uk.ac.ebi.eva.server.ws.ga4gh.GA4GHVariantWSServer.java Source code

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Here is the source code for uk.ac.ebi.eva.server.ws.ga4gh.GA4GHVariantWSServer.java

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/*
 * European Variation Archive (EVA) - Open-access database of all types of genetic
 * variation data from all species
 *
 * Copyright 2014-2016 EMBL - European Bioinformatics Institute
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *   http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

package uk.ac.ebi.eva.server.ws.ga4gh;

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

import javax.servlet.http.HttpServletResponse;

import org.apache.commons.lang.StringUtils;
import org.opencb.biodata.ga4gh.GASearchVariantRequest;
import org.opencb.biodata.ga4gh.GASearchVariantsResponse;
import org.opencb.biodata.ga4gh.GAVariant;
import org.opencb.biodata.models.feature.Region;
import org.opencb.biodata.models.variant.Variant;
import org.opencb.biodata.models.variant.ga4gh.GAVariantFactory;
import org.opencb.datastore.core.QueryOptions;
import org.opencb.datastore.core.QueryResult;
import org.opencb.opencga.lib.auth.IllegalOpenCGACredentialsException;
import org.opencb.opencga.storage.core.variant.adaptors.VariantDBAdaptor;
import org.springframework.http.HttpStatus;
import org.springframework.web.bind.annotation.ExceptionHandler;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.RestController;

import io.swagger.annotations.Api;
import uk.ac.ebi.eva.lib.datastore.DBAdaptorConnector;
import uk.ac.ebi.eva.server.ws.EvaWSServer;

/**
 *
 * @author Cristina Yenyxe Gonzalez Garcia <cyenyxe@ebi.ac.uk>
 */
@RestController
@RequestMapping(value = "/v1/ga4gh/variants", produces = "application/json")
@Api(tags = { "ga4gh", "variants" })
public class GA4GHVariantWSServer extends EvaWSServer {

    public GA4GHVariantWSServer() {
    }

    /**
     * "start" and "end" are 0-based, whereas all the position stored are 1-based
     * 
     * @see http://ga4gh.org/documentation/api/v0.5/ga4gh_api.html#/schema/org.ga4gh.GASearchVariantsRequest
     */
    @RequestMapping(value = "/search", method = RequestMethod.GET)
    public GASearchVariantsResponse getVariantsByRegion(@RequestParam("referenceName") String chromosome,
            @RequestParam("start") int start, @RequestParam("end") int end,
            //                                        @RequestParam("variantName") String id,
            @RequestParam(name = "variantSetIds", required = false) List<String> files,
            //                                        @RequestParam(name = "callSetIds", required = false) String samples,
            @RequestParam(name = "pageToken", required = false) String pageToken,
            @RequestParam(name = "pageSize", defaultValue = "10") int limit)
            throws IllegalOpenCGACredentialsException, UnknownHostException, IOException {
        initializeQueryOptions();

        VariantDBAdaptor variantMongoDbAdaptor = DBAdaptorConnector.getVariantDBAdaptor("hsapiens_grch37");

        if (files != null && !files.isEmpty()) {
            queryOptions.put("files", files);
        }

        int idxCurrentPage = 0;
        if (pageToken != null && !pageToken.isEmpty() && StringUtils.isNumeric(pageToken)) {
            idxCurrentPage = Integer.parseInt(pageToken);
            queryOptions.put("skip", idxCurrentPage * limit);
        }
        queryOptions.put("limit", limit);

        // Create the provided region, whose size can't exceed 1 million positions
        Region region = new Region(chromosome, start, end);
        int regionSize = region.getEnd() - region.getStart();

        if (regionSize > 1000000) {
            throw new IllegalArgumentException("The size of the region is larger than 1 million nucleotides");
        }

        QueryResult<Variant> qr = variantMongoDbAdaptor.getAllVariantsByRegion(region, queryOptions);
        // Convert Variant objects to GAVariant
        List<GAVariant> gaVariants = GAVariantFactory.create(qr.getResult());
        // Calculate the next page token
        int idxLastElement = idxCurrentPage * limit + limit;
        String nextPageToken = (idxLastElement < qr.getNumTotalResults()) ? String.valueOf(idxCurrentPage + 1)
                : null;

        // Create the custom response for the GA4GH API
        return new GASearchVariantsResponse(gaVariants, nextPageToken);
    }

    @RequestMapping(value = "/search", method = RequestMethod.POST, consumes = "application/json")
    public GASearchVariantsResponse getVariantsByRegion(GASearchVariantRequest request)
            throws IllegalOpenCGACredentialsException, UnknownHostException, IOException {
        request.validate();
        return getVariantsByRegion(request.getReferenceName(), (int) request.getStart(), (int) request.getEnd(),
                request.getVariantSetIds(), request.getPageToken(), request.getPageSize());
    }

    @ExceptionHandler(IllegalArgumentException.class)
    public void handleException(IllegalArgumentException e, HttpServletResponse response) throws IOException {
        response.sendError(HttpStatus.PAYLOAD_TOO_LARGE.value(), e.getMessage());
    }

}