cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/FloreGabonActivator.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.HashSet;
  14 import java.util.List;
  15 import java.util.Set;
  16 import java.util.UUID;
  17
  18 import org.apache.log4j.Logger;
  19 import org.springframework.transaction.TransactionStatus;
  20
  21 import eu.etaxonomy.cdm.api.service.ITermService;
  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.events.IIoObserver;
  27 import eu.etaxonomy.cdm.io.common.events.LoggingIoObserver;
  28 import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
  29 import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
  30 import eu.etaxonomy.cdm.io.eflora.floraMalesiana.FloraMalesianaTransformer;
  31 import eu.etaxonomy.cdm.io.markup.MarkupImportConfigurator;
  32 import eu.etaxonomy.cdm.model.description.Feature;
  33 import eu.etaxonomy.cdm.model.description.FeatureNode;
  34 import eu.etaxonomy.cdm.model.description.FeatureTree;
  35 import eu.etaxonomy.cdm.model.description.PolytomousKey;
  36 import eu.etaxonomy.cdm.model.reference.Reference;
  37 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  38
  39 /**
  40  * @author a.mueller
  41  * @created 20.06.2008
  42  * @version 1.0
  43  */
  44 public class FloreGabonActivator {
  45         private static final Logger logger = Logger.getLogger(FloreGabonActivator.class);
  46
  47         //database validation status (create, update, validate ...)
  48         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  49         static final URI fg_sample = EfloraSources.fg_sample();
  50
  51
  52 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flore_gabon_preview();
  53 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flore_gabon_production();
  54         static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  55 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
  56
  57
  58         //feature tree uuid
  59         public static final UUID featureTreeUuid = UUID.fromString("ee688973-2595-4d4d-b11e-6df71e96a5c2");
  60
  61         //classification
  62         static final UUID classificationUuid = UUID.fromString("2f892452-ff49-48cf-834f-52ca29600719");
  63
  64         //check - import
  65         private boolean h2ForCheck = true;
  66         static CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  67
  68         static boolean doPrintKeys = false;
  69
  70         //taxa
  71         static final boolean doTaxa = true;
  72
  73         private boolean includeFgSample = true;
  74
  75
  76
  77         private boolean replaceStandardKeyTitles = false;
  78
  79         private IIoObserver observer = new LoggingIoObserver();
  80         private Set<IIoObserver> observerList = new HashSet<IIoObserver>();
  81
  82
  83         private void doImport(ICdmDataSource cdmDestination){
  84                 observerList.add(observer);
  85                 if (h2ForCheck && cdmDestination.getDatabaseType().equals(CdmDestinations.localH2().getDatabaseType())){
  86                         check = CHECK.CHECK_ONLY;
  87                 }
  88
  89                 //make Source
  90                 URI source = fg_sample;
  91                 MarkupImportConfigurator markupConfig= MarkupImportConfigurator.NewInstance(source, cdmDestination);
  92                 markupConfig.setClassificationUuid(classificationUuid);
  93                 markupConfig.setDoTaxa(doTaxa);
  94                 markupConfig.setCheck(check);
  95                 markupConfig.setDoPrintKeys(doPrintKeys);
  96                 markupConfig.setDbSchemaValidation(hbm2dll);
  97                 markupConfig.setObservers(observerList);
  98                 markupConfig.setReplaceStandardKeyTitles(replaceStandardKeyTitles);
  99
 100
 101                 markupConfig.setSourceReference(getSourceReference("Flore Gabon -  Sample"));
 102
 103                 CdmDefaultImport<MarkupImportConfigurator> myImport = new CdmDefaultImport<MarkupImportConfigurator>();
 104
 105                 //Vol13_2
 106                 if (includeFgSample){
 107                         System.out.println("\nStart import from ("+ fg_sample.toString() + ") ...");
 108                         source = fg_sample;
 109                         markupConfig.setSource(source);
 110                         myImport.invoke(markupConfig);
 111                         System.out.println("End import from ("+ fg_sample.toString() + ")...");
 112                 }
 113
 114
 115
 116
 117 //                      makeGeoService();
 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         }
 134
 135         private Reference<?> getSourceReference(String string) {
 136                 Reference<?> result = ReferenceFactory.newGeneric();
 137                 result.setTitleCache(string);
 138                 return result;
 139         }
 140
 141         private FeatureTree makeFeatureNode(ITermService service){
 142                 FloraMalesianaTransformer transformer = new FloraMalesianaTransformer();
 143
 144                 FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);
 145                 result.setTitleCache("Flore Gabon Presentation Feature Tree");
 146                 FeatureNode root = result.getRoot();
 147                 FeatureNode newNode;
 148
 149                 newNode = FeatureNode.NewInstance(Feature.DESCRIPTION());
 150                 root.addChild(newNode);
 151
 152                 addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service);
 153
 154                 addFeataureNodesByStringList(generellDescriptionsUpToAnatomyList, root, transformer, service);
 155                 newNode = FeatureNode.NewInstance(Feature.ANATOMY());
 156                 addFeataureNodesByStringList(anatomySubfeatureList, newNode, transformer, service);
 157
 158                 newNode = addFeataureNodesByStringList(generellDescriptionsFromAnatomyToPhytoChemoList, root, transformer, service);
 159                 addFeataureNodesByStringList(phytoChemoSubFeaturesList, newNode, transformer, service);
 160
 161                 newNode = addFeataureNodesByStringList(generellDescriptionsFromPhytoChemoList, 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.CITATION());
 177                 root.addChild(newNode);
 178
 179                 return result;
 180         }
 181
 182         private static String [] chomosomesList = new String[]{
 183                 "Chromosomes",
 184         };
 185
 186
 187         private static String [] habitatEcologyList = new String[]{
 188                 "Habitat",
 189                 "Habitat & Ecology"
 190         };
 191
 192
 193         private static String [] generellDescriptionsUpToAnatomyList = new String[]{
 194                 "Fossils",
 195                 "Morphology and anatomy",
 196                 "Morphology",
 197                 "Vegetative morphology and anatomy",
 198         };
 199
 200
 201         private static String [] anatomySubfeatureList = new String[]{
 202                 "Leaf anatomy",
 203                 "Wood anatomy"
 204         };
 205
 206         private static String [] generellDescriptionsFromAnatomyToPhytoChemoList = new String[]{
 207                 "Flower morphology",
 208                 "Palynology",
 209                 "Pollination",
 210                 "Pollen morphology",
 211                 "embryology",
 212                 "cytology",
 213                 "Life cycle",
 214                 "Fruits and embryology",
 215                 "Dispersal",
 216                 "Chromosome numbers",
 217                 "Phytochemistry and Chemotaxonomy",
 218         };
 219
 220
 221         private static String [] phytoChemoSubFeaturesList = new String[]{
 222                 "Alkaloids",
 223                 "Iridoid glucosides",
 224                 "Leaf phenolics",
 225                 "Storage products of seeds",
 226                 "Aluminium",
 227                 "Chemotaxonomy",
 228         };
 229
 230
 231         private static String [] generellDescriptionsFromPhytoChemoList = new String[]{
 232                 "Phytochemistry",
 233                 "Taxonomy",
 234                 "history",
 235                 "cultivation",
 236                 "Notes"
 237         };
 238
 239
 240         private static String [] descriptionFeatureList = new String[]{
 241                 "lifeform",
 242                 "Bark",
 243                 //new
 244                 "wood",
 245                 "Indumentum",
 246                 "endophytic body",
 247                 "flowering buds",
 248                 "Branchlets",
 249                 "Branches",
 250                 "Branch",
 251                 "Flowering branchlets",
 252                 "Trees",
 253                 "Twigs",
 254                 "stem",
 255                 "Stems",
 256                 "stem leaves",
 257                 "Leaves",
 258                 "flower-bearing stems",
 259                 "Petiole",
 260                 "Petiolules",
 261                 "Leaflets",
 262                 "Thyrsus",
 263                 "Thyrses",
 264                 "Inflorescences",
 265                 "Inflorescence",
 266                 "Young inflorescences",
 267                 "Male inflorescences",
 268                 "Female inflorescences",
 269                 "Bracts",
 270                 "Pedicels",
 271                 "flowering buds",
 272                 "scales",
 273                 "Buds",
 274                 "Flowers",
 275                 "Flower",
 276                 "Flowering",
 277                 "Stigma",
 278                 "perianth",
 279                 "Sepals",
 280                 "Sepal",
 281                 "Outer Sepals",
 282                 "Axillary",
 283                 "cymes",
 284                 "Calyx",
 285                 "Petal",
 286                 "Petals",
 287                 "perigone",
 288                 "perigone lobes",
 289                 "perigone tube",
 290                 "Disc",
 291                 "corolla",
 292                 "Stamens",
 293                 "Staminodes",
 294                 "Ovary",
 295                 "Anthers",
 296                 "anther",
 297                 "Pistil",
 298                 "Pistillode",
 299                 "Ovules",
 300                 "androecium",
 301                 "gynoecium",
 302                 "Filaments",
 303                 "Style",
 304                 "annulus",
 305                 "female flowers",
 306                 "Male flowers",
 307                 "Female",
 308                 "Infructescences",    //order not consistent (sometimes before "Flowers")
 309                 "Fruit",
 310                 "Fruits",
 311                 "fruiting axes",
 312                 "drupes",
 313                 "Arillode",
 314                 "seed",
 315                 "Seeds",
 316                 "Seedling",
 317                 "flower tube",
 318                 "nutlets",
 319                 "pollen",
 320                 "secondary xylem",
 321                 "chromosome number",
 322
 323                 "figure",
 324                 "fig",
 325                 "figs",
 326
 327
 328
 329         };
 330
 331         public FeatureNode addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
 332                 FeatureNode lastChild = null;
 333                 try {
 334                         for (String featureString : featureStringList){
 335                                 UUID featureUuid;
 336                                 featureUuid = transformer.getFeatureUuid(featureString);
 337                                 Feature feature = (Feature)termService.find(featureUuid);
 338                                 if (feature != null){
 339                                         FeatureNode child = FeatureNode.NewInstance(feature);
 340                                         root.addChild(child);
 341                                 }
 342                         }
 343
 344                 } catch (UndefinedTransformerMethodException e) {
 345                         logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");
 346                 }
 347                 return lastChild;
 348         }
 349
 350
 351
 352         /**
 353          * @param args
 354          */
 355         public static void main(String[] args) {
 356                 FloreGabonActivator me = new FloreGabonActivator();
 357                 me.doImport(cdmDestination);
 358         }
 359 }