How to use

isCyclicRelationship

method

in

uk.ac.ebi.intact.bridges.ontologies.OntologyDocument

  /**
   * Used to exclude any document that does not have an "is_a" relationship or it is not a root node
   * (null relationship) or it is cyclic.
   * @param ontologyDocument
   * @return
   */
  public boolean accept(OntologyDocument ontologyDocument) {
    if (ontologyDocument.getRelationshipType() == null) {
      return true;
    }

    final String type = ontologyDocument.getRelationshipType();
    // note that the types are ordered by decreasing likelyhood of appearence to improve performance
    return (    type.equals( "OBO_REL:is_a" )
         || type.equals( "part_of" )
         || type.equals( "is_a" )
         || type.equals( "OBO_REL:part_of" )
        )
        && ! ontologyDocument.isCyclicRelationship();
  }
}

  /**
   * Used to exclude any document that does not have an "is_a" relationship or it is not a root node
   * (null relationship) or it is cyclic.
   * @param ontologyDocument
   * @return
   */
  public boolean accept(OntologyDocument ontologyDocument) {
    if (ontologyDocument.getRelationshipType() == null) {
      return true;
    }

    final String type = ontologyDocument.getRelationshipType();
    // note that the types are ordered by decreasing likelyhood of appearence to improve performance
    return (    type.equals( "OBO_REL:is_a" )
         || type.equals( "part_of" )
         || type.equals( "is_a" )
         || type.equals( "OBO_REL:part_of" )
        )
        && ! ontologyDocument.isCyclicRelationship();
  }
}

public void addDocument(OntologyDocument ontologyDoc) throws IOException {
  Document doc = new Document();
  doc.add(new Field(FieldName.ONTOLOGY, ontologyDoc.getOntology(), Field.Store.YES, Field.Index.UN_TOKENIZED));
  if (ontologyDoc.getParentId() != null) {
    doc.add(new Field(FieldName.PARENT_ID, ontologyDoc.getParentId(), Field.Store.YES, Field.Index.UN_TOKENIZED));
    doc.add(new Field(FieldName.PARENT_NAME, ontologyDoc.getParentName(), Field.Store.YES, Field.Index.TOKENIZED));
    doc.add(new Field(FieldName.PARENT_NAME_SORTABLE, ontologyDoc.getParentName(), Field.Store.YES, Field.Index.UN_TOKENIZED));
  }
  if (ontologyDoc.getChildId() != null) {
    doc.add(new Field(FieldName.CHILDREN_ID, ontologyDoc.getChildId(), Field.Store.YES, Field.Index.UN_TOKENIZED));
    doc.add(new Field(FieldName.CHILDREN_NAME, ontologyDoc.getChildName(), Field.Store.YES, Field.Index.TOKENIZED));
    doc.add(new Field(FieldName.CHILDREN_NAME_SORTABLE, ontologyDoc.getChildName(), Field.Store.YES, Field.Index.UN_TOKENIZED));
  }
  if (ontologyDoc.getRelationshipType() != null) {
    doc.add(new Field(FieldName.RELATIONSHIP_TYPE, ontologyDoc.getRelationshipType(), Field.Store.YES, Field.Index.UN_TOKENIZED));
  }
  doc.add(new Field(FieldName.RELATIONSHIP_CYCLIC, String.valueOf(ontologyDoc.isCyclicRelationship()),
           Field.Store.YES, Field.Index.UN_TOKENIZED));
  doc.add(new Field(FieldName.PARENT_SYNONYMS, StringUtils.join(ontologyDoc.getParentSynonyms(), SYNONYM_SEPARATOR), Field.Store.YES, Field.Index.UN_TOKENIZED));
  doc.add(new Field(FieldName.CHILDREN_SYNONYMS, StringUtils.join(ontologyDoc.getChildSynonyms(), SYNONYM_SEPARATOR), Field.Store.YES, Field.Index.UN_TOKENIZED));
  this.indexWriter.addDocument(doc);
}

private SolrInputDocument createSolrInputDocument(OntologyDocument ontologyDocument) {
  SolrInputDocument doc = new SolrInputDocument();
  String uniqueKey = ontologyDocument.getOntology() + "_" + ontologyDocument.getParentId() + "_" + ontologyDocument.getChildId() + "_" + ontologyDocument.getRelationshipType();
  addField(doc, OntologyFieldNames.ID, uniqueKey, false);
  addField(doc, OntologyFieldNames.ONTOLOGY, ontologyDocument.getOntology(), false);
  addField(doc, OntologyFieldNames.PARENT_ID, ontologyDocument.getParentId(), false);
  addField(doc, OntologyFieldNames.PARENT_NAME, ontologyDocument.getParentName(), true);
  addField(doc, OntologyFieldNames.CHILD_ID, ontologyDocument.getChildId(), false);
  addField(doc, OntologyFieldNames.CHILD_NAME, ontologyDocument.getChildName(), true);
  addField(doc, OntologyFieldNames.RELATIONSHIP_TYPE, ontologyDocument.getRelationshipType(), false);
  addField(doc, OntologyFieldNames.CYCLIC, ontologyDocument.isCyclicRelationship(), false);
  
  for (String synonym : ontologyDocument.getParentSynonyms()) {
    addField(doc, OntologyFieldNames.PARENT_SYNONYMS, synonym, false);
  }
  for (String synonym : ontologyDocument.getChildSynonyms()) {
    addField(doc, OntologyFieldNames.CHILDREN_SYNONYMS, synonym, false);
  }
  return doc;
}