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Citation Extraction Services/Database Connectors

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Re: Citation Extraction Services/Database Connectors

Postby Albert » Sat Nov 02, 2013 3:18 pm

Hello There,

I contacted my brother that lives in Miami. He log in the site as Journal Manager and tried unsuccessfully adding items on Citation Extraction Services and Citation Database Connectors. He had the same problem with flying “OK.” I thought might be in his network the result could be okay.

Later on, he tried in an OJS installed in a locahost in his computer. I was watching everything using Mikogo 4. The “Add an Item” button for Citation Extraction Services was not there, but it was for Citation Database Connectors. He pressed Add an Item button and the OK was gone soon after. Nevertheless, he selected CrossRef and immediately a lower window opened up asking for CrossRef email address. He entered our address and the service was added. Later I did the same thing on the web nevertheless after selecting a service the wizard did not pup up.

Then, it seems that the OK is not necessary if once you select a service, it opens up the wizard to add your user information in that service. I think that we can conclude that this is a bug on OJS 2.4.2 and 2.4.1 that needs to be fixed. In the mean time, I can do the same thing in a localhost here and then how can I add that information on the site running on the server? Can I add it directly on the database? If yes, how?

Another question, can I upload XML files (issue and articles) on CrossRef without having added Citation Database Connectors on the journal? We are very much behind with the publication of this, the first journal’s issue.

Regards,
Albert
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Re: Citation Extraction Services/Database Connectors

Postby Albert » Sat Nov 02, 2013 5:13 pm

Hello There,

With the intention of fixing the problems of Citation Extraction Services/Database Connectors, would be possible for someone with knowledge about config.TEMPLATE.inc. php to give a look to all the off’s and on’s on this file to see if there is something that can be changed to solve adding items to Citation Extraction Services/Database Connectors? I looked at its 467 lines and changed lines 62 and 84 to On but nothing changed. Therefore, I left them On.
We would appreciate very much your help!
Regards,

Albert
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Re: Citation Extraction Services/Database Connectors

Postby aadilsi » Mon Nov 04, 2013 9:19 am

Hi Alec,
Back to the citation extraction OK button not being displayed issue.
While using chrome's development tool, this is what I found.
While selecting the elements tab on the left bottom pan and the style tab on the right bottom pan, if one puts the cursor next to the element.style {
display: none;
and un-check it, the OK button appears back.
I wouldn't know how to debug that. :( Attaching a prt sc for you.
Best wishes,
--
eddy
Attachments
ojs-citation-extraction-button-error.jpg
ojs-citation-extraction-button-error.jpg (611.96 KiB) Viewed 1562 times
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Re: Citation Extraction Services/Database Connectors

Postby asmecher » Mon Nov 04, 2013 12:43 pm

Hi Eddy and Albert,

The "OK" button is disapperaing because it's being disabled by Javascript. Have you tried the solution posted above on this thread?

Regards,
Alec Smecher
Public Knowledge Project Team
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Re: Citation Extraction Services/Database Connectors

Postby aadilsi » Sat Nov 09, 2013 7:05 am

Hi Alec,
Tried the patch in the solution posted.
Nothing worked. :(
I managed to get the citation extraction services and database connectors installed, but still cant get to read or edit the references in the citation markup assistant.
I need to get the citation assistant sorted out.
Still following this thread for any solution that may be posted.
Regards,
--
Eddy
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Re: Citation Extraction Services/Database Connectors

Postby asmecher » Sat Nov 09, 2013 8:58 am

Hi Eddy,

Did you also run the suggested command?

Regards,
Alec Smecher
Public Knowledge Project Team
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Posts: 8470
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Re: Citation Extraction Services/Database Connectors

Postby aadilsi » Sat Nov 16, 2013 1:42 pm

Hi Alec,
Yeah, applied the patch.
Ran the command.
This is what I get
Code: Select all
-bash-3.2$ php tools/dbXMLtoSQL.php -data execute registry/citationAssistantData.xml

PHP Deprecated: Comments starting with '#' are deprecated in /web/conf/php5.ini on line 1256 in Unknown on line 0
PHP Deprecated: Comments starting with '#' are deprecated in /web/conf/php5.ini on line 1257 in Unknown on line 0

Deprecated: Directive 'magic_quotes_gpc' is deprecated in PHP 5.3 and greater in Unknown on line 0
Input file "registry/citationAssistantData.xml" does not exist!
-bash-3.2$
Any clue? Thanks for the help!
--
Eddy
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Re: Citation Extraction Services/Database Connectors

Postby asmecher » Mon Nov 18, 2013 10:10 am

Hi Eddy,

That file is available at https://github.com/pkp/ojs/blob/ojs-2_3_8-0/registry/citationAssistantData.xml.

Regards,
Alec Smecher
Public Knowledge Project Team
asmecher
 
Posts: 8470
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Re: Citation Extraction Services/Database Connectors

Postby aadilsi » Mon Nov 18, 2013 1:32 pm

Hi Alec,
Thanks for the help. Uploaded the file. Why was this missing in the first place? Is there any thing else that might be missing too? The Citation Assistant is up for now, i.e. at least letting me manually edit citations. But not identifying citations on its own. Will work around a bit, and post the details later.
Best wishes,
--
Eddy
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Re: Citation Extraction Services/Database Connectors

Postby asmecher » Mon Nov 18, 2013 2:31 pm

Hi Eddy,

That file relates to data that should be installed upon upgrade but in some cases does not get installed. We have not been able to track this down, but it appears platform-related. What you've just run through is a work-around that shouldn't be necessary but will restore the data where it is missing.

Regards,
Alec Smecher
Public Knowledge Project Team
asmecher
 
Posts: 8470
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Re: Citation Extraction Services/Database Connectors

Postby aadilsi » Sun Nov 24, 2013 7:41 am

Hi Alec,
Still some issues with the Citation Markup Assistant (CMA)!
Editors are having to put citations manually in the CMA. But after those are done in the CMA window, they don't show up in the summary section, down in the metadata.
Moreover, citations put manually, while editing the metadata section, they don't show up in the CMA window. I guess there is still something wrong, or, I may be missing something here. Will be glad for any help.
Thanks.
--
Eddy
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Re: Citation Extraction Services/Database Connectors

Postby asmecher » Thu Nov 28, 2013 12:02 pm

Hi Eddy,

Can you report the results of the following query:
Code: Select all
SELECT COUNT(*) FROM controlled_vocabs WHERE symbolic IN ('nlm30-publication-types', 'openurl10-journal-genres', 'openurl10-book-genres');
Regards,
Alec Smecher
Public Knowledge Project Team
asmecher
 
Posts: 8470
Joined: Wed Aug 10, 2005 12:56 pm

Re: Citation Extraction Services/Database Connectors

Postby aadilsi » Thu Nov 28, 2013 2:27 pm

Hi Alec,
Working on a thanksgivings day?
Here is the result:

SQL query: SELECT COUNT(*) FROM controlled_vocabs WHERE symbolic IN ('nlm30-publication-types', 'openurl10-journal-genres', 'openurl10-book-genres');
Rows: 1

COUNT(*)
3


Thanks for looking into it.
Regards,
--
Eddy
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Re: Citation Extraction Services/Database Connectors

Postby asmecher » Fri Nov 29, 2013 3:50 pm

Hi Eddy,

The data looks to have been properly installed. Which citation parsing service(s) have you got configured in your setup?

Regards,
Alec Smecher
Public Knowledge Project Team
asmecher
 
Posts: 8470
Joined: Wed Aug 10, 2005 12:56 pm

Re: Citation Extraction Services/Database Connectors

Postby aadilsi » Sat Nov 30, 2013 1:01 am

Hi Alec,
Have installed all the services available.
Is there only a particular combination that works?
Thanks.
--
Eddy
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