The problem I had accessing the sqlite db file I created in my java (jersey) server had solely to due with path. Some of the docs say the jdbc connect url should look like "jdbc:sqlite://path-to-file/sample.db". I thought the double-slash was part of a htt protocol-style path and would map properly when deployed, but in actuality, it's an absolute or relative path. So, when I placed the file at the root of the WebContent folder (tomcat project), a uri like this worked "jdbc:sqlite:sample.db".
The one thing that was throwing me was that when I was stepping through the debugger, I received a message that said "opening db: ... permission denied". I thought it was a matter of file system permissions or perhaps sql user permissions. After finding out that SQLite doesn't have the concept of roles/permissions like MySQL, etc, I did eventually change the file permissions before I came to what I believe was the correct solution, but I think it was just a bad message (i.e. permission denied, instead of File not found).
Hope this helps someone.