/*
@Override
protected TaskResult createReference(Connection connection) throws Exception {
if (!resultsFile.exists()) throw new ResourceException(Status.SERVER_ERROR_INTERNAL,"No results available!");
try {
RemoteTask task = new RemoteTask(new Reference(dataset_service),MediaType.TEXT_URI_LIST,
new FileRepresentation(resultsFile,MediaType.APPLICATION_RDF_XML),Method.POST);
//wait to complete, so that we can delete the tmp file
Thread.sleep(200);
while (!task.isDone()) {
task.poll();
Thread.sleep(800);
Thread.yield();
}
if (task.isERROR())
throw task.getError();
else
return new TaskResult(task.getResult().toString());
} catch (Exception x) {
throw x;
} finally {
try { if (resultsFile.exists()) resultsFile.delete();} catch (Exception x) {}
try { if (target.exists()) target.delete();} catch (Exception x) {}
}
return null;
}
*/
@Override
protected ProcessorsChain<IStructureRecord, IBatchStatistics, IProcessor> createProcessors()
throws Exception {
ProcessorsChain<IStructureRecord, IBatchStatistics, IProcessor> p1 =
new ProcessorsChain<IStructureRecord, IBatchStatistics, IProcessor>();
IProcessor<IStructureRecord, IStructureRecord> writer = getWriter();
if (writer != null) p1.add(writer);
return p1;
}
protected ProcessorsChain<IStructureRecord, IBatchStatistics, IProcessor> createProcessors()
throws Exception {
ProcessorsChain<IStructureRecord, IBatchStatistics, IProcessor> p1 =
new ProcessorsChain<IStructureRecord, IBatchStatistics, IProcessor>();
p1.add(new ProcessorStructureRetrieval());
p1.add(new MoleculeReader());
p1.add(new FingerprintGenerator(new Fingerprinter()));
p1.add(
new DefaultAmbitProcessor<BitSet, BitSet>() {
/** */
private static final long serialVersionUID = -2978697147490545478L;
public BitSet process(BitSet target) throws AmbitException {
builder.getTrainingData().add(target);
return target;
}
});
p1.setAbortOnError(true);
return p1;
}