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Somehow checked in a version that was building extensions for everything ("") instead of selected packages. Fixed. 

Also added more logging when extension generation fails.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5812 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2011-05-16 16:58:37 +00:00
parent a27e8b1dc6
commit 541b5f7a80
1 changed files with 35 additions and 25 deletions
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60
java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
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@ -24,7 +24,6 @@
package org.broadinstitute.sting.queue.extensions.gatk;
import net.sf.picard.filter.SamRecordFilter;
import org.apache.commons.io.FileUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
@ -136,37 +135,48 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
for (Class<? extends CommandLineProgram> clp: clpManager.getPlugins()) {
if (!isGatkProgram(clp))
continue;
try {
if (!isGatkProgram(clp)) {
logger.debug("Skipping: " + clp);
continue;
}
String clpClassName = clpManager.getName(clp);
String clpConstructor = String.format("analysisName = \"%s\"%njavaMainClass = \"%s\"%n", clpClassName, clp.getName());
logger.debug("Generating: " + clp);
String clpClassName = clpManager.getName(clp);
String clpConstructor = String.format("analysisName = \"%s\"%njavaMainClass = \"%s\"%n", clpClassName, clp.getName());
writeClass("org.broadinstitute.sting.queue.function.JavaCommandLineFunction", clpClassName,
false, clpConstructor, ArgumentDefinitionField.getArgumentFields(parser,clp), dependents);
writeClass("org.broadinstitute.sting.queue.function.JavaCommandLineFunction", clpClassName,
false, clpConstructor, ArgumentDefinitionField.getArgumentFields(parser,clp), dependents);
if (clp == CommandLineGATK.class) {
for (Entry<String, Collection<Class<? extends Walker>>> walkersByPackage: walkerManager.getWalkerNamesByPackage(false).entrySet()) {
for(Class<? extends Walker> walkerType: walkersByPackage.getValue()) {
String walkerName = walkerManager.getName(walkerType);
List<ArgumentField> argumentFields = new ArrayList<ArgumentField>();
if (clp == CommandLineGATK.class) {
for (Entry<String, Collection<Class<? extends Walker>>> walkersByPackage: walkerManager.getWalkerNamesByPackage(false).entrySet()) {
for(Class<? extends Walker> walkerType: walkersByPackage.getValue()) {
try {
String walkerName = walkerManager.getName(walkerType);
List<ArgumentField> argumentFields = new ArrayList<ArgumentField>();
argumentFields.addAll(ArgumentDefinitionField.getArgumentFields(parser,walkerType));
argumentFields.addAll(RodBindField.getRodArguments(walkerType, trackBuilder));
argumentFields.addAll(ReadFilterField.getFilterArguments(parser,walkerType));
argumentFields.addAll(ArgumentDefinitionField.getArgumentFields(parser,walkerType));
argumentFields.addAll(RodBindField.getRodArguments(walkerType, trackBuilder));
argumentFields.addAll(ReadFilterField.getFilterArguments(parser,walkerType));
String constructor = String.format("analysisName = \"%1$s\"%nanalysis_type = \"%1$s\"%n", walkerName);
String scatterClass = getScatterClass(walkerType);
boolean isScatter = false;
if (scatterClass != null) {
isScatter = true;
constructor += String.format("scatterClass = classOf[%s]%n", scatterClass);
String constructor = String.format("analysisName = \"%1$s\"%nanalysis_type = \"%1$s\"%n", walkerName);
String scatterClass = getScatterClass(walkerType);
boolean isScatter = false;
if (scatterClass != null) {
isScatter = true;
constructor += String.format("scatterClass = classOf[%s]%n", scatterClass);
}
writeClass(GATK_EXTENSIONS_PACKAGE_NAME + "." + clpClassName, walkerName,
isScatter, constructor, argumentFields, dependents);
} catch (Exception e) {
throw new ReviewedStingException("Error generating wrappers for walker " + walkerType, e);
}
}
writeClass(GATK_EXTENSIONS_PACKAGE_NAME + "." + clpClassName, walkerName,
isScatter, constructor, argumentFields, dependents);
}
}
} catch (Exception e) {
throw new ReviewedStingException("Error generating wrappers for " + clp, e);
}
}
@ -190,7 +200,7 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
private static final List<String> gatkPackages = Arrays.asList(
"org.broadinstitute.sting.gatk",
"org.broadinstitute.sting.analyzecovariates",
"");
"org.broadinstitute.sting.gatk.datasources.reads.utilities");
/**
* Returns true if the class is part of the GATK.