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ValidateVariants exception message improvement #6076

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merged 4 commits into from
Oct 30, 2019
Merged

ValidateVariants exception message improvement #6076

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db893e5
Add a test as supposedly described in #4642
ldgauthier Aug 2, 2019
9385c69
Fix and improve error message
ldgauthier Aug 2, 2019
84b9e10
Comment explaining test
ldgauthier Aug 5, 2019
d9e299c
finals
ldgauthier Aug 6, 2019
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2 changes: 1 addition & 1 deletion src/main/java/org/broadinstitute/hellbender/exceptions/UserException.java
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Original file line number Diff line number Diff line change
Expand Up @@ -326,7 +326,7 @@ public static class FailsStrictValidation extends UserException {
public final ValidateVariants.ValidationType type;

public FailsStrictValidation(String f, ValidateVariants.ValidationType type, String message) {
super(String.format("Input %s fails strict validation: %s of type:", f, message, type));
super(String.format("Input %s fails strict validation of type %s: %s", f, type, message));
this.type = type;
}
}
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13 changes: 11 additions & 2 deletions ...est/java/org/broadinstitute/hellbender/tools/walkers/ValidateVariantsIntegrationTest.java
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Expand Up @@ -37,7 +37,7 @@ public String baseTestStringWithoutReference(boolean sharedFile, String file, bo
}

private static String excludeValidationTypesButString(ValidateVariants.ValidationType type) {
if (type.equals(ALL)) {
if (type == null || type.equals(ALL)) {
return "";
}
final StringBuilder sbuilder = new StringBuilder();
Expand Down Expand Up @@ -153,13 +153,22 @@ public void testBadRefBase2() throws IOException {

@Test
public void testBadChrCount1() throws IOException {
IntegrationTestSpec spec = new IntegrationTestSpec(
final IntegrationTestSpec spec = new IntegrationTestSpec(
baseTestString(false, "validationExampleBad.vcf", false, CHR_COUNTS),
0,
UserException.FailsStrictValidation.class
);

spec.executeTest("test bad chr counts #1", this);

//test with no reference and no validations specified
final IntegrationTestSpec spec2 = new IntegrationTestSpec(
baseTestStringWithoutReference(false, "validationExampleBad.vcf", false, null),
0,
UserException.FailsStrictValidation.class
);

spec2.executeTest("test bad chr counts with no ref and no validations specified", this);
}

@Test
Expand Down