app-import/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.service.ITermService;
  21 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  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.IImportConfigurator.CHECK;
  26 import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
  27 import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
  28 import eu.etaxonomy.cdm.io.eflora.EfloraImportConfigurator;
  29 import eu.etaxonomy.cdm.io.eflora.centralAfrica.ericaceae.CentralAfricaEricaceaeImportConfigurator;
  30 import eu.etaxonomy.cdm.io.eflora.centralAfrica.ericaceae.CentralAfricaEricaceaeTransformer;
  31 import eu.etaxonomy.cdm.model.agent.Person;
  32 import eu.etaxonomy.cdm.model.agent.Team;
  33 import eu.etaxonomy.cdm.model.common.Language;
  34 import eu.etaxonomy.cdm.model.description.Feature;
  35 import eu.etaxonomy.cdm.model.description.FeatureNode;
  36 import eu.etaxonomy.cdm.model.description.FeatureTree;
  37 import eu.etaxonomy.cdm.model.description.PolytomousKey;
  38 import eu.etaxonomy.cdm.model.reference.Reference;
  39 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  40
  41 /**
  42  * @author a.mueller
  43  * @created 20.06.2008
  44  * @version 1.0
  45  */
  46 public class CentralAfricaEricaceaeActivator {
  47         private static final Logger logger = Logger.getLogger(CentralAfricaEricaceaeActivator.class);
  48
  49         //database validation status (create, update, validate ...)
  50         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  51         static final URI source = EfloraSources.ericacea_local();
  52
  53
  54 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_andreasM3();
  55 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_preview();
  56 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_production();
  57         static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  58 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_postgres_CdmTest();
  59 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
  60
  61         //feature tree uuid
  62         public static final UUID featureTreeUuid = UUID.fromString("051d35ee-22f1-42d8-be07-9e9bfec5bcf7");
  63
  64         public static UUID defaultLanguageUuid = Language.uuidFrench;
  65
  66         //classification
  67         static final UUID classificationUuid = UUID.fromString("10e5efcc-6e13-4abc-ad42-e0b46e50cbe7");
  68
  69         //check - import
  70         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  71
  72         static boolean doPrintKeys = false;
  73
  74         //taxa
  75         static final boolean doTaxa = true;
  76         static final boolean doDeduplicate = false;
  77
  78         private boolean includeEricaceae = true;
  79
  80
  81
  82         private void doImport(ICdmDataSource cdmDestination){
  83
  84 //              CdmUpdater su = CdmUpdater.NewInstance();
  85 //
  86 //              try {
  87 //                      //su.updateToCurrentVersion(cdmDestination, DefaultProgressMonitor.NewInstance());
  88 //              } catch (Exception e) {
  89 //                      e.printStackTrace();
  90 //              }
  91 //              if (false){
  92 //                      return;
  93 //              }
  94
  95                 //make Source
  96                 CentralAfricaEricaceaeImportConfigurator config= CentralAfricaEricaceaeImportConfigurator.NewInstance(source, cdmDestination);
  97                 config.setClassificationUuid(classificationUuid);
  98                 config.setDoTaxa(doTaxa);
  99                 config.setCheck(check);
 100                 config.setDefaultLanguageUuid(defaultLanguageUuid);
 101                 config.setDoPrintKeys(doPrintKeys);
 102                 config.setDbSchemaValidation(hbm2dll);
 103
 104                 CdmDefaultImport<EfloraImportConfigurator> myImport = new CdmDefaultImport<EfloraImportConfigurator>();
 105
 106
 107                 //Ericaceae
 108                 if (includeEricaceae){
 109                         System.out.println("Start import from ("+ source.toString() + ") ...");
 110                         config.setSourceReference(getSourceReference(config.getSourceReferenceTitle()));
 111                         myImport.invoke(config);
 112                         System.out.println("End import from ("+ source.toString() + ")...");
 113                 }
 114
 115                 FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
 116                 myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
 117
 118                 //check keys
 119                 if (doPrintKeys){
 120                         TransactionStatus tx = myImport.getCdmAppController().startTransaction();
 121                         List<PolytomousKey> keys = myImport.getCdmAppController().getPolytomousKeyService().list(PolytomousKey.class, null, null, null, null);
 122                         for(PolytomousKey key : keys){
 123                                 key.print(System.out);
 124                                 System.out.println();
 125                         }
 126                         myImport.getCdmAppController().commitTransaction(tx);
 127                 }
 128
 129                 //deduplicate
 130                 if (doDeduplicate){
 131                         CdmApplicationController app = myImport.getCdmAppController();
 132                         int count = app.getAgentService().deduplicate(Person.class, null, null);
 133                         logger.warn("Deduplicated " + count + " persons.");
 134                         count = app.getAgentService().deduplicate(Team.class, null, null);
 135                         logger.warn("Deduplicated " + count + " teams.");
 136                         count = app.getReferenceService().deduplicate(Reference.class, null, null);
 137                         logger.warn("Deduplicated " + count + " references.");
 138                 }
 139
 140         }
 141
 142         private Reference getSourceReference(String string) {
 143                 Reference result = ReferenceFactory.newGeneric();
 144                 result.setTitleCache(string);
 145                 return result;
 146         }
 147
 148         private FeatureTree makeFeatureNode(ITermService service){
 149                 CentralAfricaEricaceaeTransformer transformer = new CentralAfricaEricaceaeTransformer();
 150
 151                 FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);
 152                 result.setTitleCache("Central Africa Ericaceae Feature Tree");
 153                 FeatureNode root = result.getRoot();
 154                 FeatureNode newNode;
 155
 156                 newNode = FeatureNode.NewInstance(Feature.DESCRIPTION());
 157                 root.addChild(newNode);
 158
 159                 addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service);
 160
 161                 addFeataureNodesByStringList(generellDescriptionsList, root, transformer, service);
 162
 163
 164                 newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 165                 root.addChild(newNode);
 166
 167                 newNode = FeatureNode.NewInstance(Feature.ECOLOGY());
 168                 root.addChild(newNode);
 169                 addFeataureNodesByStringList(habitatEcologyList, root, transformer, service);
 170
 171                 newNode = FeatureNode.NewInstance(Feature.USES());
 172                 root.addChild(newNode);
 173
 174                 addFeataureNodesByStringList(chomosomesList, root, transformer, service);
 175
 176                 newNode = FeatureNode.NewInstance(Feature.COMMON_NAME());
 177                 root.addChild(newNode);
 178
 179                 newNode = FeatureNode.NewInstance(Feature.CITATION());
 180                 root.addChild(newNode);
 181
 182                 return result;
 183         }
 184
 185         private static String [] chomosomesList = new String[]{
 186                 "Chromosomes",
 187         };
 188
 189
 190         private static String [] habitatEcologyList = new String[]{
 191                 "Habitat",
 192                 "Habitat & Ecology"
 193         };
 194
 195
 196         private static String [] generellDescriptionsList = new String[]{
 197                 "Fossils",
 198                 "Morphology and anatomy",
 199                 "Morphology",
 200                 "Vegetative morphology and anatomy",
 201                 "Flower morphology",
 202                 "Palynology",
 203                 "Pollination",
 204                 "Pollen morphology",
 205                 "Life cycle",
 206                 "Fruits and embryology",
 207                 "Dispersal",
 208                 "Wood anatomy",
 209                 "Leaf anatomy",
 210                 "Chromosome numbers",
 211                 "Phytochemistry and Chemotaxonomy",
 212                 "Phytochemistry",
 213                 "Taxonomy",
 214         };
 215
 216         private static String [] descriptionFeatureList = new String[]{
 217                 "lifeform",
 218                 "Bark",
 219                 "Indumentum",
 220                 "endophytic body",
 221                 "flowering buds",
 222                 "Branchlets",
 223                 "Branches",
 224                 "Branch",
 225                 "Flowering branchlets",
 226                 "Trees",
 227                 "Twigs",
 228                 "stem",
 229                 "Stems",
 230                 "stem leaves",
 231                 "Leaves",
 232                 "flower-bearing stems",
 233                 "Petiole",
 234                 "Petiolules",
 235                 "Leaflets",
 236                 "Thyrsus",
 237                 "Thyrses",
 238                 "Inflorescences",
 239                 "Inflorescence",
 240                 "Young inflorescences",
 241                 "Bracts",
 242                 "Pedicels",
 243                 "flowering buds",
 244                 "scales",
 245                 "Buds",
 246                 "Flowers",
 247                 "Flower",
 248                 "Flowering",
 249                 "Stigma",
 250                 "perianth",
 251                 "Sepals",
 252                 "Sepal",
 253                 "Outer Sepals",
 254                 "Axillary",
 255                 "cymes",
 256                 "Calyx",
 257                 "Petal",
 258                 "Petals",
 259                 "perigone tube",
 260                 "Disc",
 261                 "corolla",
 262                 "Stamens",
 263                 "Staminodes",
 264                 "Ovary",
 265                 "Anthers",
 266                 "anther",
 267                 "Pistil",
 268                 "Pistillode",
 269                 "Ovules",
 270                 "androecium",
 271                 "gynoecium",
 272                 "Filaments",
 273                 "Style",
 274                 "annulus",
 275                 "female flowers",
 276                 "Male flowers",
 277                 "Female",
 278                 "Infructescences",    //order not consistent (sometimes before "Flowers")
 279                 "Fruit",
 280                 "Fruits",
 281                 "fruiting axes",
 282                 "drupes",
 283                 "Arillode",
 284                 "seed",
 285                 "Seeds",
 286                 "Seedling",
 287                 "flower tube",
 288                 "nutlets",
 289                 "pollen",
 290                 "secondary xylem",
 291                 "chromosome number",
 292
 293                 "figure",
 294                 "fig",
 295                 "figs",
 296
 297
 298
 299
 300         };
 301
 302         public void addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
 303                 try {
 304                         for (String featureString : featureStringList){
 305                         UUID featureUuid;
 306                         featureUuid = transformer.getFeatureUuid(featureString);
 307                         Feature feature = (Feature)termService.find(featureUuid);
 308                         if (feature != null){
 309                                 FeatureNode child = FeatureNode.NewInstance(feature);
 310                                 root.addChild(child);
 311                         }
 312                 }
 313                 } catch (UndefinedTransformerMethodException e) {
 314                         logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");
 315                 }
 316         }
 317
 318
 319
 320         /**
 321          * @param args
 322          */
 323         public static void main(String[] args) {
 324                 CentralAfricaEricaceaeActivator me = new CentralAfricaEricaceaeActivator();
 325                 me.doImport(cdmDestination);
 326         }
 327
 328 }