Re: [Bibdesk-users] Escaped characters in filename using autofile

[Peter Cowan]

On Wed, Apr 14, 2010 at 3:09 PM, Christiaan Hofman  wrote:
>
> On Apr 14, 2010, at 23:40, Peter Cowan wrote:
>
>> On Tue, Apr 13, 2010 at 2:22 AM, Christiaan Hofman  
>> wrote:
>>>
>>> On Apr 13, 2010, at 11:06, Christiaan Hofman wrote:
>>>
>>>>
>>>> On Apr 13, 2010, at 2:45, Peter Cowan wrote:
>>>>
>>>>> All,
>>>>>
>>>>> Two of my favorite issues in BibDesk are the autofile feature and the
>>>>> "Send via Email" features.  Recently I ran into an issue where when
>>>>> certain citations were selected the "Send via Email" silently failed.
>>>>> This turned out to be because the associated pdf filename was
>>>>>
>>>>> "Sax D & Gaines S 2003 Trends In Ecology \& Evolution.pdf"
>>>>>
>>>>> Getting rid of the slash before "&" fixed the issue.
>>>>>
>>>>> My autofile format string is: %A[ & ][ ]3 %Y%u0 %f{Journal}30%e
>>>>>
>>>>> and I have selected "Clean by removing Tex".  This produces the above
>>>>> file for the citation:
>>>>>
>>>>> Sax DF, Gaines SD (2003) Species diversity: from global decreases to
>>>>> local increases. Trends In Ecology & Evolution 18, 561–566.
>>>>>
>>>>> To summarize, some of my journal names have "&" in them which is
>>>>> escaped as "\&", which is subsequently in the filename when using
>>>>> autofile.  These files then cause "Send via Email" to fail.
>>>>>
>>>>> What am I doing wrong? Is there a work around?
>>>>>
>>>>> Thanks
>>>>>
>>>>> Peter
>>>>>
>>>>
>>>> Unfortunately, I think you're doing nothing wrong and there's no 
>>>> workaround.
>>>>
>>>> Christiaan
>>>
>>> I've fixed this for tomorrow's nightly, please test it out.
>>
>> Christiaan,
>>
>> Thanks for such a quick response.  I tried the nightly marked
>> "BibDesk-20100413.dmg" (is there a way to tell which SVN revision that
>> is?).  And, I also checked out the source and attempted to build it
>> myself (which seemed successful with the debug type selected).
>>
>> Unfortunately, both versions also fail silently, with the file: "Sax D
>> & Gaines S 2003 Trends In Ecology \& Evolution.pdf".   I get the
>> following message in the console:
>>
>> 4/14/10 2:34:25 PM    BibDesk[11223]  Error compiling mail to script: {
>>    NSAppleScriptErrorBriefMessage = "Expected \U201c\"\U201d but
>> found unknown token.";
>>    NSAppleScriptErrorMessage = "Expected \U201c\"\U201d but found
>> unknown token.";
>>    NSAppleScriptErrorNumber = "-2741";
>>    NSAppleScriptErrorRange = "NSRange: {463, 1}";
>> }
>>
>> Did the nightly I grabbed not have the relevant update?   I appreciate
>> you attention, to this minor issue!
>>
>> Peter
>>
>>
>>>
>>> Christiaan
>
> It seems I escaped one type of ampersand but not the other. Please try 
> tomorrow's nightly (dated for today).

I'm still getting the same error as above.   I tried to look at the
code and see if I could fix it myself (it is open source after all),
but my objective C is too weak.

I do notice that the changes you made over the last couple of days
escape the body of the email message.  To my untrained eyes it seems
that the problem is with the file name.  For example, my autofile
format yields the following filename.

Sax D & Gaines S 2003 Trends In Ecology \& Evolution.pdf

This give the above error in the console and mail doesn't open.  If I
go and manually change the name of the linked file to

Sax D & Gaines S 2003 Trends In Ecology Evolution.pdf

Send via Email works perfectly.  I tried to look at how the array of
files is constructed, but it was beyond me.

Sorry to take up your time with this minor issue.  I do appreciate
your efforts to help.

Peter

> Christiaan
>
>
> --
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Re: [Bibdesk-users] Escaped characters in filename using autofile

[Peter Cowan]

On Tue, Apr 13, 2010 at 2:22 AM, Christiaan Hofman  wrote:
>
> On Apr 13, 2010, at 11:06, Christiaan Hofman wrote:
>
>>
>> On Apr 13, 2010, at 2:45, Peter Cowan wrote:
>>
>>> All,
>>>
>>> Two of my favorite issues in BibDesk are the autofile feature and the
>>> "Send via Email" features.  Recently I ran into an issue where when
>>> certain citations were selected the "Send via Email" silently failed.
>>> This turned out to be because the associated pdf filename was
>>>
>>> "Sax D & Gaines S 2003 Trends In Ecology \& Evolution.pdf"
>>>
>>> Getting rid of the slash before "&" fixed the issue.
>>>
>>> My autofile format string is: %A[ & ][ ]3 %Y%u0 %f{Journal}30%e
>>>
>>> and I have selected "Clean by removing Tex".  This produces the above
>>> file for the citation:
>>>
>>> Sax DF, Gaines SD (2003) Species diversity: from global decreases to
>>> local increases. Trends In Ecology & Evolution 18, 561–566.
>>>
>>> To summarize, some of my journal names have "&" in them which is
>>> escaped as "\&", which is subsequently in the filename when using
>>> autofile.  These files then cause "Send via Email" to fail.
>>>
>>> What am I doing wrong? Is there a work around?
>>>
>>> Thanks
>>>
>>> Peter
>>>
>>
>> Unfortunately, I think you're doing nothing wrong and there's no workaround.
>>
>> Christiaan
>
> I've fixed this for tomorrow's nightly, please test it out.

Christiaan,

Thanks for such a quick response.  I tried the nightly marked
"BibDesk-20100413.dmg" (is there a way to tell which SVN revision that
is?).  And, I also checked out the source and attempted to build it
myself (which seemed successful with the debug type selected).

Unfortunately, both versions also fail silently, with the file: "Sax D
& Gaines S 2003 Trends In Ecology \& Evolution.pdf".   I get the
following message in the console:

4/14/10 2:34:25 PM  BibDesk[11223]  Error compiling mail to script: {
NSAppleScriptErrorBriefMessage = "Expected \U201c\"\U201d but
found unknown token.";
NSAppleScriptErrorMessage = "Expected \U201c\"\U201d but found
unknown token.";
NSAppleScriptErrorNumber = "-2741";
NSAppleScriptErrorRange = "NSRange: {463, 1}";
}

Did the nightly I grabbed not have the relevant update?   I appreciate
you attention, to this minor issue!

Peter


>
> Christiaan
>
>
>
> --
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
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>

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[Bibdesk-users] Escaped characters in filename using autofile

[Peter Cowan]

All,

Two of my favorite issues in BibDesk are the autofile feature and the
"Send via Email" features.  Recently I ran into an issue where when
certain citations were selected the "Send via Email" silently failed.
This turned out to be because the associated pdf filename was

"Sax D & Gaines S 2003 Trends In Ecology \& Evolution.pdf"

Getting rid of the slash before "&" fixed the issue.

My autofile format string is: %A[ & ][ ]3 %Y%u0 %f{Journal}30%e

and I have selected "Clean by removing Tex".  This produces the above
file for the citation:

Sax DF, Gaines SD (2003) Species diversity: from global decreases to
local increases. Trends In Ecology & Evolution 18, 561–566.

To summarize, some of my journal names have "&" in them which is
escaped as "\&", which is subsequently in the filename when using
autofile.  These files then cause "Send via Email" to fail.

What am I doing wrong? Is there a work around?

Thanks

Peter

--
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Re: [Bibdesk-users] Script hook to protect Address field

[Peter Cowan]

On Sat, Apr 3, 2010 at 10:29 AM, Christiaan Hofman  wrote:
>
> On Apr 3, 2010, at 18:01, Adam R. Maxwell wrote:
>
>>
>> On Apr 3, 2010, at 3:26 AM, Fischlin Andreas wrote:
>>
>>> You write: "However, this citation causes an error using my tex preview 
>>> template (below, require biblatex). The relevant part of the log is:
>>>
>>> Too many commas in name 1 of "PORTERS SOUTH, 4 CRINAN ST, LONDON N1 9XW, 
>>> ENGLAND" for entry cite-key"
>>>
>>> This indicates that there is an error in your tex preview template.
>>
>> You apparently missed the part where he said he's using biblatex.  Standard 
>> BibTeX has no problems with this, as you say.  A quick read of the biblatex 
>> manual [1] indicates that it expects "address" to be a list separated by 
>> "and."  It almost sounds like biblatex is using BibTeX name parsing rules to 
>> split a list of addresses, which seems…odd.
>>
>> [1] 
>> http://www.ctan.org/tex-archive/macros/latex/exptl/biblatex/doc/biblatex.pdf
>>

Christian,

I also read that in the biblatex manual.  It appears there are two
types of lists, one specifically for names and the other a general
list type.  Perhaps the wrong type of list is used for address.  In
any case, I need to take this up with the biblatex folks.   Oddly
enough it does work in a .tex file if it's complied using latexmk.pl.

> That's what I called a bug in biblatex earlier. IMHO.

Agreed, as soon as I can confirm that no one else has filed the issue, I will.

Thanks

Peter

> Christiaan
>
>
> --
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>

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Re: [Bibdesk-users] Script hook to protect Address field

[Peter Cowan]

On Sat, Apr 3, 2010 at 3:26 AM, Fischlin  Andreas
 wrote:
> Dear Peter,
>
> Sorry, it is very difficult to understand what your actual problem is. First 
> I see no problem whatsoever in BD, nor in the bib file generated, nor in the 
> preview and most of all I do not understand why you try to do something with 
> AppleScripts. I base this conclusion on trying to repeat your problem using 
> your example. I can't.

I didn't mean to suggest that there was a problem with BD, more it was
a question about how I could further harness it's power to work around
another issue I was having.

> 2) I clicked on BD's Import button and the record was correctly imported into 
> BD, no errors encountered, and all is as it should.  I see no problem there.
>
> 3) The Address field contains the string "PORTERS SOUTH, 4 CRINAN ST, LONDON 
> N1 9XW, ENGLAND" correctly as it should be, though I don't like the 
> capitalization and you could edit that. But I guess that is beside the point.
>
> 4) If I do (still in BD) menu command "Window -> TeX Preview" I encounter no 
> errors and the opened preview window shows the record fine. Even the 
> capitalization problem is gone.

Did you try with the TeX preview Template I included in my previous email?

> So where is a problem?
>
> a) Do you want an AppleScript to edit any of the fields in that record? If 
> yes, why? What should be the purpose?
>
> b) Curly braces do not protect anything. We are not talking about shell 
> scripts, we have BibTeX encoded data stored on bib-files that are managed by 
> BD. Curly braces merely delimit the begin and end of fields in the records 
> and enclose the entire record. They serve any scanner to delimit information 
> and correctly interpret begin and end of records and fields. Moreover curly 
> braces may be used within fields to encode special characters, abbreviations, 
> macros etc. Ex.: Author = {Kurt G{\"o}del}, Title = {The \TeX{}book}, . The 
> field author is very special, since it is treated into several subfields 
> automatically and uses for convenience reasons commas and optionally curly 
> braces to delimit its subfields. That may be the source for your 
> misinterpretation that you protect something with curly braces. See e.g. 
> Kopka & Daly, 2004, p. 235 for more on this.
>
> You write: "However, this citation causes an error using my tex preview 
> template (below, require biblatex). The relevant part of the log is:
>
> Too many commas in name 1 of "PORTERS SOUTH, 4 CRINAN ST, LONDON N1 9XW, 
> ENGLAND" for entry cite-key"
>
> This indicates that there is an error in your tex preview template. It seems 
> you entered the content of the address field into the author field or made 
> some other error causing such an interpretation by the BibTeX interpretation. 
>  This has all absolutely nothing to do with curly braces nor AppleScripts 
> AFAIK. If my interpretation is correct, fix first your preview template so 
> that no longer any address information is interpreted as an author field.
>
> c) Have you indeed changed any templates? If yes, reverse that and your 
> problems might be gone. Writing a TeX paper using BibTeX will only need the 
> correctly stored bib file and should be independent from any preview 
> template. There seems to be nothing wrong in your case with all the software 
> components involved there, except for those you may have tampered with. You 
> may have altered preview templates or otherwise deviated from a default BD 
> installation or you have wrongly changed BibTeX styles you use in your TeX 
> setup.

Yes, as attached above, I did modify my TeX template, but I would
prefer to stick with the templates provided by biblatex which more
closely resemble the ones I use on a daily basis.

> d) Why writing a bug report? AFAI can see there is no bug anywhere in BD nor 
> its default templates as used by Preview, nor is there any real biblatex 
> problem involved. It seems you would have to write the bug report to 
> yourself. ;-)

I apologize that I wasn't clear, I'm not suggesting a bug in BD, but
there may be one in biblatex (which I use in my own TeX preview
template).

Thanks

Peter

> Hope this clarifies some of the issues.
>
> Regards,
> Andreas
>
> Cited References:
> 
> Kopka, H. & Daly, P. W., 2004 (ed. 4). Guide to LaTeX. Addison-Wesley: 
> Boston, US. 597pp.     Ko089
>
>
>
> ETH Zurich
> Prof. Dr. Andreas Fischlin
> Systems Ecology - Institute of Integrative Biology
> CHN E 21.1
> Universitaetstrasse 16
> 8092 Zurich
> SWITZERLAND
>
> andreas.fisch...@env.ethz.ch
> www.sysecol.ethz.ch
>
> +41 44 633-6090 phone
> +41 44 633-1136 fax

Re: [Bibdesk-users] Script hook to protect Address field

[Peter Cowan]

On Fri, Apr 2, 2010 at 2:13 PM, Christiaan Hofman  wrote:
>
> On Apr 2, 2010, at 21:54, Peter Cowan wrote:
>
>> On Fri, Apr 2, 2010 at 9:53 AM, Christiaan Hofman  wrote:
>>>
>>> On Apr 1, 2010, at 23:29, Peter Cowan wrote:
>>>
>>>> On Thu, Apr 1, 2010 at 2:03 PM, Christiaan Hofman  
>>>> wrote:
>>>>>
>>>>> On Apr 1, 2010, at 22:15, Peter Cowan wrote:
>>>>>
>>>>>> I'm using biblatex in the TeX preview window.  And, since I often
>>>>>> import directly from ISI using the Web of Science Search function, I
>>>>>> get regular errors related to commas in the address or institution
>>>>>> field.  Perhaps there is a solution through biblatex to this problem,
>>>>>> but I'm fine with either protecting or deleting the
>>>>>> Address/Institution field on import.
>>>>>>
>>>>>> Script hooks seem like the perfect solution to this problem, but I am
>>>>>> not an applescript users.  I've tried to cobble something together
>>>>>> based on the available example and got the following which doesn't
>>>>>> appear to work, on import (from Web of Science) nothing happens no
>>>>>> errors no braces.  Any nudges in the right direction are appreciated.
>>>>>>
>>>>>> I apologize if this has been discussed on the list before, my searches
>>>>>> did not reveal anything aside from confirmation of the biblatex TeX
>>>>>> preview issue.
>>>>>>
>>>>>> Cheers
>>>>>>
>>>>>> Peter
>>>>>>
>>>> [snip old code]
>>>>>
>>>>> This won't work, because you call the external scripts outside the 
>>>>> "perform BibDesk action..." handler. The script hook will only call that 
>>>>> handler, so anything outside it (like defining the protectLib and 
>>>>> errorLib) will be ignored. Therefore reference to those external scripts 
>>>>> will fail. You'll have to move everything to inside the script hook 
>>>>> handler.
>>>>
>>>> Christiaan,
>>>>
>>>> Thanks for the reply, I've moved the load script calls inside of the
>>>> handler, but alas it still doesn't work.  The current version is
>>>> below.
>>>>
>>>> I apologize for being such an applescript newb, but is there a
>>>> workflow you follow for developing this applescripts, e.g. debugging
>>>> hints, setting "breakpoints" etc.
>>>>
>>>> Cheers
>>>>
>>>> Peter
>>>
>>>
>>> [snip]
>>>
>>> BTW, another possibility is that this actually works, but you expect it to 
>>> do something different from what it actually does. What this most certainly 
>>> does NOT do is to enclose the Address value in braces, and the check you 
>>> added make me think that that's what you (wrongly) expect it to do. So 
>>> perhaps you should also say what you expect it to do, and what you did 
>>> exactly to make it do that, perhaps with explicit samples.
>>
>> Christian and Fischlin,
>>
>> Thanks for your replies.   Indeed I'm trying to wrap the Address Field
>> in curly braces so that biblatex won't puke on those bib items.  I
>> thought that wrapping something in braces was called protecting, but
>> perhaps I am wrong.
>>
>> You are correct the above script most definitely did not do what I was
>> hoping for.
>>
>> An explicit example:
>>
>> I usually use the Web of Science SCI search to import references.  If
>> I search for au=(watson AND crick) the first hit is
>>
>> CRICK, FHC and WATSON, JD. 1956. STRUCTURE OF SMALL VIRUSES. Nature.
>> 177(4506):473-475.
>>
>> However, this citation causes an error using my tex preview template
>> (below, require biblatex).  The relevant part of the log is:
>>
>> Too many commas in name 1 of "PORTERS SOUTH, 4 CRINAN ST, LONDON N1
>> 9XW, ENGLAND" for entry cite-key
>>
>> If I change the address field to
>>
>> {PORTERS SOUTH, 4 CRINAN ST, LONDON N1 9XW, ENGLAND}
>>
>> it is compiled and previewed correctly.
>>
>
> That sounds like a totally different problem. The warning says it's 
> interpreting this as a name. So either you've put the address in an author 

Re: [Bibdesk-users] Script hook to protect Address field

[Peter Cowan]

On Fri, Apr 2, 2010 at 9:53 AM, Christiaan Hofman  wrote:
>
> On Apr 1, 2010, at 23:29, Peter Cowan wrote:
>
>> On Thu, Apr 1, 2010 at 2:03 PM, Christiaan Hofman  wrote:
>>>
>>> On Apr 1, 2010, at 22:15, Peter Cowan wrote:
>>>
>>>> I'm using biblatex in the TeX preview window.  And, since I often
>>>> import directly from ISI using the Web of Science Search function, I
>>>> get regular errors related to commas in the address or institution
>>>> field.  Perhaps there is a solution through biblatex to this problem,
>>>> but I'm fine with either protecting or deleting the
>>>> Address/Institution field on import.
>>>>
>>>> Script hooks seem like the perfect solution to this problem, but I am
>>>> not an applescript users.  I've tried to cobble something together
>>>> based on the available example and got the following which doesn't
>>>> appear to work, on import (from Web of Science) nothing happens no
>>>> errors no braces.  Any nudges in the right direction are appreciated.
>>>>
>>>> I apologize if this has been discussed on the list before, my searches
>>>> did not reveal anything aside from confirmation of the biblatex TeX
>>>> preview issue.
>>>>
>>>> Cheers
>>>>
>>>> Peter
>>>>
>> [snip old code]
>>>
>>> This won't work, because you call the external scripts outside the "perform 
>>> BibDesk action..." handler. The script hook will only call that handler, so 
>>> anything outside it (like defining the protectLib and errorLib) will be 
>>> ignored. Therefore reference to those external scripts will fail. You'll 
>>> have to move everything to inside the script hook handler.
>>
>> Christiaan,
>>
>> Thanks for the reply, I've moved the load script calls inside of the
>> handler, but alas it still doesn't work.  The current version is
>> below.
>>
>> I apologize for being such an applescript newb, but is there a
>> workflow you follow for developing this applescripts, e.g. debugging
>> hints, setting "breakpoints" etc.
>>
>> Cheers
>>
>> Peter
>
>
> [snip]
>
> BTW, another possibility is that this actually works, but you expect it to do 
> something different from what it actually does. What this most certainly does 
> NOT do is to enclose the Address value in braces, and the check you added 
> make me think that that's what you (wrongly) expect it to do. So perhaps you 
> should also say what you expect it to do, and what you did exactly to make it 
> do that, perhaps with explicit samples.

Christian and Fischlin,

Thanks for your replies.   Indeed I'm trying to wrap the Address Field
in curly braces so that biblatex won't puke on those bib items.  I
thought that wrapping something in braces was called protecting, but
perhaps I am wrong.

You are correct the above script most definitely did not do what I was
hoping for.

An explicit example:

I usually use the Web of Science SCI search to import references.  If
I search for au=(watson AND crick) the first hit is

CRICK, FHC and WATSON, JD. 1956. STRUCTURE OF SMALL VIRUSES. Nature.
177(4506):473-475.

However, this citation causes an error using my tex preview template
(below, require biblatex).  The relevant part of the log is:

Too many commas in name 1 of "PORTERS SOUTH, 4 CRINAN ST, LONDON N1
9XW, ENGLAND" for entry cite-key

If I change the address field to

{PORTERS SOUTH, 4 CRINAN ST, LONDON N1 9XW, ENGLAND}

it is compiled and previewed correctly.

The applescript I sent before was an effort to do that wrapping on
import.  I however was unable to get the protectLib to work at all so
I ended up with this *working* script hook.  A couple of caveats, the
errorLib has never produced anything to me, it seem unlikely given my
applescript skills, that I produced no errors.  And, secondly this
method won't, of course, catch cases where the field is already in
braces, so some Address fields could end up double wrapped.
Suggestions for improvements are welcome.

property theFieldToSet : "Address"

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

set errorLib to (load script file ¬
  ((path to home folder as string) &
"Library:ScriptingAdditions:Error Reporting.scpt"))
-- we only report all errors at the end

tell errorLib
  delayReportErrors()
  set its defaultErrorFileName to "BibDeskScriptErrors"
end tell

repeat with thePub in thePubs
  

Re: [Bibdesk-users] Script hook to protect Address field

[Peter Cowan]

On Thu, Apr 1, 2010 at 2:03 PM, Christiaan Hofman  wrote:
>
> On Apr 1, 2010, at 22:15, Peter Cowan wrote:
>
>> I'm using biblatex in the TeX preview window.  And, since I often
>> import directly from ISI using the Web of Science Search function, I
>> get regular errors related to commas in the address or institution
>> field.  Perhaps there is a solution through biblatex to this problem,
>> but I'm fine with either protecting or deleting the
>> Address/Institution field on import.
>>
>> Script hooks seem like the perfect solution to this problem, but I am
>> not an applescript users.  I've tried to cobble something together
>> based on the available example and got the following which doesn't
>> appear to work, on import (from Web of Science) nothing happens no
>> errors no braces.  Any nudges in the right direction are appreciated.
>>
>> I apologize if this has been discussed on the list before, my searches
>> did not reveal anything aside from confirmation of the biblatex TeX
>> preview issue.
>>
>> Cheers
>>
>> Peter
>>
[snip old code]
>
> This won't work, because you call the external scripts outside the "perform 
> BibDesk action..." handler. The script hook will only call that handler, so 
> anything outside it (like defining the protectLib and errorLib) will be 
> ignored. Therefore reference to those external scripts will fail. You'll have 
> to move everything to inside the script hook handler.

Christiaan,

Thanks for the reply, I've moved the load script calls inside of the
handler, but alas it still doesn't work.  The current version is
below.

I apologize for being such an applescript newb, but is there a
workflow you follow for developing this applescripts, e.g. debugging
hints, setting "breakpoints" etc.

Cheers

Peter


property theFieldToSet : "Address"

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

set protectLib to (load script file ¬
((path to home folder as string) & "Library:Application
Support:BibDesk:Scripts:Add Protect Strings.scpt"))
-- load the Error Reporting script library
set errorLib to (load script file ¬
((path to home folder as string) &
"Library:ScriptingAdditions:Error Reporting.scpt"))
-- we only report all errors at the end

tell errorLib
delayReportErrors()
set its defaultErrorFileName to "BibDeskScriptErrors"
end tell

-- here you could return depending on theName or theField
tell protectLib
-- protect chars between balanced {}
set its startProtectChar to "{"
set its endProtectChar to "}"

repeat with thePub in thePubs

try
tell thePub
set curValue to value of field 
theFieldToSet
-- generate a new value for the 
field
set theField to field 
theFieldToSet
set newValue to 
protectString(curValue)
if newValue is not "{}" then ¬
set value of theField 
to newValue
end tell

on error errorMessage number errorNumber
tell errorLib to 
reportError(errorMessage, errorNumber)

end try

end repeat
end tell --protectLib

end perform BibDesk action with publications
end using terms from

-- see if we had any errors
tell errorLib to checkForErrors()

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[Bibdesk-users] Script hook to protect Address field

[Peter Cowan]

I'm using biblatex in the TeX preview window.  And, since I often
import directly from ISI using the Web of Science Search function, I
get regular errors related to commas in the address or institution
field.  Perhaps there is a solution through biblatex to this problem,
but I'm fine with either protecting or deleting the
Address/Institution field on import.

Script hooks seem like the perfect solution to this problem, but I am
not an applescript users.  I've tried to cobble something together
based on the available example and got the following which doesn't
appear to work, on import (from Web of Science) nothing happens no
errors no braces.  Any nudges in the right direction are appreciated.

I apologize if this has been discussed on the list before, my searches
did not reveal anything aside from confirmation of the biblatex TeX
preview issue.

Cheers

Peter

set protectLib to (load script file ¬
((path to home folder as string) & "Library:Application
Support:BibDesk:Scripts:Add Protect Strings.scpt"))
-- load the Error Reporting script library
set errorLib to (load script file ¬
((path to home folder as string) & "Library:ScriptingAdditions:Error
Reporting.scpt"))
-- we only report all errors at the end
tell errorLib
delayReportErrors()
set its defaultErrorFileName to "BibDeskScriptErrors"
end tell

property theFieldToSet : "Address"

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

-- here you could return depending on theName or theField
tell protectLib
-- protect chars between balanced {}
set its startProtectChar to "{"
set its endProtectChar to "}"

repeat with thePub in thePubs

try
tell thePub
set curValue to value of field 
theFieldToSet
-- generate a new value for the 
field
set theField to field 
theFieldToSet
set newValue to 
protectString(curValue)
if newValue is not "{}" then ¬
set value of theField 
to newValue
end tell

on error errorMessage number errorNumber
tell errorLib to 
reportError(errorMessage, errorNumber)

end try

end repeat
end tell --protectLib

end perform BibDesk action with publications
end using terms from

-- see if we had any errors
tell errorLib to checkForErrors()

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Re: [Bibdesk-users] Is there a way to set a 'flag' for one or more publications

[Peter Cowan]

On Mon, May 25, 2009 at 6:42 PM, David Nicholls  wrote:
> In (eg) Thunderbird it's possible to set a small flag icon on particular
> emails, making them easy to find.
>
> Is there a way to set flags for particular publications in Bibdesk?
>

Check the "Fields" section of the preferences

HTH

Peter

> It would also be useful to set a "printed hard copy" flag.
>
> Thanks
>
> DN
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Re: [Bibdesk-users] Send via Email

[Peter Cowan]

Thanks! It works perfectly now.  What a great feature.

On Thu, Mar 5, 2009 at 2:31 AM, Christiaan Hofman  wrote:
> Thanks, that should be fixed in the current nightly.
>
> Christiaan
>
> On 5 Mar 2009, at 1:57 AM, Peter Cowan wrote:
>
>> First, thanks to the developers for all the time and effort they put
>> into developing and improving BibDesk.
>>
>> I notice that when I select a publication and choose Send via Email
>> nothing happens.  Mail.app is set as my default mail program as per
>> the help and the following is reported to the console.
>>
>> 3/4/09 4:27:25 PM BibDesk[427] Error compiling mail to script: {
>>    NSAppleScriptErrorBriefMessage = "Expected \U201c:\U201d but found
>> property.";
>>    NSAppleScriptErrorMessage = "Expected \U201c:\U201d but found
>> property.";
>>    NSAppleScriptErrorNumber = -2741;
>>    NSAppleScriptErrorRange = NSRange: {185, 4};
>> }
>>
>> I'm using a recently nightly of  BibDesk on mac os x 10.5.6.
>>
>> Is this a bug, or a problem with my setup?
>>
>> Peter
>
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[Bibdesk-users] Send via Email

[Peter Cowan]

First, thanks to the developers for all the time and effort they put
into developing and improving BibDesk.

I notice that when I select a publication and choose Send via Email
nothing happens.  Mail.app is set as my default mail program as per
the help and the following is reported to the console.

3/4/09 4:27:25 PM BibDesk[427] Error compiling mail to script: {
NSAppleScriptErrorBriefMessage = "Expected \U201c:\U201d but found
property.";
NSAppleScriptErrorMessage = "Expected \U201c:\U201d but found property.";
NSAppleScriptErrorNumber = -2741;
NSAppleScriptErrorRange = NSRange: {185, 4};
}

I'm using a recently nightly of  BibDesk on mac os x 10.5.6.

Is this a bug, or a problem with my setup?

Peter

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Re: [Bibdesk-users] BibDesk and glossaries package

[Peter Cowan]

On Thu, Jan 29, 2009 at 10:36 AM, Christian  wrote:
> Am 28.01.2009 um 22:06 schrieb Christiaan Hofman:
>> On 28 Jan 2009, at 9:33 PM, Christian wrote:
>>> Am 28.01.2009 um 20:43 schrieb Christiaan Hofman:
 On 28 Jan 2009, at 8:16 PM, Christian wrote:
> Hi,
>
> I know that BibDesk works together with the gloss package to create
> libraries for a glossar.
> Because the glossaries package is more up to date and more
> flexible,
> it would be nice if BibDesk would work for glossaries as it does
> for
> gloss.
> I think it would be necessary to provide a gui with the appropriate
> fields and save it as a tex file.
>
> Would there be a way that this will happen in the future?
>
>
> Thanks
> Christian

 I don't know anything about what you're talking. is it some kind of
 bibtex support package? Any bibtex type can be supported as is with
 BibDesk. You may need to add custom types and fields though in the
 Default Fields preferences to support types that are not used in the
 standard styles.

 Christiaan
>>>
>>> No, it is not a bibtex supported format.
>>> The glossary entry with glossaries looks like:
>>>
>>> \newglossaryentry{perl}{name=Perl,description=A scripting language}
>>>
>>> within an extra file saved as *.tex.
>>>
>>> And within the text you use for example
>>>
>>> \gls{perl}.
>>>
>>> Because of the great usability of BibDesk and its ablity of working
>>> together with gloss, I thought it would be possible to also provide
>>> support for the glossaries package.
>>>
>>> Christian
>>
>> I'm not sure what kind of support you're thinking of? Remember that
>> BibDesk is mostly a manager of citation information. So what kind of
>> support are you thinking of? Note I know next to nothing about the
>> workflow for glossaries. One thing I could imagine BibDesk could do is
>> to maintain information of the glossary entries in items of a new
>> 'glossary' type. Then you can write a template for a glossary entry,
>> which you can then use to copy or drag into your tex file. This can
>> already be done. Is this what you want?
>>
>> Christiaan
>
> Exactly Christiaaa! That was what I tried to explain. How would be the
> procedure to implement this?
> The glossaries package requires certain entries for an item and the
> drag an drop procedure needs to generate something like \gls{label}.
>
> Christian

Christian,

Both of these steps are documented in the BidDesk help.  See:

11.9.1 Custom Types and Fields

and

10. Templates

HTH

Peter

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Re: [Bibdesk-users] o/t question re: SVN

[Peter Cowan]

I use mercurial, mostly because before leopard it was easiest to get a
repository up and running on.  Leopard comes with SVN so this is less
true now.  As for latex specific diff I've had luck with both of
these.




Peter

On Wed, Jul 9, 2008 at 12:19 PM, Mark Eli Kalderon <[EMAIL PROTECTED]> wrote:
>>
>> This is a bit off-topic but I have been thinking about using
>> subversion to manage versioning etc. on several writing projects.
>> Everything I've seen seems to be oriented towards team / multi-user
>> scenarios but it also seems that people use it for single-authored
>> projects.  Stephan (and others!) , do you have any recommendations on
>> SVN workflow, helper apps, shortcomings etc?  Prefs. for SVN vs.
>> Mercurial or other alternatives?
>> thanks
>> Derick
>
> Multi-user workflows are readily adaptable to the single user if you
> work at multiple sites (at home and at work, say). If you have a
> repository on a server somewhere, you can access your files (and their
> histories!) wherever you are.
>
> I used to use subversion. Now I use git. Most of the problems that I
> had with subversion had to doing with merging. These have been
> addressed in subversion 1.5.
>
> However, a case can be made for using distributed version control such
> as git or mercurial especially wrt BibTeX files---to facilitate
> sharing. See:
>
> http://markelikalderon.com/blog/2008/06/17/gitting-bibtex/
> http://orgtheory.wordpress.com/2008/06/29/git-bibs/
>
> All the best, Mark
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Re: [Bibdesk-users] BibDesk and Papers

[Peter Cowan]

On Tue, Mar 18, 2008 at 12:55 AM, Niels Kobschaetzki
<[EMAIL PROTECTED]> wrote:
>
> On Tue, Mar 18, 2008 at 8:50 AM, Peter Cowan <[EMAIL PROTECTED]> wrote:
>  > >  Bibdesk is nice for manage my references (and getting a good bib-file
>  >  >  out of it) and pdfs in the file-system but it is missing the full-text
>  >  >  search over the pdfs like Papers is doing and it gets the whole
>  >  >  web-search thing more nicely done than Bibdesk (like automatically
>  >  >  search for the most recent papers from the selected author or from the
>  >  >  journal and stuff like that) and the interface just looks overall
>  >  >  quite nice.
>  >
>  >  Bibdesk has full content searching,  when I type something into the
>  >  search bar "File Content" comes up along with "Title", "Author" etc.
>  >  It's a bit slow the first time as it builds the search index, but fast
>  >  afterwards (is it cached at all after quit?).  I've been using the
>  >  nightly build for a while, perhaps this isn't in the release version
>  >  yet?
>
>  You are right…well, it never occured to me that the file content is
>  searched as well…
>  well it seems then that only the nicer interface and the way the
>  web-search stuff works are only points for Papers

I've never used Papers before, would you mind explaining what it is
that you like and how it differs from BibDesk?

Peter

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Re: [Bibdesk-users] BibDesk and Papers

[Peter Cowan]

>  Bibdesk is nice for manage my references (and getting a good bib-file
>  out of it) and pdfs in the file-system but it is missing the full-text
>  search over the pdfs like Papers is doing and it gets the whole
>  web-search thing more nicely done than Bibdesk (like automatically
>  search for the most recent papers from the selected author or from the
>  journal and stuff like that) and the interface just looks overall
>  quite nice.

Bibdesk has full content searching,  when I type something into the
search bar "File Content" comes up along with "Title", "Author" etc.
It's a bit slow the first time as it builds the search index, but fast
afterwards (is it cached at all after quit?).  I've been using the
nightly build for a while, perhaps this isn't in the release version
yet?

Peter

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Re: [Bibdesk-users] Feature-Request regarding auto-filing and auto-generation of cite-keys

[Peter Cowan]

Your specific case can partially be achieved with %P, see [^1].  As
far as I know there is no if/then operator (and I think no plans to
add one).

[1] 

HTH

Peter

On Mon, Mar 17, 2008 at 11:57 PM, Niels Kobschaetzki
<[EMAIL PROTECTED]> wrote:
> Hi!
>
>  I have sometimes the problem that I have some work that is from an
>  organization w/out any author. While I am able to put in the
>  organization it would be great that if a cite-key is auto-generated or
>  a file auto-filed that there are options for an "if/then"-operator.
>  Something like: If there are no authors, try to use the editors-field,
>  if there aren't authors or editors use the organization field for the
>  cite-key and the auto-filing.
>
>  Niels
>
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Re: [Bibdesk-users] web group problems

[Peter Cowan]

On 11/3/07, Adam R. Maxwell <[EMAIL PROTECTED]> wrote:
>
> On Nov 3, 2007, at 4:21 PM, Adam R. Maxwell wrote:
>
> > starting a new thread
> >
> > On Nov 3, 2007, at 4:06 PM, Adam M.Goldstein wrote:
> >
> >> Next question: I do a search, and I am looking at a google scholar
> >> search page in the upper part of the window, and the scraped-off
> >> bibtex records in the bottom part. Then, I go to the next page of the
> >> search by selecting the "2" at the bottom of the page for page 2 of
> >> the search. But the BibTeX at the bottom of the window stays the
> >> same.
> >> How do I get the new references on page 2?
> >
> > What do you mean by "BibTeX"?  I see the usual publications table and
> > whatever preview I've selected.  The new references should be
> > automatically loaded up, and they are in my test here.
>
> The Google Scholar scraper would fail to load an entire page if it
> encountered a single bad reference, but this should be fixed for the
> next nightly build.  Hopefully that fixes the random load failures
> we've seen with it.

The web group, now works here.  I had to quit and restart BibDesk but
it now works perfectly.  Google scholar loads quickly and changes the
references here.  Thanks for the quick response.

I'll download the next nightly and continue testing.

Peter

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Re: [Bibdesk-users] votes on 1.3.11?

[Peter Cowan]

I downloaded the latest nightly and don't understand the web group thing.

I visited the three sites in the release notes, citeulike.org,
acm.org/dl, and Google Scholar and, followed the directions on the
mailing list (e.g. changing my google preferences).  However I see
only the various web pages in the top panel and nothing in the lower
two.  Is this feature documented anywhere?  What am I doing wrong?

Thanks for all the wonderful work!  Off to check out the templates next...

Peter

On 11/3/07, Adam M. Goldstein <[EMAIL PROTECTED]> wrote:
> On Nov 3, 2007, at 3:26 PM, Adam R. Maxwell wrote:
>
> >
> > On Nov 3, 2007, at 12:00 PM, Adam M. Goldstein wrote:
> >
> >> Not terribly recent, but Version 1.3.10 (v900) has worked, well,
> >> pretty much flawlessly.
> >
> > That's over 3 weeks old, which is pretty ancient for a nightly build!
> >
>
> Yes, ok, I'm downloading the most recent one and will give it a
> workout in the next 24 hours or so and get back to you again.
>
> -Adam
>
> > --
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> >
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> =
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Re: [Bibdesk-users] Persistent search groups

[Peter Cowan]

On 8/17/07, Adam R. Maxwell <[EMAIL PROTECTED]> wrote:
>
> On Friday, August 17, 2007, at 04:44PM, "Christiaan Hofman" <[EMAIL 
> PROTECTED]> wrote:
> >
> >On 18 Aug 2007, at 1:33 AM, Peter Cowan wrote:
> >
> >> What I want is for an empty WOS search group to remain persistently
> >> (e.g. from launch to launch) in the group sidebar.  I use it for
> >> different searches almost every time I launch Bibdesk, and I'd rather
> >> not select it from the menu every time (though I could give it a
> >> shortcut which would be a workable solution).
> >>
> >
> >You cannot add search group persistently to a document. At some point
> >we decided we didn't want to do that, and there are some technical
> >problems related to that. You can add bookmarks for search groups so
> >you can quickly add them again to your document.
>
> Beware that WoS bookmarks are broken in 1.3.7, but fixed in the last nightly 
> build.  If you try using them in 1.3.7 the search will never return (PubMed 
> and z39.50 are unaffected by this).  It sounds like you really just want a 
> keyboard shortcut for the WoS bookmark?  There's really not that much 
> difference between clicking an empty search group and selecting the menu 
> item, as far as I can see, so keeping search groups in the source list 
> doesn't seem like much of a win.

If I understand correctly you don't want to store them in the bib
file?  I wouldn't mind having it in a general preference file, thus
showing up in all databases.  However, that might lead to a confusing
experience for other users.  I agree that it doesn't seem that
different that selecting something from a menu, I just don't like
using menus much.

A shortcut will be fine for me so I tried using the system preferences
to set the WOS menu item to control-W.  This appears to work, the
shortcut shows up in the menu.  However, while selecting the item from
the menu works as expected, the key command just beeps at me.  Any
suggestions?  I'm using the nightly from the 17th.

Peter

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Re: [Bibdesk-users] Persistent search groups

[Peter Cowan]

On 8/17/07, Christiaan Hofman <[EMAIL PROTECTED]> wrote:
>
> On 18 Aug 2007, at 1:33 AM, Peter Cowan wrote:
>
> > Hello,
> >
> > Thanks to the developers for adding Web of Science searching, between
> > this and Alex's excellent OpenURL script I use a web browser far less
> > and have a much more organized collection of references!
> >
> > I understand WOS searching is new so perhaps what I want already
> > exists and I haven't found it.
> >
> > What I want is for an empty WOS search group to remain persistently
> > (e.g. from launch to launch) in the group sidebar.  I use it for
> > different searches almost every time I launch Bibdesk, and I'd rather
> > not select it from the menu every time (though I could give it a
> > shortcut which would be a workable solution).
> >
>
> You cannot add search group persistently to a document. At some point
> we decided we didn't want to do that, and there are some technical
> problems related to that. You can add bookmarks for search groups so
> you can quickly add them again to your document.
>
> > I am also confused by the following line on the Bibdesk wiki:
> >
> > """
> >> You can also permanently add a search group added using 1. to the
> >> list of default search groups. Choose the Edit->Get Info menu item
> >> with the search group selected, or double-click on its icon, and
> >> hit the Add button.
> > """
> >
> > I don't see an 'add' button, what am I doing incorrectly.
> >
> > Thank in advance,
> >
> > Peter
>
> You may need to hit the button with the arrow to the right of the
> default server popup.
>
> Christiaan

If I'm clicking the same button you're describing I see buttons to
'remove', 'edit', 'reset all' and below 'cancel' and 'OK', but not
add.  Is this the same function as the 'add search bookmark' in the
Searches menu?  If so that works well for me.

Peter

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[Bibdesk-users] Persistent search groups

[Peter Cowan]

Hello,

Thanks to the developers for adding Web of Science searching, between
this and Alex's excellent OpenURL script I use a web browser far less
and have a much more organized collection of references!

I understand WOS searching is new so perhaps what I want already
exists and I haven't found it.

What I want is for an empty WOS search group to remain persistently
(e.g. from launch to launch) in the group sidebar.  I use it for
different searches almost every time I launch Bibdesk, and I'd rather
not select it from the menu every time (though I could give it a
shortcut which would be a workable solution).

I am also confused by the following line on the Bibdesk wiki:

"""
> You can also permanently add a search group added using 1. to the list of 
> default search groups. Choose the Edit->Get Info menu item with the search 
> group selected, or double-click on its icon, and hit the Add button.
"""

I don't see an 'add' button, what am I doing incorrectly.

Thank in advance,

Peter

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