app-import/src/main/java/eu/etaxonomy/cdm/app/cyprus/CyprusActivator.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.cyprus;
  11
  12 import java.io.File;
  13 import java.net.MalformedURLException;
  14 import java.net.URI;
  15 import java.net.URISyntaxException;
  16 import java.net.URL;
  17 import java.util.List;
  18 import java.util.UUID;
  19
  20 import org.apache.log4j.Logger;
  21 import org.springframework.transaction.TransactionStatus;
  22
  23 import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  24 import eu.etaxonomy.cdm.api.service.ITermService;
  25 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  26 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  27 import eu.etaxonomy.cdm.database.ICdmDataSource;
  28 import eu.etaxonomy.cdm.database.update.CdmUpdater;
  29 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  30 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  31 import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
  32 import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
  33 import eu.etaxonomy.cdm.io.cyprus.CyprusImportConfigurator;
  34 import eu.etaxonomy.cdm.io.eflora.EfloraImportConfigurator;
  35 import eu.etaxonomy.cdm.io.eflora.centralAfrica.ericaceae.CentralAfricaEricaceaeImportConfigurator;
  36 import eu.etaxonomy.cdm.io.eflora.centralAfrica.ericaceae.CentralAfricaEricaceaeTransformer;
  37 import eu.etaxonomy.cdm.model.agent.Person;
  38 import eu.etaxonomy.cdm.model.agent.Team;
  39 import eu.etaxonomy.cdm.model.common.Language;
  40 import eu.etaxonomy.cdm.model.description.Feature;
  41 import eu.etaxonomy.cdm.model.description.FeatureNode;
  42 import eu.etaxonomy.cdm.model.description.FeatureTree;
  43 import eu.etaxonomy.cdm.model.description.PolytomousKey;
  44 import eu.etaxonomy.cdm.model.reference.Reference;
  45 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  46
  47 /**
  48  * @author a.mueller
  49  * @created 16.12.2010
  50  * @version 1.0
  51  */
  52 public class CyprusActivator {
  53         private static final Logger logger = Logger.getLogger(CyprusActivator.class);
  54
  55         //database validation status (create, update, validate ...)
  56         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  57         static final URI source = cyprus_local();
  58
  59
  60 //      static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  61 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_postgres_CdmTest();
  62         static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
  63 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cyprus_dev();
  64 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cyprus_production();
  65
  66
  67         //feature tree uuid
  68         public static final UUID featureTreeUuid = UUID.fromString("14d1e912-5ec2-4d10-878b-828788b70a87");
  69
  70         //classification
  71         static final UUID classificationUuid = UUID.fromString("0c2b5d25-7b15-4401-8b51-dd4be0ee5cab");
  72
  73         //check - import
  74         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  75
  76         //taxa
  77         static final boolean doTaxa = true;
  78         static final boolean doDeduplicate = false;
  79
  80
  81         private void doImport(ICdmDataSource cdmDestination){
  82
  83                 //make Source
  84                 CyprusImportConfigurator config= CyprusImportConfigurator.NewInstance(source, cdmDestination);
  85                 config.setClassificationUuid(classificationUuid);
  86                 config.setDoTaxa(doTaxa);
  87                 config.setCheck(check);
  88 //              config.setDefaultLanguageUuid(defaultLanguageUuid);
  89 //              config.setDoPrintKeys(doPrintKeys);
  90                 config.setDbSchemaValidation(hbm2dll);
  91
  92                 CdmDefaultImport myImport = new CdmDefaultImport();
  93
  94
  95                 //...
  96                 if (true){
  97                         System.out.println("Start import from ("+ source.toString() + ") ...");
  98                         config.setSourceReference(getSourceReference(config.getSourceReferenceTitle()));
  99                         myImport.invoke(config);
 100                         System.out.println("End import from ("+ source.toString() + ")...");
 101                 }
 102
 103                 FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
 104                 myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
 105
 106
 107                 //deduplicate
 108                 if (doDeduplicate){
 109                         CdmApplicationController app = myImport.getCdmAppController();
 110                         int count = app.getAgentService().deduplicate(Person.class, null, null);
 111                         logger.warn("Deduplicated " + count + " persons.");
 112                         count = app.getAgentService().deduplicate(Team.class, null, null);
 113                         logger.warn("Deduplicated " + count + " teams.");
 114                         count = app.getReferenceService().deduplicate(Reference.class, null, null);
 115                         logger.warn("Deduplicated " + count + " references.");
 116                 }
 117
 118         }
 119
 120         private Reference getSourceReference(String string) {
 121                 Reference result = ReferenceFactory.newGeneric();
 122                 result.setTitleCache(string);
 123                 return result;
 124         }
 125
 126         private FeatureTree makeFeatureNode(ITermService service){
 127                 CentralAfricaEricaceaeTransformer transformer = new CentralAfricaEricaceaeTransformer();
 128
 129                 FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);
 130                 result.setTitleCache("Central Africa Ericaceae Feature Tree");
 131                 FeatureNode root = result.getRoot();
 132                 FeatureNode newNode;
 133
 134                 newNode = FeatureNode.NewInstance(Feature.DESCRIPTION());
 135                 root.addChild(newNode);
 136
 137                 addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service);
 138
 139                 addFeataureNodesByStringList(generellDescriptionsList, root, transformer, service);
 140
 141
 142                 newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 143                 root.addChild(newNode);
 144
 145                 newNode = FeatureNode.NewInstance(Feature.ECOLOGY());
 146                 root.addChild(newNode);
 147                 addFeataureNodesByStringList(habitatEcologyList, root, transformer, service);
 148
 149                 newNode = FeatureNode.NewInstance(Feature.USES());
 150                 root.addChild(newNode);
 151
 152                 addFeataureNodesByStringList(chomosomesList, root, transformer, service);
 153
 154                 newNode = FeatureNode.NewInstance(Feature.COMMON_NAME());
 155                 root.addChild(newNode);
 156
 157                 newNode = FeatureNode.NewInstance(Feature.CITATION());
 158                 root.addChild(newNode);
 159
 160                 return result;
 161         }
 162
 163         private static String [] chomosomesList = new String[]{
 164                 "Chromosomes",
 165         };
 166
 167
 168         private static String [] habitatEcologyList = new String[]{
 169                 "Habitat",
 170                 "Habitat & Ecology"
 171         };
 172
 173
 174         private static String [] generellDescriptionsList = new String[]{
 175                 "Fossils",
 176                 "Morphology and anatomy",
 177                 "Morphology",
 178                 "Vegetative morphology and anatomy",
 179                 "Flower morphology",
 180                 "Palynology",
 181                 "Pollination",
 182                 "Pollen morphology",
 183                 "Life cycle",
 184                 "Fruits and embryology",
 185                 "Dispersal",
 186                 "Wood anatomy",
 187                 "Leaf anatomy",
 188                 "Chromosome numbers",
 189                 "Phytochemistry and Chemotaxonomy",
 190                 "Phytochemistry",
 191                 "Taxonomy",
 192         };
 193
 194         private static String [] descriptionFeatureList = new String[]{
 195                 "lifeform",
 196                 "Bark",
 197                 "Indumentum",
 198                 "endophytic body",
 199                 "flowering buds",
 200                 "Branchlets",
 201                 "Branches",
 202                 "Branch",
 203                 "Flowering branchlets",
 204                 "Trees",
 205                 "Twigs",
 206                 "stem",
 207                 "Stems",
 208                 "stem leaves",
 209                 "Leaves",
 210                 "flower-bearing stems",
 211                 "Petiole",
 212                 "Petiolules",
 213                 "Leaflets",
 214                 "Thyrsus",
 215                 "Thyrses",
 216                 "Inflorescences",
 217                 "Inflorescence",
 218                 "Young inflorescences",
 219                 "Bracts",
 220                 "Pedicels",
 221                 "flowering buds",
 222                 "scales",
 223                 "Buds",
 224                 "Flowers",
 225                 "Flower",
 226                 "Flowering",
 227                 "Stigma",
 228                 "perianth",
 229                 "Sepals",
 230                 "Sepal",
 231                 "Outer Sepals",
 232                 "Axillary",
 233                 "cymes",
 234                 "Calyx",
 235                 "Petal",
 236                 "Petals",
 237                 "perigone tube",
 238                 "Disc",
 239                 "corolla",
 240                 "Stamens",
 241                 "Staminodes",
 242                 "Ovary",
 243                 "Anthers",
 244                 "anther",
 245                 "Pistil",
 246                 "Pistillode",
 247                 "Ovules",
 248                 "androecium",
 249                 "gynoecium",
 250                 "Filaments",
 251                 "Style",
 252                 "annulus",
 253                 "female flowers",
 254                 "Male flowers",
 255                 "Female",
 256                 "Infructescences",    //order not consistent (sometimes before "Flowers")
 257                 "Fruit",
 258                 "Fruits",
 259                 "fruiting axes",
 260                 "drupes",
 261                 "Arillode",
 262                 "seed",
 263                 "Seeds",
 264                 "Seedling",
 265                 "flower tube",
 266                 "nutlets",
 267                 "pollen",
 268                 "secondary xylem",
 269                 "chromosome number",
 270
 271                 "figure",
 272                 "fig",
 273                 "figs",
 274
 275
 276
 277
 278         };
 279
 280         public void addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
 281                 try {
 282                         for (String featureString : featureStringList){
 283                         UUID featureUuid;
 284                         featureUuid = transformer.getFeatureUuid(featureString);
 285                         Feature feature = (Feature)termService.find(featureUuid);
 286                         if (feature != null){
 287                                 FeatureNode child = FeatureNode.NewInstance(feature);
 288                                 root.addChild(child);
 289                         }
 290                 }
 291                 } catch (UndefinedTransformerMethodException e) {
 292                         logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");
 293                 }
 294         }
 295
 296
 297         //Cyprus
 298         public static URI cyprus_local() {
 299                 URI sourceUrl;
 300                 try {
 301                         sourceUrl = new URI("file:/C:/localCopy/Data/zypern/Zypern.xls");
 302                         return sourceUrl;
 303                 } catch (URISyntaxException e) {
 304                         e.printStackTrace();
 305                         return null;
 306                 }
 307         }
 308
 309
 310         /**
 311          * @param args
 312          */
 313         public static void main(String[] args) {
 314                 CyprusActivator me = new CyprusActivator();
 315                 me.doImport(cdmDestination);
 316         }
 317
 318 }