app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/diptera/DipteraActivator.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.diptera;
  11
  12 import java.lang.reflect.Method;
  13 import java.util.UUID;
  14
  15 import org.apache.log4j.Logger;
  16
  17 import eu.etaxonomy.cdm.api.application.ICdmRepository;
  18 import eu.etaxonomy.cdm.app.berlinModelImport.BerlinModelSources;
  19 import eu.etaxonomy.cdm.app.berlinModelImport.TreeCreator;
  20 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  21 import eu.etaxonomy.cdm.common.CdmUtils;
  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.berlinModel.in.BerlinModelTaxonImport.PublishMarkerChooser;
  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.ImportResult;
  31 import eu.etaxonomy.cdm.io.common.Source;
  32 import eu.etaxonomy.cdm.model.description.Feature;
  33 import eu.etaxonomy.cdm.model.description.FeatureNode;
  34 import eu.etaxonomy.cdm.model.description.FeatureTree;
  35 import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
  36 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  37
  38
  39 /**
  40  * TODO add the following to a wiki page:
  41  * 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
  42  * you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.
  43  *
  44  *
  45  * @author a.mueller
  46  *
  47  */
  48 public class DipteraActivator {
  49         private static final Logger logger = Logger.getLogger(DipteraActivator.class);
  50
  51         //database validation status (create, update, validate ...)
  52         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  53         static final Source berlinModelSource = BerlinModelSources.EDIT_Diptera();
  54         static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  55
  56         static final UUID secUuid = UUID.fromString("06fd671f-1226-4e3b-beca-1959b3b32e20");
  57         static final UUID treeUuid = UUID.fromString("1e3093f6-c761-4e96-8065-2c1334ddd0c1");
  58         static final int sourceSecId = 1000000;
  59         static final UUID featureTreeUuid = UUID.fromString("ae9615b8-bc60-4ed0-ad96-897f9226d568");
  60         static final Object[] featureKeyList = new Integer[]{1, 4, 5, 10, 11, 12, 99};
  61
  62         static boolean useClassification = true;
  63         //editor - import
  64         static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR;
  65         //check - import
  66         static final CHECK check = CHECK.CHECK_AND_IMPORT;
  67         //taxon publish marker
  68         static final PublishMarkerChooser taxonPublish = PublishMarkerChooser.NO_MARKER;
  69
  70         static final boolean doDistributionParser = true;  //also run DipteraDistributionParser
  71
  72         //NomenclaturalCode
  73         static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICZN;
  74
  75 //      //ignore null
  76         static final boolean ignoreNull = true;
  77
  78
  79
  80         //update citations ?
  81         static final boolean updateCitations = true;
  82
  83         //include collections and add to specimen
  84         static final boolean updateCollections = true;
  85
  86         //authors
  87         static final boolean doAuthors = true;
  88         //references
  89         static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;
  90         //names
  91         static final boolean doTaxonNames = true;
  92         static final boolean doRelNames = true;
  93         static final boolean doNameStatus = true;
  94         static final boolean doTypes = true;
  95         static final boolean doNameFacts = true;
  96
  97         //taxa
  98         static final boolean doTaxa = true;
  99         static final boolean doRelTaxa = true;
 100         static final boolean doFacts = true;
 101         static final boolean doOccurences = false; //There are no occurrence data in diptera
 102         static final boolean doCommonNames = false; //no common names in diptera
 103
 104         //etc.
 105         static final boolean doMarker = true;
 106         static final boolean doUser = true;
 107
 108 // **************** SELECTED *********************
 109
 110 //      //authors
 111 //      static final boolean doAuthors = false;
 112 //      //references
 113 //      static final DO_REFERENCES doReferences =  DO_REFERENCES.NONE;
 114 //      //names
 115 //      static final boolean doTaxonNames = true;
 116 //      static final boolean doRelNames = false;
 117 //      static final boolean doNameStatus = false;
 118 //      static final boolean doTypes = true;
 119 //      static final boolean doNameFacts = false;
 120 //
 121 //      //taxa
 122 //      static final boolean doTaxa = false;
 123 //      static final boolean doRelTaxa = false;
 124 //      static final boolean doFacts = false;
 125 //      static final boolean doOccurences = false;
 126 //
 127 //      //etc.
 128 //      static final boolean doMarker = false;
 129 //      static final boolean doUser = true;
 130
 131
 132         /**
 133          * @param destination
 134          * @param args
 135          */
 136         public ImportResult doImport(ICdmDataSource destination) {
 137                 ImportResult success;
 138                 System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") ...");
 139
 140                 //make BerlinModel Source
 141                 Source source = berlinModelSource;
 142
 143
 144                 BerlinModelImportConfigurator bmImportConfigurator = BerlinModelImportConfigurator.NewInstance(source,  destination);
 145
 146                 bmImportConfigurator.setClassificationUuid(treeUuid);
 147                 bmImportConfigurator.setSourceSecId(sourceSecId);
 148                 bmImportConfigurator.setNomenclaturalCode(nomenclaturalCode);
 149
 150                 bmImportConfigurator.setIgnoreNull(ignoreNull);
 151                 bmImportConfigurator.setDoAuthors(doAuthors);
 152                 bmImportConfigurator.setDoReferences(doReferences);
 153                 bmImportConfigurator.setDoTaxonNames(doTaxonNames);
 154                 bmImportConfigurator.setDoRelNames(doRelNames);
 155                 bmImportConfigurator.setDoNameStatus(doNameStatus);
 156                 bmImportConfigurator.setDoTypes(doTypes);
 157                 bmImportConfigurator.setDoNameFacts(doNameFacts);
 158                 bmImportConfigurator.setUseClassification(useClassification);
 159
 160                 bmImportConfigurator.setDoTaxa(doTaxa);
 161                 bmImportConfigurator.setDoRelTaxa(doRelTaxa);
 162                 bmImportConfigurator.setDoFacts(doFacts);
 163                 bmImportConfigurator.setDoOccurrence(doOccurences);
 164                 bmImportConfigurator.setDoCommonNames(doCommonNames);
 165
 166                 bmImportConfigurator.setDoMarker(doMarker);
 167                 bmImportConfigurator.setDoUser(doUser);
 168                 bmImportConfigurator.setEditor(editor);
 169                 bmImportConfigurator.setTaxonPublishMarker(taxonPublish);
 170                 try {
 171                         Method nameTypeDesignationStatusMethod = DipteraActivator.class.getDeclaredMethod("nameTypeDesignationStatueMethod", String.class);
 172                         bmImportConfigurator.setNameTypeDesignationStatusMethod(nameTypeDesignationStatusMethod);
 173                 } catch (Exception e) {
 174                         e.printStackTrace();
 175                         success = new ImportResult();
 176                         success.addException(e);
 177                         return success;
 178                 }
 179
 180                 bmImportConfigurator.setDbSchemaValidation(hbm2dll);
 181
 182                 bmImportConfigurator.setCheck(check);
 183
 184                 // invoke import
 185                 CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>();
 186                 success = bmImport.invoke(bmImportConfigurator);
 187
 188                 if (bmImportConfigurator.getCheck().equals(CHECK.CHECK_AND_IMPORT)  || bmImportConfigurator.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK)    ){
 189                         ICdmRepository app = bmImport.getCdmAppController();
 190
 191                         //parse distributions
 192                         if (doDistributionParser){
 193                                 DipteraDistributionParser dipDist = new DipteraDistributionParser();
 194                                 dipDist.doDistribution(app);
 195                         }
 196                         //make feature tree
 197                         app = bmImport.getCdmAppController();
 198                         FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, bmImportConfigurator.getFeatureMap(), featureKeyList);
 199                         // add image
 200                         FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE());
 201                         tree.getRoot().addChild(imageNode);
 202                         // add distribution
 203                         FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 204                         tree.getRoot().addChild(distributionNode);
 205                         app.getFeatureTreeService().saveOrUpdate(tree);
 206                 }
 207                 System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
 208                 return success;
 209         }
 210
 211         public static void main(String[] args) {
 212                 ImportResult success;
 213                 logger.debug("start");
 214                 ICdmDataSource destination = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
 215                 DipteraActivator me = new DipteraActivator();
 216                 success = me.doImport(destination);
 217
 218                 DipteraPostImportUpdater updater = new DipteraPostImportUpdater();
 219                 if (updateCitations){
 220                         success = updater.updateCitations(destination);
 221                 }
 222
 223                 if (updateCollections){
 224                         success = updater.updateCollections(destination);
 225                 }
 226
 227
 228         }
 229
 230
 231
 232
 233
 234         private static NameTypeDesignationStatus nameTypeDesignationStatueMethod(String note){
 235                 if (CdmUtils.isEmpty(note)){
 236                         return null;
 237                 }
 238                 note = note.trim();
 239                 if (note.equalsIgnoreCase("aut.") || note.equalsIgnoreCase("automatic")){
 240                         return NameTypeDesignationStatus.AUTOMATIC();
 241                 }else if (note.equalsIgnoreCase("subs. mon.") ){
 242                         return NameTypeDesignationStatus.SUBSEQUENT_MONOTYPY();
 243                 }else if (note.startsWith("mon.") ){
 244                         return NameTypeDesignationStatus.MONOTYPY();
 245                 }else if (note.startsWith("orig. des") ){
 246                         return NameTypeDesignationStatus.ORIGINAL_DESIGNATION();
 247                 }else if (note.startsWith("des") ){
 248                         return NameTypeDesignationStatus.SUBSEQUENT_DESIGNATION();
 249                 }else{
 250                         logger.warn("NameTypeDesignationStatus could not be defined for: " + note);
 251                         return null;
 252                 }
 253
 254
 255         }
 256
 257 }