diff --git a/public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java b/public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java index 013a37a88..f04731214 100755 --- a/public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java @@ -40,6 +40,8 @@ import java.util.EnumSet; * Test suite for the parsing engine. */ public class ParsingEngineUnitTest extends BaseTest { + /** we absolutely cannot have this file existing, or we'll fail the UnitTest */ + private final static String NON_EXISTANT_FILENAME_VCF = "this_file_should_not_exist_on_disk_123456789.vcf"; private ParsingEngine parsingEngine; @BeforeMethod @@ -636,7 +638,7 @@ public class ParsingEngineUnitTest extends BaseTest { @Test public void basicRodBindingArgumentTest() { - final String[] commandLine = new String[] {"-V:vcf","foo.vcf"}; + final String[] commandLine = new String[] {"-V:vcf",NON_EXISTANT_FILENAME_VCF}; parsingEngine.addArgumentSource( SingleRodBindingArgProvider.class ); parsingEngine.parse( commandLine ); @@ -646,7 +648,7 @@ public class ParsingEngineUnitTest extends BaseTest { parsingEngine.loadArgumentsIntoObject( argProvider ); Assert.assertEquals(argProvider.binding.getName(), "binding", "Name isn't set properly"); - Assert.assertEquals(argProvider.binding.getSource(), "foo.vcf", "Source isn't set to its expected value"); + Assert.assertEquals(argProvider.binding.getSource(), NON_EXISTANT_FILENAME_VCF, "Source isn't set to its expected value"); Assert.assertEquals(argProvider.binding.getType(), Feature.class, "Type isn't set to its expected value"); Assert.assertEquals(argProvider.binding.isBound(), true, "Bound() isn't returning its expected value"); Assert.assertEquals(argProvider.binding.getTags().getPositionalTags().size(), 1, "Tags aren't correctly set"); @@ -659,7 +661,7 @@ public class ParsingEngineUnitTest extends BaseTest { @Test public void shortNameOnlyRodBindingArgumentTest() { - final String[] commandLine = new String[] {"-short:vcf","foo.vcf"}; + final String[] commandLine = new String[] {"-short:vcf",NON_EXISTANT_FILENAME_VCF}; parsingEngine.addArgumentSource( ShortNameOnlyRodBindingArgProvider.class ); parsingEngine.parse( commandLine ); @@ -669,7 +671,7 @@ public class ParsingEngineUnitTest extends BaseTest { parsingEngine.loadArgumentsIntoObject( argProvider ); Assert.assertEquals(argProvider.binding.getName(), "binding", "Name isn't set properly"); - Assert.assertEquals(argProvider.binding.getSource(), "foo.vcf", "Source isn't set to its expected value"); + Assert.assertEquals(argProvider.binding.getSource(), NON_EXISTANT_FILENAME_VCF, "Source isn't set to its expected value"); Assert.assertEquals(argProvider.binding.getType(), Feature.class, "Type isn't set to its expected value"); Assert.assertEquals(argProvider.binding.isBound(), true, "Bound() isn't returning its expected value"); Assert.assertEquals(argProvider.binding.getTags().getPositionalTags().size(), 1, "Tags aren't correctly set"); @@ -711,7 +713,7 @@ public class ParsingEngineUnitTest extends BaseTest { @Test(expectedExceptions = UserException.class) public void rodBindingArgumentTestMissingType() { - final String[] commandLine = new String[] {"-V","foo.vcf"}; + final String[] commandLine = new String[] {"-V",NON_EXISTANT_FILENAME_VCF}; parsingEngine.addArgumentSource( SingleRodBindingArgProvider.class ); parsingEngine.parse( commandLine ); @@ -723,7 +725,7 @@ public class ParsingEngineUnitTest extends BaseTest { @Test(expectedExceptions = UserException.class) public void rodBindingArgumentTestTooManyTags() { - final String[] commandLine = new String[] {"-V:x,y,z","foo.vcf"}; + final String[] commandLine = new String[] {"-V:x,y,z",NON_EXISTANT_FILENAME_VCF}; parsingEngine.addArgumentSource( SingleRodBindingArgProvider.class ); parsingEngine.parse( commandLine ); @@ -740,7 +742,7 @@ public class ParsingEngineUnitTest extends BaseTest { @Test public void variantContextBindingArgumentTest() { - final String[] commandLine = new String[] {"-V:vcf","foo.vcf"}; + final String[] commandLine = new String[] {"-V:vcf",NON_EXISTANT_FILENAME_VCF}; parsingEngine.addArgumentSource( VariantContextRodBindingArgProvider.class ); parsingEngine.parse( commandLine ); @@ -750,14 +752,14 @@ public class ParsingEngineUnitTest extends BaseTest { parsingEngine.loadArgumentsIntoObject( argProvider ); Assert.assertEquals(argProvider.binding.getName(), "binding", "Name isn't set properly"); - Assert.assertEquals(argProvider.binding.getSource(), "foo.vcf", "Source isn't set to its expected value"); + Assert.assertEquals(argProvider.binding.getSource(), NON_EXISTANT_FILENAME_VCF, "Source isn't set to its expected value"); Assert.assertEquals(argProvider.binding.getType(), VariantContext.class, "Type isn't set to its expected value"); Assert.assertEquals(argProvider.binding.getTags().getPositionalTags().size(), 1, "Tags aren't correctly set"); } @Test public void variantContextBindingArgumentTestVCF3() { - final String[] commandLine = new String[] {"-V:vcf3","foo.vcf"}; + final String[] commandLine = new String[] {"-V:vcf3",NON_EXISTANT_FILENAME_VCF}; parsingEngine.addArgumentSource( VariantContextRodBindingArgProvider.class ); parsingEngine.parse( commandLine ); @@ -767,7 +769,7 @@ public class ParsingEngineUnitTest extends BaseTest { parsingEngine.loadArgumentsIntoObject( argProvider ); Assert.assertEquals(argProvider.binding.getName(), "binding", "Name isn't set properly"); - Assert.assertEquals(argProvider.binding.getSource(), "foo.vcf", "Source isn't set to its expected value"); + Assert.assertEquals(argProvider.binding.getSource(), NON_EXISTANT_FILENAME_VCF, "Source isn't set to its expected value"); Assert.assertEquals(argProvider.binding.getType(), VariantContext.class, "Type isn't set to its expected value"); Assert.assertEquals(argProvider.binding.getTags().getPositionalTags().size(), 1, "Tags aren't correctly set"); } @@ -779,7 +781,7 @@ public class ParsingEngineUnitTest extends BaseTest { @Test public void listRodBindingArgumentTest() { - final String[] commandLine = new String[] {"-V:vcf","foo.vcf"}; + final String[] commandLine = new String[] {"-V:vcf",NON_EXISTANT_FILENAME_VCF}; parsingEngine.addArgumentSource( ListRodBindingArgProvider.class ); parsingEngine.parse( commandLine ); @@ -791,14 +793,14 @@ public class ParsingEngineUnitTest extends BaseTest { Assert.assertEquals(argProvider.bindings.size(), 1, "Unexpected number of bindings"); RodBinding binding = argProvider.bindings.get(0); Assert.assertEquals(binding.getName(), "binding", "Name isn't set properly"); - Assert.assertEquals(binding.getSource(), "foo.vcf", "Source isn't set to its expected value"); + Assert.assertEquals(binding.getSource(), NON_EXISTANT_FILENAME_VCF, "Source isn't set to its expected value"); Assert.assertEquals(binding.getType(), Feature.class, "Type isn't set to its expected value"); Assert.assertEquals(binding.getTags().getPositionalTags().size(), 1, "Tags aren't correctly set"); } @Test public void listRodBindingArgumentTest2Args() { - final String[] commandLine = new String[] {"-V:vcf","foo.vcf", "-V:vcf", "bar.vcf"}; + final String[] commandLine = new String[] {"-V:vcf",NON_EXISTANT_FILENAME_VCF, "-V:vcf", "bar.vcf"}; parsingEngine.addArgumentSource( ListRodBindingArgProvider.class ); parsingEngine.parse( commandLine ); @@ -811,7 +813,7 @@ public class ParsingEngineUnitTest extends BaseTest { RodBinding binding = argProvider.bindings.get(0); Assert.assertEquals(binding.getName(), "binding", "Name isn't set properly"); - Assert.assertEquals(binding.getSource(), "foo.vcf", "Source isn't set to its expected value"); + Assert.assertEquals(binding.getSource(), NON_EXISTANT_FILENAME_VCF, "Source isn't set to its expected value"); Assert.assertEquals(binding.getType(), Feature.class, "Type isn't set to its expected value"); Assert.assertEquals(binding.getTags().getPositionalTags().size(), 1, "Tags aren't correctly set"); @@ -838,7 +840,7 @@ public class ParsingEngineUnitTest extends BaseTest { @Test public void listRodBindingArgumentTestExplicitlyNamed() { - final String[] commandLine = new String[] {"-V:foo,vcf","foo.vcf", "-V:foo,vcf", "bar.vcf"}; + final String[] commandLine = new String[] {"-V:foo,vcf",NON_EXISTANT_FILENAME_VCF, "-V:foo,vcf", "bar.vcf"}; parsingEngine.addArgumentSource( ListRodBindingArgProvider.class ); parsingEngine.parse( commandLine );