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         static final boolean importOriginalSizeMedia = false;
  70
  71         //check - import
  72         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  73
  74         private boolean ignoreNull = true;
  75
  76         private boolean includeFlatClassifications = true;
  77         private boolean includeAllNonMisappliedRelatedClassifications = true;
  78
  79         private EDITOR editor = EDITOR.EDITOR_AS_EDITOR;
  80
  81         //NomeclaturalCode
  82         static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP;
  83
  84         static String factFilter = " factCategoryFk NOT IN (7, 201, 202, 203, 204, 205, 206, 207, 208, 1000 ) ";
  85
  86
  87 // ****************** ALL *****************************************
  88
  89         //authors
  90         static final boolean doAuthors = true;
  91         //references
  92         static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;
  93         //names
  94         static final boolean doTaxonNames = true;
  95         static final boolean doRelNames = true;
  96         static final boolean doNameStatus = true;
  97         static final boolean doTypes = true;
  98
  99         //taxa
 100         static final boolean doTaxa = true;
 101         static final boolean doRelTaxa = true;
 102         static final boolean doFacts = true;
 103
 104         //alga terra specific
 105         static final boolean ecoFacts = true;
 106         static final boolean doFactEcology = true;
 107         static final boolean doImages = false;
 108         static final boolean doDna = true;
 109         static final boolean doMorphology = true;
 110
 111 // ************************ NONE **************************************** //
 112
 113 //      //authors
 114 //      static final boolean doAuthors = false;
 115 //      //references
 116 //      static final DO_REFERENCES doReferences =  DO_REFERENCES.NONE;
 117 //      //names
 118 //      static final boolean doTaxonNames = false;
 119 //      static final boolean doRelNames = false;
 120 //      static final boolean doNameStatus = false;
 121 //      static final boolean doTypes = false;
 122 //      static final boolean doNameFacts = false;
 123 //
 124 //      //taxa
 125 //      static final boolean doTaxa = false;
 126 //      static final boolean doRelTaxa = false;
 127 //      static final boolean doFacts = false;
 128 //
 129 //  //alga terra specific
 130 //      static final boolean ecoFacts = true;
 131 //      static final boolean doFactEcology = false;
 132 //      static final boolean doImages = false;
 133 //      static final boolean doDna = false;
 134 //      static final boolean doMorphology = true;
 135
 136
 137         public void invoke(String[] args){
 138                 System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") ...");
 139                 logger.debug("Start");
 140                 //make BerlinModel Source
 141                 Source source = berlinModelSource;
 142                 ICdmDataSource destination = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
 143
 144                 AlgaTerraImportConfigurator config = AlgaTerraImportConfigurator.NewInstance(source,  destination);
 145
 146                 config.setClassificationUuid(treeUuid);
 147                 config.setSourceSecId(sourceSecId);
 148                 config.setNomenclaturalCode(nomenclaturalCode);
 149
 150                 config.setDoAuthors(doAuthors);
 151                 config.setDoReferences(doReferences);
 152                 config.setDoTaxonNames(doTaxonNames);
 153                 config.setDoRelNames(doRelNames);
 154                 config.setDoNameStatus(doNameStatus);
 155                 config.setDoTypes(doTypes);
 156
 157                 config.setDoTaxa(doTaxa);
 158                 config.setDoRelTaxa(doRelTaxa);
 159                 config.setDoFacts(doFacts);
 160                 config.setDoEcoFacts(ecoFacts);
 161                 config.setDoImages(doImages);
 162                 config.setDoFactEcology(doFactEcology);
 163                 config.setDoDna(doDna);
 164                 config.setDoMorphology(doMorphology);
 165
 166                 config.setSourceRefUuid(sourceRefUuid);
 167                 config.setIgnoreNull(ignoreNull);
 168                 config.setRemoveRestricted(removeRestricted);
 169                 config.setImportOriginalSizeMedia(importOriginalSizeMedia);
 170
 171                 config.setIncludeFlatClassifications(includeFlatClassifications);
 172                 config.setIncludeAllNonMisappliedRelatedClassifications(includeAllNonMisappliedRelatedClassifications);
 173                 config.setFactFilter(factFilter);
 174
 175                 config.setDbSchemaValidation(hbm2dll);
 176
 177                 config.setCheck(check);
 178                 config.setEditor(editor);
 179
 180                 if (loginAsDefaultAdmin){
 181                         config.authenticateAsDefaultAdmin();
 182                 }
 183
 184                 // invoke import
 185                 CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>();
 186                 bmImport.invoke(config);
 187
 188                 if (doFacts && (config.getCheck().equals(CHECK.CHECK_AND_IMPORT)  || config.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK) )   ){
 189                         ICdmApplicationConfiguration app = bmImport.getCdmAppController();
 190
 191                         //make feature tree
 192                         makeTaxonFeatureTree(config, app);
 193
 194                         //make specimen feature tree
 195                         //TODO more specimen specific
 196                         makeSpecimenFeatureTree(config, app);
 197
 198                 }
 199
 200
 201                 System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
 202         }
 203
 204
 205         /**
 206          * @param config
 207          * @param app
 208          */
 209         private void makeTaxonFeatureTree(AlgaTerraImportConfigurator config, ICdmApplicationConfiguration app) {
 210                 FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, config.getFeatureMap(), featureKeyList);
 211                 tree.setTitleCache("AlgaTerra Taxon Feature Tree", true);
 212
 213                 FeatureNode node = FeatureNode.NewInstance(Feature.HABITAT());
 214                 tree.getRoot().addChild(node);
 215
 216 //              node = FeatureNode.NewInstance(Feature.OBSERVATION());
 217 //              tree.getRoot().addChild(node);
 218 //
 219 //              node = FeatureNode.NewInstance(Feature.SPECIMEN());
 220 //              tree.getRoot().addChild(node);
 221 //
 222 //              node = FeatureNode.NewInstance(Feature.INDIVIDUALS_ASSOCIATION());
 223 //              tree.getRoot().addChild(node);
 224
 225                 //needed ??
 226                 FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 227                 tree.getRoot().addChild(distributionNode, 2);
 228
 229 //              //needed ??
 230 //              FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE());
 231 //              tree.getRoot().addChild(imageNode);
 232
 233                 app.getFeatureTreeService().saveOrUpdate(tree);
 234         }
 235
 236
 237         /**
 238          * @param config
 239          * @param app
 240          * @param tree
 241          */
 242         private void makeSpecimenFeatureTree(AlgaTerraImportConfigurator config, ICdmApplicationConfiguration app) {
 243                 ITermService termService = app.getTermService();
 244                 FeatureTree specimenTree = FeatureTree.NewInstance(specimenFeatureTreeUuid);
 245 //              FeatureTree specimenTree = TreeCreator.flatTree(specimenFeatureTreeUuid, config.getFeatureMap(), featureKeyList);
 246                 specimenTree.setTitleCache("AlgaTerra Specimen Feature Tree", true);
 247                 FeatureNode root = specimenTree.getRoot();
 248
 249
 250                 FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE());
 251                 root.addChild(imageNode);
 252
 253                 addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureAlgaTerraClimate);
 254                 FeatureNode node = FeatureNode.NewInstance(Feature.HABITAT());
 255                 root.addChild(node);
 256                 addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureHabitatExplanation);
 257                 addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureAlgaTerraLifeForm);
 258
 259                 addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureAdditionalData);
 260                 addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureSpecimenCommunity);
 261
 262                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeaturePH);
 263                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureConductivity);
 264                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureWaterTemperature);
 265                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureSilica);
 266                 FeatureNode nitrogenNode = makeNitrogenNode(root, termService);
 267                 addFeatureNodeByUuid(nitrogenNode, termService, AlgaTerraImportTransformer.uuidFeatureNitrate);
 268                 addFeatureNodeByUuid(nitrogenNode, termService, AlgaTerraImportTransformer.uuidFeatureNitrite);
 269                 addFeatureNodeByUuid(nitrogenNode, termService, AlgaTerraImportTransformer.uuidFeatureAmmonium);
 270                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeaturePhosphate);
 271                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureOrthoPhosphate);
 272                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureNPRation);
 273                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureDIN);
 274                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureSRP);
 275                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureOxygenSaturation);
 276                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureCl);
 277                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureSecchiDepth);
 278                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureCommunity);
 279                 app.getFeatureTreeService().saveOrUpdate(specimenTree);
 280         }
 281
 282         private FeatureNode makeNitrogenNode(FeatureNode root, ITermService termService) {
 283                 Feature nFeature = Feature.NewInstance("Supra feature for all Nitrogen related subfeatures", "Nitrogen", "N");
 284                 termService.save(nFeature);
 285                 FeatureNode nNode = FeatureNode.NewInstance(nFeature);
 286                 root.addChild(nNode);
 287                 return nNode;
 288         }
 289
 290
 291 //      private FeatureNode addFeataureNodesByUuidList(UUID[] featureUuidList, FeatureNode root, ITermService termService){
 292 //              FeatureNode lastChild = null;
 293 //              for (UUID featureUuid : featureUuidList){
 294 //                      addFeatureNodeByUuid(root, termService, featureUuid);
 295 //              }
 296 //
 297 //              return lastChild;
 298 //      }
 299
 300
 301         /**
 302          * @param root
 303          * @param termService
 304          * @param featureUuid
 305          */
 306         private void addFeatureNodeByUuid(FeatureNode root, ITermService termService, UUID featureUuid) {
 307                 Feature feature = (Feature)termService.find(featureUuid);
 308                 if (feature != null){
 309                         FeatureNode child = FeatureNode.NewInstance(feature);
 310                         root.addChild(child);
 311                 }
 312         }
 313
 314
 315         /**
 316          * @param args
 317          */
 318         public static void main(String[] args) {
 319                 AlgaTerraActivator activator = new AlgaTerraActivator();
 320                 activator.invoke(args);
 321         }
 322
 323 }