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January 09, 2009, 03:57:07 AM *
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Author Topic: Conversion issue  (Read 1659 times)
Marco Bruno
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« on: July 21, 2007, 12:43:41 AM »

This is a truly great and usefull tool. Love it!!!
Just a quick question. It may be my ignorance, but how does one get from the Reference Manager standard to the bibtex format??? If I would know the answer, life would be even more easy...
Thanks for taking the trouble to answer my question.

Marco Bruno
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Mark Austin
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« Reply #1 on: July 23, 2007, 07:35:39 AM »

I assume by this that you mean how to get from the manual input fields to a bibtex string?  If that is the case then using the "Download bibtex string for all x results " will give you the bibtex format for all of the references displayed.
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Marco Bruno
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« Reply #2 on: July 23, 2007, 10:24:12 PM »

Marc,

Thanks for your quick reply.
I probably was not to clear with my question so I will try to be more specific.

I am a medical specialist who publishes a lot. To prepare my manuscripts I use Reference Manager Professional Edition Version 11 (Thomson ISI ResearchSoft) and I download my references from www.pubmed.com.  What I would like to do is to export a set of references from pubmed or even better from Reference Manager into your application. To do so I need to export references from either pubmed or Reference Manager into the bibtex format. That's my problem. I do not know how to do this. For example, in Ref Man I do not see any option to export in the bibtex format.

A second thing that came while I integrated your application is that in the upper part of my screen I get this message:
Notice: Only variable references should be returned by reference in W:\www\DGRF\includes\joomla.php on line 364
What is wrong and how can I fix this?
(by the way I am preparing this website offline with JSAS)

Your help is much appreciated!!!

MB
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Mark Austin
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« Reply #3 on: July 25, 2007, 12:21:26 PM »

Perhaps you could try the ris2bib tool on this site to convert from Reference Manager:

http://www.mackichan.com/index.html?bibdb/tools.html~mainFrame

I have not idea why you are getting that error in the joomla file, which version of joomla are you using?  Perhaps I could look into this when I have time.

Mark
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Mark Austin
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« Reply #4 on: July 27, 2007, 03:39:57 PM »

Are you using SMF on your site too?  I googled that error and the line in joomla.php and the only thing that came up was people having problems with SMF.  If not what version of php are you using, that came up occasionally too?  I don't see that that line can have anything to do with Joomla BibTeX,  but I could be wrong.
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Rudolf Maleri
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« Reply #5 on: August 04, 2007, 04:22:04 PM »

Hi Marco,
I had the very same problem. We use Reference Manager 10, and I was not able to convert the files.
Some time ago, I also found the machichan-Site, but I did not manage to get it working.
In the end, I found a solution which worked quite well:
http://www.potse.nl/software/bibfrob/HOWTO/RM-to-BibTeX-HOWTO
I only had to try out several of these bibtex.os files from that page until I found one which worked with my version of the Reference Manager.
To the bibtex.os you can also add additional fields to export to bibtex.

The only point is, that my .bib-files are about 2,4MBs big. For that reason I have to split the Reference Manager database in three parts before exporting them.

But in that context, I've got another question:
I've different custom fields in my reference manager and can export them to bibtex by adding the neccessary strings manually to the output style. So far, so good.
But I'd also like to have one of these custom fields in my Joomla-Bibtex-output.
I installed Joomla on our Universities' intranet and I'd like to offer the pdf files  of our references to download for my students. The filenames contain our internal repository number (e.g. 08-0573.pdf).
So I'd like to have another column in my joomla-bibtex-output table in the frontend (e.g. pdfs or something like that)  that the students can see the actual filename of the references and download it from our docman-download section.
Is there any possibility to add columns manually?

Rossi
« Last Edit: August 04, 2007, 04:53:26 PM by Rudolf Maleri » Logged
Mark Austin
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« Reply #6 on: August 05, 2007, 08:11:43 AM »

Can you not use the eprint field to add the pdf link?  Adding a new column would require some knowledge of php and html if you are willing to try you need to look at the showTable function starting line 584 in jombib.html.php.  If you want to add custom fields to the application you would need to add them to the jombib.xml file, which sets up the database on install.  You would then need to reinstall the component.

Let me know if I can give you any more help.
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Rudolf Maleri
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« Reply #7 on: August 05, 2007, 10:27:19 PM »

Can you not use the eprint field to add the pdf link?

Initially, I also thought about that and I also tried it. But then, I've got another two problems:
- what I want to see then, is not the acrobat-icon, but the filename. I don't have all publications as pdfs on the server, as - especially some of the older publications - some publications we only have as paper copies (under similar repository numbers as the pdf filenames.
- maybe I'm making a mistake during the import of the bibtex-files, but the links to the pdf files point into the root directory of my joomla installation and I dont want to copy the pdfs into the root directory. Also, I don't want to type in the links to 1.700+ files  manually.

Quote
Adding a new column would require some knowledge of php and html if you are willing to try you need to look at the showTable function starting line 584 in jombib.html.php.  If you want to add custom fields to the application you would need to add them to the jombib.xml file, which sets up the database on install.  You would then need to reinstall the component.

Hmmm. Maybe that's the way to go.  I'll try to play around with that a little and then I'll see.  Fortunately, the code is very well written and without lots of frills.

Rudolf
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Mark Austin
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« Reply #8 on: August 06, 2007, 09:39:37 AM »

Line 803 of bibtex.html.php is where the link for eprint is generated, you could easily change that to print the name of the file.  The link will default to a relative link, but it you put in a full absolute link then that will work to.  Unfortunately if the 1700 links are not absolute links but just file names there is no easy way round it.  Perhaps a find and replace.
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Rudolf Maleri
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« Reply #9 on: August 06, 2007, 10:04:14 AM »

In the meantime, I did it the brute way.
In JabRef, I created a field called "pdf" for the file names and then I just replaced the term 'eprint' by 'pdf' via find and replace in each of your com_bibtex files. Also, I removed all hyperlinks previously found under 'eprint'.
Maybe I could have had that way easier, but it works and I get exactly what I want. It's really a great tool.

Thank you, Rudolf
« Last Edit: August 06, 2007, 10:06:13 AM by Rudolf Maleri » Logged
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