On Sat, Apr 3, 2010 at 3:26 AM, Fischlin Andreas
<andreas.fisch...@env.ethz.ch> 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
> +41 79 221-4657 mobile
>
> Make it as simple as possible, but distrust it!
> ________________________________________________________________________
>
>
>
> On 03/Apr/2010, at 00:34 , Peter Cowan wrote:
>
>> On Fri, Apr 2, 2010 at 2:13 PM, Christiaan Hofman <cmhof...@gmail.com> wrote:
>>>
>>> On Apr 2, 2010, at 21:54, Peter Cowan wrote:
>>>
>>>> On Fri, Apr 2, 2010 at 9:53 AM, Christiaan Hofman <cmhof...@gmail.com>
>>>> wrote:
>>>>>
>>>>> On Apr 1, 2010, at 23:29, Peter Cowan wrote:
>>>>>
>>>>>> On Thu, Apr 1, 2010 at 2:03 PM, Christiaan Hofman <cmhof...@gmail.com>
>>>>>> 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
>>> field or something, or biblatex has a problem. It should never interpret an
>>> address as a name IMHO.
>>
>> This is from a direct import using the "Import" button while searching
>> WOS from bibdesk. I agree it seems like a biblatex problem to me, but
>> I've not found mention of it on the biblatex list, I may send a bug
>> report that way.
>>
>> This is the how the above example is imported by BibDesk:
>>
>> @article{CRICK.F:1956,
>> Address = {PORTERS SOUTH, 4 CRINAN ST, LONDON N1 9XW, ENGLAND},
>> Author = {CRICK, FHC and WATSON, JD},
>> Date-Added = {2010-04-02 15:28:17 -0700},
>> Date-Modified = {2010-04-02 15:28:17 -0700},
>> Isi = {A1956ZQ08700022},
>> Isi-Recid = {3737785},
>> Isi-Ref-Recids = {1399833 25231 154301 694402 25230 239834 3611023
>> 3395518 3500753 3437398 176937 3474554 175967 2741553 137080 43856
>> 3395520 3397795 3437394 3742607 103203 3611269 2741574 3395809 3397793
>> 261765 3649114 665053 3742608 2741559 3742609 482156},
>> Journal = {Nature},
>> Number = {4506},
>> Pages = {473-475},
>> Publisher = {MACMILLAN MAGAZINES LTD},
>> Times-Cited = {327},
>> Title = {STRUCTURE OF SMALL VIRUSES},
>> Volume = {177},
>> Year = {1956},
>> Bdsk-Url-1 =
>> {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1956ZQ08700022}}
>>
>>>> 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
>>>
>>> That's probably because you haven't really used it. This protects
>>> individual words or phrases (which is really the correct thing to do in
>>> bibtex), and you have to tell it which words and phrases to protect. Just
>>> enclosing a value in braces is crude and generally the wrong thing to do,
>>> because the capitalization is supposed to be determined by the style and
>>> not by the data, except for certain special words (like acronyms.)
>>
>> Ahh. I agree that bracing the whole field is not a good strategy.
>> However, I hardly ever use the Address field (for journal articles it
>> is usually the publishers address and thus not in the styles I use).
>> But, bracing it is safer than deleting it for the cases when it is
>> used.
>>
>>>
>>>> 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.
>>>
>>> Errors really mean errors, in that they would normally fail the script if
>>> you don't escape them.
>>>
>>>> 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.
>>>
>>> Define the following in your applescript and use it instead of
>>> protectString():
>>>
>>> on encloseInBraces(theString)
>>> if (theString is "") or (character 1 of theString is "{" and character
>>> -1 of theString is "}") then
>>> return theString
>>> else
>>> return "{" & theString & "}"
>>> end if
>>> end encloseInBraces
>>>
>>
>> Thanks for this.
>>
>> Peter
>>
>>>
>>> Christiaan
>>>
>>>
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