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Revision 55d8bf29

Added by Andreas Müller over 9 years ago

latest Vibrant Activator DwcA import changes

View differences:

app-import/src/main/java/eu/etaxonomy/cdm/app/vibrant/DwcaScratchpadImportActivator.java
10 10 
package eu.etaxonomy.cdm.app.vibrant;
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import java.net.URI;


  		




  
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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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	//database validation status (create, update, validate ...)


  		




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	static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;


  		




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	static final URI source = dwca_test_scratch_test();


  		




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	//	static final URI source =  dwca_emonocots_dioscoreaceae();


  		




  
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	static final URI source =  dwca_emonocots_zingiberaceae();


  		




  
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//	static final URI source =  dwca_emonocots_cypripedioideae();


  		




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//	static final ICdmDataSource cdmDestination = CdmDestinations.localH2();


  		




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	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_dwca();


  		




  
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	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();


  		




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//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();


  		




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	//default nom code is ICZN as it allows adding publication year 


  		




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	static final NomenclaturalCode defaultNomCode = null;


  		




  
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	static final NomenclaturalCode defaultNomCode = NomenclaturalCode.ICBN;


  		




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	//title


  		




  
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	static final String title = "Scratchpad test import";


  		




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	//check - import


  		




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	static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;


  		




  
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	static int partitionSize = 1000;


  		




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	//config


  		




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	static DatasetUse datasetUse = DatasetUse.CLASSIFICATION;


  		




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	//validate


  		




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	static boolean validateRankConsistency = true;


  		




  
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	static boolean validateRankConsistency = false;


  		




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	//taxa


  		




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	static final boolean doTaxa = true;


  		




  
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	static final boolean doDistribution = true;


  		




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	static final MappingType mappingType = MappingType.InMemoryMapping;


  		




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	private void doImport(ICdmDataSource cdmDestination){


  		




  
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	//classification


  		




  
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	static final UUID classificationUuid = UUID.fromString("d9d199b6-eaf4-47c8-a732-0639bc445c56");


  		




  
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	//config


  		




  
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	static boolean scientificNameIdAsOriginalSourceId = true;


  		




  
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	static boolean guessNomRef = false;


  		




  
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	private boolean handleAllRefsAsCitation = false;


  		




  
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	private static final boolean useSourceReferenceAsSec = true;


  		




  
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	//deduplicate


  		




  
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	static final boolean doDeduplicate = false;


  		




  
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	protected void doImport(URI source, ICdmDataSource cdmDestination, UUID classificationUuid, String title, DbSchemaValidation hbm2dll){


  		




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		//make Source


  		




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		DwcaImportConfigurator config= DwcaImportConfigurator.NewInstance(source, cdmDestination);


  		




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		config.addObserver(new LoggingIoObserver());


  		




  
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		config.setClassificationUuid(classificationUuid);


  		




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		config.setCheck(check);


  		




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		config.setDbSchemaValidation(hbm2dll);


  		




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		config.setMappingType(mappingType);


  		




  
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		config.setScientificNameIdAsOriginalSourceId(scientificNameIdAsOriginalSourceId);


  		




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		config.setValidateRankConsistency(validateRankConsistency);


  		




  
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		config.setDefaultPartitionSize(partitionSize);


  		




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		config.setNomenclaturalCode(defaultNomCode);


  		




  
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		config.setDatasetUse(datasetUse);


  		




  
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		config.setGuessNomenclaturalReferences(guessNomRef);


  		




  
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		config.setHandleAllRefsAsCitation(handleAllRefsAsCitation);


  		




  
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		config.setUseSourceReferenceAsSec(useSourceReferenceAsSec);


  		




  
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		config.setSourceReferenceTitle(title);


  		




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		CdmDefaultImport myImport = new CdmDefaultImport();


  		




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  ......




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		return result;


  		




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	}


  		




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	//Dwca


  		




  
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	public static URI dwca_emonocots_local() {


  		




  
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		URI sourceUrl = URI.create("file:///C:/localCopy/Data/dwca/import/Scratchpads/dwca_dioscoreaceae_emonocots.zip");


  		




  
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		return sourceUrl;


  		




  
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	}


  		




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	//Scratchpads test


  		




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	public static URI dwca_test_scratch_test() {


  		




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		URI sourceUrl = URI.create("file:////PESIIMPORT3/vibrant/dwca/dwca_export_scratchpads_test.zip");


  		




  
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	//emonocots_dioscoreaceae


  		




  
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	public static URI dwca_emonocots_dioscoreaceae() {


  		




  
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		URI sourceUrl = URI.create("file:////PESIIMPORT3/vibrant/dwca/dwca_emonocots_dioscoreaceae.zip");


  		




  
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		return sourceUrl;


  		




  
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	}


  		




  
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	//emonocots_zingiberaceae


  		




  
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	public static URI dwca_emonocots_zingiberaceae() {


  		




  
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		URI sourceUrl = URI.create("file:////PESIIMPORT3/vibrant/dwca/dwca_emonocots_zingiberaceae.zip");


  		




  
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		return sourceUrl;


  		




  
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	}


  		




  
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	//emonocots_cypripedioideae


  		




  
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	public static URI dwca_emonocots_cypripedioideae() {


  		




  
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		URI sourceUrl = URI.create("file:////PESIIMPORT3/vibrant/dwca/dwca_emonocots_cypripedioideae.zip");


  		




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		return sourceUrl;


  		




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	}


  		




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  ......




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	 */


  		




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	public static void main(String[] args) {


  		




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		DwcaScratchpadImportActivator me = new DwcaScratchpadImportActivator();


  		




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		me.doImport(cdmDestination);


  		




  
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		me.doImport(source, cdmDestination, classificationUuid, title, hbm2dll);


  		




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	}


  		




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}


  		












  

    
      app-import/src/main/java/eu/etaxonomy/cdm/app/vibrant/VibrantActivator.java
    
  





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package eu.etaxonomy.cdm.app.vibrant;


  		




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import java.net.URI;


  		




  
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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.berlinModelImport.BerlinModelSources;


  		




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	private static final Logger logger = Logger.getLogger(VibrantActivator.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 DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;


  		




  
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	static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;


  		




  
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	static final Source iopiSource = BerlinModelSources.iopi();


  		




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	static final Source mclSource = BerlinModelSources.mcl();


  		




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	static final Source emSource = BerlinModelSources.PESI3_euroMed();


  		




  
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	static final URI dioscoreaceaeSource = DwcaScratchpadImportActivator.dwca_emonocots_dioscoreaceae();


  		




  
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	static final URI cypripedioideaeSource = DwcaScratchpadImportActivator.dwca_emonocots_cypripedioideae();


  		




  
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	static final URI zingiberaceaeSource = DwcaScratchpadImportActivator.dwca_emonocots_zingiberaceae();


  		




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//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();


  		




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	static final ICdmDataSource cdmDestination = cdm_test_local_vibrant();


  		




  
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//	static final ICdmDataSource cdmDestination = cdm_test_local_vibrant();


  		




  
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//	static final ICdmDataSource cdmDestination = cdm_vibrant_dev();


  		




  
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	static final ICdmDataSource cdmDestination = cdm_vibrant_emonoctos_dev();


  		




  
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	static final boolean doMcl = true;


  		




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	static final boolean doEuroMed = true;


  		




  
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	static final boolean doMcl = false;


  		




  
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	static final boolean doEuroMed = false;


  		




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	static final boolean doIopi = false;


  		




  
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	static final boolean doDioscoreaceae = true;


  		




  
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	static final boolean doZingiberaceae = false;


  		




  
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	static final boolean doCypripedioideae = false;


  		




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	/**


  		




  ......




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			hbm2dll = DbSchemaValidation.NONE;


  		




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		}


  		




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		if (doDioscoreaceae){


  		




  
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			DwcaScratchpadImportActivator scratchpadActivator = new DwcaScratchpadImportActivator();


  		




  
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			UUID uuid = UUID.fromString("3bf59b32-9269-4225-944f-570256d40a9b");


  		




  
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			scratchpadActivator.doImport(dioscoreaceaeSource, cdmRepository,uuid , "Dioscoreaceae (Scratchpads)", hbm2dll);


  		




  
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			hbm2dll = DbSchemaValidation.NONE;


  		




  
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		}


  		




  
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		if (doZingiberaceae){


  		




  
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			DwcaScratchpadImportActivator scratchpadActivator = new DwcaScratchpadImportActivator();


  		




  
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			UUID uuid = UUID.fromString("8fb0f951-ccd8-41c4-8d0b-99ba1fbd2dc2");


  		




  
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			scratchpadActivator.doImport(zingiberaceaeSource, cdmRepository, uuid, " (Scratchpads)", hbm2dll);


  		




  
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			hbm2dll = DbSchemaValidation.NONE;


  		




  
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		}


  		




  
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		if (doCypripedioideae){


  		




  
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			DwcaScratchpadImportActivator scratchpadActivator = new DwcaScratchpadImportActivator();


  		




  
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			UUID uuid = UUID.fromString("a2b0ecf5-1a9d-4d94-a9ef-f57717a49bfd");


  		




  
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			scratchpadActivator.doImport(cypripedioideaeSource, cdmRepository, uuid, " (Scratchpads)", hbm2dll);


  		




  
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			hbm2dll = DbSchemaValidation.NONE;


  		




  
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		}


  		




  
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		if (doEuroMed){


  		




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			logger.warn("DON'T FORGET to reset E+M filter");


  		




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			System.out.println("DON'T FORGET to reset E+M filter");


  		




  ......




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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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	public static ICdmDataSource cdm_vibrant_dev(){


  		




  
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		DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;


  		




  
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		String cdmServer = "160.45.63.201";


  		




  
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		String cdmDB = "cdm_vibrant_index"; 


  		




  
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		String cdmUserName = "edit";


  		




  
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		return CdmDestinations.makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);


  		




  
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	}


  		




  
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	public static ICdmDataSource cdm_vibrant_emonoctos_dev(){


  		




  
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		DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;


  		




  
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		String cdmServer = "160.45.63.201";


  		




  
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		String cdmDB = "cdm_vibrant_index_emonocots"; 


  		




  
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		String cdmUserName = "edit";


  		




  
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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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