org.cbioportal.genome_nexus.annotation.domain.internal.VariantAnnotationRepositoryImpl.java Source code

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Here is the source code for org.cbioportal.genome_nexus.annotation.domain.internal.VariantAnnotationRepositoryImpl.java

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/*
 * Copyright (c) 2016 Memorial Sloan-Kettering Cancer Center.
 *
 * This library is distributed in the hope that it will be useful, but WITHOUT
 * ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS
 * FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder
 * is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no
 * obligations to provide maintenance, support, updates, enhancements or
 * modifications. In no event shall Memorial Sloan-Kettering Cancer Center be
 * liable to any party for direct, indirect, special, incidental or
 * consequential damages, including lost profits, arising out of the use of this
 * software and its documentation, even if Memorial Sloan-Kettering Cancer
 * Center has been advised of the possibility of such damage.
 */

/*
 * This file is part of cBioPortal Genome Nexus.
 *
 * cBioPortal is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Affero General Public License as
 * published by the Free Software Foundation, either version 3 of the
 * License.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Affero General Public License for more details.
 *
 * You should have received a copy of the GNU Affero General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
*/

package org.cbioportal.genome_nexus.annotation.domain.internal;

import com.fasterxml.jackson.databind.ObjectMapper;
import com.mongodb.DBObject;
import com.mongodb.util.JSON;
import org.cbioportal.genome_nexus.annotation.domain.VariantAnnotation;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.mongodb.core.MongoTemplate;

import java.io.IOException;
import java.util.List;

/**
 * @author Selcuk Onur Sumer
 */
public class VariantAnnotationRepositoryImpl implements VariantAnnotationRepositoryCustom {
    @Autowired
    private MongoTemplate mongoTemplate;

    public final String DEFAULT_COLLECTION = "vep.annotation";

    /**
     * Parses and saves the entire content of the annotation JSON object to the database.
     *
     * @param variant           variant key (used as an id)
     * @param annotationJSON    raw annotation JSON (obtained from the service)
     */
    @Override
    public void saveAnnotationJson(String variant, String annotationJSON) {
        // parse the given annotation JSON string to get a proper object
        DBObject dbObject = convertToDbObject(annotationJSON);

        // update the _id field to the given variant
        dbObject.put("_id", variant);

        // save the object into the correct repository
        this.mongoTemplate.save(dbObject, DEFAULT_COLLECTION);
    }

    /**
     * Maps the given raw annotation JSON string onto a VariantAnnotation instance.
     *
     * @param variant           variant key
     * @param annotationJSON    raw annotation JSON string
     * @return a VariantAnnotation instance
     * @throws IOException
     */
    @Override
    public VariantAnnotation mapAnnotationJson(String variant, String annotationJSON) throws IOException {
        //String toMap = removeArrayBrackets(annotationJSON);
        String toMap = JSON.serialize(convertToDbObject(annotationJSON));

        VariantAnnotation vepVariantAnnotation;
        ObjectMapper mapper = new ObjectMapper();

        // map annotation string onto VariantAnnotation instance
        vepVariantAnnotation = mapper.readValue(toMap, VariantAnnotation.class);
        // include original variant value too
        vepVariantAnnotation.setVariant(variant);
        //vepVariantAnnotation.setAnnotationJSON(annotationJSON);

        return vepVariantAnnotation;
    }

    /**
      * Transforms the given annotationJSON to a DBObject instance.
      * If the given annotation JSON is an array, returns only the first element.
      *
      * @param annotationJSON    annotation JSON as a string
      * @return DBObject instance
      */
    private DBObject convertToDbObject(String annotationJSON) {
        DBObject dbObject = (DBObject) JSON.parse(annotationJSON);

        // if it is a list, get the first element of the list
        if (dbObject instanceof List) {
            List list = ((List) dbObject);

            // get the first element, ignore the rest
            if (list.size() > 0) {
                dbObject = (DBObject) list.iterator().next();
            }
        }

        return dbObject;
    }

    /**
      *
      * @param annotationJSON    annotation JSON as a string
      * @return  stripped string with array brackets removed
      */
    private String removeArrayBrackets(String annotationJSON) {
        String stripped = annotationJSON;

        // if annotation JSON is actually an array, assume it is an array of size 1,
        // and convert it to a single object by removing array brackets
        if (annotationJSON.trim().startsWith("[")) {
            int start = annotationJSON.indexOf("[");
            int end = annotationJSON.lastIndexOf("]");
            stripped = annotationJSON.substring(start + 1, end);
        }

        return stripped;
    }
}