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.reference.Reference;
  48 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  49
  50 /**
  51  * @author a.mueller
  52  * @created 20.06.2008
  53  * @version 1.0
  54  */
  55 public class CentralAfricaEricaceaeActivator {
  56         private static final Logger logger = Logger.getLogger(CentralAfricaEricaceaeActivator.class);
  57
  58         //database validation status (create, update, validate ...)
  59         static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
  60         static final URI source = EfloraSources.ericacea_local();
  61
  62         static final URI specimenSource = EfloraSources.ericacea_specimen_local();
  63
  64
  65 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_andreasM3();
  66 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_preview();
  67 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_production();
  68         static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  69 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_postgres_CdmTest();
  70 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
  71 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_jaxb();
  72 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_edit_cichorieae_preview();
  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         //check - import
  84         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  85
  86         static boolean doPrintKeys = false;
  87
  88         //taxa
  89         private boolean includeEricaceae = true;
  90         static final boolean doTaxa = true;
  91         static final boolean doDeduplicate = false;
  92
  93
  94         private boolean doNewNamedAreas = false;
  95         private boolean doFeatureTree = false;
  96
  97         private boolean doSpecimen = false;
  98         private TermMatchMode specimenAreaMatchMode = TermMatchMode.UUID_ABBREVLABEL;
  99
 100
 101         private void doImport(ICdmDataSource cdmDestination){
 102
 103                 CdmUpdater su = CdmUpdater.NewInstance();
 104                 IProgressMonitor monitor = DefaultProgressMonitor.NewInstance();
 105 //
 106 //              try {
 107 //                      su.updateToCurrentVersion(cdmDestination, monitor);
 108 //              } catch (Exception e) {
 109 //                      e.printStackTrace();
 110 //              }
 111 //              if (true){
 112 //                      return;
 113 //              }
 114
 115                 //make Source
 116                 CentralAfricaEricaceaeImportConfigurator config= CentralAfricaEricaceaeImportConfigurator.NewInstance(source, cdmDestination);
 117                 config.setClassificationUuid(classificationUuid);
 118                 config.setDoTaxa(doTaxa);
 119                 config.setCheck(check);
 120                 config.setDefaultLanguageUuid(defaultLanguageUuid);
 121                 config.setDoPrintKeys(doPrintKeys);
 122                 config.setDbSchemaValidation(hbm2dll);
 123
 124                 CdmDefaultImport<EfloraImportConfigurator> myImport = new CdmDefaultImport<EfloraImportConfigurator>();
 125
 126
 127                 //Ericaceae
 128                 if (includeEricaceae){
 129                         System.out.println("Start import from ("+ source.toString() + ") ...");
 130                         config.setSourceReference(getSourceReference(config.getSourceReferenceTitle()));
 131                         myImport.invoke(config);
 132                         System.out.println("End import from ("+ source.toString() + ")...");
 133                 }
 134
 135                 if (doFeatureTree){
 136                         FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
 137                         myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
 138                 }
 139
 140                 //check keys
 141                 if (doPrintKeys){
 142                         TransactionStatus tx = myImport.getCdmAppController().startTransaction();
 143                         List<PolytomousKey> keys = myImport.getCdmAppController().getPolytomousKeyService().list(PolytomousKey.class, null, null, null, null);
 144                         for(PolytomousKey key : keys){
 145                                 key.print(System.out);
 146                                 System.out.println();
 147                         }
 148                         myImport.getCdmAppController().commitTransaction(tx);
 149                 }
 150
 151                 //deduplicate
 152                 if (doDeduplicate){
 153                         ICdmApplicationConfiguration app = myImport.getCdmAppController();
 154                         if (app == null){
 155                                 app = CdmApplicationController.NewInstance(cdmDestination, hbm2dll, false);
 156                         }
 157                         app.getAgentService().updateTitleCache(Team.class, null, null, null);
 158                         return;
 159 //                      int count = app.getAgentService().deduplicate(Person.class, null, null);
 160 //
 161 //                      logger.warn("Deduplicated " + count + " persons.");
 162 ////                    count = app.getAgentService().deduplicate(Team.class, null, null);
 163 ////                    logger.warn("Deduplicated " + count + " teams.");
 164 //                      count = app.getReferenceService().deduplicate(Reference.class, null, null);
 165 //                      logger.warn("Deduplicated " + count + " references.");
 166                 }
 167
 168                 if(doNewNamedAreas){
 169                         newNamedAreas(myImport);
 170                 }
 171
 172                 if (doSpecimen){
 173                         logger.warn("Start specimen import");
 174                         ICdmApplicationConfiguration app = myImport.getCdmAppController();
 175                         SpecimenCdmExcelImportConfigurator specimenConfig= SpecimenCdmExcelImportConfigurator.NewInstance(specimenSource, cdmDestination);
 176                         specimenConfig.setCdmAppController((CdmApplicationController)app);
 177                         specimenConfig.setAreaMatchMode(specimenAreaMatchMode);
 178
 179                         config.setDbSchemaValidation(DbSchemaValidation.VALIDATE);
 180                         specimenConfig.setSourceReference(getSourceReference(specimenConfig.getSourceReferenceTitle()));
 181
 182                         CdmDefaultImport<SpecimenCdmExcelImportConfigurator> specimenImport = new CdmDefaultImport<SpecimenCdmExcelImportConfigurator>();
 183                         specimenImport.setCdmAppController(app);
 184                         specimenImport.invoke(specimenConfig);
 185
 186
 187                 }
 188                 return;
 189
 190
 191
 192         }
 193
 194         private void newNamedAreas(CdmDefaultImport<EfloraImportConfigurator> myImport) {
 195                 ICdmApplicationConfiguration app = myImport.getCdmAppController();
 196                 if (app == null){
 197                         app = CdmApplicationController.NewInstance(cdmDestination, hbm2dll, false);
 198                 }
 199                 TransactionStatus tx = app.startTransaction();
 200
 201                 OrderedTermVocabulary<NamedArea> areaVoc = OrderedTermVocabulary.NewInstance(TermType.NamedArea, "Phytogeographic Regions of Central Africa", "Phytogeographic Regions of Central Africa", "FdAC regions", null);
 202                 app.getVocabularyService().save(areaVoc);
 203
 204                 NamedAreaLevel level = NamedAreaLevel.NewInstance("Phytogeographic Regions of Central Africa", "Phytogeographic Regions of Central Africa", "FdAC regions");
 205                 ITermService termService = app.getTermService();
 206
 207                 termService.save(level);
 208
 209                 NamedArea area = NamedArea.NewInstance("C\u00F4tier", "C\u00F4tier", "I");
 210                 area.setLevel(level);
 211                 area.setType(NamedAreaType.NATURAL_AREA());
 212                 areaVoc.addTerm(area);
 213                 termService.save(area);
 214
 215
 216                 area = NamedArea.NewInstance("Mayumbe", "Mayumbe", "II");
 217                 area.setLevel(level);
 218                 area.setType(NamedAreaType.NATURAL_AREA());
 219                 areaVoc.addTerm(area);
 220                 termService.save(area);
 221
 222                 area = NamedArea.NewInstance("Bas-Congo", "Bas-Congo", "III");
 223                 area.setLevel(level);
 224                 area.setType(NamedAreaType.NATURAL_AREA());
 225                 areaVoc.addTerm(area);
 226                 termService.save(area);
 227
 228                 area = NamedArea.NewInstance("Kasai", "Kasai", "IV");
 229                 area.setLevel(level);
 230                 area.setType(NamedAreaType.NATURAL_AREA());
 231                 areaVoc.addTerm(area);
 232                 termService.save(area);
 233
 234                 area = NamedArea.NewInstance("Bas-Katanga", "Bas-Katanga", "V");
 235                 area.setLevel(level);
 236                 area.setType(NamedAreaType.NATURAL_AREA());
 237                 areaVoc.addTerm(area);
 238                 termService.save(area);
 239
 240                 area = NamedArea.NewInstance("Forestier Central", "Forestier Central", "VI");
 241                 area.setLevel(level);
 242                 area.setType(NamedAreaType.NATURAL_AREA());
 243                 areaVoc.addTerm(area);
 244                 termService.save(area);
 245
 246                 area = NamedArea.NewInstance("Ubangi-Uele", "Ubangi-Uele", "VII");
 247                 area.setLevel(level);
 248                 area.setType(NamedAreaType.NATURAL_AREA());
 249                 areaVoc.addTerm(area);
 250                 termService.save(area);
 251
 252                 area = NamedArea.NewInstance("Lac Albert", "Lac Albert", "VIII");
 253                 area.setLevel(level);
 254                 area.setType(NamedAreaType.NATURAL_AREA());
 255                 areaVoc.addTerm(area);
 256                 termService.save(area);
 257
 258                 area = NamedArea.NewInstance("Lacs \u00C9douard et Kivu", "Lacs \u00C9douard et Kivu", "IX");
 259                 area.setLevel(level);
 260                 area.setType(NamedAreaType.NATURAL_AREA());
 261                 areaVoc.addTerm(area);
 262                 termService.save(area);
 263
 264                 area = NamedArea.NewInstance("Rwanda-Burundi", "Rwanda-Burundi", "X");
 265                 area.setLevel(level);
 266                 area.setType(NamedAreaType.NATURAL_AREA());
 267                 areaVoc.addTerm(area);
 268                 termService.save(area);
 269
 270                 area = NamedArea.NewInstance("Haut-Katanga", "Haut-Katanga", "XI");
 271                 area.setLevel(level);
 272                 area.setType(NamedAreaType.NATURAL_AREA());
 273                 areaVoc.addTerm(area);
 274                 termService.save(area);
 275
 276                 app.getVocabularyService().save(areaVoc);
 277
 278                 app.commitTransaction(tx);
 279
 280         }
 281
 282         private Reference getSourceReference(String string) {
 283                 Reference result = ReferenceFactory.newGeneric();
 284                 result.setTitleCache(string);
 285                 return result;
 286         }
 287
 288         private FeatureTree makeFeatureNode(ITermService service){
 289                 CentralAfricaEricaceaeTransformer transformer = new CentralAfricaEricaceaeTransformer();
 290
 291                 FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);
 292                 result.setTitleCache("Central Africa Ericaceae Feature Tree");
 293                 FeatureNode root = result.getRoot();
 294                 FeatureNode newNode;
 295
 296                 newNode = FeatureNode.NewInstance(Feature.DESCRIPTION());
 297                 root.addChild(newNode);
 298
 299                 addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service);
 300
 301                 addFeataureNodesByStringList(generellDescriptionsList, root, transformer, service);
 302
 303
 304                 newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 305                 root.addChild(newNode);
 306
 307                 newNode = FeatureNode.NewInstance(Feature.ECOLOGY());
 308                 root.addChild(newNode);
 309                 addFeataureNodesByStringList(habitatEcologyList, root, transformer, service);
 310
 311                 newNode = FeatureNode.NewInstance(Feature.USES());
 312                 root.addChild(newNode);
 313
 314                 addFeataureNodesByStringList(chomosomesList, root, transformer, service);
 315
 316                 newNode = FeatureNode.NewInstance(Feature.COMMON_NAME());
 317                 root.addChild(newNode);
 318
 319                 newNode = FeatureNode.NewInstance(Feature.CITATION());
 320                 root.addChild(newNode);
 321
 322                 return result;
 323         }
 324
 325         private static String [] chomosomesList = new String[]{
 326                 "Chromosomes",
 327         };
 328
 329
 330         private static String [] habitatEcologyList = new String[]{
 331                 "Habitat",
 332                 "Habitat & Ecology"
 333         };
 334
 335
 336         private static String [] generellDescriptionsList = new String[]{
 337                 "Fossils",
 338                 "Morphology and anatomy",
 339                 "Morphology",
 340                 "Vegetative morphology and anatomy",
 341                 "Flower morphology",
 342                 "Palynology",
 343                 "Pollination",
 344                 "Pollen morphology",
 345                 "Life cycle",
 346                 "Fruits and embryology",
 347                 "Dispersal",
 348                 "Wood anatomy",
 349                 "Leaf anatomy",
 350                 "Chromosome numbers",
 351                 "Phytochemistry and Chemotaxonomy",
 352                 "Phytochemistry",
 353                 "Taxonomy",
 354         };
 355
 356         private static String [] descriptionFeatureList = new String[]{
 357                 "lifeform",
 358                 "Bark",
 359                 "Indumentum",
 360                 "endophytic body",
 361                 "flowering buds",
 362                 "Branchlets",
 363                 "Branches",
 364                 "Branch",
 365                 "Flowering branchlets",
 366                 "Trees",
 367                 "Twigs",
 368                 "stem",
 369                 "Stems",
 370                 "stem leaves",
 371                 "Leaves",
 372                 "flower-bearing stems",
 373                 "Petiole",
 374                 "Petiolules",
 375                 "Leaflets",
 376                 "Thyrsus",
 377                 "Thyrses",
 378                 "Inflorescences",
 379                 "Inflorescence",
 380                 "Young inflorescences",
 381                 "Bracts",
 382                 "Pedicels",
 383                 "flowering buds",
 384                 "scales",
 385                 "Buds",
 386                 "Flowers",
 387                 "Flower",
 388                 "Flowering",
 389                 "Stigma",
 390                 "perianth",
 391                 "Sepals",
 392                 "Sepal",
 393                 "Outer Sepals",
 394                 "Axillary",
 395                 "cymes",
 396                 "Calyx",
 397                 "Petal",
 398                 "Petals",
 399                 "perigone tube",
 400                 "Disc",
 401                 "corolla",
 402                 "Stamens",
 403                 "Staminodes",
 404                 "Ovary",
 405                 "Anthers",
 406                 "anther",
 407                 "Pistil",
 408                 "Pistillode",
 409                 "Ovules",
 410                 "androecium",
 411                 "gynoecium",
 412                 "Filaments",
 413                 "Style",
 414                 "annulus",
 415                 "female flowers",
 416                 "Male flowers",
 417                 "Female",
 418                 "Infructescences",    //order not consistent (sometimes before "Flowers")
 419                 "Fruit",
 420                 "Fruits",
 421                 "fruiting axes",
 422                 "drupes",
 423                 "Arillode",
 424                 "seed",
 425                 "Seeds",
 426                 "Seedling",
 427                 "flower tube",
 428                 "nutlets",
 429                 "pollen",
 430                 "secondary xylem",
 431                 "chromosome number",
 432
 433                 "figure",
 434                 "fig",
 435                 "figs",
 436
 437
 438
 439
 440         };
 441
 442         public void addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
 443                 try {
 444                         for (String featureString : featureStringList){
 445                         UUID featureUuid;
 446                         featureUuid = transformer.getFeatureUuid(featureString);
 447                         Feature feature = (Feature)termService.find(featureUuid);
 448                         if (feature != null){
 449                                 FeatureNode child = FeatureNode.NewInstance(feature);
 450                                 root.addChild(child);
 451                         }
 452                 }
 453                 } catch (UndefinedTransformerMethodException e) {
 454                         logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");
 455                 }
 456         }
 457
 458
 459
 460         /**
 461          * @param args
 462          */
 463         public static void main(String[] args) {
 464                 CentralAfricaEricaceaeActivator me = new CentralAfricaEricaceaeActivator();
 465                 me.doImport(cdmDestination);
 466         }
 467
 468 }