date:20210924

Re: [Bibdesk-users] Can't preview imported citation

2021-09-24 Thread Christiaan Hofman

“using search term" uses PubMed to download the bibliographic information (by 
default), basically using the same method as a (PubMed) search group. How well 
that works probably depends on what type of publication you are looking for. 
Using the “from” argument essentially does the same thing as pasting on the 
main table and New Publication from Clipboard, which for a DOI string gets 
bibtex data from the DOI site. That probably is valid more generally.

Christiaan


> On 24 Sep 2021, at 17:46, Fischlin Andreas  
> wrote:
> 
> Dear Christiaan,
> 
> Indeed. I have so far always used only
> 
> set theDOI to (get the clipboard as string)
> tell front document of application "BibDesk"
> set theImportPubs to import for search term theDOI
> end tell
> 
> which rarely works well, so I stopped using it. Is these day your variant the 
> way to go then?
> 
> Thanks.
> Andreas
> 
> 
> ETH Zurich
> Prof. em. Dr. Andreas Fischlin
> IPCC Vice-Chair WGII
> Systems Ecology - Institute of Biogeochemistry and Pollutant Dynamics
> CHN E 24
> Universitaetstrasse 16
> 8092 Zurich
> SWITZERLAND
> 
> andreas.fisch...@env.ethz.ch 
> www.sysecol.ethz.ch/people/andreas.fischlin.html 
> 
> 
> +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 24/09/2021, at 16:09, Christiaan Hofman > > wrote:
>> 
>> And when you want to use AppleScript, you can use the import command:
>> 
>> set theDOI to (get the clipboard as string)
>> tell application “BibDesk"
>> tell front document
>> import from theDOI
>> end tell
>> end tell
>> 
>> Christiaan
>> 
>>> On 24 Sep 2021, at 15:51, Christiaan Hofman >> > wrote:
>>> 
>>> So you get the  bibtex from the website? That is more a problem of that web 
>>> site then.
>>> 
>>> Why not just get the bibtex directly from within BibDesk? There are various 
>>> ways. You can open the URL in a web group, and you will get publication (it 
>>> is downloaded from the DOI site). Or even simpler, copy the DOI, and paste 
>>> on the main window or use Publication > New Publication from Clipboard. The 
>>> bibtex is basically the same as the one from doi2bib.
>>> 
>>> Christiaan
>> 

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Re: [Bibdesk-users] Can't preview imported citation

2021-09-24 Thread Fischlin Andreas

Dear Christiaan,

Indeed. I have so far always used only

set theDOI to (get the clipboard as string)
tell front document of application "BibDesk"
set theImportPubs to import for search term theDOI
end tell

which rarely works well, so I stopped using it. Is these day your variant the 
way to go then?

Thanks.
Andreas


ETH Zurich
Prof. em. Dr. Andreas Fischlin
IPCC Vice-Chair WGII
Systems Ecology - Institute of Biogeochemistry and Pollutant Dynamics
CHN E 24
Universitaetstrasse 16
8092 Zurich
SWITZERLAND

andreas.fisch...@env.ethz.ch
www.sysecol.ethz.ch/people/andreas.fischlin.html

+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 24/09/2021, at 16:09, Christiaan Hofman 
mailto:cmhof...@gmail.com>> wrote:

And when you want to use AppleScript, you can use the import command:

set theDOI to (get the clipboard as string)
tell application “BibDesk"
tell front document
import from theDOI
end tell
end tell

Christiaan

On 24 Sep 2021, at 15:51, Christiaan Hofman 
mailto:cmhof...@gmail.com>> wrote:

So you get the  bibtex from the website? That is more a problem of that web 
site then.

Why not just get the bibtex directly from within BibDesk? There are various 
ways. You can open the URL in a web group, and you will get publication (it is 
downloaded from the DOI site). Or even simpler, copy the DOI, and paste on the 
main window or use Publication > New Publication from Clipboard. The bibtex is 
basically the same as the one from doi2bib.

Christiaan



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Re: [Bibdesk-users] Can't preview imported citation

2021-09-24 Thread Christiaan Hofman

And when you want to use AppleScript, you can use the import command:

set theDOI to (get the clipboard as string)
tell application “BibDesk"
tell front document
import from theDOI
end tell
end tell

Christiaan

> On 24 Sep 2021, at 15:51, Christiaan Hofman  wrote:
> 
> So you get the  bibtex from the website? That is more a problem of that web 
> site then.
> 
> Why not just get the bibtex directly from within BibDesk? There are various 
> ways. You can open the URL in a web group, and you will get publication (it 
> is downloaded from the DOI site). Or even simpler, copy the DOI, and paste on 
> the main window or use Publication > New Publication from Clipboard. The 
> bibtex is basically the same as the one from doi2bib.
> 
> Christiaan



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Re: [Bibdesk-users] Can't preview imported citation

2021-09-24 Thread Christiaan Hofman

So you get the  bibtex from the website? That is more a problem of that web 
site then.

Why not just get the bibtex directly from within BibDesk? There are various 
ways. You can open the URL in a web group, and you will get publication (it is 
downloaded from the DOI site). Or even simpler, copy the DOI, and paste on the 
main window or use Publication > New Publication from Clipboard. The bibtex is 
basically the same as the one from doi2bib.

Christiaan

> On 24 Sep 2021, at 11:52, Fischlin Andreas  
> wrote:
> 
> Dear Christiaan,
> 
> I guess it is following:
> 
> If you download the bib file using the cite service from the web site of the 
> paper (all manually), then the TeX preview fails with an error
> 
> 
> 
> However when you enter doi2bib created output into BibDesk, the preview works 
> right away:
> 
> 
> 
> 
> 
> I guess that is all what is behind this.
> 
> I attach a BibDesk file that contains both records for your convenience.
> 
> Andreas
> 
> 
> ETH Zurich
> Prof. em. Dr. Andreas Fischlin
> IPCC Vice-Chair WGII
> Systems Ecology - Institute of Biogeochemistry and Pollutant Dynamics
> CHN E 24
> Universitaetstrasse 16
> 8092 Zurich
> SWITZERLAND
> 
> andreas.fisch...@env.ethz.ch 
> www.sysecol.ethz.ch/people/andreas.fischlin.html 
> 
> 
> +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 24/09/2021, at 11:43, Christiaan Hofman > > wrote:
>> 
>> I still do not get what the problem is. And the bibtex I get from doi2bib is 
>> essentially the same as what BibDesk gets.
>> 
>> Christiaan
>> 
>>> On 24 Sep 2021, at 11:27, Fischlin Andreas >> > wrote:
>>> 
>>> Here an AppleScript that may help in using doi2bib
>>> 
>>> (*
>>> 
>>> Name
>>> GoTo doi2bib
>>> 
>>> Purpose
>>> Access the services of doi2bib with a minimum of effort, e.g. if a DOI is 
>>> already in the clipboard get the BibTeX entry right away or you are asked 
>>> to provide the DOI to this script
>>>  
>>> Installation  
>>> Copy this script to any AppleScript holding folder, e.g. 
>>> '~/Library/Application Support/BibDesk/Scripts/'
>>> 
>>> Usage Run this script, preferably the DOI of the wanted reference already 
>>> in the clipboard, and then click button 'Copy Bib to Clipboard'. Paste the 
>>> clipboard into any BibTeX manager such as BibDesk.
>>> 
>>> Programing
>>> Andreas Fischlin, andreas.fisch...@env.ethz.ch 
>>> , 24.Sep.2021
>>> 
>>>  
>>> History
>>> 
>>>   af
>>> 24.Sep.2021 v 0.9: First implementation (works under OS X 10.14.6 Mojave 
>>> with Safari as the default browser)
>>>  
>>> *)
>>> 
>>> property enterKey : (ASCII character of 3) -- ENTER is ASCII 3 (MacOS Roman)
>>> property theURL : "https://www.doi2bib.org/ "
>>> 
>>> on run {}
>>> set theDOI to (get the clipboard as string)
>>> if theDOI does not start with "10." then
>>> set theDOI to my EnterString("DOI?")
>>> end if
>>> if theDOI is not "" then
>>> set the clipboard to theDOI
>>> open location theURL
>>> delay 1
>>> tell application "System Events"
>>> keystroke "v" using {command down}
>>> end tell
>>> 
>>> tell application "System Events"
>>> keystroke enterKey
>>> end tell
>>> 
>>> -- Copy Bib to Clipboard needs to be done manually
>>> end if
>>> end run
>>> 
>>> 
>>> ()
>>> (* Generic routines *)
>>> ()
>>> 
>>> on EnterString(promptTxt)
>>> set Input to display dialog promptTxt with title "Text Entry" with icon 
>>> note default answer "" buttons {"Cancel", "OK"} default button 2 giving up 
>>> after 295
>>> return text returned of Input as string
>>> end EnterString
>>> 
>>> 
>>> Andreas
>>> 
>>> 
>>> ETH Zurich
>>> Prof. em. Dr. Andreas Fischlin
>>> IPCC Vice-Chair WGII
>>> Systems Ecology - Institute of Biogeochemistry and Pollutant Dynamics
>>> CHN E 24
>>> Universitaetstrasse 16
>>> 8092 Zurich
>>> SWITZERLAND
>>> 
>>> andreas.fisch...@env.ethz.ch 
>>> www.sysecol.ethz.ch/people/andreas.fischlin.html 
>>> 
>>> 
>>> +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 23/09/2021, at 20:15, Dr Eberhard W Lisse >>> > wrote:
 
 I find that
 
 
 https://www.doi2bib.org/#/doi 
 
 works very well for single citations.
 
 On 2021-09-23 19:46 , Christiaan Hofman wrote:
>> On 23 Sep 2021, at 19:36, Trevor Jenkins

Re: [Bibdesk-users] Can't preview imported citation

2021-09-24 Thread Dr Eberhard W Lisse


Andreas,

That doesn't help that much because you still have to manually copy to
the Buffer.

What would really, really be sexy would be copying the DoI into the
Clipboard (CMD-C) constructing the complete link from the Clipboard
(using pbpaste?)  and then pipe the resulting BIB entry through pbcopy
into the Clipboard again and then make BibDesk take the entry from the
clipboard :-)-O

el


On 24/09/2021 11:27, Fischlin Andreas wrote:
[...]

Usage Run this script, preferably the DOI of the wanted reference
already in the clipboard, and then click button 'Copy Bib to
Clipboard'.  Paste the clipboard into any BibTeX manager such as
BibDesk.

[...]
--
Dr. Eberhard W. Lisse   \ /   Obstetrician & Gynaecologist
e...@lisse.na / *  |  Telephone: +264 81 124 6733 (cell)
PO Box 8421 Bachbrecht  \  /  If this email is signed with GPG/PGP
10007, Namibia   ;/ Sect 20 of Act No. 4 of 2019 may apply
  Book your Covid-10 Vaccination at https://c19.idtoday.com.na


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Re: [Bibdesk-users] Can't preview imported citation

2021-09-24 Thread Dr Eberhard W Lisse


Andreas,

You are overthinking this :-)-O

I just copy and paste :-)-O

el

On 24/09/2021 10:53, Fischlin Andreas wrote:

Dear Eberhard,

Sorry, I do not really understand what you mean with that URL. Why
'#/doi’?  The URL

www.doi2bib.org>

is all what is needed to get to the site.  Or is there a hidden trick
I do not get, e.g. direct import into BibDesk?

Thanks for any clarification.

Andreas

[...]

On 23/09/2021, at 20:15, Dr Eberhard W Lisse  wrote:

I find that


https://www.doi2bib.org/#/doi

--
Dr. Eberhard W. Lisse   \ /   Obstetrician & Gynaecologist
e...@lisse.na / *  |  Telephone: +264 81 124 6733 (cell)
PO Box 8421 Bachbrecht  \  /  If this email is signed with GPG/PGP
10007, Namibia   ;/ Sect 20 of Act No. 4 of 2019 may apply
  Book your Covid-10 Vaccination at https://c19.idtoday.com.na


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Re: [Bibdesk-users] Can't preview imported citation

2021-09-24 Thread Christiaan Hofman

I still do not get what the problem is. And the bibtex I get from doi2bib is 
essentially the same as what BibDesk gets.

Christiaan

> On 24 Sep 2021, at 11:27, Fischlin Andreas  
> wrote:
> 
> Here an AppleScript that may help in using doi2bib
> 
> (*
> 
> Name
> GoTo doi2bib
> 
> Purpose
> Access the services of doi2bib with a minimum of effort, e.g. if a DOI is 
> already in the clipboard get the BibTeX entry right away or you are asked to 
> provide the DOI to this script
>  
> Installation  
> Copy this script to any AppleScript holding folder, e.g. 
> '~/Library/Application Support/BibDesk/Scripts/'
> 
> Usage Run this script, preferably the DOI of the wanted reference already in 
> the clipboard, and then click button 'Copy Bib to Clipboard'. Paste the 
> clipboard into any BibTeX manager such as BibDesk.
> 
> Programing
> Andreas Fischlin, andreas.fisch...@env.ethz.ch 
> , 24.Sep.2021
> 
>  
> History
> 
>   af
> 24.Sep.2021 v 0.9: First implementation (works under OS X 10.14.6 Mojave with 
> Safari as the default browser)
>  
> *)
> 
> property enterKey : (ASCII character of 3) -- ENTER is ASCII 3 (MacOS Roman)
> property theURL : "https://www.doi2bib.org/ "
> 
> on run {}
> set theDOI to (get the clipboard as string)
> if theDOI does not start with "10." then
> set theDOI to my EnterString("DOI?")
> end if
> if theDOI is not "" then
> set the clipboard to theDOI
> open location theURL
> delay 1
> tell application "System Events"
> keystroke "v" using {command down}
> end tell
> 
> tell application "System Events"
> keystroke enterKey
> end tell
> 
> -- Copy Bib to Clipboard needs to be done manually
> end if
> end run
> 
> 
> ()
> (* Generic routines *)
> ()
> 
> on EnterString(promptTxt)
> set Input to display dialog promptTxt with title "Text Entry" with icon note 
> default answer "" buttons {"Cancel", "OK"} default button 2 giving up after 
> 295
> return text returned of Input as string
> end EnterString
> 
> 
> Andreas
> 
> 
> ETH Zurich
> Prof. em. Dr. Andreas Fischlin
> IPCC Vice-Chair WGII
> Systems Ecology - Institute of Biogeochemistry and Pollutant Dynamics
> CHN E 24
> Universitaetstrasse 16
> 8092 Zurich
> SWITZERLAND
> 
> andreas.fisch...@env.ethz.ch 
> www.sysecol.ethz.ch/people/andreas.fischlin.html 
> 
> 
> +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 23/09/2021, at 20:15, Dr Eberhard W Lisse > > wrote:
>> 
>> I find that
>> 
>> 
>> https://www.doi2bib.org/#/doi 
>> 
>> works very well for single citations.
>> 
>> On 2021-09-23 19:46 , Christiaan Hofman wrote:
 On 23 Sep 2021, at 19:36, Trevor Jenkins  wrote:
 
 Downloaded the (auto-generated) citation from
 https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1003763
 
 The import into BibDesk was successful but the TeX Preview breaks
 with various error depending upon what fields are “adjusted”.
 
 
 Regards, Trevor.
 
 <>< Re: deemed!
>>> That is more a question about tex generation.  If the data is
>>> problematic for the tex generation, you should update the data.  That
>>> is the main function of the tex preview: to check that it is valid for
>>> tex.  So I am not precisely sure what your question is.
>>> Christiaan

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Re: [Bibdesk-users] Can't preview imported citation

2021-09-24 Thread Fischlin Andreas

Here an AppleScript that may help in using doi2bib

(*

Name GoTo doi2bib


Purpose Access the services of doi2bib with a minimum of effort, e.g. if a DOI 
is already in the clipboard get the BibTeX entry right away or you are asked to 
provide the DOI to this script



Installation
Copy this script to any AppleScript holding folder, e.g. '~/Library/Application 
Support/BibDesk/Scripts/'


Usage Run this script, preferably the DOI of the wanted reference already in 
the clipboard, and then click button 'Copy Bib to Clipboard'. Paste the 
clipboard into any BibTeX manager such as BibDesk.


Programing Andreas Fischlin, 
andreas.fisch...@env.ethz.ch, 24.Sep.2021




History


  af 24.Sep.2021 v 0.9: First implementation (works under OS X 10.14.6 Mojave 
with Safari as the default browser)



*)

property enterKey : (ASCII character of 3) -- ENTER is ASCII 3 (MacOS Roman)
property theURL : "https://www.doi2bib.org/;

on run {}
set theDOI to (get the clipboard as string)
if theDOI does not start with "10." then
set theDOI to my EnterString("DOI?")
end if
if theDOI is not "" then
set the clipboard to theDOI
open location theURL
delay 1
tell application "System Events"
keystroke "v" using {command down}
end tell


tell application "System Events"
keystroke enterKey
end tell


-- Copy Bib to Clipboard needs to be done manually
end if
end run


()
(* Generic routines *)
()

on EnterString(promptTxt)
set Input to display dialog promptTxt with title "Text Entry" with icon note 
default answer "" buttons {"Cancel", "OK"} default button 2 giving up after 295
return text returned of Input as string
end EnterString


Andreas


ETH Zurich
Prof. em. Dr. Andreas Fischlin
IPCC Vice-Chair WGII
Systems Ecology - Institute of Biogeochemistry and Pollutant Dynamics
CHN E 24
Universitaetstrasse 16
8092 Zurich
SWITZERLAND

andreas.fisch...@env.ethz.ch
www.sysecol.ethz.ch/people/andreas.fischlin.html

+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 23/09/2021, at 20:15, Dr Eberhard W Lisse 
mailto:e...@lisse.na>> wrote:

I find that


https://www.doi2bib.org/#/doi

works very well for single citations.

On 2021-09-23 19:46 , Christiaan Hofman wrote:
On 23 Sep 2021, at 19:36, Trevor Jenkins  wrote:

Downloaded the (auto-generated) citation from
https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1003763

The import into BibDesk was successful but the TeX Preview breaks
with various error depending upon what fields are “adjusted”.


Regards, Trevor.

<>< Re: deemed!
That is more a question about tex generation.  If the data is
problematic for the tex generation, you should update the data.  That
is the main function of the tex preview: to check that it is valid for
tex.  So I am not precisely sure what your question is.
Christiaan

--
Dr. Eberhard W. Lisse   \ /   Obstetrician & Gynaecologist
e...@lisse.na / *  |  Telephone: +264 81 124 6733 (cell)
PO Box 8421 Bachbrecht  \  /  If this email is signed with GPG/PGP
10007, Namibia   ;/ Sect 20 of Act No. 4 of 2019 may apply
Book your Covid-10 Vaccination at https://c19.idtoday.com.na


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Re: [Bibdesk-users] Can't preview imported citation

2021-09-24 Thread Fischlin Andreas

Dear Eberhard,

Sorry, I do not really understand what you mean with that URL. Why '#/doi’? The 
URL

www.doi2bib.org

is all what is needed to get to the site. Or is there a hidden trick I do not 
get, e.g. direct import into BibDesk?

Thanks for any clarification.

Andreas


ETH Zurich
Prof. em. Dr. Andreas Fischlin
IPCC Vice-Chair WGII
Systems Ecology - Institute of Biogeochemistry and Pollutant Dynamics
CHN E 24
Universitaetstrasse 16
8092 Zurich
SWITZERLAND

andreas.fisch...@env.ethz.ch
www.sysecol.ethz.ch/people/andreas.fischlin.html

+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 23/09/2021, at 20:15, Dr Eberhard W Lisse 
mailto:e...@lisse.na>> wrote:

I find that


https://www.doi2bib.org/#/doi

works very well for single citations.

On 2021-09-23 19:46 , Christiaan Hofman wrote:
On 23 Sep 2021, at 19:36, Trevor Jenkins  wrote:

Downloaded the (auto-generated) citation from
https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1003763

The import into BibDesk was successful but the TeX Preview breaks
with various error depending upon what fields are “adjusted”.


Regards, Trevor.

<>< Re: deemed!
That is more a question about tex generation.  If the data is
problematic for the tex generation, you should update the data.  That
is the main function of the tex preview: to check that it is valid for
tex.  So I am not precisely sure what your question is.
Christiaan

--
Dr. Eberhard W. Lisse   \ /   Obstetrician & Gynaecologist
e...@lisse.na / *  |  Telephone: +264 81 124 6733 (cell)
PO Box 8421 Bachbrecht  \  /  If this email is signed with GPG/PGP
10007, Namibia   ;/ Sect 20 of Act No. 4 of 2019 may apply
Book your Covid-10 Vaccination at https://c19.idtoday.com.na


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Re: [Bibdesk-users] Can't preview imported citation

Re: [Bibdesk-users] Can't preview imported citation

Re: [Bibdesk-users] Can't preview imported citation

Re: [Bibdesk-users] Can't preview imported citation

Re: [Bibdesk-users] Can't preview imported citation

Re: [Bibdesk-users] Can't preview imported citation

Re: [Bibdesk-users] Can't preview imported citation

Re: [Bibdesk-users] Can't preview imported citation

Re: [Bibdesk-users] Can't preview imported citation

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