public void readManifestXML()

in taverna-robundle/src/main/java/org/apache/taverna/robundle/manifest/combine/CombineManifest.java [497:567]
62 lines of code
16 McCabe index (conditional complexity)

	public void readManifestXML() throws IOException {
		Path manifestXml = manifestXmlPath(bundle);
		OmexManifest omexManifest;
		try (InputStream inStream = newInputStream(manifestXml)) {
			InputSource src = new InputSource(inStream);
			Source source = new SAXSource(src);
			omexManifest = createUnMarshaller().unmarshal(source,
					OmexManifest.class).getValue();
			// omexManifest = (OmexManifest) createUnMarshaller().unmarshal(inStream);
		} catch (JAXBException | ClassCastException e) {
			// logger.warning("Could not parse " + manifestXml);
			throw new IOException("Could not parse " + manifestXml, e);
		}
		if (!manifest.getManifest().contains(manifestXml))
			manifest.getManifest().add(manifestXml);

		for (Content c : omexManifest.getContent()) {
			PathMetadata metadata;
			if (c.getLocation().contains(":")) {
				try {
					URI uri = new URI(c.getLocation());
					if (!uri.isAbsolute()) {
						logger.warning("Not an absolute URI, but contains :"
								+ c.getLocation());
						continue;
					}
					metadata = manifest.getAggregation(uri);
				} catch (URISyntaxException e) {
					logger.warning("Invalid URI " + c.getLocation());
					continue;
				}
			} else {
				Path path = bundle.getRoot().resolve(c.getLocation());
				if (Files.isSameFile(bundle.getRoot(), path)) {
					// metadata about the archive itself
					if (c.getFormat() != null && ! c.getFormat().isEmpty()) {
						URI uri;
						try {
							uri = new URI(c.getFormat());
						} catch (URISyntaxException e) {
							logger.warning(MANIFEST_XML + " non-URI format for . expected http://identifiers.org/combine.specifications/omex");
							continue;
						}
						if (! manifest.getConformsTo().contains(uri)) {
							manifest.getConformsTo().add(uri);
						}
					}
					// Don't add / to the list of aggregations in RO,
					// as / is the RO itself!
					continue;
				}

				if (!exists(path)) {
					logger.warning(MANIFEST_XML + " listed relative path "
							+ path + ", but it does not exist in bundle");
					continue;
				}
				metadata = manifest.getAggregation(path);
			}

			// Format - is it an URI or media type?
			if (c.getFormat().contains(":")) {
				metadata.setConformsTo(URI.create(c.getFormat()));
			} else if (!c.getFormat().isEmpty()) {
				metadata.setMediatype(c.getFormat());
			} else if (metadata.getFile() != null) {
				metadata.setMediatype(manifest.guessMediaType(metadata
						.getFile()));
			} // else: Not needed for URIs
		}
	}