Examples with Annotation org.sbolstandard.core2.Annotation used on opensource projects

Example 46 with Annotation

use of org.sbolstandard.core2.Annotation in project libSBOLj by SynBioDex.

the class Provenance_SpecifyBuildOperations method specifyCutOperation.

/**
 * specifies to perform a cut operation in order to linearize a vector using a restriction enzyme
 *
 * @throws Exception
 */
public static void specifyCutOperation() throws Exception {
    // instantiate a document
    SBOLDocument document = new SBOLDocument();
    document.setDefaultURIprefix(BUILD_PREFIX);
    ComponentDefinition vector = document.createComponentDefinition("vector", VECTOR_PLASMID);
    vector.setName("vector");
    ComponentDefinition enzyme = document.createComponentDefinition("restriction_enzyme", RESTRICTION_ENZYME);
    enzyme.setName("restriction_enzyme");
    // Create the generic top level entity for the cut operation
    Activity activity = document.createActivity("cut_" + vector.getName() + "_with_" + enzyme.getName());
    activity.setName("cut(" + vector.getName() + ", " + enzyme.getName() + ")");
    // Create the qualifiedUsage annotation to describe the inputs of the cut operation
    activity.createUsage("vector", vector.getIdentity()).addRole(VECTOR_PLASMID);
    activity.createUsage("enzyme", enzyme.getIdentity()).addRole(RESTRICTION_ENZYME);
    // the result of the cut operation
    ComponentDefinition linearized_vector = document.createComponentDefinition("linearized_vector", LINEAR_DOUBLE_STRANDED_DNA);
    linearized_vector.setName("linearized_vector");
    linearized_vector.addWasGeneratedBy(activity.getIdentity());
    // serialize the document to a file
    SBOLWriter.write(document, System.out);
}

Example 47 with Annotation

use of org.sbolstandard.core2.Annotation in project libSBOLj by SynBioDex.

the class AnnotationOutput method main.

public static void main(String[] args) throws Exception {
    String prURI = "http://partsregistry.org/";
    String prPrefix = "pr";
    SBOLDocument document = new SBOLDocument();
    document.setDefaultURIprefix(prURI);
    document.setTypesInURIs(true);
    document.addNamespace(URI.create(prURI), prPrefix);
    ComponentDefinition promoter = document.createComponentDefinition("BBa_J23119", "", new HashSet<URI>(Arrays.asList(URI.create("http://www.biopax.org/release/biopax-level3.owl#DnaRegion"))));
    promoter.addRole(SequenceOntology.PROMOTER);
    promoter.setName("J23119");
    promoter.setDescription("Constitutive promoter");
    promoter.createAnnotation(new QName(prURI, "group", prPrefix), "iGEM2006_Berkeley");
    promoter.createAnnotation(new QName(prURI, "experience", prPrefix), URI.create("http://parts.igem.org/cgi/partsdb/part_info.cgi?part_name=BBa_J23119"));
    Annotation sigmaFactor = new Annotation(QName(prURI, "sigmafactor", prPrefix), "//rnap/prokaryote/ecoli/sigma70");
    Annotation regulation = new Annotation(QName(prURI, "regulation", prPrefix), "//regulation/constitutive");
    promoter.createAnnotation(new QName(prURI, "information", prPrefix), new QName(prURI, "Information", prPrefix), URI.create("http://partsregistry.org/cd/BBa_J23119/information"), new ArrayList<Annotation>(Arrays.asList(sigmaFactor, regulation)));
    SBOLWriter.write(document, (System.out));
}

Example 48 with Annotation

use of org.sbolstandard.core2.Annotation in project zipkin by openzipkin.

the class JacksonSpanDecoder method parseSpan.

static Span parseSpan(JsonParser jsonParser) throws IOException {
    if (!jsonParser.isExpectedStartObjectToken()) {
        throw new IOException("Not a valid JSON object, start token: " + jsonParser.currentToken());
    }
    Span.Builder result = Span.newBuilder();
    while (jsonParser.nextToken() != JsonToken.END_OBJECT) {
        String fieldName = jsonParser.currentName();
        JsonToken value = jsonParser.nextToken();
        if (value == JsonToken.VALUE_NULL) {
            continue;
        }
        switch(fieldName) {
            case "traceId":
                result.traceId(jsonParser.getValueAsString());
                break;
            case "parentId":
                result.parentId(jsonParser.getValueAsString());
                break;
            case "id":
                result.id(jsonParser.getValueAsString());
                break;
            case "kind":
                result.kind(Span.Kind.valueOf(jsonParser.getValueAsString()));
                break;
            case "name":
                result.name(jsonParser.getValueAsString());
                break;
            case "timestamp":
                result.timestamp(jsonParser.getValueAsLong());
                break;
            case "duration":
                result.duration(jsonParser.getValueAsLong());
                break;
            case "localEndpoint":
                result.localEndpoint(parseEndpoint(jsonParser));
                break;
            case "remoteEndpoint":
                result.remoteEndpoint(parseEndpoint(jsonParser));
                break;
            case "annotations":
                if (!jsonParser.isExpectedStartArrayToken()) {
                    throw new IOException("Invalid span, expecting annotations array start, got: " + value);
                }
                while (jsonParser.nextToken() != JsonToken.END_ARRAY) {
                    Annotation a = parseAnnotation(jsonParser);
                    result.addAnnotation(a.timestamp(), a.value());
                }
                break;
            case "tags":
                if (value != JsonToken.START_OBJECT) {
                    throw new IOException("Invalid span, expecting tags object, got: " + value);
                }
                while (jsonParser.nextToken() != JsonToken.END_OBJECT) {
                    result.putTag(jsonParser.currentName(), jsonParser.nextTextValue());
                }
                break;
            case "debug":
                result.debug(jsonParser.getBooleanValue());
                break;
            case "shared":
                result.shared(jsonParser.getBooleanValue());
                break;
            default:
                jsonParser.skipChildren();
        }
    }
    return result.build();
}

Example 49 with Annotation

use of org.sbolstandard.core2.Annotation in project zipkin by openzipkin.

the class V2SpanWriter method write.

@Override
public void write(Span value, WriteBuffer b) {
    b.writeAscii("{\"traceId\":\"");
    b.writeAscii(value.traceId());
    b.writeByte('"');
    if (value.parentId() != null) {
        b.writeAscii(",\"parentId\":\"");
        b.writeAscii(value.parentId());
        b.writeByte('"');
    }
    b.writeAscii(",\"id\":\"");
    b.writeAscii(value.id());
    b.writeByte('"');
    if (value.kind() != null) {
        b.writeAscii(",\"kind\":\"");
        b.writeAscii(value.kind().toString());
        b.writeByte('"');
    }
    if (value.name() != null) {
        b.writeAscii(",\"name\":\"");
        b.writeUtf8(jsonEscape(value.name()));
        b.writeByte('"');
    }
    if (value.timestampAsLong() != 0L) {
        b.writeAscii(",\"timestamp\":");
        b.writeAscii(value.timestampAsLong());
    }
    if (value.durationAsLong() != 0L) {
        b.writeAscii(",\"duration\":");
        b.writeAscii(value.durationAsLong());
    }
    if (value.localEndpoint() != null) {
        b.writeAscii(",\"localEndpoint\":");
        writeEndpoint(value.localEndpoint(), b, false);
    }
    if (value.remoteEndpoint() != null) {
        b.writeAscii(",\"remoteEndpoint\":");
        writeEndpoint(value.remoteEndpoint(), b, false);
    }
    if (!value.annotations().isEmpty()) {
        b.writeAscii(",\"annotations\":");
        b.writeByte('[');
        for (int i = 0, length = value.annotations().size(); i < length; ) {
            Annotation a = value.annotations().get(i++);
            writeAnnotation(a.timestamp(), a.value(), null, b);
            if (i < length)
                b.writeByte(',');
        }
        b.writeByte(']');
    }
    if (!value.tags().isEmpty()) {
        b.writeAscii(",\"tags\":{");
        Iterator<Map.Entry<String, String>> i = value.tags().entrySet().iterator();
        while (i.hasNext()) {
            Map.Entry<String, String> entry = i.next();
            b.writeByte('"');
            b.writeUtf8(jsonEscape(entry.getKey()));
            b.writeAscii("\":\"");
            b.writeUtf8(jsonEscape(entry.getValue()));
            b.writeByte('"');
            if (i.hasNext())
                b.writeByte(',');
        }
        b.writeByte('}');
    }
    if (Boolean.TRUE.equals(value.debug())) {
        b.writeAscii(",\"debug\":true");
    }
    if (Boolean.TRUE.equals(value.shared())) {
        b.writeAscii(",\"shared\":true");
    }
    b.writeByte('}');
}

Example 50 with Annotation

use of org.sbolstandard.core2.Annotation in project zipkin by openzipkin.

the class QueryRequest method test.

/**
 * Tests the supplied trace against the current request.
 *
 * <p>This is used when the backend cannot fully refine a trace query.
 */
public boolean test(List<Span> spans) {
    // v2 returns raw spans in any order, get the root's timestamp or the first timestamp
    long timestamp = 0L;
    for (Span span : spans) {
        if (span.timestampAsLong() == 0L)
            continue;
        if (span.parentId() == null) {
            timestamp = span.timestampAsLong();
            break;
        }
        if (timestamp == 0L || timestamp > span.timestampAsLong()) {
            timestamp = span.timestampAsLong();
        }
    }
    if (timestamp == 0L || timestamp < (endTs() - lookback()) * 1000 || timestamp > endTs() * 1000) {
        return false;
    }
    boolean testedDuration = minDuration() == null && maxDuration() == null;
    String serviceNameToMatch = serviceName();
    String remoteServiceNameToMatch = remoteServiceName();
    String spanNameToMatch = spanName();
    Map<String, String> annotationQueryRemaining = new LinkedHashMap<String, String>(annotationQuery());
    for (Span span : spans) {
        String localServiceName = span.localServiceName();
        // service name, when present, constrains other queries.
        if (serviceName() == null || serviceName().equals(localServiceName)) {
            serviceNameToMatch = null;
            for (Annotation a : span.annotations()) {
                if ("".equals(annotationQueryRemaining.get(a.value()))) {
                    annotationQueryRemaining.remove(a.value());
                }
            }
            for (Map.Entry<String, String> t : span.tags().entrySet()) {
                String value = annotationQueryRemaining.get(t.getKey());
                if (value == null)
                    continue;
                if (value.isEmpty() || value.equals(t.getValue())) {
                    annotationQueryRemaining.remove(t.getKey());
                }
            }
            if (remoteServiceNameToMatch != null && remoteServiceNameToMatch.equals(span.remoteServiceName())) {
                remoteServiceNameToMatch = null;
            }
            if (spanNameToMatch != null && spanNameToMatch.equals(span.name())) {
                spanNameToMatch = null;
            }
            if (!testedDuration) {
                if (minDuration() != null && maxDuration() != null) {
                    testedDuration = span.durationAsLong() >= minDuration() && span.durationAsLong() <= maxDuration();
                } else if (minDuration() != null) {
                    testedDuration = span.durationAsLong() >= minDuration();
                }
            }
        }
    }
    return (serviceName() == null || serviceNameToMatch == null) && remoteServiceNameToMatch == null && spanNameToMatch == null && annotationQueryRemaining.isEmpty() && testedDuration;
}