From de2ec4c9caf88cb6e9bd1b3821dd170d132f851e Mon Sep 17 00:00:00 2001
From: Louis Bergelson <louisb@broadinstitute.org>
Date: Fri, 4 Oct 2024 10:38:22 -0400
Subject: [PATCH] Use full path with scheme in beta VCFDecoder

* Replace toPath().toString() with toUriString() this should prevent the scheme from being cutoff unintentionally
---
 .../beta/codecs/variants/vcf/VCFDecoder.java  |  4 ++--
 .../codecs/variants/vcf/HtsVCFCodecTest.java  | 24 ++++++++++++++++++-
 2 files changed, 25 insertions(+), 3 deletions(-)

diff --git a/src/main/java/htsjdk/beta/codecs/variants/vcf/VCFDecoder.java b/src/main/java/htsjdk/beta/codecs/variants/vcf/VCFDecoder.java
index 1413f6ef58..6e2c5f79a0 100644
--- a/src/main/java/htsjdk/beta/codecs/variants/vcf/VCFDecoder.java
+++ b/src/main/java/htsjdk/beta/codecs/variants/vcf/VCFDecoder.java
@@ -206,9 +206,9 @@ private static FeatureReader<VariantContext> getVCFReader(
         //TODO: this resolves the index automatically. it should check to make sure the provided index
         // matches the one that is automatically resolved, otherwise throw since the request will not be honored
         return AbstractFeatureReader.getFeatureReader(
-                variantsIOPath.toPath().toString(),
+                variantsIOPath.getURIString(),
                 indexIOPath.isPresent() ?
-                        indexIOPath.get().toPath().toString() :
+                        indexIOPath.get().getURIString() :
                         null,
                 vcfCodec,
                 indexIOPath.isPresent(),
diff --git a/src/test/java/htsjdk/beta/codecs/variants/vcf/HtsVCFCodecTest.java b/src/test/java/htsjdk/beta/codecs/variants/vcf/HtsVCFCodecTest.java
index 0c9e6c458b..a565233868 100644
--- a/src/test/java/htsjdk/beta/codecs/variants/vcf/HtsVCFCodecTest.java
+++ b/src/test/java/htsjdk/beta/codecs/variants/vcf/HtsVCFCodecTest.java
@@ -1,5 +1,8 @@
 package htsjdk.beta.codecs.variants.vcf;
 
+import com.google.common.jimfs.Configuration;
+import com.google.common.jimfs.Jimfs;
+import com.google.common.jimfs.SystemJimfsFileSystemProvider;
 import htsjdk.HtsjdkTest;
 import htsjdk.beta.codecs.variants.vcf.vcfv3_2.VCFCodecV3_2;
 import htsjdk.beta.codecs.variants.vcf.vcfv3_3.VCFCodecV3_3;
@@ -26,6 +29,7 @@
 import htsjdk.beta.plugin.variants.VariantsEncoder;
 import htsjdk.beta.plugin.variants.VariantsFormats;
 import htsjdk.samtools.util.IOUtil;
+import htsjdk.tribble.TestUtils;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.vcf.VCFHeader;
 import org.testng.Assert;
@@ -36,6 +40,9 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
+import java.nio.file.FileSystem;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.function.Function;
@@ -60,11 +67,26 @@ private Object[][] vcfReadWriteTests() {
         };
     }
 
+    @Test
+    public void testRoundTripNio() throws IOException {
+        try(FileSystem fs = Jimfs.newFileSystem("test", Configuration.unix())){
+            final IOPath outputPath = IOUtils.createTempPath("roundTripVCFThroughPath", ".vcf");
+            Path tribbleFileInJimfs = TestUtils.getTribbleFileInJimfs(TEST_VCF_WITH_INDEX.getRawInputString(), TEST_VCF_INDEX.getRawInputString(), fs);
+            HtsPath vcf = new HtsPath(tribbleFileInJimfs.toUri().toString());
+            checkCodecAndReadWriteVcf( vcf , VCFCodecV4_0.VCF_V40_VERSION , outputPath);
+        }
+    }
+    
     @Test(dataProvider = "vcfReadWriteTests")
     public void testRoundTripVCFThroughPath(final IOPath inputPath, final HtsVersion expectedCodecVersion) {
+        final IOPath outputPath = IOUtils.createTempPath("roundTripVCFThroughPath", ".vcf");
+
+        checkCodecAndReadWriteVcf(inputPath, expectedCodecVersion, outputPath);
+    }
+
+    private void checkCodecAndReadWriteVcf(IOPath inputPath, HtsVersion expectedCodecVersion, IOPath outputPath) {
         // some test files require "AllowMissingFields" options for writing
         final VariantsEncoderOptions variantsEncoderOptions = new VariantsEncoderOptions().setAllowFieldsMissingFromHeader(true);
-        final IOPath outputPath = IOUtils.createTempPath("roundTripVCFThroughPath", ".vcf");
 
         try (final VariantsDecoder variantsDecoder = HtsDefaultRegistry.getVariantsResolver().getVariantsDecoder(inputPath);
              final VariantsEncoder variantsEncoder = HtsDefaultRegistry.getVariantsResolver().getVariantsEncoder(