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package org.apache.ctakes.fhir.cr;

import org.apache.ctakes.core.util.RelationArgumentUtil;
import org.apache.ctakes.fhir.element.FhirElementParser;
import org.apache.ctakes.fhir.resource.*;
import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;

import java.io.IOException;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import static org.apache.ctakes.fhir.element.FhirElementFactory.CTAKES_FHIR_URL;
import static org.apache.ctakes.fhir.element.FhirElementFactory.RELATION_EXT_PREFIX;
import static org.apache.ctakes.fhir.resource.AnnotationCreator.ID_NAME_ANNOTATION;
import static org.apache.ctakes.fhir.resource.BaseTokenCreator.ID_NAME_BASE_TOKEN;
import static org.apache.ctakes.fhir.resource.IdentifiedAnnotationCreator.ID_NAME_IDENTIFIED_ANNOTATION;
import static org.apache.ctakes.fhir.resource.ParagraphCreator.ID_NAME_PARAGRAPH;
import static org.apache.ctakes.fhir.resource.SectionCreator.ID_NAME_SECTION;
import static org.apache.ctakes.fhir.resource.SentenceCreator.ID_NAME_SENTENCE;

/**
 * @author SPF , chip-nlp
 * @version %I%
 * @since 5/1/2020
 */
final public class BundleParser {

   private BundleParser() {
   }


   static public void parseBundle( final JCas jCas, final Bundle bundle ) throws IOException {
      final CompositionParser compositionParser = new CompositionParser();
      final SectionParser sectionParser = new SectionParser();
      final ParagraphParser paragraphParser = new ParagraphParser();
      final SentenceParser sentenceParser = new SentenceParser();
      final BaseTokenParser baseTokenParser = new BaseTokenParser();
      final AnnotationParser annotationParser = new AnnotationParser();
      final IdentifiedAnnotationParser iaParser = new IdentifiedAnnotationParser();
      // Build map of resources to annotations, sections, etc.
      final List entries = bundle.getEntry();
      final Map resourceAnnotations = parseResources( jCas, entries,
            compositionParser, sectionParser, paragraphParser, sentenceParser, baseTokenParser,
            annotationParser, iaParser );

      // Go through the (Basic) entries in the map and build relations
      for ( Map.Entry resourceAnnotation : resourceAnnotations.entrySet() ) {
         if ( !Basic.class.isInstance( resourceAnnotation.getKey() ) ) {
            continue;
         }
         final Basic basic = (Basic)resourceAnnotation.getKey();
         final List extensions = basic.getExtension();
         for ( Extension extension : extensions ) {
            final String url = extension.getUrl();
            if ( url.startsWith( CTAKES_FHIR_URL + RELATION_EXT_PREFIX ) ) {
               final Type type = extension.getValue();
               if ( type instanceof Reference ) {
                  final IBaseResource resource = ((Reference)type).getResource();
                  final Annotation target = resourceAnnotations.get( resource );
                  if ( target != null ) {
                     createRelation( jCas, url, resourceAnnotation.getValue(), target );
                  }
               }
            }
         }
      }

      // TODO build Map> with coref chain index to annotations that belong from the Basic Extensions
   }


   static private Map parseResources( final JCas jCas,
                                                                 final List entries,
                                                                 final CompositionParser compositionParser,
                                                                 final SectionParser sectionParser,
                                                                 final ParagraphParser paragraphParser,
                                                                 final SentenceParser sentenceParser,
                                                                 final BaseTokenParser baseTokenParser,
                                                                 final AnnotationParser annotationParser,
                                                                 final IdentifiedAnnotationParser iaParser ) {
      final Map resourceAnnotations = new HashMap<>( entries.size() );
      for ( Bundle.BundleEntryComponent entry : entries ) {
         final IBaseResource resource = entry.getResource();
         final Annotation annotation = parseResource( jCas, resource,
               compositionParser, sectionParser, paragraphParser, sentenceParser, baseTokenParser,
               annotationParser, iaParser );
         if ( annotation != null ) {
            resourceAnnotations.put( resource, annotation );
         }
      }
      return resourceAnnotations;
   }

   static private Annotation parseResource( final JCas jCas,
                                            final IBaseResource resource,
                                            final CompositionParser compositionParser,
                                            final SectionParser sectionParser,
                                            final ParagraphParser paragraphParser,
                                            final SentenceParser sentenceParser,
                                            final BaseTokenParser baseTokenParser,
                                            final AnnotationParser annotationParser,
                                            final IdentifiedAnnotationParser iaParser ) {
      if ( resource instanceof Composition ) {
         final Narrative narrative = ((Composition)resource).getText();
         final XhtmlNode html = narrative.getDiv();
         final String docText = html.allText();
         jCas.setDocumentText( docText );
         return null;
      }
      Annotation annotation = null;
      if ( resource instanceof Basic ) {
         final Basic basic = (Basic)resource;
         final String idName = FhirElementParser.getIdName( basic.getId() );
         switch ( idName ) {
            case ID_NAME_SECTION:
               annotation = sectionParser.parseResource( jCas, basic );
               break;
            case ID_NAME_PARAGRAPH:
               annotation = paragraphParser.parseResource( jCas, basic );
               break;
            case ID_NAME_SENTENCE:
               annotation = sentenceParser.parseResource( jCas, basic );
               break;
            case ID_NAME_BASE_TOKEN:
               annotation = baseTokenParser.parseResource( jCas, basic );
               break;
            case ID_NAME_ANNOTATION:
               annotation = annotationParser.parseResource( jCas, basic );
               break;
            case ID_NAME_IDENTIFIED_ANNOTATION:
               annotation = iaParser.parseResource( jCas, basic );
               break;
         }
         if ( annotation != null ) {
            annotation.addToIndexes();
            return annotation;
         }
      }
      return null;
   }

   static private void createRelation( final JCas jCas, final String url,
                                       final Annotation source, final Annotation target ) {
      if ( source instanceof IdentifiedAnnotation && target instanceof IdentifiedAnnotation ) {
         final String category = url.substring( (CTAKES_FHIR_URL + RELATION_EXT_PREFIX).length() );
         final BinaryTextRelation relation
               = RelationArgumentUtil.createRelation( jCas, (IdentifiedAnnotation)source, (IdentifiedAnnotation)target,
               category );
         relation.addToIndexes();
      }
   }


   // TODO
   static private void createCoreference( final JCas jCas, Collection marked ) {

   }


}