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.common.DefaultProgressMonitor;
  23 import eu.etaxonomy.cdm.common.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.IImportConfigurator.CHECK;
  29 import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
  30 import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
  31 import eu.etaxonomy.cdm.io.eflora.EfloraImportConfigurator;
  32 import eu.etaxonomy.cdm.io.eflora.centralAfrica.ericaceae.CentralAfricaEricaceaeImportConfigurator;
  33 import eu.etaxonomy.cdm.io.eflora.centralAfrica.ericaceae.CentralAfricaEricaceaeTransformer;
  34 import eu.etaxonomy.cdm.model.agent.Person;
  35 import eu.etaxonomy.cdm.model.common.Language;
  36 import eu.etaxonomy.cdm.model.description.Feature;
  37 import eu.etaxonomy.cdm.model.description.FeatureNode;
  38 import eu.etaxonomy.cdm.model.description.FeatureTree;
  39 import eu.etaxonomy.cdm.model.description.PolytomousKey;
  40 import eu.etaxonomy.cdm.model.reference.Reference;
  41 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  42
  43 /**
  44  * @author a.mueller
  45  * @created 20.06.2008
  46  * @version 1.0
  47  */
  48 public class CentralAfricaEricaceaeActivator {
  49         private static final Logger logger = Logger.getLogger(CentralAfricaEricaceaeActivator.class);
  50
  51         //database validation status (create, update, validate ...)
  52         static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
  53         static final URI source = EfloraSources.ericacea_local();
  54
  55
  56 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_andreasM3();
  57 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_preview();
  58 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_production();
  59 //      static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  60 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_postgres_CdmTest();
  61         static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
  62 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_jaxb();
  63
  64         //feature tree uuid
  65         public static final UUID featureTreeUuid = UUID.fromString("051d35ee-22f1-42d8-be07-9e9bfec5bcf7");
  66
  67         public static UUID defaultLanguageUuid = Language.uuidFrench;
  68
  69         //classification
  70         static final UUID classificationUuid = UUID.fromString("10e5efcc-6e13-4abc-ad42-e0b46e50cbe7");
  71
  72         //check - import
  73         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  74
  75         static boolean doPrintKeys = false;
  76
  77         //taxa
  78         static final boolean doTaxa = true;
  79         static final boolean doDeduplicate = true;
  80
  81         private boolean includeEricaceae = true;
  82
  83
  84
  85         private void doImport(ICdmDataSource cdmDestination){
  86
  87                 CdmUpdater su = CdmUpdater.NewInstance();
  88                 IProgressMonitor monitor = DefaultProgressMonitor.NewInstance();
  89
  90 //              try {
  91 //                      su.updateToCurrentVersion(cdmDestination, monitor);
  92 //              } catch (Exception e) {
  93 //                      e.printStackTrace();
  94 //              }
  95 //              if (true){
  96 //                      return;
  97 //              }
  98
  99                 //make Source
 100                 CentralAfricaEricaceaeImportConfigurator config= CentralAfricaEricaceaeImportConfigurator.NewInstance(source, cdmDestination);
 101                 config.setClassificationUuid(classificationUuid);
 102                 config.setDoTaxa(doTaxa);
 103                 config.setCheck(check);
 104                 config.setDefaultLanguageUuid(defaultLanguageUuid);
 105                 config.setDoPrintKeys(doPrintKeys);
 106                 config.setDbSchemaValidation(hbm2dll);
 107
 108                 CdmDefaultImport<EfloraImportConfigurator> myImport = new CdmDefaultImport<EfloraImportConfigurator>();
 109
 110
 111                 //Ericaceae
 112                 if (includeEricaceae){
 113                         System.out.println("Start import from ("+ source.toString() + ") ...");
 114                         config.setSourceReference(getSourceReference(config.getSourceReferenceTitle()));
 115                         myImport.invoke(config);
 116                         System.out.println("End import from ("+ source.toString() + ")...");
 117                 }
 118
 119                 FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
 120                 myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
 121
 122                 //check keys
 123                 if (doPrintKeys){
 124                         TransactionStatus tx = myImport.getCdmAppController().startTransaction();
 125                         List<PolytomousKey> keys = myImport.getCdmAppController().getPolytomousKeyService().list(PolytomousKey.class, null, null, null, null);
 126                         for(PolytomousKey key : keys){
 127                                 key.print(System.out);
 128                                 System.out.println();
 129                         }
 130                         myImport.getCdmAppController().commitTransaction(tx);
 131                 }
 132
 133                 //deduplicate
 134                 if (doDeduplicate){
 135                         CdmApplicationController app = myImport.getCdmAppController();
 136                         int count = app.getAgentService().deduplicate(Person.class, null, null);
 137                         logger.warn("Deduplicated " + count + " persons.");
 138 //                      count = app.getAgentService().deduplicate(Team.class, null, null);
 139 //                      logger.warn("Deduplicated " + count + " teams.");
 140                         count = app.getReferenceService().deduplicate(Reference.class, null, null);
 141                         logger.warn("Deduplicated " + count + " references.");
 142                 }
 143
 144         }
 145
 146         private Reference getSourceReference(String string) {
 147                 Reference result = ReferenceFactory.newGeneric();
 148                 result.setTitleCache(string);
 149                 return result;
 150         }
 151
 152         private FeatureTree makeFeatureNode(ITermService service){
 153                 CentralAfricaEricaceaeTransformer transformer = new CentralAfricaEricaceaeTransformer();
 154
 155                 FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);
 156                 result.setTitleCache("Central Africa Ericaceae Feature Tree");
 157                 FeatureNode root = result.getRoot();
 158                 FeatureNode newNode;
 159
 160                 newNode = FeatureNode.NewInstance(Feature.DESCRIPTION());
 161                 root.addChild(newNode);
 162
 163                 addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service);
 164
 165                 addFeataureNodesByStringList(generellDescriptionsList, root, transformer, service);
 166
 167
 168                 newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 169                 root.addChild(newNode);
 170
 171                 newNode = FeatureNode.NewInstance(Feature.ECOLOGY());
 172                 root.addChild(newNode);
 173                 addFeataureNodesByStringList(habitatEcologyList, root, transformer, service);
 174
 175                 newNode = FeatureNode.NewInstance(Feature.USES());
 176                 root.addChild(newNode);
 177
 178                 addFeataureNodesByStringList(chomosomesList, root, transformer, service);
 179
 180                 newNode = FeatureNode.NewInstance(Feature.COMMON_NAME());
 181                 root.addChild(newNode);
 182
 183                 newNode = FeatureNode.NewInstance(Feature.CITATION());
 184                 root.addChild(newNode);
 185
 186                 return result;
 187         }
 188
 189         private static String [] chomosomesList = new String[]{
 190                 "Chromosomes",
 191         };
 192
 193
 194         private static String [] habitatEcologyList = new String[]{
 195                 "Habitat",
 196                 "Habitat & Ecology"
 197         };
 198
 199
 200         private static String [] generellDescriptionsList = new String[]{
 201                 "Fossils",
 202                 "Morphology and anatomy",
 203                 "Morphology",
 204                 "Vegetative morphology and anatomy",
 205                 "Flower morphology",
 206                 "Palynology",
 207                 "Pollination",
 208                 "Pollen morphology",
 209                 "Life cycle",
 210                 "Fruits and embryology",
 211                 "Dispersal",
 212                 "Wood anatomy",
 213                 "Leaf anatomy",
 214                 "Chromosome numbers",
 215                 "Phytochemistry and Chemotaxonomy",
 216                 "Phytochemistry",
 217                 "Taxonomy",
 218         };
 219
 220         private static String [] descriptionFeatureList = new String[]{
 221                 "lifeform",
 222                 "Bark",
 223                 "Indumentum",
 224                 "endophytic body",
 225                 "flowering buds",
 226                 "Branchlets",
 227                 "Branches",
 228                 "Branch",
 229                 "Flowering branchlets",
 230                 "Trees",
 231                 "Twigs",
 232                 "stem",
 233                 "Stems",
 234                 "stem leaves",
 235                 "Leaves",
 236                 "flower-bearing stems",
 237                 "Petiole",
 238                 "Petiolules",
 239                 "Leaflets",
 240                 "Thyrsus",
 241                 "Thyrses",
 242                 "Inflorescences",
 243                 "Inflorescence",
 244                 "Young inflorescences",
 245                 "Bracts",
 246                 "Pedicels",
 247                 "flowering buds",
 248                 "scales",
 249                 "Buds",
 250                 "Flowers",
 251                 "Flower",
 252                 "Flowering",
 253                 "Stigma",
 254                 "perianth",
 255                 "Sepals",
 256                 "Sepal",
 257                 "Outer Sepals",
 258                 "Axillary",
 259                 "cymes",
 260                 "Calyx",
 261                 "Petal",
 262                 "Petals",
 263                 "perigone tube",
 264                 "Disc",
 265                 "corolla",
 266                 "Stamens",
 267                 "Staminodes",
 268                 "Ovary",
 269                 "Anthers",
 270                 "anther",
 271                 "Pistil",
 272                 "Pistillode",
 273                 "Ovules",
 274                 "androecium",
 275                 "gynoecium",
 276                 "Filaments",
 277                 "Style",
 278                 "annulus",
 279                 "female flowers",
 280                 "Male flowers",
 281                 "Female",
 282                 "Infructescences",    //order not consistent (sometimes before "Flowers")
 283                 "Fruit",
 284                 "Fruits",
 285                 "fruiting axes",
 286                 "drupes",
 287                 "Arillode",
 288                 "seed",
 289                 "Seeds",
 290                 "Seedling",
 291                 "flower tube",
 292                 "nutlets",
 293                 "pollen",
 294                 "secondary xylem",
 295                 "chromosome number",
 296
 297                 "figure",
 298                 "fig",
 299                 "figs",
 300
 301
 302
 303
 304         };
 305
 306         public void addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
 307                 try {
 308                         for (String featureString : featureStringList){
 309                         UUID featureUuid;
 310                         featureUuid = transformer.getFeatureUuid(featureString);
 311                         Feature feature = (Feature)termService.find(featureUuid);
 312                         if (feature != null){
 313                                 FeatureNode child = FeatureNode.NewInstance(feature);
 314                                 root.addChild(child);
 315                         }
 316                 }
 317                 } catch (UndefinedTransformerMethodException e) {
 318                         logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");
 319                 }
 320         }
 321
 322
 323
 324         /**
 325          * @param args
 326          */
 327         public static void main(String[] args) {
 328                 CentralAfricaEricaceaeActivator me = new CentralAfricaEricaceaeActivator();
 329                 me.doImport(cdmDestination);
 330         }
 331
 332 }