Copy & Paste ?

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Copy & Paste ?

bestenborstel
Dear all,
I always asked Google Scholar to show me the reference for BibTeX in Safari. Then I simply copied and pasted into my library. With 1.5.7 this seem not possible anymore. Bibdesk says not supported file format. Syntax wrong.
It is only:

@article{mittelbach1962röntgenkleinwinkelstreuung,
  title={Zur R{\"o}ntgenkleinwinkelstreuung verd{\"u}nnter kolloider Systeme. VII. Die Berechnung der Streukurven von dreiachsigen Ellipsoiden},
  author={Mittelbach, P. and Porod, G.},
  journal={Acta Phys. Austriaca},
  volume={15},
  pages={122--147},
  year={1962}
}
Could somebody point me in the right direction please? 

Using the data base in that case does not work as the reference is not recognised.
Regards
G.

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Re: Copy & Paste ?

Christiaan Hofman

On Mar 9, 2012, at 16:26, bestenborstel wrote:

Dear all,
I always asked Google Scholar to show me the reference for BibTeX in Safari. Then I simply copied and pasted into my library. With 1.5.7 this seem not possible anymore. Bibdesk says not supported file format. Syntax wrong.
It is only:

@article{mittelbach1962röntgenkleinwinkelstreuung,
  title={Zur R{\"o}ntgenkleinwinkelstreuung verd{\"u}nnter kolloider Systeme. VII. Die Berechnung der Streukurven von dreiachsigen Ellipsoiden},
  author={Mittelbach, P. and Porod, G.},
  journal={Acta Phys. Austriaca},
  volume={15},
  pages={122--147},
  year={1962}
}
Could somebody point me in the right direction please? 

Using the data base in that case does not work as the reference is not recognised.
Regards
G.

Special characters like ö are not allowed in the cite key. This is a bibtex requirement.

Christiaan



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Re: Copy & Paste ?

Stian Håklev
In reply to this post by bestenborstel
The reason is that BibDesk does not accept non-ASCII characters in the citekey (mittelbach1962röntgenkleinwinkelstreuung), but both Google Scholar and dx.doi.org generate BibTeX with UTF8 citekeys. I personally made a small script to "clean" bibtex before importing it - regenerate citekey, remove keyword field (I hate when I get 8 new keyword categories just from importing one article).

I raised this as a bug report, but the developers closed it because the BibTeX specs (designed in 1985) do not allow for UTF8 citekeys. (Personally I think there should be an option to disregard the citekey completely and generate a new one according to your own preferences). 


The code I'm using to clean up citations is here https://github.com/houshuang/folders2web/blob/master/utility-functions.rb#L68-78 - note that it's part of a bigger project, so it might require a bit of work to extract.
Stian

On Fri, Mar 9, 2012 at 10:26, bestenborstel <[hidden email]> wrote:
Dear all,
I always asked Google Scholar to show me the reference for BibTeX in Safari. Then I simply copied and pasted into my library. With 1.5.7 this seem not possible anymore. Bibdesk says not supported file format. Syntax wrong.
It is only:

@article{mittelbach1962röntgenkleinwinkelstreuung,
  title={Zur R{\"o}ntgenkleinwinkelstreuung verd{\"u}nnter kolloider Systeme. VII. Die Berechnung der Streukurven von dreiachsigen Ellipsoiden},
  author={Mittelbach, P. and Porod, G.},
  journal={Acta Phys. Austriaca},
  volume={15},
  pages={122--147},
  year={1962}
}
Could somebody point me in the right direction please? 

Using the data base in that case does not work as the reference is not recognised.
Regards
G.

------------------------------------------------------------------------------
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also focuses on allowing computing to be delivered as a service.
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Re: Copy & Paste ?

Fischlin  Andreas
Dear Stian,

The problem with this is not with BibDesk nor BibTeX. The problem is with Google Scholar or whoever is responsible for that silly BibTeX export that violates BibTeX syntax rules. Unfortunately we have these days many people who are responsible for such BibTeX export services who bother not the least to carefully look into the syntax rules when they implement such an export service. One has therefore to give them feedback and ask them to fix their mistakes and that they learn the basics of coding including what ASCII code is. Shouldn't be too much to ask from a programer, should it?

Regards,
Andreas


ETH Zurich
Prof. Dr. Andreas Fischlin
Systems Ecology - Institute of Integrative Biology
CHN E 21.1
Universitaetstrasse 16
8092 Zurich
SWITZERLAND

[hidden email]<mailto:[hidden email]>
www.sysecol.ethz.ch<http://www.sysecol.ethz.ch>

+41 44 633-6090 phone
+41 44 633-1136 fax
+41 79 595-4050 mobile

             Make it as simple as possible, but distrust it!
________________________________________________________________________







On 09/03/2012, at 16:52 , Stian Håklev wrote:

The reason is that BibDesk does not accept non-ASCII characters in the citekey (mittelbach1962röntgenkleinwinkelstreuung), but both Google Scholar and dx.doi.org<http://dx.doi.org/> generate BibTeX with UTF8 citekeys. I personally made a small script to "clean" bibtex before importing it - regenerate citekey, remove keyword field (I hate when I get 8 new keyword categories just from importing one article).

I raised this as a bug report, but the developers closed it because the BibTeX specs (designed in 1985) do not allow for UTF8 citekeys. (Personally I think there should be an option to disregard the citekey completely and generate a new one according to your own preferences).

You can see the bug I filed here: http://sourceforge.net/tracker/?func=detail&aid=3489467&group_id=61487&atid=497426

The code I'm using to clean up citations is here https://github.com/houshuang/folders2web/blob/master/utility-functions.rb#L68-78 - note that it's part of a bigger project, so it might require a bit of work to extract.
Stian

On Fri, Mar 9, 2012 at 10:26, bestenborstel <[hidden email]<mailto:[hidden email]>> wrote:
Dear all,
I always asked Google Scholar to show me the reference for BibTeX in Safari. Then I simply copied and pasted into my library. With 1.5.7 this seem not possible anymore. Bibdesk says not supported file format. Syntax wrong.
It is only:


@article{mittelbach1962röntgenkleinwinkelstreuung,
  title={Zur R{\"o}ntgenkleinwinkelstreuung verd{\"u}nnter kolloider Systeme. VII. Die Berechnung der Streukurven von dreiachsigen Ellipsoiden},
  author={Mittelbach, P. and Porod, G.},
  journal={Acta Phys. Austriaca},
  volume={15},
  pages={122--147},
  year={1962}
}


Could somebody point me in the right direction please?

Using the data base in that case does not work as the reference is not recognised.
Regards
G.

------------------------------------------------------------------------------
Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing
also focuses on allowing computing to be delivered as a service.
http://www.accelacomm.com/jaw/sfnl/114/51521223/
_______________________________________________
Bibdesk-users mailing list
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Re: Copy & Paste ?

Stian Håklev
Dear Andreas,

there's the idealistic and the pragmatic approach. I have a million ideas about how Google Scholar could have been made so much better. For example, I made a proof of concept of a database that would fingerprint PDF files, and let you retrieve metadata based on this. Imagine if Google Scholar enabled this - it would probably be quite easy. Then, anytime you had a PDF file you didn't know where came from, you could quickly send a query, and receive the metadata back. Of course, I have no great hopes that GScholar will do this anytime soon... So I am building such a service with a few friends (much smaller, but concentrated on one disciplin it might still be useful): http://www.youtube.com/watch?v=X9FqaqgAlG8

I believe that the world desperately needs an open competitor to Google Scholar - just like Open Streetmap is currently slowly replacing Google Maps for embedded applications. There is no official API to GScholar, and it aggressively restricts robots, etc. Even just starting with getting every OA journal, open access repository etc in the world to share their "canonical" metadata would be a great start...

But until then we have to live with imperfection :) To me, it's more user-friendly to say "the metadata you imported is incorrect, but still recognizable as bibtex, let me clean that up for you" (I'm not asking you to actually store incorrect BibTeX in the database).

Luckily, I'm able to create scripts, and one of the reasons why I chose BibDesk after evaluating all the other tools - Mendeley, EndNotes, Zotero etc - was it's great scriptability, both because it has really good AppleScript support, and because the database is always available in a very well understood format (I chose it despite the fact that I don't even use LaTeX in my writing :) I am looking into MultiMarkdown with PanDoc or my own solution). Currently there are several people using BibDesk because they really wanted to use my integrated workflow, and it is built on BibDesk (if I could ever get it to work on MacRuby and avoid the difficult installation this would probably expand to a much larger group). 

And given that I am able to script, I'm also able to avoid this very annoying problem of trying to import something from Google Scholar and having BibDesk say "no, can't do that"... 

Anyway thanks to all the programmers for all their hard work on BibDesk,
Stian

(here are some other videos, all very short, of stuff we are working on - let us know if anyone are interested in collaborating - all is open source, open standards etc http://www.youtube.com/watch?v=O5LgG_K3y8A http://www.youtube.com/watch?v=YFPM1S27InU)

Stian

On Fri, Mar 9, 2012 at 11:06, Fischlin Andreas <[hidden email]> wrote:
Dear Stian,

The problem with this is not with BibDesk nor BibTeX. The problem is with Google Scholar or whoever is responsible for that silly BibTeX export that violates BibTeX syntax rules. Unfortunately we have these days many people who are responsible for such BibTeX export services who bother not the least to carefully look into the syntax rules when they implement such an export service. One has therefore to give them feedback and ask them to fix their mistakes and that they learn the basics of coding including what ASCII code is. Shouldn't be too much to ask from a programer, should it?

Regards,
Andreas


ETH Zurich
Prof. Dr. Andreas Fischlin
Systems Ecology - Institute of Integrative Biology
CHN E 21.1
Universitaetstrasse 16
8092 Zurich
SWITZERLAND

[hidden email]<mailto:[hidden email]>
www.sysecol.ethz.ch<http://www.sysecol.ethz.ch>

<a href="tel:%2B41%2044%20633-6090" value="+41446336090">+41 44 633-6090 phone
<a href="tel:%2B41%2044%20633-1136" value="+41446331136">+41 44 633-1136 fax
<a href="tel:%2B41%2079%20595-4050" value="+41795954050">+41 79 595-4050 mobile

            Make it as simple as possible, but distrust it!
________________________________________________________________________







On 09/03/2012, at 16:52 , Stian Håklev wrote:

The reason is that BibDesk does not accept non-ASCII characters in the citekey (mittelbach1962röntgenkleinwinkelstreuung), but both Google Scholar and dx.doi.org<http://dx.doi.org/> generate BibTeX with UTF8 citekeys. I personally made a small script to "clean" bibtex before importing it - regenerate citekey, remove keyword field (I hate when I get 8 new keyword categories just from importing one article).

I raised this as a bug report, but the developers closed it because the BibTeX specs (designed in 1985) do not allow for UTF8 citekeys. (Personally I think there should be an option to disregard the citekey completely and generate a new one according to your own preferences).

You can see the bug I filed here: http://sourceforge.net/tracker/?func=detail&aid=3489467&group_id=61487&atid=497426

The code I'm using to clean up citations is here https://github.com/houshuang/folders2web/blob/master/utility-functions.rb#L68-78 - note that it's part of a bigger project, so it might require a bit of work to extract.
Stian

On Fri, Mar 9, 2012 at 10:26, bestenborstel <[hidden email]<mailto:[hidden email]>> wrote:
Dear all,
I always asked Google Scholar to show me the reference for BibTeX in Safari. Then I simply copied and pasted into my library. With 1.5.7 this seem not possible anymore. Bibdesk says not supported file format. Syntax wrong.
It is only:


@article{mittelbach1962röntgenkleinwinkelstreuung,
 title={Zur R{\"o}ntgenkleinwinkelstreuung verd{\"u}nnter kolloider Systeme. VII. Die Berechnung der Streukurven von dreiachsigen Ellipsoiden},
 author={Mittelbach, P. and Porod, G.},
 journal={Acta Phys. Austriaca},
 volume={15},
 pages={122--147},
 year={1962}
}


Could somebody point me in the right direction please?

Using the data base in that case does not work as the reference is not recognised.
Regards
G.

------------------------------------------------------------------------------
Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing
also focuses on allowing computing to be delivered as a service.
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Re: Copy & Paste ?

Adam R. Maxwell
In reply to this post by Stian Håklev

On Mar 9, 2012, at 07:52 , Stian Håklev wrote:

> I raised this as a bug report, but the developers closed it because the BibTeX specs (designed in 1985) do not allow for UTF8 citekeys. (Personally I think there should be an option to disregard the citekey completely and generate a new one according to your own preferences).

I agree with you in principle, and I know this is a nuisance to work around.  There are technical reasons why there can't be an easy fix in BibDesk, though.  The problem is that BibDesk's BibTeX parser (btparse) does not allow this, so it happens too early in the process to do anything with it; it's still just a stream of unstructured bytes.  Any preprocessing is fraught with peril, due to the vagaries of the BibTeX format itself, and would be terrible for performance.  Modifying the lexer or parser is theoretically possible, but I think it would have to be regenerated with PCCTS...

--
Adam



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Re: Copy & Paste ?

Stian Håklev
Hi Adam,
thanks a lot for this detailed explanation. This makes it much more clear.

Indeed, in my own little script I had the same problem, as bibtex-ruby also refuses to ingest this kind of bibtex, so I do a quick regexp to clean up the citekey before passing it to bibtex (https://github.com/houshuang/folders2web/blob/master/utility-functions.rb#L71)

I understand if this is not a good solution for all cases in BibDesk.

It would make sense to contact these two organizations and encourage them to change - after all it's not something that would be hard for them to do. No idea how to get the attention of GScholar (I have a lot of things I'd like to tell them if I did), but it might be easier to at least get the ear of dx.doi.org - and given that they're a non-profit which is supposed to be "standard-setting", should be easier to get them to change too. I will try this.

Thanks
Stian

On Fri, Mar 9, 2012 at 12:21, Adam R. Maxwell <[hidden email]> wrote:

On Mar 9, 2012, at 07:52 , Stian Håklev wrote:

> I raised this as a bug report, but the developers closed it because the BibTeX specs (designed in 1985) do not allow for UTF8 citekeys. (Personally I think there should be an option to disregard the citekey completely and generate a new one according to your own preferences).

I agree with you in principle, and I know this is a nuisance to work around.  There are technical reasons why there can't be an easy fix in BibDesk, though.  The problem is that BibDesk's BibTeX parser (btparse) does not allow this, so it happens too early in the process to do anything with it; it's still just a stream of unstructured bytes.  Any preprocessing is fraught with peril, due to the vagaries of the BibTeX format itself, and would be terrible for performance.  Modifying the lexer or parser is theoretically possible, but I think it would have to be regenerated with PCCTS...

--
Adam



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Re: Copy & Paste ?

Stian Håklev
I left a comment about this issue here: http://www.crossref.org/CrossTech/2011/11/turning_dois_into_formatted_ci.html (it's being held for moderation right now).

Stian
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