use of net.idea.modbcum.i.batch.IBatchStatistics in project ambit-mirror by ideaconsult.
the class CallableFileImport method importFile.
public TaskResult importFile(File file) throws Exception {
try {
// if target dataset is not defined, create new dataset
final SourceDataset dataset = targetDataset != null ? targetDataset : datasetMeta(file);
if (targetDataset == null)
dataset.setId(-1);
final BatchDBProcessor<String> batch = new BatchDBProcessor<String>() {
/**
*/
private static final long serialVersionUID = -7971761364143510120L;
@Override
public Iterator<String> getIterator(IInputState target) throws AmbitException {
try {
File file = ((FileInputState) target).getFile();
RDFIteratingReader i = getRDFIterator(file, getReporter().getBaseReference().toString());
if (i == null) {
IIteratingChemObjectReader ni = getNanoCMLIterator(file, getReporter().getBaseReference().toString());
if (ni == null)
return super.getIterator(target);
else
return ni;
} else {
/*
* RDFMetaDatasetIterator datasets = null; try {
* datasets = new
* RDFMetaDatasetIterator(i.getJenaModel());
* datasets
* .setBaseReference(getReporter().getBaseReference
* ()); while (datasets.hasNext()) { SourceDataset d
* = datasets.next(); dataset.setId(d.getId());
* dataset.setName(d.getName());
* dataset.setTitle(d.getTitle());
* dataset.setURL(d.getURL()); } } catch (Exception
* x) { x.printStackTrace(); } finally { try {
* datasets.close();} catch (Exception x) {} }
*/
return i;
}
} catch (AmbitException x) {
throw x;
} catch (Exception x) {
throw new AmbitException(x);
}
}
@Override
public void onItemProcessed(String input, Object output, IBatchStatistics stats) {
super.onItemProcessed(input, output, stats);
if (firstCompoundOnly && (stats.getRecords(RECORDS_STATS.RECORDS_PROCESSED) >= 1)) {
cancelled = true;
if (output != null)
if ((output instanceof ArrayList) && ((ArrayList) output).size() > 0) {
if (((ArrayList) output).get(0) instanceof IStructureRecord)
recordImported = (IStructureRecord) ((ArrayList) output).get(0);
} else if (output instanceof IStructureRecord)
recordImported = (IStructureRecord) output;
}
}
};
batch.setReference(dataset.getReference());
batch.setConnection(connection);
final RepositoryWriter writer = new RepositoryWriter();
writer.setUseExistingStructure(isPropertyOnly());
writer.setPropertyKey(getMatcher());
writer.setDataset(dataset);
final ProcessorsChain<String, IBatchStatistics, IProcessor> chain = new ProcessorsChain<String, IBatchStatistics, IProcessor>();
chain.add(writer);
batch.setProcessorChain(chain);
writer.setConnection(connection);
FileInputState fin = new FileInputState(file);
IBatchStatistics stats = batch.process(fin);
if (firstCompoundOnly) {
if (recordImported == null)
throw new Exception("No compound imported");
if (compoundReporter == null)
compoundReporter = new ConformerURIReporter("", null, false);
try {
batch.close();
} catch (Exception xx) {
}
return new TaskResult(compoundReporter.getURI(recordImported));
} else {
ReadDataset q = new ReadDataset();
q.setValue(dataset);
QueryExecutor<ReadDataset> x = new QueryExecutor<ReadDataset>();
x.setConnection(connection);
ResultSet rs = x.process(q);
ISourceDataset newDataset = null;
while (rs.next()) {
newDataset = q.getObject(rs);
break;
}
x.closeResults(rs);
x.setConnection(null);
if (newDataset == null)
throw new ResourceException(Status.SUCCESS_NO_CONTENT);
if (reporter == null)
reporter = new DatasetURIReporter<IQueryRetrieval<ISourceDataset>, ISourceDataset>();
try {
batch.close();
} catch (Exception xx) {
}
return new TaskResult(reporter.getURI(newDataset));
}
} catch (ResourceException x) {
throw x;
} catch (Exception x) {
throw new ResourceException(new Status(Status.SERVER_ERROR_INTERNAL, x.getMessage()));
} finally {
try {
connection.close();
} catch (Exception x) {
}
connection = null;
}
}
use of net.idea.modbcum.i.batch.IBatchStatistics in project ambit-mirror by ideaconsult.
the class CallableFingerprintsModelCreator method createProcessors.
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;
}
use of net.idea.modbcum.i.batch.IBatchStatistics in project ambit-mirror by ideaconsult.
the class CallableUpdateDataset method createProcessors.
@Override
protected ProcessorsChain<String, IBatchStatistics, IProcessor> createProcessors() throws Exception {
final RepositoryWriter writer = new RepositoryWriter();
writer.setDataset(dataset);
final ProcessorsChain<String, IBatchStatistics, IProcessor> chain = new ProcessorsChain<String, IBatchStatistics, IProcessor>();
chain.add(writer);
return chain;
}
use of net.idea.modbcum.i.batch.IBatchStatistics in project ambit-mirror by ideaconsult.
the class BatchProcessor method process.
/*
protected Iterator getIterator(IInputState target) throws AmbitException {
return target.getReader();
}
protected void closeIterator(Iterator iterator) throws AmbitException {
iterator.close();
}
*/
public IBatchStatistics process(INPUT target) throws AmbitException {
try {
DefaultBatchStatistics stats = new DefaultBatchStatistics();
stats.setResultCaption("Read");
stats.setFrequency(1);
Iterator reader = getIterator(target);
ProcessorsChain<Target, IBatchStatistics, IProcessor> processor = getProcessorChain();
if (processor == null)
throw new AmbitException("Processor not defined");
long started = System.currentTimeMillis();
while (reader.hasNext() && !cancelled) {
if ((stats.getRecords(IBatchStatistics.RECORDS_STATS.RECORDS_READ) % stats.getFrequency()) == 0)
propertyChangeSupport.firePropertyChange(PROPERTY_BATCHSTATS, null, stats);
Object object = null;
long ms = System.currentTimeMillis();
try {
object = reader.next();
stats.increment(IBatchStatistics.RECORDS_STATS.RECORDS_READ);
stats.incrementTimeElapsed(IBatchStatistics.RECORDS_STATS.RECORDS_READ, System.currentTimeMillis() - ms);
} catch (Exception x) {
stats.increment(IBatchStatistics.RECORDS_STATS.RECORDS_ERROR);
stats.incrementTimeElapsed(IBatchStatistics.RECORDS_STATS.RECORDS_ERROR, System.currentTimeMillis() - ms);
continue;
}
ms = System.currentTimeMillis();
try {
processor.process((Target) object);
stats.increment(IBatchStatistics.RECORDS_STATS.RECORDS_PROCESSED);
stats.incrementTimeElapsed(IBatchStatistics.RECORDS_STATS.RECORDS_PROCESSED, System.currentTimeMillis() - ms);
} catch (Exception x) {
stats.increment(IBatchStatistics.RECORDS_STATS.RECORDS_ERROR);
stats.incrementTimeElapsed(IBatchStatistics.RECORDS_STATS.RECORDS_ERROR, System.currentTimeMillis() - ms);
continue;
}
long elapsed = System.currentTimeMillis() - started;
if ((timeout > 0) && (elapsed > timeout)) {
stats.increment(IBatchStatistics.RECORDS_STATS.RECORDS_ERROR);
stats.incrementTimeElapsed(IBatchStatistics.RECORDS_STATS.RECORDS_ERROR, System.currentTimeMillis() - ms);
break;
}
}
propertyChangeSupport.firePropertyChange(PROPERTY_BATCHSTATS, null, stats);
closeIterator(reader);
return stats;
} catch (Exception x) {
throw new AmbitException(x);
}
}
use of net.idea.modbcum.i.batch.IBatchStatistics in project ambit-mirror by ideaconsult.
the class DbReaderTest method testProcess.
@Test
public void testProcess() throws Exception {
setUpDatabaseFromResource("ambit2/db/processors/test/descriptors-datasets.xml");
IDatabaseConnection c = getConnection();
ITable names = c.createQueryTable("EXPECTED_NAMES", "SELECT * FROM properties");
Assert.assertEquals(5, names.getRowCount());
ITable values = c.createQueryTable("EXPECTED_VALUES", "SELECT * FROM property_values");
Assert.assertEquals(2, values.getRowCount());
ProcessorsChain<IStructureRecord, IBatchStatistics, IProcessor> p = new ProcessorsChain<IStructureRecord, IBatchStatistics, IProcessor>();
p.add(new ProcessorStructureRetrieval());
p.add(new IProcessor<IStructureRecord, IStructureRecord>() {
public boolean isEnabled() {
return true;
}
public IStructureRecord process(IStructureRecord target) throws AmbitException {
// System.out.println(target.getContent());
return target;
}
public void setEnabled(boolean value) {
}
public long getID() {
return 0;
}
@Override
public void open() throws Exception {
}
@Override
public void close() throws Exception {
}
});
p.add(new MoleculeReader());
p.add(new AtomConfigurator());
p.add(new FunctionalGroup("Test", "P", "Test"));
p.add(new IProcessor<VerboseDescriptorResult, String>() {
/**
*/
private static final long serialVersionUID = -3923864774580483348L;
public String process(VerboseDescriptorResult target) throws AmbitException {
Assert.assertEquals("1", target.getResult().toString());
return target.toString();
}
public boolean isEnabled() {
return true;
}
public void setEnabled(boolean value) {
}
public long getID() {
return 0;
}
@Override
public void open() throws Exception {
}
@Override
public void close() throws Exception {
}
});
batch.setProcessorChain(p);
QueryStructureByID query = new QueryStructureByID(100215);
batch.setConnection(c.getConnection());
batch.open();
IBatchStatistics stats = batch.process(query);
Assert.assertEquals(1, stats.getRecords(IBatchStatistics.RECORDS_STATS.RECORDS_READ));
Assert.assertEquals(1, stats.getRecords(IBatchStatistics.RECORDS_STATS.RECORDS_PROCESSED));
// C20H20BrP
}
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