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.ICdmRepository;
  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_local_cuba();
  47 //  static final ICdmDataSource cdmDestination = CdmDestinations.cdm_production_flora_cuba();
  48
  49         static boolean invers = true;
  50
  51     boolean doAsteraceae = include;
  52     boolean doConvolvulaceae = include;
  53     boolean doCyperaceae = include;
  54     boolean doDicotA_C = include;
  55     boolean doDicotD_M = include;
  56     boolean doDicotN_Z = include;
  57     boolean doEuphorbiaceae = include;
  58     boolean doFabaceae = include;
  59     boolean doGymnospermae = include;
  60     boolean doLamVerbenaceae = include;
  61     boolean doMalpighiaceae = include;
  62     boolean doMelastomataceae = include;
  63     boolean doMonocots = include;
  64     boolean doMyrtaceae = include;
  65     boolean doOrchidaceae = include;
  66     boolean doRubiaceae = include;
  67     boolean doUrticaceae = include;
  68     boolean doPteridophyta = !include;
  69
  70     static boolean include = !invers;
  71
  72
  73         //feature tree uuid
  74         public static final UUID featureTreeUuid = UUID.fromString("dad6b9b5-693f-4367-a7aa-076cc9c99476");
  75
  76         //classification
  77         static final UUID classificationUuid = UUID.fromString("5de394de-9c76-4b97-b04d-71be31c7f44b");
  78         private static final String classificationName = "Cuba Checklist";
  79
  80         static final String sourceReferenceTitle = "Cuba Checklist Word Documents";
  81
  82         //check - import
  83         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  84
  85         boolean doVocabularies = (hbm2dll == DbSchemaValidation.CREATE);
  86         static final boolean doTaxa = true;
  87         static final boolean doDeduplicate = false;
  88
  89         static final boolean doAltFlorasSanchez2017 = true;
  90         static final boolean doAltFlorasFRC = true;
  91         static final boolean doAltFlorasFC = false;
  92         static final boolean doAltFlorasAS = false;
  93
  94
  95         private void doImport(ICdmDataSource cdmDestination){
  96
  97             URI source = monocots();  //just any
  98
  99                 //make Source
 100                 CubaImportConfigurator config= CubaImportConfigurator.NewInstance(source, cdmDestination);
 101                 config.setClassificationUuid(classificationUuid);
 102         config.setClassificationName(classificationName);
 103         config.setCheck(check);
 104 //              config.setDoDistribution(doDistribution);
 105                 config.setDoTaxa(doTaxa);
 106                 config.setDbSchemaValidation(hbm2dll);
 107                 config.setSourceReferenceTitle(sourceReferenceTitle);
 108                 config.setDoVocabularies(doVocabularies);
 109                 config.setDoAltFlorasAS(doAltFlorasAS);
 110                 config.setDoAltFlorasFC(doAltFlorasFC);
 111                 config.setDoAltFlorasFRC(doAltFlorasFRC);
 112                 config.setDoAltFlorasSanchez2017(doAltFlorasSanchez2017);
 113
 114                 CdmDefaultImport<CubaImportConfigurator> myImport = new CdmDefaultImport<>();
 115
 116
 117                 //...
 118         if (doAsteraceae){
 119             doSingleSource(asteraceae(), config, myImport, doVocabularies);
 120         }
 121         if (doConvolvulaceae){
 122             doSingleSource(convolvulaceae(), config, myImport, doVocabularies);
 123         }
 124         if (doCyperaceae){
 125             doSingleSource(cyperaceae(), config, myImport, doVocabularies);
 126         }
 127         if (doDicotA_C){
 128             doSingleSource(dicotA_C(), config, myImport, doVocabularies);
 129         }
 130         if (doDicotD_M){
 131             doSingleSource(dicotD_M(), config, myImport, doVocabularies);
 132         }
 133         if (doDicotN_Z){
 134             doSingleSource(dicotN_Z(), config, myImport, doVocabularies);
 135         }
 136         if (doEuphorbiaceae){
 137             doSingleSource(euphorbiaceae(), config, myImport, doVocabularies);
 138         }
 139         if (doFabaceae){
 140             doSingleSource(fabaceae(), config, myImport, doVocabularies);
 141         }
 142         if (doGymnospermae){
 143             doSingleSource(gymnospermae(), config, myImport, doVocabularies);
 144         }
 145         if (doLamVerbenaceae){
 146             doSingleSource(lamVerbenaceae(), config, myImport, doVocabularies);
 147         }
 148         if (doMalpighiaceae){
 149             doSingleSource(malpighiaceae(), config, myImport, doVocabularies);
 150         }
 151         if (doMelastomataceae){
 152             doSingleSource(melastomataceae(), config, myImport, doVocabularies);
 153         }
 154         if (doMonocots){
 155             doSingleSource(monocots(), config, myImport, doVocabularies);
 156         }
 157         if (doMyrtaceae){
 158             doSingleSource(myrtaceae(), config, myImport, doVocabularies);
 159         }
 160         if (doOrchidaceae){
 161             doSingleSource(orchidaceae(), config, myImport, doVocabularies);
 162         }
 163         if (doRubiaceae){
 164             doSingleSource(rubiaceae(), config, myImport, doVocabularies);
 165         }
 166         if (doUrticaceae){
 167             doSingleSource(urticaceae(), config, myImport, doVocabularies);
 168         }
 169         if (doPteridophyta){
 170             doSingleSource(pteridophyta(), config, myImport, doVocabularies);
 171         }
 172
 173
 174                 //deduplicate
 175                 if (doDeduplicate){
 176                     logger.warn("Start deduplication ...");
 177
 178                     ICdmRepository app = myImport.getCdmAppController();
 179                         if (app == null){
 180                 app = CdmApplicationController.NewInstance(cdmDestination, hbm2dll, false);
 181             }
 182                         int count = app.getAgentService().deduplicate(Person.class, null, null);
 183                         logger.warn("Deduplicated " + count + " persons.");
 184 //                      count = app.getAgentService().deduplicate(Team.class, null, null);
 185 //                      logger.warn("Deduplicated " + count + " teams.");
 186 //                      count = app.getReferenceService().deduplicate(Reference.class, null, null);
 187 //                      logger.warn("Deduplicated " + count + " references.");
 188                 }
 189
 190                 System.exit(0);
 191
 192         }
 193
 194     /**
 195      * @param source
 196      * @param config
 197      * @param myImport
 198      */
 199     private void doSingleSource(URI source, CubaImportConfigurator config,
 200             CdmDefaultImport<CubaImportConfigurator> myImport, boolean doVocabularies) {
 201         config.setSource(source);
 202         String fileName = source.toString();
 203         fileName = fileName.substring(fileName.lastIndexOf("/") + 1 );
 204
 205         String message = "Start import from ("+ fileName + ") ...";
 206         System.out.println(message);
 207         logger.warn(message);
 208         config.setSourceReference(getSourceReference(fileName));
 209         config.setDoVocabularies(doVocabularies);
 210         myImport.invoke(config);
 211
 212         if (doVocabularies){
 213             FeatureTree tree = makeFeatureNodes(myImport.getCdmAppController().getTermService());
 214             myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
 215             this.doVocabularies = false;
 216         }
 217         System.out.println("End import from ("+ source.toString() + ")...");
 218     }
 219
 220     private final Reference inRef = ReferenceFactory.newGeneric();
 221         private Reference getSourceReference(String string) {
 222                 Reference result = ReferenceFactory.newGeneric();
 223                 result.setTitleCache(string, true);
 224                 result.setInReference(inRef);
 225                 inRef.setTitleCache(sourceReferenceTitle, true);
 226                 return result;
 227         }
 228
 229         private FeatureTree makeFeatureNodes(ITermService service){
 230 //              CyprusTransformer transformer = new CyprusTransformer();
 231
 232                 FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);
 233                 result.setTitleCache("Cuba Feature Tree", true);
 234                 FeatureNode root = result.getRoot();
 235                 FeatureNode newNode;
 236
 237                 newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 238                 root.addChild(newNode);
 239
 240 //              Feature featurAltFam = (Feature)service.find(CubaTransformer.uuidAlternativeFamily);
 241 //              newNode = FeatureNode.NewInstance(featurAltFam);
 242 //              root.addChild(newNode);
 243
 244             Feature featurAltFam2 = (Feature)service.find(CubaTransformer.uuidAlternativeFamily2);
 245             newNode = FeatureNode.NewInstance(featurAltFam2);
 246             root.addChild(newNode);
 247
 248                 return result;
 249         }
 250
 251
 252         //Monocots
 253         public static URI monocots() {
 254             return URI.create("file:////BGBM-PESIHPC/Cuba/Monocot.xlsx");
 255         }
 256         //Cyperaceae
 257         public static URI cyperaceae() {
 258             return URI.create("file:////BGBM-PESIHPC/Cuba/Cyper_Poaceae.xlsx");
 259         }
 260     //Fabaceae
 261     public static URI fabaceae() {
 262         return URI.create("file:////BGBM-PESIHPC/Cuba/Fabaceae.xlsx");
 263     }
 264     //Urticaceae
 265     public static URI urticaceae() {
 266         return URI.create("file:////BGBM-PESIHPC/Cuba/Urticaceae.xlsx");
 267     }
 268     //Asteraceae
 269     public static URI asteraceae() {
 270         return URI.create("file:////BGBM-PESIHPC/Cuba/Asteraceae.xlsx");
 271     }
 272     //Convolvulaceae
 273     public static URI convolvulaceae() {
 274         return URI.create("file:////BGBM-PESIHPC/Cuba/Convolvulaceae.xlsx");
 275     }
 276     //dicot A-C
 277     public static URI dicotA_C() {
 278         return URI.create("file:////BGBM-PESIHPC/Cuba/dicotA_C.xlsx");
 279     }
 280     //dicot D-M
 281     public static URI dicotD_M() {
 282         return URI.create("file:////BGBM-PESIHPC/Cuba/dicotD_M.xlsx");
 283     }
 284     //dicot N-Z
 285     public static URI dicotN_Z() {
 286         return URI.create("file:////BGBM-PESIHPC/Cuba/dicotN_Z.xlsx");
 287     }
 288     //Euphorbiaceae
 289     public static URI euphorbiaceae() {
 290         return URI.create("file:////BGBM-PESIHPC/Cuba/Euphorbiaceae.xlsx");
 291     }
 292     //Gymnospermae
 293     public static URI gymnospermae() {
 294         return URI.create("file:////BGBM-PESIHPC/Cuba/gymnospermae.xlsx");
 295     }
 296     //Lam.Verbenaceae
 297     public static URI lamVerbenaceae() {
 298         return URI.create("file:////BGBM-PESIHPC/Cuba/Lam_Verbenaceae.xlsx");
 299     }
 300     //Malpighiaceae
 301     public static URI malpighiaceae() {
 302         return URI.create("file:////BGBM-PESIHPC/Cuba/Malpighiaceae.xlsx");
 303     }
 304     //Melastomataceae
 305     public static URI melastomataceae() {
 306         return URI.create("file:////BGBM-PESIHPC/Cuba/Melastomataceae.xlsx");
 307     }
 308     //Myrtaceae
 309     public static URI myrtaceae() {
 310         return URI.create("file:////BGBM-PESIHPC/Cuba/Myrtaceae.xlsx");
 311     }
 312     //Orchidaceae
 313     public static URI orchidaceae() {
 314         return URI.create("file:////BGBM-PESIHPC/Cuba/Orchidaceae.xlsx");
 315     }
 316     //Rubiaceae
 317     public static URI rubiaceae() {
 318         return URI.create("file:////BGBM-PESIHPC/Cuba/Rubiaceae.xlsx");
 319     }
 320     //Rubiaceae
 321     public static URI pteridophyta() {
 322         return URI.create("file:////BGBM-PESIHPC/Cuba/Pteridophyta.xlsx");
 323     }
 324
 325         /**
 326          * @param args
 327          */
 328         public static void main(String[] args) {
 329             CubaActivator me = new CubaActivator();
 330                 me.doImport(cdmDestination);
 331             System.exit(0);
 332         }
 333
 334 }