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.CdmApplicationController;
  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.Source;
  28 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  29 import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;
  30 import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR;
  31 import eu.etaxonomy.cdm.model.description.Feature;
  32 import eu.etaxonomy.cdm.model.description.FeatureNode;
  33 import eu.etaxonomy.cdm.model.description.FeatureTree;
  34 import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
  35 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  36
  37
  38 /**
  39  * TODO add the following to a wiki page:
  40  * 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
  41  * you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.
  42  *
  43  *
  44  * @author a.mueller
  45  *
  46  */
  47 public class DipteraActivator {
  48         private static final Logger logger = Logger.getLogger(DipteraActivator.class);
  49
  50         //database validation status (create, update, validate ...)
  51         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  52         static final Source berlinModelSource = BerlinModelSources.EDIT_Diptera();
  53         static final ICdmDataSource cdmDestination = CdmDestinations.localH2Diptera();
  54
  55         static final UUID secUuid = UUID.fromString("06fd671f-1226-4e3b-beca-1959b3b32e20");
  56         static final UUID treeUuid = UUID.fromString("1e3093f6-c761-4e96-8065-2c1334ddd0c1");
  57         static final int sourceSecId = 1000000;
  58         static final UUID featureTreeUuid = UUID.fromString("ae9615b8-bc60-4ed0-ad96-897f9226d568");
  59         static final Object[] featureKeyList = new Integer[]{1, 4, 5, 10, 11, 12, 99};
  60
  61         static boolean useClassification = true;
  62         //editor - import
  63         static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR;
  64         //check - import
  65         static final CHECK check = CHECK.CHECK_AND_IMPORT;
  66         //taxon publish marker
  67         static final PublishMarkerChooser taxonPublish = PublishMarkerChooser.NO_MARKER;
  68
  69         static final boolean doDistributionParser = true;  //also run DipteraDistributionParser
  70
  71         //NomeclaturalCode
  72         static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICZN;
  73
  74 //      //ignore null
  75         static final boolean ignoreNull = true;
  76
  77
  78
  79         //update citations ?
  80         static final boolean updateCitations = true;
  81
  82         //include collections and add to specimen
  83         static final boolean updateCollections = true;
  84
  85         //authors
  86         static final boolean doAuthors = true;
  87         //references
  88         static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;
  89         //names
  90         static final boolean doTaxonNames = true;
  91         static final boolean doRelNames = true;
  92         static final boolean doNameStatus = true;
  93         static final boolean doTypes = true;
  94         static final boolean doNameFacts = true;
  95
  96         //taxa
  97         static final boolean doTaxa = true;
  98         static final boolean doRelTaxa = true;
  99         static final boolean doFacts = true;
 100         static final boolean doOccurences = false; //There are no occurrence data in diptera
 101         static final boolean doCommonNames = false; //no common names in diptera
 102
 103         //etc.
 104         static final boolean doMarker = true;
 105         static final boolean doUser = true;
 106
 107 // **************** SELECTED *********************
 108
 109 //      //authors
 110 //      static final boolean doAuthors = false;
 111 //      //references
 112 //      static final DO_REFERENCES doReferences =  DO_REFERENCES.NONE;
 113 //      //names
 114 //      static final boolean doTaxonNames = true;
 115 //      static final boolean doRelNames = false;
 116 //      static final boolean doNameStatus = false;
 117 //      static final boolean doTypes = true;
 118 //      static final boolean doNameFacts = false;
 119 //
 120 //      //taxa
 121 //      static final boolean doTaxa = false;
 122 //      static final boolean doRelTaxa = false;
 123 //      static final boolean doFacts = false;
 124 //      static final boolean doOccurences = false;
 125 //
 126 //      //etc.
 127 //      static final boolean doMarker = false;
 128 //      static final boolean doUser = true;
 129
 130
 131         /**
 132          * @param destination
 133          * @param args
 134          */
 135         public boolean doImport(ICdmDataSource destination) {
 136                 boolean success = true;
 137                 System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") ...");
 138
 139                 //make BerlinModel Source
 140                 Source source = berlinModelSource;
 141
 142
 143                 BerlinModelImportConfigurator bmImportConfigurator = BerlinModelImportConfigurator.NewInstance(source,  destination);
 144
 145                 bmImportConfigurator.setClassificationUuid(treeUuid);
 146                 bmImportConfigurator.setSourceSecId(sourceSecId);
 147                 bmImportConfigurator.setNomenclaturalCode(nomenclaturalCode);
 148
 149                 bmImportConfigurator.setIgnoreNull(ignoreNull);
 150                 bmImportConfigurator.setDoAuthors(doAuthors);
 151                 bmImportConfigurator.setDoReferences(doReferences);
 152                 bmImportConfigurator.setDoTaxonNames(doTaxonNames);
 153                 bmImportConfigurator.setDoRelNames(doRelNames);
 154                 bmImportConfigurator.setDoNameStatus(doNameStatus);
 155                 bmImportConfigurator.setDoTypes(doTypes);
 156                 bmImportConfigurator.setDoNameFacts(doNameFacts);
 157                 bmImportConfigurator.setUseClassification(useClassification);
 158
 159                 bmImportConfigurator.setDoTaxa(doTaxa);
 160                 bmImportConfigurator.setDoRelTaxa(doRelTaxa);
 161                 bmImportConfigurator.setDoFacts(doFacts);
 162                 bmImportConfigurator.setDoOccurrence(doOccurences);
 163                 bmImportConfigurator.setDoCommonNames(doCommonNames);
 164
 165                 bmImportConfigurator.setDoMarker(doMarker);
 166                 bmImportConfigurator.setDoUser(doUser);
 167                 bmImportConfigurator.setEditor(editor);
 168                 bmImportConfigurator.setTaxonPublishMarker(taxonPublish);
 169                 try {
 170                         Method nameTypeDesignationStatusMethod = DipteraActivator.class.getDeclaredMethod("nameTypeDesignationStatueMethod", String.class);
 171                         bmImportConfigurator.setNameTypeDesignationStatusMethod(nameTypeDesignationStatusMethod);
 172                 } catch (Exception e) {
 173                         e.printStackTrace();
 174                         return false;
 175                 }
 176
 177                 bmImportConfigurator.setDbSchemaValidation(hbm2dll);
 178
 179                 bmImportConfigurator.setCheck(check);
 180
 181                 // invoke import
 182                 CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>();
 183                 success &= bmImport.invoke(bmImportConfigurator);
 184
 185                 if (bmImportConfigurator.getCheck().equals(CHECK.CHECK_AND_IMPORT)  || bmImportConfigurator.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK)    ){
 186                         CdmApplicationController app = bmImport.getCdmAppController();
 187
 188                         //parse distributions
 189                         if (doDistributionParser){
 190                                 DipteraDistributionParser dipDist = new DipteraDistributionParser();
 191                                 dipDist.doDistribution(app);
 192                         }
 193                         //make feature tree
 194                         app = bmImport.getCdmAppController();
 195                         FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, bmImportConfigurator.getFeatureMap(), featureKeyList);
 196                         // add image
 197                         FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE());
 198                         tree.getRoot().addChild(imageNode);
 199                         // add distribution
 200                         FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 201                         tree.getRoot().addChild(distributionNode);
 202                         app.getFeatureTreeService().saveOrUpdate(tree);
 203                 }
 204                 System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
 205                 return success;
 206         }
 207
 208         public static void main(String[] args) {
 209                 boolean success = true;
 210                 logger.debug("start");
 211                 ICdmDataSource destination = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
 212                 DipteraActivator me = new DipteraActivator();
 213                 success &= me.doImport(destination);
 214
 215                 DipteraPostImportUpdater updater = new DipteraPostImportUpdater();
 216                 if (updateCitations){
 217                         success &= updater.updateCitations(destination);
 218                 }
 219
 220                 if (updateCollections){
 221                         success &= updater.updateCollections(destination);
 222                 }
 223
 224
 225         }
 226
 227
 228
 229
 230
 231         private static NameTypeDesignationStatus nameTypeDesignationStatueMethod(String note){
 232                 if (CdmUtils.isEmpty(note)){
 233                         return null;
 234                 }
 235                 note = note.trim();
 236                 if (note.equalsIgnoreCase("aut.") || note.equalsIgnoreCase("automatic")){
 237                         return NameTypeDesignationStatus.AUTOMATIC();
 238                 }else if (note.equalsIgnoreCase("subs. mon.") ){
 239                         return NameTypeDesignationStatus.SUBSEQUENT_MONOTYPY();
 240                 }else if (note.startsWith("mon.") ){
 241                         return NameTypeDesignationStatus.MONOTYPY();
 242                 }else if (note.startsWith("orig. des") ){
 243                         return NameTypeDesignationStatus.ORIGINAL_DESIGNATION();
 244                 }else if (note.startsWith("des") ){
 245                         return NameTypeDesignationStatus.SUBSEQUENT_DESIGNATION();
 246                 }else{
 247                         logger.warn("NameTypeDesignationStatus could not be defined for: " + note);
 248                         return null;
 249                 }
 250
 251
 252         }
 253
 254 }