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Bugfix for file that must not exist on disk

This commit is contained in:
Mark DePristo 2011-08-29 17:00:10 -04:00
parent 3b09d42ed6
commit 3af001fff2
1 changed files with 17 additions and 15 deletions
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32
public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java
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@ -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<Feature> 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<Feature> 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 );