based on what you need: forget the PHP java bridge for now.
- Do a HTTP POST to Java server from PHP, you can find many examples. Unfortunately you will need to send the PDF ( in Body) over the network, which can be slow.
- Write an AppEngine app, which takes the POST and gets the PDF from body ( pdf file transfered over HTTP to Java hosting) -here you can find many examples.
- Parse the PDF file, convert to text. Here you will find many examples on API documentation of your PDF manipulation library
- at response parameter send back the text in Java side
- at PHP get the Text, do what you want / HANDLE THE LOST CONNECTION TO JAVA SERVER AND TO SLOW RESPONSE ON PHP SIDE!!!
As I remember the AppEngine can schedule a POST to your PHP, in case of taking to long the parsing. I did with a cron job? -can't remember, but I did a connection to outside, however AppEngine hosting is different from PHP, isn't just an FTP upload file, but there are tutorials how to do it from Eclipse.