Enum support for command-line argument system, and some cleanup for hacks to the CleanedReadInjector that were required because Enum support was missing.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1199 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java

@@ -157,7 +157,7 @@ public class CommandLineGATK extends CommandLineProgram {
             public Object createArgument( Class type, String repr ) {
                 if (type == SAMFileReader.class) {
                     SAMFileReader samFileReader = new SAMFileReader(new File(repr),true);
-                    samFileReader.setValidationStringency(GenomeAnalysisEngine.getValidationStringency(argCollection));
+                    samFileReader.setValidationStringency(argCollection.strictnessLevel);
                     return samFileReader;
                 }
                 return null;

java/src/org/broadinstitute/sting/gatk/GATKArgumentCollection.java

@@ -14,6 +14,8 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
+import net.sf.samtools.SAMFileReader;
+
 /**
  *
  * User: aaron
@@ -118,7 +120,7 @@ public class GATKArgumentCollection {
 
     @Element(required = false)
     @Argument(fullName = "validation_strictness", shortName = "S", doc = "How strict should we be with validation (LENIENT|SILENT|STRICT)", required = false)
-    public String strictnessLevel = "silent";
+    public SAMFileReader.ValidationStringency strictnessLevel = SAMFileReader.ValidationStringency.SILENT;
 
     @Element(required = false)
     @Argument(fullName = "unsafe", shortName = "U", doc = "If set, enables unsafe operations, nothing will be checked at runtime.", required = false)

java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

@@ -124,10 +124,7 @@ public class GenomeAnalysisEngine {
             GenomeLocParser.setupRefContigOrdering(refFile);
         }
 
-        // Determine the validation stringency.  Default to ValidationStringency.STRICT.
-        ValidationStringency strictness = getValidationStringency(argCollection);
-
-        logger.info("Strictness is " + strictness);
+        logger.info("Strictness is " + argCollection.strictnessLevel);
 
         // perform validation steps that are common to all the engines
         genericEngineSetup();
@@ -219,7 +216,7 @@ public class GenomeAnalysisEngine {
      */
     private Reads extractSourceInfoFromArguments( GATKArgumentCollection argCollection ) {
         return new Reads( argCollection.samFiles,
-                          getValidationStringency(argCollection),
+                          argCollection.strictnessLevel,
                           argCollection.downsampleFraction,
                           argCollection.downsampleCoverage,
                           !argCollection.unsafe,
@@ -262,22 +259,6 @@ public class GenomeAnalysisEngine {
         }
     }
 
-    /**
-     * Default to ValidationStringency.STRICT.
-     * TODO: Store ValidationStringency as pre-parsed enum in GATKArgumentCollection.
-     * @return the validation stringency
-     */
-    public static ValidationStringency getValidationStringency( GATKArgumentCollection argCollection ) {
-        ValidationStringency strictness = ValidationStringency.SILENT;
-        try {
-            strictness = Enum.valueOf(ValidationStringency.class, argCollection.strictnessLevel.toUpperCase().trim());
-        }
-        catch (IllegalArgumentException ex) {
-            logger.debug("Unable to parse strictness from command line.  Assuming SILENT");
-        }
-        return strictness;
-    }
-
     /**
      * Default to 5 (based on research by Alec Wysoker)
      *

java/src/org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java

@@ -468,6 +468,8 @@ public class ParsingEngine {
                 throw new StingException("Unable to parse argument '" + str + "' into a character.");
             Character c = str.trim().charAt(0);
             return c;
+        } else if (type.isEnum()) {
+            return Enum.valueOf(type,str.toUpperCase().trim());
         } else {
             Constructor ctor = null;
             try {

java/test/org/broadinstitute/sting/gatk/GATKArgumentCollectionTest.java

@@ -10,6 +10,8 @@ import org.junit.Test;
 import java.io.File;
 import java.util.*;
 
+import net.sf.samtools.SAMFileReader;
+
 /*
  * Copyright (c) 2009 The Broad Institute
  *
@@ -79,7 +81,7 @@ public class GATKArgumentCollectionTest extends BaseTest {
         input.add(new File("test.file"));
         collect.samFiles = input;
         collect.maximumEngineIterations = -1;
-        collect.strictnessLevel = "strict";
+        collect.strictnessLevel = SAMFileReader.ValidationStringency.STRICT;
         collect.referenceFile = new File("referenceFile".toLowerCase());
         collect.analysisName = "analysisName".toLowerCase();
         collect.DBSNPFile = "DBSNPFile".toLowerCase();

java/test/org/broadinstitute/sting/utils/cmdLine/ParsingEngineTest.java

@@ -140,6 +140,55 @@ public class ParsingEngineTest extends BaseTest {
         public String[] inputFile;
     }
 
+    @Test
+    public void enumTest() {
+        final String[] commandLine = new String[] {  "--test_enum", "TWO" };
+
+        parsingEngine.addArgumentSource( EnumArgProvider.class );
+        parsingEngine.parse( commandLine );
+        parsingEngine.validate();
+
+        EnumArgProvider argProvider = new EnumArgProvider();
+        parsingEngine.loadArgumentsIntoObject( argProvider );
+
+        Assert.assertEquals("Enum value is not correct", TestEnum.TWO, argProvider.testEnum);
+    }
+
+    @Test
+    public void enumMixedCaseTest() {
+        final String[] commandLine = new String[] {  "--test_enum", "oNe" };
+
+        parsingEngine.addArgumentSource( EnumArgProvider.class );
+        parsingEngine.parse( commandLine );
+        parsingEngine.validate();
+
+        EnumArgProvider argProvider = new EnumArgProvider();
+        parsingEngine.loadArgumentsIntoObject( argProvider );
+
+        Assert.assertEquals("Enum value is not correct", TestEnum.ONE, argProvider.testEnum);
+    }
+    
+    @Test
+    public void enumDefaultTest() {
+        final String[] commandLine = new String[] {};
+
+        parsingEngine.addArgumentSource( EnumArgProvider.class );
+        parsingEngine.parse( commandLine );
+        parsingEngine.validate();
+
+        EnumArgProvider argProvider = new EnumArgProvider();
+        parsingEngine.loadArgumentsIntoObject( argProvider );
+
+        Assert.assertEquals("Enum value is not correct", TestEnum.THREE, argProvider.testEnum);
+    }
+
+    public enum TestEnum { ONE, TWO, THREE };
+
+    private class EnumArgProvider {
+        @Argument(fullName="test_enum",shortName="ti",doc="test enum",required=false)
+        public TestEnum testEnum = TestEnum.THREE;
+    }
+
     @Test
     public void typedCollectionTest() {
         final String[] commandLine = new String[] { "-N","2","-N","4","-N","6","-N","8","-N","10" };