Revision 24bf3f9c
Added by Andreas Müller about 12 years ago
| .gitattributes | ||
|---|---|---|
| 1254 | 1254 |
cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/PesiSources.java -text |
| 1255 | 1255 |
cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/merging/FaunaEuErmsFindIdenticalNamesActivator.java -text |
| 1256 | 1256 |
cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/merging/FaunaEuErmsMergeActivator.java -text |
| 1257 |
cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/vibrant/IopiActivator.java -text |
|
| 1258 |
cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/vibrant/MclActivator.java -text |
|
| 1259 |
cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/vibrant/VibrantActivator.java -text |
|
| 1260 | 1257 |
cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsAreaImport.java -text |
| 1261 | 1258 |
cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsDrImport.java -text |
| 1262 | 1259 |
cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsImageImport.java -text |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/vibrant/IopiActivator.java | ||
|---|---|---|
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/** |
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* Copyright (C) 2007 EDIT |
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* European Distributed Institute of Taxonomy |
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* http://www.e-taxonomy.eu |
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* |
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* The contents of this file are subject to the Mozilla Public License Version 1.1 |
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* See LICENSE.TXT at the top of this package for the full license terms. |
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*/ |
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package eu.etaxonomy.cdm.app.vibrant; |
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import java.util.UUID; |
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import org.apache.log4j.Logger; |
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|
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import eu.etaxonomy.cdm.app.common.BerlinModelSources; |
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import eu.etaxonomy.cdm.app.common.CdmDestinations; |
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import eu.etaxonomy.cdm.database.DatabaseTypeEnum; |
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import eu.etaxonomy.cdm.database.DbSchemaValidation; |
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import eu.etaxonomy.cdm.database.ICdmDataSource; |
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator; |
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import eu.etaxonomy.cdm.io.common.CdmDefaultImport; |
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK; |
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES; |
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR; |
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import eu.etaxonomy.cdm.io.common.Source; |
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import eu.etaxonomy.cdm.io.pesi.out.PesiTransformer; |
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
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/** |
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* TODO add the following to a wiki page: |
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* 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 |
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* you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names. |
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* |
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* |
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* @author a.mueller |
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* |
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*/ |
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public class IopiActivator {
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(IopiActivator.class); |
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//database validation status (create, update, validate ...) |
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static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE; |
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static final Source berlinModelSource = BerlinModelSources.iopi(); |
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql(); |
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static final ICdmDataSource cdmDestination = cdm_test_local_iopi(); |
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static final boolean useSingleClassification = false; |
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static final Integer sourceSecId = null; //7000000; |
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static final UUID classificationUuid = null; //UUID.fromString("aa3fbaeb-f5dc-4e75-8d60-c8f93beb7ba6");
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static final UUID sourceRefUuid = UUID.fromString("df68c748-3c64-4b96-9a47-db51fb9d387e");
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// set to zero for unlimited nameFacts |
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static final int maximumNumberOfNameFacts = 0; |
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static final int partitionSize = 1500; |
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//check - import |
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static final CHECK check = CHECK.CHECK_AND_IMPORT; |
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//editor - import |
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static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR; |
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//NomeclaturalCode |
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static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICBN; |
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//ignore null |
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static final boolean ignoreNull = true; |
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static boolean useClassification = true; |
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// **************** ALL ********************* |
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//authors |
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static final boolean doAuthors = true; |
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//references |
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static final DO_REFERENCES doReferences = DO_REFERENCES.ALL; |
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//names |
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static final boolean doTaxonNames = true; |
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static final boolean doRelNames = true; |
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static final boolean doNameStatus = true; |
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//taxa |
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static final boolean doTaxa = true; |
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static final boolean doRelTaxa = true; |
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static final boolean doFacts = true; |
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//etc. |
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// **************** SELECTED ********************* |
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// static final boolean doUser = true; |
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// //authors |
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// static final boolean doAuthors = false; |
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// //references |
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// static final DO_REFERENCES doReferences = DO_REFERENCES.NONE; |
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// //names |
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// static final boolean doTaxonNames = false; |
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// static final boolean doRelNames = false; |
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// static final boolean doNameStatus = false; |
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// static final boolean doTypes = false; |
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// static final boolean doNameFacts = false; |
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// |
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// //taxa |
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// static final boolean doTaxa = false; |
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// static final boolean doRelTaxa = false; |
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// static final boolean doFacts = false; |
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// |
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// //etc. |
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// static final boolean doMarker = false; |
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//******** ALWAYS IGNORE ***************************** |
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static final boolean doUser = false; |
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static final boolean doOccurences = false; |
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static final boolean doCommonNames = false; |
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static final boolean doTypes = false; |
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static final boolean doNameFacts = false; |
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static final boolean doMarker = false; |
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public void importIopi (Source source, ICdmDataSource destination, DbSchemaValidation hbm2dll){
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System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") to " + cdmDestination.getDatabase() + " ...");
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//make BerlinModel Source |
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BerlinModelImportConfigurator config = BerlinModelImportConfigurator.NewInstance(source, destination); |
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config.setClassificationUuid(classificationUuid); |
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config.setSourceSecId(sourceSecId); |
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config.setNomenclaturalCode(nomenclaturalCode); |
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config.setIgnoreNull(ignoreNull); |
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config.setDoAuthors(doAuthors); |
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config.setDoReferences(doReferences); |
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config.setDoTaxonNames(doTaxonNames); |
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config.setDoRelNames(doRelNames); |
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config.setDoNameStatus(doNameStatus); |
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config.setDoTypes(doTypes); |
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config.setDoNameFacts(doNameFacts); |
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config.setUseClassification(useClassification); |
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config.setSourceRefUuid(sourceRefUuid); |
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config.setDoTaxa(doTaxa); |
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config.setDoRelTaxa(doRelTaxa); |
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config.setDoFacts(doFacts); |
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config.setDoOccurrence(doOccurences); |
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config.setDoCommonNames(doCommonNames); |
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config.setDoMarker(doMarker); |
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config.setDoUser(doUser); |
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config.setEditor(editor); |
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config.setDbSchemaValidation(hbm2dll); |
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// maximum number of name facts to import |
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config.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts); |
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config.setUseSingleClassification(useSingleClassification); |
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config.setCheck(check); |
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config.setEditor(editor); |
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config.setRecordsPerTransaction(partitionSize); |
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// invoke import |
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CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>(); |
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bmImport.invoke(config); |
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System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
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} |
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/** |
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* @param args |
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*/ |
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public static void main(String[] args) {
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IopiActivator importActivator = new IopiActivator(); |
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Source source = berlinModelSource; |
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ICdmDataSource cdmRepository = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination; |
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importActivator.importIopi(source, cdmRepository, hbm2dll); |
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} |
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public static ICdmDataSource cdm_test_local_iopi(){
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DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
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String cdmServer = "127.0.0.1"; |
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String cdmDB = "iopi"; |
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String cdmUserName = "root"; |
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return CdmDestinations.makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
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} |
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} |
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| cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/vibrant/MclActivator.java | ||
|---|---|---|
| 1 |
/** |
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| 2 |
* Copyright (C) 2007 EDIT |
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| 3 |
* European Distributed Institute of Taxonomy |
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| 4 |
* http://www.e-taxonomy.eu |
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| 5 |
* |
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* The contents of this file are subject to the Mozilla Public License Version 1.1 |
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* See LICENSE.TXT at the top of this package for the full license terms. |
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*/ |
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package eu.etaxonomy.cdm.app.vibrant; |
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import java.util.UUID; |
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import org.apache.log4j.Logger; |
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import eu.etaxonomy.cdm.app.common.BerlinModelSources; |
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import eu.etaxonomy.cdm.app.common.CdmDestinations; |
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import eu.etaxonomy.cdm.database.DatabaseTypeEnum; |
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import eu.etaxonomy.cdm.database.DbSchemaValidation; |
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import eu.etaxonomy.cdm.database.ICdmDataSource; |
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator; |
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import eu.etaxonomy.cdm.io.common.CdmDefaultImport; |
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK; |
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES; |
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR; |
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import eu.etaxonomy.cdm.io.common.Source; |
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import eu.etaxonomy.cdm.io.pesi.out.PesiTransformer; |
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
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|
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/** |
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* TODO add the following to a wiki page: |
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| 33 |
* 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 |
|
| 34 |
* you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names. |
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* |
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* |
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* @author a.mueller |
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* |
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*/ |
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public class MclActivator {
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(MclActivator.class); |
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//database validation status (create, update, validate ...) |
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static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE; |
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static final Source berlinModelSource = BerlinModelSources.mcl(); |
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static final ICdmDataSource cdmDestination = cdm_test_local_mcl(); |
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql(); |
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static final boolean useSingleClassification = true; |
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static final int sourceSecId = 1272; |
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static final UUID classificationUuid = UUID.fromString("ba6efd26-5b45-4ce6-915d-4f9576e0bf0a");
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static final UUID sourceRefUuid = UUID.fromString("ca8b25d6-e251-4d2b-8b45-142e1e6448f7");
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// set to zero for unlimited nameFacts |
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static final int maximumNumberOfNameFacts = 0; |
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static final int partitionSize = 5000; |
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//check - import |
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static final CHECK check = CHECK.CHECK_AND_IMPORT; |
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//editor - import |
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static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR; |
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//NomeclaturalCode |
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static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICBN; |
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//ignore null |
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static final boolean ignoreNull = true; |
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static boolean useClassification = true; |
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// **************** ALL ********************* |
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//authors |
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static final boolean doAuthors = true; |
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//references |
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static final DO_REFERENCES doReferences = DO_REFERENCES.ALL; |
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//names |
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static final boolean doTaxonNames = true; |
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static final boolean doRelNames = true; |
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static final boolean doNameStatus = true; |
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//taxa |
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static final boolean doTaxa = true; |
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static final boolean doRelTaxa = true; |
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static final boolean doFacts = true; |
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// **************** SELECTED ********************* |
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// //authors |
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// static final boolean doAuthors = false; |
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// //references |
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// static final DO_REFERENCES doReferences = DO_REFERENCES.NONE; |
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// //names |
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// static final boolean doTaxonNames = false; |
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// static final boolean doRelNames = false; |
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// static final boolean doNameStatus = false; |
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// |
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// //taxa |
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// static final boolean doTaxa = false; |
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// static final boolean doRelTaxa = true; |
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// static final boolean doFacts = false; |
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// **********Always IGNORE:*********************************************** |
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//etc. |
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static final boolean doUser = false; |
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static final boolean doTypes = false; //not available in MCL |
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static final boolean doNameFacts = false; //not available in MCL |
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static final boolean doOccurences = false; //not available in MCL |
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static final boolean doCommonNames = false; //not available in MCL |
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static final boolean doMarker = false; //not available in MCL |
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public void importMcl (Source source, ICdmDataSource destination, DbSchemaValidation hbm2dll){
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System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") to " + cdmDestination.getDatabase() + " ...");
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//make BerlinModel Source |
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BerlinModelImportConfigurator config = BerlinModelImportConfigurator.NewInstance(source, destination); |
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config.setClassificationUuid(classificationUuid); |
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config.setSourceSecId(sourceSecId); |
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config.setNomenclaturalCode(nomenclaturalCode); |
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config.setIgnoreNull(ignoreNull); |
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config.setDoAuthors(doAuthors); |
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config.setDoReferences(doReferences); |
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config.setDoTaxonNames(doTaxonNames); |
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config.setDoRelNames(doRelNames); |
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config.setDoNameStatus(doNameStatus); |
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config.setDoTypes(doTypes); |
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config.setDoNameFacts(doNameFacts); |
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config.setUseClassification(useClassification); |
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config.setSourceRefUuid(sourceRefUuid); |
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config.setDoTaxa(doTaxa); |
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config.setDoRelTaxa(doRelTaxa); |
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config.setDoFacts(doFacts); |
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config.setDoOccurrence(doOccurences); |
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config.setDoCommonNames(doCommonNames); |
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config.setDoMarker(doMarker); |
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config.setDoUser(doUser); |
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config.setEditor(editor); |
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config.setDbSchemaValidation(hbm2dll); |
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// maximum number of name facts to import |
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config.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts); |
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config.setUseSingleClassification(useSingleClassification); |
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config.setCheck(check); |
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config.setEditor(editor); |
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config.setRecordsPerTransaction(partitionSize); |
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// invoke import |
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CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>(); |
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bmImport.invoke(config); |
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System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
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} |
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|
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/** |
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* @param args |
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*/ |
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public static void main(String[] args) {
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MclActivator importActivator = new MclActivator(); |
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Source source = berlinModelSource; |
|
| 183 |
ICdmDataSource cdmRepository = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination; |
|
| 184 |
|
|
| 185 |
importActivator.importMcl(source, cdmRepository, hbm2dll); |
|
| 186 |
|
|
| 187 |
} |
|
| 188 |
|
|
| 189 |
public static ICdmDataSource cdm_test_local_mcl(){
|
|
| 190 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
|
| 191 |
String cdmServer = "127.0.0.1"; |
|
| 192 |
String cdmDB = "mcl"; |
|
| 193 |
String cdmUserName = "root"; |
|
| 194 |
return CdmDestinations.makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
|
| 195 |
} |
|
| 196 |
|
|
| 197 |
} |
|
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/vibrant/VibrantActivator.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.util.UUID; |
|
| 13 |
|
|
| 14 |
import org.apache.log4j.Logger; |
|
| 15 |
|
|
| 16 |
import eu.etaxonomy.cdm.app.common.BerlinModelSources; |
|
| 17 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
|
| 18 |
import eu.etaxonomy.cdm.app.pesi.EuroMedActivator; |
|
| 19 |
import eu.etaxonomy.cdm.database.DatabaseTypeEnum; |
|
| 20 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
|
| 21 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
|
| 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.io.pesi.out.PesiTransformer; |
|
| 29 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
|
| 30 |
|
|
| 31 |
|
|
| 32 |
/** |
|
| 33 |
* TODO add the following to a wiki page: |
|
| 34 |
* 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 |
|
| 35 |
* you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names. |
|
| 36 |
* |
|
| 37 |
* |
|
| 38 |
* @author a.mueller |
|
| 39 |
* |
|
| 40 |
*/ |
|
| 41 |
public class VibrantActivator {
|
|
| 42 |
@SuppressWarnings("unused")
|
|
| 43 |
private static final Logger logger = Logger.getLogger(VibrantActivator.class); |
|
| 44 |
|
|
| 45 |
//database validation status (create, update, validate ...) |
|
| 46 |
static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE; |
|
| 47 |
static final Source iopiSource = BerlinModelSources.iopi(); |
|
| 48 |
static final Source mclSource = BerlinModelSources.mcl(); |
|
| 49 |
static final Source emSource = BerlinModelSources.euroMed_local(); |
|
| 50 |
|
|
| 51 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql(); |
|
| 52 |
static final ICdmDataSource cdmDestination = cdm_test_local_vibrant(); |
|
| 53 |
|
|
| 54 |
static final boolean doMcl = true; |
|
| 55 |
static final boolean doEuroMed = false; |
|
| 56 |
static final boolean doIopi = true; |
|
| 57 |
|
|
| 58 |
|
|
| 59 |
/** |
|
| 60 |
* @param args |
|
| 61 |
*/ |
|
| 62 |
public static void main(String[] args) {
|
|
| 63 |
ICdmDataSource cdmRepository = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination; |
|
| 64 |
|
|
| 65 |
if (doMcl){
|
|
| 66 |
MclActivator mclActivator = new MclActivator(); |
|
| 67 |
mclActivator.importMcl(mclSource, cdmRepository, hbm2dll); |
|
| 68 |
hbm2dll = DbSchemaValidation.NONE; |
|
| 69 |
} |
|
| 70 |
|
|
| 71 |
if (doEuroMed){
|
|
| 72 |
EuroMedActivator emActivator = new EuroMedActivator(); |
|
| 73 |
emActivator.importEm2CDM(emSource, cdmRepository, hbm2dll); |
|
| 74 |
hbm2dll = DbSchemaValidation.NONE; |
|
| 75 |
} |
|
| 76 |
|
|
| 77 |
if (doIopi){
|
|
| 78 |
IopiActivator iopiActivator = new IopiActivator(); |
|
| 79 |
iopiActivator.importIopi(iopiSource, cdmRepository, hbm2dll); |
|
| 80 |
hbm2dll = DbSchemaValidation.NONE; |
|
| 81 |
} |
|
| 82 |
|
|
| 83 |
} |
|
| 84 |
|
|
| 85 |
public static ICdmDataSource cdm_test_local_vibrant(){
|
|
| 86 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
|
| 87 |
String cdmServer = "127.0.0.1"; |
|
| 88 |
String cdmDB = "vibrant"; |
|
| 89 |
String cdmUserName = "root"; |
|
| 90 |
return CdmDestinations.makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
|
| 91 |
} |
|
| 92 |
|
|
| 93 |
} |
|
Also available in: Unified diff
moved vibrant to app-import