/** {@inheritDoc} */
@Override
public SBOLDocument read(InputStream in) throws IOException, SBOLValidationException {
try {
Unmarshaller unmarshaller = JAXB.CONTEXT.createUnmarshaller();
if (validate) {
unmarshaller.setSchema(JAXB.SCHEMA);
}
SBOLDocument doc = (SBOLDocument) unmarshaller.unmarshal(in);
doc.accept(new PrecedeReferenceFinder());
doc.accept(new DuplicateRemover());
if (validate) {
new SBOLValidatorImpl().validateWithoutSchema(doc);
}
return doc;
} catch (SBOLValidationException e) {
throw e;
} catch (UnmarshalException e) {
if (e.getLinkedException() != null) {
throw new SBOLValidationException(e.getLinkedException());
} else {
throw new SBOLValidationException(e);
}
} catch (Exception e) {
throw new IOException(e);
}
}
public ArrayList validateXML(String xmlMessage) {
StringBuffer validationError = new StringBuffer("");
String result = "Pass";
ArrayList list = new ArrayList();
SubmitManufacturerPartyData sb = null;
InputStream inFile = null;
try {
inFile = new ByteArrayInputStream(xmlMessage.getBytes());
SchemaFactory schemaFactory = SchemaFactory.newInstance(XMLConstants.W3C_XML_SCHEMA_NS_URI);
Schema schema = schemaFactory.newSchema(new File("PartydataManufacturer.xsd"));
JAXBContext ctx = JAXBContext.newInstance(new Class[] {SubmitManufacturerPartyData.class});
Unmarshaller um = ctx.createUnmarshaller();
um.setSchema(schema);
sb = (SubmitManufacturerPartyData) um.unmarshal(inFile);
} catch (SAXException e) {
result = "Fail";
e.printStackTrace();
} catch (UnmarshalException umex) {
result = "Fail";
System.out.println("---------- XML Validation Error -------------- ");
System.out.println("#######" + umex.getLinkedException().getMessage());
umex.printStackTrace();
} catch (Exception e) {
result = "Fail";
e.printStackTrace();
}
list.add(sb);
list.add(result);
return list;
}