app-import/src/main/java/eu/etaxonomy/cdm/app/eflora/FloraMalesianaVol13Activator.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.app.common.CdmDestinations;
  23 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  24 import eu.etaxonomy.cdm.database.ICdmDataSource;
  25 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  26 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  27 import eu.etaxonomy.cdm.io.common.events.IIoObserver;
  28 import eu.etaxonomy.cdm.io.common.events.LoggingIoObserver;
  29 import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
  30 import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
  31 import eu.etaxonomy.cdm.io.eflora.floraMalesiana.FloraMalesianaTransformer;
  32 import eu.etaxonomy.cdm.io.markup.MarkupImportConfigurator;
  33 import eu.etaxonomy.cdm.model.description.Feature;
  34 import eu.etaxonomy.cdm.model.description.FeatureNode;
  35 import eu.etaxonomy.cdm.model.description.FeatureTree;
  36 import eu.etaxonomy.cdm.model.description.PolytomousKey;
  37 import eu.etaxonomy.cdm.model.reference.Reference;
  38 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  39
  40 /**
  41  * @author a.mueller
  42  * @created 20.06.2008
  43  * @version 1.0
  44  */
  45 public class FloraMalesianaVol13Activator {
  46         private static final Logger logger = Logger.getLogger(FloraMalesianaVol13Activator.class);
  47
  48         //database validation status (create, update, validate ...)
  49         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  50         static final URI fmSource13_small = EfloraSources.fm_13_small_families();
  51         static final URI fmSource13_large = EfloraSources.fm_13_large_families();
  52
  53
  54 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_andreasM3();
  55 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_malesiana_preview();
  56 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_malesiana_production();
  57         static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  58 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
  59 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();
  60
  61         private boolean includeVol13_small = true;
  62         private boolean includeVol13_large = true;
  63
  64         private boolean h2ForCheck = true;
  65
  66
  67         //feature tree uuid
  68         public static final UUID featureTreeUuid = UUID.fromString("168df0c6-6429-484c-b26f-ded1f7e44bd9");
  69
  70         //classification
  71         static final UUID classificationUuid = UUID.fromString("ca4e4bcb-a1d1-4124-a358-a3d3c41dd450");
  72
  73         //check - import
  74         static CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  75
  76         static boolean doPrintKeys = false;
  77
  78         //taxa
  79         static final boolean doTaxa = true;
  80
  81
  82         private boolean replaceStandardKeyTitles = false;
  83
  84         private IIoObserver observer = new LoggingIoObserver();
  85         private Set<IIoObserver> observerList = new HashSet<IIoObserver>();
  86
  87
  88         private void doImport(ICdmDataSource cdmDestination){
  89                 observerList.add(observer);
  90                 if (h2ForCheck && cdmDestination.getDatabaseType().equals(CdmDestinations.localH2().getDatabaseType())){
  91                         check = CHECK.CHECK_ONLY;
  92                 }
  93
  94                 //make Source
  95                 URI source = fmSource13_small;
  96                 MarkupImportConfigurator markupConfig= MarkupImportConfigurator.NewInstance(source, cdmDestination);
  97                 markupConfig.setClassificationUuid(classificationUuid);
  98                 markupConfig.setDoTaxa(doTaxa);
  99                 markupConfig.setCheck(check);
 100                 markupConfig.setDoPrintKeys(doPrintKeys);
 101                 markupConfig.setDbSchemaValidation(hbm2dll);
 102                 markupConfig.setObservers(observerList);
 103                 markupConfig.setReplaceStandardKeyTitles(replaceStandardKeyTitles);
 104
 105
 106                 markupConfig.setSourceReference(getSourceReference("Flora Malesiana - Vol. 13"));
 107
 108                 CdmDefaultImport<MarkupImportConfigurator> myImport = new CdmDefaultImport<MarkupImportConfigurator>();
 109
 110                 //Vol13_2
 111                 if (includeVol13_large){
 112                         System.out.println("\nStart import from ("+ fmSource13_large.toString() + ") ...");
 113                         source = fmSource13_large;
 114                         markupConfig.setSource(source);
 115                         myImport.invoke(markupConfig);
 116                         System.out.println("End import from ("+ fmSource13_large.toString() + ")...");
 117                 }
 118
 119                 //Vol13_1
 120                 if (includeVol13_small){
 121                         System.out.println("\nStart import from ("+ fmSource13_small.toString() + ") ...");
 122                         source = fmSource13_small;
 123                         markupConfig.setSource(source);
 124                         myImport.invoke(markupConfig);
 125                         System.out.println("End import from ("+ fmSource13_small.toString() + ")...");
 126                 }
 127
 128
 129 //              makeGeoService();
 130
 131                 FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
 132                 myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
 133
 134                 //check keys
 135                 if (doPrintKeys){
 136                         TransactionStatus tx = myImport.getCdmAppController().startTransaction();
 137                         List<PolytomousKey> keys = myImport.getCdmAppController().getPolytomousKeyService().list(PolytomousKey.class, null, null, null, null);
 138                         for(PolytomousKey key : keys){
 139                                 key.print(System.out);
 140                                 System.out.println();
 141                         }
 142                         myImport.getCdmAppController().commitTransaction(tx);
 143                 }
 144
 145         }
 146
 147         private Reference getSourceReference(String string) {
 148                 Reference result = ReferenceFactory.newGeneric();
 149                 result.setTitleCache(string);
 150                 return result;
 151         }
 152
 153         private FeatureTree makeFeatureNode(ITermService service){
 154                 FloraMalesianaTransformer transformer = new FloraMalesianaTransformer();
 155
 156                 FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);
 157                 result.setTitleCache("Flora Malesiana Presentation Feature Tree");
 158                 FeatureNode root = result.getRoot();
 159                 FeatureNode newNode;
 160
 161                 newNode = FeatureNode.NewInstance(Feature.DESCRIPTION());
 162                 root.addChild(newNode);
 163
 164                 addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service);
 165
 166                 addFeataureNodesByStringList(generellDescriptionsUpToAnatomyList, root, transformer, service);
 167                 newNode = FeatureNode.NewInstance(Feature.ANATOMY());
 168                 addFeataureNodesByStringList(anatomySubfeatureList, newNode, transformer, service);
 169
 170                 newNode = addFeataureNodesByStringList(generellDescriptionsFromAnatomyToPhytoChemoList, root, transformer, service);
 171                 addFeataureNodesByStringList(phytoChemoSubFeaturesList, newNode, transformer, service);
 172
 173                 newNode = addFeataureNodesByStringList(generellDescriptionsFromPhytoChemoList, root, transformer, service);
 174
 175
 176                 newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 177                 root.addChild(newNode);
 178
 179                 newNode = FeatureNode.NewInstance(Feature.ECOLOGY());
 180                 root.addChild(newNode);
 181                 addFeataureNodesByStringList(habitatEcologyList, root, transformer, service);
 182
 183                 newNode = FeatureNode.NewInstance(Feature.USES());
 184                 root.addChild(newNode);
 185
 186                 addFeataureNodesByStringList(chomosomesList, root, transformer, service);
 187
 188                 newNode = FeatureNode.NewInstance(Feature.CITATION());
 189                 root.addChild(newNode);
 190
 191                 return result;
 192         }
 193
 194         private static String [] chomosomesList = new String[]{
 195                 "Chromosomes",
 196         };
 197
 198
 199         private static String [] habitatEcologyList = new String[]{
 200                 "Habitat",
 201                 "Habitat & Ecology"
 202         };
 203
 204
 205         private static String [] generellDescriptionsUpToAnatomyList = new String[]{
 206                 "Fossils",
 207                 "Morphology and anatomy",
 208                 "Morphology",
 209                 "Vegetative morphology and anatomy",
 210         };
 211
 212
 213         private static String [] anatomySubfeatureList = new String[]{
 214                 "Leaf anatomy",
 215                 "Wood anatomy"
 216         };
 217
 218         private static String [] generellDescriptionsFromAnatomyToPhytoChemoList = new String[]{
 219                 "Flower morphology",
 220                 "Palynology",
 221                 "Pollination",
 222                 "Pollen morphology",
 223                 "embryology",
 224                 "cytology",
 225                 "Life cycle",
 226                 "Fruits and embryology",
 227                 "Dispersal",
 228                 "Chromosome numbers",
 229                 "Phytochemistry and Chemotaxonomy",
 230         };
 231
 232
 233         private static String [] phytoChemoSubFeaturesList = new String[]{
 234                 "Alkaloids",
 235                 "Iridoid glucosides",
 236                 "Leaf phenolics",
 237                 "Storage products of seeds",
 238                 "Aluminium",
 239                 "Chemotaxonomy",
 240         };
 241
 242
 243         private static String [] generellDescriptionsFromPhytoChemoList = new String[]{
 244                 "Phytochemistry",
 245                 "Taxonomy",
 246                 "history",
 247                 "cultivation",
 248                 "Notes"
 249         };
 250
 251
 252         private static String [] descriptionFeatureList = new String[]{
 253                 "lifeform",
 254                 "Bark",
 255                 //new
 256                 "wood",
 257                 "Indumentum",
 258                 "endophytic body",
 259                 "flowering buds",
 260                 "Branchlets",
 261                 "Branches",
 262                 "Branch",
 263                 "Flowering branchlets",
 264                 "Trees",
 265                 "Twigs",
 266                 "stem",
 267                 "Stems",
 268                 "stem leaves",
 269                 "Leaves",
 270                 "flower-bearing stems",
 271                 "Petiole",
 272                 "Petiolules",
 273                 "Leaflets",
 274                 "Thyrsus",
 275                 "Thyrses",
 276                 "Inflorescences",
 277                 "Inflorescence",
 278                 "Young inflorescences",
 279                 "Male inflorescences",
 280                 "Female inflorescences",
 281                 "Bracts",
 282                 "Pedicels",
 283                 "flowering buds",
 284                 "scales",
 285                 "Buds",
 286                 "Flowers",
 287                 "Flower",
 288                 "Flowering",
 289                 "Stigma",
 290                 "perianth",
 291                 "Sepals",
 292                 "Sepal",
 293                 "Outer Sepals",
 294                 "Axillary",
 295                 "cymes",
 296                 "Calyx",
 297                 "Petal",
 298                 "Petals",
 299                 "perigone",
 300                 "perigone lobes",
 301                 "perigone tube",
 302                 "Disc",
 303                 "corolla",
 304                 "Stamens",
 305                 "Staminodes",
 306                 "Ovary",
 307                 "Anthers",
 308                 "anther",
 309                 "Pistil",
 310                 "Pistillode",
 311                 "Ovules",
 312                 "androecium",
 313                 "gynoecium",
 314                 "Filaments",
 315                 "Style",
 316                 "annulus",
 317                 "female flowers",
 318                 "Male flowers",
 319                 "Female",
 320                 "Infructescences",    //order not consistent (sometimes before "Flowers")
 321                 "Fruit",
 322                 "Fruits",
 323                 "fruiting axes",
 324                 "drupes",
 325                 "Arillode",
 326                 "seed",
 327                 "Seeds",
 328                 "Seedling",
 329                 "flower tube",
 330                 "nutlets",
 331                 "pollen",
 332                 "secondary xylem",
 333                 "chromosome number",
 334
 335                 "figure",
 336                 "fig",
 337                 "figs",
 338
 339
 340
 341         };
 342
 343         public FeatureNode addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
 344                 FeatureNode lastChild = null;
 345                 try {
 346                         for (String featureString : featureStringList){
 347                                 UUID featureUuid;
 348                                 featureUuid = transformer.getFeatureUuid(featureString);
 349                                 Feature feature = (Feature)termService.find(featureUuid);
 350                                 if (feature != null){
 351                                         FeatureNode child = FeatureNode.NewInstance(feature);
 352                                         root.addChild(child);
 353                                 }
 354                         }
 355
 356                 } catch (UndefinedTransformerMethodException e) {
 357                         logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");
 358                 }
 359                 return lastChild;
 360         }
 361
 362
 363
 364         /**
 365          * @param args
 366          */
 367         public static void main(String[] args) {
 368                 FloraMalesianaVol13Activator me = new FloraMalesianaVol13Activator();
 369                 me.doImport(cdmDestination);
 370         }
 371
 372 }