Examples with IIteratingChemObjectReader org.openscience.cdk.io.iterator.IIteratingChemObjectReader used on opensource projects

Example 1 with IIteratingChemObjectReader

use of org.openscience.cdk.io.iterator.IIteratingChemObjectReader 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 IIteratingChemObjectReader

use of org.openscience.cdk.io.iterator.IIteratingChemObjectReader in project ambit-mirror by ideaconsult.

the class FileInputState method getI5DReader.

public static IIteratingChemObjectReader getI5DReader(File file) throws FileNotFoundException, AmbitIOException, CDKException {
    try {
        Class clazz = Class.forName("net.idea.i5.io.I5DReader");
        Constructor constructor = clazz.getConstructor(File.class);
        return (IIteratingChemObjectReader) constructor.newInstance(file);
    } catch (Exception x) {
        return new I5ReaderSimple(new FileReader(file));
    }
}

Example 3 with IIteratingChemObjectReader

use of org.openscience.cdk.io.iterator.IIteratingChemObjectReader in project ambit-mirror by ideaconsult.

the class RawIteratingFolderReader method getItemReader.

protected IRawReader<IStructureRecord> getItemReader(int index) throws Exception {
    String name = files[index].getName().toLowerCase();
    if (name.endsWith(FileInputState._FILE_TYPE.SDF_INDEX.getExtension())) {
        RawIteratingSDFReader r = new RawIteratingSDFReader(new FileReader(files[index]));
        r.setReference(LiteratureEntry.getInstance(files[index].getName(), "file:///" + files[index].getAbsolutePath()));
        return (IRawReader<IStructureRecord>) r;
    } else if (name.endsWith(FileInputState._FILE_TYPE.MOL_INDEX.getExtension())) {
        RawIteratingMOLReader r = new RawIteratingMOLReader(new FileReader(files[index]));
        r.setReference(LiteratureEntry.getInstance(files[index].getName(), "file:///" + files[index].getAbsolutePath()));
        return (IRawReader<IStructureRecord>) r;
    } else if (name.endsWith(FileInputState._FILE_TYPE.I5D_INDEX.getExtension())) {
        IIteratingChemObjectReader r = FileInputState.getI5DReader(files[index]);
        if (r instanceof ICiteable) {
            ((ICiteable) r).setReference(LiteratureEntry.getI5UUIDReference());
        }
        return (IRawReader<IStructureRecord>) r;
    } else if (name.endsWith(FileInputState._FILE_TYPE.ZIP_INDEX.getExtension())) {
        return new ZipReader(files[index]);
    } else if (name.endsWith(FileInputState._FILE_TYPE.GZ_INDEX.getExtension())) {
        // assuming gzipped sdf only...
        InputStreamReader reader = new InputStreamReader(new GZIPInputStream(new FileInputStream(files[index])));
        return new RawIteratingSDFReader(reader);
    } else
        throw new Exception("Unsupported format " + name);
}

Example 4 with IIteratingChemObjectReader

use of org.openscience.cdk.io.iterator.IIteratingChemObjectReader in project ambit-mirror by ideaconsult.

the class I5ParserTest method testi5z.

@Test
public void testi5z() throws Exception {
    URL url = getClass().getClassLoader().getResource("ambit2/core/data/i5z/RefSub_030913110311.i5z");
    IIteratingChemObjectReader ireader = FileInputState.getReader(new File(url.getFile()));
    ireader.setErrorHandler(new IChemObjectReaderErrorHandler() {

        @Override
        public void handleError(String message, int row, int colStart, int colEnd, Exception exception) {
        }

        @Override
        public void handleError(String message, int row, int colStart, int colEnd) {
        }

        @Override
        public void handleError(String message, Exception exception) {
            exception.printStackTrace();
        }

        @Override
        public void handleError(String message) {
        }
    });
    int count = 0;
    int foundCas = 0;
    int foundName = 0;
    RawIteratingFolderReader reader = (RawIteratingFolderReader) ireader;
    while (reader.hasNext()) {
        IStructureRecord record = reader.nextRecord();
        /*
			for (Property p : record.getProperties())
				System.out.println(String.format("%s [%s] = %s",p.getName(),p.getReference().getTitle(),record.getProperty(p)));
			System.out.println();
			*/
        count++;
        for (Property p : record.getRecordProperties()) {
            foundCas += record.getRecordProperty(p).equals("59-87-0") ? 1 : 0;
            foundName += record.getRecordProperty(p).equals("5-nitro-2-furaldehyde semicarbazone") ? 1 : 0;
            System.out.println(p.getName() + " = " + record.getRecordProperty(p));
        }
    // Assert.assertNotNull(record.getSmiles());
    // Assert.assertNotNull(record.getInchi());
    // Assert.assertNotNull(record.getProperty(Property.getI5UUIDInstance()));
    }
    reader.close();
    Assert.assertEquals(10, count);
    Assert.assertEquals(1, foundCas);
    Assert.assertEquals(1, foundName);
}

Example 5 with IIteratingChemObjectReader

use of org.openscience.cdk.io.iterator.IIteratingChemObjectReader in project ambit-mirror by ideaconsult.

the class MDLV2000ReaderExtendedTest method testMol_without_Mend.

@Test
public void testMol_without_Mend() throws Exception {
    IIteratingChemObjectReader reader = FileInputState.getReader(getClass().getClassLoader().getResourceAsStream("ambit2/core/data/mdl/test_no_mend.mol"), "test_no_mend.mol");
    int count = 0;
    while (reader.hasNext()) {
        Object o = reader.next();
        Assert.assertTrue(o instanceof IAtomContainer);
        Assert.assertEquals(23, ((IAtomContainer) o).getAtomCount());
        count++;
    }
    reader.close();
    Assert.assertEquals(1, count);
}