Examples with Reference com.google.api.expr.v1alpha1.Reference used on opensource projects

Example 31 with Reference

use of com.google.api.expr.v1alpha1.Reference in project dishevelled by heuermh.

the class ImportGfa2Task method run.

@Override
public void run(final TaskMonitor taskMonitor) throws Exception {
    taskMonitor.setTitle("Import a network in Graphical Fragment Assembly (GFA) 2.0 format");
    final Map<String, Segment> segmentsById = new HashMap<String, Segment>();
    taskMonitor.setStatusMessage("Reading segments from file ...");
    try (BufferedReader readable = new BufferedReader(new FileReader(inputFile))) {
        // stream segments, building cache
        stream(readable, new Gfa2Adapter() {

            @Override
            protected boolean segment(final Segment segment) {
                segmentsById.put(segment.getId(), segment);
                return true;
            }
        });
    }
    taskMonitor.setStatusMessage("Finding reverse orientation references ...");
    final Table<String, Orientation, Segment> segmentsByOrientation = HashBasedTable.create();
    final List<Edge> edges = new ArrayList<Edge>();
    final List<Gap> gaps = new ArrayList<Gap>();
    final List<Path> paths = new ArrayList<Path>();
    try (BufferedReader readable = new BufferedReader(new FileReader(inputFile))) {
        // stream edges, gaps, and paths, looking for reverse orientation references
        stream(readable, new Gfa2Adapter() {

            private void putIfAbsent(final Reference reference) {
                Segment segment = segmentsById.get(reference.getId());
                if (segment == null) {
                    throw new RuntimeException("could not find segment by id " + reference.getId());
                }
                if (!segmentsByOrientation.contains(reference.getId(), reference.getOrientation())) {
                    segmentsByOrientation.put(reference.getId(), reference.getOrientation(), segment);
                }
            }

            @Override
            public boolean edge(final Edge edge) {
                putIfAbsent(edge.getSource());
                putIfAbsent(edge.getTarget());
                edges.add(edge);
                return true;
            }

            @Override
            public boolean gap(final Gap gap) {
                putIfAbsent(gap.getSource());
                putIfAbsent(gap.getTarget());
                gaps.add(gap);
                return true;
            }

            @Override
            public boolean path(final Path path) {
                for (Reference reference : path.getReferences()) {
                    putIfAbsent(reference);
                }
                if (loadPaths) {
                    paths.add(path);
                }
                return true;
            }
        });
    }
    logger.info("read {} segments, {} edges, {} gaps, and {} paths from {}", new Object[] { segmentsById.size(), edges.size(), gaps.size(), paths.size(), inputFile });
    segmentsById.clear();
    taskMonitor.setStatusMessage("Building Cytoscape nodes from segments ...");
    final CyNetwork network = applicationManager.getCurrentNetwork();
    final Map<String, CyNode> nodes = new HashMap<String, CyNode>(segmentsByOrientation.size());
    for (Table.Cell<String, Orientation, Segment> c : segmentsByOrientation.cellSet()) {
        String id = c.getRowKey();
        Orientation orientation = c.getColumnKey();
        Segment segment = c.getValue();
        String name = id + (orientation.isForward() ? "+" : "-");
        if (!nodes.containsKey(name)) {
            CyNode node = network.addNode();
            CyTable nodeTable = network.getDefaultNodeTable();
            CyRow nodeRow = nodeTable.getRow(node.getSUID());
            Integer length = segment.getLength();
            Integer readCount = segment.getReadCountOpt().orElse(null);
            Integer fragmentCount = segment.getFragmentCountOpt().orElse(null);
            Integer kmerCount = segment.getKmerCountOpt().orElse(null);
            String sequenceChecksum = segment.containsSequenceChecksum() ? String.valueOf(segment.getSequenceChecksum()) : null;
            String sequenceUri = segment.getSequenceUriOpt().orElse(null);
            setValue(nodeTable, nodeRow, "name", String.class, name);
            setValue(nodeTable, nodeRow, "length", Integer.class, length);
            setValue(nodeTable, nodeRow, "readCount", Integer.class, readCount);
            setValue(nodeTable, nodeRow, "fragmentCount", Integer.class, fragmentCount);
            setValue(nodeTable, nodeRow, "kmerCount", Integer.class, kmerCount);
            setValue(nodeTable, nodeRow, "sequenceChecksum", String.class, sequenceChecksum);
            setValue(nodeTable, nodeRow, "sequenceUri", String.class, sequenceUri);
            // default display length to length
            Integer displayLength = length;
            String sequence = orientation.isForward() ? segment.getSequence() : reverseComplement(segment.getSequence());
            if (sequence != null) {
                Integer sequenceLength = sequence.length();
                String displaySequence = trimFromMiddle(sequence, displaySequenceLimit);
                Integer displaySequenceLength = displaySequence.length();
                if (loadSequences) {
                    setValue(nodeTable, nodeRow, "sequence", String.class, sequence);
                }
                setValue(nodeTable, nodeRow, "sequenceLength", Integer.class, sequenceLength);
                setValue(nodeTable, nodeRow, "displaySequence", String.class, displaySequence);
                setValue(nodeTable, nodeRow, "displaySequenceLength", Integer.class, displaySequenceLength);
                // override display length with sequence length if necessary
                if (length == null || length != sequenceLength) {
                    displayLength = sequenceLength;
                }
            }
            StringBuilder sb = new StringBuilder();
            sb.append(name);
            if (displayLength != null) {
                sb.append("  ");
                sb.append(displayLength);
                sb.append(" bp");
            }
            String displayName = sb.toString();
            if (readCount != null) {
                sb.append(" ");
                sb.append(readCount);
                sb.append(" reads");
            }
            if (fragmentCount != null) {
                sb.append(" ");
                sb.append(fragmentCount);
                sb.append(" fragments");
            }
            if (kmerCount != null) {
                sb.append(" ");
                sb.append(kmerCount);
                sb.append(" kmers");
            }
            String displayLabel = sb.toString();
            setValue(nodeTable, nodeRow, "displayName", String.class, displayName);
            setValue(nodeTable, nodeRow, "displayLength", Integer.class, displayLength);
            setValue(nodeTable, nodeRow, "displayLabel", String.class, displayLabel);
            nodes.put(name, node);
        }
    }
    logger.info("converted segments and orientation to " + nodes.size() + " nodes");
    segmentsByOrientation.clear();
    taskMonitor.setStatusMessage("Building Cytoscape edges from edges and gaps ...");
    for (Edge edge : edges) {
        String sourceId = edge.getSource().getId();
        String sourceOrientation = edge.getSource().isForwardOrientation() ? "+" : "-";
        String targetId = edge.getTarget().getId();
        String targetOrientation = edge.getTarget().isForwardOrientation() ? "+" : "-";
        CyNode sourceNode = nodes.get(sourceId + sourceOrientation);
        CyNode targetNode = nodes.get(targetId + targetOrientation);
        CyEdge cyEdge = network.addEdge(sourceNode, targetNode, true);
        CyTable edgeTable = network.getDefaultEdgeTable();
        CyRow edgeRow = edgeTable.getRow(cyEdge.getSUID());
        setValue(edgeTable, edgeRow, "id", String.class, edge.getIdOpt().orElse(null));
        setValue(edgeTable, edgeRow, "type", String.class, "edge");
        setValue(edgeTable, edgeRow, "sourceId", String.class, sourceId);
        setValue(edgeTable, edgeRow, "sourceOrientation", String.class, sourceOrientation);
        setValue(edgeTable, edgeRow, "targetId", String.class, targetId);
        setValue(edgeTable, edgeRow, "targetOrientation", String.class, targetOrientation);
        setValue(edgeTable, edgeRow, "sourceStart", String.class, edge.getSourceStart().toString());
        setValue(edgeTable, edgeRow, "sourceEnd", String.class, edge.getSourceEnd().toString());
        setValue(edgeTable, edgeRow, "targetStart", String.class, edge.getTargetStart().toString());
        setValue(edgeTable, edgeRow, "targetEnd", String.class, edge.getTargetEnd().toString());
        setValue(edgeTable, edgeRow, "alignment", String.class, edge.hasAlignment() ? edge.getAlignment().toString() : null);
        setValue(edgeTable, edgeRow, "readCount", Integer.class, edge.getReadCountOpt().orElse(null));
        setValue(edgeTable, edgeRow, "fragmentCount", Integer.class, edge.getFragmentCountOpt().orElse(null));
        setValue(edgeTable, edgeRow, "kmerCount", Integer.class, edge.getKmerCountOpt().orElse(null));
        setValue(edgeTable, edgeRow, "mappingQuality", Integer.class, edge.getMappingQualityOpt().orElse(null));
        setValue(edgeTable, edgeRow, "mismatchCount", Integer.class, edge.getMismatchCountOpt().orElse(null));
    }
    logger.info("converted edges to " + edges.size() + " edges");
    for (Gap gap : gaps) {
        String sourceId = gap.getSource().getId();
        String sourceOrientation = gap.getSource().isForwardOrientation() ? "+" : "-";
        String targetId = gap.getTarget().getId();
        String targetOrientation = gap.getTarget().isForwardOrientation() ? "+" : "-";
        CyNode sourceNode = nodes.get(sourceId + sourceOrientation);
        CyNode targetNode = nodes.get(targetId + targetOrientation);
        CyEdge edge = network.addEdge(sourceNode, targetNode, true);
        CyTable edgeTable = network.getDefaultEdgeTable();
        CyRow edgeRow = edgeTable.getRow(edge.getSUID());
        setValue(edgeTable, edgeRow, "id", String.class, gap.getIdOpt().orElse(null));
        setValue(edgeTable, edgeRow, "type", String.class, "gap");
        setValue(edgeTable, edgeRow, "sourceId", String.class, sourceId);
        setValue(edgeTable, edgeRow, "sourceOrientation", String.class, sourceOrientation);
        setValue(edgeTable, edgeRow, "targetId", String.class, targetId);
        setValue(edgeTable, edgeRow, "targetOrientation", String.class, targetOrientation);
        setValue(edgeTable, edgeRow, "distance", Integer.class, gap.getDistance());
        setValue(edgeTable, edgeRow, "variance", Integer.class, gap.getVarianceOpt().orElse(null));
    }
    logger.info("converted gaps to " + gaps.size() + " edges");
    nodes.clear();
    edges.clear();
    gaps.clear();
    // pass paths to AssemblyApp if requested
    if (loadPaths && !paths.isEmpty()) {
        taskMonitor.setStatusMessage("Loading paths in path view ...");
        assemblyModel.setInputFileName(inputFile.toString());
    // todo: convert to gfa1 paths?
    // note paths in gfa2 can have references to segments, edges, or other groups
    // assemblyModel.setPaths(paths, traversalsByPathName);
    }
}

Example 32 with Reference

use of com.google.api.expr.v1alpha1.Reference in project geotoolkit by Geomatys.

the class ExecuteTest method testRequestAndMarshall.

@Test
public void testRequestAndMarshall() throws Exception {
    final WebProcessingClient client = new WebProcessingClient(new URL("http://test.com"), null, WPSVersion.v100);
    final ExecuteRequest request = client.createExecute();
    final Execute execute = request.getContent();
    final GeographicCRS epsg4326 = CommonCRS.WGS84.geographic();
    final GeneralEnvelope env = new GeneralEnvelope(epsg4326);
    env.setRange(0, 10, 10);
    env.setRange(1, 10, 10);
    execute.setIdentifier("identifier");
    final List<DataInput> inputs = execute.getInput();
    inputs.add(new DataInput("literal", new Data(new LiteralValue("10", null, null))));
    inputs.add(new DataInput("bbox", new Data(new BoundingBoxType(env))));
    inputs.add(new DataInput("complex", new Data(new Format("UTF-8", WPSMimeType.APP_GML.val(), WPSSchema.OGC_GML_3_1_1.getValue(), null), new PointType(new DirectPosition2D(epsg4326, 0, 0)))));
    inputs.add(new DataInput("reference", new Reference("http://link.to/reference/", null, null)));
    execute.getOutput().add(new OutputDefinition("output", false));
    assertEquals("WPS", execute.getService());
    assertEquals("1.0.0", execute.getVersion().toString());
    assertEquals(execute.getIdentifier().getValue(), "identifier");
    final StringWriter stringWriter = new StringWriter();
    final Marshaller marshaller = WPSMarshallerPool.getInstance().acquireMarshaller();
    marshaller.marshal(execute, stringWriter);
    String result = stringWriter.toString();
    try (final InputStream expected = expectedRequest()) {
        assertXmlEquals(expected, result, "xmlns:*", "crs", "srsName");
    }
    WPSMarshallerPool.getInstance().recycle(marshaller);
}

Example 33 with Reference

use of com.google.api.expr.v1alpha1.Reference in project eclipselink by eclipse-ee4j.

the class MetadataResource method buildQuerySchema.

private ResourceSchema buildQuerySchema(PersistenceContext context, DatabaseQuery query) {
    final ResourceSchema schema = new ResourceSchema();
    schema.setTitle(query.getName());
    schema.setSchema(HrefHelper.buildQueryMetadataHref(context, query.getName()) + "#");
    schema.addAllOf(new Reference(HrefHelper.buildBaseRestSchemaRef("#/collectionBaseResource")));
    // Link
    final String method = query.isReadQuery() ? "GET" : "POST";
    schema.setLinks((new ItemLinksBuilder()).addExecute(HrefHelper.buildQueryHref(context, query.getName(), getQueryParamString(query)), method).getList());
    // Definitions
    if (query.isReportQuery()) {
        // In case of report query we need to define a returned type
        final ResourceSchema returnType = new ResourceSchema();
        query.checkPrepare((AbstractSession) context.getServerSession(), new DatabaseRecord());
        for (ReportItem item : ((ReportQuery) query).getItems()) {
            final Property property;
            if (item.getMapping() != null) {
                if (item.getAttributeExpression() != null && item.getAttributeExpression().isMapEntryExpression()) {
                    if (((MapEntryExpression) item.getAttributeExpression()).shouldReturnMapEntry()) {
                        property = buildProperty(context, Map.Entry.class);
                    } else {
                        property = buildProperty(context, ((Class<?>) item.getMapping().getContainerPolicy().getKeyType()));
                    }
                } else {
                    property = buildProperty(context, item.getMapping().getAttributeClassification());
                }
            } else if (item.getResultType() != null) {
                property = buildProperty(context, item.getResultType());
            } else if (item.getDescriptor() != null) {
                property = buildProperty(context, item.getDescriptor().getJavaClass());
            } else if (item.getAttributeExpression() != null && item.getAttributeExpression().isConstantExpression()) {
                property = buildProperty(context, ((ConstantExpression) item.getAttributeExpression()).getValue().getClass());
            } else {
                // Use Object.class by default.
                property = buildProperty(context, Object.class);
            }
            returnType.addProperty(item.getName(), property);
        }
        schema.addDefinition("result", returnType);
        final Property items = new Property();
        items.setType("array");
        items.setItems(new Property("#/definitions/result"));
        schema.addProperty("items", items);
    } else {
        // Read all query. Each item is an entity. Make a JSON pointer.
        if (query.getReferenceClassName() != null) {
            final Property items = new Property();
            items.setType("array");
            items.setItems(new Property(HrefHelper.buildEntityMetadataHref(context, query.getReferenceClass().getSimpleName()) + "#"));
            schema.addProperty("items", items);
        }
    }
    return schema;
}

Example 34 with Reference

use of com.google.api.expr.v1alpha1.Reference in project geotoolkit by Geomatys.

the class ConvertersTestUtils method createReference.

/**
 * Helper method that creates a Reference with all its field filled
 * @param mimeType can be null
 * @param encoding can be null
 * @param schema can be null
 * @param url must be set
 * @return the reference with its field filled using the above parameters
 */
public static final Reference createReference(String version, String mimeType, String encoding, String schema, URL url) {
    final Reference reference = new Reference();
    reference.setMimeType(mimeType);
    reference.setEncoding(encoding);
    reference.setSchema(schema);
    reference.setHref(url.toString());
    return reference;
}

Example 35 with Reference

use of com.google.api.expr.v1alpha1.Reference in project geotoolkit by Geomatys.

the class FeatureSetToReferenceConverter method convert.

/**
 * {@inheritDoc}
 */
@Override
public Reference convert(final FeatureSet 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 FeatureSet)) {
        throw new UnconvertibleObjectException("The requested output data is not an instance of FeatureSet.");
    }
    Reference reference = new Reference();
    reference.setMimeType((String) params.get(MIME));
    reference.setEncoding((String) params.get(ENCODING));
    final FeatureType ft;
    try {
        ft = source.getType();
    } catch (DataStoreException ex) {
        throw new UnconvertibleObjectException("Can't write acess FeatureSet type.", ex);
    }
    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;
}