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.Reference;
  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 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
  57
  58
  59         //feature tree uuid
  60         public static final UUID featureTreeUuid = UUID.fromString("168df0c6-6429-484c-b26f-ded1f7e44bd9");
  61
  62         //classification
  63         static final UUID classificationUuid = UUID.fromString("ca4e4bcb-a1d1-4124-a358-a3d3c41dd450");
  64
  65         //check - import
  66         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  67
  68         static boolean doPrintKeys = false;
  69
  70         //taxa
  71         static final boolean doTaxa = true;
  72
  73         private boolean includeSapindaceae1 = true;
  74         private boolean includeSapindaceae2 = true;
  75         private boolean includeVol13_1 = false;
  76         private boolean includeVol13_2 = false;
  77
  78
  79         private void doImport(ICdmDataSource cdmDestination){
  80
  81                 //make Source
  82                 URI source = fmSource1;
  83                 EfloraImportConfigurator floraMalesianaConfig= EfloraImportConfigurator.NewInstance(source, cdmDestination);
  84                 floraMalesianaConfig.setClassificationUuid(classificationUuid);
  85                 floraMalesianaConfig.setDoTaxa(doTaxa);
  86                 floraMalesianaConfig.setCheck(check);
  87                 floraMalesianaConfig.setDoPrintKeys(doPrintKeys);
  88                 floraMalesianaConfig.setDbSchemaValidation(hbm2dll);
  89
  90                 CdmDefaultImport<EfloraImportConfigurator> myImport = new CdmDefaultImport<EfloraImportConfigurator>();
  91
  92
  93                 //Sapindaceae1
  94                 if (includeSapindaceae1){
  95                         System.out.println("Start import from ("+ fmSource1.toString() + ") ...");
  96                         floraMalesianaConfig.setSourceReference(getSourceReference("Flora Malesiana - Sapindaceae I"));
  97                         myImport.invoke(floraMalesianaConfig);
  98                         System.out.println("End import from ("+ fmSource1.toString() + ")...");
  99                 }
 100
 101                 //Sapindaceae2
 102                 if (includeSapindaceae2){
 103                         System.out.println("\nStart import from ("+ fmSource2.toString() + ") ...");
 104                         source = fmSource2;
 105                         floraMalesianaConfig.setSource(source);
 106                         floraMalesianaConfig.setSourceReference(getSourceReference("Flora Malesiana - Sapindaceae II"));
 107                         myImport.invoke(floraMalesianaConfig);
 108                         System.out.println("End import from ("+ fmSource2.toString() + ")...");
 109                 }
 110
 111                 floraMalesianaConfig.setSourceReference(getSourceReference("Flora Malesiana - Vol. 13"));
 112                 //Vol13_1
 113                 if (includeVol13_1){
 114                         System.out.println("\nStart import from ("+ fmSource13_1.toString() + ") ...");
 115                         source = fmSource13_1;
 116                         floraMalesianaConfig.setSource(source);
 117                         myImport.invoke(floraMalesianaConfig);
 118                         System.out.println("End import from ("+ fmSource13_1.toString() + ")...");
 119                 }
 120
 121                 //Vol13_2
 122                 if (includeVol13_2){
 123                         System.out.println("\nStart import from ("+ fmSource13_2.toString() + ") ...");
 124                         source = fmSource13_2;
 125                         floraMalesianaConfig.setSource(source);
 126                         myImport.invoke(floraMalesianaConfig);
 127                         System.out.println("End import from ("+ fmSource13_2.toString() + ")...");
 128                 }
 129
 130                 FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
 131                 myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
 132
 133                 //check keys
 134                 if (doPrintKeys){
 135                         TransactionStatus tx = myImport.getCdmAppController().startTransaction();
 136                         List<PolytomousKey> keys = myImport.getCdmAppController().getPolytomousKeyService().list(PolytomousKey.class, null, null, null, null);
 137                         for(PolytomousKey key : keys){
 138                                 key.print(System.out);
 139                                 System.out.println();
 140                         }
 141                         myImport.getCdmAppController().commitTransaction(tx);
 142                 }
 143
 144         }
 145
 146         private Reference getSourceReference(String string) {
 147                 Reference result = ReferenceFactory.newGeneric();
 148                 result.setTitleCache(string);
 149                 return result;
 150         }
 151
 152         private FeatureTree makeFeatureNode(ITermService service){
 153                 FloraMalesianaTransformer transformer = new FloraMalesianaTransformer();
 154
 155                 FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);
 156                 result.setTitleCache("Flora Malesiana Presentation Feature Tree");
 157                 FeatureNode root = result.getRoot();
 158                 FeatureNode newNode;
 159
 160                 newNode = FeatureNode.NewInstance(Feature.DESCRIPTION());
 161                 root.addChild(newNode);
 162
 163                 addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service);
 164
 165                 addFeataureNodesByStringList(generellDescriptionsList, root, transformer, service);
 166
 167
 168                 newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 169                 root.addChild(newNode);
 170
 171                 newNode = FeatureNode.NewInstance(Feature.ECOLOGY());
 172                 root.addChild(newNode);
 173                 addFeataureNodesByStringList(habitatEcologyList, root, transformer, service);
 174
 175                 newNode = FeatureNode.NewInstance(Feature.USES());
 176                 root.addChild(newNode);
 177
 178                 addFeataureNodesByStringList(chomosomesList, root, transformer, service);
 179
 180                 newNode = FeatureNode.NewInstance(Feature.CITATION());
 181                 root.addChild(newNode);
 182
 183                 return result;
 184         }
 185
 186         private static String [] chomosomesList = new String[]{
 187                 "Chromosomes",
 188         };
 189
 190
 191         private static String [] habitatEcologyList = new String[]{
 192                 "Habitat",
 193                 "Habitat & Ecology"
 194         };
 195
 196
 197         private static String [] generellDescriptionsList = new String[]{
 198                 "Fossils",
 199                 "Morphology and anatomy",
 200                 "Morphology",
 201                 "Vegetative morphology and anatomy",
 202                 "Flower morphology",
 203                 "Palynology",
 204                 "Pollination",
 205                 "Pollen morphology",
 206                 "Life cycle",
 207                 "Fruits and embryology",
 208                 "Dispersal",
 209                 "Wood anatomy",
 210                 "Leaf anatomy",
 211                 "Chromosome numbers",
 212                 "Phytochemistry and Chemotaxonomy",
 213                 "Phytochemistry",
 214                 "Taxonomy",
 215         };
 216
 217         private static String [] descriptionFeatureList = new String[]{
 218                 "lifeform",
 219                 "Bark",
 220                 "Indumentum",
 221                 "endophytic body",
 222                 "flowering buds",
 223                 "Branchlets",
 224                 "Branches",
 225                 "Branch",
 226                 "Flowering branchlets",
 227                 "Trees",
 228                 "Twigs",
 229                 "stem",
 230                 "Stems",
 231                 "stem leaves",
 232                 "Leaves",
 233                 "flower-bearing stems",
 234                 "Petiole",
 235                 "Petiolules",
 236                 "Leaflets",
 237                 "Thyrsus",
 238                 "Thyrses",
 239                 "Inflorescences",
 240                 "Inflorescence",
 241                 "Young inflorescences",
 242                 "Bracts",
 243                 "Pedicels",
 244                 "flowering buds",
 245                 "scales",
 246                 "Buds",
 247                 "Flowers",
 248                 "Flower",
 249                 "Flowering",
 250                 "Stigma",
 251                 "perianth",
 252                 "Sepals",
 253                 "Sepal",
 254                 "Outer Sepals",
 255                 "Axillary",
 256                 "cymes",
 257                 "Calyx",
 258                 "Petal",
 259                 "Petals",
 260                 "perigone tube",
 261                 "Disc",
 262                 "corolla",
 263                 "Stamens",
 264                 "Staminodes",
 265                 "Ovary",
 266                 "Anthers",
 267                 "anther",
 268                 "Pistil",
 269                 "Pistillode",
 270                 "Ovules",
 271                 "androecium",
 272                 "gynoecium",
 273                 "Filaments",
 274                 "Style",
 275                 "annulus",
 276                 "female flowers",
 277                 "Male flowers",
 278                 "Female",
 279                 "Infructescences",    //order not consistent (sometimes before "Flowers")
 280                 "Fruit",
 281                 "Fruits",
 282                 "fruiting axes",
 283                 "drupes",
 284                 "Arillode",
 285                 "seed",
 286                 "Seeds",
 287                 "Seedling",
 288                 "flower tube",
 289                 "nutlets",
 290                 "pollen",
 291                 "secondary xylem",
 292                 "chromosome number",
 293
 294                 "figure",
 295                 "fig",
 296                 "figs",
 297
 298
 299
 300
 301         };
 302
 303         public void addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
 304                 try {
 305                         for (String featureString : featureStringList){
 306                         UUID featureUuid;
 307                         featureUuid = transformer.getFeatureUuid(featureString);
 308                         Feature feature = (Feature)termService.find(featureUuid);
 309                         if (feature != null){
 310                                 FeatureNode child = FeatureNode.NewInstance(feature);
 311                                 root.addChild(child);
 312                         }
 313                 }
 314                 } catch (UndefinedTransformerMethodException e) {
 315                         logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");
 316                 }
 317         }
 318
 319
 320
 321         /**
 322          * @param args
 323          */
 324         public static void main(String[] args) {
 325                 FloraMalesianaActivator me = new FloraMalesianaActivator();
 326                 me.doImport(cdmDestination);
 327         }
 328
 329 }