Individual.java

/*
 * Copyright 2015-2016 OpenCB
 *
 * 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.opencb.opencga.catalog.models;

import org.opencb.opencga.catalog.models.acls.permissions.IndividualAclEntry;
import org.opencb.opencga.core.common.TimeUtils;

import java.util.*;

import static java.lang.Math.toIntExact;

/**
 * Created by jacobo on 11/09/14.
 */
public class Individual extends Annotable<IndividualAclEntry> {

    private long id;
    private String name;
    private long fatherId;
    private long motherId;
    private String family;
    private Sex sex;
    private KaryotypicSex karyotypicSex;
    private String ethnicity;
    private Species species;
    private Population population;
    private String dateOfBirth;
    private String creationDate;
    private Status status;
    private LifeStatus lifeStatus;
    private AffectationStatus affectationStatus;
    private List<OntologyTerm> ontologyTerms;

//    private List<IndividualAclEntry> acl;
//    private List<AnnotationSet> annotationSets;

    private Map<String, Object> attributes;

    public enum Sex {
        MALE, FEMALE, UNKNOWN, UNDETERMINED
    }

    public enum LifeStatus {
        ALIVE, ABORTED, DECEASED, UNBORN, STILLBORN, MISCARRIAGE, UNKNOWN
    }

    public enum AffectationStatus {
        AFFECTED, UNAFFECTED, UNKNOWN
    }

    public enum KaryotypicSex {
        UNKNOWN, XX, XY, XO, XXY, XXX, XXYY, XXXY, XXXX, XYY, OTHER
    }

    public Individual() {
        this(-1, null, -1, -1, null, null, null, new Species(), new Population(), new LinkedList<>(), new HashMap<>());
    }

    public Individual(long id, String name, long fatherId, long motherId, String family, Sex sex, String ethnicity, Species species,
                      Population population, List<AnnotationSet> annotationSets, Map<String, Object> attributes) {
        this(id, name, fatherId, motherId, family, sex, ethnicity, species, population, new Status(), Collections.emptyList(),
                annotationSets, attributes);
    }

    public Individual(long id, String name, long fatherId, long motherId, String family, Sex sex, String ethnicity, Species species,
                      Population population, Status status, List<IndividualAclEntry> acl, List<AnnotationSet> annotationSets,
                      Map<String, Object> attributes) {
        this(id, name, fatherId, motherId, family, sex, KaryotypicSex.UNKNOWN, ethnicity, species, population, "", TimeUtils.getTime(),
                status, LifeStatus.UNKNOWN, AffectationStatus.UNKNOWN, Collections.emptyList(), acl, annotationSets, attributes);

        if (sex == null) {
            this.sex = Sex.UNKNOWN;
        }

        if (this.sex.equals(Sex.MALE)) {
            this.karyotypicSex = KaryotypicSex.XY;
        } else if (this.sex.equals(Sex.FEMALE)) {
            this.karyotypicSex = KaryotypicSex.XX;
        } else {
            this.karyotypicSex = KaryotypicSex.UNKNOWN;
        }
    }

    @Deprecated
    public Individual(long id, String name, long fatherId, long motherId, String family, Sex sex, KaryotypicSex karyotypicSex,
                      String ethnicity, Species species, Population population, LifeStatus lifeStatus,
                      AffectationStatus affectationStatus) {
        this(id, name, fatherId, motherId, family, sex, karyotypicSex, ethnicity, species, population, lifeStatus, affectationStatus, "");
    }

    public Individual(long id, String name, long fatherId, long motherId, String family, Sex sex, KaryotypicSex karyotypicSex,
                      String ethnicity, Species species, Population population, LifeStatus lifeStatus,
                      AffectationStatus affectationStatus, String dateOfBirth) {
        this(id, name, fatherId, motherId, family, sex, karyotypicSex, ethnicity, species, population, dateOfBirth, TimeUtils.getTime(),
                new Status(), lifeStatus, affectationStatus, new LinkedList<>(), new LinkedList<>(), new LinkedList<>(),
                Collections.emptyMap());

        if (sex == null) {
            this.sex = Sex.UNKNOWN;
        }

        if (karyotypicSex == null) {
            this.karyotypicSex = KaryotypicSex.UNKNOWN;
        }

        if (population == null) {
            new Population();
        }

        if (species == null) {
            new Species();
        }
    }

    public Individual(long id, String name, long fatherId, long motherId, String family, Sex sex, KaryotypicSex karyotypicSex, String
            ethnicity, Species species, Population population, String dateOfBirth, String creationDate, Status status, LifeStatus
            lifeStatus, AffectationStatus affectationStatus, List<OntologyTerm> ontologyTerms, List<IndividualAclEntry> acl,
                      List<AnnotationSet> annotationSets, Map<String, Object> attributes) {
        this.id = id;
        this.name = name;
        this.fatherId = fatherId;
        this.motherId = motherId;
        this.family = family;
        this.sex = sex;
        this.karyotypicSex = karyotypicSex;
        this.ethnicity = ethnicity;
        this.species = species;
        this.population = population;
        this.dateOfBirth = dateOfBirth;
        this.creationDate = creationDate;
        this.status = status;
        this.lifeStatus = lifeStatus;
        this.affectationStatus = affectationStatus;
        this.ontologyTerms = ontologyTerms;
        this.acl = acl;
        this.annotationSets = annotationSets;
        this.attributes = attributes;
    }

    @Override
    public boolean equals(Object o) {
        if (this == o) {
            return true;
        }
        if (!(o instanceof Individual)) {
            return false;
        }

        Individual that = (Individual) o;

        if (id != that.id) {
            return false;
        }
        if (fatherId != that.fatherId) {
            return false;
        }
        if (motherId != that.motherId) {
            return false;
        }
        if (name != null ? !name.equals(that.name) : that.name != null) {
            return false;
        }
        if (family != null ? !family.equals(that.family) : that.family != null) {
            return false;
        }
        if (sex != that.sex) {
            return false;
        }
        if (ethnicity != null ? !ethnicity.equals(that.ethnicity) : that.ethnicity != null) {
            return false;
        }
        if (species != null ? !species.equals(that.species) : that.species != null) {
            return false;
        }
        if (population != null ? !population.equals(that.population) : that.population != null) {
            return false;
        }
        if (attributes != null ? !attributes.equals(that.attributes) : that.attributes != null) {
            return false;
        }

        return true;
    }

    @Override
    public int hashCode() {
        long result = id;
        result = 31 * result + (name != null ? name.hashCode() : 0);
        result = 31 * result + fatherId;
        result = 31 * result + motherId;
        result = 31 * result + (family != null ? family.hashCode() : 0);
        result = 31 * result + (sex != null ? sex.hashCode() : 0);
        result = 31 * result + (ethnicity != null ? ethnicity.hashCode() : 0);
        result = 31 * result + (species != null ? species.hashCode() : 0);
        result = 31 * result + (population != null ? population.hashCode() : 0);
        result = 31 * result + (attributes != null ? attributes.hashCode() : 0);
        return toIntExact(result);
    }


    public static class Species {

        private String taxonomyCode;
        private String scientificName;
        private String commonName;


        public Species() {
            this.taxonomyCode = "";
            this.scientificName = "";
            this.commonName = "";
        }

        public Species(String commonName, String scientificName, String taxonomyCode) {
            this.taxonomyCode = taxonomyCode;
            this.scientificName = scientificName;
            this.commonName = commonName;
        }

        @Override
        public String toString() {
            final StringBuilder sb = new StringBuilder("Species{");
            sb.append("taxonomyCode='").append(taxonomyCode).append('\'');
            sb.append(", scientificName='").append(scientificName).append('\'');
            sb.append(", commonName='").append(commonName).append('\'');
            sb.append('}');
            return sb.toString();
        }

        @Override
        public boolean equals(Object o) {
            if (this == o) {
                return true;
            }
            if (!(o instanceof Species)) {
                return false;
            }

            Species species = (Species) o;

            if (taxonomyCode != null ? !taxonomyCode.equals(species.taxonomyCode) : species.taxonomyCode != null) {
                return false;
            }
            if (scientificName != null ? !scientificName.equals(species.scientificName) : species.scientificName != null) {
                return false;
            }
            return !(commonName != null ? !commonName.equals(species.commonName) : species.commonName != null);

        }

        @Override
        public int hashCode() {
            int result = taxonomyCode != null ? taxonomyCode.hashCode() : 0;
            result = 31 * result + (scientificName != null ? scientificName.hashCode() : 0);
            result = 31 * result + (commonName != null ? commonName.hashCode() : 0);
            return result;
        }

        public String getTaxonomyCode() {
            return taxonomyCode;
        }

        public void setTaxonomyCode(String taxonomyCode) {
            this.taxonomyCode = taxonomyCode;
        }

        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 static class Population {

        private String name;
        private String subpopulation;
        private String description;


        public Population() {
            this.name = "";
            this.subpopulation = "";
            this.description = "";
        }

        public Population(String name, String subpopulation, String description) {
            this.name = name;
            this.subpopulation = subpopulation;
            this.description = description;
        }

        @Override
        public String toString() {
            final StringBuilder sb = new StringBuilder("Population{");
            sb.append("name='").append(name).append('\'');
            sb.append(", subpopulation='").append(subpopulation).append('\'');
            sb.append(", description='").append(description).append('\'');
            sb.append('}');
            return sb.toString();
        }

        @Override
        public boolean equals(Object o) {
            if (this == o) {
                return true;
            }
            if (!(o instanceof Population)) {
                return false;
            }

            Population that = (Population) o;

            if (name != null ? !name.equals(that.name) : that.name != null) {
                return false;
            }
            if (subpopulation != null ? !subpopulation.equals(that.subpopulation) : that.subpopulation != null) {
                return false;
            }
            return !(description != null ? !description.equals(that.description) : that.description != null);

        }

        @Override
        public int hashCode() {
            int result = name != null ? name.hashCode() : 0;
            result = 31 * result + (subpopulation != null ? subpopulation.hashCode() : 0);
            result = 31 * result + (description != null ? description.hashCode() : 0);
            return result;
        }

        public String getName() {
            return name;
        }

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

        public String getSubpopulation() {
            return subpopulation;
        }

        public void setSubpopulation(String subpopulation) {
            this.subpopulation = subpopulation;
        }

        public String getDescription() {
            return description;
        }

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


    @Override
    public String toString() {
        final StringBuilder sb = new StringBuilder("Individual{");
        sb.append("acl=").append(acl);
        sb.append(", id=").append(id);
        sb.append(", name='").append(name).append('\'');
        sb.append(", fatherId=").append(fatherId);
        sb.append(", annotationSets=").append(annotationSets);
        sb.append(", motherId=").append(motherId);
        sb.append(", family='").append(family).append('\'');
        sb.append(", sex=").append(sex);
        sb.append(", karyotypicSex=").append(karyotypicSex);
        sb.append(", ethnicity='").append(ethnicity).append('\'');
        sb.append(", species=").append(species);
        sb.append(", population=").append(population);
        sb.append(", dateOfBirth='").append(dateOfBirth).append('\'');
        sb.append(", creationDate='").append(creationDate).append('\'');
        sb.append(", status=").append(status);
        sb.append(", lifeStatus=").append(lifeStatus);
        sb.append(", affectationStatus=").append(affectationStatus);
        sb.append(", ontologyTerms=").append(ontologyTerms);
        sb.append(", attributes=").append(attributes);
        sb.append('}');
        return sb.toString();
    }

    public long getId() {
        return id;
    }

    public Individual setId(long id) {
        this.id = id;
        return this;
    }

    public String getName() {
        return name;
    }

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

    public long getFatherId() {
        return fatherId;
    }

    public Individual setFatherId(long fatherId) {
        this.fatherId = fatherId;
        return this;
    }

    public long getMotherId() {
        return motherId;
    }

    public Individual setMotherId(long motherId) {
        this.motherId = motherId;
        return this;
    }

    public String getFamily() {
        return family;
    }

    public Individual setFamily(String family) {
        this.family = family;
        return this;
    }

    public Sex getSex() {
        return sex;
    }

    public Individual setSex(Sex sex) {
        this.sex = sex;
        return this;
    }

    public KaryotypicSex getKaryotypicSex() {
        return karyotypicSex;
    }

    public Individual setKaryotypicSex(KaryotypicSex karyotypicSex) {
        this.karyotypicSex = karyotypicSex;
        return this;
    }

    public String getEthnicity() {
        return ethnicity;
    }

    public Individual setEthnicity(String ethnicity) {
        this.ethnicity = ethnicity;
        return this;
    }

    public Species getSpecies() {
        return species;
    }

    public Individual setSpecies(Species species) {
        this.species = species;
        return this;
    }

    public Population getPopulation() {
        return population;
    }

    public Individual setPopulation(Population population) {
        this.population = population;
        return this;
    }

    public String getCreationDate() {
        return creationDate;
    }

    public Individual setCreationDate(String creationDate) {
        this.creationDate = creationDate;
        return this;
    }

    public String getDateOfBirth() {
        return dateOfBirth;
    }

    public Individual setDateOfBirth(String dateOfBirth) {
        this.dateOfBirth = dateOfBirth;
        return this;
    }

    public Status getStatus() {
        return status;
    }

    public Individual setStatus(Status status) {
        this.status = status;
        return this;
    }


    public LifeStatus getLifeStatus() {
        return lifeStatus;
    }

    public Individual setLifeStatus(LifeStatus lifeStatus) {
        this.lifeStatus = lifeStatus;
        return this;
    }

    public AffectationStatus getAffectationStatus() {
        return affectationStatus;
    }

    public Individual setAffectationStatus(AffectationStatus affectationStatus) {
        this.affectationStatus = affectationStatus;
        return this;
    }

    public List<OntologyTerm> getOntologyTerms() {
        return ontologyTerms;
    }

    public Individual setOntologyTerms(List<OntologyTerm> ontologyTerms) {
        this.ontologyTerms = ontologyTerms;
        return this;
    }

    public Individual setAcl(List<IndividualAclEntry> acl) {
        this.acl = acl;
        return this;
    }

//    public List<AnnotationSet> getAnnotationSets() {
//        return annotationSets;
//    }
//
//    public Individual setAnnotationSets(List<AnnotationSet> annotationSets) {
//        this.annotationSets = annotationSets;
//        return this;
//    }

    public Map<String, Object> getAttributes() {
        return attributes;
    }

    public Individual setAttributes(Map<String, Object> attributes) {
        this.attributes = attributes;
        return this;
    }

}