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Add DeprecatedFeature annotation. #8100

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merged 2 commits into from
Dec 19, 2022
Merged

Add DeprecatedFeature annotation. #8100

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9926f15
Add DeprecatedFeature annotation.
cmnbroad Nov 21, 2022
d8d7f27
Upgrade Barclay to pick up the DeprecatedFeature annotation.
cmnbroad Nov 22, 2022
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2 changes: 1 addition & 1 deletion build.gradle
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Expand Up @@ -62,7 +62,7 @@ repositories {

final htsjdkVersion = System.getProperty('htsjdk.version','3.0.1')
final picardVersion = System.getProperty('picard.version','2.27.5')
final barclayVersion = System.getProperty('barclay.version','4.0.2')
final barclayVersion = System.getProperty('barclay.version','4.1.0')
final sparkVersion = System.getProperty('spark.version', '2.4.5')
final scalaVersion = System.getProperty('scala.version', '2.11')
final hadoopVersion = System.getProperty('hadoop.version', '3.3.1')
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4 changes: 2 additions & 2 deletions src/main/java/org/broadinstitute/hellbender/cmdline/DeprecatedToolsRegistry.java
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Expand Up @@ -6,8 +6,8 @@
import java.util.Map;

/**
* When a tool is removed from GATK (after having been @Deprecated for a suitable period), an entry should
* be added to this list to issue a message when the user tries to run that tool.
* When a tool is removed from GATK (after having been tagged with @DeprecatedFeature for a suitable period), an
* entry should be added to this list to issue a message when the user tries to run that tool.
*
* NOTE: Picard tools should be listed here as well, since by definition such tools will not be found in
* the Picard jar.
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3 changes: 2 additions & 1 deletion ...adinstitute/hellbender/tools/walkers/genotyper/GenotypeCalculationArgumentCollection.java
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Expand Up @@ -3,6 +3,7 @@
import htsjdk.variant.variantcontext.VariantContext;
import org.broadinstitute.barclay.argparser.Advanced;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.barclay.argparser.DeprecatedFeature;
import org.broadinstitute.hellbender.engine.FeatureInput;
import org.broadinstitute.hellbender.exceptions.GATKException;
import org.broadinstitute.hellbender.utils.variant.HomoSapiensConstants;
Expand Down Expand Up @@ -61,7 +62,7 @@ public GenotypeCalculationArgumentCollection clone() {
/**
* As of version 4.1.0.0, this argument is no longer needed because the new qual score is now on by default. See GATK 3.3 release notes for more details.
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Does javadoc on arguments get output in our docs at all?

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Yes, it gets included in the full text description.

*/
@Deprecated
@DeprecatedFeature(detail="New qual score is on by default")
@Argument(fullName = "use-new-qual-calculator", shortName = "new-qual", doc = "Use the new AF model instead of the so-called exact model", optional = true)
public boolean useNewAFCalculator = true;

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3 changes: 2 additions & 1 deletion ...ools/walkers/haplotypecaller/HaplotypeCallerReadThreadingAssemblerArgumentCollection.java
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Expand Up @@ -2,6 +2,7 @@

import org.broadinstitute.barclay.argparser.Advanced;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.barclay.argparser.DeprecatedFeature;
import org.broadinstitute.barclay.argparser.Hidden;
import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler;

Expand Down Expand Up @@ -32,7 +33,7 @@ public class HaplotypeCallerReadThreadingAssemblerArgumentCollection extends Rea
/**
* As of version 3.3, this argument is no longer needed because dangling end recovery is now the default behavior. See GATK 3.3 release notes for more details.
*/
@Deprecated
@DeprecatedFeature
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This has been deprecated since 3.3... maybe we can remove it.

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Can we put the reason in the description?

@Argument(fullName= RECOVER_DANGLING_HEADS_LONG_NAME, doc="This argument is deprecated since version 3.3", optional = true)
public boolean DEPRECATED_RecoverDanglingHeads = false;

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3 changes: 2 additions & 1 deletion src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2ArgumentCollection.java
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Expand Up @@ -5,6 +5,7 @@
import org.broadinstitute.barclay.argparser.Advanced;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.barclay.argparser.ArgumentCollection;
import org.broadinstitute.barclay.argparser.DeprecatedFeature;
import org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions;
import org.broadinstitute.hellbender.engine.FeatureInput;
import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentArgumentCollection;
Expand Down Expand Up @@ -115,7 +116,7 @@ public ReadThreadingAssembler createReadThreadingAssembler(){
public File f1r2TarGz;

// As of GATK 4.1, any sample not specified as the normal is considered a tumor sample
@Deprecated
@DeprecatedFeature
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Should we move the reason into here?

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Sure. Done.

@Argument(fullName = TUMOR_SAMPLE_LONG_NAME, shortName = TUMOR_SAMPLE_SHORT_NAME, doc = "BAM sample name of tumor. May be URL-encoded as output by GetSampleName with -encode argument.", optional = true)
protected String tumorSample = null;

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5 changes: 5 additions & 0 deletions src/main/java/org/broadinstitute/hellbender/utils/help/GATKGSONWorkUnit.java
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@@ -1,5 +1,6 @@
package org.broadinstitute.hellbender.utils.help;

import org.broadinstitute.barclay.help.DocWorkUnit;
import org.broadinstitute.barclay.help.GSONWorkUnit;

/**
Expand All @@ -11,6 +12,10 @@ public class GATKGSONWorkUnit extends GSONWorkUnit {

private String walkerType;

public GATKGSONWorkUnit(DocWorkUnit workUnit) {
super(workUnit);
}

public void setWalkerType(final String walkerType){
this.walkerType = walkerType;
}
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2 changes: 1 addition & 1 deletion src/main/java/org/broadinstitute/hellbender/utils/help/GATKHelpDoclet.java
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Expand Up @@ -79,7 +79,7 @@ protected GSONWorkUnit createGSONWorkUnit(
final List<Map<String, String>> groupMaps,
final List<Map<String, String>> featureMaps)
{
GATKGSONWorkUnit gatkGSONWorkUnit = new GATKGSONWorkUnit();
GATKGSONWorkUnit gatkGSONWorkUnit = new GATKGSONWorkUnit(workUnit);
gatkGSONWorkUnit.setWalkerType((String)workUnit.getRootMap().get(WALKER_TYPE_MAP_ENTRY));
return gatkGSONWorkUnit;
}
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2 changes: 2 additions & 0 deletions ...n/resources/org/broadinstitute/hellbender/utils/helpTemplates/generic.index.template.html
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Expand Up @@ -48,6 +48,8 @@ <h4>${group.name}</h4>
<td>**EXPERIMENTAL** ${datum.summary} </td>
<#elseif datum.beta?? && datum.beta == "true">
<td>**BETA** ${datum.summary}</td>
<#elseif datum.deprecated?? && datum.deprecated == "true">
<td>**DEPRECATED** ${datum.summary}</a></td>
<#else>
<td>${datum.summary}</td>
</#if>
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21 changes: 19 additions & 2 deletions src/main/resources/org/broadinstitute/hellbender/utils/helpTemplates/generic.template.html
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Expand Up @@ -36,6 +36,21 @@

<#include "common.html"/>

<#macro flagDeprecated arg>
<#if arg.deprecated == true> (Deprecated)</#if>
</#macro>

<#macro flagDeprecatedWithReason arg>
<#if arg.deprecated == true>
<#if arg.deprecationDetail??>
This argument is deprecated. ${arg.deprecationDetail}</br>
<#else>
This argument is deprecated.</br>
</#if>
</#if>
</#macro>


<#macro argumentlist name myargs>
<#if myargs?size != 0>
<tr>
Expand All @@ -56,7 +71,7 @@
<#else>
<td></td>
</#if>
<td>${arg.summary}</td>
<td><@flagDeprecated arg=arg/>${arg.summary}</td>
</tr>
</#list>
</#if>
Expand All @@ -68,7 +83,7 @@ <h3><a name="${arg.name}">${arg.name} </a>
<#if arg.synonyms?? && arg.synonyms != "NA"> / <small>${arg.synonyms}</small></#if>
</h3>
<p class="args">
<b>${arg.summary}</b><br />
<b><@flagDeprecated arg=arg/>${arg.summary}</b><br />
${arg.fulltext}
</p>
<#if arg.otherArgumentRequired != "NA">
Expand Down Expand Up @@ -132,6 +147,8 @@ <h3>Browse tools by category</h3>
<h1>**BETA** ${name}</h1>
<#elseif experimental?? && experimental == true>
<h1>**EXPERIMENTAL** ${name}</h1>
<#elseif deprecated?? && deprecated == true>
<h1>**DEPRECATED** ${name} ${deprecationDetail}</h1>
<#else>
<h1>${name}</h1>
</#if>
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