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

Example 21 with Annotation

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

the class SBOLReader method parseCollection.

/**
 * @param SBOLDoc
 * @param topLevel
 * @return
 * @throws SBOLValidationException if either of the following conditions is satisfied:
 * <ul>
 * <li>any of the following SBOL validation rules was violated:
 * 10202, 10203, 10204, 10206, 10208, 10212, 10213, 12102; or</li>
 * <li>an SBOL validation rule violation occurred in the following constructor or methods:
 * 	<ul>
 * 		<li>{@link Collection#Collection(URI)}, </li>
 * 		<li>{@link Collection#setDisplayId(String)}, </li>
 * 		<li>{@link Collection#setVersion(String)}, </li>
 * 		<li>{@link Collection#setMembers(Set)}, </li>
 * 		<li>{@link Collection#setWasDerivedFrom(URI)}, </li>
 * 		<li>{@link Identified#setAnnotations(List)}, or</li>
 * 		<li>{@link SBOLDocument#addCollection(Collection)}.</li>
 * 	</ul>
 * </li>
 * </ul>
 */
@SuppressWarnings({ "rawtypes", "unchecked" })
private static Collection parseCollection(SBOLDocument SBOLDoc, IdentifiableDocument<QName> topLevel, Map<URI, NestedDocument<QName>> nested) throws SBOLValidationException {
    // URIcompliance.extractDisplayId(topLevel.getIdentity());
    String displayId = null;
    String name = null;
    String description = null;
    // URI.create(URIcompliance.extractPersistentId(topLevel.getIdentity()));
    URI persistentIdentity = null;
    String version = null;
    Set<URI> wasDerivedFroms = new HashSet<>();
    Set<URI> wasGeneratedBys = new HashSet<>();
    Set<URI> attachments = new HashSet<>();
    Set<URI> members = new HashSet<>();
    List<Annotation> annotations = new ArrayList<>();
    for (NamedProperty<QName> namedProperty : topLevel.getProperties()) {
        if (namedProperty.getName().equals(Sbol2Terms.Identified.persistentIdentity)) {
            if (!(namedProperty.getValue() instanceof Literal) || persistentIdentity != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10203", topLevel.getIdentity());
            }
            persistentIdentity = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.version)) {
            if (!(namedProperty.getValue() instanceof Literal) || version != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10206", topLevel.getIdentity());
            }
            version = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.displayId)) {
            if (!(namedProperty.getValue() instanceof Literal) || displayId != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10204", topLevel.getIdentity());
            }
            displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Collection.hasMembers)) {
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-12102", topLevel.getIdentity());
                }
                members.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
            } else if (namedProperty.getValue() instanceof NestedDocument) {
                if (((IdentifiableDocument) namedProperty).getType().equals(Sbol2Terms.Collection.Collection))
                    parseCollection(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.ModuleDefinition.ModuleDefinition))
                    parseModuleDefinition(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Model.Model))
                    parseModel(SBOLDoc, (IdentifiableDocument) namedProperty);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Sequence.Sequence))
                    parseSequence(SBOLDoc, (IdentifiableDocument) namedProperty);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.ComponentDefinition.ComponentDefinition))
                    parseComponentDefinition(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.CombinatorialDerivation.CombinatorialDerivation))
                    parseCombinatorialDerivation(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Implementation.Implementation))
                    parseImplementation(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Attachment.Attachment))
                    parseAttachment(SBOLDoc, (IdentifiableDocument) namedProperty);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Activity.Activity))
                    parseActivity(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Agent.Agent))
                    parseAgent(SBOLDoc, (IdentifiableDocument) namedProperty);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Plan.Plan))
                    parsePlan(SBOLDoc, (IdentifiableDocument) namedProperty);
                else
                    parseGenericTopLevel(SBOLDoc, (IdentifiableDocument) namedProperty);
            } else {
                throw new SBOLValidationException("sbol-12102", topLevel.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.title)) {
            if (!(namedProperty.getValue() instanceof Literal) || name != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10212", topLevel.getIdentity());
            }
            name = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.description)) {
            if (!(namedProperty.getValue() instanceof Literal) || description != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10213", topLevel.getIdentity());
            }
            description = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.wasDerivedFrom)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10208", topLevel.getIdentity());
            }
            wasDerivedFroms.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.wasGeneratedBy)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10221", topLevel.getIdentity());
            }
            wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.TopLevel.hasAttachment)) {
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-XXXXX", topLevel.getIdentity());
                }
                attachments.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
            } else if (namedProperty.getValue() instanceof IdentifiableDocument) {
                if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.Attachment.Attachment)) {
                    Attachment attachment = parseAttachment(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue());
                    attachments.add(attachment.getIdentity());
                } else {
                    throw new SBOLValidationException("sbol-XXXXX", topLevel.getIdentity());
                }
            } else {
                throw new SBOLValidationException("sbol-XXXXX", topLevel.getIdentity());
            }
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    Collection c = new Collection(topLevel.getIdentity());
    if (displayId != null)
        c.setDisplayId(displayId);
    if (version != null)
        c.setVersion(version);
    if (persistentIdentity != null)
        c.setPersistentIdentity(persistentIdentity);
    if (!members.isEmpty())
        c.setMembers(members);
    if (name != null)
        c.setName(name);
    if (description != null)
        c.setDescription(description);
    c.setWasDerivedFroms(wasDerivedFroms);
    c.setWasGeneratedBys(wasGeneratedBys);
    c.setAttachments(attachments);
    if (!annotations.isEmpty())
        c.setAnnotations(annotations);
    Collection oldC = SBOLDoc.getCollection(topLevel.getIdentity());
    if (oldC == null) {
        SBOLDoc.addCollection(c);
    } else {
        if (!c.equals(oldC)) {
            throw new SBOLValidationException("sbol-10202", c);
        }
    }
    return c;
}

Example 22 with Annotation

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

the class ComponentDefinition method createSequenceAnnotation.

/**
 * Creates a child sequence annotation for this component definition with the given arguments,
 * and then adds to this component definition's list of sequence annotations.
 *
 * @param displayId the display ID of the sequence annotation to be created
 * @param location the location of the sequence annotation to be created
 * @return the created sequence annotation
 * @throws SBOLValidationException if any of the following condition is satisfied:
 * <ul>
 * <li>an SBOL validation rule violation occurred in {@link URIcompliance#createCompliantURI(String, String, String)};</li>
 * <li>an SBOL validation rule violation occurred in {@link #createSequenceAnnotation(URI, Set)};</li>
 * <li>an SBOL validation rule violation occurred in {@link SequenceAnnotation#setDisplayId(String)}; or</li>
 * <li>an SBOL validation rule violation occurred in {@link SequenceAnnotation#setVersion(String)}.</li>
 * </ul>
 */
private SequenceAnnotation createSequenceAnnotation(String displayId, Location location) throws SBOLValidationException {
    String URIprefix = this.getPersistentIdentity().toString();
    String version = this.getVersion();
    URI newSequenceAnnotationURI = createCompliantURI(URIprefix, displayId, version);
    Set<Location> locations = new HashSet<>();
    locations.add(location);
    SequenceAnnotation sa = createSequenceAnnotation(newSequenceAnnotationURI, locations);
    sa.setPersistentIdentity(createCompliantURI(URIprefix, displayId, ""));
    sa.setDisplayId(displayId);
    sa.setVersion(version);
    return sa;
}

Example 23 with Annotation

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

the class BulkIndexWriter method addSearchFields.

static void addSearchFields(Span span, JsonGenerator writer) throws IOException {
    long timestampMillis = span.timestampAsLong() / 1000L;
    if (timestampMillis != 0L)
        writer.writeNumberField("timestamp_millis", timestampMillis);
    if (!span.tags().isEmpty() || !span.annotations().isEmpty()) {
        writer.writeArrayFieldStart("_q");
        for (Annotation a : span.annotations()) {
            if (a.value().length() > SHORT_STRING_LENGTH)
                continue;
            writer.writeString(a.value());
        }
        for (Map.Entry<String, String> tag : span.tags().entrySet()) {
            int length = tag.getKey().length() + tag.getValue().length() + 1;
            if (length > SHORT_STRING_LENGTH)
                continue;
            // search is possible by key alone
            writer.writeString(tag.getKey());
            writer.writeString(tag.getKey() + "=" + tag.getValue());
        }
        writer.writeEndArray();
    }
}

Example 24 with Annotation

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

the class CassandraUtil method annotationQuery.

/**
 * Returns a set of annotation getValues and tags joined on equals, delimited by ░
 *
 * <p>Values over {@link RecyclableBuffers#SHORT_STRING_LENGTH} are not considered. Zipkin's
 * {@link QueryRequest#annotationQuery()} are equals match. Not all values are lookup values. For
 * example, {@code sql.query} isn't something that is likely to be looked up by value and indexing
 * that could add a potentially kilobyte partition key on {@link Schema#TABLE_SPAN}
 *
 * @see QueryRequest#annotationQuery()
 */
@Nullable
static String annotationQuery(Span span) {
    if (span.annotations().isEmpty() && span.tags().isEmpty())
        return null;
    // as very unlikely to be in the query
    char delimiter = '░';
    StringBuilder result = new StringBuilder().append(delimiter);
    for (Annotation a : span.annotations()) {
        if (a.value().length() > SHORT_STRING_LENGTH)
            continue;
        result.append(a.value()).append(delimiter);
    }
    for (Map.Entry<String, String> tag : span.tags().entrySet()) {
        if (tag.getValue().length() > SHORT_STRING_LENGTH)
            continue;
        // search is possible by key alone
        result.append(tag.getKey()).append(delimiter);
        result.append(tag.getKey()).append('=').append(tag.getValue()).append(delimiter);
    }
    return result.length() == 1 ? null : result.toString();
}

Example 25 with Annotation

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

the class V2SpanWriter method sizeInBytes.

@Override
public int sizeInBytes(Span value) {
    // {"traceId":""
    int sizeInBytes = 13;
    sizeInBytes += value.traceId().length();
    if (value.parentId() != null) {
        // ,"parentId":"0123456789abcdef"
        sizeInBytes += 30;
    }
    // ,"id":"0123456789abcdef"
    sizeInBytes += 24;
    if (value.kind() != null) {
        // ,"kind":""
        sizeInBytes += 10;
        sizeInBytes += value.kind().name().length();
    }
    if (value.name() != null) {
        // ,"name":""
        sizeInBytes += 10;
        sizeInBytes += jsonEscapedSizeInBytes(value.name());
    }
    if (value.timestampAsLong() != 0L) {
        // ,"timestamp":
        sizeInBytes += 13;
        sizeInBytes += asciiSizeInBytes(value.timestampAsLong());
    }
    if (value.durationAsLong() != 0L) {
        // ,"duration":
        sizeInBytes += 12;
        sizeInBytes += asciiSizeInBytes(value.durationAsLong());
    }
    if (value.localEndpoint() != null) {
        // ,"localEndpoint":
        sizeInBytes += 17;
        sizeInBytes += endpointSizeInBytes(value.localEndpoint(), false);
    }
    if (value.remoteEndpoint() != null) {
        // ,"remoteEndpoint":
        sizeInBytes += 18;
        sizeInBytes += endpointSizeInBytes(value.remoteEndpoint(), false);
    }
    if (!value.annotations().isEmpty()) {
        // ,"annotations":[]
        sizeInBytes += 17;
        int length = value.annotations().size();
        // comma to join elements
        if (length > 1)
            sizeInBytes += length - 1;
        for (int i = 0; i < length; i++) {
            Annotation a = value.annotations().get(i);
            sizeInBytes += annotationSizeInBytes(a.timestamp(), a.value(), 0);
        }
    }
    if (!value.tags().isEmpty()) {
        // ,"tags":{}
        sizeInBytes += 10;
        int tagCount = value.tags().size();
        // comma to join elements
        if (tagCount > 1)
            sizeInBytes += tagCount - 1;
        for (Map.Entry<String, String> entry : value.tags().entrySet()) {
            // "":""
            sizeInBytes += 5;
            sizeInBytes += jsonEscapedSizeInBytes(entry.getKey());
            sizeInBytes += jsonEscapedSizeInBytes(entry.getValue());
        }
    }
    if (Boolean.TRUE.equals(value.debug())) {
        // ,"debug":true
        sizeInBytes += 13;
    }
    if (Boolean.TRUE.equals(value.shared())) {
        // ,"shared":true
        sizeInBytes += 14;
    }
    // }
    return ++sizeInBytes;
}