From e199562c2521032abd003bd315cbfad294208e93 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 27 Nov 2012 10:26:17 -0500 Subject: [PATCH] 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). --- .../sting/commandline/CommandLineProgram.java | 3 ++- .../sting/gatk/CommandLineGATK.java | 24 ++++++++++++------- .../sting/gatk/filters/FilterManager.java | 6 ++--- .../gatk/walkers/diffengine/DiffEngine.java | 3 ++- .../gatk/walkers/diffengine/DiffObjects.java | 3 ++- .../stratifications/JexlExpression.java | 2 +- .../VariantDataManager.java | 3 ++- .../VariantValidationAssessor.java | 3 +-- .../sting/utils/exceptions/UserException.java | 5 ++-- .../sting/utils/help/ForumAPIUtils.java | 8 +++---- .../sting/utils/help/GATKDocUtils.java | 2 +- .../sting/utils/help/HelpUtils.java | 9 +++++++ .../SortingVariantContextWriterBase.java | 1 - .../utils/codecs/vcf/VCFIntegrationTest.java | 1 - 14 files changed, 43 insertions(+), 30 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java b/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java index d77ae67cf..fb15a3722 100644 --- a/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java +++ b/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java @@ -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"); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java index 0daad2c2b..d1711ba4c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java +++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java @@ -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 header = new ArrayList(); 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; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java b/public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java index 5ca8a1779..89099c587 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java @@ -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 { 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> filters) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java index 40ed26608..579b84d96 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java @@ -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"); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java index 92e2e2dc4..5951ee7d0 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java @@ -138,7 +138,8 @@ public class DiffObjects extends RodWalker { /** * 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; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java index dc5438358..c89c4be66 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java @@ -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 diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java index aacd987d5..3382a1d9b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java @@ -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); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java index a301867fc..9236247f1 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java @@ -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. * *

Input

*

diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java index a49a12292..a2ec35ae2 100755 --- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java +++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java @@ -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))); } diff --git a/public/java/src/org/broadinstitute/sting/utils/help/ForumAPIUtils.java b/public/java/src/org/broadinstitute/sting/utils/help/ForumAPIUtils.java index fe5f48a48..64238dc73 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/ForumAPIUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/ForumAPIUtils.java @@ -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 getPostedTools(String forumKey) { Gson gson = new Gson(); List output = new ArrayList(); - 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() {} } } diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java b/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java index 4ec2ac6d7..21054a794 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java @@ -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 */ diff --git a/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java b/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java index 645ab34c1..1bc20d5a0 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java @@ -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); diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/SortingVariantContextWriterBase.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/SortingVariantContextWriterBase.java index 18d91ef3f..1f3cdd0fe 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/SortingVariantContextWriterBase.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/SortingVariantContextWriterBase.java @@ -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(50, new VariantContextComparator()); this.mostUpstreamWritableLoc = BEFORE_MOST_UPSTREAM_LOC; diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java index b2a4ac2da..b9ce58992 100644 --- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java @@ -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";