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.util.List;
  13 import java.util.UUID;
  14
  15 import org.apache.log4j.Logger;
  16 import org.springframework.transaction.TransactionStatus;
  17
  18 import eu.etaxonomy.cdm.api.service.ITermService;
  19 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  20 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  21 import eu.etaxonomy.cdm.database.ICdmDataSource;
  22 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  23 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  24 import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
  25 import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
  26 import eu.etaxonomy.cdm.io.eflora.EfloraImportConfigurator;
  27 import eu.etaxonomy.cdm.io.eflora.centralAfrica.ericaceae.CentralAfricaEricaceaeImportConfigurator;
  28 import eu.etaxonomy.cdm.io.eflora.floraMalesiana.FloraMalesianaTransformer;
  29 import eu.etaxonomy.cdm.model.description.Feature;
  30 import eu.etaxonomy.cdm.model.description.FeatureNode;
  31 import eu.etaxonomy.cdm.model.description.FeatureTree;
  32 import eu.etaxonomy.cdm.model.description.PolytomousKey;
  33 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  34 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  35
  36 /**
  37  * @author a.mueller
  38  * @created 20.06.2008
  39  * @version 1.0
  40  */
  41 public class CentralAfricaEricaceaeActivator {
  42         private static final Logger logger = Logger.getLogger(CentralAfricaEricaceaeActivator.class);
  43
  44         //database validation status (create, update, validate ...)
  45         static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
  46         static final String source = EfloraSources.ericacea_local();
  47
  48
  49 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_andreasM3();
  50         static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_preview();
  51 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_production();
  52 //      static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  53
  54         //feature tree uuid
  55         public static final UUID featureTreeUuid = UUID.fromString("051d35ee-22f1-42d8-be07-9e9bfec5bcf7");
  56
  57         //classification
  58         static final UUID classificationUuid = UUID.fromString("10e5efcc-6e13-4abc-ad42-e0b46e50cbe7");
  59
  60         //check - import
  61         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  62
  63         static boolean doPrintKeys = false;
  64
  65         //taxa
  66         static final boolean doTaxa = true;
  67
  68         private boolean includeSapindaceae1 = true;
  69
  70
  71
  72         private void doImport(ICdmDataSource cdmDestination){
  73
  74                 //make Source
  75                 CentralAfricaEricaceaeImportConfigurator config= CentralAfricaEricaceaeImportConfigurator.NewInstance(source, cdmDestination);
  76                 config.setTaxonomicTreeUuid(classificationUuid);
  77                 config.setDoTaxa(doTaxa);
  78                 config.setCheck(check);
  79                 config.setDoPrintKeys(doPrintKeys);
  80                 config.setDbSchemaValidation(hbm2dll);
  81
  82                 CdmDefaultImport<EfloraImportConfigurator> myImport = new CdmDefaultImport<EfloraImportConfigurator>();
  83
  84
  85                 //Sapindaceae1
  86                 if (includeSapindaceae1){
  87                         System.out.println("Start import from ("+ source.toString() + ") ...");
  88                         config.setSourceReference(getSourceReference(config.getSourceReferenceTitle()));
  89                         myImport.invoke(config);
  90                         System.out.println("End import from ("+ source.toString() + ")...");
  91                 }
  92
  93
  94                 FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
  95                 myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
  96
  97                 //check keys
  98                 if (doPrintKeys){
  99                         TransactionStatus tx = myImport.getCdmAppController().startTransaction();
 100                         List<FeatureTree> keys = myImport.getCdmAppController().getFeatureTreeService().list(PolytomousKey.class, null, null, null, null);
 101                         for(FeatureTree key : keys){
 102                                 ((PolytomousKey)key).print(System.out);
 103                                 System.out.println();
 104                         }
 105                         myImport.getCdmAppController().commitTransaction(tx);
 106                 }
 107
 108         }
 109
 110         private ReferenceBase getSourceReference(String string) {
 111                 ReferenceBase result = ReferenceFactory.newGeneric();
 112                 result.setTitleCache(string);
 113                 return result;
 114         }
 115
 116         private FeatureTree makeFeatureNode(ITermService service){
 117                 FloraMalesianaTransformer transformer = new FloraMalesianaTransformer();
 118
 119                 FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);
 120                 result.setTitleCache("Flora Malesiana Presentation Feature Tree");
 121                 FeatureNode root = result.getRoot();
 122                 FeatureNode newNode;
 123
 124                 newNode = FeatureNode.NewInstance(Feature.CITATION());
 125                 root.addChild(newNode);
 126
 127                 newNode = FeatureNode.NewInstance(Feature.DESCRIPTION());
 128                 root.addChild(newNode);
 129
 130                 addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service);
 131
 132                 addFeataureNodesByStringList(generellDescriptionsList, root, transformer, service);
 133
 134
 135                 newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 136                 root.addChild(newNode);
 137
 138                 newNode = FeatureNode.NewInstance(Feature.ECOLOGY());
 139                 root.addChild(newNode);
 140                 addFeataureNodesByStringList(habitatEcologyList, root, transformer, service);
 141
 142                 newNode = FeatureNode.NewInstance(Feature.USES());
 143                 root.addChild(newNode);
 144
 145                 addFeataureNodesByStringList(chomosomesList, root, transformer, service);
 146
 147                 return result;
 148         }
 149
 150         private static String [] chomosomesList = new String[]{
 151                 "Chromosomes",
 152         };
 153
 154
 155         private static String [] habitatEcologyList = new String[]{
 156                 "Habitat",
 157                 "Habitat & Ecology"
 158         };
 159
 160
 161         private static String [] generellDescriptionsList = new String[]{
 162                 "Fossils",
 163                 "Morphology and anatomy",
 164                 "Morphology",
 165                 "Vegetative morphology and anatomy",
 166                 "Flower morphology",
 167                 "Palynology",
 168                 "Pollination",
 169                 "Pollen morphology",
 170                 "Life cycle",
 171                 "Fruits and embryology",
 172                 "Dispersal",
 173                 "Wood anatomy",
 174                 "Leaf anatomy",
 175                 "Chromosome numbers",
 176                 "Phytochemistry and Chemotaxonomy",
 177                 "Phytochemistry",
 178                 "Taxonomy",
 179         };
 180
 181         private static String [] descriptionFeatureList = new String[]{
 182                 "lifeform",
 183                 "Bark",
 184                 "Indumentum",
 185                 "endophytic body",
 186                 "flowering buds",
 187                 "Branchlets",
 188                 "Branches",
 189                 "Branch",
 190                 "Flowering branchlets",
 191                 "Trees",
 192                 "Twigs",
 193                 "stem",
 194                 "Stems",
 195                 "stem leaves",
 196                 "Leaves",
 197                 "flower-bearing stems",
 198                 "Petiole",
 199                 "Petiolules",
 200                 "Leaflets",
 201                 "Thyrsus",
 202                 "Thyrses",
 203                 "Inflorescences",
 204                 "Inflorescence",
 205                 "Young inflorescences",
 206                 "Bracts",
 207                 "Pedicels",
 208                 "flowering buds",
 209                 "scales",
 210                 "Buds",
 211                 "Flowers",
 212                 "Flower",
 213                 "Flowering",
 214                 "Stigma",
 215                 "perianth",
 216                 "Sepals",
 217                 "Sepal",
 218                 "Outer Sepals",
 219                 "Axillary",
 220                 "cymes",
 221                 "Calyx",
 222                 "Petal",
 223                 "Petals",
 224                 "perigone tube",
 225                 "Disc",
 226                 "corolla",
 227                 "Stamens",
 228                 "Staminodes",
 229                 "Ovary",
 230                 "Anthers",
 231                 "anther",
 232                 "Pistil",
 233                 "Pistillode",
 234                 "Ovules",
 235                 "androecium",
 236                 "gynoecium",
 237                 "Filaments",
 238                 "Style",
 239                 "annulus",
 240                 "female flowers",
 241                 "Male flowers",
 242                 "Female",
 243                 "Infructescences",    //order not consistent (sometimes before "Flowers")
 244                 "Fruit",
 245                 "Fruits",
 246                 "fruiting axes",
 247                 "drupes",
 248                 "Arillode",
 249                 "seed",
 250                 "Seeds",
 251                 "Seedling",
 252                 "flower tube",
 253                 "nutlets",
 254                 "pollen",
 255                 "secondary xylem",
 256                 "chromosome number",
 257
 258                 "figure",
 259                 "fig",
 260                 "figs",
 261
 262
 263
 264
 265         };
 266
 267         public void addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
 268                 try {
 269                         for (String featureString : featureStringList){
 270                         UUID featureUuid;
 271                         featureUuid = transformer.getFeatureUuid(featureString);
 272                         Feature feature = (Feature)termService.find(featureUuid);
 273                         if (feature != null){
 274                                 FeatureNode child = FeatureNode.NewInstance(feature);
 275                                 root.addChild(child);
 276                         }
 277                 }
 278                 } catch (UndefinedTransformerMethodException e) {
 279                         logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");
 280                 }
 281         }
 282
 283
 284
 285         /**
 286          * @param args
 287          */
 288         public static void main(String[] args) {
 289                 CentralAfricaEricaceaeActivator me = new CentralAfricaEricaceaeActivator();
 290                 me.doImport(cdmDestination);
 291         }
 292
 293 }