public void parseAnnotations()

in taverna-scufl2-t2flow/src/main/java/org/apache/taverna/scufl2/translator/t2flow/T2FlowParser.java [653:758]
91 lines of code
19 McCabe index (conditional complexity)

	public void parseAnnotations(WorkflowBean annotatedBean,
			Annotations annotations) throws ReaderException {
		// logger.fine("Checking annotations for " + annotatedSubject);

		Map<String, NetSfTavernaT2AnnotationAnnotationAssertionImpl> annotationElems = new HashMap<>();
		if (annotations == null
				|| annotations.getAnnotationChainOrAnnotationChain22() == null)
			return;
		for (JAXBElement<AnnotationChain> el : annotations
				.getAnnotationChainOrAnnotationChain22()) {
			NetSfTavernaT2AnnotationAnnotationAssertionImpl ann = el.getValue()
					.getNetSfTavernaT2AnnotationAnnotationChainImpl()
					.getAnnotationAssertions()
					.getNetSfTavernaT2AnnotationAnnotationAssertionImpl();
			String annClass = ann.getAnnotationBean().getClazz();
			if (annotationElems.containsKey(annClass)
					&& annotationElems.get(annClass).getDate()
							.compareToIgnoreCase(ann.getDate()) > 0)
				// ann.getDate() is less than current 'latest' annotation, skip
				continue;
			annotationElems.put(annClass, ann);
		}

		for (String clazz : annotationElems.keySet()) {
			NetSfTavernaT2AnnotationAnnotationAssertionImpl ann = annotationElems.get(clazz);
			Calendar cal = parseDate(ann.getDate());					
			String value = null;	
			String semanticMediaType = TEXT_TURTLE;
			for (Object obj : ann.getAnnotationBean().getAny()) {
				if (!(obj instanceof Element))
					continue;
				Element elem = (Element) obj;
				if (!(elem.getNamespaceURI() == null))
					continue;
				if (elem.getLocalName().equals("text")) {
					value = elem.getTextContent().trim();
					break;
				}
				if (clazz.equals(SEMANTIC_ANNOTATION)) {
					if (elem.getLocalName().equals("content"))
						value = elem.getTextContent().trim();
					if (elem.getLocalName().equals("mimeType"))
						semanticMediaType = elem.getTextContent().trim();
				}
			}
			if (value != null) {
				// Add the annotation
				Annotation annotation = new Annotation();
				WorkflowBundle workflowBundle = parserState.get()
						.getCurrentWorkflowBundle();
				annotation.setParent(workflowBundle);

				String path = "annotation/" + annotation.getName() + ".ttl";
				URI bodyURI = URI.create(path);

				annotation.setTarget(annotatedBean);
				annotation.setAnnotatedAt(cal);
				// annotation.setAnnotator();
				annotation.setSerializedBy(t2flowParserURI);
				annotation.setSerializedAt(new GregorianCalendar());
				URI annotatedSubject = uriTools.relativeUriForBean(
						annotatedBean, annotation);
				String body;
				if (clazz.equals(SEMANTIC_ANNOTATION)) {
					String baseStr = "@base <"
							+ annotatedSubject.toASCIIString() + "> .\n";
					body = baseStr + value;
				} else {
					// Generate Turtle from 'classic' annotation
					URI predicate = getPredicatesForClass().get(clazz);
					if (predicate == null) {
						if (isStrict())
							throw new ReaderException(
									"Unsupported annotation class " + clazz);
						return;
					}

					StringBuilder turtle = new StringBuilder();
					turtle.append("<");
					turtle.append(annotatedSubject.toASCIIString());
					turtle.append("> ");

					turtle.append("<");
					turtle.append(predicate.toASCIIString());
					turtle.append("> ");

					// A potentially multi-line string
					turtle.append("\"\"\"");
					// Escape existing \ to \\
					String escaped = value.replace("\\", "\\\\");
					// Escape existing " to \" (beware Java's escaping of \ and " below)
					escaped = escaped.replace("\"", "\\\"");
					turtle.append(escaped);
					turtle.append("\"\"\"");
					turtle.append(" .");
					body = turtle.toString();
				}
                try {
                    workflowBundle.getResources().addResource(body, path, semanticMediaType);
                } catch (IOException e) {
                    throw new ReaderException("Could not store annotation body to " + path, e);
                }
                annotation.setBody(bodyURI);
			}
		}
	}