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0
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1 package de.mpiwg.itgroup.eSciDoc.harvesting;
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2
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3 import java.io.IOException;
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2
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4 import java.io.InputStream;
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3
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5 import java.io.UnsupportedEncodingException;
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0
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6 import java.net.URL;
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7 import java.util.ArrayList;
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4
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8 import java.util.List;
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3
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9 import java.util.Map;
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0
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10
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2
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11 import org.apache.http.HttpEntity;
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0
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12 import org.apache.http.HttpResponse;
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13 import org.apache.log4j.Level;
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14 import org.apache.log4j.Logger;
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15 import org.apache.log4j.xml.DOMConfigurator;
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16 import org.jdom.JDOMException;
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17
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18 import de.mpiwg.itgroup.eSciDoc.Tools.EScidocBasicHandler;
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19 import de.mpiwg.itgroup.eSciDoc.Tools.EScidocTools;
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20 import de.mpiwg.itgroup.eSciDoc.echoObjects.ECHOObject;
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21 import de.mpiwg.itgroup.eSciDoc.echoObjects.ECHORessource;
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3
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22 import de.mpiwg.itgroup.eSciDoc.exceptions.ConnectorException;
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23 import de.mpiwg.itgroup.eSciDoc.exceptions.ESciDocXmlObjectException;
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24 import de.mpiwg.itgroup.eSciDoc.exceptions.ObjectNotUniqueError;
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25 import de.mpiwg.itgroup.eSciDoc.exceptions.TransformerException;
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0
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26 import de.mpiwg.itgroup.eSciDoc.importer.ECHOImporter;
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27 import de.mpiwg.itgroup.eSciDoc.importer.Importer;
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28 import de.mpiwg.itgroup.eSciDoc.transformer.ECHOTransformer;
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29 import de.mpiwg.itgroup.eSciDoc.transformer.Transformer;
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30 import de.mpiwg.itgroup.eSciDoc.utils.eSciDocXmlObject;
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31
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3
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32 /**
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33 * @author dwinter
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34 * Main class for data harveting from index.meta files into eScidoc
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35 */
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0
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36 public class ESciDocDataHarvester {
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3
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37 static int MAX_REC=1000; // maximale Anzahl von Records die in einem Stueck eingelesen bzw. bearbeitet werden.
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2
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38 //static int MAX_REC=5;
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39 protected Logger logger = Logger.getRootLogger();
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40 protected Importer importer;
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41 protected EScidocBasicHandler connector;
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42 protected Transformer transformer;
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8
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43
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6
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44 private String context;
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45 private Logger addedFile = Logger.getLogger("addedFilesLogger");
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46 private Logger notAddedFile = Logger.getLogger("notAddedFilesLogger");
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2
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47
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3
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48 /**
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49 * @param importer Importer for dataObjects, describes how to access the objects
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50 * @param transformer Transformer, generates the eScidocMetaDatasets
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51 * @param connector connects to the eScidocRepository
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52 * @param context Escidoc context path z.b. /ir/context/escidoc:12001
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53 */
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54 public ESciDocDataHarvester(Importer importer, Transformer transformer,
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55 EScidocBasicHandler connector, String context) {
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56 this.importer = importer;
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57 this.transformer = transformer;
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58 this.connector = connector;
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3
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59 //this.tools = new EScidocTools(connector);
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60 this.context = context;
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61
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62 }
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63
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64 /** Read objects into eScidoc or updates the objects if indexMeta has changed.
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65 * @param type restrict the imported objects to a specific type, possible types should be defined in
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66 * the given importer @see {@link #importer}
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67 * @return
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68 * @throws ConnectorException
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69 * @throws TransformerException
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70 * @throws ESciDocXmlObjectException
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71 */
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72 @Deprecated
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73 public Boolean readObjectsFromInstanceOLD(String type) throws ConnectorException, TransformerException, ESciDocXmlObjectException {
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74 ArrayList<String> addedObjects = new ArrayList<String>();
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75 ArrayList<String> notAddedObjects = new ArrayList<String>();
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76 for (ECHOObject obj : importer.getObjectList(type)) {
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77
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78 if (ECHORessource.class.isInstance(obj)) {
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79 try {
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80 ECHOObject old;
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81 try {
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8
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82 old = connector.alreadyExists(
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83 "admin.archivePath",
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84 ((ECHORessource) obj).archivePath, context,"=");
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85 if (old==null){ //FIXME Problem bei der Erfassungder Metadaten sollte eigentlich nicht vorkommen!
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86 old = connector.alreadyExists(
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87 "admin.archivePath",
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88 ((ECHORessource) obj).archivePath.replace("/mpiwg/online/permanent", "/Volumes/online/permanent"), context,"=");
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89 }
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90 if (old==null){
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91 old = connector.alreadyExists(
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92 "admin.archivePath",
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93 ((ECHORessource) obj).archivePath.replace("/mpiwg/online/experimental", "/Volumes/online/experimental"), context,"=");
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94 }
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95 } catch (ObjectNotUniqueError e) {
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96 // TODO Auto-generated catch block
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97 e.printStackTrace();
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98 continue;
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99 }
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100 if (old!=null) {
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101 logger.debug("already exist:"
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102 + ((ECHORessource) obj).archivePath);
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103 handleExistingObject(obj,old);
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104 continue;
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105 }
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106 } catch (ConnectorException e) {
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107 logger.debug("already exist error:");
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108 e.printStackTrace();
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109 continue;
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110 }
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111 }
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112
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113 obj.context = context;
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114
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115 String contid = connector.getIDfromPID(obj.pid, context);
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116 if (contid != null) {
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117 System.out.println("------- belongsTo:" + contid);
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118 } else {
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119
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120 eSciDocXmlObject escidocItem = transformer.transform(obj);
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121
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122
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123 try {
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124 logger.info(escidocItem.printXML());
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125 // TODO write PID to back to echo-obj
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126 Boolean result = connector.createItem(escidocItem);
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127 if (result) {
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128 addedObjects.add(escidocItem.getESciDocId());
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129 addedFile.debug(escidocItem.getESciDocId() + "\n");
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130
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131 } else {
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132 notAddedObjects.add(obj.echoUrl);
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133 notAddedFile.debug(obj.echoUrl);
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134
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135 }
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136
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137 } catch (IOException e) {
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138 // TODO Auto-generated catch block
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139 e.printStackTrace();
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140 throw new ESciDocXmlObjectException();
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141 } catch (JDOMException e) {
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142 // TODO Auto-generated catch block
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143 e.printStackTrace();
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144 throw new ESciDocXmlObjectException();
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145 }
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146
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4
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147 }
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148 }
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149 if (logger.getLevel() == Level.DEBUG) {
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150 for (String addedObject : addedObjects) {
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151 logger.debug(addedObject);
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152 }
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153 }
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154
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155 return true;
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156 }
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157
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158
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159 /** Read objects into eScidoc or updates the objects if indexMeta has changed.
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160 * @param type restrict the imported objects to a specific type, possible types should be defined in
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161 * the given importer @see {@link #importer}
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162 * @return
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163 * @throws ConnectorException
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164 * @throws TransformerException
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165 * @throws ESciDocXmlObjectException
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166 */
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167 public Boolean readObjectsFromInstance(String type) throws ConnectorException, TransformerException, ESciDocXmlObjectException {
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168 ArrayList<String> addedObjects = new ArrayList<String>();
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169 ArrayList<String> notAddedObjects = new ArrayList<String>();
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170 for (ECHOObject obj : importer.getObjectList(type)) {
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171 if (obj==null)
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172 continue;
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173 if (ECHORessource.class.isInstance(obj)) {
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174 try {
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175
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176 // checke zuerst, ob die MD5 schon im publiziert Teil der Metadaten ist, dann tue nichts
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177 String md5 = ((ECHORessource) obj).getIndexMetaMD5onServer();
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178 //List<eSciDocXmlObject> results = connector.getObjectsFromSearch("escidoc.component.checksum",md5);
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179 List<eSciDocXmlObject> results = connector.getObjectsFromSearch("escidoc.component.checksum",md5,context);
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180 if (results.size()>0){ //index.meta schon abgespeichert
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181 notAddedFile.debug("alredy exist:"+obj.echoUrl);
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182
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183 ((ECHORessource) obj).writeEsciDocIDToIndexMeta(results.get(0));
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184
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185 continue;
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186 }
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187
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188
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189
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190
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191 ECHOObject old;
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192 try {
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193
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194 old = connector.alreadyExists(
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195 "admin.archivePath",
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196 ((ECHORessource) obj).archivePath, context,"=");
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197 if (old==null){ //FIXME Problem bei der Erfassungder Metadaten sollte eigentlich nicht vorkommen!
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198 old = connector.alreadyExists(
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199 "admin.archivePath",
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200 ((ECHORessource) obj).archivePath.replace("/mpiwg/online/permanent", "/Volumes/online_permanent"), context,"=");
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201 }
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202 if (old==null){
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203 old = connector.alreadyExists(
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204 "admin.archivePath",
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205 ((ECHORessource) obj).archivePath.replace("/mpiwg/online/experimental", "/Volumes/online_experimental"), context,"=");
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206 }
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207 } catch (ObjectNotUniqueError e) {
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208 // TODO Auto-generated catch block
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209 e.printStackTrace();
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210 continue;
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211 }
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212 if (old!=null) {
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213 logger.debug("already exist:"
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214 + ((ECHORessource) obj).archivePath);
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215 handleExistingObject(obj,old);
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216 continue;
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217 }
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218 } catch (ConnectorException e) {
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219 logger.debug("already exist error:");
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220 e.printStackTrace();
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221 continue;
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222 }
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223 }
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224
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225 obj.context = context;
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226
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227 String contid=null;
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228
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229 if (obj.pid!=null)
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230 contid = connector.getIDfromPID(obj.pid, context);
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231 if (contid != null) {
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232 System.out.println("------- belongsTo:" + contid);
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233 } else {
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234
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235 eSciDocXmlObject escidocItem = transformer.transform(obj);
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236
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237
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238 try {
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239 logger.info(escidocItem.printXML());
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240 // TODO write PID to back to echo-obj
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241 Boolean result = connector.createItem(escidocItem);
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242 if (result) {
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243 String objID=escidocItem.getESciDocId();
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244 addedObjects.add(objID);
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245 addedFile.debug(objID + "\n");
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246 ((ECHORessource)obj).writeEsciDocIDToIndexMeta(objID.replace("/ir/item/",""));
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8
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247 } else {
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248 notAddedObjects.add(obj.echoUrl);
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249 notAddedFile.debug(obj.echoUrl);
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250
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251 }
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252
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253 } catch (IOException e) {
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254 // TODO Auto-generated catch block
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255 e.printStackTrace();
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256 throw new ESciDocXmlObjectException();
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257 } catch (JDOMException e) {
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258 // TODO Auto-generated catch block
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259 e.printStackTrace();
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260 throw new ESciDocXmlObjectException();
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261 }
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262
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263 }
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264 }
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265 if (logger.getLevel() == Level.DEBUG) {
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266 for (String addedObject : addedObjects) {
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267 logger.debug(addedObject);
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268 }
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269 }
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270
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271 return true;
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272 }
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273
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274
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275
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3
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276
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277 /**
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278 * Deal with existing objects, do nothing if md5 of stored metadata and metadata on the server is the same otherwise call {@link #updateObject(ECHOObject)}.
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279 * @param objNew
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280 * @param old
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281 * @throws TransformerException
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282 * @throws ESciDocXmlObjectException
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283 */
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284 private void handleExistingObject(ECHOObject objNew, ECHOObject old) throws TransformerException, ESciDocXmlObjectException {
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285 ECHORessource objNewRes = (ECHORessource)objNew;
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286 ECHORessource objOldRes = (ECHORessource)old;
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287 String md5onServer = objNewRes.getIndexMetaMD5onServer();
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288 String md5=objOldRes.getIndexMetaMD5stored();
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289
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290 objNewRes.writeEsciDocIDToIndexMeta(objOldRes.eScidocId);
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291
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3
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292 if (md5onServer.equals(md5))
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293 return;
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294 else {
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8
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295
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3
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296 updateObject(objNew, old);
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297
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298
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3
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299 }
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300
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3
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301 }
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302
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303 private void updateObject(ECHOObject objNew, ECHOObject objOld) throws TransformerException, ESciDocXmlObjectException {
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304 objNew.context = context;
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305
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306 //erzeuge erst einmal ein neues XML Object aus den neuen Daten.
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307 eSciDocXmlObject escidocItem = transformer.transform(objNew);
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308 String lastModificationDateOld = objOld.lastModificationDate;
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309
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310 //jetzt das alte ModeificationDate dort rein (wegen, optimitistic locking)
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311 escidocItem.setLastModificationDate(lastModificationDateOld);
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312 try {
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313 HttpResponse ret = connector.eScidocPut("/ir/item/"+objOld.eScidocId, EScidocBasicHandler.convertStringToStream(escidocItem.printXML()));
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3
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314 HttpEntity ent = ret.getEntity();
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315 if (ret.getStatusLine().getStatusCode() != 200) {
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316 logger.debug("Can not update:" + objOld.eScidocId);
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317 // res.getEntity().consumeContent(); // necessary to release
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318 // the conneciton
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319 ent.consumeContent();
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320
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321 }
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322 InputStream restream = ret.getEntity().getContent();
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323 logger.debug(EScidocBasicHandler.convertStreamToString(restream));
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324 } catch (UnsupportedEncodingException e) {
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325 // TODO Auto-generated catch block
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326 e.printStackTrace();
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327 } catch (IOException e) {
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328 // TODO Auto-generated catch block
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329 e.printStackTrace();
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330 }
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8
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331
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5
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332 addedFile.debug("updated:"+objOld.eScidocId);
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3
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333 }
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334
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2
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335 /**
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336 * @param command
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337 * @param objectXPath
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8
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338 * @param comment der in escidoc bei der Operation abgespeichert wird.
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2
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339 * @param mode 0 : only submit, 1:only release, 2:release and submit
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340 * @throws Exception
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341 */
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8
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342 public void releaseAndSubmitObjects(String command, String objectXPath,String comment,int mode)
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2
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343 throws Exception {
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344
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345 Integer numberOfHits = connector.getNumberOfHitsFromFilterResult(
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346 command, objectXPath,mode);
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8
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347
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10
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348 logger.info(String.format("%s objects found.", numberOfHits));
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2
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349 int tausend = ((numberOfHits-1) / MAX_REC);
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8
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350
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2
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351 String queryRestrict="";
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352 if(mode==0 | mode==2){
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353 queryRestrict="query=%22/properties/version/status%22=pending";
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354 } else {
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355 queryRestrict="query=%22/properties/version/status%22=submitted";
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356 }
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10
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357 int counter=0;
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2
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358 for (int t = 0; t <= tausend; t++) {
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359 int start = t * MAX_REC+1;
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360 // int max=Math.min((t+1)*1000, numberOfHits);
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361 String query = "?maximumRecords="+String.valueOf(MAX_REC)+"&startRecord="
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362 + String.valueOf(start)+"&"+queryRestrict;
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363 for (eSciDocXmlObject obj : connector
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4
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364 .getObjectsFromFilterResult(command+query, objectXPath)) {
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8
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365
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10
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366 logger.info(String.format("%s/%s", counter,numberOfHits));
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367 counter+=1;
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368
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2
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369 //TODO is the following really necessary, currently the obj in the list is sometimes not the current one.
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370 try{
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8
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371 HttpResponse resObj = connector.eScidocGet(obj.getESciDocId());
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372 HttpEntity ent = resObj.getEntity();
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373 if (ent!=null){
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374 obj= new eSciDocXmlObject(ent.getContent());
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375 } else {
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376 logger.debug("Can not retrieve:" + obj.getESciDocId());
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377 continue;
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378 }
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2
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379 } catch (Exception e){
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380 logger.debug("Can not retrieve:" + obj.getESciDocId());
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381 continue;
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382 }
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383 if (mode==0 | mode==2){
|
|
|
384 HttpResponse res = connector.submitAnObject(obj,
|
|
8
|
385 comment);
|
|
2
|
386 logger.debug(res.getStatusLine());
|
|
8
|
387
|
|
2
|
388 if (res.getStatusLine().getStatusCode() != 200) {
|
|
|
389 logger.debug("Can not submit:" + obj.getESciDocId());
|
|
|
390 // res.getEntity().consumeContent(); // necessary to release
|
|
|
391 // the conneciton
|
|
8
|
392
|
|
2
|
393 }
|
|
|
394 InputStream restream = res.getEntity().getContent();
|
|
|
395 logger.debug(EScidocBasicHandler.convertStreamToString(restream));
|
|
|
396 //res.getEntity().consumeContent(); // necessary to release the
|
|
8
|
397 // conneciton
|
|
|
398
|
|
2
|
399 if (!connector.upDateObject(obj)) {
|
|
|
400 logger.debug("Can not update:" + obj.getESciDocId());
|
|
|
401 // continue;
|
|
8
|
402
|
|
2
|
403 }
|
|
|
404 }
|
|
8
|
405
|
|
2
|
406 if (mode==1 | mode==2){
|
|
8
|
407 HttpResponse res = connector.releaseAnObject(obj, comment);
|
|
2
|
408 logger.debug(res.getStatusLine());
|
|
|
409 if (res.getStatusLine().getStatusCode() != 200) {
|
|
|
410 logger.debug("Can not release:" + obj.getESciDocId());
|
|
|
411 res.getEntity().consumeContent(); // necessary to release
|
|
8
|
412 // the conneciton
|
|
2
|
413 continue;
|
|
|
414 }
|
|
|
415 addedFile.debug("RELEASED:" + obj.getESciDocId());
|
|
|
416 res.getEntity().consumeContent(); // necessary to release the
|
|
8
|
417 // connecito
|
|
2
|
418 }
|
|
0
|
419 }
|
|
|
420 }
|
|
2
|
421
|
|
0
|
422 }
|
|
2
|
423
|
|
|
424 public static void main(String[] args) throws Exception {
|
|
|
425
|
|
0
|
426 Logger rl = Logger.getRootLogger();
|
|
8
|
427 DOMConfigurator.configure("/etc/escidocImportConfig.xml");
|
|
2
|
428 rl.setLevel(Level.DEBUG);
|
|
0
|
429
|
|
8
|
430
|
|
9
|
431 EScidocBasicHandler connector = new EScidocBasicHandler("escidoc.mpiwg-berlin.mpg.de",8080,"dwinter","weikiki7");
|
|
8
|
432
|
|
|
433
|
|
|
434 //ECHOImporter newimporter = new ECHOImporter(new URL(
|
|
|
435 // "file:///Users/dwinter/libcoll.rdf"));
|
|
|
436
|
|
2
|
437 ECHOImporter newimporter = new ECHOImporter(new URL(
|
|
8
|
438 "http://xserve09.mpiwg-berlin.mpg.de:19280/echo_nav/echo_pages/content/showRDF"));
|
|
2
|
439 ESciDocDataHarvester hv = new ESciDocDataHarvester(newimporter,
|
|
|
440 new ECHOTransformer(), connector, "/ir/context/escidoc:1001");
|
|
|
441
|
|
|
442 // hv.readObjectsFromInstance("ECHO_collection");
|
|
10
|
443 //hv.readObjectsFromInstance("ECHO_resource");
|
|
2
|
444
|
|
|
445 hv.releaseAndSubmitObjects(
|
|
|
446 "/ir/context/escidoc:1001/resources/members",
|
|
8
|
447 "//escidocItem:item","first release",0);
|
|
|
448 hv.releaseAndSubmitObjects(
|
|
|
449 "/ir/context/escidoc:1001/resources/members",
|
|
|
450 "//escidocItem:item","first release",1);
|
|
|
451
|
|
2
|
452
|
|
|
453 // newimporter.organizeRessourcesInCollections(connector,
|
|
|
454 // "/ir/context/escidoc:1001");
|
|
|
455 // hv.releaseAndSubmitObjects("/ir/containers","//container:container");
|
|
0
|
456 }
|
|
|
457 }
|
