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
  60
  61         //feature tree uuid
  62         public static final UUID featureTreeUuid = UUID.fromString("168df0c6-6429-484c-b26f-ded1f7e44bd9");
  63
  64         //classification
  65         static final UUID classificationUuid = UUID.fromString("ca4e4bcb-a1d1-4124-a358-a3d3c41dd450");
  66
  67         //check - import
  68         static final CHECK check = CHECK.CHECK_AND_IMPORT;
  69
  70         static boolean doPrintKeys = false;
  71
  72         //taxa
  73         static final boolean doTaxa = true;
  74
  75         private boolean includeVol13_small = true;
  76         private boolean includeVol13_large = false;
  77
  78         private IIoObserver observer = new LoggingIoObserver();
  79         private Set<IIoObserver> observerList = new HashSet<IIoObserver>();
  80
  81
  82         private void doImport(ICdmDataSource cdmDestination){
  83                 observerList.add(observer);
  84
  85                 //make Source
  86                 URI source = fmSource13_small;
  87                 MarkupImportConfigurator markupConfig= MarkupImportConfigurator.NewInstance(source, cdmDestination);
  88                 markupConfig.setClassificationUuid(classificationUuid);
  89                 markupConfig.setDoTaxa(doTaxa);
  90                 markupConfig.setCheck(check);
  91                 markupConfig.setDoPrintKeys(doPrintKeys);
  92                 markupConfig.setDbSchemaValidation(hbm2dll);
  93                 markupConfig.setObservers(observerList);
  94
  95                 CdmDefaultImport<MarkupImportConfigurator> myImport = new CdmDefaultImport<MarkupImportConfigurator>();
  96
  97
  98                 markupConfig.setSourceReference(getSourceReference("Flora Malesiana - Vol. 13"));
  99                 //Vol13_1
 100                 if (includeVol13_small){
 101                         System.out.println("\nStart import from ("+ fmSource13_small.toString() + ") ...");
 102                         source = fmSource13_small;
 103                         markupConfig.setSource(source);
 104                         myImport.invoke(markupConfig);
 105                         System.out.println("End import from ("+ fmSource13_small.toString() + ")...");
 106                 }
 107
 108                 //Vol13_2
 109                 if (includeVol13_large){
 110                         System.out.println("\nStart import from ("+ fmSource13_large.toString() + ") ...");
 111                         source = fmSource13_large;
 112                         markupConfig.setSource(source);
 113                         myImport.invoke(markupConfig);
 114                         System.out.println("End import from ("+ fmSource13_large.toString() + ")...");
 115                 }
 116
 117                 FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
 118                 myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
 119
 120                 //check keys
 121                 if (doPrintKeys){
 122                         TransactionStatus tx = myImport.getCdmAppController().startTransaction();
 123                         List<PolytomousKey> keys = myImport.getCdmAppController().getPolytomousKeyService().list(PolytomousKey.class, null, null, null, null);
 124                         for(PolytomousKey key : keys){
 125                                 key.print(System.out);
 126                                 System.out.println();
 127                         }
 128                         myImport.getCdmAppController().commitTransaction(tx);
 129                 }
 130
 131         }
 132
 133         private Reference getSourceReference(String string) {
 134                 Reference result = ReferenceFactory.newGeneric();
 135                 result.setTitleCache(string);
 136                 return result;
 137         }
 138
 139         private FeatureTree makeFeatureNode(ITermService service){
 140                 FloraMalesianaTransformer transformer = new FloraMalesianaTransformer();
 141
 142                 FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);
 143                 result.setTitleCache("Flora Malesiana Presentation Feature Tree");
 144                 FeatureNode root = result.getRoot();
 145                 FeatureNode newNode;
 146
 147                 newNode = FeatureNode.NewInstance(Feature.DESCRIPTION());
 148                 root.addChild(newNode);
 149
 150                 addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service);
 151
 152                 addFeataureNodesByStringList(generellDescriptionsList, root, transformer, service);
 153
 154
 155                 newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 156                 root.addChild(newNode);
 157
 158                 newNode = FeatureNode.NewInstance(Feature.ECOLOGY());
 159                 root.addChild(newNode);
 160                 addFeataureNodesByStringList(habitatEcologyList, root, transformer, service);
 161
 162                 newNode = FeatureNode.NewInstance(Feature.USES());
 163                 root.addChild(newNode);
 164
 165                 addFeataureNodesByStringList(chomosomesList, root, transformer, service);
 166
 167                 newNode = FeatureNode.NewInstance(Feature.CITATION());
 168                 root.addChild(newNode);
 169
 170                 return result;
 171         }
 172
 173         private static String [] chomosomesList = new String[]{
 174                 "Chromosomes",
 175         };
 176
 177
 178         private static String [] habitatEcologyList = new String[]{
 179                 "Habitat",
 180                 "Habitat & Ecology"
 181         };
 182
 183
 184         private static String [] generellDescriptionsList = new String[]{
 185                 "Fossils",
 186                 "Morphology and anatomy",
 187                 "Morphology",
 188                 "Vegetative morphology and anatomy",
 189                 "Flower morphology",
 190                 "Palynology",
 191                 "Pollination",
 192                 "Pollen morphology",
 193                 "Life cycle",
 194                 "Fruits and embryology",
 195                 "Dispersal",
 196                 "Wood anatomy",
 197                 "Leaf anatomy",
 198                 "Chromosome numbers",
 199                 "Phytochemistry and Chemotaxonomy",
 200                 "Phytochemistry",
 201                 "Taxonomy",
 202         };
 203
 204         private static String [] descriptionFeatureList = new String[]{
 205                 "lifeform",
 206                 "Bark",
 207                 "Indumentum",
 208                 "endophytic body",
 209                 "flowering buds",
 210                 "Branchlets",
 211                 "Branches",
 212                 "Branch",
 213                 "Flowering branchlets",
 214                 "Trees",
 215                 "Twigs",
 216                 "stem",
 217                 "Stems",
 218                 "stem leaves",
 219                 "Leaves",
 220                 "flower-bearing stems",
 221                 "Petiole",
 222                 "Petiolules",
 223                 "Leaflets",
 224                 "Thyrsus",
 225                 "Thyrses",
 226                 "Inflorescences",
 227                 "Inflorescence",
 228                 "Young inflorescences",
 229                 "Bracts",
 230                 "Pedicels",
 231                 "flowering buds",
 232                 "scales",
 233                 "Buds",
 234                 "Flowers",
 235                 "Flower",
 236                 "Flowering",
 237                 "Stigma",
 238                 "perianth",
 239                 "Sepals",
 240                 "Sepal",
 241                 "Outer Sepals",
 242                 "Axillary",
 243                 "cymes",
 244                 "Calyx",
 245                 "Petal",
 246                 "Petals",
 247                 "perigone tube",
 248                 "Disc",
 249                 "corolla",
 250                 "Stamens",
 251                 "Staminodes",
 252                 "Ovary",
 253                 "Anthers",
 254                 "anther",
 255                 "Pistil",
 256                 "Pistillode",
 257                 "Ovules",
 258                 "androecium",
 259                 "gynoecium",
 260                 "Filaments",
 261                 "Style",
 262                 "annulus",
 263                 "female flowers",
 264                 "Male flowers",
 265                 "Female",
 266                 "Infructescences",    //order not consistent (sometimes before "Flowers")
 267                 "Fruit",
 268                 "Fruits",
 269                 "fruiting axes",
 270                 "drupes",
 271                 "Arillode",
 272                 "seed",
 273                 "Seeds",
 274                 "Seedling",
 275                 "flower tube",
 276                 "nutlets",
 277                 "pollen",
 278                 "secondary xylem",
 279                 "chromosome number",
 280
 281                 "figure",
 282                 "fig",
 283                 "figs",
 284
 285
 286
 287
 288         };
 289
 290         public void addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
 291                 try {
 292                         for (String featureString : featureStringList){
 293                         UUID featureUuid;
 294                         featureUuid = transformer.getFeatureUuid(featureString);
 295                         Feature feature = (Feature)termService.find(featureUuid);
 296                         if (feature != null){
 297                                 FeatureNode child = FeatureNode.NewInstance(feature);
 298                                 root.addChild(child);
 299                         }
 300                 }
 301                 } catch (UndefinedTransformerMethodException e) {
 302                         logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");
 303                 }
 304         }
 305
 306
 307
 308         /**
 309          * @param args
 310          */
 311         public static void main(String[] args) {
 312                 FloraMalesianaVol13Activator me = new FloraMalesianaVol13Activator();
 313                 me.doImport(cdmDestination);
 314         }
 315
 316 }