Examples with RDFMetaDatasetIterator ambit2.rest.rdf.RDFMetaDatasetIterator used on opensource projects

Example 1 with RDFMetaDatasetIterator

use of ambit2.rest.rdf.RDFMetaDatasetIterator in project ambit-mirror by ideaconsult.

the class MetadatasetResource method createObjectIterator.

@Override
protected RDFObjectIterator<M> createObjectIterator(Representation entity) throws ResourceException {
    RDFMetaDatasetIterator iterator = new RDFMetaDatasetIterator(entity, entity.getMediaType()) {

        @Override
        protected ISourceDataset createRecord() {
            return new SourceDataset();
        }
    };
    iterator.setForceReadRDFLocalObjects(true);
    iterator.setBaseReference(getRequest().getRootRef());
    return iterator;
}

Example 2 with RDFMetaDatasetIterator

use of ambit2.rest.rdf.RDFMetaDatasetIterator 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 RDFMetaDatasetIterator

use of ambit2.rest.rdf.RDFMetaDatasetIterator in project ambit-mirror by ideaconsult.

the class MetaDatasetResourceTest method testRDFXML.

@Test
public void testRDFXML() throws Exception {
    Reference ref = new Reference(String.format("http://localhost:%d/dataset/1/metadata", port));
    RDFMetaDatasetIterator<ISourceDataset> iterator = new RDFMetaDatasetIterator<ISourceDataset>(ref, "test") {

        @Override
        protected ISourceDataset createRecord() {
            return new SourceDataset();
        }
    };
    iterator.setBaseReference(new Reference(String.format("http://localhost:%d", port)));
    int count = 0;
    while (iterator.hasNext()) {
        ISourceDataset target = iterator.next();
        Assert.assertEquals(1, target.getID());
        Assert.assertEquals("Dbunit dataset", target.getName());
        Assert.assertEquals("XLogP", target.getSource());
        if (target instanceof SourceDataset)
            Assert.assertEquals("XLogP reference", ((SourceDataset) target).getURL());
        count++;
    }
    Assert.assertEquals(1, count);
    iterator.close();
}

Example 4 with RDFMetaDatasetIterator

use of ambit2.rest.rdf.RDFMetaDatasetIterator in project ambit-mirror by ideaconsult.

the class MetaRDatasetResourceTest method testRDFXML.

@Test
public void testRDFXML() throws Exception {
    Reference ref = new Reference(String.format("http://localhost:%d/dataset/R1/metadata", port));
    RDFMetaDatasetIterator<ISourceDataset> iterator = new RDFMetaDatasetIterator<ISourceDataset>(ref, "test") {

        @Override
        protected ISourceDataset createRecord() {
            return new SourceDataset();
        }
    };
    iterator.setBaseReference(new Reference(String.format("http://localhost:%d", port)));
    int count = 0;
    while (iterator.hasNext()) {
        ISourceDataset target = iterator.next();
        Assert.assertEquals(1, target.getID());
        Assert.assertEquals("test query", target.getName());
        // Assert.assertEquals("XLogP", target.getTitle());
        // Assert.assertEquals("XLogP", target.getURL());
        count++;
    }
    Assert.assertEquals(1, count);
    iterator.close();
}