org.cbioportal.annotation.pipeline.MutationRecordWriter.java Source code

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Here is the source code for org.cbioportal.annotation.pipeline.MutationRecordWriter.java

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/*
 * Copyright (c) 2016 Memorial Sloan-Kettering Cancer Center.
 *
 * This library is distributed in the hope that it will be useful, but WITHOUT
 * ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS
 * FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder
 * is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no
 * obligations to provide maintenance, support, updates, enhancements or
 * modifications. In no event shall Memorial Sloan-Kettering Cancer Center be
 * liable to any party for direct, indirect, special, incidental or
 * consequential damages, including lost profits, arising out of the use of this
 * software and its documentation, even if Memorial Sloan-Kettering Cancer
 * Center has been advised of the possibility of such damage.
 */

/*
 * This file is part of cBioPortal CMO-Pipelines.
 *
 * cBioPortal is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Affero General Public License as
 * published by the Free Software Foundation, either version 3 of the
 * License.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Affero General Public License for more details.
 *
 * You should have received a copy of the GNU Affero General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
*/

package org.cbioportal.annotation.pipeline;

import java.io.*;
import java.util.*;
import java.nio.file.*;
import org.apache.commons.lang.StringUtils;
import org.springframework.batch.item.*;
import org.springframework.batch.item.file.*;
import org.springframework.batch.item.file.transform.PassThroughLineAggregator;
import org.cbioportal.models.AnnotatedRecord;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.core.io.FileSystemResource;

/**
 *
 * @author Zachary Heins
 */
public class MutationRecordWriter implements ItemStreamWriter<String> {

    @Value("#{jobParameters[outputFilename]}")
    private String outputFilename;

    @Value("#{stepExecutionContext['commentLines']}")
    private List<String> commentLines;

    @Value("#{stepExecutionContext['mutation_header']}")
    private List<String> header;

    private Path stagingFile;
    private FlatFileItemWriter<String> flatFileItemWriter = new FlatFileItemWriter<>();

    // Set up the writer and print the json from CVR to a file
    @Override
    public void open(ExecutionContext ec) throws ItemStreamException {
        stagingFile = Paths.get(outputFilename);

        PassThroughLineAggregator aggr = new PassThroughLineAggregator();
        flatFileItemWriter.setLineAggregator(aggr);
        flatFileItemWriter.setResource(new FileSystemResource(stagingFile.toString()));
        flatFileItemWriter.setHeaderCallback(new FlatFileHeaderCallback() {
            @Override
            public void writeHeader(Writer writer) throws IOException {
                AnnotatedRecord record = new AnnotatedRecord();

                // first write out the comment lines, then write the actual header
                for (String comment : commentLines) {
                    writer.write(comment + "\n");
                }
                writer.write(StringUtils.join(header, "\t"));
            }
        });
        flatFileItemWriter.open(ec);
    }

    @Override
    public void update(ExecutionContext ec) throws ItemStreamException {
    }

    @Override
    public void close() throws ItemStreamException {
        flatFileItemWriter.close();
    }

    @Override
    public void write(List<? extends String> items) throws Exception {
        flatFileItemWriter.write(items);
    }
}