Mysql file upload and pdf browser viewer failing to work - php

Question

I am trying to build an interface with between my Wordpress page and my practice management software. When I upload files directly to my practice management software a physical copy shows up in the patient file. When browsing files within the software, on first click, I am able to view them in a browser based pdf viewer. If I click again on the file link, the file downloads and opens on my PC's PDF software.
PROBLEM: currently my file uploads to the server and a physical file is placed in the patient file. When browsing files it will not show up in my PDF viewer. It downloads to my PC on the first click and opens into my PDF software. However, the same file, when uploaded directly to the software behaves as expected.
I see no difference in the two files. So I assume there must be a problem with the $contents variable in my query. I am only working with PDF files. To upload attachments in my private messaging software I am using the following code:
function action_getmsgup($uploadid) {
global $wpdb, $out;
$query = $wpdb->prepare("SELECT ID, post_mime_type, guid FROM {$wpdb->prefix}posts WHERE ID = %d", array($uploadid));
$rows = $wpdb->get_results($query, ARRAY_A);
foreach ($rows as $row) {
$url = $row['guid'];
$filename = basename($url);
$path = parse_url($url, PHP_URL_PATH); // just the path part of the URL
$parts = explode('/', $path); // all the components
$parts = array_slice($parts, -6); // the last six
$path = implode('/', $parts);
$filepath = ABSPATH . $path;
// Get file contents and make a blob.
$tmpfile = fopen($filepath, "r");
$contents = fread($tmpfile, filesize($filepath));
$out['filename'] = $filename;
$out['mimetype'] = $row['mimetype'];
$out['contents'] = $contents;
}
}
QUESTION: Is there a problem with my upload method that is not filling $contents correctly?