app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/EuroMedActivator.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 import org.springframework.transaction.TransactionStatus;
  16
  17 import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
  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.berlinModel.BerlinModelTransformer;
  22 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;
  23 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  24 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  25 import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;
  26 import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR;
  27 import eu.etaxonomy.cdm.io.common.Source;
  28 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  29 import eu.etaxonomy.cdm.model.common.Language;
  30 import eu.etaxonomy.cdm.model.common.Representation;
  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.NomenclaturalCode;
  35 import eu.etaxonomy.cdm.model.name.Rank;
  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 EuroMedActivator {
  48         @SuppressWarnings("unused")
  49         private static final Logger logger = Logger.getLogger(EuroMedActivator.class);
  50
  51         //database validation status (create, update, validate ...)
  52         static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
  53         static final Source berlinModelSource = BerlinModelSources.euroMed_BGBM42();
  54 //      static final Source berlinModelSource = BerlinModelSources.euroMed_PESI3();
  55
  56 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_euroMed();
  57
  58         static final ICdmDataSource cdmDestination = CdmDestinations.cdm_pesi_euromed();
  59 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_euromed3();
  60 //      static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  61
  62         static final boolean includePesiExport = false;
  63
  64         static final int sourceSecId = 7000000; //500000
  65         static final UUID classificationUuid = UUID.fromString("314a68f9-8449-495a-91c2-92fde8bcf344");
  66         static final boolean useSingleClassification = true;
  67         static final String classificationName = "Euro+Med 2014";
  68         static final UUID featureTreeUuid = UUID.fromString("6a5e1c2b-ec0d-46c8-9c7d-a2059267ffb7");
  69         static final Object[] featureKeyList = new Integer[]{1, 31, 4, 98, 41};
  70
  71         // set to zero for unlimited nameFacts
  72         static final int maximumNumberOfNameFacts = 0;
  73
  74         static final int partitionSize = 2500;
  75
  76         //check - import
  77         static final CHECK check = CHECK.CHECK_AND_IMPORT;
  78
  79         //editor - import
  80         static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR;
  81
  82         //NomenclaturalCode
  83         static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP;
  84
  85         //ignore null
  86         static final boolean ignoreNull = true;
  87
  88         static final boolean switchSpeciesGroup = true;
  89
  90         static boolean useClassification = true;
  91
  92         static boolean isSplitTdwgCodes = false;
  93         static boolean useEmAreaVocabulary = true;
  94
  95         private boolean removeHttpMapsAnchor = true;
  96
  97
  98         static final String infrGenericRankAbbrev = "[unranked]";
  99         static final String infrSpecificRankAbbrev = "[unranked]";
 100
 101
 102         static String taxonTable = "v_cdm_exp_taxaAll";
 103         static String classificationQuery = " SELECT DISTINCT t.PTRefFk, r.RefCache FROM PTaxon t INNER JOIN Reference r ON t.PTRefFk = r.RefId WHERE t.PTRefFk = " + sourceSecId;
 104         static String relPTaxonIdQuery = " SELECT r.RelPTaxonId " +
 105                                         " FROM RelPTaxon AS r INNER JOIN v_cdm_exp_taxaDirect AS a ON r.PTNameFk2 = a.PTNameFk AND r.PTRefFk2 = a.PTRefFk" +
 106                                         " WHERE r.RelPTaxonID NOT IN (1883791,1883800,1883823,1883852,1883853,1883864,1883896,1883921,1883943,1883944,1883955,1883972,1884008,1884030,1884031,1884035) " + //Unpublished Kew taxa which are not imported anymore
 107                                         " ";  // AND r.RelQualifierFk =1
 108         static String nameIdTable = " v_cdm_exp_namesAll ";
 109         static String referenceIdTable = " v_cdm_exp_refAll ";
 110         static String refDetailFilter =  " RefDetailID IN (SELECT RefDetailID FROM v_cdm_exp_RefDetail) ";
 111         static String factFilter = " factId IN ( SELECT factId FROM v_cdm_exp_factsAll WHERE FactCategoryFk NOT IN (12, 14, 249, 251))";
 112         static String occurrenceFilter = " occurrenceId IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";
 113         static String occurrenceSourceFilter = " occurrenceFk IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";
 114         static String commonNameFilter = " commonNameId IN ( SELECT commonNameId FROM v_cdm_exp_commonNamesAll )";
 115         static String webMarkerFilter = " TableNameFk <> 500 OR ( RIdentifierFk IN (SELECT RIdentifier FROM v_cdm_exp_taxaAll)) ";
 116         static String authorTeamFilter = null; // " authorTeamId IN (SELECT authorTeamId FROM v_cdm_exp_authorTeamsAll) ";
 117         static String authorFilter = null;  // " authorId IN (SELECT authorId FROM v_cdm_exp_authorsAll) ";
 118
 119
 120
 121 // **************** ALL *********************
 122
 123         boolean invers =   !(hbm2dll == DbSchemaValidation.CREATE);
 124
 125         static final boolean doUser = true;
 126 //      //authors
 127         static final boolean doAuthors = true;
 128         //references
 129         static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;
 130         //names
 131         static final boolean doTaxonNames = true;
 132         static final boolean doRelNames = true;
 133         static final boolean doNameStatus = true;
 134         static final boolean doTypes = false;  //serious types do not exist in E+M
 135         static final boolean doNameFacts = true;
 136
 137         //taxa
 138         static final boolean doTaxa = true;
 139         static final boolean doRelTaxa = false;
 140         static final boolean doFacts = true;
 141         static final boolean doOccurences = true;
 142         static final boolean doCommonNames = true;
 143
 144         //etc.
 145         static final boolean doMarker = true;
 146
 147
 148         public void importEm2CDM (Source source, ICdmDataSource destination, DbSchemaValidation hbm2dll){
 149                 System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") to " + cdmDestination.getDatabase() + " ...");
 150                 //make BerlinModel Source
 151
 152                 BerlinModelImportConfigurator config = BerlinModelImportConfigurator.NewInstance(source,  destination);
 153
 154                 config.setClassificationName(classificationName);
 155
 156                 config.setClassificationUuid(classificationUuid);
 157                 config.setSourceSecId(sourceSecId);
 158                 config.setNomenclaturalCode(nomenclaturalCode);
 159                 config.setIgnoreNull(ignoreNull);
 160
 161                 config.setDoAuthors(doAuthors ^ invers);
 162                 config.setDoReferences(invers ? doReferences.invers() : doReferences);
 163                 config.setDoTaxonNames(doTaxonNames ^ invers);
 164                 config.setDoRelNames(doRelNames ^ invers);
 165                 config.setDoNameStatus(doNameStatus ^ invers);
 166                 config.setDoTypes(doTypes);  //always false
 167                 config.setDoNameFacts(doNameFacts ^ invers);
 168                 config.setDoTaxa(doTaxa ^ invers);
 169                 config.setDoRelTaxa(doRelTaxa ^ invers);
 170                 config.setDoFacts(doFacts ^ invers);
 171                 config.setDoOccurrence(doOccurences ^ invers);
 172                 config.setDoCommonNames(doCommonNames ^ invers);
 173
 174                 config.setDoMarker(doMarker ^ invers);
 175                 config.setDoUser(doUser ^ invers);
 176
 177                 config.setUseClassification(useClassification);
 178                 config.setSourceRefUuid(BerlinModelTransformer.uuidSourceRefEuroMed);
 179                 config.setEditor(editor);
 180                 config.setDbSchemaValidation(hbm2dll);
 181
 182                 // maximum number of name facts to import
 183                 config.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts);
 184
 185                 config.setInfrGenericRankAbbrev(infrGenericRankAbbrev);
 186                 config.setInfrSpecificRankAbbrev(infrSpecificRankAbbrev);
 187                 config.setRemoveHttpMapsAnchor(removeHttpMapsAnchor);
 188
 189 //              filter
 190                 config.setTaxonTable(taxonTable);
 191                 config.setClassificationQuery(classificationQuery);
 192                 config.setRelTaxaIdQuery(relPTaxonIdQuery);
 193                 config.setNameIdTable(nameIdTable);
 194                 config.setReferenceIdTable(referenceIdTable);
 195                 config.setAuthorTeamFilter(authorTeamFilter);
 196                 config.setAuthorFilter(authorFilter);
 197                 config.setFactFilter(factFilter);
 198                 config.setRefDetailFilter(refDetailFilter);
 199                 config.setCommonNameFilter(commonNameFilter);
 200                 config.setOccurrenceFilter(occurrenceFilter);
 201                 config.setOccurrenceSourceFilter(occurrenceSourceFilter);
 202                 config.setWebMarkerFilter(webMarkerFilter);
 203                 config.setUseSingleClassification(useSingleClassification);
 204
 205                 //TDWG codes
 206                 config.setSplitTdwgCodes(isSplitTdwgCodes);
 207                 config.setUseEmAreaVocabulary(useEmAreaVocabulary);
 208
 209                 config.setCheck(check);
 210                 config.setEditor(editor);
 211                 config.setRecordsPerTransaction(partitionSize);
 212
 213                 config.setSwitchSpeciesGroup(switchSpeciesGroup);
 214
 215                 // invoke import
 216                 CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>();
 217                 bmImport.invoke(config);
 218
 219                 if (config.isDoTaxonNames() && (config.getCheck().equals(CHECK.CHECK_AND_IMPORT)  || config.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK)  )  ){
 220                         ICdmApplicationConfiguration app = bmImport.getCdmAppController();
 221                         TransactionStatus tx = app.startTransaction();
 222                         try {
 223                                 Rank sectBot = (Rank)app.getTermService().find(Rank.SECTION_BOTANY().getUuid());
 224                                 Representation repr = sectBot.getRepresentation(Language.ENGLISH());
 225                                 repr.setAbbreviatedLabel(repr.getAbbreviatedLabel().replace("(bot.)", "").trim());
 226                                 repr.setLabel(repr.getLabel().replace("(Botany)", "").trim());
 227                                 sectBot.setTitleCache(null, false);  //to definetely update the titleCache also
 228                                 app.getTermService().saveOrUpdate(sectBot);
 229
 230                                 Rank subSectBot = (Rank)app.getTermService().find(Rank.SECTION_BOTANY().getUuid());
 231                                 repr = subSectBot.getRepresentation(Language.ENGLISH());
 232                                 repr.setAbbreviatedLabel(repr.getAbbreviatedLabel().replace("(bot.)", "").trim());
 233                                 repr.setLabel(repr.getLabel().replace("(Botany)", "").trim());
 234                                 subSectBot.setTitleCache(null, false);  //to definetely update the titleCache also
 235                                 app.getTermService().saveOrUpdate(subSectBot);
 236                                 app.commitTransaction(tx);
 237                         } catch (Exception e) {
 238                                 e.printStackTrace();
 239                         }
 240                 }
 241
 242                 if (config.isDoFacts() && (config.getCheck().equals(CHECK.CHECK_AND_IMPORT)  || config.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK)  )  ){
 243                         ICdmApplicationConfiguration app = bmImport.getCdmAppController();
 244                         TransactionStatus tx = app.startTransaction();
 245
 246                         //make feature tree
 247                         FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, config.getFeatureMap(), featureKeyList);
 248                         FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE());
 249                         tree.getRoot().addChild(imageNode);
 250                         FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 251                         tree.getRoot().addChild(distributionNode, 1);
 252                         FeatureNode commonNameNode = FeatureNode.NewInstance(Feature.COMMON_NAME());
 253                         tree.getRoot().addChild(commonNameNode, 2);
 254                         app.getFeatureTreeService().saveOrUpdate(tree);
 255
 256                         //Change common name label
 257                         DefinedTermBase<?> commonNameFeature = app.getTermService().find(Feature.COMMON_NAME().getUuid());
 258                         commonNameFeature.setLabel("Common Names", Language.ENGLISH());
 259                         commonNameFeature.setTitleCache(null, false);  //to definetely update the titleCache also
 260                         app.getTermService().saveOrUpdate(commonNameFeature);
 261                         app.commitTransaction(tx);
 262                 }
 263
 264                 if (config.isDoRelTaxa()){
 265
 266                 }
 267
 268                 System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
 269
 270         }
 271
 272         /**
 273          * @param args
 274          */
 275         public static void main(String[] args) {
 276                 EuroMedActivator importActivator = new EuroMedActivator();
 277                 Source source = berlinModelSource;
 278                 ICdmDataSource cdmRepository = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
 279
 280                 importActivator.importEm2CDM(source, cdmRepository, hbm2dll);
 281                 if (includePesiExport){
 282                         //not available from here since E+M was moved to app-import
 283 //                      PesiExportActivatorEM exportActivator = new PesiExportActivatorEM();
 284 //                      exportActivator.doExport(cdmRepository);
 285                 }
 286
 287         }
 288
 289 }