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.description.Feature;
  40 import eu.etaxonomy.cdm.model.description.FeatureNode;
  41 import eu.etaxonomy.cdm.model.description.FeatureTree;
  42 import eu.etaxonomy.cdm.model.description.PolytomousKey;
  43 import eu.etaxonomy.cdm.model.location.NamedArea;
  44 import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
  45 import eu.etaxonomy.cdm.model.location.NamedAreaType;
  46 import eu.etaxonomy.cdm.model.reference.Reference;
  47 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  48
  49 /**
  50  * @author a.mueller
  51  * @created 20.06.2008
  52  * @version 1.0
  53  */
  54 public class CentralAfricaEricaceaeActivator {
  55         private static final Logger logger = Logger.getLogger(CentralAfricaEricaceaeActivator.class);
  56
  57         //database validation status (create, update, validate ...)
  58         static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
  59         static final URI source = EfloraSources.ericacea_local();
  60
  61         static final URI specimenSource = EfloraSources.ericacea_specimen_local();
  62
  63
  64 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_andreasM3();
  65 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_preview();
  66 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_production();
  67         static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  68 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_postgres_CdmTest();
  69 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
  70 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_jaxb();
  71 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_edit_cichorieae_preview();
  72 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_campanulaceae_production();
  73
  74         //feature tree uuid
  75         public static final UUID featureTreeUuid = UUID.fromString("051d35ee-22f1-42d8-be07-9e9bfec5bcf7");
  76
  77         public static UUID defaultLanguageUuid = Language.uuidFrench;
  78
  79         //classification
  80         static final UUID classificationUuid = UUID.fromString("10e5efcc-6e13-4abc-ad42-e0b46e50cbe7");
  81
  82         //check - import
  83         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  84
  85         static boolean doPrintKeys = false;
  86
  87         //taxa
  88         private boolean includeEricaceae = true;
  89         static final boolean doTaxa = true;
  90         static final boolean doDeduplicate = false;
  91
  92
  93         private boolean doNewNamedAreas = false;
  94         private boolean doFeatureTree = false;
  95
  96         private boolean doSpecimen = false;
  97         private TermMatchMode specimenAreaMatchMode = TermMatchMode.UUID_ABBREVLABEL;
  98
  99
 100         private void doImport(ICdmDataSource cdmDestination){
 101
 102                 CdmUpdater su = CdmUpdater.NewInstance();
 103                 IProgressMonitor monitor = DefaultProgressMonitor.NewInstance();
 104 //
 105 //              try {
 106 //                      su.updateToCurrentVersion(cdmDestination, monitor);
 107 //              } catch (Exception e) {
 108 //                      e.printStackTrace();
 109 //              }
 110 //              if (true){
 111 //                      return;
 112 //              }
 113
 114                 //make Source
 115                 CentralAfricaEricaceaeImportConfigurator config= CentralAfricaEricaceaeImportConfigurator.NewInstance(source, cdmDestination);
 116                 config.setClassificationUuid(classificationUuid);
 117                 config.setDoTaxa(doTaxa);
 118                 config.setCheck(check);
 119                 config.setDefaultLanguageUuid(defaultLanguageUuid);
 120                 config.setDoPrintKeys(doPrintKeys);
 121                 config.setDbSchemaValidation(hbm2dll);
 122
 123                 CdmDefaultImport<EfloraImportConfigurator> myImport = new CdmDefaultImport<EfloraImportConfigurator>();
 124
 125
 126                 //Ericaceae
 127                 if (includeEricaceae){
 128                         System.out.println("Start import from ("+ source.toString() + ") ...");
 129                         config.setSourceReference(getSourceReference(config.getSourceReferenceTitle()));
 130                         myImport.invoke(config);
 131                         System.out.println("End import from ("+ source.toString() + ")...");
 132                 }
 133
 134                 if (doFeatureTree){
 135                         FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
 136                         myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
 137                 }
 138
 139                 //check keys
 140                 if (doPrintKeys){
 141                         TransactionStatus tx = myImport.getCdmAppController().startTransaction();
 142                         List<PolytomousKey> keys = myImport.getCdmAppController().getPolytomousKeyService().list(PolytomousKey.class, null, null, null, null);
 143                         for(PolytomousKey key : keys){
 144                                 key.print(System.out);
 145                                 System.out.println();
 146                         }
 147                         myImport.getCdmAppController().commitTransaction(tx);
 148                 }
 149
 150                 //deduplicate
 151                 if (doDeduplicate){
 152                         ICdmApplicationConfiguration app = myImport.getCdmAppController();
 153                         if (app == null){
 154                                 app = CdmApplicationController.NewInstance(cdmDestination, hbm2dll, false);
 155                         }
 156                         app.getAgentService().updateTitleCache(Team.class, null, null, null);
 157                         return;
 158 //                      int count = app.getAgentService().deduplicate(Person.class, null, null);
 159 //
 160 //                      logger.warn("Deduplicated " + count + " persons.");
 161 ////                    count = app.getAgentService().deduplicate(Team.class, null, null);
 162 ////                    logger.warn("Deduplicated " + count + " teams.");
 163 //                      count = app.getReferenceService().deduplicate(Reference.class, null, null);
 164 //                      logger.warn("Deduplicated " + count + " references.");
 165                 }
 166
 167                 if(doNewNamedAreas){
 168                         newNamedAreas(myImport);
 169                 }
 170
 171                 if (doSpecimen){
 172                         logger.warn("Start specimen import");
 173                         ICdmApplicationConfiguration app = myImport.getCdmAppController();
 174                         SpecimenCdmExcelImportConfigurator specimenConfig= SpecimenCdmExcelImportConfigurator.NewInstance(specimenSource, cdmDestination);
 175                         specimenConfig.setCdmAppController((CdmApplicationController)app);
 176                         specimenConfig.setAreaMatchMode(specimenAreaMatchMode);
 177
 178                         config.setDbSchemaValidation(DbSchemaValidation.VALIDATE);
 179                         specimenConfig.setSourceReference(getSourceReference(specimenConfig.getSourceReferenceTitle()));
 180
 181                         CdmDefaultImport<SpecimenCdmExcelImportConfigurator> specimenImport = new CdmDefaultImport<SpecimenCdmExcelImportConfigurator>();
 182                         specimenImport.setCdmAppController(app);
 183                         specimenImport.invoke(specimenConfig);
 184
 185
 186                 }
 187                 return;
 188
 189
 190
 191         }
 192
 193         private void newNamedAreas(CdmDefaultImport<EfloraImportConfigurator> myImport) {
 194                 ICdmApplicationConfiguration app = myImport.getCdmAppController();
 195                 if (app == null){
 196                         app = CdmApplicationController.NewInstance(cdmDestination, hbm2dll, false);
 197                 }
 198                 TransactionStatus tx = app.startTransaction();
 199
 200                 OrderedTermVocabulary<NamedArea> voc = OrderedTermVocabulary.NewInstance("Phytogeographic Regions of Central Africa", "Phytogeographic Regions of Central Africa", "FdAC regions", null);
 201                 app.getVocabularyService().save(voc);
 202
 203                 NamedAreaLevel level = NamedAreaLevel.NewInstance("Phytogeographic Regions of Central Africa", "Phytogeographic Regions of Central Africa", "FdAC regions");
 204                 ITermService termService = app.getTermService();
 205
 206                 termService.save(level);
 207
 208                 NamedArea area = NamedArea.NewInstance("C\u00F4tier", "C\u00F4tier", "I");
 209                 area.setLevel(level);
 210                 area.setType(NamedAreaType.NATURAL_AREA());
 211                 voc.addTerm(area);
 212                 termService.save(area);
 213
 214
 215                 area = NamedArea.NewInstance("Mayumbe", "Mayumbe", "II");
 216                 area.setLevel(level);
 217                 area.setType(NamedAreaType.NATURAL_AREA());
 218                 voc.addTerm(area);
 219                 termService.save(area);
 220
 221                 area = NamedArea.NewInstance("Bas-Congo", "Bas-Congo", "III");
 222                 area.setLevel(level);
 223                 area.setType(NamedAreaType.NATURAL_AREA());
 224                 voc.addTerm(area);
 225                 termService.save(area);
 226
 227                 area = NamedArea.NewInstance("Kasai", "Kasai", "IV");
 228                 area.setLevel(level);
 229                 area.setType(NamedAreaType.NATURAL_AREA());
 230                 voc.addTerm(area);
 231                 termService.save(area);
 232
 233                 area = NamedArea.NewInstance("Bas-Katanga", "Bas-Katanga", "V");
 234                 area.setLevel(level);
 235                 area.setType(NamedAreaType.NATURAL_AREA());
 236                 voc.addTerm(area);
 237                 termService.save(area);
 238
 239                 area = NamedArea.NewInstance("Forestier Central", "Forestier Central", "VI");
 240                 area.setLevel(level);
 241                 area.setType(NamedAreaType.NATURAL_AREA());
 242                 voc.addTerm(area);
 243                 termService.save(area);
 244
 245                 area = NamedArea.NewInstance("Ubangi-Uele", "Ubangi-Uele", "VII");
 246                 area.setLevel(level);
 247                 area.setType(NamedAreaType.NATURAL_AREA());
 248                 voc.addTerm(area);
 249                 termService.save(area);
 250
 251                 area = NamedArea.NewInstance("Lac Albert", "Lac Albert", "VIII");
 252                 area.setLevel(level);
 253                 area.setType(NamedAreaType.NATURAL_AREA());
 254                 voc.addTerm(area);
 255                 termService.save(area);
 256
 257                 area = NamedArea.NewInstance("Lacs \u00C9douard et Kivu", "Lacs \u00C9douard et Kivu", "IX");
 258                 area.setLevel(level);
 259                 area.setType(NamedAreaType.NATURAL_AREA());
 260                 voc.addTerm(area);
 261                 termService.save(area);
 262
 263                 area = NamedArea.NewInstance("Rwanda-Burundi", "Rwanda-Burundi", "X");
 264                 area.setLevel(level);
 265                 area.setType(NamedAreaType.NATURAL_AREA());
 266                 voc.addTerm(area);
 267                 termService.save(area);
 268
 269                 area = NamedArea.NewInstance("Haut-Katanga", "Haut-Katanga", "XI");
 270                 area.setLevel(level);
 271                 area.setType(NamedAreaType.NATURAL_AREA());
 272                 voc.addTerm(area);
 273                 termService.save(area);
 274
 275                 app.getVocabularyService().save(voc);
 276
 277                 app.commitTransaction(tx);
 278
 279         }
 280
 281         private Reference getSourceReference(String string) {
 282                 Reference result = ReferenceFactory.newGeneric();
 283                 result.setTitleCache(string);
 284                 return result;
 285         }
 286
 287         private FeatureTree makeFeatureNode(ITermService service){
 288                 CentralAfricaEricaceaeTransformer transformer = new CentralAfricaEricaceaeTransformer();
 289
 290                 FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);
 291                 result.setTitleCache("Central Africa Ericaceae Feature Tree");
 292                 FeatureNode root = result.getRoot();
 293                 FeatureNode newNode;
 294
 295                 newNode = FeatureNode.NewInstance(Feature.DESCRIPTION());
 296                 root.addChild(newNode);
 297
 298                 addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service);
 299
 300                 addFeataureNodesByStringList(generellDescriptionsList, root, transformer, service);
 301
 302
 303                 newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 304                 root.addChild(newNode);
 305
 306                 newNode = FeatureNode.NewInstance(Feature.ECOLOGY());
 307                 root.addChild(newNode);
 308                 addFeataureNodesByStringList(habitatEcologyList, root, transformer, service);
 309
 310                 newNode = FeatureNode.NewInstance(Feature.USES());
 311                 root.addChild(newNode);
 312
 313                 addFeataureNodesByStringList(chomosomesList, root, transformer, service);
 314
 315                 newNode = FeatureNode.NewInstance(Feature.COMMON_NAME());
 316                 root.addChild(newNode);
 317
 318                 newNode = FeatureNode.NewInstance(Feature.CITATION());
 319                 root.addChild(newNode);
 320
 321                 return result;
 322         }
 323
 324         private static String [] chomosomesList = new String[]{
 325                 "Chromosomes",
 326         };
 327
 328
 329         private static String [] habitatEcologyList = new String[]{
 330                 "Habitat",
 331                 "Habitat & Ecology"
 332         };
 333
 334
 335         private static String [] generellDescriptionsList = new String[]{
 336                 "Fossils",
 337                 "Morphology and anatomy",
 338                 "Morphology",
 339                 "Vegetative morphology and anatomy",
 340                 "Flower morphology",
 341                 "Palynology",
 342                 "Pollination",
 343                 "Pollen morphology",
 344                 "Life cycle",
 345                 "Fruits and embryology",
 346                 "Dispersal",
 347                 "Wood anatomy",
 348                 "Leaf anatomy",
 349                 "Chromosome numbers",
 350                 "Phytochemistry and Chemotaxonomy",
 351                 "Phytochemistry",
 352                 "Taxonomy",
 353         };
 354
 355         private static String [] descriptionFeatureList = new String[]{
 356                 "lifeform",
 357                 "Bark",
 358                 "Indumentum",
 359                 "endophytic body",
 360                 "flowering buds",
 361                 "Branchlets",
 362                 "Branches",
 363                 "Branch",
 364                 "Flowering branchlets",
 365                 "Trees",
 366                 "Twigs",
 367                 "stem",
 368                 "Stems",
 369                 "stem leaves",
 370                 "Leaves",
 371                 "flower-bearing stems",
 372                 "Petiole",
 373                 "Petiolules",
 374                 "Leaflets",
 375                 "Thyrsus",
 376                 "Thyrses",
 377                 "Inflorescences",
 378                 "Inflorescence",
 379                 "Young inflorescences",
 380                 "Bracts",
 381                 "Pedicels",
 382                 "flowering buds",
 383                 "scales",
 384                 "Buds",
 385                 "Flowers",
 386                 "Flower",
 387                 "Flowering",
 388                 "Stigma",
 389                 "perianth",
 390                 "Sepals",
 391                 "Sepal",
 392                 "Outer Sepals",
 393                 "Axillary",
 394                 "cymes",
 395                 "Calyx",
 396                 "Petal",
 397                 "Petals",
 398                 "perigone tube",
 399                 "Disc",
 400                 "corolla",
 401                 "Stamens",
 402                 "Staminodes",
 403                 "Ovary",
 404                 "Anthers",
 405                 "anther",
 406                 "Pistil",
 407                 "Pistillode",
 408                 "Ovules",
 409                 "androecium",
 410                 "gynoecium",
 411                 "Filaments",
 412                 "Style",
 413                 "annulus",
 414                 "female flowers",
 415                 "Male flowers",
 416                 "Female",
 417                 "Infructescences",    //order not consistent (sometimes before "Flowers")
 418                 "Fruit",
 419                 "Fruits",
 420                 "fruiting axes",
 421                 "drupes",
 422                 "Arillode",
 423                 "seed",
 424                 "Seeds",
 425                 "Seedling",
 426                 "flower tube",
 427                 "nutlets",
 428                 "pollen",
 429                 "secondary xylem",
 430                 "chromosome number",
 431
 432                 "figure",
 433                 "fig",
 434                 "figs",
 435
 436
 437
 438
 439         };
 440
 441         public void addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
 442                 try {
 443                         for (String featureString : featureStringList){
 444                         UUID featureUuid;
 445                         featureUuid = transformer.getFeatureUuid(featureString);
 446                         Feature feature = (Feature)termService.find(featureUuid);
 447                         if (feature != null){
 448                                 FeatureNode child = FeatureNode.NewInstance(feature);
 449                                 root.addChild(child);
 450                         }
 451                 }
 452                 } catch (UndefinedTransformerMethodException e) {
 453                         logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");
 454                 }
 455         }
 456
 457
 458
 459         /**
 460          * @param args
 461          */
 462         public static void main(String[] args) {
 463                 CentralAfricaEricaceaeActivator me = new CentralAfricaEricaceaeActivator();
 464                 me.doImport(cdmDestination);
 465         }
 466
 467 }