Description:
Reading PDF file in Java activity with Adobe APIs works fine with TIBCO Businessworks (BW) 5.9.2 and backward versions but fails with java.net.MalformedURLException in TIBCO Businessworks (BW) 5.9.3 and newer versions.
Symptoms:
Steps to reproduce:

1). Download the attached jar file and the project.
2). Set the alias library in the AdobeUtilities/AlliasLibrary folder.
3). Set the full path of a sample pdf file in the input tab of the Java code activity.
4). Run the "read pdf from-file" process.
5). The process will run fine with BW 5.9.2, but will fail with the following exception with BW 5.9.3 and newer. The exception happens while executing doc.exportAnnotations() method in the Java code.

2013 Feb 06 12:19:44:780 GMT -8 BW.PDFReader Debug [BW-Core] Job-22000 Error in [read pdf form - file.process/read pdf file] While executing [invoke] encountered [com.adobe.pdf.exceptions.XFDFException] : [java.net.MalformedURLException at com.adobe.pdf.impl.PDFDocumentImpl.exportAnnotations(Unknown Source)]
2013 Feb 06 12:19:44:783 GMT -8 BW.PDFReader Debug [BW-Core] <= read pdf form - file.process/read pdf file.eval(Job-22000) returned ERROR
2013 Feb 06 12:19:44:784 GMT -8 BW.PDFReader Error [BW_Plugin] BW-JAVA-100001 Job-22000 Error in [read pdf form - file.process/read pdf file]
While executing [invoke] encountered [com.adobe.pdf.exceptions.XFDFException] : [java.net.MalformedURLException at com.adobe.pdf.impl.PDFDocumentImpl.exportAnnotations(Unknown Source)]
at com.tibco.plugin.java.JavaActivity.eval(JavaActivity.java:420)
at com.tibco.pe.plugin.Activity.eval(Activity.java:240)
at com.tibco.pe.core.TaskImpl.eval(TaskImpl.java:775)
at com.tibco.pe.core.Job.step(Job.java:729)
at com.tibco.pe.core.Job.checkStep(Job.java:518)
at com.tibco.pe.core.JobDispatcher$JobCourier.runx(JobDispatcher.java:249)
at com.tibco.pe.core.JobDispatcher$JobCourier.run(JobDispatcher.java:200)
<?xml version="1.0" encoding="UTF-8"?>

<Data>
<ns0:InvocationException xmlns:ns0="http://schemas.tibco.com/bw/plugins/java/5.0/javaExceptions">
<msg>While executing [invoke] encountered [com.adobe.pdf.exceptions.XFDFException] : [java.net.MalformedURLException at com.adobe.pdf.impl.PDFDocumentImpl.exportAnnotations(Unknown Source)]</msg>
<msgCode>BW-JAVA-100001</msgCode>
<methodName>invoke</methodName>
<exceptionClassName>com.adobe.pdf.exceptions.XFDFException</exceptionClassName>
<exceptionMessage>java.net.MalformedURLException at com.adobe.pdf.impl.PDFDocumentImpl.exportAnnotations(Unknown Source)</exceptionMessage>
</ns0:InvocationException>
</Data>
Cause:
The issue is due to jar xmlparsers.jar which provides the object of TransformFactoryImpl concrete class. It was changed starting with BW 5.9.3 for a security fix related to XML parsing. If you copy the engine.jar from BW 5.9.2 to the hotfix/lib directory of BW 5.9.3, the project will work fine even with BW 5.9.3.

1). Adding the following line into the beginning of your Java code:  
     System.setProperty("javax.xml.transform.TransformerFactory", "net.sf.saxon.TransformerFactoryImpl");

2). Adding the following line into your Java code:
    System.setProperty("javax.xml.transform.TransformerFactory","com.sun.org.apache.xalan.internal.xsltc.trax.TransformerFactoryImpl");

3). Disable the XML parser security feature introduced in BW 5.9.3 in the application’s tra (runtime) or designer.tra (design time) file, so that it will work like BW 5.9.2 and prior versions:
     java.property.com.tibco.xml.parsers.disabled true

Reading a PDF file using Java Code activity implementing Adobe APIs does not work.