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 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_algaterra_production();
  56
  57
  58         static final UUID treeUuid = UUID.fromString("1f617402-78dc-4bf1-ac77-d260600a8879");
  59         static final int sourceSecId = 7331;
  60         static final UUID sourceRefUuid = UUID.fromString("7e1a2500-93a5-40c2-ba34-0213d7822379");
  61
  62         static final UUID featureTreeUuid = UUID.fromString("a970168a-36fd-4c7c-931e-87214a965c14");
  63         static final Object[] featureKeyList = new Integer[]{7,201,203,204,206,207};
  64         static final UUID specimenFeatureTreeUuid = UUID.fromString("ba86246e-d4d0-419f-832e-86d70b1e4bd7");
  65
  66         static final boolean loginAsDefaultAdmin = true;
  67         static final boolean removeRestricted = true;
  68
  69         //check - import
  70         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  71
  72         private boolean ignoreNull = true;
  73
  74         private boolean includeFlatClassifications = true;
  75         private boolean includeAllNonMisappliedRelatedClassifications = true;
  76
  77         private EDITOR editor = EDITOR.EDITOR_AS_EDITOR;
  78
  79         //NomeclaturalCode
  80         static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP;
  81
  82         static String factFilter = " factCategoryFk NOT IN (7, 201, 202, 203, 204, 205, 206, 207, 208, 1000 ) ";
  83
  84
  85 // ****************** ALL *****************************************
  86
  87         //authors
  88         static final boolean doAuthors = true;
  89         //references
  90         static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;
  91         //names
  92         static final boolean doTaxonNames = true;
  93         static final boolean doRelNames = true;
  94         static final boolean doNameStatus = true;
  95         static final boolean doTypes = true;
  96
  97         //taxa
  98         static final boolean doTaxa = true;
  99         static final boolean doRelTaxa = true;
 100         static final boolean doFacts = true;
 101
 102         //alga terra specific
 103         static final boolean ecoFacts = true;
 104         static final boolean doFactEcology = true;
 105         static final boolean doImages = true;
 106         static final boolean doDna = true;
 107         static final boolean doMorphology = false;
 108
 109 // ************************ NONE **************************************** //
 110
 111 //      //authors
 112 //      static final boolean doAuthors = false;
 113 //      //references
 114 //      static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;
 115 //      //names
 116 //      static final boolean doTaxonNames = false;
 117 //      static final boolean doRelNames = false;
 118 //      static final boolean doNameStatus = false;
 119 //      static final boolean doTypes = false;
 120 //      static final boolean doNameFacts = false;
 121 //
 122 //      //taxa
 123 //      static final boolean doTaxa = true;
 124 //      static final boolean doRelTaxa = false;
 125 //      static final boolean doFacts = false;
 126 //
 127 //  //alga terra specific
 128 //      static final boolean ecoFacts = true;
 129 //      static final boolean doFactEcology = false;
 130 //      static final boolean doImages = false;
 131 //      static final boolean doDna = true;
 132 //      static final boolean doMorphology = false;
 133
 134
 135         public void invoke(String[] args){
 136                 System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") ...");
 137                 logger.debug("Start");
 138                 //make BerlinModel Source
 139                 Source source = berlinModelSource;
 140                 ICdmDataSource destination = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
 141
 142                 AlgaTerraImportConfigurator config = AlgaTerraImportConfigurator.NewInstance(source,  destination);
 143
 144                 config.setClassificationUuid(treeUuid);
 145                 config.setSourceSecId(sourceSecId);
 146                 config.setNomenclaturalCode(nomenclaturalCode);
 147
 148                 config.setDoAuthors(doAuthors);
 149                 config.setDoReferences(doReferences);
 150                 config.setDoTaxonNames(doTaxonNames);
 151                 config.setDoRelNames(doRelNames);
 152                 config.setDoNameStatus(doNameStatus);
 153                 config.setDoTypes(doTypes);
 154
 155                 config.setDoTaxa(doTaxa);
 156                 config.setDoRelTaxa(doRelTaxa);
 157                 config.setDoFacts(doFacts);
 158                 config.setDoEcoFacts(ecoFacts);
 159                 config.setDoImages(doImages);
 160                 config.setDoFactEcology(doFactEcology);
 161                 config.setDoDna(doDna);
 162                 config.setDoMorphology(doMorphology);
 163
 164                 config.setSourceRefUuid(sourceRefUuid);
 165                 config.setIgnoreNull(ignoreNull);
 166                 config.setRemoveRestricted(removeRestricted);
 167
 168                 config.setIncludeFlatClassifications(includeFlatClassifications);
 169                 config.setIncludeAllNonMisappliedRelatedClassifications(includeAllNonMisappliedRelatedClassifications);
 170                 config.setFactFilter(factFilter);
 171
 172                 config.setDbSchemaValidation(hbm2dll);
 173
 174                 config.setCheck(check);
 175                 config.setEditor(editor);
 176
 177                 if (loginAsDefaultAdmin){
 178                         config.authenticateAsDefaultAdmin();
 179                 }
 180
 181                 // invoke import
 182                 CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>();
 183                 bmImport.invoke(config);
 184
 185                 if (doFacts && (config.getCheck().equals(CHECK.CHECK_AND_IMPORT)  || config.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK) )   ){
 186                         ICdmApplicationConfiguration app = bmImport.getCdmAppController();
 187
 188                         //make feature tree
 189                         makeTaxonFeatureTree(config, app);
 190
 191                         //make specimen feature tree
 192                         //TODO more specimen specific
 193                         makeSpecimenFeatureTree(config, app);
 194
 195                 }
 196
 197
 198                 System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
 199         }
 200
 201
 202         /**
 203          * @param config
 204          * @param app
 205          */
 206         private void makeTaxonFeatureTree(AlgaTerraImportConfigurator config, ICdmApplicationConfiguration app) {
 207                 FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, config.getFeatureMap(), featureKeyList);
 208                 tree.setTitleCache("AlgaTerra Taxon Feature Tree", true);
 209
 210                 FeatureNode node = FeatureNode.NewInstance(Feature.HABITAT());
 211                 tree.getRoot().addChild(node);
 212
 213 //              node = FeatureNode.NewInstance(Feature.OBSERVATION());
 214 //              tree.getRoot().addChild(node);
 215 //
 216 //              node = FeatureNode.NewInstance(Feature.SPECIMEN());
 217 //              tree.getRoot().addChild(node);
 218 //
 219 //              node = FeatureNode.NewInstance(Feature.INDIVIDUALS_ASSOCIATION());
 220 //              tree.getRoot().addChild(node);
 221
 222                 //needed ??
 223                 FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 224                 tree.getRoot().addChild(distributionNode, 2);
 225
 226 //              //needed ??
 227 //              FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE());
 228 //              tree.getRoot().addChild(imageNode);
 229
 230                 app.getFeatureTreeService().saveOrUpdate(tree);
 231         }
 232
 233
 234         /**
 235          * @param config
 236          * @param app
 237          * @param tree
 238          */
 239         private void makeSpecimenFeatureTree(AlgaTerraImportConfigurator config, ICdmApplicationConfiguration app) {
 240                 ITermService termService = app.getTermService();
 241                 FeatureTree specimenTree = FeatureTree.NewInstance(specimenFeatureTreeUuid);
 242 //              FeatureTree specimenTree = TreeCreator.flatTree(specimenFeatureTreeUuid, config.getFeatureMap(), featureKeyList);
 243                 specimenTree.setTitleCache("AlgaTerra Specimen Feature Tree", true);
 244                 FeatureNode root = specimenTree.getRoot();
 245
 246
 247                 FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE());
 248                 root.addChild(imageNode);
 249
 250                 addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureAlgaTerraClimate);
 251                 FeatureNode node = FeatureNode.NewInstance(Feature.HABITAT());
 252                 root.addChild(node);
 253                 addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureHabitatExplanation);
 254                 addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureAlgaTerraLifeForm);
 255
 256                 addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureAdditionalData);
 257                 addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureSpecimenCommunity);
 258
 259                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeaturePH);
 260                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureConductivity);
 261                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureWaterTemperature);
 262                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureSilica);
 263                 FeatureNode nitrogenNode = makeNitrogenNode(root, termService);
 264                 addFeatureNodeByUuid(nitrogenNode, termService, AlgaTerraImportTransformer.uuidFeatureNitrate);
 265                 addFeatureNodeByUuid(nitrogenNode, termService, AlgaTerraImportTransformer.uuidFeatureNitrite);
 266                 addFeatureNodeByUuid(nitrogenNode, termService, AlgaTerraImportTransformer.uuidFeatureAmmonium);
 267                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeaturePhosphate);
 268                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureOrthoPhosphate);
 269                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureNPRation);
 270                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureDIN);
 271                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureSRP);
 272                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureOxygenSaturation);
 273                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureCl);
 274                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureSecchiDepth);
 275                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureCommunity);
 276                 app.getFeatureTreeService().saveOrUpdate(specimenTree);
 277         }
 278
 279         private FeatureNode makeNitrogenNode(FeatureNode root, ITermService termService) {
 280                 Feature nFeature = Feature.NewInstance("Supra feature for all Nitrogen related subfeatures", "Nitrogen", "N");
 281                 termService.save(nFeature);
 282                 FeatureNode nNode = FeatureNode.NewInstance(nFeature);
 283                 root.addChild(nNode);
 284                 return nNode;
 285         }
 286
 287
 288 //      private FeatureNode addFeataureNodesByUuidList(UUID[] featureUuidList, FeatureNode root, ITermService termService){
 289 //              FeatureNode lastChild = null;
 290 //              for (UUID featureUuid : featureUuidList){
 291 //                      addFeatureNodeByUuid(root, termService, featureUuid);
 292 //              }
 293 //
 294 //              return lastChild;
 295 //      }
 296
 297
 298         /**
 299          * @param root
 300          * @param termService
 301          * @param featureUuid
 302          */
 303         private void addFeatureNodeByUuid(FeatureNode root, ITermService termService, UUID featureUuid) {
 304                 Feature feature = (Feature)termService.find(featureUuid);
 305                 if (feature != null){
 306                         FeatureNode child = FeatureNode.NewInstance(feature);
 307                         root.addChild(child);
 308                 }
 309         }
 310
 311
 312         /**
 313          * @param args
 314          */
 315         public static void main(String[] args) {
 316                 AlgaTerraActivator activator = new AlgaTerraActivator();
 317                 activator.invoke(args);
 318         }
 319
 320 }