コード例 #1
0
ファイル: OntologyMapper.java プロジェクト: hardikgw/BioSolr
 @Override
 public void run() {
   OntologyHelper helper = helpers.get(threadKey);
   if (helper != null) {
     // Check if the last call time was longer ago than the maximum
     if (System.currentTimeMillis() - DELETE_CHECK_DELAY_MS > helper.getLastCallTime()) {
       // Assume helper is out of use - dispose of it to allow memory to be freed
       helper.dispose();
       helpers.remove(threadKey);
     }
   }
 }
コード例 #2
0
ファイル: OntologyMapper.java プロジェクト: hardikgw/BioSolr
  public static OntologyHelper getHelper(OntologySettings settings, ThreadPool threadPool)
      throws OntologyHelperException {
    String helperKey = buildHelperKey(settings);
    OntologyHelper helper = helpers.get(helperKey);

    if (helper == null) {
      helper = new ElasticOntologyHelperFactory(settings).buildOntologyHelper();
      OntologyCheckRunnable checker = new OntologyCheckRunnable(helperKey);
      threadPool.scheduleWithFixedDelay(checker, TimeValue.timeValueMillis(DELETE_CHECK_DELAY_MS));
      helpers.put(helperKey, helper);
      helper.updateLastCallTime();
    }

    return helper;
  }
コード例 #3
0
ファイル: OntologyMapper.java プロジェクト: hardikgw/BioSolr
  @Override
  public void parse(ParseContext context) throws IOException {
    String iri;
    XContentParser parser = context.parser();
    XContentParser.Token token = parser.currentToken();

    if (token == XContentParser.Token.VALUE_STRING) {
      iri = parser.text();
    } else {
      throw new MapperParsingException(name() + " does not contain String value");
    }

    ContentPath.Type origPathType = context.path().pathType();
    context.path().pathType(ContentPath.Type.FULL);
    context.path().add(names.name());

    try {
      OntologyHelper helper = getHelper(ontologySettings, threadPool);

      OntologyData data = findOntologyData(helper, iri);
      if (data == null) {
        logger.debug("Cannot find OWL class for IRI {}", iri);
      } else {
        addFieldData(
            context,
            getPredefinedMapper(FieldMappings.URI, context),
            Collections.singletonList(iri));

        // Look up the label(s)
        addFieldData(context, getPredefinedMapper(FieldMappings.LABEL, context), data.getLabels());

        // Look up the synonyms
        addFieldData(
            context, getPredefinedMapper(FieldMappings.SYNONYMS, context), data.getLabels());

        // Add the child details
        addRelatedNodesWithLabels(
            context,
            data.getChildIris(),
            getPredefinedMapper(FieldMappings.CHILD_URI, context),
            data.getChildLabels(),
            getPredefinedMapper(FieldMappings.CHILD_LABEL, context));

        // Add the parent details
        addRelatedNodesWithLabels(
            context,
            data.getParentIris(),
            getPredefinedMapper(FieldMappings.PARENT_URI, context),
            data.getParentLabels(),
            getPredefinedMapper(FieldMappings.PARENT_LABEL, context));

        if (ontologySettings.isIncludeIndirect()) {
          // Add the descendant details
          addRelatedNodesWithLabels(
              context,
              data.getDescendantIris(),
              getPredefinedMapper(FieldMappings.DESCENDANT_URI, context),
              data.getDescendantLabels(),
              getPredefinedMapper(FieldMappings.DESCENDANT_LABEL, context));

          // Add the ancestor details
          addRelatedNodesWithLabels(
              context,
              data.getAncestorIris(),
              getPredefinedMapper(FieldMappings.ANCESTOR_URI, context),
              data.getAncestorLabels(),
              getPredefinedMapper(FieldMappings.ANCESTOR_LABEL, context));
        }

        if (ontologySettings.isIncludeRelations()) {
          // Add the related nodes
          Map<String, Collection<String>> relations = data.getRelationIris();

          for (String relation : relations.keySet()) {
            // Sanitise the relation name
            String sanRelation = relation.replaceAll("\\W+", "_");
            String uriMapperName = sanRelation + DYNAMIC_URI_FIELD_SUFFIX;
            String labelMapperName = sanRelation + DYNAMIC_LABEL_FIELD_SUFFIX;

            // Get the mapper for the relation
            FieldMapper<String> uriMapper =
                mappers.get(context.path().fullPathAsText(uriMapperName));
            FieldMapper<String> labelMapper =
                mappers.get(context.path().fullPathAsText(labelMapperName));

            if (uriMapper == null) {
              // No mappers created yet - build new ones for URI and label
              BuilderContext builderContext =
                  new BuilderContext(context.indexSettings(), context.path());
              uriMapper =
                  MapperBuilders.stringField(uriMapperName)
                      .store(true)
                      .index(true)
                      .tokenized(false)
                      .build(builderContext);
              labelMapper =
                  MapperBuilders.stringField(labelMapperName)
                      .store(true)
                      .index(true)
                      .tokenized(true)
                      .build(builderContext);
            }

            addRelatedNodesWithLabels(
                context,
                relations.get(relation),
                uriMapper,
                helper.findLabelsForIRIs(relations.get(relation)),
                labelMapper);
          }
        }
      }

      helper.updateLastCallTime();
    } catch (OntologyHelperException e) {
      throw new ElasticsearchException("Could not initialise ontology helper", e);
    } finally {
      context.path().remove();
      context.path().pathType(origPathType);
    }
  }