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org.broadinstitute.hellbender.utils.help.GATKWDLDoclet Maven / Gradle / Ivy
package org.broadinstitute.hellbender.utils.help;
import freemarker.template.Configuration;
import freemarker.template.Template;
import freemarker.template.TemplateException;
import jdk.javadoc.doclet.Doclet;
import org.apache.commons.io.FilenameUtils;
import org.broadinstitute.barclay.help.*;
import javax.lang.model.element.Element;
import java.io.*;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
/**
* Custom Barclay-based Javadoc Doclet used for generating tool WDL.
*
* NOTE: Methods in this class are intended to be called by Gradle/Javadoc only, and should not be called
* by methods that are used by the GATK runtime. This class has a dependency on com.sun.javadoc classes,
* which may not be present since they're not provided as part of the normal GATK runtime classpath.
*/
@SuppressWarnings("removal")
public class GATKWDLDoclet extends WDLDoclet {
// emit an index file with links to all the .wdl files
private final static String GATK_FREEMARKER_INDEX_TEMPLATE_NAME = "wdlIndexTemplate.html.ftl";
// the directory where the wdlgen build is running
public final static String OPT_BUILD_DIR = "-build-dir";
private String buildDir;
@Override
public String getIndexFileExtension() { return "html"; }
@Override
public Set getSupportedOptions() {
final Set options = new LinkedHashSet<>();
options.addAll(super.getSupportedOptions());
final Doclet.Option localOption =
new BarclayDocletOption.SimpleStandardOption(OPT_BUILD_DIR) {
@Override
public boolean process(String option, List arguments) {
buildDir = arguments.get(0);
return true;
}
};
options.add(localOption);
return options;
}
/**
* @return the location where the build is running; used in the cromwell validation tests to generate a dummy
* input file to satisfy cromwell file localization
*/
public String getBuildDir() { return buildDir; }
/**
* Return the name of the freemarker template to be used for the index generated by Barclay.
* For WDL gen, we create an index file that links to each of the generated WDL files.
* Must reside in the folder passed to the Barclay Javadc Doclet via the "-settings-dir" parameter.
* @return name of freemarker index template
*/
@Override
public String getIndexTemplateName() {
return GATK_FREEMARKER_INDEX_TEMPLATE_NAME;
}
/**
* @return Create and return a DocWorkUnit-derived object to handle documentation
* for the target feature(s) represented by documentedFeature.
*
* @param classElement the Element for the class for this workunit
* @param clazz class of the target feature
* @param documentedFeature DocumentedFeature annotation for the target feature
* @return
*/
@Override
public DocWorkUnit createWorkUnit(
final Element classElement,
final Class clazz,
final DocumentedFeature documentedFeature)
{
return includeInDocs(documentedFeature, clazz) ?
// for WDL we don't need to customize the work unit, only the handler, so just use the
// Barclay default WorkUnit class
new DocWorkUnit(
new GATKWDLWorkUnitHandler(this),
classElement,
clazz,
documentedFeature) :
null;
}
@Override
protected void processWorkUnitTemplate(
final Configuration cfg,
final DocWorkUnit workUnit,
final List> indexByGroupMaps,
final List> featureMaps)
{
final String defaultWDLOutputFileName = workUnit.getTargetFileName();
final String defaultJSONOutputFileName = workUnit.getJSONFileName();
// generate the default WDL and input JSON, which expose only required args
exportWorkUnitTemplate(
cfg,
workUnit,
workUnit.getTemplateName(),
new File(getDestinationDir(), defaultWDLOutputFileName));
exportWorkUnitTemplate(
cfg,
workUnit,
"wdlJSONTemplate.json.ftl",
new File(getDestinationDir(), defaultJSONOutputFileName));
// generate a second pair of files containing ALL arguments
exportWorkUnitTemplate(
cfg,
workUnit,
"wdlToolTemplateAllArgs.wdl.ftl",
new File(getDestinationDir(),
String.format("%sAllArgs.%s",
FilenameUtils.getBaseName(defaultWDLOutputFileName),
FilenameUtils.getExtension(defaultWDLOutputFileName)))
);
exportWorkUnitTemplate(
cfg,
workUnit,
"wdlJSONTemplateAllArgs.json.ftl",
new File(getDestinationDir(),
String.format("%sAllArgsInputs.json",
FilenameUtils.getBaseName(defaultWDLOutputFileName)))
);
// Finally, we need to emit a test WDL and JSON pair for use by the cromwell execution test (which
// runs GATK in command line evaluation only mode). The JSON file is primed with dummy values for any
// required args. The test WDL specifies no docker image, and has no runtime outputs, since in
// command line validation mode no outputs are produced, so otherwise cromwell will fail attempting to
// de-localize them.
exportWorkUnitTemplate(
cfg,
workUnit,
"wdlToolTemplateAllArgsTest.wdl.ftl",
new File(getDestinationDir(),
String.format("%sAllArgsTest.%s",
FilenameUtils.getBaseName(defaultWDLOutputFileName),
FilenameUtils.getExtension(defaultWDLOutputFileName)))
);
exportWorkUnitTemplate(
cfg,
workUnit,
"wdlJSONTemplateAllArgsTest.json.ftl",
new File(getDestinationDir(),
String.format("%sAllArgsTestInputs.json",
FilenameUtils.getBaseName(defaultWDLOutputFileName)))
);
}
/**
* Export the generated files from templates for a single work unit.
*
* @param cfg freemarker config
* @param workUnit the WorkUnit being processed
* @param wdlTemplateName name of the template to use
* @param wdlOutputPath output file
*/
protected final void exportWorkUnitTemplate(
final Configuration cfg,
final DocWorkUnit workUnit,
final String wdlTemplateName,
final File wdlOutputPath) {
try {
// Merge data-model with wdl template
final Template wdlTemplate = cfg.getTemplate(wdlTemplateName);
try (final Writer out = new OutputStreamWriter(new FileOutputStream(wdlOutputPath))) {
wdlTemplate.process(workUnit.getRootMap(), out);
}
} catch (IOException e) {
throw new DocException("IOException during documentation creation", e);
} catch (TemplateException e) {
throw new DocException("TemplateException during documentation creation", e);
}
}
/**
* Return the group map for this workunit. This adds the custom super-category property so that we can
* order the categories in the documentation index.
*
* @param docWorkUnit the DocWorkUnit being processed
* @return the group map for this work unit, updated to include any custom properties
*/
@Override
protected final Map getGroupMap(final DocWorkUnit docWorkUnit) {
final Map root = super.getGroupMap(docWorkUnit);
/**
* Add-on super-category definitions. The super-category needs to match the string(s) used
* in the Freemarker template.
*/
root.put("supercat", HelpConstants.getSuperCategoryProperty(docWorkUnit.getGroupName()));
return root;
}
}
