app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/cichorieae/TaraxacumActivator.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 java.util.Set;
  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.application.CdmApplicationController;
  20 import eu.etaxonomy.cdm.app.berlinModelImport.BerlinModelSources;
  21 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  22 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  23 import eu.etaxonomy.cdm.database.ICdmDataSource;
  24 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;
  25 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  26 import eu.etaxonomy.cdm.io.common.Source;
  27 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  28 import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;
  29 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  30 import eu.etaxonomy.cdm.model.reference.Reference;
  31 import eu.etaxonomy.cdm.model.taxon.Taxon;
  32 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  33 import eu.etaxonomy.cdm.model.taxon.Classification;
  34
  35
  36 /**
  37  * TODO add the following to a wiki page:
  38  * 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
  39  * you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.
  40  *
  41  *
  42  * @author a.mueller
  43  *
  44  */
  45 public class TaraxacumActivator {
  46         private static final Logger logger = Logger.getLogger(TaraxacumActivator.class);
  47
  48         //database validation status (create, update, validate ...)
  49         static DbSchemaValidation hbm2dll = DbSchemaValidation.UPDATE;
  50         static final Source berlinModelSource = BerlinModelSources.EDIT_Taraxacum();
  51         static final ICdmDataSource cdmDestination = CdmDestinations.localH2Cichorieae();
  52
  53         static final UUID treeUuid = UUID.fromString("019c4b4d-736b-4d2e-883c-e3244167080a");
  54 //      static final UUID treeUuid = UUID.fromString("00db28a7-50e1-4abc-86ec-b2a8ce870de9");
  55 //      static final UUID treeUuid = UUID.fromString("534e190f-3339-49ba-95d9-fa27d5493e3e");
  56         static final int sourceSecId = 7800000;
  57
  58         static final UUID featureTreeUuid = UUID.fromString("ab007336-d853-4f2f-a490-7c8232eafe7b");
  59         static final Object[] featureKeyList = new Integer[]{1, 31, 4, 98, 41};
  60
  61         //TODO update for Taraxacum
  62         static final String mediaUrlString = "http://wp5.e-taxonomy.eu/dataportal/cichorieae/media/protolog/";
  63         //Mac
  64         //static final File mediaPath = new File("/Volumes/protolog/protolog/");
  65         //Windows
  66         //static final File mediaPath = new File("\\\\media\\editwp6\\protolog");
  67         // set to zero for unlimited nameFacts
  68         static final int maximumNumberOfNameFacts = 0;
  69
  70
  71         //check - import
  72         //static final CHECK check = CHECK.CHECK_ONLY;
  73         static final CHECK check = CHECK.CHECK_AND_IMPORT;
  74
  75         //NomeclaturalCode
  76         static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICBN;
  77
  78         //ignore null
  79         static final boolean ignoreNull = true;
  80
  81
  82 // **************** ALL *********************
  83     //authors
  84         static final boolean doAuthors = true;
  85         //references
  86         static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;
  87         //names
  88         static final boolean doTaxonNames = true;
  89         static final boolean doRelNames = true;
  90         static final boolean doNameStatus = true;
  91         static final boolean doTypes = true;
  92         static final boolean doNameFacts = true;
  93
  94         //taxa
  95         static final boolean doTaxa = true;
  96         static final boolean doRelTaxa = true;
  97         static final boolean doFacts = true;
  98         static final boolean doOccurences = true;
  99         static final boolean doCommonNames = true;
 100
 101
 102 // **************** SELECTED *********************
 103 //
 104 //      //authors
 105 //      static final boolean doAuthors = false;
 106 //      //references
 107 //      static final DO_REFERENCES doReferences =  DO_REFERENCES.NONE;
 108 //      //names
 109 //      static final boolean doTaxonNames = false;
 110 //      static final boolean doRelNames = false;
 111 //      static final boolean doNameStatus = false;
 112 //      static final boolean doTypes = false;
 113 //      static final boolean doNameFacts = false;
 114 //
 115 //      //taxa
 116 //      static final boolean doTaxa = false;
 117 //      static final boolean doRelTaxa = false;
 118 //      static final boolean doFacts = false;
 119 //      static final boolean doOccurences = false;
 120
 121         /**
 122          * @param args
 123          */
 124         public boolean doImport(ICdmDataSource destination, DbSchemaValidation hbm2dll) {
 125                 boolean success = true;
 126                 logger.info("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") to " + cdmDestination.getDatabase() + " ...");
 127
 128                 //make BerlinModel Source
 129                 Source source = berlinModelSource;
 130
 131                 BerlinModelImportConfigurator bmImportConfigurator = BerlinModelImportConfigurator.NewInstance(source,  destination);
 132
 133                 bmImportConfigurator.setClassificationUuid(treeUuid);
 134 //              bmImportConfigurator.setSecUuid(secUuid);
 135                 bmImportConfigurator.setSourceSecId(sourceSecId);
 136
 137                 bmImportConfigurator.setNomenclaturalCode(nomenclaturalCode);
 138
 139                 bmImportConfigurator.setIgnoreNull(ignoreNull);
 140                 bmImportConfigurator.setDoAuthors(doAuthors);
 141                 bmImportConfigurator.setDoReferences(doReferences);
 142                 bmImportConfigurator.setDoTaxonNames(doTaxonNames);
 143                 bmImportConfigurator.setDoRelNames(doRelNames);
 144                 bmImportConfigurator.setDoNameStatus(doNameStatus);
 145                 bmImportConfigurator.setDoTypes(doTypes);
 146                 bmImportConfigurator.setDoNameFacts(doNameFacts);
 147
 148                 bmImportConfigurator.setDoTaxa(doTaxa);
 149                 bmImportConfigurator.setDoRelTaxa(doRelTaxa);
 150                 bmImportConfigurator.setDoFacts(doFacts);
 151                 bmImportConfigurator.setDoOccurrence(doOccurences);
 152                 bmImportConfigurator.setDoCommonNames(doCommonNames);
 153
 154                 bmImportConfigurator.setDbSchemaValidation(hbm2dll);
 155
 156
 157                 // mediaResourceLocations
 158                 File mediaPath = CichorieaeActivator.protologuePath;
 159                 if ( mediaPath.exists() && mediaPath.isDirectory()){
 160                         bmImportConfigurator.setMediaUrl(mediaUrlString);
 161                         bmImportConfigurator.setMediaPath(mediaPath);
 162                 }else{
 163                         logger.warn("Could not configure mediaResourceLocations");
 164                 }
 165
 166                 // maximum number of name facts to import
 167                 bmImportConfigurator.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts);
 168
 169
 170                 bmImportConfigurator.setCheck(check);
 171
 172                 // invoke import
 173                 CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>();
 174                 success &= bmImport.invoke(bmImportConfigurator);
 175
 176                 if (bmImportConfigurator.getCheck().equals(CHECK.CHECK_AND_IMPORT)  || bmImportConfigurator.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK)    ){
 177                         CdmApplicationController app = bmImport.getCdmAppController();
 178                         TransactionStatus tx = app.startTransaction();
 179                         //make feature tree
 180 //                      FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, bmImportConfigurator.getFeatureMap(), featureKeyList);
 181 //                      FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE());
 182 //                      tree.getRoot().addChild(imageNode);
 183 //                      FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 184 //                      FeatureNode featureNode = tree.getRoot();
 185 //                      tree.getRoot().addChild(distributionNode, featureNode.getChildCount() + 1);
 186 //                      app.getFeatureTreeService().saveOrUpdate(tree);
 187                         mergeIntoCichorieae(app);
 188                         app.commitTransaction(tx);
 189                 }
 190
 191                 logger.info("End import from BerlinModel ("+ source.getDatabase() + ")...");
 192                 return success;
 193         }
 194
 195
 196         public boolean mergeIntoCichorieae(CdmApplicationController app){
 197                 boolean success = true;
 198         //      String taraxTaraxacumUuidStr = "9a7bced0-fa1a-432e-9cca-57b62219cde6";
 199                 String taraxTaraxacumUuidStr = "b86f1156-091c-494d-a9c9-c84d71058f98";
 200                 UUID taraxTaraxacumUUID = UUID.fromString(taraxTaraxacumUuidStr);
 201
 202                 String cichTaraxacumUuidStr = "c946ac62-b6c6-493b-8ed9-278fa38b931a";
 203                 UUID cichTaraxacumUUID = UUID.fromString(cichTaraxacumUuidStr);
 204
 205                 Taxon taraxacumInCichTaxon = (Taxon)app.getTaxonService().find(cichTaraxacumUUID);
 206                 if (taraxacumInCichTaxon != null) {
 207                         logger.info("Merge Taraxacum");
 208                         Set<TaxonNode> taxonNodesInCich = taraxacumInCichTaxon.getTaxonNodes();
 209                         TaxonNode taxonNodeInCich = null;
 210                         TaxonNode parentNodeInCich = null;
 211                         Taxon parentInCich = null;
 212                         TaxonNode taxonNodeInTarax = null;
 213
 214                         if (taxonNodesInCich == null || taxonNodesInCich.isEmpty()) {
 215                                 logger.error("No taxon nodes found for Taraxacum in cichorieae database");
 216                                 success = false;
 217                         } else {
 218                                 logger.info(taxonNodesInCich.size()+ " taxon node(s) found for Taraxacum in Cich DB");
 219                                 taxonNodeInCich = taxonNodesInCich.iterator().next();
 220                                 parentNodeInCich = (TaxonNode) taxonNodeInCich.getParent();
 221                                 parentInCich = parentNodeInCich.getTaxon();
 222                         }
 223
 224                         Taxon taraxacumInTaraxTaxon = (Taxon)app.getTaxonService().find(taraxTaraxacumUUID);
 225
 226                         Set<TaxonNode> taxonNodesInTarax = taraxacumInTaraxTaxon.getTaxonNodes();
 227
 228                         Classification treeInTaraxacum = null;
 229                         if (taxonNodesInTarax == null || taxonNodesInTarax.isEmpty()) {
 230                                 logger.warn("No taxon nodes found for Taraxacum in taraxacum database");
 231                                 success = false;
 232                         }else{
 233                                 taxonNodeInTarax = taxonNodesInTarax.iterator().next();
 234                                 treeInTaraxacum = taxonNodeInTarax.getClassification();
 235                         }
 236
 237                         //TODO reference
 238                         Reference citation = null;
 239                         String microcitation = null;
 240
 241                         taxonNodeInTarax = parentNodeInCich.addChildNode(taxonNodeInTarax, citation, microcitation, null);
 242                         //parentNodeInCich.getClassification().addParentChild(parentInCich, taraxacumInTaraxTaxon, null, null);
 243
 244                         parentNodeInCich.deleteChildNode(taxonNodeInCich);
 245
 246                         app.getTaxonService().save(parentInCich);
 247                         app.getTaxonService().delete(taraxacumInCichTaxon);
 248                         try {
 249 //                              app.getClassificationService().delete(treeInTaraxacum); //throws exception
 250                         } catch (Exception e) {
 251                                 e.printStackTrace();
 252                                 return false;
 253                         }
 254                 }else{
 255                         logger.warn("Taraxacum in cichorieae not found");
 256                         success = false;
 257                 }
 258                 return success;
 259         }
 260
 261         public static void main(String[] args) {
 262                 TaraxacumActivator ta = new TaraxacumActivator();
 263                 ICdmDataSource destination = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
 264
 265                 ta.doImport(destination, hbm2dll);
 266
 267         }
 268
 269 }