/*
    * The baseCode project
    *
    * Copyright (c) 2012 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;
  
  import org.apache.commons.lang3.StringUtils;
  import org.junit.Test;
  import org.slf4j.Logger;
  import org.slf4j.LoggerFactory;
  import ubic.basecode.ontology.model.OntologyTerm;
  import ubic.basecode.ontology.providers.CellLineOntologyService;
  import ubic.basecode.ontology.providers.DiseaseOntologyService;
  import ubic.basecode.ontology.providers.NIFSTDOntologyService;
  
  import java.io.InputStream;
  import java.util.Collection;
  import java.util.zip.GZIPInputStream;
  
  import static java.util.Objects.requireNonNull;
  import static org.junit.Assert.*;
  
  /**
   * @author Paul
   */
  public class OntologyTermTest extends AbstractOntologyTest {
  
      private static final Logger log = LoggerFactory.getLogger( OntologyTermTest.class );
  
      @Test
      public void testGetChildren() throws Exception {
          // DOID:4159
          DiseaseOntologyService s = new DiseaseOntologyService();
          InputStream is = new GZIPInputStream( requireNonNull( this.getClass().getResourceAsStream( "/data/doid.short.owl.gz" ) ) );
          s.initialize( is, false );
  
          assertTrue( s.getAdditionalPropertyUris().contains( "http://purl.obolibrary.org/obo/BFO_0000050" ) );
          assertTrue( s.getAdditionalPropertyUris().contains( "http://www.obofoundry.org/ro/ro.owl#proper_part_of" ) );
  
          OntologyTerm t = s.getTerm( "http://purl.obolibrary.org/obo/DOID_4159" );
          assertNotNull( t );
  
          // test of getting basic properties thrown in here
          assertEquals( "skin cancer", t.getLabel() );
  
          Collection<OntologyTerm> children = t.getChildren( true );
          assertEquals( 2, children.size() );
          boolean found = false;
          for ( OntologyTerm par : children ) {
              if ( par.getUri().equals( "http://purl.obolibrary.org/obo/DOID_8923" ) ) {
                  found = true;
              }
          }
          assertTrue( found );
  
          Collection<OntologyTerm> allchildren = t.getChildren( false );
          found = false;
          assertEquals( 6, allchildren.size() );
          for ( OntologyTerm chil : allchildren ) {
              if ( chil.getUri().equals( "http://purl.obolibrary.org/obo/DOID_10054" ) ) {
                  found = true;
              }
              // exercise other things.
              log.info( "Annotations: " + StringUtils.join( chil.getAnnotations(), "," ) );
              log.info( "Comment: " + chil.getComment() );
              log.info( "Individuals: " + StringUtils.join( chil.getIndividuals(), "," ) );
              log.info( "Individuals: " + StringUtils.join( chil.getIndividuals( true ), "," ) );
              log.info( "Individuals: " + StringUtils.join( chil.getIndividuals( false ), "," ) );
              log.info( "Restrictions: " + StringUtils.join( chil.getRestrictions(), "," ) );
              log.info( "AlternativeIDs: " + StringUtils.join( chil.getAlternativeIds(), "," ) );
          }
          assertTrue( found );
      }
  
      /**
       * FIXME this uses NIF, which we are no longer using actively - not a big deal since this just tests mechanics
       */
      @Test
      public void testGetChildrenHasProperPart() throws Exception {
          NIFSTDOntologyService s = new NIFSTDOntologyService();
          InputStream is = new GZIPInputStream( requireNonNull( this.getClass().getResourceAsStream(
                  "/data/NIF-GrossAnatomy.small.owl.xml.gz" ) ) );
          s.initialize( is, false );
  
          OntologyTerm t = s.getTerm( "http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#birnlex_734" );
          assertNotNull( t );
  
          Collection<OntologyTerm> c = t.getChildren( true );
          assertEquals( 6, c.size() );
         // Dorsal hypothalamic area [birnlex_777]
         // Lateral hypothalamic area [birnlex_4037]
         // Medial forebrain bundle [birnlex_908]
         // Postcommissural fornix [birnlex_914]
         // Posterior hypothalamic region [birnlex_1651]
         // Dorsal longitudinal fasciculus of hypothalamus [birnlex_898]
         // Anterior hypothalamic region [birnlex_1005]
         // Intermediate hypothalamic region [birnlex_1015]
         // Regional part of hypothalamus [birnlex_995]
         OntologyTerm t1 = s.getTerm( "http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#birnlex_898" );
         assertNotNull( t1 );
         assertTrue( c.contains( t1 ) );
 
         Collection<OntologyTerm> c2 = t.getChildren( false );
         assertEquals( 7, c2.size() );
         OntologyTerm t2 = s.getTerm( "http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#birnlex_4037" );
         assertNotNull( t2 );
         assertTrue( c.contains( t2 ) );
     }
 
     @Test
     public void testGetParents() throws Exception {
 
         DiseaseOntologyService s = new DiseaseOntologyService();
         InputStream is = new GZIPInputStream( requireNonNull( this.getClass().getResourceAsStream( "/data/doid.short.owl.gz" ) ) );
 
         s.initialize( is, false );
 
         /*
          * Note that this test uses the 'new style' URIs for DO, but at this writing we actually use purl.org not
          * purl.obolibrary.org.
          */
 
         OntologyTerm t = s.getTerm( "http://purl.obolibrary.org/obo/DOID_10040" );
         assertNotNull( t );
         Collection<OntologyTerm> parents = t.getParents( true );
         assertEquals( 1, parents.size() );
         OntologyTerm p = parents.iterator().next();
         assertEquals( "http://purl.obolibrary.org/obo/DOID_8923", p.getUri() );
 
         Collection<OntologyTerm> parents2 = t.getParents( false );
         assertEquals( 7, parents2.size() );
         boolean found = false;
         for ( OntologyTerm par : parents2 ) {
             if ( par.getUri().equals( "http://purl.obolibrary.org/obo/DOID_0060122" ) ) {
                 found = true;
             }
 
             // exercise other things.
             log.info( "Annotations: " + StringUtils.join( par.getAnnotations(), "," ) );
             log.info( "Comment: " + par.getComment() );
             log.info( "Individuals: " + StringUtils.join( par.getIndividuals(), "," ) );
             log.info( "Individuals: " + StringUtils.join( par.getIndividuals( true ), "," ) );
             log.info( "Individuals: " + StringUtils.join( par.getIndividuals( false ), "," ) );
             log.info( "Restrictions: " + StringUtils.join( par.getRestrictions(), "," ) );
             log.info( "AlternativeIDs: " + StringUtils.join( par.getAlternativeIds(), "," ) );
         }
 
         assertTrue( found );
     }
 
     @Test
     public void testGetParentsHasProperPart() throws Exception {
         NIFSTDOntologyService s = new NIFSTDOntologyService();
 
         assertFalse( s.getProcessImports() );
 
         InputStream is = new GZIPInputStream( requireNonNull( this.getClass().getResourceAsStream(
                 "/data/NIF-GrossAnatomy.small.owl.xml.gz" ) ) );
         assertNotNull( is );
         s.initialize( is, false );
 
         // Mammillary princeps fasciculus: part of white matter, hypothalamus, etc.
         OntologyTerm t = s
                 .getTerm( "http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#birnlex_1492" );
 
         assertNotNull( t );
 
         Collection<OntologyTerm> parents = t.getParents( true );
         assertEquals( 3, parents.size() );
 
         // Nerve tract [birnlex_1649]
         // White matter [nlx_anat_101177]
         // Posterior hypothalamic region [birnlex_1651]
         boolean found = false;
         for ( OntologyTerm p : parents ) {
             if ( p.getUri().equals(
                     "http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#nlx_anat_101177" ) ) {
                 found = true;
             }
         }
         assertTrue( found );
         // Part of neuraxis [nlx_anat_1010010] x
         // Nerve tract [birnlex_1649] x
         // White matter [nlx_anat_101177] x
         // Posterior hypothalamic region [birnlex_1651] x
         // Forebrain [birnlex_1509] x
         // Hypothalamus [birnlex_734] x
         // Regional part of brain [birnlex_1167] x
         // Diencephalon [birnlex_1503] x
 
         Collection<OntologyTerm> parents2 = t.getParents( false );
         assertEquals( 14, parents2.size() );
 
         // does not includes 'continuant' and 'independent continuant' or parents of those terms.
         assertTrue( parents2.contains( s.getTerm( "http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#birnlex_1503" ) ) );
         assertFalse( parents2.contains( ( OntologyTerm ) s.getResource( "http://www.ifomis.org/bfo/1.1/snap#Continuant" ) ) );
     }
 
     @Test
     public void testRejectNonEnglish() throws Exception {
         CellLineOntologyService s = new CellLineOntologyService();
         InputStream is = new GZIPInputStream( requireNonNull( this.getClass().getResourceAsStream( "/data/clo_merged.sample.owl.xml.gz" ) ) );
         s.initialize( is, false );
 
         OntologyTerm t = s.getTerm( "http://purl.obolibrary.org/obo/CLO_0000292" );
         assertNotNull( t );
         assertEquals( "immortal larynx-derived cell line cell", t.getLabel() );
     }
 }