app-import/src/main/java/eu/etaxonomy/cdm/app/cuba/CubaActivator.java

   1 /**
   2 * Copyright (C) 2007 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9
  10 package eu.etaxonomy.cdm.app.cuba;
  11
  12 import java.net.URI;
  13 import java.util.UUID;
  14
  15 import org.apache.log4j.Logger;
  16
  17 import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  18 import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
  19 import eu.etaxonomy.cdm.api.service.ITermService;
  20 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  21 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  22 import eu.etaxonomy.cdm.database.ICdmDataSource;
  23 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  24 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  25 import eu.etaxonomy.cdm.io.cuba.CubaImportConfigurator;
  26 import eu.etaxonomy.cdm.io.cuba.CubaTransformer;
  27 import eu.etaxonomy.cdm.model.agent.Person;
  28 import eu.etaxonomy.cdm.model.description.Feature;
  29 import eu.etaxonomy.cdm.model.description.FeatureNode;
  30 import eu.etaxonomy.cdm.model.description.FeatureTree;
  31 import eu.etaxonomy.cdm.model.reference.Reference;
  32 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  33
  34 /**
  35  * @author a.mueller
  36  * @created 04.01.2016
  37  */
  38 public class CubaActivator {
  39         private static final Logger logger = Logger.getLogger(CubaActivator.class);
  40
  41         //database validation status (create, update, validate ...)
  42         static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
  43
  44     static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  45 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();
  46 //    static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cuba_production();
  47
  48         static boolean invers = true;
  49
  50     boolean doAsteraceae = include;
  51     boolean doConvolvulaceae = include;
  52     boolean doCyperaceae = include;
  53     boolean doDicotA_C = include;
  54     boolean doDicotD_M = include;
  55     boolean doDicotN_Z = include;
  56     boolean doEuphorbiaceae = include;
  57     boolean doFabaceae = include;
  58     boolean doGymnospermae = include;
  59     boolean doLamVerbenaceae = include;
  60     boolean doMalpighiaceae = include;
  61     boolean doMelastomataceae = include;
  62     boolean doMonocots = include;
  63     boolean doMyrtaceae = include;
  64     boolean doOrchidaceae = include;
  65     boolean doRubiaceae = include;
  66     boolean doUrticaceae = include;
  67
  68     static boolean include = !invers;
  69
  70
  71         //feature tree uuid
  72         public static final UUID featureTreeUuid = UUID.fromString("dad6b9b5-693f-4367-a7aa-076cc9c99476");
  73
  74         //classification
  75         static final UUID classificationUuid = UUID.fromString("5de394de-9c76-4b97-b04d-71be31c7f44b");
  76         private static final String classificationName = "Cuba Checklist";
  77
  78         static final String sourceReferenceTitle = "Cuba Checklist Word Documents";
  79
  80         //check - import
  81         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  82
  83         boolean doVocabularies = (hbm2dll == DbSchemaValidation.CREATE);
  84         static final boolean doTaxa = false;
  85         static final boolean doDeduplicate = true;
  86
  87
  88         private void doImport(ICdmDataSource cdmDestination){
  89
  90             URI source = monocots();  //just any
  91
  92                 //make Source
  93                 CubaImportConfigurator config= CubaImportConfigurator.NewInstance(source, cdmDestination);
  94                 config.setClassificationUuid(classificationUuid);
  95         config.setClassificationName(classificationName);
  96         config.setCheck(check);
  97 //              config.setDoDistribution(doDistribution);
  98                 config.setDoTaxa(doTaxa);
  99                 config.setDbSchemaValidation(hbm2dll);
 100                 config.setSourceReferenceTitle(sourceReferenceTitle);
 101                 config.setDoVocabularies(doVocabularies);
 102
 103                 CdmDefaultImport<CubaImportConfigurator> myImport = new CdmDefaultImport<CubaImportConfigurator>();
 104
 105
 106                 //...
 107         if (doAsteraceae){
 108             doSingleSource(asteraceae(), config, myImport, doVocabularies);
 109         }
 110         if (doConvolvulaceae){
 111             doSingleSource(convolvulaceae(), config, myImport, doVocabularies);
 112         }
 113         if (doCyperaceae){
 114             doSingleSource(cyperaceae(), config, myImport, doVocabularies);
 115         }
 116         if (doDicotA_C){
 117             doSingleSource(dicotA_C(), config, myImport, doVocabularies);
 118         }
 119         if (doDicotD_M){
 120             doSingleSource(dicotD_M(), config, myImport, doVocabularies);
 121         }
 122         if (doDicotN_Z){
 123             doSingleSource(dicotN_Z(), config, myImport, doVocabularies);
 124         }
 125         if (doEuphorbiaceae){
 126             doSingleSource(euphorbiaceae(), config, myImport, doVocabularies);
 127         }
 128         if (doFabaceae){
 129             doSingleSource(fabaceae(), config, myImport, doVocabularies);
 130         }
 131         if (doGymnospermae){
 132             doSingleSource(gymnospermae(), config, myImport, doVocabularies);
 133         }
 134         if (doLamVerbenaceae){
 135             doSingleSource(lamVerbenaceae(), config, myImport, doVocabularies);
 136         }
 137         if (doMalpighiaceae){
 138             doSingleSource(malpighiaceae(), config, myImport, doVocabularies);
 139         }
 140         if (doMelastomataceae){
 141             doSingleSource(melastomataceae(), config, myImport, doVocabularies);
 142         }
 143         if (doMonocots){
 144             doSingleSource(monocots(), config, myImport, doVocabularies);
 145         }
 146         if (doMyrtaceae){
 147             doSingleSource(myrtaceae(), config, myImport, doVocabularies);
 148         }
 149         if (doOrchidaceae){
 150             doSingleSource(orchidaceae(), config, myImport, doVocabularies);
 151         }
 152         if (doRubiaceae){
 153             doSingleSource(rubiaceae(), config, myImport, doVocabularies);
 154         }
 155         if (doUrticaceae){
 156             doSingleSource(urticaceae(), config, myImport, doVocabularies);
 157         }
 158
 159
 160                 //deduplicate
 161                 if (doDeduplicate){
 162                     logger.warn("Start deduplication ...");
 163
 164                     ICdmApplicationConfiguration app = myImport.getCdmAppController();
 165                         if (app == null){
 166                 app = CdmApplicationController.NewInstance(cdmDestination, hbm2dll, false);
 167             }
 168                         int count = app.getAgentService().deduplicate(Person.class, null, null);
 169                         logger.warn("Deduplicated " + count + " persons.");
 170 //                      count = app.getAgentService().deduplicate(Team.class, null, null);
 171 //                      logger.warn("Deduplicated " + count + " teams.");
 172 //                      count = app.getReferenceService().deduplicate(Reference.class, null, null);
 173 //                      logger.warn("Deduplicated " + count + " references.");
 174                 }
 175
 176                 System.exit(0);
 177
 178         }
 179
 180     /**
 181      * @param source
 182      * @param config
 183      * @param myImport
 184      */
 185     private void doSingleSource(URI source, CubaImportConfigurator config,
 186             CdmDefaultImport<CubaImportConfigurator> myImport, boolean doVocabularies) {
 187         config.setSource(source);
 188         String fileName = source.toString();
 189         fileName = fileName.substring(fileName.lastIndexOf("/") + 1 );
 190
 191         String message = "Start import from ("+ fileName + ") ...";
 192         System.out.println(message);
 193         logger.warn(message);
 194         config.setSourceReference(getSourceReference(fileName));
 195         config.setDoVocabularies(doVocabularies);
 196         myImport.invoke(config);
 197
 198         if (doVocabularies){
 199             FeatureTree tree = makeFeatureNodes(myImport.getCdmAppController().getTermService());
 200             myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
 201             this.doVocabularies = false;
 202         }
 203         System.out.println("End import from ("+ source.toString() + ")...");
 204     }
 205
 206     private final Reference inRef = ReferenceFactory.newGeneric();
 207         private Reference getSourceReference(String string) {
 208                 Reference result = ReferenceFactory.newGeneric();
 209                 result.setTitleCache(string, true);
 210                 result.setInReference(inRef);
 211                 inRef.setTitleCache(sourceReferenceTitle, true);
 212                 return result;
 213         }
 214
 215         private FeatureTree makeFeatureNodes(ITermService service){
 216 //              CyprusTransformer transformer = new CyprusTransformer();
 217
 218                 FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);
 219                 result.setTitleCache("Cuba Feature Tree", true);
 220                 FeatureNode root = result.getRoot();
 221                 FeatureNode newNode;
 222
 223                 newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 224                 root.addChild(newNode);
 225
 226 //              Feature featurAltFam = (Feature)service.find(CubaTransformer.uuidAlternativeFamily);
 227 //              newNode = FeatureNode.NewInstance(featurAltFam);
 228 //              root.addChild(newNode);
 229
 230             Feature featurAltFam2 = (Feature)service.find(CubaTransformer.uuidAlternativeFamily2);
 231             newNode = FeatureNode.NewInstance(featurAltFam2);
 232             root.addChild(newNode);
 233
 234                 return result;
 235         }
 236
 237
 238         //Monocots
 239         public static URI monocots() {
 240             return URI.create("file:////BGBM-PESIHPC/Cuba/Monocot.xlsx");
 241         }
 242         //Cyperaceae
 243         public static URI cyperaceae() {
 244             return URI.create("file:////BGBM-PESIHPC/Cuba/Cyper_Poaceae.xlsx");
 245         }
 246     //Fabaceae
 247     public static URI fabaceae() {
 248         return URI.create("file:////BGBM-PESIHPC/Cuba/Fabaceae.xlsx");
 249     }
 250     //Urticaceae
 251     public static URI urticaceae() {
 252         return URI.create("file:////BGBM-PESIHPC/Cuba/Urticaceae.xlsx");
 253     }
 254     //Asteraceae
 255     public static URI asteraceae() {
 256         return URI.create("file:////BGBM-PESIHPC/Cuba/Asteraceae.xlsx");
 257     }
 258     //Convolvulaceae
 259     public static URI convolvulaceae() {
 260         return URI.create("file:////BGBM-PESIHPC/Cuba/Convolvulaceae.xlsx");
 261     }
 262     //dicot A-C
 263     public static URI dicotA_C() {
 264         return URI.create("file:////BGBM-PESIHPC/Cuba/dicotA_C.xlsx");
 265     }
 266     //dicot D-M
 267     public static URI dicotD_M() {
 268         return URI.create("file:////BGBM-PESIHPC/Cuba/dicotD_M.xlsx");
 269     }
 270     //dicot N-Z
 271     public static URI dicotN_Z() {
 272         return URI.create("file:////BGBM-PESIHPC/Cuba/dicotN_Z.xlsx");
 273     }
 274     //Euphorbiaceae
 275     public static URI euphorbiaceae() {
 276         return URI.create("file:////BGBM-PESIHPC/Cuba/Euphorbiaceae.xlsx");
 277     }
 278     //Gymnospermae
 279     public static URI gymnospermae() {
 280         return URI.create("file:////BGBM-PESIHPC/Cuba/gymnospermae.xlsx");
 281     }
 282     //Lam.Verbenaceae
 283     public static URI lamVerbenaceae() {
 284         return URI.create("file:////BGBM-PESIHPC/Cuba/Lam_Verbenaceae.xlsx");
 285     }
 286     //Malpighiaceae
 287     public static URI malpighiaceae() {
 288         return URI.create("file:////BGBM-PESIHPC/Cuba/Malpighiaceae.xlsx");
 289     }
 290     //Melastomataceae
 291     public static URI melastomataceae() {
 292         return URI.create("file:////BGBM-PESIHPC/Cuba/Melastomataceae.xlsx");
 293     }
 294     //Myrtaceae
 295     public static URI myrtaceae() {
 296         return URI.create("file:////BGBM-PESIHPC/Cuba/Myrtaceae.xlsx");
 297     }
 298     //Orchidaceae
 299     public static URI orchidaceae() {
 300         return URI.create("file:////BGBM-PESIHPC/Cuba/Orchidaceae.xlsx");
 301     }
 302     //Rubiaceae
 303     public static URI rubiaceae() {
 304         return URI.create("file:////BGBM-PESIHPC/Cuba/Rubiaceae.xlsx");
 305     }
 306
 307         /**
 308          * @param args
 309          */
 310         public static void main(String[] args) {
 311             CubaActivator me = new CubaActivator();
 312                 me.doImport(cdmDestination);
 313         }
 314
 315 }