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Update URL for phone home / GATK key documentation output by the GATK upon error

This commit is contained in:
David Roazen 2012-08-08 09:29:54 -04:00
parent cda8d944b7
commit a7811d673f
4 changed files with 12 additions and 11 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
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@ -130,8 +130,8 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
getArgumentCollection().phoneHomeType == GATKRunReport.PhoneHomeOption.STDOUT ) { getArgumentCollection().phoneHomeType == GATKRunReport.PhoneHomeOption.STDOUT ) {
if ( getArgumentCollection().gatkKeyFile == null ) { if ( getArgumentCollection().gatkKeyFile == null ) {
throw new UserException("Running with the -et NO_ET or -et STDOUT option requires a GATK Key file. " + throw new UserException("Running with the -et NO_ET or -et STDOUT option requires a GATK Key file. " +
"Please see http://www.broadinstitute.org/gsa/wiki/index.php/Phone_home " + "Please see " + GATKRunReport.PHONE_HOME_DOCS_URL +
"for more information and instructions on how to obtain a key."); " for more information and instructions on how to obtain a key.");
} }
else { else {
PublicKey gatkPublicKey = CryptUtils.loadGATKDistributedPublicKey(); PublicKey gatkPublicKey = CryptUtils.loadGATKDistributedPublicKey();

4
public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -66,10 +66,10 @@ public class GATKArgumentCollection {
@Argument(fullName = "read_buffer_size", shortName = "rbs", doc="Number of reads per SAM file to buffer in memory", required = false) @Argument(fullName = "read_buffer_size", shortName = "rbs", doc="Number of reads per SAM file to buffer in memory", required = false)
public Integer readBufferSize = null; public Integer readBufferSize = null;
@Argument(fullName = "phone_home", shortName = "et", doc="What kind of GATK run report should we generate? STANDARD is the default, can be NO_ET so nothing is posted to the run repository. Please see http://www.broadinstitute.org/gsa/wiki/index.php/Phone_home for details.", required = false) @Argument(fullName = "phone_home", shortName = "et", doc="What kind of GATK run report should we generate? STANDARD is the default, can be NO_ET so nothing is posted to the run repository. Please see " + GATKRunReport.PHONE_HOME_DOCS_URL + " for details.", required = false)
public GATKRunReport.PhoneHomeOption phoneHomeType = GATKRunReport.PhoneHomeOption.STANDARD; public GATKRunReport.PhoneHomeOption phoneHomeType = GATKRunReport.PhoneHomeOption.STANDARD;
@Argument(fullName = "gatk_key", shortName = "K", doc="GATK Key file. Required if running with -et NO_ET. Please see http://www.broadinstitute.org/gsa/wiki/index.php/Phone_home for details.", required = false) @Argument(fullName = "gatk_key", shortName = "K", doc="GATK Key file. Required if running with -et NO_ET. Please see " + GATKRunReport.PHONE_HOME_DOCS_URL + " for details.", required = false)
public File gatkKeyFile = null; public File gatkKeyFile = null;
@Argument(fullName = "read_filter", shortName = "rf", doc = "Specify filtration criteria to apply to each read individually", required = false) @Argument(fullName = "read_filter", shortName = "rf", doc = "Specify filtration criteria to apply to each read individually", required = false)

1
public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
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@ -88,6 +88,7 @@ public class GATKRunReport {
// number of milliseconds before the S3 put operation is timed-out: // number of milliseconds before the S3 put operation is timed-out:
private static final long S3PutTimeOut = 10 * 1000; private static final long S3PutTimeOut = 10 * 1000;
public static final String PHONE_HOME_DOCS_URL = "http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest";
/** /**
* our log * our log

14
public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
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@ -27,6 +27,7 @@ package org.broadinstitute.sting.utils.exceptions;
import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMSequenceDictionary; import net.sf.samtools.SAMSequenceDictionary;
import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.sam.ReadUtils;
@ -351,8 +352,8 @@ public class UserException extends ReviewedStingException {
public static class UnreadableKeyException extends UserException { public static class UnreadableKeyException extends UserException {
public UnreadableKeyException ( File f, Exception e ) { public UnreadableKeyException ( File f, Exception e ) {
super(String.format("Key file %s cannot be read (possibly the key file is corrupt?). Error was: %s. " + 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.", "Please see %s for help.",
f.getAbsolutePath(), getMessage(e))); f.getAbsolutePath(), getMessage(e), GATKRunReport.PHONE_HOME_DOCS_URL));
} }
public UnreadableKeyException ( String message, Exception e ) { public UnreadableKeyException ( String message, Exception e ) {
@ -361,8 +362,8 @@ public class UserException extends ReviewedStingException {
public UnreadableKeyException ( String message ) { public UnreadableKeyException ( String message ) {
super(String.format("Key file cannot be read (possibly the key file is corrupt?): %s. " + super(String.format("Key file cannot be read (possibly the key file is corrupt?): %s. " +
"Please see http://www.broadinstitute.org/gsa/wiki/index.php/Phone_home for help.", "Please see %s for help.",
message)); message, GATKRunReport.PHONE_HOME_DOCS_URL));
} }
} }
@ -370,9 +371,8 @@ public class UserException extends ReviewedStingException {
public KeySignatureVerificationException ( File f ) { public KeySignatureVerificationException ( File f ) {
super(String.format("The signature in key file %s failed cryptographic verification. " + super(String.format("The signature in key file %s failed cryptographic verification. " +
"If this key was valid in the past, it's likely been revoked. " + "If this key was valid in the past, it's likely been revoked. " +
"Please see http://www.broadinstitute.org/gsa/wiki/index.php/Phone_home " + "Please see %s for help.",
"for help.", f.getAbsolutePath(), GATKRunReport.PHONE_HOME_DOCS_URL));
f.getAbsolutePath()));
} }
} }
} }