Re: [Bibdesk-users] Bibdesk file paths and Google Drive

[Nathan]

The trick that Christiaan suggested is more relevant to this particular 
problem, but I thought I would mention that if one needs to convert the encoded 
bdsk-file path data to plain text (for example, if one is exporting to another 
app such as Zotero or JabRef), one can use the Python script written by Ed 
Summers, bibdesk2zotero: https://github.com/edsu/bibdesk2zotero

Nathan

> On Feb 8, 2023, at 4:55 AM, Christiaan Hofman  wrote:
> 
> No, the saved links are not in plain text, they are encoded data.
> 
> Christiaan
> 
>> On 8 Feb 2023, at 00:17, Andy Jacobson via Bibdesk-users 
>>  wrote:
>> 
>> Can't you just edit the bib file and do a wholesale edit/replace of the path?
>> 
>> Best,
>> 
>> Andy



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Re: [Bibdesk-users] Imports

[Nathan]

Martin: The way I would achieve your goal (although I may be describing the 
obvious) is:

Sort the main publication table by date-added.
Select recently added publications that I want to review.
Drag the selected publications to an empty static group.
Sort the publication table in the static group by any desired field and review 
the publications.

If it is important to me to restrict the groups table to show only data about a 
selection of publications (and not about all publications in my main database), 
then I open a separate BibDesk database with the desired groups already 
configured but empty of publications, and I drag the selected publications to 
the separate database temporarily where I can visually analyze the groups 
table. (But I do not drag publications back and forth between databases, 
because this changes the date-added field, which I want to keep intact; I treat 
the separate database as a temporary "read-only" view that is destroyed after 
use.)

Nathan

> On Sep 11, 2023, at 10:15 AM, Christiaan Hofman  wrote:
> 
>> On 11 Sep 2023, at 16:08, Martin Gillis > <mailto:mr790...@dal.ca>> wrote:
>> 
>> Hi Folks,
>> 
>> Wondering if there is a way to have the "Last Import" group maintain a list 
>> of imports for the current open session for BibDesk. The general idea is 
>> that I would like to imports article and the review them as a list. Is this 
>> possible?
>> 
>> Thanks in advance,
>> 
>> -Martin
> 
> 
> No, this only contains items for the database where it belongs to. We do not 
> maintain a database containing all items for all open documents.
> 
> Christiaan

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Re: [Bibdesk-users] App icon

[Nathan]

Themis: What do you think of the old icon of Skim 1.4? You could download the 
older version of the app, copy the icon from the old version, and paste it onto 
the latest version of Skim in your Applications folder.

Here is Apple's instructions for how to copy and paste icons (it's very easy):

https://support.apple.com/lv-lv/guide/mac-help/mchlp2313

Here is the download link for Skim 1.4 with the old icon:

https://sourceforge.net/projects/skim-app/files/Skim/Skim-1.4.41/

That would be a much easier solution than redesigning the current icon.


> On Feb 7, 2024, at 8:43 AM, Themis Matsoukas via Bibdesk-users 
>  wrote:
> 
> I don’t know if this qualifies as a request, but...
> 
> ...I use both Bibdesk and Skim and have them permanently on the dock but the 
> color of the apps is very similar and I have to think (yeah, I know…) each 
> time I need to choose one or the other. Could the art department come up with 
> a color scheme that complements the two apps so they look like siblings but 
> not like twins?
> 
> Thanks regardless,
> 
> Themis
> 
> PS To distinguish them a bit better I have them to the left and right of 
> sublime text, which I use for latexing. 



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Re: [Bibdesk-users] Underscore in DOI or Url in BibDesk

[Nathan]

> On May 23, 2024, at 5:16 AM, Christiaan Hofman  wrote:
> 
> I am not sure what to do exactly about the underscore and the dueling 
> requirements for URL and tex. I am also not completely sure about what tex 
> can handle, also combined with the \url command. One option may be to use a 
> tex conversion  for the underscore, so it its saved as {\_} in .bib, but in 
> BibDesk it turns up as _.

I don't think TeX conversion of URL and DOI fields is a good idea, although I 
haven't analyzed all the implications of such a choice. Adam R. Maxwell's 
response seemed right to me: you "need to edit the BibTeX style to 
interpret/display those fields correctly, instead of altering the underlying 
data to be incorrect".

> On May 22, 2024, at 9:02 PM, Adam R. Maxwell via Bibdesk-users 
>  wrote:
> 
> You are missing something, although I don't know if it's obvious. You (or 
> Elsevier) need to edit the BibTeX style to interpret/display those fields 
> correctly, instead of altering the underlying data to be incorrect. Take a 
> look at how abbrvnat.bst (to pick a random example) handles this. 
> Unfortunately, not all styles handle a "doi" field correctly, so you may not 
> find a one-size-fits-all solution. 
> 
> If you can't modify the style or are sending your input files to Elsevier, 
> you might look into wrapping the doi field contents in a \url command (style 
> will be tricky here), or just export a minimal BibTeX file without doi and 
> send that.
> 
> A final option if you can't modify the style would be to send the contents of 
> your .bbl file after you correctly handle doi (or just insert the \bibitem 
> commands to your document to produce camera-ready copy). IIRC some publishers 
> require this, as they won't use BibTeX.


By the way, I encountered similar URL encoding issues some years ago when 
exporting citations to HTML with a BibDesk export template. As I recall, the 
problem was that I needed to translate some characters in URLs to HTML entities 
such as "&", ">", "<". I solved that particular problem by 
post-processing the exported HTML with a simple regex shell script.

Nathan

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Re: [Bibdesk-users] Underscore in DOI or Url in BibDesk

[Nathan]

> On May 23, 2024, at 11:33 AM, quark67 via Bibdesk-users 
>  wrote:
> 
> THE SOLUTION:
> 
> It works with doi and url field filled with the _ character. [...]


I agree that it's best to store all DOIs and URLs in BibTeX files as raw data, 
i.e., without any backslash escaping. This has at least several advantages:

1. The DOI and URL icons in BibDesk can be clicked and they work.
2. URLs can be selected from BibTeX files in a text editor and opened in a web 
browser without any need to strip the backslashes from them.
3. The BibTeX file can be used with non-LaTeX workflows, notably: using Pandoc 
with CiteProc: https://en.wikipedia.org/wiki/Pandoc

If you use a LaTeX template (or style file) that seems to require using BibTeX 
files with backslash escaping in DOIs and URLs, then it's best to edit the 
template to eliminate that requirement.



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Re: [Bibdesk-users] Exporting a bibliography and removing the crossrefs

[Nathan]

> On Jun 15, 2024, at 6:39 PM, Alexander,J wrote:
> 
> Is there a way to export a bibliography with all of the cross-references 
> removed, so that each individual entry is a complete, stand-alone entry with 
> no dependencies?
> 
> I ask because I’ve been writing some JavaScript to automatically create and 
> format bibliographies in webpages using citation.js, but it seems 
> cross-references make things much more complicated — so it would be much more 
> convenient to be able to save a version with the crossrefs removed.
> 
> Best wishes,
> 
> Jason

I do this with bibtool, a command-line tool by Gerd Neugebauer. The relevant 
argument in bibtool is expand.crossref. After installing bibtool (with 
Homebrew, MacPorts, etc.), run a command of the form:

bibtool -- expand.crossref=on -i input.bib -o output.bib

There are also many other arguments/commands in bibtool. For example, there are 
commands for sorting entries, deleting fields, renaming fields, and rewriting 
fields with regular expressions. You can list many commands in a separate text 
file called a resource file and instruct bibtool to read and execute them all 
at once, with the following command form (where options.rsc, for example, is 
the name of a resource file with a list of commands):

bibtool -r options.rsc -i input.bib -o output.bib

It's a very fast and useful tool. Let me know if you have any questions about 
it; I can probably help.

Some links for bibtool:
CTAN: https://ctan.org/pkg/bibtool
GitHub: https://github.com/ge-ne/bibtool



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Re: [Bibdesk-users] Issue with page range character when retrieving entry through DOI

[Nathan]

> On Jun 18, 2024, at 7:45 AM, Bertolt Meyer wrote:
> 
> Dear fellow bibdesk users,
> 
> since a few bibdesk updates ago, I encounter the following issue when pasting 
> a doi into bibdesk in order to make it retrieve an entire entry from the 
> internet (i.e., I paste a doi into the list of refrerences view with cmd+v): 
> In the resulting entry, in the Pages field, the character between the first 
> and the last page of the given entry is rendered as „â“ (e.g., Pages 
> 87–102), breaking the preview and LaTeX/BibTex rendering unless I manually 
> correct it to - or -- every time. Any idea how I can fix this? I am on 
> bibdesk 1.9.2.

I don't know if this is a bug that requires a software fix (perhaps Christiaan 
can address that).

I will mention that I often encounter various small data quality issues similar 
to this one, depending on the data source. Whenever I encounter such a 
recurrent problematic character, I create a smart group in BibDesk to catch it. 
For example, in your case the smart group rule would be: Pages contains â. Then 
if you have "Show group counts" enabled in BibDesk's Display preferences, the 
list of smart groups in the sidebar will show you how many publications have 
the problematic character. If the count is non-zero, you can do a Database Find 
and Replace within the smart group to replace the problematic character.

Nathan

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Re: [Bibdesk-users] what is bibdesk? at a tangent

[Nathan Paxton]

	We might take a look at http://thedata.org/citation and http:// 
gking.harvard.edu/files/cite.pdf


	These try to take a look at linking to the thing itself rather than  
a location for the thing.


-N
On 9 Oct 2007, at 11:47 AM, Jason Davies wrote:


incidentally, is there an 'accepted' way to link to things like
podcasts (yet)? As more and more become legitimate sources
(prestigious speakers and stable access), is anyone thinking
about how to cite them? In the meantime, does anyone have any
sugestions (eg can we get a unique link to use in BibDesk that
will open a podcast? I know that you can be taken to a
particular podcast on the web, but what about when you have it?
just the usual local-file route to open iTunes? can we jump to a
particular moment to hear a quote?)

I realise the last is very unrealistic (currently) but this is
becoming an issue for me in my work (chiefly when i do Education  
materials).




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--
Nathan A. Paxton
Ph.D. Candidate
Dept. of Government, Harvard University

Resident Tutor
John Winthrop House, Harvard University

napaxton AT fas DOT harvard DOT edu
http://www.fas.harvard.edu/~napaxton
 
===
When you have to stay eight years away from California, you live in a  
perpetual state of homesickness.

- Ronald Reagan

The most courageous act is still to think for yourself.  Aloud.
-Coco Chanel
 
===






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[Bibdesk-users] URLs in formatted citations, deprecated fields, and such

[Nathan Paxton]

Hi all,

	I've done some searching, but I can't figure out what search terms  
would work best to narrow all of this down.


	Here's the problem. I do most of my citation work with natbib, using  
a chicago bst file. The bst is set up to include URLs of articles,  
periodicals, and so forth, where they exist, in line with Chicago's  
style on this sort of thing. So, for example, the front page article  
of today's New York Times should look like (in Chicago author-date in- 
text style):


Vlasic, Bill. 2008. U.A.W. Makes Concessions to Help Automakers. New  
York Times, 3 December 2008. http://www.nytimes.com/2008/12/04/business/04auto.html 
 (accessed 3 December 2008).


	But with the deprecation of the URL field in the most recent BibDesk  
versions, I no longer get the URL and access information. How can I  
restore the stylistically correct behavior?


Best,
-Nathan
--
Nathan A. Paxton
Ph.D. Candidate
Dept. of Government, Harvard University

Resident Tutor
John Winthrop House, Harvard University

napaxton AT fas DOT harvard DOT edu
http://www.fas.harvard.edu/~napaxton
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If every professor who backed a lunatic politician were to be sacked,  
half the interesting minds in

academia would be lost.
- The Economist, 5 Jan 2002

A morning without coffee is like something without something else.
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-
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Re: [Bibdesk-users] URLs in formatted citations, deprecated fields, and such

[Nathan Paxton]

Thanks!

I'm not an Applescript genius, so what are teh names of the scripts?

	Will these make sure than I don't run into this problem each time I  
update BD?


Best,
-Nathan
------
Nathan A. Paxton
Ph.D. Candidate
Dept. of Government, Harvard University

Resident Tutor
John Winthrop House, Harvard University

napaxton AT fas DOT harvard DOT edu
http://www.fas.harvard.edu/~napaxton
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When you have to stay eight years away from California, you live in a  
perpetual state of homesickness.

- Ronald Reagan

The most courageous act is still to think for yourself.  Aloud.
-Coco Chanel
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On 4 Dec 2008, at 11:25 AM, Christiaan Hofman wrote:

You can duplicate the linked files/URLs to fields. Best to do that  
using AppleScript. I recently posted an applescript on this list  
that duplicates the linked files and URLs to fields like Local-Url  
and Url. You can also automate the task (for newly added linked  
files and URLs) using a script hook. A sample script for this is  
linked on the Wiki.


Christiaan

On 4 Dec 2008, at 5:16 PM, Nathan Paxton wrote:


Hi all,

	I've done some searching, but I can't figure out what search terms  
would work best to narrow all of this down.


	Here's the problem. I do most of my citation work with natbib,  
using a chicago bst file. The bst is set up to include URLs of  
articles, periodicals, and so forth, where they exist, in line with  
Chicago's style on this sort of thing. So, for example, the front  
page article of today's New York Times should look like (in Chicago  
author-date in-text style):


Vlasic, Bill. 2008. U.A.W. Makes Concessions to Help Automakers.  
New York Times, 3 December 2008. http://www.nytimes.com/2008/12/04/business/04auto.html 
 (accessed 3 December 2008).


	But with the deprecation of the URL field in the most recent  
BibDesk versions, I no longer get the URL and access information.  
How can I restore the stylistically correct behavior?


Best,
-Nathan
--
Nathan A. Paxton
Ph.D. Candidate
Dept. of Government, Harvard University

Resident Tutor
John Winthrop House, Harvard University

napaxton AT fas DOT harvard DOT edu
http://www.fas.harvard.edu/~napaxton
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If every professor who backed a lunatic politician were to be  
sacked, half the interesting minds in

academia would be lost.
- The Economist, 5 Jan 2002

A morning without coffee is like something without something else.
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-
This SF.Net email is sponsored by the Moblin Your Move Developer's  
challenge
Build the coolest Linux based applications with Moblin SDK & win  
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Grand prize is a trip for two to an Open Source event anywhere in  
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Bibdesk-users mailing list
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https://lists.sourceforge.net/lists/listinfo/bibdesk-users


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Re: [Bibdesk-users] URLs in formatted citations, deprecated fields, and such

[Nathan Paxton]

	Okey-dokey, I found the file posted recently, with a script called  
LinkedFilesToFields.scpt. I added that to the scripts menu. I tried to  
run it. And the following happened.


AppleScript reported the following error:
Finder got an error: Can’t get container of file "Macintosh  
HD:Users:nathanpaxton:Library:texmf:bibtex:bib:disslibrary.bib".


As for keeping these fields, make sure you use the correct settings  
in the Default Fields preferences for automatic conversions (in  
particular don't automatically delete URL fields). Updating BD does  
not make a difference, as you're not changing anything in the BD  
bundle.

I must have allowed an automatic deletion.

	I don't know any AppleScript at all, and I am sorry for that. I only  
really want to have two things happen here:


1. I'd like there to be a URL field, so that my .bst can pick it up  
and work correctly (as it did before). How can I back convert my .bib  
file?
2. Will I be able to continue having URL/local file fields in my .bib  
file in the future?


	Perhaps we could add a small warning to the conversion process,  
indicating that allowing the original fields to be deleted will change  
the behavior of bibliographic output in one's documents? I read the  
"fields are being deprecated" language and that made me think that  
they were not necessary anymore


Thanks, Christiaan, in advance for your help.

Best,
-Nathan
--
Nathan A. Paxton
Ph.D. Candidate
Dept. of Government, Harvard University

Resident Tutor
John Winthrop House, Harvard University

napaxton AT fas DOT harvard DOT edu
http://www.fas.harvard.edu/~napaxton
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If every professor who backed a lunatic politician were to be sacked,  
half the interesting minds in

academia would be lost.
- The Economist, 5 Jan 2002

A morning without coffee is like something without something else.
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On 4 Dec 2008, at 11:56 AM, Christiaan Hofman wrote:

Well, just look in the archive of this list and on the Wiki. It  
should be pretty obvious.


As for keeping these fields, make sure you use the correct settings  
in the Default Fields preferences for automatic conversions (in  
particular don't automatically delete URL fields). Updating BD does  
not make a difference, as you're not changing anything in the BD  
bundle.


Christiaan


On 4 Dec 2008, at 5:30 PM, Nathan Paxton wrote:


Thanks!

I'm not an Applescript genius, so what are teh names of the scripts?

	Will these make sure than I don't run into this problem each time  
I update BD?


Best,
-Nathan
--
Nathan A. Paxton
Ph.D. Candidate
Dept. of Government, Harvard University

Resident Tutor
John Winthrop House, Harvard University

napaxton AT fas DOT harvard DOT edu
http://www.fas.harvard.edu/~napaxton
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When you have to stay eight years away from California, you live in  
a perpetual state of homesickness.

- Ronald Reagan

The most courageous act is still to think for yourself.  Aloud.
-Coco Chanel
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On 4 Dec 2008, at 11:25 AM, Christiaan Hofman wrote:

You can duplicate the linked files/URLs to fields. Best to do that  
using AppleScript. I recently posted an applescript on this list  
that duplicates the linked files and URLs to fields like Local-Url  
and Url. You can also automate the task (for newly added linked  
files and URLs) using a script hook. A sample script for this is  
linked on the Wiki.


Christiaan

On 4 Dec 2008, at 5:16 PM, Nathan Paxton wrote:


Hi all,

	I've done some searching, but I can't figure out what search  
terms would work best to narrow all of this down.


	Here's the problem. I do most of my citation work with natbib,  
using a chicago bst file. The bst is set up to include URLs of  
articles, periodicals, and so forth, where they exist, in line  
with Chicago's style on this sort of thing. So, for example, the  
front page article of today's New York Times should look like (in  
Chicago author-date in-text style):


Vlasic, Bill. 2008. U.A.W. Makes Concessions to Help Automakers.  
New York Times, 3 December 2008. http://www.nytimes.com/2008/12/04/business/04auto.html 
 (accessed 3 December 2008).


	But with the deprecation of the URL field in the most recent  

Re: [Bibdesk-users] URLs in formatted citations, deprecated fields, and such

[Nathan Paxton]

Following the discussion of the script in question, I changed  
"theFile" to "(theFile as file)". The new error message I get is:
"BibDesk got an error: Can’t make linked URL into type text."

Best,
-Nathan
--
Nathan A. Paxton
Ph.D. Candidate
Dept. of Government, Harvard University

Resident Tutor
John Winthrop House, Harvard University

napaxton AT fas DOT harvard DOT edu
http://www.fas.harvard.edu/~napaxton
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If every professor who backed a lunatic politician were to be sacked,  
half the interesting minds in
academia would be lost.
- The Economist, 5 Jan 2002

A morning without coffee is like something without something else.
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On 4 Dec 2008, at 12:20 PM, Nathan Paxton wrote:

>   Okey-dokey, I found the file posted recently, with a script called  
> LinkedFilesToFields.scpt. I added that to the scripts menu. I tried  
> to run it. And the following happened.
>
> AppleScript reported the following error:
> Finder got an error: Can’t get container of file "Macintosh  
> HD:Users:nathanpaxton:Library:texmf:bibtex:bib:disslibrary.bib".
>
>>> As for keeping these fields, make sure you use the correct  
>>> settings in the Default Fields preferences for automatic  
>>> conversions (in particular don't automatically delete URL fields).  
>>> Updating BD does not make a difference, as you're not changing  
>>> anything in the BD bundle.
>   I must have allowed an automatic deletion.
>
>   I don't know any AppleScript at all, and I am sorry for that. I  
> only really want to have two things happen here:
>
> 1. I'd like there to be a URL field, so that my .bst can pick it up  
> and work correctly (as it did before). How can I back convert  
> my .bib file?
> 2. Will I be able to continue having URL/local file fields in  
> my .bib file in the future?
>
>   Perhaps we could add a small warning to the conversion process,  
> indicating that allowing the original fields to be deleted will  
> change the behavior of bibliographic output in one's documents? I  
> read the "fields are being deprecated" language and that made me  
> think that they were not necessary anymore
>
>   Thanks, Christiaan, in advance for your help.
>
> Best,
> -Nathan
> --
> Nathan A. Paxton
> Ph.D. Candidate
> Dept. of Government, Harvard University
>
> Resident Tutor
> John Winthrop House, Harvard University
>
> napaxton AT fas DOT harvard DOT edu
> http://www.fas.harvard.edu/~napaxton
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> If every professor who backed a lunatic politician were to be  
> sacked, half the interesting minds in
> academia would be lost.
>   - The Economist, 5 Jan 2002
>
> A morning without coffee is like something without something else.
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> On 4 Dec 2008, at 11:56 AM, Christiaan Hofman wrote:
>
>> Well, just look in the archive of this list and on the Wiki. It  
>> should be pretty obvious.
>>
>> As for keeping these fields, make sure you use the correct settings  
>> in the Default Fields preferences for automatic conversions (in  
>> particular don't automatically delete URL fields). Updating BD does  
>> not make a difference, as you're not changing anything in the BD  
>> bundle.
>>
>> Christiaan
>>
>>
>> On 4 Dec 2008, at 5:30 PM, Nathan Paxton wrote:
>>
>>> Thanks!
>>>
>>> I'm not an Applescript genius, so what are teh names of the  
>>> scripts?
>>>
>>> Will these make sure than I don't run into this problem each time  
>>> I update BD?
>>>
>>> Best,
>>> -Nathan
>>> --
>>> Nathan A. Paxton
>>> Ph.D. Candida

Re: [Bibdesk-users] URLs in formatted citations, deprecated fields, and such

[Nathan Paxton]

On 4 Dec 2008, at 12:50 PM, Christiaan Hofman wrote:



Use the script after fixing it. The fix was described in the thread  
where you found it. Open the script in Script Editor, and replace  
"theFile" with "(theFile as alias)" inside the containerPath routine.


Done. Also made the changes suggested in the following e-mail:

Replace "(get linked URL)" with "(get linked URL i)"

Christiaan





2. Will I be able to continue having URL/local file fields in  
my .bib file in the future?




Use the script hook from the Wiki.


	I'm really sorry. I don't understand how scripts, script hooks, and  
all this works. I guess that all I want to do is be able to have  
bibliographic entries that follow the Chicago format, and  that  
requires the inclusion of URLs and access dates. (See the next comment  
also.) I don't know how to do AppleScript, and I don't have time this  
month to learn, unfortunately.




	Perhaps we could add a small warning to the conversion process,  
indicating that allowing the original fields to be deleted will  
change the behavior of bibliographic output in one's documents? I  
read the "fields are being deprecated" language and that made me  
think that they were not necessary anymore




That just depends. Be aware that these are not even standard bibtex  
fields.


*Sigh*
	So how are these being done now? (I'm using a standard .bst file,  
just modified with the urlbst macro package from CTAN.) I guess I'm  
frustrated by doing what I thought had been the "right" way, only to  
find out that I was either led astray at some point, or things have  
changed.


	What's the way that people get URLs and such into bibliographic  
references? Any help here would be appreciated; I like tex'ing, but  
sometimes these changes are confusing.


	Can anyone suggest a good working chicago-style bst, preferably for  
natbib?


Thanks.

Best,
-Nathan

-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
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Re: [Bibdesk-users] URLs in formatted citations, deprecated fields, and such

[Nathan Paxton]

	Ah, *that's* what the script hooks pref menu is for! I've never  
understood that.


	So I simply go to Script Hooks in the preferences, select Add to File  
or URL (and Did Auto File), and then select LinkedFilesToFields.scpt  
for the script file? And this will then automagically take the url/ 
location of the included files (over in the preview sidebar) and put  
it in URL/file/DOI fields that the script has just created?


	I would wager that there are other non-beginner users out there who  
don't quite understand what the script hooks preferences and all are  
about. How could the BD project go about explaining the script hooks  
preferences panel, what the hooks are, and so forth? I know there's  
basic documentation on the wiki, but I can't say that I quite  
understand what's going on based on that. I'd be happy to help, but  
since I'm only fuzzily understanding this myself, I'm not good to lead/ 
start a beefing up of the documentation.


Best,
-Nathan
--
Nathan A. Paxton
Ph.D. Candidate
Dept. of Government, Harvard University

Resident Tutor
John Winthrop House, Harvard University

napaxton AT fas DOT harvard DOT edu
http://www.fas.harvard.edu/~napaxton
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When you have to stay eight years away from California, you live in a  
perpetual state of homesickness.

- Ronald Reagan

The most courageous act is still to think for yourself.  Aloud.
-Coco Chanel
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On 4 Dec 2008, at 1:19 PM, Christiaan Hofman wrote:



On 4 Dec 2008, at 7:12 PM, Nathan Paxton wrote:



On 4 Dec 2008, at 12:50 PM, Christiaan Hofman wrote:



Use the script after fixing it. The fix was described in the  
thread where you found it. Open the script in Script Editor, and  
replace "theFile" with "(theFile as alias)" inside the  
containerPath routine.


Done. Also made the changes suggested in the following e-mail:

Replace "(get linked URL)" with "(get linked URL i)"

Christiaan





2. Will I be able to continue having URL/local file fields in  
my .bib file in the future?




Use the script hook from the Wiki.


	I'm really sorry. I don't understand how scripts, script hooks,  
and all this works. I guess that all I want to do is be able to  
have bibliographic entries that follow the Chicago format, and   
that requires the inclusion of URLs and access dates. (See the next  
comment also.) I don't know how to do AppleScript, and I don't have  
time this month to learn, unfortunately.




You don't need to learn AppleScript to do this, as the script is  
already available form the Wiki. Just add it in the Script Hook  
preferences for Add File and/or Did Auto File. It will automatically  
be invoked when the corresponding event happens.


Christiaan





	Perhaps we could add a small warning to the conversion process,  
indicating that allowing the original fields to be deleted will  
change the behavior of bibliographic output in one's documents? I  
read the "fields are being deprecated" language and that made me  
think that they were not necessary anymore




That just depends. Be aware that these are not even standard  
bibtex fields.


*Sigh*
	So how are these being done now? (I'm using a standard .bst file,  
just modified with the urlbst macro package from CTAN.) I guess I'm  
frustrated by doing what I thought had been the "right" way, only  
to find out that I was either led astray at some point, or things  
have changed.


	What's the way that people get URLs and such into bibliographic  
references? Any help here would be appreciated; I like tex'ing, but  
sometimes these changes are confusing.


	Can anyone suggest a good working chicago-style bst, preferably  
for natbib?


Thanks.

Best,
-Nathan

-
This SF.Net email is sponsored by the Moblin Your Move Developer's  
challenge
Build the coolest Linux based applications with Moblin SDK & win  
great prizes
Grand prize is a trip for two to an Open Source event anywhere in  
the world

http://moblin-contest.org/redirect.php?banner_id=100&url=/___
Bibdesk-users mailing list
Bibdesk-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/bibdesk-users


-
This SF.Net email is sponsored by the Moblin Your Move Developer's  
challenge
Build the coolest Linux based applications

Re: [Bibdesk-users] URLs in formatted citations, deprecated fields, and such

[Nathan Paxton]

Alex (et al.),

	That was exactly what I needed. I had sort of inferred that something  
like that might be the case.


	And Christiaan's clarification that the hook only gets invoked (in  
this case) upon some action helps also.


	So, I'd be happy to write some clarification of what each of the  
hooks do, after I figure that out.


	Now, I've added the LinkedFilesToFields script to the Add File or URL  
hook. My understanding is that when I drop a webpage or PDF document  
into the entry window sidebar, I should get a Url or Local-Url field  
generated, with the path to the webpage or document in it.
	Is that it? Because the Url field generation only occurs when I  
manually run the script on the entry, not automatically upon dropping  
a weblink onto the sidebar.


Thanks for all the help, all.

Best,
-Nathan
--
Nathan A. Paxton
Ph.D. Candidate
Dept. of Government, Harvard University

Resident Tutor
John Winthrop House, Harvard University

napaxton AT fas DOT harvard DOT edu
http://www.fas.harvard.edu/~napaxton
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When you have to stay eight years away from California, you live in a  
perpetual state of homesickness.

- Ronald Reagan

The most courageous act is still to think for yourself.  Aloud.
-Coco Chanel
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On 4 Dec 2008, at 7:06 PM, Alex Hamann wrote:



On 04.12.2008, at 22:12, Nathan Paxton wrote:


Ah, *that's* what the script hooks pref menu is for! I've never
understood that.

So I simply go to Script Hooks in the preferences, select Add to
File or URL (and Did Auto File), and then select
LinkedFilesToFields.scpt for the script file? And this will then
automagically take the url/location of the included files (over in
the preview sidebar) and put it in URL/file/DOI fields that the
script has just created?

I would wager that there are other non-beginner users out there
who don't quite understand what the script hooks preferences and
all are about. How could the BD project go about explaining the
script hooks preferences panel, what the hooks are, and so forth? I
know there's basic documentation on the wiki, but I can't say that
I quite understand what's going on based on that. I'd be happy to
help, but since I'm only fuzzily understanding this myself, I'm not
good to lead/start a beefing up of the documentation.

Best,
-Nathan
--
Nathan A. Paxton
Ph.D. Candidate
Dept. of Government, Harvard University

Resident Tutor
John Winthrop House, Harvard University

napaxton AT fas DOT harvard DOT edu
http://www.fas.harvard.edu/~napaxton



Hi Nathan,

I might be too basic here but maybe it helps clarify things. You
should be aware of the difference between a script and a script hook.
An applescript is a small script file that is being kept in the
respective BibDeks scrip folder and that can be invoked via the
script menu in BD's menu bar. This will run the specific script and
perform the relevant actions.
A script hook is a way of automatically invoking such a script
whenever a specific action is performed. Nevertheless, the script
will be basically the same type of file, just the way it is being
invoked is different: manually in the first case, automatically in
the latter.
Applescript is a tricky thing to get into: I myself have made several
attempts and ended them in frustration each time. Still, the best
approach seems to be to try to understand a simple script and then
try to think about ways it would work using a script hook.
Sorry, if this was all clear to you.

Alex



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Re: [Bibdesk-users] *****SPAM***** Re: URLs in formatted citations, deprecated fields, and such

[Nathan Paxton]

	Hmm. This helps. I will try it post-haste, but there does not seem to  
be an automatic generation of the linked file on my hard drive when I  
drop the PDF onto the sidebar.


Best,
-Nathan
--
Nathan A. Paxton
Ph.D. Candidate
Dept. of Government, Harvard University

Resident Tutor
John Winthrop House, Harvard University

napaxton AT fas DOT harvard DOT edu
http://www.fas.harvard.edu/~napaxton
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When you have to stay eight years away from California, you live in a  
perpetual state of homesickness.

- Ronald Reagan

The most courageous act is still to think for yourself.  Aloud.
-Coco Chanel
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On 4 Dec 2008, at 7:41 PM, Christiaan Hofman wrote:



On 5 Dec 2008, at 1:28 AM, Nathan Paxton wrote:


Alex (et al.),

	That was exactly what I needed. I had sort of inferred that  
something like that might be the case.


	And Christiaan's clarification that the hook only gets invoked (in  
this case) upon some action helps also.


	So, I'd be happy to write some clarification of what each of the  
hooks do, after I figure that out.


	Now, I've added the LinkedFilesToFields script to the Add File or  
URL hook. My understanding is that when I drop a webpage or PDF  
document into the entry window sidebar, I should get a Url or Local- 
Url field generated, with the path to the webpage or document in it.
	Is that it? Because the Url field generation only occurs when I  
manually run the script on the entry, not automatically upon  
dropping a weblink onto the sidebar.




The script hook on the Wiki only handles linked files, not linked  
URLs. It's not too hard though to modify the script to also handle  
remote URLs. Basically, you should copy the "if" block for "Local  
File", and add a "else if" block to it for "Remote URL". Something  
like this:


...
else if theField is "Remote URL" then
repeat with thePub in thePubs
tell thePub
if ((count of (get linked URLs)) > 0) then
set theURL to linked URL 1
set the value of field "Url" to theURL
end if
end tell
end repeat
end if

Also note that the script hook only copies the first linked file,  
while the script from the list copies all linked files or URLs (if  
there are more than one).


Christiaan


Thanks for all the help, all.

Best,
-Nathan
--
Nathan A. Paxton
Ph.D. Candidate
Dept. of Government, Harvard University

Resident Tutor
John Winthrop House, Harvard University

napaxton AT fas DOT harvard DOT edu
http://www.fas.harvard.edu/~napaxton
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When you have to stay eight years away from California, you live in  
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- Ronald Reagan

The most courageous act is still to think for yourself.  Aloud.
-Coco Chanel
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On 4 Dec 2008, at 7:06 PM, Alex Hamann wrote:



On 04.12.2008, at 22:12, Nathan Paxton wrote:


Ah, *that's* what the script hooks pref menu is for! I've never
understood that.

So I simply go to Script Hooks in the preferences, select Add to
File or URL (and Did Auto File), and then select
LinkedFilesToFields.scpt for the script file? And this will then
automagically take the url/location of the included files (over in
the preview sidebar) and put it in URL/file/DOI fields that the
script has just created?

I would wager that there are other non-beginner users out there
who don't quite understand what the script hooks preferences and
all are about. How could the BD project go about explaining the
script hooks preferences panel, what the hooks are, and so forth? I
know there's basic documentation on the wiki, but I can't say that
I quite understand what's going on based on that. I'd be happy to
help, but since I'm only fuzzily understanding this myself, I'm not
good to lead/start a beefing up of the documentation.

Best,
-Nathan
--
Nathan A. Paxton
Ph.D. Candidate
Dept. of Government, Harvard University

Resident Tutor
John Winthrop House, Harvard University

napaxton AT fas DOT harvard DOT edu
http://www.fas.harvard.edu/~napaxton



Hi Nathan,

I might be too basic here but maybe it helps clarify things. You
should be aware of the difference between a script an

Re: [Bibdesk-users] *****SPAM***** Re: URLs in formatted citations, deprecated fields, and such

[Nathan Paxton]

Actually, the following was in the script I got:

-- convert linked URLs
set theCount to count of (get linked URLs)
repeat with i from 1 to theCount
set theURL to (get linked URL i)
set theFieldName to "Url"
if i > 1 then set theFieldName to "Url-" 
& i
set the value of field theFieldName to 
theURL
end repeat

	When I run the script manually, it sets the remote URLs.  I'll add  
the suggestion you had for remote URLs once I can get the automatic  
action working for local files.


Best,
-Nathan
--
Nathan A. Paxton
Ph.D. Candidate
Dept. of Government, Harvard University

Resident Tutor
John Winthrop House, Harvard University

napaxton AT fas DOT harvard DOT edu
http://www.fas.harvard.edu/~napaxton
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When you have to stay eight years away from California, you live in a  
perpetual state of homesickness.

- Ronald Reagan

The most courageous act is still to think for yourself.  Aloud.
-Coco Chanel
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On 4 Dec 2008, at 7:41 PM, Christiaan Hofman wrote:



On 5 Dec 2008, at 1:28 AM, Nathan Paxton wrote:


Alex (et al.),

	That was exactly what I needed. I had sort of inferred that  
something like that might be the case.


	And Christiaan's clarification that the hook only gets invoked (in  
this case) upon some action helps also.


	So, I'd be happy to write some clarification of what each of the  
hooks do, after I figure that out.


	Now, I've added the LinkedFilesToFields script to the Add File or  
URL hook. My understanding is that when I drop a webpage or PDF  
document into the entry window sidebar, I should get a Url or Local- 
Url field generated, with the path to the webpage or document in it.
	Is that it? Because the Url field generation only occurs when I  
manually run the script on the entry, not automatically upon  
dropping a weblink onto the sidebar.




The script hook on the Wiki only handles linked files, not linked  
URLs. It's not too hard though to modify the script to also handle  
remote URLs. Basically, you should copy the "if" block for "Local  
File", and add a "else if" block to it for "Remote URL". Something  
like this:


...
else if theField is "Remote URL" then
repeat with thePub in thePubs
tell thePub
if ((count of (get linked URLs)) > 0) then
set theURL to linked URL 1
set the value of field "Url" to theURL
end if
end tell
end repeat
end if

Also note that the script hook only copies the first linked file,  
while the script from the list copies all linked files or URLs (if  
there are more than one).


Christiaan


Thanks for all the help, all.

Best,
-Nathan
--
Nathan A. Paxton
Ph.D. Candidate
Dept. of Government, Harvard University

Resident Tutor
John Winthrop House, Harvard University

napaxton AT fas DOT harvard DOT edu
http://www.fas.harvard.edu/~napaxton
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When you have to stay eight years away from California, you live in  
a perpetual state of homesickness.

- Ronald Reagan

The most courageous act is still to think for yourself.  Aloud.
-Coco Chanel
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On 4 Dec 2008, at 7:06 PM, Alex Hamann wrote:



On 04.12.2008, at 22:12, Nathan Paxton wrote:


Ah, *that's* what the script hooks pref menu is for! I've never
understood that.

So I simply go to Script Hooks in the preferences, select Add to
File or URL (and Did Auto File), and then select
LinkedFilesToFields.scpt for the script file? And this will then
automagically take the url/location of the included files (over in
the preview sidebar) and put it in URL/file/DOI fields that the
script has just created?

I would wager that there are other non-beginner users out there
who don't quite understand what the script hooks preferences and
all are about. How could the BD project go about explaining the
script hooks preferences panel, what the hooks are, and so forth? I
know there's basic documentati

Re: [Bibdesk-users] *****SPAM***** Re: *****SPAM***** Re: URLs in formatted citations, deprecated fields, and such

[Nathan Paxton]

	Sorry, I should be clearer. This is what happens when you try to work  
through a headache.


	The script hook does not generate a local-url field when I drop a  
file from my hard drive onto the sidebar. When I drop a local file  
onto the sidebar, I can see no change in the entry (as opposed to when  
I run the same script manually, when the Local-Url and Url fields are  
generated immediately).


Best,
-Nathan
--
Nathan A. Paxton
Ph.D. Candidate
Dept. of Government, Harvard University

Resident Tutor
John Winthrop House, Harvard University

napaxton AT fas DOT harvard DOT edu
http://www.fas.harvard.edu/~napaxton
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When you have to stay eight years away from California, you live in a  
perpetual state of homesickness.

- Ronald Reagan

The most courageous act is still to think for yourself.  Aloud.
-Coco Chanel
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On 4 Dec 2008, at 7:53 PM, Christiaan Hofman wrote:


Huh? It does not generate a file, it only generates a Local-Url field.

Christiaan

On 5 Dec 2008, at 1:46 AM, Nathan Paxton wrote:

	Hmm. This helps. I will try it post-haste, but there does not seem  
to be an automatic generation of the linked file on my hard drive  
when I drop the PDF onto the sidebar.


Best,
-Nathan
--
Nathan A. Paxton
Ph.D. Candidate
Dept. of Government, Harvard University

Resident Tutor
John Winthrop House, Harvard University

napaxton AT fas DOT harvard DOT edu
http://www.fas.harvard.edu/~napaxton
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When you have to stay eight years away from California, you live in  
a perpetual state of homesickness.

- Ronald Reagan

The most courageous act is still to think for yourself.  Aloud.
-Coco Chanel
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On 4 Dec 2008, at 7:41 PM, Christiaan Hofman wrote:



On 5 Dec 2008, at 1:28 AM, Nathan Paxton wrote:


Alex (et al.),

	That was exactly what I needed. I had sort of inferred that  
something like that might be the case.


	And Christiaan's clarification that the hook only gets invoked  
(in this case) upon some action helps also.


	So, I'd be happy to write some clarification of what each of the  
hooks do, after I figure that out.


	Now, I've added the LinkedFilesToFields script to the Add File  
or URL hook. My understanding is that when I drop a webpage or  
PDF document into the entry window sidebar, I should get a Url or  
Local-Url field generated, with the path to the webpage or  
document in it.
	Is that it? Because the Url field generation only occurs when I  
manually run the script on the entry, not automatically upon  
dropping a weblink onto the sidebar.




The script hook on the Wiki only handles linked files, not linked  
URLs. It's not too hard though to modify the script to also handle  
remote URLs. Basically, you should copy the "if" block for "Local  
File", and add a "else if" block to it for "Remote URL". Something  
like this:


...
else if theField is "Remote URL" then
repeat with thePub in thePubs
tell thePub
if ((count of (get linked URLs)) > 0) then
set theURL to linked URL 1
set the value of field "Url" to theURL
end if
end tell
end repeat
end if

Also note that the script hook only copies the first linked file,  
while the script from the list copies all linked files or URLs (if  
there are more than one).


Christiaan


Thanks for all the help, all.

Best,
-Nathan
--
Nathan A. Paxton
Ph.D. Candidate
Dept. of Government, Harvard University

Resident Tutor
John Winthrop House, Harvard University

napaxton AT fas DOT harvard DOT edu
http://www.fas.harvard.edu/~napaxton
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When you have to stay eight years away from California, you live  
in a perpetual state of homesickness.

- Ronald Reagan

The most courageous act is still to think for yourself.  Aloud.
-Coco Chanel
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On 4 Dec 2008, at 7:06 PM, Alex Hamann wrote:



On 04.12.2008, at 22

Re: [Bibdesk-users] Documentation

[Nathan Paxton]

	I'm totally happy to contribute to the Wiki. I'd join the list on a  
more continuing basis, but I have to admit that I'm swamped (aren't we  
all, I know) in e-mail, and the thought of one more list sends shivers  
up and down my body.


	I understand that documentation is the last thing our developers want  
to do, but to get more people to use the program at its full range of  
capacities, it's probably the most important thing one can do. There  
will always be people who join/use a feature after the discussion on  
it took place, and they'll want to know what/how to do stuff. So, with  
script hooks, for example, even the short description that Alex gave  
yesterday, combined with a fuller description of what each of the  
hooks means (for example, I don't quite get the difference between  
"will" and "did" in the auto file and cite key pairs of hooks, at  
least based on the descriptor in the preference pane) would go a  
significant way toward making them less mysterious.


I will start a page in the wiki on script hooks later today.

Best,
-Nathan
--
Nathan A. Paxton
Ph.D. Candidate
Dept. of Government, Harvard University

Resident Tutor
John Winthrop House, Harvard University

napaxton AT fas DOT harvard DOT edu
http://www.fas.harvard.edu/~napaxton
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When you have to stay eight years away from California, you live in a  
perpetual state of homesickness.

- Ronald Reagan

The most courageous act is still to think for yourself.  Aloud.
-Coco Chanel
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On 5 Dec 2008, at 7:38 AM, Alex Hamann wrote:





On 5 Dec 2008, at 7:43 AM, Dan T. Abell wrote:


[Starting this as a new thread]

On 4 Dec 2008, at 16:06, Christiaan Hofman wrote:


...
We have said many times on the list: we developers are not the
ones who should write the Help, because for us everything is
trivial. It should be written by users. So far not many users
have responded.


Ahhh ... THE, THE fundamental challenge of software development.

Write documentation. Rewrite documentation. Deal with complaints.
Re-rewrite documentation.
Read Tufte (The Work of Edward Tufte and Graphics Press).
Put new ideas to use. Raise signal-to-noise ratio on help pages.
Deal with more complaints. Re--re-rewrite documentation.
Read more Tufte.
Get some sleep.

Repeat. ('Twas ever thus!)

So ... a long-time user of BibTeX, but a novice user of BibDesk, I
have been learning BibDesk mostly by trial and error.  I find the
help pages frustrating---not because they are poorly written---but
because I feel that I'm constantly drilling down in search of an
answer, then drilling back up to the last branch point, then down
some more, still searching  On your opening help page you list
thirteen help topics, each with a brief (< nine word) description.
You also list seven appendices. When opened to display most of
that information, the help page takes up more than a third of my
screen's real estate. The information density seems painfully thin.

Then at the VERY bottom of the page, BELOW the copyright notice, is
the real meat. Driven there by sheer curiosity, I found "Contents".
WHAT is that link doing down there? I mean .. WAY down there beyond
the notice of most of us?

As another example: consider your list of help topics. To identify
the description of AutoFile, your eye must span a yawning gap made
more difficult by the tight line separation. An arrangement of the
form shown here



occupies about the same amount of real estate, but now with clear
associations between topic and description. As a bonus, you now
see that "Searching External Databases" will tell you about, ummm,
"searching external databases". Well, an added advantage of this
format is that now a fuller, more meaningful description will not
harm the association between topic and description. Indeed, a more
complete description here will save a lot of drilling. Add another
column to further increase the resolution of information at this
level. (Sarah Palin may like drilling here and now, but not I.)

My $0.02,
-Dan







On 05.12.2008, at 10:56, Christiaan Hofman wrote:
Remember that BibDesk is an open source project completely driven
by volunteers who put in lots of precious free time. And writing
the Help is really the last thing we like to do. From this
perspective, you should only be happy to have any Help pages.

Christiaan



Also, BD has become quite complex and powerful over the years. I
myself found that the best way to learn more about BD is to monitor
this list, use the nightlies and experiment a bit. I agree that 

Re: [Bibdesk-users] Documentation

[Nathan Paxton]

Sure.

	For many users, however, the point about whether a problem is a BD or  
BT problem is less relevant. They just want to know what has to be  
done to make it work. If we made it clear that a problem was  
underlying to BT or the Finder or whatever, when we know, that at  
least helps the user to know where to go off to look for more help. We  
could even wikily include a "Go ask about this (here)" list or at  
least tell a reader it can't be addressed right now. That's closer to  
pareto-efficiency than expecting everyone to know what to look up in a  
search engine, annoying developers, etc.


	Tufte would tell us that good presentation is as important as  
content. In this arena, good documentation is (nearly) as important as  
a good tool, so that one know how the awesome tool can be used most  
optimally---especially as the tool and the matter acted upon change.


Best,
-Nathan
--
Nathan A. Paxton
Ph.D. Candidate
Dept. of Government, Harvard University

Resident Tutor
John Winthrop House, Harvard University

napaxton AT fas DOT harvard DOT edu
http://www.fas.harvard.edu/~napaxton
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When you have to stay eight years away from California, you live in a  
perpetual state of homesickness.

- Ronald Reagan

The most courageous act is still to think for yourself.  Aloud.
-Coco Chanel
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On 5 Dec 2008, at 7:38 AM, Alex Hamann wrote:




Also, BD has become quite complex and powerful over the years. I
myself found that the best way to learn more about BD is to monitor
this list, use the nightlies and experiment a bit. I agree that the
Help is not perfect but every attempt to think about how to improve
it just showed me how complex a comprehensive documentation project
would be. Also, we have the Wiki that should provide some more
information. One of the problems in documenting is that many often it
is not clear to a user whether the problem he runs into are really
BibDesk or BibTeX problems. A comprehensive documentation would
really be quite an effort. But one way of approaching it would be if
people would be willing to contribute to the Wiki. As the Wiki
expands it would become an easier job to review all information there
and compile from it a BibDesk Help. That way a more experienced user
willing to do the Help would also see where new users are coming from
and what they are primarily concerned with.

A.

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Re: [Bibdesk-users] URLs in formatted citations, deprecated fields, and such

[Nathan Paxton]

	Okey-dokey. I got this working. SInce I can't post this rev'd bit of  
script to the wiki, I'll post the text here. And I'll document what it  
is supposed to do. So maybe it can be found on a search engine search.


Begin documentation

	This is the "LocalFileToLocal-UrlScriptHook" with the alteration that  
Christiaan suggested to do the same to the Bibtex entry with remote  
URLs as is done with local files; that is, it automatically generates  
a "Url" field when a website is added to the entry's sidebar (just as  
it does with local files and generating a Local-Url). To make it work,  
you must go to the Script Hook preferences, and add it for the value  
for "Add File or URL."


(*
Use this as a script hook for "Did Auto File" or "Add File or URL".
*)

-- the format of the Local-Url field
property useFileURL : false
property useRelativePath : true

using terms from application "BibDesk"
	on perform BibDesk action with publications thePubs for script hook  
theScriptHook

tell application "BibDesk"
set theField to get field name of theScriptHook as 
string
set theDoc to get document of theScriptHook
set theDocDir to my containerPath(get file of theDoc)
if theField is "Local File" then
repeat with thePub in thePubs
tell thePub
if ((count of (get linked files)) 
> 0) then
if useFileURL then
set thePath to 
URL of linked file 1
else
set thePath to 
POSIX path of (get linked file 1)
if 
useRelativePath then
set 
thePath to my relativePath(thePath, theDocDir)
end if
end if
set the value of field 
"Local-Url" to thePath
end if
end tell
end repeat
else if theField is "Remote URL" then
repeat with thePub in thePubs
tell thePub
if ((count of (get linked URLs)) 
> 0) then
set theURL to linked 
URL 1
set the value of field 
"Url" to theURL
end if
end tell
end repeat
end if
end tell
end perform BibDesk action with publications
end using terms from

on containerPath(theFile)
tell application "Finder"
set theContainer to get container of (theFile as alias)
return POSIX path of (theContainer as alias)
end tell
end containerPath

on relativePath(fullPath, basePath)
set theLength to length of basePath
	if (length of fullPath > theLength) and (text 1 thru theLength of  
fullPath) = basePath then

return text theLength thru end of fullPath
else
return fullPath
end if
end relativePath
(* end script
*)

	I really did not do much here, except take the suggestion made about  
remote URLs in an e-mail sometime yesterday and add it to the modified  
script that C. posted on the wiki. (That is, I copied the lines given  
in yesterday's e-mail [for the if statement beginning with "else if  
theField is "Remote URL"..." ] and pasted them in what seemed an  
appropriate spot. This is just an aggregation of different pieces of  
script floating on the wiki, mailing list, etc.)
	But this is a more complete/alternate version of the script, if you  
want both local and remote files to be added to the entry as fields  
for Bibtex to use in creating a bibliography.


End semi-documentation

Hope this helps someone else!

Best,
-Nathan
--
Nathan A. Paxton
Ph.D. Candidate
Dept. of Government, Harvard University

Resident Tutor
John Winthrop House, Harvard University

napaxton AT fas DOT harvard DOT edu
http://www.fas.harvard.edu/~napaxton
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[Bibdesk-users] Question about using macros

[Nathan Paxton]

Hi all,

I have a set of macros at the beginning of my database:

@string{cup = {Cambridge University Press}}
@string{pup = {Princeton University Press}}

I created these in BD using the Database -> Macros feature. I think I  
must not quite understand how the macros work, because when I enter,  
e.g., "pup" in the publisher field of a book entry, the abbreviation  
is not expanded when I run latex and bibtex. I get "pup" in the  
reference list instead of my intended Princeton University Press.


	This behavior occurs no matter which style I use (at least on  
plplain, plainnat, and my home-cooked file). What do I need to be  
doing to make the macro expand?


Best,
-Nathan
--
Nathan A. Paxton
Ph.D. Candidate
Dept. of Government, Harvard University

Resident Tutor
John Winthrop House, Harvard University

napaxton AT fas DOT harvard DOT edu
http://www.fas.harvard.edu/~napaxton
=
When you have to stay eight years away from California, you live in a  
perpetual state of homesickness.

- Ronald Reagan

The most courageous act is still to think for yourself.  Aloud.
-Coco Chanel
=

--
Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA
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Re: [Bibdesk-users] Question about using macros

[Nathan Paxton]

Sorry, Adam. I don't quite understand. Here's what is in the entry:

@book{grmek1990a,
Author = {Grmek, Mirko D.},
	Booktitle = {History of {AIDS}: emergence and origin of a modern  
pandemic},

Date-Added = {2009-02-23 10:52:19 -0500},
Date-Modified = {2009-02-23 11:14:24 -0500},
Publisher = {pup},
Title = {History of {AIDS}: emergence and origin of a modern pandemic},
Translator = {Maulitz, Russell C. and Duffin, Jacalyn},
Year = {1990}}

I just put the "pup" string in the entry window.

Best,
-Nathan
--
Nathan A. Paxton
Ph.D. Candidate
Dept. of Government, Harvard University

Resident Tutor
John Winthrop House, Harvard University

napaxton AT fas DOT harvard DOT edu
http://www.fas.harvard.edu/~napaxton

If every professor who backed a lunatic politician were to be sacked,  
half the interesting minds in academia would be lost.

- The Economist, 5 Jan 2002

A morning without coffee is like something without something else.


On 23 Feb 2009, at 11:41 AM, Maxwell, Adam R wrote:


On 02/23/09 08:30, "Nathan Paxton"  wrote:

I created these in BD using the Database -> Macros feature. I think  
I must not
quite understand how the macros work, because when I enter, e.g.,  
"pup" in the
publisher field of a book entry, the abbreviation is not expanded  
when I run
latex and bibtex. I get "pup" in the reference list instead of my  
intended

Princeton University Press.


Make sure you hit cmd-r in the editor window and delete the curly  
braces
when entering "pup."  If that's not the problem, copy a sample entry  
to the

list.


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Re: [Bibdesk-users] Question about using macros

[Nathan Paxton]

On 23 Feb 2009, at 11:58 AM, Maxwell, Adam R wrote:


On 02/23/09 08:49, "Nathan Paxton"  wrote:


Publisher = {pup},


should be "Publisher = pup" (no quotes).
	Why does BD put the braces in? I simply entered pup and Princeton  
University Press in the applicable blanks in the Macros panel.






I just put the "pup" string in the entry window.


Open the editor window for this entry, choose the Publisher field,  
and hit
cmd-r.  Delete the outer curly braces and tab out of the field.  It  
will

then show up in blue.

This should be covered in the help on macros.  Look for "raw bibtex"  
or

something.


	Sort of. There is mention of the use of raw Bibtex in the field if  
one wants to use macros, but it wasn't clear that that was necessary.  
The info sounds like there are several ways that this can be done, not  
that Cmd-R has to be invoked and then one can go about using macros...


    Thanks for the help.

--
Nathan A. Paxton
Ph.D. Candidate
Dept. of Government, Harvard University

Resident Tutor
John Winthrop House, Harvard University

napaxton AT fas DOT harvard DOT edu
http://www.fas.harvard.edu/~napaxton
=
When you have to stay eight years away from California, you live in a  
perpetual state of homesickness.

- Ronald Reagan

The most courageous act is still to think for yourself.  Aloud.
-Coco Chanel
=--
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-OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
-Strategies to boost innovation and cut costs with open source participation
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Re: [Bibdesk-users] Question about using macros

[Nathan Paxton]

This feature is support for bibtex's macros. You're basically  
supposed to be familiar with bibtex if you use this feature,  
otherwise you're not supposed to be interested in it.


Christiaan



	Sorry. I hadn't realized that Macros were one of the advanced things  
I should avoid interest in. I shall try to be less curious from here on.


Best,
-Nathan --
Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA
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[Bibdesk-users] double hyphen autoreplace in Abstract field in BibDesk v1.6.5

[nathan . artist]

I encountered a problem in BibDesk v1.6.5, and I found a solution to the 
problem that I am sharing here in case anyone else encounters this problem. 

I am using Mac OS X 10.9.5 Mavericks. After I upgraded to BibDesk v1.6.5, I 
encountered a problem that I did not have in BibDesk v1.6.4: After 
upgrading, when I typed a space and a double hyphen (" --") into the 
Abstract field of the Editor window in BibDesk, the double hyphen was 
automatically replaced by an em dash (" —"). This was a problem for me 
because I use LaTeX, and in LaTeX an em dash is represented by three 
hyphens, not two hyphens. So BibDesk would save the em dash as three 
hyphens, not two hyphens as I wanted! Therefore this autoreplace behavior 
was highly undesirable for me. 

The solution I found was to go to the Keyboard preference pane in System 
Preferences, select the Text pane, and uncheck "Use smart quotes and 
dashes". Of course, this change applies in all applications. 

It is very interesting that BibDesk v1.6.4 did not respect the system-wide 
"Use smart quotes and dashes" preference (at least in Mavericks) but BibDesk 
v1.6.5 does. The change is probably an improvement, but one needs to know 
how to turn it off if desired, as I described above.

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Re: [Bibdesk-users] double hyphen autoreplace in Abstract field in BibDesk v1.6.5

[nathan . artist]

Christiaan asked: "Are you sure this was not the case in 1.6.4, not just 
that you happened to use that on an older OS system? Because I can assure 
you that BibDesk was not changed in any way in handling dashes." 

I am 100% certain. I upgraded to BibDesk v1.6.5 a few days ago (when I 
installed MacTeX-2016) and continued using Mavericks just as I had before. 
When I recognized the hyphen problem I switched back and forth several times 
between v1.6.4 and v1.6.5 editing the same .bib file. When I was typing in 
the Abstract field of the Editor window, BibDesk v1.6.4 ignored the system 
"Use smart quotes and dashes" preference; it did not replace straight quotes 
and hyphens with curly quotes and dashes. BibDesk v1.6.5 does the 
replacement, therefore I have now unchecked "Use smart quotes and dashes" in 
System Preferences to get the behavior I was accustomed to with v1.6.4.

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Re: [Bibdesk-users] Modifying Display Title

[nathan . artist]

Br. Samuel: It appears to me, based on your question, that you are not using 
the correct BibTeX type and you may not be using the fields correctly. 



For chapters in edited books I use the BibTeX type @incollection, not 
@inbook. (In fact I have never had an occasion to use @inbook; for an 
argument against @inbook see below.) 



When I want to put multiple chapters from the same book into a BibTeX 
database, I first add the whole book as an item of BibTeX type @book. Then I 
select that item in the publication list and use the "New Publication with 
Crossref" command (keyboard shortcut: option-command-N) to create a new item 
that is a chapter in that book. Then I change the BibTeX type of the new 
item to @incollection. Then I copy the title field to the booktitle field. 
(This could be automated with AppleScript, but I just do it manually.) Then 
I put the chapter title in the title field. Then I add the page numbers in 
the pages field. The chapter number (NOT the title of the chapter) would go 
in the chapter field (although I almost never add the chapter number). 



As you can see if you are following what I am saying, an item's title ALWAYS 
goes in the title field, whether it is a chapter title, book title, thesis 
title, etc. So if you include the title field as a column in BibDesk's 
publication list, it will always show the title of any item, regardless of 
its BibTeX type. 



For an argument against @inbook, see Jukka Suomela's answer to the question 
"How to cite chapter in book?" here: https://tex.stackexchange.com/a/2568


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[Bibdesk-users] BibDesk and Microsoft Word in 2020

[nathan . artist]

This is a response to Carlos, who yesterday asked for help using BibDesk to 
insert citations and a bibliography in Microsoft Word. First, I would ask 
Carlos: Have you considered using Zotero as a reference manager? Zotero has 
a Word plugin. You can import a BibDesk file into Zotero. Second, I don't 
use Word directly (but sometimes I convert my plain-text documents to Word 
format using Pandoc), so using BibDesk to insert citations and a 
bibliography in Word is not a problem I have needed to solve, but I can see 
that there would be a variety of methods to solve it. 



1. The easiest method that I can imagine is to use Pandoc for the 
bibliography: you would write citations manually in Word; then when finished 
writing, you would generate the bibliography by feeding to Pandoc: a list of 
citekeys + your BibDesk file + a CSL (Citation Style Language) file; then 
you would copy the generated bibliography into your written document. This 
would likely be easier (once you have learned to use Pandoc) than the 
following alternative, because there are many ready-made CSL files available 
on the Web for any bibliographic style. (Zotero also uses CSL files.) 



2. Another method is to use BibDesk's templates: you would set up a 
citations template for the citation style and a bibliography template for 
the bibliography style; then set the default and alternate copying and 
dragging formats in BibDesk's citation preference pane to those templates; 
when citing you would select a publication in BibDesk, copy with the 
citation template, and paste into Word; when finished writing you would 
select all the cited publications in BibDesk, copy with the bibliography 
template, and paste into Word. This way may be harder than the previously 
mentioned method because you may have to write your own templates. 



3. A third method would be not to write in Word at all: you would write in 
plain text using Pandoc's Markdown syntax (which is very simple); cite 
publications by writing @ in front of each citekey; when finished you would 
generate the Word document by feeding to Pandoc: your plain-text file + your 
BibDesk file + a CSL (Citation Style Language) file. This is actually what I 
do (although Word is not often my destination format). 



4. David Sanson posted to GitHub some BibDesk export templates for Pandoc 
that allow a fourth method that is like a hybrid of the first and second 
methods mentioned above: 
https://github.com/dsanson/bibdesk-pandoc-export-templates 



In summary, you can use Zotero, use BibDesk's templates, or use Pandoc in 
various ways. Not to mention other possible methods.



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Re: [Bibdesk-users] Hook integration for BibDesk?

[nathan . artist]

Matthew Heun via Bibdesk-users writes: 


it says that "A document must always produce the same URL even if the document is 
moved renamed or edited."  The script below will not meet that requirement if the 
cite key changes.  Should we rather use the DOI of an entry as the primary URL, if the 
DOI is present?  (The scheme you suggested (using the cite key) could be a backup scheme 
when no DOI is present.)



Based on my experience, I would say that it's the responsibility of the user 
to maintain the cite key as a permanent identifier. In other words, the user 
shouldn't change the cite key, and it should be fine to use the cite key as 
a permanent identifier. If the user changes the cite key, they are going to 
have bigger problems than Hook not working: all the LaTeX commands that use 
that cite key won't work, any other x-bdsk://citekey URLs you've created 
won't work, etc. Just don't change the cite key and you'll be fine. You 
should set up a standard cite key format at the start and use it until you 
die. That's my experience (though I haven't died yet). 




Should the URL returned by this script also encode an identifier for the .bib 
file in which the entry is embedded?  It seems like Hook will need to know 
which .bib file to open before finding the entry within that .bib file.



Christiaan can correct me if I'm wrong, but the way x-bdsk://citekey URLs 
work does not need an identifier for the .bib file. 



Nathan 



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Re: [Bibdesk-users] Hook integration for BibDesk?

[nathan . artist]

Matthew Heun via Bibdesk-users writes: 


it says that "A document must always produce the same URL even if the document is 
moved renamed or edited."  The script below will not meet that requirement if the 
cite key changes.  Should we rather use the DOI of an entry as the primary URL, if the 
DOI is present?  (The scheme you suggested (using the cite key) could be a backup scheme 
when no DOI is present.)


Based on my experience, I would say that it's the responsibility of the user to maintain the cite key as a permanent identifier. In other words, the user shouldn't change the cite key, and it should be fine to use the cite key as a permanent identifier. If the user changes the cite key, they are going to have bigger problems than Hook not working: all the LaTeX commands that use that cite key won't work, any other x-bdsk://citekey URLs you've created won't work, etc. Just don't change the cite key and you'll be fine. You should set up a standard cite key format at the start and use it until you die. That's my experience (though I haven't died yet). 


OK.  You have convinced me ..



Matt, one more tip: it's also the user's responsibility to think about which 
cite keys are in which BibTeX databases. A couple of weeks ago someone asked 
on this list why an x-bdsk://citekey URL was not working. Christiaan 
recommended saving the BibTeX database again, and that fixed the issue. But 
if you use the same cite key in multiple BibTeX databases, the 
x-bdsk://citekey URL will point (I think) to whichever database you last 
saved in BibDesk. And if you move to a new computer, or to a new user 
account on the same computer, you will need to re-save the BibTeX 
database(s) in BibDesk for the x-bdsk://citekey URLs to work again. So that 
is something to keep in mind. BibDesk saves the relevant metadata files for 
the cite keys (at least on my system) at 
~/Library/Caches/Metadata/edu.ucsd.cs.mmccrack.bibdesk/ 



Nathan 



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Re: [Bibdesk-users] New AppleScript to fully integrate with Word

[nathan . artist]

This is an ambitious AppleScript! As I wrote in a message to this list last 
year about "BibDesk and Microsoft Word in 2020", Pandoc is also a useful 
intermediary between BibDesk and Word. Pandoc is what I use when I need 
output in Word format. One of Pandoc's advantages is that one can use a wide 
variety of existing CSL (Citation Style Language) files for different 
bibliography styles. Zotero also uses CSL files. It's not clear from 
WordScript's README file which bibliography styles it supports. Does one 
have to write a different BibDesk export template if one wants to use a 
different bibliography style? That could end up being much extra work for a 
user who needs to switch bibliography styles frequently, and Pandoc or 
Zotero may be a better option for such a user.



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Re: [Bibdesk-users] New AppleScript to fully integrate with Word

[nathan . artist]

Hi David, what you've done is impressive. I am a BibDesk user and I have 
written many AppleScripts but this is much larger than anything I've done. 
Pandoc is a command-line program, so it can be integrated into AppleScripts. 
For example, it could be integrated into WordScript so that Pandoc creates 
the bibliography using CSL instead of doing it with a BibDesk export 
template. Then you could use the huge library of ready-made CSL files. Have 
you tried using Zotero's Word plugin? It seems like it would be much easier 
just to periodically sync your BibDesk file to Zotero and use Zotero's Word 
plugin instead, though I understand the pleasure of trying to solve a 
problem with your own code. (Though maintaining an AppleScript of that size 
doesn't look like much fun to me!) 



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Re: [Bibdesk-users] BibDesk slowdowns

[nathan . artist]

I am a long-time BibDesk user with a large .bib file (30k+ entries, 140+ 
MB), and I am familiar with a couple of factors that slow down BibDesk, 
although they may not be related to Simon's situation. 

(1) First, if I search for keywords in the quick search field, and I edit 
one or more of the entries in the search results without clearing the search 
first, there is a short delay (five seconds?) after editing the entries, 
presumably because BibDesk is doing some recalculating. 

(2) Second, I have a very long list of smart groups, and whenever I open the 
large .bib file (which I don't do often because I always keep the file open 
since BibDesk is my external brain) BibDesk locks up for several minutes 
while it calculates so many smart groups for so many entries. After BibDesk 
finishes doing that, I immediately collapse the list of smart groups (which 
serve an important purpose but are rarely used) so that BibDesk does not 
recalculate them every time I edit an entry, which would be tortuously slow. 

There is another simple way of avoiding these slowdowns in practice: 
Whenever I want to edit many entries that are in a list of search results or 
in a smart group, I drag the contents of the search results or of the smart 
group to one or more temporary static groups (I keep many empty static 
groups ready for this purpose), and then I clear the search or collapse the 
list of smart groups, and then I can edit the entries in the static groups 
without any slowdown. 



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Re: [Bibdesk-users] BibDesk slowdowns

[nathan . artist]

Thanks! During all these years I had never tried unchecking "Show group 
counts". That's a helpful option. 



Christiaan Hofman writes: 

Especially for 2, you may want to collapse the smart groups whenever you close the file, so it won't be opened when you open the file. Or better, in your situation you may want to consider hiding the group counts in the Display prefs; BibDesk doesn.t bother calculating them when they are hidden, which would probably avoid the delay. 


Christiaan




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[Bibdesk-users] bibdesk topic on GitHub

[nathan . artist]

I noticed today that there is a bibdesk topic on GitHub (topics are a way of 
categorizing software repositories). See: https://github.com/topics/bibdesk 

If you have a BibDesk-related repo on GitHub, add the repo to the bibdesk 
topic by clicking on the gear icon next to "About" on the repo page, then 
type "bibdesk" into the topics box. 

I am sending this to the bibdesk-users list because there must be people on 
this list who maintain BibDesk-related repos on GitHub (for AppleScripts, 
etc.); one was mentioned on this list last month, for example. There is also 
a bibtex topic for BibTeX-related repos more generally. 


Thanks,
Nathan


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[Bibdesk-users] How you can support the BibDesk community on the web

[nathan . artist]

To everyone who has asked how to support BibDesk by, for example, "writing a 
review somewhere", and to everyone else on this list, I have a suggestion: 
If you have a blog, or if you read a tech blog that accepts guest 
submissions, write a blog post about how you use BibDesk. Whenever I search 
for BibDesk-related topics on the web, I am always surprised by how little I 
can find in the "blogosphere" about BibDesk. You can also answer questions 
about BibDesk on Q&A sites like the Stack Exchange network, but writing your 
own blog post allows you write about arbitrary BibDesk-related topics that 
may not be directly related to a specific question. Thanks! Nathan 



John Burt writes: 


Can I just add, Bravo! I too love Bibdesk, and I too find it an essential
tool for my work!
John Burt
Brandeis University 


On Fri, Feb 26, 2021 at 3:39 AM Luc Bourhis via Bibdesk-users <
bibdesk-users@lists.sourceforge.net> wrote: 

Hi, 


Jenniffer makes me realise I have never thanked Christaan for the
beautiful craft over so many years, and also Adam and Michael judging from
the .About... I just could not work without Bibdesk either. The cherry on
the cake for me is its fantastic scripting abilities. I second Jennifer for
the review: if there is anywhere I can spread the message that Bibdesk is
awesome, I.ll do it! 

Best wishes, 

Luc J Bourhis 



On 25 Feb 2021, at 01:37, Jennifer Claro via Bibdesk-users <
bibdesk-users@lists.sourceforge.net> wrote: 

I like the new logo! [image: Emoji] 


By the way, I just want to say how very important BibDesk is for my work.
Essential! I use it every day and have always found it so user-friendly
and efficient. 


Should I write a review somewhere? Vote for it somewhere? Support somehow?
I did describe BibDesk as part of my workflow at an online conference last
year,
but that's the only support I have ever given, I think. 


Thank you very much for all your hard work on BibDesk over the years.
It's awesome!!!
On Monday, May 18, 2020, 06:07:21 PM GMT+9, Christiaan Hofman <
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] Custom cite keys

[nathan . artist]

Jan David Hauck via Bibdesk-users writes: 


This is a nice change. But I'm curious, what does "unique characters based on the 
item" mean, i.e., if it's not random what information from the item does it use?
Also, it seems that %u0 still generates citekeys starting with "a" (for the 
first one that would clash), but when I change it to %u1 it generates a different letter. 
Just curious what the logic here is.



Christiaan can explain the details; I will just note that the ticket related 
to this change, with related discussion, is here: 
https://sourceforge.net/p/bibdesk/feature-requests/878/



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Re: [Bibdesk-users] AppleScript to look up EU court cases

[nathan . artist]

A couple of suggestions: 



First, when using Git and GitHub with AppleScript, it is best to save the 
script in plain-text format (which uses the file extension .applescript) 
instead of binary format (which uses the file extension .scpt). This can be 
done by choosing Text from the File Format menu of the Save panel in Script 
Editor. When the script is in text format, Git can track changes in the 
code, and users can see the content of the script on GitHub. 



Second, if this is a BibDesk-related AppleScript, you should add its 
repository to GitHub's bibdesk topic. Topics are a way of categorizing 
software repositories. Add the repository to the bibdesk topic by clicking 
on the gear icon next to "About" on the GitHub repository main page, then 
type bibdesk into the topics box. See also: 
https://github.com/topics/bibdesk 



Timothy Roes writes: 

And here's the correct link to GitHub: https://github.com/flimofly/eurlexlookup 


Best,
Timothy  

On 25 Apr 2021, at 18:56, Timothy Roes  wrote: 

Dear all, 


Are there any users who put EU court cases in BibDesk, preferably using the fields 
described in the OSCOLA Biblatex 
 
style?



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Re: [Bibdesk-users] [EXTERNAL] BibDesk 1.8.4

[Nathan Paxton]

Blergh. If that’s the case, where can I download 1.8.2, which did work, until 
I’m ready to go to OS 11?

-Nathan Paxton

Please excuse misspelling and autocorrect artifacts as this is "Sent from my 
iPhone"

> On Sep 11, 2021, at 05:04, Christiaan Hofman  wrote:
> 
> Yes, it really does seem to be a problem with older systems. That makes it 
> very hard to fix, as I cannot see it myself, and the problem is deep inside 
> Apple’s very basic code, so that sounds like a system bug.
> 
> Christiaan
> 
>> On 11 Sep 2021, at 03:14, Gilberto C  wrote:
>> 
>> I’m not having this problem. Could it be because I’m running it on MacOS Big 
>> Sur (11.5.2)?
>> —G
>> 
>> 
>>> On Sep 10, 2021, at 6:40 PM, Nathan A. Paxton  wrote:
>>> 
>>> I am having the same problem, trying to open 1.8.4. I click, and I get 
>>> ehet the rainbow beach ball of death.
>>> 
>>> I’ve attached the diagnostic report from the Console; there was no Spin 
>>> Report. If there is other info you need, I’d be happy to help.
>>> 
>>> -N
>>> 
>>> 
>>> -
>>> Nathan Paxton
>>> napax...@gmail.com
>>> 
>>> Outside of a dog, a book is man's best friend. Inside of a dog, it's too 
>>> dark to read.
>>> —Mark Twain
>>> (It's kind of cramped, too.)
>>> 
>>>> On 10 Sep 2021, at 5:58 PM, Christiaan Hofman  wrote:
>>>> 
>>>> I have uploaded a test version to 
>>>> <https://bibdesk.sourceforge.io/BibDesk.dmg>. Perhaps you can download it 
>>>> and test it out, it may do the group table layout a bit more efficiently.
>>>> 
>>>> Christiaan
>>>> 
>>>>> On 10 Sep 2021, at 22:56, Klassen, David R.  wrote:
>>>>> 
>>>>> The file I was opening had a lot of unique keywords in all the entries—I 
>>>>> assume by “groups” you mean those created by that.  I opened the .bib 
>>>>> file in vim, deleted all the keywords lines from every entry, and now it 
>>>>> opens.  It takes, literally, 2 minutes to open (53 entries) and overall 
>>>>> navigation in the system seems a bit sluggish, but I can see all the 
>>>>> entries.
>>>>> 
>>>>> While that’s open I tried to open the original version with all the 
>>>>> keywords still in it and the beachball spins and spins and the MEM and 
>>>>> CPU ramp up.
>>>>> 
>>>>> --
>>>>> Dr. David R. Klassen, Chair (he/him/his)
>>>>> Department of Physics & Astronomy
>>>>> Rowan University
>>>>> 201 Mullica Hill Road
>>>>> Glassboro, NJ  08028
>>>>> 
>>>>> SCI 130E
>>>>> 856-256-4391
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>>> On Sep 10, 2021, at 4:45 PM, Jan David Hauck via Bibdesk-users 
>>>>>>  wrote:
>>>>>> 
>>>>>> Just standard fonts, but yes, I do have quite a large number of groups.  
>>>>>> Opening an empty file works just fine, but when I open my default bib 
>>>>>> file it hangs.  
>>>>>> 
>>>>>> Attaching another sample, this time I opened BibDesk with an empty file 
>>>>>> first, and then tried the default bib file. 
>>>>>> I’ve waited a couple of minutes now, but it remains unresponsive.  
>>>>>> 
>>>>>> Also, I’m still on an old OS, Mojave, maybe that’s an issue?  
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>>> On Sep 10, 2021, at 11:13 AM, Christiaan Hofman  
>>>>>>> wrote:
>>>>>>> 
>>>>>>> Or could it be that you are using some non standard font for the group 
>>>>>>> table?
>>>>>>> 
>>>>>>> Christiaan
>>>>>>> 
>>>>>>>> On 10 Sep 2021, at 20:01, Christiaan Hofman  wrote:
>>>>>>>> 
>>>>>>>> Unfortunately not too much. It seems to take a long time to layout the 
>>>>>>>> group table.I would expect that the systems auto layout would be 
>>>>>>>> efficient, we’re not doing anything really complicated and expensive 
>>>>>>>> for this particular view. Do you have a really large number

Re: [Bibdesk-users] Is there any feature to search within keywords

[nathan . artist]

Also note that you can right-click (or control-click) on a group in the list of 
groups to see a contextual menu where you can toggle between "Show Items 
Contained in Any Group" (union) and "Show Items Contained in All Groups" 
(intersection). This is a global setting that controls which publications are 
displayed in the publications list when multiple groups are selected in the 
list of groups. This is the primary way that I exploit keywords in BibDesk: via 
selection of multiple field groups in the groups list.


After selecting multiple groups, I can do a quick search or a database find and 
replace within the selected groups. Or I can select all the publications in a 
set of groups and then select a different group instead, and only the subset of 
the previously selected publications that are in the newly selected group will 
remain selected. Or, after I have selected all the publications in a set of 
groups, I can clear the selected groups by selecting the "Library" group (so 
that all publications are displayed but the previously selected publications 
stay selected), and then I can make a new group with all the publications that 
are NOT those selected publications by choosing the menu item "Edit > Invert 
Selection" and dragging the newly selected publications to a new group for 
further operations.


All of the above permits sophisticated exploitation of keywords.


I have very often wished for a separate quick search field in the list of 
groups that could filter the list of groups in the same way that the existing 
quick search field filters the publications list. When the list of field groups 
is very long, it can be time-consuming to scroll through them looking for 
something. (This would be roughly analogous to Zotero's tags search, which 
Roberto mentioned, but even without this feature, I have always found BibDesk's 
ability to exploit field groups to be more sophisticated than Zotero.)


Nathan




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Re: [Bibdesk-users] Is there any feature to search within keywords

[nathan . artist]

I understand the desire to datestamp groups, which I've been doing since I 
started using BibDesk in 2008. I have over a thousand static groups now and 
their names all start with (manually created) datestamps, except for a few 
groups where dates are not needed. So most of my static groups are listed by 
date in the list of groups. I also have a script that I run periodically that 
extracts the static groups from my main BibTeX file and lists them in a 
separate text file so I can search that text file when needed to determine if I 
have already created a static group that mentions a word.


Figuring out when a keyword was added to a BibTeX entry would be a more 
difficult problem to solve. Most of the keywords that I add to a publication 
are added at time of creation. Any keywords that I add later are added to the 
end of the keywords field. So if I select a keyword field group and sort the 
publications in it by the date-added field, I see a rough estimate of when 
keywords were added, since most of the keywords were added when the publication 
was added to the database.


The publication editor in BibDesk features completion suggestions in the 
keywords field and other fields. I rely on the completion suggestions there to 
make sure that whatever I add conforms to my existing controlled vocabulary.


Roberto wrote:
> Thanks for these inputs. These are new ways I am learning how to use
> groups. However I think other ways are worth exploring.
> Tag search in Zotero has completion suggestions. I do not see any way
> suggestions for completion of the search string can be obtained in Bibdesk.
> Furthermore groups and keyword do not have time information, as it is not
> stored at all in the dictionary. This prevents any organization (or
> completion suggestions) based on recent usage of a keyword or addition to a
> group. This is missing  in Zotero as well afaik. I think would be rather
> useful.




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Re: [Bibdesk-users] Smart group for incomplete publications?

[nathan . artist]

I think of this issue as bibliographic quality control. I have many different 
smart groups dedicated to data quality issues, i.e., just different aspects 
that over the years I have noticed tend to be problems about the data in 
fields: missing data, incorrect data, bad characters, etc. So you could set up 
a smart group for each of the fields that you notice tend to be missing, or 
combine some of the fields into one smart group, etc. Like Christiaan said, the 
problem is that smart groups are updated frequently, so I have to keep my smart 
groups hidden all the time except when I am checking data quality. You could 
also deal with this issue by creating the smart groups, then saving and closing 
the database, then manually cutting and pasting the smart groups into a 
separate file with a text editor, and only reinsert the smart groups when you 
need to use them.




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Re: [Bibdesk-users] Smart group for incomplete publications?

[nathan . artist]

But it seems that the easiest solution for what Luc wants to do is simply to do 
Select Incomplete Publications and then drag all the selected publications into 
an empty static group and then work with them in the static group. By the way, 
I have found that "drag them all into an empty static group and then work with 
them in the static group" is a solution to many, many practical issues when 
working with publications.




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Re: [Bibdesk-users] v1.8.6: 'Searching External Databases' is limited to an arbitrary short number of results?

[nathan . artist]

Mike, I would guess from my own experience that it would be easier to do the 
kind of systematic review that you're trying to do in some other software and 
then import the results into BibDesk. You said "it gets difficult for me to 
keep track over what's done and what remains tbd". I think that's because 
BibDesk is not designed for that. Don't get me wrong, I love BibDesk, but what 
you specifically mentioned about tracking the research process is something I 
do in other software. Cheers, Nathan



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Re: [Bibdesk-users] Exporting fields with special characters

[nathan . artist]

Adding to what Christiaan said, I see several options: (1) BibDesk can export 
the full BibTeX record(s) without using an export template. (2) If you want 
only a subset of the fields in the full BibTeX record(s), you could export the 
full BibTeX record(s) and then remove the unwanted fields from the exported 
file outside of BibDesk with a tool like Gerd Neugebauer's BibTool, which is 
fairly easy to learn if you are comfortable with the Terminal. (3) You can 
change the name of the field in your BibDesk file from "author+an" to 
"author-an", since your export template will work with a hyphen instead of a 
plus. Then use a text editor or shell script to do a find-and-replace in the 
exported file to change "author-an =" to "author+an =".



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Re: [Bibdesk-users] Customizing the table header with a custom image

[nathan . artist]

If Christiaan is able and willing to implement the hidden preference that Jason 
suggested, I see no reason to object, but I would object to the claim that "an 
'Annote' or 'Abstract' field is going to have far too many characters to 
display any useful information": I have been displaying the Abstract field in 
the publications table for many years, and the presence or absence of content 
in that field (or any other field) in the publications table has been useful 
information for me. Of course, if one wants to see the whole field when there 
is a lot of content then one has to look at the preview pane using an 
appropriate template. I will note that smart groups can also be useful for 
keeping track of publications that are missing field content. Cheers, Nathan



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Re: [Bibdesk-users] Template question - conditioning on the journal name

[nathan . artist]

Responding to Jason's question about BibDesk's HTML rendering, Christiaan can 
correct me if I'm wrong, but I would guess that BibDesk's preview uses Apple's 
Cocoa text system to interpret the HTML as rich text. I don't know if Apple has 
documented anywhere exactly which tags are interpreted by the Cocoa text 
system, but it's a small subset of HTML+CSS, nothing like WebKit's 
capabilities. Cheers, Nathan



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Re: [Bibdesk-users] RTF/text preview in the TeX Preview window

[Nathan A. Paxton]

Many thanks for a quick and helpful response!

-Nathan


On 28 Jan 2014, at 5:06 PM, Maxwell, Adam R wrote:

> 
> On Jan 28, 2014, at 13:45, Christiaan Hofman  wrote:
> 
>> No, this has been removed. It depended on a third party tool that was not 
>> reliable, including causing crashes. And the main reason for its existence 
>> is not relevant anymore.
> 
> You can now copy formatted text from the PDF preview panel just by selecting 
> and copying. The RTF feature was from the days of OS X 10.2/10.3, when you 
> couldn't select text in a PDF.
> 
> Adam
> 
> 
> --
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> a virtual appliance and go from zero to informed in seconds.
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Re: [Bibdesk-users] RTF/text preview in the TeX Preview window

[Nathan A. Paxton]

So I'm having the same problem. I'm on 10.7.5, with the latest BD.

I copy from the floating preview window in BD, paste into Scrivener or 
TextEdit, and the formatting disappears. This is with a Cmd-V paste, not a 
Shift-Option-Cmd-V.

-N
-----
Nathan Paxton
napax...@gmail.com

If every professor who backed a lunatic politician were to be sacked, half the 
interesting minds in academia would be lost.
- The Economist, 5 Jan 2002

On 31 Jan 2014, at 7:07 AM, Ken Mankoff wrote:

> 
> 
> On Thu, Jan 30, 2014 at 11:02 PM, Adam R. Maxwell  wrote:
> 
> Yes, italics and other formatting are preserved (and so are hyphens in line 
> breaks, unfortunately). Does it change if you use a different font, or 
> install the Latin Modern fonts for GUI apps? I just tried pasting into 
> TextEdit on 10.9, and had no problems.
> 
> 
> I opened FontBook and searched for "Latin" and I do not have that installed. 
> The bibdesk preview template is unmodified and uses the default LaTeX font. 
> When I paste into TextEdit, making sure it is in RTF mode, I can use 
> Helvetica or Times or any other font and the bold and italics do not show up.
> 
> I will try to install Latin Modern and see if that helps.
> 
>   -k. 
> --
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> security intelligence. It gives you real-time visual feedback on key
> security issues and trends.  Skip the complicated setup - simply import
> a virtual appliance and go from zero to informed in seconds.
> http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk___
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Re: [Bibdesk-users] [EXTERNAL] BibDesk 1.8.4

[Nathan A. Paxton]

	I am having the same problem, trying to open 1.8.4. I click, and I get ehet the rainbow beach ball of death.	I’ve attached the diagnostic report from the Console; there was no Spin Report. If there is other info you need, I’d be happy to help.-N

BibDesk_2021-09-10-192932_MacintoshNAP.cpu_resource.diag
Description: Binary data

-Nathan Paxtonnapax...@gmail.comOutside of a dog, a book is man's best friend. Inside of a dog, it's too dark to read.	—Mark Twain(It's kind of cramped, too.)

On 10 Sep 2021, at 5:58 PM, Christiaan Hofman <cmhof...@gmail.com> wrote:I have uploaded a test version to <https://bibdesk.sourceforge.io/BibDesk.dmg>. Perhaps you can download it and test it out, it may do the group table layout a bit more efficiently.ChristiaanOn 10 Sep 2021, at 22:56, Klassen, David R. <klas...@rowan.edu> wrote:




The file I was opening had a lot of unique keywords in all the entries—I assume by “groups” you mean those created by that.  I opened the .bib file in vim, deleted all the keywords lines from every entry, and now it opens.  It takes, literally, 2 minutes to
 open (53 entries) and overall navigation in the system seems a bit sluggish, but I can see all the entries.



While that’s open I tried to open the original version with all the keywords still in it and the beachball spins and spins and the MEM and CPU ramp up.





--

Dr. David R. Klassen, Chair (he/him/his)

Department of Physics & Astronomy

Rowan University

201 Mullica Hill Road

Glassboro, NJ  08028




SCI 130E

856-256-4391










On Sep 10, 2021, at 4:45 PM, Jan David Hauck via Bibdesk-users <bibdesk-users@lists.sourceforge.net> wrote:

Just
 standard fonts, but yes, I do have quite a large number of groups.  

Opening an empty file works just fine, but when I open my default bib file it hangs.  




Attaching another sample, this time I opened BibDesk with an empty file first, and then tried the default bib file. 

I’ve waited a couple of minutes now, but it remains unresponsive.  




Also, I’m still on an old OS, Mojave, maybe that’s an issue?  











On Sep 10, 2021, at 11:13 AM, Christiaan Hofman <cmhof...@gmail.com> wrote:



Or could it be that you are using some non standard font for the group table?


Christiaan


On 10 Sep 2021, at 20:01, Christiaan Hofman <cmhof...@gmail.com> wrote:



Unfortunately not too much. It seems to take a long time to layout the group table.I would expect that the systems auto layout would be efficient, we’re not doing anything really complicated and expensive for this particular view. Do you have a really large
 number groups?


Christiaan


On 10 Sep 2021, at 19:47, Jan David Hauck via Bibdesk-users <bibdesk-users@lists.sourceforge.net> wrote:



Does that help any? 













On Sep 10, 2021, at 10:40 AM, Christiaan Hofman <cmhof...@gmail.com> wrote:



I really see no problem with a 1000+ file. And I have really no idea what could give a problem. I cannot say anything without seeing a sample from someone who has this problem.


Christiaan


On 10 Sep 2021, at 19:18, Klassen, David R. <klas...@rowan.edu> wrote:



Opened BibDesk; MEM = 20.4 MB, CPU = 0.0%.  


Opening refs.bib (67 kb) from ~/Desktop via File → Open… 
MEM = 1.04 GB (and rising!), CPU = 99.9%
Also has it’s in red with (Not Responding) behind the name.


If I wait a super long time, the file will open but the lag in trying to do anything is horrible.  So, basically, I can’t do any work with it.


Running macOS Catalina (10.15.7), 2.6 GHz 6-core I7 with 32 GB RAM.


[After about 1 minute, and file still not opened, MEM = 8.07 GB and rising.]






--

Dr. David R. Klassen, Chair (he/him/his)

Department of Physics & Astronomy

Rowan University

201 Mullica Hill Road

Glassboro, NJ  08028




SCI 130E

856-256-4391










On Sep 10, 2021, at 12:56 PM, Christiaan Hofman <cmhof...@gmail.com> wrote:



Strange, I am having no problem.


Perhaps you could make a Sample of BiBdesk using Activity Monitor, and send it to me off list?


Christiaan


On 10 Sep 2021, at 18:41, Jodi Schneider <jschnei...@pobox.com> wrote:


I updated. My default is an empty library (0 references) so BibDesk does open for me. However, on trying to open RIS and BibTeX files, I too get Mac's spinning beach ball. (Mac 10.14.6 if that is has an impact.)


On Fri, Sep 10, 2021 at 9:51 AM Jan David Hauck via Bibdesk-users <bibdesk-users@lists.sourceforge.net> wrote:


I’ve just updated, but now when I open BibDesk I get the spinning beach ball :(  






On Sep 10, 2021, at 4:16 AM, Christiaan Hofman <cmhof...@gmail.com> wrote:









The BibDesk development team is pleased to announce that a new version of BibDesk, version 1.8.4, 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 &quo

Re: [Bibdesk-users] [EXTERNAL] BibDesk 1.8.4

[Nathan A. Paxton]

It now opens and works mostly as expected. Preview is quite slow, but 
that could always be a different issue, so I will start a new thread about  
that (I’m using biblatex and biber to do chicago-authordate, so that requires a 
couple edits to the template.

-NAP
-
Nathan Paxton
napax...@gmail.com

Outside of a dog, a book is man's best friend. Inside of a dog, it's too dark 
to read.
—Mark Twain
(It's kind of cramped, too.)

> On 11 Sep 2021, at 1:02 PM, Christiaan Hofman  wrote:
> 
> Did anyone try the latest test version at 
> <https://bibdesk.sourceforge.io/BibDesk.dmg 
> <https://bibdesk.sourceforge.io/BibDesk.dmg>>? It could give me some idea 
> about what the problems and how to possibly fix it.
> 
> Christiaan
> 
>> On 11 Sep 2021, at 18:51, Christiaan Hofman > <mailto:cmhof...@gmail.com>> wrote:
>> 
>> It’s linked to on the web site.
>> 
>> Christiaan
>> 
>>> On 11 Sep 2021, at 18:29, Nathan Paxton >> <mailto:napax...@gmail.com>> wrote:
>>> 
>>> Blergh. If that’s the case, where can I download 1.8.2, which did work, 
>>> until I’m ready to go to OS 11?
>>> 
>>> -Nathan Paxton
>>> 
>>> Please excuse misspelling and autocorrect artifacts as this is "Sent from 
>>> my iPhone"
>>> 
>>>> On Sep 11, 2021, at 05:04, Christiaan Hofman >>> <mailto:cmhof...@gmail.com>> wrote:
>>>> 
>>>> Yes, it really does seem to be a problem with older systems. That makes 
>>>> it very hard to fix, as I cannot see it myself, and the problem is deep 
>>>> inside Apple’s very basic code, so that sounds like a system bug.
>>>> 
>>>> Christiaan
>>>> 
>>>>> On 11 Sep 2021, at 03:14, Gilberto C >>>> <mailto:ah.gilbert...@gmail.com>> wrote:
>>>>> 
>>>>> I’m not having this problem. Could it be because I’m running it on MacOS 
>>>>> Big Sur (11.5.2)?
>>>>> —G
>>>>> 
>>>>> 
>>>>>> On Sep 10, 2021, at 6:40 PM, Nathan A. Paxton >>>>> <mailto:napax...@gmail.com>> wrote:
>>>>>> 
>>>>>>  I am having the same problem, trying to open 1.8.4. I click, and I get 
>>>>>> ehet the rainbow beach ball of death.
>>>>>> 
>>>>>>  I’ve attached the diagnostic report from the Console; there was no Spin 
>>>>>> Report. If there is other info you need, I’d be happy to help.
>>>>>> 
>>>>>> -N
>>>>>> 
>>>>>> 
>>>>>> -
>>>>>> Nathan Paxton
>>>>>> napax...@gmail.com <mailto:napax...@gmail.com>
>>>>>> 
>>>>>> Outside of a dog, a book is man's best friend. Inside of a dog, it's too 
>>>>>> dark to read.
>>>>>>  —Mark Twain
>>>>>> (It's kind of cramped, too.)
>>>>>> 
>>>>>>> On 10 Sep 2021, at 5:58 PM, Christiaan Hofman >>>>>> <mailto:cmhof...@gmail.com>> wrote:
>>>>>>> 
>>>>>>> I have uploaded a test version to 
>>>>>>> <https://bibdesk.sourceforge.io/BibDesk.dmg 
>>>>>>> <https://bibdesk.sourceforge.io/BibDesk.dmg>>. Perhaps you can download 
>>>>>>> it and test it out, it may do the group table layout a bit more 
>>>>>>> efficiently.
>>>>>>> 
>>>>>>> Christiaan
>>>>>>> 
>>>>>>>> On 10 Sep 2021, at 22:56, Klassen, David R. >>>>>>> <mailto:klas...@rowan.edu>> wrote:
>>>>>>>> 
>>>>>>>> The file I was opening had a lot of unique keywords in all the 
>>>>>>>> entries—I assume by “groups” you mean those created by that.  I opened 
>>>>>>>> the .bib file in vim, deleted all the keywords lines from every entry, 
>>>>>>>> and now it opens.  It takes, literally, 2 minutes to open (53 entries) 
>>>>>>>> and overall navigation in the system seems a bit sluggish, but I can 
>>>>>>>> see all the entries.
>>>>>>>> 
>>>>>>>> While that’s open I tried to open the original version with all the 
>>>>>>>> keywords still in it and the beachball sp

[Bibdesk-users] BibDesk update incorrectly signed?

[Nathan A. Paxton]

All,

Went to try to update, via the (what I assume is) Sparkle mechanism 
(App menu -> Check for Updates…). Received the following message: "The update 
is improperly signed and could not be validated. Please try again later or 
contact the app developer.”

Any troubleshooting suggestions?

-NAP

-
Nathan Paxton
napax...@gmail.com

Outside of a dog, a book is man's best friend. Inside of a dog, it's too dark 
to read.
—Mark Twain
(It's kind of cramped, too.)

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