org.molgenis.ontology.roc.InformationContentService Maven / Gradle / Ivy

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Plugin module containing SORTA (system for ontology-based re-coding and technical annotation) plugins.
There is a newer version: 8.4.5
package org.molgenis.ontology.roc;

import static java.util.Objects.requireNonNull;
import static org.molgenis.ontology.core.meta.OntologyMetadata.ONTOLOGY;
import static org.molgenis.ontology.core.meta.OntologyTermMetadata.ONTOLOGY_TERM;

import com.google.common.cache.CacheBuilder;
import com.google.common.cache.CacheLoader;
import com.google.common.cache.LoadingCache;
import com.google.common.collect.Sets;
import com.google.common.util.concurrent.UncheckedExecutionException;
import java.math.BigDecimal;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.TimeUnit;
import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import org.molgenis.data.DataService;
import org.molgenis.data.Entity;
import org.molgenis.data.QueryRule;
import org.molgenis.data.QueryRule.Operator;
import org.molgenis.data.support.QueryImpl;
import org.molgenis.ontology.core.meta.OntologyMetadata;
import org.molgenis.ontology.core.meta.OntologyTermMetadata;
import org.molgenis.semanticsearch.string.NGramDistanceAlgorithm;
import org.molgenis.semanticsearch.string.Stemmer;

public class InformationContentService {
  private static final String NON_WORD_SEPARATOR = "[^a-zA-Z0-9]";
  private static final String SINGLE_WHITESPACE = " ";

  private final LoadingCache cachedTotalWordCount =
      CacheBuilder.newBuilder()
          .maximumSize(Integer.MAX_VALUE)
          .expireAfterWrite(1, TimeUnit.DAYS)
          .build(
              new CacheLoader() {
                @Override
                public Long load(String ontologyIri) {
                  Entity ontologyEntity =
                      dataService.findOne(
                          ONTOLOGY,
                          new QueryImpl<>().eq(OntologyMetadata.ONTOLOGY_IRI, ontologyIri));
                  if (ontologyEntity != null) {
                    return dataService.count(
                        ONTOLOGY_TERM,
                        new QueryImpl<>().eq(OntologyTermMetadata.ONTOLOGY, ontologyEntity));
                  }
                  return (long) 0;
                }
              });
  private final LoadingCache cachedInverseDocumentFreq =
      CacheBuilder.newBuilder()
          .maximumSize(Integer.MAX_VALUE)
          .expireAfterWrite(1, TimeUnit.DAYS)
          .build(
              new CacheLoader() {
                public Double load(OntologyWord key) throws ExecutionException {
                  String ontologyIri = key.getOntologyIri();
                  Entity ontologyEntity =
                      dataService.findOne(
                          ONTOLOGY,
                          new QueryImpl<>().eq(OntologyMetadata.ONTOLOGY_IRI, ontologyIri));
                  if (ontologyEntity != null) {
                    QueryRule queryRule =
                        new QueryRule(
                            Arrays.asList(
                                new QueryRule(
                                    OntologyTermMetadata.ONTOLOGY_TERM_SYNONYM,
                                    Operator.FUZZY_MATCH,
                                    key.getWord())));
                    queryRule.setOperator(Operator.DIS_MAX);
                    QueryRule finalQuery =
                        new QueryRule(
                            Arrays.asList(
                                new QueryRule(
                                    OntologyTermMetadata.ONTOLOGY, Operator.EQUALS, ontologyEntity),
                                new QueryRule(Operator.AND),
                                queryRule));
                    long wordCount = dataService.count(ONTOLOGY_TERM, new QueryImpl<>(finalQuery));
                    Long total = cachedTotalWordCount.get(ontologyIri);
                    BigDecimal idfValue =
                        BigDecimal.valueOf(
                            total == null ? 0 : (1 + Math.log((double) total / (wordCount + 1))));
                    return idfValue.doubleValue();
                  }
                  return (double) 0;
                }
              });

  private final DataService dataService;

  public InformationContentService(DataService dataService) {
    this.dataService = requireNonNull(dataService);
  }

  public Map redistributedNGramScore(String queryString, String ontologyIri) {
    Map wordIDFMap = createWordIDF(queryString, ontologyIri);
    Map wordWeightedSimilarity = new HashMap<>();

    if (wordIDFMap.size() > 0) {
      double averageIDFValue =
          wordIDFMap.values().stream().mapToDouble(Double::doubleValue).average().getAsDouble();
      double queryStringLength =
          StringUtils.join(createStemmedWordSet(queryString), SINGLE_WHITESPACE).trim().length();
      double totalContribution = 0;
      double totalDenominator = 0;

      for (Entry entry : wordIDFMap.entrySet()) {
        double diff = entry.getValue() - averageIDFValue;
        if (diff < 0) {
          Double contributedSimilarity =
              (entry.getKey().length() / queryStringLength * 100) * (diff / averageIDFValue);
          totalContribution += Math.abs(contributedSimilarity);
          wordWeightedSimilarity.put(entry.getKey(), contributedSimilarity);
        } else {
          totalDenominator += diff;
        }
      }

      for (Entry entry : wordIDFMap.entrySet()) {
        double diff = entry.getValue() - averageIDFValue;
        if (diff > 0) {
          if (totalDenominator == 0) {
            throw new IllegalStateException("totalDenominator is 0");
          }
          wordWeightedSimilarity.put(
              entry.getKey(), ((diff / totalDenominator) * totalContribution));
        }
      }
    }
    return wordWeightedSimilarity;
  }

  Map createWordIDF(String queryString, String ontologyIri) {
    Map wordFreqMap = new HashMap<>();
    Set wordsInQueryString = createStemmedWordSet(queryString);
    wordsInQueryString.stream()
        .forEach(
            word -> {
              Double wordIDF = null;
              try {
                wordIDF = cachedInverseDocumentFreq.get(new OntologyWord(ontologyIri, word));
              } catch (ExecutionException e) {
                throw new UncheckedExecutionException(e);
              }

              if (wordIDF != null && wordIDF != 0) {
                wordFreqMap.put(word, wordIDF);
              }
            });
    return wordFreqMap;
  }

  public Set createStemmedWordSet(String queryString) {
    Set uniqueTerms =
        Sets.newHashSet(queryString.toLowerCase().trim().split(NON_WORD_SEPARATOR)).stream()
            .filter(term -> !NGramDistanceAlgorithm.STOPWORDSLIST.contains(term))
            .map(Stemmer::stem)
            .filter(StringUtils::isNotBlank)
            .collect(Collectors.toSet());
    return Sets.newHashSet(uniqueTerms);
  }
}