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DataCite plugin

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DataCite plugin

Postby gemusehandler » Sat Oct 19, 2013 6:49 am

Hello Alec, hope you can help me out with this one. We have been struggling with the DataCite doi plugin and finally got it to work. My local DataCite provider had to install its own API, and adjust the url in the plugin. Its works with most of the journals, but not all of them.

In the case of the newer journals (that have a limited number issues and articles) submitting and updating doi's works like a charm. However, I have one journal that starts way back in 1899. We have all full issues online and all articles from 1989 on. http://bulletin.knob.nl

It seems that this is too much to handle for OJS. The 'export specific articles' page returns blank. The 'export specific issues' pages list only 40 issues without a possibility to browse or select further. I was able to register those 40 issues though. The export 'all unregistered issues, article and galleys' page stops loading when it reaches the issues published in the early 20th century. It is not able to display articles or galleys or display buttons that allow me to register.

Is there somewhere a download limit that I can raise, or something else? The only work around would be that I unpublish the issues until I have about 10 or 20 left and start registering them, unpublish the registered issues, republish another 10 to 20 issue and work my way up. Although this will probably work I am not looking forward to go down that road.
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Re: DataCite plugin

Postby JasonNugent » Sun Oct 20, 2013 4:27 am

Hi gemusehandler,

Out of curiosity, have you looked in your error log for a PHP problem for the blank page? Does exporting specific articles work if you choose fewer than 40 articles? You might be hitting a PHP memory limit or a script execution time limit in that case. If it doesn't work at all, then it may be a bug in the plugin that may already be fixed in a patch some place.

Regards,
Jason
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Re: DataCite plugin

Postby asmecher » Tue Oct 22, 2013 10:51 am

Hi gemusehandler,

What version of OJS are you using? If 2.4.x, and you haven't patched it already, try applying https://github.com/pkp/pkp-lib/commit/cc4be218320d7cf4480a3dc1b15a54b29d3e5a6e in lib/pkp (ignore the parts of the patch that deal with the tests/ subdirectory). That should resolve a memory leak that can make intensive operations consume more memory than PHP is configured to give. Otherwise, check your PHP error logs -- often blank pages indicate that a PHP error occurred, and the details should be in the log file.

Regards,
Alec Smecher
Public Knowledge Project Team
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Re: DataCite plugin

Postby gemusehandler » Wed Nov 20, 2013 6:53 am

Alec, as always: spot on. Problem solved with your advise.
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Re: DataCite plugin

Postby tabber » Tue Nov 26, 2013 9:55 am

Hello Alec,
The fix in the Hook registry works fine (OJS 2.4.2). But ever since, I get emails (empty) from the cron running php /var/www/html/ojs/tools/runScheduledTasks.php. When I restore the original HookRegistry.inc.php file, I get no emails. I've turned on show_stacktrace. Pls look at the attachment for the log file.
Attachments
ojs_hookfix.txt
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Re: DataCite plugin

Postby asmecher » Tue Nov 26, 2013 10:06 am

Hi tabber,

Cron will send an email when it gets any output, so a blank email is not necessarily bad news -- it suggests that there's a single line feed or something coming out of PHP that cron thinks it's worth notifying you about. (It's still worth figuring out where that line feed is coming from, but it may just be a blank line added somewhere and not an error condition.)

When invoking OJS from the command line, there is no request object describing the web request because no web request triggered the execution. That seems to be what one of the error messages in the attached file are describing: some piece of code attempts to access the request object, but it doesn't exist. I wonder if it's not a plugin that's attempting to extend built-in functionality without checking whether or not we're dealing with a command-line request first. Unfortunately the stack trace doesn't go deeper than 10 levels and what we're looking for is probably around the 12th level or so.

The "permission denied" message relates to file permissions in your file storage directory; it looks like OJS is trying to access a file stored there, discovering that an expected directory doesn't exist, and trying to create it. It's harmless because it'll be created empty and then OJS will discover that there are no files in it (surprise!) but does suggest you should fix file permissions.

Regards,
Alec Smecher
Public Knowledge Project Team
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