uk.ac.ebi.bioinvindex.model.Protocol.java Source code

Introduction

Here is the source code for uk.ac.ebi.bioinvindex.model.Protocol.java

Source

package uk.ac.ebi.bioinvindex.model;

/*
 * __________
 * CREDITS
 * __________
 *
 * Team page: http://isatab.sf.net/
 * - Marco Brandizi (software engineer: ISAvalidator, ISAconverter, BII data management utility, BII model)
 * - Eamonn Maguire (software engineer: ISAcreator, ISAcreator configurator, ISAvalidator, ISAconverter,  BII data management utility, BII web)
 * - Nataliya Sklyar (software engineer: BII web application, BII model,  BII data management utility)
 * - Philippe Rocca-Serra (technical coordinator: user requirements and standards compliance for ISA software, ISA-tab format specification, BII model, ISAcreator wizard, ontology)
 * - Susanna-Assunta Sansone (coordinator: ISA infrastructure design, standards compliance, ISA-tab format specification, BII model, funds raising)
 *
 * Contributors:
 * - Manon Delahaye (ISA team trainee:  BII web services)
 * - Richard Evans (ISA team trainee: rISAtab)
 *
 *
 * ______________________
 * Contacts and Feedback:
 * ______________________
 *
 * Project overview: http://isatab.sourceforge.net/
 *
 * To follow general discussion: isatab-devel@list.sourceforge.net
 * To contact the developers: isatools@googlegroups.com
 *
 * To report bugs: http://sourceforge.net/tracker/?group_id=215183&atid=1032649
 * To request enhancements:  http://sourceforge.net/tracker/?group_id=215183&atid=1032652
 *
 *
 * __________
 * License:
 * __________
 *
 * This work is licenced under the Creative Commons Attribution-Share Alike 2.0 UK: England & Wales License. To view a copy of this licence, visit http://creativecommons.org/licenses/by-sa/2.0/uk/ or send a letter to Creative Commons, 171 Second Street, Suite 300, San Francisco, California 94105, USA.
 *
 * __________
 * Sponsors
 * __________
 * This work has been funded mainly by the EU Carcinogenomics (http://www.carcinogenomics.eu) [PL 037712] and in part by the
 * EU NuGO [NoE 503630](http://www.nugo.org/everyone) projects and in part by EMBL-EBI.
 */

import org.apache.commons.lang.StringUtils;

import uk.ac.ebi.bioinvindex.model.term.Parameter;
import uk.ac.ebi.bioinvindex.model.term.ProtocolComponent;
import uk.ac.ebi.bioinvindex.model.term.ProtocolType;

import javax.persistence.Entity;
import javax.persistence.JoinColumn;
import javax.persistence.Lob;
import javax.persistence.ManyToOne;
import javax.persistence.OneToMany;
import javax.persistence.Table;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;

/**
 * Object representing wet/dry laboratory operating procedures.
 * 
 * @author Nataliya Sklyar (nsklyar@ebi.ac.uk)
 * Date: Nov 20, 2007
 */
@Entity
@Table(name = "PROTOCOL")
public class Protocol extends Accessible {

    private String name;
    private ProtocolType type;
    private String description;
    private String uri;
    private String version;
    private Collection<Parameter> parameters = new ArrayList<Parameter>();
    private Collection<ProtocolComponent> components = new ArrayList<ProtocolComponent>();

    protected Protocol() {
        super();
    }

    public Protocol(String name, ProtocolType type) {
        this.name = name;
        this.type = type;
    }

    public String getName() {
        return name;
    }

    public void setName(String name) {
        this.name = name;
    }

    @ManyToOne(targetEntity = ProtocolType.class)
    @JoinColumn(name = "type", nullable = true)
    public ProtocolType getType() {
        return type;
    }

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

    @Lob
    public String getDescription() {
        return description;
    }

    public void setDescription(String description) {
        this.description = description;
    }

    public String getUri() {
        return uri;
    }

    public void setUri(String uri) {
        this.uri = uri;
    }

    public String getVersion() {
        return version;
    }

    public void setVersion(String version) {
        this.version = version;
    }

    @OneToMany(targetEntity = Parameter.class)
    @JoinColumn(name = "PROTOCOL_ID", nullable = true)
    // TODO: Remove
    //   @JoinTable(
    //         name = "Protocol2Property",
    //         joinColumns = {@JoinColumn(name = "PROTOCOL_ID")},
    //         inverseJoinColumns = @JoinColumn(name = "PROPERTY_ID")
    //   )
    public Collection<Parameter> getParameters() {
        return Collections.unmodifiableCollection(parameters);
    }

    public void addParameter(Parameter parameter) {
        this.parameters.add(parameter);
    }

    protected void setParameters(Collection<Parameter> parameters) {
        this.parameters = parameters;
    }

    public boolean removeParameter(Parameter parameter) {
        return this.parameters.remove(parameter);
    }

    public Parameter findParameterByName(String name) {
        for (Parameter param : getParameters()) {
            if (param != null && name.equals(param.getValue()))
                return param;
        }
        return null;
    }

    @OneToMany(targetEntity = ProtocolComponent.class)
    @JoinColumn(name = "protocol_id", nullable = true)
    public Collection<ProtocolComponent> getComponents() {
        return Collections.unmodifiableCollection(components);
    }

    protected void setComponents(Collection<ProtocolComponent> components) {
        this.components = components;
    }

    public void addComponent(ProtocolComponent component) {
        components.add(component);
    }

    public boolean equals(Object o) {
        if (this == o)
            return true;
        if (o == null || getClass() != o.getClass())
            return false;
        if (!super.equals(o))
            return false;

        Protocol protocol = (Protocol) o;

        if (description != null ? !description.equals(protocol.description) : protocol.description != null)
            return false;
        if (!name.equals(protocol.name))
            return false;
        if (parameters != null ? !parameters.equals(protocol.parameters) : protocol.parameters != null)
            return false;
        if (components != null ? !components.equals(protocol.components) : protocol.components != null)
            return false;
        if (type != null ? !type.equals(protocol.type) : protocol.type != null)
            return false;

        return true;
    }

    public int hashCode() {
        int result = super.hashCode();
        result = 31 * result + name.hashCode();
        result = 31 * result + (type != null ? type.hashCode() : 0);
        result = 31 * result + (description != null ? description.hashCode() : 0);
        result = 31 * result + (parameters != null ? parameters.hashCode() : 0);
        result = 31 * result + (components != null ? components.hashCode() : 0);
        return result;
    }

    public String toString() {
        return "Protocol{" + "id=" + getId() + ", acc='" + getAcc() + '\'' + ", name='" + name + "'" + ", type="
                + type + ", uri='" + uri + "'" + ", version='" + version + "'" + ", description='"
                + StringUtils.substring(description, 0, 20) + '\'' + ", parameters=" + parameters + ", components="
                + components + '}';
    }

}