Created new DeprecatedToolChecks class
--Based on existing code in GenomeAnalysisEngine --Hashmaps hold mapping of deprecated tool name to version number and recommended replacement (if any) --Using FastUtils for maps; specifically Object2ObjectMap but there could be a better type for Strings... --Added user exception for deprecated annotations --Added deprecation check to AnnotationInterfaceManager.validateAnnotations --Run when annotations are initialized --Made annotation sets instead of lists
This commit is contained in:
Geraldine Van der Auwera
parent
6b4d88ebe9
commit
d70bf64737
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@ -67,6 +67,9 @@ import java.io.File;
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import java.util.*;
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import java.util.concurrent.TimeUnit;
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import static org.broadinstitute.sting.utils.DeprecatedToolChecks.getWalkerDeprecationInfo;
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import static org.broadinstitute.sting.utils.DeprecatedToolChecks.isDeprecatedWalker;
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/**
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* A GenomeAnalysisEngine that runs a specified walker.
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*/
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@ -288,40 +291,6 @@ public class GenomeAnalysisEngine {
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//return result;
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}
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// TODO -- Let's move this to a utility class in unstable - but which one?
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// **************************************************************************************
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// * Handle Deprecated Walkers *
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// **************************************************************************************
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// Mapping from walker name to major version number where the walker first disappeared
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private static Map<String, String> deprecatedGATKWalkers = new HashMap<String, String>();
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static {
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deprecatedGATKWalkers.put("CountCovariates", "2.0");
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deprecatedGATKWalkers.put("TableRecalibration", "2.0");
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deprecatedGATKWalkers.put("AlignmentWalker", "2.2");
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deprecatedGATKWalkers.put("CountBestAlignments", "2.2");
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}
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/**
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* Utility method to check whether a given walker has been deprecated in a previous GATK release
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*
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* @param walkerName the walker class name (not the full package) to check
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*/
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public static boolean isDeprecatedWalker(final String walkerName) {
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return deprecatedGATKWalkers.containsKey(walkerName);
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}
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/**
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* Utility method to check whether a given walker has been deprecated in a previous GATK release
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*
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* @param walkerName the walker class name (not the full package) to check
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*/
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public static String getDeprecatedMajorVersionNumber(final String walkerName) {
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return deprecatedGATKWalkers.get(walkerName);
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}
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// **************************************************************************************
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/**
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* Retrieves an instance of the walker based on the walker name.
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*
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@ -333,7 +302,7 @@ public class GenomeAnalysisEngine {
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return walkerManager.createByName(walkerName);
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} catch ( UserException e ) {
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if ( isDeprecatedWalker(walkerName) ) {
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e = new UserException.DeprecatedWalker(walkerName, getDeprecatedMajorVersionNumber(walkerName));
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e = new UserException.DeprecatedWalker(walkerName, getWalkerDeprecationInfo(walkerName));
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}
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throw e;
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}
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@ -565,6 +534,8 @@ public class GenomeAnalysisEngine {
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if ( intervals != null && intervals.isEmpty() ) {
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logger.warn("The given combination of -L and -XL options results in an empty set. No intervals to process.");
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}
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// TODO: add a check for ActiveRegion walkers to prevent users from passing an entire contig/chromosome
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}
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/**
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@ -44,6 +44,7 @@ import org.broadinstitute.variant.vcf.*;
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import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
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import org.broadinstitute.variant.variantcontext.VariantContext;
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import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
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import it.unimi.dsi.fastutil.objects.ObjectOpenHashSet;
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import java.util.*;
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@ -155,7 +156,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
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* If multiple records in the rod overlap the given position, one is chosen arbitrarily.
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*/
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@Argument(fullName="expression", shortName="E", doc="One or more specific expressions to apply to variant calls; see documentation for more details", required=false)
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protected List<String> expressionsToUse = new ArrayList<String>();
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protected Set<String> expressionsToUse = new ObjectOpenHashSet();
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/**
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* Note that the -XL argument can be used along with this one to exclude annotations.
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@ -189,9 +190,10 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
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*/
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public void initialize() {
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if ( LIST )
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if ( LIST ) {
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HelpUtils.listAnnotations();
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System.exit(0);
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}
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// get the list of all sample names from the variant VCF input rod, if applicable
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List<String> rodName = Arrays.asList(variantCollection.variants.getName());
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@ -104,7 +104,7 @@ public class VariantAnnotatorEngine {
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}
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// select specific expressions to use
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public void initializeExpressions(List<String> expressionsToUse) {
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public void initializeExpressions(Set<String> expressionsToUse) {
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// set up the expressions
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for ( String expression : expressionsToUse )
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requestedExpressions.add(new VAExpression(expression, walker.getResourceRodBindings()));
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@ -25,6 +25,7 @@
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package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
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import org.broadinstitute.sting.utils.DeprecatedToolChecks;
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import org.broadinstitute.sting.utils.classloader.PluginManager;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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@ -58,7 +59,7 @@ public class AnnotationInterfaceManager {
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if ( interfaceClass == null )
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interfaceClass = classMap.get(group + "Annotation");
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if ( interfaceClass == null )
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throw new UserException.BadArgumentValue("group", "Class " + group + " is not found; please check that you have specified the class name correctly");
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throw new UserException.BadArgumentValue("group", "Annotation group " + group + " was not found; please check that you have specified the group name correctly");
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}
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}
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@ -67,8 +68,13 @@ public class AnnotationInterfaceManager {
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Class annotationClass = classMap.get(annotation);
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if ( annotationClass == null )
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annotationClass = classMap.get(annotation + "Annotation");
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if ( annotationClass == null )
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throw new UserException.BadArgumentValue("annotation", "Class " + annotation + " is not found; please check that you have specified the class name correctly");
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if ( annotationClass == null ) {
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if (DeprecatedToolChecks.isDeprecatedAnnotation(annotation) ) {
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throw new UserException.DeprecatedAnnotation(annotation, DeprecatedToolChecks.getAnnotationDeprecationInfo(annotation));
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} else {
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throw new UserException.BadArgumentValue("annotation", "Annotation " + annotation + " was not found; please check that you have specified the annotation name correctly");
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}
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}
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}
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}
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@ -0,0 +1,95 @@
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/*
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* Copyright (c) 2012 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.utils;
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import it.unimi.dsi.fastutil.objects.Object2ObjectMap;
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import it.unimi.dsi.fastutil.objects.Object2ObjectOpenHashMap;
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import java.util.*;
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/**
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* Utility class for handling deprecated tools gracefully
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*
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* @author vdauwera
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* @since 3/11/13
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*/
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public class DeprecatedToolChecks {
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// Mapping from walker name to major version number where the walker first disappeared and optional replacement options
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private static Object2ObjectMap deprecatedGATKWalkers = new Object2ObjectOpenHashMap();
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static {
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// Indicate recommended replacement in parentheses if applicable
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deprecatedGATKWalkers.put("CountCovariates", "2.0 (use BaseRecalibrator instead; see documentation for usage)");
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deprecatedGATKWalkers.put("AnalyzeCovariates", "2.0 (use BaseRecalibrator instead; see documentation for usage)");
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deprecatedGATKWalkers.put("TableRecalibration", "2.0 (use PrintReads with -BQSR instead; see documentation for usage)");
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deprecatedGATKWalkers.put("AlignmentWalker", "2.2 (no replacement)");
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deprecatedGATKWalkers.put("CountBestAlignments", "2.2 (no replacement)");
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}
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// Mapping from walker name to major version number where the walker first disappeared and optional replacement options
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private static Object2ObjectMap deprecatedGATKAnnotations = new Object2ObjectOpenHashMap();
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static {
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// Same comments as for walkers
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deprecatedGATKAnnotations.put("DepthOfCoverage", "2.4 (renamed to Coverage)");
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}
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/**
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* Utility method to check whether a given walker has been deprecated in a previous GATK release
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*
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* @param walkerName the walker class name (not the full package) to check
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*/
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public static boolean isDeprecatedWalker(final String walkerName) {
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return deprecatedGATKWalkers.containsKey(walkerName);
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}
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/**
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* Utility method to check whether a given annotation has been deprecated in a previous GATK release
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*
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* @param annotationName the annotation class name (not the full package) to check
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*/
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public static boolean isDeprecatedAnnotation(final String annotationName) {
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return deprecatedGATKAnnotations.containsKey(annotationName);
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}
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/**
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* Utility method to pull up the version number at which a walker was deprecated and the suggested replacement, if any
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*
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* @param walkerName the walker class name (not the full package) to check
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*/
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public static String getWalkerDeprecationInfo(final String walkerName) {
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return deprecatedGATKWalkers.get(walkerName).toString();
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}
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/**
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* Utility method to pull up the version number at which an annotation was deprecated and the suggested replacement, if any
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*
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* @param annotationName the annotation class name (not the full package) to check
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*/
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public static String getAnnotationDeprecationInfo(final String annotationName) {
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return deprecatedGATKAnnotations.get(annotationName).toString();
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}
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}
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@ -371,14 +371,18 @@ public class UserException extends ReviewedStingException {
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}
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}
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public static class DeprecatedWalker extends UserException {
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public DeprecatedWalker(String walkerName, String version) {
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super(String.format("Walker %s is no longer available in the GATK; it has been deprecated since version %s", walkerName, version));
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}
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}
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public static class DeprecatedAnnotation extends UserException {
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public DeprecatedAnnotation(String annotationName, String version) {
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super(String.format("Annotation %s is no longer available in the GATK; it has been deprecated since version %s", annotationName, version));
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}
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}
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public static class CannotExecuteQScript extends UserException {
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public CannotExecuteQScript(String message) {
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super(String.format("Unable to execute QScript: " + message));
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