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I have pulled out all of the documentation URLs and put them into the HelpUtils class as static variables; this way, Appistry can change links as needed to point commercial users to their own internal forum without having to muck things up all over our source. Added some TODOs for Geraldine to update links in the GATK docs that still point to the old wiki. Sorry that I am pushing into stable, but that's what Appistry is pulling from for their release next week (and unstable has been failing forever).

This commit is contained in:
Eric Banks 2012-11-27 10:26:17 -05:00
parent d978cfe835
commit e199562c25
14 changed files with 43 additions and 30 deletions
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3
public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java
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@ -33,6 +33,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.help.ApplicationDetails;
import org.broadinstitute.sting.utils.help.HelpFormatter;
import org.broadinstitute.sting.utils.help.HelpUtils;
import java.io.IOException;
import java.util.*;
@ -288,7 +289,7 @@ public abstract class CommandLineProgram {
*/
private static void printDocumentationReference() {
errorPrintf("Visit our website and forum for extensive documentation and answers to %n");
errorPrintf("commonly asked questions http://www.broadinstitute.org/gatk%n");
errorPrintf("commonly asked questions " + HelpUtils.BASE_GATK_URL + "%n");
}

24
public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
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@ -39,6 +39,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.ApplicationDetails;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.GATKDocUtils;
import org.broadinstitute.sting.utils.help.HelpUtils;
import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import java.util.*;
@ -118,17 +119,24 @@ public class CommandLineGATK extends CommandLineExecutable {
public static final String DISK_QUOTA_EXCEEDED_ERROR = "Disk quota exceeded";
private static void checkForMaskedUserErrors(final Throwable t) {
// masked out of memory error
if ( t instanceof OutOfMemoryError )
exitSystemWithUserError(new UserException.NotEnoughMemory());
// masked user error
if ( t instanceof UserException || t instanceof TribbleException )
exitSystemWithUserError(new UserException(t.getMessage()));
// no message means no masked error
final String message = t.getMessage();
if ( message == null )
return;
// we know what to do about the common "Too many open files" error
// too many open files error
if ( message.contains("Too many open files") )
exitSystemWithUserError(new UserException.TooManyOpenFiles());
// malformed BAM looks like a SAM file
if ( message.contains(PICARD_TEXT_SAM_FILE_ERROR_1) ||
message.contains(PICARD_TEXT_SAM_FILE_ERROR_2) )
if ( message.contains(PICARD_TEXT_SAM_FILE_ERROR_1) || message.contains(PICARD_TEXT_SAM_FILE_ERROR_2) )
exitSystemWithSamError(t);
// can't close tribble index when writing
@ -138,12 +146,10 @@ public class CommandLineGATK extends CommandLineExecutable {
// disk is full
if ( message.contains(NO_SPACE_LEFT_ON_DEVICE_ERROR) || message.contains(DISK_QUOTA_EXCEEDED_ERROR) )
exitSystemWithUserError(new UserException.NoSpaceOnDevice());
if ( t.getCause() != null && (t.getCause().getMessage().contains(NO_SPACE_LEFT_ON_DEVICE_ERROR) || t.getCause().getMessage().contains(DISK_QUOTA_EXCEEDED_ERROR)) )
exitSystemWithUserError(new UserException.NoSpaceOnDevice());
// masked out of memory error
if ( t.getCause() != null && t.getCause() instanceof OutOfMemoryError )
exitSystemWithUserError(new UserException.NotEnoughMemory());
// masked error wrapped in another one
if ( t.getCause() != null )
checkForMaskedUserErrors(t.getCause());
}
/**
@ -155,7 +161,7 @@ public class CommandLineGATK extends CommandLineExecutable {
List<String> header = new ArrayList<String>();
header.add(String.format("The Genome Analysis Toolkit (GATK) v%s, Compiled %s",getVersionNumber(), getBuildTime()));
header.add("Copyright (c) 2010 The Broad Institute");
header.add("For support and documentation go to http://www.broadinstitute.org/gatk");
header.add("For support and documentation go to " + HelpUtils.BASE_GATK_URL);
return header;
}

6
public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java
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@ -25,11 +25,9 @@
package org.broadinstitute.sting.gatk.filters;
import com.google.common.base.Function;
import com.google.common.collect.Collections2;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.help.GATKDocUtils;
import org.broadinstitute.sting.utils.help.HelpUtils;
import java.util.Collection;
import java.util.List;
@ -73,7 +71,7 @@ public class FilterManager extends PluginManager<ReadFilter> {
return String.format("Read filter %s not found. Available read filters:%n%n%s%n%n%s",pluginName,
userFriendlyListofReadFilters(availableFilters),
"Please consult the GATK Documentation (http://www.broadinstitute.org/gatk/gatkdocs/) for more information.");
"Please consult the GATK Documentation (" + HelpUtils.GATK_DOCS_URL + ") for more information.");
}
private String userFriendlyListofReadFilters(List<Class<? extends ReadFilter>> filters) {

3
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
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@ -282,7 +282,8 @@ public class DiffEngine {
// now that we have a specific list of values we want to show, display them
GATKReport report = new GATKReport();
final String tableName = "differences";
report.addTable(tableName, "Summarized differences between the master and test files. See http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine for more information", 3);
// TODO for Geraldine -- link needs to be updated below
report.addTable(tableName, "Summarized differences between the master and test files. See [ask Geraldine to fix link to DiffEngine wiki] for more information", 3);
final GATKReportTable table = report.getTable(tableName);
table.addColumn("Difference");
table.addColumn("NumberOfOccurrences");

3
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java
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@ -138,7 +138,8 @@ public class DiffObjects extends RodWalker<Integer, Integer> {
/**
* Writes out a file of the DiffEngine format:
*
* http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine
* TODO for Geraldine -- link needs to be updated below (and also in SelectVariants and RefSeqCodec GATK docs)
* http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine
*/
@Output(doc="File to which results should be written",required=true)
protected PrintStream out;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java
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@ -13,7 +13,7 @@ import java.util.Set;
/**
* Stratifies the eval RODs by user-supplied JEXL expressions
*
* See http://www.broadinstitute.org/gsa/wiki/index.php/Using_JEXL_expressions for more details
* See http://gatkforums.broadinstitute.org/discussion/1255/what-are-jexl-expressions-and-how-can-i-use-them-with-the-gatk for more details
*/
public class JexlExpression extends VariantStratifier implements StandardStratification {
// needs to know the jexl expressions

3
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
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@ -32,6 +32,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.help.HelpUtils;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
import org.broadinstitute.sting.utils.exceptions.UserException;
@ -80,7 +81,7 @@ public class VariantDataManager {
final double theSTD = standardDeviation(theMean, iii);
logger.info( annotationKeys.get(iii) + String.format(": \t mean = %.2f\t standard deviation = %.2f", theMean, theSTD) );
if( Double.isNaN(theMean) ) {
throw new UserException.BadInput("Values for " + annotationKeys.get(iii) + " annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. See http://www.broadinstitute.org/gsa/wiki/index.php/VariantAnnotator");
throw new UserException.BadInput("Values for " + annotationKeys.get(iii) + " annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. See " + HelpUtils.GATK_FORUM_URL + "discussion/49/using-variant-annotator");
}
foundZeroVarianceAnnotation = foundZeroVarianceAnnotation || (theSTD < 1E-6);

3
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
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@ -51,8 +51,7 @@ import java.util.*;
* The Variant Validation Assessor is a tool for vetting/assessing validation data (containing genotypes).
* The tool produces a VCF that is annotated with information pertaining to plate quality control and by
* default is soft-filtered by high no-call rate or low Hardy-Weinberg probability.
* If you have .ped files, please first convert them to VCF format
* (see http://www.broadinstitute.org/gsa/wiki/index.php/Converting_ped_to_vcf).
* If you have .ped files, please first convert them to VCF format.
*
* <h2>Input</h2>
* <p>

5
public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
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@ -30,6 +30,7 @@ import net.sf.samtools.SAMSequenceDictionary;
import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpUtils;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@ -267,7 +268,7 @@ public class UserException extends ReviewedStingException {
public static class ReadMissingReadGroup extends MalformedBAM {
public ReadMissingReadGroup(SAMRecord read) {
super(read, String.format("Read %s is either missing the read group or its read group is not defined in the BAM header, both of which are required by the GATK. Please use http://www.broadinstitute.org/gsa/wiki/index.php/ReplaceReadGroups to fix this problem", read.getReadName()));
super(read, String.format("Read %s is either missing the read group or its read group is not defined in the BAM header, both of which are required by the GATK. Please use " + HelpUtils.GATK_FORUM_URL + "discussion/59/companion-utilities-replacereadgroups to fix this problem", read.getReadName()));
}
}
@ -343,7 +344,7 @@ public class UserException extends ReviewedStingException {
super(String.format("Lexicographically sorted human genome sequence detected in %s."
+ "\nFor safety's sake the GATK requires human contigs in karyotypic order: 1, 2, ..., 10, 11, ..., 20, 21, 22, X, Y with M either leading or trailing these contigs."
+ "\nThis is because all distributed GATK resources are sorted in karyotypic order, and your processing will fail when you need to use these files."
+ "\nYou can use the ReorderSam utility to fix this problem: http://www.broadinstitute.org/gsa/wiki/index.php/ReorderSam"
+ "\nYou can use the ReorderSam utility to fix this problem: " + HelpUtils.GATK_FORUM_URL + "discussion/58/companion-utilities-reordersam"
+ "\n %s contigs = %s",
name, name, ReadUtils.prettyPrintSequenceRecords(dict)));
}

8
public/java/src/org/broadinstitute/sting/utils/help/ForumAPIUtils.java
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@ -44,14 +44,13 @@ public class ForumAPIUtils {
/**
* How we post to the forum
*/
private final static String API_URL = "https://gatkforums.broadinstitute.org/api/v1/";
final private static String ACCESS_TOKEN = "access_token=";
public static List<String> getPostedTools(String forumKey) {
Gson gson = new Gson();
List<String> output = new ArrayList<String>();
String text = httpGet(API_URL + "categories.json?CategoryIdentifier=tool-bulletin&page=1-100000&" + ACCESS_TOKEN + forumKey);
String text = httpGet(HelpUtils.GATK_FORUM_API_URL + "categories.json?CategoryIdentifier=tool-bulletin&page=1-100000&" + ACCESS_TOKEN + forumKey);
APIQuery details = gson.fromJson(text, APIQuery.class);
ForumDiscussion[] discussions = details.Discussions;
@ -159,7 +158,7 @@ public class ForumAPIUtils {
Gson gson = new Gson();
String data = gson.toJson(post.getPostData());
httpPost(data, API_URL + "post/discussion.json?" + ACCESS_TOKEN + forumKey);
httpPost(data, HelpUtils.GATK_FORUM_API_URL + "post/discussion.json?" + ACCESS_TOKEN + forumKey);
}
@ -167,8 +166,7 @@ public class ForumAPIUtils {
class APIQuery {
ForumDiscussion[] Discussions;
public APIQuery() {
}
public APIQuery() {}
}
}

2
public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java
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@ -28,7 +28,7 @@ public class GATKDocUtils {
/**
* The URL root for RELEASED GATKDOC units
*/
public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gatk/gatkdocs/";
public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = HelpUtils.GATK_DOCS_URL;
/**
* The URL root for STABLE GATKDOC units
*/

9
public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java
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@ -32,6 +32,15 @@ import org.broadinstitute.sting.utils.classloader.JVMUtils;
import java.lang.reflect.Field;
public class HelpUtils {
public final static String BASE_GATK_URL = "http://www.broadinstitute.org/gatk";
public final static String GATK_DOCS_URL = BASE_GATK_URL + "/gatkdocs/";
public final static String GATK_FORUM_URL = "http://gatkforums.broadinstitute.org/";
public final static String GATK_FORUM_API_URL = "https://gatkforums.broadinstitute.org/api/v1/";
protected static boolean assignableToClass(ProgramElementDoc classDoc, Class lhsClass, boolean requireConcrete) {
try {
Class type = getClassForDoc(classDoc);

1
public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/SortingVariantContextWriterBase.java
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@ -71,7 +71,6 @@ abstract class SortingVariantContextWriterBase implements VariantContextWriter {
this.takeOwnershipOfInner = takeOwnershipOfInner;
// has to be PriorityBlockingQueue to be thread-safe
// see http://getsatisfaction.com/gsa/topics/missing_loci_output_in_multi_thread_mode_when_implement_sortingvcfwriterbase?utm_content=topic_link&utm_medium=email&utm_source=new_topic
this.queue = new PriorityBlockingQueue<VCFRecord>(50, new VariantContextComparator());
this.mostUpstreamWritableLoc = BEFORE_MOST_UPSTREAM_LOC;

1
public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
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@ -28,7 +28,6 @@ public class VCFIntegrationTest extends WalkerTest {
}
@Test(enabled = true)
// See https://getsatisfaction.com/gsa/topics/support_vcf_4_1_structural_variation_breakend_alleles?utm_content=topic_link&utm_medium=email&utm_source=new_topic
public void testReadingAndWritingBreakpointAlleles() {
String testVCF = privateTestDir + "breakpoint-example.vcf";