deprecating the old method and adding comments

src/main/java/htsjdk/samtools/CoordinateSortedPairInfoMap.java

@@ -56,7 +56,7 @@ public class CoordinateSortedPairInfoMap<KEY, REC> implements Iterable<Map.Entry
     /**
      * directory where files will go
      */
-    private final File workDir = IOUtil.createTempDir("CSPI.", null);
+    private final File workDir = IOUtil.createTempDir("CSPI.tmp").toFile();
     private int sequenceIndexOfMapInRam = INVALID_SEQUENCE_INDEX;
     private Map<KEY, REC> mapInRam = null;
     private final FileAppendStreamLRUCache outputStreams;

src/main/java/htsjdk/samtools/util/IOUtil.java

@@ -974,19 +974,34 @@ public static void copyDirectoryTree(final File fileOrDirectory, final File dest
     }
 
     /**
-     * Create a temporary subdirectory in the default temporary-file directory, using the given prefix and suffix to generate the name.
+     * Create a temporary subdirectory in the default temporary-file directory, using the given prefix and morePrefix to generate the name.
      * Note that this method is not completely safe, because it create a temporary file, deletes it, and then creates
      * a directory with the same name as the file.  Should be good enough.
      *
-     * @param prefix The prefix string to be used in generating the file's name; must be at least three characters long
-     * @param suffix The suffix string to be used in generating the file's name; may be null, in which case the suffix ".tmp" will be used
+     * This has been updated to avoid the problem in https://github.com/samtools/htsjdk/pull/1617
+     *
+     * @param prefix The prefix string to be used in generating the file's name;
+     * @param morePrefix This was previously a suffix but the implementation changed; may be null, in which case the morePrefix ".tmp" will be used
      * @return File object for new directory
+     * @deprecated  Use {@link #createTempDir(String)} instead.
+     *              It turns out the mechanism was not "good enough" and caused security issues, the new implementation
+     *              combines the prefix/morePrefix into a single prefix.  The security flaw is fixed but due to the now
+     *              extraneous morePrefix argument it is recommended to use the 1 argument form.
+     */
+    @Deprecated
+    public static File createTempDir(final String prefix, final String morePrefix) {
+        final String dotSeparatedSuffix = morePrefix == null ? ".tmp" : morePrefix.startsWith(".") ? morePrefix : "." + morePrefix;
+        return createTempDir(prefix + dotSeparatedSuffix).toFile() ;
+    }
+
+    /*
+     * Create a temporary subdirectory in the default temporary-file directory, using the given prefix and suffix to generate the name.
+     * @param prefix The prefix string to be used in generating the file's name, may be null
      */
-    public static File createTempDir(final String prefix, final String suffix) {
+    public static Path createTempDir(final String prefix) {
         try {
-            final File tmp = Files.createTempDirectory(prefix + suffix).toFile();
-            return tmp;
-        } catch (IOException e) {
+            return Files.createTempDirectory(prefix);
+        } catch (final IOException e) {
             throw new SAMException("Exception creating temporary directory.", e);
         }
     }

src/test/java/htsjdk/samtools/BAMMergerTest.java

@@ -222,7 +222,7 @@ private static Path textIndexBai(Path bai) {
 
     @Test
     public void test() throws IOException {
-        final Path outputDir = IOUtil.createTempDir(this.getClass().getSimpleName() + ".", ".tmp").toPath();
+        final Path outputDir = IOUtil.createTempDir(this.getClass().getSimpleName() + ".tmp");
         IOUtil.deleteOnExit(outputDir);
 
         final Path outputBam = File.createTempFile(this.getClass().getSimpleName() + ".", ".bam").toPath();

src/test/java/htsjdk/samtools/CRAMFileWriterTest.java

@@ -271,11 +271,11 @@ public void test_roundtrip_tlen_preserved() throws IOException {
     public void test_roundtrip_many_reads() throws IOException {
 
         // Create the input file
-        final File outputDir = IOUtil.createTempDir(this.getClass().getSimpleName() + ".", ".tmp");
+        final File outputDir = IOUtil.createTempDir(this.getClass().getSimpleName() + ".tmp").toFile();
         outputDir.deleteOnExit();
         final Path output = new File(outputDir, "input.cram").toPath();
         IOUtil.deleteOnExit(output);
-        final Path fastaDir = IOUtil.createTempDir("CRAMFileWriterTest", "").toPath();
+        final Path fastaDir = IOUtil.createTempDir("CRAMFileWriterTest");
         IOUtil.deleteOnExit(fastaDir);
         final Path newFasta = fastaDir.resolve("input.fasta");
         IOUtil.deleteOnExit(newFasta);

src/test/java/htsjdk/samtools/CRAMMergerTest.java

@@ -193,7 +193,7 @@ private static Path indexCram(Path cram, Path crai) throws IOException {
 
     @Test
     public void test() throws IOException {
-        final Path outputDir = IOUtil.createTempDir(this.getClass().getSimpleName() + ".", ".tmp").toPath();
+        final Path outputDir = IOUtil.createTempDir(this.getClass().getSimpleName() + ".tmp");
         IOUtil.deleteOnExit(outputDir);
 
         final Path outputCram = File.createTempFile(this.getClass().getSimpleName() + ".", FileExtensions.CRAM).toPath();

src/test/java/htsjdk/samtools/reference/FastaSequenceIndexCreatorTest.java

@@ -63,7 +63,7 @@ public void testBuildFromFasta(final File indexedFile) throws Exception {
     @Test(dataProvider = "indexedSequences")
     public void testCreate(final File indexedFile) throws Exception {
         // copy the file to index
-        final File tempDir = IOUtil.createTempDir("FastaSequenceIndexCreatorTest", "testCreate");
+        final File tempDir = IOUtil.createTempDir("FastaSequenceIndexCreatorTest.testCreate").toFile();
         final File copied = new File(tempDir, indexedFile.getName());
         copied.deleteOnExit();
         Files.copy(indexedFile.toPath(), copied.toPath());

src/test/java/htsjdk/samtools/seekablestream/SeekableStreamFactoryTest.java

@@ -52,7 +52,7 @@ public void testPathWithEmbeddedSpace() throws IOException {
         final File testBam =  new File(TEST_DATA_DIR, "BAMFileIndexTest/index_test.bam");
 
         //create a temp dir with a space in the name and copy the test file there
-        final File tempDir = IOUtil.createTempDir("test spaces", "");
+        final File tempDir = IOUtil.createTempDir("test spaces").toFile();
         Assert.assertTrue(tempDir.getAbsolutePath().contains(" "));
         tempDir.deleteOnExit();
         final File inputBam = new File(tempDir, "index_test.bam");

src/test/java/htsjdk/samtools/util/IOUtilTest.java

@@ -312,7 +312,7 @@ public void testGetDefaultTmpDirPath() throws Exception {
 
     @Test(dataProvider = "fileNamesForDelete")
     public void testDeletePathLocal(final List<String> fileNames) throws Exception {
-        final File tmpDir = IOUtil.createTempDir("testDeletePath", "");
+        final Path tmpDir = IOUtil.createTempDir("testDeletePath");
         final List<Path> paths = createLocalFiles(tmpDir, fileNames);
         testDeletePaths(paths);
     }
@@ -341,7 +341,7 @@ public void testDeletePathJims(final List<String> fileNames) throws Exception {
 
     @Test(dataProvider = "fileNamesForDelete")
     public void testDeleteArrayPathLocal(final List<String> fileNames) throws Exception {
-        final File tmpDir = IOUtil.createTempDir("testDeletePath", "");
+        final Path tmpDir = IOUtil.createTempDir("testDeletePath");
         final List<Path> paths = createLocalFiles(tmpDir, fileNames);
         testDeletePathArray(paths);
     }
@@ -365,12 +365,11 @@ private static void testDeletePathArray(final List<Path> paths) {
         paths.forEach(p -> Assert.assertFalse(Files.exists(p)));
     }
 
-    private static List<Path> createLocalFiles(final File tmpDir, final List<String> fileNames) throws Exception {
+    private static List<Path> createLocalFiles(final Path tmpDir, final List<String> fileNames) throws Exception {
         final List<Path> paths = new ArrayList<>(fileNames.size());
         for (final String f: fileNames) {
-            final File file = new File(tmpDir, f);
-            Assert.assertTrue(file.createNewFile(), "failed to create test file" +file);
-            paths.add(file.toPath());
+            final Path file = Files.createFile(tmpDir.resolve(f));
+            paths.add(file);
         }
         return paths;
     }

src/test/java/htsjdk/tribble/index/IndexFactoryTest.java

@@ -166,7 +166,7 @@ public void testCreateTabixIndexFromVCF(
             final File inputVCF,
             final Interval queryInterval) throws IOException {
         // copy the original file and create the index for the copy
-        final File tempDir = IOUtil.createTempDir("testCreateTabixIndexFromVCF", null);
+        final File tempDir = IOUtil.createTempDir("testCreateTabixIndexFromVCF").toFile();
         tempDir.deleteOnExit();
         final File tmpVCF = new File(tempDir, inputVCF.getName());
         Files.copy(inputVCF, tmpVCF);
@@ -208,7 +208,7 @@ public Object[][] getBCFData(){
     @Test(dataProvider = "bcfDataFactory")
     public void testCreateLinearIndexFromBCF(final File inputBCF) throws IOException {
         // copy the original file and create the index for the copy
-        final File tempDir = IOUtil.createTempDir("testCreateIndexFromBCF", null);
+        final File tempDir = IOUtil.createTempDir("testCreateIndexFromBCF").toFile();
         tempDir.deleteOnExit();
         final File tmpBCF = new File(tempDir, inputBCF.getName());
         Files.copy(inputBCF, tmpBCF);
@@ -250,7 +250,7 @@ public Object[][] getRedirectFiles(){
     @Test(dataProvider = "getRedirectFiles")
     public void testIndexRedirectedFiles(String input, IndexFactory.IndexType type) throws IOException {
         final VCFRedirectCodec codec = new VCFRedirectCodec();
-        final File dir = IOUtil.createTempDir("redirec-test", "dir");
+        final File dir = IOUtil.createTempDir("redirec-test.dir").toFile();
         try {
             final File tmpInput = new File(dir, new File(input).getName());
             Files.copy(new File(input), tmpInput);

src/test/java/htsjdk/tribble/index/IndexTest.java

@@ -131,7 +131,7 @@ public void testWritePathIndex(final File inputFile, final IndexFactory.IndexTyp
 
     @Test(dataProvider = "writeIndexData")
     public void testWriteBasedOnNonRegularFeatureFile(final File inputFile, final IndexFactory.IndexType type, final  FeatureCodec codec) throws Exception {
-        final File tmpFolder = IOUtil.createTempDir("NonRegultarFeatureFile", null);
+        final File tmpFolder = IOUtil.createTempDir("NonRegultarFeatureFile").toFile();
         // create the index
         final Index index = IndexFactory.createIndex(inputFile, codec, type);
         // try to write based on the tmpFolder

src/test/java/htsjdk/tribble/index/tabix/TabixIndexTest.java

@@ -190,7 +190,7 @@ public void testBedTabixIndex(
             final List<Interval> queryIntervals
     ) throws Exception {
         // copy the input file and create an index for the copy
-        final File tempDir = IOUtil.createTempDir("testBedTabixIndex", null);
+        final File tempDir = IOUtil.createTempDir("testBedTabixIndex.tmp").toFile();
         tempDir.deleteOnExit();
         final File tmpBed = new File(tempDir, inputBed.getName());
         Files.copy(inputBed, tmpBed);

src/test/java/htsjdk/variant/vcf/VCFFileReaderTest.java

@@ -110,7 +110,7 @@ public void testTabixFileWithEmbeddedSpaces() throws IOException {
         // Copy the input files into a temporary directory with embedded spaces in the name.
         // This test needs to include the associated .tbi file because we want to force execution
         // of the tabix code path.
-        final File tempDir = IOUtil.createTempDir("test spaces", "");
+        final File tempDir = IOUtil.createTempDir("test spaces").toFile();
         Assert.assertTrue(tempDir.getAbsolutePath().contains(" "));
         tempDir.deleteOnExit();
         final File inputVCF = new File(tempDir, "HiSeq.10000.vcf.bgz");

src/test/java/htsjdk/variant/vcf/VCFMergerTest.java

@@ -206,7 +206,7 @@ private static Path indexVcf(Path vcf, Path tbi) throws IOException {
 
     @Test
     public void test() throws IOException {
-        final Path outputDir = IOUtil.createTempDir(this.getClass().getSimpleName() + ".", ".tmp").toPath();
+        final Path outputDir = IOUtil.createTempDir(this.getClass().getSimpleName() + ".tmp");
         IOUtil.deleteOnExit(outputDir);
 
         final Path outputVcf = File.createTempFile(this.getClass().getSimpleName() + ".", FileExtensions.COMPRESSED_VCF).toPath();