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.ICdmApplicationConfiguration;
  18 import eu.etaxonomy.cdm.api.service.ITermService;
  19 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  20 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  21 import eu.etaxonomy.cdm.database.ICdmDataSource;
  22 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  23 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  24 import eu.etaxonomy.cdm.io.cuba.CubaImportConfigurator;
  25 import eu.etaxonomy.cdm.io.cuba.CubaTransformer;
  26 import eu.etaxonomy.cdm.model.agent.Person;
  27 import eu.etaxonomy.cdm.model.description.Feature;
  28 import eu.etaxonomy.cdm.model.description.FeatureNode;
  29 import eu.etaxonomy.cdm.model.description.FeatureTree;
  30 import eu.etaxonomy.cdm.model.reference.Reference;
  31 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  32
  33 /**
  34  * @author a.mueller
  35  * @created 04.01.2016
  36  */
  37 public class CubaActivator {
  38         private static final Logger logger = Logger.getLogger(CubaActivator.class);
  39
  40         //database validation status (create, update, validate ...)
  41         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  42
  43 //    static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  44 //  static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();
  45     static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cuba_production();
  46
  47         static boolean invers = false;
  48
  49     boolean doAsteraceae = include;
  50     boolean doConvolvulaceae = include;
  51     boolean doCyperaceae = include;
  52     boolean doDicotA_C = include;
  53     boolean doDicotD_M = include;
  54     boolean doDicotN_Z = include;
  55     boolean doEuphorbiaceae = include;
  56     boolean doFabaceae = include;
  57     boolean doGymnospermae = include;
  58     boolean doLamVerbenaceae = include;
  59     boolean doMalpighiaceae = include;
  60     boolean doMelastomataceae = include;
  61     boolean doMonocots = include;
  62     boolean doMyrtaceae = include;
  63     boolean doOrchidaceae = include;
  64     boolean doRubiaceae = include;
  65     boolean doUrticaceae = include;
  66
  67     static boolean include = !invers;
  68
  69
  70
  71
  72         //feature tree uuid
  73         public static final UUID featureTreeUuid = UUID.fromString("dad6b9b5-693f-4367-a7aa-076cc9c99476");
  74
  75         //classification
  76         static final UUID classificationUuid = UUID.fromString("5de394de-9c76-4b97-b04d-71be31c7f44b");
  77         private static final String classificationName = "Flora of Cuba";
  78
  79         static final String sourceReferenceTitle = "Cuba import";
  80
  81         //check - import
  82         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  83
  84         boolean doVocabularies = (hbm2dll == DbSchemaValidation.CREATE);
  85         static final boolean doTaxa = true;
  86         static final boolean doDeduplicate = false;
  87
  88
  89         private void doImport(ICdmDataSource cdmDestination){
  90
  91             URI source = monocots();  //just any
  92
  93                 //make Source
  94                 CubaImportConfigurator config= CubaImportConfigurator.NewInstance(source, cdmDestination);
  95                 config.setClassificationUuid(classificationUuid);
  96         config.setClassificationName(classificationName);
  97         config.setCheck(check);
  98 //              config.setDoDistribution(doDistribution);
  99                 config.setDoTaxa(doTaxa);
 100                 config.setDbSchemaValidation(hbm2dll);
 101                 config.setSourceReferenceTitle(sourceReferenceTitle);
 102                 config.setDoVocabularies(doVocabularies);
 103
 104                 CdmDefaultImport<CubaImportConfigurator> myImport = new CdmDefaultImport<CubaImportConfigurator>();
 105
 106
 107                 //...
 108         if (doAsteraceae){
 109             doSource(asteraceae(), config, myImport, doVocabularies);
 110         }
 111         if (doConvolvulaceae){
 112             doSource(convolvulaceae(), config, myImport, doVocabularies);
 113         }
 114         if (doCyperaceae){
 115             doSource(cyperaceae(), config, myImport, doVocabularies);
 116         }
 117         if (doDicotA_C){
 118             doSource(dicotA_C(), config, myImport, doVocabularies);
 119         }
 120         if (doDicotD_M){
 121             doSource(dicotD_M(), config, myImport, doVocabularies);
 122         }
 123         if (doDicotN_Z){
 124             doSource(dicotN_Z(), config, myImport, doVocabularies);
 125         }
 126         if (doEuphorbiaceae){
 127             doSource(euphorbiaceae(), config, myImport, doVocabularies);
 128         }
 129         if (doFabaceae){
 130             doSource(fabaceae(), config, myImport, doVocabularies);
 131         }
 132         if (doGymnospermae){
 133             doSource(gymnospermae(), config, myImport, doVocabularies);
 134         }
 135         if (doLamVerbenaceae){
 136             doSource(lamVerbenaceae(), config, myImport, doVocabularies);
 137         }
 138         if (doMalpighiaceae){
 139             doSource(malpighiaceae(), config, myImport, doVocabularies);
 140         }
 141         if (doMelastomataceae){
 142             doSource(melastomataceae(), config, myImport, doVocabularies);
 143         }
 144         if (doMonocots){
 145             doSource(monocots(), config, myImport, doVocabularies);
 146         }
 147         if (doMyrtaceae){
 148             doSource(myrtaceae(), config, myImport, doVocabularies);
 149         }
 150         if (doOrchidaceae){
 151             doSource(orchidaceae(), config, myImport, doVocabularies);
 152         }
 153         if (doRubiaceae){
 154             doSource(rubiaceae(), config, myImport, doVocabularies);
 155         }
 156         if (doUrticaceae){
 157             doSource(urticaceae(), config, myImport, doVocabularies);
 158         }
 159
 160
 161
 162                 //deduplicate
 163                 if (doDeduplicate){
 164                         ICdmApplicationConfiguration app = myImport.getCdmAppController();
 165                         int count = app.getAgentService().deduplicate(Person.class, null, null);
 166                         logger.warn("Deduplicated " + count + " persons.");
 167 //                      count = app.getAgentService().deduplicate(Team.class, null, null);
 168 //                      logger.warn("Deduplicated " + count + " teams.");
 169                         count = app.getReferenceService().deduplicate(Reference.class, null, null);
 170                         logger.warn("Deduplicated " + count + " references.");
 171                 }
 172
 173
 174                 System.exit(0);
 175
 176         }
 177
 178     /**
 179      * @param source
 180      * @param config
 181      * @param myImport
 182      */
 183     private void doSource(URI source, CubaImportConfigurator config,
 184             CdmDefaultImport<CubaImportConfigurator> myImport, boolean doVocabularies) {
 185         config.setSource(source);
 186         String message = "Start import from ("+ source.toString() + ") ...";
 187         System.out.println(message);
 188         logger.warn(message);
 189         config.setSourceReference(getSourceReference(sourceReferenceTitle));
 190         config.setDoVocabularies(doVocabularies);
 191         myImport.invoke(config);
 192
 193         if (doVocabularies){
 194             FeatureTree tree = makeFeatureNodes(myImport.getCdmAppController().getTermService());
 195             myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
 196             this.doVocabularies = false;
 197         }
 198         System.out.println("End import from ("+ source.toString() + ")...");
 199     }
 200
 201         private Reference<?> getSourceReference(String string) {
 202                 Reference<?> result = ReferenceFactory.newGeneric();
 203                 result.setTitleCache(string, true);
 204                 return result;
 205         }
 206
 207         private FeatureTree makeFeatureNodes(ITermService service){
 208 //              CyprusTransformer transformer = new CyprusTransformer();
 209
 210                 FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);
 211                 result.setTitleCache("Cuba Feature Tree", true);
 212                 FeatureNode root = result.getRoot();
 213                 FeatureNode newNode;
 214
 215 //              newNode = FeatureNode.NewInstance(Feature.STATUS());
 216 //              root.addChild(newNode);
 217
 218                 newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 219                 root.addChild(newNode);
 220
 221                 Feature featurAltFam = (Feature)service.find(CubaTransformer.uuidAlternativeFamily);
 222                 newNode = FeatureNode.NewInstance(featurAltFam);
 223                 root.addChild(newNode);
 224
 225             Feature featurAltFam2 = (Feature)service.find(CubaTransformer.uuidAlternativeFamily2);
 226             newNode = FeatureNode.NewInstance(featurAltFam2);
 227             root.addChild(newNode);
 228
 229 //              newNode = FeatureNode.NewInstance(Feature.SYSTEMATICS());
 230 //              root.addChild(newNode);
 231
 232                 //user defined features
 233 //              String [] featureList = new String[]{"Red Book", "Endemism"};
 234 //              addFeataureNodesByStringList(featureList, root, transformer, service);
 235
 236                 return result;
 237         }
 238
 239
 240         //Monocots
 241         public static URI monocots() {
 242             return URI.create("file:////BGBM-PESIHPC/Cuba/Monocot.xlsx");
 243         }
 244         //Cyperaceae
 245         public static URI cyperaceae() {
 246             return URI.create("file:////BGBM-PESIHPC/Cuba/Cyper_Poaceae.xlsx");
 247         }
 248     //Fabaceae
 249     public static URI fabaceae() {
 250         return URI.create("file:////BGBM-PESIHPC/Cuba/Fabaceae.xlsx");
 251     }
 252     //Urticaceae
 253     public static URI urticaceae() {
 254         return URI.create("file:////BGBM-PESIHPC/Cuba/Urticaceae.xlsx");
 255     }
 256     //Asteraceae
 257     public static URI asteraceae() {
 258         return URI.create("file:////BGBM-PESIHPC/Cuba/Asteraceae.xlsx");
 259     }
 260     //Convolvulaceae
 261     public static URI convolvulaceae() {
 262         return URI.create("file:////BGBM-PESIHPC/Cuba/Convolvulaceae.xlsx");
 263     }
 264     //dicot A-C
 265     public static URI dicotA_C() {
 266         return URI.create("file:////BGBM-PESIHPC/Cuba/dicotA_C.xlsx");
 267     }
 268     //dicot D-M
 269     public static URI dicotD_M() {
 270         return URI.create("file:////BGBM-PESIHPC/Cuba/dicotD_M.xlsx");
 271     }
 272     //dicot N-Z
 273     public static URI dicotN_Z() {
 274         return URI.create("file:////BGBM-PESIHPC/Cuba/dicotN_Z.xlsx");
 275     }
 276     //Euphorbiaceae
 277     public static URI euphorbiaceae() {
 278         return URI.create("file:////BGBM-PESIHPC/Cuba/Euphorbiaceae.xlsx");
 279     }
 280     //Gymnospermae
 281     public static URI gymnospermae() {
 282         return URI.create("file:////BGBM-PESIHPC/Cuba/gymnospermae.xlsx");
 283     }
 284     //Lam.Verbenaceae
 285     public static URI lamVerbenaceae() {
 286         return URI.create("file:////BGBM-PESIHPC/Cuba/Lam_Verbenaceae.xlsx");
 287     }
 288     //Malpighiaceae
 289     public static URI malpighiaceae() {
 290         return URI.create("file:////BGBM-PESIHPC/Cuba/Malpighiaceae.xlsx");
 291     }
 292     //Melastomataceae
 293     public static URI melastomataceae() {
 294         return URI.create("file:////BGBM-PESIHPC/Cuba/Melastomataceae.xlsx");
 295     }
 296     //Myrtaceae
 297     public static URI myrtaceae() {
 298         return URI.create("file:////BGBM-PESIHPC/Cuba/Myrtaceae.xlsx");
 299     }
 300     //Orchidaceae
 301     public static URI orchidaceae() {
 302         return URI.create("file:////BGBM-PESIHPC/Cuba/Orchidaceae.xlsx");
 303     }
 304     //Rubiaceae
 305     public static URI rubiaceae() {
 306         return URI.create("file:////BGBM-PESIHPC/Cuba/Rubiaceae.xlsx");
 307     }
 308
 309         /**
 310          * @param args
 311          */
 312         public static void main(String[] args) {
 313             CubaActivator me = new CubaActivator();
 314                 me.doImport(cdmDestination);
 315         }
 316
 317 }