adding ability to control jexl expression behavior when missing values

src/main/java/htsjdk/variant/variantcontext/JEXLMap.java

@@ -5,61 +5,95 @@
 import org.apache.commons.jexl2.JexlException;
 import org.apache.commons.jexl2.MapContext;
 
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Set;
+import java.util.*;
 
 /**
  * This is an implementation of a Map of {@link JexlVCMatchExp} to true or false values.
  * It lazily initializes each value as requested to save as much processing time as possible.
  */
 
 class JEXLMap implements Map<JexlVCMatchExp, Boolean> {
+    /**
+     * If a JEXL expression contains values that are not available in the given context, the default behavior is to
+     * treat that expression as a miss match.
+     */
+    public static final JexlMissingValueTreatment DEFAULT_MISSING_VALUE_TREATMENT = JexlMissingValueTreatment.TREAT_AS_MISMATCH;
+
     // our variant context and/or Genotype
     private final VariantContext vc;
     private final Genotype g;
 
-    // our context
-    private JexlContext jContext = null;
+    private final JexlMissingValueTreatment howToTreatMissingValues;
 
     /**
      * our mapping from {@link JexlVCMatchExp} to {@link Boolean}s, which will be set to {@code NULL}
      * for previously un-cached {@link JexlVCMatchExp}.
      */
-    private Map<JexlVCMatchExp,Boolean> jexl;
+    private final Map<JexlVCMatchExp,Boolean> jexl;
 
-    public JEXLMap(final Collection<JexlVCMatchExp> jexlCollection, final VariantContext vc, final Genotype g) {
-        initialize(jexlCollection);
+    // our context
+    private JexlContext jContext = null;
+
+    /**
+     * Construct a new JEXLMap which can evaluate expressions against a specific genotype and variant context
+     * @param jexlCollection collection of expressions to be evaluated
+     * @param vc VariantContext to evaluate expressions against
+     * @param g genotype to evaluate expressions against, may be null
+     * @param howToTreatMissingValues how missing values in vc and g should be treated
+     */
+    public JEXLMap(final Collection<JexlVCMatchExp> jexlCollection, final VariantContext vc, final Genotype g, final JexlMissingValueTreatment howToTreatMissingValues) {
+        this.jexl = initializeMap(jexlCollection);
         this.vc = vc;
         this.g = g;
+        this.howToTreatMissingValues = howToTreatMissingValues;
     }
 
+
+    /**
+     * Construct a new JEXLMap which can evaluate expressions against a specific genotype and variant context
+     * @param jexlCollection collection of expressions to be evaluated
+     * @param vc VariantContext to evaluate expressions against
+     * @param g genotype to evaluate expressions against, may be null
+     *
+     * missing values are treated as false
+     */
+    public JEXLMap(final Collection<JexlVCMatchExp> jexlCollection, final VariantContext vc, final Genotype g) {
+        this(jexlCollection, vc, g, DEFAULT_MISSING_VALUE_TREATMENT);
+    }
+
+    /**
+     * Construct a new JEXLMap which can evaluate expressions against a specific VariantContext
+     * @param jexlCollection collection of expressions to be evaluated
+     * @param vc VariantContext to evaluate expressions against
+     *
+     * missing values are treated as non matches (false)
+     */
     public JEXLMap(final Collection<JexlVCMatchExp> jexlCollection, final VariantContext vc) {
-        this(jexlCollection, vc, null);
+        this(jexlCollection, vc, null, DEFAULT_MISSING_VALUE_TREATMENT);
     }
 
     /**
      * Note: due to laziness, this accessor actually modifies the instance by possibly forcing evaluation of an Jexl expression.
      *
-     * @throws IllegalArgumentException when {@code o} is {@code null} or
+     * @throws IllegalArgumentException when {@code key} is {@code null} or
      *                                  when any of the JexlVCMatchExp (i.e. keys) contains invalid Jexl expressions.
      */
-    public Boolean get(Object o) {
-        if (o == null) {
+    public Boolean get(Object key) {
+        if (key == null) {
             throw new IllegalArgumentException("Query key is null");
         }
 
         // if we've already determined the value, return it
-        if (jexl.containsKey(o) && jexl.get(o) != null) {
-            return jexl.get(o);
+        final Boolean value = jexl.get(key);
+        if (jexl.containsKey(key) && value != null) {
+            return value;
         }
 
         // otherwise cast the expression and try again
-        final JexlVCMatchExp e = (JexlVCMatchExp) o;
-        evaluateExpression(e);
-        return jexl.get(e);
+        final JexlVCMatchExp exp = (JexlVCMatchExp) key;
+        final boolean matches = evaluateExpression(exp);
+        jexl.put(exp, matches);
+        return matches;
     }
 
     /**
@@ -87,9 +121,7 @@ public Boolean get(Object o) {
      */
     public Collection<Boolean> values() {
         for (final JexlVCMatchExp exp : jexl.keySet()) {
-            if (jexl.get(exp) == null) {
-                evaluateExpression(exp);
-            }
+            jexl.computeIfAbsent(exp, k -> evaluateExpression(exp));
         }
         return jexl.values();
     }
@@ -112,55 +144,60 @@ public void putAll(Map<? extends JexlVCMatchExp, ? extends Boolean> map) {
     }
 
     /**
-     * Initializes all keys with null values indicating that they have not yet been evaluated.
+     * Initializes a map and give all keys with null values indicating that they have not yet been evaluated.
      * The actual value will be computed only when the key is requested via {@link #get(Object)} or {@link #values()}.
+     *
+     * @return an initialized map of jexlExpression -> null
      */
-    private void initialize(Collection<JexlVCMatchExp> jexlCollection) {
-        jexl = new HashMap<>();
+    private static Map<JexlVCMatchExp,Boolean> initializeMap(final Collection<JexlVCMatchExp> jexlCollection) {
+        final Map<JexlVCMatchExp,Boolean> jexlMap = new HashMap<>(jexlCollection.size());
         for (final JexlVCMatchExp exp: jexlCollection) {
-            jexl.put(exp, null);
+            jexlMap.put(exp, null);
         }
+
+        return jexlMap;
     }
 
     /**
      * Evaluates a {@link JexlVCMatchExp}'s expression, given the current context (and setup the context if it's {@code null}).
      *
      * @param exp the {@link JexlVCMatchExp} to evaluate
-     *
+     * @return true if the expression matched the context
      * @throws IllegalArgumentException when {@code exp} is {@code null}, or
      *                                  when the Jexl expression in {@code exp} fails to evaluate the JexlContext
      *                                  constructed with the input VC or genotype.
      */
-    private void evaluateExpression(final JexlVCMatchExp exp) {
+    private boolean evaluateExpression(final JexlVCMatchExp exp) {
         // if the context is null, we need to create it to evaluate the JEXL expression
         if (this.jContext == null) {
-            createContext();
+            jContext = createContext();
         }
 
         try {
+            //TODO figure out of this can ever evaluate to null or if that isn't actually possible
             final Boolean value = (Boolean) exp.exp.evaluate(jContext);
-            // treat errors as no match
-            jexl.put(exp, value == null ? false : value);
+            return value == null ? howToTreatMissingValues.getMissingValueOrExplode() : value;
         } catch (final JexlException.Variable e) {
-            // if exception happens because variable is undefined (i.e. field in expression is not present), evaluate to FALSE
-            jexl.put(exp,false);
+            //this occurs when the jexl expression contained a literal that didn't match anything in the given context
+            return howToTreatMissingValues.getMissingValueOrExplode();
         } catch (final JexlException e) {
             // todo - might be better if no exception is caught here but let's user decide how to deal with them; note this will propagate to get() and values()
             throw new IllegalArgumentException(String.format("Invalid JEXL expression detected for %s", exp.name), e);
         }
     }
 
     /**
-     * Create the internal JexlContext, only when required.
+     * Create a new JexlContext
      * This code is where new JEXL context variables should get added.
+     * @return a new jexl context initialized appropriately
      */
-    private void createContext() {
+    private JexlContext createContext() {
         if (vc == null) {
-            jContext = new MapContext(Collections.emptyMap());
+            return new MapContext(Collections.emptyMap());
         } else if (g == null) {
-            jContext = new VariantJEXLContext(vc);
+            return new VariantJEXLContext(vc);
         } else {
-            jContext = new GenotypeJEXLContext(vc, g);
+            return new GenotypeJEXLContext(vc, g);
         }
     }
 
@@ -181,7 +218,7 @@ public Boolean remove(Object o) {
 
 
     public Set<Entry<JexlVCMatchExp, Boolean>> entrySet() {
-        throw new UnsupportedOperationException("clear() not supported on a JEXLMap");
+        throw new UnsupportedOperationException("entrySet() not supported on a JEXLMap");
     }
 
     // nope

src/main/java/htsjdk/variant/variantcontext/JexlMissingValueTreatment.java

@@ -0,0 +1,39 @@
+package htsjdk.variant.variantcontext;
+
+import java.util.function.Supplier;
+
+/**
+ * How to treat values that appear in a jexl expression but are missing in the context it's applied to
+ */
+public enum JexlMissingValueTreatment {
+    /**
+     * Treat expressions with a missing value as a mismatch and evaluate to false
+     */
+    TREAT_AS_MISMATCH(() -> false),
+
+    /**
+     * Treat expressions with a missing value as a match and evaluate to true
+     */
+    TREAT_AS_MATCH(() -> true),
+
+    /**
+     * Treat expressions with a missing value as an error and throw an {@link IllegalArgumentException}
+     */
+    THROW(() -> {throw new IllegalArgumentException("Jexl Expression couldn't be evaluated because there was a missing value.");});
+
+    private final Supplier<Boolean> resultSupplier;
+
+    JexlMissingValueTreatment(final Supplier<Boolean> resultSupplier){
+        this.resultSupplier = resultSupplier;
+    }
+
+    /**
+     * get the missing value that corresponds to this option or throw an exception
+     * @return the value that should be used in case of a missing value
+     * @throws IllegalArgumentException if this should be treated as an error
+     */
+    boolean getMissingValueOrExplode(){
+        return resultSupplier.get();
+    }
+
+}

src/main/java/htsjdk/variant/variantcontext/VariantContextUtils.java

@@ -307,6 +307,7 @@ public static boolean match(VariantContext vc, JexlVCMatchExp exp) {
      * This the best way to apply JEXL expressions to {@link VariantContext} records.
      * Use the various {@code initializeMatchExps()}'s to create the list of {@link JexlVCMatchExp} expressions.
      *
+     * Expressions that contain literals not available in the VariantContext or Genotype will be treated as not matching
      * @param vc    variant context
      * @param exps  expressions
      * @return      true if there is a match
@@ -324,7 +325,20 @@ public static boolean match(VariantContext vc, JexlVCMatchExp exp) {
      * @return      true if there is a match
      */
     public static boolean match(VariantContext vc, Genotype g, JexlVCMatchExp exp) {
-        return match(vc,g, Collections.singletonList(exp)).get(exp);
+        return match(vc, g, Collections.singletonList(exp), JEXLMap.DEFAULT_MISSING_VALUE_TREATMENT).get(exp);
+    }
+
+    /**
+     * Returns true if {@code exp} match {@code vc}, {@code g}.
+     * See {@link #match(VariantContext, Genotype, Collection)} for full docs.
+     * @param vc    variant context
+     * @param g     genotype
+     * @param exp   expression
+     * @param howToTreatMissingValues what to do if the jexl expression contains literals that aren't in the context
+     * @return      true if there is a match
+     */
+    public static boolean match(VariantContext vc, Genotype g, JexlVCMatchExp exp, JexlMissingValueTreatment howToTreatMissingValues) {
+        return match(vc, g, Collections.singletonList(exp), howToTreatMissingValues).get(exp);
     }
 
     /**
@@ -333,13 +347,30 @@ public static boolean match(VariantContext vc, Genotype g, JexlVCMatchExp exp) {
      * This the best way to apply JEXL expressions to {@link VariantContext} records.
      * Use the various {@code initializeMatchExps()}'s to create the list of {@link JexlVCMatchExp} expressions.
      *
+     * Expressions that contain literals not available in the VariantContext or Genotype will be treated as not matching
      * @param vc    variant context
      * @param g     genotype
      * @param exps  expressions
      * @return      true if there is a match
      */
     public static Map<JexlVCMatchExp, Boolean> match(VariantContext vc, Genotype g, Collection<JexlVCMatchExp> exps) {
-        return new JEXLMap(exps,vc,g);
+        return match(vc, g, exps, JEXLMap.DEFAULT_MISSING_VALUE_TREATMENT);
+    }
+
+    /**
+     * Matches each {@link JexlVCMatchExp} exp against the data contained in {@code vc}, {@code g},
+     * and returns a map from these expressions to {@code true} (if they matched) or {@code false} (if they didn't).
+     * This the best way to apply JEXL expressions to {@link VariantContext} records.
+     * Use the various {@code initializeMatchExps()}'s to create the list of {@link JexlVCMatchExp} expressions.
+     *
+     * @param vc    variant context
+     * @param g     genotype
+     * @param exps  expressions
+     * @param howToTreatMissingValues what to do if the jexl expression contains literals that aren't in the context
+     * @return      true if there is a match
+     */
+    public static Map<JexlVCMatchExp, Boolean> match(VariantContext vc, Genotype g, Collection<JexlVCMatchExp> exps, JexlMissingValueTreatment howToTreatMissingValues) {
+        return new JEXLMap(exps, vc, g, howToTreatMissingValues);
     }
 
     /**

src/test/java/htsjdk/variant/variantcontext/VariantJEXLContextUnitTest.java

@@ -31,14 +31,10 @@
 
 import htsjdk.variant.vcf.VCFConstants;
 import org.testng.Assert;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 
 
 /**
@@ -55,6 +51,10 @@
     private static final VariantContextUtils.JexlVCMatchExp exp
             = new VariantContextUtils.JexlVCMatchExp("name", VariantContextUtils.engine.get().createExpression("QUAL > 500.0"));
 
+    private static final JexlVCMatchExp missingValueExpression = new VariantContextUtils.JexlVCMatchExp(
+            "Zis10", VariantContextUtils.engine.get().createExpression("Z==10"));
+
+
     // SNP alleles: A[ref]/T[alt] at chr1:10. One (crappy) sample, one (bare minimum) VC.
     private static final SimpleFeature eventLoc = new SimpleFeature("chr1", 10, 10);
     private static final Allele Aref = Allele.create("A", true);
@@ -87,7 +87,45 @@ public void testGetValue() {
         // eval our known expression
         Assert.assertTrue(!jexlMap.get(exp));
     }
-    
+
+    @Test(dataProvider = "getMissingValueTestData")
+    public void testMissingBehaviorThroughMatch(VariantContext vc, JexlMissingValueTreatment missingValueTreatment, boolean expected, Class<? extends Exception> expectedException){
+        if(expectedException == null) {
+            Assert.assertEquals(VariantContextUtils.match(vc, null, missingValueExpression, missingValueTreatment), expected);
+        } else {
+            Assert.assertThrows(expectedException, () -> VariantContextUtils.match(vc, null, missingValueExpression, missingValueTreatment));
+        }
+    }
+
+    @Test(dataProvider = "getMissingValueTestData")
+    public void testMissingBehavior(VariantContext vc, JexlMissingValueTreatment missingValueTreatment, boolean expected, Class<? extends Exception> expectedException){
+        final JEXLMap jexlMap = new JEXLMap(Collections.singletonList(missingValueExpression), vc, null, missingValueTreatment);
+        if(expectedException == null) {
+            Assert.assertEquals((boolean) jexlMap.get(missingValueExpression), expected);
+        } else {
+            Assert.assertThrows(expectedException, () -> jexlMap.get(missingValueExpression));
+        }
+    }
+
+    @DataProvider
+    public Object[][] getMissingValueTestData(){
+        final List<Allele> alleles = Arrays.asList(Aref, Talt);
+        VariantContextBuilder vcb = new VariantContextBuilder("test", "chr1", 10, 10, alleles);
+        VariantContext noZ = vcb.make();
+        VariantContext hasZ = vcb.attribute("Z", 0).make();
+
+        return new Object[][]{
+                {noZ, JEXLMap.DEFAULT_MISSING_VALUE_TREATMENT, false, null},
+                {hasZ, JEXLMap.DEFAULT_MISSING_VALUE_TREATMENT, false, null}, //the value isn't missing but the expression is false
+                {noZ, JexlMissingValueTreatment.TREAT_AS_MATCH, true, null},
+                {hasZ, JexlMissingValueTreatment.TREAT_AS_MATCH, false, null}, //the value isn't missing but the expression is false
+                {noZ, JexlMissingValueTreatment.TREAT_AS_MISMATCH, false, null},
+                {hasZ, JexlMissingValueTreatment.TREAT_AS_MISMATCH, false, null},
+                {noZ, JexlMissingValueTreatment.THROW, false, IllegalArgumentException.class},
+                {hasZ, JexlMissingValueTreatment.THROW, false, null}
+        };
+    }
+
     // Testing the new 'FT' and 'isPassFT' expressions in the JEXL map
     @Test
     public void testJEXLGenotypeFilters() {