EDIT

package eu.etaxonomy.cdm.io.prometheus;

import java.io.IOException;

import java.net.URI;

import org.apache.log4j.Logger;

import eu.etaxonomy.cdm.app.common.CdmDestinations;

import eu.etaxonomy.cdm.database.DatabaseTypeEnum;

import eu.etaxonomy.cdm.database.DbSchemaValidation;

import eu.etaxonomy.cdm.database.ICdmDataSource;

import eu.etaxonomy.cdm.io.common.CdmDefaultImport;

import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;

/**

 *

 * @author pplitzner

 * @date 18.02.2019

 *

 */

public class PrometheusPropertiesActivator {

	@SuppressWarnings("unused")

	private static final Logger logger = Logger.getLogger(PrometheusPropertiesActivator.class);

	private void doImport(ICdmDataSource cdmDestination) throws IOException{

	    /*

	     * Source file:

	     * extracted data from xml-exported prometheus ontology

	     */

	    URI uri = URI.create("file:/home/pplitzner/projects/Additivity/prometheus_extract/new_qualitative_properties.csv");

		PrometheusPropertiesCsvImportConfigurator config = PrometheusPropertiesCsvImportConfigurator.NewInstance(uri, cdmDestination);

		config.setCheck(CHECK.IMPORT_WITHOUT_CHECK);

		config.setDbSchemaValidation(DbSchemaValidation.VALIDATE);

		CdmDefaultImport<PrometheusPropertiesCsvImportConfigurator> myImport = new CdmDefaultImport<>();

		System.out.println("Start import from ("+ cdmDestination.toString() + ") ...");

		myImport.invoke(config);

		System.out.println("End import from ("+ cdmDestination.toString() + ")...");

	}

	public static void main(String[] args) {

		PrometheusPropertiesActivator activator = new PrometheusPropertiesActivator();

		try {

	        ICdmDataSource dataSource = CdmDestinations.makeDestination(DatabaseTypeEnum.MySQL, "127.0.0.1", "empty", 3306, "root", null);

//		    ICdmDataSource dataSource = CdmDestinations.cdm_additivity_ontology();

            activator.doImport(dataSource);

        } catch (IOException e) {

            e.printStackTrace();

        }

	}

}

/**

* Copyright (C) 2017 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.io.prometheus;

import java.io.IOException;

import java.net.URI;

import eu.etaxonomy.cdm.database.ICdmDataSource;

import eu.etaxonomy.cdm.io.csv.in.CsvImportConfiguratorBase;

/**

*

* @author pplitzner

* @date 18.02.2019

*

*/

public class PrometheusPropertiesCsvImportConfigurator

        extends CsvImportConfiguratorBase{

    private static final long serialVersionUID = 987286481306951779L;

    public static PrometheusPropertiesCsvImportConfigurator NewInstance(URI source,

            ICdmDataSource cdmDestination) throws IOException {

        return new PrometheusPropertiesCsvImportConfigurator(source, cdmDestination);

    }

// ****************** CONSTRUCTOR *****************************/

    private PrometheusPropertiesCsvImportConfigurator(URI source,

            ICdmDataSource cdmDestination) throws IOException{

        super(source, cdmDestination, null);

    }

// *************************************

    @Override

    @SuppressWarnings("unchecked")

    protected void makeIoClassList() {

        ioClassList = new Class[] {

                PrometheusPropertiesImport.class };

    }

    @Override

    public PrometheusPropertiesCsvImportState getNewState() {

        return new PrometheusPropertiesCsvImportState(this);

    }

}

/**

* Copyright (C) 2017 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.io.prometheus;

import java.util.ArrayList;

import java.util.List;

import eu.etaxonomy.cdm.api.service.ITermService;

import eu.etaxonomy.cdm.io.csv.in.CsvImportState;

import eu.etaxonomy.cdm.model.agent.Person;

import eu.etaxonomy.cdm.model.common.TermType;

import eu.etaxonomy.cdm.model.common.TermVocabulary;

import eu.etaxonomy.cdm.model.common.VerbatimTimePeriod;

import eu.etaxonomy.cdm.model.description.Feature;

import eu.etaxonomy.cdm.model.description.State;

import eu.etaxonomy.cdm.model.reference.Reference;

import eu.etaxonomy.cdm.model.reference.ReferenceFactory;

/**

*

* @author pplitzner

* @date 18.02.2019

*

*/

public class PrometheusPropertiesCsvImportState extends CsvImportState<PrometheusPropertiesCsvImportConfigurator> {

    private List<State> existingTerms = new ArrayList<>();

    private final TermVocabulary<Feature> propertiesVoc;

    private final Reference citation;

    protected PrometheusPropertiesCsvImportState(PrometheusPropertiesCsvImportConfigurator config) {

        super(config);

        propertiesVoc = TermVocabulary.NewInstance(TermType.Feature);

        propertiesVoc.setLabel("Properties");

        citation = ReferenceFactory.newGeneric();

        citation.setTitle("The Prometheus Description Model: an examination of the taxonomic description-building process and its representation.");

        Person author = Person.NewInstance(null, "Pullan", null, "M.");

        citation.setAuthorship(author);

        VerbatimTimePeriod datePublished = VerbatimTimePeriod.NewVerbatimInstance();

        datePublished.setStartYear(2005);

        citation.setDatePublished(datePublished);

        citation.setVolume("54");

        citation.setPages("751-756");

    }

    @Override

    public void resetSession(){

        super.resetSession();

    }

    public boolean isTermPresent(String termName, ITermService termService) {

        if(existingTerms.isEmpty()){

            existingTerms = termService.list(State.class, null, null, null, null);

        }

        return existingTerms.stream().map(term->term.getLabel()).anyMatch(label->label.equals(termName));

    }

    public TermVocabulary<Feature> getPropertiesVoc() {

        return propertiesVoc;

    }

    Reference getCitation() {

        return citation;

    }

}

/**

* Copyright (C) 2017 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.io.prometheus;

import java.io.File;

import java.util.Map;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

import eu.etaxonomy.cdm.common.CdmUtils;

import eu.etaxonomy.cdm.io.csv.in.CsvImportBase;

import eu.etaxonomy.cdm.model.common.IdentifiableSource;

import eu.etaxonomy.cdm.model.common.OriginalSourceType;

import eu.etaxonomy.cdm.model.common.TermVocabulary;

import eu.etaxonomy.cdm.model.description.Feature;

/**

*

* @author pplitzner

* @date 18.02.2019

*

*/

@Component

public class PrometheusPropertiesImport extends CsvImportBase<PrometheusPropertiesCsvImportConfigurator, PrometheusPropertiesCsvImportState, File>{

    private static final long serialVersionUID = -5600766240192189822L;

    private static Logger logger = Logger.getLogger(PrometheusPropertiesImport.class);

    final String HEADER_LABEL = "NEW_QUALITATIVE_PROPERTIES - NEW_QUALITATIVE_PROPERTY - term";

    @Override

    protected void handleSingleLine(PrometheusPropertiesCsvImportState importState) {

        Map<String, String> currentRecord = importState.getCurrentRecord();

        String termLabel = currentRecord.get(HEADER_LABEL);

        //check if already present

        if(CdmUtils.isBlank(termLabel) || importState.isTermPresent(termLabel, getTermService())){

            return;

        }

        Feature structure = Feature.NewInstance(null, termLabel, null);

        structure.setIdInVocabulary(termLabel);

        TermVocabulary vocabulary = importState.getPropertiesVoc();

        vocabulary.addTerm(structure);

        IdentifiableSource source = IdentifiableSource.NewInstance(OriginalSourceType.Import, importState.getCitation().getTitle(), null, importState.getCitation(), null);

        source.setIdInSource(termLabel);

        structure.addSource(source);

        getVocabularyService().saveOrUpdate(vocabulary);

        getTermService().saveOrUpdate(structure);

    }

}