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Revision 0d21320d

Added by Andreas Müller about 12 years ago

deleting some old sources

View differences:

.gitattributes
61 61 
app-import/src/main/java/eu/etaxonomy/cdm/app/sdd/ViolaExportActivator.java -text
62 62 
app-import/src/main/java/eu/etaxonomy/cdm/app/sdd/ViolaUpdateActivator.java -text
63 63 
app-import/src/main/java/eu/etaxonomy/cdm/app/sdd/applicationContext.xml -text
64 
app-import/src/main/java/eu/etaxonomy/cdm/app/synthesysImport/SpecimenImport.java -text
64 
app-import/src/main/java/eu/etaxonomy/cdm/app/synthesysImport/SpecimenImportActivator.java -text
65 65 
app-import/src/main/java/eu/etaxonomy/cdm/app/synthesysImport/SynthesysCacheActivator.java -text
66 66 
app-import/src/main/java/eu/etaxonomy/cdm/app/synthesysImport/SynthesysSpecimenTestActivator.java -text
67 67 
app-import/src/main/java/eu/etaxonomy/cdm/app/tcs/TcsRdfTestActivator.java -text
app-import/src/main/java/eu/etaxonomy/cdm/app/abcdImport/SynthesysCacheActivator.java
205 205 
		TransactionStatus tx = null;
206 206 

  		




  207
  207
  
    

  		




  208
  
  
    
		app = CdmApplicationController.NewInstance(CdmDestinations.cdm_test_patricia(), hbm2dll);


  		




  
  208
  
    
		app = CdmApplicationController.NewInstance(CdmDestinations.localH2(), hbm2dll);


  		




  209
  209
  
    
		


  		




  210
  210
  
    
		tx = app.startTransaction();


  		




  211
  211
  
    
		try {


  		












  

    
      app-import/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java
    
  





  51
  51
  
    
		return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);


  		




  52
  52
  
    
	}


  		




  53
  53
  
    
	


  		




  54
  
  
    
	public static ICdmDataSource cdm_test_jaxb(){


  		




  55
  
  
    
		DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;


  		




  56
  
  
    
		String cdmServer = "192.168.2.10";


  		




  57
  
  
    
		String cdmDB = "cdm_test_jaxb"; 


  		




  58
  
  
    
		String cdmUserName = "edit";


  		




  59
  
  
    
		return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);


  		




  60
  
  
    
	}


  		




  61
  
  
    
	


  		




  62
  
  
    
	public static ICdmDataSource cdm_test_jaxb2(){


  		




  63
  
  
    
		DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;


  		




  64
  
  
    
		String cdmServer = "192.168.2.10";


  		




  65
  
  
    
		String cdmDB = "cdm_test_jaxb2"; 


  		




  66
  
  
    
		String cdmUserName = "edit";


  		




  67
  
  
    
		return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);


  		




  68
  
  
    
	}


  		




  69
  
  
    

  		




  70
  
  
    
	public static ICdmDataSource cdm_test_andreasM(){


  		




  71
  
  
    
		DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;


  		




  72
  
  
    
		String cdmServer = "192.168.2.10";


  		




  73
  
  
    
		String cdmDB = "cdm_test_andreasM"; 


  		




  74
  
  
    
		String cdmUserName = "edit";


  		




  75
  
  
    
		return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);


  		




  76
  
  
    
	}


  		




  77
  
  
    
	


  		




  78
  
  
    
	public static ICdmDataSource cdm_test_andreasM2(){


  		




  79
  
  
    
		DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;


  		




  80
  
  
    
		String cdmServer = "192.168.2.10";


  		




  81
  
  
    
		String cdmDB = "cdm_test_andreasM2"; 


  		




  82
  
  
    
		String cdmUserName = "edit";


  		




  83
  
  
    
		return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);


  		




  84
  
  
    
	}


  		




  85
  
  
    
	


  		




  86
  54
  
    
	public static ICdmDataSource cdm_test_local_mysql(){


  		




  87
  55
  
    
		DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;


  		




  88
  56
  
    
		String cdmServer = "127.0.0.1";


  		




  ......




  148
  116
  
    
		String cdmUserName = "edit";


  		




  149
  117
  
    
		return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);


  		




  150
  118
  
    
	}


  		




  151
  
  
    
	


  		




  152
  
  
    
	public static ICdmDataSource cdm_test_patricia(){


  		




  153
  
  
    
		DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;


  		




  154
  
  
    
		String cdmServer = "192.168.2.10";


  		




  155
  
  
    
		String cdmDB = "cdm_test_patricia";


  		




  156
  
  
    
		String cdmUserName = "edit";


  		




  157
  
  
    
		return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);


  		




  158
  
  
    
	}


  		




  159
  
  
    
	


  		




  160
  
  
    
	//


  		




  161
  
  
    
	public static ICdmDataSource cdm_test_andreasK1(){


  		




  162
  
  
    
		DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;


  		




  163
  
  
    
		String cdmServer = "192.168.2.10";


  		




  164
  
  
    
		String cdmDB = "cdm_test_andreasK1";


  		




  165
  
  
    
		String cdmUserName = "edit";


  		




  166
  
  
    
		return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);


  		




  167
  
  
    
	}


  		




  168
  
  
    
	


  		




  169
  119
  
    

  		




  170
  120
  
    
	public static ICdmDataSource cdm_pesi_erms(){


  		




  171
  121
  
    
		DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;


  		




  ......




  174
  124
  
    
		String cdmUserName = "edit";


  		




  175
  125
  
    
		return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);


  		




  176
  126
  
    
	}


  		




  177
  
  
    
	


  		




  178
  
  
    
	public static ICdmDataSource cdm_campanulaceae(){


  		




  179
  
  
    
		DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;


  		




  180
  
  
    
		String cdmServer = "192.168.2.10";


  		




  181
  
  
    
		String cdmDB = "cdm_campanulaceae";


  		




  182
  
  
    
		String cdmUserName = "edit";


  		




  183
  
  
    
		return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);


  		




  184
  
  
    
	}


  		




  
  127
  
    

  		




  185
  128
  
    

  		




  186
  129
  
    
	public static ICdmDataSource cdm_ildis_dev(){


  		




  187
  130
  
    
		DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;


  		












  

    
      app-import/src/main/java/eu/etaxonomy/cdm/app/dwca/DwcaImportActivator.java
    
  





  41
  41
  
    
	static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;


  		




  42
  42
  
    
//	static final URI source = dwca_test_in();


  		




  43
  43
  
    
//	static final URI source = dwca_test_cich_len();


  		




  44
  
  
    
//	static final URI source = dwca_test_col_cichorium();


  		




  
  44
  
    
	static final URI source = dwca_test_col_cichorium();


  		




  45
  45
  
    
//	static final URI source = dwca_test_col_All();


  		




  46
  
  
    
	static final URI source = dwca_test_col_All_Pesi2();


  		




  
  46
  
    
//	static final URI source = dwca_test_col_All_Pesi2();


  		




  47
  47
  
    
	


  		




  48
  48
  
    
	


  		




  49
  49
  
    
//	static final ICdmDataSource cdmDestination = CdmDestinations.localH2();


  		




  50
  
  
    
	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_pesi_test();


  		




  51
  
  
    
//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();


  		




  
  50
  
    
//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_pesi_test();


  		




  
  51
  
    
	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();


  		




  52
  52
  
    

  		




  53
  53
  
    
	


  		




  54
  54
  
    
	//classification


  		




  ......




  64
  64
  
    
	//config


  		




  65
  65
  
    
	static DatasetUse datasetUse = DatasetUse.SECUNDUM;


  		




  66
  66
  
    
	static boolean scientificNameIdAsOriginalSourceId = true;


  		




  
  67
  
    
	static boolean guessNomRef = true;


  		




  
  68
  
    
	private boolean handleAllRefsAsCitation = true;


  		




  67
  69
  
    
	


  		




  68
  70
  
    
	//validate


  		




  69
  71
  
    
	static boolean validateRankConsistency = false;


  		




  ......




  88
  90
  
    
		config.setCheck(check);


  		




  89
  91
  
    
		config.setDbSchemaValidation(hbm2dll);


  		




  90
  92
  
    
		config.setMappingType(mappingType);


  		




  
  93
  
    
		


  		




  91
  94
  
    
		config.setScientificNameIdAsOriginalSourceId(scientificNameIdAsOriginalSourceId);


  		




  92
  95
  
    
		config.setValidateRankConsistency(validateRankConsistency);


  		




  93
  96
  
    
		config.setNomenclaturalCode(defaultNomCode);


  		




  
  97
  
    
		config.setDatasetUse(datasetUse);


  		




  
  98
  
    
		config.setGuessNomenclaturalReferences(guessNomRef);


  		




  
  99
  
    
		config.setHandleAllRefsAsCitation(handleAllRefsAsCitation);


  		




  94
  100
  
    
		


  		




  95
  101
  
    
		CdmDefaultImport myImport = new CdmDefaultImport();


  		




  96
  102
  
    

  		












  

    
      app-import/src/main/java/eu/etaxonomy/cdm/app/jaxb/CdmDiffActivator.java
    
  





  28
  28
  
    

  		




  29
  29
  
    
	static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;


  		




  30
  30
  
    

  		




  31
  
  
    
	static final ICdmDataSource cdmSourceOne = CdmDestinations.cdm_test_jaxb();


  		




  32
  
  
    
	static final ICdmDataSource cdmSourceTwo = CdmDestinations.cdm_test_jaxb2();


  		




  
  31
  
    
	static final ICdmDataSource cdmSourceOne = CdmDestinations.localH2();


  		




  
  32
  
    
	static final ICdmDataSource cdmSourceTwo = CdmDestinations.localH2();


  		




  33
  33
  
    

  		




  34
  34
  
    
}


  		












  

    
      app-import/src/main/java/eu/etaxonomy/cdm/app/jaxb/JaxbImportActivator.java
    
  





  36
  36
  
    

  		




  37
  37
  
    
	/* SerializeFrom DB **/


  		




  38
  38
  
    
	//private static final ICdmDataSource cdmSource = CdmDestinations.localH2Diptera();


  		




  39
  
  
    
	private static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_jaxb();


  		




  
  39
  
    
	private static final ICdmDataSource cdmDestination = CdmDestinations.localH2();


  		




  40
  40
  
    
	


  		




  41
  41
  
    
	// Import:


  		




  42
  42
  
    
	private static String importFileNameString = 


  		












  

    
      app-import/src/main/java/eu/etaxonomy/cdm/app/synthesysImport/SpecimenImport.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.synthesysImport;


  		




  11
  
  
    
import java.net.URI;


  		




  12
  
  
    
import java.net.URISyntaxException;


  		




  13
  
  
    

  		




  14
  
  
    
import org.apache.log4j.Logger;


  		




  15
  
  
    

  		




  16
  
  
    
import eu.etaxonomy.cdm.app.common.CdmDestinations;


  		




  17
  
  
    
import eu.etaxonomy.cdm.database.DbSchemaValidation;


  		




  18
  
  
    
import eu.etaxonomy.cdm.database.ICdmDataSource;


  		




  19
  
  
    
import eu.etaxonomy.cdm.io.common.CdmDefaultImport;


  		




  20
  
  
    
import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;


  		




  21
  
  
    
import eu.etaxonomy.cdm.io.specimen.excel.in.SpecimenSynthesysExcelImportConfigurator;


  		




  22
  
  
    

  		




  23
  
  
    
public class SpecimenImport {


  		




  24
  
  
    
private static Logger logger = Logger.getLogger(SpecimenImport.class);


  		




  25
  
  
    
	


  		




  26
  
  
    
	//database validation status (create, update, validate ...)


  		




  27
  
  
    
	static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;


  		




  28
  
  
    
	final static String excelSource = "/home/patricia/Desktop/CDMtabular6493890c4d_18_11_08.xls";


  		




  29
  
  
    
//	final static String xmlSource = "C:\\localCopy\\eclipse\\cdmlib\\app-import\\src\\main\\resources\\specimenABCD\\CDMtabular9c04a474e2_23_09_08.xls";	


  		




  30
  
  
    
	


  		




  31
  
  
    
	


  		




  32
  
  
    
	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_patricia();


  		




  33
  
  
    
	//check - import


  		




  34
  
  
    
	static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;


  		




  35
  
  
    
	


  		




  36
  
  
    
	/**


  		




  37
  
  
    
	 * @param args


  		




  38
  
  
    
	 */


  		




  39
  
  
    
	public static void main(String[] args) {


  		




  40
  
  
    
		URI source;


  		




  41
  
  
    
		try {


  		




  42
  
  
    
			source = new URI(excelSource);


  		




  43
  
  
    
			System.out.println(source);


  		




  44
  
  
    
			System.out.println("Start import from  Synthesys Specimen data("+ source.toString() + ") ...");


  		




  45
  
  
    
			


  		




  46
  
  
    
			ICdmDataSource destination = cdmDestination;


  		




  47
  
  
    
			SpecimenSynthesysExcelImportConfigurator specimenImportConfigurator = SpecimenSynthesysExcelImportConfigurator.NewInstance(source,  destination);


  		




  48
  
  
    
			


  		




  49
  
  
    
			specimenImportConfigurator.setSourceSecId("specimen");


  		




  50
  
  
    
			specimenImportConfigurator.setCheck(check);


  		




  51
  
  
    
			specimenImportConfigurator.setDbSchemaValidation(hbm2dll);


  		




  52
  
  
    
			specimenImportConfigurator.setDoAutomaticParsing(true);


  		




  53
  
  
    
			specimenImportConfigurator.setReUseExistingMetadata(true);


  		




  54
  
  
    
			specimenImportConfigurator.setReUseTaxon(true);


  		




  55
  
  
    
			specimenImportConfigurator.setSourceReference(null);


  		




  56
  
  
    
			specimenImportConfigurator.setTaxonReference(null);


  		




  57
  
  
    
			


  		




  58
  
  
    
			// invoke import


  		




  59
  
  
    
			CdmDefaultImport<SpecimenSynthesysExcelImportConfigurator> specimenImport = new CdmDefaultImport<SpecimenSynthesysExcelImportConfigurator>();


  		




  60
  
  
    
			//new Test().invoke(tcsImportConfigurator);


  		




  61
  
  
    
			specimenImport.invoke(specimenImportConfigurator);


  		




  62
  
  
    
			System.out.println("End import from SpecimenData ("+ source.toString() + ")...");


  		




  63
  
  
    
		} catch (URISyntaxException e) {


  		




  64
  
  
    
			e.printStackTrace();


  		




  65
  
  
    
		}


  		




  66
  
  
    
		


  		




  67
  
  
    
	}


  		




  68
  
  
    

  		




  69
  
  
    
}


  		












  

    
      app-import/src/main/java/eu/etaxonomy/cdm/app/synthesysImport/SpecimenImportActivator.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.synthesysImport;


  		




  
  11
  
    
import java.net.URI;


  		




  
  12
  
    
import java.net.URISyntaxException;


  		




  
  13
  
    

  		




  
  14
  
    
import org.apache.log4j.Logger;


  		




  
  15
  
    

  		




  
  16
  
    
import eu.etaxonomy.cdm.app.common.CdmDestinations;


  		




  
  17
  
    
import eu.etaxonomy.cdm.database.DbSchemaValidation;


  		




  
  18
  
    
import eu.etaxonomy.cdm.database.ICdmDataSource;


  		




  
  19
  
    
import eu.etaxonomy.cdm.io.common.CdmDefaultImport;


  		




  
  20
  
    
import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;


  		




  
  21
  
    
import eu.etaxonomy.cdm.io.specimen.excel.in.SpecimenSynthesysExcelImportConfigurator;


  		




  
  22
  
    

  		




  
  23
  
    
public class SpecimenImportActivator {


  		




  
  24
  
    
	@SuppressWarnings("unused")


  		




  
  25
  
    
	private static Logger logger = Logger.getLogger(SpecimenImportActivator.class);


  		




  
  26
  
    
	


  		




  
  27
  
    
	//database validation status (create, update, validate ...)


  		




  
  28
  
    
	static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;


  		




  
  29
  
    
	final static String excelSource = "/home/patricia/Desktop/CDMtabular6493890c4d_18_11_08.xls";


  		




  
  30
  
    
//	final static String xmlSource = "C:\\localCopy\\eclipse\\cdmlib\\app-import\\src\\main\\resources\\specimenABCD\\CDMtabular9c04a474e2_23_09_08.xls";	


  		




  
  31
  
    
	


  		




  
  32
  
    
	


  		




  
  33
  
    
	static final ICdmDataSource cdmDestination = CdmDestinations.localH2();


  		




  
  34
  
    
	//check - import


  		




  
  35
  
    
	static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;


  		




  
  36
  
    
	


  		




  
  37
  
    
	/**


  		




  
  38
  
    
	 * @param args


  		




  
  39
  
    
	 */


  		




  
  40
  
    
	public static void main(String[] args) {


  		




  
  41
  
    
		URI source;


  		




  
  42
  
    
		try {


  		




  
  43
  
    
			source = new URI(excelSource);


  		




  
  44
  
    
			System.out.println(source);


  		




  
  45
  
    
			System.out.println("Start import from  Synthesys Specimen data("+ source.toString() + ") ...");


  		




  
  46
  
    
			


  		




  
  47
  
    
			ICdmDataSource destination = cdmDestination;


  		




  
  48
  
    
			SpecimenSynthesysExcelImportConfigurator specimenImportConfigurator = SpecimenSynthesysExcelImportConfigurator.NewInstance(source,  destination);


  		




  
  49
  
    
			


  		




  
  50
  
    
			specimenImportConfigurator.setSourceSecId("specimen");


  		




  
  51
  
    
			specimenImportConfigurator.setCheck(check);


  		




  
  52
  
    
			specimenImportConfigurator.setDbSchemaValidation(hbm2dll);


  		




  
  53
  
    
			specimenImportConfigurator.setDoAutomaticParsing(true);


  		




  
  54
  
    
			specimenImportConfigurator.setReUseExistingMetadata(true);


  		




  
  55
  
    
			specimenImportConfigurator.setReUseTaxon(true);


  		




  
  56
  
    
			specimenImportConfigurator.setSourceReference(null);


  		




  
  57
  
    
			specimenImportConfigurator.setTaxonReference(null);


  		




  
  58
  
    
			


  		




  
  59
  
    
			// invoke import


  		




  
  60
  
    
			CdmDefaultImport<SpecimenSynthesysExcelImportConfigurator> specimenImport = new CdmDefaultImport<SpecimenSynthesysExcelImportConfigurator>();


  		




  
  61
  
    
			//new Test().invoke(tcsImportConfigurator);


  		




  
  62
  
    
			specimenImport.invoke(specimenImportConfigurator);


  		




  
  63
  
    
			System.out.println("End import from SpecimenData ("+ source.toString() + ")...");


  		




  
  64
  
    
		} catch (URISyntaxException e) {


  		




  
  65
  
    
			e.printStackTrace();


  		




  
  66
  
    
		}


  		




  
  67
  
    
		


  		




  
  68
  
    
	}


  		




  
  69
  
    

  		




  
  70
  
    
}


  		












  

    
      app-import/src/main/java/eu/etaxonomy/cdm/app/viennaImport/ViennaActivator.java
    
  





  66
  66
  
    
		


  		




  67
  67
  
    
		try {


  		




  68
  68
  
    
			if (withCdm){


  		




  69
  
  
    
				app = CdmApplicationController.NewInstance(CdmDestinations.cdm_test_patricia());


  		




  
  69
  
    
				app = CdmApplicationController.NewInstance(CdmDestinations.localH2());


  		




  70
  70
  
    
			}else{


  		




  71
  71
  
    
				//app = CdmApplicationController.NewInstance(DbSchemaValidation.VALIDATE);


  		




  72
  72
  
    
			}


  		












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