Basic unit tests for ReferenceOrderedView, ShardDataProvider. Addressing GSA-25.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@844 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/dataSources/providers/ShardDataProvider.java

@@ -141,7 +141,7 @@ public class ShardDataProvider {
             Collection<Class<? extends View>> conflicts = registeredView.getConflictingViews();
             for( Class<? extends View> conflict: conflicts ) {
                 if( conflict.isInstance(view) )
-                    throw new StingException(String.format("Tried to registered two conflicting views: %s and %s",
+                    throw new StingException(String.format("Tried to register two conflicting views: %s and %s",
                                                            registeredView.getClass().getSimpleName(),
                                                            view.getClass().getSimpleName()));
             }
@@ -151,7 +151,7 @@ public class ShardDataProvider {
         for( Class<? extends View> conflict: view.getConflictingViews() ) {
             for( View registeredView: registeredViews ) {
                 if( conflict.isInstance(registeredView) )
-                    throw new StingException(String.format("Tried to registered two conflicting views: %s and %s",
+                    throw new StingException(String.format("Tried to register two conflicting views: %s and %s",
                                                            registeredView.getClass().getSimpleName(),
                                                            view.getClass().getSimpleName()));
             }

java/test/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceOrderedViewTest.java

@@ -0,0 +1,116 @@
+package org.broadinstitute.sting.gatk.dataSources.providers;
+
+import org.junit.Test;
+import org.junit.BeforeClass;
+import org.junit.Assert;
+import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
+import org.broadinstitute.sting.gatk.refdata.TabularROD;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
+import org.broadinstitute.sting.gatk.dataSources.shards.LocusShard;
+import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.ReferenceOrderedDataSource;
+import org.broadinstitute.sting.BaseTest;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.util.Collections;
+import java.util.Arrays;
+/**
+ * User: hanna
+ * Date: May 27, 2009
+ * Time: 3:07:23 PM
+ * BROAD INSTITUTE SOFTWARE COPYRIGHT NOTICE AND AGREEMENT
+ * Software and documentation are copyright 2005 by the Broad Institute.
+ * All rights are reserved.
+ *
+ * Users acknowledge that this software is supplied without any warranty or support.
+ * The Broad Institute is not responsible for its use, misuse, or
+ * functionality.
+ */
+
+/**
+ * Test the transparent view into the reference-ordered data.  At the moment, just do some basic bindings and make
+ * sure the data comes through correctly.
+ */
+public class ReferenceOrderedViewTest extends BaseTest {
+    /**
+     * Sequence file.
+     */
+    private static IndexedFastaSequenceFile seq;
+
+    @BeforeClass
+    public static void init() throws FileNotFoundException {
+        // sequence
+        seq = new IndexedFastaSequenceFile(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
+        GenomeLoc.setupRefContigOrdering(seq);
+    }
+
+    /**
+     * Make sure binding to an empty list produces an empty tracker.
+     */
+    @Test
+    public void testNoBindings() {
+        Shard shard = new LocusShard(new GenomeLoc("chrM",1,30));
+        ShardDataProvider provider = new ShardDataProvider(shard, null, seq, Collections.<ReferenceOrderedDataSource>emptyList());
+        ReferenceOrderedView view = new ReferenceOrderedView( provider );
+
+        RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(new GenomeLoc("chrM",10));
+        Assert.assertNull("The tracker should not have produced any data", tracker.lookup("tableTest",null));
+    }
+
+    /**
+     * Test a single ROD binding.
+     */
+    @Test
+    public void testSingleBinding() {
+        File file = new File(testDir + "TabularDataTest.dat");
+        ReferenceOrderedData rod = new ReferenceOrderedData("tableTest", file, TabularROD.class);
+        ReferenceOrderedDataSource dataSource = new ReferenceOrderedDataSource(rod);
+
+        Shard shard = new LocusShard(new GenomeLoc("chrM",1,30));
+
+        ShardDataProvider provider = new ShardDataProvider(shard, null, seq, Collections.singletonList(dataSource));
+        ReferenceOrderedView view = new ReferenceOrderedView( provider );
+
+        RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(new GenomeLoc("chrM",20));
+        TabularROD datum = (TabularROD)tracker.lookup("tableTest",null);
+
+        Assert.assertEquals("datum parameter for COL1 is incorrect", "C", datum.get("COL1"));
+        Assert.assertEquals("datum parameter for COL2 is incorrect", "D", datum.get("COL2"));
+        Assert.assertEquals("datum parameter for COL3 is incorrect", "E", datum.get("COL3"));
+    }
+
+    /**
+     * Make sure multiple bindings are visible from the view.
+     */
+    @Test
+    public void testMultipleBinding() {
+        File file = new File(testDir + "TabularDataTest.dat");
+
+        ReferenceOrderedData rod1 = new ReferenceOrderedData("tableTest1", file, TabularROD.class);
+        ReferenceOrderedDataSource dataSource1 = new ReferenceOrderedDataSource(rod1);
+        ReferenceOrderedData rod2 = new ReferenceOrderedData("tableTest2", file, TabularROD.class);
+        ReferenceOrderedDataSource dataSource2 = new ReferenceOrderedDataSource(rod2);
+
+
+        Shard shard = new LocusShard(new GenomeLoc("chrM",1,30));
+
+        ShardDataProvider provider = new ShardDataProvider(shard, null, seq, Arrays.asList(dataSource1,dataSource2));
+        ReferenceOrderedView view = new ReferenceOrderedView( provider );
+
+        RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(new GenomeLoc("chrM",20));
+        TabularROD datum1 = (TabularROD)tracker.lookup("tableTest1",null);
+
+        Assert.assertEquals("datum1 parameter for COL1 is incorrect", "C", datum1.get("COL1"));
+        Assert.assertEquals("datum1 parameter for COL2 is incorrect", "D", datum1.get("COL2"));
+        Assert.assertEquals("datum1 parameter for COL3 is incorrect", "E", datum1.get("COL3"));
+
+        TabularROD datum2 = (TabularROD)tracker.lookup("tableTest2",null);
+
+        Assert.assertEquals("datum2 parameter for COL1 is incorrect", "C", datum2.get("COL1"));
+        Assert.assertEquals("datum2 parameter for COL2 is incorrect", "D", datum2.get("COL2"));
+        Assert.assertEquals("datum2 parameter for COL3 is incorrect", "E", datum2.get("COL3"));
+    }
+}

java/test/org/broadinstitute/sting/gatk/dataSources/providers/ShardDataProviderTest.java

@@ -0,0 +1,125 @@
+package org.broadinstitute.sting.gatk.dataSources.providers;
+
+import org.junit.Before;
+import org.junit.Assert;
+import org.junit.Test;
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.StingException;
+
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Arrays;
+/**
+ * User: hanna
+ * Date: May 27, 2009
+ * Time: 1:56:02 PM
+ * BROAD INSTITUTE SOFTWARE COPYRIGHT NOTICE AND AGREEMENT
+ * Software and documentation are copyright 2005 by the Broad Institute.
+ * All rights are reserved.
+ *
+ * Users acknowledge that this software is supplied without any warranty or support.
+ * The Broad Institute is not responsible for its use, misuse, or
+ * functionality.
+ */
+
+/**
+ * Test basic functionality of the shard data provider.
+ */
+
+public class ShardDataProviderTest extends BaseTest {
+    /**
+     * Provider to test.  Should be recreated for every test.
+     */
+    private ShardDataProvider provider = null;
+
+    @Before
+    public void createProvider() {
+        provider = new ShardDataProvider( null,null,null,null );
+    }
+
+    /**
+     * Test whether views are closed when the provider closes.
+     */
+    @Test
+    public void testClose() {
+        TestView testView = new TestView( provider );
+        Assert.assertFalse("View is currently closed but should be open", testView.closed);
+
+        provider.close();
+        Assert.assertTrue("View is currently open but should be closed", testView.closed);
+    }
+
+    /**
+     * Test whether multiple of the same view can be registered and all get a close method.
+     */
+    @Test
+    public void testMultipleClose() {
+        Collection<TestView> testViews = Arrays.asList(new TestView(provider),new TestView(provider));
+        for( TestView testView: testViews )
+            Assert.assertFalse("View is currently closed but should be open", testView.closed);
+
+        provider.close();
+        for( TestView testView: testViews )
+            Assert.assertTrue("View is currently open but should be closed", testView.closed);        
+    }
+
+    /**
+     * Try adding a view which conflicts with some other view that's already been registered.
+     */
+    @Test(expected=StingException.class)
+    public void testAddViewWithExistingConflict() {
+        View initial = new ConflictingTestView( provider );
+        View conflictsWithInitial = new TestView( provider );
+    }
+
+    /**
+     * Try adding a view which has a conflict with a previously registered view.
+     */
+    @Test(expected=StingException.class)
+    public void testAddViewWithNewConflict() {
+        View conflictsWithInitial = new TestView( provider );
+        View initial = new ConflictingTestView( provider );
+    }
+
+    /**
+     * A simple view for testing interactions between views attached to the ShardDataProvider.
+     */
+    private class TestView implements View {
+        /**
+         * Is the test view currently closed.
+         */
+        private boolean closed = false;
+
+        /**
+         * Create a new test view wrapping the given provider.
+         * @param provider
+         */
+        public TestView( ShardDataProvider provider ) {
+            provider.register(this);            
+        }
+
+        /**
+         * Gets conflicting views.  In this case, none conflict.
+         * @return
+         */
+        public Collection<Class<? extends View>> getConflictingViews() { return Collections.emptyList(); }
+
+        /**
+         * Close this view.
+         */
+        public void close() { this.closed = true; }
+    }
+
+    /**
+     * Another view that conflicts with the one above.
+     */
+    private class ConflictingTestView implements View {
+        public ConflictingTestView( ShardDataProvider provider ) { provider.register(this); }
+
+        public Collection<Class<? extends View>> getConflictingViews() {
+            return Collections.<Class<? extends View>>singleton(TestView.class);
+        }
+
+        public void close() {}
+    }
+}