cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/FloraMalesianaActivator.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  */
  43 public class FloraMalesianaActivator extends EfloraActivatorBase {
  44         private static final Logger logger = Logger.getLogger(FloraMalesianaActivator.class);
  45
  46         //database validation status (create, update, validate ...)
  47         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  48
  49         static final URI fmSource12_1 = EfloraSources.fm_12_1();
  50         static final URI fmSource12_2 = EfloraSources.fm_12_2();
  51         static final URI fmSource13 = EfloraSources.fm_13();
  52         static final URI fmSource14 = EfloraSources.fm_14();
  53         static final URI fmSource15 = EfloraSources.fm_15();
  54         static final URI fmSource16 = EfloraSources.fm_16();
  55         static final URI fmSource17_1 = EfloraSources.fm_17_1();
  56         static final URI fmSource17_2 = EfloraSources.fm_17_2();
  57         static final URI fmSource18 = EfloraSources.fm_18();
  58         static final URI fmSource19 = EfloraSources.fm_19();
  59         static final URI fmSource20 = EfloraSources.fm_20();
  60
  61         static final URI fmSource_Ser2_02 = EfloraSources.fm_ser2_2();
  62         static final URI fmSource_Ser2_03 = EfloraSources.fm_ser2_3();
  63
  64
  65 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_malesiana_preview();
  66 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_malesiana_production();
  67         static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  68 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
  69 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();
  70
  71         private boolean includeBase = true;
  72         private boolean includeVol12_1 = includeBase;
  73         private boolean includeVol12_2 = includeBase;
  74         private boolean includeVol13 = includeBase;
  75         private boolean includeVol14 = includeBase;
  76         private boolean includeVol15 = includeBase;
  77         private boolean includeVol16 = includeBase;
  78         private boolean includeVol17_1 = includeBase;
  79         private boolean includeVol17_2 = includeBase;
  80         private boolean includeVol18 = includeBase;
  81         private boolean includeVol19 = includeBase;
  82         private boolean includeVol20 = includeBase;
  83         private boolean includeVol2_2 = includeBase;
  84         private boolean includeVol2_3 = includeBase;
  85
  86         private boolean h2ForCheck = false;
  87
  88         static final boolean reuseState = true;  //when running multiple imports
  89
  90
  91         //feature tree uuid
  92         public static final UUID featureTreeUuid = UUID.fromString("168df0c6-6429-484c-b26f-ded1f7e44bd9");
  93         private static final String featureTreeTitle = "Flora Malesiana Presentation Feature Tree";
  94
  95         //classification
  96         static final UUID classificationUuid = UUID.fromString("ca4e4bcb-a1d1-4124-a358-a3d3c41dd450");
  97         static final String classificationTitle = "Flora Malesiana";
  98
  99         //check - import
 100         static CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
 101
 102         static boolean doPrintKeys = false;
 103
 104         //taxa
 105         static final boolean doTaxa = true;
 106
 107
 108         private boolean replaceStandardKeyTitles = false;
 109
 110         private IIoObserver observer = new LoggingIoObserver();
 111         private Set<IIoObserver> observerList = new HashSet<IIoObserver>();
 112
 113
 114         private void doImport(ICdmDataSource cdmDestination){
 115                 observerList.add(observer);
 116                 if (h2ForCheck && cdmDestination.getDatabaseType().equals(CdmDestinations.localH2().getDatabaseType())){
 117                         check = CHECK.CHECK_ONLY;
 118                 }
 119
 120                 //make Source
 121 //              URI source = fmSource13_small;
 122                 URI source = null;
 123
 124                 MarkupImportConfigurator markupConfig= MarkupImportConfigurator.NewInstance(source, cdmDestination);
 125                 markupConfig.setClassificationUuid(classificationUuid);
 126                 markupConfig.setClassificationName(classificationTitle);
 127                 markupConfig.setDoTaxa(doTaxa);
 128                 markupConfig.setCheck(check);
 129                 markupConfig.setDoPrintKeys(doPrintKeys);
 130                 markupConfig.setDbSchemaValidation(hbm2dll);
 131                 markupConfig.setObservers(observerList);
 132                 markupConfig.setReplaceStandardKeyTitles(replaceStandardKeyTitles);
 133                 markupConfig.setReuseExistingState(reuseState);
 134
 135                 markupConfig.setSourceReference(getSourceReference("Flora Malesiana - Vol. 13"));
 136
 137                 CdmDefaultImport<MarkupImportConfigurator> myImport = new CdmDefaultImport<MarkupImportConfigurator>();
 138
 139
 140
 141                 //Vol16
 142                 doSource(includeVol16, fmSource16, "Flora Malesiana - vol. 16", markupConfig, myImport);
 143
 144
 145                 //Vol12_1
 146                 doSource(includeVol12_1, fmSource12_1, "Flora Malesiana - vol. 12, pt.1", markupConfig, myImport);
 147
 148                 //Vol12_2
 149                 doSource(includeVol12_2, fmSource12_2, "Flora Malesiana - vol. 12, pt.2", markupConfig, myImport);
 150
 151                 //Vol13_large
 152                 doSource(includeVol13, fmSource13, "Flora Malesiana - vol. 13", markupConfig, myImport);
 153
 154                 //Vol14
 155                 doSource(includeVol14, fmSource14, "Flora Malesiana - vol. 14", markupConfig, myImport);
 156
 157                 //Vol15
 158                 doSource(includeVol15, fmSource15, "Flora Malesiana - vol. 15", markupConfig, myImport);
 159                 //Vol17, part1
 160                 doSource(includeVol17_1, fmSource17_1, "Flora Malesiana - vol. 17, part I", markupConfig, myImport);
 161
 162                 //Vol17, part2
 163                 doSource(includeVol17_2, fmSource17_2, "Flora Malesiana - vol. 17, part II", markupConfig, myImport);
 164
 165                 //Vol18
 166                 doSource(includeVol18, fmSource18, "Flora Malesiana - vol. 18", markupConfig, myImport);
 167
 168                 //Vol19
 169                 doSource(includeVol19, fmSource19, "Flora Malesiana - vol. 19", markupConfig, myImport);
 170
 171                 //Vol20
 172                 doSource(includeVol20, fmSource20, "Flora Malesiana - vol. 20", markupConfig, myImport);
 173
 174                 //Vol_2_2
 175                 doSource(includeVol2_2, fmSource_Ser2_02, "Flora Malesiana - Ser.2, vol. 2", markupConfig, myImport);
 176
 177                 //Vol_2_3
 178                 doSource(includeVol2_3, fmSource_Ser2_03, "Flora Malesiana - Ser.2, vol. 3", markupConfig, myImport);
 179
 180                 makeAutomatedFeatureTree(myImport.getCdmAppController(), markupConfig.getState(),
 181                                 featureTreeUuid, featureTreeTitle);
 182
 183 //              makeGeoService();
 184
 185                 FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
 186                 myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
 187
 188                 //check keys
 189                 if (doPrintKeys){
 190                         TransactionStatus tx = myImport.getCdmAppController().startTransaction();
 191                         List<PolytomousKey> keys = myImport.getCdmAppController().getPolytomousKeyService().list(PolytomousKey.class, null, null, null, null);
 192                         for(PolytomousKey key : keys){
 193                                 key.print(System.out);
 194                                 System.out.println();
 195                         }
 196                         myImport.getCdmAppController().commitTransaction(tx);
 197                 }
 198
 199         }
 200
 201         private void doSource(boolean doInclude, URI source, String sourceTitle, MarkupImportConfigurator markupConfig,
 202                         CdmDefaultImport<MarkupImportConfigurator> myImport) {
 203                 if (doInclude){
 204                         System.out.println("\nStart import from ("+ source.toString() + ") ...");
 205                         markupConfig.setSource(source);
 206                         markupConfig.setSourceReference(getSourceReference(sourceTitle));
 207                         myImport.invoke(markupConfig);
 208                         System.out.println("End import from ("+ source.toString() + ")...");
 209                 }
 210         }
 211
 212         private Reference<?> getSourceReference(String string) {
 213                 Reference<?> result = ReferenceFactory.newGeneric();
 214                 result.setTitleCache(string);
 215                 return result;
 216         }
 217
 218         private FeatureTree makeFeatureNode(ITermService service){
 219                 FloraMalesianaTransformer transformer = new FloraMalesianaTransformer();
 220
 221                 FeatureTree result = FeatureTree.NewInstance(UUID.randomUUID());
 222                 result.setTitleCache("Flora Malesiana Presentation Feature Tree - Old");
 223                 FeatureNode root = result.getRoot();
 224                 FeatureNode newNode;
 225
 226                 newNode = FeatureNode.NewInstance(Feature.DESCRIPTION());
 227                 root.addChild(newNode);
 228
 229                 addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service);
 230
 231                 addFeataureNodesByStringList(generellDescriptionsUpToAnatomyList, root, transformer, service);
 232                 newNode = FeatureNode.NewInstance(Feature.ANATOMY());
 233                 addFeataureNodesByStringList(anatomySubfeatureList, newNode, transformer, service);
 234
 235                 newNode = addFeataureNodesByStringList(generellDescriptionsFromAnatomyToPhytoChemoList, root, transformer, service);
 236                 addFeataureNodesByStringList(phytoChemoSubFeaturesList, newNode, transformer, service);
 237
 238                 newNode = addFeataureNodesByStringList(generellDescriptionsFromPhytoChemoList, root, transformer, service);
 239
 240
 241                 newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 242                 root.addChild(newNode);
 243
 244                 newNode = FeatureNode.NewInstance(Feature.ECOLOGY());
 245                 root.addChild(newNode);
 246                 addFeataureNodesByStringList(habitatEcologyList, root, transformer, service);
 247
 248                 newNode = FeatureNode.NewInstance(Feature.USES());
 249                 root.addChild(newNode);
 250
 251                 addFeataureNodesByStringList(chomosomesList, root, transformer, service);
 252
 253                 newNode = FeatureNode.NewInstance(Feature.CITATION());
 254                 root.addChild(newNode);
 255
 256                 return result;
 257         }
 258
 259         private static String [] chomosomesList = new String[]{
 260                 "Chromosomes",
 261         };
 262
 263
 264         private static String [] habitatEcologyList = new String[]{
 265                 "Habitat",
 266                 "Habitat & Ecology"
 267         };
 268
 269
 270         private static String [] generellDescriptionsUpToAnatomyList = new String[]{
 271                 "Fossils",
 272                 "Morphology and anatomy",
 273                 "Morphology",
 274                 "Vegetative morphology and anatomy",
 275         };
 276
 277
 278         private static String [] anatomySubfeatureList = new String[]{
 279                 "Leaf anatomy",
 280                 "Wood anatomy"
 281         };
 282
 283         private static String [] generellDescriptionsFromAnatomyToPhytoChemoList = new String[]{
 284                 "Flower morphology",
 285                 "Palynology",
 286                 "Pollination",
 287                 "Pollen morphology",
 288                 "embryology",
 289                 "cytology",
 290                 "Life cycle",
 291                 "Fruits and embryology",
 292                 "Dispersal",
 293                 "Chromosome numbers",
 294                 "Phytochemistry and Chemotaxonomy",
 295         };
 296
 297
 298         private static String [] phytoChemoSubFeaturesList = new String[]{
 299                 "Alkaloids",
 300                 "Iridoid glucosides",
 301                 "Leaf phenolics",
 302                 "Storage products of seeds",
 303                 "Aluminium",
 304                 "Chemotaxonomy",
 305         };
 306
 307
 308         private static String [] generellDescriptionsFromPhytoChemoList = new String[]{
 309                 "Phytochemistry",
 310                 "Taxonomy",
 311                 "history",
 312                 "cultivation",
 313                 "Notes"
 314         };
 315
 316
 317         private static String [] descriptionFeatureList = new String[]{
 318                 "lifeform",
 319                 "Bark",
 320                 //new
 321                 "wood",
 322                 "Indumentum",
 323                 "endophytic body",
 324                 "flowering buds",
 325                 "Branchlets",
 326                 "Branches",
 327                 "Branch",
 328                 "Flowering branchlets",
 329                 "Trees",
 330                 "Twigs",
 331                 "stem",
 332                 "Stems",
 333                 "stem leaves",
 334                 "Leaves",
 335                 "flower-bearing stems",
 336                 "Petiole",
 337                 "Petiolules",
 338                 "Leaflets",
 339                 "Thyrsus",
 340                 "Thyrses",
 341                 "Inflorescences",
 342                 "Inflorescence",
 343                 "Young inflorescences",
 344                 "Male inflorescences",
 345                 "Female inflorescences",
 346                 "Bracts",
 347                 "Pedicels",
 348                 "flowering buds",
 349                 "scales",
 350                 "Buds",
 351                 "Flowers",
 352                 "Flower",
 353                 "Flowering",
 354                 "Stigma",
 355                 "perianth",
 356                 "Sepals",
 357                 "Sepal",
 358                 "Outer Sepals",
 359                 "Axillary",
 360                 "cymes",
 361                 "Calyx",
 362                 "Petal",
 363                 "Petals",
 364                 "perigone",
 365                 "perigone lobes",
 366                 "perigone tube",
 367                 "Disc",
 368                 "corolla",
 369                 "Stamens",
 370                 "Staminodes",
 371                 "Ovary",
 372                 "Anthers",
 373                 "anther",
 374                 "Pistil",
 375                 "Pistillode",
 376                 "Ovules",
 377                 "androecium",
 378                 "gynoecium",
 379                 "Filaments",
 380                 "Style",
 381                 "annulus",
 382                 "female flowers",
 383                 "Male flowers",
 384                 "Female",
 385                 "Infructescences",    //order not consistent (sometimes before "Flowers")
 386                 "Fruit",
 387                 "Fruits",
 388                 "fruiting axes",
 389                 "drupes",
 390                 "Arillode",
 391                 "seed",
 392                 "Seeds",
 393                 "Seedling",
 394                 "flower tube",
 395                 "nutlets",
 396                 "pollen",
 397                 "secondary xylem",
 398                 "chromosome number",
 399
 400                 "figure",
 401                 "fig",
 402                 "figs",
 403
 404
 405
 406         };
 407
 408         public FeatureNode addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
 409                 FeatureNode lastChild = null;
 410                 try {
 411                         for (String featureString : featureStringList){
 412                                 UUID featureUuid;
 413                                 featureUuid = transformer.getFeatureUuid(featureString);
 414                                 Feature feature = (Feature)termService.find(featureUuid);
 415                                 if (feature != null){
 416                                         FeatureNode child = FeatureNode.NewInstance(feature);
 417                                         root.addChild(child);
 418                                 }
 419                         }
 420
 421                 } catch (UndefinedTransformerMethodException e) {
 422                         logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");
 423                 }
 424                 return lastChild;
 425         }
 426
 427
 428
 429         /**
 430          * @param args
 431          */
 432         public static void main(String[] args) {
 433                 FloraMalesianaActivator me = new FloraMalesianaActivator();
 434                 me.doImport(cdmDestination);
 435         }
 436
 437 }