Java tutorial
/* * This is eMonocot, a global online biodiversity information resource. * * Copyright 20112015 The Board of Trustees of the Royal Botanic Gardens, Kew and The University of Oxford * * eMonocot is free software: you can redistribute it and/or modify it under the terms of the * GNU Affero General Public License as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. * * eMonocot is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even * the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Affero General Public License for more details. * * The complete text of the GNU Affero General Public License is in the source repository as the file * COPYING. It is also available from <http://www.gnu.org/licenses/>. */ package org.emonocot.model; import java.util.ArrayList; import java.util.HashSet; import java.util.List; import java.util.Set; import javax.persistence.Entity; import javax.persistence.FetchType; import javax.persistence.GeneratedValue; import javax.persistence.GenerationType; import javax.persistence.Id; import javax.persistence.JoinColumn; import javax.persistence.JoinTable; import javax.persistence.Lob; import javax.persistence.ManyToMany; import javax.persistence.ManyToOne; import javax.persistence.OneToMany; import javax.persistence.OrderBy; import javax.persistence.Transient; import org.apache.solr.common.SolrInputDocument; import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.databind.annotation.JsonDeserialize; import com.fasterxml.jackson.databind.annotation.JsonSerialize; import org.emonocot.model.constants.MediaType; import org.emonocot.model.marshall.json.ReferenceDeserializer; import org.emonocot.model.marshall.json.ReferenceSerializer; import org.emonocot.model.marshall.json.TaxonDeserializer; import org.emonocot.model.marshall.json.TaxonSerializer; import org.hibernate.annotations.Cascade; import org.hibernate.annotations.CascadeType; import org.hibernate.annotations.Where; @Entity public class PhylogeneticTree extends Multimedia { /** * */ private static final long serialVersionUID = 6377124432983928528L; private Long id; private Set<Taxon> taxa = new HashSet<Taxon>(); private Set<Taxon> leaves = new HashSet<Taxon>(); private Set<Annotation> annotations = new HashSet<Annotation>(); private String phylogeny; private List<Comment> comments = new ArrayList<Comment>(); private Long numberOfExternalNodes; private Reference bibliographicReference; private boolean hasBranchLengths; public Long getNumberOfExternalNodes() { return numberOfExternalNodes; } public void setNumberOfExternalNodes(Long numberOfExternalNodes) { this.numberOfExternalNodes = numberOfExternalNodes; } @ManyToOne(fetch = FetchType.LAZY) @Cascade({ CascadeType.SAVE_UPDATE }) @JsonSerialize(using = ReferenceSerializer.class) public Reference getBibliographicReference() { return bibliographicReference; } @JsonDeserialize(using = ReferenceDeserializer.class) public void setBibliographicReference(Reference bibliographicReference) { this.bibliographicReference = bibliographicReference; } @Override @Id @GeneratedValue(generator = "table-hilo", strategy = GenerationType.TABLE) public Long getId() { return id; } @Override @OneToMany(fetch = FetchType.LAZY, orphanRemoval = true) @JoinColumn(name = "annotatedObjId") @Where(clause = "annotatedObjType = 'PhylogeneticTree'") @Cascade({ CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE }) @JsonIgnore public Set<Annotation> getAnnotations() { return annotations; } @Override public void setAnnotations(Set<Annotation> annotations) { this.annotations = annotations; } @Override @ManyToMany(fetch = FetchType.LAZY) @JoinTable(name = "Taxon_PhylogeneticTree", joinColumns = { @JoinColumn(name = "trees_id") }, inverseJoinColumns = { @JoinColumn(name = "Taxon_id") }) @Cascade({ CascadeType.SAVE_UPDATE, CascadeType.MERGE }) @JsonSerialize(contentUsing = TaxonSerializer.class) public Set<Taxon> getTaxa() { return taxa; } @Override @JsonDeserialize(contentUsing = TaxonDeserializer.class) public void setTaxa(Set<Taxon> taxa) { this.taxa = taxa; } @ManyToMany(fetch = FetchType.LAZY) @JoinTable(name = "PhylogeneticTree_Taxon", joinColumns = { @JoinColumn(name = "PhylogeneticTree_id") }, inverseJoinColumns = { @JoinColumn(name = "leaves_id") }) @Cascade({ CascadeType.SAVE_UPDATE, CascadeType.MERGE }) @JsonSerialize(contentUsing = TaxonSerializer.class) public Set<Taxon> getLeaves() { return leaves; } @JsonDeserialize(contentUsing = TaxonDeserializer.class) public void setLeaves(Set<Taxon> leaves) { this.leaves = leaves; } @Lob public String getPhylogeny() { return phylogeny; } public void setPhylogeny(String phylogeny) { this.phylogeny = phylogeny; } public void setHasBranchLengths(boolean hasBranchLengths) { this.hasBranchLengths = hasBranchLengths; } public boolean getHasBranchLengths() { return hasBranchLengths; } @OneToMany(fetch = FetchType.LAZY, orphanRemoval = true) @JoinColumn(name = "commentPage_id") @OrderBy("created DESC") @Where(clause = "commentPage_type = 'PhylogeneticTree'") @Cascade({ CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE }) @JsonIgnore public List<Comment> getComments() { return comments; } /** * @param comments - Comments made about this tree */ @JsonIgnore public void setComments(List<Comment> comments) { this.comments = comments; } public void setId(Long id) { this.id = id; } /* (non-Javadoc) * @see org.emonocot.model.Multimedia#getType() */ @Override @Transient public MediaType getType() { return MediaType.InteractiveResource; } @Override public SolrInputDocument toSolrInputDocument() { SolrInputDocument sid = super.toSolrInputDocument(); //sid.addField("phylogeny.title_t", getTitle()); //addField(sid,"phylogeny.creator_t", getCreator()); //addField(sid,"phylogeny.description_t", getDescription()); StringBuilder summary = new StringBuilder().append(getTitle()).append(" ").append(getCreator()).append(" ") .append(getDescription()); if (getTaxa() != null) { boolean first = true; for (Taxon t : getTaxa()) { if (first) { //addField(sid,"taxon.class_s", t.getClazz()); //addField(sid,"taxon.kingdom_s", t.getKingdom()); //addField(sid,"taxon.phylum_s", t.getPhylum()); addField(sid, "taxon.subgenus_s", t.getSubgenus()); addField(sid, "taxon.order_s", t.getOrder()); } addField(sid, "taxon.family_ss", t.getFamily()); addField(sid, "taxon.genus_ss", t.getGenus()); addField(sid, "taxon.subfamily_ss", t.getSubfamily()); addField(sid, "taxon.subtribe_ss", t.getSubtribe()); addField(sid, "taxon.tribe_ss", t.getTribe()); summary.append(" ").append(t.getClazz()).append(" ").append(t.getClazz()).append(" ") .append(t.getFamily()).append(" ").append(t.getGenus()).append(" ").append(t.getKingdom()) .append(" ").append(t.getOrder()).append(" ").append(t.getPhylum()).append(" ") .append(t.getSubfamily()).append(" ").append(t.getSubgenus()).append(" ") .append(t.getSubtribe()).append(" ").append(t.getTribe()); first = false; } } sid.addField("searchable.solrsummary_t", summary.toString()); return sid; } }