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When an underlying exception occurs because of the user error, if the exception instance does not include a message instead of telling the user "because null", tell them "because <exception class name>".

This commit is contained in:
Khalid Shakir 2012-05-30 16:39:06 -04:00
parent 421d0d1435
commit c4f7df4dce
1 changed files with 18 additions and 15 deletions
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33
public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
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@ -27,14 +27,12 @@ package org.broadinstitute.sting.utils.exceptions;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMSequenceDictionary;
import net.sf.samtools.SAMSequenceRecord;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.File;
import java.util.Arrays;
/**
* Represents the common user errors detected by Sting / GATK
@ -53,6 +51,11 @@ public class UserException extends ReviewedStingException {
public UserException(String msg, Throwable e) { super(msg, e); }
private UserException(Throwable e) { super("", e); } // cannot be called, private access
protected static String getMessage(Throwable t) {
String message = t.getMessage();
return message != null ? message : t.getClass().getName();
}
public static class CommandLineException extends UserException {
public CommandLineException(String message) {
super(String.format("Invalid command line: %s", message));
@ -121,7 +124,7 @@ public class UserException extends ReviewedStingException {
public static class CouldNotReadInputFile extends UserException {
public CouldNotReadInputFile(String message, Exception e) {
super(String.format("Couldn't read file because %s caused by %s", message, e.getMessage()));
super(String.format("Couldn't read file because %s caused by %s", message, getMessage(e)));
}
public CouldNotReadInputFile(File file) {
@ -133,11 +136,11 @@ public class UserException extends ReviewedStingException {
}
public CouldNotReadInputFile(File file, String message, Exception e) {
super(String.format("Couldn't read file %s because %s with exception %s", file.getAbsolutePath(), message, e.getMessage()));
super(String.format("Couldn't read file %s because %s with exception %s", file.getAbsolutePath(), message, getMessage(e)));
}
public CouldNotReadInputFile(File file, Exception e) {
this(file, e.getMessage());
this(file, getMessage(e));
}
public CouldNotReadInputFile(String message) {
@ -148,7 +151,7 @@ public class UserException extends ReviewedStingException {
public static class CouldNotCreateOutputFile extends UserException {
public CouldNotCreateOutputFile(File file, String message, Exception e) {
super(String.format("Couldn't write file %s because %s with exception %s", file.getAbsolutePath(), message, e.getMessage()));
super(String.format("Couldn't write file %s because %s with exception %s", file.getAbsolutePath(), message, getMessage(e)));
}
public CouldNotCreateOutputFile(File file, String message) {
@ -156,11 +159,11 @@ public class UserException extends ReviewedStingException {
}
public CouldNotCreateOutputFile(String filename, String message, Exception e) {
super(String.format("Couldn't write file %s because %s with exception %s", filename, message, e.getMessage()));
super(String.format("Couldn't write file %s because %s with exception %s", filename, message, getMessage(e)));
}
public CouldNotCreateOutputFile(File file, Exception e) {
super(String.format("Couldn't write file %s because exception %s", file.getAbsolutePath(), e.getMessage()));
super(String.format("Couldn't write file %s because exception %s", file.getAbsolutePath(), getMessage(e)));
}
public CouldNotCreateOutputFile(String message, Exception e) {
@ -241,7 +244,7 @@ public class UserException extends ReviewedStingException {
public static class MissortedFile extends UserException {
public MissortedFile(File file, String message, Exception e) {
super(String.format("Missorted Input file: %s is must be sorted in coordinate order. %s and got error %s", file, message, e.getMessage()));
super(String.format("Missorted Input file: %s is must be sorted in coordinate order. %s and got error %s", file, message, getMessage(e)));
}
}
@ -251,7 +254,7 @@ public class UserException extends ReviewedStingException {
}
public MalformedFile(String message, Exception e) {
super(String.format("Unknown file is malformed: %s caused by %s", message, e.getMessage()));
super(String.format("Unknown file is malformed: %s caused by %s", message, getMessage(e)));
}
public MalformedFile(File f, String message) {
@ -259,7 +262,7 @@ public class UserException extends ReviewedStingException {
}
public MalformedFile(File f, String message, Exception e) {
super(String.format("File %s is malformed: %s caused by %s", f.getAbsolutePath(), message, e.getMessage()));
super(String.format("File %s is malformed: %s caused by %s", f.getAbsolutePath(), message, getMessage(e)));
}
public MalformedFile(String name, String message) {
@ -267,7 +270,7 @@ public class UserException extends ReviewedStingException {
}
public MalformedFile(String name, String message, Exception e) {
super(String.format("File associated with name %s is malformed: %s caused by %s", name, message, e.getMessage()));
super(String.format("File associated with name %s is malformed: %s caused by %s", name, message, getMessage(e)));
}
}
@ -326,7 +329,7 @@ public class UserException extends ReviewedStingException {
public CouldNotCreateReferenceIndexFile(File f, String message, Exception e) {
super(String.format("Index file %s does not exist but could not be created because: %s. ", f, message)
+ (e == null ? "" : e.getMessage()));
+ (e == null ? "" : getMessage(e)));
}
}
@ -343,11 +346,11 @@ public class UserException extends ReviewedStingException {
public UnreadableKeyException ( File f, Exception e ) {
super(String.format("Key file %s cannot be read (possibly the key file is corrupt?). Error was: %s. " +
"Please see http://www.broadinstitute.org/gsa/wiki/index.php/Phone_home for help.",
f.getAbsolutePath(), e.getMessage()));
f.getAbsolutePath(), getMessage(e)));
}
public UnreadableKeyException ( String message, Exception e ) {
this(String.format("%s. Error was: %s", message, e.getMessage()));
this(String.format("%s. Error was: %s", message, getMessage(e)));
}
public UnreadableKeyException ( String message ) {