Add FQZComp Interop tests

src/test/java/htsjdk/samtools/cram/FQZCompInteropTest.java

@@ -19,92 +19,66 @@
 
 public class FQZCompInteropTest extends HtsjdkTest {
 
-    public static final String COMPRESSED_FQZComp_DIR = "fqzcomp";
+    public static final String COMPRESSED_FQZCOMP_DIR = "fqzcomp";
 
-    @DataProvider(name = "allFQZCompFiles")
-    public Object[][] getAllFQZCompCodecsForRoundTrip() throws IOException {
+    // uses the available compressed interop test files
+    @DataProvider(name = "decodeOnlyTestCases")
+    public Object[][] getDecodeOnlyTestCases() throws IOException {
 
         // params:
-        // compressed testfile path, uncompressed testfile path, FQZComp decoder
+        // compressed testfile path, uncompressed testfile path,
+        // FQZComp decoder
         final List<Object[]> testCases = new ArrayList<>();
-        for (Path path : getInteropFQZCompCompressedFiles()) {
+        for (Path path : CRAMInteropTestUtils.getInteropCompressedFilePaths(COMPRESSED_FQZCOMP_DIR)) {
             Object[] objects = new Object[]{
                     path,
-                    getFQZCompUnCompressedFilePath(path),
-                    new FQZCompDecode(),
+                    CRAMInteropTestUtils.getUnCompressedFilePath(path),
+                    new FQZCompDecode()
             };
             testCases.add(objects);
         }
         return testCases.toArray(new Object[][]{});
     }
 
     @Test(description = "Test if CRAM Interop Test Data is available")
-    public void testGetHTSCodecsCorpus() {
+    public void testHtsCodecsCorpusIsAvailable() {
         if (!CRAMInteropTestUtils.isInteropTestDataAvailable()) {
             throw new SkipException(String.format("CRAM Interop Test Data is not available at %s",
                     CRAMInteropTestUtils.INTEROP_TEST_FILES_PATH));
         }
     }
 
-    @Test(
-            dependsOnMethods = "testGetHTSCodecsCorpus",
-            dataProvider = "allFQZCompFiles",
-            description = "Uncompress the existing compressed file using htsjdk FQZComp Codec and compare it with the original file.")
-    public void testFQZCompPreCompressed(
+    @Test (
+            dependsOnMethods = "testHtsCodecsCorpusIsAvailable",
+            dataProvider = "decodeOnlyTestCases",
+            description = "Uncompress the existing compressed file using htsjdk FQZcomp codec and compare it with the original file.")
+    public void testDecodeOnly(
             final Path compressedFilePath,
-            final Path uncompressedFilePath,
-//            final NameTokenisationEncode unsusednameTokenisationEncode,
-            final FQZCompDecode fqzCompDecode) throws IOException {
-//        final Path compressedFilePath= Paths.get("../htscodecs_1/tests/dat/fqzcomp/q4.1");
-//        final Path uncompressedFilePath = Paths.get("../htscodecs_1/tests/dat/q4");
-        try(final InputStream preCompressedInteropStream = Files.newInputStream(compressedFilePath);
-            final InputStream unCompressedInteropStream = Files.newInputStream(uncompressedFilePath)){
+            final Path uncompressedInteropPath,
+            final FQZCompDecode fqzcompDecode) throws IOException {
+        try (final InputStream uncompressedInteropStream = Files.newInputStream(uncompressedInteropPath);
+             final InputStream preCompressedInteropStream = Files.newInputStream(compressedFilePath)
+        ) {
+            // preprocess the uncompressed data (to match what the htscodecs-library test harness does)
+            // by filtering out the embedded newlines, and then round trip through FQZComp codec
+            // and compare the results
+
             final ByteBuffer preCompressedInteropBytes = ByteBuffer.wrap(IOUtils.toByteArray(preCompressedInteropStream));
-            final ByteBuffer unCompressedInteropBytes = ByteBuffer.wrap(IOUtils.toByteArray(unCompressedInteropStream));
 
             // Use htsjdk to uncompress the precompressed file from htscodecs repo
-            final ByteBuffer uncompressedHtsjdkBytes = fqzCompDecode.uncompress(preCompressedInteropBytes);
+            final ByteBuffer uncompressedHtsjdkBytes = fqzcompDecode.uncompress(preCompressedInteropBytes);
+
+            final ByteBuffer uncompressedInteropBytes = ByteBuffer.wrap(IOUtils.toByteArray(uncompressedInteropStream));
+            // TODO!!: the precompressed interop files seem different to the other codecs.
+            //  For htslib compression using FQZComp, "\n" was not filtered out of these test files
+            //  unlike what we observed in the RANS, Range or Name Tokenizer compressed interop test files.
 
             // Compare the htsjdk uncompressed bytes with the original input file from htscodecs repo
-            Assert.assertEquals(uncompressedHtsjdkBytes, unCompressedInteropBytes);
+            Assert.assertEquals(uncompressedHtsjdkBytes, uncompressedInteropBytes);
         } catch (final NoSuchFileException ex){
-            throw new SkipException("Skipping testNameTokenizationPrecompressed as either input file " +
+            throw new SkipException("Skipping testDecodeOnly as either input file " +
                     "or precompressed file is missing.", ex);
         }
     }
 
-    // return a list of all FQZComp encoded test data files in the htscodecs/tests/dat/fqzcomp directory
-    private List<Path> getInteropFQZCompCompressedFiles() throws IOException {
-        final List<Path> paths = new ArrayList<>();
-        Files.newDirectoryStream(
-                        CRAMInteropTestUtils.getInteropTestDataLocation().resolve("dat/"+COMPRESSED_FQZComp_DIR),
-                        path -> Files.isRegularFile(path))
-                .forEach(path -> paths.add(path));
-        return paths;
-    }
-
-    // Given a compressed test file path, return the corresponding uncompressed file path
-    public static final Path getFQZCompUnCompressedFilePath(final Path compressedInteropPath) {
-        String uncompressedFileName = getUncompressedFileName(compressedInteropPath.getFileName().toString());
-        // Example compressedInteropPath: ../dat/fqzcomp/q4.0 => unCompressedFilePath: ../dat/q4
-        return compressedInteropPath.getParent().getParent().resolve(uncompressedFileName);
-    }
-
-    public static final String getUncompressedFileName(final String compressedFileName) {
-        // Returns original filename from compressed file name
-        int lastDotIndex = compressedFileName.lastIndexOf(".");
-        if (lastDotIndex >= 0) {
-            String fileName = compressedFileName.substring(0, lastDotIndex);
-            return fileName;
-        } else {
-            throw new CRAMException("The format of the compressed File Name is not as expected. " +
-                    "The name of the compressed file should contain a period followed by a number that " +
-                    "indicates type of compression. Actual compressed file name = "+ compressedFileName);
-        }
-    }
-
-
-
-
-
 }