app-import/src/main/java/eu/etaxonomy/cdm/app/vibrant/IopiActivator.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 package eu.etaxonomy.cdm.app.vibrant;
  10
  11 import java.lang.reflect.Method;
  12 import java.sql.ResultSet;
  13 import java.util.UUID;
  14
  15 import org.apache.logging.log4j.LogManager;
  16 import org.apache.logging.log4j.Logger;
  17
  18 import eu.etaxonomy.cdm.app.berlinModelImport.BerlinModelSources;
  19 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  20 import eu.etaxonomy.cdm.database.DatabaseTypeEnum;
  21 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  22 import eu.etaxonomy.cdm.database.ICdmDataSource;
  23 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;
  24 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  25 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  26 import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;
  27 import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR;
  28 import eu.etaxonomy.cdm.io.common.Source;
  29 import eu.etaxonomy.cdm.model.common.ExtensionType;
  30 import eu.etaxonomy.cdm.model.name.INonViralName;
  31 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  32 import eu.etaxonomy.cdm.model.name.Rank;
  33 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  34
  35 /**
  36  * TODO add the following to a wiki page:
  37  * 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
  38  * you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.
  39  *
  40  * @author a.mueller
  41  */
  42 public class IopiActivator {
  43
  44     private static final Logger logger = LogManager.getLogger();
  45
  46         //database validation status (create, update, validate ...)
  47         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  48         static final Source berlinModelSource = BerlinModelSources.iopi();
  49
  50 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
  51         static final ICdmDataSource cdmDestination = cdm_test_local_iopi();
  52
  53         static final boolean useSingleClassification = true;
  54         static final Integer sourceSecId = 1892; //7000000;
  55         static final UUID classificationUuid = null; //UUID.fromString("aa3fbaeb-f5dc-4e75-8d60-c8f93beb7ba6");
  56
  57         static final UUID sourceRefUuid = UUID.fromString("df68c748-3c64-4b96-9a47-db51fb9d387e");
  58
  59         // set to zero for unlimited nameFacts
  60         static final int maximumNumberOfNameFacts = 0;
  61
  62         static final int partitionSize = 1500;
  63
  64         //check - import
  65         static final CHECK check = CHECK.CHECK_AND_IMPORT;
  66
  67         //editor - import
  68         static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR;
  69
  70         //NomenclaturalCode
  71         static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP;
  72
  73         //ignore null
  74         static final boolean ignoreNull = true;
  75
  76         static boolean useClassification = true;
  77
  78
  79         //filter
  80         static String taxonTable = "v_cdm_exp_taxaAll";
  81         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;
  82         static String relPTaxonIdQuery = " SELECT r.RelPTaxonId " +
  83                                         " FROM RelPTaxon AS r INNER JOIN v_cdm_exp_taxaDirect AS a ON r.PTNameFk2 = a.PTNameFk AND r.PTRefFk2 = a.PTRefFk ";
  84         static String nameIdTable = " v_cdm_exp_namesAll ";
  85         static String referenceIdTable = " v_cdm_exp_refAll ";
  86         static String factFilter = " factId IN ( SELECT factId FROM v_cdm_exp_factsAll )";
  87         static String authorTeamFilter = null; // " authorTeamId IN (SELECT authorTeamId FROM v_cdm_exp_authorTeamsAll) ";
  88         static String authorFilter = null;  // " authorId IN (SELECT authorId FROM v_cdm_exp_authorsAll) ";
  89         //not used
  90         static String occurrenceFilter = " occurrenceId IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";
  91         static String occurrenceSourceFilter = " occurrenceFk IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";
  92         static String commonNameFilter = " commonNameId IN ( SELECT commonNameId FROM v_cdm_exp_commonNamesAll )";
  93
  94
  95
  96 // **************** ALL *********************
  97
  98         //authors
  99         static final boolean doAuthors = true;
 100         //references
 101         static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;
 102         //names
 103         static final boolean doTaxonNames = true;
 104         static final boolean doRelNames = true;
 105         static final boolean doNameStatus = true;
 106
 107         //taxa
 108         static final boolean doTaxa = true;
 109         static final boolean doRelTaxa = true;
 110         static final boolean doFacts = true;
 111
 112         //etc.
 113
 114
 115 // **************** SELECTED *********************
 116
 117 //      static final boolean doUser = true;
 118 //      //authors
 119 //      static final boolean doAuthors = false;
 120 //      //references
 121 //      static final DO_REFERENCES doReferences =  DO_REFERENCES.NONE;
 122 //      //names
 123 //      static final boolean doTaxonNames = false;
 124 //      static final boolean doRelNames = false;
 125 //      static final boolean doNameStatus = false;
 126 //      static final boolean doTypes = false;
 127 //      static final boolean doNameFacts = false;
 128 //
 129 //      //taxa
 130 //      static final boolean doTaxa = false;
 131 //      static final boolean doRelTaxa = false;
 132 //      static final boolean doFacts = false;
 133 //
 134 //      //etc.
 135 //      static final boolean doMarker = false;
 136
 137
 138 //******** ALWAYS IGNORE *****************************
 139
 140         static final boolean doUser = false;
 141         static final boolean doOccurences = false;
 142         static final boolean doCommonNames = false;
 143         static final boolean doTypes = false;
 144         static final boolean doNameFacts = false;
 145         static final boolean doMarker = false;
 146
 147
 148         public void importIopi (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.setClassificationUuid(classificationUuid);
 155                 config.setSourceSecId(sourceSecId);
 156
 157                 config.setNomenclaturalCode(nomenclaturalCode);
 158
 159                 try {
 160                         Method makeUrlMethod = this.getClass().getDeclaredMethod("makeUrlForTaxon", TaxonBase.class, ResultSet.class);
 161                         config.setMakeUrlForTaxon(makeUrlMethod);
 162                 } catch (Exception e) {
 163                         e.printStackTrace();
 164                         return;
 165                 }
 166
 167                 config.setIgnoreNull(ignoreNull);
 168                 config.setDoAuthors(doAuthors);
 169                 config.setDoReferences(doReferences);
 170                 config.setDoTaxonNames(doTaxonNames);
 171                 config.setDoRelNames(doRelNames);
 172                 config.setDoNameStatus(doNameStatus);
 173                 config.setDoTypes(doTypes);
 174                 config.setDoNameFacts(doNameFacts);
 175                 config.setUseClassification(useClassification);
 176                 config.setSourceRefUuid(sourceRefUuid);
 177
 178                 config.setDoTaxa(doTaxa);
 179                 config.setDoRelTaxa(doRelTaxa);
 180                 config.setDoFacts(doFacts);
 181                 config.setDoOccurrence(doOccurences);
 182                 config.setDoCommonNames(doCommonNames);
 183
 184                 config.setDoMarker(doMarker);
 185                 config.setDoUser(doUser);
 186                 config.setEditor(editor);
 187                 config.setDbSchemaValidation(hbm2dll);
 188
 189                 // maximum number of name facts to import
 190                 config.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts);
 191
 192                 config.setUseSingleClassification(useSingleClassification);
 193
 194                 config.setCheck(check);
 195                 config.setEditor(editor);
 196                 config.setRecordsPerTransaction(partitionSize);
 197
 198 //              filter
 199                 config.setTaxonTable(taxonTable);
 200                 config.setClassificationQuery(classificationQuery);
 201                 config.setRelTaxaIdQuery(relPTaxonIdQuery);
 202                 config.setNameIdTable(nameIdTable);
 203                 config.setReferenceIdTable(referenceIdTable);
 204                 config.setAuthorTeamFilter(authorTeamFilter);
 205                 config.setAuthorFilter(authorFilter);
 206                 config.setFactFilter(factFilter);
 207                 config.setCommonNameFilter(commonNameFilter);
 208                 config.setOccurrenceFilter(occurrenceFilter);
 209                 config.setOccurrenceSourceFilter(occurrenceSourceFilter);
 210                 config.setUseSingleClassification(useSingleClassification);
 211
 212
 213
 214                 // invoke import
 215                 CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>();
 216                 bmImport.invoke(config);
 217
 218                 System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
 219
 220         }
 221
 222         /**
 223          * @param args
 224          */
 225         public static void main(String[] args) {
 226                 IopiActivator importActivator = new IopiActivator();
 227                 Source source = berlinModelSource;
 228                 ICdmDataSource cdmRepository = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
 229
 230                 importActivator.importIopi(source, cdmRepository, hbm2dll);
 231
 232         }
 233
 234         public static ICdmDataSource cdm_test_local_iopi(){
 235                 DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
 236                 String cdmServer = "127.0.0.1";
 237                 String cdmDB = "iopi";
 238                 String cdmUserName = "root";
 239                 return CdmDestinations.makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
 240         }
 241
 242
 243         //for FAUNA Europaea (http://rbg-web2.rbge.org.uk/FE/fe.html)
 244         private static final String URLbase = "http://rbg-web2.rbge.org.uk/cgi-bin/nph-readbtree.pl/feout?FAMILY_XREF=%s&GENUS_XREF=%s&SPECIES_XREF=%s&TAXON_NAME_XREF=%s&RANK=%s";
 245         public static Method makeUrlForTaxon(TaxonBase<?> taxon, ResultSet rs){
 246                 Method result = null;
 247                 ExtensionType urlExtensionType = ExtensionType.URL();
 248
 249                 String family = "";
 250                 String genus = "";
 251                 String species = "";
 252                 String taxonName = "";
 253                 String rankStr = "";
 254
 255                 INonViralName  name = taxon.getName();
 256                 Rank rank = name.getRank();
 257                 rankStr = transformFeRanks(rank);
 258
 259
 260                 if (rank.equals(Rank.FAMILY())){
 261                         family = name.getGenusOrUninomial();
 262                         taxonName = name.getGenusOrUninomial();
 263                 }else if (rank.isSupraGeneric()){
 264                         taxonName = name.getGenusOrUninomial();
 265                 }else if (rank.isGenus()){
 266                         genus = name.getGenusOrUninomial();
 267                         rankStr = "genus";
 268                 }else if (rank.isInfraGeneric()){
 269                         genus = name.getGenusOrUninomial();
 270                         taxonName = name.getInfraGenericEpithet();
 271                 }else if (rank.isSpecies()){
 272                         genus = name.getGenusOrUninomial();
 273                         species = name.getSpecificEpithet();
 274                         rankStr = "species";
 275                 }else if (rank.isInfraSpecific()){
 276                         genus = name.getGenusOrUninomial();
 277                         species = name.getSpecificEpithet();
 278                         taxonName = name.getInfraSpecificEpithet();
 279                 }
 280
 281
 282                 String url = String.format(URLbase ,family, genus, species, taxonName, rankStr);
 283                 taxon.addExtension(url, urlExtensionType);
 284
 285                 return result;
 286         }
 287
 288         private static String transformFeRanks(Rank rank){
 289                 if (rank.equals(Rank.SPECIESAGGREGATE())){ return "agg.";
 290                 }else if (rank.equals(Rank.CLASS())){ return "Class";
 291                 }else if (rank.equals(Rank.DIVISION())){ return "Division";
 292                 }else if (rank.equals(Rank.FAMILY())){ return "family";
 293                 }else if (rank.equals(Rank.FORM())){ return "forma";
 294                 }else if (rank.equals(Rank.GENUS())){ return "genus";
 295                 }else if (rank.equals(Rank.GREX_INFRASPEC())){ return "grex";
 296                 }else if (rank.equals(Rank.SPECIESGROUP())){ return "group";
 297                 }else if (rank.equals(Rank.ORDER())){ return "Order";
 298 //              }else if (rank.equals(Rank.PROL())){ return "proles";
 299 //--            }else if (rank.equals(Rank.RACE())){ return "race";
 300                 }else if (rank.equals(Rank.SECTION_BOTANY())){ return "Sect.";
 301                 }else if (rank.equals(Rank.SERIES())){ return "Ser.";
 302                 }else if (rank.equals(Rank.SPECIES())){ return "species";
 303                 }else if (rank.equals(Rank.SUBCLASS())){ return "Subclass";
 304                 }else if (rank.equals(Rank.SUBDIVISION())){ return "Subdivision";
 305                 }else if (rank.equals(Rank.SUBFORM())){ return "Subf.";
 306                 }else if (rank.equals(Rank.SUBGENUS())){ return "Subgen.";
 307                 }else if (rank.equals(Rank.SUBORDER())){ return "Suborder";
 308                 }else if (rank.equals(Rank.SUBSECTION_BOTANY())){ return "Subsect.";
 309                 }else if (rank.equals(Rank.SUBSERIES())){ return "Subser.";
 310                 }else if (rank.equals(Rank.SUBSPECIES())){ return "subsp";
 311                 }else if (rank.equals(Rank.SUBVARIETY())){ return "subvar.";
 312                 }else if (rank.equals(Rank.SUPERORDER())){ return "Superorder";
 313                 }else if (rank.equals(Rank.TRIBE())){ return "Tribe";
 314                 }else if (rank.equals(Rank.VARIETY())){ return "var.";
 315                 }else{
 316                         logger.debug("Rank not found: " + rank.getTitleCache());
 317                         return "";
 318                 }
 319         }
 320
 321
 322 }