SqwFile.java

package net.sourceforge.seqware.pipeline.workflowV2.model;

import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;

/**
 * a file object which has all information for provision
 *
 */
public class SqwFile {
    private boolean attached = false;
    private String type;
    private String location;
    private String outputLocation;
    private boolean input = true;
    private boolean forceCopy;
    private final String uniqueDir;
    private final List<String> parentAccessions;
    private boolean skipIfMissing = false;
    private final Map<String, String> annotations = new HashMap<>();

    public SqwFile() {
        // need to create a random directory for later reference
        this.uniqueDir = Long.toString(System.nanoTime());
        this.parentAccessions = new ArrayList<>();
    }

    public String getType() {
        return type;
    }

    public void setType(String type) {
        this.type = type;
    }

    public String getSourcePath() {
        return location;
    }

    public void setSourcePath(String location) {
        this.location = location;
    }

    public String getOutputPath() {
        return outputLocation;
    }

    public void setOutputPath(String location) {
        this.outputLocation = location;
    }

    /**
     * is an output file?
     *
     * @return
     */
    public boolean isOutput() {
        return !input;
    }

    /**
     * is an input file?
     *
     * @return
     */
    public boolean isInput() {
        return input;
    }

    /**
     * isInput = @param isInput isOutput = !@param isInput
     *
     * @param isInupt
     */
    public void setIsInput(boolean isInupt) {
        this.input = isInupt;
    }

    /**
     * isInput = !@param isOutput isOutput = @param isOutput
     *
     * @param isOutput
     */
    public void setIsOutput(boolean isOutput) {
        this.input = !isOutput;
    }

    @Override
    public boolean equals(Object obj) {
        if (obj instanceof SqwFile == false) return false;
        if (obj == this) return true;
        SqwFile rhs = (SqwFile) obj;
        return new EqualsBuilder().appendSuper(super.equals(obj)).append(type, rhs.type).append(location, rhs.location)
                .append(input, rhs.input).isEquals();
    }

    @Override
    public int hashCode() {
        return new HashCodeBuilder(17, 37).append(type).append(location).append(input).toHashCode();
    }

    public boolean isForceCopy() {
        return forceCopy;
    }

    /**
     * when forceCopy is true, it will pass "--forcecopy" argument to provisionFileJob
     *
     * @param forceCopy
     */
    public void setForceCopy(boolean forceCopy) {
        this.forceCopy = forceCopy;
    }

    /**
     *
     * @return the file path after provisioned.
     */
    public String getProvisionedPath() {
        return "provisionfiles/" + this.uniqueDir + "/" + FilenameUtils.getName(this.getSourcePath());
    }

    /**
     * return the unique dir associate with the file if the file type is input, the provisioned file will be output to
     * provisionfiles/uniquedir + filename
     *
     * @return
     */
    public String getUniqueDir() {
        return this.uniqueDir;
    }

    /**
     * set the parent accessions for provision file job
     *
     * @param parentAccessions
     */
    public void setParentAccessions(Collection<String> parentAccessions) {
        this.parentAccessions.addAll(parentAccessions);
    }

    public Collection<String> getParentAccessions() {
        return this.parentAccessions;
    }

    /**
     * @return the attached
     */
    public boolean isAttached() {
        return attached;
    }

    /**
     * @param attached
     *            the attached to set
     */
    public void setAttached(boolean attached) {
        this.attached = attached;
    }

    /**
     * @return the skipIfMissing
     */
    public boolean isSkipIfMissing() {
        return skipIfMissing;
    }

    /**
     * @param skipIfMissing
     *            only relevant for provision output, this sets the skip if missing parameter of the provision files module allowing for the
     *            additional of optional files
     */
    public void setSkipIfMissing(boolean skipIfMissing) {
        this.skipIfMissing = skipIfMissing;
    }

    /**
     * Set arbitrary key-value annotations on provisioned files.
     *
     * @return
     */
    public Map<String, String> getAnnotations() {
        return annotations;
    }
}