app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/cichorieae/CichorieaeActivator.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.wp6.cichorieae;
  11
  12 import java.io.File;
  13 import eu.etaxonomy.cdm.common.URI;
  14 import java.net.URISyntaxException;
  15 import java.util.UUID;
  16
  17 import org.apache.log4j.Logger;
  18
  19 import eu.etaxonomy.cdm.api.application.ICdmRepository;
  20 import eu.etaxonomy.cdm.app.berlinModelImport.BerlinModelSources;
  21 import eu.etaxonomy.cdm.app.berlinModelImport.TreeCreator;
  22 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  23 import eu.etaxonomy.cdm.app.images.ImageImportConfigurator;
  24 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  25 import eu.etaxonomy.cdm.database.ICdmDataSource;
  26 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;
  27 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  28 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
  29 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  30 import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;
  31 import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR;
  32 import eu.etaxonomy.cdm.io.common.ImportResult;
  33 import eu.etaxonomy.cdm.io.common.Source;
  34 import eu.etaxonomy.cdm.io.wp6.CichorieaeImageImport;
  35 import eu.etaxonomy.cdm.model.description.Feature;
  36 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  37 import eu.etaxonomy.cdm.model.name.TaxonName;
  38 import eu.etaxonomy.cdm.model.term.TermTree;
  39
  40
  41 /**
  42  * TODO add the following to a wiki page:
  43  * HINT: If you are about to import into a mysql data base running under windows and if you wish to dump and restore the resulting data bas under another operation systen
  44  * you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.
  45  *
  46  *
  47  * @author a.mueller
  48  *
  49  */
  50 public class CichorieaeActivator {
  51         private static final Logger logger = Logger.getLogger(CichorieaeActivator.class);
  52
  53         //database validation status (create, update, validate ...)
  54         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  55         static final Source berlinModelSource = BerlinModelSources.EDIT_CICHORIEAE();
  56         static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();
  57
  58         static final UUID secUuid = UUID.fromString("6924c75d-e0d0-4a6d-afb7-3dd8c71195ca");
  59         static final UUID classificationUuid = UUID.fromString("534e190f-3339-49ba-95d9-fa27d5493e3e");
  60 //      static final UUID treeUuid = UUID.fromString("00db28a7-50e1-4abc-86ec-b2a8ce870de9");
  61         static final int sourceSecId = 7800000;
  62
  63         static final UUID featureTreeUuid = UUID.fromString("ae9615b8-bc60-4ed0-ad96-897f9226d568");
  64         static final Object[] featureKeyList = new Integer[]{1, 43, 31, 4, 12, 98, 41};
  65
  66         /* --------- MEDIA recources ------------ */
  67         static final boolean stopOnMediaErrors = false;
  68         static final String protologueUrlString = "http://wp5.e-taxonomy.eu/dataportal/cichorieae/media/protolog/";
  69         //Mac
  70         //static final File protologuePath = new File("/Volumes/protolog/protolog/");
  71         //Windows
  72         public static final String imageFolderString  = "//media/editwp6/photos";
  73         static final File protologuePath = new File("//media/editwp6/protolog");
  74 //      public static final File imageFolder  = new File("/media/photos");
  75 //      static final File protologuePath = new File("/media/protolog");
  76         /* -------------------------------------- */
  77
  78         // set to zero for unlimited nameFacts
  79         static final int maximumNumberOfNameFacts = 0;
  80         static final int recordsPerTransaction = 2000;
  81
  82         //should the other imports run as well?
  83         static final boolean includeTaraxacum = true;
  84         static final boolean includeImages = false;
  85
  86
  87         //check - import
  88         static final CHECK check = CHECK.CHECK_AND_IMPORT;
  89
  90         //editor - import
  91         static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR;
  92
  93         //NomenclaturalCode
  94         static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP;
  95
  96         //ignore null
  97         static final boolean ignoreNull = true;
  98
  99         static boolean useClassification = true;
 100
 101
 102 // **************** ALL *********************
 103
 104         static final boolean doUser = true;
 105         //authors
 106         static final boolean doAuthors = true;
 107         //references
 108         static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;
 109         //names
 110         static final boolean doTaxonNames = true;
 111         static final boolean doRelNames = true;
 112         static final boolean doNameStatus = true;
 113         static final boolean doTypes = true;
 114         static final boolean doNameFacts = true;
 115
 116         //taxa
 117         static final boolean doTaxa = true;
 118         static final boolean doRelTaxa = true;
 119         static final boolean doFacts = false;
 120         static final boolean doOccurences = false;
 121         static final boolean doCommonNames = true;
 122
 123         //etc.
 124         static final boolean doMarker = false;
 125
 126
 127 // **************** SELECTED *********************
 128 //
 129 //      static final boolean doUser = false;
 130 //      //authors
 131 //      static final boolean doAuthors = false;
 132 //      //references
 133 //      static final DO_REFERENCES doReferences =  DO_REFERENCES.NONE;
 134 //      //names
 135 //      static final boolean doTaxonNames = false;
 136 //      static final boolean doRelNames = false;
 137 //      static final boolean doNameStatus = false;
 138 //      static final boolean doTypes = false;
 139 //      static final boolean doNameFacts = false;
 140 //
 141 //      //taxa
 142 //      static final boolean doTaxa = false;
 143 //      static final boolean doRelTaxa = false;
 144 //      static final boolean doCommonNames = false;
 145 //      static final boolean doFacts = false;
 146 //      static final boolean doOccurences = false;
 147 //
 148 //      //etc.
 149 //      static final boolean doMarker = false;
 150
 151
 152         private ImportResult doInvoke(ICdmDataSource destination){
 153                 ImportResult success = new ImportResult();
 154                 Source source = berlinModelSource;
 155
 156                 BerlinModelImportConfigurator bmImportConfigurator = BerlinModelImportConfigurator.NewInstance(source,  destination);
 157
 158                 bmImportConfigurator.setClassificationUuid(classificationUuid);
 159                 bmImportConfigurator.setSourceSecId(sourceSecId);
 160
 161                 bmImportConfigurator.setNomenclaturalCode(nomenclaturalCode);
 162
 163                 bmImportConfigurator.setIgnoreNull(ignoreNull);
 164                 bmImportConfigurator.setDoAuthors(doAuthors);
 165                 bmImportConfigurator.setDoReferences(doReferences);
 166                 bmImportConfigurator.setDoTaxonNames(doTaxonNames);
 167                 bmImportConfigurator.setDoRelNames(doRelNames);
 168                 bmImportConfigurator.setDoNameStatus(doNameStatus);
 169                 bmImportConfigurator.setDoTypes(doTypes);
 170                 bmImportConfigurator.setDoNameFacts(doNameFacts);
 171                 bmImportConfigurator.setUseClassification(useClassification);
 172
 173                 bmImportConfigurator.setDoTaxa(doTaxa);
 174                 bmImportConfigurator.setDoRelTaxa(doRelTaxa);
 175                 bmImportConfigurator.setDoFacts(doFacts);
 176                 bmImportConfigurator.setDoOccurrence(doOccurences);
 177                 bmImportConfigurator.setDoCommonNames(doCommonNames);
 178
 179                 bmImportConfigurator.setDoMarker(doMarker);
 180                 bmImportConfigurator.setDoUser(doUser);
 181                 bmImportConfigurator.setEditor(editor);
 182                 bmImportConfigurator.setDbSchemaValidation(hbm2dll);
 183                 bmImportConfigurator.setRecordsPerTransaction(recordsPerTransaction);
 184
 185
 186                 // protologueResourceLocations
 187                 if ( protologuePath.exists() && protologuePath.isDirectory()){
 188                         bmImportConfigurator.setMediaUrl(protologueUrlString);
 189                         bmImportConfigurator.setMediaPath(protologuePath);
 190                 }else{
 191                         if(stopOnMediaErrors){
 192                                 logger.error("Could not configure protologue ResourceLocations -> will quit.");
 193                                 System.exit(-1);
 194                         }
 195                         logger.error("Could not configure protologue ResourceLocations");
 196                 }
 197
 198                 File imageFolder = new File(imageFolderString);
 199                 // also check the image source folder
 200                 if ( !imageFolder.exists() || !imageFolder.isDirectory()){
 201                         if(stopOnMediaErrors){
 202                                 logger.error("Could not configure imageFolder  -> will quit.");
 203                                 System.exit(-1);
 204                         }
 205                         logger.error("Could not configure imageFolder");
 206                 }
 207
 208                 // maximum number of name facts to import
 209                 bmImportConfigurator.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts);
 210
 211
 212                 bmImportConfigurator.setCheck(check);
 213                 bmImportConfigurator.setEditor(editor);
 214
 215                 // invoke import
 216                 CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>();
 217                 success = bmImport.invoke(bmImportConfigurator);
 218
 219                 if (doFacts && (bmImportConfigurator.getCheck().equals(CHECK.CHECK_AND_IMPORT)  || bmImportConfigurator.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK) )   ){
 220                         ICdmRepository app = bmImport.getCdmAppController();
 221                         TaxonName obj = app.getCommonService().getSourcedObjectByIdInSource(TaxonName.class, "1000027", null);
 222                         logger.info(obj);
 223
 224                         //make feature tree
 225                         TermTree<Feature> tree = TreeCreator.flatTree(featureTreeUuid, bmImportConfigurator.getFeatureMap(), featureKeyList);
 226                         tree.getRoot().addChild(Feature.IMAGE());
 227                         tree.getRoot().addChild(Feature.DISTRIBUTION(), 2);
 228                         app.getFeatureTreeService().saveOrUpdate(tree);
 229                 }
 230
 231                 System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
 232
 233
 234                 try {
 235                         if (includeTaraxacum) {
 236                                 System.out.println("Start Taraxacum import from BerlinModel ...");
 237                                 TaraxacumActivator taraxacumActivator = new TaraxacumActivator();
 238                                 ImportResult successTaraxacum =  taraxacumActivator.doImport(destination, DbSchemaValidation.UPDATE);
 239                                 success.merge(successTaraxacum);
 240                                 logger.warn("Taraxacum import still needs to be tested");
 241                                 System.out.println("End Taraxacum import from BerlinModel ...");
 242                         }
 243                 } catch (Exception e) {
 244                     success.addException(e);
 245                         logger.error("Exception occurred during Taraxacum import.");
 246                         e.printStackTrace();
 247                 }
 248
 249
 250
 251                 if (includeImages) {
 252                         System.out.println("Start importing images ...");
 253                         CdmDefaultImport<IImportConfigurator> imageImporter = new CdmDefaultImport<IImportConfigurator>();
 254                         URI imageFolderCichorieae;
 255                         try {
 256                                 imageFolderCichorieae = new URI(CichorieaeActivator.imageFolderString);
 257                                 ImageImportConfigurator imageConfigurator = ImageImportConfigurator.NewInstance(
 258                                                 imageFolderCichorieae, destination, CichorieaeImageImport.class);
 259                                 imageConfigurator.setSecUuid(secUuid);
 260                                 imageConfigurator.setClassificationUuid(classificationUuid);
 261                                 ImportResult resultImageImport = imageImporter.invoke(imageConfigurator);
 262                                 success.merge(resultImageImport);
 263                         } catch (URISyntaxException e) {
 264                                 e.printStackTrace();
 265                         }
 266                         System.out.println("End importing images ...");
 267                 }
 268                 logger.warn("!!!! NOTE: RefDetail notes and RelPTaxon notes are not imported automatically. Please check for these notes and import them manually.");
 269
 270                 return success;
 271
 272         }
 273
 274         /**
 275          * @param args
 276          */
 277         public static void main(String[] args) {
 278                 ICdmDataSource destination = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
 279
 280                 System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") to " + destination.getDatabase() + " ...");
 281                 CichorieaeActivator me = new CichorieaeActivator();
 282                 me.doInvoke(destination);
 283
 284         }
 285
 286 }