Revision 0f8489d7
Added by Andreas Müller almost 10 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java | ||
|---|---|---|
| 86 | 86 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 87 | 87 |
String cdmServer = "127.0.0.1"; |
| 88 | 88 |
String cdmDB = "test"; |
| 89 |
String cdmUserName = "edit"; //root on pesiimport2
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|
| 89 |
String cdmUserName = "root"; //root on pesiimport2
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|
| 90 | 90 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 91 | 91 |
} |
| 92 | 92 |
|
| ... | ... | |
| 377 | 377 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 378 | 378 |
} |
| 379 | 379 |
|
| 380 |
public static ICdmDataSource local_cdm_edit_cichorieae_a(){
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DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
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String cdmServer = "127.0.0.1"; |
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String cdmDB = "cdm_edit_cichorieae_a"; |
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String cdmUserName = "edit"; |
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return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
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} |
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|
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public static ICdmDataSource cdm_edit_palmae_a(){
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DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
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String cdmServer = "192.168.2.10"; |
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String cdmDB = "cdm_edit_palmae_a"; |
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String cdmUserName = "edit"; |
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return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
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} |
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|
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| 396 | 380 |
public static ICdmDataSource cdm_edit_cichorieae_preview(){
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| 397 | 381 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 398 | 382 |
String cdmServer = "127.0.0.1"; |
| ... | ... | |
| 411 | 395 |
return makeDestination(dbType, cdmServer, cdmDB, port, cdmUserName, null); |
| 412 | 396 |
} |
| 413 | 397 |
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public static ICdmDataSource cdm_edit_cichorieae_integration(){
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DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
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String cdmServer = "127.0.0.1"; |
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String cdmDB = "cdm_integration_cichorieae"; |
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String cdmUserName = "edit"; |
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int port = 13306; |
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return makeDestination(dbType, cdmServer, cdmDB, port, cdmUserName, null); |
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} |
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|
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public static ICdmDataSource cdm_edit_palmae_preview(){
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public static ICdmDataSource cdm_production_piB(String database){
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| 424 | 399 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
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String cdmServer = "127.0.0.1"; |
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String cdmDB = "cdm_edit_palmae"; |
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String cdmUserName = "edit"; |
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int port = 13306; |
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return makeDestination(dbType, cdmServer, cdmDB, port, cdmUserName, null); |
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} |
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|
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public static ICdmDataSource cdm_edit_salvador(){
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DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
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String cdmServer = "192.168.2.10"; |
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String cdmDB = "cdm_edit_salvador"; |
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String cdmUserName = "edit"; |
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return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
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} |
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public static ICdmDataSource cdm_import_salvador() {
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DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
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String cdmServer = "192.168.2.10"; |
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String cdmDB = "cdm_import_salvador"; |
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String cdmServer = "160.45.63.171"; |
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String cdmDB = "cdm_prodcution_" + database + "_pilot"; |
|
| 444 | 402 |
String cdmUserName = "edit"; |
| 445 | 403 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 446 | 404 |
} |
| 447 |
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public static ICdmDataSource cdm_salvador_production() {
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DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
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String cdmServer = "192.168.2.10"; |
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String cdmDB = "salvador_cdm"; |
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String cdmUserName = "salvador"; |
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return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
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} |
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| 456 | 406 |
/** |
| 457 | 407 |
* patricia |
| 458 | 408 |
*/ |
| app-import/src/main/java/eu/etaxonomy/cdm/app/proibiosphere/TaxonXImportLauncher.java | ||
|---|---|---|
| 51 | 51 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql(); |
| 52 | 52 |
static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); |
| 53 | 53 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test(); |
| 54 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_production_piB("piB_spiders");
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|
| 54 | 55 |
|
| 55 | 56 |
static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK; |
| 56 | 57 |
|
| ... | ... | |
| 79 | 80 |
|
| 80 | 81 |
String defaultClassification="Spiders"; |
| 81 | 82 |
boolean alwaysUseDefaultClassification = true; |
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boolean useOldUnparsedSynonymExtraction = false; |
|
| 82 | 85 |
|
| 83 | 86 |
|
| 84 | 87 |
|
| ... | ... | |
| 95 | 98 |
loadTreatmentIfPresent(filterType,taxonList, documentMap); |
| 96 | 99 |
// loadTreatmentIfPresent(FilterType.MODS,modsList, documents,documentMap); |
| 97 | 100 |
|
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TaxonXImportConfigurator taxonxImportConfigurator =null; |
|
| 99 | 101 |
CdmDefaultImport<TaxonXImportConfigurator> taxonImport = new CdmDefaultImport<TaxonXImportConfigurator>(); |
| 100 | 102 |
|
| 101 | 103 |
ICdmDataSource destination = cdmDestination; |
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taxonxImportConfigurator = prepareTaxonXImport(destination,reuseSecundum, secundum, tnomenclature, alwaysUseDefaultClassification); |
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taxonxImportConfigurator.setImportClassificationName(defaultClassification); |
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TaxonXImportConfigurator config = prepareTaxonXImport(destination,reuseSecundum, secundum, tnomenclature, alwaysUseDefaultClassification); |
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config.setUseOldUnparsedSynonymExtraction(useOldUnparsedSynonymExtraction); |
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config.setImportClassificationName(defaultClassification); |
|
| 105 | 108 |
log.info("Start import from TaxonX Data");
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| 106 | 109 |
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taxonxImportConfigurator.setLastImport(false);
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config.setLastImport(false);
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| 108 | 111 |
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| 109 | 112 |
int j=0; |
| 110 | 113 |
for (String document : documentMap.keySet()){
|
| ... | ... | |
| 115 | 118 |
System.out.println("START "+document+" "+i+" ("+(documentMap.get(document)).size()+"): "+source.getPath());
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| 116 | 119 |
i++; |
| 117 | 120 |
if (j==documentMap.keySet().size() && i==documentMap.get(document).size()) {
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taxonxImportConfigurator.setLastImport(true);
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config.setLastImport(true);
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| 119 | 122 |
} |
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prepareReferenceAndSource(taxonxImportConfigurator,source);
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prepareReferenceAndSource(config,source);
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| 121 | 124 |
// taxonxImportConfigurator.setTaxonReference(null); |
| 122 |
taxonImport.invoke(taxonxImportConfigurator);
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taxonImport.invoke(config);
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| 123 | 126 |
log.info("End import from SpecimenData ("+ source.toString() + ")...");
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| 124 | 127 |
|
| 125 | 128 |
// //deduplicate |
| ... | ... | |
| 221 | 224 |
e1.printStackTrace(); |
| 222 | 225 |
} |
| 223 | 226 |
|
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// sourcesStr.add("/home/pkelbert/Documents/Proibiosphere/ChenopodiumXML/1362148061170_Chenopodium_K_hn_U_1993_tx.xml");
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|
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| 226 | 227 |
//System.out.println(documents); |
| 227 | 228 |
for (String docId : docs.keySet()){
|
| 228 | 229 |
List<String> treatments = new ArrayList<String>(new HashSet<String>(docs.get(docId))); |
| ... | ... | |
| 243 | 244 |
// log.info(pages); |
| 244 | 245 |
|
| 245 | 246 |
log.info("Document "+docId+" should have "+treatments.size()+" treatments");
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//don't test if all the treatments are really online, it should be working without problems now |
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// int cnt=0; |
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// if(treatments.size()<150){
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// |
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// for (String source:treatments){
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// DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); |
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// DocumentBuilder builder; |
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// URL url; |
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// |
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// try {
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// builder = factory.newDocumentBuilder(); |
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// url = new URL(source.split("---")[3]);
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// Object o = url.getContent(); |
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// InputStream is = (InputStream) o; |
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// Document document = builder.parse(is); |
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// cnt++; |
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// }catch(Exception e){
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// // e.printStackTrace(); |
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// log.warn(e); |
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// } |
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// } |
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// log.info("Document "+docId+" has "+cnt+" treatments available");
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// } |
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// if(treatments.size() != cnt) |
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// {
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// File file = new File("/home/pkelbert/Bureau/urlTaxonXToDoLater.txt");
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// FileWriter writer; |
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// try {
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// writer = new FileWriter(file ,true); |
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// writer.write(docId+"\n"); |
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// writer.flush(); |
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// writer.close(); |
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// } catch (IOException e1) {
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// // TODO Auto-generated catch block |
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// e1.printStackTrace(); |
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// } |
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// |
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// } |
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// else{
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| 285 | 247 |
List<URI> uritmp = documentMap.get(docId); |
| 286 | 248 |
if (uritmp == null) {
|
| 287 | 249 |
uritmp = new ArrayList<URI>(); |
| ... | ... | |
| 305 | 267 |
|
| 306 | 268 |
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| 307 | 269 |
|
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// } |
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////// log.info("NB SOURCES : "+sourcesStr.size());
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// List<URI> sourcesStr = new ArrayList<URI>(); |
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// try {
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//// documentMap = new HashMap<String, List<URI>>(); |
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// sourcesStr.add(new URI("http://plazi.cs.umb.edu/GgServer/cdmSync/8F5B3EA099D371BC41CC5DDBFEDCFBED"));
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// documentMap.put("singlesource", sourcesStr);
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// } catch (URISyntaxException e) {
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// // TODO Auto-generated catch block |
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// e.printStackTrace(); |
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// } |
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| 319 | 271 |
|
| 320 | 272 |
return documentMap; |
| 321 | 273 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/sdd/CichorieaeActivator.java | ||
|---|---|---|
| 41 | 41 |
* ALTER TABLE `statisticalmeasurementvalue_definedtermbase` DROP INDEX `modifiers_id`; |
| 42 | 42 |
* |
| 43 | 43 |
********************************************************************************/ |
| 44 |
static final ICdmDataSource cdmDestination = CdmDestinations.local_cdm_edit_cichorieae_a();
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static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
|
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| 45 | 45 |
static final String sddSource = SDDSources.Cichorieae_DA_export_sdd(); |
| 46 | 46 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_portal_test_localhost(); |
| 47 | 47 |
|
Also available in: Unified diff
removed some destinations