org.icgc.dcc.release.job.summarize.function.SummarizeDonorGene.java Source code

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Here is the source code for org.icgc.dcc.release.job.summarize.function.SummarizeDonorGene.java

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/*
 * Copyright (c) 2015 The Ontario Institute for Cancer Research. All rights reserved.                             
 *                                                                                                               
 * This program and the accompanying materials are made available under the terms of the GNU Public License v3.0.
 * You should have received a copy of the GNU General Public License along with                                  
 * this program. If not, see <http://www.gnu.org/licenses/>.                                                     
 *                                                                                                               
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY                           
 * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES                          
 * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT                           
 * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,                                
 * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED                          
 * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;                               
 * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER                              
 * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN                         
 * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */
package org.icgc.dcc.release.job.summarize.function;

import lombok.val;

import org.apache.spark.api.java.function.PairFunction;

import scala.Tuple2;

import com.fasterxml.jackson.databind.node.ObjectNode;
import com.google.common.collect.Iterables;

public class SummarizeDonorGene
        implements PairFunction<Tuple2<ObjectNode, Iterable<ObjectNode>>, String, ObjectNode> {

    @Override
    public Tuple2<String, ObjectNode> call(Tuple2<ObjectNode, Iterable<ObjectNode>> tuple) throws Exception {
        val fields = tuple._1;
        val group = tuple._2;

        val donorId = fields.get("_donor_id").asText();
        val geneId = fields.get("_gene_id").asText();
        val summary = fields.objectNode();
        summary.put("_ssm_count", Iterables.size(group));

        val geneSummary = fields.objectNode();
        geneSummary.put("_gene_id", geneId);
        geneSummary.set("_summary", summary);

        return new Tuple2<String, ObjectNode>(donorId, geneSummary);
    }

}