cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/CentralAfricaEricaceaeActivator.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.eflora;
  11
  12 import java.net.URI;
  13 import java.util.List;
  14 import java.util.UUID;
  15
  16 import org.apache.log4j.Logger;
  17 import org.springframework.transaction.TransactionStatus;
  18
  19 import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  20 import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
  21 import eu.etaxonomy.cdm.api.service.ITermService;
  22 import eu.etaxonomy.cdm.common.monitor.DefaultProgressMonitor;
  23 import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
  24 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  25 import eu.etaxonomy.cdm.database.ICdmDataSource;
  26 import eu.etaxonomy.cdm.database.update.CdmUpdater;
  27 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  28 import eu.etaxonomy.cdm.io.common.CdmImportBase.TermMatchMode;
  29 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  30 import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
  31 import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
  32 import eu.etaxonomy.cdm.io.eflora.EfloraImportConfigurator;
  33 import eu.etaxonomy.cdm.io.eflora.centralAfrica.ericaceae.CentralAfricaEricaceaeImportConfigurator;
  34 import eu.etaxonomy.cdm.io.eflora.centralAfrica.ericaceae.CentralAfricaEricaceaeTransformer;
  35 import eu.etaxonomy.cdm.io.specimen.excel.in.SpecimenCdmExcelImportConfigurator;
  36 import eu.etaxonomy.cdm.model.agent.Team;
  37 import eu.etaxonomy.cdm.model.common.Language;
  38 import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
  39 import eu.etaxonomy.cdm.model.common.TermType;
  40 import eu.etaxonomy.cdm.model.description.Feature;
  41 import eu.etaxonomy.cdm.model.description.FeatureNode;
  42 import eu.etaxonomy.cdm.model.description.FeatureTree;
  43 import eu.etaxonomy.cdm.model.description.PolytomousKey;
  44 import eu.etaxonomy.cdm.model.location.NamedArea;
  45 import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
  46 import eu.etaxonomy.cdm.model.location.NamedAreaType;
  47 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  48 import eu.etaxonomy.cdm.model.reference.Reference;
  49 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  50
  51 /**
  52  * @author a.mueller
  53  * @created 20.06.2008
  54  * @version 1.0
  55  */
  56 public class CentralAfricaEricaceaeActivator {
  57         private static final Logger logger = Logger.getLogger(CentralAfricaEricaceaeActivator.class);
  58
  59         //database validation status (create, update, validate ...)
  60         static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
  61         static final URI source = EfloraSources.ericacea_local();
  62
  63         static final URI specimenSource = EfloraSources.vittaria_specimen_pesiimport3();
  64
  65
  66         static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_local();
  67
  68 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_preview();
  69 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_production();
  70 //      static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  71 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_postgres_CdmTest();
  72 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
  73 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_campanulaceae_production();
  74
  75         //feature tree uuid
  76         public static final UUID featureTreeUuid = UUID.fromString("051d35ee-22f1-42d8-be07-9e9bfec5bcf7");
  77
  78         public static UUID defaultLanguageUuid = Language.uuidFrench;
  79
  80         //classification
  81         static final UUID classificationUuid = UUID.fromString("10e5efcc-6e13-4abc-ad42-e0b46e50cbe7");
  82
  83         NomenclaturalCode nc = NomenclaturalCode.ICNAFP;
  84
  85         //check - import
  86         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  87
  88         static boolean doPrintKeys = false;
  89
  90         //taxa
  91         private boolean includeEricaceae = false;
  92         static final boolean doTaxa = false;
  93         static final boolean doDeduplicate = false;
  94
  95
  96         private boolean doNewNamedAreas = false;
  97         private boolean doFeatureTree = false;
  98
  99         private boolean doSpecimen = true;
 100         private TermMatchMode specimenAreaMatchMode = TermMatchMode.UUID_ABBREVLABEL;
 101
 102
 103         private void doImport(ICdmDataSource cdmDestination){
 104
 105 //              CdmUpdater su = CdmUpdater.NewInstance();
 106 //              IProgressMonitor monitor = DefaultProgressMonitor.NewInstance();
 107 //
 108 //              try {
 109 //                      su.updateToCurrentVersion(cdmDestination, monitor);
 110 //              } catch (Exception e) {
 111 //                      e.printStackTrace();
 112 //              }
 113 //              if (true){
 114 //                      return;
 115 //              }
 116
 117                 //make Source
 118                 CentralAfricaEricaceaeImportConfigurator config= CentralAfricaEricaceaeImportConfigurator.NewInstance(source, cdmDestination);
 119                 config.setClassificationUuid(classificationUuid);
 120                 config.setDoTaxa(doTaxa);
 121                 config.setCheck(check);
 122                 config.setDefaultLanguageUuid(defaultLanguageUuid);
 123                 config.setDoPrintKeys(doPrintKeys);
 124                 config.setDbSchemaValidation(hbm2dll);
 125                 config.setNomenclaturalCode(nc);
 126
 127                 CdmDefaultImport<EfloraImportConfigurator> myImport = new CdmDefaultImport<EfloraImportConfigurator>();
 128
 129
 130                 //Ericaceae
 131                 if (includeEricaceae){
 132                         System.out.println("Start import from ("+ source.toString() + ") ...");
 133                         config.setSourceReference(getSourceReference(config.getSourceReferenceTitle()));
 134                         myImport.invoke(config);
 135                         System.out.println("End import from ("+ source.toString() + ")...");
 136                 }
 137
 138                 if (doFeatureTree){
 139                         FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
 140                         myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
 141                 }
 142
 143                 //check keys
 144                 if (doPrintKeys){
 145                         TransactionStatus tx = myImport.getCdmAppController().startTransaction();
 146                         List<PolytomousKey> keys = myImport.getCdmAppController().getPolytomousKeyService().list(PolytomousKey.class, null, null, null, null);
 147                         for(PolytomousKey key : keys){
 148                                 key.print(System.out);
 149                                 System.out.println();
 150                         }
 151                         myImport.getCdmAppController().commitTransaction(tx);
 152                 }
 153
 154                 //deduplicate
 155                 if (doDeduplicate){
 156                         ICdmApplicationConfiguration app = myImport.getCdmAppController();
 157                         if (app == null){
 158                                 app = CdmApplicationController.NewInstance(cdmDestination, hbm2dll, false);
 159                         }
 160                         app.getAgentService().updateTitleCache(Team.class, null, null, null);
 161                         return;
 162 //                      int count = app.getAgentService().deduplicate(Person.class, null, null);
 163 //
 164 //                      logger.warn("Deduplicated " + count + " persons.");
 165 ////                    count = app.getAgentService().deduplicate(Team.class, null, null);
 166 ////                    logger.warn("Deduplicated " + count + " teams.");
 167 //                      count = app.getReferenceService().deduplicate(Reference.class, null, null);
 168 //                      logger.warn("Deduplicated " + count + " references.");
 169                 }
 170
 171                 if(doNewNamedAreas){
 172                         newNamedAreas(myImport);
 173                 }
 174
 175                 if (doSpecimen){
 176                         logger.warn("Start specimen import");
 177                         ICdmApplicationConfiguration app = myImport.getCdmAppController();
 178                         SpecimenCdmExcelImportConfigurator specimenConfig= SpecimenCdmExcelImportConfigurator.NewInstance(specimenSource, cdmDestination);
 179                         specimenConfig.setCdmAppController((CdmApplicationController)app);
 180                         specimenConfig.setAreaMatchMode(specimenAreaMatchMode);
 181                         specimenConfig.setNomenclaturalCode(nc);
 182
 183                         config.setDbSchemaValidation(DbSchemaValidation.VALIDATE);
 184                         specimenConfig.setSourceReference(getSourceReference(specimenConfig.getSourceReferenceTitle()));
 185
 186                         CdmDefaultImport<SpecimenCdmExcelImportConfigurator> specimenImport = new CdmDefaultImport<SpecimenCdmExcelImportConfigurator>();
 187                         specimenImport.setCdmAppController(app);
 188                         specimenImport.invoke(specimenConfig);
 189
 190                 }
 191                 return;
 192
 193
 194
 195         }
 196
 197         private void newNamedAreas(CdmDefaultImport<EfloraImportConfigurator> myImport) {
 198                 ICdmApplicationConfiguration app = myImport.getCdmAppController();
 199                 if (app == null){
 200                         app = CdmApplicationController.NewInstance(cdmDestination, hbm2dll, false);
 201                 }
 202                 TransactionStatus tx = app.startTransaction();
 203
 204                 OrderedTermVocabulary<NamedArea> areaVoc = OrderedTermVocabulary.NewInstance(TermType.NamedArea, "Phytogeographic Regions of Central Africa", "Phytogeographic Regions of Central Africa", "FdAC regions", null);
 205                 app.getVocabularyService().save(areaVoc);
 206
 207                 NamedAreaLevel level = NamedAreaLevel.NewInstance("Phytogeographic Regions of Central Africa", "Phytogeographic Regions of Central Africa", "FdAC regions");
 208                 ITermService termService = app.getTermService();
 209
 210                 termService.save(level);
 211
 212                 NamedArea area = NamedArea.NewInstance("C\u00F4tier", "C\u00F4tier", "I");
 213                 area.setLevel(level);
 214                 area.setType(NamedAreaType.NATURAL_AREA());
 215                 areaVoc.addTerm(area);
 216                 termService.save(area);
 217
 218
 219                 area = NamedArea.NewInstance("Mayumbe", "Mayumbe", "II");
 220                 area.setLevel(level);
 221                 area.setType(NamedAreaType.NATURAL_AREA());
 222                 areaVoc.addTerm(area);
 223                 termService.save(area);
 224
 225                 area = NamedArea.NewInstance("Bas-Congo", "Bas-Congo", "III");
 226                 area.setLevel(level);
 227                 area.setType(NamedAreaType.NATURAL_AREA());
 228                 areaVoc.addTerm(area);
 229                 termService.save(area);
 230
 231                 area = NamedArea.NewInstance("Kasai", "Kasai", "IV");
 232                 area.setLevel(level);
 233                 area.setType(NamedAreaType.NATURAL_AREA());
 234                 areaVoc.addTerm(area);
 235                 termService.save(area);
 236
 237                 area = NamedArea.NewInstance("Bas-Katanga", "Bas-Katanga", "V");
 238                 area.setLevel(level);
 239                 area.setType(NamedAreaType.NATURAL_AREA());
 240                 areaVoc.addTerm(area);
 241                 termService.save(area);
 242
 243                 area = NamedArea.NewInstance("Forestier Central", "Forestier Central", "VI");
 244                 area.setLevel(level);
 245                 area.setType(NamedAreaType.NATURAL_AREA());
 246                 areaVoc.addTerm(area);
 247                 termService.save(area);
 248
 249                 area = NamedArea.NewInstance("Ubangi-Uele", "Ubangi-Uele", "VII");
 250                 area.setLevel(level);
 251                 area.setType(NamedAreaType.NATURAL_AREA());
 252                 areaVoc.addTerm(area);
 253                 termService.save(area);
 254
 255                 area = NamedArea.NewInstance("Lac Albert", "Lac Albert", "VIII");
 256                 area.setLevel(level);
 257                 area.setType(NamedAreaType.NATURAL_AREA());
 258                 areaVoc.addTerm(area);
 259                 termService.save(area);
 260
 261                 area = NamedArea.NewInstance("Lacs \u00C9douard et Kivu", "Lacs \u00C9douard et Kivu", "IX");
 262                 area.setLevel(level);
 263                 area.setType(NamedAreaType.NATURAL_AREA());
 264                 areaVoc.addTerm(area);
 265                 termService.save(area);
 266
 267                 area = NamedArea.NewInstance("Rwanda-Burundi", "Rwanda-Burundi", "X");
 268                 area.setLevel(level);
 269                 area.setType(NamedAreaType.NATURAL_AREA());
 270                 areaVoc.addTerm(area);
 271                 termService.save(area);
 272
 273                 area = NamedArea.NewInstance("Haut-Katanga", "Haut-Katanga", "XI");
 274                 area.setLevel(level);
 275                 area.setType(NamedAreaType.NATURAL_AREA());
 276                 areaVoc.addTerm(area);
 277                 termService.save(area);
 278
 279                 app.getVocabularyService().save(areaVoc);
 280
 281                 app.commitTransaction(tx);
 282
 283         }
 284
 285         private Reference<?> getSourceReference(String string) {
 286                 Reference<?> result = ReferenceFactory.newGeneric();
 287                 result.setTitleCache(string, true);
 288                 return result;
 289         }
 290
 291         private FeatureTree makeFeatureNode(ITermService service){
 292                 CentralAfricaEricaceaeTransformer transformer = new CentralAfricaEricaceaeTransformer();
 293
 294                 FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);
 295                 result.setTitleCache("Central Africa Ericaceae Feature Tree", true);
 296                 FeatureNode root = result.getRoot();
 297                 FeatureNode newNode;
 298
 299                 newNode = FeatureNode.NewInstance(Feature.DESCRIPTION());
 300                 root.addChild(newNode);
 301
 302                 addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service);
 303
 304                 addFeataureNodesByStringList(generellDescriptionsList, root, transformer, service);
 305
 306
 307                 newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 308                 root.addChild(newNode);
 309
 310                 newNode = FeatureNode.NewInstance(Feature.ECOLOGY());
 311                 root.addChild(newNode);
 312                 addFeataureNodesByStringList(habitatEcologyList, root, transformer, service);
 313
 314                 newNode = FeatureNode.NewInstance(Feature.USES());
 315                 root.addChild(newNode);
 316
 317                 addFeataureNodesByStringList(chomosomesList, root, transformer, service);
 318
 319                 newNode = FeatureNode.NewInstance(Feature.COMMON_NAME());
 320                 root.addChild(newNode);
 321
 322                 newNode = FeatureNode.NewInstance(Feature.CITATION());
 323                 root.addChild(newNode);
 324
 325                 return result;
 326         }
 327
 328         private static String [] chomosomesList = new String[]{
 329                 "Chromosomes",
 330         };
 331
 332
 333         private static String [] habitatEcologyList = new String[]{
 334                 "Habitat",
 335                 "Habitat & Ecology"
 336         };
 337
 338
 339         private static String [] generellDescriptionsList = new String[]{
 340                 "Fossils",
 341                 "Morphology and anatomy",
 342                 "Morphology",
 343                 "Vegetative morphology and anatomy",
 344                 "Flower morphology",
 345                 "Palynology",
 346                 "Pollination",
 347                 "Pollen morphology",
 348                 "Life cycle",
 349                 "Fruits and embryology",
 350                 "Dispersal",
 351                 "Wood anatomy",
 352                 "Leaf anatomy",
 353                 "Chromosome numbers",
 354                 "Phytochemistry and Chemotaxonomy",
 355                 "Phytochemistry",
 356                 "Taxonomy",
 357         };
 358
 359         private static String [] descriptionFeatureList = new String[]{
 360                 "lifeform",
 361                 "Bark",
 362                 "Indumentum",
 363                 "endophytic body",
 364                 "flowering buds",
 365                 "Branchlets",
 366                 "Branches",
 367                 "Branch",
 368                 "Flowering branchlets",
 369                 "Trees",
 370                 "Twigs",
 371                 "stem",
 372                 "Stems",
 373                 "stem leaves",
 374                 "Leaves",
 375                 "flower-bearing stems",
 376                 "Petiole",
 377                 "Petiolules",
 378                 "Leaflets",
 379                 "Thyrsus",
 380                 "Thyrses",
 381                 "Inflorescences",
 382                 "Inflorescence",
 383                 "Young inflorescences",
 384                 "Bracts",
 385                 "Pedicels",
 386                 "flowering buds",
 387                 "scales",
 388                 "Buds",
 389                 "Flowers",
 390                 "Flower",
 391                 "Flowering",
 392                 "Stigma",
 393                 "perianth",
 394                 "Sepals",
 395                 "Sepal",
 396                 "Outer Sepals",
 397                 "Axillary",
 398                 "cymes",
 399                 "Calyx",
 400                 "Petal",
 401                 "Petals",
 402                 "perigone tube",
 403                 "Disc",
 404                 "corolla",
 405                 "Stamens",
 406                 "Staminodes",
 407                 "Ovary",
 408                 "Anthers",
 409                 "anther",
 410                 "Pistil",
 411                 "Pistillode",
 412                 "Ovules",
 413                 "androecium",
 414                 "gynoecium",
 415                 "Filaments",
 416                 "Style",
 417                 "annulus",
 418                 "female flowers",
 419                 "Male flowers",
 420                 "Female",
 421                 "Infructescences",    //order not consistent (sometimes before "Flowers")
 422                 "Fruit",
 423                 "Fruits",
 424                 "fruiting axes",
 425                 "drupes",
 426                 "Arillode",
 427                 "seed",
 428                 "Seeds",
 429                 "Seedling",
 430                 "flower tube",
 431                 "nutlets",
 432                 "pollen",
 433                 "secondary xylem",
 434                 "chromosome number",
 435
 436                 "figure",
 437                 "fig",
 438                 "figs",
 439
 440
 441
 442
 443         };
 444
 445         public void addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
 446                 try {
 447                         for (String featureString : featureStringList){
 448                         UUID featureUuid;
 449                         featureUuid = transformer.getFeatureUuid(featureString);
 450                         Feature feature = (Feature)termService.find(featureUuid);
 451                         if (feature != null){
 452                                 FeatureNode child = FeatureNode.NewInstance(feature);
 453                                 root.addChild(child);
 454                         }
 455                 }
 456                 } catch (UndefinedTransformerMethodException e) {
 457                         logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");
 458                 }
 459         }
 460
 461
 462
 463         /**
 464          * @param args
 465          */
 466         public static void main(String[] args) {
 467                 CentralAfricaEricaceaeActivator me = new CentralAfricaEricaceaeActivator();
 468                 me.doImport(cdmDestination);
 469         }
 470
 471 }