Revision 246e1070
Added by Andreas Müller about 13 years ago
| .gitattributes | ||
|---|---|---|
| 69 | 69 |
app-import/src/main/java/eu/etaxonomy/cdm/app/sdd/applicationContext.xml -text |
| 70 | 70 |
app-import/src/main/java/eu/etaxonomy/cdm/app/synthesysImport/SpecimenImport.java -text |
| 71 | 71 |
app-import/src/main/java/eu/etaxonomy/cdm/app/synthesysImport/SynthesysCacheActivator.java -text |
| 72 |
app-import/src/main/java/eu/etaxonomy/cdm/app/synthesysImport/SynthesysSpecimenTestActivator.java -text |
|
| 72 | 73 |
app-import/src/main/java/eu/etaxonomy/cdm/app/tcs/TcsRdfTestActivator.java -text |
| 73 | 74 |
app-import/src/main/java/eu/etaxonomy/cdm/app/tcs/TcsSources.java -text |
| 74 | 75 |
app-import/src/main/java/eu/etaxonomy/cdm/app/tcs/TcsXmlTestActivator.java -text |
| ... | ... | |
| 132 | 133 |
app-import/src/main/resources/sdd/Xper2-import-export.sdd.xml -text |
| 133 | 134 |
app-import/src/main/resources/sdd/cichorieae-Xper2.xml -text |
| 134 | 135 |
app-import/src/main/resources/sdd/phlebo.sdd.xml -text |
| 135 |
app-import/src/main/resources/specimenABCD/CDMtabular9c04a474e2_23_09_08.xls -text
|
|
| 136 |
app-import/src/main/resources/specimen/SynthesysSpecimenExample.xls -text
|
|
| 136 | 137 |
app-import/src/main/resources/specimenABCD/multiABCD.xml -text |
| 137 | 138 |
app-import/src/main/resources/taxonX/palm_tc_100446.xml -text |
| 138 | 139 |
app-import/src/main/resources/taxonX/palm_tc_101019.xml -text |
| app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/SalvadorExport.java | ||
|---|---|---|
| 19 | 19 |
import eu.etaxonomy.cdm.io.common.CdmDefaultExport; |
| 20 | 20 |
import eu.etaxonomy.cdm.io.common.Source; |
| 21 | 21 |
import eu.etaxonomy.cdm.io.common.IExportConfigurator.CHECK; |
| 22 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;
|
|
| 22 |
import eu.etaxonomy.cdm.io.common.IExportConfigurator.DO_REFERENCES;
|
|
| 23 | 23 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| 24 | 24 |
|
| 25 | 25 |
|
| ... | ... | |
| 104 | 104 |
bmExportConfigurator.setDoReferences(doReferences); |
| 105 | 105 |
bmExportConfigurator.setDoTaxonNames(doTaxonNames); |
| 106 | 106 |
bmExportConfigurator.setDoRelNames(doRelNames); |
| 107 |
bmExportConfigurator.setDoTypes(doTypes); |
|
| 108 | 107 |
bmExportConfigurator.setDoNameFacts(doNameFacts); |
| 109 | 108 |
|
| 110 | 109 |
bmExportConfigurator.setDoTaxa(doTaxa); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/cyprus/CyprusActivator.java | ||
|---|---|---|
| 73 | 73 |
//make Source |
| 74 | 74 |
CyprusImportConfigurator config= CyprusImportConfigurator.NewInstance(source, cdmDestination); |
| 75 | 75 |
config.setClassificationUuid(classificationUuid); |
| 76 |
config.setDoTaxa(doTaxa); |
|
| 77 | 76 |
config.setCheck(check); |
| 78 | 77 |
// config.setDefaultLanguageUuid(defaultLanguageUuid); |
| 79 | 78 |
// config.setDoPrintKeys(doPrintKeys); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/eflora/CentralAfricaEricaceaeActivator.java | ||
|---|---|---|
| 56 | 56 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_andreasM3(); |
| 57 | 57 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_preview(); |
| 58 | 58 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_production(); |
| 59 |
static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); |
|
| 59 |
// static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
|
|
| 60 | 60 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_postgres_CdmTest(); |
| 61 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
|
|
| 61 |
static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();
|
|
| 62 | 62 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_jaxb(); |
| 63 | 63 |
|
| 64 | 64 |
//feature tree uuid |
| app-import/src/main/java/eu/etaxonomy/cdm/app/exel/NormalExplicitTestActivator.java | ||
|---|---|---|
| 66 | 66 |
config.setClassificationUuid(treeUuid); |
| 67 | 67 |
config.setSourceSecId(sourceSecId); |
| 68 | 68 |
|
| 69 |
config.setDoReferences(doReferences); |
|
| 70 |
config.setDoTaxonNames(doTaxonNames); |
|
| 71 |
|
|
| 72 | 69 |
config.setDoMatchTaxa(doMatchTaxa); |
| 73 |
config.setDoTaxa(doTaxa); |
|
| 74 |
config.setDoRelTaxa(doRelTaxa); |
|
| 75 | 70 |
|
| 76 | 71 |
config.setCheck(check); |
| 77 | 72 |
config.setDbSchemaValidation(hbm2dll); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/globis/GlobisActivator.java | ||
|---|---|---|
| 101 | 101 |
config.setIgnoreNull(ignoreNull); |
| 102 | 102 |
config.setDoReferences(doReferences); |
| 103 | 103 |
|
| 104 |
config.setDoTaxa(doTaxa); |
|
| 105 |
config.setDoRelTaxa(doRelTaxa); |
|
| 104 |
// config.setDoTaxa(doTaxa);
|
|
| 105 |
// config.setDoRelTaxa(doRelTaxa);
|
|
| 106 | 106 |
config.setDoLinks(doLinks); |
| 107 | 107 |
config.setDoOccurrence(doOccurences); |
| 108 | 108 |
config.setDbSchemaValidation(hbm2dll); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/pesi/PesiExportActivator.java | ||
|---|---|---|
| 91 | 91 |
|
| 92 | 92 |
PesiExportConfigurator pesiExportConfigurator = PesiExportConfigurator.NewInstance(destination, source); |
| 93 | 93 |
|
| 94 |
pesiExportConfigurator.setDoAuthors(doAuthors); |
|
| 95 |
pesiExportConfigurator.setDoReferences(doReferences); |
|
| 96 |
pesiExportConfigurator.setDoTaxonNames(doTaxonNames); |
|
| 97 |
pesiExportConfigurator.setDoTypes(doTypes); |
|
| 98 | 94 |
pesiExportConfigurator.setDoNameFacts(doNameFacts); |
| 99 | 95 |
|
| 100 | 96 |
pesiExportConfigurator.setDoTaxa(doTaxa); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/pilotOutputHtml/SimpleDescriptionOutput.java | ||
|---|---|---|
| 15 | 15 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 16 | 16 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| 17 | 17 |
import eu.etaxonomy.cdm.io.common.CdmDefaultExport; |
| 18 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;
|
|
| 18 |
import eu.etaxonomy.cdm.io.common.IExportConfigurator.DO_REFERENCES;
|
|
| 19 | 19 |
import eu.etaxonomy.cdm.io.pilotOutputHtml.PilotOutputExportConfigurator; |
| 20 | 20 |
|
| 21 | 21 |
/** |
| app-import/src/main/java/eu/etaxonomy/cdm/app/sdd/ViolaExportActivator.java | ||
|---|---|---|
| 14 | 14 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 15 | 15 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| 16 | 16 |
import eu.etaxonomy.cdm.io.common.CdmDefaultExport; |
| 17 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;
|
|
| 17 |
import eu.etaxonomy.cdm.io.common.IExportConfigurator.DO_REFERENCES;
|
|
| 18 | 18 |
import eu.etaxonomy.cdm.io.sdd.out.SDDExportConfigurator; |
| 19 | 19 |
|
| 20 | 20 |
/** |
| app-import/src/main/java/eu/etaxonomy/cdm/app/synthesysImport/SynthesysCacheActivator.java | ||
|---|---|---|
| 24 | 24 |
import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
| 25 | 25 |
import eu.etaxonomy.cdm.api.service.pager.Pager; |
| 26 | 26 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 27 |
import eu.etaxonomy.cdm.app.common.CdmImportSources; |
|
| 27 | 28 |
import eu.etaxonomy.cdm.common.ExcelUtils; |
| 28 | 29 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 30 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
|
| 29 | 31 |
import eu.etaxonomy.cdm.model.agent.AgentBase; |
| 30 | 32 |
import eu.etaxonomy.cdm.model.agent.Institution; |
| 31 | 33 |
import eu.etaxonomy.cdm.model.agent.Person; |
| ... | ... | |
| 73 | 75 |
protected ArrayList<String> gatheringAgentList = new ArrayList<String>(); |
| 74 | 76 |
protected ArrayList<String> identificationList = new ArrayList<String>(); |
| 75 | 77 |
|
| 76 |
static DbSchemaValidation hbm2dll = DbSchemaValidation.UPDATE; |
|
| 77 |
|
|
| 78 |
static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE; |
|
| 79 |
|
|
| 80 |
static ICdmDataSource desitination = CdmDestinations.localH2(); |
|
| 81 |
|
|
| 78 | 82 |
protected HSSFWorkbook hssfworkbook = null; |
| 79 | 83 |
|
| 80 | 84 |
|
| ... | ... | |
| 123 | 127 |
} catch (Exception e) {
|
| 124 | 128 |
} |
| 125 | 129 |
try {String coll =unit.get("collector");
|
| 126 |
coll=coll.replaceAll("None", null);
|
|
| 127 |
this.gatheringAgentList.add(coll); |
|
| 130 |
coll=coll.replaceAll("None", null);
|
|
| 131 |
this.gatheringAgentList.add(coll);
|
|
| 128 | 132 |
} catch (Exception e) {
|
| 129 | 133 |
} |
| 130 | 134 |
try {this.identificationList.add(taxonName+" "+author);
|
| ... | ... | |
| 138 | 142 |
CdmApplicationController app = null; |
| 139 | 143 |
TransactionStatus tx = null; |
| 140 | 144 |
|
| 141 |
app = CdmApplicationController.NewInstance(CdmDestinations.cdm_test_patricia(), hbm2dll);
|
|
| 145 |
app = CdmApplicationController.NewInstance(desitination, hbm2dll);
|
|
| 142 | 146 |
|
| 143 | 147 |
tx = app.startTransaction(); |
| 144 | 148 |
try {
|
| ... | ... | |
| 434 | 438 |
* @throws URISyntaxException |
| 435 | 439 |
*/ |
| 436 | 440 |
public static void main(String[] args) throws URISyntaxException {
|
| 437 |
URI uri = new URI("file:///home/patricia/Desktop/CDMtabular9c04a474e2_23_09_08.xls");
|
|
| 438 |
|
|
| 441 |
URI uri = CdmImportSources.SYNTHESYS_SPECIMEN(); |
|
| 439 | 442 |
logger.info("main method");
|
| 440 | 443 |
SynthesysCacheActivator abcdAct = new SynthesysCacheActivator(); |
| 444 |
|
|
| 441 | 445 |
ArrayList<HashMap<String, String>> units; |
| 442 | 446 |
try {
|
| 443 | 447 |
units = ExcelUtils.parseXLS(uri); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/synthesysImport/SynthesysSpecimenTestActivator.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 |
|
|
| 12 |
import java.net.URI; |
|
| 13 |
import java.util.UUID; |
|
| 14 |
|
|
| 15 |
import org.apache.log4j.Logger; |
|
| 16 |
|
|
| 17 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
|
| 18 |
import eu.etaxonomy.cdm.app.common.CdmImportSources; |
|
| 19 |
import eu.etaxonomy.cdm.app.tcs.TcsSources; |
|
| 20 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
|
| 21 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
|
| 22 |
import eu.etaxonomy.cdm.io.common.CdmDefaultImport; |
|
| 23 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK; |
|
| 24 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES; |
|
| 25 |
import eu.etaxonomy.cdm.io.excel.taxa.NormalExplicitImportConfigurator; |
|
| 26 |
import eu.etaxonomy.cdm.io.specimen.excel.in.SpecimenExcelImportConfigurator; |
|
| 27 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
|
| 28 |
|
|
| 29 |
/** |
|
| 30 |
* @author a.mueller |
|
| 31 |
* @created 20.06.2008 |
|
| 32 |
* @version 1.0 |
|
| 33 |
*/ |
|
| 34 |
public class SynthesysSpecimenTestActivator {
|
|
| 35 |
private static final Logger logger = Logger.getLogger(SynthesysSpecimenTestActivator.class); |
|
| 36 |
|
|
| 37 |
//database validation status (create, update, validate ...) |
|
| 38 |
static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE; |
|
| 39 |
// static final String mySources = TcsSources.taxonX_local(); |
|
| 40 |
static final URI mySource = CdmImportSources.SYNTHESYS_SPECIMEN(); |
|
| 41 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_tdwg2010(); |
|
| 42 |
static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); |
|
| 43 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_postgres_CdmTest(); |
|
| 44 |
|
|
| 45 |
static final UUID treeUuid = UUID.fromString("190d9456-12e8-47a4-a235-bab36adb247c");
|
|
| 46 |
static final String sourceSecId = "TestSynthesysSpecimen"; |
|
| 47 |
|
|
| 48 |
//check - import |
|
| 49 |
static final CHECK check = CHECK.CHECK_AND_IMPORT; |
|
| 50 |
|
|
| 51 |
static final boolean doMatchTaxa = true; |
|
| 52 |
|
|
| 53 |
//references |
|
| 54 |
static final DO_REFERENCES doReferences = DO_REFERENCES.ALL; |
|
| 55 |
//names |
|
| 56 |
static final boolean doTaxonNames = true; |
|
| 57 |
static final boolean doRelNames = true; |
|
| 58 |
|
|
| 59 |
//taxa |
|
| 60 |
static final boolean doTaxa = true; |
|
| 61 |
static final boolean doRelTaxa = true; |
|
| 62 |
|
|
| 63 |
|
|
| 64 |
public void doImport(ICdmDataSource destination, DbSchemaValidation hbm2dll){
|
|
| 65 |
System.out.println("Start import from Tcs("+ mySource.toString() + ") ...");
|
|
| 66 |
|
|
| 67 |
SpecimenExcelImportConfigurator config = SpecimenExcelImportConfigurator.NewInstance(mySource, destination); |
|
| 68 |
|
|
| 69 |
config.setClassificationUuid(treeUuid); |
|
| 70 |
config.setSourceSecId(sourceSecId); |
|
| 71 |
|
|
| 72 |
// config.setDoReferences(doReferences); |
|
| 73 |
// config.setDoTaxonNames(doTaxonNames); |
|
| 74 |
// |
|
| 75 |
// config.setDoMatchTaxa(doMatchTaxa); |
|
| 76 |
// config.setDoTaxa(doTaxa); |
|
| 77 |
// config.setDoRelTaxa(doRelTaxa); |
|
| 78 |
|
|
| 79 |
config.setCheck(check); |
|
| 80 |
config.setDbSchemaValidation(hbm2dll); |
|
| 81 |
|
|
| 82 |
// invoke import |
|
| 83 |
CdmDefaultImport<SpecimenExcelImportConfigurator> myImport = new CdmDefaultImport<SpecimenExcelImportConfigurator>(); |
|
| 84 |
//new Test().invoke(tcsImportConfigurator); |
|
| 85 |
myImport.invoke(config); |
|
| 86 |
|
|
| 87 |
|
|
| 88 |
logger.info("End");
|
|
| 89 |
System.out.println("End import from Normal Explicit ("+ mySource.toString() + ")...");
|
|
| 90 |
|
|
| 91 |
} |
|
| 92 |
|
|
| 93 |
/** |
|
| 94 |
* @param args |
|
| 95 |
*/ |
|
| 96 |
public static void main(String[] args) {
|
|
| 97 |
SynthesysSpecimenTestActivator me = new SynthesysSpecimenTestActivator(); |
|
| 98 |
me.doImport(cdmDestination, hbm2dll); |
|
| 99 |
} |
|
| 100 |
|
|
| 101 |
} |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/cichorieae/CichorieaeCacheUpdater.java | ||
|---|---|---|
| 20 | 20 |
import eu.etaxonomy.cdm.io.common.CacheUpdaterConfigurator; |
| 21 | 21 |
import eu.etaxonomy.cdm.io.common.CdmDefaultImport; |
| 22 | 22 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 23 |
import eu.etaxonomy.cdm.model.reference.Reference; |
|
| 24 | 23 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| 25 | 24 |
|
| 26 | 25 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/diptera/DipteraPostImportUpdater.java | ||
|---|---|---|
| 88 | 88 |
String originalNameString = parseOriginalNameString(text); |
| 89 | 89 |
String newText = parseNewText(text); |
| 90 | 90 |
citation.removeText(language); |
| 91 |
citation.putText(newText, language);
|
|
| 91 |
citation.putText(language, newText);
|
|
| 92 | 92 |
TaxonNameBase scientificName = getScientificName(originalNameString, nameMap, nameDuplicateMap); |
| 93 | 93 |
|
| 94 | 94 |
Set<DescriptionElementSource> sources = citation.getSources(); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/palmae/PalmaeActivator.java | ||
|---|---|---|
| 101 | 101 |
tcsImportConfigurator.setSecUuid(secUuid); |
| 102 | 102 |
tcsImportConfigurator.setSourceSecId(sourceSecId); |
| 103 | 103 |
|
| 104 |
tcsImportConfigurator.setDoAuthors(doAuthors); |
|
| 105 | 104 |
tcsImportConfigurator.setDoReferences(doReferences); |
| 106 | 105 |
tcsImportConfigurator.setDoTaxonNames(doTaxonNames); |
| 107 | 106 |
tcsImportConfigurator.setDoRelNames(doRelNames); |
| app-import/src/main/java/eu/etaxonomy/cdm/io/cyprus/CyprusRow.java | ||
|---|---|---|
| 11 | 11 |
|
| 12 | 12 |
import java.util.TreeMap; |
| 13 | 13 |
|
| 14 |
import org.apache.log4j.Logger; |
|
| 15 |
|
|
| 14 | 16 |
/** |
| 15 | 17 |
* @author a.babadshanjan |
| 16 | 18 |
* @created 13.01.2009 |
| 17 | 19 |
* @version 1.0 |
| 18 | 20 |
*/ |
| 19 | 21 |
public class CyprusRow {
|
| 20 |
|
|
| 22 |
@SuppressWarnings("unused")
|
|
| 23 |
private static final Logger logger = Logger.getLogger(CyprusRow.class); |
|
| 24 |
|
|
| 21 | 25 |
private String species; |
| 22 | 26 |
private String subspecies; |
| 23 | 27 |
private String homotypicSynonyms; |
| app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisImportConfigurator.java | ||
|---|---|---|
| 18 | 18 |
import eu.etaxonomy.cdm.io.common.ImportConfiguratorBase; |
| 19 | 19 |
import eu.etaxonomy.cdm.io.common.ImportStateBase; |
| 20 | 20 |
import eu.etaxonomy.cdm.io.common.Source; |
| 21 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES; |
|
| 21 | 22 |
import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer; |
| 22 | 23 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| 23 | 24 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| ... | ... | |
| 48 | 49 |
private boolean doNotes = true; |
| 49 | 50 |
private boolean doImages = true; |
| 50 | 51 |
private boolean doOccurrence = true; |
| 52 |
private DO_REFERENCES doReferences = DO_REFERENCES.ALL; |
|
| 53 |
|
|
| 51 | 54 |
|
| 52 | 55 |
private static IInputTransformer defaultTransformer = new GlobisTransformer(); |
| 53 | 56 |
|
| ... | ... | |
| 132 | 135 |
public int getRecordsPerTransaction() {
|
| 133 | 136 |
return recordsPerTransaction; |
| 134 | 137 |
} |
| 135 |
|
|
| 136 | 138 |
/** |
| 137 | 139 |
* @param limitSave the limitSave to set |
| 138 | 140 |
*/ |
| ... | ... | |
| 162 | 164 |
public void setDoLinks(boolean doLinks) {
|
| 163 | 165 |
this.doLinks = doLinks; |
| 164 | 166 |
} |
| 165 |
|
|
| 166 |
|
|
| 167 |
|
|
| 168 | 167 |
/** |
| 169 | 168 |
* @return the doLinks |
| 170 | 169 |
*/ |
| ... | ... | |
| 180 | 179 |
public void setDoNotes(boolean doNotes) {
|
| 181 | 180 |
this.doNotes = doNotes; |
| 182 | 181 |
} |
| 183 |
|
|
| 184 |
|
|
| 185 |
|
|
| 186 | 182 |
/** |
| 187 | 183 |
* @return the doNotes |
| 188 | 184 |
*/ |
| ... | ... | |
| 190 | 186 |
return doNotes; |
| 191 | 187 |
} |
| 192 | 188 |
|
| 193 |
|
|
| 194 |
|
|
| 195 | 189 |
/** |
| 196 | 190 |
* @param doImages the doImages to set |
| 197 | 191 |
*/ |
| 198 | 192 |
public void setDoImages(boolean doImages) {
|
| 199 | 193 |
this.doImages = doImages; |
| 200 | 194 |
} |
| 201 |
|
|
| 202 |
|
|
| 203 |
|
|
| 204 | 195 |
/** |
| 205 | 196 |
* @return the doImages |
| 206 | 197 |
*/ |
| ... | ... | |
| 215 | 206 |
public void setDoOccurrence(boolean doOccurrence) {
|
| 216 | 207 |
this.doOccurrence = doOccurrence; |
| 217 | 208 |
} |
| 209 |
|
|
| 210 |
|
|
| 211 |
public DO_REFERENCES getDoReferences() {
|
|
| 212 |
return doReferences; |
|
| 213 |
} |
|
| 214 |
public void setDoReferences(DO_REFERENCES doReferences) {
|
|
| 215 |
this.doReferences = doReferences; |
|
| 216 |
} |
|
| 217 |
|
|
| 218 | 218 |
|
| 219 | 219 |
|
| 220 | 220 |
|
| app-import/src/main/resources/sdd/SDD-Test-Simple.xml | ||
|---|---|---|
| 1 | 1 |
<?xml version="1.0" encoding="UTF-8"?> |
| 2 |
<Datasets xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://rs.tdwg.org/UBIF/2006/" xsi:schemaLocation="http://rs.tdwg.org/UBIF/2006/ ../SDD.xsd">
|
|
| 2 |
<Datasets xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://rs.tdwg.org/UBIF/2006/" xsi:schemaLocation="http://rs.tdwg.org/UBIF/2006/ C:/localCopy/schema/sdd/UBIF_TypeLib.xsd">
|
|
| 3 | 3 |
<TechnicalMetadata created="2006-04-20T10:00:00"> |
| 4 | 4 |
<Generator name="n/a, handcrafted instance document" version="n/a"/> |
| 5 | 5 |
</TechnicalMetadata> |
| ... | ... | |
| 80 | 80 |
</Representation> |
| 81 | 81 |
</TextCharacter> |
| 82 | 82 |
</Characters> |
| 83 |
<CodedDescriptions> |
|
| 83 |
|
|
| 84 |
<CharacterTrees> |
|
| 85 |
<CharacterTree> |
|
| 86 |
<Representation> |
|
| 87 |
<Label>Main character list</Label> |
|
| 88 |
<Detail>Default arrangement of characters; used for editing and identification purposes. Each character occurs only a single time and all characters should be present.</Detail> |
|
| 89 |
</Representation> |
|
| 90 |
<DesignedFor> |
|
| 91 |
<Role>DescriptionEditing</Role> |
|
| 92 |
<Role>InteractiveIdentification</Role> |
|
| 93 |
<Role>TerminologyReporting</Role> |
|
| 94 |
</DesignedFor> |
|
| 95 |
<ShouldContainAllCharacters>true</ShouldContainAllCharacters> |
|
| 96 |
<Nodes> |
|
| 97 |
<CharNode> |
|
| 98 |
<Character ref="c1"/> |
|
| 99 |
</CharNode> |
|
| 100 |
<CharNode> |
|
| 101 |
<Character ref="c2"/> |
|
| 102 |
</CharNode> |
|
| 103 |
<CharNode> |
|
| 104 |
<Character ref="c3"/> |
|
| 105 |
</CharNode> |
|
| 106 |
<CharNode> |
|
| 107 |
<Character ref="c4"/> |
|
| 108 |
</CharNode> |
|
| 109 |
</Nodes> |
|
| 110 |
|
|
| 111 |
</CharacterTree> |
|
| 112 |
</CharacterTrees> |
|
| 113 |
<CodedDescriptions> |
|
| 84 | 114 |
<CodedDescription id="D101"> |
| 85 | 115 |
<Representation> |
| 86 | 116 |
<Label><i>Viola hederacea</i> Labill. as revised by R. Morris April 8, 2006</Label> |
| cdmlib-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/EfloraImportConfigurator.java | ||
|---|---|---|
| 36 | 36 |
return new EfloraImportConfigurator(uri, destination); |
| 37 | 37 |
} |
| 38 | 38 |
|
| 39 |
private boolean doTaxa = true; |
|
| 40 |
|
|
| 41 |
|
|
| 39 | 42 |
//TODO |
| 40 | 43 |
private static IInputTransformer defaultTransformer = null; |
| 41 | 44 |
private String classificationTitle = "E-Flora Import"; |
| ... | ... | |
| 180 | 183 |
public void setDefaultLanguageUuid(UUID defaultLanguageUuid) {
|
| 181 | 184 |
this.defaultLanguageUuid = defaultLanguageUuid; |
| 182 | 185 |
} |
| 183 |
|
|
| 186 |
|
|
| 187 |
public boolean isDoTaxa() {
|
|
| 188 |
return doTaxa; |
|
| 189 |
} |
|
| 190 |
public void setDoTaxa(boolean doTaxa) {
|
|
| 191 |
this.doTaxa = doTaxa; |
|
| 192 |
} |
|
| 193 |
|
|
| 184 | 194 |
|
| 185 | 195 |
|
| 186 | 196 |
|
| cdmlib-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/checklist/CentralAfricaChecklistImportConfigurator.java | ||
|---|---|---|
| 52 | 52 |
private boolean doLinks = true; |
| 53 | 53 |
private boolean doNotes = true; |
| 54 | 54 |
private boolean doImages = true; |
| 55 |
private DO_REFERENCES doReferences = DO_REFERENCES.ALL; |
|
| 56 |
private boolean doTaxa = true; |
|
| 57 |
|
|
| 55 | 58 |
|
| 56 | 59 |
private static IInputTransformer defaultTransformer = new CentralAfricaChecklistTransformer(); |
| 57 | 60 |
|
| ... | ... | |
| 231 | 234 |
} |
| 232 | 235 |
|
| 233 | 236 |
|
| 237 |
public DO_REFERENCES getDoReferences() {
|
|
| 238 |
return doReferences; |
|
| 239 |
} |
|
| 240 |
public void setDoReferences(DO_REFERENCES doReferences) {
|
|
| 241 |
this.doReferences = doReferences; |
|
| 242 |
} |
|
| 243 |
|
|
| 244 |
public boolean isDoTaxa() {
|
|
| 245 |
return doTaxa; |
|
| 246 |
} |
|
| 247 |
public void setDoTaxa(boolean doTaxa) {
|
|
| 248 |
this.doTaxa = doTaxa; |
|
| 249 |
} |
|
| 250 |
|
|
| 251 |
|
|
| 234 | 252 |
|
| 235 | 253 |
} |
| cdmlib-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/checklist/CentralAfricaChecklistReferenceImport.java | ||
|---|---|---|
| 23 | 23 |
|
| 24 | 24 |
import eu.etaxonomy.cdm.api.service.IClassificationService; |
| 25 | 25 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| 26 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator; |
|
| 26 | 27 |
import eu.etaxonomy.cdm.io.common.IOValidator; |
| 27 | 28 |
import eu.etaxonomy.cdm.io.common.ResultSetPartitioner; |
| 28 | 29 |
import eu.etaxonomy.cdm.io.common.mapping.DbImportMapping; |
| ... | ... | |
| 143 | 144 |
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator) |
| 144 | 145 |
*/ |
| 145 | 146 |
protected boolean isIgnore(CentralAfricaChecklistImportState state){
|
| 146 |
return ! state.getConfig().isDoTaxa();
|
|
| 147 |
return state.getConfig().getDoReferences().equals(IImportConfigurator.DO_REFERENCES.NONE);
|
|
| 147 | 148 |
} |
| 148 | 149 |
|
| 149 | 150 |
|
| cdmlib-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/ferns/CentralAfricaFernsImportConfigurator.java | ||
|---|---|---|
| 18 | 18 |
import eu.etaxonomy.cdm.io.common.ImportConfiguratorBase; |
| 19 | 19 |
import eu.etaxonomy.cdm.io.common.ImportStateBase; |
| 20 | 20 |
import eu.etaxonomy.cdm.io.common.Source; |
| 21 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES; |
|
| 21 | 22 |
import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer; |
| 22 | 23 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| 23 | 24 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| ... | ... | |
| 47 | 48 |
private boolean doLinks = true; |
| 48 | 49 |
private boolean doNotes = true; |
| 49 | 50 |
private boolean doImages = true; |
| 51 |
private DO_REFERENCES doReferences = DO_REFERENCES.ALL; |
|
| 52 |
private boolean doTaxa = true; |
|
| 53 |
private boolean doRelTaxa = true; |
|
| 54 |
|
|
| 50 | 55 |
|
| 51 | 56 |
private static IInputTransformer defaultTransformer = new CentralAfricaFernsTransformer(); |
| 52 | 57 |
|
| ... | ... | |
| 122 | 127 |
public int getRecordsPerTransaction() {
|
| 123 | 128 |
return recordsPerTransaction; |
| 124 | 129 |
} |
| 125 |
|
|
| 126 | 130 |
/** |
| 127 | 131 |
* @param limitSave the limitSave to set |
| 128 | 132 |
*/ |
| ... | ... | |
| 136 | 140 |
public void setDoVernaculars(boolean doVernaculars) {
|
| 137 | 141 |
this.doVernaculars = doVernaculars; |
| 138 | 142 |
} |
| 139 |
|
|
| 140 | 143 |
/** |
| 141 | 144 |
* @return the doVernaculars |
| 142 | 145 |
*/ |
| ... | ... | |
| 152 | 155 |
public void setDoLinks(boolean doLinks) {
|
| 153 | 156 |
this.doLinks = doLinks; |
| 154 | 157 |
} |
| 155 |
|
|
| 156 |
|
|
| 157 |
|
|
| 158 | 158 |
/** |
| 159 | 159 |
* @return the doLinks |
| 160 | 160 |
*/ |
| ... | ... | |
| 170 | 170 |
public void setDoNotes(boolean doNotes) {
|
| 171 | 171 |
this.doNotes = doNotes; |
| 172 | 172 |
} |
| 173 |
|
|
| 174 |
|
|
| 175 |
|
|
| 176 | 173 |
/** |
| 177 | 174 |
* @return the doNotes |
| 178 | 175 |
*/ |
| ... | ... | |
| 180 | 177 |
return doNotes; |
| 181 | 178 |
} |
| 182 | 179 |
|
| 183 |
|
|
| 184 |
|
|
| 185 | 180 |
/** |
| 186 | 181 |
* @param doImages the doImages to set |
| 187 | 182 |
*/ |
| 188 | 183 |
public void setDoImages(boolean doImages) {
|
| 189 | 184 |
this.doImages = doImages; |
| 190 | 185 |
} |
| 191 |
|
|
| 192 |
|
|
| 193 |
|
|
| 194 | 186 |
/** |
| 195 | 187 |
* @return the doImages |
| 196 | 188 |
*/ |
| ... | ... | |
| 198 | 190 |
return doImages; |
| 199 | 191 |
} |
| 200 | 192 |
|
| 193 |
|
|
| 194 |
public DO_REFERENCES getDoReferences() {
|
|
| 195 |
return doReferences; |
|
| 196 |
} |
|
| 197 |
public void setDoReferences(DO_REFERENCES doReferences) {
|
|
| 198 |
this.doReferences = doReferences; |
|
| 199 |
} |
|
| 200 |
|
|
| 201 |
public boolean isDoTaxa() {
|
|
| 202 |
return doTaxa; |
|
| 203 |
} |
|
| 204 |
public void setDoTaxa(boolean doTaxa) {
|
|
| 205 |
this.doTaxa = doTaxa; |
|
| 206 |
} |
|
| 207 |
|
|
| 208 |
public boolean isDoRelTaxa() {
|
|
| 209 |
return doRelTaxa; |
|
| 210 |
} |
|
| 211 |
public void setDoRelTaxa(boolean doRelTaxa) {
|
|
| 212 |
this.doRelTaxa = doRelTaxa; |
|
| 213 |
} |
|
| 201 | 214 |
|
| 202 | 215 |
|
| 203 | 216 |
} |
| cdmlib-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/ferns/CentralAfricaFernsTaxonRelationImport.java | ||
|---|---|---|
| 1181 | 1181 |
*/ |
| 1182 | 1182 |
@Override |
| 1183 | 1183 |
protected boolean isIgnore(CentralAfricaFernsImportState state){
|
| 1184 |
return ! state.getConfig().isDoTaxa(); |
|
| 1184 |
return ! state.getConfig().isDoRelTaxa();
|
|
| 1185 | 1185 |
} |
| 1186 | 1186 |
|
| 1187 | 1187 |
|
| cdmlib-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsImportConfigurator.java | ||
|---|---|---|
| 18 | 18 |
import eu.etaxonomy.cdm.io.common.ImportConfiguratorBase; |
| 19 | 19 |
import eu.etaxonomy.cdm.io.common.ImportStateBase; |
| 20 | 20 |
import eu.etaxonomy.cdm.io.common.Source; |
| 21 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES; |
|
| 21 | 22 |
import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer; |
| 22 | 23 |
import eu.etaxonomy.cdm.io.pesi.erms.validation.ErmsGeneralImportValidator; |
| 23 | 24 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| ... | ... | |
| 49 | 50 |
private boolean doNotes = true; |
| 50 | 51 |
private boolean doImages = true; |
| 51 | 52 |
private boolean doOccurrence = true; |
| 53 |
private DO_REFERENCES doReferences = DO_REFERENCES.ALL; |
|
| 54 |
private boolean doTaxa = true; |
|
| 55 |
private boolean doRelTaxa = true; |
|
| 56 |
|
|
| 52 | 57 |
|
| 53 | 58 |
private static IInputTransformer defaultTransformer = new ErmsTransformer(); |
| 54 | 59 |
|
| ... | ... | |
| 232 | 237 |
public void setDoOccurrence(boolean doOccurrence) {
|
| 233 | 238 |
this.doOccurrence = doOccurrence; |
| 234 | 239 |
} |
| 240 |
|
|
| 241 |
|
|
| 242 |
public DO_REFERENCES getDoReferences() {
|
|
| 243 |
return doReferences; |
|
| 244 |
} |
|
| 245 |
public void setDoReferences(DO_REFERENCES doReferences) {
|
|
| 246 |
this.doReferences = doReferences; |
|
| 247 |
} |
|
| 248 |
|
|
| 249 |
public boolean isDoTaxa() {
|
|
| 250 |
return doTaxa; |
|
| 251 |
} |
|
| 252 |
public void setDoTaxa(boolean doTaxa) {
|
|
| 253 |
this.doTaxa = doTaxa; |
|
| 254 |
} |
|
| 255 |
|
|
| 256 |
public boolean isDoRelTaxa() {
|
|
| 257 |
return doRelTaxa; |
|
| 258 |
} |
|
| 259 |
public void setDoRelTaxa(boolean doRelTaxa) {
|
|
| 260 |
this.doRelTaxa = doRelTaxa; |
|
| 261 |
} |
|
| 262 |
|
|
| 263 |
|
|
| 235 | 264 |
|
| 236 | 265 |
} |
| cdmlib-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaImportConfigurator.java | ||
|---|---|---|
| 14 | 14 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator; |
| 15 | 15 |
import eu.etaxonomy.cdm.io.common.ImportConfiguratorBase; |
| 16 | 16 |
import eu.etaxonomy.cdm.io.common.Source; |
| 17 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES; |
|
| 17 | 18 |
import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer; |
| 18 | 19 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| 19 | 20 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| ... | ... | |
| 230 | 231 |
public void setDoOccurrence(boolean doOccurrence) {
|
| 231 | 232 |
this.doOccurrence = doOccurrence; |
| 232 | 233 |
} |
| 234 |
|
|
| 235 |
|
|
| 236 |
private boolean doAuthors = true; |
|
| 237 |
//references |
|
| 238 |
private DO_REFERENCES doReferences = DO_REFERENCES.ALL; |
|
| 239 |
//names |
|
| 240 |
private boolean doTypes = true; |
|
| 241 |
|
|
| 242 |
//taxa |
|
| 243 |
private boolean doTaxa = true; |
|
| 244 |
private boolean doRelTaxa = true; |
|
| 245 |
|
|
| 246 |
public boolean isDoAuthors() {
|
|
| 247 |
return doAuthors; |
|
| 248 |
} |
|
| 249 |
public void setDoAuthors(boolean doAuthors) {
|
|
| 250 |
this.doAuthors = doAuthors; |
|
| 251 |
} |
|
| 252 |
|
|
| 253 |
public DO_REFERENCES getDoReferences() {
|
|
| 254 |
return doReferences; |
|
| 255 |
} |
|
| 256 |
public void setDoReferences(DO_REFERENCES doReferences) {
|
|
| 257 |
this.doReferences = doReferences; |
|
| 258 |
} |
|
| 259 |
|
|
| 260 |
// public boolean isDoTypes() {
|
|
| 261 |
// return doTypes; |
|
| 262 |
// } |
|
| 263 |
// public void setDoTypes(boolean doTypes) {
|
|
| 264 |
// this.doTypes = doTypes; |
|
| 265 |
// } |
|
| 266 |
|
|
| 267 |
public boolean isDoTaxa() {
|
|
| 268 |
return doTaxa; |
|
| 269 |
} |
|
| 270 |
public void setDoTaxa(boolean doTaxa) {
|
|
| 271 |
this.doTaxa = doTaxa; |
|
| 272 |
} |
|
| 273 |
|
|
| 274 |
public boolean isDoRelTaxa() {
|
|
| 275 |
return doRelTaxa; |
|
| 276 |
} |
|
| 277 |
public void setDoRelTaxa(boolean doRelTaxa) {
|
|
| 278 |
this.doRelTaxa = doRelTaxa; |
|
| 279 |
} |
|
| 280 |
|
|
| 281 |
|
|
| 233 | 282 |
} |
| cdmlib-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiExportConfigurator.java | ||
|---|---|---|
| 16 | 16 |
import eu.etaxonomy.cdm.io.common.ExportStateBase; |
| 17 | 17 |
import eu.etaxonomy.cdm.io.common.IExportConfigurator; |
| 18 | 18 |
import eu.etaxonomy.cdm.io.common.Source; |
| 19 |
import eu.etaxonomy.cdm.io.common.IExportConfigurator.DO_REFERENCES; |
|
| 19 | 20 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 20 | 21 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 21 | 22 |
|
| ... | ... | |
| 28 | 29 |
@SuppressWarnings("unused")
|
| 29 | 30 |
private static Logger logger = Logger.getLogger(PesiExportConfigurator.class); |
| 30 | 31 |
private int limitSave = 1000; |
| 32 |
|
|
| 31 | 33 |
private Reference<?> auctReference; |
| 32 | 34 |
private boolean doOccurrence = true; |
| 33 | 35 |
private boolean doFacts = true; |
| 34 | 36 |
private boolean doNameFacts = true; |
| 37 |
private DO_REFERENCES doReferences = DO_REFERENCES.ALL; |
|
| 38 |
private boolean doTaxa = true; |
|
| 39 |
private boolean doRelTaxa = true; |
|
| 40 |
|
|
| 35 | 41 |
|
| 36 | 42 |
public static PesiExportConfigurator NewInstance(Source pesiDestination, ICdmDataSource source) {
|
| 37 | 43 |
return new PesiExportConfigurator(pesiDestination, source); |
| ... | ... | |
| 120 | 126 |
public void setDoNameFacts(boolean doNameFacts) {
|
| 121 | 127 |
this.doNameFacts = doNameFacts; |
| 122 | 128 |
} |
| 129 |
|
|
| 130 |
|
|
| 131 |
|
|
| 132 |
public DO_REFERENCES getDoReferences() {
|
|
| 133 |
return doReferences; |
|
| 134 |
} |
|
| 135 |
public void setDoReferences(DO_REFERENCES doReferences) {
|
|
| 136 |
this.doReferences = doReferences; |
|
| 137 |
} |
|
| 138 |
|
|
| 139 |
public boolean isDoTaxa() {
|
|
| 140 |
return doTaxa; |
|
| 141 |
} |
|
| 142 |
public void setDoTaxa(boolean doTaxa) {
|
|
| 143 |
this.doTaxa = doTaxa; |
|
| 144 |
} |
|
| 145 |
|
|
| 146 |
public boolean isDoRelTaxa() {
|
|
| 147 |
return doRelTaxa; |
|
| 148 |
} |
|
| 149 |
public void setDoRelTaxa(boolean doRelTaxa) {
|
|
| 150 |
this.doRelTaxa = doRelTaxa; |
|
| 151 |
} |
|
| 152 |
|
|
| 153 |
|
|
| 123 | 154 |
|
| 124 | 155 |
|
| 125 | 156 |
|
Also available in: Unified diff
removing all doXXX from IImportConfigurator