
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486 | |
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487 | Calendar cal = Calendar.getInstance(); |
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488 | |
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489 | long time = cal.getTimeInMillis(); |
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490 | |
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491 | return String.format("%s%s%s", ANNOTATION_URI_BASE, prefix, time); |
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492 | |
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493 | } |
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494 | |
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495 | } |
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