/*
    * The baseCode project
    *
    * Copyright (c) 2013 University of British Columbia
    *
    * 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 ubic.basecode.ontology.jena;
  
  import com.hp.hpl.jena.ontology.OntClass;
  import com.hp.hpl.jena.ontology.OntResource;
  import com.hp.hpl.jena.ontology.Restriction;
  import com.hp.hpl.jena.rdf.model.*;
  import com.hp.hpl.jena.util.iterator.ExtendedIterator;
  import ubic.basecode.ontology.jena.vocabulary.OBO;
  import ubic.basecode.ontology.model.AnnotationProperty;
  import ubic.basecode.ontology.model.OntologyIndividual;
  import ubic.basecode.ontology.model.OntologyRestriction;
  import ubic.basecode.ontology.model.OntologyTerm;
  
  import javax.annotation.Nullable;
  import java.util.*;
  import java.util.stream.Collectors;
  
  import static ubic.basecode.ontology.jena.JenaUtils.where;
  
  /**
   * Represents a class in an ontology
   *
   * @author Paul
   */
  public class OntologyTermImpl extends AbstractOntologyResource implements OntologyTerm {
  
      private static final String HAS_ALTERNATE_ID = "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId";
  
      /**
       * Ontology class underlying this term.
       */
      private final transient OntClass ontResource;
  
      /**
       * Extra sets of properties to use when navigating parents and children of a term.
       */
      private final transient Set<Restriction> additionalRestrictions;
  
      public OntologyTermImpl( OntClass resource, @Nullable Set<Restriction> additionalRestrictions ) {
          super( resource );
          this.ontResource = resource;
          this.additionalRestrictions = additionalRestrictions;
      }
  
      public OntologyTermImpl( OntClass resource, Set<Restriction> additionalRestrictions, double score ) {
          super( resource, score );
          this.ontResource = resource;
          this.additionalRestrictions = additionalRestrictions;
      }
  
      @Override
      public Collection<String> getAlternativeIds() {
          Collection<String> results = new HashSet<>();
  
          Property alternate = ResourceFactory.createProperty( HAS_ALTERNATE_ID );
          StmtIterator it = this.ontResource.listProperties( alternate );
          while ( it.hasNext() ) {
              Statement statement = it.next();
              results.add( statement.asTriple().getMatchObject().getLiteralLexicalForm() );
          }
  
          return results;
  
      }
  
      @Override
      public Collection<AnnotationProperty> getAnnotations() {
          Collection<AnnotationProperty> annots = new HashSet<>();
          StmtIterator iterator = ontResource.listProperties();
          // this is a little slow because we have to go through all statements for the term.
          while ( iterator.hasNext() ) {
              Statement state = iterator.next();
              OntResource res = state.getPredicate().as( OntResource.class );
              if ( res.isAnnotationProperty() ) {
                  com.hp.hpl.jena.ontology.AnnotationProperty p = res.asAnnotationProperty();
                  RDFNode n = state.getObject();
                  annots.add( new AnnotationPropertyImpl( p, n ) );
              }
          }
          return annots;
      }
  
      @Override
      public Collection<OntologyTerm> getChildren( boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes ) {
          return JenaUtils.getChildren( ontResource.getOntModel(), Collections.singleton( ontResource ), direct, includeAdditionalProperties ? additionalRestrictions : null )
                 .stream()
                 .map( o -> new OntologyTermImpl( o, additionalRestrictions ) )
                 .filter( o -> keepObsoletes || !o.isObsolete() )
                 .collect( Collectors.toSet() );
     }
 
     /*
      * (non-Javadoc)
      *
      * @see ubic.gemma.ontology.OntologyTerm#getComment()
      */
     @Override
     public String getComment() {
         String comment = this.ontResource.getComment( null );
         return comment == null ? "" : comment;
     }
 
     @Override
     public Collection<OntologyIndividual> getIndividuals( boolean direct ) {
         return this.ontResource.listInstances( direct )
                 .filterKeep( where( OntResource::isIndividual ) )
                 .mapWith( r -> ( OntologyIndividual ) new OntologyIndividualImpl( r.asIndividual(), additionalRestrictions ) )
                 .toSet();
     }
 
     @Override
     public String getLocalName() {
         return ontResource.getLocalName();
     }
 
     @Override
     public Object getModel() {
         return ontResource.getModel();
     }
 
     @Override
     public Collection<OntologyTerm> getParents( boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes ) {
         return JenaUtils.getParents( ontResource.getOntModel(), Collections.singleton( ontResource ), direct, includeAdditionalProperties ? additionalRestrictions : null )
                 .stream()
                 .map( o -> new OntologyTermImpl( o, additionalRestrictions ) )
                 .filter( o -> keepObsoletes || !o.isObsolete() )
                 .collect( Collectors.toSet() );
     }
 
     /**
      *
      */
     @Override
     public Collection<OntologyRestriction> getRestrictions() {
         /*
          * Remember that restrictions are superclasses.
          */
         Collection<OntologyRestriction> result = new HashSet<>();
         ExtendedIterator<OntClass> iterator = ontResource.listSuperClasses( false );
         while ( iterator.hasNext() ) {
             OntClass c = iterator.next();
             if ( c.isRestriction() ) {
                 result.add( RestrictionFactory.asRestriction( c.asRestriction(), additionalRestrictions ) );
             }
         }
 
         // Check superclasses for any ADDITIONAL restrictions.
         iterator = ontResource.listSuperClasses( false );
         while ( iterator.hasNext() ) {
             OntClass c = iterator.next();
 
             try {
                 c.asRestriction(); // throw it away, we already processed it above.
             } catch ( Exception e ) {
                 // not a restriction, but a superclass that might have restrictions
                 ExtendedIterator<OntClass> supClassesIt = c.listSuperClasses( false );
                 loop:
                 while ( supClassesIt.hasNext() ) {
                     OntClass sc = supClassesIt.next();
                     Restriction sr;
                     try {
                         sr = sc.asRestriction();
 
                         // only add it if the class doesn't already have one.
                         OntologyRestriction candidateRestriction = RestrictionFactory.asRestriction( sr, additionalRestrictions );
                         for ( OntologyRestriction restr : result ) {
                             if ( restr.getRestrictionOn().equals( candidateRestriction.getRestrictionOn() ) )
                                 continue loop;
                         }
                         result.add( candidateRestriction );
 
                     } catch ( Exception ex ) {
                         // superclass isn't a restriction.
                     }
                 }
             }
 
         }
 
         return result;
     }
 
     /*
      * (non-Javadoc)
      *
      * @see ubic.gemma.analysis.ontology.OntologyTerm#getTerm()
      */
     @Override
     public String getTerm() {
         String res = getLabel();
         if ( res == null ) {
             res = ontResource.toString();
         }
         return res;
     }
 
     @Override
     public boolean isObsolete() {
         return super.isObsolete() || ontResource.hasSuperClass( OBO.ObsoleteClass );
     }
 
     /*
      * (non-Javadoc)
      *
      * @see ubic.gemma.analysis.ontology.OntologyTerm#isRoot()
      */
     @Override
     public boolean isRoot() {
         return getParents( true, true, true ).isEmpty();
     }
 
     /*
      * (non-Javadoc)
      *
      * @see ubic.basecode.ontology.model.OntologyTerm#isTermObsolete()
      */
     @Override
     public boolean isTermObsolete() {
         return isObsolete();
     }
 }