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Revision 273e1f05

ID273e1f055ea0cb2420db3bf9e7e149b9c95fbe63
Parent d3622550
Child 21e704da

Added by Patrick Plitzner 4 months ago

Implement Prometheus properties import

View differences:

app-import/src/main/java/eu/etaxonomy/cdm/io/prometheus/PrometheusPropertiesActivator.java
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package eu.etaxonomy.cdm.io.prometheus;
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import java.io.IOException;
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import java.net.URI;
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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.database.DatabaseTypeEnum;
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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.IImportConfigurator.CHECK;
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/**
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 *
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 * @author pplitzner
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 * @date 18.02.2019
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 *
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 */
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public class PrometheusPropertiesActivator {
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	@SuppressWarnings("unused")
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	private static final Logger logger = Logger.getLogger(PrometheusPropertiesActivator.class);
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	private void doImport(ICdmDataSource cdmDestination) throws IOException{
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	    /*
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	     * Source file:
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	     * extracted data from xml-exported prometheus ontology
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	     */
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	    URI uri = URI.create("file:/home/pplitzner/projects/Additivity/prometheus_extract/new_qualitative_properties.csv");
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		PrometheusPropertiesCsvImportConfigurator config = PrometheusPropertiesCsvImportConfigurator.NewInstance(uri, cdmDestination);
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		config.setCheck(CHECK.IMPORT_WITHOUT_CHECK);
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		config.setDbSchemaValidation(DbSchemaValidation.VALIDATE);
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		CdmDefaultImport<PrometheusPropertiesCsvImportConfigurator> myImport = new CdmDefaultImport<>();
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		System.out.println("Start import from ("+ cdmDestination.toString() + ") ...");
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		myImport.invoke(config);
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		System.out.println("End import from ("+ cdmDestination.toString() + ")...");
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	}
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	public static void main(String[] args) {
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		PrometheusPropertiesActivator activator = new PrometheusPropertiesActivator();
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		try {
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	        ICdmDataSource dataSource = CdmDestinations.makeDestination(DatabaseTypeEnum.MySQL, "127.0.0.1", "empty", 3306, "root", null);
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//		    ICdmDataSource dataSource = CdmDestinations.cdm_additivity_ontology();
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            activator.doImport(dataSource);
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        } catch (IOException e) {
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            e.printStackTrace();
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        }
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	}
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}
app-import/src/main/java/eu/etaxonomy/cdm/io/prometheus/PrometheusPropertiesCsvImportConfigurator.java
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/**
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* Copyright (C) 2017 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.io.prometheus;
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import java.io.IOException;
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import java.net.URI;
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import eu.etaxonomy.cdm.database.ICdmDataSource;
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import eu.etaxonomy.cdm.io.csv.in.CsvImportConfiguratorBase;
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/**
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*
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* @author pplitzner
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* @date 18.02.2019
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*
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*/
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public class PrometheusPropertiesCsvImportConfigurator
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        extends CsvImportConfiguratorBase{
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    private static final long serialVersionUID = 987286481306951779L;
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    public static PrometheusPropertiesCsvImportConfigurator NewInstance(URI source,
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            ICdmDataSource cdmDestination) throws IOException {
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        return new PrometheusPropertiesCsvImportConfigurator(source, cdmDestination);
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    }
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// ****************** CONSTRUCTOR *****************************/
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    private PrometheusPropertiesCsvImportConfigurator(URI source,
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            ICdmDataSource cdmDestination) throws IOException{
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        super(source, cdmDestination, null);
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    }
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// *************************************
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    @Override
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    @SuppressWarnings("unchecked")
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    protected void makeIoClassList() {
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        ioClassList = new Class[] {
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                PrometheusPropertiesImport.class };
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    }
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    @Override
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    public PrometheusPropertiesCsvImportState getNewState() {
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        return new PrometheusPropertiesCsvImportState(this);
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    }
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}
app-import/src/main/java/eu/etaxonomy/cdm/io/prometheus/PrometheusPropertiesCsvImportState.java
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/**
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* Copyright (C) 2017 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.io.prometheus;
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import java.util.ArrayList;
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import java.util.List;
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import eu.etaxonomy.cdm.api.service.ITermService;
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import eu.etaxonomy.cdm.io.csv.in.CsvImportState;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.common.TermType;
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import eu.etaxonomy.cdm.model.common.TermVocabulary;
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import eu.etaxonomy.cdm.model.common.VerbatimTimePeriod;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.State;
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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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*
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* @author pplitzner
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* @date 18.02.2019
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*
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*/
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public class PrometheusPropertiesCsvImportState extends CsvImportState<PrometheusPropertiesCsvImportConfigurator> {
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    private List<State> existingTerms = new ArrayList<>();
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    private final TermVocabulary<Feature> propertiesVoc;
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    private final Reference citation;
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    protected PrometheusPropertiesCsvImportState(PrometheusPropertiesCsvImportConfigurator config) {
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        super(config);
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        propertiesVoc = TermVocabulary.NewInstance(TermType.Feature);
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        propertiesVoc.setLabel("Properties");
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        citation = ReferenceFactory.newGeneric();
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        citation.setTitle("The Prometheus Description Model: an examination of the taxonomic description-building process and its representation.");
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        Person author = Person.NewInstance(null, "Pullan", null, "M.");
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        citation.setAuthorship(author);
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        VerbatimTimePeriod datePublished = VerbatimTimePeriod.NewVerbatimInstance();
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        datePublished.setStartYear(2005);
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        citation.setDatePublished(datePublished);
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        citation.setVolume("54");
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        citation.setPages("751-756");
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    }
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    @Override
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    public void resetSession(){
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        super.resetSession();
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    }
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    public boolean isTermPresent(String termName, ITermService termService) {
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        if(existingTerms.isEmpty()){
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            existingTerms = termService.list(State.class, null, null, null, null);
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        }
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        return existingTerms.stream().map(term->term.getLabel()).anyMatch(label->label.equals(termName));
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    }
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    public TermVocabulary<Feature> getPropertiesVoc() {
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        return propertiesVoc;
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    }
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    Reference getCitation() {
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        return citation;
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    }
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}
app-import/src/main/java/eu/etaxonomy/cdm/io/prometheus/PrometheusPropertiesImport.java
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/**
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* Copyright (C) 2017 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.io.prometheus;
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import java.io.File;
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import java.util.Map;
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import org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.io.csv.in.CsvImportBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.common.OriginalSourceType;
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import eu.etaxonomy.cdm.model.common.TermVocabulary;
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import eu.etaxonomy.cdm.model.description.Feature;
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/**
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*
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* @author pplitzner
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* @date 18.02.2019
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*
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*/
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@Component
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public class PrometheusPropertiesImport extends CsvImportBase<PrometheusPropertiesCsvImportConfigurator, PrometheusPropertiesCsvImportState, File>{
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    private static final long serialVersionUID = -5600766240192189822L;
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    private static Logger logger = Logger.getLogger(PrometheusPropertiesImport.class);
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    final String HEADER_LABEL = "NEW_QUALITATIVE_PROPERTIES - NEW_QUALITATIVE_PROPERTY - term";
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    @Override
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    protected void handleSingleLine(PrometheusPropertiesCsvImportState importState) {
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        Map<String, String> currentRecord = importState.getCurrentRecord();
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        String termLabel = currentRecord.get(HEADER_LABEL);
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        //check if already present
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        if(CdmUtils.isBlank(termLabel) || importState.isTermPresent(termLabel, getTermService())){
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            return;
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        }
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        Feature structure = Feature.NewInstance(null, termLabel, null);
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        structure.setIdInVocabulary(termLabel);
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        TermVocabulary vocabulary = importState.getPropertiesVoc();
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        vocabulary.addTerm(structure);
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        IdentifiableSource source = IdentifiableSource.NewInstance(OriginalSourceType.Import, importState.getCitation().getTitle(), null, importState.getCitation(), null);
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        source.setIdInSource(termLabel);
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        structure.addSource(source);
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        getVocabularyService().saveOrUpdate(vocabulary);
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        getTermService().saveOrUpdate(structure);
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    }
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}

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