app-import/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.List;
  14 import java.util.UUID;
  15
  16 import org.apache.log4j.Logger;
  17 import org.springframework.transaction.TransactionStatus;
  18
  19 import eu.etaxonomy.cdm.api.service.ITermService;
  20 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  21 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  22 import eu.etaxonomy.cdm.database.ICdmDataSource;
  23 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  24 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  25 import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
  26 import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
  27 import eu.etaxonomy.cdm.io.eflora.EfloraImportConfigurator;
  28 import eu.etaxonomy.cdm.io.eflora.floraMalesiana.FloraMalesianaTransformer;
  29 import eu.etaxonomy.cdm.model.description.Feature;
  30 import eu.etaxonomy.cdm.model.description.FeatureNode;
  31 import eu.etaxonomy.cdm.model.description.FeatureTree;
  32 import eu.etaxonomy.cdm.model.description.PolytomousKey;
  33 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  34 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  35
  36 /**
  37  * @author a.mueller
  38  * @created 20.06.2008
  39  * @version 1.0
  40  */
  41 public class FloraMalesianaActivator {
  42         private static final Logger logger = Logger.getLogger(FloraMalesianaActivator.class);
  43
  44         //database validation status (create, update, validate ...)
  45         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  46         static final URI fmSource1 = EfloraSources.fm_sapindaceae_local();
  47         static final URI fmSource2 = EfloraSources.fm_sapindaceae2_local();
  48         static final URI fmSource13_1 = EfloraSources.fm_13_1_local();
  49         static final URI fmSource13_2 = EfloraSources.fm_13_2_local();
  50
  51
  52 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_andreasM3();
  53 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_malesiana_preview();
  54 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_malesiana_production();
  55         static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  56
  57         //feature tree uuid
  58         public static final UUID featureTreeUuid = UUID.fromString("168df0c6-6429-484c-b26f-ded1f7e44bd9");
  59
  60         //classification
  61         static final UUID classificationUuid = UUID.fromString("ca4e4bcb-a1d1-4124-a358-a3d3c41dd450");
  62
  63         //check - import
  64         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  65
  66         static boolean doPrintKeys = false;
  67
  68         //taxa
  69         static final boolean doTaxa = true;
  70
  71         private boolean includeSapindaceae1 = true;
  72         private boolean includeSapindaceae2 = true;
  73         private boolean includeVol13_1 = false;
  74         private boolean includeVol13_2 = false;
  75
  76
  77         private void doImport(ICdmDataSource cdmDestination){
  78
  79                 //make Source
  80                 URI source = fmSource1;
  81                 EfloraImportConfigurator floraMalesianaConfig= EfloraImportConfigurator.NewInstance(source, cdmDestination);
  82                 floraMalesianaConfig.setTaxonomicTreeUuid(classificationUuid);
  83                 floraMalesianaConfig.setDoTaxa(doTaxa);
  84                 floraMalesianaConfig.setCheck(check);
  85                 floraMalesianaConfig.setDoPrintKeys(doPrintKeys);
  86                 floraMalesianaConfig.setDbSchemaValidation(hbm2dll);
  87
  88                 CdmDefaultImport<EfloraImportConfigurator> myImport = new CdmDefaultImport<EfloraImportConfigurator>();
  89
  90
  91                 //Sapindaceae1
  92                 if (includeSapindaceae1){
  93                         System.out.println("Start import from ("+ fmSource1.toString() + ") ...");
  94                         floraMalesianaConfig.setSourceReference(getSourceReference("Flora Malesiana - Sapindaceae I"));
  95                         myImport.invoke(floraMalesianaConfig);
  96                         System.out.println("End import from ("+ fmSource1.toString() + ")...");
  97                 }
  98
  99                 //Sapindaceae2
 100                 if (includeSapindaceae2){
 101                         System.out.println("\nStart import from ("+ fmSource2.toString() + ") ...");
 102                         source = fmSource2;
 103                         floraMalesianaConfig.setSource(source);
 104                         floraMalesianaConfig.setSourceReference(getSourceReference("Flora Malesiana - Sapindaceae II"));
 105                         myImport.invoke(floraMalesianaConfig);
 106                         System.out.println("End import from ("+ fmSource2.toString() + ")...");
 107                 }
 108
 109                 floraMalesianaConfig.setSourceReference(getSourceReference("Flora Malesiana - Vol. 13"));
 110                 //Vol13_1
 111                 if (includeVol13_1){
 112                         System.out.println("\nStart import from ("+ fmSource13_1.toString() + ") ...");
 113                         source = fmSource13_1;
 114                         floraMalesianaConfig.setSource(source);
 115                         myImport.invoke(floraMalesianaConfig);
 116                         System.out.println("End import from ("+ fmSource13_1.toString() + ")...");
 117                 }
 118
 119                 //Vol13_2
 120                 if (includeVol13_2){
 121                         System.out.println("\nStart import from ("+ fmSource13_2.toString() + ") ...");
 122                         source = fmSource13_2;
 123                         floraMalesianaConfig.setSource(source);
 124                         myImport.invoke(floraMalesianaConfig);
 125                         System.out.println("End import from ("+ fmSource13_2.toString() + ")...");
 126                 }
 127
 128                 FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
 129                 myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
 130
 131                 //check keys
 132                 if (doPrintKeys){
 133                         TransactionStatus tx = myImport.getCdmAppController().startTransaction();
 134                         List<FeatureTree> keys = myImport.getCdmAppController().getFeatureTreeService().list(PolytomousKey.class, null, null, null, null);
 135                         for(FeatureTree key : keys){
 136                                 ((PolytomousKey)key).print(System.out);
 137                                 System.out.println();
 138                         }
 139                         myImport.getCdmAppController().commitTransaction(tx);
 140                 }
 141
 142         }
 143
 144         private ReferenceBase getSourceReference(String string) {
 145                 ReferenceBase result = ReferenceFactory.newGeneric();
 146                 result.setTitleCache(string);
 147                 return result;
 148         }
 149
 150         private FeatureTree makeFeatureNode(ITermService service){
 151                 FloraMalesianaTransformer transformer = new FloraMalesianaTransformer();
 152
 153                 FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);
 154                 result.setTitleCache("Flora Malesiana Presentation Feature Tree");
 155                 FeatureNode root = result.getRoot();
 156                 FeatureNode newNode;
 157
 158                 newNode = FeatureNode.NewInstance(Feature.DESCRIPTION());
 159                 root.addChild(newNode);
 160
 161                 addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service);
 162
 163                 addFeataureNodesByStringList(generellDescriptionsList, root, transformer, service);
 164
 165
 166                 newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 167                 root.addChild(newNode);
 168
 169                 newNode = FeatureNode.NewInstance(Feature.ECOLOGY());
 170                 root.addChild(newNode);
 171                 addFeataureNodesByStringList(habitatEcologyList, root, transformer, service);
 172
 173                 newNode = FeatureNode.NewInstance(Feature.USES());
 174                 root.addChild(newNode);
 175
 176                 addFeataureNodesByStringList(chomosomesList, root, transformer, service);
 177
 178                 newNode = FeatureNode.NewInstance(Feature.CITATION());
 179                 root.addChild(newNode);
 180
 181                 return result;
 182         }
 183
 184         private static String [] chomosomesList = new String[]{
 185                 "Chromosomes",
 186         };
 187
 188
 189         private static String [] habitatEcologyList = new String[]{
 190                 "Habitat",
 191                 "Habitat & Ecology"
 192         };
 193
 194
 195         private static String [] generellDescriptionsList = new String[]{
 196                 "Fossils",
 197                 "Morphology and anatomy",
 198                 "Morphology",
 199                 "Vegetative morphology and anatomy",
 200                 "Flower morphology",
 201                 "Palynology",
 202                 "Pollination",
 203                 "Pollen morphology",
 204                 "Life cycle",
 205                 "Fruits and embryology",
 206                 "Dispersal",
 207                 "Wood anatomy",
 208                 "Leaf anatomy",
 209                 "Chromosome numbers",
 210                 "Phytochemistry and Chemotaxonomy",
 211                 "Phytochemistry",
 212                 "Taxonomy",
 213         };
 214
 215         private static String [] descriptionFeatureList = new String[]{
 216                 "lifeform",
 217                 "Bark",
 218                 "Indumentum",
 219                 "endophytic body",
 220                 "flowering buds",
 221                 "Branchlets",
 222                 "Branches",
 223                 "Branch",
 224                 "Flowering branchlets",
 225                 "Trees",
 226                 "Twigs",
 227                 "stem",
 228                 "Stems",
 229                 "stem leaves",
 230                 "Leaves",
 231                 "flower-bearing stems",
 232                 "Petiole",
 233                 "Petiolules",
 234                 "Leaflets",
 235                 "Thyrsus",
 236                 "Thyrses",
 237                 "Inflorescences",
 238                 "Inflorescence",
 239                 "Young inflorescences",
 240                 "Bracts",
 241                 "Pedicels",
 242                 "flowering buds",
 243                 "scales",
 244                 "Buds",
 245                 "Flowers",
 246                 "Flower",
 247                 "Flowering",
 248                 "Stigma",
 249                 "perianth",
 250                 "Sepals",
 251                 "Sepal",
 252                 "Outer Sepals",
 253                 "Axillary",
 254                 "cymes",
 255                 "Calyx",
 256                 "Petal",
 257                 "Petals",
 258                 "perigone tube",
 259                 "Disc",
 260                 "corolla",
 261                 "Stamens",
 262                 "Staminodes",
 263                 "Ovary",
 264                 "Anthers",
 265                 "anther",
 266                 "Pistil",
 267                 "Pistillode",
 268                 "Ovules",
 269                 "androecium",
 270                 "gynoecium",
 271                 "Filaments",
 272                 "Style",
 273                 "annulus",
 274                 "female flowers",
 275                 "Male flowers",
 276                 "Female",
 277                 "Infructescences",    //order not consistent (sometimes before "Flowers")
 278                 "Fruit",
 279                 "Fruits",
 280                 "fruiting axes",
 281                 "drupes",
 282                 "Arillode",
 283                 "seed",
 284                 "Seeds",
 285                 "Seedling",
 286                 "flower tube",
 287                 "nutlets",
 288                 "pollen",
 289                 "secondary xylem",
 290                 "chromosome number",
 291
 292                 "figure",
 293                 "fig",
 294                 "figs",
 295
 296
 297
 298
 299         };
 300
 301         public void addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
 302                 try {
 303                         for (String featureString : featureStringList){
 304                         UUID featureUuid;
 305                         featureUuid = transformer.getFeatureUuid(featureString);
 306                         Feature feature = (Feature)termService.find(featureUuid);
 307                         if (feature != null){
 308                                 FeatureNode child = FeatureNode.NewInstance(feature);
 309                                 root.addChild(child);
 310                         }
 311                 }
 312                 } catch (UndefinedTransformerMethodException e) {
 313                         logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");
 314                 }
 315         }
 316
 317
 318
 319         /**
 320          * @param args
 321          */
 322         public static void main(String[] args) {
 323                 FloraMalesianaActivator me = new FloraMalesianaActivator();
 324                 me.doImport(cdmDestination);
 325         }
 326
 327 }