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