From fe0e908530a46e755dd31f97662dba129af62688 Mon Sep 17 00:00:00 2001
From: Chris Norman <cnorman@broadinstitute.org>
Date: Tue, 27 Feb 2024 16:25:54 -0500
Subject: [PATCH] Update to use the locally checked in CRAM 3.1 interop test
 data.

---
 .../samtools/cram/CRAMInteropTestUtils.java   | 21 +++----------------
 .../htsjdk/samtools/cram/RANSInteropTest.java | 18 ++--------------
 .../java/htsjdk/utils/SamtoolsTestUtils.java  |  5 +++++
 3 files changed, 10 insertions(+), 34 deletions(-)

diff --git a/src/test/java/htsjdk/samtools/cram/CRAMInteropTestUtils.java b/src/test/java/htsjdk/samtools/cram/CRAMInteropTestUtils.java
index 71b7b39555..8085693302 100644
--- a/src/test/java/htsjdk/samtools/cram/CRAMInteropTestUtils.java
+++ b/src/test/java/htsjdk/samtools/cram/CRAMInteropTestUtils.java
@@ -8,29 +8,14 @@
 import java.util.ArrayList;
 import java.util.List;
 
-import htsjdk.utils.SamtoolsTestUtils;
-
-/**
- * Interop test data is kept in a separate repository, currently at https://github.com/samtools/htscodecs
- * so it can be shared across htslib/samtools/htsjdk.
- */
 public class CRAMInteropTestUtils {
-    public static final String INTEROP_TEST_FILES_PATH = SamtoolsTestUtils.getCRAMInteropData();
-
-    /**
-     * @return true if interop test data is available, otherwise false
-     */
-    public static boolean isInteropTestDataAvailable() {
-        final Path testDataPath = getInteropTestDataLocation();
-        return Files.exists(testDataPath);
-    }
 
     /**
-     * @return the name and location of the local interop test data as specified by the
-     * variable INTEROP_TEST_FILES_PATH
+     * Return the location of the locally checked-in test CRAM 3.1 test interop data dir (the files
+     * there are copied from the originals in htscodecs), and should be updated periodically.
      */
     public static Path getInteropTestDataLocation() {
-        return Paths.get(INTEROP_TEST_FILES_PATH);
+        return Paths.get("src/test/resources/htsjdk/samtools/cram/3.1_streams/");
     }
 
     // the input files have embedded newlines that the test remove before round-tripping...
diff --git a/src/test/java/htsjdk/samtools/cram/RANSInteropTest.java b/src/test/java/htsjdk/samtools/cram/RANSInteropTest.java
index 9c1abafc29..a99c97aa97 100644
--- a/src/test/java/htsjdk/samtools/cram/RANSInteropTest.java
+++ b/src/test/java/htsjdk/samtools/cram/RANSInteropTest.java
@@ -30,12 +30,8 @@
 
 /**
  * RANSInteropTest tests if the htsjdk RANS4x8 and RANSNx16 implementations are interoperable
- * with the htslib implementations. The test files for Interop tests is kept in a separate repository,
- * currently at https://github.com/samtools/htscodecs so it can be shared across htslib/samtools/htsjdk.
- *
- * For local development env, the Interop test files must be downloaded locally and made available at "../htscodecs/tests"
- * For CI env, the Interop test files are made available from the existing samtools installation
- * at "/samtools-1.14/htslib-1.14/htscodecs/tests"
+ * with the htslib implementations. The test files for Interop tests originate a separate repository,
+ * currently at https://github.com/samtools/htscodecs, but are checked into this repo as wrll.
  */
 public class RANSInteropTest extends HtsjdkTest {
     public static final String COMPRESSED_RANS4X8_DIR = "r4x8";
@@ -155,16 +151,7 @@ public Object[][] getDecodeOnlyTestCases() throws IOException {
                 .toArray(Object[][]::new);
     }
 
-    @Test(description = "Test if CRAM Interop Test Data is available")
-    public void testHtsCodecsCorpusIsAvailable() {
-        if (!CRAMInteropTestUtils.isInteropTestDataAvailable()) {
-            throw new SkipException(String.format("RANS Interop Test Data is not available at %s",
-                    CRAMInteropTestUtils.INTEROP_TEST_FILES_PATH));
-        }
-    }
-
     @Test (
-            dependsOnMethods = "testHtsCodecsCorpusIsAvailable",
             dataProvider = "roundTripTestCases",
             description = "Roundtrip using htsjdk RANS. Compare the output with the original file" )
     public void testRANSRoundTrip(
@@ -192,7 +179,6 @@ public void testRANSRoundTrip(
     }
 
     @Test (
-            dependsOnMethods = "testHtsCodecsCorpusIsAvailable",
             dataProvider = "decodeOnlyTestCases",
             description = "Uncompress the existing compressed file using htsjdk RANS and compare it with the original file.")
     public void testDecodeOnly(
diff --git a/src/test/java/htsjdk/utils/SamtoolsTestUtils.java b/src/test/java/htsjdk/utils/SamtoolsTestUtils.java
index a4c1cc1918..c62c8a5fef 100644
--- a/src/test/java/htsjdk/utils/SamtoolsTestUtils.java
+++ b/src/test/java/htsjdk/utils/SamtoolsTestUtils.java
@@ -48,6 +48,11 @@ public static String getSamtoolsBin() {
         return samtoolsPath == null ? "/usr/local/bin/samtools" : samtoolsPath;
     }
 
+    public static String getCRAMInteropData() {
+        final String samtoolsPath = System.getenv(SAMTOOLS_BINARY_ENV_VARIABLE);
+        return samtoolsPath == null ? "../htscodecs/tests" : "./samtools-"+expectedSamtoolsVersion+ "/htslib-"+expectedHtslibVersion+"/htscodecs/tests";
+    }
+
     /**
      * Execute a samtools command line if a local samtools executable is available see {@link #isSamtoolsAvailable()}.
      *