More testng fallout: fixing another seemingly 'random' issue arising from an

alternate test ordering.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5160 348d0f76-0448-11de-a6fe-93d51630548a

java/test/org/broadinstitute/sting/WalkerTest.java

@@ -40,14 +40,8 @@ import java.io.File;
 import java.util.*;
 
 public class WalkerTest extends BaseTest {
-    // the default output path for the integration test
-    private File outputFileLocation = null;
     private static final boolean ENABLE_REPORTING = false;
 
-    public void setOutputFileLocation(File outputFileLocation) {
-        this.outputFileLocation = outputFileLocation;
-    }
-
     public String assertMatchingMD5(final String name, final File resultsFile, final String expectedMD5) {
         return assertMatchingMD5(name, resultsFile, expectedMD5, parameterize());
     }
@@ -84,6 +78,9 @@ public class WalkerTest extends BaseTest {
         List<String> exts = null;
         Class expectedException = null;
 
+        // the default output path for the integration test
+        private File outputFileLocation = null;
+
         protected Map<String, File> auxillaryFiles = new HashMap<String, File>();
 
         public WalkerTestSpec(String args, List<String> md5s) {
@@ -113,6 +110,14 @@ public class WalkerTest extends BaseTest {
             this.expectedException = expectedException;
         }
 
+        public void setOutputFileLocation(File outputFileLocation) {
+            this.outputFileLocation = outputFileLocation;
+        }        
+
+        protected File getOutputFileLocation() {
+            return outputFileLocation;
+        }
+        
         public boolean expectsException() {
             return expectedException != null;
         }
@@ -125,6 +130,7 @@ public class WalkerTest extends BaseTest {
         public void addAuxFile(String expectededMD5sum, File outputfile) {
             auxillaryFiles.put(expectededMD5sum, outputfile);
         }
+
     }
 
     protected boolean parameterize() {
@@ -163,7 +169,7 @@ public class WalkerTest extends BaseTest {
 
         if ( spec.expectsException() ) {
             // this branch handles the case were we are testing that a walker will fail as expected
-            return executeTest(name, null, tmpFiles, args, spec.getExpectedException());
+            return executeTest(name, spec.getOutputFileLocation(), null, tmpFiles, args, spec.getExpectedException());
         } else {
             List<String> md5s = new LinkedList<String>();
             md5s.addAll(spec.md5s);
@@ -173,7 +179,7 @@ public class WalkerTest extends BaseTest {
                 md5s.add(md5);
                 tmpFiles.add(spec.auxillaryFiles.get(md5));
             }
-            return executeTest(name, md5s, tmpFiles, args, null);
+            return executeTest(name, spec.getOutputFileLocation(), md5s, tmpFiles, args, null);
         }
     }
 
@@ -186,9 +192,9 @@ public class WalkerTest extends BaseTest {
      * @param expectedException the expected exception or null
      * @return a pair of file and string lists
      */
-    private Pair<List<File>, List<String>> executeTest(String name, List<String> md5s, List<File> tmpFiles, String args, Class expectedException) {
+    private Pair<List<File>, List<String>> executeTest(String name, File outputFileLocation, List<String> md5s, List<File> tmpFiles, String args, Class expectedException) {
         if (outputFileLocation != null)
-            args += " -o " + this.outputFileLocation.getAbsolutePath();
+            args += " -o " + outputFileLocation.getAbsolutePath();
         executeTest(name, args, expectedException);
 
         if ( expectedException != null ) {

java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java

@@ -50,10 +50,6 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest {
 
     @Test
     public void testMapQ0Only() {
-        // our base file
-        File baseOutputFile = this.createTempFile("depthofcoveragemapq0",".tmp");
-        this.setOutputFileLocation(baseOutputFile);
-
         String[] intervals = {"1:10,000,000-10,002,000","1:10,003,000-10,004,000"};
         String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam"};
 
@@ -61,6 +57,10 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest {
 
         WalkerTestSpec spec = new WalkerTestSpec(cmd,0,new ArrayList<String>());
 
+        // our base file
+        File baseOutputFile = this.createTempFile("depthofcoveragemapq0",".tmp");
+
+        spec.setOutputFileLocation(baseOutputFile);
         spec.addAuxFile("f39af6ad99520fd4fb27b409ab0344a0",baseOutputFile);
         spec.addAuxFile("6b15f5330414b6d4e2f6caea42139fa1", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts"));
         spec.addAuxFile("cc6640d82077991dde8a2b523935cdff", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions"));
@@ -74,14 +74,15 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest {
 
     @Test
     public void testLotsOfSamples() {
-        File baseOutputFile = this.createTempFile("testManySamples",".tmp");
-        this.setOutputFileLocation(baseOutputFile);
         String[] intervals = {"1:1105290-1105295"};
         String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/pilot3.CEU+TSI.5loci.bam"};
         String cmd = buildRootCmd(b36KGReference, new ArrayList<String>(Arrays.asList(bams)), new ArrayList<String>(Arrays.asList(intervals)));
 
         WalkerTestSpec spec = new WalkerTestSpec(cmd,0,new ArrayList<String>());
 
+        File baseOutputFile = this.createTempFile("testManySamples",".tmp");
+        
+        spec.setOutputFileLocation(baseOutputFile);
         spec.addAuxFile("c9561b52344536d2b06ab97b0bb1a234",baseOutputFile);
 
         execute("testLotsOfSamples",spec);

java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java

@@ -44,16 +44,16 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
 
     @Test
     public void testBaseOutputNoFiltering() {
-        // our base file
-        File baseOutputFile = this.createTempFile("depthofcoveragenofiltering",".tmp");
-        this.setOutputFileLocation(baseOutputFile);
-
         String[] intervals = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/fhs_jhs_30_targts.interval_list"};
         String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/FHS_indexed_subset.bam"};
 
         String cmd = buildRootCmd(hg18Reference,new ArrayList<String>(Arrays.asList(bams)),new ArrayList<String>(Arrays.asList(intervals))) + " -mmq 0 -mbq 0 -dels -baseCounts -pt readgroup -pt sample -pt library --outputFormat csv -ct 10 -ct 15 -ct 20 -ct 25";
         WalkerTestSpec spec = new WalkerTestSpec(cmd,0, new ArrayList<String>());
 
+        // our base file
+        File baseOutputFile = this.createTempFile("depthofcoveragenofiltering",".tmp");
+        spec.setOutputFileLocation(baseOutputFile);
+
         // now add the expected files that get generated
         spec.addAuxFile("423571e4c05e7934322172654ac6dbb7", baseOutputFile);
         spec.addAuxFile("9df5e7e07efeb34926c94a724714c219", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_counts"));
@@ -80,15 +80,15 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
 
     @Test
     public void testNoCoverageDueToFiltering() {
-        File baseOutputFile = this.createTempFile("depthofcoveragenofiltering",".tmp");
-        this.setOutputFileLocation(baseOutputFile);
-
         String[] intervals = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/fhs_jhs_30_targts.interval_list"};
         String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/FHS_indexed_subset.bam"};
 
         String cmd = buildRootCmd(hg18Reference,new ArrayList<String>(Arrays.asList(bams)),new ArrayList<String>(Arrays.asList(intervals))) + " -mmq 0 -mbq 5 --maxBaseQuality 4 -dels -baseCounts -pt readgroup -pt sample -pt library --outputFormat csv";
         WalkerTestSpec spec = new WalkerTestSpec(cmd,0, new ArrayList<String>());
 
+        File baseOutputFile = this.createTempFile("depthofcoveragenofiltering",".tmp");
+        spec.setOutputFileLocation(baseOutputFile);
+
         spec.addAuxFile("6ccd7d8970ba98cb95fe41636a070c1c",baseOutputFile);
         spec.addAuxFile("0ee40f3e5091536c14e077b77557083a",createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
 

java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java

@@ -75,7 +75,7 @@ public class IntervalIntegrationTest extends WalkerTest {
 
         // our base file
         File baseOutputFile = createTempFile("testUnmappedReadInclusion",".bam");
-        this.setOutputFileLocation(baseOutputFile);
+        spec.setOutputFileLocation(baseOutputFile);
         spec.addAuxFile("fcd11cfa8474472c617d400623a30fcd",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
         spec.addAuxFile("3d1f077727e6b68e20a2095d034e56d7", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));
 
@@ -95,7 +95,7 @@ public class IntervalIntegrationTest extends WalkerTest {
 
         // our base file
         File baseOutputFile = createTempFile("testUnmappedReadExclusion",".bam");
-        this.setOutputFileLocation(baseOutputFile);
+        spec.setOutputFileLocation(baseOutputFile);
         spec.addAuxFile("3153593c9f9ff80a8551fff5655e65ec",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
         spec.addAuxFile("7fc574ac72211623e4df74d9f75a4e48", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));