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.common.DoubleResult;
  23 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  24 import eu.etaxonomy.cdm.database.ICdmDataSource;
  25 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;
  26 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState;
  27 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  28 import eu.etaxonomy.cdm.io.common.Source;
  29 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  30 import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;
  31 import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR;
  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 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  38
  39
  40 /**
  41  * TODO add the following to a wiki page:
  42  * 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
  43  * you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.
  44  *
  45  *
  46  * @author a.mueller
  47  *
  48  */
  49 public class DipteraActivator {
  50         private static final Logger logger = Logger.getLogger(DipteraActivator.class);
  51
  52         //database validation status (create, update, validate ...)
  53         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  54         static final Source berlinModelSource = BerlinModelSources.EDIT_Diptera();
  55         static final ICdmDataSource cdmDestination = CdmDestinations.localH2Diptera();
  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[]{1,4,5,10,11,12,13,99};
  61
  62         static boolean useTaxonomicTree = 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
  68         static final boolean doDistributionParser = true;  //also run DipteraDistributionParser
  69
  70         //NomeclaturalCode
  71         static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICZN;
  72
  73 //      //ignore null
  74         static final boolean ignoreNull = true;
  75
  76         //authors
  77         static final boolean doAuthors = true;
  78         //references
  79         static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;
  80         //names
  81         static final boolean doTaxonNames = true;
  82         static final boolean doRelNames = true;
  83         static final boolean doNameStatus = true;
  84         static final boolean doTypes = true;
  85         static final boolean doNameFacts = true;
  86
  87         //taxa
  88         static final boolean doTaxa = true;
  89         static final boolean doRelTaxa = true;
  90         static final boolean doFacts = true;
  91         static final boolean doOccurences = false; //There are no occurrence data in diptera
  92
  93         //etc.
  94         static final boolean doMarker = true;
  95         static final boolean doUser = true;
  96
  97 // **************** SELECTED *********************
  98
  99 //      //authors
 100 //      static final boolean doAuthors = true;
 101 //      //references
 102 //      static final DO_REFERENCES doReferences =  DO_REFERENCES.NONE;
 103 //      //names
 104 //      static final boolean doTaxonNames = false;
 105 //      static final boolean doRelNames = false;
 106 //      static final boolean doNameStatus = false;
 107 //      static final boolean doTypes = false;
 108 //      static final boolean doNameFacts = false;
 109 //
 110 //      //taxa
 111 //      static final boolean doTaxa = true;
 112 //      static final boolean doRelTaxa = false;
 113 //      static final boolean doFacts = true;
 114 //      static final boolean doOccurences = false;
 115 //
 116 //      //etc.
 117 //      static final boolean doMarker = false;
 118 //      static final boolean doUser = false;
 119
 120
 121         /**
 122          * @param args
 123          */
 124         public static void main(String[] args) {
 125                 System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") ...");
 126
 127                 //make BerlinModel Source
 128                 Source source = berlinModelSource;
 129                 ICdmDataSource destination = cdmDestination;
 130
 131                 BerlinModelImportConfigurator bmImportConfigurator = BerlinModelImportConfigurator.NewInstance(source,  destination);
 132
 133                 bmImportConfigurator.setTreeUuid(treeUuid);
 134                 bmImportConfigurator.setSourceSecId(sourceSecId);
 135                 bmImportConfigurator.setNomenclaturalCode(nomenclaturalCode);
 136
 137                 bmImportConfigurator.setIgnoreNull(ignoreNull);
 138                 bmImportConfigurator.setDoAuthors(doAuthors);
 139                 bmImportConfigurator.setDoReferences(doReferences);
 140                 bmImportConfigurator.setDoTaxonNames(doTaxonNames);
 141                 bmImportConfigurator.setDoRelNames(doRelNames);
 142                 bmImportConfigurator.setDoNameStatus(doNameStatus);
 143                 bmImportConfigurator.setDoTypes(doTypes);
 144                 bmImportConfigurator.setDoNameFacts(doNameFacts);
 145                 bmImportConfigurator.setUseTaxonomicTree(useTaxonomicTree);
 146
 147                 bmImportConfigurator.setDoTaxa(doTaxa);
 148                 bmImportConfigurator.setDoRelTaxa(doRelTaxa);
 149                 bmImportConfigurator.setDoFacts(doFacts);
 150                 bmImportConfigurator.setDoOccurrence(doOccurences);
 151
 152                 bmImportConfigurator.setDoMarker(doMarker);
 153                 bmImportConfigurator.setDoUser(doUser);
 154                 bmImportConfigurator.setEditor(editor);
 155                 try {
 156                         Method nameTypeDesignationStatusMethod = DipteraActivator.class.getDeclaredMethod("nameTypeDesignationStatueMethod", String.class);
 157                         bmImportConfigurator.setNameTypeDesignationStatusMethod(nameTypeDesignationStatusMethod);
 158                 } catch (Exception e) {
 159                         e.printStackTrace();
 160                         return;
 161                 }
 162
 163                 bmImportConfigurator.setDbSchemaValidation(hbm2dll);
 164
 165                 bmImportConfigurator.setCheck(check);
 166
 167                 // invoke import
 168                 CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>();
 169                 bmImport.invoke(bmImportConfigurator);
 170
 171                 if (bmImportConfigurator.getCheck().equals(CHECK.CHECK_AND_IMPORT)  || bmImportConfigurator.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK)    ){
 172                         CdmApplicationController app = bmImport.getCdmAppController();
 173
 174                         //parse distributions
 175                         if (doDistributionParser){
 176                                 DipteraDistributionParser dipDist = new DipteraDistributionParser();
 177                                 dipDist.doDistribution(app);
 178                         }
 179                         //make feature tree
 180                         app = bmImport.getCdmAppController();
 181                         FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, bmImportConfigurator.getFeatureMap(), featureKeyList);
 182                         // add image
 183                         FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE());
 184                         tree.getRoot().addChild(imageNode);
 185                         // add distribution
 186                         FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 187                         tree.getRoot().addChild(distributionNode);
 188                         app.getDescriptionService().saveFeatureTree(tree);
 189                 }
 190                 System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
 191         }
 192
 193         private static NameTypeDesignationStatus nameTypeDesignationStatueMethod(String note){
 194                 if (CdmUtils.isEmpty(note)){
 195                         return null;
 196                 }
 197                 note = note.trim();
 198                 if (note.equalsIgnoreCase("aut.") || note.equalsIgnoreCase("automatic")){
 199                         return NameTypeDesignationStatus.AUTOMATIC();
 200                 }else if (note.equalsIgnoreCase("subs. mon.") ){
 201                         return NameTypeDesignationStatus.SUBSEQUENT_MONOTYPY();
 202                 }else if (note.startsWith("mon.") ){
 203                         return NameTypeDesignationStatus.MONOTYPY();
 204                 }else if (note.startsWith("orig. des") ){
 205                         return NameTypeDesignationStatus.ORIGINAL_DESIGNATION();
 206                 }else if (note.startsWith("des") ){
 207                         return NameTypeDesignationStatus.SUBSEQUENT_DESIGNATION();
 208                 }else{
 209                         logger.warn("NameTypeDesignationStatus could not be defined for: " + note);
 210                         return null;
 211                 }
 212
 213
 214         }
 215
 216 }