Revision 81bba387
Added by Andreas Müller almost 12 years ago
| .gitattributes | ||
|---|---|---|
| 46 | 46 |
app-import/src/main/java/eu/etaxonomy/cdm/app/jaxb/CdmDiffActivator.java -text |
| 47 | 47 |
app-import/src/main/java/eu/etaxonomy/cdm/app/jaxb/JaxbExportActivator.java -text |
| 48 | 48 |
app-import/src/main/java/eu/etaxonomy/cdm/app/jaxb/JaxbImportActivator.java -text |
| 49 |
app-import/src/main/java/eu/etaxonomy/cdm/app/pesi/ErmsActivator.java -text |
|
| 50 |
app-import/src/main/java/eu/etaxonomy/cdm/app/pesi/EuroMedActivator.java -text |
|
| 51 |
app-import/src/main/java/eu/etaxonomy/cdm/app/pesi/FaunaEuropaeaActivator.java -text |
|
| 52 |
app-import/src/main/java/eu/etaxonomy/cdm/app/pesi/FaunaEuropaeaSources.java -text |
|
| 53 |
app-import/src/main/java/eu/etaxonomy/cdm/app/pesi/PesiDestinations.java -text |
|
| 54 |
app-import/src/main/java/eu/etaxonomy/cdm/app/pesi/PesiExportActivator.java -text |
|
| 55 |
app-import/src/main/java/eu/etaxonomy/cdm/app/pesi/erms/ErmsActivator.java -text |
|
| 56 |
app-import/src/main/java/eu/etaxonomy/cdm/app/pesi/merging/FaunaEuErmsFindIdenticalNamesActivator.java -text |
|
| 57 |
app-import/src/main/java/eu/etaxonomy/cdm/app/pesi/merging/FaunaEuErmsMergeActivator.java -text |
|
| 58 | 49 |
app-import/src/main/java/eu/etaxonomy/cdm/app/pilotOutputHtml/SimpleDescriptionOutput.java -text |
| 59 | 50 |
app-import/src/main/java/eu/etaxonomy/cdm/app/references/EndNoteImportActivator.java -text |
| 60 | 51 |
app-import/src/main/java/eu/etaxonomy/cdm/app/sdd/AnthuriumActivator.java -text |
| app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/AlgaTerraActivator.java | ||
|---|---|---|
| 19 | 19 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| 20 | 20 |
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator; |
| 21 | 21 |
import eu.etaxonomy.cdm.io.common.CdmDefaultImport; |
| 22 |
import eu.etaxonomy.cdm.io.common.Source; |
|
| 23 | 22 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK; |
| 24 | 23 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES; |
| 25 |
import eu.etaxonomy.cdm.model.common.ISourceable;
|
|
| 24 |
import eu.etaxonomy.cdm.io.common.Source;
|
|
| 26 | 25 |
import eu.etaxonomy.cdm.model.description.Feature; |
| 27 | 26 |
import eu.etaxonomy.cdm.model.description.FeatureNode; |
| 28 | 27 |
import eu.etaxonomy.cdm.model.description.FeatureTree; |
| 29 | 28 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| 30 |
import eu.etaxonomy.cdm.model.name.ZoologicalName; |
|
| 31 | 29 |
|
| 32 | 30 |
|
| 33 | 31 |
/** |
| app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/CampanulaceaeActivator.java | ||
|---|---|---|
| 13 | 13 |
|
| 14 | 14 |
import org.apache.log4j.Logger; |
| 15 | 15 |
|
| 16 |
import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
|
| 17 | 16 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration; |
| 18 | 17 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 18 |
import eu.etaxonomy.cdm.app.berlinModelImport.TreeCreator; |
|
| 19 | 19 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 20 | 20 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| 21 | 21 |
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator; |
| app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/IldisActivator.java | ||
|---|---|---|
| 15 | 15 |
|
| 16 | 16 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration; |
| 17 | 17 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 18 |
import eu.etaxonomy.cdm.app.pesi.FaunaEuropaeaActivator; |
|
| 19 | 18 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 20 | 19 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| 21 | 20 |
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator; |
| ... | ... | |
| 36 | 35 |
*/ |
| 37 | 36 |
public class IldisActivator {
|
| 38 | 37 |
@SuppressWarnings("unused")
|
| 39 |
private static final Logger logger = Logger.getLogger(FaunaEuropaeaActivator.class);
|
|
| 38 |
private static final Logger logger = Logger.getLogger(IldisActivator.class);
|
|
| 40 | 39 |
//database validation status (create, update, validate ...) |
| 41 | 40 |
static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE; |
| 42 | 41 |
static final Source berlinModelSource = BerlinModelSources.ILDIS(); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/SalvadorActivator.java | ||
|---|---|---|
| 14 | 14 |
|
| 15 | 15 |
import org.apache.log4j.Logger; |
| 16 | 16 |
|
| 17 |
import eu.etaxonomy.cdm.app.berlinModelImport.BerlinModelSources; |
|
| 17 | 18 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 18 | 19 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 19 | 20 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/TreeCreator.java | ||
|---|---|---|
| 15 | 15 |
|
| 16 | 16 |
import org.apache.log4j.Logger; |
| 17 | 17 |
|
| 18 |
import eu.etaxonomy.cdm.app.berlinModelImport.TreeCreator; |
|
| 18 | 19 |
import eu.etaxonomy.cdm.model.description.Feature; |
| 19 | 20 |
import eu.etaxonomy.cdm.model.description.FeatureNode; |
| 20 | 21 |
import eu.etaxonomy.cdm.model.description.FeatureTree; |
| app-import/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 |
|
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| 12 |
import java.util.UUID; |
|
| 13 |
|
|
| 14 |
import org.apache.log4j.Logger; |
|
| 15 |
|
|
| 16 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration; |
|
| 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.berlinModel.in.BerlinModelImportConfigurator; |
|
| 21 |
import eu.etaxonomy.cdm.io.common.CdmDefaultImport; |
|
| 22 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK; |
|
| 23 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES; |
|
| 24 |
import eu.etaxonomy.cdm.io.common.Source; |
|
| 25 |
import eu.etaxonomy.cdm.model.common.ISourceable; |
|
| 26 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
|
| 27 |
import eu.etaxonomy.cdm.model.name.ZoologicalName; |
|
| 28 |
|
|
| 29 |
|
|
| 30 |
/** |
|
| 31 |
* TODO add the following to a wiki page: |
|
| 32 |
* HINT: If you are about to import into a mysql data base running under windows and if you wish to dump and restore the resulting data base under another operation systen |
|
| 33 |
* you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names. |
|
| 34 |
* |
|
| 35 |
* |
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| 36 |
* @author a.mueller |
|
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* |
|
| 38 |
*/ |
|
| 39 |
public class ErmsActivator {
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private static final Logger logger = Logger.getLogger(ErmsActivator.class); |
|
| 41 |
|
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| 42 |
//database validation status (create, update, validate ...) |
|
| 43 |
static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE; |
|
| 44 |
static final Source berlinModelSource = FaunaEuropaeaSources.PESI_ERMS(); |
|
| 45 |
static final ICdmDataSource cdmDestination = CdmDestinations.cdm_pesi_erms(); |
|
| 46 |
static final UUID treeUuid = UUID.fromString("8bd27d84-fd4f-4bfa-bde0-3e6b7311b334");
|
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| 47 |
static final int sourceSecId = 500000; |
|
| 48 |
static final UUID featureTreeUuid = UUID.fromString("33cbf7a8-0c47-4d47-bd11-b7d77a38d0f6");
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static final Object[] featureKeyList = new Integer[]{1,4,5,10,11,12,13,14, 249, 250, 251, 252, 253};
|
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| 50 |
|
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//check - import |
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static final CHECK check = CHECK.CHECK_AND_IMPORT; |
|
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|
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| 54 |
|
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//NomeclaturalCode |
|
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static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICZN; |
|
| 57 |
|
|
| 58 |
//ignore null |
|
| 59 |
static final boolean ignoreNull = true; |
|
| 60 |
|
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// ***************** ALL ************************************************// |
|
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|
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| 63 |
//authors |
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static final boolean doAuthors = true; |
|
| 65 |
//references |
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static final DO_REFERENCES doReferences = DO_REFERENCES.CONCEPT_REFERENCES; |
|
| 67 |
//names |
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static final boolean doTaxonNames = false; |
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static final boolean doRelNames = true; |
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static final boolean doNameStatus = true; |
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static final boolean doTypes = true; |
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static final boolean doNameFacts = true; |
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|
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//taxa |
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static final boolean doTaxa = true; |
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static final boolean doRelTaxa = true; |
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static final boolean doFacts = true; |
|
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static final boolean doOccurences = false; |
|
| 79 |
|
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| 80 |
|
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//******************** NONE ***************************************// |
|
| 82 |
|
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// //authors |
|
| 84 |
// static final boolean doAuthors = true; |
|
| 85 |
// //references |
|
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// static final DO_REFERENCES doReferences = DO_REFERENCES.NONE; |
|
| 87 |
// //names |
|
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// static final boolean doTaxonNames = false; |
|
| 89 |
// static final boolean doRelNames = false; |
|
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// static final boolean doNameStatus = false; |
|
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// static final boolean doTypes = false; |
|
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// static final boolean doNameFacts = false; |
|
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// |
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// //taxa |
|
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// static final boolean doTaxa = true; |
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// static final boolean doRelTaxa = false; |
|
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// static final boolean doFacts = false; |
|
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// static final boolean doOccurences = false; |
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// |
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/** |
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* @param args |
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*/ |
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public static void main(String[] args) {
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System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") ...");
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//make BerlinModel Source |
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Source source = berlinModelSource; |
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ICdmDataSource destination = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination; |
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BerlinModelImportConfigurator bmImportConfigurator = BerlinModelImportConfigurator.NewInstance(source, destination); |
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bmImportConfigurator.setClassificationUuid(treeUuid); |
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bmImportConfigurator.setSourceSecId(sourceSecId); |
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bmImportConfigurator.setNomenclaturalCode(nomenclaturalCode); |
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bmImportConfigurator.setIgnoreNull(ignoreNull); |
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bmImportConfigurator.setDoAuthors(doAuthors); |
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bmImportConfigurator.setDoReferences(doReferences); |
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bmImportConfigurator.setDoTaxonNames(doTaxonNames); |
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bmImportConfigurator.setDoRelNames(doRelNames); |
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bmImportConfigurator.setDoNameStatus(doNameStatus); |
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bmImportConfigurator.setDoTypes(doTypes); |
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bmImportConfigurator.setDoNameFacts(doNameFacts); |
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bmImportConfigurator.setDoTaxa(doTaxa); |
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bmImportConfigurator.setDoRelTaxa(doRelTaxa); |
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bmImportConfigurator.setDoFacts(doFacts); |
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bmImportConfigurator.setDoOccurrence(doOccurences); |
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bmImportConfigurator.setDbSchemaValidation(hbm2dll); |
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bmImportConfigurator.setCheck(check); |
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// invoke import |
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CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>(); |
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bmImport.invoke(bmImportConfigurator); |
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if (bmImportConfigurator.getCheck().equals(CHECK.CHECK_AND_IMPORT) || bmImportConfigurator.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK) ){
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ICdmApplicationConfiguration app = bmImport.getCdmAppController(); |
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ISourceable obj = app.getCommonService().getSourcedObjectByIdInSource(ZoologicalName.class, "1000027", null); |
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logger.info(obj); |
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// //make feature tree |
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// FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, bmImportConfigurator.getFeatureMap(), featureKeyList); |
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// app = bmImport.getCdmAppController(); |
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// app.getFeatureTreeService().saveOrUpdate(tree); |
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} |
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System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
|
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} |
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} |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/pesi/EuroMedActivator.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 |
|
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| 10 |
package eu.etaxonomy.cdm.app.pesi; |
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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.api.application.ICdmApplicationConfiguration; |
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import eu.etaxonomy.cdm.app.berlinModelImport.BerlinModelSources; |
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import eu.etaxonomy.cdm.app.berlinModelImport.TreeCreator; |
|
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import eu.etaxonomy.cdm.app.common.CdmDestinations; |
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import eu.etaxonomy.cdm.database.DbSchemaValidation; |
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import eu.etaxonomy.cdm.database.ICdmDataSource; |
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator; |
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import eu.etaxonomy.cdm.io.common.CdmDefaultImport; |
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK; |
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES; |
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR; |
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import eu.etaxonomy.cdm.io.common.Source; |
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import eu.etaxonomy.cdm.model.description.Feature; |
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import eu.etaxonomy.cdm.model.description.FeatureNode; |
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import eu.etaxonomy.cdm.model.description.FeatureTree; |
|
| 31 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
|
| 32 |
|
|
| 33 |
|
|
| 34 |
/** |
|
| 35 |
* TODO add the following to a wiki page: |
|
| 36 |
* HINT: If you are about to import into a mysql data base running under windows and if you wish to dump and restore the resulting data bas under another operation systen |
|
| 37 |
* you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names. |
|
| 38 |
* |
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| 39 |
* |
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| 40 |
* @author a.mueller |
|
| 41 |
* |
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*/ |
|
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public class EuroMedActivator {
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@SuppressWarnings("unused")
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| 45 |
private static final Logger logger = Logger.getLogger(EuroMedActivator.class); |
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|
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| 47 |
//database validation status (create, update, validate ...) |
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static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE; |
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// static final Source berlinModelSource = BerlinModelSources.euroMed(); |
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static final Source berlinModelSource = BerlinModelSources.EDIT_CICHORIEAE(); |
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// static final Source berlinModelSource = BerlinModelSources.EDIT_Diptera(); |
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|
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static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_andreasM(); |
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static final int sourceSecId = 7000000; //500000 |
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| 55 |
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static final UUID classificationUuid = UUID.fromString("314a68f9-8449-495a-91c2-92fde8bcf344");
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| 57 |
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| 58 |
static final UUID featureTreeUuid = UUID.fromString("6a5e1c2b-ec0d-46c8-9c7d-a2059267ffb7");
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| 59 |
static final Object[] featureKeyList = new Integer[]{1, 31, 4, 98, 41};
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| 60 |
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// set to zero for unlimited nameFacts |
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static final int maximumNumberOfNameFacts = 0; |
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static final int partitionSize = 2000; |
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//check - import |
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static final CHECK check = CHECK.CHECK_AND_IMPORT; |
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| 68 |
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//editor - import |
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| 70 |
static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR; |
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| 72 |
//NomeclaturalCode |
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static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICBN; |
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| 74 |
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| 75 |
//ignore null |
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static final boolean ignoreNull = true; |
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| 77 |
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| 78 |
static boolean useClassification = true; |
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| 79 |
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| 80 |
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| 81 |
// **************** ALL ********************* |
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| 82 |
// |
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| 83 |
static final boolean doUser = true; |
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| 84 |
//authors |
|
| 85 |
static final boolean doAuthors = true; |
|
| 86 |
//references |
|
| 87 |
static final DO_REFERENCES doReferences = DO_REFERENCES.ALL; |
|
| 88 |
//names |
|
| 89 |
static final boolean doTaxonNames = true; |
|
| 90 |
static final boolean doRelNames = true; |
|
| 91 |
static final boolean doNameStatus = true; |
|
| 92 |
static final boolean doTypes = true; |
|
| 93 |
static final boolean doNameFacts = true; |
|
| 94 |
|
|
| 95 |
//taxa |
|
| 96 |
static final boolean doTaxa = true; |
|
| 97 |
static final boolean doRelTaxa = true; |
|
| 98 |
static final boolean doFacts = true; |
|
| 99 |
static final boolean doOccurences = true; |
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| 100 |
static final boolean doCommonNames = true; |
|
| 101 |
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| 102 |
//etc. |
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| 103 |
static final boolean doMarker = true; |
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| 104 |
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| 105 |
|
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| 106 |
// **************** SELECTED ********************* |
|
| 107 |
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| 108 |
// static final boolean doUser = true; |
|
| 109 |
// //authors |
|
| 110 |
// static final boolean doAuthors = false; |
|
| 111 |
// //references |
|
| 112 |
// static final DO_REFERENCES doReferences = DO_REFERENCES.NONE; |
|
| 113 |
// //names |
|
| 114 |
// static final boolean doTaxonNames = false; |
|
| 115 |
// static final boolean doRelNames = false; |
|
| 116 |
// static final boolean doNameStatus = false; |
|
| 117 |
// static final boolean doTypes = false; |
|
| 118 |
// static final boolean doNameFacts = false; |
|
| 119 |
// |
|
| 120 |
// //taxa |
|
| 121 |
// static final boolean doTaxa = false; |
|
| 122 |
// static final boolean doRelTaxa = false; |
|
| 123 |
// static final boolean doFacts = false; |
|
| 124 |
// static final boolean doOccurences = false; |
|
| 125 |
// |
|
| 126 |
// //etc. |
|
| 127 |
// static final boolean doMarker = false; |
|
| 128 |
|
|
| 129 |
|
|
| 130 |
/** |
|
| 131 |
* @param args |
|
| 132 |
*/ |
|
| 133 |
public static void main(String[] args) {
|
|
| 134 |
System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") to " + cdmDestination.getDatabase() + " ...");
|
|
| 135 |
|
|
| 136 |
//make BerlinModel Source |
|
| 137 |
Source source = berlinModelSource; |
|
| 138 |
ICdmDataSource destination = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination; |
|
| 139 |
|
|
| 140 |
BerlinModelImportConfigurator bmImportConfigurator = BerlinModelImportConfigurator.NewInstance(source, destination); |
|
| 141 |
|
|
| 142 |
bmImportConfigurator.setClassificationUuid(classificationUuid); |
|
| 143 |
bmImportConfigurator.setSourceSecId(sourceSecId); |
|
| 144 |
|
|
| 145 |
bmImportConfigurator.setNomenclaturalCode(nomenclaturalCode); |
|
| 146 |
|
|
| 147 |
bmImportConfigurator.setIgnoreNull(ignoreNull); |
|
| 148 |
bmImportConfigurator.setDoAuthors(doAuthors); |
|
| 149 |
bmImportConfigurator.setDoReferences(doReferences); |
|
| 150 |
bmImportConfigurator.setDoTaxonNames(doTaxonNames); |
|
| 151 |
bmImportConfigurator.setDoRelNames(doRelNames); |
|
| 152 |
bmImportConfigurator.setDoNameStatus(doNameStatus); |
|
| 153 |
bmImportConfigurator.setDoTypes(doTypes); |
|
| 154 |
bmImportConfigurator.setDoNameFacts(doNameFacts); |
|
| 155 |
bmImportConfigurator.setUseClassification(useClassification); |
|
| 156 |
|
|
| 157 |
bmImportConfigurator.setDoTaxa(doTaxa); |
|
| 158 |
bmImportConfigurator.setDoRelTaxa(doRelTaxa); |
|
| 159 |
bmImportConfigurator.setDoFacts(doFacts); |
|
| 160 |
bmImportConfigurator.setDoOccurrence(doOccurences); |
|
| 161 |
bmImportConfigurator.setDoCommonNames(doCommonNames); |
|
| 162 |
|
|
| 163 |
bmImportConfigurator.setDoMarker(doMarker); |
|
| 164 |
bmImportConfigurator.setDoUser(doUser); |
|
| 165 |
bmImportConfigurator.setEditor(editor); |
|
| 166 |
bmImportConfigurator.setDbSchemaValidation(hbm2dll); |
|
| 167 |
|
|
| 168 |
// maximum number of name facts to import |
|
| 169 |
bmImportConfigurator.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts); |
|
| 170 |
|
|
| 171 |
bmImportConfigurator.setCheck(check); |
|
| 172 |
bmImportConfigurator.setEditor(editor); |
|
| 173 |
bmImportConfigurator.setRecordsPerTransaction(partitionSize); |
|
| 174 |
|
|
| 175 |
// invoke import |
|
| 176 |
CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>(); |
|
| 177 |
bmImport.invoke(bmImportConfigurator); |
|
| 178 |
|
|
| 179 |
if (doFacts && bmImportConfigurator.getCheck().equals(CHECK.CHECK_AND_IMPORT) || bmImportConfigurator.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK) ){
|
|
| 180 |
ICdmApplicationConfiguration app = bmImport.getCdmAppController(); |
|
| 181 |
|
|
| 182 |
//make feature tree |
|
| 183 |
FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, bmImportConfigurator.getFeatureMap(), featureKeyList); |
|
| 184 |
FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE()); |
|
| 185 |
tree.getRoot().addChild(imageNode); |
|
| 186 |
FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION()); |
|
| 187 |
tree.getRoot().addChild(distributionNode, 2); |
|
| 188 |
app.getFeatureTreeService().saveOrUpdate(tree); |
|
| 189 |
} |
|
| 190 |
|
|
| 191 |
System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
|
|
| 192 |
|
|
| 193 |
} |
|
| 194 |
|
|
| 195 |
} |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/pesi/FaunaEuropaeaActivator.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.ICdmApplicationConfiguration; |
|
| 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.faunaEuropaea.FaunaEuropaeaImportConfigurator; |
|
| 25 |
import eu.etaxonomy.cdm.model.description.Feature; |
|
| 26 |
import eu.etaxonomy.cdm.model.description.FeatureNode; |
|
| 27 |
import eu.etaxonomy.cdm.model.description.FeatureTree; |
|
| 28 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
|
| 29 |
|
|
| 30 |
/** |
|
| 31 |
* @author a.babadshanjan |
|
| 32 |
* @created 12.05.2009 |
|
| 33 |
*/ |
|
| 34 |
public class FaunaEuropaeaActivator {
|
|
| 35 |
@SuppressWarnings("unused")
|
|
| 36 |
private static final Logger logger = Logger.getLogger(FaunaEuropaeaActivator.class); |
|
| 37 |
|
|
| 38 |
static final Source faunaEuropaeaSource = FaunaEuropaeaSources.faunaEu_1_3(); |
|
| 39 |
static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_andreasM(); |
|
| 40 |
|
|
| 41 |
static final int limitSave = 2000; |
|
| 42 |
|
|
| 43 |
// static final CHECK check = CHECK.CHECK_AND_IMPORT; |
|
| 44 |
static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK; |
|
| 45 |
static DbSchemaValidation dbSchemaValidation = DbSchemaValidation.CREATE; |
|
| 46 |
// static DbSchemaValidation dbSchemaValidation = DbSchemaValidation.UPDATE; |
|
| 47 |
// static DbSchemaValidation dbSchemaValidation = DbSchemaValidation.VALIDATE; |
|
| 48 |
static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICZN; |
|
| 49 |
|
|
| 50 |
// ****************** ALL ***************************************** |
|
| 51 |
|
|
| 52 |
// Fauna Europaea to CDM import |
|
| 53 |
static final boolean doAuthors = true; |
|
| 54 |
static final boolean doTaxa = true; |
|
| 55 |
static final boolean doBasionyms = true; |
|
| 56 |
static final boolean doTaxonomicallyIncluded = true; |
|
| 57 |
static final boolean doMisappliedNames = true; |
|
| 58 |
static final boolean doHeterotypicSynonyms = true; |
|
| 59 |
static final DO_REFERENCES doReferences = DO_REFERENCES.ALL; |
|
| 60 |
static final boolean doDistributions = true; |
|
| 61 |
static final boolean makeFeatureTree = true; |
|
| 62 |
// CDM to CDM import |
|
| 63 |
static final boolean doHeterotypicSynonymsForBasionyms = true; |
|
| 64 |
|
|
| 65 |
// ************************ NONE **************************************** // |
|
| 66 |
|
|
| 67 |
// Fauna Europaea to CDM import |
|
| 68 |
// static final boolean doAuthors = false; |
|
| 69 |
// static final boolean doTaxa = false; |
|
| 70 |
// static final boolean doBasionyms = false; |
|
| 71 |
// static final boolean doTaxonomicallyIncluded = false; |
|
| 72 |
// static final boolean doMisappliedNames = false; |
|
| 73 |
// static final boolean doHeterotypicSynonyms = false; |
|
| 74 |
// static final DO_REFERENCES doReferences = DO_REFERENCES.NONE; |
|
| 75 |
// static final boolean doDistributions = false; |
|
| 76 |
// static final boolean makeFeatureTree = false; |
|
| 77 |
// // CDM to CDM import |
|
| 78 |
// static final boolean doHeterotypicSynonymsForBasionyms = false; |
|
| 79 |
|
|
| 80 |
|
|
| 81 |
/** |
|
| 82 |
* @param args |
|
| 83 |
*/ |
|
| 84 |
public static void main(String[] args) {
|
|
| 85 |
|
|
| 86 |
ICdmDataSource destination = cdmDestination; |
|
| 87 |
System.out.println("Starting import from Fauna Europaea (" + faunaEuropaeaSource.getDatabase() + ") to CDM (" + destination.getDatabase() + ")...");
|
|
| 88 |
|
|
| 89 |
// invoke Fauna Europaea to CDM import |
|
| 90 |
|
|
| 91 |
FaunaEuropaeaImportConfigurator fauEuImportConfigurator = |
|
| 92 |
FaunaEuropaeaImportConfigurator.NewInstance(faunaEuropaeaSource, destination); |
|
| 93 |
|
|
| 94 |
fauEuImportConfigurator.setDbSchemaValidation(dbSchemaValidation); |
|
| 95 |
fauEuImportConfigurator.setNomenclaturalCode(nomenclaturalCode); |
|
| 96 |
fauEuImportConfigurator.setCheck(check); |
|
| 97 |
|
|
| 98 |
fauEuImportConfigurator.setDoAuthors(doAuthors); |
|
| 99 |
fauEuImportConfigurator.setDoTaxa(doTaxa); |
|
| 100 |
fauEuImportConfigurator.setDoReferences(doReferences); |
|
| 101 |
fauEuImportConfigurator.setDoOccurrence(doDistributions); |
|
| 102 |
fauEuImportConfigurator.setDoTaxonomicallyIncluded(doTaxonomicallyIncluded); |
|
| 103 |
fauEuImportConfigurator.setDoBasionyms(doBasionyms); |
|
| 104 |
fauEuImportConfigurator.setDoMisappliedNames(doMisappliedNames); |
|
| 105 |
fauEuImportConfigurator.setDoHeterotypicSynonyms(doHeterotypicSynonyms); |
|
| 106 |
fauEuImportConfigurator.setDoHeterotypicSynonymsForBasionyms(doHeterotypicSynonymsForBasionyms); |
|
| 107 |
|
|
| 108 |
CdmDefaultImport<FaunaEuropaeaImportConfigurator> fauEuImport = |
|
| 109 |
new CdmDefaultImport<FaunaEuropaeaImportConfigurator>(); |
|
| 110 |
try {
|
|
| 111 |
fauEuImport.invoke(fauEuImportConfigurator); |
|
| 112 |
} catch (Exception e) {
|
|
| 113 |
System.out.println("ERROR in Fauna Europaea to CDM import");
|
|
| 114 |
e.printStackTrace(); |
|
| 115 |
} |
|
| 116 |
|
|
| 117 |
// invoke CDM to CDM import |
|
| 118 |
|
|
| 119 |
// System.out.println("Starting import from CDM to CDM (" + destination.getDatabase() + ")...");
|
|
| 120 |
// |
|
| 121 |
// CdmImportConfigurator cdmImportConfigurator = |
|
| 122 |
// CdmImportConfigurator.NewInstance(destination, destination); |
|
| 123 |
// |
|
| 124 |
// cdmImportConfigurator.setDbSchemaValidation(DbSchemaValidation.VALIDATE); |
|
| 125 |
// cdmImportConfigurator.setNomenclaturalCode(nomenclaturalCode); |
|
| 126 |
// cdmImportConfigurator.setCheck(check); |
|
| 127 |
// |
|
| 128 |
// cdmImportConfigurator.setDoHeterotypicSynonymsForBasionyms(doHeterotypicSynonymsForBasionyms); |
|
| 129 |
// cdmImportConfigurator.setDoAuthors(false); |
|
| 130 |
// cdmImportConfigurator.setDoTaxa(false); |
|
| 131 |
// cdmImportConfigurator.setDoReferences(DO_REFERENCES.NONE); |
|
| 132 |
// cdmImportConfigurator.setDoOccurrence(false); |
|
| 133 |
// cdmImportConfigurator.setLimitSave(limitSave); |
|
| 134 |
// |
|
| 135 |
// CdmDefaultImport<CdmImportConfigurator> cdmImport = |
|
| 136 |
// new CdmDefaultImport<CdmImportConfigurator>(); |
|
| 137 |
// try {
|
|
| 138 |
// cdmImport.invoke(cdmImportConfigurator); |
|
| 139 |
// } catch (Exception e) {
|
|
| 140 |
// System.out.println("ERROR in CDM to CDM import");
|
|
| 141 |
// e.printStackTrace(); |
|
| 142 |
// } |
|
| 143 |
|
|
| 144 |
//make feature tree |
|
| 145 |
|
|
| 146 |
if (makeFeatureTree == true) {
|
|
| 147 |
FeatureTree featureTree = FeatureTree.NewInstance(UUID.fromString("ff59b9ad-1fb8-4aa4-a8ba-79d62123d0fb"));
|
|
| 148 |
FeatureNode root = featureTree.getRoot(); |
|
| 149 |
|
|
| 150 |
ICdmApplicationConfiguration app = fauEuImport.getCdmAppController(); |
|
| 151 |
Feature citationFeature = (Feature)app.getTermService().find(UUID.fromString("99b2842f-9aa7-42fa-bd5f-7285311e0101"));
|
|
| 152 |
FeatureNode citationNode = FeatureNode.NewInstance(citationFeature); |
|
| 153 |
root.addChild(citationNode); |
|
| 154 |
Feature distributionFeature = (Feature)app.getTermService().find(UUID.fromString("9fc9d10c-ba50-49ee-b174-ce83fc3f80c6"));
|
|
| 155 |
FeatureNode distributionNode = FeatureNode.NewInstance(distributionFeature); |
|
| 156 |
root.addChild(distributionNode); |
|
| 157 |
|
|
| 158 |
app.getFeatureTreeService().saveOrUpdate(featureTree); |
|
| 159 |
} |
|
| 160 |
|
|
| 161 |
System.out.println("End importing Fauna Europaea data");
|
|
| 162 |
} |
|
| 163 |
|
|
| 164 |
} |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/pesi/FaunaEuropaeaSources.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 org.apache.log4j.Logger; |
|
| 13 |
|
|
| 14 |
import eu.etaxonomy.cdm.app.common.ImportUtils; |
|
| 15 |
import eu.etaxonomy.cdm.common.AccountStore; |
|
| 16 |
import eu.etaxonomy.cdm.io.common.Source; |
|
| 17 |
|
|
| 18 |
/** |
|
| 19 |
* @author a.babadshanjan |
|
| 20 |
* @created 12.05.2009 |
|
| 21 |
*/ |
|
| 22 |
public class FaunaEuropaeaSources {
|
|
| 23 |
@SuppressWarnings("unused")
|
|
| 24 |
private static final Logger logger = Logger.getLogger(FaunaEuropaeaSources.class); |
|
| 25 |
|
|
| 26 |
public static Source faunEu(){
|
|
| 27 |
// Fauna Europaea |
|
| 28 |
|
|
| 29 |
String dbms = Source.SQL_SERVER_2008; |
|
| 30 |
|
|
| 31 |
String strServer = "BGBM42"; // "192.168.1.36"; |
|
| 32 |
|
|
| 33 |
String strDB = "FaunEu"; |
|
| 34 |
int port = 1433; |
|
| 35 |
String userName = "WebUser"; |
|
| 36 |
return ImportUtils.makeSource(dbms, strServer, strDB, port, userName, null); |
|
| 37 |
} |
|
| 38 |
|
|
| 39 |
public static Source faunaEu_1_3(){
|
|
| 40 |
// Fauna Europaea |
|
| 41 |
|
|
| 42 |
String dbms = Source.SQL_SERVER_2008; |
|
| 43 |
|
|
| 44 |
String strServer = "BGBM42"; // "192.168.1.36"; |
|
| 45 |
|
|
| 46 |
String strDB = "FaunaEu_1_3"; |
|
| 47 |
int port = 1433; |
|
| 48 |
String userName = "WebUser"; |
|
| 49 |
return ImportUtils.makeSource(dbms, strServer, strDB, port, userName, null); |
|
| 50 |
} |
|
| 51 |
|
|
| 52 |
|
|
| 53 |
public static Source PESI_ERMS(){
|
|
| 54 |
// BerlinModel - Pesi-ERMS |
|
| 55 |
String dbms = Source.SQL_SERVER_2008; |
|
| 56 |
String strServer = "BGBM42"; |
|
| 57 |
String strDB = "ERMS"; |
|
| 58 |
int port = 1433; |
|
| 59 |
String userName = "WebUser"; |
|
| 60 |
return makeSource(dbms, strServer, strDB, port, userName, null); |
|
| 61 |
} |
|
| 62 |
|
|
| 63 |
|
|
| 64 |
/** |
|
| 65 |
* Initializes the source. |
|
| 66 |
* @param dbms |
|
| 67 |
* @param strServer |
|
| 68 |
* @param strDB |
|
| 69 |
* @param port |
|
| 70 |
* @param userName |
|
| 71 |
* @param pwd |
|
| 72 |
* @return the source |
|
| 73 |
*/ |
|
| 74 |
private static Source makeSource(String dbms, String strServer, String strDB, int port, String userName, String pwd ){
|
|
| 75 |
//establish connection |
|
| 76 |
Source source = null; |
|
| 77 |
source = new Source(dbms, strServer, strDB); |
|
| 78 |
source.setPort(port); |
|
| 79 |
|
|
| 80 |
pwd = AccountStore.readOrStorePassword(dbms, strServer, userName, pwd); |
|
| 81 |
source.setUserAndPwd(userName, pwd); |
|
| 82 |
// write pwd to account store |
|
| 83 |
return source; |
|
| 84 |
} |
|
| 85 |
|
|
| 86 |
|
|
| 87 |
} |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/pesi/PesiDestinations.java | ||
|---|---|---|
| 1 |
// $Id$ |
|
| 2 |
/** |
|
| 3 |
* Copyright (C) 2009 EDIT |
|
| 4 |
* European Distributed Institute of Taxonomy |
|
| 5 |
* http://www.e-taxonomy.eu |
|
| 6 |
* |
|
| 7 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
|
| 8 |
* See LICENSE.TXT at the top of this package for the full license terms. |
|
| 9 |
*/ |
|
| 10 |
package eu.etaxonomy.cdm.app.pesi; |
|
| 11 |
|
|
| 12 |
|
|
| 13 |
import org.apache.log4j.Logger; |
|
| 14 |
|
|
| 15 |
import eu.etaxonomy.cdm.common.AccountStore; |
|
| 16 |
import eu.etaxonomy.cdm.io.common.Source; |
|
| 17 |
|
|
| 18 |
/** |
|
| 19 |
* @author e.-m.lee |
|
| 20 |
* @date 16.02.2010 |
|
| 21 |
* |
|
| 22 |
*/ |
|
| 23 |
public class PesiDestinations {
|
|
| 24 |
@SuppressWarnings("unused")
|
|
| 25 |
private static final Logger logger = Logger.getLogger(PesiDestinations.class); |
|
| 26 |
|
|
| 27 |
public static Source pesi_test_local_PESI_V10(){
|
|
| 28 |
// CDM - PESI |
|
| 29 |
String dbms = Source.SQL_SERVER_2008; |
|
| 30 |
String strServer = "C206\\MSSQLSERVER2"; |
|
| 31 |
String strDB = "PESI_V10"; |
|
| 32 |
int port = 1433; |
|
| 33 |
String userName = "sa"; |
|
| 34 |
String pwd = "bewell"; |
|
| 35 |
return makeSource(dbms, strServer, strDB, port, userName, pwd); |
|
| 36 |
} |
|
| 37 |
|
|
| 38 |
public static Source pesi_test_local_CDM_DWH_FaEu(){
|
|
| 39 |
// CDM - PESI |
|
| 40 |
String dbms = Source.SQL_SERVER_2008; |
|
| 41 |
String strServer = "C206\\MSSQLSERVER2"; |
|
| 42 |
String strDB = "CDM_DWH_FaEu"; |
|
| 43 |
int port = 1433; |
|
| 44 |
String userName = "sa"; |
|
| 45 |
String pwd = "bewell"; |
|
| 46 |
return makeSource(dbms, strServer, strDB, port, userName, pwd); |
|
| 47 |
} |
|
| 48 |
|
|
| 49 |
public static Source pesi_test_local_PESI_V11(){
|
|
| 50 |
// CDM - PESI |
|
| 51 |
String dbms = Source.SQL_SERVER_2008; |
|
| 52 |
String strServer = "C206\\MSSQLSERVER2"; |
|
| 53 |
String strDB = "PESI_V11_LOCAL"; |
|
| 54 |
int port = 1433; |
|
| 55 |
String userName = "sa"; |
|
| 56 |
String pwd = "bewell"; |
|
| 57 |
return makeSource(dbms, strServer, strDB, port, userName, pwd); |
|
| 58 |
} |
|
| 59 |
|
|
| 60 |
public static Source pesi_test_bgbm42_CDM_DWH_FaEu(){
|
|
| 61 |
// CDM - PESI |
|
| 62 |
String dbms = Source.SQL_SERVER_2008; |
|
| 63 |
String strServer = "BGBM42"; |
|
| 64 |
String strDB = "CDM_DWH_FaEu"; |
|
| 65 |
int port = 1433; |
|
| 66 |
String userName = "WebUser"; |
|
| 67 |
String pwd = ""; |
|
| 68 |
return makeSource(dbms, strServer, strDB, port, userName, pwd); |
|
| 69 |
} |
|
| 70 |
|
|
| 71 |
public static Source pesi_test_bgbm42_PESI_V11(){
|
|
| 72 |
// CDM - PESI |
|
| 73 |
String dbms = Source.SQL_SERVER_2008; |
|
| 74 |
String strServer = "BGBM42"; |
|
| 75 |
String strDB = "PESI_v11"; |
|
| 76 |
int port = 1433; |
|
| 77 |
String userName = "WebUser"; |
|
| 78 |
String pwd = ""; |
|
| 79 |
return makeSource(dbms, strServer, strDB, port, userName, pwd); |
|
| 80 |
} |
|
| 81 |
|
|
| 82 |
/** |
|
| 83 |
* Initializes the source. |
|
| 84 |
* @param dbms |
|
| 85 |
* @param strServer |
|
| 86 |
* @param strDB |
|
| 87 |
* @param port |
|
| 88 |
* @param userName |
|
| 89 |
* @param pwd |
|
| 90 |
* @return the source |
|
| 91 |
*/ |
|
| 92 |
private static Source makeSource(String dbms, String strServer, String strDB, int port, String userName, String pwd ){
|
|
| 93 |
//establish connection |
|
| 94 |
Source source = null; |
|
| 95 |
source = new Source(dbms, strServer, strDB); |
|
| 96 |
source.setPort(port); |
|
| 97 |
|
|
| 98 |
pwd = AccountStore.readOrStorePassword(dbms, strServer, userName, pwd); |
|
| 99 |
source.setUserAndPwd(userName, pwd); |
|
| 100 |
// write pwd to account store |
|
| 101 |
return source; |
|
| 102 |
} |
|
| 103 |
|
|
| 104 |
} |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/pesi/PesiExportActivator.java | ||
|---|---|---|
| 1 |
// $Id$ |
|
| 2 |
/** |
|
| 3 |
* Copyright (C) 2009 EDIT |
|
| 4 |
* European Distributed Institute of Taxonomy |
|
| 5 |
* http://www.e-taxonomy.eu |
|
| 6 |
* |
|
| 7 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
|
| 8 |
* See LICENSE.TXT at the top of this package for the full license terms. |
|
| 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.app.common.CdmDestinations; |
|
| 17 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
|
| 18 |
import eu.etaxonomy.cdm.io.common.CdmDefaultExport; |
|
| 19 |
import eu.etaxonomy.cdm.io.common.IExportConfigurator.CHECK; |
|
| 20 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES; |
|
| 21 |
import eu.etaxonomy.cdm.io.common.Source; |
|
| 22 |
import eu.etaxonomy.cdm.io.pesi.out.PesiExportConfigurator; |
|
| 23 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
|
| 24 |
|
|
| 25 |
/** |
|
| 26 |
* @author a.mueller |
|
| 27 |
* @author e.-m.lee |
|
| 28 |
* @date 16.02.2010 |
|
| 29 |
* |
|
| 30 |
*/ |
|
| 31 |
public class PesiExportActivator {
|
|
| 32 |
|
|
| 33 |
@SuppressWarnings("unused")
|
|
| 34 |
private static final Logger logger = Logger.getLogger(PesiExportActivator.class); |
|
| 35 |
|
|
| 36 |
//database validation status (create, update, validate ...) |
|
| 37 |
static final Source pesiDestination = PesiDestinations.pesi_test_local_CDM_DWH_FaEu(); |
|
| 38 |
static final ICdmDataSource cdmSource = CdmDestinations.cdm_test_jaxb(); |
|
| 39 |
static final UUID secUuid = UUID.fromString("d03ef02a-f226-4cb1-bdb4-f6c154f08a34");
|
|
| 40 |
static final int sourceSecId = 7331; |
|
| 41 |
static final int isHomotypicId = 72; |
|
| 42 |
static boolean useClassification = true; |
|
| 43 |
|
|
| 44 |
//check - export |
|
| 45 |
static final CHECK check = CHECK.EXPORT_WITHOUT_CHECK; |
|
| 46 |
|
|
| 47 |
//NomeclaturalCode |
|
| 48 |
static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICBN; |
|
| 49 |
|
|
| 50 |
// ****************** ALL ***************************************** |
|
| 51 |
|
|
| 52 |
//authors |
|
| 53 |
static final boolean doAuthors = true; |
|
| 54 |
//references |
|
| 55 |
static final DO_REFERENCES doReferences = DO_REFERENCES.ALL; |
|
| 56 |
//names |
|
| 57 |
static final boolean doTaxonNames = true; |
|
| 58 |
static final boolean doTypes = false; |
|
| 59 |
static final boolean doNameFacts = false; |
|
| 60 |
|
|
| 61 |
//taxa |
|
| 62 |
static final boolean doTaxa = true; |
|
| 63 |
static final boolean doRelTaxa = true; |
|
| 64 |
static final boolean doFacts = true; |
|
| 65 |
static final boolean doOccurences = true; |
|
| 66 |
|
|
| 67 |
// ************************ NONE **************************************** // |
|
| 68 |
|
|
| 69 |
// //authors |
|
| 70 |
// static final boolean doAuthors = false; |
|
| 71 |
// static final boolean doAuthorTeams = false; |
|
| 72 |
// //references |
|
| 73 |
// static final DO_REFERENCES doReferences = DO_REFERENCES.ALL; |
|
| 74 |
// //names |
|
| 75 |
// static final boolean doTaxonNames = true; |
|
| 76 |
// static final boolean doTypes = false; |
|
| 77 |
// static final boolean doNameFacts = false; |
|
| 78 |
// |
|
| 79 |
// //taxa |
|
| 80 |
// static final boolean doTaxa = false; |
|
| 81 |
// static final boolean doRelTaxa = false; |
|
| 82 |
// static final boolean doFacts = false; |
|
| 83 |
// static final boolean doOccurences = false; |
|
| 84 |
// |
|
| 85 |
|
|
| 86 |
public boolean doExport(ICdmDataSource source){
|
|
| 87 |
System.out.println("Start export to PESI ("+ pesiDestination.getDatabase() + ") ...");
|
|
| 88 |
|
|
| 89 |
//make PESI Source |
|
| 90 |
Source destination = pesiDestination; |
|
| 91 |
|
|
| 92 |
PesiExportConfigurator pesiExportConfigurator = PesiExportConfigurator.NewInstance(destination, source); |
|
| 93 |
|
|
| 94 |
pesiExportConfigurator.setDoNameFacts(doNameFacts); |
|
| 95 |
|
|
| 96 |
pesiExportConfigurator.setDoTaxa(doTaxa); |
|
| 97 |
pesiExportConfigurator.setDoRelTaxa(doRelTaxa); |
|
| 98 |
pesiExportConfigurator.setDoFacts(doFacts); |
|
| 99 |
pesiExportConfigurator.setDoOccurrence(doOccurences); |
|
| 100 |
// pesiExportConfigurator.setIsHomotypicId(isHomotypicId); |
|
| 101 |
pesiExportConfigurator.setCheck(check); |
|
| 102 |
pesiExportConfigurator.setUseClassification(useClassification); |
|
| 103 |
|
|
| 104 |
// invoke export |
|
| 105 |
CdmDefaultExport<PesiExportConfigurator> pesiExport = new CdmDefaultExport<PesiExportConfigurator>(); |
|
| 106 |
boolean result = pesiExport.invoke(pesiExportConfigurator); |
|
| 107 |
|
|
| 108 |
System.out.println("End export to PESI ("+ destination.getDatabase() + ")..." + (result? "(successful)":"(with errors)"));
|
|
| 109 |
return result; |
|
| 110 |
} |
|
| 111 |
|
|
| 112 |
/** |
|
| 113 |
* @param args |
|
| 114 |
*/ |
|
| 115 |
public static void main(String[] args) {
|
|
| 116 |
PesiExportActivator ex = new PesiExportActivator(); |
|
| 117 |
ICdmDataSource source = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmSource; |
|
| 118 |
|
|
| 119 |
ex.doExport(source); |
|
| 120 |
} |
|
| 121 |
|
|
| 122 |
} |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/pesi/erms/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.erms; |
|
| 11 |
|
|
| 12 |
import java.util.UUID; |
|
| 13 |
|
|
| 14 |
import org.apache.log4j.Logger; |
|
| 15 |
|
|
| 16 |
import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration; |
|
| 17 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
|
| 18 |
import eu.etaxonomy.cdm.app.pesi.FaunaEuropaeaSources; |
|
| 19 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
|
| 20 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
|
| 21 |
import eu.etaxonomy.cdm.io.common.CdmDefaultImport; |
|
| 22 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK; |
|
| 23 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES; |
|
| 24 |
import eu.etaxonomy.cdm.io.common.Source; |
|
| 25 |
import eu.etaxonomy.cdm.io.pesi.erms.ErmsImportConfigurator; |
|
| 26 |
import eu.etaxonomy.cdm.model.common.ISourceable; |
|
| 27 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
|
| 28 |
import eu.etaxonomy.cdm.model.name.ZoologicalName; |
|
| 29 |
|
|
| 30 |
|
|
| 31 |
/** |
|
| 32 |
* TODO add the following to a wiki page: |
|
| 33 |
* HINT: If you are about to import into a mysql data base running under windows and if you wish to dump and restore the resulting data base under another operation systen |
|
| 34 |
* you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names. |
|
| 35 |
* |
|
| 36 |
* |
|
| 37 |
* @author a.mueller |
|
| 38 |
* |
|
| 39 |
*/ |
|
| 40 |
public class ErmsActivator {
|
|
| 41 |
private static final Logger logger = Logger.getLogger(ErmsActivator.class); |
|
| 42 |
|
|
| 43 |
//database validation status (create, update, validate ...) |
|
| 44 |
static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE; |
|
| 45 |
static final Source ermsSource = FaunaEuropaeaSources.PESI_ERMS(); |
|
| 46 |
static final ICdmDataSource cdmDestination = CdmDestinations.localH2Erms(); |
|
| 47 |
static final UUID treeUuid = UUID.fromString("8bd27d84-fd4f-4bfa-bde0-3e6b7311b334");
|
|
| 48 |
static final UUID featureTreeUuid = UUID.fromString("33cbf7a8-0c47-4d47-bd11-b7d77a38d0f6");
|
|
| 49 |
//static final Object[] featureKeyList = new Integer[]{1,4,5,10,11,12,13,14, 249, 250, 251, 252, 253};
|
|
| 50 |
|
|
| 51 |
//check - import |
|
| 52 |
static final CHECK check = CHECK.CHECK_AND_IMPORT; |
|
| 53 |
|
|
| 54 |
static final int partitionSize = 2000; |
|
| 55 |
|
|
| 56 |
|
|
| 57 |
//NomeclaturalCode |
|
| 58 |
static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICZN; |
|
| 59 |
|
|
| 60 |
//ignore null |
|
| 61 |
static final boolean ignoreNull = true; |
|
| 62 |
|
|
| 63 |
// ***************** ALL ************************************************// |
|
| 64 |
|
|
| 65 |
//references |
|
| 66 |
static final DO_REFERENCES doReferences = DO_REFERENCES.ALL; |
|
| 67 |
|
|
| 68 |
//taxa |
|
| 69 |
static final boolean doTaxa = true; |
|
| 70 |
static final boolean doRelTaxa = true; |
|
| 71 |
static final boolean doLinks = true; |
|
| 72 |
static final boolean doOccurences = true; |
|
| 73 |
static final boolean doImages = true; |
|
| 74 |
|
|
| 75 |
|
|
| 76 |
//******************** NONE ***************************************// |
|
| 77 |
|
|
| 78 |
|
|
| 79 |
// //references |
|
| 80 |
// static final DO_REFERENCES doReferences = DO_REFERENCES.NONE; |
|
| 81 |
// |
|
| 82 |
// //taxa |
|
| 83 |
// static final boolean doTaxa = false; |
|
| 84 |
// static final boolean doRelTaxa = false; |
|
| 85 |
// static final boolean doLinks = false; |
|
| 86 |
// static final boolean doOccurences = false; |
|
| 87 |
// |
|
| 88 |
|
|
| 89 |
|
|
| 90 |
/** |
|
| 91 |
* @param args |
|
| 92 |
*/ |
|
| 93 |
public static void main(String[] args) {
|
|
| 94 |
System.out.println("Start import from ("+ ermsSource.getDatabase() + ") ...");
|
|
| 95 |
|
|
| 96 |
//make ERMS Source |
|
| 97 |
Source source = ermsSource; |
|
| 98 |
ICdmDataSource destination = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination; |
|
| 99 |
|
|
| 100 |
ErmsImportConfigurator ermsImportConfigurator = ErmsImportConfigurator.NewInstance(source, destination); |
|
| 101 |
|
|
| 102 |
ermsImportConfigurator.setClassificationUuid(treeUuid); |
|
| 103 |
ermsImportConfigurator.setNomenclaturalCode(nomenclaturalCode); |
|
| 104 |
|
|
| 105 |
ermsImportConfigurator.setIgnoreNull(ignoreNull); |
|
| 106 |
ermsImportConfigurator.setDoReferences(doReferences); |
|
| 107 |
|
|
| 108 |
ermsImportConfigurator.setDoTaxa(doTaxa); |
|
| 109 |
ermsImportConfigurator.setDoRelTaxa(doRelTaxa); |
|
| 110 |
ermsImportConfigurator.setDoLinks(doLinks); |
|
| 111 |
ermsImportConfigurator.setDoOccurrence(doOccurences); |
|
| 112 |
ermsImportConfigurator.setDbSchemaValidation(hbm2dll); |
|
| 113 |
|
|
| 114 |
ermsImportConfigurator.setCheck(check); |
|
| 115 |
ermsImportConfigurator.setRecordsPerTransaction(partitionSize); |
|
| 116 |
|
|
| 117 |
// invoke import |
|
| 118 |
CdmDefaultImport<ErmsImportConfigurator> ermsImport = new CdmDefaultImport<ErmsImportConfigurator>(); |
|
| 119 |
ermsImport.invoke(ermsImportConfigurator); |
|
| 120 |
|
|
| 121 |
if (ermsImportConfigurator.getCheck().equals(CHECK.CHECK_AND_IMPORT) || ermsImportConfigurator.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK) ){
|
|
| 122 |
ICdmApplicationConfiguration app = ermsImport.getCdmAppController(); |
|
| 123 |
ISourceable obj = app.getCommonService().getSourcedObjectByIdInSource(ZoologicalName.class, "1000027", null); |
|
| 124 |
logger.info(obj); |
|
| 125 |
|
|
| 126 |
// //make feature tree |
|
| 127 |
// FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, ermsImportConfigurator.getFeatureMap(), featureKeyList); |
|
| 128 |
// app = ermsImport.getCdmAppController(); |
|
| 129 |
// app.getFeatureTreeService().saveOrUpdate(tree); |
|
| 130 |
} |
|
| 131 |
System.out.println("End import from ("+ source.getDatabase() + ")...");
|
|
| 132 |
} |
|
| 133 |
|
|
| 134 |
} |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/pesi/merging/FaunaEuErmsFindIdenticalNamesActivator.java | ||
|---|---|---|
| 1 |
package eu.etaxonomy.cdm.app.pesi.merging; |
|
| 2 |
|
|
| 3 |
import java.io.FileWriter; |
|
| 4 |
import java.io.IOException; |
|
| 5 |
import java.util.ArrayList; |
|
| 6 |
import java.util.Iterator; |
|
| 7 |
import java.util.List; |
|
| 8 |
import java.util.Set; |
|
| 9 |
|
|
| 10 |
import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
|
| 11 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
|
| 12 |
import eu.etaxonomy.cdm.app.util.TestDatabase; |
|
| 13 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
|
| 14 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
|
| 15 |
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper; |
|
| 16 |
import eu.etaxonomy.cdm.io.pesi.merging.FaunaEuErmsMerging; |
|
| 17 |
import eu.etaxonomy.cdm.model.common.IdentifiableSource; |
|
| 18 |
import eu.etaxonomy.cdm.model.name.Rank; |
|
| 19 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
|
| 20 |
import eu.etaxonomy.cdm.model.name.ZoologicalName; |
|
| 21 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
|
| 22 |
import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
|
| 23 |
|
|
| 24 |
public class FaunaEuErmsFindIdenticalNamesActivator {
|
|
| 25 |
|
|
| 26 |
static final ICdmDataSource faunaEuropaeaSource = CdmDestinations.cdm_test_jaxb2(); |
|
| 27 |
//static final ICdmDataSource ermsSource = CdmDestinations.cdm_test_andreasM(); |
|
| 28 |
|
|
| 29 |
//TODO hole aus beiden DB alle TaxonNameBases |
|
| 30 |
|
|
| 31 |
|
|
| 32 |
private CdmApplicationController initDb(ICdmDataSource db) {
|
|
| 33 |
|
|
| 34 |
// Init source DB |
|
| 35 |
CdmApplicationController appCtrInit = null; |
|
| 36 |
|
|
| 37 |
appCtrInit = TestDatabase.initDb(db, DbSchemaValidation.VALIDATE, false); |
|
| 38 |
|
|
| 39 |
return appCtrInit; |
|
| 40 |
} |
|
| 41 |
|
|
| 42 |
|
|
| 43 |
/** |
|
| 44 |
* @param args |
|
| 45 |
*/ |
|
| 46 |
public static void main(String[] args) {
|
|
| 47 |
|
|
| 48 |
FaunaEuErmsFindIdenticalNamesActivator sc = new FaunaEuErmsFindIdenticalNamesActivator(); |
|
| 49 |
|
|
| 50 |
CdmApplicationController appCtrFaunaEu = sc.initDb(faunaEuropaeaSource); |
|
| 51 |
String sFileName = "c:\\test"; |
|
| 52 |
//CdmApplicationController appCtrErms = sc.initDb(ermsSource); |
|
| 53 |
List<String> propertyPaths = new ArrayList<String>(); |
|
| 54 |
propertyPaths.add("sources.*");
|
|
| 55 |
propertyPaths.add("sources.idInSource");
|
|
| 56 |
propertyPaths.add("sources.idNamespace");
|
|
| 57 |
propertyPaths.add("taxonBases.*");
|
|
| 58 |
propertyPaths.add("taxonBases.relationsFromThisTaxon");
|
|
| 59 |
propertyPaths.add("taxonBases.taxonNodes.*");
|
|
| 60 |
propertyPaths.add("taxonBases.taxonNodes.parent.*");
|
|
| 61 |
propertyPaths.add("taxonBases.taxonNodes.parent.taxon.name.*");
|
|
| 62 |
System.err.println("Start getIdenticalNames...");
|
|
| 63 |
List<TaxonNameBase> namesOfIdenticalTaxa = appCtrFaunaEu.getTaxonService().findIdenticalTaxonNameIds(propertyPaths); |
|
| 64 |
//List<UUID> namesOfIdenticalTaxa = appCtrFaunaEu.getTaxonService().findIdenticalTaxonNameIds(propertyPaths); |
|
| 65 |
|
|
| 66 |
System.err.println("first name: " + namesOfIdenticalTaxa.get(0) + " " + namesOfIdenticalTaxa.size());
|
|
| 67 |
TaxonNameBase zooName = (TaxonNameBase)namesOfIdenticalTaxa.get(0); |
|
| 68 |
System.err.println(zooName + " nr of taxa " + namesOfIdenticalTaxa.size()); |
|
| 69 |
//TaxonNameComparator taxComp = new TaxonNameComparator(); |
|
| 70 |
|
|
| 71 |
//Collections.sort(namesOfIdenticalTaxa,taxComp); |
|
| 72 |
System.err.println(namesOfIdenticalTaxa.get(0) + " - " + namesOfIdenticalTaxa.get(1) + " - " + namesOfIdenticalTaxa.get(2)); |
|
| 73 |
List<FaunaEuErmsMerging> mergingObjects = new ArrayList<FaunaEuErmsMerging>(); |
|
| 74 |
FaunaEuErmsMerging mergeObject; |
|
| 75 |
TaxonNameBase faunaEuTaxName; |
|
| 76 |
TaxonNameBase ermsTaxName; |
|
| 77 |
|
|
| 78 |
mergingObjects= sc.createMergeObjects(namesOfIdenticalTaxa, appCtrFaunaEu); |
|
| 79 |
|
|
| 80 |
sc.writeSameNamesdifferentAuthorToCsv(mergingObjects, sFileName + "_authors.csv"); |
|
| 81 |
sc.writeSameNamesdifferentStatusToCsv(mergingObjects, sFileName + "_status.csv"); |
|
| 82 |
sc.writeSameNamesToCsVFile(mergingObjects, sFileName + "_names.csv"); |
|
| 83 |
sc.writeSameNamesdifferentPhylumToCsv(mergingObjects, sFileName + "_phylum.csv"); |
|
| 84 |
|
|
| 85 |
|
|
| 86 |
System.out.println("End merging Fauna Europaea and Erms");
|
|
| 87 |
|
|
| 88 |
} |
|
| 89 |
|
|
| 90 |
private boolean writeSameNamesToCsVFile( |
|
| 91 |
List<FaunaEuErmsMerging> mergingObjects, String string) {
|
|
| 92 |
try{
|
|
| 93 |
FileWriter writer = new FileWriter(string); |
|
| 94 |
|
|
| 95 |
//create Header |
|
| 96 |
String firstLine = "same names"; |
|
| 97 |
createHeader(writer, firstLine); |
|
| 98 |
for (FaunaEuErmsMerging merging : mergingObjects){
|
|
| 99 |
writeCsvLine(writer, merging) ; |
|
| 100 |
} |
|
| 101 |
writer.flush(); |
|
| 102 |
writer.close(); |
|
| 103 |
} |
|
| 104 |
catch(IOException e) |
|
| 105 |
{
|
|
| 106 |
return false; |
|
| 107 |
} |
|
| 108 |
return true; |
|
| 109 |
} |
|
| 110 |
|
|
| 111 |
|
|
| 112 |
private boolean writeSameNamesdifferentPhylumToCsv(List<FaunaEuErmsMerging> mergingObjects, String sfileName){
|
|
| 113 |
try |
|
| 114 |
{
|
|
| 115 |
FileWriter writer = new FileWriter(sfileName); |
|
| 116 |
|
|
| 117 |
//create Header |
|
| 118 |
String firstLine = "same names but different phylum"; |
|
| 119 |
createHeader(writer, firstLine); |
|
| 120 |
|
|
| 121 |
//write data |
|
| 122 |
for (FaunaEuErmsMerging merging : mergingObjects){
|
|
| 123 |
//TODO |
|
| 124 |
if ((merging.getPhylumInErms()== null )^ (merging.getPhylumInFaunaEu()== null)){
|
|
| 125 |
writeCsvLine(writer, merging) ; |
|
| 126 |
}else if(!((merging.getPhylumInErms()==null) && (merging.getPhylumInFaunaEu()==null))){
|
|
| 127 |
if(!merging.getPhylumInErms().equals(merging.getPhylumInFaunaEu())){
|
|
| 128 |
writeCsvLine(writer, merging) ; |
|
| 129 |
} |
|
| 130 |
} |
|
| 131 |
} |
|
| 132 |
writer.flush(); |
|
| 133 |
writer.close(); |
|
| 134 |
} |
|
| 135 |
catch(IOException e) |
|
| 136 |
{
|
|
| 137 |
return false; |
|
| 138 |
} |
|
| 139 |
return true; |
|
| 140 |
} |
|
| 141 |
|
|
| 142 |
private boolean writeSameNamesdifferentRankToCsv(List<FaunaEuErmsMerging> mergingObjects, String sfileName){
|
|
| 143 |
try |
|
| 144 |
{
|
|
| 145 |
FileWriter writer = new FileWriter(sfileName); |
|
| 146 |
String firstLine = "same names but different rank"; |
|
| 147 |
//create Header |
|
| 148 |
createHeader(writer, firstLine); |
|
| 149 |
|
|
| 150 |
//write data |
|
| 151 |
for (FaunaEuErmsMerging merging : mergingObjects){
|
|
| 152 |
|
|
| 153 |
if (!merging.getRankInErms().equals(merging.getRankInFaunaEu())){
|
|
| 154 |
writeCsvLine(writer, merging); |
|
| 155 |
} |
|
| 156 |
} |
|
| 157 |
writer.flush(); |
|
| 158 |
writer.close(); |
|
| 159 |
} |
|
| 160 |
catch(IOException e) |
|
| 161 |
{
|
|
| 162 |
return false; |
|
| 163 |
} |
|
| 164 |
return true; |
|
| 165 |
} |
|
| 166 |
|
|
| 167 |
private void createHeader(FileWriter writer, String firstLine) throws IOException{
|
|
| 168 |
writer.append(firstLine); |
|
| 169 |
writer.append('\n');
|
|
| 170 |
writer.append("uuid in Fauna Europaea");
|
|
| 171 |
writer.append(';');
|
|
| 172 |
writer.append("id in Fauna Europaea");
|
|
| 173 |
writer.append(';');
|
|
| 174 |
writer.append("name");
|
|
| 175 |
writer.append(';');
|
|
| 176 |
writer.append("author");
|
|
| 177 |
writer.append(';');
|
|
| 178 |
writer.append("rank");
|
|
| 179 |
writer.append(';');
|
|
| 180 |
writer.append("state");
|
|
| 181 |
writer.append(';');
|
|
| 182 |
writer.append("phylum");
|
|
| 183 |
writer.append(';');
|
|
| 184 |
writer.append("parent");
|
|
| 185 |
writer.append(';');
|
|
| 186 |
writer.append("parent rank");
|
|
| 187 |
writer.append(';');
|
|
| 188 |
|
|
| 189 |
writer.append("uuid in Erms");
|
|
| 190 |
writer.append(';');
|
|
| 191 |
writer.append("id in Erms");
|
|
| 192 |
writer.append(';');
|
|
| 193 |
writer.append("name");
|
|
| 194 |
writer.append(';');
|
|
| 195 |
writer.append("author");
|
|
| 196 |
writer.append(';');
|
|
| 197 |
writer.append("rank");
|
|
| 198 |
writer.append(';');
|
|
| 199 |
writer.append("state");
|
|
| 200 |
writer.append(';');
|
|
| 201 |
writer.append("phylum");
|
|
| 202 |
writer.append(';');
|
|
| 203 |
writer.append("parent");
|
|
| 204 |
writer.append(';');
|
|
| 205 |
writer.append("parent rank");
|
|
| 206 |
writer.append('\n');
|
|
| 207 |
} |
|
| 208 |
|
|
| 209 |
private boolean writeSameNamesdifferentStatusToCsv(List<FaunaEuErmsMerging> mergingObjects, String sfileName){
|
|
| 210 |
try |
|
| 211 |
{
|
|
| 212 |
FileWriter writer = new FileWriter(sfileName); |
|
| 213 |
|
|
| 214 |
//create Header |
|
| 215 |
String firstLine = "same names but different status"; |
|
| 216 |
createHeader(writer, firstLine); |
|
| 217 |
|
|
| 218 |
//write data |
|
| 219 |
for (FaunaEuErmsMerging merging : mergingObjects){
|
|
| 220 |
|
|
| 221 |
if (merging.isStatInErms()^merging.isStatInFaunaEu()){
|
|
| 222 |
writeCsvLine(writer, merging); |
|
| 223 |
} |
|
| 224 |
} |
|
| 225 |
|
|
| 226 |
|
|
| 227 |
writer.flush(); |
|
| 228 |
writer.close(); |
|
| 229 |
} |
|
| 230 |
catch(IOException e) |
|
| 231 |
{
|
|
| 232 |
return false; |
|
| 233 |
} |
|
| 234 |
return true; |
|
| 235 |
} |
|
| 236 |
|
|
| 237 |
private boolean writeSameNamesdifferentAuthorToCsv(List<FaunaEuErmsMerging> mergingObjects, String sfileName){
|
|
| 238 |
try |
|
| 239 |
{
|
|
| 240 |
FileWriter writer = new FileWriter(sfileName); |
|
| 241 |
|
|
| 242 |
//create Header |
|
| 243 |
String firstLine = "same names but different authors"; |
|
| 244 |
createHeader(writer, firstLine); |
|
| 245 |
|
|
| 246 |
//write data |
|
| 247 |
for (FaunaEuErmsMerging merging : mergingObjects){
|
|
| 248 |
|
|
| 249 |
if (!merging.getAuthorInErms().equals(merging.getAuthorInFaunaEu())){
|
|
| 250 |
writeCsvLine(writer, merging); |
|
| 251 |
} |
|
| 252 |
} |
|
| 253 |
|
|
| 254 |
|
|
| 255 |
writer.flush(); |
|
| 256 |
writer.close(); |
|
| 257 |
} |
|
| 258 |
catch(IOException e) |
|
| 259 |
{
|
|
| 260 |
return false; |
|
| 261 |
} |
|
| 262 |
return true; |
|
| 263 |
} |
|
| 264 |
|
|
| 265 |
private void writeCsvLine(FileWriter writer, FaunaEuErmsMerging merging) throws IOException{
|
|
| 266 |
|
|
| 267 |
writer.append(merging.getUuidFaunaEu()); |
|
| 268 |
writer.append(';');
|
|
| 269 |
writer.append(merging.getIdInFaunaEu()); |
|
| 270 |
writer.append(';');
|
|
| 271 |
writer.append(merging.getNameCacheInFaunaEu()); |
|
| 272 |
writer.append(';');
|
|
| 273 |
writer.append(merging.getAuthorInFaunaEu()); |
|
| 274 |
writer.append(';');
|
|
| 275 |
writer.append(merging.getRankInFaunaEu()); |
|
| 276 |
writer.append(';');
|
|
| 277 |
if (merging.isStatInFaunaEu()){
|
|
| 278 |
writer.append("accepted");
|
|
| 279 |
}else{
|
|
| 280 |
writer.append("synonym");
|
|
| 281 |
} |
|
| 282 |
writer.append(';');
|
|
| 283 |
writer.append(merging.getPhylumInFaunaEu()); |
|
| 284 |
writer.append(';');
|
|
| 285 |
writer.append(merging.getParentStringInFaunaEu()); |
|
| 286 |
writer.append(';');
|
|
| 287 |
writer.append(merging.getParentRankStringInFaunaEu()); |
|
| 288 |
writer.append(';');
|
|
| 289 |
|
|
| 290 |
writer.append(merging.getUuidErms()); |
|
| 291 |
writer.append(';');
|
|
| 292 |
writer.append(merging.getIdInErms()); |
|
| 293 |
writer.append(';');
|
|
| 294 |
writer.append(merging.getNameCacheInErms()); |
|
| 295 |
writer.append(';');
|
|
| 296 |
writer.append(merging.getAuthorInErms()); |
|
| 297 |
writer.append(';');
|
|
| 298 |
writer.append(merging.getRankInErms()); |
|
| 299 |
writer.append(';');
|
|
| 300 |
if (merging.isStatInErms()){
|
|
| 301 |
writer.append("accepted");
|
|
| 302 |
}else{
|
|
| 303 |
writer.append("synonym");
|
|
| 304 |
} |
|
| 305 |
|
|
| 306 |
writer.append(';');
|
|
| 307 |
writer.append(merging.getPhylumInErms()); |
|
| 308 |
writer.append(';');
|
|
| 309 |
writer.append(merging.getParentStringInErms()); |
|
| 310 |
writer.append(';');
|
|
| 311 |
writer.append(merging.getParentRankStringInErms()); |
|
| 312 |
writer.append('\n');
|
|
| 313 |
} |
|
| 314 |
|
|
| 315 |
|
|
| 316 |
private List<FaunaEuErmsMerging> createMergeObjects(List<TaxonNameBase> names, CdmApplicationController appCtr){
|
|
| 317 |
|
|
| 318 |
List<FaunaEuErmsMerging> merge = new ArrayList<FaunaEuErmsMerging>(); |
|
| 319 |
ZoologicalName zooName, zooName2; |
|
| 320 |
FaunaEuErmsMerging mergeObject; |
|
| 321 |
String idInSource1; |
|
| 322 |
for (int i = 0; i<names.size()-1; i=i+2){
|
|
| 323 |
zooName = (ZoologicalName)names.get(i); |
|
| 324 |
zooName2 = (ZoologicalName)names.get(i+1); |
|
| 325 |
mergeObject = new FaunaEuErmsMerging(); |
|
| 326 |
//TODO:?berpr?fen, ob die beiden Namen identisch sind und aus unterschiedlichen DB kommen |
|
| 327 |
|
|
| 328 |
//getPhylum |
|
| 329 |
String phylum1 = null; |
|
| 330 |
if (!zooName.getRank().isHigher(Rank.PHYLUM())){
|
|
| 331 |
phylum1 =appCtr.getTaxonService().getPhylumName(zooName); |
|
| 332 |
} |
|
| 333 |
|
|
| 334 |
String phylum2 = null; |
|
| 335 |
if (!zooName2.getRank().isHigher(Rank.PHYLUM())){
|
|
| 336 |
phylum2 = appCtr.getTaxonService().getPhylumName(zooName2); |
|
| 337 |
} |
|
| 338 |
mergeObject.setPhylumInErms(phylum1); |
|
| 339 |
mergeObject.setPhylumInFaunaEu(phylum2); |
|
| 340 |
|
|
| 341 |
//getUuids |
|
| 342 |
mergeObject.setUuidErms(zooName.getUuid().toString()); |
|
| 343 |
mergeObject.setUuidFaunaEu(zooName.getUuid().toString()); |
|
| 344 |
|
|
| 345 |
Iterator sources = zooName.getSources().iterator(); |
|
| 346 |
if (sources.hasNext()){
|
|
| 347 |
IdentifiableSource source = (IdentifiableSource)sources.next(); |
|
| 348 |
idInSource1 = source.getIdInSource(); |
|
| 349 |
mergeObject.setIdInErms(idInSource1); |
|
| 350 |
} |
|
| 351 |
sources = zooName2.getSources().iterator(); |
|
| 352 |
if (sources.hasNext()){
|
|
| 353 |
IdentifiableSource source = (IdentifiableSource)sources.next(); |
|
| 354 |
idInSource1 = source.getIdInSource(); |
|
| 355 |
mergeObject.setIdInFaunaEu(idInSource1); |
|
| 356 |
} |
|
| 357 |
|
|
| 358 |
mergeObject.setNameCacheInErms(zooName.getNameCache()); |
|
| 359 |
mergeObject.setNameCacheInFaunaEu(zooName2.getNameCache()); |
|
| 360 |
|
|
| 361 |
mergeObject.setAuthorInErms(zooName.getAuthorshipCache()); |
|
| 362 |
mergeObject.setAuthorInFaunaEu(zooName2.getAuthorshipCache()); |
|
| 363 |
Set<Taxon> taxa = zooName.getTaxa(); |
|
| 364 |
if (!taxa.isEmpty()){
|
|
| 365 |
mergeObject.setStatInErms(true); |
|
| 366 |
Iterator taxaIterator = taxa.iterator(); |
|
| 367 |
Taxon taxon = null; |
|
| 368 |
while (taxaIterator.hasNext()){
|
|
| 369 |
taxon = (Taxon) taxaIterator.next(); |
|
| 370 |
if (!taxon.isMisapplication()){
|
|
| 371 |
break; |
|
| 372 |
} |
|
| 373 |
} |
|
| 374 |
Set<TaxonNode> nodes = taxon.getTaxonNodes(); |
|
| 375 |
Iterator taxonNodeIterator = nodes.iterator(); |
|
| 376 |
TaxonNode node, parentNode = null; |
|
| 377 |
while (taxonNodeIterator.hasNext()){
|
|
| 378 |
node = (TaxonNode)taxonNodeIterator.next(); |
|
| 379 |
if (!node.isTopmostNode()){
|
|
| 380 |
parentNode = node.getParent(); |
|
| 381 |
} |
|
| 382 |
} |
|
| 383 |
//TODO: ?ndern mit erweitertem Initializer.. |
|
| 384 |
if (parentNode != null){
|
|
| 385 |
ZoologicalName parentName = HibernateProxyHelper.deproxy(parentNode.getTaxon().getName(), ZoologicalName.class); |
|
| 386 |
String parentNameCache = parentName.getNameCache(); |
|
| 387 |
mergeObject.setParentStringInErms(parentNameCache); |
|
| 388 |
mergeObject.setParentRankStringInErms(parentName.getRank().getLabel()); |
|
Also available in: Unified diff
remove pesi activators from app-import