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/**
* The MIT License (MIT)
* Copyright (c) 2018 Univeristy of Caifornia, Los Angeles and Intel Corporation
* Copyright (c) 2023 Omics Data Automation, Inc.
*
* Permission is hereby granted, free of charge, to any person obtaining a copy of
* this software and associated documentation files (the "Software"), to deal in
* the Software without restriction, including without limitation the rights to
* use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
* the Software, and to permit persons to whom the Software is furnished to do so,
* subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
* FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
* COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
* IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
* CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
import gnu.getopt.Getopt;
import gnu.getopt.LongOpt;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.variantcontext.writer.Options;
import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder;
import htsjdk.variant.vcf.VCFFileReader;
import org.apache.hadoop.conf.Configuration;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.genomicsdb.spark.GenomicsDBConfiguration;
import org.genomicsdb.spark.GenomicsDBInputFormat;
import org.genomicsdb.importer.extensions.JsonFileExtensions;
import org.genomicsdb.model.GenomicsDBExportConfiguration;
import org.genomicsdb.model.GenomicsDBImportConfiguration;
import java.io.*;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.nio.file.StandardCopyOption;
import java.nio.charset.Charset;
import java.util.List;
import java.util.Base64;
import com.google.protobuf.Message;
import com.google.protobuf.util.JsonFormat;
public final class TestGenomicsDBSparkHDFS {
public static void main(final String[] args) throws IOException,
org.json.simple.parser.ParseException {
LongOpt[] longopts = new LongOpt[8];
longopts[0] = new LongOpt("loader", LongOpt.REQUIRED_ARGUMENT, null, 'l');
longopts[1] = new LongOpt("query", LongOpt.REQUIRED_ARGUMENT, null, 'q');
longopts[2] = new LongOpt("hostfile", LongOpt.REQUIRED_ARGUMENT, null, 'h');
longopts[3] = new LongOpt("template_vcf_header", LongOpt.REQUIRED_ARGUMENT, null, 't');
longopts[4] = new LongOpt("spark_master", LongOpt.REQUIRED_ARGUMENT, null, 's');
longopts[5] = new LongOpt("jar_dir", LongOpt.REQUIRED_ARGUMENT, null, 'j');
longopts[6] = new LongOpt("use-query-protobuf", LongOpt.NO_ARGUMENT, null, 'p');
longopts[7] = new LongOpt("use-loader-protobuf", LongOpt.NO_ARGUMENT, null, 'e');
if (args.length < 10) {
System.err.println("Usage:\n\t--loader <loader.json> --query <query.json> --hostfile <hostfile>"
+" --template_vcf_header <templateVCFHeader> --spark_master <sparkMaster> --jar_dir <jar_dir>"
+"\nOptional args:\n --hostfile <hostfile> --use-query-protobuf --user-loader-protobuf");
System.exit(-1);
}
String loaderFile, queryFile, hostfile, templateVCFHeader, sparkMaster, jarDir;
boolean useQueryProtobuf = false;
boolean useLoaderProtobuf = false;
loaderFile = queryFile = hostfile = templateVCFHeader = sparkMaster = jarDir = "";
Getopt g = new Getopt("TestGenomicsDBSparkHDFS", args, "l:q:h:t:s:j:p:e", longopts);
int c = -1;
String optarg;
while ((c = g.getopt()) != -1) {
switch (c) {
case 'l':
loaderFile = g.getOptarg();
break;
case 'q':
queryFile = g.getOptarg();
break;
case 'h':
hostfile = g.getOptarg();
break;
case 't':
templateVCFHeader = g.getOptarg();
break;
case 's':
sparkMaster = g.getOptarg();
break;
case 'j':
jarDir = g.getOptarg();
break;
case 'p':
useQueryProtobuf = true;
break;
case 'e':
useLoaderProtobuf = true;
break;
default:
System.err.println("Unknown command line option "+g.getOptarg());
System.exit(-1);
}
}
SparkConf conf = new SparkConf().setAppName("TestGenomicsDBSparkHDFS");
conf.set("spark.hadoopRDD.ignoreEmptySplits","false");
Path dstdir = Paths.get("").toAbsolutePath();
Path qSrc = Paths.get(queryFile);
Path lSrc = Paths.get(loaderFile);
File qDstFile = null;
File lDstFile = null;
JavaSparkContext sc = new JavaSparkContext(conf);
if(!useQueryProtobuf) {
qDstFile = File.createTempFile("query", ".json", new File(dstdir.toString()));
qDstFile.deleteOnExit();
Files.copy(qSrc, qDstFile.toPath(), StandardCopyOption.REPLACE_EXISTING);
sc.addFile(qDstFile.getName());
}
if (!useLoaderProtobuf) {
lDstFile = File.createTempFile("loader", ".json", new File(dstdir.toString()));
lDstFile.deleteOnExit();
Files.copy(lSrc, lDstFile.toPath(), StandardCopyOption.REPLACE_EXISTING);
sc.addFile(lDstFile.getName());
}
Configuration hadoopConf = sc.hadoopConfiguration();
if(!useLoaderProtobuf) {
hadoopConf.set(GenomicsDBConfiguration.LOADERJSON, lDstFile.getName());
}
else {
String pbString = JsonFileExtensions.getProtobufAsBase64StringFromFile(GenomicsDBImportConfiguration.ImportConfiguration.newBuilder(),
loaderFile);
hadoopConf.set(GenomicsDBConfiguration.LOADERPB, pbString);
}
if(!useQueryProtobuf) {
hadoopConf.set(GenomicsDBConfiguration.QUERYJSON, qDstFile.getName());
}
else {
String pbString = JsonFileExtensions.getProtobufAsBase64StringFromFile(GenomicsDBExportConfiguration.ExportConfiguration.newBuilder(),
queryFile);
hadoopConf.set(GenomicsDBConfiguration.QUERYPB, pbString);
}
if(!hostfile.isEmpty()) {
hadoopConf.set(GenomicsDBConfiguration.MPIHOSTFILE, hostfile);
}
JavaPairRDD<String, VariantContext> variants;
Class gformatClazz = GenomicsDBInputFormat.class;
variants = sc.newAPIHadoopRDD(hadoopConf,
gformatClazz, String.class, VariantContext.class);
// sort based on variantcontext start pos. this is limited and will not work when data for more
// than a single contig will be used. good enough for testing?
List<VariantContext> result = variants.map(x -> x._2).sortBy(x -> {return x.getStart();}, true, 1).collect();
// probably a smarter way to do this but...creating a temporary vcf file to
// grab the header from it for this test. Trying to create a VCFFileReader
// with just the inputs/template_vcf_header doesn't work...
// TODO: need to amend GenomicsDBRDD with function to write VCF file...
File tempFile = File.createTempFile("temp",".vcf");
tempFile.deleteOnExit();
BufferedReader br = new BufferedReader(new FileReader(templateVCFHeader));
BufferedWriter bw = new BufferedWriter(new FileWriter(tempFile));
String line;
while ((line=br.readLine()) != null) {
bw.write(line+'\n');
}
bw.write("#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT\t");
bw.write(String.join("\t", result.get(0).getSampleNamesOrderedByName()));
bw.write("\n");
bw.write("1 12145 . C <NON_REF> . . END=12277;DS GT:DP:GQ:MIN_DP:PL 0/0:3:0:0:0,0,0\n");
bw.close();
br.close();
VCFFileReader vcffr = new VCFFileReader(tempFile, false);
final VariantContextWriter writer =
new VariantContextWriterBuilder().setOutputVCFStream(System.out).unsetOption(
Options.INDEX_ON_THE_FLY).build();
writer.writeHeader(vcffr.getFileHeader());
vcffr.close();
// print rest of vcf
for (VariantContext vc : result) {
writer.add(vc);
}
}
}
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