com.cloudera.science.quince.FileUtils.java Source code

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Here is the source code for com.cloudera.science.quince.FileUtils.java

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/*
 * Copyright (c) 2015, Cloudera, Inc. All Rights Reserved.
 *
 * Cloudera, Inc. licenses this file to you 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
 *
 * This software 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 com.cloudera.science.quince;

import java.io.IOException;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileStatus;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.fs.PathFilter;

public final class FileUtils {
    private FileUtils() {
    }

    public static Path[] findVcfs(Path path, Configuration conf) throws IOException {
        FileSystem fs = path.getFileSystem(conf);
        if (fs.isDirectory(path)) {
            FileStatus[] fileStatuses = fs.listStatus(path, new HiddenPathFilter());
            Path[] vcfs = new Path[fileStatuses.length];
            int i = 0;
            for (FileStatus status : fileStatuses) {
                vcfs[i++] = status.getPath();
            }
            return vcfs;
        } else {
            return new Path[] { path };
        }
    }

    public static boolean sampleGroupExists(Path path, Configuration conf, String sampleGroup) throws IOException {
        FileSystem fs = path.getFileSystem(conf);
        if (!fs.exists(path)) {
            return false;
        }
        for (FileStatus chrStatus : fs.listStatus(path, new PartitionPathFilter("chr"))) {
            for (FileStatus posStatus : fs.listStatus(chrStatus.getPath(), new PartitionPathFilter("pos"))) {
                if (fs.listStatus(posStatus.getPath(),
                        new PartitionPathFilter("sample_group", sampleGroup)).length > 0) {
                    return true;
                }
            }
        }
        return false;
    }

    public static void deleteSampleGroup(Path path, Configuration conf, String sampleGroup) throws IOException {
        FileSystem fs = path.getFileSystem(conf);
        if (!fs.exists(path)) {
            return;
        }
        for (FileStatus chrStatus : fs.listStatus(path, new PartitionPathFilter("chr"))) {
            for (FileStatus posStatus : fs.listStatus(chrStatus.getPath(), new PartitionPathFilter("pos"))) {
                for (FileStatus sampleGroupStatus : fs.listStatus(posStatus.getPath(),
                        new PartitionPathFilter("sample_group", sampleGroup))) {
                    fs.delete(sampleGroupStatus.getPath(), true);
                }
            }
        }
    }

    static class HiddenPathFilter implements PathFilter {
        @Override
        public boolean accept(Path p) {
            String name = p.getName();
            return !name.startsWith("_") && !name.startsWith(".");
        }
    }

    static class PartitionPathFilter implements PathFilter {
        private final String partitionName;
        private final String partitionValue;

        public PartitionPathFilter(String partitionName) {
            this(partitionName, null);
        }

        public PartitionPathFilter(String partitionName, String partitionValue) {
            this.partitionName = partitionName;
            this.partitionValue = partitionValue;
        }

        @Override
        public boolean accept(Path path) {
            if (partitionValue == null) {
                return path.getName().startsWith(partitionName + "=");
            } else {
                return path.getName().equals(partitionName + "=" + partitionValue);
            }
        }
    }
}