Examples with Reference org.dishevelled.bio.assembly.gfa1.Reference used on opensource projects

Example 6 with Reference

use of org.dishevelled.bio.assembly.gfa1.Reference in project geotoolkit by Geomatys.

the class GeometryArrayToReferenceConverterTest method testJSONConversion.

@Test
public void testJSONConversion() throws IOException, FactoryException, URISyntaxException, DataStoreException {
    // Get test resource
    final Object testResource = ConvertersTestUtils.loadTestResource("/inputs/geometrycollection.json");
    final Reference reference = ConvertersTestUtils.initAndRunOutputConversion(Geometry[].class, Reference.class, testResource, WPSMimeType.APP_GEOJSON.val(), WPSEncoding.UTF8.getValue());
    // Test reference
    assertEquals(WPSMimeType.APP_GEOJSON.val(), reference.getMimeType());
    assertEquals(WPSEncoding.UTF8.getValue(), reference.getEncoding());
    assertNull(reference.getSchema());
    assertNotNull(reference.getHref());
    final Geometry[] geometryArray = ConvertersTestUtils.getGeometryArrayFromInputStream(new FileInputStream(new File(new URL(reference.getHref()).toURI())));
    ConvertersTestUtils.assertGeometryArrayIsValid((Geometry[]) testResource);
    ConvertersTestUtils.assertGeometryArrayIsValid(geometryArray);
}

Example 7 with Reference

use of org.dishevelled.bio.assembly.gfa1.Reference in project geotoolkit by Geomatys.

the class UrlConnectionToReferenceConverterTest method convert.

@Test
public void convert() throws Exception {
    final WPSObjectConverter<URLConnection, Reference> converter = WPSConverterRegistry.getInstance().getConverter(URLConnection.class, Reference.class);
    final URL url = new URL("https://toto.titi/tata");
    URLConnection conn = url.openConnection();
    Reference ref = converter.convert(conn, Collections.singletonMap(WPSObjectConverter.IOTYPE, (Object) WPSIO.IOType.OUTPUT.name()));
    Assert.assertEquals("Href differs !", url.toExternalForm(), ref.getHref());
}

Example 8 with Reference

use of org.dishevelled.bio.assembly.gfa1.Reference in project geotoolkit by Geomatys.

the class FeatureCollectionToReferenceConverter method convert.

/**
 * {@inheritDoc}
 */
@Override
public Reference convert(final FeatureCollection source, final Map<String, Object> params) throws UnconvertibleObjectException {
    if (params.get(TMP_DIR_PATH) == null) {
        throw new UnconvertibleObjectException("The output directory should be defined.");
    }
    if (params.get(TMP_DIR_URL) == null) {
        throw new UnconvertibleObjectException("The output directory URL should be defined.");
    }
    if (source == null) {
        throw new UnconvertibleObjectException("The output data should be defined.");
    }
    // TODO : useless test, null test above is all we need, fix this and other converters
    if (!(source instanceof FeatureCollection)) {
        throw new UnconvertibleObjectException("The requested output data is not an instance of FeatureCollection.");
    }
    Reference reference = new Reference();
    reference.setMimeType((String) params.get(MIME));
    reference.setEncoding((String) params.get(ENCODING));
    final FeatureType ft = source.getType();
    final String namespace = NamesExt.getNamespace(ft.getName());
    final Map<String, String> schemaLocation = new HashMap<>();
    final String randomFileName = UUID.randomUUID().toString();
    if (WPSMimeType.APP_GEOJSON.val().equalsIgnoreCase(reference.getMimeType())) {
        // create file
        final Path dataFile = buildPath(params, randomFileName + ".json");
        try (OutputStream fos = Files.newOutputStream(dataFile, CREATE, TRUNCATE_EXISTING, WRITE);
            GeoJSONStreamWriter writer = new GeoJSONStreamWriter(fos, ft, WPSConvertersUtils.FRACTION_DIGITS);
            Stream<Feature> st = source.features(false)) {
            Iterator<Feature> iterator = st.iterator();
            while (iterator.hasNext()) {
                Feature next = iterator.next();
                Feature neww = writer.next();
                FeatureExt.copy(next, neww, false);
                writer.write();
            }
        } catch (DataStoreException e) {
            throw new UnconvertibleObjectException("Can't write Feature into GeoJSON output stream.", e);
        } catch (IOException e) {
            throw new UnconvertibleObjectException(e);
        }
        final String relLoc = getRelativeLocation(dataFile, params);
        reference.setHref(params.get(TMP_DIR_URL) + "/" + relLoc);
        reference.setSchema(null);
    } else if (WPSMimeType.APP_GML.val().equalsIgnoreCase(reference.getMimeType()) || WPSMimeType.TEXT_XML.val().equalsIgnoreCase(reference.getMimeType()) || WPSMimeType.TEXT_GML.val().equalsIgnoreCase(reference.getMimeType())) {
        try {
            reference.setSchema(WPSConvertersUtils.writeSchema(ft, params));
            schemaLocation.put(namespace, reference.getSchema());
        } catch (JAXBException ex) {
            throw new UnconvertibleObjectException("Can't write FeatureType into xsd schema.", ex);
        } catch (IOException ex) {
            throw new UnconvertibleObjectException("Can't create xsd schema file.", ex);
        }
        // Write Feature
        final JAXPStreamFeatureWriter featureWriter = new JAXPStreamFeatureWriter(schemaLocation);
        // create file
        final Path dataFile = buildPath(params, randomFileName + ".xml");
        try (final OutputStream dataStream = Files.newOutputStream(dataFile);
            final AutoCloseable xmlCloser = () -> featureWriter.dispose()) {
            // Write feature in file
            featureWriter.write(source, dataStream);
            final String relLoc = getRelativeLocation(dataFile, params);
            reference.setHref(params.get(TMP_DIR_URL) + "/" + relLoc);
        } catch (XMLStreamException ex) {
            throw new UnconvertibleObjectException("Stax exception while writing the feature collection", ex);
        } catch (DataStoreException ex) {
            throw new UnconvertibleObjectException("FeatureStore exception while writing the feature collection", ex);
        } catch (FeatureStoreRuntimeException ex) {
            throw new UnconvertibleObjectException("FeatureStoreRuntimeException exception while writing the feature collection", ex);
        } catch (Exception ex) {
            throw new UnconvertibleObjectException(ex);
        }
    } else {
        throw new UnconvertibleObjectException("Unsupported mime-type for " + this.getClass().getName() + " : " + reference.getMimeType());
    }
    return reference;
}

Example 9 with Reference

use of org.dishevelled.bio.assembly.gfa1.Reference in project geotoolkit by Geomatys.

the class FeatureToReferenceConverter method convert.

/**
 * {@inheritDoc}
 */
@Override
public Reference convert(final Feature source, final Map<String, Object> params) throws UnconvertibleObjectException {
    if (params.get(TMP_DIR_PATH) == null) {
        throw new UnconvertibleObjectException("The output directory should be defined.");
    }
    if (source == null) {
        throw new UnconvertibleObjectException("The output directory should be defined.");
    }
    FeatureType ft = null;
    if (source instanceof Feature) {
        ft = source.getType();
    } else {
        throw new UnconvertibleObjectException("The requested output reference data is not an instance of Feature.");
    }
    Reference reference = new Reference();
    reference.setMimeType((String) params.get(MIME));
    reference.setEncoding((String) params.get(ENCODING));
    final String namespace = NamesExt.getNamespace(ft.getName());
    final Map<String, String> schemaLocation = new HashMap<>();
    final String randomFileName = UUID.randomUUID().toString();
    final String tmpDirUrl = (String) params.get(TMP_DIR_URL);
    if (WPSMimeType.APP_GEOJSON.val().equalsIgnoreCase(reference.getMimeType())) {
        // create file
        final Path dataFile = buildPath(params, randomFileName + ".json");
        try {
            try (OutputStream fos = Files.newOutputStream(dataFile);
                GeoJSONStreamWriter writer = new GeoJSONStreamWriter(fos, ft, WPSConvertersUtils.FRACTION_DIGITS)) {
                Feature next = writer.next();
                FeatureExt.copy(source, next, true);
                writer.write();
            }
        } catch (DataStoreException e) {
            throw new UnconvertibleObjectException("Can't write Feature into GeoJSON output stream.", e);
        } catch (IOException e) {
            throw new UnconvertibleObjectException(e);
        }
        final String relLoc = getRelativeLocation(dataFile, params);
        reference.setHref(tmpDirUrl + "/" + relLoc);
        reference.setSchema(null);
    } else if (WPSMimeType.APP_GML.val().equalsIgnoreCase(reference.getMimeType()) || WPSMimeType.TEXT_XML.val().equalsIgnoreCase(reference.getMimeType()) || WPSMimeType.TEXT_GML.val().equalsIgnoreCase(reference.getMimeType())) {
        // Write FeatureType
        try {
            reference.setSchema(WPSConvertersUtils.writeSchema(ft, params));
            schemaLocation.put(namespace, reference.getSchema());
        } catch (JAXBException ex) {
            throw new UnconvertibleObjectException("Can't write FeatureType into xsd schema.", ex);
        } catch (IOException ex) {
            throw new UnconvertibleObjectException("Can't create xsd schema file.", ex);
        }
        // Write Feature
        final XmlFeatureWriter featureWriter = new JAXPStreamFeatureWriter(schemaLocation);
        // create file
        final Path dataFile = buildPath(params, randomFileName + ".xml");
        try (final OutputStream dataStream = Files.newOutputStream(dataFile);
            final AutoCloseable xmlCloser = () -> featureWriter.dispose()) {
            // Write feature in file
            featureWriter.write(source, dataStream);
            final String relLoc = getRelativeLocation(dataFile, params);
            reference.setHref(tmpDirUrl + "/" + relLoc);
        } catch (XMLStreamException ex) {
            throw new UnconvertibleObjectException("Stax exception while writing the feature collection", ex);
        } catch (DataStoreException ex) {
            throw new UnconvertibleObjectException("FeatureStore exception while writing the feature collection", ex);
        } catch (FeatureStoreRuntimeException ex) {
            throw new UnconvertibleObjectException("FeatureStoreRuntimeException exception while writing the feature collection", ex);
        } catch (Exception ex) {
            throw new UnconvertibleObjectException(ex);
        }
    } else
        throw new UnconvertibleObjectException("Unsupported mime-type for " + this.getClass().getName() + " : " + reference.getMimeType());
    return reference;
}

Example 10 with Reference

use of org.dishevelled.bio.assembly.gfa1.Reference in project geotoolkit by Geomatys.

the class FeatureTypeToReferenceConverter method convert.

/**
 * {@inheritDoc}
 */
@Override
public Reference convert(final FeatureType source, final Map<String, Object> params) throws UnconvertibleObjectException {
    if (params.get(TMP_DIR_PATH) == null) {
        throw new UnconvertibleObjectException("The output directory should be defined.");
    }
    if (source == null) {
        throw new UnconvertibleObjectException("The output directory should be defined.");
    }
    Reference reference = new Reference();
    reference.setMimeType((String) params.get(MIME));
    reference.setEncoding((String) params.get(ENCODING));
    reference.setSchema((String) params.get(SCHEMA));
    reference.setMimeType((String) params.get(MIME));
    reference.setEncoding((String) params.get(ENCODING));
    final String randomFileName = UUID.randomUUID().toString();
    // Write FeatureType
    try {
        final String schemaFileName = randomFileName + "_schema" + ".xsd";
        // create file
        final Path schemaFile = buildPath(params, schemaFileName);
        final OutputStream schemaStream = Files.newOutputStream(schemaFile);
        // write featureType xsd on file
        final JAXBFeatureTypeWriter xmlFTWriter = new JAXBFeatureTypeWriter();
        xmlFTWriter.write(source, schemaStream);
        final String relLoc = getRelativeLocation(schemaFile, params);
        reference.setHref((String) params.get(TMP_DIR_URL) + "/" + relLoc);
    } catch (JAXBException ex) {
        throw new UnconvertibleObjectException("Can't write FeatureType into xsd schema.", ex);
    } catch (IOException ex) {
        throw new UnconvertibleObjectException("Can't create xsd schema file.", ex);
    }
    return reference;
}