@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);
}
}
}
/**
* 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;
}
}