Re: [Bibdesk-users] Missing "Add field" button on entry edit panel?

[Fischlin Andreas]

The button is still there in the lower left corner of the editing window. The 
icon is a plus symbol. If you hover over that button it says: Add new field.

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

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> On Tue, 05.09.23, at 12:15, Alexander,J  wrote:
> 
> Hello,
> 
> I seem to remember that, when editing bibliography entries, the panel had a 
> button for adding fields.  I’ve just noticed that in version 1.8.19, that 
> button is no longer there.  It is still possible to add fields, but you have 
> to either use the menu or the hotkey combination.
> 
> Was this a deliberate user interface change, or has it simply gone missing in 
> one of the builds?  If the latter, might it be possible to bring the “Add 
> field” button back in future builds?
> 
> Many thanks,
> 
> Jason
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Re: [Bibdesk-users] Merging Bibliographies?

[Fischlin Andreas]

If the cite keys remain constant, i.e. serve as the primary key, then you can 
clean up your new data base by using following AppleScript. Note, it overwrites 
any existing older record with the imported one. If this is not your case, you 
must not use this AppleScript.

(* 
   Name Cleanup Duplicates
   
   Purpose  If importing into a BibDesk file updated records, which have 
been imported previously, are obsolete, since outdated. Such duplicates are 
deleted while retaining static group memberships.
   
Remark  This script does also properly restore static group memberships 
even in cases where duplicates are present in multiple numbers, i.e. not only 
simple pairs (see variable 'youngestPub')
   
Installation
Copy this script to folder '~/Library/Application 
Support/BibDesk/Scripts/'

Usage   Run this script by choosing corresponding menu command 
from within BibDesk's Script menu.

Remark  Alternatively you can also run this script from anywhere on 
your system without any installation.   


Programmer  Andreas Fischlin, andreas.fisch...@env.ethz.ch, 
http://www.sysecol.ethz.ch/staff/af/ 
building on script 'Select Obsolete Duplicates' 
written by Christiaan Hofmann, as of 1.Sep.2009 and the previous, but 
comparably very slow script 'Cleanup Duplicates' written by af
 
History 

  af01.Sep.2009 v 1.0: First implementation (works with 
BibDesk Version 1.5.2 (1879) under Snow Leopard OS X 10.6.4). In contrast to 
its predecessor, this script does no logging to be as efficient as possible. 
This algorithm is considerably more efficient than its much more complex 
predecessor variant.
  af08.Oct.2011 v 1.0.1: Introducing core algorithm as a 
separte routine to enable copy/paste maintenance (identical routines used in 
scripts 'Cleanup Duplicates.scpt' and 'Fix PDF and URL Links.scpt'). 
  af15.Sep.2019 v 1.1: Enhancement: For a large library the 
algorithm becomes very time consuming. I added therefore a case working only 
within the set of currently selected pubs. This works also in the case when 
called after an import, making the importing much more efficient.
  af8.Apr.2022 v 1.2: Enhancement: Adding routine 
alertUserOfFailedDeletion to notify user when deletion of records failed
  
*)


on run {}
CleanupDuplicates()
end run


-- IMPORTANT NOTE: The following routine is an identical copy as contained in 
files 'Cleanup Duplicates.scpt' and 'Fix PDF and URL Links.scpt'. Make sure the 
two copies are always kept identical.
on CleanupDuplicates()
set theBibDeskDocu to document 1 of application "BibDesk"
tell document 1 of application "BibDesk"
set thePubs to selection
if (count of thePubs) = 0 then
-- get and sort all publications by cite key ensuring 
that in any set of publications with the same cite key the youngest comes first 
and the oldest, typically the only one of the set that is still member of any 
static groups, comes last. To retain static group memberships we have to ensure 
that such "membership info" is copied from the last to the first publication of 
any set of publications with the same cite key (see vars 'aPub', 'prevPub', 
'youngestPub').
-- with a large library this functionality becomes 
quite tedious and with BibDesk 1.7.1 under OS X 10.14.x (Mojave) it seems that 
duplicates are no longer found with the menu command 'Database -> Select 
Duplicates -> Only Duplicates'. Choosing this menu command results only in a 
beep, despite the fact that duplicates (by cite key) are present and correctly 
shown in red.
set thePubs to (sort (get publications) by "Cite Key" 
subsort by "Date-Added" without ascending)
else
-- this part of the algorithm does only search for 
duplicates for the currently selected publications regardless of the possible 
presence of additional other duplicates in the data base or not. It finds for 
every cite key within current selection a possibly matching publication in the 
data base. Only the thus constructed set of publications is then fixed for 
duplicates by keeping the younger record only. This helps to speed up things 
considerably for large libraries, in particular when importing potential 
duplicates is a relatively small set compared to the entire library.
set theCitekeys to {}
repeat with aPub in thePubs
set aCiteKey to cite key of aPub
set end of theCitekeys to aCiteKey
end repeat
set n to 

Re: [Bibdesk-users] [Bibdesk-announce] BibDesk 1.8.13

[Fischlin Andreas]

Dear Christiaan and colleagues,

Thank you very much for all your efforts you put into BibDesk. IMHO a great 
software!!!

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 21/09/2022, at 11:13, Christiaan Hofman  wrote:
> 
> The BibDesk development team is pleased to announce that a new version of 
> BibDesk, version 1.8.13, is now available.
> 
> We thank the users who have contributed to BibDesk development by sharing 
> their experiences with BibDesk, and testing nightly builds. 
> 
> This release can be obtained by selecting "check for updates" in the 
> "BibDesk" menu, visiting the Sourceforge downloads page at
> 
> https://sourceforge.net/projects/bibdesk/ 
> 
> 
> or by visiting the BibDesk home page at
> 
> https://bibdesk.sourceforge.io/ 
> 
> or by following the link below, which will begin immediate download:
> 
> https://sourceforge.net/projects/bibdesk/files/BibDesk/latest/download 
> 
> 
> For those interested follow the full release notes for this version.
> 
> Release notes for BibDesk version 1.8.13
> 
> Bugs Fixed
>   *  Fix crasher on changing preferences
>   *  Fix problems related to cite key auto-generation in detail window
>   *  Fix search groups using zoom servers
>   *  Fix search group icons
> 
> ___
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Re: [Bibdesk-users] [Bibdesk-announce] BibDesk 1.8.10

[Fischlin Andreas]

Dear Christian,

Thanks for the new BibDesk.

UPDATE FROM PREVIOUS E-MAIL: Small correction for the 2nd snippet given below

However, it seems there is something broken with the AppleScript class linked 
file or linked files that has previously worked fine. E.g. statements such as

tell thePub
add theMacFileToLink to end of linked 
files
end tell

or 

tell thePub
set theLinkedFiles to linked files
if theLinkedFiles is not {} then
repeat with theLinkedF in theLinkedFiles
delete theLinkedF
end repeat
end if
end tell

or 

tell thePub
delete linked files
end tell


all no longer work. Can you please clarify what is going on?

Thanks a lot.

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 10/06/2022, at 11:05, Christiaan Hofman  > wrote:
> 
> The BibDesk development team is pleased to announce that a new version of 
> BibDesk, version 1.8.10, is now available. 
> 
> We thank the users who have contributed to BibDesk development by sharing 
> their experiences with BibDesk, and testing nightly builds. 
> 
> This release can be obtained by selecting "check for updates" in the 
> "BibDesk" menu, visiting the Sourceforge downloads page at
> 
> https://sourceforge.net/projects/bibdesk/ 
> 
> 
> or by visiting the BibDesk home page at
> 
> https://bibdesk.sourceforge.io/ 
> 
> or by following the link below, which will begin immediate download:
> 
> https://sourceforge.net/projects/bibdesk/files/BibDesk/latest/download 
> 
> 
> For those interested follow the full release notes for this version.
> 
> Release notes for BibDesk version 1.8.10
> 
> New Features
>   *  Expose preference to choose download folder
> 
> Bugs Fixed
>   *  Fix copy or drag of templated rich text
>   *  Make template preview display a bit more robust
>   *  Fix and improve updates and edit commits in detail window
>   *  Fix arXiv web scraper for abstract pages
>   *  Fix adding linked files to parsed or copied items
>   *  Do not convert file and URL fields in external groups
> 
> ___
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> 
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Re: [Bibdesk-users] [Bibdesk-announce] BibDesk 1.8.10

[Fischlin Andreas]

Dear Christian,

Thanks for the new BibDesk.

However, it seems there is something broken with the AppleScript class linked 
file or linked files that has previously worked fine. E.g. statements such as

tell thePub
add theMacFileToLink to end of linked 
files
end tell

or 

tell thePub
set theLinkedFiles to linked files
delete linked files
end tell

or 

tell thePub
delete linked files
end tell


all no longer work. Can you please clarify what is going on?

Thanks a lot.

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 10/06/2022, at 11:05, Christiaan Hofman  wrote:
> 
> The BibDesk development team is pleased to announce that a new version of 
> BibDesk, version 1.8.10, is now available. 
> 
> We thank the users who have contributed to BibDesk development by sharing 
> their experiences with BibDesk, and testing nightly builds. 
> 
> This release can be obtained by selecting "check for updates" in the 
> "BibDesk" menu, visiting the Sourceforge downloads page at
> 
> https://sourceforge.net/projects/bibdesk/ 
> 
> 
> or by visiting the BibDesk home page at
> 
> https://bibdesk.sourceforge.io/ 
> 
> or by following the link below, which will begin immediate download:
> 
> https://sourceforge.net/projects/bibdesk/files/BibDesk/latest/download 
> 
> 
> For those interested follow the full release notes for this version.
> 
> Release notes for BibDesk version 1.8.10
> 
> New Features
>   *  Expose preference to choose download folder
> 
> Bugs Fixed
>   *  Fix copy or drag of templated rich text
>   *  Make template preview display a bit more robust
>   *  Fix and improve updates and edit commits in detail window
>   *  Fix arXiv web scraper for abstract pages
>   *  Fix adding linked files to parsed or copied items
>   *  Do not convert file and URL fields in external groups
> 
> ___
> Bibdesk-announce mailing list
> bibdesk-annou...@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/bibdesk-announce



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Re: [Bibdesk-users] Copy Rich Text hangs

[Fischlin Andreas]

This is likely to vary a lot with the amount of data you wish to process. Have 
you tried with a single reference selected?

ETH Zurich, Prof. em. Dr. Andreas Fischlin, IPCC Vice-Chair WGII, Systems 
Ecology, CHN E 24, Universitaetstrasse 16, CH-8092 Zurich, SWITZERLAND
Tel: +41 44 633-6090   Mobile: +41 79 595-4050   Mail: 
andreas.fisch...@env.ethz.ch
www.sysecol.ethz.ch/people/andreas.fischlin.html

> On 3 Mar 2022, at 02:05, Matthew Heun via Bibdesk-users 
>  wrote:
> 
> 
> 
>>> On Mar 2, 2022, at 5:56 PM, Christiaan Hofman  wrote:
>>> 
>>> 
>>> 
 On 2 Mar 2022, at 19:59, Matthew Heun via Bibdesk-users 
  wrote:
>>> 
>>> All:
>>> 
>>> When I copy a bib entry as rich text (via contextual menu and via the Edit 
>>> menu), BibDesk hangs. I see the following message at the bottom of the 
>>> BibDesk window:
>>> 
>>> "Generating data. Please wait..."
>>> 
>>> Does anyone else see this problem?
>>> 
>>> Trying to paste into another application hangs the destination application, 
>>> too.  Steps to replicate:
>>> 
>>> * Select one row (one reference) in the main BibDesk window.
>>> * Right click to choose "Copy Rich Text"
>>> * Switch to MS Word (or other application, like TextMate)
>>> * Paste
>>> 
>>> Now both applications (BibDesk and Word or other destination app) are 
>>> beachballing.  The only way to recover is to force quit both BibDesk and 
>>> the destination app.
>>> 
>>> If it matters, I'm on a 14-inch MacBook Pro (M1 Pro).  I'm using BibDesk 
>>> 1.8.8 (5799).
>>> 
>>> Any suggestions for how to work around this bug?  
>>> 
>>> Cheers,
>>> 
>>> Matt
>> 
>> 
>> This message is normal. You should be able to wait till it finishes. This 
>> may take a little while, depending on your environment and your tex 
>> installation. You should realize that it needs several tex runs to generate 
>> the data.
>> 
>> 
>> Christiaan
>> 
> 
> 
> 
> Thanks for your response.  I just tried again.  I let it go 10 minutes, but 
> it still didn't complete the copy.  Should I wait longer?  
> 
> 
> Cheers,
> 
> Matt
> 
> 
> 
> 
> 
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Re: [Bibdesk-users] Can't preview imported citation

[Fischlin Andreas]

I agree, would really be nice. But the problem is that the doi2bib website 
offers as the default button only the 'get BibTeX’ button and I found no 
solution to get the result into the clipboard, i.e. how to click the button 
‘Copy Bib to Clipboard’ I would know how to trigger via AppleScript in a robust 
manner. Clicking via page/window coordinates is probably not working as the 
size of the window varies all the time. We would need to ask the doi2bib people 
to implement such a fieature, e.g. by making the ‘Copy Bib to Clipboard’ button 
the default button once the ‘get BibTeX’ button has been clicked successfully. 
Then all would be easy to implement as you suggest.

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!



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

[Fischlin Andreas]

I agree, would really be nice. But the problem is that the doi2bib website 
offers as the default button only the 'get BibTeX’ button and I found no 
solution to get the result into the clipboard, i.e. how to click the button 
‘Copy Bib to Clipboard’ I would know how to trigger via AppleScript in a robust 
manner. Clicking via page/window coordinates is probably not working as the 
size of the window varies all the time. We would need to ask the doi2bib people 
to implement such a fieature, e.g. by making the ‘Copy Bib to Clipboard’ button 
the default button once the ‘get BibTeX’ button has been clicked successfully. 
Then all would be easy to implement as you suggest.

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<mailto:andreas.fisch...@env.ethz.ch>
www.sysecol.ethz.ch/people/andreas.fischlin.html<http://www.sysecol.ethz.ch/people/andreas.fischlin.hml>

+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 12:00, Dr Eberhard W Lisse 
mailto:e...@lisse.na>> wrote:


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<mailto: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

[Fischlin Andreas]

Thanks, Christiaan. Good to know.

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<mailto:andreas.fisch...@env.ethz.ch>
www.sysecol.ethz.ch/people/andreas.fischlin.html<http://www.sysecol.ethz.ch/people/andreas.fischlin.hml>

+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 23:59, Christiaan Hofman 
mailto:cmhof...@gmail.com>> wrote:

“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 
mailto:andreas.fisch...@env.ethz.ch>> 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<mailto:andreas.fisch...@env.ethz.ch>
www.sysecol.ethz.ch/people/andreas.fischlin.html<http://www.sysecol.ethz.ch/people/andreas.fischlin.hml>

+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

[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

[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

[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] BibDesk 1.8.3

[Fischlin Andreas]

Dear Christiaan and Colleagues,

Many thanks for BibDesk!!!

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 01/06/2021, at 11:32, Christiaan Hofman 
mailto:cmhof...@gmail.com>> wrote:


The BibDesk development team is pleased to announce that a new version of 
BibDesk, version 1.8.3, is now available.

We thank the users who have contributed to BibDesk development by sharing their 
experiences with BibDesk, and testing nightly builds.

This release can be obtained by selecting "check for updates" in the "BibDesk" 
menu, visiting the Sourceforge downloads page at

https://sourceforge.net/projects/bibdesk/

or by visiting the BibDesk home page at

http://bibdesk.sourceforge.net/

or by following the link below, which will begin immediate download:

https://sourceforge.net/projects/bibdesk/files/BibDesk/BibDesk-1.8.3/BibDesk-1.8.3.dmg/download

For those interested follow the full release notes for this version.

Release notes for BibDesk version 1.8.3

New Features
  *  Keyboard shortcut for adding a new field

Bugs Fixed
  *  Fix completion in fields combo boxes
  *  Fix layout of toolbar search fields on older systems
  *  Ignore rubbish spotlight search text from Finder
  *  Fix save and open options view layout on 10.9
  *  Fix unicode to TeX conversion
  *  Improve UI layout
  *  Fix encoding selection buttons

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Re: [Bibdesk-users] BibDesk slowdowns

[Fischlin Andreas]

Dear Simon,

Indeed this speaks rather against my feeling. Nevertheless, are those systems 
perhaps similarly configured? Therefore, do boot into the safe mode and see 
whether that the behavior that bothers you can be reproduced.

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<mailto:andreas.fisch...@env.ethz.ch>
www.sysecol.ethz.ch/people/andreas.fischlin.html<http://www.sysecol.ethz.ch/people/andreas.fischlin.hml>

+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 03/02/2021, at 14:52, Simon Spiegel 
mailto:si...@simifilm.ch>> wrote:



On 3 Feb 2021, at 14:48, Fischlin Andreas 
mailto:andreas.fisch...@env.ethz.ch>> wrote:

Dear Simon,

This is now more of a feeling than anything else and I might be totally wrong. 
But what you describe now sounds to me like a particular system setup problem.

As a first step towards nailing it down, why do you not boot your Mac into safe 
mode (Start up your Mac in safe mode - Apple Support) and check out whether the 
problem is gone or not. If yes, this means it is your system setup and not 
BibDesk.

I see this on three different machines. And while none of them is brand new, I 
think they should all be capable of handling a database of this size.

Simon

--
Simon Spiegel
Maneggplatz 18
8041 Zürich

Telephon: ++41 44 451 5334
Mobophon: ++41 76 459 6039

http://www.simifilm.ch
http://www.utopia2016.ch

„This too shall pass.“ Tom Hanks



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Re: [Bibdesk-users] BibDesk slowdowns

[Fischlin Andreas]

Dear Simon,

This is now more of a feeling than anything else and I might be totally wrong. 
But what you describe now sounds to me like a particular system setup problem.

As a first step towards nailing it down, why do you not boot your Mac into safe 
mode (Start up your Mac in safe mode - Apple 
Support<https://support.apple.com/en-ph/guide/mac-help/mh21245/11.0/mac/11.0>) 
and check out whether the problem is gone or not. If yes, this means it is your 
system setup and not BibDesk.

Regards,
Andreas


On 03/02/2021, at 13:48, Simon Spiegel 
mailto:si...@simifilm.ch>> wrote:



On 3 Feb 2021, at 12:00, Fischlin Andreas 
mailto:andreas.fisch...@env.ethz.ch>> wrote:

Dear all,

I almost daily work with a large bib file that contains currently 5347 entries, 
admitted this is only half the size of Simon's. I see no such obvious delay 
during regular work. I notice for certain AppleScripts, e.g. I have one 
searching for duplicates after an import, that has become a bit slow with the 
growing size of the bib file. But that is rather due to the nature of that 
particular algorithm, I have chosen to use than a fault of BibDesk.

I would look out for what activity triggers slow responses, what user events 
etc. I cannot confirm that BibDesk has noticeably slowed down in general only 
because of large bib files. I was first also worried about the growing size of 
my default bib file and was always positively surprised how fast BibDesk 
generally still behaves.

As always, once you try to nail it down, it suddenly stops. Seriously, it’s 
definitely a thing, but I don’t see a pattern. It seems to happen often when 
I’m in a different application, say a browser, copy something there and then 
switch to BibDesk to paste it into a field. Then I will often get considerable 
lags – though not always, and it also happens in other situations.

I am no programmer, so maybe this is all wrong, but it seems to me, although 
9000 entries is quite a number, it’s really nothing in terms of memory. The 
.bib file is something over 9mb, and according to Activity Monitor, BibDesk 
uses ~410mb of memory, which isn’t a lot compared to many other common programs.

Simon--
Simon Spiegel
Maneggplatz 18
8041 Zürich

Telephon: ++41 44 451 5334
Mobophon: ++41 76 459 6039

http://www.simifilm.ch
http://www.utopia2016.ch

„This too shall pass.“ Tom Hanks



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Re: [Bibdesk-users] BibDesk slowdowns

[Fischlin Andreas]

Dear all,

I almost daily work with a large bib file that contains currently 5347 entries, 
admitted this is only half the size of Simon's. I see no such obvious delay 
during regular work. I notice for certain AppleScripts, e.g. I have one 
searching for duplicates after an import, that has become a bit slow with the 
growing size of the bib file. But that is rather due to the nature of that 
particular algorithm, I have chosen to use than a fault of BibDesk.

I would look out for what activity triggers slow responses, what user events 
etc. I cannot confirm that BibDesk has noticeably slowed down in general only 
because of large bib files. I was first also worried about the growing size of 
my default bib file and was always positively surprised how fast BibDesk 
generally still behaves.

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 03/02/2021, at 09:38, Simon Spiegel 
mailto:si...@simifilm.ch>> wrote:

Hi everybody,

for quite some time now I’ve been experiencing considerably lags when editing 
entries in BibDesk, this is particularly noticeable in fields where BibDesk is 
suggesting autocompletion.

My .bib file has more than 9000 entries, maybe this is too much?

I am not sure when it started, whether it happened with the update t a new 
version or after reaching a certain number of entries. What I can say is that I 
see this on machines of quite different ages.

Any suggestions?

Simon

--
Simon Spiegel
Maneggplatz 18
8041 Zürich

Telephon: ++41 44 451 5334
Mobophon: ++41 76 459 6039

http://www.simifilm.ch
http://www.utopia2016.ch

„For there is always light / If only we’re brave enough to see it / If only 
we’re brave enough to be it.“ Amanda Gorman



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Re: [Bibdesk-users] importing links to attachment - a step further

[Fischlin Andreas]

Dear Ronald,

And I forgot to mention that there is also the AppleScript 'Inspect Linked 
Files’ available. That script should work fine in your case and provide you 
with helpful information to diagnose the status of your PDF’s and the current 
meta data in your BibTeX file.

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 29/12/2020, at 00:08, Ronald Haynes 
mailto:rhayne...@gmail.com>> wrote:

Correct! A hack for sure to get up and running with bibdesk.

Sincerely,

Dr. Ronald D. Haynes

Professor, Department of Mathematics and Statistics
Chair, MSc and PhD Scientific Computing Programs
Memorial University of Newfoundland

We acknowledge that the lands on which Memorial University’s campuses are 
situated are in the traditional territories of diverse Indigenous groups, and 
we acknowledge with respect the diverse histories and cultures of the Beothuk, 
Mi’kmaq, Innu, and Inuit of this province.
On Dec 28, 2020, 7:35 PM -0330, Christiaan Hofman 
mailto:cmhof...@gmail.com>>, wrote:
That looks like it just drops the second file. Also problematic when anything 
else, like a title, has a semicolon in it.

Christiaan

On 28 Dec 2020, at 22:09, Ronald Haynes 
mailto:rhayne...@gmail.com>> wrote:

Hi folks, I was able to conjure up a little vi magic to handle this:

:%s/;.*/}/

Sincerely,

Dr. Ronald D. Haynes

Professor, Department of Mathematics and Statistics
Chair, MSc and PhD Scientific Computing Programs
Memorial University of Newfoundland

We acknowledge that the lands on which Memorial University’s campuses are 
situated are in the traditional territories of diverse Indigenous groups, and 
we acknowledge with respect the diverse histories and cultures of the Beothuk, 
Mi’kmaq, Innu, and Inuit of this province.
On Dec 28, 2020, 2:40 PM -0330, Christiaan Hofman 
mailto:cmhof...@gmail.com>>, wrote:


On 28 Dec 2020, at 17:15, Ronald Haynes 
mailto:rhayne...@gmail.com>> wrote:

Hi folks, so I have made some progress with links to attachments using a .bib 
file generated by zotero/better-bibtex.  All entries work except for entries 
with multiple attachments.  Several of my .bib entries have file fields that 
look like:

/Users/rhaynes/Zotero/storage/QYXFGM6P/Peña_1995_M-matrices whose inverses are 
totally 
positive.pdf;/Users/rhaynes/Zotero/storage/ZQNHFBL9/002437959300244T.html


Bibdesk is not able to decipher the link to the pdf file.  Any suggestions?

Sincerely,

Dr. Ronald D. Haynes

Professor, Department of Mathematics and Statistics
Chair, MSc and PhD Scientific Computing Programs
Memorial University of Newfoundland

BibDesk cannot by itself understand multiple files in the same field. It is 
also ambiguous, as the semicolon is also a valid path character.

You could try to use AppleScript to convert these fields into linked files. I 
don’t know if you are versed in AppleScript?

The following script should do what you want (disclaimer: not fully tested, as 
I don’t have these fields).

tell application "BibDesk"
tell front document
set AppleScript's text item delimiters to {";"}
repeat with aPub in publications
tell (contents of aPub)
set theValue to value of field "File"
if theValue contains ";" then
set theFileNames to text items of theValue
repeat with theFileName in theFileNames
set theFileName to contents of theFileName
if theFileName ≠ "" then
set theFile to resolve theFileName
try
theFile as alias
if (get linked files) does not contain theFile then
add theFile
end if
end try
end if
end repeat
end if
end tell
end repeat
set AppleScript's text item delimiters to {""}
end tell
end tell

Christiaan

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Re: [Bibdesk-users] importing links to attachment - a step further

[Fischlin Andreas]

Dear Ronald,

On my website you find a link to 
Software I offer where you find BIbDesk 
AppleScripts. There I offer the AppleScript 'Fix PDF and URL Links’. This 
script deletes first all current links and reconstructs them from the existing 
files for the PDF’s. The script works well, yet it comes with a drawback, i.e. 
the file names are assumed to start with the cite key. Nevertheless, the script 
may help you to get the AppleScript you need to get done what you need right 
now.

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 29/12/2020, at 00:08, Ronald Haynes 
mailto:rhayne...@gmail.com>> wrote:

Correct! A hack for sure to get up and running with bibdesk.

Sincerely,

Dr. Ronald D. Haynes

Professor, Department of Mathematics and Statistics
Chair, MSc and PhD Scientific Computing Programs
Memorial University of Newfoundland

We acknowledge that the lands on which Memorial University’s campuses are 
situated are in the traditional territories of diverse Indigenous groups, and 
we acknowledge with respect the diverse histories and cultures of the Beothuk, 
Mi’kmaq, Innu, and Inuit of this province.
On Dec 28, 2020, 7:35 PM -0330, Christiaan Hofman 
mailto:cmhof...@gmail.com>>, wrote:
That looks like it just drops the second file. Also problematic when anything 
else, like a title, has a semicolon in it.

Christiaan

On 28 Dec 2020, at 22:09, Ronald Haynes 
mailto:rhayne...@gmail.com>> wrote:

Hi folks, I was able to conjure up a little vi magic to handle this:

:%s/;.*/}/

Sincerely,

Dr. Ronald D. Haynes

Professor, Department of Mathematics and Statistics
Chair, MSc and PhD Scientific Computing Programs
Memorial University of Newfoundland

We acknowledge that the lands on which Memorial University’s campuses are 
situated are in the traditional territories of diverse Indigenous groups, and 
we acknowledge with respect the diverse histories and cultures of the Beothuk, 
Mi’kmaq, Innu, and Inuit of this province.
On Dec 28, 2020, 2:40 PM -0330, Christiaan Hofman 
mailto:cmhof...@gmail.com>>, wrote:


On 28 Dec 2020, at 17:15, Ronald Haynes 
mailto:rhayne...@gmail.com>> wrote:

Hi folks, so I have made some progress with links to attachments using a .bib 
file generated by zotero/better-bibtex.  All entries work except for entries 
with multiple attachments.  Several of my .bib entries have file fields that 
look like:

/Users/rhaynes/Zotero/storage/QYXFGM6P/Peña_1995_M-matrices whose inverses are 
totally 
positive.pdf;/Users/rhaynes/Zotero/storage/ZQNHFBL9/002437959300244T.html


Bibdesk is not able to decipher the link to the pdf file.  Any suggestions?

Sincerely,

Dr. Ronald D. Haynes

Professor, Department of Mathematics and Statistics
Chair, MSc and PhD Scientific Computing Programs
Memorial University of Newfoundland

BibDesk cannot by itself understand multiple files in the same field. It is 
also ambiguous, as the semicolon is also a valid path character.

You could try to use AppleScript to convert these fields into linked files. I 
don’t know if you are versed in AppleScript?

The following script should do what you want (disclaimer: not fully tested, as 
I don’t have these fields).

tell application "BibDesk"
tell front document
set AppleScript's text item delimiters to {";"}
repeat with aPub in publications
tell (contents of aPub)
set theValue to value of field "File"
if theValue contains ";" then
set theFileNames to text items of theValue
repeat with theFileName in theFileNames
set theFileName to contents of theFileName
if theFileName ≠ "" then
set theFile to resolve theFileName
try
theFile as alias
if (get linked files) does not contain theFile then
add theFile
end if
end try
end if
end repeat
end if
end tell
end repeat
set AppleScript's text item delimiters to {""}
end tell
end tell

Christiaan

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Re: [Bibdesk-users] Installing BibDesk issues

[Fischlin Andreas]

Dear Ronel,

What Eberhard suggested may not be the best solution, since it disables for 
good all such warnings. To keep control of what’s going on on your Mac I would 
recommend an alternative. Do control-click in the Finder the application 
‘BibDesk’ and then choose in the pop-up menu to open the application. This will 
give the same warning but with an option to open the application nevertheless. 
That’s all folks.

You need to do this only once during very first use of an application not from 
Apple’s App Store. Thereafter any application opened by this technique can be 
used normally without a glitch.

Regards,
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.hml

+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 02/10/2020, at 06:31, Ronel Scheepers 
mailto:ronel.scheep...@hdr.qut.edu.au>> wrote:

Good day,

I’ve been using bibdesk for the past 5 years and have recently aquired a new 
Macbook Pro. I downloaded the software from your website and the app appears in 
my applications folder. However, when I want to open it, I get the following 
message:


Could you please advise how I can rectify this?

Thank you,

Kind regards,

Ronél
Ronél Scheepers
n8967261
email: ronel.scheep...@hdr.qut.edu.au

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Re: [Bibdesk-users] Working with a master and a local .bib file

[Fischlin Andreas]

Dear Daniele,

For all the good reasons you mention (and some others) I do not keep the large 
master file in the Dropbox. Even more importantly, my precious repository of 
pdf’s that goes with that master file, is also way too large to fit into my 
Dropbox. In cases where I needed to have the same master file and the same pdf 
repository on more than one computer, I am using syncing apps. However, for a 
particular project such as the writing of a scientific paper I use excerpts. If 
you go to my website  
you find at the bottom links to software I offer, where you also find many 
BibDesk AppleScripts that support the extraction of excerpts, with or without 
the accompanying pdf’s, including some syncing back utilities. The latter are 
of interest to me, since I like to read pdf’s on my iPad. Yet, again my 
collection is too large to have all on the iPad. Thus I also make excerpts, 
e.g. one on a particular topic, to myself, to go to the iPad. The metadata of 
an excerpt are typically all in a website created from the currently in BibDesk 
selected references. That website can be read on the iPad and its links to 
pdf’s can be used to open and read the pdf’s. For the excerpt you could use a 
Dropbox folder, but I actually use today a derivative of owncloud for syncing 
such an excerpt among all involved devices. On the iPad to actually read I use 
GoodReader, which I like for its excellent features, in particular for 
annotations. The latter are precious, the reason why I use sync back utilities 
to overwrite in my master collection the newly annotated pdf’s. The only 
discipline required on the user side is to not read the same paper on two 
devices at the same time. Otherwise only the pdf copy that received the most 
recent annotation on any of the used devices is going into the collection. But 
I find that discipline easy to observe. If I want to switch devices, e.g. stop 
reading on the iPad and continue reading on the Mac, I always first run the 
sync back utility from within BibDesk before opening the pdf.

Regards,
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.hml

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

 Make it as simple as possible, but distrust it!







On 23/08/2020, at 12:00, Daniele Avitabile 
mailto:d.avitab...@gmail.com>> wrote:

Dear All,

I'm relatively new to BibDesk, and I am trying to improve my workflow. I have 
tried to search for this information but could not find it, so feel free to 
redirect me to the documentation, or other discussions. It seems so basic to me 
that I'm almost sure it's been discussed plenty of times before.

I plan to build a master file, a large collection of entries, that I will keep 
in order, with many pdfs, sublists, etc. This master file will live in a 
Dropbox folder.

However, when I'm writing a paper, I only need some of these references, and 
the corresponding .bib file lives next to the .tex sources. It's a local file. 
I will most likely share this file with collaborators, and clearly I don't want 
to expose my master file.

How do you typically work in this setup? Do you keep the master and the local 
file open, and drag references from one to the other? There's something smarter 
to do? Am I missing something?

Thanks
Daniele
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Re: [Bibdesk-users] Feature request: remove file on disk when removing link

[Fischlin Andreas]

Dear Luc,

Indeed, that would be annoying.

BTW, I offer on my website several AppleScripts which greatly support such 
tasks. E.g. I can simply replace in the Finder an obsolete version of a PDF 
with an updated one and then trigger with a shortcut (Ctrl^F) an AppleScript 
that discards the old link and replaces it with a new link to the new file. 
There is only one drawback for this to work, I use information from the record 
to construct the file name. In my case I use only the cite key with some 
suffixes if there are several PDF’s linked to the same article, e.g. 
supplementary material, to name my PDFs.

Should you be interested, here the link: https://www.sysecol2.ethz.ch/software/

Regards,
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.hml

+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 12/06/2020, at 09:31, Luc Bourhis via Bibdesk-users 
mailto:bibdesk-users@lists.sourceforge.net>>
 wrote:

Hi,

it would be sweet if BibDesk would propose to remove the actual file on disk 
when one removes a link from a record. It happens every now and then that 
either I filed the wrong file, or more often that I want to replace a preprint 
by a later version or the published one. Currently, I have to remove the link, 
add the new one, then use “Reveal in Finder” and remove the old one. A bit 
tedious.

Best wishes,

Luc J Bourhis



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Re: [Bibdesk-users] [Bibdesk-announce] BibDesk 1.7.6

[Fischlin Andreas]

Dear Christiaan and all other developers,

Once again a big thank you! I would not know what to do without Bibdesk!

Regards,
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.hml

+41 44 633-6090 phone
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 Make it as simple as possible, but distrust it!







On 18/05/2020, at 11:01, Christiaan Hofman 
mailto:cmhof...@gmail.com>> wrote:

Greetings all

The BibDesk development team is pleased to announce that a new version of 
BibDesk, version 1.7.6, is now available.

We thank the users who have contributed to BibDesk development by sharing their 
experiences with BibDesk, and testing nightly builds.

This release can be obtained by selecting "check for updates" in the "BibDesk" 
menu, visiting the Sourceforge downloads page at

https://sourceforge.net/projects/bibdesk/

or by visiting the BibDesk home page at

http://bibdesk.sourceforge.net/

or by following the link below, which will begin immediate download:

https://sourceforge.net/projects/bibdesk/files/BibDesk/BibDesk-1.7.6/BibDesk-1.7.6.dmg/download

For those interested follow the full release notes for this version.

Release notes for BibDesk version 1.7.6

New Features
  *  Share menu instead of email command when available
  *  New option in import script command to overwrite fields without asking

Bugs Fixed
  *  Fix a crasher when automatically committing certain edits
  *  Fix import script command
  *  Don't update linked files unnecessary during save
  *  Fix color label conditions in smart groups
  *  Fix Inspire web scraper for new page format

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Re: [Bibdesk-users] Adding pdf extension to the Url field

[Fischlin Andreas]

AppleScripts can for sure do that. I offer many AppleScripts I have developed 
for BibDesk on my website (see below).

Regards,
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.hml

+41 44 633-6090 phone
+41 44 633-1136 fax
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 Make it as simple as possible, but distrust it!







On 26/10/2019, at 05:14, Danushka Bollegala 
mailto:danushka.bolleg...@gmail.com>> wrote:

Thank you for developing BibDesk which is an essential component of my research 
workflow!

I use acl anthology for importing papers into bibdesk. The Url field in the 
BibText in acl anthology does not contain .pdf extension.
For example, see https://www.aclweb.org/anthology/N18-2115/
for which the bibtex entry contains

url = "https://www.aclweb.org/anthology/N18-2115”

Unfortunately, this gets mapped to the Url field in Bibdesk and I cannot 
download the pdf but the top page by “Download Urls” menu.

Is there a way (for example a script hook etc.) that would let me automatically 
append .pdf to the url field when a bibtex entry is copied to BibDesk?

Thank you

Danushka
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Re: [Bibdesk-users] Problem: export database with citekeys only

[Fischlin Andreas]

Please see the BibDesk scripts I offer on my software website:

http://www.sysecol.ethz.ch/people/andreas.fischlin.html
Link Software

Hope this helps.

Regards,
Andreas


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

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

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

 Make it as simple as possible, but distrust it!









On 10/02/2019, at 20:17, Björn mailto:pihte...@arcor.de>> 
wrote:

Good evening,

I need to export my entire bib desk-bibliography into a csv file, but with cite 
keys only, separated by comma or anything else (that a script can later 
identify as a separator).

I was reading on export templates and export tags as well as building custom 
templates with the build-in template editor  (sources see bottom).

I was building a custom template, like:

<$publications>

<$citeKey/>



I cannot test it, though.
Problem is: when trying to export within Bibdesk, there is only a drop down 
menue with a couple of file formats (html, rtf, txt) but I cannot find my new 
one (which I put into the template folder to the other templates).

The above mentioned help sources on Sourceforge mention a dialog in which I can 
select templates. I do not have this. I do not even have the menu item "Using 
Template“ in my drop-down menu.

Question: is my Bibdesk to old or broken?
Question: am I going the right way or is there an easier way of getting all 
one´s cite keys in a csv-file?

I am using Bibdesk Version 1.6.13 (4389) on Mac OS 10.9.5

Thanks for your hints and have a good start of the week!

Peter



Sources:
Export templates:
https://sourceforge.net/p/bibdesk/wiki/Templates/

Template builder
https://bibdesk.sourceforge.io/manual/BibDeskHelp_60.html#SEC119



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Re: [Bibdesk-users] AppleScript CiteInPages

[Fischlin Andreas]

Dear Paolo,

I for one have not tweaked them.

However, to make latest versions of scripts available to everyone is certainly 
a good idea. If you can help along those lines, please do so.

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

andreas.fisch...@env.ethz.ch
www.sysecol.ethz.ch/Staff/af

+41 44 633-6090 phone
+41 44 633-1136 fax
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On 01/03/2017, at 17:00, Pier Paolo Donato 
> wrote:

Hi there,
I have a question regarding BibDesk and Pages 6: I couldn’t manage to get the 
bibliography using the CiteInPages AppleScript.
The website from which I got the AppleScript 
(http://jhh.med.virginia.edu/main/CiteInPages) is been unavailable for years 
now (at least for me).
Since the scripts are open source, I wonder if anyone has tweaked them to work 
with Pages 6.
For reference the script author said "This script used the ReplaceCite script 
from the BibDesk Wiki site 
(http://bibdesk.sourceforge.net/wiki/index.php/BibDesk_Applescripts) as a 
starting point and may still contain a few lines of that code.”
If you guys like, I still have the scripts on my computer, I could forward them 
to you for inspection.

Or hopefully someone else has written a new script for that.

Thanks in advance.
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Re: [Bibdesk-users] BibDesk 1.6.8

[Fischlin Andreas]

Dear Christiaan,

The link to the dmg is to version 1.6.7. Is that really intentional?

Regards,
Andreas


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

andreas.fisch...@env.ethz.ch
www.sysecol.ethz.ch/Staff/af

+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 13/02/2017, at 10:21, Christiaan Hofman 
> wrote:

Greetings all

The BibDesk development team is pleased to announce that a new version of 
BibDesk, version 1.6.8, is now available.

We thank the users who have contributed to BibDesk development by sharing their 
experiences with BibDesk, and testing nightly builds.

This release can be obtained by selecting "check for updates" in the "BibDesk" 
menu, visiting the Sourceforge downloads page at

https://sourceforge.net/projects/bibdesk/

or by visiting the BibDesk home page at

http://bibdesk.sourceforge.net/

or by following the link below, which will begin immediate download:

http://sourceforge.net/projects/bibdesk/files/BibDesk/BibDesk-1.6.7/BibDesk-1.6.7.dmg/download

For those interested follow the full release notes for this version.

Release notes for BibDesk version 1.6.8

Bugs Fixed
  *  Use separate PATH environment variables for tex and bibtex commands for 
preview
  *  Allow background drawing in TeX preview PDF view to avoid sluggishness on 
10.12
  *  Linked files prefer path over file object after replacing, support Dropbox
  *  Fix side pane animation

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Re: [Bibdesk-users] How to Alter the "Copy Rich Text" template?

[Fischlin Andreas]

Dear Gray,

You need merely to edit the template. You can freely do that yourself. See the 
wiki pages.

Regards,
Andreas


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

andreas.fisch...@env.ethz.ch
www.sysecol.ethz.ch/Staff/af

+41 44 633-6090 phone
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On 05/11/2016, at 16:26, Gray, Wayne  wrote:

> Using bibdesk for mac — I would like to alter the defaults for “Copy Rich 
> Text” template so that the info appearing btw the first two brackets is the 
> citekey.
> 
> For example:
> 
> RATHER THAN THE DEFAULT; I.E., THIS:
> 
> [Jones et al., 2009] Jones, M. W. G., Blue, C. S., and Smith, D. (2009). 
> Increasing speed of processing with action video games. Current Directions in 
> Game Science, 34(6):321–326.
> 
> I WOULD LIKE THIS:
> 
> [jones09cdgs] Jones, M. W. G., Blue, C. S., and Smith, D. (2009). Increasing 
> speed of processing with action video games. Current Directions in Game 
> Science, 34(6):321–326.
> 
> where “jones09cdgs” is my citekey for this citation.
> 
> Thanks,
> 
> Wayne Gray
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Re: [Bibdesk-users] The search, edit, and save sequence hides the item.

[Fischlin Andreas]

BTW, I find this behavior one of the strengths of BibDesk’s searching 
capabilities in contrast to many other applications failing miserably along 
those lines. I find myself in most applications always retyping, often several 
times, the same search strings. Not so in BibDesk.

Regards,
Andreas


On 15/07/2016, at 12:40, Masso Chailly  wrote:

> 
>> On Jul 15, 2016, at 7:20 PM, Christiaan Hofman  wrote:
>> 
>> 
>>> On Jul 15, 2016, at 11:57, Masso Chailly  wrote:
>>> 
>>> Hi.
>>> 
>>> When I search the library, edit an item of the search result, and save it, 
>>> then the modified item disappears from the list of search result. Does 
>>> anybody else have the same issue?
>>> 
>> 
>> Does the edited item still match the search? Than this works as expected. 
>> And it works like that for me: when the edited item still matches the 
>> search, it will remain, if it doesn’t match the search after the edit it 
>> will disappear. AFAIK we redo the search when relevant fields are edited.
> 
> Even when the edited item still matches, it disappears. Strange, isn’t it?
> 
> 
>>> It’s not terribly annoying, because I can search again using the same 
>>> keywords still available in the input field. Yet I find it inconvenient. 
>>> Actually, I have noticed this issue quite a while (from previous versions).
>>> 
>>> A feature request if possible: Currently, the BibDesk search shows only 
>>> exact matches. Of course, I can put * around a keyword to get all matches 
>>> containing it. Can I change the behaviour so that the latter be the default?
>>> 
>> 
>> You can search for exact matches, or with wildcards. Use the search mEnu 
>> (the contextual menu for the search field). This option will stick.
> 
> Ah, great! Sorry that I haven’t noticed the contextual menu. And thanks!
> 
> Masso
> 
> 
>>> Many thanks in advance,
>>> 
>>> Masso
>> 
>> hah
>> Christiaan
>> 
> 
> 
> 
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Re: [Bibdesk-users] why does it crash so often?

[Fischlin Andreas]

Dear Masso,

I cannot confirm that observation, however I am using mostly older OS X 
versions, currently mostly OS X 10.9.5 (Mavericks).

Given my long experience with BibDesk, one of the best programs out there in 
terms of reliability and robust functioning, I suspect a specific problem with 
your setup or even perhaps your BibTeX file. Perhaps you test, whether you can 
repeat this crash by using a virgin account on your very same system. If you 
can’t repeat the crash, this points at a specific system configuration, which 
causes the crash. If you switch to a different BibTeX file and can no longer 
repeat the crash, this points at a problem with your specific BibTeX file. 
Perhaps these hints help you to narrow it down.

Regards,
Andreas


ETH Zurich
Prof. em. Dr. Andreas Fischlin
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/Staff/af

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

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On 30 Mar 2016, at 10:33, Masso Chailly 
> wrote:

Hi.

I’ve been using BibDesk quite a while. From some point, it crashes increasingly 
often. Now I can even reproduce, at least, one instance of crash: about 10 
repeated presses of next-entry (arrow down) or previous-entry (arrow up) keys 
cause the crash.

Is it only the case for me?

For your reference, my OS X version is El Capitan (10.11.4) but I remember it 
was crashing quite a lot on earlier OS X versions as well.

Any suggestion to improve my experience with BibDesk will be appreciated.


Masso


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Re: [Bibdesk-users] Bibdesk-URLs keep changing when I save on different machines

[Fischlin Andreas]

I have avoided parts of the issue first described in this discussion by 
introducing symbolic links mirroring any system involved. The situation is, 
however, slightly different in that I sync or transfer also the BibDesk file 
among systems first. When I then open the bib-file with BibDesk on any of the 
involved systems, the symbolic links ensure that the identical path exists as 
well. E.g. two systems with two users ‘userx’ and ‘usery’ having both a 
different location where the pdf repository resides:

/Users/userx/Documents/DataBases/PDFsOfRefs
/Users/usery/MyProject/Literature/BibDesk/pdfRepository

and having on each of those systems symbolic links such that on both systems 
exist both paths. This trick avoids losing the linked files and BibDesk does 
since years honor such a change of systems without a glitch. No need to go for 
local file field and the 1 to n relationship can be maintained the usual very 
powerful and convenient manner as BD offers.

Regards,
Andreas


ETH Zurich
Prof. em. Dr. Andreas Fischlin
Systems Ecology - Institute of Biogeochemistry and Pollutant Dynamics
CHN E 21.1
Universitaetstrasse 16
8092 Zurich
SWITZERLAND

andreas.fisch...@env.ethz.ch
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 19 Nov 2015, at 11:44, Christiaan Hofman 
> wrote:


On Nov 13, 2015, at 23:23, Christiaan Hofman 
> wrote:


On Nov 13, 2015, at 20:52, Adam R. Maxwell 
> wrote:


On Nov 13, 2015, at 04:05 , macula > wrote:

Regarding the huge diffs, I am fully in agreement with Michael. Autofile
is a great feature, and so is the preview side panel, and it would be a
pity to view this as an either/or proposition.

The underlying code for files is pretty complicated, and some if it
has been there since the editor window had a drawer where you could
view a single attached PDF :).

The fileview and alias code was a massive rewrite, and it's just
not really compatible with the older attachment code. Maybe it could
be changed at the serialization level to only save a path, but reading
it would then be tricky…

I just feel that the new
BibDesk is somehow rubbing against the aesthetic and openness of the
Bib(La)TeX format.

I disagree with this; we namespace our private fields with a bdsk-
prefix, to avoid clobbering anyone else's data. By comparison,
I think BibLaTeX is not compatible with BibTeX as it's been defined
for years (notably having changed the semantics of a field or two).
This makes it impossible for BibDesk to support both.

BibDesk's Date-Modified, Date-Added, Annote, Abstract are exceptions
that predate our notion of private fields.

Many if not all of us are scholars and share our
materials with students and colleagues. Part of the appeal of this
format is that its plain-text elegance and standardization liberate the
data from any particular software. The very fact that BibDesk now
presumes to "own" the database is a bit contrary to the philosophy of
BibTeX, I think.

To be clear, we "own" the bdsk-fields, and other well-behaved software
should just ignore those. Sharing a .bib and set of attached files on
a fileserver or cloud is an extremely complicated case, especially when
multiple users can access it. Apple screws it up regularly, so I just
prefer not to even try :).

More practically, wouldn't this issue be solved if there was a scheme
for storing the links locally in a separate file? I am thinking of a
simple one-to-one index assigning each bibliographic entry (identified
either by its BibTeX key or by a BibDesk-generate UUID) to a list of
links to the entry's attachments?

Two separate files would be a disaster with Finder copies and
moving/renaming/sharing. I suppose one could store it in the resource
fork or extended attributes, but that's a different ball of hurt.

We considered doing this in a number of ways (a new data file format,
a package-based format). The former died on the vine, and the
latter makes it hard to get to the .bib file for TeX usage, and isn't
really compatible with version control systems.

For the time being, Michael, I am thinking to move my BibDesk-owned bib
file out of the git repo and into dropbox, then use bibtool to produce a
git-friendly version stripped of all links.

You can probably do this with a template also, or use the minimal
BibTeX export (but that might remove too much).

I'm not entirely unsympathetic to the problems here, but they're not
trivial to solve in a way that is robust, user-friendly, and backwards
compatible.

Adam


Optionally leaving out the alias data would lead to somewhat fragile data, so 
the link could easily be lost. 

Re: [Bibdesk-users] Bibdesk-URLs keep changing when I save on different machines

[Fischlin Andreas]

I am not convinced that a new field type is necessary here for several reasons: 
What happens if you should have both fields in a record? Why supporting files 
to be anywhere in case of relative paths? I believe that most use cases 
interested in a relative path need only a common root path to which to 
concatenate the relative path. Thus one could enforce such a common root (for 
this new hidden pref) and always extract the wanted relative path from an 
absolute path as contained in the existing field type. Following some rules, 
e.g. using the global pdf repository path as that common root, would already 
suffice to define what part of the absolute path is to be ignored. 

Regards, Andreas 

ETH Zurich, Prof. Dr. Andreas Fischlin, Systems Ecology
CHN E 21.1, Universitaetstrasse 16, 8092 Zurich, SWITZERLAND
Tel: +41 44 633-6090 - Mobile: +41 79 595-4050 - 
mailto:andreas.fisch...@env.ethz.ch
www.sysecol.ethz.ch/people/afischli

> On 19 Nov 2015, at 18:01, Maxwell, Adam R  wrote:
> 
> 
>> On Nov 19, 2015, at 02:44, Christiaan Hofman  wrote:
>> 
>> For now this is just for testing purposes. I am not sure what to do with 
>> this, whether to advertise this on the Wiki, integrate this as an actual 
>> pref (that could be dangerous), or remove it later.
> 
> Just spitballing, but the only safe way I see to make it an actual pref is by 
> adding a new field type (like Bdsk-Path-n) and doing a conversion process 
> when opening and saving.
> 
> -- 
> Adam
> 
> 
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Re: [Bibdesk-users] Auto-filing attachments of individual publications

[Fischlin Andreas]

Dear Y.,

First there is no such menu command ‘AutoFile Paper’, but I guess you mean 
‘AutoFile Linked Files’. Saving or not saving the database does not matter for 
this menu item’s availability, since it refers to linked files. Only if you 
have actually added some linked files, e.g. by drag/drop a pdf to the right 
side bar of the Edit window will this menu command become active and available. 
I presume it is greyed out in your case, because you have not created any 
linked files for that record.

Hope this clarifies the situation.

Regards,
Andreas


ETH Zurich
Prof. Dr. Andreas Fischlin
Systems Ecology - Institute of Biogeochemistry and Pollutant Dynamics
CHN E 21.1
Universitaetstrasse 16
8092 Zurich
SWITZERLAND

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
www.sysecol.ethz.chhttp://www.sysecol.ethz.ch

+41 44 633-6090 phone
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On 09/07/2014, at 10h21, Yannis Rammos ir...@me.commailto:ir...@me.com 
wrote:

Hi,

According to the help system, you can also AutoFile a single linked
file by choosing the 'AutoFile Paper' menu item in the action menu of
the Editor. On my system this option (which I presume is under the
cogwheel con). is always greyed out, both before and after saving the
database.

Thanks,

Y.

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Re: [Bibdesk-users] search within bibtex

[Fischlin Andreas]

Thomson Reuters has changed the services. However, this happened already quite 
a while ago.

Some of us are currently working on finalizing a new implementation. You need 
to use the latest nightly to profit from those efforts.

Regards,
Andreas


ETH Zurich
Prof. Dr. Andreas Fischlin
Systems Ecology - Institute of Biogeochemistry and Pollutant Dynamics (IBP)
Department of Environmental Systems Science
CHN E 21.1
Universitaetstrasse 16
8092 Zurich
SWITZERLAND

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
www.sysecol.ethz.chhttp://www.sysecol.ethz.ch

+41 44 633-6090 phone
+41 44 633-1136 fax
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On 18/04/2014, at 08:24 , Fu Feichao wrote:

Dear all,
I found that I cannot search within bibtex from the ISI web of knowledge.  Does 
anyone know what’s happened? Thx first.

Bests,
Feichao


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Re: [Bibdesk-users] pdfmeat

[Fischlin Andreas]

Dear Ken,

On 25/01/2014, at 03:11 , Ken Mankoff wrote:

Ok, it seems there is no mechanism to parse the raw BibTeX record (it is 
read-only in BibDesk AppleScript).

Of course not. You can fully read and write BibDesk records using AppleScripts. 
It is however, not fully clear what you mean by raw BibTeX record. What I know 
is that you should not meddle with those and leave that to BibDesk to manage 
the data in the bib file. Otherwise you risk getting a huge mess.


I guess a simple work-around is to import an entirely new record using the 
pdfmeat.py output, link the old file (the file link being the only thing in the 
previous empty record) to the new record, and then delete the old record.

There are plenty of example AppleScripts within the BibDesk community which can 
do what you seem to be looking for. Why don't you have a look at those (Help 
- Visit BibDesk Wiki)? Here a link to mine I offer from this web site:  
http://www.sysecol.ethz.ch/people/afischli   Link Software - BibDesk - 
AppleScripts



I have the import working, and know how to delete a record thanks to the sample 
script, but can't figure out how to move the linked file from the old to the 
new.

see above

What seems to be missing is a loop over all records in current selection, which 
may look similar to following

set thePubs to selection
if (count of thePubs)  0 then
  repeat with thePub in thePubs
tell aPub
   set theAuthor to value of field Author
   set value of field Doi to 10.1007/s10584-010-9923-5
   ...
   etc.
   ...
end tell
  end repeat
else
  beep
end if


Regards,
Andreas



   -k.





On Fri, Jan 24, 2014 at 8:11 PM, Ken Mankoff 
mank...@gmail.commailto:mank...@gmail.com wrote:
So I've made some progress on this applescript but seek some help from those on 
this list who have used applescript before and understand the BibDesk 
dictionary a bit. I now can drag PDFs into BibDesk where they get blank 
records. I can then hit CMD+SHFT+P and the full BibTeX record is displayed from 
pdfmeat.py. What I need help with is looping through each element of this 
BibTeX record and inserting it into the current blank one. My current code 
follows. Any help/hints will be much appreciated.

Thanks,

-k.

tell application BibDesk
  set theDoc to document 1
  tell theDoc
set theSel to selection
set thePub to item 1 of theSel
tell thePub
  -- current (probably empty?) BibTeX record
  set curBibTeXRecord to get BibTeX string of thePub
  -- get the BibTeX record using pdfmeat.py. Wrap it in a shell script 
because it needs a full path, write access to a folder, etc.
  set theFiles to get linked files
  set thePath to POSIX path of theFiles
  set shellCmd to /Users/mankoff/bin/pdfmeat.sh   '  thePath  '
  set pdfMeatOutput to do shell script shellCmd
  --display dialog pdfMeatOutput
  --display dialog curBibTeXRecord
end tell
  end tell
end tell




On Wed, Jan 8, 2014 at 8:49 PM, Ken Mankoff 
mank...@gmail.commailto:mank...@gmail.com wrote:
I just discovered pdfmeat at https://code.google.com/p/pdfmeat/ which as of one 
year ago includes a stand-alone CLI python script to generate BibTeX entries 
given a file. To get it working on OS X I had to change the path for the 
FireFox cookie file from ~/mozilla/firefox/ to ~/Library/Application 
Support/FireFox/Profiles/, did pip install X for each X it complained was 
missing, and it just worked. Nice.

It seems like this could be wrapped in a plugin so that drag-and-dropping PDF 
files onto BibDesk could auto-import with meta-data, just like Mendely and 
Papers and Zotero and all the other PDF/bibliography managers.

I searched for pdfmeat and bibdesk and found almost no hits. Is anyone 
aware of such a plugin, or anyone familiar with plugin writing un-aware of 
pdfmeat and now interested in creating this plugin? If not, I may have to 
figure out how BibDesk plugins work...

  -k.


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Re: [Bibdesk-users] pdfmeat

[Fischlin Andreas]

Sorry, I had a mistake in the AppleScript: Please replace tell aPub with 
tell thePub.

Regards,
Andreas


 
 What seems to be missing is a loop over all records in current selection, 
 which may look similar to following
 
 set thePubs to selection
 if (count of thePubs)  0 then
  repeat with thePub in thePubs
tell aPub
   set theAuthor to value of field Author
   set value of field Doi to 10.1007/s10584-010-9923-5
   ...
   etc.
   ...
end tell
  end repeat
 else
  beep
 end if
 
 
 Regards,
 Andreas
 
 
 
   -k.
 
 
 
 
 
 On Fri, Jan 24, 2014 at 8:11 PM, Ken Mankoff 
 mank...@gmail.commailto:mank...@gmail.com wrote:
 So I've made some progress on this applescript but seek some help from those 
 on this list who have used applescript before and understand the BibDesk 
 dictionary a bit. I now can drag PDFs into BibDesk where they get blank 
 records. I can then hit CMD+SHFT+P and the full BibTeX record is displayed 
 from pdfmeat.py. What I need help with is looping through each element of 
 this BibTeX record and inserting it into the current blank one. My current 
 code follows. Any help/hints will be much appreciated.
 
 Thanks,
 
-k.
 
 tell application BibDesk
  set theDoc to document 1
  tell theDoc
set theSel to selection
set thePub to item 1 of theSel
tell thePub
  -- current (probably empty?) BibTeX record
  set curBibTeXRecord to get BibTeX string of thePub
  -- get the BibTeX record using pdfmeat.py. Wrap it in a shell script 
 because it needs a full path, write access to a folder, etc.
  set theFiles to get linked files
  set thePath to POSIX path of theFiles
  set shellCmd to /Users/mankoff/bin/pdfmeat.sh   '  thePath  '
  set pdfMeatOutput to do shell script shellCmd
  --display dialog pdfMeatOutput
  --display dialog curBibTeXRecord
end tell
  end tell
 end tell
 
 
 
 
 On Wed, Jan 8, 2014 at 8:49 PM, Ken Mankoff 
 mank...@gmail.commailto:mank...@gmail.com wrote:
 I just discovered pdfmeat at https://code.google.com/p/pdfmeat/ which as of 
 one year ago includes a stand-alone CLI python script to generate BibTeX 
 entries given a file. To get it working on OS X I had to change the path for 
 the FireFox cookie file from ~/mozilla/firefox/ to ~/Library/Application 
 Support/FireFox/Profiles/, did pip install X for each X it complained was 
 missing, and it just worked. Nice.
 
 It seems like this could be wrapped in a plugin so that drag-and-dropping PDF 
 files onto BibDesk could auto-import with meta-data, just like Mendely and 
 Papers and Zotero and all the other PDF/bibliography managers.
 
 I searched for pdfmeat and bibdesk and found almost no hits. Is anyone 
 aware of such a plugin, or anyone familiar with plugin writing un-aware of 
 pdfmeat and now interested in creating this plugin? If not, I may have to 
 figure out how BibDesk plugins work...
 
  -k.
 
 
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Re: [Bibdesk-users] export template development

[Fischlin Andreas]

Look at my scripts at

http://www.sysecol.ethz.ch/people/afischli

Links: Software, BibDesk Applescripts

Regards,
Andreas


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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
www.sysecol.ethz.chhttp://www.sysecol.ethz.ch

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

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On 13/12/2013, at 05:59 , Christopher Eliot wrote:

Are there any BibDesk experts who might be willing to write (and possibly help 
me get working) a simple HTML export template? I would pay for time.

I imagine it would be a 10–30 minute writing project for someone who knows what 
they’re doing, but I’ve been floundering around on it for hours.

Thanks, and apologies if this is an inappropriate request for the list. Chris

Christopher Eliot
eliot...@umn.edumailto:eliot...@umn.edu




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Re: [Bibdesk-users] [ANN] BibDesk 1.6.2

[Fischlin Andreas]

Dear Christiaan and all the others who have contributed,

Many thanks. A nice X-mas gift.

I guess most have figured out the typo, the new version 1.6.2.

I wish also to warn here users that the Web of Science searches as performed by 
this BibDesk version, if they should work at all (your institution has a 
license to WOKSearchPremium web services), are likely to miss out on many 
publications. Thomson Reuters seems to deprecate the data base behind the 
interface BibDesk is currently supporting (version 2 of the SOAP interface as 
described here: 
http://search.isiknowledge.com/esti/cxf-wsclient-demo/docs/soap/).  So be not 
mislead, if you do not find some publication using current BibDesk version, 
this does not mean it is not available in the Web of Science data base at all, 
it means merely it is not available through BibDesk. Once BibDesk supports the 
new version 3 of the SOAP interface, things should be back to what they once 
were and searching with BibDesk should again yield equivalent results as when 
you are using a browser to search Web of Science.

Regards,
Andreas


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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
www.sysecol.ethz.chhttp://www.sysecol.ethz.ch

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

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On 10/12/2013, at 12:11 , Christiaan Hofman wrote:

Greetings all

The BibDesk development team is pleased to announce that a new version of 
BibDesk, version 1.6.0, is now available.

We thank the users who have contributed to BibDesk development by sharing their 
experiences with BibDesk, and testing nightly builds.

This release can be obtained by selecting check for updates in the BibDesk 
menu, visiting the Sourceforge downloads page at

https://sourceforge.net/projects/bibdesk/

or by visiting the BibDesk home page at

http://bibdesk.sourceforge.net/

or by following the link below, which will begin immediate download:

http://sourceforge.net/projects/bibdesk/files/BibDesk/BibDesk-1.6.0/BibDesk-1.6.0.dmg/download

For those interested follow the full release notes for this version.

Release notes for BibDesk version 1.6.2

New Features
  *  Allow username/passsword identification in ISI World of Science search 
groups
  *  Allow editing search bookmarks
  *  Support Quick Look in orphaned files finder and file matcher
  *  Allow phrase searching

Bugs Fixed
  *  Fix abstract import from RIS
  *  Spotlight search editors for publications without an author
  *  Fix search group URLs
  *  Fix scripting properties of markup notes
  *  Avoid creating many annote fields from RIS
  *  Fix scripting of field groups
  *  Avoid a spurious crasher
  *  Code-sign all components
  *  Avoid using discrete GPU
  *  Disable web icons for remote URLs on Mavericks for now

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Re: [Bibdesk-users] crash during adding new publication from File...

[Fischlin Andreas]

Dear Ryohei,

On 11/12/2013, at 05:41 , Ryohei SETO wrote:

Hi,

The crash happened again due to importing wrong bib file (attached).
Now I confirmed with the other machine.
As I reported, rebooting stops this behavior (sometime, not always).
But after importing bibfiles several times, it may occur again.

There should be no crash and on my machine BD never crashes with this bib file. 
What happens is of course an error, since the bib file is syntactically wrong 
and needs to be fixed. Once fixed the import/opening works fine. BTW, this has 
nothing to do with the presence of the field 'eid'.


The exported bibfile from Journal of Rheology includes this wrong line eid = 
,”.
I often download from this journal’s web site. Each time I have to remove the 
line by hand.

There is no other way unless you inform that journal's webmaster that they are 
unable to properly export a citation.


By the way, some journal uses “eid” instead of “pages”.
So far, this field name is not included in BibDesk.

It will never be included since AFAIK it does not belong to the BibTeX 
definition. This has BTW nothing to do with BibDesk and it makes no sense to 
try to fix mistakes from publishers who ignore well known standards such as 
BibTeX with another mistake in a software such as BibDesk.

Moreover, as I pointed out above, the import problem has nothing to do with the 
presence of this extra field 'eid'. Once syntactically correct, even the extra 
field 'eid' is imported and forms part of the record.

Regards,
Andreas


I think it is better to add.

Best,
Ryohei Seto



On Dec 9, 2013, at 7:44 PM, Christiaan Hofman 
cmhof...@gmail.commailto:cmhof...@gmail.com wrote:


On Dec 10, 2013, at 1:36, Adam R. Maxwell wrote:


On Dec 09, 2013, at 04:09 PM, Christiaan Hofman 
cmhof...@gmail.commailto:cmhof...@gmail.com wrote:


On Dec 10, 2013, at 0:54, Adam R. Maxwell wrote:

On Dec 09, 2013, at 02:15 PM, Christiaan Hofman 
cmhof...@gmail.commailto:cmhof...@gmail.com wrote:


On Dec 9, 2013, at 23:01, Ryohei SETO wrote:

https://dl.dropboxusercontent.com/u/9745885/BibDesk_2013-12-09-165629_seto-macbookpro.crash

Ryohei

Weird one. There does not seem to be anything specific to the problem in that 
crash report. Some generic crash when closing a file read.

I'd never seen EXC_GUARD before, and the fade2dead address looked interesting. 
With a bit of searching, it turns out this is a close on a guarded file 
descriptor (Greg Parker is an Apple engineer):

https://twitter.com/gparker/status/395678654375546881

There should be an +[NSPipe pipe] somewhere to create that autoreleased 
NSConcretePipe, but I don't recall anything in the cmd-shift-L code path that 
would do it.

Adam

Sounds more like something in the system being messed up. We only open the file 
indirectly by reading a string from it. And the parsing is the same as when you 
drop the file or paste the bibtex, and that all gives just the warning. Also 
given the tweets, it really seems more like a system bug. Otherwise something 
completely unrelated that just pops up here for some vague reason. It really 
does not look like anything related to our code related to anything of this.

I wouldn't rule out an OS bug, but does this run through the NSPipe code that I 
had in NSData category? Looks like you moved it to the parser, but it's an 
obvious NSPipe call when you try and parse bibtex data that's not a file.

adam


You're right, I forgot about that one. I don't see why that would crash now 
when it has worked all the time.

Christiaan

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Re: [Bibdesk-users] crash during adding new publication from File...

[Fischlin Andreas]

Dear Ryohei,

On 11/12/2013, at 05:41 , Ryohei SETO wrote:

Hi,

The crash happened again due to importing wrong bib file (attached).
Now I confirmed with the other machine.
As I reported, rebooting stops this behavior (sometime, not always).
But after importing bibfiles several times, it may occur again.

There should be no crash and on my machine BD never crashes with this bib file. 
What happens is of course an error, since the bib file is syntactically wrong 
and needs to be fixed. Once fixed the import/opening works fine. BTW, this has 
nothing to do with the presence of the field 'eid'.


The exported bibfile from Journal of Rheology includes this wrong line eid = 
,”.
I often download from this journal’s web site. Each time I have to remove the 
line by hand.

There is no other way unless you inform that journal's webmaster that they are 
unable to properly export a citation.


By the way, some journal uses “eid” instead of “pages”.
So far, this field name is not included in BibDesk.

It will never be included since AFAIK it does not belong to the BibTeX 
definition. This has BTW nothing to do with BibDesk and it makes no sense to 
try to fix mistakes from publishers who ignore well known standards such as 
BibTeX with another mistake in a software such as BibDesk.

Moreover, as I pointed out above, the import problem has nothing to do with the 
presence of this extra field 'eid'. Once syntactically correct, even the extra 
field 'eid' is imported and forms part of the record.

Regards,
Andreas


I think it is better to add.

Best,
Ryohei Seto



On Dec 9, 2013, at 7:44 PM, Christiaan Hofman 
cmhof...@gmail.commailto:cmhof...@gmail.com wrote:


On Dec 10, 2013, at 1:36, Adam R. Maxwell wrote:


On Dec 09, 2013, at 04:09 PM, Christiaan Hofman 
cmhof...@gmail.commailto:cmhof...@gmail.com wrote:


On Dec 10, 2013, at 0:54, Adam R. Maxwell wrote:

On Dec 09, 2013, at 02:15 PM, Christiaan Hofman 
cmhof...@gmail.commailto:cmhof...@gmail.com wrote:


On Dec 9, 2013, at 23:01, Ryohei SETO wrote:

https://dl.dropboxusercontent.com/u/9745885/BibDesk_2013-12-09-165629_seto-macbookpro.crash

Ryohei

Weird one. There does not seem to be anything specific to the problem in that 
crash report. Some generic crash when closing a file read.

I'd never seen EXC_GUARD before, and the fade2dead address looked interesting. 
With a bit of searching, it turns out this is a close on a guarded file 
descriptor (Greg Parker is an Apple engineer):

https://twitter.com/gparker/status/395678654375546881

There should be an +[NSPipe pipe] somewhere to create that autoreleased 
NSConcretePipe, but I don't recall anything in the cmd-shift-L code path that 
would do it.

Adam

Sounds more like something in the system being messed up. We only open the file 
indirectly by reading a string from it. And the parsing is the same as when you 
drop the file or paste the bibtex, and that all gives just the warning. Also 
given the tweets, it really seems more like a system bug. Otherwise something 
completely unrelated that just pops up here for some vague reason. It really 
does not look like anything related to our code related to anything of this.

I wouldn't rule out an OS bug, but does this run through the NSPipe code that I 
had in NSData category? Looks like you moved it to the parser, but it's an 
obvious NSPipe call when you try and parse bibtex data that's not a file.

adam


You're right, I forgot about that one. I don't see why that would crash now 
when it has worked all the time.

Christiaan

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Re: [Bibdesk-users] v1.6.1 crashes on 10.9

[Fischlin Andreas]

Please do not stop to support Snow Leopard   Lion I could 
care less.

Regards,
Andreas


ETH Zurich
Prof. Dr. Andreas Fischlin
Systems Ecology - Institute of Integrative Biology
CHN E 21.1
Universitaetstrasse 16
8092 Zurich
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On 14/Nov/2013, at 21:54 , Dr. Adam M. Goldstein PhD MSLIS wrote:

Apropos these comments, I wanted do a release last week, but my laptop had a 
logic board failure.

Thoughts in whether I should proceed? I'm picking up the computer from the 
repair shop today.

I had been using BD on mavericks with no problems at all for several weeks.

Related issue: are we still going to support Lion (10.7)? My 2006 laptop can't 
be updated past Lion, so we'd lose people if we dropped it, I think.

What goes into that kind of decision? Support is dropped when the current 
release is deemed too buggy to run on the OS in question? Then, what, the 
previous release is listed as the last to support the OS?

Adam G

Sent from my iPhone

On Nov 14, 2013, at 12:58, Simon Spiegel 
si...@simifilm.chmailto:si...@simifilm.ch wrote:


On 14.11.2013, at 18:48, jhgowen jhgo...@mac.commailto:jhgo...@mac.com 
wrote:

V. 1.6.1 was very stable on Mountain Lion, but on upgrading to Mavericks, I 
found that BibDesk was crashing all the time. Almost any action would cause it 
to crash, including dragging a citation from one bibliography window to 
another, attaching a file, pasting in text to the abstract pane

I recently upgraded to the nightly build 20131029, and this has fixed the 
crashing problem on Mavericks.
I don't know if it is something to do with the version, or if there was 
something messed up by the OS upgrade and a simple reinstall would have worked, 
but just wanted to let suggest that you put out a new stable version, which 
should then run well on 10.9.

If that's of any help: I don't see any problems with BibDesk on Mavericks.

Simon
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Re: [Bibdesk-users] Release

[Fischlin Andreas]

I see no obvious problems in the latest nightlies. Thanks for a new release.

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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
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On 04/09/2013, at 10:51 , Christiaan Hofman wrote:

BibDesk is now ready for release. I have enabled the localizations in the last 
release, so those can be tested. Also the release notes have been updated. So 
please test out the latest nightlies at 
https://www.dropbox.com/sh/pkt955ttu8vbsdi/E21z4ghXRy/BibDesk.

Christiaan


On Aug 12, 2013, at 16:56, Dr. Adam M. Goldstein PhD MSLIS wrote:

Hi all

Not much traffic on the users or developer's list---anything that needs to be 
nailed down before a release?

Adam



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Re: [Bibdesk-users] Improving compatibility with Dropbox when annotating PDFs

[Fischlin Andreas]

Dear Graham,

I have not responded when you contacted BibDesk developers on this. But I wish 
to do this now by making two points:

First, I understand that this problem is annoying, however, I doubt it can be 
solved, or better, I do not think this should be solved by BibDesk. Rather this 
appears to be a problem Dropbox and/or Apple has first of all to solve. Given 
your wrapper solution works, I would consider this to be nearly ideal and would 
recommend to refrain from trying to fix in BibDesk a problem present in other 
software such as Dropbox or Apple's system software. This argument being made 
more on principal grounds of software engineering. Once Dropbox fixes this, one 
may have to change the code of BibDesk back to what it is now.

Secondly, I'd like to remind us all that file linking/tracing as done by 
BibDesk is rather sophisticated and handles everything very well, including 
symbolic links and ordinary Finder aliases. It would be a pity, if any solution 
good for Dropbox would impact on any of these complex functions now very 
reliably handled by BibDesk. And I fear that may be the case. I am of course 
not sure whether that might be really the case or not, but fear there is a real 
risk. I do sync my bibliography files and pdf's among various Macs and iOS 
devices very well and encounter no problems nor glitches. I make sure on Macs 
that the file hierarchy is the same on all Macs (if necessary complemented with 
symbolic links) and use cloud services when syncing with iOS devices (my iPad, 
iPhone). I have never encountered any difficulties in my workflow and I am 
happy with the reliability by which BibDesk is handling all this. Of course, I 
need my own scripts to accomplish this all conveniently. BTW, anyone inte
 rested can find all my scripts also on my home page 
(http://www.sysecol.ethz.ch/people/afischli  link Software). All works very 
well right now, yet is sophisticated with syncing back pdf's via symbolic links 
or Finder aliases via modification date etc. I would hate if any of this would 
get disrupted.

Sorry, for these words of caution, but I wish us all to consider all aspects 
before asking perhaps rashly for changes of BibDesk.

In any case many, many thanks for your wrapper solution.

Sincerely yours,
Andreas


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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
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On 03/09/2013, at 08:49 , Graham Dennis wrote:

Hi,

There's an interaction problem between BibDesk and Dropbox which causes BibDesk 
to lose its link to files stored in Dropbox if those files are annotated on 
computer #2 while BibDesk is running on computer #1.  If you later save the 
library in BibDesk on computer #1, the link will be changed to a temporary file 
which will disappear in a few days.

I've reported this problem to the BibDesk developers, but they expressed 
concern that my approach to solving this problem might cause problems for other 
users if they have moved their PDFs.  Full details of the problem and my 
proposed solution are available here: 
https://github.com/GrahamDennis/BibDeskWrapper

If you're experiencing this problem and would like to help test my solution, 
please download BibDeskWrapper.app (http://bit.ly/18ewabY). BibDeskWrapper is a 
simple wrapper around BibDesk which modifies its behaviour to fix the problem.  
BibDeskWrapper and BibDesk can be updated independently, so using 
BibDeskWrapper doesn't prevent you from getting the latest updates to BibDesk.  
For information about getting AppleScripts to work with BibDeskWrapper see here 
(https://github.com/GrahamDennis/BibDeskWrapper#how-do-i-make-my-bibdesk-applescripts-work-with-bibdeskwrapper).


Regards,

Graham Dennis
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Re: [Bibdesk-users] Release

[Fischlin Andreas]

Dear all,

I can confirm that the new search group editing needed when using an 
UserID/password credential when searching ISI WOK (WOKSearchPremium and 
WOKSearchLite services) works fine. I have been using this feature now for 
weeks and it seems to function very reliably and to my fullest satisfaction.

However, I encounter frequent crashes during importing of publications, but 
also in other situations. Not only when importing via ISI searches, but also 
when importing via drag drop from a 2nd currently open bib file do latest 
nightlly builds regularly crash. Details on this are given in my addition to 
bug #1430https://sourceforge.net/p/bibdesk/bugs/1430/ .

Perhaps the there provided crash reports help to better track down the cause of 
the crash. I believe it would be good to look once more into this issue before 
completing the next release. By this I do not expect necessarily a resolving of 
this bug, given that it may be quite difficult to chase down because of its 
intermittent nature. Nevertheless, my overall assessment is that this is a bug 
bad enough (I often lose some work) and one that occurs way too often, so that 
it deserves some attention before the next official release.

Cheers,
Andreas


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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
www.sysecol.ethz.chhttp://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 12/08/2013, at 18:59 , Christiaan Hofman wrote:


On Aug 12, 2013, at 16:56, Dr. Adam M. Goldstein PhD MSLIS wrote:

Hi all

Not much traffic on the users or developer's list---anything that needs to be 
nailed down before a release?

Adam


Not completely sure how the ISI search group stands, as I cannot test it myself.

And the localizations need to be updated.

Christiaan


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Re: [Bibdesk-users] Question regarding cite key syntax

[Fischlin Andreas]

Of course there is. I also determine cite keys in a custom manner that is not 
directly supported by BibDesk and that works very well. Find my AppleScripts at 
my home page (Link Software):

http://www.sysecol.ethz.ch/people/afischli

Regards,
Andreas


On 10/07/2013, at 01:43 , Maxwell, Adam R wrote:


On Jul 9, 2013, at 09:58, Christiaan Hofman wrote:

Sorry, that's not possible. You can set a fixed number of characters for each 
individual name, and a fixed (maximum) number of authors to consider. Not the 
total number for all names together.

Isn't there a citekey script hook where you could do this?

-- adam


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Re: [Bibdesk-users] entry type for project reports

[Fischlin Andreas]

On 27/06/2013, at 23:02 , Hermann Maier wrote:

 Dear all,
 
 Two newbie questions:
 
 a) what entry type should I use for a project report like this:
 http://emobil-umwelt.de/images/pdf/ifeu_(2011)_-_UMBReLA_grundlagenbericht.pdf
 
 I have in my field of research actually mostly reports from publicly
 funded projects
 which have authors but no publishing house and are not peer-reviewed
 like a proper paper or edited like a proper book - any suggestions which
 entry type I should use?

This has nothing to do with BibDesk. Use techreport, unfortunately BibTeX has 
long ago made this mistake to use tech instead of simply report. Consider 
techreport to be a synonym for report.  More on sites such as 
http://en.wikipedia.org/wiki/BibTeX#Entry_types

 
 b) I have encountered an error in my first bib-entry, at least the sytem
 tells
 me that. How disencouraging... :-(
 
 You can find a screenshot of the error here (not sure if I can post
 binaries here)
 
 http://tinyurl.com/lt9svhp
 
 The original bib-entry from springerlink can be found here
 http://link.springer.com/article/10.1007/s12398-013-0105-9#
 (please see right bottom under Export Citation)
 
 I am not quite sure what the error in line 2 might be.
 
 Funny thing is, when I get the article from google scholar, bibdesk
 imports it fine,
 but then again, the entry is minimal with half the information missing.

This is because people are too often sloppy and do not correctly enter meta 
data as needed.

 
 I am not sure how to correct the entry, it tells me to change = with
 ,, but I don´t see the point, the working citation from google has the
 same equal sign in the year entry. I have tried it with a temp cite key
 but that did not help.
 
 Thanks for any suggestions on these two issues.
 
 Best
 Hermann
 
 
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Re: [Bibdesk-users] linking files to dropbox

[Fischlin Andreas]

 it.

  *   maybe some automation to retrieve the cloud link for any file stored in 
the local Dropbox folder would be useful IMHO

Automation of setting this information will not and should not be done in any 
default way. This could be done using AppleScript, possibly through script 
hooks.

I noticed that I don't know how to create a field common to the entire database

Now, I am begging all of you to consider my perspective instead of constantly 
underscoring my computer science inconsistency.

Its not about computer science. It's about your assumptions on how they work. 
That makes it really confusing, because it makes it unclear what you really 
want. The answer to what field to use depends on why you want this field and 
what you want to do with it. And actually you probably don't even want a field, 
but something else. But that is not what you asked.

If my description is not enough, I will give up.
I appreciate your cooperation
Daniele Pontillo, MD


So here is what I now think you want (rather than what you think you want):

1. You have items with linked files (not fields!) located in your local Dropbox.
2. You want to generate HTML from templates, possibly the default HTML template.
3. The generated template should contain *remote URLs* to your remote Dropbox, 
associated to those linked files.

Is that correct?

Now to get this you need at least two things:
1. Those remote URLs should be added to the item data.
2. The template should actually use those remote URLs (wherever they end up) in 
the generated text.

The point is that as it is now, the default HTML template will not do 2 for 
you, so you need to edit the template (or use a custom  template). Moreover, 
there are different ways you can do 1, which may or may not involve a field, 
and it depends on what you do in 2.

If all this is correct, I think the best solution is to put the remote URLs in 
the linked URLs (so not in a field, but a URL that turns up in the side panes.) 
Those linked URLs should also turn up in the template, but I just noticed that 
there is an error in the default HTML template. To fix that, you should edit 
the htmlItemExportTemplate.html file (see the Template prefs) using a plain 
text editor, and add $ before the word remoteURLs (twice).

An alternative is to use a field. But then you have to edit the template a bit 
more (could be in the same item template file). For instance, if you put the 
corresponding remote URL in the field Url, then you could add the following 
line:

span class=Filea 
href=$urls.Url.absoluteString/$urls.Url.absoluteString//a/spanbr /

or you could put this line instead of the 3 lines from $localFiles to 
/$localFiles.

Then the next question could be how to automate the synchronization of the 
linked local files with the corresponding remote URLs in your data. For this, 
you should use AppleScript. What this AppleScript looks like depends on whether 
you want to synchronize manually (say, generate the remote URLs in all selected 
items). Or whether you want to have this done automatically whenever you add a 
new linked file, in which case you should use a script hook. Moreover what the 
AppleScript looks like depends on the choices you make above (basically, 
whether you want to put the remote URL in the linked URLs, or in the Url field.)

Christiaan



Il giorno 04/apr/2013, alle ore 13:05, Fischlin Andreas 
andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch ha scritto:

It seems you do not like the html file. Then edit the template you use 
accordingly. This has, AFAI can understand you, nothing to do with a field of 
your publication record in BibDesk nor with Dropbox.

Regards,
Andreas


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

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On 04/04/2013, at 12:51 , Daniele Pontillo wrote:


Il giorno 04/apr/2013, alle ore 12:45, Christiaan Hofman 
cmhof...@gmail.commailto:cmhof...@gmail.commailto:cmhof...@gmail.com ha 
scritto:


On Apr 4, 2013, at 12:26, Daniele Pontillo wrote:

I am so sorry I cannot make myself understood. I'll try harder, step by step.


1.  hahah, I have a publication
2.  I have a pdf file I want to link to the publication
3.  the pdf is in my dropbox folder

Everything clear till now, OK?

When I export my database to a HTML file take a look at what I get
link.jpg

Well, I guess you have a linked file to your local dropbox folder.


1.  I don't need to display the link to my local folder (/Users/lalla/)
2.  I want to find in my publication the APPROPRIATE FIELD to paste

Re: [Bibdesk-users] Publication:Send via Email

[Fischlin Andreas]

Is there a preference in which I can set the template to be used by this 
command? I find nothing in Help nor on the wiki. That's basically a question to 
Christiaan, since you mention a template @ 
http://www.mail-archive.com/bibdesk-users@lists.sourceforge.net/msg05105.html 
but I do not know which you were thinking of and how I could cause this command 
to use a specific template instead of the default (in my case I get a 'BibTeX 
source record', not my first choice).

Regards,
Andreas


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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
www.sysecol.ethz.chhttp://www.sysecol.ethz.ch

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

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On 04/04/2013, at 18:55 , Christiaan Hofman wrote:


On Apr 4, 2013, at 17:22, Christiaan Hofman wrote:


On Apr 4, 2013, at 17:17, Gray, Wayne wrote:

All,

Since discovering this feature -- being able to go directly from BibTec to my 
mail program with a completely formatted citation, abstract, and attached PDFs, 
I have been using it a lot.

However, lately it seems as if it is not always working. Must be something in 
the files I am trying to send.  But recently I have observed the following 
behavior with no clear pattern:

A. It sends the pdfs and other files that are attached to my entry, but not the 
BibDesk citation.
B. It sends nothing - neither file nor citation
C. It works as intended sending both the formatted citation and any attached 
files.

Any ideas as to what is causing this erratic behavior?

I am using BibDesk: v1.6.0 (2779) and Mac OS 10.7.5.

Thanks for any ideas you might have on solving this mystery.

Wayne Gray


Apparently somewhere in the process it runs into an exception or something like 
that. I cannot say where from here. Try looking into Console.app to see if any 
errors are reported.

Christiaan


Another thing is the generation of the citation. What format are you using for 
email? And for the items that give you problems, is copy/paste for that format 
(Copy As) also failing?

Christiaan


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Re: [Bibdesk-users] linking files to dropbox

[Fischlin Andreas]

It seems you do not like the html file. Then edit the template you use 
accordingly. This has, AFAI can understand you, nothing to do with a field of 
your publication record in BibDesk nor with Dropbox.

Regards,
Andreas


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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
www.sysecol.ethz.chhttp://www.sysecol.ethz.ch

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

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On 04/04/2013, at 12:51 , Daniele Pontillo wrote:


Il giorno 04/apr/2013, alle ore 12:45, Christiaan Hofman 
cmhof...@gmail.commailto:cmhof...@gmail.com ha scritto:


On Apr 4, 2013, at 12:26, Daniele Pontillo wrote:

I am so sorry I cannot make myself understood. I'll try harder, step by step.


  1.  hahah, I have a publication
  2.  I have a pdf file I want to link to the publication
  3.  the pdf is in my dropbox folder

Everything clear till now, OK?

When I export my database to a HTML file take a look at what I get
link.jpg

Well, I guess you have a linked file to your local dropbox folder.


  1.  I don't need to display the link to my local folder (/Users/lalla/)
  2.  I want to find in my publication the APPROPRIATE FIELD to paste the 
Dropbox server-generated link instead of getting the local file link


The appropriate field is the field where you put the URL you're talking about. 
If you did not put a URL in a field, then there is no appropriate field.

Christiaan

Dear Christiaan, I guess that this  Italian cardiologist is really too dumb as 
for computer science. But listen carefully:
please give me the name of the field where I can place the link and that would 
be displayed in an HTML output


Il giorno 04/apr/2013, alle ore 12:15, Christiaan Hofman 
cmhof...@gmail.commailto:cmhof...@gmail.com ha scritto:


On Apr 4, 2013, at 11:47, Daniele Pontillo wrote:

Hello again everybody.
Since there are some issues in identifuing the field in which local pdfs are 
stored (in order to find and replace the url) I will ask another question
I linked my publication to the file on  the dropbox server 
(https://www.dropbox.com/s/21v1rxpvbgb65x0/2008.pdf) placing it in the 
remote-url field.
What syntax should I use and which file should I edit to get the remote-url 
link instead of the local file link displayed on the exported HTML file ?
Thanks
Dan

You're confusing again. Are you talking about linked files, linked remote URLs, 
or a field called Remote-Url?

Christiaan


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Re: [Bibdesk-users] 1.5.8 and 1.6.0: Tex preview bug difference

[Fischlin Andreas]

You can have as many layouts you want, you simply have to write the template 
and install it using BibDesk's preferences Templates.

Regards,
Andreas


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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
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On 02/03/2013, at 15:13 , David Nicholls wrote:

On 03/03/2013, at 12:33 AM, David Nicholls 
da...@mso.anu.edu.aumailto:da...@mso.anu.edu.au wrote:


On 02/03/2013, at 11:43 PM, Christiaan Hofman 
cmhof...@gmail.commailto:cmhof...@gmail.com wrote:

You can just as well copy the text from the bottom preview. The next release 
won't provide anything more than that, apart from allowing you to do it in the 
separate window. The old Text preview will be gone, as it (now) crashes and 
anyway has always been problematic. Oh, and you are aware that you can copy the 
fully prepared \bibitem?

Christiaan

No, I wasn't aware, but its layout needs to be (typically) in Astrophysical 
Journal layout: e.g.

\bibitem[Nicholls et al.(2011)]{Nicholls11}Nicholls, D.~C. et al. 2011, \aj, 
142, 83

How do I do that?  I would be very useful.


OK, it looks like it's effected by Edit  Copy As  LaTeX, but the result 
requires further editing.  Is there any source file I can edit to generate the 
layout I want?

DN


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Re: [Bibdesk-users] Citing a web page

[Fischlin Andreas]

No, URLs are treated specially, similar to linked files. Since you can have any 
number of URLs linked to a pub, i.e. a 1:n relationship, you should not misuse 
a single field having only a 1:1 relationship to a pub or you risk encountering 
difficulties. Simply drag drop URLs to the right side panel to add an URL or 
select one there and press backspace to delete it, and you should be fine.

If you want to see what BibDesk is actually doing behind the scenes use a text 
editor to have a look at the bib file.

To import URLs via a text file in BibTeX format, say from another application, 
you can use the field URL (only 1:1) and/or Bdsk-Url-1, Bdsk-Url-2, etc. (1:n) 
and then have the URL field converted as any other linked URL (if preference 
Fields is set accordingly, this happens automatically).

Other than above it is recommended to use AppleScript when you wish to 
add/link, inspect or remove/unlink URLs. Find such scripts on my website (link 
Software).

Regards,
Andreas Fischlin


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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
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On 25/02/2013, at 02:49 , Kevin Fjelsted wrote:

WHen I use the URL cite type  in BibDesk there is no field for the actualURL? 
Am I supposed to use the URLDate field for the URL?

-Kevin


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Re: [Bibdesk-users] Web of Science not working?

[Fischlin Andreas]

Dear Johan,

The answer to this is twofold:

1) Thomson Reuters have changed their services as of Aug. 31st 2012, AFAIK 
worldwide. Often without informing their clients. The change of service means a 
new version of the software, but also a split in the kind of services. One of 
the services is the premium WokSearch, comparable to what we all could enjoy 
before Aug 2012. The other is WokSearchLite, a considerably lower service 
level, to which many institutional subscriptions have now fallen subject to, it 
seems.

2) BibDesk was quickly updated to the new version, but only for the premium 
service. Colin A. Smith who did that has promised to do it for WokSearchLite 
too, but didn't have the time yet (perhaps also since his institution has the 
premium service ;-) ).

From this follows two things IMHO:

a) One should step on the toes of Thomson Reuters and complain about their 
behavior. They have done all this in a most customer unfriendly manner that has 
put off many, many users AFAIK. Unilaterally making such deep cutting decisions 
without properly consulting clients, let alone warning and/or properly 
informing them, is IMHO a misuse of a nearly-monopolistic position.

b) You could nag one owns institutional library to upgrade to the premium 
WokSearch level. I know there are some costs involved, but unfortunately TR has 
created these facts without batting an eyelash nor shifting their ground the 
slightest bit since last summer.

Of course you might argue, why not adding the ability to BibDesk to also 
support WokSearchLite? However, the welcome that stopgap is for many users, me 
one of them, it is not really what most of us need, since the information you 
can access via WokSearchLite is very limited. E.g. no doi, no abstracts etc.

BTW, of course you can always search in the browser, download those files and 
import them into BibDesk. But the real strength of BibDesk was the ability to 
avoid all these cumbersome steps and to directly search, read abstracts, decide 
what to import, run AppleScripts via hooks when this really happens etc. An 
entire suit of facilities that changed my workflow considerably. All disrupted 
now, since Switzerland has not yet decided how to go about this contract with 
Thomson Reuters (yes, this has to be done at the national level, unfortunately, 
and TR is obviously using this opportunity to squeeze out more money from our 
universities, sic). All what we have at the moment is WokSearchLite only and 
for that BibDesk can't access the information.

And pubmed, still working in this wonderful way, is no replacement for a 
natural scientist like me.

Hope this helps to understand the situation better.

Regards,
Andreas


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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
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On 12/02/2013, at 09:35 , Johan Ekh wrote:

Hi all,
I'm new to Bibdesk. I'm trying to search for papers using Web of Science from 
within Bibdesk but it does not work.
The search continues for a second and then a small triangle appears. No papers 
are found. When I search with PubMed
everything works fine.

I've searched and found some discussions on this topic a few months ago, but I 
did not find a solution. Is there a solution now?

BR / Johan
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Re: [Bibdesk-users] extracting references relevant to a publication

[Fischlin Andreas]

I mark my records with a label (field Note), search for it and then use some of 
my extract AppleScripts, e.g. Extract Bibliography, available at 
http://www.sysecol.ethz.ch/people/afischli/software, to create the wanted 
bibliography in whichever form you wish.

Regards,
Andreas


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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
www.sysecol.ethz.chhttp://www.sysecol.ethz.ch

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On 18/12/2012, at 15:17 , M. Tamer Özsu wrote:

I knew how to do this, but I cannot remember now and looking through the help 
documentation, I could not locate it. There was a way to keep a master .bib 
file and extract the references relevant to one publication from it. How do we 
do that please?

Thanks.

==Tamer
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University of Waterloo
Cheriton School of Computer Science


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Re: [Bibdesk-users] All ISI WOS search seems disrupted - How about importing from Scopus?

[Fischlin Andreas]

Dear all,

I had a visit from two official representatives from Thomson Reuters concerning 
their changed web services. A representative from the main library 
(www.library.ethz.ch/en/http://www.library.ethz.ch/en/) at my unversity, i.e. 
ETH Zurich (www.ethz.chhttp://www.ethz.ch), was also present.

The discussion was fruitful and I got promises from Thomson Reuters they would 
make efforts to give us the ISI WOS access via BibDesk back, at least to some 
extent.

Since this topic should rather be discussed in the developer mailing list I 
will stop writing on this topic until it becomes again of interest for BibDesk 
end users. For the time being none of us I guess knows exactly by when and in 
what precise form we can regain the same services we enjoyed up to August 31st 
2012 as BibDesk users from the ISI WOS data base services.

Please note also, that the delay resulted also from the inability of Thomson 
Reuters to understand the issue and to answer properly all the questions the 
main library from my university (ETH Zurich, www.ethz.chhttp://www.ethz.ch) 
and I asked them. Before I get now really these awaited answers, it is very 
difficult to assess how much effort will be required on our BibDesk side to get 
all back to what it once was and whether that will actually be possible. 
Fortunately, given the promises Thomson Reuters representatives made to me in 
terms of giving us good support, technical information, including a special 
access while modifying BibDesk I hope we will find really soon now a solution. 
But please understand, that from my understanding any promises would currently 
be premature. Therefore please wait until things have further cleared up.

On the other hand, if anyone should be able to help clarifying the situation, 
for instance if some other response from TR was given to you, please inform us 
all of this. Thanks.

Regards,
Andreas


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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
www.sysecol.ethz.chhttp://www.sysecol.ethz.ch

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

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On 12/Sep/2012, at 17:18 , Adam R. Maxwell wrote:


On Sep 12, 2012, at 07:38 , Fischlin Andreas 
andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch wrote:

In the meantime I will try to help by getting at the technical official 
specifications of the new version.

This appears to be the latest version

http://search.isiknowledge.com/esti/cxf-wsclient-demo/docs/soap/index.html

and is mostly correct insofar as the current search API is concerned.  It is 
much better than their previous documentation.  If you discover that it is 
superseded, let me know.

I have one last question at the moment: Would you know wether the SOAP protocol 
version 2.0 has already been available previously, i.e. in parallel with 
version 1.0?

No idea.  You'd have to ask TR.  BibDesk's support dates to 2007, and the 
documentation I have for the old service is copyright 2006.

adam


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Re: [Bibdesk-users] bibdesk help

[Fischlin Andreas]

Please consult 
http://sourceforge.net/apps/mediawiki/bibdesk/index.php?title=Main_Page  and 
you may find there also my Tutorial useful.  Regards,
Andreas Fischlin

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

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On 09/10/2012, at 15:44 , mir shovkat wrote:

Hi, i have just started to write my academic papers!!. I will be grateful for 
some simple instructions on using bibdesk.

1. Is it possible to - cite while you write with bib desk- on mac word11.
2. How do i add references and bibliography from bibdesk? i can drag the ref 
into the doc, but then i don't get a bibliography at the end? I am aiming for a 
numbered reference list (APA I think)
3. I cant understand how to generate a txt file?
4. Where do you insert a script? if you have more then one script do you just 
cut and paste them into the script editor?

thats it for now!!!
thanks for your help.
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Re: [Bibdesk-users] bibdesk help

[Fischlin Andreas]

But I use BibDesk also when writing with Word. You can easily do that and 
install AppleScripts or other Services to accomplish this. Regards,
Andreas


On 09/10/2012, at 15:49 , Alex Hamann wrote:

Hi,
first of all, BibDesk is a frontend for BibTeX. BibTeX is meant to be used with 
LaTeX. You should probably read up on these two to get an idea what this means.
Have a look here: http://bibdesk.sourceforge.net/manual/
I think most of your questions are answered on these pages.

Alex



On 09.10.2012, at 15:44, mir shovkat wrote:

Hi, i have just started to write my academic papers!!. I will be grateful for 
some simple instructions on using bibdesk.

1. Is it possible to - cite while you write with bib desk- on mac word11.
2. How do i add references and bibliography from bibdesk? i can drag the ref 
into the doc, but then i don't get a bibliography at the end? I am aiming for a 
numbered reference list (APA I think)
3. I cant understand how to generate a txt file?
4. Where do you insert a script? if you have more then one script do you just 
cut and paste them into the script editor?

thats it for now!!!
thanks for your help.
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Re: [Bibdesk-users] add in field from clipboard

[Fischlin Andreas]

Yes, once you opened the publication for editing.  HeGru, Andreas

On 05/10/2012, at 10:36 , Christian Pleul wrote:

I would like to add the content of the clipboard to an existing field of the 
selected publication.

Possible?

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On 30.09.2012, at 17:23, Fischlin Andreas 
andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch wrote:

Yes, see help and menu command Publications - New publication from 
clipboard...

Regards,
Andreas Fischlin


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

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On 30/09/2012, at 00:18 , Christian Pleul wrote:

Hey,

is there a script to add the content of the clipboard into field x of the 
selected publication?


Thank you
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Re: [Bibdesk-users] add in field from clipboard

[Fischlin Andreas]

Yes, see help and menu command Publications - New publication from 
clipboard...

Regards,
Andreas Fischlin


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

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On 30/09/2012, at 00:18 , Christian Pleul wrote:

Hey,

is there a script to add the content of the clipboard into field x of the 
selected publication?


Thank you
--
Christian


-Because I'm the CEO, and I think it can be done.-

Steve Jobs, 2005

--
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3 out of 4 devs don\\\'t know how their code performs in production.
Find out how slow your code is with AppDynamics Lite.
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http://info.appdynamics.com/FreeJavaPerformanceDownload.html___
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Re: [Bibdesk-users] All ISI WOS search seems disrupted - How about importing from Scopus?

[Fischlin Andreas]

Dear Adam,

Thanks for all these most useful answers.

I concur with most you are saying and would only hope that a similarly 
convenient solution can be found using BibDesk as we had in the past.

In the meantime I will try to help by getting at the technical official 
specifications of the new version. We got conflicting answers from TR inasmuch 
as some of the answers we got state that TR merely changed their web services 
from version 1.0 to version 2.0 as of Aug.31st 2012 while another answer from 
TR claimed that the recent transition has made all web sites describing web 
services obsolete and that would explain the many faults I found there.  
Notably did I detect many dead links, exactly for those that want to describe 
differences between version 1.0 and 2.0 (e.g. 
http://search.isiknowledge.com/esti/docs/index.whats.new.html, which has indeed 
a suspiciously old date, i.e. 6 Aug 2009).

I have one last question at the moment: Would you know wether the SOAP protocol 
version 2.0 has already been available previously, i.e. in parallel with 
version 1.0? The date of aforementioned web side at least surprised me to be 
from 2009. If yes, could we have developed BibDesk earlier to support that as 
well or do the changes now necessary represent further changes, perhaps made by 
TR to the same version 2.0? I am asking because of the confusion that 
resulted on my side from the conflicting information given to me by TR (see 
above).

Regards,
Andreas


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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
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On 12/09/2012, at 06:39 , Adam R. Maxwell wrote:


On Sep 11, 2012, at 03:27 , Fischlin Andreas 
andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch wrote:

Dear Adam,

Many thanks. All the links to the source code you gave me helps me a lot to 
understand the situation much better. A pity this is so elaborate.

In the meantime our case with Thomson Reuters resulted in directing us to a web 
site, of which the answer e-mail claimed, it would supersede the sites we 
discussed previously.

I did a few quick tests with Python and suds today to see how hard this would 
be.

First, using the old WSDL gives an error saying that the service is no longer 
supported; this confirms what we suspected.  Not sure why BibDesk isn't showing 
that error, but we probably need to manually check for a fault.

Second, I'm not sanguine about getting this to work with Apple's framework, as 
TR has started using complex objects instead of simple (albeit messy) string 
parameters.  Explicit authentication is also required, and you have to pass an 
HTTP cookie back with each search/retrieve request.  I've not dealt with 
serializing and deserializing objects in Apple's Web Services framework.

The easiest option at this point is shipping suds inside BibDesk, then writing 
a command-line tool that would do the Web Service stuff and echo back XML.  
Unfortunately, it's LGPL v3 and I'm not sure that's compatible with BibDesk's 
BSD license.  It's also 500 kbytes of files, though that's not a deal breaker.  
Not sure that other devs think of it.  Using gSOAP is also an option, but not 
as easy.

However, would it not be easier not to work with Mountain Lion first, in 
particular to overcome the caveats of the new protocol? Say, using the reliable 
Snow Leopard (or Lion, but I wouldn't use the word reliable in this case ;-) ). 
Once understood it might work even under Mountain Lion?

OS version is irrelevant.  Apple's Web Service code likely won't work any 
differently under 10.8.  Code that is deprecated isn't necessarily going away 
right now (though the jerks at Apple broke DataTank by removing 
XgridFoundation.framework in 10.8, after deprecating it in 10.7).

One further thought: Such SOAP like protocols 
(http://en.wikipedia.org/wiki/SOAP_(protocol)) may be of interest also in other 
cases.

BibDesk's DBLP search group also uses it.

Would it not be more robust for BibDesk to develop a generic module that can 
handle such queries while the syntax specifics of any given protocol are 
described with a meta language, e.g. similar as attributed EBNF 
(http://en.wikipedia.org/wiki/EBNF) this can do for programing languages. Then 
BibDesk could be extended by any query by simply providing the protocol 
description in form of that language?

You want a meta language on top of SOAP?  Forget it.  I'm not an expert, but 
IMO there's too much variety in Web Service interfaces to do something like 
that.  Generic isn't always better, and neither are layers of abstraction 
against a time when something might possibly

Re: [Bibdesk-users] All ISI WOS search seems disrupted - How about importing from Scopus?

[Fischlin Andreas]

Dear Adam,

Many thanks. All the links to the source code you gave me helps me a lot to 
understand the situation much better. A pity this is so elaborate.

In the meantime our case with Thomson Reuters resulted in directing us to a web 
site, of which the answer e-mail claimed, it would supersede the sites we 
discussed previously. Here is that URL, since it may also be of interest:

http://wokinfo.com/products_tools/products/related/webservices/

Despite all being very helpful what you wrote, it is certainly not good news. 
And I share several of your concerns only too easily. I am willing to help. My 
first step along this lines is currently to continue insisting that the company 
really helps us. My institution is paying AFAIK huge amounts of subscription 
fees, yet nobody seems to have informed us of the consequences of the 
transition as end of August nor do they really help at the moment to overcome 
the difficulties. The information they have provided so far are all very 
conflicting and no real progress can be seen. Obviously as an end-user one has 
to insist they help, given the way they have handled us during this recent 
transition, or we will never get anywhere. The case only exists, because I 
complained insistingly, which finally did trigger this case and so far a few 
reactions.

However, would it not be easier not to work with Mountain Lion first, in 
particular to overcome the caveats of the new protocol? Say, using the reliable 
Snow Leopard (or Lion, but I wouldn't use the word reliable in this case ;-) ). 
Once understood it might work even under Mountain Lion?

One further thought: Such SOAP like protocols 
(http://en.wikipedia.org/wiki/SOAP_(protocol)) may be of interest also in other 
cases. Would it not be more robust for BibDesk to develop a generic module that 
can handle such queries while the syntax specifics of any given protocol are 
described with a meta language, e.g. similar as attributed EBNF 
(http://en.wikipedia.org/wiki/EBNF) this can do for programing languages. Then 
BibDesk could be extended by any query by simply providing the protocol 
description in form of that language? What is your experience with these 
interfaces? Are they clean? Formally well designed or are they all just 
tedious, cumbersome patchwork full of idiosyncrasies?

Regards,
Andreas





On 11/09/2012, at 01:17 , Adam R. Maxwell wrote:


On Sep 10, 2012, at 14:48 , Fischlin Andreas 
andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch wrote:

Dear Adam,

Many thanks for this most valuable information. Indeed, in the meantime I got a 
confirmation from company Thomson Reuters that they have switched from version 
1.0 to 2.0 of their web services, including the SOAP access as of 31st August 
2012.

Well, that's a pretty clear indication of what has happened.

Unfortunately I need very urgently ISI WOS in BibDesk back.

Any idea what could be done?

New WS stub code [1] has to be generated with WSMakeStubs, it has to be checked 
for bugs, and then glue code has to be written to integrate the new service 
into BibDesk [2].  This last is the only significant task, and based on my 
cursory glance last week, it'll be a fairly extensive rewrite.  
BDSKISIWebServices.[hm] will be replace entirely, and BDSKISIGroupServer.m will 
have to be rewritten to use the new methods and error checking.

[1] 
http://bibdesk.svn.sourceforge.net/viewvc/bibdesk/trunk/bibdesk/BDSKISIWebServices.m?revision=18776view=markup

[2] 
http://bibdesk.svn.sourceforge.net/viewvc/bibdesk/trunk/bibdesk/BDSKISIGroupServer.m?revision=18776view=markup

I'd guess 4-8 hours work, assuming the new API is straightforward and not too 
different from the old one, but I have very low confidence in those 
assumptions, and I have no time to look at this myself before October.

Notably I have for sure following questions for the time being:

1) Where are search details as contained in a .bdsksearch file actually stored 
in BibDesk once such a search has been installed?
I have consulted the help pages, and examples of .bdsksearch files are also not 
that difficult to construct from scratch. But this all did not answer me this 
question. Have I overlooked something or is it really missing.

Those files are largely irrelevant for WoS searches; they just store a database 
name and human-readable counterpart.  Local additions should end up in 
~/Library/Application Support/BibDesk/SearchGroupServers.

2) What URL is Searches - Web of Science SCI using?
In the current case I opened with Thomson Reuters, they are asking me this 
question, but I do not know what to answer.

The default endpoint is

http://wok-ws.isiknowledge.com/esti/soap/SearchRetrieve

See link [1] for details.

3) Can I edit or at least see Web of Science SCI search specs at the XML level?
Is there a way to edit a search once its .bdsksearch file has been installed? I 
looked for plist files, but neither inside the application BibDesk nor in 
~/Library/Application Support

Re: [Bibdesk-users] All ISI WOS search seems disrupted - How about importing from Scopus?

[Fischlin Andreas]

Dear Adam,

Many thanks for this most valuable information. Indeed, in the meantime I got a 
confirmation from company Thomson Reuters that they have switched from version 
1.0 to 2.0 of their web services, including the SOAP access as of 31st August 
2012.

Unfortunately I need very urgently ISI WOS in BibDesk back.

Any idea what could be done?

Notably I have for sure following questions for the time being:

1) Where are search details as contained in a .bdsksearch file actually stored 
in BibDesk once such a search has been installed?
 I have consulted the help pages, and examples of .bdsksearch files are also 
not that difficult to construct from scratch. But this all did not answer me 
this question. Have I overlooked something or is it really missing.

2) What URL is Searches - Web of Science SCI using?
In the current case I opened with Thomson Reuters, they are asking me this 
question, but I do not know what to answer.

3) Can I edit or at least see Web of Science SCI search specs at the XML level?
Is there a way to edit a search once its .bdsksearch file has been installed? I 
looked for plist files, but neither inside the application BibDesk nor in 
~/Library/Application Support could I find the wanted information.

4) Can I look at a SOAP protocol during an attempt to access the ISI WOS 
service?
In the current case I opened with Thomson Reuters, they are asking me for the 
exact error message that was returned, but I can not answer that question 
unless I could look at the protocol of a query using SOAP access.

Maybe you Adam or someone else can help me a bit by at least answering some or 
all of these questions.

Thanks!

Cheers,
Andreas



On 07/09/2012, at 18:33 , Maxwell, Adam R wrote:

On Sep 7, 2012, at 08:40, Fischlin Andreas wrote:
In the last few days I have never again been able to successfully search ISI 
WOS. I have checked everything on our side and included personnel from our main 
library at ETH Zurich. Unfortunately all to no avail.

Question 1: Has anyone encountered similar difficulties?

Yes, it appears to be broken.  You can download the WSDL, so the server is 
still alive.

http://wok-ws.isiknowledge.com/esti/soap/SearchRetrieve?wsdl

There's apparently a newer version of their WS interface, but I don't have time 
to investigate it right now:

http://search.isiknowledge.com/esti/cxf-wsclient-demo/docs/soap/index.html

It uses separate authentication and searching, from what I can tell at a quick 
glance, even for IP-based auth.  Maybe they've changed auth for the old 
service, too.

Question 2: How about importing from Scopus?   
http://www.library.ethz.ch/en/Resources/Databases/Scopus

I used Scopus several years ago, and adapted BibDesk's RIS parser to deal with 
their bastardized RIS.  That should still work, but I no longer have access to 
Scopus.

If you're asking about a search group for it in BibDesk, that would require a 
suitable API from Scopus, and someone with access to write the code and test 
it.  A web group might be more appropriate, but the same access caveat applies.

Adam


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[Bibdesk-users] All ISI WOS search seems disrupted - How about importing from Scopus?

[Fischlin Andreas]

Hi all,

In the last few days I have never again been able to successfully search ISI 
WOS. I have checked everything on our side and included personnel from our main 
library at ETH Zurich. Unfortunately all to no avail.

Question 1: Has anyone encountered similar difficulties?

Note, the ISI WOS server per se is up and running, which can be checked by 
using the web browser access. But from the perspective of BibDesk it seems to 
be dead. AFAIK it is the SOAP access used by BibDesk that seems not to be 
working. BTW, I have also tried with several official versions of BibDesk 
(skipping latest nightlies) and can assure you that all tested BibDesk versions 
show the same problem: They no longer work now, BibDesk versions from which I 
know with 100% certainty that they functioned fine with respect to ISI WOS 
queries in the past.

Given my workflow I am currently under great international pressure to have 
this service up and running again, but fear that may get complicated. Therefore 
my 2nd question:

Question 2: How about importing from Scopus?   
http://www.library.ethz.ch/en/Resources/Databases/Scopus

Has anyone accomplished this with the same convenience as with ISI WOS? I 
learned that Scopus should be becoming more and more competitive with ISI WOS 
and it might in general be worse trying to support searching that service as 
well (http://www.scopus.com/home.url).

Thanks for sharing any experiences, voices, opinions on these two issues.

Regards,
Andreas Fischlin


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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
www.sysecol.ethz.chhttp://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!









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Re: [Bibdesk-users] nightly builds down

[Fischlin Andreas]

Stick pleeeaaase with 3.2.6 and support for 10.6 is still there. Moreover, if 
you do not make use of fancy stuff only available from ML, this should be no 
problem, isn't it?

Regards,
Andreas


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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
www.sysecol.ethz.chhttp://www.sysecol.ethz.ch

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

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On 22/08/2012, at 13:15 , Dr. Adam M. Goldstein PhD MSLIS wrote:


On Aug 21, 2012, at 9:45 AM, Adam R. Maxwell 
amaxw...@mac.commailto:amaxw...@mac.com wrote:

Nightly builds are down until I can get the script switched to use my dropbox 
account for hosting them.

Since we've lost the nightlies, it would be nice to get a release out ASAP 
because of that data loss bug that occurs on 10.7/10.8.


Gah. Data loss bug.

I am now on 10.8. Any advice about how to build with XCode would be 
appreciated. Stick with 3.2? My impression is that support for 10.6 is now 
being dropped.

-- adam


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Re: [Bibdesk-users] nightly builds down

[Fischlin Andreas]

Apple is really getting a pain in the a...   Awful how they try to force 
everyone to go with latest hard- and software only because they believe they 
can make this way more profits. Where are the quality goals gone, sic?

Regards,
Andreas


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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
www.sysecol.ethz.chhttp://www.sysecol.ethz.ch

+41 44 633-6090 phone
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On 22/08/2012, at 15:44 , Adam R. Maxwell wrote:


On Aug 22, 2012, at 04:15 , Dr. Adam M. Goldstein PhD MSLIS 
z_californianus-dated-1346066159.6b7...@shiftingbalance.orgmailto:z_californianus-dated-1346066159.6b7...@shiftingbalance.org
 wrote:

I am now on 10.8. Any advice about how to build with XCode would be 
appreciated. Stick with 3.2? My impression is that support for 10.6 is now 
being dropped.

Support for 10.6 is still notionally present in Xcode 4, I think, but the SDK 
is gone.  BibDesk still requires Xcode 3.2, though it's not a viable path 
forward, and can't be installed on 10.7 or later.  It still more-or-less works 
if you've preserved it through upgrades, as I have.

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Re: [Bibdesk-users] PDF drag-and-drop

[Fischlin Andreas]

Dear Sean,

(*
   Name Import by DOI



   Purpose Run this script if you wish to import an article from which you 
know the doi into the currently open BibDesk bibliography



   Remark Experience is limited, yet the script seems to successfully 
import articles that are contained in pubMed



Installation
Copy this script to folder '~/Library/Application Support/BibDesk/Scripts/'


Usage   Run this script by choosing corresponding menu command from within 
BibDesk's Script menu.


Remark  Alternatively you can also run this script from anywhere on your system 
without any installation.


Programmer Andreas Fischlin, 
andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch, 
http://www.sysecol.ethz.ch/people/afischli


References (available @ 
http://www.sysecol2.ethz.ch/intranet/How_to_write.html#LiteratureMY)


Fischlin, A.  Nemecek, T., 2001 (ed. 2 corr.). Literaturverwaltung der 
Fachgruppe Systemökologie ITÖ / D-UMNW / ETH Zürich. Institute of Terrestrial 
Ecology, Swiss Federal Institute of Technology ETH, Zurich, Switzerland, 49 pp. 
  Fi086



History


  af 02.Jun.2012 v 0.9: First implementation (works with BibDesk Version 1.5.8 
(2556) under Snow Leopard OS X 10.6.8).



*)


on run {}
tell front document of application BibDesk
set theDOI to my enterString(DOI?)
if theDOI is not  then
set theImportPubs to import for search term theDOI
if theImportPubs is not {} then
set theImportPub to (get item 1 of theImportPubs)
end if
end if
end tell
end run

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


Regards,
Andreas


P.S.: I offer this script also under my usual BibDesk offering: 
http://www.sysecol.ethz.ch/people/afischli/software

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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
www.sysecol.ethz.chhttp://www.sysecol.ethz.ch

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

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On 12/Jul/2012, at 22:55 , Sean Garrett-Roe wrote:

On a separate topic, the PDF drag-and-drop is the BEST feature ever. That is so 
awesome. It makes me so happy. Chapeau!

Some time ago I think I read that the importer searches for a doi and downloads 
citation information from that using PubMed (or HubMed or whatever). If I have 
a doi and want to do the same thing, is there a way from the gui to do the same 
thing?

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Re: [Bibdesk-users] RIS import

[Fischlin Andreas]

Why not using the import button? Is the problem there persistent?

Regards,
Andreas


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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
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+41 44 633-6090 phone
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+41 79 595-4050 mobile

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On 02/06/2012, at 01:07 , Maxwell, Adam R wrote:

On Jun 1, 2012, at 15:56, Christiaan Hofman wrote:

On Jun 2, 2012, at 0:23, Sean Garrett-Roe wrote:

But the SP field (Pages in EN RIS Documentation.xls for Type Generic and 
Journal Article) isn't recognized. I've tried BP and EP but that didn't work 
either. What field tag is Bibdesk expecting?

Thanks,
Sean

Well, quite frankly, their definitions are a bit inconsistent between places 
and times. Whenever we fix it they seem to have changed it later on.

Yeah, no kidding; that spreadsheet is new, and more complicated than what I 
recall.  There's also a lot of code in BibDesk to deal with incorrect RIS from 
various sources, too; trying to massage each publisher's homegrown RIS into 
BibTeX is not trivial.

BibDesk expects SP and EP as start page and end page, respectively.  It used to 
accept PG, but it looks like that won't work anymore.  If you can do this

SP  - 2665
EP  - 2667

it ought to work.

--
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Re: [Bibdesk-users] 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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
www.sysecol.ethz.chhttp://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.orghttp://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=detailaid=3489467group_id=61487atid=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 
bestenbors...@gmail.commailto:bestenbors...@gmail.com 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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[Bibdesk-users] My Google scholar preferences get forgotten all the time

[Fischlin Andreas]

Hi all,

Does anyone know what I need to do to get Google scholar to honor my preference 
settings when visiting it via BibDesk? When I use a browser such as Safari I 
can easily set my preferences, e.g. to remember that I do not want to use 
Deutsch only because my IP# is Swiss and import in the BibTeX format. My 
settings are preserved among sessions. In BibDesk they are regularly forgotten 
and I have at least every day once to set my prefs again. Does anyone know what 
I could do to avoid that?

I first hoped that registering with Google would help. But I fear I possible 
managed the opposite. I am mentioning that since about the time when I got 
annoyed about this silly behavior by Google scholar I tried all sorts of things 
to control it and I am no longer sure whether it was BibDesk having changed (I 
regularly use nightly builds) or whether I did open an account first. 
Regardless how that may be, any help in regaining control by setting the prefs 
of Google scholar for good when searching via BibDesk would be most welcome.

Regards,
Andreas

NOTE: I have a new mobile number!

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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
www.sysecol.ethz.chhttp://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!








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Re: [Bibdesk-users] Release

[Fischlin Andreas]

I concur.

Regards,
Andreas


On 26/01/2012, at 14:15 , Christiaan Hofman wrote:

 
 On Jan 25, 2012, at 21:28, Dr. Adam M. Goldstein PhD MSLIS wrote:
 
 Hi all
 
 Judging by the absence of reports of problems on the users list, I take it 
 that there are no objections to a new release.
 
 Right?
 
 Best
 
 Adam
 
 Agreed
 
 Christiaan
 
 
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Re: [Bibdesk-users] Adding Kindle books to BibDesk records

[Fischlin Andreas]

Dear Derick,

Thanks for this useful hint. However, I believe your instructions contain 
errors. At least the Content Folder by default seems to be another one (you 
probably changed yours via the preferences or have a different history of the 
application on your system). AFAIK the default location is:

- ~/Library/Application Support/Kindle/My Kindle Content/

but you can change it to any other location via the preferences.

Moreover, it seems quite important to use only a Finder alias, and not a 
symbolic link or BibDesk will remove the .azw from the Kindle repository if you 
have Auto File active.

Regards,
Andreas




On 20/Jan/2012, at 19:25 , Derick Fay wrote:

 Here's something I just figured out.  I am in the habit of using BibDesk as 
 an organizer / file manager for all of my scholarly reading these days, and I 
 have some books on Kindle for the Mac that I wanted to be able to launch from 
 BibDesk.
 
 Kindle books are stored in ~/Documents/My Kindle Content but the filenames 
 are meaningless.  So the solution I found was
 
 1) navigate to ~/Documents/My Kindle Content
 
 2) open a .azw file - this will launch Kindle for Mac and open the book so 
 you can see which book it is
 
 3) (in the Finder) make an alias for the .azw file you just opened, with a 
 recognizable name
 
 4) add the alias to the appropriate BibDesk record.
 
 This will work - allowing launching of the Kindle book from within BibDesk - 
 even if Autofile is on.  I didn't try it, but I assume that if one just 
 Autofiled the .azw files, Kindle for Mac would have problems since they'd no 
 longer be in the expected location.
 
 It's a bit of a pain at first, if you have a lot of books, but unless Amazon 
 makes book titles visible through Applescript (fat chance!) I don't see a way 
 it could be automated.
 
 --Derick
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Re: [Bibdesk-users] BibDesk testing

[Fischlin Andreas]

Will do. Regards,
Andreas


On 13/01/2012, at 23:03 , Christiaan Hofman wrote:

 We're ready for a next release. For those brave enough, please download the 
 latest nightly builds and start (or continue) testing! Check the release 
 notes on what has been changed since the last release.
 
 thanks!
 Christiaan
 
 
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Re: [Bibdesk-users] Applescript Question

[Fischlin Andreas]

Don't do any hacks with BibDesk. BibDesk allows to do everything with 
AppleScripts quite nicely.  To remove a field, make it empty, i.e. assign an 
empty string value and the filed will be gone. For actual code examples see my 
script collection at http://www.sysecol.ethz.ch/people/afischli/software

Regards,
Andreas

NOTE: I have a new mobile number!

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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
www.sysecol.ethz.chhttp://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 23/11/2011, at 16:41 , Di Xiao wrote:

On Wed, Nov 23, 2011 at 5:25 AM, Christiaan Hofman 
cmhof...@gmail.commailto:cmhof...@gmail.com wrote:

On Nov 23, 2011, at 3:10, Di Xiao wrote:

I'm writing an applescript to do the following

1) import bibtex from a webpage in safari
2) generate a cite key according to the auto generation rule set in preferences

Below is the part of applescript

tell document 1 of application BibDesk
  activate
  set myPub to first item of (import from theBibTeXString)
  set selection to {myPub}
  tell application System Events to keystroke k using {command down}
end tell

However, I ran into the following problem.  I use keyword groups.  If
BibDesk is already running and one of the keyword groups is selected,
then the the last line won't run because, unless the imported entry
has the same keyword, it won't be selected.  I checked the BibDesk
dictionary in Applescript Editor.  It seems that I can first select
the library group right after activate.  But I cannot figure out
the proper way to do it.  Any help is appreciated.

D.

Using system events to simulate key strokes is something of a hack, you should 
not use that if it's not necessary. In this case you can simply generate and 
set the cite key in applescript.

tell application BibDesk
   activate
   set theFormat to cite key format
   tell document 1
   set thePubs to (import from theBibTeXString)
   if count of thePubs  0 then
   set myPub to (get first item of thePubs)
   set theCiteKey to parse format theFormat for Cite Key 
from myPub
   set cite key of myPub to theCiteKey
   end if
   end tell
end tell

Christiaan


Hi Christiaan,

Thanks a lot!  I was wondering if there is a more elegant way to do
the cite key generation.

I have another question.  I have a script saved in BibDesk's script
folder to do some format cleaning after a record is imported, i.e.,
remove some unnecessary field added by the publisher.  Right now what
I'm doing is again to assign a menu shortcut to that script, then call
it using the system events.  Is there a way to call that script from
the current applescript?

Di

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Re: [Bibdesk-users] Local-Url field

[Fischlin Andreas]

Yes, AppleScript and check out my AppleScript Inspect Linked Files you can 
download at http://www.sysecol.ethz.ch/people/afischli/software

Regards,
Andreas


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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
www.sysecol.ethz.chhttp://www.sysecol.ethz.ch

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On 17/11/2011, at 11:48 , FZiegler wrote:

Christiaan Hofman wrote:

That was instant to do with find  replace in a text editor.

Note that BibDesk has that same feature, that you can use for specific fields.

I probably missed something, but I could not see how to do it at one
stroke for all 6000+ entries in my database. (Replace all seemed to
work per-entry.)

Another option is to use the linked files anyway, but have them backed up in 
the Local-Url field. Is it really such a problem when others see one extra 
field?

Their point of view is that bibtex is cross-platform, but my mac aliases
1) break that and 2) considerably enlarge the file's size. But yes, they
might forgive as long as I duplicate the path in plain text. How do I go
about this?  (Still applescript?)

Thanks,
Francois

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Re: [Bibdesk-users] Odd quirk on Lion - zero bytes

[Fischlin Andreas]

This has probably nothing to do with BibDesk but with a missing update of the 
Finder information. You can usually force more uptodate the Finder information 
by closing and reopening the window where you suspect the information is not 
correct.

Regards,
Andreas


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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
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On 15/11/2011, at 13:09 , David Nicholls wrote:

I have just installed Bibdesk 1.5.6 on Lion 10.7.2.  In the Finder, the size is 
given as Zero bytes, but when I use Getinfo, it reports 20.7 Meg.  Why is 
this so?

I also inherited a second copy (in sub folder) of Bibdesk 1.5.4 when I instal 
MacTex.  It shows its size correctly in Finder.  I have not run the second 
version.

Any ideas?  Bug?

DN
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Re: [Bibdesk-users] iCloud support BibDesk

[Fischlin Andreas]

Hi all,

From all what I read my verdict is crystal clear: Forget iCloud, in particular 
for anything as precious as a personal separata collection revolving around 
BibDesk (my assessment assumes most of us are scientists).

Let me explain:

1) I am since years a MobileMe user. I pay my yearly 99$ fee to have synced 
among 3 Macs (some of my collaborators need to see my calendar, address book), 
an iPad, and an iPhone:
- iDisk (10 GB)
- Calendar
- Contacts (Address book)
- Safari bookmarks
- Mail accounts
- Mail rules, signatures, and smart mailboxes

iDisk is pertinent to our topic, which is where I store pdf's as extracted from 
BibDesk's pdf repository including the needed AppleScripts 
(http://www.sysecol.ethz.ch/people/afischli/software) to sync back any 
annotations I made on my Wi-Fi only iPad using GoodReader.

2) This system works reliably, albeit iDisk is very slow and has failed me 
often in the past (I live in Switzerland). More recently (Mac OS X 10.6.5 and 
later) it started to improve and Apple's iDisk software got more reliable (no 
unfixable out of sync anymore, requiring a full resync lasting hours for only a 
few GB and this regardless of fast internet connections). I do not expect 
iCloud to become faster than iDisk was at its best times. Only incremental 
syncing is speed-wise acceptable, yet still slow and I often find myself when 
leaving my office missing the tram or bus because the syncing takes so long. 
Concerning all other sync services apart iDisk work efficiently. I was often 
surprised how well, entering an appointment on my Mac into the calendar, 
closing the lid, getting up and picking up my iPhone out of my pocket and it is 
already there.

3) As of June next year MobileMe will stop functioning and my iDisk will be 
gone and AFAIK iCloud will NOT provide any replacement. 

4) From what I know so far DropBox appears to me to be clearly the only 
replacement for iDisk, not iCloud. I have Dropbox installed since quite a while 
but have not yet moved fully from iDisk to it and still do most document 
syncing via iDisk. But having read about the clumsy way you can officially 
exchange documents between a Mac and iCloud, see e.g. 
http://www.macworld.com/article/163173/2011/10/bugs_and_fixes_losing_iwork_documents_in_icloud.html,
 iCloud does not look attractive to me at all. But Dropbox does. Unless Apple 
offers again something similar to iDisk with official, i.e. warranted 
functioning, why should we even think about using iCloud for BibDesk?

5) For all the other syncing services (see list above) I expect from iCloud to 
provide a full and functioning replacement for all other MobileMe syncing 
services I currently use (list above), given I can move to Lion. I try to push 
the latter as far off into the future as possible, given the fact that Rosetta 
is no longer available. Our modeling software RAMSES still partly depends on it 
(http://www.sysecol.ethz.ch/ramses/).  If iCloud manages to sync some files 
between my iPad and iPhone behind the scenes, that is fine, but this is not 
really important for my workflow. But I have not the least reason wanting to 
use the iCloud for really important working files such as TeX, Word documents, 
paper pdfs, possibly annotated, or my BibDesk reference file, Keynote 
presentations etc. given Dropbox works fine.

6) At some point in the near future I plan to start paying Dropbox my 99$ (Pro 
50) an year and Apple can forget it.

I am looking forward to learn about other workflow philosophies and perhaps 
someone has an even better solution to the messy realms Apple seems to move us 
into. ;-) I only hope I err with the latter sentiment.

Regards,
Andreas


On 12/11/2011, at 17:35 , Adam R. Maxwell wrote:

 
 On Nov 11, 2011, at 08:21 , M A wrote:
 
 Well, it does give notification to the OS (or so they claim) or
 through Growl if it's installed. It seems like it should be possible
 to hook into that somehow, though I don't know enough about what
 Dropbox is doing to know how.
 
 [...]
 
 It's more about
 giving the user the choice of which bib file to use once BibDesk gets
 notified that the one on disk was changed.
 
 The point I was trying to make (badly) in bringing up NSDocument is that this
 should happen automatically, right now.  If you try to save a .bib file that
 has been modified externally, BibDesk should give you an alert with the option
 to overwrite the external changes or cancel the save.
 
 -- 
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Re: [Bibdesk-users] Applescript for Bibdesk to Endnote X4 synchronisation

[Fischlin Andreas]

What's the difference what I provide since a long time?  
http://www.sysecol.ethz.ch/people/afischli/software

Regards,
Andreas


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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
www.sysecol.ethz.chhttp://www.sysecol.ethz.ch

+41 44 633-6090 phone
+41 44 633-1136 fax
+41 79 221-4657 mobile

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On 31/10/2011, at 18:51 , Peadar Grant wrote:

Good Evening Everyone,

Although I use LaTeX and Bibdesk for as much of my publication output as 
possible, there are still times when I have to complete an academic document 
that includes references in Microsoft Word.  Seen as I have access to Endnote, 
I have put together a script to automate the transfer from Bibdesk to Endnote 
X4.

Note that this script deletes everything in the Endnote database and re-creates 
it on every run, so do not make changes to the Endnote database unless you 
don't mind losing them.  I am working on a new version to do incremental 
updates, but it's still early in development.

Developers - please feel free to post this on the Bibdesk Wiki.

Best regards,

Peadar.




Script follows below:



--- Script to pre-load Endnote from BibDesk
--- Peadar Grant 2009, updated 2011.

--- Start with an empty Endnote library
--- This applescript will save the Bibdesk bibliography as
--- endnote XML and then will open Endnote,
--- delete all the references in your Endnote library
--- and populate it with your BibDesk references.

--- You need to set the three filenames:
--- bibdeskFile : your bibdesk file
--- exportFile : the interim file that's used to dump data
--- endnoteFile : your endnote library
--- ... and the filenames need to be specified
--- in applescript (as opposed to POSIX) format.

--- This has been tested to work with Endnote X4 for Mac only.

--- There seems to be a file access problem unless the applications
--- are both quit.

set bibdeskFile to ((path to home folder as text)  
Documents:Bibliography:Bibliography.bib)
set exportFile to ((path to home folder as text)  
Documents:Bibliography:ExportedFromBibdesk.xml)
set endnoteFile to ((path to home folder as text)  
Documents:Bibliography:EndnoteLibrary.enl)


tell application BibDesk
activate
open bibdeskFile
set theDoc to get first document
save theDoc in exportFile as EndNote XML
quit
end tell

tell application Finder
set myXMLFile to open for access exportFile without write permission
set refsToImport to read myXMLFile
close access myXMLFile
end tell

tell application EndNote X4
activate
set myDB to open endnoteFile
set res to find  
delete record res
import refsToImport into myDB
close myDB saving yes
quit
end tell

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Re: [Bibdesk-users] Importing PDF files

[Fischlin Andreas]

AFAIK those services cost a lot. I do not see how that is compatible with an 
open source BibDesk.

Regards,
Andreas


On 13/10/2011, at 02:35 , Maxwell, Adam R wrote:

 
 On Oct 12, 2011, at 17:29, Douglas Stebila wrote:
 
 On 2011-10-13, at 0:52, Adam R. Maxwell amaxw...@mac.com wrote:
 
 AFAIK, none of the screen-scraping sites in the web group are suitable for 
 a query, unfortunately.  You need a service such as PubMed or Web of 
 Science with an actual API.
 
 Couldn't you visit the page defined by the DOI, and, if it's a page from a 
 site that the web group scrapers know how to scrape, then it scrapes that 
 data?  Obviously suffers from the limitations of scraping being inaccurate / 
 fragile, but it should work a bit.
 
 Oh, that's a neat idea, and it probably would work.  I was thinking you'd 
 somehow craft a query string for each site, which is harder.
 
 -- 
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Re: [Bibdesk-users] Output format of the bib file

[Fischlin Andreas]

Dear Fabian,

I do not see why your end users are a problem for the solution I suggested as 
long as you know what I am talking about. Because you can build all this into a 
solution that is as easy as choosing a menu command. That is what I do. I 
program it and then I forget, i.e. I get as dumb as any other end-user when I 
concentrate on something scientific again. This means I use an AppleScript that 
is accessible from BibDesk like any other menu command (Extract 
Bibliography). I guess any end-user of BibDesk can do that, right?

That AppleScript uses templates and sed grep and all sorts of Unix commands in 
the post processing shell script that BibDesk so nicely supports (I have 
forgotten what it all does). If I remember correctly I use grep to customize my 
html output, i.e. setting the title of the web page to something else than the 
default. This happens by grepping from a simple text file some of the 
parameters used by the AppleScript Extract Bibliography. But you could also 
have a dialog to ask the user, if editing a text file is too difficult for your 
end users. 

Be welcome to have a look at my BibDesk scripts, which I offer for download 
here 

http://www.sysecol.ethz.ch/people/afischli/software

together with all templates etc.

Regards,
Andreas


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

andreas.fisch...@env.ethz.ch
www.sysecol.ethz.ch

+41 44 633-6090 phone
+41 44 633-1136 fax
+41 79 221-4657 mobile

 Make it as simple as possible, but distrust it!




On 12/10/2011, at 19:17 , Fabian Dorsch wrote:

 Andreas, Adam, thanks a lot for your quick replies!
 
 My aim is to dynamically display the publications of our research
 group on our Modx website in different and complex ways (e.g.,
 filtered by author, year, keyword, research project, etc.). This is
 why I need a php script, rather than the option of html output from
 BibDesk.
 
 Also, members of the group should be able to add new publications in a
 simple way, i.e. by nothing more complicated than using software like
 BibDesk or JabRef. They are all from the humanities and typically have
 no idea of unix, scripts, etc. - it would just scare them away. This
 is why sed is not an option, either.
 
 I could just use JabRef since it provides the desired output. But it
 doesn't (easily?) allow the user to add custom fields, which are
 needed for the script.
 
 I guess I'll have to continue to look around for a simpler solution.
 
 Fabian
 
 
 On Wed, Oct 12, 2011 at 6:06 PM, Fabian Dorsch
 fabian.dor...@uclmail.net wrote:
 Hi,
 
 the answer to my question is probably simple, but I couldn't find it
 myself. I would like to use a script to display references in html.
 But the script requires a special format of the bibtex entries.
 
 When I save my bibliography with BibDesk, each entry looks like this:
 
 @article{...
...
Year = {2007}}
 
 But what I need would be this (which is also the output from, say,
 Google Scholar):
 
 @article{...
...
Year = {2007}
 }
 
 I looked at the preferences of BibDesk, but did not find any way to
 change this. I also tried out different encodings, with no success.
 Any suggestions?
 
 Thanks a lot!
 
 Fabian
 
 
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 www.unifr.ch/philo/de/department/modern/dorsch.php
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Re: [Bibdesk-users] Cite Key Autogeneration

[Fischlin Andreas]

Container does exactly that for you. You got already the advice. Why don't you 
try and see for yourself?

If you don't believe us, read the BibDesk help Browsing References and the 
description of the field Container whether Container is for you.

Regards,
Andreas


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

andreas.fisch...@env.ethz.ch
www.sysecol.ethz.ch

+41 44 633-6090 phone
+41 44 633-1136 fax
+41 79 221-4657 mobile

 Make it as simple as possible, but distrust it!




On 13/10/2011, at 10:14 , Masahiro Takahashi wrote:

 Thanks Andreas,
 
 If I understand correctly, the way you taught is just a normal way.
 
 My question is that if there is a way changing Container part
 for different types of references.
 
 I want to set parameters as:
 
 %a1_%f{Journal}_%Y_v%n
 for articles
 
 and
 
 %a1_%f{Booktitle}_%Y_v%n
 for inbook.
 
 Thanks in advance.
 
 Best regards,
 masa
 
 p.s.
 I just recognize that if I set
 %a1_%f{Journal}%f{Booktitle}_%Y_v%n
 then I probably get what I want.
 If there is a better idea or default functionality, please.
 
 On 2011/10/13木, at 16:40, Fischlin Andreas wrote:
 
 Use %f{Container} to specify how cite keys are generated (menu BibDesk - 
 Preferences... - Cite Key in the Format String having set the Preset 
 Format to Custom)
 
 and you fill in the fields of the publications the normal way.
 
 Regards,
 Andreas
 
 
 ETH Zurich
 Prof. Dr. Andreas Fischlin
 Systems Ecology - Institute of Integrative Biology
 CHN E 21.1
 Universitaetstrasse 16
 8092 Zurich
 SWITZERLAND
 
 andreas.fisch...@env.ethz.ch
 www.sysecol.ethz.ch
 
 +41 44 633-6090 phone
 +41 44 633-1136 fax
 +41 79 221-4657 mobile
 
Make it as simple as possible, but distrust it!
 
 
 
 
 On 13/10/2011, at 07:55 , Masahiro Takahashi wrote:
 
 Thank you, Christiaan,
 
 I need more detailed explanations.
 How do I define Container for articles and inbook?
 You can use %f{Container} for this.
 
 I checked following link, but I couldn't figured out.
 http://bibdesk.sourceforge.net/manual/BibDesk%20Help_91.html#SEC159
 
 Thank you for your advices in advance.
 
 Sincerely,
 masa
 
 On 2011/10/11火, at 16:35, Christiaan Hofman wrote:
 
 
 On Oct 11, 2011, at 5:31, Masahiro Takahashi wrote:
 
 Dear all,
 
 I'm using BibDesk with several kinds of materials,
 for example article, inbook, etc...
 
 I'm using Cite Key Autogeneration functionality as
 
 %a1_%f{Journal}_%Y_v%n
 
 gives an example of the cite key:
 
 McCracken_Source-Forge_2004_v0
 
 However, for inbook, there is no ENTRY Journal,
 so autogeneration just skip the part.
 
 McCracken__2004_v0
 
 Is there any way of replacing Journal by (for example) Booktitle,
 if there is no ENTRY journal?
 Or is it possible to tell BibDesk use Booktitle for inbook.
 
 Sorry if there is a same question.
 
 Sincerely,
 masa
 
 You can use %f{Container} for this.
 
 Christiaan
 
 
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Re: [Bibdesk-users] Importing PDF files

[Fischlin Andreas]

I was talking only on the web scraping. That AFAIK costs a lot, e.g. 
http://www.automationanywhere.com/solutions/screenScrape.htm. But perhaps 
that's not an issue at all.

Regards,
Andreas


On 13/10/2011, at 15:00 , Adam R. Maxwell wrote:

 
 On Oct 13, 2011, at 00:57 , Fischlin Andreas wrote:
 
 AFAIK those services cost a lot. I do not see how that is compatible with an 
 open source BibDesk.
 
 I don't see what on earth you're talking about.  We've supported Web of 
 Science searching in BibDesk for several years, and many (most?) of the web 
 groups are for-pay sites such as IEEE.
 
 -- 
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Re: [Bibdesk-users] Importing PDF files

[Fischlin Andreas]

Indeed, I would support that suggestion. I have it on since years and never 
regretted (so far) ;-)

Regards,
Andreas


On 13/10/2011, at 16:32 , Gregory Jefferis wrote:

 
 On 12 Oct 2011, at 14:23, Adam R. Maxwell wrote:
 
 
 On Oct 12, 2011, at 05:09 , M. Tamer Özsu wrote:
 
 I was simply wondering out loud how some of these other programs manage to 
 extract the title/author/... data from the PDF files to at least attempt to 
 generate some of this citation information. I now understand that Bibdesk 
 does not do this, and that is perfectly fine.
 
 They do it by scraping information from the PDF, including the DOI.  BibDesk 
 can also do this, using the BDSKShouldParsePDFToGeneratePubMedSearchTerm 
 hidden preference.  I don't use it myself, since it only searches PubMed.  
 Pretty similar code could probably be used to run a Web of Science search, 
 though, come to think of it...
 
 Is there any reason why this is turned off by default? I actually wrote most 
 of that code and I thought that it had broken because I did not notice the 
 hidden pref. For biologists/medics, this is an incredibly timesaver and it 
 works with nearly all modern PDFs in this domain.
 
 People don't normally drop PDFs onto BibDesk unless they have an existing 
 reference. So I don't see that setting this to true by default would much 
 inconvenience anyone. Setting it to false means that very few people will 
 ever notice and use it.
 
 Best,
 
 Greg.
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Re: [Bibdesk-users] Importing PDF files

[Fischlin Andreas]

Hi Tamer Özsu,

Look at the data you provided:

file = {:Users/tozsu/Documents/Collected Papers/Proceedings Papers/EDBT/EDBT 
2011/LID11(EDBT)\_a6-zaniolo.pdf},

This is AFAIK not a valid file path, e.g. it starts with a :. I guess 
Christiaan's word use 'junk' is more too often true than not. Making wild 
guesses, as perhaps other programs such as Papers do, may also not be always 
helpful, because it can be very confusing if it once works and once not for 
reasons very difficult to comprehend. And if you look at other program 
characteristics, e.g. Papers' lousy cite key generation, you find that perhaps 
a small advantage as guessing when pdf metadata are bad is paid with 
deficiencies that are intolerable (at least for me).

This is just meant as some considerations to also take into account before 
criticizing BibDesk too much.

Sincerely yours,
Andreas Fischlin


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

andreas.fisch...@env.ethz.ch
www.sysecol.ethz.ch

+41 44 633-6090 phone
+41 44 633-1136 fax
+41 79 221-4657 mobile

 Make it as simple as possible, but distrust it!




On 12/10/2011, at 10:10 , M. Tamer Özsu wrote:

 Thank you. I'll study that. 
 
 I wonder how programs such as Papers and Mendeley are able to extract that 
 info from PDF files -- or do they not extract them from the PDFs?
 
 ==Tamer
 
 On 2011-10-11, at 11:20 PM, Maxwell, Adam R wrote:
 
 
 On Oct 11, 2011, at 14:16, M. Tamer Özsu wrote:
 
 Some PDF files do have this information included as metadata that some 
 programs are able to extract. I thought there might be a mechanism such as 
 that, but I understand that there isn't.
 
 There is, but most of that metadata is junk.  Look for 
 BDSKShouldUsePDFMetadata on this page:
 
 http://sourceforge.net/apps/mediawiki/bibdesk/index.php?title=Tips_and_Tricks
 
 
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Re: [Bibdesk-users] Importing PDF files

[Fischlin Andreas]

No, they often do not extract them from the pdf. They often search in the pdf 
for a doi and then provide the actual data from a provider such as ISI WOS or 
other data base sources. BibDesk does not do that. As a consequence you see in 
BibDesk how lousy the meta data in the pdf generally actually are (at least in 
my experience).

Regards,
Andreas


ETH Zurich
Prof. Dr. Andreas Fischlin
Systems Ecology - Institute of Integrative Biology
CHN E 21.1
Universitaetstrasse 16
8092 Zurich
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On 12/10/2011, at 10:10 , M. Tamer Özsu wrote:

 Thank you. I'll study that. 
 
 I wonder how programs such as Papers and Mendeley are able to extract that 
 info from PDF files -- or do they not extract them from the PDFs?
 
 ==Tamer
 
 On 2011-10-11, at 11:20 PM, Maxwell, Adam R wrote:
 
 
 On Oct 11, 2011, at 14:16, M. Tamer Özsu wrote:
 
 Some PDF files do have this information included as metadata that some 
 programs are able to extract. I thought there might be a mechanism such as 
 that, but I understand that there isn't.
 
 There is, but most of that metadata is junk.  Look for 
 BDSKShouldUsePDFMetadata on this page:
 
 http://sourceforge.net/apps/mediawiki/bibdesk/index.php?title=Tips_and_Tricks
 
 
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Re: [Bibdesk-users] merging databases and their pdfs

[Fischlin Andreas]

You have two options to accomplish what you want (if I understood correctly):

1) Use the Finder (or some synchronizing tool such as Synchronize Pro 
http://www.qdea.com/) and BibDesk tracks the moving.

2) (i) choose a new pdf repository (BD prefs); (ii) Select the new 
publications; (iii) Choose menu command Publication - Autofile Linked 
Files...

Regards,
Andreas


ETH Zurich
Prof. Dr. Andreas Fischlin
Systems Ecology - Institute of Integrative Biology
CHN E 21.1
Universitaetstrasse 16
8092 Zurich
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On 30/09/2011, at 15:08 , Themis Matsoukas wrote:

 In my bibliographies use the auto file string
 
 /%b/%a1-%c{Journal}%y%u0%e
 
 so that the pdfs associated with databaseXYZ.bib are stored in sub-folder 
 /databaseXYZ of a folder that I have designated in the auto file options. Now 
 I want to merge two my databases into one but when I copy records from one 
 bib file to another, the pdfs are not transferred to the corresponding 
 subfolder. Is there an automatic way to do the transfer of pdfs? 
 
 Themis
 
 
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Re: [Bibdesk-users] BibDesk 1.5.5 released

[Fischlin Andreas]

Many thanks Christiaan! :-)

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

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On 20/09/2011, at 12:00 , Christiaan Hofman wrote:

The BibDesk development team is pleased to announce the release of BibDesk 
1.5.5, the latest version. We thank the contributors to the bibdesk-users 
mailing list and others who contributed code or bug reports.

It can be accessed at

BibDesk  Check for Updates

from within the application itself, or by visiting the BibDesk home page at

http://bibdesk.sourceforge.net/

Here is some information about the new release:

Changes since 1.5.4

New Features
  *  New select AppleScript command
  *  Support Outlook email client
  *  New service to open a URL in a web group
  *  Add recent searches to menu of quick search menu
  *  Enable Lion's full screen support
  *  Disable Lion's built-in window restoration feature.

Bugs Fixed
  *  Don't open remote URLs twice
  *  Update authors and groups when macros change
  *  Add full abstract text to Entrez search results
  *  Don't allow = in cite keys
  *  Allow changing raw BibTeX values that expand to the same value
  *  Fix key view loop in preference window
  *  Fix a crasher that sometimes can happen with saving new documents
  *  Remember secondary sort key
  *  Allow numeric pad keys in type select
  *  Extra optional arguments for %k and %w format specifiers for separator
  *  Improved efficiency when selecting the Publication Date column
  *  Fix setting scripting properties in make command
  *  Allow some more characters in cite key when sniffing for bibtex
  *  Improved preference window layout
  *  Fix link to feature requests
  *  Make sure search field is always shown when initiating a quick search
  *  Avoid a crash when a linked URL contains PDF
  *  Fix zoom popups in previews on Lion
  *  Don't save template in empty documents
  *  Support INSPIRE in web group

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Re: [Bibdesk-users] Fields for entry types

[Fischlin Andreas]

It stores them in the .bib file only for that particular publication.

Regards,
Andreas


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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
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On 02/09/2011, at 13:47 , Christian Pleul wrote:

On 02.09.2011, at 13:26, Christiaan Hofman wrote:


On Sep 2, 2011, at 13:20, Christian Pleul wrote:

Hi,

Where does BD save the fields (e.g. Author, Title, URL etc) to make them 
available when manually adding a new field to a publication via Publication  
Add Field


Best
--
Christian

What do you mean? Field names are arbitrary, as long as they don't contain some 
special characters.

Christiaan

I mean the fields I can select when using Publication  Add Field.

Best
--
Christian


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Re: [Bibdesk-users] J App Phys bibtex not recognized by bibdesk

[Fischlin Andreas]

Indeed. Regards,
Andreas
 

On 18/Aug/2011, at 17:13 , Themis Matsoukas wrote:

 On Aug 17, 2011, at 12:25 PM, Fischlin Andreas wrote:
 
 Yes, it may be a problem with the APL exporter. You need to teach those web 
 guys proper BibTeX. Unfortunately, in my experience you have to do that with 
 many. I sent feedback on these simple mistakes already to Science, Nature, 
 PNAS and many more. At least that's the only thing I see we can do, and 
 gradually they learn and things get slowly, slowly better.
 
 Well, it is good to know that AIP is responsive:
 
 From: Scitation Help Desk h...@aip.org
 Subject: RE: Bibtex downloads are broken
 Date: August 18, 2011 10:45:43 AM EDT
 To: 'Themis Matsoukas' matsou...@engr.psu.edu
 
 Dear Themis Matsoukas,
 
 Thank you for contacting the Scitation Help Desk and providing the below 
 information.
 
 Our technicial department is aware of the bibtex error and are working 
 diligently to have it fixed.
 
 If you have any questions or concerns, please let us know.
 
 Sincerely,
 Esther Zirkiev
 
 Scitation Online Services Help Desk
 American Institute of Physics
 Email:  h...@scitation.org
 Toll Free US/Canada:  1 800 874-6383
 International:  1 516 576-2664
 FAX:  1 516 349-9704
 
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Re: [Bibdesk-users] J App Phys bibtex not recognized by bibdesk

[Fischlin Andreas]

Yes, it may be a problem with the APL exporter. You need to teach those web 
guys proper BibTeX. Unfortunately, in my experience you have to do that with 
many. I sent feedback on these simple mistakes already to Science, Nature, PNAS 
and many more. At least that's the only thing I see we can do, and gradually 
they learn and things get slowly, slowly better.

Regards,
Andreas


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

andreas.fisch...@env.ethz.ch
www.sysecol.ethz.ch

+41 44 633-6090 phone
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 Make it as simple as possible, but distrust it!




On 17/08/2011, at 18:17 , Simon Spiegel wrote:

 
 On 17.08.2011, at 17:33, Adam R. Maxwell wrote:
 
 
 On Aug 17, 2011, at 08:12 , Themis Matsoukas wrote:
 
 The problem is fixed by changing @journal article to @article but I 
 shouldn't have to do this manually. Is this a problem with APL's bibtex 
 exporter?
 
 Yes, this is terribly broken; @article is the correct type.  There is no 
 @journal, and there must be no space in the type.
 
 Biblatex actually has a type @journal, but @journal article is definitely 
 broken.
 
 Simon
 
 
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Re: [Bibdesk-users] Texshop / Bibdesk

[Fischlin Andreas]

Dear Christiaan,

While having selected a cite key, e.g. in TeXShop and then choosing from the 
services menu item BibDesk:  Show Reference With Cite Key the record is 
opened. I would have expected just that record being selected, but not opened. 
Is that the wanted behavior and yes, is there any way to influence the way that 
service works, e.g. to have a preference not opening the record for editing, 
but merely selecting the pub?

Regards,
Andreas


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

andreas.fisch...@env.ethz.ch
www.sysecol.ethz.ch

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On 02/07/2011, at 23:24 , Christiaan Hofman wrote:

 
 On Jul 2, 2011, at 22:53, ccl4 wrote:
 
 thanks.
 
 but i only see something like dictionary entries. how can i make the list of
 the references in bibdesk be visible instead?
 
 --
 View this message in context: 
 http://bibdesk-users.661331.n2.nabble.com/Texshop-Bibdesk-tp6541514p6541651.html
 Sent from the bibdesk users mailing list archive at Nabble.com.
 
 You said autocompletion, not lookup. For lookup you can use Services, this 
 looks up by cite key. You can also use that for citation, though that tries 
 to match certain search criteria title=Title or author=Author).
 
 Christiaan
 
 
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Re: [Bibdesk-users] Problem importing paper from journal with name containing

[Fischlin Andreas]

 I really do have to say that I find it so astonishing that major producers of 
 BibTeX records like JSTOR  cannot get these formats right. Rarely does a 
 record come into the database without my having to tinker with it. Something 
 is always missing or else wrong. I don't think the basic structure of a BT 
 record is that complicated.

I fully concur. I almost always have to send feedback to most journals, 
including Science, Nature, PNAS etc. A shame on the current IT responsible 
people, who seem to be unable to do even the simplest things right...

Regards,
Andreas


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Re: [Bibdesk-users] review of Papers 2

[Fischlin Andreas]

I concur. ;-)

Regards,
Andreas


ETH Zurich
Prof. Dr. Andreas Fischlin
Systems Ecology - Institute of Integrative Biology
CHN E 21.1
Universitaetstrasse 16
8092 Zurich
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On 16/May/2011, at 22:17 , Jens Nöckel wrote:

 
 On May 16, 2011, at 12:03 PM, Themis Matsoukas wrote:
 
 
 On May 16, 2011, at 2:36 PM, Adam M. Goldstein wrote:
 
 I don't know if this is what bothers Themis, but what bothers me is the 
 ugly icons in the left-han-pane and also the toolbar and its counterpart 
 below the main table/cover view area. 
 
 I have always thought that the main icon looks something like a cross 
 between a barn, a bank or courthouse, and a small house. Libraries have red 
 carpets?
 
 That's exactly what I was talking about. The icon has excruciating detail, 
 you can look through the windows of the barn and see computers, and if you 
 look more closely you might even see what the prof/farmer/librarian ate for 
 lunch... Look like Animal Crossings on Wii (my daughter plays it, not me). 
 
 The menu on the left is equally annoying. Reports and references, for 
 example shows a spreadsheet with heading rows and columns, and possibly with 
 equations in the cells. Such nano-minute detail gives me a headache. 
 
 
 Just a note from a lurker: I've been using BibDesk consistently for many 
 years and just want to encourage the developers to stay the course. Eye-candy 
 is irrelevant to serious users (which I'm sure make up the silent 
 majority). 
 
 Thanks,
 Jens
 
 
 
 
 
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Re: [Bibdesk-users] Way to make Skim default only in Bibdesk?

[Fischlin Andreas]

Inspecting BD a bit with 

defaults read edu.ucsd.cs.mmccrack.bibdesk

lead me first to conclude that Adam might be right. At least I could not figure 
out that it is not a BD specific preference. However, I have set in the Finder 
to open all pdf with Adobe Reader. Double-clicking a pdf in the Finder opens it 
with that wanted reader. When changing in BD the pdf reader to say Skim, then 
opening a pdf from within BD opens it in Skim. This tells me clearly that there 
is a BD preference for pdf reading which is different from the system wide.

However, I agree with kbostroem that it is not well placed under tab 'Fields'. 
I opt to have it under tab AutoFile or perhaps General. AutoFile has mostly to 
do with pdf's, doesn't it? Therefore users might find it easier when it would 
be offered there.

What can Chrstiaan tell us on this?

Regards,
Andreas

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

andreas.fisch...@env.ethz.ch
www.sysecol.ethz.ch

+41 44 633-6090 phone
+41 44 633-1136 fax
+41 79 221-4657 mobile

 Make it as simple as possible, but distrust it!




On 29/Apr/2011, at 14:38 , Adam M. Goldstein wrote:

 On Apr 29, 2011, at 8:25, kbostroem b...@kim-bostroem.de wrote:
 
 Sorry if I'm stepping into this discussion that lately, but I'm also one of
 those people with a burning desire for a default-PDF-viewer preference at a
 transparent place in BibDesk. In fact, I just didn't find this preference
 although I was looking for it in the BibDesk preference pane. I then googled
 it and  stumbled into this forum, so I'm happy that the setting exists and
 works!
 
 
 I don't like it in General, if not just because it's not a primary  
 preference. Personally, I would rather side with Adam and remove it  
 all together than moving it to the General preferences. As it's really  
 an advanced preference that arguable should not be there at all,  
 there's a strong case to make it hidden. 
 
 Why do you developers often see things so deeply different than ordinary
 users?
 As an ordinary user, I simply don't care if the PDF-viewer setting is an
 advanced preference or a primary preference or whatever, I just want to
 set it, and I want to find it at a location where I expect it to be, which
 is definitely not under Fields. 
 But more to the point: What exactly is wrong with putting the setting under
 General? As far as I can see, the setting does not influence my
 system-wide default PDF-viewer setting, but just and only the BibDesk-wide
 viewer setting. It simply lets me define what viewer to use within BibDesk,
 so it is a veritable BibDesk setting and not in any way suspicious or
 dangerous. How come you and Adam think to the contrary, that it's an evil
 setting which should be hidden from the user or even removed?
 
 
 I suspect it's because there is a system-wide setting, and that if people 
 were to change this just for BD, it would conflict with that setting.
 
 In contrast with TeXShop, whose PDF viewer is built in, BibDesk relies on an 
 external program, and changing the preference for it in BD would take over a 
 system function.
 
 Also I am pretty sure you can right-click on a PDF icon or image and choose 
 open with as a way of opting out of the system-wide setting. 
 
 
 --
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 Sent from the bibdesk users mailing list archive at Nabble.com.
 
 
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Re: [Bibdesk-users] Way to make Skim default only in Bibdesk?

[Fischlin Andreas]

Christiaan's and my mail crossed each other. I side with Christiaan, having 
read the thread. And true, there are many arguments to consider, not just a 
particular user's ones.

One last advanced ;-) question to Christiaan: I wish just to better 
understand the implementation: Is there a systemwide setting that is controlled 
here? What is it's name, in which plist? Then that setting must be different 
from the setting you can make using the Finder (Get Info - Open with - Change 
All...). A rather complicated situation. Moreover, using utilities such as 
MisFox (http://mac.clauss-net.de/misfox/) show still another setting exists on 
the system for .pdf (AFAIK the so-called internet settings). An even more 
complicated situation.  Thus, can you please clarify a bit and tell me what 
system preference exactly is controlled via BD? Or can you give me the URL 
where the BD code is that does this? Thanks.

Regards,
Andreas

P.S.: Please don't get tired too quickly. These discussions are unavoidable in 
such projects. ;-)


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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
www.sysecol.ethz.chhttp://www.sysecol.ethz.ch

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On 29/Apr/2011, at 14:52 , Christiaan Hofman wrote:


On Apr 29, 2011, at 14:25, kbostroem wrote:

Sorry if I'm stepping into this discussion that lately, but I'm also one of
those people with a burning desire for a default-PDF-viewer preference at a
transparent place in BibDesk. In fact, I just didn't find this preference
although I was looking for it in the BibDesk preference pane. I then googled
it and  stumbled into this forum, so I'm happy that the setting exists and
works!


I don't like it in General, if not just because it's not a primary
preference. Personally, I would rather side with Adam and remove it
all together than moving it to the General preferences. As it's really
an advanced preference that arguable should not be there at all,
there's a strong case to make it hidden.

Why do you developers often see things so deeply different than ordinary
users?

Because users have deeply different views among themselves (I can assure you), 
and we have to take into account all of these views and in particular logic and 
Apple's Human Interface Guidelines.

As an ordinary user, I simply don't care if the PDF-viewer setting is an
advanced preference or a primary preference or whatever, I just want to
set it, and I want to find it at a location where I expect it to be, which
is definitely not under Fields.

The placement under Fields has been explained. And above I explained why it 
does not matter whether YOU don't care, the point is that we DO care.

But more to the point: What exactly is wrong with putting the setting under
General?

That was explained, you apparently read that, so why you ask?

As far as I can see, the setting does not influence my
system-wide default PDF-viewer setting, but just and only the BibDesk-wide
viewer setting. It simply lets me define what viewer to use within BibDesk,
so it is a veritable BibDesk setting and not in any way suspicious or
dangerous. How come you and Adam think to the contrary, that it's an evil
setting which should be hidden from the user or even removed?

But it does overrule a standard system setting, and therefore does things that 
can be unexpected, and arguably should not be done.

In hindsight, we should have never added this setting. And there is a good 
chance that in the future it will be a hidden preference, as for the default 
browser (more arguing about this will enhance the chances of this happening, as 
it makes me tired of it).

Christiaan


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Re: [Bibdesk-users] Way to make Skim default only in Bibdesk?

[Fischlin Andreas]

To kbostroem,

No, OS X is pretty good in keeping user accounts separate and I guess this is 
not the issue. The issue with system wide preferences within your account, 
since it may affect other applications. If the only program you would be 
running is BD, then BD could do what it wants. But in case you use another 
application you as an end-user could be irritated, since you may prefer another 
pdf reader in that other app. E.g. with TeX I prefer TeXShop, in general I 
prefer Adobe Reader, and with BD I may prefer Skim as THE pdf reader. If each 
of those programs would have a preference that overrides the very same system 
wide preference, then each app would interfere with the other and you would end 
up having to set the preferences each time you use the other app. And what 
happens if you switch between those apps frequently? You set the pref anew 
after each switch? I guess not. Therefore one needs to consider all these 
aspects here. 

Moreover, if there are several system wide preferences, things can get very 
messy. There are fora full of discussions on this issue (see e.g. ThunderBird, 
FireFox download disputes since years without any progress, open source). And 
my small experimenting showed that this is AFAI understand so far the case with 
BD and pdf reading. And please, don't tell me this is only of interest to the 
programmer. On the contrary, a smooth and logical workflow is of primary 
interest to an end-user, isn't it? However, with system wide prefs you can 
easily confuse yourself and get a messy, instead of a logical workflow.

Regards,
Andreas
 

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

andreas.fisch...@env.ethz.ch
www.sysecol.ethz.ch

+41 44 633-6090 phone
+41 44 633-1136 fax
+41 79 221-4657 mobile

 Make it as simple as possible, but distrust it!




On 29/Apr/2011, at 16:17 , kbostroem wrote:

 
 
 For a user that didn't know you had set it this way, there would be.
 Expecting Preview if coming from finder, but getting Skim in BD, an
 element of chaos wd be introduced into user experience. Same if
 vice-versa. 
 
 Well, I wouldn't call it chaos but user-friendly flexibility. What program
 to launch depends on the context. System-wide: launch Preview, in BibDesk:
 launch Skim. Different context, different needs. And finally it's me, the
 user, who sets this preference. There's no other user using my account and
 my BibDesk preferences. 
 But... wait ... maybe now I see: Does the setting influence the
 BibDesk-PDF-viewer defaults of other user-accounts on the same machine? If
 this is the case, then I understand ... --
 View this message in context: 
 http://bibdesk-users.661331.n2.nabble.com/Way-to-make-Skim-default-only-in-Bibdesk-tp2201367p6317057.html
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Re: [Bibdesk-users] Way to make Skim default only in Bibdesk?

[Fischlin Andreas]

To kbostroem,

If you wish to have as an end-user a simple workflow in a logical and 
transparent manner then you should let programmers do their job properly. 
There are good reasons for thinking carefully about an implementation and 
striking the balance right. Arguing it is so simple for me therefore it 
should be as simple for anyone else is not really helping. I am saying this 
having plenty of experience on both sides, i.e. programming and end-user sides. 
Moreover open source projects are done on a mere voluntary basis, yet require 
much work on the side of the programmers. Yes BibDesk is great exactly thanks 
to the care and attention paid by the involved programmers. I am involved (here 
as a programmer) in other open source projects (e.g. AlphaX), where things 
don't go as smoothly as in BD, precisely from the perspective  of the end-use. 
One reason possibly because less discipline is bestowed on wishes than is the 
custom in the BD project. 

The consequence, where users and programmers meet, a busy frontier in open 
source projects, is, we need most of all respect and gratitude. Let me use this 
as an opportunity to thank once again to all programmers and not the least to 
Christiaan in particular for all the excellent work they have been doing (I am 
not programming on BD) and perhaps stop or at least tone down this discussion a 
notch.

Regards,
Andreas


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

andreas.fisch...@env.ethz.ch
www.sysecol.ethz.ch

+41 44 633-6090 phone
+41 44 633-1136 fax
+41 79 221-4657 mobile

 Make it as simple as possible, but distrust it!




On 29/Apr/2011, at 15:37 , kbostroem wrote:

 
 
 I suspect it's because there is a system-wide setting, and that if people
 were to change this just for BD, it would conflict with that setting.
 
 I have the system-wide default set to Preview.app and in BibDesk to
 Skim.app. It works as expected. No conflict.
 
 
 
 In contrast with TeXShop, whose PDF viewer is built in, BibDesk relies on
 an external program, and changing the preference for it in BD would take
 over a system function.
 
 Yes but who cares? That's typical for the difference between developers and
 ordinary users. Ordinary users just want the software to simplify their
 workflow in a logical and transparent manner. The software should just work.
 They absolutely do not care if internally, in the guts of the Cocoa
 framework, some comfortable and much beloved preference setting actually
 takes over a system function. Honestly: Is there (or will there ever be) any
 true problem with taking over a system function from within BibDesk
 preferences (besides, perhaps, violating some programmer's dogma)?
 
 
 
 Also I am pretty sure you can right-click on a PDF icon or image and
 choose open with as a way of opting out of the system-wide setting.
 
 Yes, of course. It's right-click/cmd-click, then go down the context menu to
 open with, wait for the extension menu to unfold, scroll down a list of
 about 20 items and then click on the item near the very bottom (in case of
 Skim, at least). That makes 4 operations instead of one simple
 double-click every time you want to view a paper! I assume nobody here among
 the proponents truly claims that it's impossible to do so. It's just very
 ... tedious. Tedious enough to explain many user's otherwise unexplainable
 desire for a default setting in the preference pane.--
 View this message in context: 
 http://bibdesk-users.661331.n2.nabble.com/Way-to-make-Skim-default-only-in-Bibdesk-tp2201367p6316928.html
 Sent from the bibdesk users mailing list archive at Nabble.com.
 
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Re: [Bibdesk-users] BibDesk 1.5.4 release

[Fischlin Andreas]

Many thanks!  Regards,
Andreas


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

andreas.fisch...@env.ethz.ch
www.sysecol.ethz.ch

+41 44 633-6090 phone
+41 44 633-1136 fax
+41 79 221-4657 mobile

 Make it as simple as possible, but distrust it!




On 14/Mar/2011, at 05:52 , Adam M. Goldstein wrote:

 The BibDesk development team is pleased to announce the release of BibDesk 
 1.5.4. Obtain by going to BibDesk  Check for Updates from with the BibDesk 
 application, or by visiting 
 
 http://sourceforge.net/projects/bibdesk/
 
 and downloading manually or by visiting
 
 http://sourceforge.net/projects/bibdesk/files/BibDesk/BibDesk-1.5.4/BibDesk-1.5.4.dmg/download
 
 which will cause an immediate download of the disk image.
 
 We thank all of our user-testers and the contributors to the BibDesk user and 
 developer mailing lists, and, of course, all of our users everywhere.
 
 New features and bug fixes:
 
 New Features
   •   Support Web Archive rich text templates
   •   Support template tags in links in rich text templates
   •   Added German localization (thanks Florian Beyerlein)
   •   Support for multiple web groups
   •   Download management in web groups
   •   Hidden preference to suppress initial web group
   •   More web group improvements
   •   Web history submenu of Bookmarks menu
 
 Bugs Fixed
   •   Allow opening author info from detail window through shortcut
   •   Improve %-escapes in URLs from fields
   •   Improvements to 'add' scripting command
   •   Fix crasher due to editor not being cleaned up properly
   •   Accept RIS with extra comments at the top
   •   Improvements to template-based preview: use accessory files and 
 background color
   •   Import article number from new import format in ISI search 
 groups
   •   Allow HTML preview templates with accessory files
   •   Fix creation of new groups from AppleScript
   •   Reset file search index when reverting
   •   Escape @ character in saved groups
   •   Fixes and improvements to template documents, in particular 
 when reading from file
   •   Use user's calendar settings to interpret smart group date 
 conditions
   •   Don't reset document when reading fails
   •   Make Revert undoable
   •   Complete support for webarchive templates
   •   Fix IEEE Xplore web parser
   •   Don't crash on corrupted bookmarks data
   •   Don't show duplicate error alert when opening a file was 
 already cancelled
   •   Default to printing all items as bibtex, add a separate print 
 command to print the selection or the preview
   •   Fix some display problems after resorting
   •   Update Springer and ACM web site parsers
   •   Fix journal parsing of COinS web parser
 
 
 --
 Adam M. Goldstein PhD, MSLIS
 --
 z_california...@shiftingbalance.org
 http://www.shiftingbalance.org
 http://www.twitter.com/shiftingbalance
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 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSNsearch_value=180621
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Re: [Bibdesk-users] Include references in .bib file

[Fischlin Andreas]

AFAIK that's far from easy and I know of no tool to help you with that. I fear 
you still need distributing lots of it manually to the various BibTeX fields.

Regards,
Andreas


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

andreas.fisch...@env.ethz.chmailto:andreas.fisch...@env.ethz.ch
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+41 44 633-6090 phone
+41 44 633-1136 fax
+41 79 221-4657 mobile

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On 12/Mar/2011, at 20:47 , Ursula Molter wrote:

hello all,

I recently received a latex paper with a large reference list. I have access to 
both: .tex file or .bbl file.

Does anyone know how to include these references into a .bib file?
thank you very much for your help.

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umol...@gmail.commailto:umol...@gmail.com
***

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Re: [Bibdesk-users] Release is back on schedule

[Fischlin Andreas]

Nothing, despite me using BD daily. Thanks for the effort.

Regards,
Andreas


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

andreas.fisch...@env.ethz.ch
www.sysecol.ethz.ch

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On 10/Mar/2011, at 00:58 , Adam M. Goldstein wrote:

 Hello all
 
 I have been swamped and have had to put off the release still further. Now 
 that school, etc., have calmed down, I would like to do this release this 
 weekend. People have not been reporting problems with the localizations or 
 anything else, but if there is anything we should be aware of before the 
 release, please do speak up.
 
 Best
 
 Adam
 
 --
 Adam M. Goldstein PhD, MSLIS
 --
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 http://www.shiftingbalance.org
 http://www.twitter.com/shiftingbalance
 --
 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSNsearch_value=180621
 --
 Associate Editor
 Reviews Editor
 Evolution: Education  Outreach
 http://www.springer.com/life+sci/journal/12052
 --
 Spellman 205
 (914) 637-2717 (msg)
 --
 Dept of Philosophy
 Iona College
 715 North Avenue
 New Rochelle NY 10801
 http://www.iona.edu/faculty/agoldstein
 
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Re: [Bibdesk-users] multiple entries to one citation key

[Fischlin Andreas]

It is difficult to understand what the goal should be. Regardless of what the 
people do, to merge the various records into a single, usable bib file means 
having to assign new cite keys to avoid duplicate cite keys. BibDesk helps you 
in this by highlighting the records, which have duplicates and helps you in 
finding/selecting the culprits. Then a manual fixing of the duplicate cite keys 
is most likely unavoidable and asking the people who have contributed the 
records to fix the problem in their data bases as well to support smooth 
collaboration in the future.

If the issue is another one, e.g. redundant records that are not identical and 
use different cite keys, again BibDesk helps you there to find those and to 
possibly weed out redundant records (Menu command Database - Select 
Duplicates).

If the issue should be multiple bib files with possible redundancies, I suggest 
to merge them all into one bib file and then resolve the issues I understood 
might be present as described above.

Perhaps I misunderstood, which means, I guess, you have to explain better what 
your problem really is.

Regards,
Andreas

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

andreas.fisch...@env.ethz.ch
www.sysecol.ethz.ch

+41 44 633-6090 phone
+41 44 633-1136 fax
+41 79 221-4657 mobile

 Make it as simple as possible, but distrust it!




On 19/Jan/2011, at 02:15 , Uli Wienands wrote:

 Dear List,
 
 I am new to Bibdesk, but not new to LaTeX  friends.
 
 In my present project (editing parts of a design report with multiple  
 authors giving me LaTeX sources of their contributions) I have the  
 following issue:
 
 We have a number of citations. Some authors have several documents  
 listed under one citation key.
 
 E.g.
 
 \bibitem[ref:key1] {A. Author, Title, Journal etc... and\\
 B.Author, Title, Journal etc..}
 
 (There are variations to this theme like lab reports bearing the  
 number of several labs [don't ask; in physics all sorts of things  
 happen..)
 
 While I can handle these in manual bibliographies (\bibliography 
 {99} ... \end{bibliography}) I am not sure how to put these in to  
 BibTeX and, by extension, BibDesk. The multiple report numbers I  
 think I can do using the Note field, but for the true multiple  
 documents I do not know a good way. I suppose the Note would work  
 here as well, with manually formatting things, but maybe someone has  
 a smarter idea?
 
 Because I am editor, not author of the contributions I cannot make  
 too drastic changes (so I can't tell my people not to do this). Also,  
 I am not getting .bib files but the bibliographies are in the  
 contribs. This is SOP in my area of work  not easily changed.
 
 While I am at it; is there a way to add fields to the BibDesk records  
 en masse i.e. by selecting multiple records? Sort-of like in iTunes  
 where I can select multiple tracks and then add the composer in one  
 operation.
 
 Thanks in advance
 
 Uli
 
 
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[Bibdesk-users] Importing some .ris files from AGU journal citation exports

[Fischlin Andreas]

Hi all,

The AGU journal REVIEWS OF GEOPHYSICS - as many other AGU journals - offers a 
Export RIS Citation service. I found that these files contain a DOI field 
encoded similar to this

DO  - 10.1029/2010RG000345

yet, when I import such a ris file into BibDesk (latest nightly Version 1.5.3 
(2069) from 29.Dec.2010) a field 'Do' is generated, not a field 'Doi'. Can 
anyone enlighten me where to tackle this problem? Should BibDesk be improved to 
make a Doi field instead of the Do field? Should AGU be asked to use a 
different encoding?

Thanks for any ideas on this issue.

Regards,
Andreas
 

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

andreas.fisch...@env.ethz.ch
www.sysecol.ethz.ch

+41 44 633-6090 phone
+41 44 633-1136 fax
+41 79 221-4657 mobile

 Make it as simple as possible, but distrust it!





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Re: [Bibdesk-users] Importing some .ris files from AGU journal citation exports

[Fischlin Andreas]

Indeed. I sent Thomson ResearchSoft a suggestion to define a tag for DOI in the 
RIS format. However, as I know that company I do not expect much response from 
them and it may well take years before they will do anything about that issue. 
They are known to have tried to delay the use of doi for years, since they 
wanted us to depend on their IS GOTO system (ISI WOS misuses its monopolistic 
position since a long time) and they prefer to do with the tags what the want 
as EndNote or Reference Manager advance (slowly of course, very slowly).

Thus I think we could add DO - DOI as a valid translation in BibDesk might 
be a useful way to go. BTW, I have already written an AppleScript fixing all 
sorts of errors exporting services are making and have just added a fix for the 
'Do' 'Doi' issue. But other users of BD might profit more if that enhancement 
would be done in BD itself.

Regards,
Andreas
 

On 30/Dec/2010, at 11:47 , Christiaan Hofman wrote:

 The problem is that DO is not a valid RIS tag 
 http://www.refman.com/support/risformat_intro.asp. In fact, RIS does not 
 define any tag for DOI, which also means that it can be basically anywhere, 
 see e.g. http://support.biblioscape.com/node/1571. I guess ID would be the 
 most appropriate valid tag, but the problem is that it would not be possible 
 to know whether it's a DOI. Ideally, the RIS format should be updated adding 
 the DO tag, but chances for that are very small. In this case, as it would 
 not otherwise seem to lead to problems with the way we set things up, we 
 could add DO - DOI as a valid translation in BibDesk. You could also use a 
 script hook to change Do to Doi.
 
 Christiaan
 
 On Dec 30, 2010, at 10:49, Fischlin Andreas wrote:
 
 Hi all,
 
 The AGU journal REVIEWS OF GEOPHYSICS - as many other AGU journals - offers 
 a Export RIS Citation service. I found that these files contain a DOI 
 field encoded similar to this
 
  DO  - 10.1029/2010RG000345
 
 yet, when I import such a ris file into BibDesk (latest nightly Version 
 1.5.3 (2069) from 29.Dec.2010) a field 'Do' is generated, not a field 'Doi'. 
 Can anyone enlighten me where to tackle this problem? Should BibDesk be 
 improved to make a Doi field instead of the Do field? Should AGU be asked to 
 use a different encoding?
 
 Thanks for any ideas on this issue.
 
 Regards,
 Andreas
 
 
 ETH Zurich
 Prof. Dr. Andreas Fischlin
 Systems Ecology - Institute of Integrative Biology
 CHN E 21.1
 Universitaetstrasse 16
 8092 Zurich
 SWITZERLAND
 
 andreas.fisch...@env.ethz.ch
 www.sysecol.ethz.ch
 
 +41 44 633-6090 phone
 +41 44 633-1136 fax
 +41 79 221-4657 mobile
 
Make it as simple as possible, but distrust it!
 
 
 
 
 
 --
 Learn how Oracle Real Application Clusters (RAC) One Node allows customers
 to consolidate database storage, standardize their database environment, 
 and, 
 should the need arise, upgrade to a full multi-node Oracle RAC database 
 without downtime or disruption
 http://p.sf.net/sfu/oracle-sfdevnl
 ___
 Bibdesk-users mailing list
 Bibdesk-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/bibdesk-users
 
 
 --
 Learn how Oracle Real Application Clusters (RAC) One Node allows customers
 to consolidate database storage, standardize their database environment, and, 
 should the need arise, upgrade to a full multi-node Oracle RAC database 
 without downtime or disruption
 http://p.sf.net/sfu/oracle-sfdevnl
 ___
 Bibdesk-users mailing list
 Bibdesk-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/bibdesk-users


--
Learn how Oracle Real Application Clusters (RAC) One Node allows customers
to consolidate database storage, standardize their database environment, and, 
should the need arise, upgrade to a full multi-node Oracle RAC database 
without downtime or disruption
http://p.sf.net/sfu/oracle-sfdevnl
___
Bibdesk-users mailing list
Bibdesk-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/bibdesk-users