cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/FloraGuianasActivator.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.markup.MarkupImportConfigurator;
  31 import eu.etaxonomy.cdm.io.markup.MarkupTransformer;
  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 FloraGuianasActivator {
  45         private static final Logger logger = Logger.getLogger(FloraGuianasActivator.class);
  46
  47         //database validation status (create, update, validate ...)
  48         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  49 //      static final URI source = EfloraSources.fdg_sample();
  50         static final URI fgu1 = EfloraSources.fgu_1();
  51 //      static final URI fgu2 = EfloraSources.fgu_2();
  52 //      static final URI fgu3 = EfloraSources.fgu_3();
  53 //      static final URI fgu4 = EfloraSources.fgu_4();
  54
  55
  56 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_guianas_preview();
  57 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_guianas_production();
  58         static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  59 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
  60
  61
  62         //feature tree uuid
  63         public static final UUID featureTreeUuid = UUID.fromString("2be99595-92fc-4f80-b9c4-b48d38505f5d");
  64
  65         //classification
  66         static final UUID classificationUuid = UUID.fromString("5e3a1b07-2609-4597-bbda-7b02dfe8c2b3");
  67
  68         private static final String SOURCE_REFERENCE_TITLE = "Flora of the Guianas";
  69         private static final String FEATURE_TREE_TITLE = "Flora of the Guianas Feature Tree";
  70
  71         //check - import
  72         private boolean h2ForCheck = true;
  73         static CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  74
  75         static boolean doPrintKeys = false;
  76
  77         //taxa
  78         static final boolean doTaxa = true;
  79
  80         private boolean includeFgu1 = true;
  81         private boolean includeFgu2 = false;
  82         private boolean includeFgu3 = false;
  83         private boolean includeFgu4 = false;
  84
  85
  86         private boolean replaceStandardKeyTitles = true;
  87
  88         private IIoObserver observer = new LoggingIoObserver();
  89         private Set<IIoObserver> observerList = new HashSet<IIoObserver>();
  90
  91
  92         private void doImport(ICdmDataSource cdmDestination){
  93                 observerList.add(observer);
  94                 if (h2ForCheck && cdmDestination.getDatabaseType().equals(CdmDestinations.localH2().getDatabaseType())){
  95                         check = CHECK.CHECK_ONLY;
  96                 }
  97
  98                 //make config
  99                 URI source = fgu1;
 100                 MarkupImportConfigurator markupConfig= MarkupImportConfigurator.NewInstance(source, cdmDestination);
 101                 markupConfig.setClassificationUuid(classificationUuid);
 102                 markupConfig.setDoTaxa(doTaxa);
 103                 markupConfig.setCheck(check);
 104                 markupConfig.setDoPrintKeys(doPrintKeys);
 105                 markupConfig.setDbSchemaValidation(hbm2dll);
 106                 markupConfig.setObservers(observerList);
 107                 markupConfig.setReplaceStandardKeyTitles(replaceStandardKeyTitles);
 108
 109
 110                 markupConfig.setSourceReference(getSourceReference(SOURCE_REFERENCE_TITLE));
 111
 112                 CdmDefaultImport<MarkupImportConfigurator> myImport = new CdmDefaultImport<MarkupImportConfigurator>();
 113
 114                 //Vol1
 115                 if (includeFgu1){
 116                         source = fgu1;
 117                         System.out.println("\nStart import from ("+ fgu1.toString() + ") ...");
 118                         markupConfig.setSource(source);
 119                         myImport.invoke(markupConfig);
 120                         System.out.println("End import from ("+ fgu1.toString() + ")...");
 121                 }
 122
 123 //              //Vol2
 124 //              if (includeFgu2){
 125 //                      source = fgu2;
 126 //                      System.out.println("\nStart import from ("+ source.toString() + ") ...");
 127 //                      markupConfig.setSource(source);
 128 //                      myImport.invoke(markupConfig);
 129 //                      System.out.println("End import from ("+ source.toString() + ")...");
 130 //              }
 131 //
 132 //              //Vol3
 133 //              if (includeFgu3){
 134 //                      source = fgu3;
 135 //                      System.out.println("\nStart import from ("+ source.toString() + ") ...");
 136 //                      markupConfig.setSource(source);
 137 //                      myImport.invoke(markupConfig);
 138 //                      System.out.println("End import from ("+ source.toString() + ")...");
 139 //              }
 140 //
 141 //              //Vol4
 142 //              if (includeFgu4){
 143 //                      source = fgu4;
 144 //                      System.out.println("\nStart import from ("+ source.toString() + ") ...");
 145 //                      markupConfig.setSource(source);
 146 //                      myImport.invoke(markupConfig);
 147 //                      System.out.println("End import from ("+ source.toString() + ")...");
 148 //              }
 149
 150                 FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
 151                 myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
 152
 153                 //check keys
 154                 if (doPrintKeys){
 155                         TransactionStatus tx = myImport.getCdmAppController().startTransaction();
 156                         List<PolytomousKey> keys = myImport.getCdmAppController().getPolytomousKeyService().list(PolytomousKey.class, null, null, null, null);
 157                         for(PolytomousKey key : keys){
 158                                 key.print(System.out);
 159                                 System.out.println();
 160                         }
 161                         myImport.getCdmAppController().commitTransaction(tx);
 162                 }
 163
 164         }
 165
 166         private Reference<?> getSourceReference(String string) {
 167                 Reference<?> result = ReferenceFactory.newGeneric();
 168                 result.setTitleCache(string);
 169                 return result;
 170         }
 171
 172         private FeatureTree makeFeatureNode(ITermService service){
 173                 MarkupTransformer transformer = new MarkupTransformer();
 174
 175                 FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);
 176                 result.setTitleCache(FEATURE_TREE_TITLE);
 177                 FeatureNode root = result.getRoot();
 178                 FeatureNode newNode;
 179
 180                 newNode = FeatureNode.NewInstance(Feature.DESCRIPTION());
 181                 root.addChild(newNode);
 182
 183                 addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service);
 184
 185                 addFeataureNodesByStringList(generellDescriptionsUpToAnatomyList, root, transformer, service);
 186                 newNode = FeatureNode.NewInstance(Feature.ANATOMY());
 187                 addFeataureNodesByStringList(anatomySubfeatureList, newNode, transformer, service);
 188
 189                 newNode = addFeataureNodesByStringList(generellDescriptionsFromAnatomyToPhytoChemoList, root, transformer, service);
 190                 addFeataureNodesByStringList(phytoChemoSubFeaturesList, newNode, transformer, service);
 191
 192                 newNode = addFeataureNodesByStringList(generellDescriptionsFromPhytoChemoList, root, transformer, service);
 193
 194
 195                 newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 196                 root.addChild(newNode);
 197
 198                 newNode = FeatureNode.NewInstance(Feature.COMMON_NAME());
 199                 root.addChild(newNode);
 200
 201                 newNode = FeatureNode.NewInstance(Feature.PHENOLOGY());
 202                 root.addChild(newNode);
 203
 204                 newNode = FeatureNode.NewInstance(Feature.ECOLOGY());
 205                 root.addChild(newNode);
 206                 addFeataureNodesByStringList(habitatEcologyList, root, transformer, service);
 207
 208                 newNode = FeatureNode.NewInstance(Feature.USES());
 209                 root.addChild(newNode);
 210
 211                 addFeataureNodesByStringList(chomosomesList, root, transformer, service);
 212
 213                 newNode = FeatureNode.NewInstance(Feature.CITATION());
 214                 root.addChild(newNode);
 215
 216                 String sql = "\nSELECT feature.titleCache " +
 217                                 " FROM DescriptionElementBase deb INNER JOIN DefinedTermBase feature ON deb.feature_id = feature.id " +
 218                                 " GROUP BY feature.id " +
 219                                 " HAVING feature.id NOT IN (SELECT DISTINCT fn.feature_id " +
 220                                 " FROM FeatureNode fn " +
 221                                 " WHERE fn.feature_id IS NOT NULL) ";
 222                 logger.warn("Check for missing features in feature tree: " + sql);
 223
 224                 return result;
 225         }
 226
 227         private static String [] chomosomesList = new String[]{
 228                 "Chromosomes",
 229         };
 230
 231
 232         private static String [] habitatEcologyList = new String[]{
 233                 "Habitat",
 234                 "Habitat & Ecology"
 235         };
 236
 237
 238         private static String [] generellDescriptionsUpToAnatomyList = new String[]{
 239                 "Fossils",
 240                 "Morphology and anatomy",
 241                 "Morphology",
 242                 "Vegetative morphology and anatomy",
 243         };
 244
 245
 246         private static String [] anatomySubfeatureList = new String[]{
 247                 "Leaf anatomy",
 248                 "Wood anatomy"
 249         };
 250
 251         private static String [] generellDescriptionsFromAnatomyToPhytoChemoList = new String[]{
 252                 "Flower morphology",
 253                 "Palynology",
 254                 "Pollination",
 255                 "Pollen morphology",
 256                 "embryology",
 257                 "cytology",
 258                 "Life cycle",
 259                 "Fruits and embryology",
 260                 "Dispersal",
 261                 "Chromosome numbers",
 262                 "Phytochemistry and Chemotaxonomy",
 263         };
 264
 265
 266         private static String [] phytoChemoSubFeaturesList = new String[]{
 267                 "Alkaloids",
 268                 "Iridoid glucosides",
 269                 "Leaf phenolics",
 270                 "Storage products of seeds",
 271                 "Aluminium",
 272                 "Chemotaxonomy",
 273         };
 274
 275
 276         private static String [] generellDescriptionsFromPhytoChemoList = new String[]{
 277                 "Phytochemistry",
 278                 "Taxonomy",
 279                 "history",
 280                 "cultivation",
 281                 "Notes"
 282         };
 283
 284
 285         private static String [] descriptionFeatureList = new String[]{
 286                 "lifeform",
 287                 "Juvenile parts",
 288                 "Bark",
 289                 //new
 290                 "wood",
 291                 "Indumentum",
 292                 "endophytic body",
 293                 "flowering buds",
 294                 "Branchlets",
 295                 "Branches",
 296                 "Branch",
 297                 "Flowering branchlets",
 298                 "Trees",
 299                 "Twigs",
 300                 "stem",
 301                 "Stems",
 302                 "stem leaves",
 303                 "Leaves",
 304                 "extraxylary sclerenchyma",
 305                 "flower-bearing stems",
 306                 "Petiole",
 307                 "Petiolules",
 308                 "Leaflets",
 309                 "Lamina",
 310                 "Veins",
 311                 "Thyrsus",
 312                 "Thyrses",
 313                 "Inflorescences",
 314                 "Inflorescence",
 315                 "Young inflorescences",
 316                 "Male inflorescences",
 317                 "Female inflorescences",
 318                 "rachises",
 319                 "Pedicels",
 320                 "Bracts",
 321                 "flowering buds",
 322                 "scales",
 323                 "Buds",
 324                 "Flowers",
 325                 "Flower",
 326                 "Flowering",
 327                 "Stigma",
 328                 "perianth",
 329                 "Sepals",
 330                 "Sepal",
 331                 "Outer Sepals",
 332                 "Axillary",
 333                 "cymes",
 334                 "Calyx",
 335                 "Petal",
 336                 "Petals",
 337                 "perigone",
 338                 "perigone lobes",
 339                 "perigone tube",
 340                 "Disc",
 341                 "corolla",
 342                 "Stamens",
 343                 "Staminodes",
 344                 "Ovary",
 345                 "Anthers",
 346                 "anther",
 347                 "Pistil",
 348                 "Pistillode",
 349                 "Ovules",
 350                 "androecium",
 351                 "gynoecium",
 352                 "Filaments",
 353                 "Style",
 354                 "annulus",
 355                 "female flowers",
 356                 "Male flowers",
 357                 "Female",
 358                 "Infructescences",    //order not consistent (sometimes before "Flowers")
 359                 "Fruit",
 360                 "Fruits",
 361                 "fruiting axes",
 362                 "drupes",
 363                 "Arillode",
 364                 "seed",
 365                 "Seeds",
 366                 "Seedling",
 367                 "flower tube",
 368                 "nutlets",
 369                 "pollen",
 370                 "secondary xylem",
 371                 "chromosome number",
 372
 373                 "figure",
 374                 "fig",
 375                 "figs",
 376
 377
 378
 379         };
 380
 381         public FeatureNode addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
 382                 FeatureNode lastChild = null;
 383                 try {
 384                         for (String featureString : featureStringList){
 385                                 UUID featureUuid;
 386                                 featureUuid = transformer.getFeatureUuid(featureString);
 387                                 Feature feature = (Feature)termService.find(featureUuid);
 388                                 if (feature != null){
 389                                         FeatureNode child = FeatureNode.NewInstance(feature);
 390                                         root.addChild(child);
 391                                 }
 392                         }
 393
 394                 } catch (UndefinedTransformerMethodException e) {
 395                         logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");
 396                 }
 397                 return lastChild;
 398         }
 399
 400
 401
 402         /**
 403          * @param args
 404          */
 405         public static void main(String[] args) {
 406                 FloraGuianasActivator me = new FloraGuianasActivator();
 407                 me.doImport(cdmDestination);
 408         }
 409 }