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JEXL expressions now generate exceptions, not warnings. Tools should catch the runtime exception to handle correctly. Removed unncessary complexity from the JEXL contexts 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4695 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-11-17 16:08:16 +00:00
parent 539651de30
commit d86ab2becb
6 changed files with 49 additions and 62 deletions
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27
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
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@ -39,6 +39,10 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
public class VariantContextUtils {
final public static JexlEngine engine = new JexlEngine();
static {
engine.setSilent(false); // will throw errors now for selects that don't evaluate properly
engine.setLenient(false);
}
/**
* Create a new VariantContext
@ -211,7 +215,7 @@ public class VariantContextUtils {
Expression exp = engine.createExpression(expStr);
exps.add(new JexlVCMatchExp(name, exp));
} catch (Exception e) {
throw new UserException.BadArgumentValue(name, "Invalid expression used (" + expStr + "). Please see the JEXL docs for correct syntax.") ;
throw new UserException.BadArgumentValue(name, "Invalid expression used (" + expStr + "). Please see the JEXL docs for correct syntax.") ;
}
}
@ -224,8 +228,8 @@ public class VariantContextUtils {
* @param exp expression
* @return true if there is a match
*/
public static boolean match(GenomeLocParser genomeLocParser,VariantContext vc, JexlVCMatchExp exp) {
return match(genomeLocParser,vc,Arrays.asList(exp)).get(exp);
public static boolean match(VariantContext vc, JexlVCMatchExp exp) {
return match(vc,Arrays.asList(exp)).get(exp);
}
/**
@ -238,8 +242,8 @@ public class VariantContextUtils {
* @param exps expressions
* @return true if there is a match
*/
public static Map<JexlVCMatchExp, Boolean> match(GenomeLocParser genomeLocParser,VariantContext vc, Collection<JexlVCMatchExp> exps) {
return new JEXLMap(genomeLocParser,exps,vc);
public static Map<JexlVCMatchExp, Boolean> match(VariantContext vc, Collection<JexlVCMatchExp> exps) {
return new JEXLMap(exps,vc);
}
@ -250,8 +254,8 @@ public class VariantContextUtils {
* @param exp expression
* @return true if there is a match
*/
public static boolean match(GenomeLocParser genomeLocParser,VariantContext vc, Genotype g, JexlVCMatchExp exp) {
return match(genomeLocParser,vc,g,Arrays.asList(exp)).get(exp);
public static boolean match(VariantContext vc, Genotype g, JexlVCMatchExp exp) {
return match(vc,g,Arrays.asList(exp)).get(exp);
}
/**
@ -265,9 +269,8 @@ public class VariantContextUtils {
* @param exps expressions
* @return true if there is a match
*/
public static Map<JexlVCMatchExp, Boolean> match(GenomeLocParser genomeLocParser,VariantContext vc, Genotype g, Collection<JexlVCMatchExp> exps) {
return new JEXLMap(genomeLocParser,exps,vc,g);
public static Map<JexlVCMatchExp, Boolean> match(VariantContext vc, Genotype g, Collection<JexlVCMatchExp> exps) {
return new JEXLMap(exps,vc,g);
}
public static double computeHardyWeinbergPvalue(VariantContext vc) {
@ -354,7 +357,7 @@ public class VariantContextUtils {
for (VariantContext vc : prepaddedVCs) {
// also a reasonable place to remove filtered calls, if needed
if ( ! filteredAreUncalled || vc.isNotFiltered() )
VCs.add(VariantContext.createVariantContextWithPaddedAlleles(vc,inputRefBase,false));
VCs.add(VariantContext.createVariantContextWithPaddedAlleles(vc,inputRefBase,false));
}
if ( VCs.size() == 0 ) // everything is filtered out and we're filteredareUncalled
return null;
@ -454,7 +457,7 @@ public class VariantContextUtils {
s.add( vc.isFiltered() ? "filterIn" + vc.getSource() : vc.getSource() );
setValue = Utils.join("-", s);
}
if ( setKey != null ) attributes.put(setKey, setValue);
}

37
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantJEXLContext.java
View File

@ -27,7 +27,6 @@ import org.apache.commons.jexl2.JexlContext;
import org.apache.commons.jexl2.MapContext;
import org.broad.tribble.util.variantcontext.Genotype;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.Utils;
import org.broad.tribble.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.UserException;
@ -50,7 +49,6 @@ import java.util.*;
*/
class VariantJEXLContext implements JexlContext {
private GenomeLocParser genomeLocParser;
// our stored variant context
private VariantContext vc;
@ -75,16 +73,10 @@ class VariantJEXLContext implements JexlContext {
x.put("homVarCount", new AttributeGetter() { public Object get(VariantContext vc) { return vc.getHomVarCount(); }});
}
public VariantJEXLContext(GenomeLocParser genomeLocParser,VariantContext vc) {
this.genomeLocParser = genomeLocParser;
public VariantJEXLContext(VariantContext vc) {
this.vc = vc;
}
// public VariantJEXLContext(VariantContext vc, Genotype g) {
// this.vc = vc;
// //throw new UnsupportedOperationException("Cannot instantiate VariantJEXLContext");
// }
public Object get(String name) {
Object result = null;
if ( x.containsKey(name) ) { // dynamic resolution of name -> value via map
@ -122,7 +114,6 @@ class VariantJEXLContext implements JexlContext {
*/
class JEXLMap implements Map<VariantContextUtils.JexlVCMatchExp, Boolean> {
private final GenomeLocParser genomeLocParser;
// our variant context and/or Genotype
private final VariantContext vc;
private final Genotype g;
@ -134,19 +125,18 @@ class JEXLMap implements Map<VariantContextUtils.JexlVCMatchExp, Boolean> {
private Map<VariantContextUtils.JexlVCMatchExp,Boolean> jexl;
public JEXLMap(GenomeLocParser genomeLocParser,Collection<VariantContextUtils.JexlVCMatchExp> jexlCollection, VariantContext vc, Genotype g) {
this.genomeLocParser = genomeLocParser;
public JEXLMap(Collection<VariantContextUtils.JexlVCMatchExp> jexlCollection, VariantContext vc, Genotype g) {
this.vc = vc;
this.g = g;
initialize(jexlCollection);
}
public JEXLMap(GenomeLocParser genomeLocParser,Collection<VariantContextUtils.JexlVCMatchExp> jexlCollection, VariantContext vc) {
this(genomeLocParser,jexlCollection, vc, null);
public JEXLMap(Collection<VariantContextUtils.JexlVCMatchExp> jexlCollection, VariantContext vc) {
this(jexlCollection, vc, null);
}
public JEXLMap(GenomeLocParser genomeLocParser,Collection<VariantContextUtils.JexlVCMatchExp> jexlCollection, Genotype g) {
this(genomeLocParser,jexlCollection, null, g);
public JEXLMap(Collection<VariantContextUtils.JexlVCMatchExp> jexlCollection, Genotype g) {
this(jexlCollection, null, g);
}
private void initialize(Collection<VariantContextUtils.JexlVCMatchExp> jexlCollection) {
@ -164,14 +154,17 @@ class JEXLMap implements Map<VariantContextUtils.JexlVCMatchExp, Boolean> {
private void createContext() {
if ( g == null ) {
// todo -- remove dependancy on g to the entire system
jContext = new VariantJEXLContext(genomeLocParser,vc);
jContext = new VariantJEXLContext(vc);
} else {
//
// this whole branch is here just to support G jexl operations
//
Map<String, Object> infoMap = new HashMap<String, Object>();
if ( vc != null ) {
// create a mapping of what we know about the variant context, its Chromosome, positions, etc.
infoMap.put("CHROM", VariantContextUtils.getLocation(genomeLocParser,vc).getContig());
infoMap.put("POS", String.valueOf(VariantContextUtils.getLocation(genomeLocParser,vc).getStart()));
infoMap.put("CHROM", vc.getChr());
infoMap.put("POS", vc.getStart());
infoMap.put("TYPE", vc.getType().toString());
infoMap.put("QUAL", String.valueOf(vc.getPhredScaledQual()));
@ -195,10 +188,8 @@ class JEXLMap implements Map<VariantContextUtils.JexlVCMatchExp, Boolean> {
// addAttributesToMap(infoMap, g.getAttributes(), prefix);
// infoMap.put(prefix + "GT", g.getGenotypeString());
// }
}
// add specific genotype if one is provided
if ( g != null ) {
// add specific genotype if one is provided
infoMap.put(VCFConstants.GENOTYPE_KEY, g.getGenotypeString());
infoMap.put("isHomRef", g.isHomRef() ? "1" : "0");
infoMap.put("isHet", g.isHet() ? "1" : "0");
@ -206,7 +197,7 @@ class JEXLMap implements Map<VariantContextUtils.JexlVCMatchExp, Boolean> {
infoMap.put(VCFConstants.GENOTYPE_QUALITY_KEY, new Double(g.getPhredScaledQual()));
for ( Map.Entry<String, Object> e : g.getAttributes().entrySet() ) {
if ( e.getValue() != null && !e.getValue().equals(VCFConstants.MISSING_VALUE_v4) )
infoMap.put(e.getKey(), e.getValue());
infoMap.put(e.getKey(), e.getValue());
}
}

4
java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
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@ -188,7 +188,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
Set<String> filters = new LinkedHashSet<String>(g.getFilters());
for ( VariantContextUtils.JexlVCMatchExp exp : genotypeFilterExps ) {
if ( VariantContextUtils.match(getToolkit().getGenomeLocParser(),vc, g, exp) )
if ( VariantContextUtils.match(vc, g, exp) )
filters.add(exp.name);
}
genotypes.put(genotype.getKey(), new Genotype(genotype.getKey(), g.getAlleles(), g.getNegLog10PError(), filters, g.getAttributes(), g.genotypesArePhased()));
@ -211,7 +211,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
filters.add(CLUSTERED_SNP_FILTER_NAME);
for ( VariantContextUtils.JexlVCMatchExp exp : filterExps ) {
if ( VariantContextUtils.match(getToolkit().getGenomeLocParser(),vc, exp) )
if ( VariantContextUtils.match(vc, exp) )
filters.add(exp.name);
}

18
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -620,6 +620,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
}
}
private static Set<String> seenJEXLExceptions = new HashSet<String>();
private boolean applyVCtoEvaluation(VariantContext vc, Map<String, VariantContext> vcs, EvaluationContext group) {
if ( vc == null )
return true;
@ -643,8 +644,21 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
else if ( group.requiresNovel() && vcKnown )
return false;
if ( group.selectExp != null && ! VariantContextUtils.match(getToolkit().getGenomeLocParser(),vc, group.selectExp) )
return false;
if ( group.selectExp != null ) {
try {
if ( ! VariantContextUtils.match(vc, group.selectExp) )
return false;
} catch ( RuntimeException e ) {
if ( ! seenJEXLExceptions.contains(group.selectExp.name) ) {
seenJEXLExceptions.add(group.selectExp.name);
logger.warn("JEXL evaluation error for SELECT " + group.selectExp.name + ": " + e.getMessage() +
"; this may be an error or may simply result from some variants not having INFO fields keys " +
"referenced in the JEXL expressions. Variants generating exceptions will *NOT* be matched " +
"by the expression. Occurred with variant " + vc);
}
return false;
}
}
// nothing invalidated our membership in this set
return true;

23
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -169,27 +169,6 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
jexls = VariantContextUtils.initializeMatchExps(selectNames, SELECT_EXPRESSIONS);
}
// This is commented out rather than just deleted in case I want to enable JEXL matching *before* sample subsetting.
// /**
// * If JEXL expressions are supplied, include only records that satisfy the expression
// *
// * @param tracker the ROD tracker
// * @param ref reference information
// * @param context alignment info
// * @return true if no JEXL expressions are supplied or if a record satisfies all JEXL criteria, false if otherwise
// */
// public boolean filter(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
// VariantContext vc = tracker.getVariantContext(ref, "variant", null, context.getLocation(), true);
//
// for ( VariantContextUtils.JexlVCMatchExp jexl : jexls ) {
// if ( !VariantContextUtils.match(vc, jexl) ) {
// return false;
// }
// }
//
// return true;
// }
/**
* Subset VC record if necessary and emit the modified record (provided it satisfies criteria for printing)
*
@ -214,7 +193,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
if ( (sub.isPolymorphic() || !EXCLUDE_NON_VARIANTS) && (!sub.isFiltered() || !EXCLUDE_FILTERED) ) {
//System.out.printf("%s%n",sub.toString());
for ( VariantContextUtils.JexlVCMatchExp jexl : jexls ) {
if ( !VariantContextUtils.match(getToolkit().getGenomeLocParser(),sub, jexl) ) {
if ( !VariantContextUtils.match(sub, jexl) ) {
return 0;
}
}

2
java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantJEXLContextUnitTest.java
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@ -146,7 +146,7 @@ public class VariantJEXLContextUnitTest extends BaseTest {
List<Allele> alleles = Arrays.asList(Aref, T);
VariantContext vc = new VariantContext("test", snpLoc.getContig(), snpLoc.getStart(), snpLoc.getStop(), alleles);
return new JEXLMap(genomeLocParser,Arrays.asList(exp),vc);
return new JEXLMap(Arrays.asList(exp),vc);
}