Notify Reviewer Gives 503 Error - OJS 2.4.1.0

[inertin]

OJS Version : 2.3.3.2 Upgraded to 2.4.1.0 by Full installation Database Upgrade.
Notify Reviewer mail link (/index.php/xxxx/editor/notifyReviewer?reviewId=xxx) gives 503 error.
From the submissionReview section: /index.php/xxxxx/editor/submissionReview/
Error Details:
Error: 503 Service Unavailable, The server is temporarily busy, try again later!
All other notifier links are working
PHP: Version 5.3.18

Gives same error in Apache in local XAMPP installation.
Also, in XAMPP after increasing memory limit, gives the following error : "Fatal error: Allowed memory size of 268435456 bytes exhausted (tried to allocate 261904 bytes) in D:\xampp\htdocs\lib\pkp\classes\file\FileManager.inc.php on line 337"

A new database installation works fine by the way...

Any Insights please... The old database contains 4500 users and 750 articles, so it is really troublesome to do a new mysql database installation...

[inertin]

::bump::

[bdgregg]

Can I ask how much memory does the whole system have that you are running this on?

From the messages you have given it seems like the system may be starved for memory. The 503 Error from the web server "Service unavailable" indicates a temporary overloading or maintenance of the server (http://www.checkupdown.com/status/E503.html). This could be a memory issue. Additionally the memory error you posted" Fatal error: Allowed memory size of 268435456 bytes exhausted (tried to allocate 261904 bytes) in D:\xampp\htdocs\lib\pkp\classes\file\FileManager.inc.php on line 337" shows that it has trouble allocating a chunk of RAM to handle the request.

Might I suggest that you reboot your server, make sure everything starts up properly and see if the error does go away as a first step to resolving this.

If the system still has issues afterwards please post the relevant parts of your web server error log showing any entries that are relevant to the time in which you are seeing the error.

[asmecher]

Hi inertin,

What page are you on when you receive the "out of memory" error? 256MB ought to be enough allocated to PHP for a single request. (In my experience, rebooting doesn't affect this kind of issue.)

Regards,
Alec Smecher
Public Knowledge Project Team

[inertin]

Hi inertin,

What page are you on when you receive the "out of memory" error? 256MB ought to be enough allocated to PHP for a single request. (In my experience, rebooting doesn't affect this kind of issue.)

Regards,
Alec Smecher
Public Knowledge Project Team

Can I ask how much memory does the whole system have that you are running this on?

Thank you for helping out Brian and Alec... Your help is much appreciated...
Firstly the memory limit as Alec suggested was already increased to 256MB and still memory allocation failed, as you can see...
Rebooting the server in VPS and XAMPP was also done several times and in other two servers.
memory allocation error was seen only in XAMPP local installation. In my Los Angeles VPS with 2GB RAM, the database upgrade from 2.3.3.2 to 2.4.1 went okay but with same error with page load failed in the page http://website.com/index.php/xxxx/edito ... eview/xxxx. it occurs after selecting reviewer and then clicking on the notify reviewer button. I have to specify that this error never occurs in a fresh installation with new database; so may I suggest that we can safely rule out 2.4.1 installation file system bugs and may be because there is some goof up in the database upgrade process from 2.3.3.2 to 2.4.1 ???
My production site runs in a reseller and shared centos 5 and 6 with cpanel. The error was duplicated with all kinds of server modes- Apache with mod_php, mod_php; mod_php_ruid2, su_php variations etc with path_info on and off...
php version upgrade by ISP to 5.3.8 with shared server failed my OJS-2.3.3.2 running version, that is why I had to upgrade in the first place....
I am attaching the debug output from the error page too below...
I can actually give you people the whole Los Angeles High RAM VPS login where the old and new journal systems are tested in; so that you can see the logs and stuff... It is running on kloxo now, with centos 5.8

[asmecher]

Hi inertin,

That's strange, because the "notify reviewer" function isn't one of the more memory-intensive ones. It suggests to me that you're hitting some kind of recursion limit due to memory usage.

Could you try resetting the file permissions in your files directory (the one configured under files_dir in config.inc.php)? All contents and subdirectories need to be writable by the account under which PHP scripts run (which will depend on what SAPI you're using).

Regards,
Alec Smecher
Public Knowledge Project Team

[inertin]

The permissions in files_dir location were "0755" for folders and "0644" for files...
When same files directory was tested with old installation of 2.3.3.2 with old dataabase, there is no notification e-mail page error...
Also, Author e-mailing and Editor-emailing from the same page works fast with absolutely no database lag !!!
The files directory comes to about 1GB, so we were using the same files storage directory for upgraded and old installation testing...
Also now tested with a new files directory with file permissions 0755 for folder and 0644 under public_html for files_dir and the error is present...

[asmecher]

Hi inertin,

Note that just the numeric permissions (e.g. 644 or 755) aren't necessarily enough -- you also need to make sure the owner and group users are appropriate.

Regards,
Alec Smecher
Public Knowledge Project Team

[inertin]

The permissions as far as I can see, are set okay in the shared server with cpanel where upgraded installation was running and also in VPS test server.
Is there any permission differences for files directory between OJS 2.3.3.2 and OJS 2.4.1 ?

[asmecher]

Hi inertin,

No, there weren't any changes in how files were stored between the two versions.

Regards,
Alec Smecher
Public Knowledge Project Team

[inertin]

Thank you Alec...
Because we couldn't find any workable solutions this far; we have started the long and arduous process of exporting and importing issues into a fresh database for 2.4.1.0...
Anyway; I have kept copies of old and problem databases; just in case you would suggest some workable solutions...

[asmecher]

Hi intertin,

Hmm, I suspect you're going to spend a lot of time avoiding a fix that'll turn out to be pretty trivial in the end. I'm wondering why a notification link would end up trying to make a directory anyway; if you drop a fatalError('...') call into that function temporarily (near where the code is dying), and turn on stack traces in config.inc.php, it would be a good start to tracking it down.

Regards,
Alec Smecher
Public Knowledge Project Team

[inertin]

That I would try and get back to you...
But I am happy to say that I found out how to get out of this problem; at least partially...
The problem seems to be in selecting the second option of E-Mailing Reviewer the submission during Notifier function - which is in setup-policies. The Notifier function goes through normally when standard review is selected...which I accidentally found out just today...

So, as you have suggested, the TemporaryFileManager.inc.php seems to be called only when E-Mail attachment option is selected and then the memory error props up...

I have (supposedly ) narrowed down the problem code in the E-Mail attachment option selection, to be the lines 277-287 in SectionEditorAction.inc.php :
" if ($isEmailBasedReview) {
// An email-based review process was selected. Attach
// the current review version.
import('classes.file.TemporaryFileManager');
$temporaryFileManager = new TemporaryFileManager();
$reviewVersion =& $sectionEditorSubmission->getReviewFile();
if ($reviewVersion) {
$temporaryFile = $temporaryFileManager->articleToTemporaryFile($reviewVersion, $user->getId());
$email->addPersistAttachment($temporaryFile);
}
}"

When I remove this code; the NotifyReviewer function continues on normally; albeit a missing review file attachment....

This does so seems to be a temporary file creation or manipulation problem; as far as I could understand...


I have seen the following erros when "Display an error message when something goes wrong." is turned On in config.nic.php - In E-Mail Attachment Reviewer Notifier Mode:

NOTICE: Undefined property: TemporaryFileManager::$filesDir (D:\xampp\htdocs\241\classes\file\TemporaryFileManager.inc.php:38)
NOTICE: Undefined property: TemporaryFileManager::$filesDir (D:\xampp\htdocs\241\classes\file\TemporaryFileManager.inc.php:40)

While database is loaded in XAMPP and trying "notifyReviewer" function;
and the following errors when "deprecation_warnings = On" alongwith "display_errors = On" :

ojs2 has produced an error Message: USER NOTICE: Deprecated function. In file: D:\xampp\htdocs\241\lib\pkp\classes\user\PKPUserDAO.inc.php At line: 59 Stacktrace: File: (unknown) line (unknown) Function: PKPApplication->errorHandler(1024, "Deprecated function.", "D:\xampp\htdocs\241\lib\pkp\classes\user\PKPUserDAO.inc.php", 59, Array(2)) File: D:\xampp\htdocs\241\lib\pkp\classes\user\PKPUserDAO.inc.php line 59 Function: trigger_error("Deprecated function.") File: D:\xampp\htdocs\241\classes\submission\sectionEditor\SectionEditorAction.inc.php line 217 Function: PKPUserDAO->getUser("2760") File: D:\xampp\htdocs\241\pages\sectionEditor\SubmissionEditHandler.inc.php line 679 Function: SectionEditorAction->notifyReviewer(Object(SectionEditorSubmission), 370, False, Object(Request)) File: (unknown) line (unknown) Function: SubmissionEditHandler->notifyReviewer(Array(0), Object(Request)) File: D:\xampp\htdocs\241\lib\pkp\classes\core\PKPRouter.inc.php line 370 Function: call_user_func(Array(2), Array(0), Object(Request)) File: D:\xampp\htdocs\241\lib\pkp\classes\core\PKPPageRouter.inc.php line 266 Function: PKPRouter->_authorizeInitializeAndCallRequest(Array(2), Object(Request), Array(0), False) File: D:\xampp\htdocs\241\lib\pkp\classes\core\Dispatcher.inc.php line 133 Function: PKPPageRouter->route(Object(Request)) File: D:\xampp\htdocs\241\lib\pkp\classes\core\PKPApplication.inc.php line 189 Function: Dispatcher->dispatch(Object(Request)) File: D:\xampp\htdocs\241\index.php line 63 Function: PKPApplication->execute() Server info: OS: WINNT PHP Version: 5.3.1 Apache Version: Apache/2.2.14 (Win32) DAV/2 mod_ssl/2.2.14 OpenSSL/0.9.8l mod_autoindex_color PHP/5.3.1 mod_apreq2-20090110/2.7.1 mod_perl/2.0.4 Perl/v5.10.1 DB Driver: mysql DB server version: 5.1.41
ojs2 has produced an error Message: USER NOTICE: Deprecated function. In file: D:\xampp\htdocs\241\lib\pkp\classes\user\PKPUserDAO.inc.php At line: 59 Stacktrace: File: (unknown) line (unknown) Function: PKPApplication->errorHandler(1024, "Deprecated function.", "D:\xampp\htdocs\241\lib\pkp\classes\user\PKPUserDAO.inc.php", 59, Array(2)) File: D:\xampp\htdocs\241\lib\pkp\classes\user\PKPUserDAO.inc.php line 59 Function: trigger_error("Deprecated function.") File: D:\xampp\htdocs\241\classes\security\Validation.inc.php line 255 Function: PKPUserDAO->getUser("2760") File: D:\xampp\htdocs\241\classes\submission\sectionEditor\SectionEditorAction.inc.php line 274 Function: Validation->generatePasswordResetHash("2760") File: D:\xampp\htdocs\241\pages\sectionEditor\SubmissionEditHandler.inc.php line 679 Function: SectionEditorAction->notifyReviewer(Object(SectionEditorSubmission), 370, False, Object(Request)) File: (unknown) line (unknown) Function: SubmissionEditHandler->notifyReviewer(Array(0), Object(Request)) File: D:\xampp\htdocs\241\lib\pkp\classes\core\PKPRouter.inc.php line 370 Function: call_user_func(Array(2), Array(0), Object(Request)) File: D:\xampp\htdocs\241\lib\pkp\classes\core\PKPPageRouter.inc.php line 266 Function: PKPRouter->_authorizeInitializeAndCallRequest(Array(2), Object(Request), Array(0), False) File: D:\xampp\htdocs\241\lib\pkp\classes\core\Dispatcher.inc.php line 133 Function: PKPPageRouter->route(Object(Request)) File: D:\xampp\htdocs\241\lib\pkp\classes\core\PKPApplication.inc.php line 189 Function: Dispatcher->dispatch(Object(Request)) File: D:\xampp\htdocs\241\index.php line 63 Function: PKPApplication->execute() Server info: OS: WINNT PHP Version: 5.3.1 Apache Version: Apache/2.2.14 (Win32) DAV/2 mod_ssl/2.2.14 OpenSSL/0.9.8l mod_autoindex_color PHP/5.3.1 mod_apreq2-20090110/2.7.1 mod_perl/2.0.4 Perl/v5.10.1 DB Driver: mysql DB server version: 5.1.41
NOTICE: Undefined property: TemporaryFileManager::$filesDir (D:\xampp\htdocs\241\classes\file\TemporaryFileManager.inc.php:38)
NOTICE: Undefined property: TemporaryFileManager::$filesDir (D:\xampp\htdocs\241\classes\file\TemporaryFileManager.inc.php:40)


Introducing fatalError('function'); with "stack trace on" into Notify function below line 285 for $email produced on screen error:

"Fatal error: Allowed memory size of 268435456 bytes exhausted (tried to allocate 24 bytes) in D:\xampp\htdocs\241\lib\pkp\classes\file\FileManager.inc.php on line 336"

[asmecher]

Hi inertin,

Are you able to upload file attachments manually to emails?

Regards,
Alec Smecher
Public Knowledge Project Team

[inertin]

Yes... We can manually upload attachments to E-Mails....