VariantWSServer.java

/*
 * Copyright 2015 OpenCB
 *
 * 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 org.opencb.hpg.bigdata.app.rest.ws;

import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import io.swagger.annotations.ApiParam;
import org.opencb.commons.datastore.core.Query;
import org.opencb.hpg.bigdata.core.lib.VariantParseQuery;

import javax.servlet.http.HttpServletRequest;
import javax.ws.rs.GET;
import javax.ws.rs.Path;
import javax.ws.rs.Produces;
import javax.ws.rs.QueryParam;
import javax.ws.rs.core.Context;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Response;
import javax.ws.rs.core.UriInfo;
import java.io.IOException;

/**
 * Created by jacobo on 15/12/14.
 */
@Path("/{version}/variant")
@Produces(MediaType.APPLICATION_JSON)
@Api(value = "Cohorts", position = 9, description = "Methods for working with 'cohorts' endpoint")
public class VariantWSServer {


    public VariantWSServer(@Context UriInfo uriInfo, @Context HttpServletRequest httpServletRequest) throws IOException {
//        super(uriInfo, httpServletRequest);
    }

    @GET
    @Path("/sql")
    @ApiOperation(value = "Create a cohort", position = 1, notes = "", response = String.class)
    public Response getSqlQuery(@ApiParam(value = "table", required = true) @QueryParam("table") String table,
                                @ApiParam(value = "id") @QueryParam("id") String id,
                                @ApiParam(value = "ancestralAllele") @QueryParam("ancestralAllele") String ancestralAllele,
                                @ApiParam(value = "displayConsequenceType")
                                    @QueryParam("displayConsequenceType") String displayConsequenceType,
                                @ApiParam(value = "xrefs") @QueryParam("xrefs") String xrefs,
                                @ApiParam(value = "hgvs") @QueryParam("hgvs") String hgvs,
                                @ApiParam(value = "consequenceTypes") @QueryParam("consequenceTypes") String consequenceTypes,
                                @ApiParam(value = "consequenceTypes.sequenceOntologyTerms.accession")
                                    @QueryParam("consequenceTypes.sequenceOntologyTerms.accession") String consequenceSoAccession,
                                @ApiParam(value = "consequenceTypes.sequenceOntologyTerms.name")
                                    @QueryParam("consequenceTypes.sequenceOntologyTerms.name") String consequenceSoName,
                                @ApiParam(value = "populationFrequencies")
                                    @QueryParam("populationFrequencies") String populationFrequencies,
                                @ApiParam(value = "conservation") @QueryParam("conservation") String conservation,
                                @ApiParam(value = "variantTraitAssociation")
                                    @QueryParam("variantTraitAssociation") String variantTraitAssociation) {
        try {
            Query query = new Query();
            query.putIfNotEmpty("id", id);
            query.putIfNotEmpty("ancestralAllele", ancestralAllele);
            query.putIfNotEmpty("displayConsequenceType", displayConsequenceType);
            query.putIfNotEmpty("xrefs", xrefs);
            query.putIfNotEmpty("hgvs", hgvs);
            query.putIfNotEmpty("annotation.consequenceTypes", consequenceTypes);
            query.putIfNotEmpty("annotation.populationFrequencies", populationFrequencies);
            query.putIfNotEmpty("annotation.consequenceTypes.sequenceOntologyTerms.accession", consequenceSoAccession);
            query.putIfNotEmpty("annotation.consequenceTypes.sequenceOntologyTerms.name", consequenceSoName);
            query.putIfNotEmpty("annotation.conservation", conservation);
            query.putIfNotEmpty("annotation.variantTraitAssociation", variantTraitAssociation);

            VariantParseQuery variantParseQuery = new VariantParseQuery();
            String sql = variantParseQuery.parse(query, null, table);
            return Response.ok(sql).build();
        } catch (Exception e) {
            return Response.ok(e.toString()).build();
        }
    }

}