Examples with RDFIteratingReader ambit2.rest.dataset.RDFIteratingReader used on opensource projects

Example 1 with RDFIteratingReader

use of ambit2.rest.dataset.RDFIteratingReader in project ambit-mirror by ideaconsult.

the class RepositoryWriterRDFTest method testWrite.

public void testWrite(String baseref) throws Exception {
    setUpDatabaseFromResource("src-datasets.xml");
    IDatabaseConnection c = getConnection();
    ITable chemicals = c.createQueryTable("EXPECTED", "SELECT * FROM chemicals");
    Assert.assertEquals(4, chemicals.getRowCount());
    ITable strucs = c.createQueryTable("EXPECTED", "SELECT * FROM structure");
    Assert.assertEquals(5, strucs.getRowCount());
    ITable srcdataset = c.createQueryTable("EXPECTED", "SELECT * FROM src_dataset");
    Assert.assertEquals(3, srcdataset.getRowCount());
    ITable struc_src = c.createQueryTable("EXPECTED", "SELECT * FROM struc_dataset");
    Assert.assertEquals(8, struc_src.getRowCount());
    ITable property = c.createQueryTable("EXPECTED", "SELECT * FROM properties");
    Assert.assertEquals(3, property.getRowCount());
    ITable tuples = c.createQueryTable("EXPECTED", "SELECT * FROM tuples");
    Assert.assertEquals(1, tuples.getRowCount());
    ITable property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values");
    Assert.assertEquals(1, property_values.getRowCount());
    ITable p_tuples = c.createQueryTable("EXPECTED", "SELECT * FROM property_tuples");
    Assert.assertEquals(1, p_tuples.getRowCount());
    InputStream in = this.getClass().getClassLoader().getResourceAsStream("import_dataset2.rdf");
    Assert.assertNotNull(in);
    RDFIteratingReader reader = new RDFIteratingReader(in, SilentChemObjectBuilder.getInstance(), baseref, "RDF/XML");
    // reader.setReference(LiteratureEntry.getInstance("input.rdf"));
    write(reader, c.getConnection());
    c.close();
    c = getConnection();
    chemicals = c.createQueryTable("EXPECTED", "SELECT * FROM chemicals");
    Assert.assertEquals(4, chemicals.getRowCount());
    chemicals = c.createQueryTable("EXPECTED", "SELECT * FROM chemicals where smiles is not null and inchi is not null and formula is not null");
    Assert.assertEquals(0, chemicals.getRowCount());
    strucs = c.createQueryTable("EXPECTED", "SELECT * FROM structure");
    Assert.assertEquals(5, strucs.getRowCount());
    srcdataset = c.createQueryTable("EXPECTED", "SELECT * FROM src_dataset where name='TEST INPUT'");
    Assert.assertEquals(1, srcdataset.getRowCount());
    struc_src = c.createQueryTable("EXPECTED", "SELECT * FROM struc_dataset");
    Assert.assertEquals(8, struc_src.getRowCount());
    property = c.createQueryTable("EXPECTED", "SELECT * FROM properties");
    Assert.assertEquals(33, property.getRowCount());
    property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values");
    Assert.assertEquals(57, property_values.getRowCount());
    tuples = c.createQueryTable("EXPECTED", "SELECT * FROM tuples");
    Assert.assertEquals(3, tuples.getRowCount());
    p_tuples = c.createQueryTable("EXPECTED", "SELECT * FROM property_tuples");
    Assert.assertEquals(57, p_tuples.getRowCount());
    p_tuples = c.createQueryTable("EXPECTED", "SELECT * FROM values_string where name=\"Property 1\" and value = \"XXXXX\" and idstructure=100215");
    Assert.assertEquals(1, p_tuples.getRowCount());
    p_tuples = c.createQueryTable("EXPECTED", "SELECT value_num FROM property_values join properties using(idproperty) where name='http://anotherservice.com:8080/feature/1' and idstructure=100215");
    Assert.assertEquals(1, p_tuples.getRowCount());
    Assert.assertEquals("3.14", p_tuples.getValue(0, "value_num").toString());
    c.close();
}

Example 2 with RDFIteratingReader

use of ambit2.rest.dataset.RDFIteratingReader 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 3 with RDFIteratingReader

use of ambit2.rest.dataset.RDFIteratingReader in project ambit-mirror by ideaconsult.

the class RepositoryWriterRDFTest method testWriteForeign.

/**
 * Writes "Property 1" = "XXXXX" for structure 100215
 *
 * @throws Exception
 */
@Test
public void testWriteForeign() throws Exception {
    setUpDatabaseFromResource("src-datasets.xml");
    IDatabaseConnection c = getConnection();
    ITable chemicals = c.createQueryTable("EXPECTED", "SELECT * FROM chemicals");
    Assert.assertEquals(4, chemicals.getRowCount());
    ITable strucs = c.createQueryTable("EXPECTED", "SELECT * FROM structure");
    Assert.assertEquals(5, strucs.getRowCount());
    ITable srcdataset = c.createQueryTable("EXPECTED", "SELECT * FROM src_dataset");
    Assert.assertEquals(3, srcdataset.getRowCount());
    ITable struc_src = c.createQueryTable("EXPECTED", "SELECT * FROM struc_dataset");
    Assert.assertEquals(8, struc_src.getRowCount());
    ITable property = c.createQueryTable("EXPECTED", "SELECT * FROM properties");
    Assert.assertEquals(3, property.getRowCount());
    ITable tuples = c.createQueryTable("EXPECTED", "SELECT * FROM tuples");
    Assert.assertEquals(1, tuples.getRowCount());
    ITable property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values");
    Assert.assertEquals(1, property_values.getRowCount());
    ITable p_tuples = c.createQueryTable("EXPECTED", "SELECT * FROM property_tuples");
    Assert.assertEquals(1, p_tuples.getRowCount());
    InputStream in = this.getClass().getClassLoader().getResourceAsStream("import_dataset2.rdf");
    Assert.assertNotNull(in);
    RDFIteratingReader reader = new RDFIteratingReader(in, SilentChemObjectBuilder.getInstance(), String.format("http://somethingelse.com:%d", port), "RDF/XML");
    // reader.setReference(LiteratureEntry.getInstance("input.rdf"));
    write(reader, c.getConnection());
    c.close();
    c = getConnection();
    chemicals = c.createQueryTable("EXPECTED", "SELECT * FROM chemicals");
    Assert.assertEquals(5, chemicals.getRowCount());
    chemicals = c.createQueryTable("EXPECTED", "SELECT * FROM chemicals where smiles is not null and inchi is not null and formula is not null");
    Assert.assertEquals(2, chemicals.getRowCount());
    strucs = c.createQueryTable("EXPECTED", "SELECT * FROM structure");
    Assert.assertEquals(7, strucs.getRowCount());
    srcdataset = c.createQueryTable("EXPECTED", "SELECT * FROM src_dataset where name='TEST INPUT'");
    Assert.assertEquals(1, srcdataset.getRowCount());
    struc_src = c.createQueryTable("EXPECTED", "SELECT * FROM struc_dataset");
    Assert.assertEquals(10, struc_src.getRowCount());
    property = c.createQueryTable("EXPECTED", "SELECT * FROM properties");
    Assert.assertEquals(34, property.getRowCount());
    property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values");
    Assert.assertEquals(57, property_values.getRowCount());
    tuples = c.createQueryTable("EXPECTED", "SELECT * FROM tuples");
    Assert.assertEquals(3, tuples.getRowCount());
    p_tuples = c.createQueryTable("EXPECTED", "SELECT * FROM property_tuples");
    Assert.assertEquals(57, p_tuples.getRowCount());
    p_tuples = c.createQueryTable("EXPECTED", "SELECT * FROM values_string where name=\"http://localhost:8181/feature/1\" and value = \"XXXXX\"");
    Assert.assertEquals(1, p_tuples.getRowCount());
    p_tuples = c.createQueryTable("EXPECTED", "SELECT value_num FROM property_values join properties using(idproperty) where name='http://anotherservice.com:8080/feature/1'");
    Assert.assertEquals(1, p_tuples.getRowCount());
    Assert.assertEquals("3.14", p_tuples.getValue(0, "value_num").toString());
    c.close();
}