WordPress frontend upload issue - php

Question

In frontend I have created a form that use upload_user_file() to upload files from fronted theme and every image is stored fine in WordPress media library (well it seems like so).
So when I upload a file named test.jpg its relative thumbnails is created and visible in media library.
test-150x150.jpg
test-300x225.jpg
test-1024x768.jpg
The problem I have is when I delete this image from the media library. Only the created thumbnails is deleted and test.jpg is left intact in the upload folder. If I upload this file directly from media library, and then delete it all files is deleted including test.jpg.
Heres the code that stores values in a database and also upload files to the medialibrary. Is there another WordPress function to use? I guess upload_user_file() is not storing image data correctly in database?
global $wpdb;
global $post;
//$table = 'wp_verk1_project'; //$post_slug=$post->post_name;
$table = $wpdb->prefix . "project_name_" . $post_slug=$post->post_name;
$data = array(
'contributorname' => $_POST['yourname'],
'email' => $_POST['email'],
'telephone' => $_POST['telephone'],
'description' => $_POST['description'],
'date' => date('Y-m-d'),
'time' => date('H:i:s'),
'upload' => upload_user_file($_FILES['file']),
'upload2' => upload_user_file($_FILES['file2']),
'upload3' => upload_user_file($_FILES['file3']),
'upload4' => upload_user_file($_FILES['file4']),
'upload5' => upload_user_file($_FILES['file5']),
'rate' => '0'
);
$format = array(
'%s',
'%s'
);
$success = $wpdb->insert($table, $data, $format);
if ($success) {
header("Location: " . get_bloginfo('url') . "/thank-you/");
exit();
}
edit_user_file():
function upload_user_file( $file = array() ) {
require_once( ABSPATH . 'wp-admin/includes/admin.php' );
$file_return = wp_handle_upload( $file, array('test_form' => false ) );
if( isset( $file_return['error'] ) || isset( $file_return['upload_error_handler'] ) ) {
return false;
} else {
$filename = $file_return['file'];
$attachment = array(
'post_mime_type' => $file_return['type'],
'post_title' => preg_replace( '/\.[^.]+$/', '', basename( $filename ) ),
'post_content' => '',
'post_status' => 'inherit',
'guid' => $file_return['url']
);
$attachment_id = wp_insert_attachment( $attachment, $file_return['url'] );
require_once (ABSPATH . 'wp-admin/includes/image.php' );
$attachment_data = wp_generate_attachment_metadata( $attachment_id, $filename );
wp_update_attachment_metadata( $attachment_id, $attachment_data );
if( 0 < intval( $attachment_id ) ) {
return $attachment_id;
}
}
return false;
}
Kind regards
Johan

Answer 1

I manage to solve my own question.
I digged into the WordPress core-files.
Ireplaced the following line:
$attachment_id = wp_insert_attachment( $attachment, $file_return['url'] );
with this:
$attachment_id = wp_insert_attachment( $attachment, $filename );
In wp_postmeta, meta_value for the upload was set to the complete url (http://sitenamen.com/wp-content/upload/2014/12/file.jpg) while it should be stored like this: 2014/12/file.jpg
Now all files is deleted.