/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */

package org.biojava.nbio.ontology;

import org.biojava.nbio.ontology.utils.AssertionFailure;

import java.util.*;




/**
 * An ontology.
 *
 * <p>This is just a set of Term objects, and a set of
 * Triple objects describing relationships between these terms.
 * This class does not itself contain any reasoning functionality. Ontology is
 * a collection of facts, or axioms.</p>
 *
 * @author Thomas Down
 * @author Matthew Pocock
 *
 * @since 1.4
 */

public interface Ontology  {


        /**
         * Return the name of this ontology
         * @return the name of the ontology
         */

        public String getName();

        /** Set the name for this ontology
         *
         * @param name - the name
         *
         */
        public void setName(String name);

        /**
         * Return a human-readable description of this ontology, or the empty
         * string if none is available
         * @return the description of the term
         */

        public String getDescription();

        /** set the description of this ontology
         *
         * @param description
         */
        public void setDescription(String description);



        /**
         * Return all the terms in this ontology
         * @return a Set of all Terms of the ontology.
         */

        public Set<Term> getTerms();

        /**
         * Fetch the term with the specified name.
         * @param name the name of the term
         *
         * @return The term named <code>name</code>
         * @throws NoSuchElementException if no term exists with that name
         */

        public Term getTerm(String name);

        /**
         * Return all triples from this ontology which match the supplied
         * pattern.  If any of the parameters of this method are <code>null</code>,
         * they are treated as wildcards.
         *
         * @param subject The subject to search for, or <code>null</code>
         * @param object The object to search for, or <code>null</code>
         * @param predicate The relationship to search for, or <code>null</code>.
         * @return a Set of triples
         */

        public Set<Triple> getTriples(Term subject, Term object, Term predicate);

        /**
         * Return the associated OntologyOps.
         *
         * This method should be implemented by ontology
         * implementors to allow OntoTools
         * to get optimized access to some usefull ontology operations. It is not
         * intended that users will ever invoke this. A sensible dumb implementation
         * of this would return a per-ontology instance of DefaultOps.
         *
         * @return the OntologyOps instance associated with this instance.
         */

        public OntologyOps getOps();

        /**
         * Create a new term in this ontology.
         *
         * @param name The name of the term (must be unique))
         * @throws IllegalArgumentException if either <code>name</code> or
         *         <code>description</code> is <code>null</code>, or violates
         *         some other constraint of this implementation.
         * @throws AlreadyExistsException if a term of this name already exists
         * @return The newly created term.
         */

        public Term createTerm(String name)
                        throws
                        AlreadyExistsException

        ;

        /**
         * Create a new term in this ontology.
         *
         * @param name The name of the term (must be unique)
         * @param description A human-readable description (may be empty)
         * @throws IllegalArgumentException if either <code>name</code> or
         *         <code>description</code> is <code>null</code>, or violates
         *         some other constraint of this implementation.
         * @throws AlreadyExistsException if a term of this name already exists
         * @return The newly created term.
         */

        public Term createTerm(String name, String description)
                        throws
                        AlreadyExistsException

        ;

        /**
         * Create a new term in this ontology.
         *
         * @param name The name of the term (must be unique)
         * @param description A human-readable description (may be empty)
         * @param synonyms Some synonyms for this term.
         * @throws IllegalArgumentException if either <code>name</code> or
         *         <code>description</code> is <code>null</code>, or violates
         *         some other constraint of this implementation.
         * @throws AlreadyExistsException if a term of this name already exists
         * @return The newly created term.
         */

        public Term createTerm(String name, String description, Object[] synonyms)
                        throws
                        AlreadyExistsException

        ;

        /**
         * Create a new term in this ontology that is used as a variable.
         *
         * @param name The name of the term (must be unique)
         * @param description A human-readable description (may be empty)
         * @throws IllegalArgumentException if either <code>name</code> or
         *         <code>description</code> is <code>null</code>, or violates
         *         some other constraint of this implementation.
         * @throws AlreadyExistsException if a term of this name already exists
         * @return The newly created term.
         */

        public Variable createVariable(String name, String description)
                        throws
                        AlreadyExistsException

        ;

        /**
         * Create a view of a term from another ontology.  If the requested term
         * has already been imported under that name, this method returns the existing
         * RemoteTerm object. If the term that is being imported is itself a
         * RemoteTerm instance then first unwrap the term back to the orriginal
         * term it represents and then produce a RemoteTerm from that. If the term
         * being imported orriginated from this ontology, then return that term
         * unaltered.
         *
         * @param t  the Term to import
         * @param localName  the local name to import it under, optionally null
         * @return a Term
         * @throws IllegalArgumentException
         */

        public Term importTerm(Term t, String localName)
                

        ;

        /**
         * Creates a new Triple.
         *
         * @param subject     the subject Term
         * @param object      the object Term
         * @param predicate    the predicate Term
         * @param name        the name of the triple, or null
         * @param description the description of the triple, or null
         * @return  a new Triple over these three terms
         * @throws AlreadyExistsException if a triple already exists with the same
         *      subject, object and predicate, regardless of the name and description
         * @throws NullPointerException if subject, object or predicate are null
         * @throws IllegalArgumentException if subject, object or predicate are not all
         *      from the same ontology
         */
        public Triple createTriple(Term subject, Term object, Term predicate, String name, String description)
                        throws
                        AlreadyExistsException
                        ;

        /**
         * See if a triple exists in this ontology
         * @param subject
         * @param object
         * @param predicate
         * @return true if contained
         */

        public boolean containsTriple(Term subject, Term object, Term predicate);

        /**
         * Remove a term from an ontology, together with all triples which refer to it.
         * @param t
         */

        public void deleteTerm(Term t) ;

        /**
         * Determines if this ontology currently contains a term named <code>name</code>
         * @param name
         * @return true is contained
         */

        public boolean containsTerm(String name);

        /**
         * A basic in-memory implementation of an ontology
         *
         * @author Thomas Down
         * @author Matthew Pocock
         * @since 1.3
         */

        // AP: I am setting name and description to public changeable fields
        // e.g during parsing of an .obo file we don't know them when the ontology is instanciated
        public final class Impl

        implements Ontology, java.io.Serializable {
                /**
                 *
                 */
                private static final long serialVersionUID = -8064461497813727957L;
                private final Map<String,Term> terms;
                private final Set<Triple> triples;
                private final Map<Term, Set<Triple>> subjectTriples;
                private final Map<Term, Set<Triple>> objectTriples;
                private final Map<Term, Set<Triple>> relationTriples;
                private final Map<Term,RemoteTerm> remoteTerms;
                private final Set<Term> localRemoteTerms;

                private /*final*/ String name;
                private /*final*/ String description;
                private final OntologyOps ops;

                {
                        terms            = new HashMap<>();
                        triples          = new HashSet<>();
                        subjectTriples   = new HashMap<>();
                        objectTriples    = new HashMap<>();
                        relationTriples  = new HashMap<>();
                        remoteTerms      = new HashMap<>();
                        localRemoteTerms = new HashSet<>();
                }

                public Impl(String name, String description) {
                        this.name = name;
                        this.description = description;
                        ops = new DefaultOps() {
                                /**
                                 *
                                 */
                                private static final long serialVersionUID = -2135777733685713181L;

                                @Override
                                public Set<Term> getRemoteTerms() {
                                        return localRemoteTerms;
                                }
                        };
                }

                @Override
                public String getName() {
                        return name;
                }

                @Override
                public String getDescription() {
                        return description;
                }


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

                @Override
                public Set<Term> getTerms() {
                        return new HashSet<>(terms.values());
                }

                @Override
                public Term getTerm(String name)
                
                        {
                        Term t = terms.get(name);
                        if (t == null) {
                                throw new NoSuchElementException("No term named '" + name + "'");
                        } else {
                                return terms.get(name);
                        }
                                }

                @Override
                public Set<Triple> getTriples(Term subject, Term object, Term predicate) {
                        if(subject != null && subject.getOntology() != this) {
                                throw new IllegalArgumentException("Subject is not in this ontology: " + subject + " " + this);
                        }

                        if(object != null && object.getOntology() != this) {
                                throw new IllegalArgumentException("Object is not in this ontology: " + object + " " + this);
                        }

                        if(predicate != null && predicate.getOntology() != this) {
                                throw new IllegalArgumentException("Predicate is not in this ontology: " + predicate + " " + this);
                        }

                        if (subject != null) {
                                return filterTriples( subjectTriples.get(subject), null, object, predicate);
                        } else if (object != null) {
                                return filterTriples( objectTriples.get(object), subject, null, predicate);
                        } else if (predicate != null) {
                                return filterTriples( relationTriples.get(predicate), subject, object, null);
                        } else {
                                return filterTriples(triples, subject, object, predicate);
                        }
                }

                private Set<Triple> filterTriples(Set<Triple> base, Term subject, Term object, Term predicate) {
                        if (base == null) {
                                return Collections.EMPTY_SET;
                        } else if (subject == null && object == null && predicate == null) {
                                return Collections.unmodifiableSet(new HashSet<Triple>(base));
                        }

                        Set<Triple> retval = new HashSet<>();
                        for (Iterator<Triple> i = base.iterator(); i.hasNext(); ) {
                                Triple t = i.next();
                                if (subject != null && t.getSubject() != subject) {
                                        continue;
                                }
                                if (object != null && t.getObject() != object) {
                                        continue;
                                }
                                if (predicate != null && t.getPredicate() != predicate) {
                                        continue;
                                }
                                retval.add(t);
                        }
                        return retval;
                }

                private void addTerm(Term t)
                                throws AlreadyExistsException 
                        {
                        if (terms.containsKey(t.getName())) {
                                throw new AlreadyExistsException("Ontology " + getName() + " already contains " + t.toString());
                        }


                        terms.put(t.getName(), t);

                                }

                @Override
                public Term createTerm(String name)
                                throws AlreadyExistsException 
                        {
                        Term t = new Term.Impl(this, name);
                        addTerm(t);
                        return t;
                                }

                @Override
                public Term createTerm(String name, String description)
                                throws AlreadyExistsException 
                        {
                        Term t = new Term.Impl(this, name, description);
                        addTerm(t);
                        return t;
                                }

                @Override
                public Term createTerm(String name, String description, Object[] synonyms)
                                throws AlreadyExistsException 
                        {
                        Term t = new Term.Impl(this, name, description, synonyms);
                        addTerm(t);
                        return t;
                                }

                @Override
                public Variable createVariable(String name, String description)
                                throws
                                AlreadyExistsException

         {
                        Variable var = new Variable.Impl(this, name, description);
                        addTerm(var);
                        return var;
                }

                public OntologyTerm createOntologyTerm(Ontology o)
                                throws AlreadyExistsException
                                {
                        OntologyTerm ot = new OntologyTerm.Impl(this, o);
                        addTerm(ot);
                        return ot;
                                }


                @Override
                public Term importTerm(Term t, String name)
                
                        {
                        // unpack any potential indirection - belt & braces
                        while(t instanceof RemoteTerm) {
                                t = ((RemoteTerm) t).getRemoteTerm();
                        }

                        if(t.getOntology() == this) {
                                return t;
                        }

                        RemoteTerm rt = remoteTerms.get(t);
                        if (rt == null) {
                                rt = new RemoteTerm.Impl(this, t, name);
                                try {
                                        addTerm(rt);
                                } catch (AlreadyExistsException e) {
                                        throw new AssertionFailure("This term can not exist", e);
                                }
                                if(name == null) {
                                        remoteTerms.put(t, rt);
                                }
                                localRemoteTerms.add(rt);
                        }
                        return rt;
                                }

                @Override
                public void deleteTerm(Term t)

                {
                        String name = t.getName();
                        if (terms.get(name) != t) {
                                return; // Should this be an exception?
                        }

                        terms.remove(name);
                        if(t instanceof Triple) {
                                removeTriple((Triple) t);
                        }

                }

                @Override
                public boolean containsTerm(String name) {
                        return terms.containsKey(name);
                }

                private boolean containsTerm(Term t) {
                        return (terms.get(t.getName()) == t);
                }

                @Override
                public boolean containsTriple(Term subject, Term object, Term predicate) {
                        if(!(subject.getOntology() == this)) return false;
                        if(!(object.getOntology() == this)) return false;
                        if(!(predicate.getOntology() == this)) return false;

                        return triples.contains(new Triple.Impl(subject, object, predicate));
                }

                @Override
                public Triple createTriple(Term subject,
                                Term object,
                                Term predicate,
                                String name,
                                String description)
                                                throws
                                                AlreadyExistsException
                
                
                
                                        {
                        Triple t = new Triple.Impl(subject, object, predicate, name, description);
                        if (!containsTerm(subject)) {
                                throw new IllegalArgumentException("Ontology " + getName() + " doesn't contain " + subject);
                        }
                        if (!containsTerm(predicate)) {
                                throw new IllegalArgumentException("Ontology " + getName() + " doesn't contain " + predicate);
                        }
                        if (!containsTerm(object)) {
                                throw new IllegalArgumentException("Ontology " + getName() + " doesn't contain " + object);
                        }
                        if (triples.contains(t)) {
                                throw new AlreadyExistsException("Ontology " + getName() + " already contains " + t.toString());
                        }


                        addTerm(t);
                        addTriple(t);

                        return t;
                                                }

                private void addTriple(Triple t) {
                        triples.add(t);
                        pushTriple(subjectTriples, t.getSubject(), t);
                        pushTriple(objectTriples, t.getObject(), t);
                        pushTriple(relationTriples, t.getPredicate(), t);
                }

                private void pushTriple(Map<Term,Set<Triple>> m, Term key, Triple t) {
                        Set<Triple> s = m.get(key);
                        if (s == null) {
                                s = new HashSet<>();
                                m.put(key, s);
                        }
                        s.add(t);
                }

                private void removeTriple(Triple t) {
                        triples.remove(t);
                        pullTriple(subjectTriples, t.getSubject(), t);
                        pullTriple(objectTriples, t.getObject(), t);
                        pullTriple(relationTriples, t.getPredicate(), t);
                }

                private void pullTriple(Map<Term, Set<Triple>> subjectTriples2, Term key, Triple t) {
                        Set<Triple> s = subjectTriples2.get(key);
                        if (s != null) {
                                s.remove(t);
                        }
                }

                @Override
                public OntologyOps getOps() {
                        return ops;
                }

                @Override
                public String toString() {
                        return "ontology: " + getName();
                }

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

                }
        }
}