Sample.java

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 * and open the template in the editor.
 */
package io.seqware.webservice.generated.model;

import com.sun.xml.bind.CycleRecoverable;
import java.io.Serializable;
import java.sql.Timestamp;
import java.util.Collection;
import java.util.Date;
import javax.persistence.Basic;
import javax.persistence.CascadeType;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.EntityManager;
import javax.persistence.EntityManagerFactory;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
import javax.persistence.JoinColumn;
import javax.persistence.JoinTable;
import javax.persistence.ManyToMany;
import javax.persistence.ManyToOne;
import javax.persistence.NamedQueries;
import javax.persistence.NamedQuery;
import javax.persistence.OneToMany;
import javax.persistence.Persistence;
import javax.persistence.PostLoad;
import javax.persistence.Query;
import javax.persistence.Table;
import javax.persistence.Temporal;
import javax.persistence.TemporalType;
import javax.persistence.Version;
import javax.validation.constraints.NotNull;
import javax.validation.constraints.Size;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.Marshaller;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlTransient;
import org.apache.log4j.Logger;

/**
 * 
 * @author boconnor
 */
@Entity
@Table(name = "sample")
@XmlRootElement
@NamedQueries({
        @NamedQuery(name = "Sample.findAll", query = "SELECT s FROM Sample s"),
        @NamedQuery(name = "Sample.findBySampleId", query = "SELECT s FROM Sample s WHERE s.sampleId = :sampleId"),
        @NamedQuery(name = "Sample.findByName", query = "SELECT s FROM Sample s WHERE s.name = :name"),
        @NamedQuery(name = "Sample.findByTitle", query = "SELECT s FROM Sample s WHERE s.title = :title"),
        @NamedQuery(name = "Sample.findByAlias", query = "SELECT s FROM Sample s WHERE s.alias = :alias"),
        @NamedQuery(name = "Sample.findByType", query = "SELECT s FROM Sample s WHERE s.type = :type"),
        @NamedQuery(name = "Sample.findByScientificName", query = "SELECT s FROM Sample s WHERE s.scientificName = :scientificName"),
        @NamedQuery(name = "Sample.findByCommonName", query = "SELECT s FROM Sample s WHERE s.commonName = :commonName"),
        @NamedQuery(name = "Sample.findByAnonymizedName", query = "SELECT s FROM Sample s WHERE s.anonymizedName = :anonymizedName"),
        @NamedQuery(name = "Sample.findByIndividualName", query = "SELECT s FROM Sample s WHERE s.individualName = :individualName"),
        @NamedQuery(name = "Sample.findByDescription", query = "SELECT s FROM Sample s WHERE s.description = :description"),
        @NamedQuery(name = "Sample.findByTaxonId", query = "SELECT s FROM Sample s WHERE s.taxonId = :taxonId"),
        @NamedQuery(name = "Sample.findByTags", query = "SELECT s FROM Sample s WHERE s.tags = :tags"),
        @NamedQuery(name = "Sample.findByAdapters", query = "SELECT s FROM Sample s WHERE s.adapters = :adapters"),
        @NamedQuery(name = "Sample.findByRegions", query = "SELECT s FROM Sample s WHERE s.regions = :regions"),
        @NamedQuery(name = "Sample.findByExpectedNumberRuns", query = "SELECT s FROM Sample s WHERE s.expectedNumberRuns = :expectedNumberRuns"),
        @NamedQuery(name = "Sample.findByExpectedNumberSpots", query = "SELECT s FROM Sample s WHERE s.expectedNumberSpots = :expectedNumberSpots"),
        @NamedQuery(name = "Sample.findByExpectedNumberReads", query = "SELECT s FROM Sample s WHERE s.expectedNumberReads = :expectedNumberReads"),
        @NamedQuery(name = "Sample.findBySkip", query = "SELECT s FROM Sample s WHERE s.skip = :skip"),
        @NamedQuery(name = "Sample.findByIsPublic", query = "SELECT s FROM Sample s WHERE s.isPublic = :isPublic"),
        @NamedQuery(name = "Sample.findBySwAccession", query = "SELECT s FROM Sample s WHERE s.swAccession = :swAccession"),
        @NamedQuery(name = "Sample.findByCreateTstmp", query = "SELECT s FROM Sample s WHERE s.createTstmp = :createTstmp"),
        @NamedQuery(name = "Sample.findByUpdateTstmp", query = "SELECT s FROM Sample s WHERE s.updateTstmp = :updateTstmp") })
public class Sample implements Serializable, CycleRecoverable {
    private static final long serialVersionUID = 1L;
    @Id
    @GeneratedValue(strategy = GenerationType.IDENTITY)
    @Basic(optional = false)
    @Column(name = "sample_id")
    private Integer sampleId;
    @Size(max = 2147483647)
    @Column(name = "name")
    private String name;
    @Size(max = 2147483647)
    @Column(name = "title")
    private String title;
    @Size(max = 2147483647)
    @Column(name = "alias")
    private String alias;
    @Size(max = 2147483647)
    @Column(name = "type")
    private String type;
    @Size(max = 2147483647)
    @Column(name = "scientific_name")
    private String scientificName;
    @Size(max = 2147483647)
    @Column(name = "common_name")
    private String commonName;
    @Size(max = 2147483647)
    @Column(name = "anonymized_name")
    private String anonymizedName;
    @Size(max = 2147483647)
    @Column(name = "individual_name")
    private String individualName;
    @Size(max = 2147483647)
    @Column(name = "description")
    private String description;
    @Column(name = "taxon_id")
    private Integer taxonId;
    @Size(max = 2147483647)
    @Column(name = "tags")
    private String tags;
    @Size(max = 2147483647)
    @Column(name = "adapters")
    private String adapters;
    @Size(max = 2147483647)
    @Column(name = "regions")
    private String regions;
    @Column(name = "expected_number_runs")
    private Integer expectedNumberRuns;
    @Column(name = "expected_number_spots")
    private Integer expectedNumberSpots;
    @Column(name = "expected_number_reads")
    private Integer expectedNumberReads;
    @Column(name = "skip")
    private Boolean skip;
    @Column(name = "is_public")
    private Boolean isPublic;
    @Column(name = "sw_accession", insertable = false, updatable = false)
    private Integer swAccession;
    @Basic(optional = false)
    @NotNull
    @Column(name = "create_tstmp")
    @Temporal(TemporalType.TIMESTAMP)
    private Date createTstmp;
    @Column(name = "update_tstmp")
    @Version
    private Timestamp updateTstmp;
    @JoinTable(name = "sample_hierarchy", joinColumns = { @JoinColumn(name = "parent_id", referencedColumnName = "sample_id") }, inverseJoinColumns = { @JoinColumn(name = "sample_id", referencedColumnName = "sample_id") })
    @ManyToMany
    private Collection<Sample> sampleCollection;
    @ManyToMany(mappedBy = "sampleCollection")
    private Collection<Sample> sampleCollection1;
    @OneToMany(mappedBy = "sampleId")
    private Collection<Lane> laneCollection;
    @JoinColumn(name = "owner_id", referencedColumnName = "registration_id")
    @ManyToOne
    private Registration ownerId;
    @JoinColumn(name = "organism_id", referencedColumnName = "organism_id")
    @ManyToOne
    private Organism organismId;
    @JoinColumn(name = "experiment_id", referencedColumnName = "experiment_id")
    @ManyToOne
    private Experiment experimentId;
    @OneToMany(cascade = CascadeType.ALL, mappedBy = "sampleId")
    private Collection<Ius> iusCollection;
    @OneToMany(cascade = CascadeType.ALL, mappedBy = "sampleId")
    private Collection<ProcessingSamples> processingSamplesCollection;
    @OneToMany(cascade = CascadeType.ALL, mappedBy = "sampleId")
    private Collection<SampleAttribute> sampleAttributeCollection;
    @OneToMany(mappedBy = "parentId")
    private Collection<SampleRelationship> sampleRelationshipCollection;
    @OneToMany(mappedBy = "childId")
    private Collection<SampleRelationship> sampleRelationshipCollection1;

    public Sample() {
    }

    public Sample(Integer sampleId) {
        this.sampleId = sampleId;
    }

    public Sample(Integer sampleId, Date createTstmp) {
        this.sampleId = sampleId;
        this.createTstmp = createTstmp;
    }

    public Integer getSampleId() {
        return sampleId;
    }

    public void setSampleId(Integer sampleId) {
        this.sampleId = sampleId;
    }

    public String getName() {
        return name;
    }

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

    public String getTitle() {
        return title;
    }

    public void setTitle(String title) {
        this.title = title;
    }

    public String getAlias() {
        return alias;
    }

    public void setAlias(String alias) {
        this.alias = alias;
    }

    public String getType() {
        return type;
    }

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

    public String getScientificName() {
        return scientificName;
    }

    public void setScientificName(String scientificName) {
        this.scientificName = scientificName;
    }

    public String getCommonName() {
        return commonName;
    }

    public void setCommonName(String commonName) {
        this.commonName = commonName;
    }

    public String getAnonymizedName() {
        return anonymizedName;
    }

    public void setAnonymizedName(String anonymizedName) {
        this.anonymizedName = anonymizedName;
    }

    public String getIndividualName() {
        return individualName;
    }

    public void setIndividualName(String individualName) {
        this.individualName = individualName;
    }

    public String getDescription() {
        return description;
    }

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

    public Integer getTaxonId() {
        return taxonId;
    }

    public void setTaxonId(Integer taxonId) {
        this.taxonId = taxonId;
    }

    public String getTags() {
        return tags;
    }

    public void setTags(String tags) {
        this.tags = tags;
    }

    public String getAdapters() {
        return adapters;
    }

    public void setAdapters(String adapters) {
        this.adapters = adapters;
    }

    public String getRegions() {
        return regions;
    }

    public void setRegions(String regions) {
        this.regions = regions;
    }

    public Integer getExpectedNumberRuns() {
        return expectedNumberRuns;
    }

    public void setExpectedNumberRuns(Integer expectedNumberRuns) {
        this.expectedNumberRuns = expectedNumberRuns;
    }

    public Integer getExpectedNumberSpots() {
        return expectedNumberSpots;
    }

    public void setExpectedNumberSpots(Integer expectedNumberSpots) {
        this.expectedNumberSpots = expectedNumberSpots;
    }

    public Integer getExpectedNumberReads() {
        return expectedNumberReads;
    }

    public void setExpectedNumberReads(Integer expectedNumberReads) {
        this.expectedNumberReads = expectedNumberReads;
    }

    public Boolean getSkip() {
        return skip;
    }

    public void setSkip(Boolean skip) {
        this.skip = skip;
    }

    public Boolean getIsPublic() {
        return isPublic;
    }

    public void setIsPublic(Boolean isPublic) {
        this.isPublic = isPublic;
    }

    public Integer getSwAccession() {
        return swAccession;
    }

    public void setSwAccession(Integer swAccession) {
        this.swAccession = swAccession;
    }

    public Date getCreateTstmp() {
        return createTstmp;
    }

    public void setCreateTstmp(Date createTstmp) {
        this.createTstmp = createTstmp;
    }

    public Timestamp getUpdateTstmp() {
        return updateTstmp;
    }

    public void setUpdateTstmp(Timestamp updateTstmp) {
        this.updateTstmp = updateTstmp;
    }

    public Collection<Sample> getSampleCollection() {
        return sampleCollection;
    }

    public void setSampleCollection(Collection<Sample> sampleCollection) {
        this.sampleCollection = sampleCollection;
    }

    public Collection<Sample> getSampleCollection1() {
        return sampleCollection1;
    }

    public void setSampleCollection1(Collection<Sample> sampleCollection1) {
        this.sampleCollection1 = sampleCollection1;
    }

    @XmlTransient
    public Collection<Lane> getLaneCollection() {
        return laneCollection;
    }

    public void setLaneCollection(Collection<Lane> laneCollection) {
        this.laneCollection = laneCollection;
    }

    public Registration getOwnerId() {
        return ownerId;
    }

    public void setOwnerId(Registration ownerId) {
        this.ownerId = ownerId;
    }

    public Organism getOrganismId() {
        return organismId;
    }

    public void setOrganismId(Organism organismId) {
        this.organismId = organismId;
    }

    public Experiment getExperimentId() {
        return experimentId;
    }

    public void setExperimentId(Experiment experimentId) {
        this.experimentId = experimentId;
    }

    @XmlTransient
    public Collection<Ius> getIusCollection() {
        return iusCollection;
    }

    public void setIusCollection(Collection<Ius> iusCollection) {
        this.iusCollection = iusCollection;
    }

    @XmlTransient
    public Collection<ProcessingSamples> getProcessingSamplesCollection() {
        return processingSamplesCollection;
    }

    public void setProcessingSamplesCollection(Collection<ProcessingSamples> processingSamplesCollection) {
        this.processingSamplesCollection = processingSamplesCollection;
    }

    @XmlTransient
    public Collection<SampleAttribute> getSampleAttributeCollection() {
        return sampleAttributeCollection;
    }

    public void setSampleAttributeCollection(Collection<SampleAttribute> sampleAttributeCollection) {
        this.sampleAttributeCollection = sampleAttributeCollection;
    }

    @XmlTransient
    public Collection<SampleRelationship> getSampleRelationshipCollection() {
        return sampleRelationshipCollection;
    }

    public void setSampleRelationshipCollection(Collection<SampleRelationship> sampleRelationshipCollection) {
        this.sampleRelationshipCollection = sampleRelationshipCollection;
    }

    @XmlTransient
    public Collection<SampleRelationship> getSampleRelationshipCollection1() {
        return sampleRelationshipCollection1;
    }

    public void setSampleRelationshipCollection1(Collection<SampleRelationship> sampleRelationshipCollection1) {
        this.sampleRelationshipCollection1 = sampleRelationshipCollection1;
    }

    @Override
    public int hashCode() {
        int hash = 0;
        hash += (sampleId != null ? sampleId.hashCode() : 0);
        return hash;
    }

    @Override
    public boolean equals(Object object) {
        // TODO: Warning - this method won't work in the case the id fields are not set
        if (!(object instanceof Sample)) {
            return false;
        }
        Sample other = (Sample) object;
        if ((this.sampleId == null && other.sampleId != null) || (this.sampleId != null && !this.sampleId.equals(other.sampleId))) {
            return false;
        }
        return true;
    }

    @Override
    public String toString() {
        return "io.seqware.webservice.model.Sample[ sampleId=" + sampleId + " ]";
    }

    /**
     * from http://wiki.eclipse.org/EclipseLink/Release/2.4.0/JAXB_RI_Extensions/Cycle_Recoverable
     * 
     * @param cntxt
     * @return
     */
    @Override
    public Object onCycleDetected(Context cntxt) {
        return this.getSampleId();
    }

    /**
     * For debugging (silly generated classes have no model base class) TODO: create a base class and fix this
     */
    public void toXml() {
        try {
            JAXBContext ctx = JAXBContext.newInstance(this.getClass());
            Marshaller marshaller = ctx.createMarshaller();
            marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
            marshaller.marshal(this, System.out);
        } catch (Exception e) {

            // catch exception
        }
    }

    @PostLoad
    public void loadRootSampleFlag() {
        Logger.getLogger(Sample.class).info(this.getSampleId() + ": Attempting to find root sample flag");
        EntityManagerFactory emFactory = Persistence.createEntityManagerFactory("io.seqware_seqware-admin-webservice_war_1.0-SNAPSHOTPU");
        EntityManager em = emFactory.createEntityManager();
        Query query = selectNullParentCountQuery(em, this.getSampleId());
        Long firstResult = (Long) query.getSingleResult();
        if (firstResult != null && firstResult > 0) {
            Logger.getLogger(Sample.class).info(this.getSampleId() + ": Found root sample flag");
            this.getSampleCollection1().add(null);
            return;
        }
        Logger.getLogger(Sample.class).info(this.getSampleId() + ": Did not find root sample flag");
    }

    public static Query selectNullParentCountQuery(EntityManager em, int id) {
        Query query = em.createNativeQuery("select count(*) from sample_hierarchy where sample_id = " + id + " and parent_id IS NULL;");
        return query;
    }
}