I think you will have to ask this question in a different place: it's something to do with the way that the catalog is working. It's certainly nothing to do with Saxon - Saxon doesn't get involved with dereferencing external entity references.
(Sorry if that sounds unhelpful. I'm happy to help with questions that fall outside the strict boundaries of Saxon if I happen to know the answer. But in this case I don't.)
Michael Kay

From: saxon-help-bounces@lists.sourceforge.net [mailto:saxon-help-bounces@lists.sourceforge.net] On Behalf Of Panthera 5000
Sent: 04 December 2007 22:17
To: saxon-help@lists.sourceforge.net
Subject: [saxon] net.sf.saxon.trans.DynamicError:java.net.MalformedURLException: no protocol: file_01.xml

My apology for the format error in my previous email. I didn't realize I cut & paste the html link as well. The clean version is below.
I have a Java program that transform XML files to another format using Saxon 8.7. It works fine for a single full XML file. When I try to transform a XML with entity file references, I got the no protocol error.
The XML looks like this:
<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE document PUBLIC "-//My Document DTD v1.1 20030520//EN" "mydtd/project.dtd" [
      <!ENTITY file_01 SYSTEM "file_01.xml">
      <!ENTITY file_02 SYSTEM "file_02.xml">
      <!ENTITY file_03 SYSTEM "file_03.xml">
      <!ENTITY file_04 SYSTEM "file_04.xml">
<document xmlns:xlink=" http://www.w3.org/1999/xlink">
      <title>Title here</title>

The error is:
net.sf.saxon.trans.DynamicError: java.net.MalformedURLException: no protocol: file_01.xml

I have catalog file to map my DTD so those are working fine. But as for the entity files, each project has different file so I don't think I map each of them.

Is there any solution in transforming this without getting the protocol error? Thank you for any help.

Owon. S.