app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/AlgaTerraActivator.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.berlinModelImport;
  11
  12 import java.util.UUID;
  13
  14 import org.apache.log4j.Logger;
  15
  16 import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
  17 import eu.etaxonomy.cdm.api.service.ITermService;
  18 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  19 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  20 import eu.etaxonomy.cdm.database.ICdmDataSource;
  21 import eu.etaxonomy.cdm.io.algaterra.AlgaTerraImportConfigurator;
  22 import eu.etaxonomy.cdm.io.algaterra.AlgaTerraImportTransformer;
  23 import eu.etaxonomy.cdm.io.algaterra.AlgaTerraSpecimenImportBase;
  24 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;
  25 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  26 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  27 import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;
  28 import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR;
  29 import eu.etaxonomy.cdm.io.common.Source;
  30 import eu.etaxonomy.cdm.model.description.Feature;
  31 import eu.etaxonomy.cdm.model.description.FeatureNode;
  32 import eu.etaxonomy.cdm.model.description.FeatureTree;
  33 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  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 AlgaTerraActivator {
  46         private static final Logger logger = Logger.getLogger(AlgaTerraActivator.class);
  47
  48         //database validation status (create, update, validate ...)
  49         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  50         static final Source berlinModelSource = BerlinModelSources.AlgaTerra();
  51         static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  52 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
  53
  54 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_algaterra_preview();
  55
  56
  57         static final UUID treeUuid = UUID.fromString("1f617402-78dc-4bf1-ac77-d260600a8879");
  58         static final int sourceSecId = 7331;
  59         static final UUID sourceRefUuid = UUID.fromString("7e1a2500-93a5-40c2-ba34-0213d7822379");
  60
  61         static final UUID featureTreeUuid = UUID.fromString("a970168a-36fd-4c7c-931e-87214a965c14");
  62         static final Object[] featureKeyList = new Integer[]{7,201,202,203,204,205,206,207};
  63         static final UUID specimenFeatureTreeUuid = UUID.fromString("ba86246e-d4d0-419f-832e-86d70b1e4bd7");
  64
  65
  66         //check - import
  67         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  68
  69         private boolean ignoreNull = true;
  70
  71         private boolean includeFlatClassifications = true;
  72         private boolean includeAllNonMisappliedRelatedClassifications = true;
  73
  74         private EDITOR editor = EDITOR.EDITOR_AS_EDITOR;
  75
  76         //NomeclaturalCode
  77         static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICBN;
  78
  79         static String factFilter = " factCategoryFk NOT IN (7, 202, 1000 ) ";
  80
  81
  82 // ****************** ALL *****************************************
  83
  84 //      //authors
  85 //      static final boolean doAuthors = true;
  86 //      //references
  87 //      static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;
  88 //      //names
  89 //      static final boolean doTaxonNames = true;
  90 //      static final boolean doRelNames = true;
  91 //      static final boolean doNameStatus = true;
  92 //      static final boolean doTypes = true;
  93 //
  94 //      //taxa
  95 //      static final boolean doTaxa = true;
  96 //      static final boolean doRelTaxa = true;
  97 //      static final boolean doFacts = true;
  98 //
  99 //      //alga terra specific
 100 //      static final boolean ecoFacts = true;
 101 //      static final boolean doFactEcology = true;
 102 //      static final boolean doImages = true;
 103
 104 // ************************ NONE **************************************** //
 105
 106         //authors
 107         static final boolean doAuthors = false;
 108         //references
 109         static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;
 110         //names
 111         static final boolean doTaxonNames = false;
 112         static final boolean doRelNames = false;
 113         static final boolean doNameStatus = false;
 114         static final boolean doTypes = false;
 115         static final boolean doNameFacts = false;
 116
 117         //taxa
 118         static final boolean doTaxa = true;
 119         static final boolean doRelTaxa = false;
 120         static final boolean doFacts = true;
 121
 122   //alga terra specific
 123         static final boolean ecoFacts = true;
 124         static final boolean doFactEcology = false;
 125         static final boolean doImages = true;
 126
 127
 128         public void invoke(String[] args){
 129                 System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") ...");
 130                 logger.debug("Start");
 131                 //make BerlinModel Source
 132                 Source source = berlinModelSource;
 133                 ICdmDataSource destination = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
 134
 135                 AlgaTerraImportConfigurator config = AlgaTerraImportConfigurator.NewInstance(source,  destination);
 136
 137                 config.setClassificationUuid(treeUuid);
 138                 config.setSourceSecId(sourceSecId);
 139                 config.setNomenclaturalCode(nomenclaturalCode);
 140
 141                 config.setDoAuthors(doAuthors);
 142                 config.setDoReferences(doReferences);
 143                 config.setDoTaxonNames(doTaxonNames);
 144                 config.setDoRelNames(doRelNames);
 145                 config.setDoNameStatus(doNameStatus);
 146                 config.setDoTypes(doTypes);
 147
 148                 config.setDoTaxa(doTaxa);
 149                 config.setDoRelTaxa(doRelTaxa);
 150                 config.setDoFacts(doFacts);
 151                 config.setDoEcoFacts(ecoFacts);
 152                 config.setDoImages(doImages);
 153                 config.setDoFactEcology(doFactEcology);
 154
 155                 config.setSourceRefUuid(sourceRefUuid);
 156                 config.setIgnoreNull(ignoreNull);
 157
 158                 config.setIncludeFlatClassifications(includeFlatClassifications);
 159                 config.setIncludeAllNonMisappliedRelatedClassifications(includeAllNonMisappliedRelatedClassifications);
 160                 config.setFactFilter(factFilter);
 161
 162                 config.setDbSchemaValidation(hbm2dll);
 163
 164                 config.setCheck(check);
 165                 config.setEditor(editor);
 166
 167                 // invoke import
 168                 CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>();
 169                 bmImport.invoke(config);
 170
 171                 if (doFacts && (config.getCheck().equals(CHECK.CHECK_AND_IMPORT)  || config.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK) )   ){
 172                         ICdmApplicationConfiguration app = bmImport.getCdmAppController();
 173
 174                         //make feature tree
 175                         makeTaxonFeatureTree(config, app);
 176
 177                         //make specimen feature tree
 178                         //TODO more specimen specific
 179                         makeSpecimenFeatureTree(config, app);
 180
 181                 }
 182
 183
 184                 System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
 185         }
 186
 187
 188         /**
 189          * @param config
 190          * @param app
 191          */
 192         private void makeTaxonFeatureTree(AlgaTerraImportConfigurator config, ICdmApplicationConfiguration app) {
 193                 FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, config.getFeatureMap(), featureKeyList);
 194                 tree.setTitleCache("AlgaTerra Taxon Feature Tree", true);
 195
 196                 FeatureNode node = FeatureNode.NewInstance(Feature.HABITAT());
 197                 tree.getRoot().addChild(node);
 198
 199                 node = FeatureNode.NewInstance(Feature.OBSERVATION());
 200                 tree.getRoot().addChild(node);
 201
 202                 node = FeatureNode.NewInstance(Feature.SPECIMEN());
 203                 tree.getRoot().addChild(node);
 204
 205                 node = FeatureNode.NewInstance(Feature.INDIVIDUALS_ASSOCIATION());
 206                 tree.getRoot().addChild(node);
 207
 208                 //needed ??
 209                 FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 210                 tree.getRoot().addChild(distributionNode, 2);
 211
 212                 //needed ??
 213                 FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE());
 214                 tree.getRoot().addChild(imageNode);
 215
 216                 app.getFeatureTreeService().saveOrUpdate(tree);
 217         }
 218
 219
 220         /**
 221          * @param config
 222          * @param app
 223          * @param tree
 224          */
 225         private void makeSpecimenFeatureTree(AlgaTerraImportConfigurator config, ICdmApplicationConfiguration app) {
 226                 ITermService termService = app.getTermService();
 227                 FeatureTree specimenTree = FeatureTree.NewInstance(specimenFeatureTreeUuid);
 228 //              FeatureTree specimenTree = TreeCreator.flatTree(specimenFeatureTreeUuid, config.getFeatureMap(), featureKeyList);
 229                 specimenTree.setTitleCache("AlgaTerra Specimen Feature Tree", true);
 230                 FeatureNode root = specimenTree.getRoot();
 231
 232
 233                 FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE());
 234                 root.addChild(imageNode);
 235
 236                 addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureAlgaTerraClimate);
 237                 FeatureNode node = FeatureNode.NewInstance(Feature.HABITAT());
 238                 root.addChild(node);
 239                 addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureHabitatExplanation);
 240                 addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureAlgaTerraLifeForm);
 241
 242                 addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureAdditionalData);
 243                 addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureSpecimenCommunity);
 244
 245                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeaturePH);
 246                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureConductivity);
 247                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureWaterTemperature);
 248                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureSilica);
 249                 FeatureNode nitrogenNode = makeNitrogenNode(root, termService);
 250                 addFeatureNodeByUuid(nitrogenNode, termService, AlgaTerraImportTransformer.uuidFeatureNitrate);
 251                 addFeatureNodeByUuid(nitrogenNode, termService, AlgaTerraImportTransformer.uuidFeatureNitrite);
 252                 addFeatureNodeByUuid(nitrogenNode, termService, AlgaTerraImportTransformer.uuidFeatureAmmonium);
 253                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeaturePhosphate);
 254                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureOrthoPhosphate);
 255                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureNPRation);
 256                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureDIN);
 257                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureSRP);
 258                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureOxygenSaturation);
 259                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureCl);
 260                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureSecchiDepth);
 261                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureCommunity);
 262                 app.getFeatureTreeService().saveOrUpdate(specimenTree);
 263         }
 264
 265         private FeatureNode makeNitrogenNode(FeatureNode root, ITermService termService) {
 266                 Feature nFeature = Feature.NewInstance("Supra feature for all Nitrogen related subfeatures", "Nitrogen", "N");
 267                 termService.save(nFeature);
 268                 FeatureNode nNode = FeatureNode.NewInstance(nFeature);
 269                 root.addChild(nNode);
 270                 return nNode;
 271         }
 272
 273
 274 //      private FeatureNode addFeataureNodesByUuidList(UUID[] featureUuidList, FeatureNode root, ITermService termService){
 275 //              FeatureNode lastChild = null;
 276 //              for (UUID featureUuid : featureUuidList){
 277 //                      addFeatureNodeByUuid(root, termService, featureUuid);
 278 //              }
 279 //
 280 //              return lastChild;
 281 //      }
 282
 283
 284         /**
 285          * @param root
 286          * @param termService
 287          * @param featureUuid
 288          */
 289         private void addFeatureNodeByUuid(FeatureNode root, ITermService termService, UUID featureUuid) {
 290                 Feature feature = (Feature)termService.find(featureUuid);
 291                 if (feature != null){
 292                         FeatureNode child = FeatureNode.NewInstance(feature);
 293                         root.addChild(child);
 294                 }
 295         }
 296
 297
 298         /**
 299          * @param args
 300          */
 301         public static void main(String[] args) {
 302                 AlgaTerraActivator activator = new AlgaTerraActivator();
 303                 activator.invoke(args);
 304         }
 305
 306 }