File pdfFile = new File("...test.pdf");
byte[] pdfData = new byte[(int) pdfFile.length()];
DataInputStream dis = new DataInputStream(new FileInputStream(pdfFile));
dis.readFully(pdfData);  // read from file into byte[] array
dis.close();

String myConnectionString = "jdbc:mysql:...";
String user = "user";
String password = "password";
dbConnection = DriverManager.getConnection(myConnectionString, user, password);
PreparedStatement ps = dbConnection.prepareStatement(
        "INSERT INTO project (filename, pdf_file) VALUES (?,?)");
ps.setString(1, "test");
ps.setBytes(2, pdfData);  // byte[] array
ps.executeUpdate();