@Override
  protected void processInput(String keggGeneId, String keggGeneRecord, Resource output) {
    Map<String, String> recordSections = KeggUtils.getSectionsFromKeggRecord(keggGeneRecord);
    StrTokenizer tokenizer = new StrTokenizer();

    if (recordSections.containsKey(PATHWAY_RECORD_SECTION)) {
      for (String line : recordSections.get(PATHWAY_RECORD_SECTION).split("\\r?\\n")) {
        String keggPathwayId = tokenizer.reset(line).nextToken();
        Resource keggPathwayNode =
            LSRNUtils.createInstance(
                output.getModel(), LSRNUtils.getClass(LSRN.Namespace.KEGG_PATHWAY), keggPathwayId);
        output.addProperty(SIO.is_participant_in, keggPathwayNode);
      }
    }
  }
Exemplo n.º 2
0
 /**
  * Converts a String back to connection parameters.
  *
  * @param input String from configuration
  * @return JDBC connection parameters
  */
 protected static Properties propertiesFromString(String input) {
   if (input != null && !input.isEmpty()) {
     Properties result = new Properties();
     StrTokenizer propertyTokenizer = StrTokenizer.getCSVInstance(input);
     StrTokenizer valueTokenizer = StrTokenizer.getCSVInstance();
     valueTokenizer.setDelimiterChar('=');
     while (propertyTokenizer.hasNext()) {
       valueTokenizer.reset(propertyTokenizer.nextToken());
       String[] values = valueTokenizer.getTokenArray();
       if (values.length == 2) {
         result.put(values[0], values[1]);
       }
     }
     return result;
   } else {
     return null;
   }
 }