All Downloads are FREE. Search and download functionalities are using the official Maven repository.

org.broadinstitute.barclay.help.DocWorkUnit Maven / Gradle / Ivy

The newest version!
package org.broadinstitute.barclay.help;

import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.broadinstitute.barclay.argparser.CommandLineException;
import org.broadinstitute.barclay.argparser.CommandLineProgramGroup;
import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
import org.broadinstitute.barclay.argparser.BetaFeature;
import org.broadinstitute.barclay.argparser.DeprecatedFeature;
import org.broadinstitute.barclay.argparser.ExperimentalFeature;
import org.broadinstitute.barclay.utils.Utils;

import javax.lang.model.element.Element;
import java.lang.reflect.InvocationTargetException;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

/**
 * Collection of all relevant information about a single feature the HelpDoclet can document
 */
public class DocWorkUnit implements Comparable {
    final protected static Logger logger = LogManager.getLogger(DocWorkUnit.class);

    private final String name;                          // name of this work unit/feature

    private final Class clazz;                       // class that's being documented
    private final Element docElement;                  // javadoc documentation for clazz
    private final DocWorkUnitHandler workUnitHandler;   // handler for this work unit

    // Annotations attached to the feature class being documented by this work unit
    private final DocumentedFeature documentedFeature;
    private final CommandLineProgramProperties commandLineProperties;
    private final ExperimentalFeature experimentalFeature;
    private final BetaFeature betaFeature;
    private final DeprecatedFeature deprecatedFeature;

    private Map propertyMap = new HashMap<>(); // propertyMap for this unit's template

    // Cached values derived by fallback policies that are implemented by the work unit handler.
    protected String summary;         // summary description of this feature
    protected String groupName;       // name of the feature group to which this feature belongs
    protected String groupSummary;    // summary description of this feature's feature group

    /**
     * @param workUnitHandler
     * @param docElement
     * @param clazz
     * @param documentedFeatureAnnotation
     */
    public DocWorkUnit(
            final DocWorkUnitHandler workUnitHandler,
            final Element docElement,
            final Class clazz,
            final DocumentedFeature documentedFeatureAnnotation)
    {
        Utils.nonNull(workUnitHandler, "workUnitHandler cannot be null");
        Utils.nonNull(documentedFeatureAnnotation, "DocumentedFeature annotation cannot be null");
        Utils.nonNull(docElement, "classDoc cannot be null");
        Utils.nonNull(clazz, "class cannot be null");

        this.name = clazz.getSimpleName();

        this.documentedFeature = documentedFeatureAnnotation;
        this.commandLineProperties = clazz.getAnnotation(CommandLineProgramProperties.class);
        this.experimentalFeature = clazz.getAnnotation(ExperimentalFeature.class);
        this.betaFeature = clazz.getAnnotation(BetaFeature.class);
        this.deprecatedFeature = clazz.getAnnotation(DeprecatedFeature.class);
        checkForMultipleMutexAnnotations();

        this.workUnitHandler = workUnitHandler;
        this.docElement = docElement;
        this.clazz = clazz;

        // summary, groupName and groupSummary can each be determined via fallback policies dictated
        // by the feature handler, so delegate back to the handler to allow it to do the initialization
        // once, and then cache the results so that all consumers see consistent values.
        summary = workUnitHandler.getSummaryForWorkUnit(this);
        groupName = workUnitHandler.getGroupNameForWorkUnit(this);
        groupSummary = workUnitHandler.getGroupSummaryForWorkUnit(this);

    }

    private void checkForMultipleMutexAnnotations() {
        int count =
                (this.experimentalFeature != null ? 1 : 0) +
                (this.betaFeature != null ? 1 : 0) +
                (this.deprecatedFeature != null ? 1 : 0);
        if (count > 1) {
            throw new CommandLineException.CommandLineParserInternalException(String.format(
                    "Multiple annotations detected on class %s. The Deprecated, Beta, and Experimental annotations are mutually exclusive.",
                    clazz.getSimpleName()));
        }
    }

    /**
     * Get the root property map used for this work unit.
     * @return Root property map for this work unit.
     */
    public Map getRootMap() {
        return (this.propertyMap);
    }

    /**
     * Set a property on the root property map for this work unit.
     * @param key
     * @param value
     */
    public void setProperty(final String key, final Object value) {
        propertyMap.put(key, value);
    }

    /**
     * Get a property from the root property map for this work unit
     * @param key
     * @return Object value for the given property, or null if property not found.
     */
    public Object getProperty(final String key) {
        return propertyMap.get(key);
    }

    /**
     * Get the DocumentedFeature annotation object for this class.
     * @return DocumentedFeature object. Will not be null.
     */
    public DocumentedFeature getDocumentedFeature() { return documentedFeature; }

    /**
     * Get the Java language Element for this work unit.
     * @return Element for this work unit. Will not be null.
     */
    public Element getDocElement() { return docElement; }

    /**
     * The name of this documentation unit
     */
    public String getName() {
        return name;
    }

    /**
     * The name of the documentation group (e.g., walkers, read filters) class belongs to
     */
    public String getGroupName() {
        return groupName;
    }

    /**
     * The group summary for the group for this object
     */
    public String getGroupSummary() {
        return groupSummary;
    }

    /**
     * The summary of the documentation object
     */
    public String getSummary() { return summary; }

    public Class getClazz() { return clazz; }

    /**
     * Populate the property map for this work unit by delegating to the documented feature handler for this work unit.
     * @param featureMaps map of all features included in this javadoc run
     * @param groupMaps map of all groups included in the javadoc run
     */
    public void processDoc(final List> featureMaps, final List> groupMaps) {
        workUnitHandler.processWorkUnit(this, featureMaps, groupMaps);

    };

    /**
     * Get the template to be used for this work unit. Delegates to the feature handler.
     * @return name of the template (relative to the input path specified to the doclet) for the template to be used
     * for this work unit.
     */
    public String getTemplateName() { return workUnitHandler.getTemplateName(this); }

    public String getTargetFileName() { return workUnitHandler.getDestinationFilename(this); }

    public String getJSONFileName() { return workUnitHandler.getJSONFilename(this); }

    /**
     * Get the CommandLineProgramProperties annotation for this work unit.
     * @return CommandLineProgramProperties object for this work unit. May be null for features that are not
     * command line programs.
     */
    public CommandLineProgramProperties getCommandLineProperties() { return commandLineProperties; }

    /**
     * @return a boolean determining if this documented feature is marked as a beta feature
     */
    public boolean isBetaFeature() { return betaFeature != null; }

    /**
     * @return a boolean determining if this documented feature is marked as an experimental feature
     */
    public boolean isExperimentalFeature() { return experimentalFeature != null; }

    /**
     * @return a boolean determining if this documented feature is marked as a deprecated feature
     */
    public boolean isDeprecatedFeature() { return deprecatedFeature != null; }

    /**
     * Get the deprecation detail string.
     * @return a String containing the detail (may be null if the work unit is not annotated with the {@code
     * @DeprecatedFeature} annotation or if no deprecation detail was provided).
     */
    public String getDeprecationDetail() { return isDeprecatedFeature() ? deprecatedFeature.detail() : null; }

    /**
     * Get the CommandLineProgramGroup object from the CommandLineProgramProperties of this work unit.
     * @return CommandLineProgramGroup if the feature has one, otherwise null.
     */
    public CommandLineProgramGroup getCommandLineProgramGroup() {
        if (commandLineProperties != null) {
            try {
                return commandLineProperties.programGroup().getDeclaredConstructor().newInstance();
            } catch (final NoSuchMethodException e) {
                throw new CommandLineException.CommandLineParserInternalException(
                        String.format ("Command line program class %s does not have the required no argument constructor",
                                getClazz()), e);
            } catch (final InvocationTargetException |IllegalAccessException | InstantiationException e) {
                logger.warn(
                        String.format("Can't instantiate program group class to retrieve summary for group %s for class %s",
                                commandLineProperties.programGroup().getName(),
                                clazz.getName()));
            }
        }
        return null;
    }

    /**
     * Sort in order of the name of this WorkUnit
     */
    public int compareTo(DocWorkUnit other) {
        return this.name.compareTo(other.name);
    }

    @Override
    public boolean equals(Object o) {
        if (this == o) return true;
        if (!(o instanceof DocWorkUnit)) return false;

        DocWorkUnit that = (DocWorkUnit) o;

        if (!name.equals(that.name)) return false;
        if (!clazz.equals(that.clazz)) return false;
        if (!docElement.equals(that.docElement)) return false;
        if (documentedFeature != null ? !documentedFeature.equals(that.documentedFeature) :
                that.documentedFeature != null)
            return false;
        if (commandLineProperties != null ? !commandLineProperties.equals(that.commandLineProperties) :
                that.commandLineProperties != null)
            return false;
        if (experimentalFeature != null ? !experimentalFeature.equals(that.experimentalFeature) :
                that.experimentalFeature != null)
            return false;
        if (betaFeature != null ? !betaFeature.equals(that.betaFeature) : that.betaFeature != null) return false;
        if (!propertyMap.equals(that.propertyMap)) return false;
        if (summary != null ? !summary.equals(that.summary) : that.summary != null) return false;
        if (groupName != null ? !groupName.equals(that.groupName) : that.groupName != null) return false;
        return groupSummary != null ? groupSummary.equals(that.groupSummary) : that.groupSummary == null;
    }

    @Override
    public int hashCode() {
        int result = name.hashCode();
        result = 31 * result + clazz.hashCode();
        result = 31 * result + docElement.hashCode();
        result = 31 * result + (documentedFeature != null ? documentedFeature.hashCode() : 0);
        result = 31 * result + (commandLineProperties != null ? commandLineProperties.hashCode() : 0);
        result = 31 * result + (experimentalFeature != null ? experimentalFeature.hashCode() : 0);
        result = 31 * result + (betaFeature != null ? betaFeature.hashCode() : 0);
        result = 31 * result + propertyMap.hashCode();
        result = 31 * result + (summary != null ? summary.hashCode() : 0);
        result = 31 * result + (groupName != null ? groupName.hashCode() : 0);
        result = 31 * result + (groupSummary != null ? groupSummary.hashCode() : 0);
        return result;
    }

}




© 2015 - 2025 Weber Informatics LLC | Privacy Policy