Taxonomy2.java

/**
 * Copyright 2014 Global Crop Diversity Trust
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *   http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 **/

package org.genesys.server.model.genesys;

import java.text.MessageFormat;
import java.util.Arrays;
import java.util.List;
import java.util.concurrent.atomic.AtomicBoolean;

import javax.persistence.Cacheable;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.FetchType;
import javax.persistence.JoinColumn;
import javax.persistence.Lob;
import javax.persistence.ManyToOne;
import javax.persistence.OneToMany;
import javax.persistence.PrePersist;
import javax.persistence.Table;
import javax.persistence.Transient;
import javax.persistence.UniqueConstraint;

import lombok.Getter;
import lombok.NoArgsConstructor;
import lombok.Setter;
import org.apache.commons.lang3.StringUtils;
import org.genesys.blocks.model.AuditedVersionedModel;
import org.genesys.server.api.model.Api1Constants;
import org.genesys.server.model.GlobalModel;
import org.genesys.server.model.grin.TaxonomySpecies;
import org.hibernate.annotations.Type;
import org.springframework.data.elasticsearch.annotations.Field;
import org.springframework.data.elasticsearch.annotations.FieldType;

import com.fasterxml.jackson.annotation.JsonIdentityInfo;
import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.annotation.JsonProperty.Access;
import com.fasterxml.jackson.annotation.ObjectIdGenerators;

@Cacheable
@Entity
// Add index on all fields
@Table(name = "taxonomy2", uniqueConstraints = { @UniqueConstraint(name="UK_taxonomy2", columnNames = { "genus", "species", "spAuthor", "subtaxa", "subtAuthor" }) })
@JsonIgnoreProperties(ignoreUnknown = true)
@JsonIdentityInfo(generator = ObjectIdGenerators.PropertyGenerator.class, property = "id", scope = Taxonomy2.class)
@Getter
@Setter
@NoArgsConstructor
public class Taxonomy2 extends AuditedVersionedModel implements GlobalModel {

	private static final long serialVersionUID = 8881324404490162933L;

	@Column(length = 500)
	private String rdfUri;

	@Column(nullable = false, length = 100)
	@JsonProperty(value = Api1Constants.Accession.GENUS)
	private String genus;

	@Column(nullable = false, length = 100)
	@JsonProperty(value = Api1Constants.Accession.SPECIES)
	private String species;

	@Column(length = 25)
	private String family;

	@Column(nullable = false, length = 100)
	@JsonProperty(value = Api1Constants.Accession.SPAUTHOR)
	private String spAuthor;

	@Column(nullable = false, length = 100)
	@Field(type = FieldType.Text)
	@JsonProperty(value = Api1Constants.Accession.SUBTAXA)
	private String subtaxa;

	@Column(nullable = false, length = 100)
	@JsonProperty(value = Api1Constants.Accession.SUBTAUTHOR)
	private String subtAuthor;

	@Column(nullable = false)
	@Lob
	@Type(type = "org.hibernate.type.TextType")
	private String taxonName;

	private Long taxGenus;

	private Long taxSpecies;
	
	@Transient
	@Field(type = FieldType.Keyword)
	@JsonInclude
	private String genusSpecies;

	@ManyToOne(cascade = {}, fetch = FetchType.EAGER, optional = true)
	@JoinColumn(name = "grinTaxonomySpecies")
	@JsonProperty(access = Access.READ_ONLY)
	@Field(type = FieldType.Object)
	@JsonIgnoreProperties({ "currentTaxonomySpecies", "taxonomyGenus" })
	private TaxonomySpecies grinTaxonomySpecies;

	@ManyToOne(cascade = {}, fetch = FetchType.EAGER, optional = true)
	@JoinColumn(name = "currentTaxonomySpecies")
	@JsonProperty(access = Access.READ_ONLY)
	@Field(type = FieldType.Object)
	@JsonIgnoreProperties({ "currentTaxonomySpecies", "taxonomyGenus" })
	private TaxonomySpecies currentTaxonomySpecies;

	@ManyToOne(cascade = {}, fetch = FetchType.EAGER, optional = true)
	@JoinColumn(name = "overrideTaxonomySpecies")
	@JsonIgnore
	private TaxonomySpecies overrideTaxonomySpecies;

	@OneToMany(cascade = {}, fetch = FetchType.LAZY, mappedBy = "taxonomy")
	@JsonIgnore
	private List<Accession> accessions;

	public Taxonomy2(Taxonomy2 taxonomy) {
		if (taxonomy != null) {
			this.genus = taxonomy.genus;
			this.species = taxonomy.species;
			this.spAuthor = taxonomy.spAuthor;
			this.subtaxa = taxonomy.subtaxa;
			this.subtAuthor = taxonomy.subtAuthor;
		}
	}

	@PrePersist
	private void prePersist() {
		this.taxonName = getTaxonName();
	}
	
	public String getGenusSpecies() {
		return this.genus + " " + this.species;
	}

	public String getTaxonName() {
		final StringBuilder sb = new StringBuilder();
		sb.append(genus).append(" ").append(species);
		if (StringUtils.isNotBlank(spAuthor)) {
			sb.append(" ").append(spAuthor);
		}
		if (StringUtils.isNotBlank(subtaxa)) {
			sb.append(" ").append(subtaxa);
		}
		if (StringUtils.isNotBlank(subtAuthor)) {
			sb.append(" ").append(subtAuthor);
		}
		return sb.toString();
	}
	
	public String getTaxonNameHtml() {
		final StringBuilder sb = new StringBuilder();
		sb.append("<i>").append(genus).append("</i>");
		if (species.equals("sp.") || species.equals("spp.")) {
			sb.append(" ").append(species);
		} else {
			sb.append(" <i>").append(species).append("</i>");
		}
		if (StringUtils.isNotBlank(spAuthor)) {
			sb.append(" ").append(spAuthor);
		}
		if (StringUtils.isNotBlank(subtaxa)) {
			sb.append(" ").append(getSubtaxaHtml());
			if (StringUtils.isNotBlank(subtAuthor)) {
				sb.append(" ").append(subtAuthor);
			}
		}
		return sb.toString();
	}

	public String getSubtaxaHtml() {
		if (StringUtils.isNotBlank(subtaxa)) {
			final StringBuilder sb = new StringBuilder();
			final AtomicBoolean inLatin = new AtomicBoolean(false);
			Arrays.stream(subtaxa.split("\\s+")).forEach((part) -> {
				if (part.endsWith(".") || part.toLowerCase().equals("group")) {
					sb.append(" ").append(part);
					inLatin.set(true);
				} else {
					if (inLatin.get()) {
						sb.append(" <i>").append(part).append("</i>");
					} else {
						sb.append(" ").append(part);
					}
				}
			});
			return sb.toString().trim().replaceAll("</i> <i>", " ");
		}
		return null;
	}

	public void setTaxonName(String taxonName) {
		// Ignore what they provide
		this.taxonName = getTaxonName();
	}

	// public List<CropTaxonomy> getCropTaxonomies() {
	// return cropTaxonomies;
	// }
	//
	// public void setCropTaxonomies(List<CropTaxonomy> cropTaxonomies) {
	// this.cropTaxonomies = cropTaxonomies;
	// }

	public boolean sameAs(Taxonomy2 taxonomy) {
		return taxonomy == null ? false : getId().equals(taxonomy.getId());
	}

	public Long getTaxGenus() {
		return this.taxGenus == null ? this.getId() : this.taxGenus;
	}
	
	public Long getTaxSpecies() {
		return this.taxSpecies == null ? this.getId() : this.taxSpecies;
	}
	
	@Override
	public String toString() {
		return MessageFormat.format("Tax id={0} taxonName={1} genus={2} sp={3} spauthor={4} subtaxa={5} subtauthor={6}", getId(), getTaxonName(), genus, species,
				spAuthor, subtaxa, subtAuthor);
	}

	/**
	 * Clean up nulls and stuff...
	 * 
	 * @return
	 */
	public Taxonomy2 sanitize() {
		genus = StringUtils.trimToEmpty(genus);
		species = StringUtils.trimToEmpty(species);
		spAuthor = StringUtils.trimToEmpty(spAuthor);
		subtaxa = StringUtils.trimToEmpty(subtaxa);
		subtAuthor = StringUtils.trimToEmpty(subtAuthor);

		if (StringUtils.isBlank(species) || "sp".equalsIgnoreCase(species) || "spp".equalsIgnoreCase(species) || "spp.".equalsIgnoreCase(species)) {
			species = "sp.";
		}

		// Force blank subtAuthor when subtaxa is blank
		if (StringUtils.isBlank(subtaxa)) {
			subtAuthor = "";
		}

		return this;
	}

	public boolean equalTo(Taxonomy2 other) {
		if (other == null) {
			return false;
		}
		if (! StringUtils.equalsIgnoreCase(genus, other.genus)) {
			return false;
		}
		if (! StringUtils.equalsIgnoreCase(species, other.species)) {
			return false;
		}
		if (! StringUtils.equalsIgnoreCase(spAuthor, other.spAuthor)) {
			return false;
		}
		if (! StringUtils.equalsIgnoreCase(subtaxa, other.subtaxa)) {
			return false;
		}
		if (! StringUtils.equalsIgnoreCase(subtAuthor, other.subtAuthor)) {
			return false;
		}

		return true;
	}

	@Override
	public boolean canEqual(Object other) {
		return other instanceof Taxonomy2;
	}
}