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Revision 8804a550

Added by Andreas Müller over 4 years ago

ref #1444 update pesi/erms sources and destinations

View differences:

cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java
55 55
        return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
56 56
    }
57 57

  
58

  
59 58
	public static ICdmDataSource cdm_test_local_indexFungorum(){
60 59
		DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
61 60
		String cdmServer = "127.0.0.1";
......
64 63
		return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
65 64
	}
66 65

  
67

  
68 66
	public static ICdmDataSource cdm_test_local_mysql_erms(){
69 67
		DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
70 68
		String cdmServer = "127.0.0.1";
......
73 71
		return CdmDestinations.makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
74 72
	}
75 73

  
74
    public static ICdmDataSource cdm_test_local_mysql_erms2(){
75
        DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
76
        String cdmServer = "127.0.0.1";
77
        String cdmDB = "cdm_pesi_erms2";
78
        String cdmUserName = "edit";
79
        return CdmDestinations.makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
80
    }
76 81

  
77 82
	public static ICdmDataSource cdm_test_local_mysql_test(){
78 83
		DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
......
81 86
		String cdmUserName = "edit";
82 87
		return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
83 88
	}
84
	public static ICdmDataSource cdm_portal_test_localhost(){
85
		DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
86
		String cdmServer = "127.0.0.1";
87
		String cdmDB = "cdm_portal_test";
88
		String cdmUserName = "edit";
89
		return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
90
	}
91

  
92
	public static ICdmDataSource cdm_portal_test_localhost2(){
93
		DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
94
		String cdmServer = "127.0.0.1";
95
		String cdmDB = "cdm_portal_test2";
96
		String cdmUserName = "edit";
97
		return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
98
	}
99

  
100
	public static ICdmDataSource cdm_local_postgres_CdmTest(){
101
		DatabaseTypeEnum dbType = DatabaseTypeEnum.PostgreSQL;
102
		String cdmServer = "127.0.0.1";
103
		String cdmDB = "CdmTest";
104
		String cdmUserName = "edit";
105
		return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
106
	}
107

  
108 89

  
109 90
	public static ICdmDataSource NULL(){
110 91
		return null;
......
123 104
		return CdmDataSource.NewH2EmbeddedInstance("erms", "sa", "");
124 105
	}
125 106

  
126
	public static ICdmDataSource cdm_algaterra_preview(){
127
		DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
128
		String cdmServer = "160.45.63.201";
129
		String cdmDB = "cdm_edit_algaterra";
130
		String cdmUserName = "edit";
131
		return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
132
	}
133

  
134

  
135 107
	public static ICdmDataSource test_cdm_pesi_euroMed(){
136 108
		DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
137 109
		String cdmServer = "160.45.63.175";
......
183 155
			throw new RuntimeException("Unsupported DatabaseType");
184 156
		}
185 157
		return destination;
186

  
187 158
	}
188 159

  
189 160

  
cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/ErmsActivator.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.pesi;
11

  
12
import java.util.UUID;
13

  
14
import org.apache.log4j.Logger;
15

  
16
import eu.etaxonomy.cdm.api.application.ICdmRepository;
17
import eu.etaxonomy.cdm.app.common.CdmDestinations;
18
import eu.etaxonomy.cdm.database.DbSchemaValidation;
19
import eu.etaxonomy.cdm.database.ICdmDataSource;
20
import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
21
import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
22
import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;
23
import eu.etaxonomy.cdm.io.common.Source;
24
import eu.etaxonomy.cdm.io.pesi.erms.ErmsImportConfigurator;
25
import eu.etaxonomy.cdm.io.pesi.out.PesiTransformer;
26
import eu.etaxonomy.cdm.model.name.TaxonName;
27
import eu.etaxonomy.cdm.model.reference.ISourceable;
28

  
29

  
30
/**
31
 * @author a.mueller
32
 */
33
public class ErmsActivator {
34
	private static final Logger logger = Logger.getLogger(ErmsActivator.class);
35

  
36
	//database validation status (create, update, validate ...)
37
	static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
38
//	static final Source ermsSource = PesiSources.PESI3_ERMS();
39
	static final Source ermsSource = PesiSources.PESI2019_ERMS();
40
//	static final ICdmDataSource cdmDestination = CdmDestinations.test_cdm_pesi_erms();
41
	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_erms();
42

  
43
	static final UUID classificationUuid = UUID.fromString("6fa988a9-10b7-48b0-a370-2586fbc066eb");
44

  
45
	static final String classificationName = "ERMS 2019";
46

  
47
	//check - import
48
	static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
49

  
50
	static final int partitionSize = 5000;
51

  
52
	//ignore null
53
	static final boolean ignoreNull = true;
54

  
55
	static final boolean includeExport = true;
56

  
57
// ***************** ALL ************************************************//
58

  
59
	//references
60
	static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;
61

  
62
	//taxa
63
	static final boolean doTaxa = true;
64
	static final boolean doRelTaxa = true;
65
	static final boolean doLinks = true;
66
	static final boolean doOccurences = true;
67
	static final boolean doImages = true;
68

  
69

  
70
//******************** NONE ***************************************//
71

  
72

  
73
//	//references
74
//	static final DO_REFERENCES doReferences =  DO_REFERENCES.NONE;
75
//
76
//	//taxa
77
//	static final boolean doTaxa = false;
78
//	static final boolean doRelTaxa = false;
79
//	static final boolean doLinks = false;
80
//	static final boolean doOccurences = false;
81
//
82

  
83

  
84
	private void doImport(Source source, ICdmDataSource destination, DbSchemaValidation hbm2dll){
85
		System.out.println("Start import from ("+ ermsSource.getDatabase() + ") ...");
86

  
87
		//make ERMS Source
88

  
89
		ErmsImportConfigurator config = ErmsImportConfigurator.NewInstance(source,  destination);
90

  
91
		config.setClassificationUuid(classificationUuid);
92

  
93
		config.setIgnoreNull(ignoreNull);
94
		config.setDoReferences(doReferences);
95

  
96
		config.setDoTaxa(doTaxa);
97
		config.setDoRelTaxa(doRelTaxa);
98
		config.setDoLinks(doLinks);
99
		config.setDoOccurrence(doOccurences);
100
		config.setDbSchemaValidation(hbm2dll);
101

  
102
		config.setCheck(check);
103
		config.setRecordsPerTransaction(partitionSize);
104
		config.setSourceRefUuid(PesiTransformer.uuidSourceRefErms);
105
		config.setClassificationName(classificationName);
106

  
107
		// invoke import
108
		CdmDefaultImport<ErmsImportConfigurator> ermsImport = new CdmDefaultImport<ErmsImportConfigurator>();
109
		ermsImport.invoke(config);
110

  
111
		if (config.getCheck().equals(CHECK.CHECK_AND_IMPORT)  || config.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK)    ){
112
			ICdmRepository app = ermsImport.getCdmAppController();
113
			ISourceable<?> obj = app.getCommonService().getSourcedObjectByIdInSource(TaxonName.class, "1000027", null);
114
			logger.info(obj);
115

  
116
//			//make feature tree
117
//			FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, ermsImportConfigurator.getFeatureMap(), featureKeyList);
118
//			app = ermsImport.getCdmAppController();
119
//			app.getFeatureTreeService().saveOrUpdate(tree);
120
		}
121
		System.out.println("End import from ("+ source.getDatabase() + ")...");
122
	}
123

  
124
	/**
125
	 * @param args
126
	 */
127
	public static void main(String[] args) {
128
		ICdmDataSource cdmDB = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
129
		ErmsActivator ermsImport = new ErmsActivator();
130
		ermsImport.doImport(ermsSource, cdmDB, hbm2dll);
131

  
132
		if (includeExport){
133
			PesiExportActivatorERMS ermsExport = new PesiExportActivatorERMS();
134
			ermsExport.doExport(cdmDB);
135
		}
136
		System.exit(0);
137
	}
138

  
139
}
cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/ErmsImportActivator.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.pesi;
11

  
12
import java.util.UUID;
13

  
14
import org.apache.log4j.Logger;
15

  
16
import eu.etaxonomy.cdm.api.application.ICdmRepository;
17
import eu.etaxonomy.cdm.app.common.CdmDestinations;
18
import eu.etaxonomy.cdm.database.DbSchemaValidation;
19
import eu.etaxonomy.cdm.database.ICdmDataSource;
20
import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
21
import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
22
import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;
23
import eu.etaxonomy.cdm.io.common.Source;
24
import eu.etaxonomy.cdm.io.pesi.erms.ErmsImportConfigurator;
25
import eu.etaxonomy.cdm.io.pesi.out.PesiTransformer;
26
import eu.etaxonomy.cdm.model.name.TaxonName;
27
import eu.etaxonomy.cdm.model.reference.ISourceable;
28

  
29

  
30
/**
31
 * @author a.mueller
32
 */
33
public class ErmsActivator {
34
	private static final Logger logger = Logger.getLogger(ErmsActivator.class);
35

  
36
	//database validation status (create, update, validate ...)
37
	static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
38
//	static final Source ermsSource = PesiSources.PESI3_ERMS();
39
	static final Source ermsSource = PesiSources.PESI2019_ERMS();
40
//	static final ICdmDataSource cdmDestination = CdmDestinations.test_cdm_pesi_erms();
41
	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_erms();
42

  
43
	static final UUID classificationUuid = UUID.fromString("6fa988a9-10b7-48b0-a370-2586fbc066eb");
44

  
45
	static final String classificationName = "ERMS 2019";
46

  
47
	//check - import
48
	static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
49

  
50
	static final int partitionSize = 5000;
51

  
52
	//ignore null
53
	static final boolean ignoreNull = true;
54

  
55
	static final boolean includeExport = true;
56

  
57
// ***************** ALL ************************************************//
58

  
59
	//references
60
	static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;
61

  
62
	//taxa
63
	static final boolean doTaxa = true;
64
	static final boolean doRelTaxa = true;
65
	static final boolean doLinks = true;
66
	static final boolean doOccurences = true;
67
	static final boolean doImages = true;
68

  
69

  
70
//******************** NONE ***************************************//
71

  
72

  
73
//	//references
74
//	static final DO_REFERENCES doReferences =  DO_REFERENCES.NONE;
75
//
76
//	//taxa
77
//	static final boolean doTaxa = false;
78
//	static final boolean doRelTaxa = false;
79
//	static final boolean doLinks = false;
80
//	static final boolean doOccurences = false;
81
//
82

  
83

  
84
	private void doImport(Source source, ICdmDataSource destination, DbSchemaValidation hbm2dll){
85
		System.out.println("Start import from ("+ ermsSource.getDatabase() + ") ...");
86

  
87
		//make ERMS Source
88

  
89
		ErmsImportConfigurator config = ErmsImportConfigurator.NewInstance(source,  destination);
90

  
91
		config.setClassificationUuid(classificationUuid);
92

  
93
		config.setIgnoreNull(ignoreNull);
94
		config.setDoReferences(doReferences);
95

  
96
		config.setDoTaxa(doTaxa);
97
		config.setDoRelTaxa(doRelTaxa);
98
		config.setDoLinks(doLinks);
99
		config.setDoOccurrence(doOccurences);
100
		config.setDbSchemaValidation(hbm2dll);
101

  
102
		config.setCheck(check);
103
		config.setRecordsPerTransaction(partitionSize);
104
		config.setSourceRefUuid(PesiTransformer.uuidSourceRefErms);
105
		config.setClassificationName(classificationName);
106

  
107
		// invoke import
108
		CdmDefaultImport<ErmsImportConfigurator> ermsImport = new CdmDefaultImport<ErmsImportConfigurator>();
109
		ermsImport.invoke(config);
110

  
111
		if (config.getCheck().equals(CHECK.CHECK_AND_IMPORT)  || config.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK)    ){
112
			ICdmRepository app = ermsImport.getCdmAppController();
113
			ISourceable<?> obj = app.getCommonService().getSourcedObjectByIdInSource(TaxonName.class, "1000027", null);
114
			logger.info(obj);
115

  
116
//			//make feature tree
117
//			FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, ermsImportConfigurator.getFeatureMap(), featureKeyList);
118
//			app = ermsImport.getCdmAppController();
119
//			app.getFeatureTreeService().saveOrUpdate(tree);
120
		}
121
		System.out.println("End import from ("+ source.getDatabase() + ")...");
122
	}
123

  
124
	/**
125
	 * @param args
126
	 */
127
	public static void main(String[] args) {
128
		ICdmDataSource cdmDB = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
129
		ErmsActivator ermsImport = new ErmsActivator();
130
		ermsImport.doImport(ermsSource, cdmDB, hbm2dll);
131

  
132
		if (includeExport){
133
			PesiExportActivatorERMS ermsExport = new PesiExportActivatorERMS();
134
			ermsExport.doExport(cdmDB);
135
		}
136
		System.exit(0);
137
	}
138

  
139
}
cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/PesiDestinations.java
17 17
/**
18 18
 * @author e.-m.lee
19 19
 * @since 16.02.2010
20
 *
21 20
 */
22 21
public class PesiDestinations {
23 22
	@SuppressWarnings("unused")
......
70 69
		String strServer = "pesiimport3";
71 70
		String strDB = "CDM_ERMS2PESI";
72 71
		int port = 1433;
73
		String userName = "pesiexport";
72
		String userName = "pesi2019";
74 73
		return makeSource(dbms, strServer, strDB, port, userName, null);
75 74
	}
76 75

  
cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/PesiExportActivator.java
30 30
	@SuppressWarnings("unused")
31 31
	private static final Logger logger = Logger.getLogger(PesiExportActivator.class);
32 32

  
33
	//database validation status (create, update, validate ...)
34
//	static final Source pesiDestination = PesiDestinations.pesi_test_local_CDM_EM2PESI();
35
//	static final Source pesiDestination = PesiDestinations.pesi_test_local_CDM_FE2PESI();
36
	static final Source pesiDestination = PesiDestinations.pesi_test_local_CDM_ERMS2PESI();
37

  
38 33
	static final ICdmDataSource cdmSource = CdmDestinations.cdm_test_local_faunaEu_mysql();
39 34
//	static final ICdmDataSource cdmSource = CdmDestinations.cdm_test_local_mysql();
40 35
//	static final ICdmDataSource cdmSource = CdmDestinations.cdm_test_local_mysql_test();
41 36

  
37
//	static final Source pesiDestination = PesiDestinations.pesi_test_local_CDM_EM2PESI();
38
//	static final Source pesiDestination = PesiDestinations.pesi_test_local_CDM_FE2PESI();
39
	static final Source pesiDestination = PesiDestinations.pesi_test_local_CDM_ERMS2PESI();
40

  
42 41
	//Taxon names can't be mapped to their CDM ids as PESI Taxon table mainly holds taxa and there IDs. We ad nameIdStart to the TaxonName id to get a unique id
43 42
	static final int nameIdStart = 10000000;
44 43

  
cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/PesiExportActivatorEM.java
25 25
 * @author a.mueller
26 26
 * @author e.-m.lee
27 27
 * @since 16.02.2010
28
 *
29 28
 */
30 29
public class PesiExportActivatorEM {
31 30
	@SuppressWarnings("unused")
32 31
	private static final Logger logger = Logger.getLogger(PesiExportActivatorEM.class);
33 32

  
33
	static final ICdmDataSource cdmSource = CdmDestinations.test_cdm_pesi_euroMed();
34

  
34 35
	//database validation status (create, update, validate ...)
35 36
	static final Source pesiDestination = PesiDestinations.pesi_test_local_CDM_EM2PESI();
36 37
//	static final Source pesiDestination = PesiDestinations.pesi_test_local_CDM_FE2PESI();
37 38
//	static final Source pesiDestination = PesiDestinations.pesi_test_local_CDM_ERMS2PESI();
38 39

  
39
	static final ICdmDataSource cdmSource = CdmDestinations.cdm_pesi_erms();
40 40
	//Taxon names can't be mapped to their CDM ids as PESI Taxon table mainly holds taxa and there IDs. We ad nameIdStart to the TaxonName id to get a unique id
41 41
	static final int nameIdStart = 10000000;
42 42
	static final IdType idType = IdType.CDM_ID_WITH_EXCEPTIONS;
......
128 128
		}
129 129

  
130 130
		// invoke export
131
		CdmDefaultExport<PesiExportConfigurator> pesiExport = new CdmDefaultExport<PesiExportConfigurator>();
131
		CdmDefaultExport<PesiExportConfigurator> pesiExport = new CdmDefaultExport<>();
132 132
		boolean result = pesiExport.invoke(config).isSuccess();
133 133

  
134 134
		System.out.println("End export to PESI ("+ destination.getDatabase() + ")..." + (result? "(successful)":"(with errors)"));
135 135
		return result;
136 136
	}
137 137

  
138
	/**
139
	 * @param args
140
	 */
141 138
	public static void main(String[] args) {
142 139
		PesiExportActivatorEM ex = new PesiExportActivatorEM();
143 140
		ICdmDataSource source = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmSource;
144 141
//		Connection con = pesiDestination.getConnection();
145 142
//		System.out.println(con);
146 143
		ex.doExport(source);
144
		System.exit(0);
147 145
	}
148 146

  
149 147
}
cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/PesiExportActivatorERMS.java
25 25
 * @author a.mueller
26 26
 * @author e.-m.lee
27 27
 * @since 16.02.2010
28
 *
29 28
 */
30 29
public class PesiExportActivatorERMS {
31 30
	@SuppressWarnings("unused")
32 31
	private static final Logger logger = Logger.getLogger(PesiExportActivatorERMS.class);
33 32

  
34
	static final ICdmDataSource cdmSource = CdmDestinations.cdm_test_local_mysql_erms();
33
//	static final ICdmDataSource cdmSource = CdmDestinations.cdm_test_local_mysql_erms();
34
    static final ICdmDataSource cdmSource = CdmDestinations.cdm_test_local_mysql_erms2();
35 35

  
36 36
	//database validation status (create, update, validate ...)
37 37
	static final Source pesiDestination = PesiDestinations.pesi_test_local_CDM_ERMS2PESI();
......
131 131
		return result;
132 132
	}
133 133

  
134
	/**
135
	 * @param args
136
	 */
137 134
	public static void main(String[] args) {
138 135
		PesiExportActivatorERMS ex = new PesiExportActivatorERMS();
139 136
		ICdmDataSource source = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmSource;
140 137

  
141 138
		ex.doExport(source);
139
		System.exit(0);
142 140
	}
143

  
144 141
}

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