com.dnastack.bob.service.processor.impl.BeaconizerBeaconProcessor.java Source code

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Here is the source code for com.dnastack.bob.service.processor.impl.BeaconizerBeaconProcessor.java

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/*
 * The MIT License
 *
 * Copyright 2014 Miroslav Cupak (mirocupak@gmail.com).
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */
package com.dnastack.bob.service.processor.impl;

import com.dnastack.bob.persistence.entity.Beacon;
import com.dnastack.bob.persistence.entity.Query;
import com.dnastack.bob.persistence.enumerated.Reference;
import com.google.common.collect.ImmutableSet;
import java.io.UnsupportedEncodingException;
import java.net.MalformedURLException;
import java.util.Set;
import java.util.concurrent.Future;
import javax.ejb.AsyncResult;
import javax.ejb.Asynchronous;
import org.apache.http.client.methods.HttpRequestBase;

import static com.dnastack.bob.service.processor.util.HttpUtils.createRequest;
import static com.dnastack.bob.service.processor.util.HttpUtils.executeRequest;
import static com.dnastack.bob.service.processor.util.ParsingUtils.parseBooleanFromJson;

/**
 * Beaconizer beacon service.
 *
 * @author Miroslav Cupak (mirocupak@gmail.com)
 * @version 1.0
 */
public abstract class BeaconizerBeaconProcessor extends AbstractBeaconProcessor {

    private static final long serialVersionUID = 112L;
    private static final Set<Reference> SUPPORTED_REFS = ImmutableSet.of(Reference.HG19);

    protected abstract String getParamTemplate();

    protected abstract String getBaseUrl();

    private String getQueryUrl(String beacon, String chrom, Long pos, String allele) throws MalformedURLException {
        String params = String.format(getParamTemplate(), beacon, chrom, pos, allele);

        return getBaseUrl() + params;
    }

    @Override
    @Asynchronous
    public Future<String> getQueryResponse(Beacon beacon, Query query) {
        String res = null;

        // should be POST, but the server accepts GET as well
        try {
            HttpRequestBase request = createRequest(getQueryUrl(beacon.getId(), query.getChromosome().toString(),
                    query.getPosition(), query.getAllele()), false, null);
            request.setHeader("Accept", "application/json");
            res = executeRequest(request);
        } catch (MalformedURLException | UnsupportedEncodingException ex) {
            // ignore, already null
        }

        return new AsyncResult<>(res);
    }

    @Override
    @Asynchronous
    public Future<Boolean> parseQueryResponse(Beacon b, String response) {
        Boolean res = parseBooleanFromJson(response, "exists");

        return new AsyncResult<>(res);
    }

    @Override
    public Set<Reference> getSupportedReferences() {
        return SUPPORTED_REFS;
    }
}