Here is the method I used to load the main xslt and do the transformation:

String xslt = "src/main/resources/xslt/main.xslt";
....
InputStream is_xml =".....";
InputStream is_xslt = new FileInputStream(xsltPath);

Source xsltSource = new StreamSource(is_xslt);
Source xmlSource = new StreamSource(is_xml);

TransformerFactory transFact = TransformerFactory.newInstance();
Result result = new StreamResult(baos);
Transformer trans = transFact.newTransformer(xsltSource);
 trans.transform(xmlSource, result);