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[SECURITY] Fix Temporary File Information Disclosure Vulnerability #214

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[SECURITY] Fix Temporary File Information Disclosure Vulnerability #214

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5 changes: 3 additions & 2 deletions src/test/java/org/seqdoop/hadoop_bam/BAMTestUtil.java
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@
import htsjdk.samtools.SamReaderFactory;
import java.io.File;
import java.io.IOException;
import java.nio.file.Files;

class BAMTestUtil {
public static File writeBamFile(int numPairs, SAMFileHeader.SortOrder sortOrder)
Expand Down Expand Up @@ -42,7 +43,7 @@ public static File writeBamFile(int numPairs, SAMFileHeader.SortOrder sortOrder)
("test-read-%03d-unplaced-unmapped", numPairs++));
}

final File bamFile = File.createTempFile("test", ".bam");
final File bamFile = Files.createTempFile("test", ".bam").toFile();
bamFile.deleteOnExit();
SAMFileHeader samHeader = samRecordSetBuilder.getHeader();
final SAMFileWriter bamWriter = new SAMFileWriterFactory()
Expand Down Expand Up @@ -75,7 +76,7 @@ public static File writeBamFileWithLargeHeader() throws IOException {
start2);
}

final File bamFile = File.createTempFile("test", ".bam");
final File bamFile = Files.createTempFile("test", ".bam").toFile();
bamFile.deleteOnExit();
SAMFileHeader samHeader = samRecordSetBuilder.getHeader();
StringBuffer sb = new StringBuffer();
Expand Down
12 changes: 6 additions & 6 deletions src/test/java/org/seqdoop/hadoop_bam/TestBAMOutputFormat.java
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Expand Up @@ -91,7 +91,7 @@ public void setup() throws Exception {

@Test
public void testBAMRecordWriterNoHeader() throws Exception {
final File outFile = File.createTempFile("testBAMWriter", ".bam");
final File outFile = Files.createTempFile("testBAMWriter", ".bam").toFile();
outFile.deleteOnExit();
final Path outPath = new Path(outFile.toURI());

Expand Down Expand Up @@ -120,7 +120,7 @@ public void testBAMRecordWriterNoHeader() throws Exception {

@Test
public void testBAMRecordWriterWithHeader() throws Exception {
final File outFile = File.createTempFile("testBAMWriter", ".bam");
final File outFile = Files.createTempFile("testBAMWriter", ".bam").toFile();
outFile.deleteOnExit();
final Path outPath = new Path(outFile.toURI());

Expand Down Expand Up @@ -150,7 +150,7 @@ public void testBAMRecordWriterWithHeader() throws Exception {
@Test
public void testBAMOutput() throws Exception {
final Path outputPath = doMapReduce(testBAMFileName);
final File outFile = File.createTempFile("testBAMWriter", ".bam");
final File outFile = Files.createTempFile("testBAMWriter", ".bam").toFile();
outFile.deleteOnExit();
SAMFileMerger.mergeParts(outputPath.toUri().toString(), outFile.toURI().toString(),
SAMFormat.BAM, samFileHeader);
Expand All @@ -164,7 +164,7 @@ public void testEmptyBAM() throws Exception {
SAMFileHeader.SortOrder.coordinate).toURI().toString();
conf.setBoolean(BAMOutputFormat.WRITE_SPLITTING_BAI, true);
final Path outputPath = doMapReduce(bam);
final File outFile = File.createTempFile("testBAMWriter", ".bam");
final File outFile = Files.createTempFile("testBAMWriter", ".bam").toFile();
outFile.deleteOnExit();
SAMFileMerger.mergeParts(outputPath.toUri().toString(), outFile.toURI().toString(),
SAMFormat.BAM, new SAMRecordSetBuilder(true, SAMFileHeader.SortOrder.coordinate).getHeader());
Expand Down Expand Up @@ -194,7 +194,7 @@ public void testBAMWithSplittingBai() throws Exception {
recordsAtSplits.addAll(getRecordsAtSplits(bamFile, index));
}

final File outFile = File.createTempFile("testBAMWriter", ".bam");
final File outFile = Files.createTempFile("testBAMWriter", ".bam").toFile();
//outFile.deleteOnExit();
SAMFileMerger.mergeParts(outputPath.toUri().toString(), outFile.toURI().toString(),
SAMFormat.BAM,
Expand Down Expand Up @@ -231,7 +231,7 @@ public void testBAMRoundTrip() throws Exception {
Path outputPath = doMapReduce(testBAMFileName);

// merge the parts, and write to a temp file
final File outFile = File.createTempFile("testBAMWriter", ".bam");
final File outFile = Files.createTempFile("testBAMWriter", ".bam").toFile();
outFile.deleteOnExit();
SAMFileMerger.mergeParts(outputPath.toUri().toString(), outFile.toURI().toString(),
SAMFormat.BAM, samFileHeader);
Expand Down
8 changes: 4 additions & 4 deletions src/test/java/org/seqdoop/hadoop_bam/TestCRAMOutputFormat.java
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Expand Up @@ -95,7 +95,7 @@ public void setup() throws Exception {

@Test
public void testCRAMRecordWriterNoHeader() throws Exception {
final File outFile = File.createTempFile("testCRAMWriter", ".cram");
final File outFile = Files.createTempFile("testCRAMWriter", ".cram").toFile();
outFile.deleteOnExit();
final Path outPath = new Path(outFile.toURI());

Expand Down Expand Up @@ -125,7 +125,7 @@ public void testCRAMRecordWriterNoHeader() throws Exception {

@Test
public void testCRAMRecordWriterWithHeader() throws Exception {
final File outFile = File.createTempFile("testCRAMWriter", ".cram");
final File outFile = Files.createTempFile("testCRAMWriter", ".cram").toFile();
outFile.deleteOnExit();
final Path outPath = new Path(outFile.toURI());

Expand Down Expand Up @@ -155,7 +155,7 @@ public void testCRAMRecordWriterWithHeader() throws Exception {
@Test
public void testCRAMOutput() throws Exception {
final Path outputPath = doMapReduce(testCRAMFileName);
final File outFile = File.createTempFile("testCRAMWriter", ".cram");
final File outFile = Files.createTempFile("testCRAMWriter", ".cram").toFile();
outFile.deleteOnExit();
SAMFileMerger.mergeParts(outputPath.toUri().toString(), outFile.toURI().toString(),
SAMFormat.CRAM, samFileHeader);
Expand All @@ -171,7 +171,7 @@ public void testCRAMRoundTrip() throws Exception {
Path outputPath = doMapReduce(testCRAMFileName);

// merge the parts, and write to a temp file
final File outFile = File.createTempFile("testCRAMWriter", ".cram");
final File outFile = Files.createTempFile("testCRAMWriter", ".cram").toFile();
outFile.deleteOnExit();
SAMFileMerger.mergeParts(outputPath.toUri().toString(), outFile.toURI().toString(),
SAMFormat.CRAM, samFileHeader);
Expand Down
5 changes: 3 additions & 2 deletions src/test/java/org/seqdoop/hadoop_bam/TestFastqInputFormat.java
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Expand Up @@ -27,6 +27,7 @@
import java.io.File;
import java.io.IOException;
import java.io.PrintWriter;
import java.nio.file.Files;
import java.io.BufferedWriter;
import java.io.FileWriter;
import java.io.FileOutputStream;
Expand Down Expand Up @@ -137,8 +138,8 @@ public class TestFastqInputFormat
@Before
public void setup() throws IOException
{
tempFastq = File.createTempFile("test_fastq_input_format", "fastq");
tempGz = File.createTempFile("test_fastq_input_format", ".gz");
tempFastq = Files.createTempFile("test_fastq_input_format", "fastq").toFile();
tempGz = Files.createTempFile("test_fastq_input_format", ".gz").toFile();
conf = new JobConf();
key = new Text();
fragment = new SequencedFragment();
Expand Down
5 changes: 3 additions & 2 deletions src/test/java/org/seqdoop/hadoop_bam/TestQseqInputFormat.java
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Expand Up @@ -29,6 +29,7 @@
import java.io.File;
import java.io.IOException;
import java.io.PrintWriter;
import java.nio.file.Files;
import java.io.BufferedWriter;
import java.io.FileWriter;
import java.io.FileOutputStream;
Expand Down Expand Up @@ -92,8 +93,8 @@ public class TestQseqInputFormat
@Before
public void setup() throws IOException
{
tempQseq = File.createTempFile("test_qseq_input_format", "qseq");
tempGz = File.createTempFile("test_qseq_input_format", ".gz");
tempQseq = Files.createTempFile("test_qseq_input_format", "qseq").toFile();
tempGz = Files.createTempFile("test_qseq_input_format", ".gz").toFile();
conf = new JobConf();
key = new Text();
fragment = new SequencedFragment();
Expand Down
3 changes: 2 additions & 1 deletion src/test/java/org/seqdoop/hadoop_bam/TestVCFOutputFormat.java
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Expand Up @@ -22,6 +22,7 @@

import java.io.*;
import java.lang.reflect.InvocationTargetException;
import java.nio.file.Files;
import java.util.*;

import htsjdk.samtools.seekablestream.SeekableFileStream;
Expand Down Expand Up @@ -54,7 +55,7 @@ public class TestVCFOutputFormat {

@Before
public void setup() throws IOException, NoSuchMethodException, IllegalAccessException, InvocationTargetException, InstantiationException {
test_vcf_output = File.createTempFile("test_vcf_output", "");
test_vcf_output = Files.createTempFile("test_vcf_output", "").toFile();
test_vcf_output.delete();
writable = new VariantContextWritable();
Configuration conf = new Configuration();
Expand Down
6 changes: 3 additions & 3 deletions src/test/java/org/seqdoop/hadoop_bam/TestVCFRoundTrip.java
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Expand Up @@ -32,6 +32,7 @@
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.nio.file.Files;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
Expand Down Expand Up @@ -199,8 +200,7 @@ public void testRoundTripWithMerge() throws Exception {
// merge the output
VCFHeader vcfHeader = VCFHeaderReader.readHeaderFrom(new SeekableFileStream(new
File(testVCFFileName)));
final File outFile = File.createTempFile("testVCFWriter",
testVCFFileName.substring(testVCFFileName.lastIndexOf(".")));
final File outFile = Files.createTempFile("testVCFWriter", testVCFFileName.substring(testVCFFileName.lastIndexOf("."))).toFile();
outFile.deleteOnExit();
VCFFileMerger.mergeParts(outputPath.toUri().toString(), outFile.toURI().toString(),
vcfHeader);
Expand Down Expand Up @@ -256,7 +256,7 @@ private static VCFFileReader parseVcf(File vcf) throws IOException {
File actualVcf;
// work around TribbleIndexedFeatureReader not reading header from .bgz files
if (vcf.getName().endsWith(".bgz")) {
actualVcf = File.createTempFile(vcf.getName(), ".gz");
actualVcf = Files.createTempFile(vcf.getName(), ".gz").toFile();
actualVcf.deleteOnExit();
Files.copy(vcf, actualVcf);
} else {
Expand Down