From 8d814236252feed3c3486514f44e4d0eb4fbf44c Mon Sep 17 00:00:00 2001
From: orlicohen <107129422+orlicohen@users.noreply.github.com>
Date: Thu, 4 Aug 2022 10:09:00 -0400
Subject: [PATCH] Cloud tests for CompareReferences and
 CheckReferenceCompatibility tools (#7973)

* Comprehensive cloud tests for CompareReferences and CheckReferenceCompatibility tools.
---
 .../tools/reference/CompareReferences.java    |  2 +-
 ...ReferenceCompatibilityIntegrationTest.java | 47 +++++++++++++++++++
 .../CompareReferencesIntegrationTest.java     | 43 +++++++++++++++++
 3 files changed, 91 insertions(+), 1 deletion(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/reference/CompareReferences.java b/src/main/java/org/broadinstitute/hellbender/tools/reference/CompareReferences.java
index 882612a89ae..fc3d44f8322 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/reference/CompareReferences.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/reference/CompareReferences.java
@@ -56,7 +56,7 @@
  * <pre>
  * gatk CompareReferences \
  *   -R reference1.fasta \
- *   -refcomp reference2.fasta
+ *   -refcomp reference2.fasta \
  *   -O output.fasta \
  *   -md5-calculation-mode USE_DICT
  * </pre>
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/reference/CheckReferenceCompatibilityIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/reference/CheckReferenceCompatibilityIntegrationTest.java
index 885f99fee5d..7c9f6df6074 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/reference/CheckReferenceCompatibilityIntegrationTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/reference/CheckReferenceCompatibilityIntegrationTest.java
@@ -8,6 +8,9 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
 
 public class CheckReferenceCompatibilityIntegrationTest extends CommandLineProgramTest {
 
@@ -209,4 +212,48 @@ public void testReferenceCompatibilityNoBAMOrVCF() throws IOException {
         final String[] args = new String[]{"-refcomp", ref1.getAbsolutePath()};
         runCommandLine(args);
     }
+
+    @DataProvider(name = "cloudInputData")
+    public Object[][] cloudInputData() {
+        String testBucket = getGCPTestInputPath() + "org/broadinstitute/hellbender/tools/reference/";
+        return new Object[][]{
+                // dict, list of refs, expected output, isBAM, isVCF
+                new Object[]{testBucket + "reads_data_source_test1_withmd5s.bam",
+                        Arrays.asList(testBucket + "hg19mini.fasta"),
+                        new File(getToolTestDataDir(), "expected.testReferenceCompatibilityBAMWithMD5s_exactmatch.table"),
+                        true, false
+                },
+                new Object[]{ testBucket + "example_variants_withSequenceDict_withmd5.vcf",
+                        Arrays.asList(testBucket + "hg19mini.fasta"),
+                        new File(getToolTestDataDir(), "expected.testReferenceCompatibilityVCFWithMD5s.table"),
+                        false, true
+                },
+        };
+    }
+
+    @Test(dataProvider = "cloudInputData", groups = "bucket")
+    public void testReferenceCompatibilityCloudInputs(String dict, List<String> fastas, File expected, boolean isBAM, boolean isVCF) throws IOException{
+        final File output = createTempFile("testCompareReferencesCloudInputs", ".table");
+
+        List<String> arguments = new ArrayList<>();
+        for(int i = 0; i < fastas.size(); i++){
+            arguments.add("-refcomp");
+            arguments.add(fastas.get(i));
+        }
+
+        if(isBAM){
+            arguments.add("-I");
+        } else if(isVCF){
+            arguments.add("-V");
+        }
+
+        arguments.add(dict);
+        arguments.add("-O");
+        arguments.add(output.getAbsolutePath());
+
+        final String[] args = arguments.toArray(new String[0]);
+        runCommandLine(args);
+
+        IntegrationTestSpec.assertEqualTextFiles(output, expected);
+    }
 }
\ No newline at end of file
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/reference/CompareReferencesIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/reference/CompareReferencesIntegrationTest.java
index 64ab4b7a9d3..6bf0b6ec380 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/reference/CompareReferencesIntegrationTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/reference/CompareReferencesIntegrationTest.java
@@ -8,6 +8,9 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
 
 public class CompareReferencesIntegrationTest extends CommandLineProgramTest {
 
@@ -98,6 +101,46 @@ public void testCompareReferencesUseDictMD5MissingValue() throws IOException{
         runCommandLine(args);
     }
 
+    @DataProvider(name = "cloudInputData")
+    public Object[][] cloudInputData() {
+        String testBucket = getGCPTestInputPath() + "org/broadinstitute/hellbender/tools/reference/";
+        return new Object[][]{
+                // list of refs, expected output
+                new Object[]{ Arrays.asList(testBucket + "hg19mini.fasta",
+                        testBucket + "hg19mini_chr2snp.fasta"),
+                        new File(getToolTestDataDir(), "expected.testCompareReferencesMissingValue.table")
+                },
+                new Object[]{ Arrays.asList(testBucket + "hg19mini.fasta",
+                        testBucket + "hg19mini_1renamed.fasta",
+                        testBucket + "hg19mini_chr2snp.fasta"),
+                        new File(getToolTestDataDir(), "expected.testCompareReferencesMultipleReferences.table")
+                },
+        };
+    }
+
+    @Test(dataProvider = "cloudInputData", groups = "bucket")
+    public void testCompareReferencesCloudInputs(List<String> fastas, File expected) throws IOException{
+        final File output = createTempFile("testCompareReferencesCloudInputs", ".table");
+        List<String> arguments = new ArrayList<>();
+        for(int i = 0; i < fastas.size(); i++){
+            if(i == 0){
+                arguments.add("-R");
+
+            }
+            else{
+                arguments.add("-refcomp");
+            }
+            arguments.add(fastas.get(i));
+        }
+        arguments.add("-O");
+        arguments.add(output.getAbsolutePath());
+
+        final String[] args = arguments.toArray(new String[0]);
+        runCommandLine(args);
+
+        IntegrationTestSpec.assertEqualTextFiles(output, expected);
+    }
+
     // no assertions made, testing tool runs successfully without -O argument
     @Test
     public void testCompareReferencesToStdOutput() throws IOException{