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Fatal Error with CrossRef XML Export Plugin using 2.4.3

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Fatal Error with CrossRef XML Export Plugin using 2.4.3

Postby jamilj » Mon Jan 27, 2014 2:01 pm

Hello,

I am getting a fatal error when I attempt to export DOI data using the CrossRef XML Export Plugin:

Fatal error: Maximum execution time of 30 seconds exceeded in ~/public_html/archives_ojs/lib/pkp/classes/plugins/HookRegistry.inc.php on line 22


This seems to be a new problem since installing the 2.4.3 version of OJS. Is anyone else having this issue?
jamilj
 
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Re: Fatal Error with CrossRef XML Export Plugin using 2.4.3

Postby asmecher » Mon Jan 27, 2014 2:35 pm

Hi Jamil,

Are there any third-party plugins or modifications to your install (i.e. anything besides the OJS 2.4.3 tarball)?

Regards,
Alec Smecher
Public Knowledge Project Team
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Re: Fatal Error with CrossRef XML Export Plugin using 2.4.3

Postby jamilj » Mon Jan 27, 2014 8:39 pm

Dear Alex,

Unfortunately no, I only ran the patches after the install. I did a complete swap of the files, and then went back and added the changes to the config.inc.php file. Other than that, it should be a fresh install so I'm not sure what is up.
jamilj
 
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Re: Fatal Error with CrossRef XML Export Plugin using 2.4.3

Postby swing » Tue Jan 28, 2014 1:09 am

Hi jamilj,

Could you tell us what exactly are you trying to export? Does this error always occur, no matter what object you try to export the DOIs for? Could it be that you are trying to export the DOIs for lots of objects? Hmmm... Any further information would be very helpful.

Thanks!
Bozana Bokan
swing
 
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Re: Fatal Error with CrossRef XML Export Plugin using 2.4.3

Postby mrcardoso » Tue Jan 28, 2014 8:45 am

I'm having a similar error. Whenever I try do export articles or issues through
Home > User > Journal Manager > Import/Export Data > CrossRef XML Export Plugin > Select an Issue to export.
or
Home > User > Journal Manager > Import/Export Data > CrossRef XML Export Plugin > Select Articles to export.

the list always comes empty, and it started since I've upgraded to OJS 2.4.3.0
mrcardoso
 
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Re: Fatal Error with CrossRef XML Export Plugin using 2.4.3

Postby jamilj » Tue Jan 28, 2014 9:19 am

Hello,

In my case, it happens before I even get to the step of actually downloading an XML file. As I said, whether I click on "Articles" or "Issues" (the only two options) I get the above error. I am aware of the fact that there can be PHP memory errors if you try and export too many articles or issues. However, this is not the problem that I am having.

Just to be clear, it is the following page that I cannot get past:

http://archive.monthlyreview.org/index. ... portPlugin

However, when I tried it again today, I am now getting a different error when I click "Export Articles":

Fatal error: Maximum execution time of 30 seconds exceeded in /home/jhpm3s/public_html/archives_ojs/lib/pkp/classes/site/VersionDAO.inc.php on line 117


And when I click "Export Issues" I get a blank page. Here is what I found in the error log:

[28-Jan-2014 16:22:36 UTC] PHP Fatal error: Maximum execution time of 30 seconds exceeded in ~/public_html/archives_ojs/lib/pkp/classes/site/VersionDAO.inc.php on line 117
Last edited by jamilj on Tue Jan 28, 2014 9:31 am, edited 3 times in total.
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Re: Fatal Error with CrossRef XML Export Plugin using 2.4.3

Postby swing » Tue Jan 28, 2014 9:20 am

/* Ohhh, this is getting worse... :-( */

Hi mrcardoso,

What version did you upgrade from?
Do you get the same error message as jamilj?
If you go to Home > User > Journal Manager > Import/Export Data > CrossRef XML Export Plugin > Select an Issue to export, is the page displayed fully/correctly but with no issue listed or an error occurs and the page is not correctly displayed? Could you try to see if there is an error in the log file?

Thanks!
Bozana Bokan
swing
 
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Re: Fatal Error with CrossRef XML Export Plugin using 2.4.3

Postby swing » Tue Jan 28, 2014 9:35 am

Hi jamilj,

Is the max_execution_time = 30 in your php.ini? If so, could you please try to increase it and see if the error is therefore (because this part of code needs longer to execute)? This part of code is looking into each issue and article to assign a DOI to it, so it could last longer if there are lots of issues and/or articles. Hmmm... And I will try to reproduce it in order to understand what's happening...

Thanks!
Bozana Bokan
swing
 
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Re: Fatal Error with CrossRef XML Export Plugin using 2.4.3

Postby jamilj » Tue Jan 28, 2014 9:57 am

When I changed it to 60 seconds, it still hung when I clicked "Export Articles" but gave a different error. However, it worked when I chose to "Export Issues". Many thanks for the suggestion!

Does this mean that I need to increase the execution time even more for articles? If so, what time period is safe? I don't want my server to get bogged down if the script is poorly written.
jamilj
 
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Re: Fatal Error with CrossRef XML Export Plugin using 2.4.3

Postby mrcardoso » Tue Jan 28, 2014 10:26 am

swing wrote:/* Ohhh, this is getting worse... :-( */

Hi mrcardoso,

What version did you upgrade from?
Do you get the same error message as jamilj?
If you go to Home > User > Journal Manager > Import/Export Data > CrossRef XML Export Plugin > Select an Issue to export, is the page displayed fully/correctly but with no issue listed or an error occurs and the page is not correctly displayed? Could you try to see if there is an error in the log file?

Thanks!
Bozana Bokan


I´ve upgraded from 2.4.2.0 to 2.4.3.0 as you can see in version history:
2.4.3.0 2 4 3 0 13-01-2014
2.4.2.0 2 4 2 0 18-06-2013

And that's what i found in the error.log file:
ojs2 has produced an error
Message: WARNING: reset() expects parameter 1 to be array, null given
In file: /usr/share/ojs/ojs/lib/pkp/classes/core/VirtualArrayIterator.inc.php
At line: 54
Stacktrace:
Server info:
OS: Linux
PHP Version: 5.3.3-7+squeeze18
Apache Version: Apache/2.2.16 (Debian)
DB Driver: mysql
DB server version: 5.1.73-1, referer: http://proxy.furb.br/ojs/index.php/rbdr ... portPlugin

FYI, it doesn't happen to all journals hosted.
mrcardoso
 
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Re: Fatal Error with CrossRef XML Export Plugin using 2.4.3

Postby swing » Wed Jan 29, 2014 9:19 am

Hi jamilj,

The concept behind the automatic DOI generation is complex and the new script tries to consider and list only published articles a DOI is/could be assigned to -- there could exist published articles a DOI shouldn't/couldn't be assigned to (e.g. if the DOI suffix is empty). Thus the script has to find all published articles, goes through each and check if the DOI is/could be assigned to it, and split the result into pages. This all apparently leads to a longer execution time :-( I/we will have to think about how to eventually solve this in another way and hope to come back to you with a solution soon.

Best!
Bozana
swing
 
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Re: Fatal Error with CrossRef XML Export Plugin using 2.4.3

Postby swing » Wed Jan 29, 2014 10:22 am

Hi mrcardoso,

Hmmm... Somehow I cannot reproduce it :-( but will try further. However, it is a warning and not error, thus it shouldn't make such a problem, I think. What do you see when you go to Home > User > Journal Manager > Import/Export Data > CrossRef XML Export Plugin > Select an Issue ? Is the page displayed fully/correctly but with no issue listed?

Thanks!
Bozana Bokan
swing
 
Posts: 139
Joined: Tue Oct 09, 2007 2:59 am

Re: Fatal Error with CrossRef XML Export Plugin using 2.4.3

Postby mrcardoso » Thu Jan 30, 2014 4:53 am

swing wrote:Hi mrcardoso,

Hmmm... Somehow I cannot reproduce it :-( but will try further. However, it is a warning and not error, thus it shouldn't make such a problem, I think. What do you see when you go to Home > User > Journal Manager > Import/Export Data > CrossRef XML Export Plugin > Select an Issue ? Is the page displayed fully/correctly but with no issue listed?

Thanks!
Bozana Bokan


The list of articles come empty as you can see here Image

But if you go to http://proxy.furb.br/ojs/index.php/rbdr/index you'll see that the journal already has 2 issues and articles published.
mrcardoso
 
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Re: Fatal Error with CrossRef XML Export Plugin using 2.4.3

Postby swing » Thu Jan 30, 2014 5:51 am

Hi mrcardoso,

:-P What a strange issue! :-(
Is maybe your setting for 'items per page' = 0? -- You will find the setting as journal manager in the setup 5.8 Lists.

Best!
Bozana Bokan
swing
 
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Re: Fatal Error with CrossRef XML Export Plugin using 2.4.3

Postby mrcardoso » Thu Jan 30, 2014 5:59 am

swing wrote:Hi mrcardoso,

:-P What a strange issue! :-(
Is maybe your setting for 'items per page' = 0? -- You will find the setting as journal manager in the setup 5.8 Lists.

Best!
Bozana Bokan



A kind of magic! That was the trick, worked like a charm!

Thank you very much for the help! :D
mrcardoso
 
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