gedi.oml.remote.Pipeline.Receiver.java Source code

Introduction

Here is the source code for gedi.oml.remote.Pipeline.Receiver.java

Source

/**
 * 
 *    Copyright 2017 Florian Erhard
 *
 *   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 gedi.oml.remote.Pipeline;

import gedi.core.data.mapper.DisablingGenomicRegionDataMapper;
import gedi.core.data.mapper.GenomicRegionDataMapping;
import gedi.core.reference.ReferenceSequence;
import gedi.core.region.GenomicRegion;
import gedi.core.region.MutableReferenceGenomicRegion;
import gedi.gui.genovis.pixelMapping.PixelLocationMapping;
import io.netty.channel.ChannelHandlerContext;
import io.netty.channel.ChannelInboundHandlerAdapter;
import io.netty.util.ReferenceCountUtil;

import java.util.concurrent.LinkedBlockingQueue;
import java.util.logging.Level;
import java.util.logging.Logger;

@GenomicRegionDataMapping(fromType = Void.class, toType = Object.class)
public class Receiver extends ChannelInboundHandlerAdapter
        implements DisablingGenomicRegionDataMapper<Void, Object> {

    private String id;
    private String server;

    private boolean disabled = true;

    public Receiver(String on) {
        this.server = on;
    }

    public void setId(String id) {
        this.id = id;
    }

    public String getId() {
        return id;
    }

    @Override
    public boolean isDisabled(ReferenceSequence reference, GenomicRegion region,
            PixelLocationMapping pixelMapping) {
        return disabled;
    }

    public void setDisabled(boolean disabled) {
        this.disabled = disabled;
    }

    @Override
    public Object map(ReferenceSequence reference, GenomicRegion region, PixelLocationMapping pixelMapping,
            Void data) {

        synchronized (location) {
            location.set(reference, region, pixelMapping.getXmapper());
        }

        try {
            for (;;) {
                RemotePipelineData re = answer.take();

                synchronized (location) {
                    boolean thisCorrect = reference.equals(location.getReference())
                            && region.equals(location.getRegion());
                    boolean answerCorrect = re.getData().getReference().equals(location.getReference())
                            && re.getData().getRegion().equals(location.getRegion());
                    if (thisCorrect) {
                        if (answerCorrect) {
                            Object ret = re.getData().getData();
                            return ret;
                        }
                        // otherwise, the answer is not interesting anymore, wait for next answer
                    } else {
                        if (answerCorrect)
                            answer.offer(re);
                        else
                            return null;
                        //                  throw new RuntimeException("This should not happen as the thread is supposed to be interrupted already!");
                    }
                }
            }

        } catch (InterruptedException e) {
            return null;
        }
    }

    private static final Logger log = Logger.getLogger(Receiver.class.getName());

    private MutableReferenceGenomicRegion location = new MutableReferenceGenomicRegion();
    private LinkedBlockingQueue<RemotePipelineData> answer = new LinkedBlockingQueue<RemotePipelineData>(1);

    @Override
    public void channelRead(ChannelHandlerContext ctx, Object msg) throws Exception {
        if (!(msg instanceof RemotePipelineData)) {
            ctx.fireChannelRead(msg);
            return;
        }

        RemotePipelineData data = (RemotePipelineData) msg;

        boolean release = true;
        try {

            synchronized (location) {
                if (data.getId().equals(id))
                    answer.offer(data);
                else {
                    release = false;
                    ctx.fireChannelRead(msg);
                }

            }

        } finally {
            if (release) {
                ReferenceCountUtil.release(msg);
            }
        }
    }

    @Override
    public void exceptionCaught(ChannelHandlerContext ctx, Throwable cause) throws Exception {
        log.log(Level.SEVERE, "Receiver caught exception!", cause);
    }

}