Paper.java

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package cedar.hepdata.model;

import java.util.*;
import javax.persistence.*;

@Entity
@Table(name="Papers")
public class Paper extends Storeable {
    @Id @GeneratedValue
    @Column(name="PAPER_ID")
    private Long _id;


    @Column(name="SpiresId", unique=true, nullable=true)
    private Long _spiresId = null;


    @Column(name="RedId", unique=true, nullable=true)
    private Long _redId = null;


    @Column(name="Title", unique=false, nullable=true)
    private String _title = "";


    @org.hibernate.annotations.CollectionOfElements
    @JoinTable(name="PaperExpts", joinColumns=@JoinColumn(name="PAPER_ID"))
    @org.hibernate.annotations.CollectionId(columns=@Column(name="PaperExptId"), type=@org.hibernate.annotations.Type(type="long"), generator="sequence")
    @org.hibernate.annotations.Sort(type=org.hibernate.annotations.SortType.NATURAL)
    private SortedSet<Experiment> _experiments = new TreeSet<Experiment>();


    @org.hibernate.annotations.CollectionOfElements
    @JoinTable(name="PaperAuthors", joinColumns=@JoinColumn(name="PAPER_ID"))
    @org.hibernate.annotations.Sort(type=org.hibernate.annotations.SortType.NATURAL)
    @org.hibernate.annotations.BatchSize(size=2)
    private SortedSet<String> _authors = new TreeSet<String>();


    @org.hibernate.annotations.CollectionOfElements
    @JoinTable(name="PaperRefs", joinColumns=@JoinColumn(name="PAPER_ID"))
    @org.hibernate.annotations.CollectionId(columns=@Column(name="PaperRefId"), type=@org.hibernate.annotations.Type(type="long"), generator="sequence")
    @org.hibernate.annotations.Sort(type=org.hibernate.annotations.SortType.NATURAL)
    private SortedSet<Reference> _references = new TreeSet<Reference>();


    @org.hibernate.annotations.CollectionOfElements
    @JoinTable(name="PaperComments", joinColumns=@JoinColumn(name="PAPER_ID"))
    @org.hibernate.annotations.IndexColumn(name="Posn")
    @Column(length=10000)
    private List<String> _comments = new Vector<String>();


    @org.hibernate.annotations.CollectionOfElements
    @JoinTable(name="PaperMods", joinColumns=@JoinColumn(name="PAPER_ID"))
    @org.hibernate.annotations.CollectionId(columns=@Column(name="PaperModId"), type=@org.hibernate.annotations.Type(type="long"), generator="sequence")
    @org.hibernate.annotations.Sort(type=org.hibernate.annotations.SortType.NATURAL)
    @org.hibernate.annotations.BatchSize(size=2)
    private SortedSet<Modification> _modifications = new TreeSet<Modification>();


    @OneToMany(mappedBy="_paper")
    @org.hibernate.annotations.Fetch(value=org.hibernate.annotations.FetchMode.SUBSELECT)
    @org.hibernate.annotations.Cascade(value={org.hibernate.annotations.CascadeType.ALL, org.hibernate.annotations.CascadeType.DELETE_ORPHAN})
    @org.hibernate.annotations.Sort(type=org.hibernate.annotations.SortType.NATURAL)
    @org.hibernate.annotations.BatchSize(size=5)
    private SortedSet<Dataset> _datasets = new TreeSet<Dataset>();




    public Paper() {}

    public Paper(String title) {
        setTitle(title);
    }

    public Paper(String title, Long spiresId) {
        this(title);
        setSpiresId(spiresId);
    }

    public Paper(String title, Integer spiresId) {
        this(title, new Long(spiresId));
    }




    public Long getSpiresId() {
        return _spiresId;
    }
    public Paper setSpiresId(Long spiresId) {
        _spiresId = spiresId;
        return this;
    }
    public Paper setSpiresId(Integer spiresId) {
        _spiresId = new Long(spiresId);
        return this;
    }


    public Long getRedId() {
        return _redId;
    }
    public Paper setRedId(Long redId) {
        _redId = redId;
        return this;
    }
    public Paper setRedId(Integer redId) {
        _redId = new Long(redId);
        return this;
    }



    public String getTitle() {
        return _title;
    }
    public Paper setTitle(String title) {
        _title = title;
        return this;
    }



    public SortedSet<Experiment> getExperiments() {
        return _experiments;
    }

    public Paper setExperiments(SortedSet<Experiment> experiments) {
        _experiments = experiments;
        return this;
    }

    public Paper addExperiment(Experiment experiment) {
        if (experiment != null) {
            _experiments.add(experiment);
        } else {
            log().warn("Tried to add a null experiment to a paper");
        }
        return this;
    }

    public Paper removeExperiment(Experiment experiment) {
        if (experiment != null) {
            _experiments.remove(experiment);
        } else {
            log().warn("Tried to remove a null experiment from a paper");
        }
        return this;
    }



    // Authors
    public SortedSet<String> getAuthors() {
        return _authors;
    }
    public Paper setAuthors(SortedSet<String> authors) {
        _authors = authors;
        return this;
    }
    public Paper addAuthor(String author) {
        if (author != null) {
            _authors.add(author);
        } else {
            log().warn("Tried to add a null author to a paper");
        }
        return this;
    }
    public Paper removeAuthor(String author) {
        if (author != null) {
            _authors.remove(author);
        } else {
            log().warn("Tried to remove a null author from a paper");
        }
        return this;
    }


    public List<String> getComments() {
        return _comments;
    }
    public Paper setComments(List<String> comments) {
        _comments = comments;
        return this;
    }
    public Paper addComment(String comment) {
        _comments.add(comment);
        return this;
    }



    public SortedSet<Dataset> getDatasets() {
        return _datasets;
    }

    public Dataset getDataset(Integer datasetId) {
        Dataset theDataset = null;
        for (Dataset d : getDatasets()) {
            if (d.getId().equals(datasetId)) {
                theDataset = d;
                break;
            }
        }
        return theDataset;
    }

    public Paper setDatasets(SortedSet<Dataset> datasets) {
        _datasets = datasets;
        return this;
    }

    public Paper setDatasets(Collection<Dataset> datasets) {
        setDatasets(new TreeSet(datasets));
        return this;
    }

    public Paper setDatasets(Dataset[] datasets) {
        setDatasets(Arrays.asList(datasets));
        return this;
    }

    public Paper addDataset(Dataset dataset) {
        if (dataset != null) {
            if (dataset.getId() == null) {
                int highestId = 0;
                if (getDatasets().size() > 0) {
                    highestId = getDatasets().last().getId();
                }
                log().debug("Incrementing dataset ID: " + (highestId + 1));
                dataset.setId(highestId + 1);
            }
            log().debug("Adding dataset: ID = " + dataset.getId());
            dataset.setPaper(this);
            _datasets.add(dataset);
        } else {
            log().warn("Tried to add null dataset to a paper");
        }
        return this;
    }

    public Paper removeDataset(Dataset dataset) {
        if (dataset != null) {
            dataset.setPaper(null); // Data orphaning
            _datasets.remove(dataset);
        } else {
            log().warn("Tried to remove a null dataset from a paper");
        }
        return this;
    }


    public SortedSet<Modification> getModifications() {
        return _modifications;
    }

    public Paper setModifications(SortedSet<Modification> modifications) {
        _modifications = modifications;
        return this;
    }

    public Paper addModification(Modification modification) {
        _modifications.add(modification);
        return this;
    }

    public Paper removeModification(Modification modification) {
        _modifications.remove(modification);
        return this;
    }



    public SortedSet<Reference> getReferences() {
        return _references;
    }

    public Paper setReferences(SortedSet<Reference> references) {
        _references = references;
        return this;
    }

    public Paper addReference(Reference reference) {
        _references.add(reference);
        return this;
    }

    public Paper removeReference(Reference reference) {
        _references.remove(reference);
        return this;
    }




    public String toString() {
        return toString(0);
    }


    public String toString(Integer indentBy) {
        StringBuffer s = new StringBuffer();
        String indent = "";
        for (int i  = 0; i < indentBy; ++i) indent += " ";

        // Title
        s.append(indent + "Title: ");
        if (getTitle() != null) {
            s.append(getTitle());
        } else {
            s.append("N/A");
        }

        // ID codes
        s.append("\n" + indent + "Spires ID: " + getSpiresId());
        if (getRedId() != null) {
            s.append("\n" + indent + "Reaction database ID: " + getRedId());
        }

        // Modifications
        s.append("\n" + indent + "Modifications: ");
        if (getModifications().size() == 0) {
            s.append("none");
        } else {
            for (Modification mod : getModifications()) {
                s.append("\n" + indent + mod.getTimestamp());
                s.append(" by " + mod.getModifier());
                if (mod.getComment() != null && mod.getComment().length() != 0)
                    s.append(": " + mod.getComment());
            }
        }

        // Comments
        s.append("\n" + indent + "Comments: ");
        if (getComments().size() == 0) {
            s.append("none");
        } else {
            for (String c : getComments()) s.append("\n" + c);
        }

        // Dataset (recursive toString)
        if (!getDatasets().isEmpty()) {
            s.append("\n" + indent + getDatasets().size() + " Datasets");
            for (Dataset ds : getDatasets()) {
                s.append("\n" + ds.toString(indentBy + 2));
            }
        }

        return s.toString();
    }
}

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