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.CdmApplicationDefaultController;
  20 import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
  21 import eu.etaxonomy.cdm.api.application.ICdmApplicationDefaultConfiguration;
  22 import eu.etaxonomy.cdm.api.service.ITermService;
  23 import eu.etaxonomy.cdm.common.monitor.DefaultProgressMonitor;
  24 import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
  25 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  26 import eu.etaxonomy.cdm.database.ICdmDataSource;
  27 import eu.etaxonomy.cdm.database.update.CdmUpdater;
  28 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  29 import eu.etaxonomy.cdm.io.common.CdmImportBase.TermMatchMode;
  30 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  31 import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
  32 import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
  33 import eu.etaxonomy.cdm.io.eflora.EfloraImportConfigurator;
  34 import eu.etaxonomy.cdm.io.eflora.centralAfrica.ericaceae.CentralAfricaEricaceaeImportConfigurator;
  35 import eu.etaxonomy.cdm.io.eflora.centralAfrica.ericaceae.CentralAfricaEricaceaeTransformer;
  36 import eu.etaxonomy.cdm.io.specimen.excel.in.SpecimenCdmExcelImportConfigurator;
  37 import eu.etaxonomy.cdm.model.agent.Team;
  38 import eu.etaxonomy.cdm.model.common.Language;
  39 import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
  40 import eu.etaxonomy.cdm.model.common.TermType;
  41 import eu.etaxonomy.cdm.model.description.Feature;
  42 import eu.etaxonomy.cdm.model.description.FeatureNode;
  43 import eu.etaxonomy.cdm.model.description.FeatureTree;
  44 import eu.etaxonomy.cdm.model.description.PolytomousKey;
  45 import eu.etaxonomy.cdm.model.location.NamedArea;
  46 import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
  47 import eu.etaxonomy.cdm.model.location.NamedAreaType;
  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.ericacea_specimen_local();
  64
  65
  66 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_andreasM3();
  67 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_preview();
  68 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_production();
  69         static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  70 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_postgres_CdmTest();
  71 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
  72 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_jaxb();
  73 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_edit_cichorieae_preview();
  74 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_campanulaceae_production();
  75
  76         //feature tree uuid
  77         public static final UUID featureTreeUuid = UUID.fromString("051d35ee-22f1-42d8-be07-9e9bfec5bcf7");
  78
  79         public static UUID defaultLanguageUuid = Language.uuidFrench;
  80
  81         //classification
  82         static final UUID classificationUuid = UUID.fromString("10e5efcc-6e13-4abc-ad42-e0b46e50cbe7");
  83
  84         //check - import
  85         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  86
  87         static boolean doPrintKeys = false;
  88
  89         //taxa
  90         private boolean includeEricaceae = true;
  91         static final boolean doTaxa = true;
  92         static final boolean doDeduplicate = false;
  93
  94
  95         private boolean doNewNamedAreas = false;
  96         private boolean doFeatureTree = false;
  97
  98         private boolean doSpecimen = false;
  99         private TermMatchMode specimenAreaMatchMode = TermMatchMode.UUID_ABBREVLABEL;
 100
 101
 102         private void doImport(ICdmDataSource cdmDestination){
 103
 104                 CdmUpdater su = CdmUpdater.NewInstance();
 105                 IProgressMonitor monitor = DefaultProgressMonitor.NewInstance();
 106 //
 107 //              try {
 108 //                      su.updateToCurrentVersion(cdmDestination, monitor);
 109 //              } catch (Exception e) {
 110 //                      e.printStackTrace();
 111 //              }
 112 //              if (true){
 113 //                      return;
 114 //              }
 115
 116                 //make Source
 117                 CentralAfricaEricaceaeImportConfigurator config= CentralAfricaEricaceaeImportConfigurator.NewInstance(source, cdmDestination);
 118                 config.setClassificationUuid(classificationUuid);
 119                 config.setDoTaxa(doTaxa);
 120                 config.setCheck(check);
 121                 config.setDefaultLanguageUuid(defaultLanguageUuid);
 122                 config.setDoPrintKeys(doPrintKeys);
 123                 config.setDbSchemaValidation(hbm2dll);
 124
 125                 CdmDefaultImport<EfloraImportConfigurator> myImport = new CdmDefaultImport<EfloraImportConfigurator>();
 126
 127
 128                 //Ericaceae
 129                 if (includeEricaceae){
 130                         System.out.println("Start import from ("+ source.toString() + ") ...");
 131                         config.setSourceReference(getSourceReference(config.getSourceReferenceTitle()));
 132                         myImport.invoke(config);
 133                         System.out.println("End import from ("+ source.toString() + ")...");
 134                 }
 135
 136                 if (doFeatureTree){
 137                         FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
 138                         myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
 139                 }
 140
 141                 //check keys
 142                 if (doPrintKeys){
 143                         TransactionStatus tx = myImport.getCdmAppController().startTransaction();
 144                         List<PolytomousKey> keys = myImport.getCdmAppController().getPolytomousKeyService().list(PolytomousKey.class, null, null, null, null);
 145                         for(PolytomousKey key : keys){
 146                                 key.print(System.out);
 147                                 System.out.println();
 148                         }
 149                         myImport.getCdmAppController().commitTransaction(tx);
 150                 }
 151
 152                 //deduplicate
 153                 if (doDeduplicate){
 154                         ICdmApplicationDefaultConfiguration app = myImport.getCdmAppController();
 155                         if (app == null){
 156                                 app = CdmApplicationDefaultController.NewInstance(cdmDestination, hbm2dll, false);
 157                         }
 158                         app.getAgentService().updateTitleCache(Team.class, null, null, null);
 159                         return;
 160 //                      int count = app.getAgentService().deduplicate(Person.class, null, null);
 161 //
 162 //                      logger.warn("Deduplicated " + count + " persons.");
 163 ////                    count = app.getAgentService().deduplicate(Team.class, null, null);
 164 ////                    logger.warn("Deduplicated " + count + " teams.");
 165 //                      count = app.getReferenceService().deduplicate(Reference.class, null, null);
 166 //                      logger.warn("Deduplicated " + count + " references.");
 167                 }
 168
 169                 if(doNewNamedAreas){
 170                         newNamedAreas(myImport);
 171                 }
 172
 173                 if (doSpecimen){
 174                         logger.warn("Start specimen import");
 175                         ICdmApplicationDefaultConfiguration app = myImport.getCdmAppController();
 176                         SpecimenCdmExcelImportConfigurator specimenConfig= SpecimenCdmExcelImportConfigurator.NewInstance(specimenSource, cdmDestination);
 177                         specimenConfig.setCdmAppController((CdmApplicationDefaultController)app);
 178                         specimenConfig.setAreaMatchMode(specimenAreaMatchMode);
 179
 180                         config.setDbSchemaValidation(DbSchemaValidation.VALIDATE);
 181                         specimenConfig.setSourceReference(getSourceReference(specimenConfig.getSourceReferenceTitle()));
 182
 183                         CdmDefaultImport<SpecimenCdmExcelImportConfigurator> specimenImport = new CdmDefaultImport<SpecimenCdmExcelImportConfigurator>();
 184                         specimenImport.setCdmAppController(app);
 185                         specimenImport.invoke(specimenConfig);
 186
 187
 188                 }
 189                 return;
 190
 191
 192
 193         }
 194
 195         private void newNamedAreas(CdmDefaultImport<EfloraImportConfigurator> myImport) {
 196                 ICdmApplicationDefaultConfiguration app = myImport.getCdmAppController();
 197                 if (app == null){
 198                         app = CdmApplicationDefaultController.NewInstance(cdmDestination, hbm2dll, false);
 199                 }
 200                 TransactionStatus tx = app.startTransaction();
 201
 202                 OrderedTermVocabulary<NamedArea> areaVoc = OrderedTermVocabulary.NewInstance(TermType.NamedArea, "Phytogeographic Regions of Central Africa", "Phytogeographic Regions of Central Africa", "FdAC regions", null);
 203                 app.getVocabularyService().save(areaVoc);
 204
 205                 NamedAreaLevel level = NamedAreaLevel.NewInstance("Phytogeographic Regions of Central Africa", "Phytogeographic Regions of Central Africa", "FdAC regions");
 206                 ITermService termService = app.getTermService();
 207
 208                 termService.save(level);
 209
 210                 NamedArea area = NamedArea.NewInstance("C\u00F4tier", "C\u00F4tier", "I");
 211                 area.setLevel(level);
 212                 area.setType(NamedAreaType.NATURAL_AREA());
 213                 areaVoc.addTerm(area);
 214                 termService.save(area);
 215
 216
 217                 area = NamedArea.NewInstance("Mayumbe", "Mayumbe", "II");
 218                 area.setLevel(level);
 219                 area.setType(NamedAreaType.NATURAL_AREA());
 220                 areaVoc.addTerm(area);
 221                 termService.save(area);
 222
 223                 area = NamedArea.NewInstance("Bas-Congo", "Bas-Congo", "III");
 224                 area.setLevel(level);
 225                 area.setType(NamedAreaType.NATURAL_AREA());
 226                 areaVoc.addTerm(area);
 227                 termService.save(area);
 228
 229                 area = NamedArea.NewInstance("Kasai", "Kasai", "IV");
 230                 area.setLevel(level);
 231                 area.setType(NamedAreaType.NATURAL_AREA());
 232                 areaVoc.addTerm(area);
 233                 termService.save(area);
 234
 235                 area = NamedArea.NewInstance("Bas-Katanga", "Bas-Katanga", "V");
 236                 area.setLevel(level);
 237                 area.setType(NamedAreaType.NATURAL_AREA());
 238                 areaVoc.addTerm(area);
 239                 termService.save(area);
 240
 241                 area = NamedArea.NewInstance("Forestier Central", "Forestier Central", "VI");
 242                 area.setLevel(level);
 243                 area.setType(NamedAreaType.NATURAL_AREA());
 244                 areaVoc.addTerm(area);
 245                 termService.save(area);
 246
 247                 area = NamedArea.NewInstance("Ubangi-Uele", "Ubangi-Uele", "VII");
 248                 area.setLevel(level);
 249                 area.setType(NamedAreaType.NATURAL_AREA());
 250                 areaVoc.addTerm(area);
 251                 termService.save(area);
 252
 253                 area = NamedArea.NewInstance("Lac Albert", "Lac Albert", "VIII");
 254                 area.setLevel(level);
 255                 area.setType(NamedAreaType.NATURAL_AREA());
 256                 areaVoc.addTerm(area);
 257                 termService.save(area);
 258
 259                 area = NamedArea.NewInstance("Lacs \u00C9douard et Kivu", "Lacs \u00C9douard et Kivu", "IX");
 260                 area.setLevel(level);
 261                 area.setType(NamedAreaType.NATURAL_AREA());
 262                 areaVoc.addTerm(area);
 263                 termService.save(area);
 264
 265                 area = NamedArea.NewInstance("Rwanda-Burundi", "Rwanda-Burundi", "X");
 266                 area.setLevel(level);
 267                 area.setType(NamedAreaType.NATURAL_AREA());
 268                 areaVoc.addTerm(area);
 269                 termService.save(area);
 270
 271                 area = NamedArea.NewInstance("Haut-Katanga", "Haut-Katanga", "XI");
 272                 area.setLevel(level);
 273                 area.setType(NamedAreaType.NATURAL_AREA());
 274                 areaVoc.addTerm(area);
 275                 termService.save(area);
 276
 277                 app.getVocabularyService().save(areaVoc);
 278
 279                 app.commitTransaction(tx);
 280
 281         }
 282
 283         private Reference getSourceReference(String string) {
 284                 Reference result = ReferenceFactory.newGeneric();
 285                 result.setTitleCache(string);
 286                 return result;
 287         }
 288
 289         private FeatureTree makeFeatureNode(ITermService service){
 290                 CentralAfricaEricaceaeTransformer transformer = new CentralAfricaEricaceaeTransformer();
 291
 292                 FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);
 293                 result.setTitleCache("Central Africa Ericaceae Feature Tree");
 294                 FeatureNode root = result.getRoot();
 295                 FeatureNode newNode;
 296
 297                 newNode = FeatureNode.NewInstance(Feature.DESCRIPTION());
 298                 root.addChild(newNode);
 299
 300                 addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service);
 301
 302                 addFeataureNodesByStringList(generellDescriptionsList, root, transformer, service);
 303
 304
 305                 newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 306                 root.addChild(newNode);
 307
 308                 newNode = FeatureNode.NewInstance(Feature.ECOLOGY());
 309                 root.addChild(newNode);
 310                 addFeataureNodesByStringList(habitatEcologyList, root, transformer, service);
 311
 312                 newNode = FeatureNode.NewInstance(Feature.USES());
 313                 root.addChild(newNode);
 314
 315                 addFeataureNodesByStringList(chomosomesList, root, transformer, service);
 316
 317                 newNode = FeatureNode.NewInstance(Feature.COMMON_NAME());
 318                 root.addChild(newNode);
 319
 320                 newNode = FeatureNode.NewInstance(Feature.CITATION());
 321                 root.addChild(newNode);
 322
 323                 return result;
 324         }
 325
 326         private static String [] chomosomesList = new String[]{
 327                 "Chromosomes",
 328         };
 329
 330
 331         private static String [] habitatEcologyList = new String[]{
 332                 "Habitat",
 333                 "Habitat & Ecology"
 334         };
 335
 336
 337         private static String [] generellDescriptionsList = new String[]{
 338                 "Fossils",
 339                 "Morphology and anatomy",
 340                 "Morphology",
 341                 "Vegetative morphology and anatomy",
 342                 "Flower morphology",
 343                 "Palynology",
 344                 "Pollination",
 345                 "Pollen morphology",
 346                 "Life cycle",
 347                 "Fruits and embryology",
 348                 "Dispersal",
 349                 "Wood anatomy",
 350                 "Leaf anatomy",
 351                 "Chromosome numbers",
 352                 "Phytochemistry and Chemotaxonomy",
 353                 "Phytochemistry",
 354                 "Taxonomy",
 355         };
 356
 357         private static String [] descriptionFeatureList = new String[]{
 358                 "lifeform",
 359                 "Bark",
 360                 "Indumentum",
 361                 "endophytic body",
 362                 "flowering buds",
 363                 "Branchlets",
 364                 "Branches",
 365                 "Branch",
 366                 "Flowering branchlets",
 367                 "Trees",
 368                 "Twigs",
 369                 "stem",
 370                 "Stems",
 371                 "stem leaves",
 372                 "Leaves",
 373                 "flower-bearing stems",
 374                 "Petiole",
 375                 "Petiolules",
 376                 "Leaflets",
 377                 "Thyrsus",
 378                 "Thyrses",
 379                 "Inflorescences",
 380                 "Inflorescence",
 381                 "Young inflorescences",
 382                 "Bracts",
 383                 "Pedicels",
 384                 "flowering buds",
 385                 "scales",
 386                 "Buds",
 387                 "Flowers",
 388                 "Flower",
 389                 "Flowering",
 390                 "Stigma",
 391                 "perianth",
 392                 "Sepals",
 393                 "Sepal",
 394                 "Outer Sepals",
 395                 "Axillary",
 396                 "cymes",
 397                 "Calyx",
 398                 "Petal",
 399                 "Petals",
 400                 "perigone tube",
 401                 "Disc",
 402                 "corolla",
 403                 "Stamens",
 404                 "Staminodes",
 405                 "Ovary",
 406                 "Anthers",
 407                 "anther",
 408                 "Pistil",
 409                 "Pistillode",
 410                 "Ovules",
 411                 "androecium",
 412                 "gynoecium",
 413                 "Filaments",
 414                 "Style",
 415                 "annulus",
 416                 "female flowers",
 417                 "Male flowers",
 418                 "Female",
 419                 "Infructescences",    //order not consistent (sometimes before "Flowers")
 420                 "Fruit",
 421                 "Fruits",
 422                 "fruiting axes",
 423                 "drupes",
 424                 "Arillode",
 425                 "seed",
 426                 "Seeds",
 427                 "Seedling",
 428                 "flower tube",
 429                 "nutlets",
 430                 "pollen",
 431                 "secondary xylem",
 432                 "chromosome number",
 433
 434                 "figure",
 435                 "fig",
 436                 "figs",
 437
 438
 439
 440
 441         };
 442
 443         public void addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
 444                 try {
 445                         for (String featureString : featureStringList){
 446                         UUID featureUuid;
 447                         featureUuid = transformer.getFeatureUuid(featureString);
 448                         Feature feature = (Feature)termService.find(featureUuid);
 449                         if (feature != null){
 450                                 FeatureNode child = FeatureNode.NewInstance(feature);
 451                                 root.addChild(child);
 452                         }
 453                 }
 454                 } catch (UndefinedTransformerMethodException e) {
 455                         logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");
 456                 }
 457         }
 458
 459
 460
 461         /**
 462          * @param args
 463          */
 464         public static void main(String[] args) {
 465                 CentralAfricaEricaceaeActivator me = new CentralAfricaEricaceaeActivator();
 466                 me.doImport(cdmDestination);
 467         }
 468
 469 }