Revision 8f2ee187
Added by Andreas Müller over 12 years ago
| .gitattributes | ||
|---|---|---|
| 29 | 29 |
app-import/src/main/java/eu/etaxonomy/cdm/app/cyprus/CyprusActivator.java -text |
| 30 | 30 |
app-import/src/main/java/eu/etaxonomy/cdm/app/cyprus/CyprusSpecimenActivator.java -text |
| 31 | 31 |
app-import/src/main/java/eu/etaxonomy/cdm/app/dwca/DwcaExportActivator.java -text |
| 32 |
app-import/src/main/java/eu/etaxonomy/cdm/app/eflora/CentralAfricaChecklistActivator.java -text |
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| 33 |
app-import/src/main/java/eu/etaxonomy/cdm/app/eflora/CentralAfricaEricaceaeActivator.java -text |
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| 34 |
app-import/src/main/java/eu/etaxonomy/cdm/app/eflora/CentralAfricaFernsActivator.java -text |
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| 35 |
app-import/src/main/java/eu/etaxonomy/cdm/app/eflora/EfloraSources.java -text |
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| 36 |
app-import/src/main/java/eu/etaxonomy/cdm/app/eflora/FloraMalesianaActivator.java -text |
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| 37 |
app-import/src/main/java/eu/etaxonomy/cdm/app/eflora/FloraMalesianaVol13Activator.java -text |
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| 38 | 32 |
app-import/src/main/java/eu/etaxonomy/cdm/app/excelImport/distribution/CichorieaeDistributionActivator.java -text |
| 39 | 33 |
app-import/src/main/java/eu/etaxonomy/cdm/app/excelImport/taxa/NormalExplicitActivator.java -text |
| 40 | 34 |
app-import/src/main/java/eu/etaxonomy/cdm/app/excelImport/taxa/UseSummaryActivator.java -text |
| app-import/src/main/java/eu/etaxonomy/cdm/app/eflora/CentralAfricaChecklistActivator.java | ||
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/** |
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* Copyright (C) 2007 EDIT |
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* European Distributed Institute of Taxonomy |
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* http://www.e-taxonomy.eu |
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* |
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* The contents of this file are subject to the Mozilla Public License Version 1.1 |
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* See LICENSE.TXT at the top of this package for the full license terms. |
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*/ |
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package eu.etaxonomy.cdm.app.eflora; |
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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.app.common.CdmDestinations; |
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import eu.etaxonomy.cdm.app.common.CdmImportSources; |
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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.common.CdmDefaultImport; |
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import eu.etaxonomy.cdm.io.common.Source; |
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK; |
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import eu.etaxonomy.cdm.io.eflora.centralAfrica.checklist.CentralAfricaChecklistImportConfigurator; |
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import eu.etaxonomy.cdm.model.reference.Reference; |
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
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/** |
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* @author a.mueller |
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* @created 20.06.2008 |
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* @version 1.0 |
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*/ |
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public class CentralAfricaChecklistActivator {
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(CentralAfricaChecklistActivator.class); |
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//database validation status (create, update, validate ...) |
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static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE; |
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static final Source mySource = CdmImportSources.AFRICA_CHECKLIST_ACCESS(); |
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_andreasM3(); |
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_preview(); |
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_production(); |
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static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); |
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int recordsPerTransaction = 1000; |
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//feature tree uuid |
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public static final UUID featureTreeUuid = UUID.fromString("ebe558b5-d04d-41d5-83d9-b61c56e6e34a");
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public static final String sourceReference = "Flora of Central Africa - Checklist"; |
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private UUID uuidGenevaReference = UUID.fromString("cf3fd13d-6cad-430c-ab70-7ea841b7159f");
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private String genevaReferenceTitle = "Geneva Database"; |
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//classification |
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public static final UUID classificationUuid = UUID.fromString("ce1d035a-79a9-4a3a-95bf-26641ecb4fbe");
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//check - import |
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static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK; |
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//taxa |
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static final boolean doTaxa = true; |
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private void doImport(ICdmDataSource cdmDestination){
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//make Source |
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Source source = mySource; |
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CentralAfricaChecklistImportConfigurator config= CentralAfricaChecklistImportConfigurator.NewInstance(source, cdmDestination); |
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config.setClassificationUuid(classificationUuid); |
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config.setDoTaxa(doTaxa); |
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config.setCheck(check); |
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config.setDbSchemaValidation(hbm2dll); |
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config.setRecordsPerTransaction(recordsPerTransaction); |
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config.setGenevaReferenceTitle(genevaReferenceTitle); |
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config.setUuidGenevaReference(uuidGenevaReference); |
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CdmDefaultImport<CentralAfricaChecklistImportConfigurator> myImport = new CdmDefaultImport<CentralAfricaChecklistImportConfigurator>(); |
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System.out.println("Start import from ("+ source.toString() + ") ...");
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config.setSourceReference(getSourceReference(sourceReference)); |
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myImport.invoke(config); |
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System.out.println("End import from ("+ source.toString() + ")...");
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// FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService()); |
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// myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree); |
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} |
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private Reference getSourceReference(String string) {
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Reference result = ReferenceFactory.newGeneric(); |
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result.setTitleCache(string); |
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return result; |
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} |
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// private FeatureTree makeFeatureNode(ITermService service){
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// FloraMalesianaTransformer transformer = new FloraMalesianaTransformer(); |
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// |
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// FeatureTree result = FeatureTree.NewInstance(featureTreeUuid); |
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// result.setTitleCache("Flora Malesiana Presentation Feature Tree");
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// FeatureNode root = result.getRoot(); |
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// FeatureNode newNode; |
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// |
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// newNode = FeatureNode.NewInstance(Feature.CITATION()); |
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// root.addChild(newNode); |
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// |
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// newNode = FeatureNode.NewInstance(Feature.DESCRIPTION()); |
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// root.addChild(newNode); |
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// |
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// return result; |
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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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CentralAfricaChecklistActivator me = new CentralAfricaChecklistActivator(); |
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me.doImport(cdmDestination); |
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} |
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} |
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| app-import/src/main/java/eu/etaxonomy/cdm/app/eflora/CentralAfricaEricaceaeActivator.java | ||
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/** |
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* Copyright (C) 2007 EDIT |
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* European Distributed Institute of Taxonomy |
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* http://www.e-taxonomy.eu |
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* |
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* The contents of this file are subject to the Mozilla Public License Version 1.1 |
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* See LICENSE.TXT at the top of this package for the full license terms. |
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*/ |
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package eu.etaxonomy.cdm.app.eflora; |
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import java.net.URI; |
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import java.util.List; |
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import java.util.UUID; |
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import org.apache.log4j.Logger; |
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import org.springframework.transaction.TransactionStatus; |
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import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
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import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration; |
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import eu.etaxonomy.cdm.api.service.ITermService; |
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import eu.etaxonomy.cdm.app.common.CdmDestinations; |
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import eu.etaxonomy.cdm.common.monitor.DefaultProgressMonitor; |
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import eu.etaxonomy.cdm.common.monitor.IProgressMonitor; |
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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.database.update.CdmUpdater; |
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import eu.etaxonomy.cdm.io.common.CdmDefaultImport; |
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import eu.etaxonomy.cdm.io.common.CdmImportBase.TermMatchMode; |
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK; |
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import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer; |
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import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; |
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import eu.etaxonomy.cdm.io.eflora.EfloraImportConfigurator; |
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import eu.etaxonomy.cdm.io.eflora.centralAfrica.ericaceae.CentralAfricaEricaceaeImportConfigurator; |
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import eu.etaxonomy.cdm.io.eflora.centralAfrica.ericaceae.CentralAfricaEricaceaeTransformer; |
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import eu.etaxonomy.cdm.io.specimen.excel.in.SpecimenCdmExcelImportConfigurator; |
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import eu.etaxonomy.cdm.model.agent.Team; |
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import eu.etaxonomy.cdm.model.common.Language; |
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import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary; |
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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; |
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import eu.etaxonomy.cdm.model.description.PolytomousKey; |
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import eu.etaxonomy.cdm.model.location.NamedArea; |
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import eu.etaxonomy.cdm.model.location.NamedAreaLevel; |
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import eu.etaxonomy.cdm.model.location.NamedAreaType; |
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import eu.etaxonomy.cdm.model.reference.Reference; |
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
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/** |
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* @author a.mueller |
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* @created 20.06.2008 |
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* @version 1.0 |
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*/ |
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public class CentralAfricaEricaceaeActivator {
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private static final Logger logger = Logger.getLogger(CentralAfricaEricaceaeActivator.class); |
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//database validation status (create, update, validate ...) |
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static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE; |
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static final URI source = EfloraSources.ericacea_local(); |
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static final URI specimenSource = EfloraSources.ericacea_specimen_local(); |
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_andreasM3(); |
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_preview(); |
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_production(); |
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static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); |
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_postgres_CdmTest(); |
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql(); |
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_jaxb(); |
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_edit_cichorieae_preview(); |
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_campanulaceae_production(); |
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//feature tree uuid |
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public static final UUID featureTreeUuid = UUID.fromString("051d35ee-22f1-42d8-be07-9e9bfec5bcf7");
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public static UUID defaultLanguageUuid = Language.uuidFrench; |
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//classification |
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static final UUID classificationUuid = UUID.fromString("10e5efcc-6e13-4abc-ad42-e0b46e50cbe7");
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//check - import |
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static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK; |
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static boolean doPrintKeys = false; |
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//taxa |
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private boolean includeEricaceae = true; |
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static final boolean doTaxa = true; |
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static final boolean doDeduplicate = false; |
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private boolean doNewNamedAreas = false; |
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private boolean doFeatureTree = false; |
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private boolean doSpecimen = false; |
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private TermMatchMode specimenAreaMatchMode = TermMatchMode.UUID_ABBREVLABEL; |
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private void doImport(ICdmDataSource cdmDestination){
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CdmUpdater su = CdmUpdater.NewInstance(); |
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IProgressMonitor monitor = DefaultProgressMonitor.NewInstance(); |
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// |
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// try {
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// su.updateToCurrentVersion(cdmDestination, monitor); |
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// } catch (Exception e) {
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// e.printStackTrace(); |
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// } |
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// if (true){
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// return; |
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// } |
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//make Source |
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CentralAfricaEricaceaeImportConfigurator config= CentralAfricaEricaceaeImportConfigurator.NewInstance(source, cdmDestination); |
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config.setClassificationUuid(classificationUuid); |
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config.setDoTaxa(doTaxa); |
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config.setCheck(check); |
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config.setDefaultLanguageUuid(defaultLanguageUuid); |
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config.setDoPrintKeys(doPrintKeys); |
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config.setDbSchemaValidation(hbm2dll); |
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CdmDefaultImport<EfloraImportConfigurator> myImport = new CdmDefaultImport<EfloraImportConfigurator>(); |
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//Ericaceae |
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if (includeEricaceae){
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System.out.println("Start import from ("+ source.toString() + ") ...");
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config.setSourceReference(getSourceReference(config.getSourceReferenceTitle())); |
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myImport.invoke(config); |
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System.out.println("End import from ("+ source.toString() + ")...");
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} |
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if (doFeatureTree){
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FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService()); |
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myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree); |
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} |
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//check keys |
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if (doPrintKeys){
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TransactionStatus tx = myImport.getCdmAppController().startTransaction(); |
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List<PolytomousKey> keys = myImport.getCdmAppController().getPolytomousKeyService().list(PolytomousKey.class, null, null, null, null); |
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for(PolytomousKey key : keys){
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key.print(System.out); |
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System.out.println(); |
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} |
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myImport.getCdmAppController().commitTransaction(tx); |
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} |
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//deduplicate |
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if (doDeduplicate){
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ICdmApplicationConfiguration app = myImport.getCdmAppController(); |
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if (app == null){
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app = CdmApplicationController.NewInstance(cdmDestination, hbm2dll, false); |
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} |
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app.getAgentService().updateTitleCache(Team.class, null, null, null); |
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return; |
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// int count = app.getAgentService().deduplicate(Person.class, null, null); |
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// |
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// logger.warn("Deduplicated " + count + " persons.");
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//// count = app.getAgentService().deduplicate(Team.class, null, null); |
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//// logger.warn("Deduplicated " + count + " teams.");
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// count = app.getReferenceService().deduplicate(Reference.class, null, null); |
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// logger.warn("Deduplicated " + count + " references.");
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} |
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if(doNewNamedAreas){
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newNamedAreas(myImport); |
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} |
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if (doSpecimen){
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logger.warn("Start specimen import");
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ICdmApplicationConfiguration app = myImport.getCdmAppController(); |
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SpecimenCdmExcelImportConfigurator specimenConfig= SpecimenCdmExcelImportConfigurator.NewInstance(specimenSource, cdmDestination); |
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specimenConfig.setCdmAppController((CdmApplicationController)app); |
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specimenConfig.setAreaMatchMode(specimenAreaMatchMode); |
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config.setDbSchemaValidation(DbSchemaValidation.VALIDATE); |
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specimenConfig.setSourceReference(getSourceReference(specimenConfig.getSourceReferenceTitle())); |
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CdmDefaultImport<SpecimenCdmExcelImportConfigurator> specimenImport = new CdmDefaultImport<SpecimenCdmExcelImportConfigurator>(); |
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specimenImport.setCdmAppController(app); |
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specimenImport.invoke(specimenConfig); |
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} |
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return; |
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} |
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private void newNamedAreas(CdmDefaultImport<EfloraImportConfigurator> myImport) {
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ICdmApplicationConfiguration app = myImport.getCdmAppController(); |
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if (app == null){
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app = CdmApplicationController.NewInstance(cdmDestination, hbm2dll, false); |
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} |
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TransactionStatus tx = app.startTransaction(); |
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OrderedTermVocabulary<NamedArea> voc = OrderedTermVocabulary.NewInstance("Phytogeographic Regions of Central Africa", "Phytogeographic Regions of Central Africa", "FdAC regions", null);
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app.getVocabularyService().save(voc); |
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NamedAreaLevel level = NamedAreaLevel.NewInstance("Phytogeographic Regions of Central Africa", "Phytogeographic Regions of Central Africa", "FdAC regions");
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ITermService termService = app.getTermService(); |
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termService.save(level); |
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NamedArea area = NamedArea.NewInstance("C?tier", "C?tier", "I");
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area.setLevel(level); |
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area.setType(NamedAreaType.NATURAL_AREA()); |
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voc.addTerm(area); |
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termService.save(area); |
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area = NamedArea.NewInstance("Mayumbe", "Mayumbe", "II");
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area.setLevel(level); |
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area.setType(NamedAreaType.NATURAL_AREA()); |
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voc.addTerm(area); |
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termService.save(area); |
|
| 221 |
|
|
| 222 |
area = NamedArea.NewInstance("Bas-Congo", "Bas-Congo", "III");
|
|
| 223 |
area.setLevel(level); |
|
| 224 |
area.setType(NamedAreaType.NATURAL_AREA()); |
|
| 225 |
voc.addTerm(area); |
|
| 226 |
termService.save(area); |
|
| 227 |
|
|
| 228 |
area = NamedArea.NewInstance("Kasai", "Kasai", "IV");
|
|
| 229 |
area.setLevel(level); |
|
| 230 |
area.setType(NamedAreaType.NATURAL_AREA()); |
|
| 231 |
voc.addTerm(area); |
|
| 232 |
termService.save(area); |
|
| 233 |
|
|
| 234 |
area = NamedArea.NewInstance("Bas-Katanga", "Bas-Katanga", "V");
|
|
| 235 |
area.setLevel(level); |
|
| 236 |
area.setType(NamedAreaType.NATURAL_AREA()); |
|
| 237 |
voc.addTerm(area); |
|
| 238 |
termService.save(area); |
|
| 239 |
|
|
| 240 |
area = NamedArea.NewInstance("Forestier Central", "Forestier Central", "VI");
|
|
| 241 |
area.setLevel(level); |
|
| 242 |
area.setType(NamedAreaType.NATURAL_AREA()); |
|
| 243 |
voc.addTerm(area); |
|
| 244 |
termService.save(area); |
|
| 245 |
|
|
| 246 |
area = NamedArea.NewInstance("Ubangi-Uele", "Ubangi-Uele", "VII");
|
|
| 247 |
area.setLevel(level); |
|
| 248 |
area.setType(NamedAreaType.NATURAL_AREA()); |
|
| 249 |
voc.addTerm(area); |
|
| 250 |
termService.save(area); |
|
| 251 |
|
|
| 252 |
area = NamedArea.NewInstance("Lac Albert", "Lac Albert", "VIII");
|
|
| 253 |
area.setLevel(level); |
|
| 254 |
area.setType(NamedAreaType.NATURAL_AREA()); |
|
| 255 |
voc.addTerm(area); |
|
| 256 |
termService.save(area); |
|
| 257 |
|
|
| 258 |
area = NamedArea.NewInstance("Lacs ?douard et Kivu", "Lacs ?douard et Kivu", "IX");
|
|
| 259 |
area.setLevel(level); |
|
| 260 |
area.setType(NamedAreaType.NATURAL_AREA()); |
|
| 261 |
voc.addTerm(area); |
|
| 262 |
termService.save(area); |
|
| 263 |
|
|
| 264 |
area = NamedArea.NewInstance("Rwanda-Burundi", "Rwanda-Burundi", "X");
|
|
| 265 |
area.setLevel(level); |
|
| 266 |
area.setType(NamedAreaType.NATURAL_AREA()); |
|
| 267 |
voc.addTerm(area); |
|
| 268 |
termService.save(area); |
|
| 269 |
|
|
| 270 |
area = NamedArea.NewInstance("Haut-Katanga", "Haut-Katanga", "XI");
|
|
| 271 |
area.setLevel(level); |
|
| 272 |
area.setType(NamedAreaType.NATURAL_AREA()); |
|
| 273 |
voc.addTerm(area); |
|
| 274 |
termService.save(area); |
|
| 275 |
|
|
| 276 |
app.getVocabularyService().save(voc); |
|
| 277 |
|
|
| 278 |
app.commitTransaction(tx); |
|
| 279 |
|
|
| 280 |
} |
|
| 281 |
|
|
| 282 |
private Reference getSourceReference(String string) {
|
|
| 283 |
Reference result = ReferenceFactory.newGeneric(); |
|
| 284 |
result.setTitleCache(string); |
|
| 285 |
return result; |
|
| 286 |
} |
|
| 287 |
|
|
| 288 |
private FeatureTree makeFeatureNode(ITermService service){
|
|
| 289 |
CentralAfricaEricaceaeTransformer transformer = new CentralAfricaEricaceaeTransformer(); |
|
| 290 |
|
|
| 291 |
FeatureTree result = FeatureTree.NewInstance(featureTreeUuid); |
|
| 292 |
result.setTitleCache("Central Africa Ericaceae Feature Tree");
|
|
| 293 |
FeatureNode root = result.getRoot(); |
|
| 294 |
FeatureNode newNode; |
|
| 295 |
|
|
| 296 |
newNode = FeatureNode.NewInstance(Feature.DESCRIPTION()); |
|
| 297 |
root.addChild(newNode); |
|
| 298 |
|
|
| 299 |
addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service); |
|
| 300 |
|
|
| 301 |
addFeataureNodesByStringList(generellDescriptionsList, root, transformer, service); |
|
| 302 |
|
|
| 303 |
|
|
| 304 |
newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION()); |
|
| 305 |
root.addChild(newNode); |
|
| 306 |
|
|
| 307 |
newNode = FeatureNode.NewInstance(Feature.ECOLOGY()); |
|
| 308 |
root.addChild(newNode); |
|
| 309 |
addFeataureNodesByStringList(habitatEcologyList, root, transformer, service); |
|
| 310 |
|
|
| 311 |
newNode = FeatureNode.NewInstance(Feature.USES()); |
|
| 312 |
root.addChild(newNode); |
|
| 313 |
|
|
| 314 |
addFeataureNodesByStringList(chomosomesList, root, transformer, service); |
|
| 315 |
|
|
| 316 |
newNode = FeatureNode.NewInstance(Feature.COMMON_NAME()); |
|
| 317 |
root.addChild(newNode); |
|
| 318 |
|
|
| 319 |
newNode = FeatureNode.NewInstance(Feature.CITATION()); |
|
| 320 |
root.addChild(newNode); |
|
| 321 |
|
|
| 322 |
return result; |
|
| 323 |
} |
|
| 324 |
|
|
| 325 |
private static String [] chomosomesList = new String[]{
|
|
| 326 |
"Chromosomes", |
|
| 327 |
}; |
|
| 328 |
|
|
| 329 |
|
|
| 330 |
private static String [] habitatEcologyList = new String[]{
|
|
| 331 |
"Habitat", |
|
| 332 |
"Habitat & Ecology" |
|
| 333 |
}; |
|
| 334 |
|
|
| 335 |
|
|
| 336 |
private static String [] generellDescriptionsList = new String[]{
|
|
| 337 |
"Fossils", |
|
| 338 |
"Morphology and anatomy", |
|
| 339 |
"Morphology", |
|
| 340 |
"Vegetative morphology and anatomy", |
|
| 341 |
"Flower morphology", |
|
| 342 |
"Palynology", |
|
| 343 |
"Pollination", |
|
| 344 |
"Pollen morphology", |
|
| 345 |
"Life cycle", |
|
| 346 |
"Fruits and embryology", |
|
| 347 |
"Dispersal", |
|
| 348 |
"Wood anatomy", |
|
| 349 |
"Leaf anatomy", |
|
| 350 |
"Chromosome numbers", |
|
| 351 |
"Phytochemistry and Chemotaxonomy", |
|
| 352 |
"Phytochemistry", |
|
| 353 |
"Taxonomy", |
|
| 354 |
}; |
|
| 355 |
|
|
| 356 |
private static String [] descriptionFeatureList = new String[]{
|
|
| 357 |
"lifeform", |
|
| 358 |
"Bark", |
|
| 359 |
"Indumentum", |
|
| 360 |
"endophytic body", |
|
| 361 |
"flowering buds", |
|
| 362 |
"Branchlets", |
|
| 363 |
"Branches", |
|
| 364 |
"Branch", |
|
| 365 |
"Flowering branchlets", |
|
| 366 |
"Trees", |
|
| 367 |
"Twigs", |
|
| 368 |
"stem", |
|
| 369 |
"Stems", |
|
| 370 |
"stem leaves", |
|
| 371 |
"Leaves", |
|
| 372 |
"flower-bearing stems", |
|
| 373 |
"Petiole", |
|
| 374 |
"Petiolules", |
|
| 375 |
"Leaflets", |
|
| 376 |
"Thyrsus", |
|
| 377 |
"Thyrses", |
|
| 378 |
"Inflorescences", |
|
| 379 |
"Inflorescence", |
|
| 380 |
"Young inflorescences", |
|
| 381 |
"Bracts", |
|
| 382 |
"Pedicels", |
|
| 383 |
"flowering buds", |
|
| 384 |
"scales", |
|
| 385 |
"Buds", |
|
| 386 |
"Flowers", |
|
| 387 |
"Flower", |
|
| 388 |
"Flowering", |
|
| 389 |
"Stigma", |
|
| 390 |
"perianth", |
|
| 391 |
"Sepals", |
|
| 392 |
"Sepal", |
|
| 393 |
"Outer Sepals", |
|
| 394 |
"Axillary", |
|
| 395 |
"cymes", |
|
| 396 |
"Calyx", |
|
| 397 |
"Petal", |
|
| 398 |
"Petals", |
|
| 399 |
"perigone tube", |
|
| 400 |
"Disc", |
|
| 401 |
"corolla", |
|
| 402 |
"Stamens", |
|
| 403 |
"Staminodes", |
|
| 404 |
"Ovary", |
|
| 405 |
"Anthers", |
|
| 406 |
"anther", |
|
| 407 |
"Pistil", |
|
| 408 |
"Pistillode", |
|
| 409 |
"Ovules", |
|
| 410 |
"androecium", |
|
| 411 |
"gynoecium", |
|
| 412 |
"Filaments", |
|
| 413 |
"Style", |
|
| 414 |
"annulus", |
|
| 415 |
"female flowers", |
|
| 416 |
"Male flowers", |
|
| 417 |
"Female", |
|
| 418 |
"Infructescences", //order not consistent (sometimes before "Flowers") |
|
| 419 |
"Fruit", |
|
| 420 |
"Fruits", |
|
| 421 |
"fruiting axes", |
|
| 422 |
"drupes", |
|
| 423 |
"Arillode", |
|
| 424 |
"seed", |
|
| 425 |
"Seeds", |
|
| 426 |
"Seedling", |
|
| 427 |
"flower tube", |
|
| 428 |
"nutlets", |
|
| 429 |
"pollen", |
|
| 430 |
"secondary xylem", |
|
| 431 |
"chromosome number", |
|
| 432 |
|
|
| 433 |
"figure", |
|
| 434 |
"fig", |
|
| 435 |
"figs", |
|
| 436 |
|
|
| 437 |
|
|
| 438 |
|
|
| 439 |
|
|
| 440 |
}; |
|
| 441 |
|
|
| 442 |
public void addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
|
|
| 443 |
try {
|
|
| 444 |
for (String featureString : featureStringList){
|
|
| 445 |
UUID featureUuid; |
|
| 446 |
featureUuid = transformer.getFeatureUuid(featureString); |
|
| 447 |
Feature feature = (Feature)termService.find(featureUuid); |
|
| 448 |
if (feature != null){
|
|
| 449 |
FeatureNode child = FeatureNode.NewInstance(feature); |
|
| 450 |
root.addChild(child); |
|
| 451 |
} |
|
| 452 |
} |
|
| 453 |
} catch (UndefinedTransformerMethodException e) {
|
|
| 454 |
logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");
|
|
| 455 |
} |
|
| 456 |
} |
|
| 457 |
|
|
| 458 |
|
|
| 459 |
|
|
| 460 |
/** |
|
| 461 |
* @param args |
|
| 462 |
*/ |
|
| 463 |
public static void main(String[] args) {
|
|
| 464 |
CentralAfricaEricaceaeActivator me = new CentralAfricaEricaceaeActivator(); |
|
| 465 |
me.doImport(cdmDestination); |
|
| 466 |
} |
|
| 467 |
|
|
| 468 |
} |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/eflora/CentralAfricaFernsActivator.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.eflora; |
|
| 11 |
|
|
| 12 |
import java.util.UUID; |
|
| 13 |
|
|
| 14 |
import org.apache.log4j.Logger; |
|
| 15 |
|
|
| 16 |
import eu.etaxonomy.cdm.api.service.ITermService; |
|
| 17 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
|
| 18 |
import eu.etaxonomy.cdm.app.common.CdmImportSources; |
|
| 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.Source; |
|
| 23 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK; |
|
| 24 |
import eu.etaxonomy.cdm.io.eflora.centralAfrica.ferns.CentralAfricaFernsImportConfigurator; |
|
| 25 |
import eu.etaxonomy.cdm.io.eflora.floraMalesiana.FloraMalesianaTransformer; |
|
| 26 |
import eu.etaxonomy.cdm.model.description.Feature; |
|
| 27 |
import eu.etaxonomy.cdm.model.description.FeatureNode; |
|
| 28 |
import eu.etaxonomy.cdm.model.description.FeatureTree; |
|
| 29 |
import eu.etaxonomy.cdm.model.reference.Reference; |
|
| 30 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
|
| 31 |
|
|
| 32 |
/** |
|
| 33 |
* @author a.mueller |
|
| 34 |
* @created 20.06.2008 |
|
| 35 |
* @version 1.0 |
|
| 36 |
*/ |
|
| 37 |
public class CentralAfricaFernsActivator {
|
|
| 38 |
@SuppressWarnings("unused")
|
|
| 39 |
private static final Logger logger = Logger.getLogger(CentralAfricaFernsActivator.class); |
|
| 40 |
|
|
| 41 |
//database validation status (create, update, validate ...) |
|
| 42 |
static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE; |
|
| 43 |
static final Source mySource = CdmImportSources.AFRICA_FERNS_ACCESS(); |
|
| 44 |
|
|
| 45 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_andreasM2(); |
|
| 46 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_preview(); |
|
| 47 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_production(); |
|
| 48 |
static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); |
|
| 49 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_postgres_CdmTest(); |
|
| 50 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql(); |
|
| 51 |
|
|
| 52 |
//feature tree uuid |
|
| 53 |
public static final UUID featureTreeUuid = UUID.fromString("62d930cb-aabb-461c-ad16-0fdbd2bae592");
|
|
| 54 |
|
|
| 55 |
public static final String sourceReference = "Flora of Central Africa"; |
|
| 56 |
|
|
| 57 |
public static final String classificationName = "Flora of Central Africa - Ferns"; |
|
| 58 |
|
|
| 59 |
//classification |
|
| 60 |
static final UUID classificationUuid = UUID.fromString("a90fa160-8f33-4a19-9c5a-ab05a1553017");
|
|
| 61 |
|
|
| 62 |
//check - import |
|
| 63 |
static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK; |
|
| 64 |
|
|
| 65 |
// static boolean doPrintKeys = false; |
|
| 66 |
|
|
| 67 |
//taxa |
|
| 68 |
static final boolean doTaxa = true; |
|
| 69 |
|
|
| 70 |
// private boolean includeSapindaceae1 = true; |
|
| 71 |
|
|
| 72 |
|
|
| 73 |
|
|
| 74 |
private void doImport(ICdmDataSource cdmDestination){
|
|
| 75 |
|
|
| 76 |
|
|
| 77 |
//make Source |
|
| 78 |
Source source = mySource; |
|
| 79 |
|
|
| 80 |
// mySource.getResultSet("SELECT * FROM tmp");
|
|
| 81 |
CentralAfricaFernsImportConfigurator config= CentralAfricaFernsImportConfigurator.NewInstance(source, cdmDestination); |
|
| 82 |
config.setClassificationUuid(classificationUuid); |
|
| 83 |
config.setClassificationName(classificationName); |
|
| 84 |
config.setDoTaxa(doTaxa); |
|
| 85 |
config.setCheck(check); |
|
| 86 |
// configsetDoPrintKeys(doPrintKeys); |
|
| 87 |
config.setDbSchemaValidation(hbm2dll); |
|
| 88 |
|
|
| 89 |
CdmDefaultImport<CentralAfricaFernsImportConfigurator> myImport = new CdmDefaultImport<CentralAfricaFernsImportConfigurator>(); |
|
| 90 |
|
|
| 91 |
|
|
| 92 |
// if (includeSapindaceae1){
|
|
| 93 |
System.out.println("Start import from ("+ source.toString() + ") ...");
|
|
| 94 |
config.setSourceReference(getSourceReference(sourceReference)); |
|
| 95 |
myImport.invoke(config); |
|
| 96 |
System.out.println("End import from ("+ source.toString() + ")...");
|
|
| 97 |
// } |
|
| 98 |
|
|
| 99 |
|
|
| 100 |
|
|
| 101 |
FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService()); |
|
| 102 |
myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree); |
|
| 103 |
|
|
| 104 |
//check keys |
|
| 105 |
// if (doPrintKeys){
|
|
| 106 |
// TransactionStatus tx = myImport.getCdmAppController().startTransaction(); |
|
| 107 |
// List<FeatureTree> keys = myImport.getCdmAppController().getFeatureTreeService().list(PolytomousKey.class, null, null, null, null); |
|
| 108 |
// for(FeatureTree key : keys){
|
|
| 109 |
// ((PolytomousKey)key).print(System.out); |
|
| 110 |
// System.out.println(); |
|
| 111 |
// } |
|
| 112 |
// myImport.getCdmAppController().commitTransaction(tx); |
|
| 113 |
// } |
|
| 114 |
|
|
| 115 |
} |
|
| 116 |
|
|
| 117 |
private Reference getSourceReference(String string) {
|
|
| 118 |
Reference result = ReferenceFactory.newGeneric(); |
|
| 119 |
result.setTitleCache(string); |
|
| 120 |
return result; |
|
| 121 |
} |
|
| 122 |
|
|
| 123 |
private FeatureTree makeFeatureNode(ITermService service){
|
|
| 124 |
FloraMalesianaTransformer transformer = new FloraMalesianaTransformer(); |
|
| 125 |
|
|
| 126 |
FeatureTree result = FeatureTree.NewInstance(featureTreeUuid); |
|
| 127 |
result.setTitleCache("Flora Malesiana Presentation Feature Tree");
|
|
| 128 |
FeatureNode root = result.getRoot(); |
|
| 129 |
FeatureNode newNode; |
|
| 130 |
|
|
| 131 |
newNode = FeatureNode.NewInstance(Feature.CITATION()); |
|
| 132 |
root.addChild(newNode); |
|
| 133 |
|
|
| 134 |
newNode = FeatureNode.NewInstance(Feature.DESCRIPTION()); |
|
| 135 |
root.addChild(newNode); |
|
| 136 |
|
|
| 137 |
return result; |
|
| 138 |
} |
|
| 139 |
|
|
| 140 |
|
|
| 141 |
|
|
| 142 |
/** |
|
| 143 |
* @param args |
|
| 144 |
*/ |
|
| 145 |
public static void main(String[] args) {
|
|
| 146 |
CentralAfricaFernsActivator me = new CentralAfricaFernsActivator(); |
|
| 147 |
me.doImport(cdmDestination); |
|
| 148 |
} |
|
| 149 |
|
|
| 150 |
} |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/eflora/EfloraSources.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.eflora; |
|
| 11 |
|
|
| 12 |
import java.io.File; |
|
| 13 |
import java.net.URI; |
|
| 14 |
|
|
| 15 |
import org.apache.log4j.Logger; |
|
| 16 |
|
|
| 17 |
/** |
|
| 18 |
* @author a.mueller |
|
| 19 |
* @date 09.06.2010 |
|
| 20 |
* |
|
| 21 |
*/ |
|
| 22 |
public class EfloraSources {
|
|
| 23 |
@SuppressWarnings("unused")
|
|
| 24 |
private static final Logger logger = Logger.getLogger(EfloraSources.class); |
|
| 25 |
|
|
| 26 |
//Ericaceae |
|
| 27 |
public static URI ericacea_local() {
|
|
| 28 |
return URI.create("file:C:/localCopy/Data/eflora/africa/Ericaceae/ericaceae_v2.xml");
|
|
| 29 |
} |
|
| 30 |
|
|
| 31 |
public static URI ericacea_specimen_local() {
|
|
| 32 |
return URI.create("file:/C:/localCopy/Data/eflora/africa/Specimen/Ericaceae/Ericaceae_CDM_specimen.xls");
|
|
| 33 |
} |
|
| 34 |
|
|
| 35 |
//Sapindaceae |
|
| 36 |
public static URI fm_sapindaceae_local(){
|
|
| 37 |
return URI.create("file:C:/localCopy/Data/eflora/floraMalesiana/sapindaceae-01v25.xml");
|
|
| 38 |
} |
|
| 39 |
|
|
| 40 |
//Sapindaceae2 |
|
| 41 |
public static URI fm_sapindaceae2_local(){
|
|
| 42 |
return URI.create("file:C:/localCopy/Data/eflora/floraMalesiana/sapindaceae-02final2.xml");
|
|
| 43 |
} |
|
| 44 |
|
|
| 45 |
//Flora Malesiana Vol 13-1 |
|
| 46 |
public static URI fm_13_1_local(){
|
|
| 47 |
return URI.create("file:C:/localCopy/Data/eflora/floraMalesiana/fm13_1_v8_final.xml");
|
|
| 48 |
} |
|
| 49 |
|
|
| 50 |
//Flora Malesiana Vol 13-2 |
|
| 51 |
public static URI fm_13_2_local(){
|
|
| 52 |
return URI.create("file:C:/localCopy/Data/eflora/floraMalesiana/fm13_2_v8_final.xml");
|
|
| 53 |
} |
|
| 54 |
|
|
| 55 |
//Flora Malesiana Vol 13 - small families |
|
| 56 |
public static URI fm_13_small_families(){
|
|
| 57 |
URI uri = URI.create("file:/C:/localCopy/Data/eflora/floraMalesiana/vol_13/vol_13_small_families.xml");
|
|
| 58 |
File file = new File(uri); |
|
| 59 |
return uri; |
|
| 60 |
} |
|
| 61 |
|
|
| 62 |
//Flora Malesiana Vol 13 - large families |
|
| 63 |
public static URI fm_13_large_families(){
|
|
| 64 |
return URI.create("file:C:/localCopy/Data/eflora/floraMalesiana/vol_13/xmlv9_large_families_vol_13.xml");
|
|
| 65 |
} |
|
| 66 |
|
|
| 67 |
|
|
| 68 |
//Flora Malesiana Vol 12 |
|
| 69 |
public static URI fm_12(){
|
|
| 70 |
return URI.create("file:C:/localCopy/Data/eflora/floraMalesiana/vol_12/xml_1995_vol_12_all_final_5.xml");
|
|
| 71 |
} |
|
| 72 |
|
|
| 73 |
//Flora Malesiana Series 2 - Vol 2 |
|
| 74 |
public static URI fm_2_2(){
|
|
| 75 |
return URI.create("file:C:/localCopy/Data/eflora/floraMalesiana/ser2_vol2/ser2vol2final1.xml");
|
|
| 76 |
} |
|
| 77 |
|
|
| 78 |
} |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/eflora/FloraMalesianaActivator.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.eflora; |
|
| 11 |
|
|
| 12 |
import java.net.URI; |
|
| 13 |
import java.util.List; |
|
| 14 |
import java.util.UUID; |
|
| 15 |
|
|
| 16 |
import org.apache.log4j.Logger; |
|
| 17 |
import org.springframework.transaction.TransactionStatus; |
|
| 18 |
|
|
| 19 |
import eu.etaxonomy.cdm.api.service.ITermService; |
|
| 20 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
|
| 21 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
|
| 22 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
|
| 23 |
import eu.etaxonomy.cdm.io.common.CdmDefaultImport; |
|
| 24 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK; |
|
| 25 |
import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer; |
|
| 26 |
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; |
|
| 27 |
import eu.etaxonomy.cdm.io.eflora.EfloraImportConfigurator; |
|
| 28 |
import eu.etaxonomy.cdm.io.eflora.floraMalesiana.FloraMalesianaTransformer; |
|
| 29 |
import eu.etaxonomy.cdm.model.description.Feature; |
|
| 30 |
import eu.etaxonomy.cdm.model.description.FeatureNode; |
|
| 31 |
import eu.etaxonomy.cdm.model.description.FeatureTree; |
|
| 32 |
import eu.etaxonomy.cdm.model.description.PolytomousKey; |
|
| 33 |
import eu.etaxonomy.cdm.model.reference.Reference; |
|
| 34 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
|
| 35 |
|
|
| 36 |
/** |
|
| 37 |
* @author a.mueller |
|
| 38 |
* @created 20.06.2008 |
|
| 39 |
* @version 1.0 |
|
| 40 |
*/ |
|
| 41 |
public class FloraMalesianaActivator {
|
|
| 42 |
private static final Logger logger = Logger.getLogger(FloraMalesianaActivator.class); |
|
| 43 |
|
|
| 44 |
//database validation status (create, update, validate ...) |
|
| 45 |
static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE; |
|
| 46 |
static final URI fmSource1 = EfloraSources.fm_sapindaceae_local(); |
|
| 47 |
static final URI fmSource2 = EfloraSources.fm_sapindaceae2_local(); |
|
| 48 |
static final URI fmSource13_1 = EfloraSources.fm_13_1_local(); |
|
| 49 |
static final URI fmSource13_2 = EfloraSources.fm_13_2_local(); |
|
| 50 |
|
|
| 51 |
|
|
| 52 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_andreasM3(); |
|
| 53 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_malesiana_preview(); |
|
| 54 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_malesiana_production(); |
|
| 55 |
static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); |
|
| 56 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql(); |
|
| 57 |
|
|
| 58 |
|
|
| 59 |
//feature tree uuid |
|
| 60 |
public static final UUID featureTreeUuid = UUID.fromString("168df0c6-6429-484c-b26f-ded1f7e44bd9");
|
|
| 61 |
|
|
| 62 |
//classification |
|
| 63 |
static final UUID classificationUuid = UUID.fromString("ca4e4bcb-a1d1-4124-a358-a3d3c41dd450");
|
|
| 64 |
|
|
| 65 |
//check - import |
|
| 66 |
static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK; |
|
| 67 |
|
|
| 68 |
static boolean doPrintKeys = false; |
|
| 69 |
|
|
| 70 |
//taxa |
|
| 71 |
static final boolean doTaxa = true; |
|
| 72 |
|
|
| 73 |
private boolean includeSapindaceae1 = true; |
|
| 74 |
private boolean includeSapindaceae2 = true; |
|
| 75 |
private boolean includeVol13_1 = false; |
|
| 76 |
private boolean includeVol13_2 = false; |
|
| 77 |
|
|
| 78 |
|
|
| 79 |
private void doImport(ICdmDataSource cdmDestination){
|
|
| 80 |
|
|
| 81 |
//make Source |
|
| 82 |
URI source = fmSource1; |
|
| 83 |
EfloraImportConfigurator floraMalesianaConfig= EfloraImportConfigurator.NewInstance(source, cdmDestination); |
|
| 84 |
floraMalesianaConfig.setClassificationUuid(classificationUuid); |
|
| 85 |
floraMalesianaConfig.setDoTaxa(doTaxa); |
|
| 86 |
floraMalesianaConfig.setCheck(check); |
|
| 87 |
floraMalesianaConfig.setDoPrintKeys(doPrintKeys); |
|
| 88 |
floraMalesianaConfig.setDbSchemaValidation(hbm2dll); |
|
| 89 |
|
|
| 90 |
CdmDefaultImport<EfloraImportConfigurator> myImport = new CdmDefaultImport<EfloraImportConfigurator>(); |
|
| 91 |
|
|
| 92 |
|
|
| 93 |
//Sapindaceae1 |
|
| 94 |
if (includeSapindaceae1){
|
|
| 95 |
System.out.println("Start import from ("+ fmSource1.toString() + ") ...");
|
|
| 96 |
floraMalesianaConfig.setSourceReference(getSourceReference("Flora Malesiana - Sapindaceae I"));
|
|
| 97 |
myImport.invoke(floraMalesianaConfig); |
|
| 98 |
System.out.println("End import from ("+ fmSource1.toString() + ")...");
|
|
| 99 |
} |
|
| 100 |
|
|
| 101 |
//Sapindaceae2 |
|
| 102 |
if (includeSapindaceae2){
|
|
| 103 |
System.out.println("\nStart import from ("+ fmSource2.toString() + ") ...");
|
|
| 104 |
source = fmSource2; |
|
| 105 |
floraMalesianaConfig.setSource(source); |
|
| 106 |
floraMalesianaConfig.setSourceReference(getSourceReference("Flora Malesiana - Sapindaceae II"));
|
|
| 107 |
myImport.invoke(floraMalesianaConfig); |
|
| 108 |
System.out.println("End import from ("+ fmSource2.toString() + ")...");
|
|
| 109 |
} |
|
| 110 |
|
|
| 111 |
floraMalesianaConfig.setSourceReference(getSourceReference("Flora Malesiana - Vol. 13"));
|
|
| 112 |
//Vol13_1 |
|
| 113 |
if (includeVol13_1){
|
|
| 114 |
System.out.println("\nStart import from ("+ fmSource13_1.toString() + ") ...");
|
|
| 115 |
source = fmSource13_1; |
|
| 116 |
floraMalesianaConfig.setSource(source); |
|
| 117 |
myImport.invoke(floraMalesianaConfig); |
|
| 118 |
System.out.println("End import from ("+ fmSource13_1.toString() + ")...");
|
|
| 119 |
} |
|
| 120 |
|
|
| 121 |
//Vol13_2 |
|
| 122 |
if (includeVol13_2){
|
|
| 123 |
System.out.println("\nStart import from ("+ fmSource13_2.toString() + ") ...");
|
|
| 124 |
source = fmSource13_2; |
|
| 125 |
floraMalesianaConfig.setSource(source); |
|
| 126 |
myImport.invoke(floraMalesianaConfig); |
|
| 127 |
System.out.println("End import from ("+ fmSource13_2.toString() + ")...");
|
|
| 128 |
} |
|
| 129 |
|
|
| 130 |
FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService()); |
|
| 131 |
myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree); |
|
| 132 |
|
|
| 133 |
//check keys |
|
| 134 |
if (doPrintKeys){
|
|
| 135 |
TransactionStatus tx = myImport.getCdmAppController().startTransaction(); |
|
| 136 |
List<PolytomousKey> keys = myImport.getCdmAppController().getPolytomousKeyService().list(PolytomousKey.class, null, null, null, null); |
|
| 137 |
for(PolytomousKey key : keys){
|
|
| 138 |
key.print(System.out); |
|
| 139 |
System.out.println(); |
|
| 140 |
} |
|
| 141 |
myImport.getCdmAppController().commitTransaction(tx); |
|
| 142 |
} |
|
| 143 |
|
|
| 144 |
} |
|
| 145 |
|
|
| 146 |
private Reference getSourceReference(String string) {
|
|
| 147 |
Reference result = ReferenceFactory.newGeneric(); |
|
| 148 |
result.setTitleCache(string); |
|
| 149 |
return result; |
|
| 150 |
} |
|
| 151 |
|
|
| 152 |
private FeatureTree makeFeatureNode(ITermService service){
|
|
| 153 |
FloraMalesianaTransformer transformer = new FloraMalesianaTransformer(); |
|
| 154 |
|
|
| 155 |
FeatureTree result = FeatureTree.NewInstance(featureTreeUuid); |
|
| 156 |
result.setTitleCache("Flora Malesiana Presentation Feature Tree");
|
|
| 157 |
FeatureNode root = result.getRoot(); |
|
| 158 |
FeatureNode newNode; |
|
| 159 |
|
|
| 160 |
newNode = FeatureNode.NewInstance(Feature.DESCRIPTION()); |
|
| 161 |
root.addChild(newNode); |
|
| 162 |
|
|
| 163 |
addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service); |
|
| 164 |
|
|
| 165 |
addFeataureNodesByStringList(generellDescriptionsList, root, transformer, service); |
|
| 166 |
|
|
| 167 |
|
|
| 168 |
newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION()); |
|
| 169 |
root.addChild(newNode); |
|
| 170 |
|
|
| 171 |
newNode = FeatureNode.NewInstance(Feature.ECOLOGY()); |
|
| 172 |
root.addChild(newNode); |
|
| 173 |
addFeataureNodesByStringList(habitatEcologyList, root, transformer, service); |
|
| 174 |
|
|
| 175 |
newNode = FeatureNode.NewInstance(Feature.USES()); |
|
| 176 |
root.addChild(newNode); |
|
| 177 |
|
|
| 178 |
addFeataureNodesByStringList(chomosomesList, root, transformer, service); |
|
| 179 |
|
|
| 180 |
newNode = FeatureNode.NewInstance(Feature.CITATION()); |
|
| 181 |
root.addChild(newNode); |
|
| 182 |
|
|
| 183 |
return result; |
|
| 184 |
} |
|
| 185 |
|
|
| 186 |
private static String [] chomosomesList = new String[]{
|
|
| 187 |
"Chromosomes", |
|
| 188 |
}; |
|
| 189 |
|
|
| 190 |
|
|
| 191 |
private static String [] habitatEcologyList = new String[]{
|
|
| 192 |
"Habitat", |
|
| 193 |
"Habitat & Ecology" |
|
| 194 |
}; |
|
| 195 |
|
|
| 196 |
|
|
| 197 |
private static String [] generellDescriptionsList = new String[]{
|
|
| 198 |
"Fossils", |
|
| 199 |
"Morphology and anatomy", |
|
| 200 |
"Morphology", |
|
| 201 |
"Vegetative morphology and anatomy", |
|
| 202 |
"Flower morphology", |
|
| 203 |
"Palynology", |
|
| 204 |
"Pollination", |
|
| 205 |
"Pollen morphology", |
|
| 206 |
"Life cycle", |
|
| 207 |
"Fruits and embryology", |
|
| 208 |
"Dispersal", |
|
| 209 |
"Wood anatomy", |
|
| 210 |
"Leaf anatomy", |
|
| 211 |
"Chromosome numbers", |
|
| 212 |
"Phytochemistry and Chemotaxonomy", |
|
| 213 |
"Phytochemistry", |
|
| 214 |
"Taxonomy", |
|
| 215 |
}; |
|
| 216 |
|
|
| 217 |
private static String [] descriptionFeatureList = new String[]{
|
|
| 218 |
"lifeform", |
|
| 219 |
"Bark", |
|
| 220 |
"Indumentum", |
|
| 221 |
"endophytic body", |
|
| 222 |
"flowering buds", |
|
| 223 |
"Branchlets", |
|
| 224 |
"Branches", |
|
| 225 |
"Branch", |
|
| 226 |
"Flowering branchlets", |
|
| 227 |
"Trees", |
|
| 228 |
"Twigs", |
|
| 229 |
"stem", |
|
| 230 |
"Stems", |
|
| 231 |
"stem leaves", |
|
| 232 |
"Leaves", |
|
| 233 |
"flower-bearing stems", |
|
| 234 |
"Petiole", |
|
| 235 |
"Petiolules", |
|
| 236 |
"Leaflets", |
|
| 237 |
"Thyrsus", |
|
| 238 |
"Thyrses", |
|
| 239 |
"Inflorescences", |
|
| 240 |
"Inflorescence", |
|
| 241 |
"Young inflorescences", |
|
| 242 |
"Bracts", |
|
| 243 |
"Pedicels", |
|
| 244 |
"flowering buds", |
|
| 245 |
"scales", |
|
| 246 |
"Buds", |
|
| 247 |
"Flowers", |
|
| 248 |
"Flower", |
|
| 249 |
"Flowering", |
|
| 250 |
"Stigma", |
|
| 251 |
"perianth", |
|
| 252 |
"Sepals", |
|
| 253 |
"Sepal", |
|
| 254 |
"Outer Sepals", |
|
| 255 |
"Axillary", |
|
| 256 |
"cymes", |
|
| 257 |
"Calyx", |
|
| 258 |
"Petal", |
|
| 259 |
"Petals", |
|
| 260 |
"perigone tube", |
|
| 261 |
"Disc", |
|
| 262 |
"corolla", |
|
| 263 |
"Stamens", |
|
| 264 |
"Staminodes", |
|
| 265 |
"Ovary", |
|
| 266 |
"Anthers", |
|
| 267 |
"anther", |
|
| 268 |
"Pistil", |
|
| 269 |
"Pistillode", |
|
| 270 |
"Ovules", |
|
| 271 |
"androecium", |
|
| 272 |
"gynoecium", |
|
| 273 |
"Filaments", |
|
| 274 |
"Style", |
|
| 275 |
"annulus", |
|
| 276 |
"female flowers", |
|
| 277 |
"Male flowers", |
|
| 278 |
"Female", |
|
| 279 |
"Infructescences", //order not consistent (sometimes before "Flowers") |
|
| 280 |
"Fruit", |
|
| 281 |
"Fruits", |
|
| 282 |
"fruiting axes", |
|
| 283 |
"drupes", |
|
| 284 |
"Arillode", |
|
| 285 |
"seed", |
|
| 286 |
"Seeds", |
|
| 287 |
"Seedling", |
|
| 288 |
"flower tube", |
|
| 289 |
"nutlets", |
|
| 290 |
"pollen", |
|
| 291 |
"secondary xylem", |
|
| 292 |
"chromosome number", |
|
| 293 |
|
|
| 294 |
"figure", |
|
| 295 |
"fig", |
|
| 296 |
"figs", |
|
| 297 |
|
|
| 298 |
|
|
| 299 |
|
|
| 300 |
|
|
| 301 |
}; |
|
| 302 |
|
|
| 303 |
public void addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
|
|
| 304 |
try {
|
|
| 305 |
for (String featureString : featureStringList){
|
|
| 306 |
UUID featureUuid; |
|
| 307 |
featureUuid = transformer.getFeatureUuid(featureString); |
|
| 308 |
Feature feature = (Feature)termService.find(featureUuid); |
|
| 309 |
if (feature != null){
|
|
| 310 |
FeatureNode child = FeatureNode.NewInstance(feature); |
|
| 311 |
root.addChild(child); |
|
| 312 |
} |
|
| 313 |
} |
|
| 314 |
} catch (UndefinedTransformerMethodException e) {
|
|
| 315 |
logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");
|
|
| 316 |
} |
|
| 317 |
} |
|
| 318 |
|
|
| 319 |
|
|
| 320 |
|
|
| 321 |
/** |
|
| 322 |
* @param args |
|
| 323 |
*/ |
|
| 324 |
public static void main(String[] args) {
|
|
| 325 |
FloraMalesianaActivator me = new FloraMalesianaActivator(); |
|
| 326 |
me.doImport(cdmDestination); |
|
| 327 |
} |
|
| 328 |
|
|
| 329 |
} |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/eflora/FloraMalesianaVol13Activator.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.eflora; |
|
| 11 |
|
|
| 12 |
import java.net.URI; |
|
| 13 |
import java.util.HashSet; |
|
| 14 |
import java.util.List; |
|
| 15 |
import java.util.Set; |
|
| 16 |
import java.util.UUID; |
|
| 17 |
|
|
| 18 |
import org.apache.log4j.Logger; |
|
| 19 |
import org.springframework.transaction.TransactionStatus; |
|
| 20 |
|
|
| 21 |
import eu.etaxonomy.cdm.api.service.ITermService; |
|
| 22 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
|
| 23 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
|
| 24 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
|
| 25 |
import eu.etaxonomy.cdm.io.common.CdmDefaultImport; |
|
| 26 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK; |
|
| 27 |
import eu.etaxonomy.cdm.io.common.events.IIoObserver; |
|
| 28 |
import eu.etaxonomy.cdm.io.common.events.LoggingIoObserver; |
|
| 29 |
import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer; |
|
| 30 |
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; |
|
| 31 |
import eu.etaxonomy.cdm.io.eflora.floraMalesiana.FloraMalesianaTransformer; |
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import eu.etaxonomy.cdm.io.markup.MarkupImportConfigurator; |
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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; |
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import eu.etaxonomy.cdm.model.description.PolytomousKey; |
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import eu.etaxonomy.cdm.model.reference.Reference; |
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
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/** |
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* @author a.mueller |
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* @created 20.06.2008 |
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* @version 1.0 |
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*/ |
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public class FloraMalesianaVol13Activator {
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private static final Logger logger = Logger.getLogger(FloraMalesianaVol13Activator.class); |
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//database validation status (create, update, validate ...) |
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static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE; |
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static final URI fmSource13_small = EfloraSources.fm_13_small_families(); |
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static final URI fmSource13_large = EfloraSources.fm_13_large_families(); |
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static final URI fmSource12 = EfloraSources.fm_12(); |
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static final URI fmSource2_2 = EfloraSources.fm_2_2(); |
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_andreasM3(); |
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_malesiana_preview(); |
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_malesiana_production(); |
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static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); |
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql(); |
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test(); |
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private boolean includeVol13_small = false; |
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private boolean includeVol13_large = false; |
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private boolean includeVol12 = false; |
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private boolean includeVol2_2 = true; |
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private boolean h2ForCheck = true; |
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//feature tree uuid |
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public static final UUID featureTreeUuid = UUID.fromString("168df0c6-6429-484c-b26f-ded1f7e44bd9");
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//classification |
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static final UUID classificationUuid = UUID.fromString("ca4e4bcb-a1d1-4124-a358-a3d3c41dd450");
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//check - import |
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static CHECK check = CHECK.IMPORT_WITHOUT_CHECK; |
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static boolean doPrintKeys = false; |
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//taxa |
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static final boolean doTaxa = true; |
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private boolean replaceStandardKeyTitles = false; |
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private IIoObserver observer = new LoggingIoObserver(); |
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private Set<IIoObserver> observerList = new HashSet<IIoObserver>(); |
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private void doImport(ICdmDataSource cdmDestination){
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observerList.add(observer); |
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if (h2ForCheck && cdmDestination.getDatabaseType().equals(CdmDestinations.localH2().getDatabaseType())){
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check = CHECK.CHECK_ONLY; |
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} |
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//make Source |
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URI source = fmSource13_small; |
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MarkupImportConfigurator markupConfig= MarkupImportConfigurator.NewInstance(source, cdmDestination); |
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markupConfig.setClassificationUuid(classificationUuid); |
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markupConfig.setDoTaxa(doTaxa); |
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markupConfig.setCheck(check); |
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markupConfig.setDoPrintKeys(doPrintKeys); |
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markupConfig.setDbSchemaValidation(hbm2dll); |
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markupConfig.setObservers(observerList); |
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markupConfig.setReplaceStandardKeyTitles(replaceStandardKeyTitles); |
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markupConfig.setSourceReference(getSourceReference("Flora Malesiana - Vol. 13"));
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CdmDefaultImport<MarkupImportConfigurator> myImport = new CdmDefaultImport<MarkupImportConfigurator>(); |
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//Vol13_2 |
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if (includeVol13_large){
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System.out.println("\nStart import from ("+ fmSource13_large.toString() + ") ...");
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source = fmSource13_large; |
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markupConfig.setSource(source); |
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myImport.invoke(markupConfig); |
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System.out.println("End import from ("+ fmSource13_large.toString() + ")...");
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} |
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//Vol13_1 |
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if (includeVol13_small){
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System.out.println("\nStart import from ("+ fmSource13_small.toString() + ") ...");
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source = fmSource13_small; |
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markupConfig.setSource(source); |
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myImport.invoke(markupConfig); |
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System.out.println("End import from ("+ fmSource13_small.toString() + ")...");
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} |
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//Vol12 |
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if (includeVol12){
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source = fmSource12; |
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System.out.println("\nStart import from ("+ source.toString() + ") ...");
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markupConfig.setSource(source); |
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myImport.invoke(markupConfig); |
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System.out.println("End import from ("+ source.toString() + ")...");
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} |
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//Vol_2_2 |
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if (includeVol2_2){
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source = fmSource2_2; |
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System.out.println("\nStart import from ("+ source.toString() + ") ...");
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markupConfig.setSource(source); |
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myImport.invoke(markupConfig); |
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System.out.println("End import from ("+ source.toString() + ")...");
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} |
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// makeGeoService(); |
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FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService()); |
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myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree); |
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//check keys |
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if (doPrintKeys){
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TransactionStatus tx = myImport.getCdmAppController().startTransaction(); |
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List<PolytomousKey> keys = myImport.getCdmAppController().getPolytomousKeyService().list(PolytomousKey.class, null, null, null, null); |
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for(PolytomousKey key : keys){
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key.print(System.out); |
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System.out.println(); |
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} |
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myImport.getCdmAppController().commitTransaction(tx); |
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} |
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} |
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private Reference getSourceReference(String string) {
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Reference result = ReferenceFactory.newGeneric(); |
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result.setTitleCache(string); |
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return result; |
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} |
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private FeatureTree makeFeatureNode(ITermService service){
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FloraMalesianaTransformer transformer = new FloraMalesianaTransformer(); |
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FeatureTree result = FeatureTree.NewInstance(featureTreeUuid); |
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result.setTitleCache("Flora Malesiana Presentation Feature Tree");
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FeatureNode root = result.getRoot(); |
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FeatureNode newNode; |
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newNode = FeatureNode.NewInstance(Feature.DESCRIPTION()); |
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root.addChild(newNode); |
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addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service); |
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addFeataureNodesByStringList(generellDescriptionsUpToAnatomyList, root, transformer, service); |
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newNode = FeatureNode.NewInstance(Feature.ANATOMY()); |
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addFeataureNodesByStringList(anatomySubfeatureList, newNode, transformer, service); |
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newNode = addFeataureNodesByStringList(generellDescriptionsFromAnatomyToPhytoChemoList, root, transformer, service); |
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addFeataureNodesByStringList(phytoChemoSubFeaturesList, newNode, transformer, service); |
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newNode = addFeataureNodesByStringList(generellDescriptionsFromPhytoChemoList, root, transformer, service); |
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newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION()); |
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root.addChild(newNode); |
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newNode = FeatureNode.NewInstance(Feature.ECOLOGY()); |
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root.addChild(newNode); |
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addFeataureNodesByStringList(habitatEcologyList, root, transformer, service); |
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newNode = FeatureNode.NewInstance(Feature.USES()); |
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root.addChild(newNode); |
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addFeataureNodesByStringList(chomosomesList, root, transformer, service); |
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newNode = FeatureNode.NewInstance(Feature.CITATION()); |
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root.addChild(newNode); |
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return result; |
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} |
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private static String [] chomosomesList = new String[]{
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"Chromosomes", |
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}; |
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private static String [] habitatEcologyList = new String[]{
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"Habitat", |
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"Habitat & Ecology" |
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}; |
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private static String [] generellDescriptionsUpToAnatomyList = new String[]{
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"Fossils", |
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"Morphology and anatomy", |
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"Morphology", |
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"Vegetative morphology and anatomy", |
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}; |
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private static String [] anatomySubfeatureList = new String[]{
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"Leaf anatomy", |
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"Wood anatomy" |
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}; |
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private static String [] generellDescriptionsFromAnatomyToPhytoChemoList = new String[]{
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"Flower morphology", |
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"Palynology", |
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"Pollination", |
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"Pollen morphology", |
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"embryology", |
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"cytology", |
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"Life cycle", |
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"Fruits and embryology", |
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"Dispersal", |
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"Chromosome numbers", |
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"Phytochemistry and Chemotaxonomy", |
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}; |
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private static String [] phytoChemoSubFeaturesList = new String[]{
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"Alkaloids", |
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"Iridoid glucosides", |
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"Leaf phenolics", |
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"Storage products of seeds", |
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"Aluminium", |
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"Chemotaxonomy", |
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}; |
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private static String [] generellDescriptionsFromPhytoChemoList = new String[]{
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"Phytochemistry", |
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"Taxonomy", |
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"history", |
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"cultivation", |
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"Notes" |
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}; |
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private static String [] descriptionFeatureList = new String[]{
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"lifeform", |
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"Bark", |
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//new |
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"wood", |
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"Indumentum", |
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"endophytic body", |
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"flowering buds", |
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"Branchlets", |
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"Branches", |
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"Branch", |
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"Flowering branchlets", |
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"Trees", |
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"Twigs", |
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"stem", |
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"Stems", |
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"stem leaves", |
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"Leaves", |
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Also available in: Unified diff
move eflora activators from app-import to cdm-eflora