Examples with RepositoryWriter ambit2.db.processors.RepositoryWriter used on opensource projects

Example 1 with RepositoryWriter

use of ambit2.db.processors.RepositoryWriter 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;
    }
}

Example 2 with RepositoryWriter

use of ambit2.db.processors.RepositoryWriter 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;
}

Example 3 with RepositoryWriter

use of ambit2.db.processors.RepositoryWriter in project ambit-mirror by ideaconsult.

the class RepositoryWriterToXMLTest method write.

public int write(IRawReader<IStructureRecord> reader, Connection connection, PropertyKey key) throws Exception {
    RepositoryWriter writer = new RepositoryWriter();
    if (key != null)
        writer.setPropertyKey(key);
    writer.setDataset(new SourceDataset("TEST INPUT", LiteratureEntry.getInstance("File", "file:study.toxml")));
    writer.setConnection(connection);
    writer.open();
    int records = 0;
    while (reader.hasNext()) {
        IStructureRecord record = reader.nextRecord();
        writer.write(record);
        records++;
    }
    reader.close();
    writer.close();
    return records;
}

Example 4 with RepositoryWriter

use of ambit2.db.processors.RepositoryWriter in project ambit-mirror by ideaconsult.

the class RepositoryWriterTest method write.

public int write(IRawReader<IStructureRecord> reader, Connection connection, PropertyKey key, boolean useExistingStructure, int maxrecords) throws Exception {
    RepositoryWriter writer = new RepositoryWriter();
    writer.setUseExistingStructure(useExistingStructure);
    if (key != null)
        writer.setPropertyKey(key);
    writer.setDataset(new SourceDataset("TEST INPUT", LiteratureEntry.getInstance("File", "file:input.sdf")));
    writer.setConnection(connection);
    writer.open();
    int records = 0;
    while (reader.hasNext()) {
        IStructureRecord record = reader.nextRecord();
        writer.write(record);
        records++;
        if (maxrecords <= 0 || (records <= maxrecords))
            continue;
        else
            break;
    }
    reader.close();
    writer.close();
    return records;
}

Example 5 with RepositoryWriter

use of ambit2.db.processors.RepositoryWriter in project ambit-mirror by ideaconsult.

the class NanoWriterTest method write.

public int write(IRawReader<IStructureRecord> reader, Connection connection, PropertyKey key) throws Exception {
    RepositoryWriter writer = new RepositoryWriter();
    if (key != null)
        writer.setPropertyKey(key);
    writer.setDataset(new SourceDataset("TEST INPUT", LiteratureEntry.getInstance("File", "file:input.nmx")));
    writer.setConnection(connection);
    writer.open();
    int records = 0;
    while (reader.hasNext()) {
        IStructureRecord record = reader.nextRecord();
        writer.write(record);
        records++;
    }
    reader.close();
    writer.close();
    return records;
}