Examples with Link org.candlepin.dto.api.v1.Link used on opensource projects

Example 1 with Link

use of org.candlepin.dto.api.v1.Link in project geotoolkit by Geomatys.

the class SmlXMLBindingTest method SystemUnmarshallMarshalingTest.

/**
 * Test simple Record Marshalling.
 *
 * @throws java.lang.Exception
 */
@Test
public void SystemUnmarshallMarshalingTest() throws Exception {
    Unmarshaller unmarshaller = SensorMLMarshallerPool.getInstance().acquireUnmarshaller();
    InputStream is = SmlXMLBindingTest.class.getResourceAsStream("/org/geotoolkit/sml/system.xml");
    Object unmarshalled = unmarshaller.unmarshal(is);
    if (unmarshalled instanceof JAXBElement) {
        unmarshalled = ((JAXBElement) unmarshalled).getValue();
    }
    assertTrue(unmarshalled instanceof SensorML);
    SensorML result = (SensorML) unmarshalled;
    Member member = new Member();
    member.setRole("urn:x-ogx:def:sensor:OGC:detector");
    SystemType system = new SystemType();
    List<JAXBElement<String>> kw = new ArrayList<JAXBElement<String>>();
    kw.add(sml100Factory.createKeywordsKeywordListKeyword("piezometer"));
    kw.add(sml100Factory.createKeywordsKeywordListKeyword("geosciences"));
    kw.add(sml100Factory.createKeywordsKeywordListKeyword("point d'eau"));
    Keywords keywords = new Keywords(new KeywordList(URI.create("urn:x-brgm:def:gcmd:keywords"), kw));
    system.setKeywords(keywords);
    Classifier cl1 = new Classifier("intendedApplication", new Term("eaux souterraines", URI.create("urn:x-ogc:def:classifier:OGC:application")));
    CodeSpacePropertyType cs = new CodeSpacePropertyType("urn:x-brgm:def:GeoPoint:bss");
    Classifier cl2 = new Classifier("sensorType", new Term(cs, "piezometer", URI.create("urn:sensor:classifier:sensorType")));
    CodeSpacePropertyType cs3 = new CodeSpacePropertyType("urn:x-sandre:def:mdo:identifier");
    Classifier cl3 = new Classifier("waterBody", new Term(cs3, "FR6221", URI.create("urn:sensor:classifier:references")));
    CodeSpacePropertyType cs4 = new CodeSpacePropertyType("urn:x-sandre:def:mdo:name");
    Classifier cl4 = new Classifier("waterBody", new Term(cs4, "Multicouche pliocene et alluvions quaternaires du Roussillon", URI.create("urn:sensor:classifier:references")));
    CodeSpacePropertyType cs5 = new CodeSpacePropertyType("urn:x-sandre:def:bdhrf:identifier");
    Classifier cl5 = new Classifier("hydrologicalEntity", new Term(cs5, "225", URI.create("urn:sensor:classifier:references")));
    CodeSpacePropertyType cs6 = new CodeSpacePropertyType("urn:x-sandre:def:bdhrf:name");
    Classifier cl6 = new Classifier("hydrologicalEntity", new Term(cs6, "Pliocene du Roussillon", URI.create("urn:sensor:classifier:references")));
    CodeSpacePropertyType cs7 = new CodeSpacePropertyType("urn:x-insee:def:commune:identifier");
    Classifier cl7 = new Classifier("commune", new Term(cs7, "66008", URI.create("urn:sensor:classifier:references")));
    CodeSpacePropertyType cs8 = new CodeSpacePropertyType("urn:x-insee:def:commune:name");
    Classifier cl8 = new Classifier("commune", new Term(cs8, "ARGELES SUR MER", URI.create("urn:sensor:classifier:references")));
    CodeSpacePropertyType cs9 = new CodeSpacePropertyType("urn:x-sandre:def:network:identifier");
    Classifier cl9 = new Classifier("network", new Term(cs9, "600000221", URI.create("urn:sensor:classifier:references")));
    CodeSpacePropertyType cs10 = new CodeSpacePropertyType("urn:x-sandre:def:network:identifier");
    Classifier cl10 = new Classifier("network", new Term(cs10, "600000025", URI.create("urn:sensor:classifier:references")));
    List<Classifier> cls = new ArrayList<Classifier>();
    cls.add(cl1);
    cls.add(cl2);
    cls.add(cl3);
    cls.add(cl4);
    cls.add(cl5);
    cls.add(cl6);
    cls.add(cl7);
    cls.add(cl8);
    cls.add(cl9);
    cls.add(cl10);
    ClassifierList claList = new ClassifierList(null, cls);
    Classification classification = new Classification(claList);
    system.setClassification(classification);
    List<Identifier> identifiers = new ArrayList<Identifier>();
    cs = new CodeSpacePropertyType("urn:x-brgm:def:samplingStation:bss");
    Identifier id1 = new Identifier("bssCode", new Term(cs, "10972X0137/PONT", URI.create("urn:x-ogc:def:identifier:OGC:modelNumber")));
    cs = new CodeSpacePropertyType("urn:x-brgm:def:sensorSystem:hydras");
    Identifier id2 = new Identifier("supervisorCode", new Term(cs, "00ARGLELES", URI.create("urn:x-ogc:def:identifier:OGC:modelNumber")));
    Identifier id3 = new Identifier("longName", new Term("ARGELES", URI.create("urn:x-ogc:def:identifier:OGC:longname")));
    identifiers.add(id1);
    identifiers.add(id2);
    identifiers.add(id3);
    IdentifierList identifierList = new IdentifierList(null, identifiers);
    Identification identification = new Identification(identifierList);
    system.setIdentification(identification);
    Capabilities capabilities = new Capabilities();
    List<DataComponentPropertyType> fields = new ArrayList<DataComponentPropertyType>();
    QuantityType quantity = new QuantityType("urn:x-ogc:def:property:temperature", new UomPropertyType(null, "urn:ogc:unit:degree:celsius"), 0.1);
    DataComponentPropertyType field1 = new DataComponentPropertyType("resolution", "urn:x-ogc:def:property:resolution", quantity);
    fields.add(field1);
    QuantityRange quantityR = new QuantityRange(new UomPropertyType(null, "urn:ogc:unit:percent"), Arrays.asList(-0.5, 0.5));
    quantityR.setDefinition("urn:x-ogc:def:property:absoluteAccuracy");
    DataComponentPropertyType field2 = new DataComponentPropertyType("accuracy", "urn:x-ogc:def:property:accuracy", quantityR);
    fields.add(field2);
    DataRecordType record = new DataRecordType("urn:x-ogc:def:property:measurementProperties", fields);
    record.setDescription("Toutes les informations sur les  contraintes sur les donnees");
    JAXBElement<? extends AbstractDataRecordType> jbRecord = swe100Factory.createDataRecord(record);
    capabilities.setAbstractDataRecord(jbRecord);
    system.setCapabilities(capabilities);
    AddressType address1 = new AddressType("SGR LRO-1039 Rue de Pinville-34000 Montpellier", "MONTPELLIER", null, null, null, "m.blaise@brgm.fr");
    ContactInfo contactInfo1 = new ContactInfo(null, address1);
    ResponsibleParty resp1 = new ResponsibleParty("BLAISE Marion (BRGM)", "BRGM", null, contactInfo1);
    Contact contact1 = new Contact("urn:x-ogc:def:role:producer", resp1);
    AddressType address2 = new AddressType("Hotel du Departement, B.P. 906, 66 906 Perpignan Cedex", "PERPIGNAN", null, null, null, null);
    ContactInfo contactInfo2 = new ContactInfo(null, address2);
    ResponsibleParty resp2 = new ResponsibleParty("ASSENS Martine (CG66)", "CONSEIL GENERAL DES PYRENEES ORIENTALES", null, contactInfo2);
    Contact contact2 = new Contact("urn:x-ogc:def:role:owner", resp2);
    system.setContact(Arrays.asList(contact1, contact2));
    IoComponentPropertyType io = new IoComponentPropertyType("level", new ObservableProperty("urn:x-ogc:def:phenomenon:OGC:level"));
    InputList inputList = new InputList(Arrays.asList(io));
    Inputs inputs = new Inputs(inputList);
    system.setInputs(inputs);
    fields = new ArrayList<DataComponentPropertyType>();
    TimeType time = new TimeType("urn:x-ogc:def:phenomenon:observationTime", new UomPropertyType(null, "urn:x-ogc:def:unit:ISO8601"));
    fields.add(new DataComponentPropertyType("time", null, time));
    QuantityType q = new QuantityType("urn:x-ogc:def:phenomenon:OGC:depth", new UomPropertyType("m", null), null);
    fields.add(new DataComponentPropertyType("depth", null, q));
    BooleanType b = new BooleanType("urn:x-ogc:def:phenomenon:BRGM:validity", null);
    fields.add(new DataComponentPropertyType("validity", null, b));
    DataRecordType outRecord = new DataRecordType(null, fields);
    outRecord.setId("outputGroup");
    IoComponentPropertyType io2 = new IoComponentPropertyType("piezoMeasurements", swe100Factory.createDataRecord(outRecord));
    OutputList outputList = new OutputList(Arrays.asList(io2));
    Outputs outputs = new Outputs(outputList);
    system.setOutputs(outputs);
    fields = new ArrayList<DataComponentPropertyType>();
    q = new QuantityType("urn:x-ogc:def:property:depth", new UomPropertyType(null, "urn:ogc:unit:m"), 166.0);
    fields.add(new DataComponentPropertyType("MaxDepth", null, q));
    DataRecordType charRecord = new DataRecordType(null, fields);
    List<DataComponentPropertyType> fields2 = new ArrayList<DataComponentPropertyType>();
    fields2.add(new DataComponentPropertyType("physicalProperties", null, swe100Factory.createDataRecord(charRecord)));
    DataRecordType ccharRecord = new DataRecordType("urn:x-ogc:def:property:physicalProperties", fields2);
    Characteristics characteristics = new Characteristics();
    characteristics.setAbstractDataRecord(swe100Factory.createDataRecord(ccharRecord));
    system.setCharacteristics(characteristics);
    DirectPositionType pos = new DirectPositionType("urn:ogc:crs:EPSG:27582", 2, Arrays.asList(65400.0, 1731368.0));
    PointType point = new PointType("STATION_LOCALISATION", pos);
    Location location = new Location(point);
    system.setSMLLocation(location);
    EngineeringDatumType engineeringDatum = new EngineeringDatumType("datum", "Sensor Datum", new CodeType("X, Y et Z sont orthogonal au regard d'un point de reference."));
    EngineeringDatumRefType usesEngineeringDatum = new EngineeringDatumRefType(engineeringDatum);
    EngineeringCRSType engineeringCRS = new EngineeringCRSType("STATION_FRAME", "Position absolue du capteur", new CoordinateSystemRefType("urn:ogc:def:crs:ogc:1.0:xyzFrame"), usesEngineeringDatum);
    SpatialReferenceFrame spatialReferenceFrame = new SpatialReferenceFrame(engineeringCRS);
    system.setSpatialReferenceFrame(spatialReferenceFrame);
    Document doc = new Document("Fiche descriptive de la station", "text/html", Arrays.asList(new OnlineResource("http://ades.eaufrance.fr/FichePtEau.aspx?code=10972X0137/PONT")));
    Documentation documentation = new Documentation(doc);
    documentation.setRole("urn:ogc:role:description");
    system.setDocumentation(Arrays.asList(documentation));
    List<ComponentPropertyType> compos = new ArrayList<ComponentPropertyType>();
    compos.add(new ComponentPropertyType("Profondeur", "urn:x-ogc:def:sensor:detector", "capteur_"));
    ComponentList componentList = new ComponentList(compos);
    Components components = new Components(componentList);
    system.setComponents(components);
    List<CoordinateType> coordinates = new ArrayList<CoordinateType>();
    QuantityType xQuant = new QuantityType("urn:ogc:def:phenomenon:distance", new UomPropertyType("m", null), 0.0);
    xQuant.setAxisID("X");
    CoordinateType xcoord = new CoordinateType("x", xQuant);
    QuantityType yQuant = new QuantityType("urn:ogc:def:phenomenon:distance", new UomPropertyType("m", null), 0.0);
    yQuant.setAxisID("Y");
    CoordinateType ycoord = new CoordinateType("y", yQuant);
    QuantityType zQuant = new QuantityType("urn:ogc:def:phenomenon:distance", new UomPropertyType("m", null), 0.0);
    zQuant.setAxisID("Z");
    CoordinateType zcoord = new CoordinateType("z", zQuant);
    coordinates.add(xcoord);
    coordinates.add(ycoord);
    coordinates.add(zcoord);
    VectorType vect = new VectorType("urn:ogc:def:phenomenon:location", coordinates);
    VectorPropertyType vectP = new VectorPropertyType(vect);
    PositionType Sposition = new PositionType(URI.create("#REFERENCE_POINT"), URI.create("#PIEZOMETER_FRAME"), vectP, null);
    Position position = new Position("piezoPosition", Sposition);
    PositionList positionList = new PositionList(null, Arrays.asList(position));
    Positions positions = new Positions(positionList);
    system.setPositions(positions);
    TemporalReferenceFrame temporalReferenceFrame = new TemporalReferenceFrame(new TemporalCRSType("temporalReference", null, null, "calendrier gregorien en heure d'ete", new TemporalCSRefType("urn:x-brgm:temporalCS:gregorian"), new TemporalDatumRefType("urn:x-brgm:temporalDatum:UniversalTime")));
    system.setTemporalReferenceFrame(temporalReferenceFrame);
    List<Connection> connecL = new ArrayList<Connection>();
    connecL.add(new Connection("inputTolevel", new Link(null, new LinkRef("this/inputs/level"), new LinkRef("piezometer/inputs/level"))));
    Connection c2 = new Connection("depthToOutput", new Link(null, new LinkRef("piezometer/outputs/depth"), new LinkRef("this/outputs/piezoMeasurements/depth")));
    ArrayLink alink = new ArrayLink();
    LinkRef sa = new LinkRef("piezometer/outputs/depth");
    alink.setSourceArray(sa);
    LinkRef si = new LinkRef("this/outputs/piezoMeasurements/depth");
    alink.setSourceIndex(si);
    LinkRef da = new LinkRef("this/outputs/piezoMeasurements/depth");
    alink.setDestinationArray(da);
    LinkRef di = new LinkRef("this/outputs/piezoMeasurements/depth");
    alink.getDestinationIndex().add(di);
    c2.setArrayLink(alink);
    connecL.add(c2);
    ConnectionList connectionList = new ConnectionList(connecL);
    Connections connections = new Connections(connectionList);
    system.setConnections(connections);
    LayerPropertyType applicationLayer = new LayerPropertyType(new Category("urn:ogc:def:protocol:applicationLink", "urn:x-brgm:def:protocol:hydrasIRIS"));
    LayerPropertyType dataLinkLayer = new LayerPropertyType(new Category("urn:ogc:def:protocol:dataLink", "urn:x-brgm:def:dataLink:RTC"));
    InterfaceDefinition definition = new InterfaceDefinition(null, applicationLayer, dataLinkLayer);
    Interface i1 = new Interface("RS-232", definition);
    List<Interface> interfaceL = new ArrayList<Interface>();
    interfaceL.add(i1);
    InterfaceList interfaceList = new InterfaceList(null, interfaceL);
    Interfaces interfaces = new Interfaces(interfaceList);
    system.setInterfaces(interfaces);
    Rights rights = new Rights(true, true, new Documentation(new Document("Donnees sous copyright du BRGM")));
    LegalConstraint legalConstraint = new LegalConstraint(rights);
    system.setLegalConstraint(legalConstraint);
    system.setDescription("information about the piezometer");
    system.setName(new DefaultIdentifier("Piezometer Test"));
    member.setProcess(sml100Factory.createSystem(system));
    SensorML expectedResult = new SensorML("1.0", Arrays.asList(member));
    assertEquals(result.getMember().size(), 1);
    assertTrue(result.getMember().get(0).getProcess() != null);
    assertTrue(result.getMember().get(0).getProcess().getValue() instanceof SystemType);
    SystemType resultProcess = (SystemType) result.getMember().get(0).getProcess().getValue();
    assertEquals(resultProcess.getCapabilities().size(), system.getCapabilities().size());
    assertTrue(resultProcess.getCapabilities().get(0).getAbstractDataRecord().getValue() instanceof DataRecordType);
    DataRecordType resultRecord = (DataRecordType) resultProcess.getCapabilities().get(0).getAbstractDataRecord().getValue();
    DataRecordType expRecord = (DataRecordType) system.getCapabilities().get(0).getAbstractDataRecord().getValue();
    assertEquals(resultRecord.getField().get(0), expRecord.getField().get(0));
    assertEquals(resultRecord.getField().get(1), expRecord.getField().get(1));
    assertEquals(resultRecord.getField(), expRecord.getField());
    assertEquals(resultProcess.getCapabilities().get(0).getAbstractDataRecord().getValue(), system.getCapabilities().get(0).getAbstractDataRecord().getValue());
    assertEquals(resultProcess.getCapabilities().get(0), system.getCapabilities().get(0));
    assertEquals(resultProcess.getCapabilities(), system.getCapabilities());
    assertTrue(resultProcess.getContact().size() == 2);
    assertEquals(resultProcess.getContact().get(0).getContactList(), system.getContact().get(0).getContactList());
    assertEquals(resultProcess.getContact().get(0).getResponsibleParty().getContactInfo(), system.getContact().get(0).getResponsibleParty().getContactInfo());
    assertEquals(resultProcess.getContact().get(0).getResponsibleParty().getOrganizationName(), system.getContact().get(0).getResponsibleParty().getOrganizationName());
    assertEquals(resultProcess.getContact().get(0).getResponsibleParty(), system.getContact().get(0).getResponsibleParty());
    assertEquals(resultProcess.getContact().get(0), system.getContact().get(0));
    assertEquals(resultProcess.getContact(), system.getContact());
    assertTrue(resultProcess.getClassification().size() == 1);
    assertTrue(resultProcess.getClassification().get(0).getClassifierList().getClassifier().size() == 10);
    assertEquals(resultProcess.getClassification().get(0).getClassifierList().getClassifier().get(0).getTerm(), system.getClassification().get(0).getClassifierList().getClassifier().get(0).getTerm());
    assertEquals(resultProcess.getClassification().get(0).getClassifierList().getClassifier().get(0), system.getClassification().get(0).getClassifierList().getClassifier().get(0));
    assertEquals(resultProcess.getClassification().get(0).getClassifierList().getClassifier(), system.getClassification().get(0).getClassifierList().getClassifier());
    assertEquals(resultProcess.getClassification().get(0).getClassifierList(), system.getClassification().get(0).getClassifierList());
    assertEquals(resultProcess.getClassification().get(0), system.getClassification().get(0));
    assertEquals(resultProcess.getClassification(), system.getClassification());
    assertEquals(resultProcess.getIdentification(), system.getIdentification());
    assertEquals(resultProcess.getValidTime(), system.getValidTime());
    assertEquals(resultProcess.getParameters(), system.getParameters());
    assertEquals(resultProcess.getInputs().getInputList().getInput(), system.getInputs().getInputList().getInput());
    assertEquals(resultProcess.getInputs().getInputList(), system.getInputs().getInputList());
    assertEquals(resultProcess.getInputs(), system.getInputs());
    assertEquals(resultProcess.getOutputs(), system.getOutputs());
    assertEquals(resultProcess.getSMLLocation(), system.getSMLLocation());
    assertEquals(resultProcess.getPosition(), system.getPosition());
    assertEquals(resultProcess.getSpatialReferenceFrame(), system.getSpatialReferenceFrame());
    assertEquals(resultProcess.getDocumentation(), system.getDocumentation());
    assertEquals(resultProcess.getCharacteristics(), system.getCharacteristics());
    assertEquals(resultProcess.getComponents(), system.getComponents());
    assertEquals(resultProcess.getPositions(), system.getPositions());
    assertEquals(resultProcess.getTemporalReferenceFrame(), system.getTemporalReferenceFrame());
    assertEquals(resultProcess.getConnections().getConnectionList().getConnection().get(0), system.getConnections().getConnectionList().getConnection().get(0));
    assertEquals(resultProcess.getConnections().getConnectionList().getConnection().get(1), system.getConnections().getConnectionList().getConnection().get(1));
    assertEquals(resultProcess.getConnections().getConnectionList().getConnection(), system.getConnections().getConnectionList().getConnection());
    assertEquals(resultProcess.getConnections().getConnectionList(), system.getConnections().getConnectionList());
    assertEquals(resultProcess.getConnections(), system.getConnections());
    assertEquals(resultProcess.getInterfaces(), system.getInterfaces());
    assertEquals(resultProcess.getLegalConstraint(), system.getLegalConstraint());
    assertEquals(resultProcess.getKeywords(), system.getKeywords());
    assertEquals(resultProcess.getId(), system.getId());
    assertEquals(resultProcess.getName(), system.getName());
    assertEquals(resultProcess, system);
    assertEquals(expectedResult.getMember().get(0), result.getMember().get(0));
    assertEquals(expectedResult.getMember(), result.getMember());
    assertEquals(expectedResult, result);
    SensorMLMarshallerPool.getInstance().recycle(unmarshaller);
}

Example 2 with Link

use of org.candlepin.dto.api.v1.Link in project flow.service.workflow by boomerang-io.

the class ModelConverterV5 method convertToEntityModel.

public static RevisionEntity convertToEntityModel(WorkflowRevision revision) {
    RevisionEntity entity = new RevisionEntity();
    entity.setVersion(revision.getVersion());
    entity.setMarkdown(revision.getMarkdown());
    entity.setConfig(revision.getConfig());
    if (revision.getDag() == null) {
        return entity;
    }
    mapBaseData(revision, entity);
    List<Link> links = revision.getDag().getLinks();
    List<ConfigNodes> configNodes = revision.getConfig().getNodes();
    Dag dag = new Dag();
    entity.setDag(dag);
    List<DAGTask> tasks = new LinkedList<>();
    dag.setTasks(tasks);
    for (TaskNode node : revision.getDag().getNodes()) {
        DAGTask dagTask = new DAGTask();
        dagTask.setId(node.getNodeId());
        dagTask.setTemplateId(node.getTaskId());
        if ("startend".equals(node.getType())) {
            if ("Start".equals(node.getPassedName())) {
                dagTask.setType(TaskType.start);
            } else if ("End".equals(node.getPassedName())) {
                dagTask.setType(TaskType.end);
            }
        } else if (TEMPLATETASKNAME.equals(node.getType())) {
            dagTask.setType(TaskType.template);
        } else if (CUSTOMTASKNAME.equals(node.getType())) {
            dagTask.setType(TaskType.customtask);
        } else {
            dagTask.setType(TaskType.valueOf(node.getType()));
        }
        List<Dependency> dependencies = new LinkedList<>();
        dagTask.setDependencies(dependencies);
        List<Port> ports = node.getPorts();
        ConfigNodes config = configNodes.stream().parallel().filter(c -> node.getNodeId().equals(c.getNodeId())).findFirst().orElse(null);
        dagTask.setLabel(node.getTaskName());
        buildConfig(dagTask, config);
        caclulateDependncies(links, dependencies, ports);
        buildMetadataSection(node, dagTask);
        tasks.add(dagTask);
    }
    return entity;
}

Example 3 with Link

use of org.candlepin.dto.api.v1.Link in project flow.service.workflow by boomerang-io.

the class ModelConverterV5 method caclulateDependncies.

private static void caclulateDependncies(List<Link> links, List<Dependency> dependencies, List<Port> ports) {
    for (Port port : ports) {
        if ("left".equals(port.getPosition()) && !port.getLinks().isEmpty()) {
            for (String linkid : port.getLinks()) {
                Link link = links.stream().parallel().filter(l -> linkid.equals(l.getId())).findFirst().orElse(null);
                if (link != null) {
                    String source = link.getSource();
                    Dependency dependency = createDependency(link, source);
                    dependencies.add(dependency);
                }
            }
        }
    }
}

Example 4 with Link

use of org.candlepin.dto.api.v1.Link in project dishevelled-bio by heuermh.

the class Gfa1ToGfa2 method call.

@Override
public Integer call() throws Exception {
    PrintWriter writer = null;
    try {
        writer = writer(outputGfa2File);
        final PrintWriter w = writer;
        Gfa1Reader.stream(reader(inputGfa1File), new Gfa1Adapter() {

            @Override
            public boolean header(final Header header) {
                // convert VN:Z:1.0 to VN:Z:2.0 annotation if present
                if (header.getAnnotations().containsKey("VN")) {
                    if (!"1.0".equals(header.getAnnotations().get("VN").getValue())) {
                        throw new RuntimeException("cannot convert input as GFA 1.0, was " + header.getAnnotations().get("VN").getValue());
                    }
                    Map<String, Annotation> annotations = new HashMap<String, Annotation>();
                    annotations.put("VN", new Annotation("VN", "Z", "2.0"));
                    for (Annotation annotation : header.getAnnotations().values()) {
                        if (!"VN".equals(annotation.getName())) {
                            annotations.put(annotation.getName(), annotation);
                        }
                    }
                    Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Header(annotations), w);
                } else {
                    Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Header(header.getAnnotations()), w);
                }
                return true;
            }

            @Override
            public boolean segment(final Segment segment) {
                if (segment.getSequence() != null) {
                    Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Segment(segment.getId(), segment.getSequence().length(), segment.getSequence(), segment.getAnnotations()), w);
                } else if (segment.getAnnotations().containsKey("LN")) {
                    Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Segment(segment.getId(), Integer.parseInt(segment.getAnnotations().get("LN").getValue()), segment.getSequence(), segment.getAnnotations()), w);
                } else {
                    Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Segment(segment.getId(), 0, segment.getSequence(), segment.getAnnotations()), w);
                }
                return true;
            }

            @Override
            public boolean link(final Link link) {
                Position unknown = new Position(0, false);
                Alignment alignment = link.getOverlap() == null ? null : Alignment.valueOf(link.getOverlap());
                Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Edge(null, toGfa2Reference(link.getSource()), toGfa2Reference(link.getTarget()), unknown, unknown, unknown, unknown, alignment, link.getAnnotations()), w);
                return true;
            }

            @Override
            public boolean containment(final Containment containment) {
                Position unknown = new Position(0, false);
                Position targetStart = new Position(containment.getPosition(), false);
                Alignment alignment = containment.getOverlap() == null ? null : Alignment.valueOf(containment.getOverlap());
                Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Edge(null, toGfa2Reference(containment.getContainer()), toGfa2Reference(containment.getContained()), unknown, unknown, targetStart, unknown, alignment, containment.getAnnotations()), w);
                return true;
            }

            @Override
            public boolean path(final Path path) {
                Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Path(path.getName(), toGfa2References(path.getSegments()), path.getAnnotations()), w);
                return true;
            }
        });
        return 0;
    } finally {
        try {
            writer.close();
        } catch (Exception e) {
        // empty
        }
    }
}

Example 5 with Link

use of org.candlepin.dto.api.v1.Link in project flowlogix by flowlogix.

the class SessionTrackerUtil method redirectToSelf.

public static void redirectToSelf(RequestGlobals rg, PageRenderLinkSource linkSource) throws IOException {
    final Link link = linkSource.createPageRenderLink(rg.getRequest().getPath().replaceFirst("\\..*", "").substring(1));
    final String url = link.toAbsoluteURI(rg.getRequest().isSecure());
    if (rg.getRequest().isXHR()) {
        try (PrintWriter writer = rg.getResponse().getPrintWriter("application/json")) {
            writer.write("{\n\t\"redirectURL\" : \"" + url + "\"\n}");
        }
    } else {
        rg.getResponse().sendRedirect(url);
    }
}