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Citation Assistant Questions.

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Citation Assistant Questions.

Postby bdgregg » Wed Nov 10, 2010 10:57 am

We are working with the 2.3.3.2 version of OJS on a test system here, we however can not seem to get the Citation Assistant to work properly.

I see our citations in the "citations" table in the database, with newly entered ones with a citation_state of "1", and I see older ones with a citation_state of "2" and a lock_id. However none of our citations are showing up as like "completed". And the web interface seems to indicate that the citations are still in processing.

Can you advise as to what to look for troubleshooting wise? We've updated the config.inc.php to include the changes that are incorporated in the version 2.3.3.2 default config.inc.php file so we should be good to go there. I didn't know if there was a log somewhere of what was going on or not that I could look at to determine why our citations are not completing.

Any help would be greatly appreciated.

Vanessa Gabler - our Journal Manager is really excited to get this working, but I have little to offer in explanation of why it isn't working.
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Re: Citation Assistant Questions.

Postby jerico » Wed Nov 10, 2010 5:17 pm

Hi Brian!

Sorry to hear that you've got trouble in getting the citation assistant to work.

Some things to check first:
- Did you activate the ParaCite citation extractor without installing the CPAN dependencies mentioned when adding the extractor to the set-up?
- Did you maybe leave the setup page 3 without setting a default citation style (the last drop-down box there)?
- Do you have some firewall or PHP function restriction in place that might prohibit PHP to access external web services from the server?
- Do you get any error message in your PHP error log when you save a reference list?

Citations usually get "caught" in state 1 or 2 if some low-level error occurs while they are being processed that causes the processing to abort. Only citations in state "3" or above will appear in the citation assistant.

You can do two things to further localize the problem (in that order):
1) Can you please make sure that PHP errors (including warnings and notices) are logged somewhere? You can not use the error display from config.inc.php as the citation processing takes place in the background. You'll have to configure error logging in php.ini and switch OJS own error display mechanism off. You can then reset all citations in the database to state "1" and press the "refresh" button in the citation assistant which should process them again. Do you get any error messages in your log then?
2) You can try the citation extractors and database connectors one by one to find the one that causes the error. Go to journal setup step 3, remove all but one citation extraction services and have no database connector switched on. If still no citation shows up in your citation assistant even when you press "refresh" once every 5 seconds or so then remove that extractor and try another one, etc. As soon as you get a result you can try switching on other services successively (first extractors then database connectors).

You'll always have to reset all citations to state "1" after you did an experiment to make sure they are eligible for processing the next time you try. Alternatively you can make a small change to your citation list in "Summary->Edit Metadata->References" and resubmit the reference list which will also cause all previous citations of that article to be deleted and the changed onces to be processed.

Additionally you'll have to execute the following SQL to make sure that the process slots for citation processing are being freed immediately (otherwise it takes 15 Minutes before OJS declares your processes "dead" and removes them from the locking table):
Code: Select all
UPDATE citations SET lock_id = NULL;
DELETE FROM processes;


If you get an error message in your log or identify the extractor/connector that causes the problem, then we can investigate further.

Hope we find the troublemaker soon. ;-)
jerico
 
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Re: Citation Assistant Questions.

Postby bdgregg » Wed Nov 10, 2010 6:55 pm

So far I think I ran into 3 issues, but I'm not sure what else I might run into:

1.) Perl - It is installed on Solaris 10 but is basically very limited and usually can't be updated. So I've installed another copy of Perl and am now pointing to it.
2.) Additional non-core Perl Modules - Obviously we need the required Perl modules to be able to use at least one of the Citation choices. So I've added those modules referenced when you enable one of the citation options.
3.) cURL needs to be included in PHP as I saw an error in the web server log about needing that as well. I'll be re-compiling PHP tomorrow to include the cURL PHP module as this is not a standard module when compiling from scratch at least not on Solaris 10.

Is there anything else that I should need to get this to work software wise that you know of?
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Re: Citation Assistant Questions.

Postby jerico » Wed Nov 10, 2010 7:15 pm

Hi Brian,

sounds as if you were really tech savvy. That makes my job much easier. :-)

Actually you need perl/CPAN for the ParaCite extractor only although this is the extractor that usually works best for articles so you really should try to get it to work. All other extractors and database connectors require PHP5 + cURL + XSL + XML DOM for web service access.

I think that's all you need.

jerico
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Re: Citation Assistant Questions.

Postby bdgregg » Thu Nov 11, 2010 9:13 am

jerico,

We've gotten further now - After some re-compiling. :D

Now all of the citations have a citation_state of '4'. However, all of our citations are complaining :( that:
"Unsupported or missing publication type. Please manually edit the citation and enter a publication type (allowed types are 'book', 'journal', 'thesis' and 'conf-proc')."

Any help with understanding this and how to fix it? :?

Brian.
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Re: Citation Assistant Questions.

Postby bdgregg » Thu Nov 11, 2010 9:21 am

I think I found it. Will post what I find out shortly.
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Re: Citation Assistant Questions.

Postby bdgregg » Thu Nov 11, 2010 9:32 am

Ok,
I thought PHP included XSL automatically, but as I found out - NOT. I had to add the module the --with-xsl to the configure command.
Some more re-compiling and now we're getting some better (expected) results. :D

Thanks for the help!
Much appreciated.
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Re: Citation Assistant Questions.

Postby jerico » Thu Nov 11, 2010 11:16 am

bdgregg wrote:"Unsupported or missing publication type."


That happens if none of the configured extraction services returns any result for your citations or if the results are so incomplete that they are being discarded by the system.
1) Please try to configure all four available extraction services in journal setup step 3 for testing. You can later disable services that do not give you useful results. You should regularly get some result from ParsCit, FreeCite and ParaCite. (See the "expert results" at the bottom of the citation assistant details pane to identify the services that work for you!)
2) Please make sure that all services are enabled "by default" for testing. You can always make them non-default later to speed up processing if you discover that some do rarely provide good results.
3) Please try all services out manually. When you add a service you find links to the home pages of the services in the explanatory text for each service. If you get a result on the web page of one of these services but not in our citation assistant then this is either a bug or a misconfiguration. If you think your configuration is correct then please tell us about the problem via the forum or via our bugzilla system.

Once you've got a good feeling which extractors and databases work for you, you should either completely delete less useful services in setup page 3 or set them "non-default", to speed up initial citation processing. You can also play a bit with the parallel citation procession option in config.inc.php, see the in-line explanation there.

BTW: Citation extractor services alone will never give you very good results. You'll only get really good results if at least one of the connected databases contains your citations. That's the reason why we mostly recommend the citation assistant for the life sciences where really good citation databases exist. Other fields will have to develop similar databases before they can expect comparable results. Obviously the availability of good research-field specific citation extraction services or citation databases is not something that we can influence. If you know about good extractor services/citation databases for your field of research which are not yet available by default then I'm happy to show you how you develop and install your own connector. If you have some PHP and XML knowledge then this will be easy for you.
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Re: Citation Assistant Questions.

Postby newbies » Wed Nov 06, 2013 10:35 pm

I have the same problem of "unsupported or missing publication type". I enabled all services and installed necessary perl module. none reference can be recognized. Below is the only warning I could find the error_log:

[06-Nov-2013 21:25:50 America/Los_Angeles] ojs2 has produced an error
Message: WARNING: call_user_func_array() expects parameter 1 to be a valid callback, class 'PKPComponentRouter' does not have a method 'getRequestedPage'
In file: /home/xxx/public_html/lib/pkp/classes/core/PKPRequest.inc.php
At line: 788
Stacktrace:
Server info:
OS: Linux
PHP Version: 5.4.19
Apache Version: N/A
DB Driver: mysql
DB server version: 5.1.70-cll
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Re: Citation Assistant Questions.

Postby asmecher » Thu Nov 07, 2013 10:00 am

Hi newbies,

Have you worked through the steps above, and if so, what were the results?

Regards,
Alec Smecher
Public Knowledge Project Team
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Re: Citation Assistant Questions.

Postby newbies » Fri Nov 08, 2013 10:55 am

thank you for asking. I got it to work. I did not know I have to click each reference which are strike-through and then click the "Process" button. I did that one by one, and everything worked out.
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