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.ICdmRepository;
  20 import eu.etaxonomy.cdm.api.service.ITermService;
  21 import eu.etaxonomy.cdm.common.URI;
  22 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  23 import eu.etaxonomy.cdm.database.ICdmDataSource;
  24 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  25 import eu.etaxonomy.cdm.io.common.CdmImportBase.TermMatchMode;
  26 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  27 import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
  28 import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
  29 import eu.etaxonomy.cdm.io.eflora.EfloraImportConfigurator;
  30 import eu.etaxonomy.cdm.io.eflora.centralAfrica.ericaceae.CentralAfricaEricaceaeImportConfigurator;
  31 import eu.etaxonomy.cdm.io.eflora.centralAfrica.ericaceae.CentralAfricaEricaceaeTransformer;
  32 import eu.etaxonomy.cdm.io.specimen.excel.in.SpecimenCdmExcelImportConfigurator;
  33 import eu.etaxonomy.cdm.model.agent.Team;
  34 import eu.etaxonomy.cdm.model.common.Language;
  35 import eu.etaxonomy.cdm.model.description.Feature;
  36 import eu.etaxonomy.cdm.model.description.PolytomousKey;
  37 import eu.etaxonomy.cdm.model.location.NamedArea;
  38 import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
  39 import eu.etaxonomy.cdm.model.location.NamedAreaType;
  40 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  41 import eu.etaxonomy.cdm.model.reference.Reference;
  42 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  43 import eu.etaxonomy.cdm.model.term.OrderedTermVocabulary;
  44 import eu.etaxonomy.cdm.model.term.TermNode;
  45 import eu.etaxonomy.cdm.model.term.TermTree;
  46 import eu.etaxonomy.cdm.model.term.TermType;
  47
  48 /**
  49  * @author a.mueller
  50  * @since 20.06.2008
  51  */
  52 public class CentralAfricaEricaceaeActivator {
  53
  54     private static Logger logger = LogManager.getLogger();
  55
  56         //database validation status (create, update, validate ...)
  57         static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
  58         static final URI source = EfloraSources.ericacea_local();
  59
  60         static final URI specimenSource = EfloraSources.vittaria_specimen_pesiimport3();
  61
  62
  63         static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_local();
  64
  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_campanulaceae_production();
  71
  72         //feature tree uuid
  73         public static final UUID featureTreeUuid = UUID.fromString("051d35ee-22f1-42d8-be07-9e9bfec5bcf7");
  74
  75         public static UUID defaultLanguageUuid = Language.uuidFrench;
  76
  77         //classification
  78         static final UUID classificationUuid = UUID.fromString("10e5efcc-6e13-4abc-ad42-e0b46e50cbe7");
  79
  80         NomenclaturalCode nc = NomenclaturalCode.ICNAFP;
  81
  82         //check - import
  83         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  84
  85         static boolean doPrintKeys = false;
  86
  87         //taxa
  88         private final boolean includeEricaceae = false;
  89         static final boolean doTaxa = false;
  90         static final boolean doDeduplicate = false;
  91
  92
  93         private final boolean doNewNamedAreas = false;
  94         private final boolean doFeatureTree = false;
  95
  96         private final boolean doSpecimen = true;
  97         private final 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                 config.setNomenclaturalCode(nc);
 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                         TermTree<Feature> tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
 137                         myImport.getCdmAppController().getTermTreeService().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                         ICdmRepository app = myImport.getCdmAppController();
 154                         if (app == null){
 155                                 app = CdmApplicationController.NewInstance(cdmDestination, hbm2dll, false);
 156                         }
 157                         app.getAgentService().updateCaches(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                         ICdmRepository app = myImport.getCdmAppController();
 175                         SpecimenCdmExcelImportConfigurator specimenConfig= SpecimenCdmExcelImportConfigurator.NewInstance(specimenSource, cdmDestination);
 176                         specimenConfig.setCdmAppController(app);
 177                         specimenConfig.setAreaMatchMode(specimenAreaMatchMode);
 178                         specimenConfig.setNomenclaturalCode(nc);
 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                 return;
 188         }
 189
 190         private void newNamedAreas(CdmDefaultImport<EfloraImportConfigurator> myImport) {
 191                 ICdmRepository app = myImport.getCdmAppController();
 192                 if (app == null){
 193                         app = CdmApplicationController.NewInstance(cdmDestination, hbm2dll, false);
 194                 }
 195                 TransactionStatus tx = app.startTransaction();
 196
 197                 OrderedTermVocabulary<NamedArea> areaVoc = OrderedTermVocabulary.NewOrderedInstance(TermType.NamedArea, NamedArea.class, "Phytogeographic Regions of Central Africa", "Phytogeographic Regions of Central Africa", "FdAC regions", null);
 198                 app.getVocabularyService().save(areaVoc);
 199
 200                 NamedAreaLevel level = NamedAreaLevel.NewInstance("Phytogeographic Regions of Central Africa", "Phytogeographic Regions of Central Africa", "FdAC regions");
 201                 ITermService termService = app.getTermService();
 202
 203                 termService.save(level);
 204
 205                 NamedArea area = NamedArea.NewInstance("C\u00F4tier", "C\u00F4tier", "I");
 206                 area.setLevel(level);
 207                 area.setType(NamedAreaType.NATURAL_AREA());
 208                 areaVoc.addTerm(area);
 209                 termService.save(area);
 210
 211
 212                 area = NamedArea.NewInstance("Mayumbe", "Mayumbe", "II");
 213                 area.setLevel(level);
 214                 area.setType(NamedAreaType.NATURAL_AREA());
 215                 areaVoc.addTerm(area);
 216                 termService.save(area);
 217
 218                 area = NamedArea.NewInstance("Bas-Congo", "Bas-Congo", "III");
 219                 area.setLevel(level);
 220                 area.setType(NamedAreaType.NATURAL_AREA());
 221                 areaVoc.addTerm(area);
 222                 termService.save(area);
 223
 224                 area = NamedArea.NewInstance("Kasai", "Kasai", "IV");
 225                 area.setLevel(level);
 226                 area.setType(NamedAreaType.NATURAL_AREA());
 227                 areaVoc.addTerm(area);
 228                 termService.save(area);
 229
 230                 area = NamedArea.NewInstance("Bas-Katanga", "Bas-Katanga", "V");
 231                 area.setLevel(level);
 232                 area.setType(NamedAreaType.NATURAL_AREA());
 233                 areaVoc.addTerm(area);
 234                 termService.save(area);
 235
 236                 area = NamedArea.NewInstance("Forestier Central", "Forestier Central", "VI");
 237                 area.setLevel(level);
 238                 area.setType(NamedAreaType.NATURAL_AREA());
 239                 areaVoc.addTerm(area);
 240                 termService.save(area);
 241
 242                 area = NamedArea.NewInstance("Ubangi-Uele", "Ubangi-Uele", "VII");
 243                 area.setLevel(level);
 244                 area.setType(NamedAreaType.NATURAL_AREA());
 245                 areaVoc.addTerm(area);
 246                 termService.save(area);
 247
 248                 area = NamedArea.NewInstance("Lac Albert", "Lac Albert", "VIII");
 249                 area.setLevel(level);
 250                 area.setType(NamedAreaType.NATURAL_AREA());
 251                 areaVoc.addTerm(area);
 252                 termService.save(area);
 253
 254                 area = NamedArea.NewInstance("Lacs \u00C9douard et Kivu", "Lacs \u00C9douard et Kivu", "IX");
 255                 area.setLevel(level);
 256                 area.setType(NamedAreaType.NATURAL_AREA());
 257                 areaVoc.addTerm(area);
 258                 termService.save(area);
 259
 260                 area = NamedArea.NewInstance("Rwanda-Burundi", "Rwanda-Burundi", "X");
 261                 area.setLevel(level);
 262                 area.setType(NamedAreaType.NATURAL_AREA());
 263                 areaVoc.addTerm(area);
 264                 termService.save(area);
 265
 266                 area = NamedArea.NewInstance("Haut-Katanga", "Haut-Katanga", "XI");
 267                 area.setLevel(level);
 268                 area.setType(NamedAreaType.NATURAL_AREA());
 269                 areaVoc.addTerm(area);
 270                 termService.save(area);
 271
 272                 app.getVocabularyService().save(areaVoc);
 273
 274                 app.commitTransaction(tx);
 275
 276         }
 277
 278         private Reference getSourceReference(String string) {
 279                 Reference result = ReferenceFactory.newGeneric();
 280                 result.setTitleCache(string, true);
 281                 return result;
 282         }
 283
 284         private TermTree<Feature> makeFeatureNode(ITermService service){
 285                 CentralAfricaEricaceaeTransformer transformer = new CentralAfricaEricaceaeTransformer();
 286
 287                 TermTree<Feature> result = TermTree.NewFeatureInstance(featureTreeUuid);
 288                 result.setTitleCache("Central Africa Ericaceae Feature Tree", true);
 289                 TermNode<Feature> root = result.getRoot();
 290
 291                 TermNode<Feature> newNode = root.addChild(Feature.DESCRIPTION());
 292
 293                 addFeatureNodesByStringList(descriptionFeatureList, newNode, transformer, service);
 294
 295                 addFeatureNodesByStringList(generellDescriptionsList, root, transformer, service);
 296
 297                 newNode = root.addChild(Feature.DISTRIBUTION());
 298
 299                 newNode = root.addChild(Feature.ECOLOGY());
 300                 addFeatureNodesByStringList(habitatEcologyList, root, transformer, service);
 301
 302                 newNode = root.addChild(Feature.USES());
 303
 304                 addFeatureNodesByStringList(chomosomesList, root, transformer, service);
 305
 306                 newNode = root.addChild(Feature.COMMON_NAME());
 307
 308                 newNode = root.addChild(Feature.CITATION());
 309
 310                 return result;
 311         }
 312
 313         private static String [] chomosomesList = new String[]{
 314                 "Chromosomes",
 315         };
 316
 317
 318         private static String [] habitatEcologyList = new String[]{
 319                 "Habitat",
 320                 "Habitat & Ecology"
 321         };
 322
 323
 324         private static String [] generellDescriptionsList = new String[]{
 325                 "Fossils",
 326                 "Morphology and anatomy",
 327                 "Morphology",
 328                 "Vegetative morphology and anatomy",
 329                 "Flower morphology",
 330                 "Palynology",
 331                 "Pollination",
 332                 "Pollen morphology",
 333                 "Life cycle",
 334                 "Fruits and embryology",
 335                 "Dispersal",
 336                 "Wood anatomy",
 337                 "Leaf anatomy",
 338                 "Chromosome numbers",
 339                 "Phytochemistry and Chemotaxonomy",
 340                 "Phytochemistry",
 341                 "Taxonomy",
 342         };
 343
 344         private static String [] descriptionFeatureList = new String[]{
 345                 "lifeform",
 346                 "Bark",
 347                 "Indumentum",
 348                 "endophytic body",
 349                 "flowering buds",
 350                 "Branchlets",
 351                 "Branches",
 352                 "Branch",
 353                 "Flowering branchlets",
 354                 "Trees",
 355                 "Twigs",
 356                 "stem",
 357                 "Stems",
 358                 "stem leaves",
 359                 "Leaves",
 360                 "flower-bearing stems",
 361                 "Petiole",
 362                 "Petiolules",
 363                 "Leaflets",
 364                 "Thyrsus",
 365                 "Thyrses",
 366                 "Inflorescences",
 367                 "Inflorescence",
 368                 "Young inflorescences",
 369                 "Bracts",
 370                 "Pedicels",
 371                 "flowering buds",
 372                 "scales",
 373                 "Buds",
 374                 "Flowers",
 375                 "Flower",
 376                 "Flowering",
 377                 "Stigma",
 378                 "perianth",
 379                 "Sepals",
 380                 "Sepal",
 381                 "Outer Sepals",
 382                 "Axillary",
 383                 "cymes",
 384                 "Calyx",
 385                 "Petal",
 386                 "Petals",
 387                 "perigone tube",
 388                 "Disc",
 389                 "corolla",
 390                 "Stamens",
 391                 "Staminodes",
 392                 "Ovary",
 393                 "Anthers",
 394                 "anther",
 395                 "Pistil",
 396                 "Pistillode",
 397                 "Ovules",
 398                 "androecium",
 399                 "gynoecium",
 400                 "Filaments",
 401                 "Style",
 402                 "annulus",
 403                 "female flowers",
 404                 "Male flowers",
 405                 "Female",
 406                 "Infructescences",    //order not consistent (sometimes before "Flowers")
 407                 "Fruit",
 408                 "Fruits",
 409                 "fruiting axes",
 410                 "drupes",
 411                 "Arillode",
 412                 "seed",
 413                 "Seeds",
 414                 "Seedling",
 415                 "flower tube",
 416                 "nutlets",
 417                 "pollen",
 418                 "secondary xylem",
 419                 "chromosome number",
 420
 421                 "figure",
 422                 "fig",
 423                 "figs",
 424
 425
 426
 427
 428         };
 429
 430         public void addFeatureNodesByStringList(String[] featureStringList, TermNode<Feature> root, IInputTransformer transformer, ITermService termService){
 431                 try {
 432                         for (String featureString : featureStringList){
 433                         UUID featureUuid;
 434                         featureUuid = transformer.getFeatureUuid(featureString);
 435                         Feature feature = (Feature)termService.find(featureUuid);
 436                         if (feature != null){
 437                                 TermNode<Feature> child = root.addChild(feature);
 438                         }
 439                 }
 440                 } catch (UndefinedTransformerMethodException e) {
 441                         logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");
 442                 }
 443         }
 444
 445
 446
 447         /**
 448          * @param args
 449          */
 450         public static void main(String[] args) {
 451                 CentralAfricaEricaceaeActivator me = new CentralAfricaEricaceaeActivator();
 452                 me.doImport(cdmDestination);
 453         }
 454
 455 }