org.icgc.dcc.portal.manifest.writer.ICGCManifestWriter.java Source code

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Here is the source code for org.icgc.dcc.portal.manifest.writer.ICGCManifestWriter.java

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/*
 * Copyright (c) 2016 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.portal.manifest.writer;

import java.io.OutputStream;
import java.util.Collection;
import java.util.List;

import org.icgc.dcc.portal.manifest.model.ManifestFile;

import com.google.common.collect.Lists;
import com.google.common.collect.Multimap;

import lombok.SneakyThrows;
import lombok.val;

public class ICGCManifestWriter extends TSVManifestWriter {

    /**
     * Constants - Fields
     */
    private static final String[] TSV_HEADERS = { "repo_code", "file_id", "object_id", "file_format", "file_name",
            "file_size", "md5_sum", "index_object_id", "donor_id/donor_count", "project_id/project_count",
            "study" };

    @SneakyThrows
    public static void write(OutputStream buffer, Multimap<String, ManifestFile> bundles) {
        val tsv = createTsv(buffer);
        tsv.writeHeader(TSV_HEADERS);

        for (val url : bundles.keySet()) {
            val bundle = bundles.get(url);
            val row = createRow(bundle);

            tsv.write(row);
        }

        tsv.flush();
    }

    private static List<String> createRow(Collection<ManifestFile> bundle) {
        val row = Lists.<String>newArrayList();
        row.add(join(bundle, ManifestFile::getRepoCode));
        row.add(join(bundle, ManifestFile::getId));
        row.add(join(bundle, ManifestFile::getObjectId));
        row.add(join(bundle, ManifestFile::getFormat));
        row.add(join(bundle, ManifestFile::getName));
        row.add(join(bundle, ManifestFile::getSize));
        row.add(join(bundle, ManifestFile::getMd5sum));
        row.add(join(bundle, ManifestFile::getIndexObjectId));
        row.add(join(bundle, ManifestFile::getDonorId));
        row.add(join(bundle, ManifestFile::getProjectCode));
        row.add(join(bundle, ManifestFile::getStudy));

        return row;
    }

}