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.logging.log4j.LogManager;
  15 import org.apache.logging.log4j.Logger;
  16
  17 import eu.etaxonomy.cdm.api.application.ICdmRepository;
  18 import eu.etaxonomy.cdm.api.service.ITermService;
  19 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  20 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  21 import eu.etaxonomy.cdm.database.ICdmDataSource;
  22 import eu.etaxonomy.cdm.io.algaterra.AlgaTerraImportConfigurator;
  23 import eu.etaxonomy.cdm.io.algaterra.AlgaTerraImportTransformer;
  24 import eu.etaxonomy.cdm.io.algaterra.AlgaTerraSpecimenImportBase;
  25 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;
  26 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  27 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  28 import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;
  29 import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR;
  30 import eu.etaxonomy.cdm.io.common.Source;
  31 import eu.etaxonomy.cdm.model.description.Feature;
  32 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  33 import eu.etaxonomy.cdm.model.term.TermNode;
  34 import eu.etaxonomy.cdm.model.term.TermTree;
  35
  36
  37 /**
  38  * TODO add the following to a wiki page:
  39  * 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
  40  * you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.
  41  *
  42  *
  43  * @author a.mueller
  44  *
  45  */
  46 public class AlgaTerraActivator {
  47
  48     private static Logger logger = LogManager.getLogger();
  49
  50     //database validation status (create, update, validate ...)
  51         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  52         static final Source berlinModelSource = BerlinModelSources.AlgaTerra();
  53         static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  54 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
  55
  56 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_algaterra_preview();
  57 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_algaterra_production();
  58
  59
  60         static final UUID treeUuid = UUID.fromString("1f617402-78dc-4bf1-ac77-d260600a8879");
  61         static final int sourceSecId = 7331;
  62         static final UUID sourceRefUuid = UUID.fromString("7e1a2500-93a5-40c2-ba34-0213d7822379");
  63
  64         static final UUID featureTreeUuid = UUID.fromString("a970168a-36fd-4c7c-931e-87214a965c14");
  65         static final Object[] featureKeyList = new Integer[]{7,201,203,204,206,207};
  66         static final UUID specimenFeatureTreeUuid = UUID.fromString("ba86246e-d4d0-419f-832e-86d70b1e4bd7");
  67
  68         static final boolean loginAsDefaultAdmin = true;
  69         //TODO set to false for final import
  70         static final boolean removeRestricted = true;
  71
  72         static final boolean importOriginalSizeMedia = false;
  73
  74         //check - import
  75         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  76
  77         private boolean ignoreNull = true;
  78
  79         private boolean includeFlatClassifications = true;
  80         private boolean includeAllNonMisappliedRelatedClassifications = true;
  81
  82         private EDITOR editor = EDITOR.EDITOR_AS_EDITOR;
  83
  84         //NomenclaturalCode
  85         static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP;
  86
  87         static String factFilter = " factCategoryFk NOT IN (7, 201, 202, 203, 204, 205, 206, 207, 208, 1000 ) ";
  88
  89
  90 // ****************** ALL *****************************************
  91
  92         //authors
  93         static final boolean doAuthors = true;
  94         //references
  95         static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;
  96         //names
  97         static final boolean doTaxonNames = true;
  98         static final boolean doRelNames = true;
  99         static final boolean doNameStatus = true;
 100         static final boolean doTypes = true;
 101
 102         //taxa
 103         static final boolean doTaxa = true;
 104         static final boolean doRelTaxa = true;
 105         static final boolean doFacts = true;
 106
 107         //alga terra specific
 108         static final boolean ecoFacts = true;
 109         static final boolean doFactEcology = true;
 110         static final boolean doImages = false;
 111         static final boolean doDna = true;
 112         static final boolean doMorphology = true;
 113
 114 // ************************ NONE **************************************** //
 115
 116 //      //authors
 117 //      static final boolean doAuthors = false;
 118 //      //references
 119 //      static final DO_REFERENCES doReferences =  DO_REFERENCES.NONE;
 120 //      //names
 121 //      static final boolean doTaxonNames = false;
 122 //      static final boolean doRelNames = false;
 123 //      static final boolean doNameStatus = false;
 124 //      static final boolean doTypes = true;
 125 //      static final boolean doNameFacts = false;
 126 //
 127 //      //taxa
 128 //      static final boolean doTaxa = false;
 129 //      static final boolean doRelTaxa = false;
 130 //      static final boolean doFacts = false;
 131 //
 132 //  //alga terra specific
 133 //      static final boolean ecoFacts = false;
 134 //      static final boolean doFactEcology = false;
 135 //      static final boolean doImages = false;
 136 //      static final boolean doDna = false;
 137 //      static final boolean doMorphology = false;
 138
 139
 140         public void invoke(String[] args){
 141                 System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") ...");
 142                 logger.debug("Start");
 143                 //make BerlinModel Source
 144                 Source source = berlinModelSource;
 145                 ICdmDataSource destination = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
 146
 147                 AlgaTerraImportConfigurator config = AlgaTerraImportConfigurator.NewInstance(source,  destination);
 148
 149                 config.setClassificationUuid(treeUuid);
 150                 config.setSourceSecId(sourceSecId);
 151                 config.setNomenclaturalCode(nomenclaturalCode);
 152
 153                 config.setDoAuthors(doAuthors);
 154                 config.setDoReferences(doReferences);
 155                 config.setDoTaxonNames(doTaxonNames);
 156                 config.setDoRelNames(doRelNames);
 157                 config.setDoNameStatus(doNameStatus);
 158                 config.setDoTypes(doTypes);
 159
 160                 config.setDoTaxa(doTaxa);
 161                 config.setDoRelTaxa(doRelTaxa);
 162                 config.setDoFacts(doFacts);
 163                 config.setDoEcoFacts(ecoFacts);
 164                 config.setDoImages(doImages);
 165                 config.setDoFactEcology(doFactEcology);
 166                 config.setDoDna(doDna);
 167                 config.setDoMorphology(doMorphology);
 168
 169                 config.setSourceRefUuid(sourceRefUuid);
 170                 config.setIgnoreNull(ignoreNull);
 171                 config.setRemoveRestricted(removeRestricted);
 172                 config.setImportOriginalSizeMedia(importOriginalSizeMedia);
 173
 174                 config.setIncludeFlatClassifications(includeFlatClassifications);
 175                 config.setIncludeAllNonMisappliedRelatedClassifications(includeAllNonMisappliedRelatedClassifications);
 176                 config.setFactFilter(factFilter);
 177
 178                 config.setDbSchemaValidation(hbm2dll);
 179
 180                 config.setCheck(check);
 181                 config.setEditor(editor);
 182
 183                 if (loginAsDefaultAdmin){
 184                         config.authenticateAsDefaultAdmin();
 185                 }
 186
 187                 // invoke import
 188                 CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>();
 189                 bmImport.invoke(config);
 190
 191                 if (doFacts && (config.getCheck().equals(CHECK.CHECK_AND_IMPORT)  || config.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK) )   ){
 192                     ICdmRepository app = bmImport.getCdmAppController();
 193
 194                         //make feature tree
 195                         makeTaxonFeatureTree(config, app);
 196
 197                         //make specimen feature tree
 198                         //TODO more specimen specific
 199                         makeSpecimenFeatureTree(config, app);
 200
 201                 }
 202
 203
 204                 System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
 205         }
 206
 207
 208         /**
 209          * @param config
 210          * @param app
 211          */
 212         private void makeTaxonFeatureTree(AlgaTerraImportConfigurator config, ICdmRepository app) {
 213             TermTree<Feature> tree = TreeCreator.flatTree(featureTreeUuid, config.getFeatureMap(), featureKeyList);
 214                 tree.setTitleCache("AlgaTerra Taxon Feature Tree", true);
 215
 216                 tree.getRoot().addChild(Feature.HABITAT());
 217
 218 //              tree.getRoot().addChild(Feature.OBSERVATION());
 219 //
 220 //              tree.getRoot().addChild(Feature.SPECIMEN());
 221 //
 222 //              tree.getRoot().addChild(Feature.INDIVIDUALS_ASSOCIATION());
 223
 224                 //needed ??
 225                 tree.getRoot().addChild(Feature.DISTRIBUTION(), 2);
 226
 227 //              //needed ??
 228 //              tree.getRoot().addChild(Feature.IMAGE());
 229
 230                 app.getTermTreeService().saveOrUpdate(tree);
 231         }
 232
 233
 234         /**
 235          * @param config
 236          * @param app
 237          * @param tree
 238          */
 239         private void makeSpecimenFeatureTree(AlgaTerraImportConfigurator config, ICdmRepository app) {
 240                 ITermService termService = app.getTermService();
 241                 TermTree<Feature> specimenTree = TermTree.NewFeatureInstance(specimenFeatureTreeUuid);
 242 //              FeatureTree specimenTree = TreeCreator.flatTree(specimenFeatureTreeUuid, config.getFeatureMap(), featureKeyList);
 243                 specimenTree.setTitleCache("AlgaTerra Specimen Feature Tree", true);
 244                 TermNode<Feature> root = specimenTree.getRoot();
 245
 246
 247                 root.addChild(Feature.IMAGE());
 248
 249                 addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureAlgaTerraClimate);
 250                 root.addChild(Feature.HABITAT());
 251                 addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureHabitatExplanation);
 252                 addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureAlgaTerraLifeForm);
 253
 254                 addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureAdditionalData);
 255                 addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureSpecimenCommunity);
 256
 257                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeaturePH);
 258                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureConductivity);
 259                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureWaterTemperature);
 260                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureSilica);
 261                 TermNode<Feature> nitrogenNode = makeNitrogenNode(root, termService);
 262                 addFeatureNodeByUuid(nitrogenNode, termService, AlgaTerraImportTransformer.uuidFeatureNitrate);
 263                 addFeatureNodeByUuid(nitrogenNode, termService, AlgaTerraImportTransformer.uuidFeatureNitrite);
 264                 addFeatureNodeByUuid(nitrogenNode, termService, AlgaTerraImportTransformer.uuidFeatureAmmonium);
 265                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeaturePhosphate);
 266                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureOrthoPhosphate);
 267                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureNPRation);
 268                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureDIN);
 269                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureSRP);
 270                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureOxygenSaturation);
 271                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureCl);
 272                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureSecchiDepth);
 273                 addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureCommunity);
 274                 app.getTermTreeService().saveOrUpdate(specimenTree);
 275         }
 276
 277         private TermNode<Feature> makeNitrogenNode(TermNode<Feature> root, ITermService termService) {
 278                 Feature nFeature = Feature.NewInstance("Supra feature for all Nitrogen related subfeatures", "Nitrogen", "N");
 279                 termService.save(nFeature);
 280                 TermNode<Feature> nNode = root.addChild(nFeature);
 281                 return nNode;
 282         }
 283
 284
 285 //      private FeatureNode addFeataureNodesByUuidList(UUID[] featureUuidList, FeatureNode root, ITermService termService){
 286 //              FeatureNode lastChild = null;
 287 //              for (UUID featureUuid : featureUuidList){
 288 //                      addFeatureNodeByUuid(root, termService, featureUuid);
 289 //              }
 290 //
 291 //              return lastChild;
 292 //      }
 293
 294
 295         /**
 296          * @param root
 297          * @param termService
 298          * @param featureUuid
 299          */
 300         private void addFeatureNodeByUuid(TermNode<Feature> root, ITermService termService, UUID featureUuid) {
 301                 Feature feature = (Feature)termService.find(featureUuid);
 302                 if (feature != null){
 303                         root.addChild(feature);
 304                 }
 305         }
 306
 307
 308         /**
 309          * @param args
 310          */
 311         public static void main(String[] args) {
 312                 AlgaTerraActivator activator = new AlgaTerraActivator();
 313                 activator.invoke(args);
 314         }
 315
 316 }