Validates that the tribble binding provides the right object types at startup

Tests to ensure this remains working

public/java/src/org/broadinstitute/sting/commandline/RodBinding.java

@@ -39,10 +39,15 @@ import java.util.List;
  * There is no constraint on the type of the ROD bound.
  */
 public class RodBinding<T extends Feature> {
-    final String variableName;
+    final private String variableName;
-    final String source;
+    final private String source;
-    final Tags tags;
+    final private Tags tags;
-    final Class<T> type;
+    final private Class<T> type;
+
+    public boolean isBound() {
+        // todo : implement me
+        return source != null;
+    }
 
     public RodBinding(Class<T> type, final String variableName, final String source, final Tags tags) {
         this.type = type;

public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java

@@ -38,10 +38,7 @@ import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.utils.text.ListFileUtils;
 
-import java.util.ArrayList;
+import java.util.*;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.List;
 
 /**
  * @author aaron
@@ -134,6 +131,7 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
         return 0;
     }
 
+
     /**
      * Generate the GATK run report for this walker using the current GATKEngine, if -et is enabled.
      * This report will be written to either STDOUT or to the run repository, depending on the options

public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2010 The Broad Institute
+ * Copyright (c) 2011, The Broad Institute
  *
  * Permission is hereby granted, free of charge, to any person
  * obtaining a copy of this software and associated documentation
@@ -12,15 +12,14 @@
  *
  * The above copyright notice and this permission notice shall be
  * included in all copies or substantial portions of the Software.
- *
  * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
  * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
  * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
  * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
  * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
  * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ * OTHER DEALINGS IN THE SOFTWARE.
  */
 
 package org.broadinstitute.sting.gatk.refdata.tracks;
@@ -100,7 +99,7 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
     public RMDTrackBuilder(SAMSequenceDictionary dict,
                            GenomeLocParser genomeLocParser,
                            ValidationExclusion.TYPE validationExclusionType) {
-        super(FeatureCodec.class, "Codecs", "Codec");
+        this();
         this.dict = dict;
         this.genomeLocParser = genomeLocParser;
         this.validationExclusionType = validationExclusionType;
@@ -108,7 +107,21 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
         classes = new HashMap<String, Class>();
         for (String name: this.getPluginsByName().keySet()) {
             classes.put(name.toUpperCase(), getPluginsByName().get(name));
-        }    }
+        }
+    }
+
+    /**
+     * Limited constructor that produces a builder capable for validating types, but not building tracks
+     */
+    public RMDTrackBuilder() {
+        super(FeatureCodec.class, "Codecs", "Codec");
+
+        classes = new HashMap<String, Class>();
+        for (String name: this.getPluginsByName().keySet()) {
+            classes.put(name.toUpperCase(), getPluginsByName().get(name));
+        }
+    }
+
 
     /** @return a list of all available track types we currently have access to create */
     public Map<String, Class> getAvailableTrackNamesAndTypes() {
@@ -125,6 +138,10 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
         return classToRecord;
     }
 
+    public Class getFeatureCodecClass(RMDTriplet fileDescriptor) {
+        return getAvailableTrackNamesAndTypes().get(fileDescriptor.getType().toUpperCase());
+    }
+
     /**
      * create a RMDTrack of the specified type
      *
@@ -136,7 +153,7 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
         String name = fileDescriptor.getName();
         File inputFile = new File(fileDescriptor.getFile());
 
-        Class featureCodecClass = getAvailableTrackNamesAndTypes().get(fileDescriptor.getType().toUpperCase());
+        Class featureCodecClass = getFeatureCodecClass(fileDescriptor);
         if (featureCodecClass == null)
             throw new UserException.BadArgumentValue("-B",fileDescriptor.getType());
 

public/java/src/org/broadinstitute/sting/utils/text/ListFileUtils.java

@@ -29,6 +29,7 @@ import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.commandline.Tags;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
 import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
+import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
@@ -134,6 +135,7 @@ public class ListFileUtils {
     public static Collection<RMDTriplet> unpackRODBindings(final Collection<RodBinding> RODBindings, final ParsingEngine parser) {
         // todo -- this is a strange home for this code.  Move into ROD system
         Collection<RMDTriplet> rodBindings = new ArrayList<RMDTriplet>();
+        RMDTrackBuilder builderForValidation = new RMDTrackBuilder();
 
         for (RodBinding rodBinding: RODBindings) {
             String argValue = rodBinding.getSource();
@@ -158,7 +160,17 @@ public class ListFileUtils {
             else
                 storageType = RMDTriplet.RMDStorageType.FILE;
 
-            rodBindings.add(new RMDTriplet(name,type,fileName,storageType,tags));
+            RMDTriplet triplet = new RMDTriplet(name,type,fileName,storageType,tags);
+
+            // validate triplet type
+            Class typeFromTribble = builderForValidation.getFeatureCodecClass(triplet);
+            if ( typeFromTribble != null && ! rodBinding.getType().isAssignableFrom(typeFromTribble) )
+                throw new UserException.BadArgumentValue(rodBinding.getVariableName(),
+                        String.format("Field %s expected type %s, but the type of the input file provided on the command line was %s",
+                                rodBinding.getVariableName(), rodBinding.getType(), typeFromTribble));
+
+
+            rodBindings.add(triplet);
         }
 
         return rodBindings;

public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java

@@ -0,0 +1,58 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.testng.annotations.Test;
+
+/**
+ *
+ */
+public class EngineFeaturesIntegrationTest extends WalkerTest {
+    private void testBadRODBindingInput(String type, String name) {
+        WalkerTestSpec spec = new WalkerTestSpec("-T SelectVariants -L 1:1 --variants:" + type + " "
+                + b37dbSNP132 + " -R " + b37KGReference + " -o %s",
+                1, UserException.class);
+        executeTest(name, spec);
+    }
+
+
+    @Test() private void testBadRODBindingInputType1() {
+        testBadRODBindingInput("beagle", "BEAGLE input to VCF expecting walker");
+    }
+
+    @Test() private void testBadRODBindingInputType2() {
+        testBadRODBindingInput("vcf3", "VCF3 input to VCF expecting walker");
+    }
+
+    @Test() private void testBadRODBindingInputType3() {
+        testBadRODBindingInput("bed", "Bed input to VCF expecting walker");
+    }
+
+    @Test() private void testBadRODBindingInputTypeUnknownType() {
+        testBadRODBindingInput("bedXXX", "Unknown input to VCF expecting walker");
+    }
+}