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
  10 package eu.etaxonomy.cdm.app.vibrant;
  11
  12 import java.lang.reflect.Method;
  13 import java.sql.ResultSet;
  14 import java.util.UUID;
  15
  16 import org.apache.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.CdmBase;
  30 import eu.etaxonomy.cdm.model.common.ExtensionType;
  31 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  32 import eu.etaxonomy.cdm.model.name.NonViralName;
  33 import eu.etaxonomy.cdm.model.name.Rank;
  34 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  35
  36
  37 /**
  38  * TODO add the following to a wiki page:
  39  * 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
  40  * you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.
  41  *
  42  *
  43  * @author a.mueller
  44  *
  45  */
  46 public class IopiActivator {
  47         private static final Logger logger = Logger.getLogger(IopiActivator.class);
  48
  49         //database validation status (create, update, validate ...)
  50         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  51         static final Source berlinModelSource = BerlinModelSources.iopi();
  52
  53 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
  54         static final ICdmDataSource cdmDestination = cdm_test_local_iopi();
  55
  56         static final boolean useSingleClassification = true;
  57         static final Integer sourceSecId = 1892; //7000000;
  58         static final UUID classificationUuid = null; //UUID.fromString("aa3fbaeb-f5dc-4e75-8d60-c8f93beb7ba6");
  59
  60         static final UUID sourceRefUuid = UUID.fromString("df68c748-3c64-4b96-9a47-db51fb9d387e");
  61
  62         // set to zero for unlimited nameFacts
  63         static final int maximumNumberOfNameFacts = 0;
  64
  65         static final int partitionSize = 1500;
  66
  67         //check - import
  68         static final CHECK check = CHECK.CHECK_AND_IMPORT;
  69
  70         //editor - import
  71         static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR;
  72
  73         //NomenclaturalCode
  74         static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP;
  75
  76         //ignore null
  77         static final boolean ignoreNull = true;
  78
  79         static boolean useClassification = true;
  80
  81
  82         //filter
  83         static String taxonTable = "v_cdm_exp_taxaAll";
  84         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;
  85         static String relPTaxonIdQuery = " SELECT r.RelPTaxonId " +
  86                                         " FROM RelPTaxon AS r INNER JOIN v_cdm_exp_taxaDirect AS a ON r.PTNameFk2 = a.PTNameFk AND r.PTRefFk2 = a.PTRefFk ";
  87         static String nameIdTable = " v_cdm_exp_namesAll ";
  88         static String referenceIdTable = " v_cdm_exp_refAll ";
  89         static String factFilter = " factId IN ( SELECT factId FROM v_cdm_exp_factsAll )";
  90         static String authorTeamFilter = null; // " authorTeamId IN (SELECT authorTeamId FROM v_cdm_exp_authorTeamsAll) ";
  91         static String authorFilter = null;  // " authorId IN (SELECT authorId FROM v_cdm_exp_authorsAll) ";
  92         //not used
  93         static String occurrenceFilter = " occurrenceId IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";
  94         static String occurrenceSourceFilter = " occurrenceFk IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";
  95         static String commonNameFilter = " commonNameId IN ( SELECT commonNameId FROM v_cdm_exp_commonNamesAll )";
  96
  97
  98
  99 // **************** ALL *********************
 100
 101         //authors
 102         static final boolean doAuthors = true;
 103         //references
 104         static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;
 105         //names
 106         static final boolean doTaxonNames = true;
 107         static final boolean doRelNames = true;
 108         static final boolean doNameStatus = true;
 109
 110         //taxa
 111         static final boolean doTaxa = true;
 112         static final boolean doRelTaxa = true;
 113         static final boolean doFacts = true;
 114
 115         //etc.
 116
 117
 118 // **************** SELECTED *********************
 119
 120 //      static final boolean doUser = true;
 121 //      //authors
 122 //      static final boolean doAuthors = false;
 123 //      //references
 124 //      static final DO_REFERENCES doReferences =  DO_REFERENCES.NONE;
 125 //      //names
 126 //      static final boolean doTaxonNames = false;
 127 //      static final boolean doRelNames = false;
 128 //      static final boolean doNameStatus = false;
 129 //      static final boolean doTypes = false;
 130 //      static final boolean doNameFacts = false;
 131 //
 132 //      //taxa
 133 //      static final boolean doTaxa = false;
 134 //      static final boolean doRelTaxa = false;
 135 //      static final boolean doFacts = false;
 136 //
 137 //      //etc.
 138 //      static final boolean doMarker = false;
 139
 140
 141 //******** ALWAYS IGNORE *****************************
 142
 143         static final boolean doUser = false;
 144         static final boolean doOccurences = false;
 145         static final boolean doCommonNames = false;
 146         static final boolean doTypes = false;
 147         static final boolean doNameFacts = false;
 148         static final boolean doMarker = false;
 149
 150
 151         public void importIopi (Source source, ICdmDataSource destination, DbSchemaValidation hbm2dll){
 152                 System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") to " + cdmDestination.getDatabase() + " ...");
 153                 //make BerlinModel Source
 154
 155                 BerlinModelImportConfigurator config = BerlinModelImportConfigurator.NewInstance(source,  destination);
 156
 157                 config.setClassificationUuid(classificationUuid);
 158                 config.setSourceSecId(sourceSecId);
 159
 160                 config.setNomenclaturalCode(nomenclaturalCode);
 161
 162                 try {
 163                         Method makeUrlMethod = this.getClass().getDeclaredMethod("makeUrlForTaxon", TaxonBase.class, ResultSet.class);
 164                         config.setMakeUrlForTaxon(makeUrlMethod);
 165                 } catch (Exception e) {
 166                         e.printStackTrace();
 167                         return;
 168                 }
 169
 170                 config.setIgnoreNull(ignoreNull);
 171                 config.setDoAuthors(doAuthors);
 172                 config.setDoReferences(doReferences);
 173                 config.setDoTaxonNames(doTaxonNames);
 174                 config.setDoRelNames(doRelNames);
 175                 config.setDoNameStatus(doNameStatus);
 176                 config.setDoTypes(doTypes);
 177                 config.setDoNameFacts(doNameFacts);
 178                 config.setUseClassification(useClassification);
 179                 config.setSourceRefUuid(sourceRefUuid);
 180
 181                 config.setDoTaxa(doTaxa);
 182                 config.setDoRelTaxa(doRelTaxa);
 183                 config.setDoFacts(doFacts);
 184                 config.setDoOccurrence(doOccurences);
 185                 config.setDoCommonNames(doCommonNames);
 186
 187                 config.setDoMarker(doMarker);
 188                 config.setDoUser(doUser);
 189                 config.setEditor(editor);
 190                 config.setDbSchemaValidation(hbm2dll);
 191
 192                 // maximum number of name facts to import
 193                 config.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts);
 194
 195                 config.setUseSingleClassification(useSingleClassification);
 196
 197                 config.setCheck(check);
 198                 config.setEditor(editor);
 199                 config.setRecordsPerTransaction(partitionSize);
 200
 201 //              filter
 202                 config.setTaxonTable(taxonTable);
 203                 config.setClassificationQuery(classificationQuery);
 204                 config.setRelTaxaIdQuery(relPTaxonIdQuery);
 205                 config.setNameIdTable(nameIdTable);
 206                 config.setReferenceIdTable(referenceIdTable);
 207                 config.setAuthorTeamFilter(authorTeamFilter);
 208                 config.setAuthorFilter(authorFilter);
 209                 config.setFactFilter(factFilter);
 210                 config.setCommonNameFilter(commonNameFilter);
 211                 config.setOccurrenceFilter(occurrenceFilter);
 212                 config.setOccurrenceSourceFilter(occurrenceSourceFilter);
 213                 config.setUseSingleClassification(useSingleClassification);
 214
 215
 216
 217                 // invoke import
 218                 CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>();
 219                 bmImport.invoke(config);
 220
 221                 System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
 222
 223         }
 224
 225         /**
 226          * @param args
 227          */
 228         public static void main(String[] args) {
 229                 IopiActivator importActivator = new IopiActivator();
 230                 Source source = berlinModelSource;
 231                 ICdmDataSource cdmRepository = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
 232
 233                 importActivator.importIopi(source, cdmRepository, hbm2dll);
 234
 235         }
 236
 237         public static ICdmDataSource cdm_test_local_iopi(){
 238                 DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
 239                 String cdmServer = "127.0.0.1";
 240                 String cdmDB = "iopi";
 241                 String cdmUserName = "root";
 242                 return CdmDestinations.makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
 243         }
 244
 245
 246         //for FAUNA Europaea (http://rbg-web2.rbge.org.uk/FE/fe.html)
 247         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";
 248         public static Method makeUrlForTaxon(TaxonBase<?> taxon, ResultSet rs){
 249                 Method result = null;
 250                 ExtensionType urlExtensionType = ExtensionType.URL();
 251
 252                 String family = "";
 253                 String genus = "";
 254                 String species = "";
 255                 String taxonName = "";
 256                 String rankStr = "";
 257
 258                 NonViralName<?>  name = CdmBase.deproxy(taxon.getName(), NonViralName.class);
 259                 Rank rank = name.getRank();
 260                 rankStr = transformFeRanks(rank);
 261
 262
 263                 if (rank.equals(Rank.FAMILY())){
 264                         family = name.getGenusOrUninomial();
 265                         taxonName = name.getGenusOrUninomial();
 266                 }else if (rank.isHigher(Rank.GENUS())){
 267                         taxonName = name.getGenusOrUninomial();
 268                 }else if (rank.isGenus()){
 269                         genus = name.getGenusOrUninomial();
 270                         rankStr = "genus";
 271                 }else if (rank.isInfraGeneric()){
 272                         genus = name.getGenusOrUninomial();
 273                         taxonName = name.getInfraGenericEpithet();
 274                 }else if (rank.isSpecies()){
 275                         genus = name.getGenusOrUninomial();
 276                         species = name.getSpecificEpithet();
 277                         rankStr = "species";
 278                 }else if (rank.isInfraSpecific()){
 279                         genus = name.getGenusOrUninomial();
 280                         species = name.getSpecificEpithet();
 281                         taxonName = name.getInfraSpecificEpithet();
 282                 }
 283
 284
 285                 String url = String.format(URLbase ,family, genus, species, taxonName, rankStr);
 286                 taxon.addExtension(url, urlExtensionType);
 287
 288                 return result;
 289         }
 290
 291         private static String transformFeRanks(Rank rank){
 292                 if (rank.equals(Rank.SPECIESAGGREGATE())){ return "agg.";
 293                 }else if (rank.equals(Rank.CLASS())){ return "Class";
 294                 }else if (rank.equals(Rank.DIVISION())){ return "Division";
 295                 }else if (rank.equals(Rank.FAMILY())){ return "family";
 296                 }else if (rank.equals(Rank.FORM())){ return "forma";
 297                 }else if (rank.equals(Rank.GENUS())){ return "genus";
 298                 }else if (rank.equals(Rank.GREX())){ return "grex";
 299                 }else if (rank.equals(Rank.SPECIESGROUP())){ return "group";
 300                 }else if (rank.equals(Rank.ORDER())){ return "Order";
 301 //              }else if (rank.equals(Rank.PROL())){ return "proles";
 302 //--            }else if (rank.equals(Rank.RACE())){ return "race";
 303                 }else if (rank.equals(Rank.SECTION_BOTANY())){ return "Sect.";
 304                 }else if (rank.equals(Rank.SERIES())){ return "Ser.";
 305                 }else if (rank.equals(Rank.SPECIES())){ return "species";
 306                 }else if (rank.equals(Rank.SUBCLASS())){ return "Subclass";
 307                 }else if (rank.equals(Rank.SUBDIVISION())){ return "Subdivision";
 308                 }else if (rank.equals(Rank.SUBFORM())){ return "Subf.";
 309                 }else if (rank.equals(Rank.SUBGENUS())){ return "Subgen.";
 310                 }else if (rank.equals(Rank.SUBORDER())){ return "Suborder";
 311                 }else if (rank.equals(Rank.SUBSECTION_BOTANY())){ return "Subsect.";
 312                 }else if (rank.equals(Rank.SUBSERIES())){ return "Subser.";
 313                 }else if (rank.equals(Rank.SUBSPECIES())){ return "subsp";
 314                 }else if (rank.equals(Rank.SUBVARIETY())){ return "subvar.";
 315                 }else if (rank.equals(Rank.SUPERORDER())){ return "Superorder";
 316                 }else if (rank.equals(Rank.TRIBE())){ return "Tribe";
 317                 }else if (rank.equals(Rank.VARIETY())){ return "var.";
 318                 }else{
 319                         logger.debug("Rank not found: " + rank.getTitleCache());
 320                         return "";
 321                 }
 322         }
 323
 324
 325 }