SbgnUtil.readFrom(InputStream is) fails when conversion from Milestone 1 or 2 necessary

[tczauderna]

SbgnUtil.readFrom(InputStream is) fails when a conversion is necessary (from Milestone 1 or 2).

The problem is that the input stream can only be used once.

This happens here Sbgn result = (Sbgn) unmarshaller.unmarshal(is);

Afterwards the input stream is closed and a conversion is not possible.

This will always fail String docUri = XmlUtil.getDocumentUri(is);

Possible fixes

1. Don't provide conversion when an input stream is used. There is other readFrom methods which don't provide a conversion.
2. Save the input stream to a file and use readFromFile

public static Sbgn readFrom(InputStream is) throws IOException, JAXBException {
	
	try {
		File tmp = File.createTempFile("sbgn-", ".sbgn");
		tmp.deleteOnExit();
		Files.copy(is, tmp.toPath(), StandardCopyOption.REPLACE_EXISTING);
		return readFromFile(tmp);
	} catch (IOException ex) {
		throw ex;
	}
}

[fbergmann]

thanks for letting me know, I have to say i was really surprised how hard it seems to be to get the namespace uri's in Java. I'll have a look ... maybe there should be an option on SbgnUtil that controls whether a conversion should be attempted or not, and only if perform the workaround. I'll think about it

[fbergmann]

added test code, and unified the way non-files are treated, i hope this resolves the issue.