edu.mayo.cts2.framework.plugin.service.lexevs.bulk.mapversion.MappingExtensionBulkDownloader.java Source code

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Here is the source code for edu.mayo.cts2.framework.plugin.service.lexevs.bulk.mapversion.MappingExtensionBulkDownloader.java

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/*
* Copyright: (c) Mayo Foundation for Medical Education and
* Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the
* triple-shield Mayo logo are trademarks and service marks of MFMER.
*
* Distributed under the OSI-approved BSD 3-Clause License.
* See http://ncip.github.com/lexevs-service/LICENSE.txt for details.
*/
package edu.mayo.cts2.framework.plugin.service.lexevs.bulk.mapversion;

import java.io.OutputStream;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import javax.annotation.Resource;

import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference;
import org.LexGrid.LexBIG.Exceptions.LBParameterException;
import org.LexGrid.LexBIG.Extensions.Generic.CodingSchemeReference;
import org.LexGrid.LexBIG.Extensions.Generic.MappingExtension;
import org.LexGrid.LexBIG.Impl.helpers.ResolvedConceptReferencesIteratorAdapter;
import org.LexGrid.LexBIG.Utility.Iterators.ResolvedConceptReferencesIterator;
import org.springframework.beans.factory.InitializingBean;
import org.springframework.stereotype.Component;

import edu.mayo.cts2.framework.plugin.service.lexevs.bulk.AbstractBulkDownloader;
import edu.mayo.cts2.framework.plugin.service.lexevs.bulk.Extractor;

/**
 * A Bulk Downloader based on the LexEVS MappingExtension.
 *
 * @author <a href="mailto:kevin.peterson@mayo.edu">Kevin Peterson</a>
 */
@Component
public class MappingExtensionBulkDownloader extends AbstractBulkDownloader
        implements MapVersionBulkDownloader, InitializingBean {

    @Resource
    private MappingExtension mappingExtension;

    private final static Map<String, Extractor> SOURCE_EXTRACTOR_MAP = new HashMap<String, Extractor>() {

        private static final long serialVersionUID = -7214815015371005224L;
        {
            {
                put(MapVersionBulkDownloader.SOURCE_CODE_FIELD, new Extractor() {
                    @Override
                    public String extract(ResolvedConceptReference ref) {
                        return ref.getCode();
                    }
                });

                put(MapVersionBulkDownloader.SOURCE_NAMESPACE_FIELD, new Extractor() {
                    @Override
                    public String extract(ResolvedConceptReference ref) {
                        return ref.getCodeNamespace();
                    }
                });

                put(MapVersionBulkDownloader.SOURCE_DESCRIPTION_FIELD, new Extractor() {
                    @Override
                    public String extract(ResolvedConceptReference ref) {
                        if (ref.getEntityDescription() != null) {
                            return ref.getEntityDescription().getContent();
                        } else {
                            return "";
                        }
                    }
                });

                put(MapVersionBulkDownloader.SOURCE_CODINGSCHEME_NAME_FIELD, new Extractor() {
                    @Override
                    public String extract(ResolvedConceptReference ref) {
                        return ref.getCodingSchemeName();
                    }
                });

                put(MapVersionBulkDownloader.SOURCE_CODINGSCHEME_URI_FIELD, new Extractor() {
                    @Override
                    public String extract(ResolvedConceptReference ref) {
                        return ref.getCodingSchemeURI();
                    }
                });

                put(MapVersionBulkDownloader.SOURCE_CODINGSCHEME_VERSION_FIELD, new Extractor() {
                    @Override
                    public String extract(ResolvedConceptReference ref) {
                        return ref.getCodingSchemeVersion();
                    }
                });

            }
        }
    };

    private final static Map<String, Extractor> TARGET_EXTRACTOR_MAP = new HashMap<String, Extractor>() {

        private ResolvedConceptReference getTarget(ResolvedConceptReference ref) {
            return ref.getSourceOf().getAssociation(0).getAssociatedConcepts().getAssociatedConcept(0);
        }

        private static final long serialVersionUID = -7214815015371005224L;
        {
            {
                put(MapVersionBulkDownloader.TARGET_CODE_FIELD, new Extractor() {
                    @Override
                    public String extract(ResolvedConceptReference ref) {
                        return getTarget(ref).getCode();
                    }
                });

                put(MapVersionBulkDownloader.TARGET_NAMESPACE_FIELD, new Extractor() {
                    @Override
                    public String extract(ResolvedConceptReference ref) {
                        return getTarget(ref).getCodeNamespace();
                    }
                });

                put(MapVersionBulkDownloader.TARGET_DESCRIPTION_FIELD, new Extractor() {
                    @Override
                    public String extract(ResolvedConceptReference ref) {
                        return getTarget(ref).getEntityDescription().getContent();
                    }
                });

                put(MapVersionBulkDownloader.TARGET_CODINGSCHEME_NAME_FIELD, new Extractor() {
                    @Override
                    public String extract(ResolvedConceptReference ref) {
                        return getTarget(ref).getCodingSchemeName();
                    }
                });

                put(MapVersionBulkDownloader.TARGET_CODINGSCHEME_URI_FIELD, new Extractor() {
                    @Override
                    public String extract(ResolvedConceptReference ref) {
                        return getTarget(ref).getCodingSchemeURI();
                    }
                });

                put(MapVersionBulkDownloader.TARGET_CODINGSCHEME_VERSION_FIELD, new Extractor() {
                    @Override
                    public String extract(ResolvedConceptReference ref) {
                        return getTarget(ref).getCodingSchemeVersion();
                    }
                });

            }
        }
    };

    private Map<String, Extractor> extractorMap;

    /* (non-Javadoc)
     * @see org.springframework.beans.factory.InitializingBean#afterPropertiesSet()
     */
    @Override
    public void afterPropertiesSet() throws Exception {
        Map<String, Extractor> map = new HashMap<String, Extractor>();
        map.putAll(SOURCE_EXTRACTOR_MAP);
        map.putAll(TARGET_EXTRACTOR_MAP);

        this.extractorMap = map;
    }

    /* (non-Javadoc)
     * @see edu.mayo.cts2.framework.plugin.service.lexevs.bulk.mapversion.MapVersionBulkDownloader#download(java.io.OutputStream, org.LexGrid.LexBIG.Extensions.Generic.CodingSchemeReference, java.util.List, char)
     */
    @Override
    public void download(OutputStream outputStream, CodingSchemeReference codingScheme, List<String> fields,
            char separator) {

        ResolvedConceptReferencesIterator itr;
        try {
            itr = this.mappingExtension.resolveMapping(codingScheme.getCodingScheme(),
                    codingScheme.getVersionOrTag(), null, null);
        } catch (LBParameterException e) {
            throw new RuntimeException(e);
        }

        this.doWrite(outputStream, new ResolvedConceptReferencesIteratorAdapter(itr), separator, fields);
    }

    @Override
    protected Map<String, Extractor> getExtractorMap() {
        return this.extractorMap;
    }

}