Align the Funcotator checkIfAlreadyAnnotated test with the Funcotator…

… engine code. (#7555)

src/main/java/org/broadinstitute/hellbender/tools/funcotator/Funcotator.java

@@ -4,7 +4,6 @@
 import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.vcf.VCFHeader;
-import htsjdk.variant.vcf.VCFHeaderLine;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.broadinstitute.barclay.argparser.ArgumentCollection;
@@ -826,10 +825,7 @@ public void onTraversalStart() {
      */
     @VisibleForTesting
     static void checkIfAlreadyAnnotated(final VCFHeader vcfHeader, GATKPath drivingVariantFile) {
-        if (vcfHeader.getOtherHeaderLine(FuncotatorConstants.VCF_HEADER_ALREADY_ANNOTATED_1) != null) {
-            throw new UserException.BadInput("Given VCF " +drivingVariantFile+ " has already been annotated!");
-        }
-        else if (vcfHeader.getOtherHeaderLine(FuncotatorConstants.VCF_HEADER_ALREADY_ANNOTATED_2) != null) {
+        if (vcfHeader.getOtherHeaderLine(FuncotatorConstants.FUNCOTATOR_VERSION_VCF_HEADERLINE_KEY) != null) {
             throw new UserException.BadInput("Given VCF " +drivingVariantFile+ " has already been annotated!");
         }
     }

src/main/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorConstants.java

@@ -44,11 +44,8 @@ public class FuncotatorConstants {
             Arrays.asList(B37_MITOCHONDRIAL_CONTIG_NAME, HG19_MITOCHONDRIAL_CONTIG_NAME, HG38_MITOCHONDRIAL_CONTIG_NAME)
     );
 
-    /** Name of one of the header line keys which indicates that a file has already been annotated. */
-    public static final String VCF_HEADER_ALREADY_ANNOTATED_1 = "Funcotator";
-
-    /** Name of the second header line key which indicates that a file has already been annotated. */
-    public static final String VCF_HEADER_ALREADY_ANNOTATED_2 = "Funcotator Version";
+    /** Name of the header line key which indicates that a file has already been annotated. */
+    public static final String FUNCOTATOR_VERSION_VCF_HEADERLINE_KEY = "Funcotator Version";
 
 
 }

src/main/java/org/broadinstitute/hellbender/tools/funcotator/vcfOutput/VcfOutputRenderer.java

@@ -1,6 +1,5 @@
 package org.broadinstitute.hellbender.tools.funcotator.vcfOutput;
 
-import com.google.common.annotations.VisibleForTesting;
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.VariantContextBuilder;
@@ -281,7 +280,7 @@ private VCFHeader createVCFHeader() {
 
         // Add in the lines about Funcotations:
         headerLines.addAll(defaultToolVcfHeaderLines);
-        headerLines.add(new VCFHeaderLine("Funcotator Version", toolVersion + " | " + getDataSourceInfoString()));
+        headerLines.add(new VCFHeaderLine(FuncotatorConstants.FUNCOTATOR_VERSION_VCF_HEADERLINE_KEY, toolVersion + " | " + getDataSourceInfoString()));
         headerLines.add(new VCFInfoHeaderLine(FUNCOTATOR_VCF_FIELD_NAME, VCFHeaderLineCount.A,
                 VCFHeaderLineType.String, "Functional annotation from the Funcotator tool.  Funcotation fields are"
                 + DESCRIPTION_PREAMBLE_DELIMITER +

src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorUnitTest.java

@@ -4,12 +4,9 @@
 import htsjdk.variant.vcf.VCFHeaderLine;
 import org.broadinstitute.hellbender.GATKBaseTest;
 import org.broadinstitute.hellbender.exceptions.UserException;
-import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
-import java.util.ArrayList;
 import java.util.LinkedHashSet;
-import java.util.List;
 import java.util.Set;
 
 /**
@@ -18,114 +15,36 @@
  */
 public class FuncotatorUnitTest extends GATKBaseTest {
 
-    /**
-     * Data provider for the unit test for checkIfAlreadyAnnotated. In this case, we have a
-     * "Funcotator" column in the vcf header, which indicates
-     * that this vcf has already been annotated and thus the program
-     * should not run on this input.
-     *
-     */
-    @DataProvider
-    Object[][] provideDataForAnnotationCheckWrong() {
-        final Set<VCFHeaderLine> headerLines = new LinkedHashSet<>();
-
-        headerLines.add(new VCFHeaderLine("fileformat", "fileformat"));
-        headerLines.add(new VCFHeaderLine("FILTER", "FILTER"));
-        headerLines.add(new VCFHeaderLine("FORMAT", "FORMAT"));
-        headerLines.add(new VCFHeaderLine("Funcotator", "Funcotator"));
-        headerLines.add(new VCFHeaderLine("GATKCommandLine", "GATKCommandLine"));
-        headerLines.add(new VCFHeaderLine("INFO", "INFO"));
-
-        return new Object[][] {
-                { headerLines }
-        };
-    }
-
-    /**
-     * Data provider for the unit test for checkIfAlreadyAnnotated. In this case, we have a
-     * "Funcotator Version" column in the vcf header, which indicates
-     * that this vcf has already been annotated and thus the program
-     * should not run on this input.
-     *
-     */
-    @DataProvider
-    Object[][] provideDataForAnnotationCheckWrongSecond() {
-        final Set<VCFHeaderLine> headerLines = new LinkedHashSet<>();
-
-        headerLines.add(new VCFHeaderLine("fileformat", "fileformat"));
-        headerLines.add(new VCFHeaderLine("FILTER", "FILTER"));
-        headerLines.add(new VCFHeaderLine("FORMAT", "FORMAT"));
-        headerLines.add(new VCFHeaderLine("Funcotator Version", "Funcotator Version"));
-        headerLines.add(new VCFHeaderLine("GATKCommandLine", "GATKCommandLine"));
-        headerLines.add(new VCFHeaderLine("INFO", "INFO"));
-
-        return new Object[][] {
-                { headerLines }
-        };
-    }
-
-
-    /**
-     * Data provider for the unit test of our annotation function when the
-     * given vcf file has not already been annotated. In this case, we see that
-     * there is no longer a column labelled "Funcotator", and all other columns
-     * are typically of a vcf file which has not been annotated yet. Thus,
-     * the function should not throw an error and we should annotate this file.
-     *
-     */
-    @DataProvider
-    Object[][] provideDataForAnnotationCheckRight() {
-        final Set<VCFHeaderLine> headerLines = new LinkedHashSet<>(); //= new List<>();
-        //return Arrays.asList(
-        headerLines.add(new VCFHeaderLine("fileformat", "VCF"));
-        headerLines.add(new VCFHeaderLine("FILTER", "FILTER"));
-        headerLines.add(new VCFHeaderLine("FORMAT", "FORMAT"));
-        headerLines.add(new VCFHeaderLine("GATKCommandLine", "GATKCommandLine"));
-        headerLines.add(new VCFHeaderLine("INFO", "INFO"));
-
-        return new Object[][] {
-                { headerLines }
-        };
-    }
-
-
-    /**
-     * Unit test to check if our checkIfAlreadyAnnotated function works correctly.
-     * In this case, we are using the data provider which has an incorrect field name
-     * in the vcf header, and thus, this function should throw an error because the given
-     * vcf file has already been annotated and we do not need to annotate again.
-     *
-     */
-    @Test(dataProvider = "provideDataForAnnotationCheckWrong", expectedExceptions = UserException.BadInput.class)
-    public void testCheckWhenAlreadyAnnotated(final Set<VCFHeaderLine> vcfHeaderLines) {
-        final VCFHeader vcfHeader = new VCFHeader(vcfHeaderLines);
-        Funcotator.checkIfAlreadyAnnotated(vcfHeader, null);
-    }
-
     /**
      * Unit test to check if our checkIfAlreadyAnnotated function works correctly.
-     * In this case, we are using the data provider which has the second incorrect field name
+     * In this case, we are using a header which does not have the
+     * {@link FuncotatorConstants#FUNCOTATOR_VERSION_VCF_HEADERLINE_KEY}
      * in the vcf header, and thus, this function should throw an error because the given
      * vcf file has already been annotated and we do not need to annotate again.
      *
      */
-    @Test(dataProvider = "provideDataForAnnotationCheckWrongSecond", expectedExceptions = UserException.BadInput.class)
-    public void testCheckWhenAlreadyAnnotatedSecond(final Set<VCFHeaderLine> vcfHeaderLines) {
+    @Test(expectedExceptions = UserException.BadInput.class)
+    public void testCheckWhenAlreadyAnnotated() {
+        final Set<VCFHeaderLine> vcfHeaderLines = new LinkedHashSet<>();
+        vcfHeaderLines.add(new VCFHeaderLine(
+                FuncotatorConstants.FUNCOTATOR_VERSION_VCF_HEADERLINE_KEY,
+                "content not relevant for this test"));
         final VCFHeader vcfHeader = new VCFHeader(vcfHeaderLines);
         Funcotator.checkIfAlreadyAnnotated(vcfHeader, null);
     }
 
     /**
      * Unit test to check if our checkIfAlreadyAnnotated function works correctly.
-     * In this case, we are using the data provider which does not have any incorrect
-     * field names in the given vcf header, and thus, this function should
+     * In this case, we are using the data provider which has the
+     * {@link FuncotatorConstants#FUNCOTATOR_VERSION_VCF_HEADERLINE_KEY} header line
+     * in the given vcf header, and thus, this function should
      * not throw an error because the given vcf file has not been annotated yet
      * and this file should be annotated.
      *
      */
-    @Test(dataProvider = "provideDataForAnnotationCheckRight")
-    public void testCheckWhenNotAlreadyAnnotated(final Set<VCFHeaderLine> vcfHeaderLines) {
-        final VCFHeader vcfHeader = new VCFHeader(vcfHeaderLines);
+    @Test
+    public void testCheckWhenNotAlreadyAnnotated() {
+        final VCFHeader vcfHeader = new VCFHeader(new LinkedHashSet<>());
         Funcotator.checkIfAlreadyAnnotated(vcfHeader, null);
         //this should not throw an exception.
     }