Examples with AmbitException net.idea.modbcum.i.exceptions.AmbitException used on opensource projects

Example 16 with AmbitException

use of net.idea.modbcum.i.exceptions.AmbitException in project ambit-mirror by ideaconsult.

the class ARFFIterator method getIterator.

@Override
public Iterator<IStructureRecord> getIterator(File[] target) throws AmbitException {
    try {
        input = new BufferedReader(new FileReader(target[0]));
        results = new BufferedReader(new FileReader(target[1]));
        arffInput = new ArffReader(input, 1);
        arffResults = new ArffReader(results, 1);
        dataInput = arffInput.getStructure();
        dataResults = arffResults.getStructure();
        properties = new Property[dataResults.numAttributes()];
        for (int i = 0; i < dataResults.numAttributes(); i++) {
            Attribute attribute = dataResults.attribute(i);
            RDFPropertyIterator reader = null;
            Property p = null;
            try {
                reader = new RDFPropertyIterator(new Reference(attribute.name()), "arff");
                reader.setBaseReference(baseReference);
                while (reader.hasNext()) {
                    p = reader.next();
                }
            } catch (Exception x) {
                p = null;
            // p.setId((Integer)OpenTox.URI.feature.getId(attribute.name(), baseReference));
            } finally {
                try {
                    reader.close();
                } catch (Exception x) {
                }
            }
            properties[i] = p;
        }
        return new Iterator<IStructureRecord>() {

            public boolean hasNext() {
                try {
                    inputInstance = arffInput.readInstance(dataInput);
                    resultInstance = arffResults.readInstance(dataResults);
                    return (inputInstance != null) && (resultInstance != null);
                } catch (Exception x) {
                    return false;
                }
            }

            public IStructureRecord next() {
                record.clear();
                Object[] ids = OpenTox.URI.conformer.getIds(inputInstance.toString(0), baseReference);
                if ((ids != null) && (ids[0] != null) && (ids[1] != null)) {
                    record.setIdchemical((Integer) ids[0]);
                    record.setIdstructure((Integer) ids[1]);
                } else {
                    Object id = OpenTox.URI.compound.getId(inputInstance.toString(0), baseReference);
                    if (id != null) {
                        record.setIdchemical((Integer) id);
                        record.setIdstructure(-1);
                    } else {
                    // retrieveStructure(uris[index]);
                    }
                }
                for (int i = 0; i < properties.length; i++) if (properties[i] != null) {
                    if (dataResults.attribute(i).isNumeric())
                        record.setRecordProperty(properties[i], resultInstance.value(i));
                    else
                        record.setRecordProperty(properties[i], resultInstance.toString(i));
                }
                return record;
            }

            public void remove() {
            }
        };
    } catch (FileNotFoundException x) {
        throw new AmbitException(x);
    } catch (Exception x) {
        throw new AmbitException(x);
    }
}

Example 17 with AmbitException

use of net.idea.modbcum.i.exceptions.AmbitException in project ambit-mirror by ideaconsult.

the class Structure2DModelBuilder method process.

public ModelQueryResults process(Algorithm algorithm) throws AmbitException {
    try {
        ModelQueryResults mr = new ModelQueryResults();
        mr.setHidden(modelHidden);
        mr.setContentMediaType(AlgorithmFormat.Structure2D.getMediaType());
        mr.setName(algorithm.getName());
        mr.setContent(algorithm.getContent().toString());
        mr.setAlgorithm(alg_reporter.getURI(algorithm));
        mr.setPredictors(algorithm.getInput());
        Template dependent = new Template("Empty");
        mr.setDependent(dependent);
        PredictedVarsTemplate predicted = new PredictedVarsTemplate("Empty");
        mr.setPredicted(predicted);
        return mr;
    } catch (Exception x) {
        throw new ResourceException(Status.SERVER_ERROR_INTERNAL, x.getCause() == null ? x.getMessage() : x.getCause().getMessage(), x);
    }
}

Example 18 with AmbitException

use of net.idea.modbcum.i.exceptions.AmbitException in project ambit-mirror by ideaconsult.

the class TaskCreator method processItem.

@Override
public Object processItem(T item) throws AmbitException {
    try {
        ICallableTask callable = getCallable(form, item);
        if (async) {
            ITask<Reference, USERID> task = createTask(callable, item);
            tasks.add(task.getUuid());
        } else {
            ITaskResult ref = callable.call();
        }
    } catch (AmbitException x) {
        throw x;
    } catch (Exception x) {
        throw new AmbitException(x);
    }
    return item;
}

Example 19 with AmbitException

use of net.idea.modbcum.i.exceptions.AmbitException in project ambit-mirror by ideaconsult.

the class ClassHolder method load.

public static List<ClassHolder> load(InputStream input) throws AmbitException {
    List<ClassHolder> classes = new ArrayList<ClassHolder>();
    try {
        BufferedReader reader = new BufferedReader(new InputStreamReader(input));
        boolean eof = false;
        String fileLine;
        while (!eof) {
            fileLine = reader.readLine();
            if (fileLine == null)
                eof = true;
            else {
                classes.add(new ClassHolder(fileLine.trim(), fileLine, "", (String) null));
            }
        }
        reader.close();
    } catch (Exception x) {
    } finally {
        try {
            input.close();
        } catch (Exception x) {
        }
    }
    return classes;
}

Example 20 with AmbitException

use of net.idea.modbcum.i.exceptions.AmbitException 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);
    }
}