On 3/18/08, Christiaan Hofman <[EMAIL PROTECTED]> wrote:
>
> On 18 Mar 2008, at 5:06 PM, P Kishor wrote:
>
> > On 3/18/08, Christiaan Hofman <[EMAIL PROTECTED]> wrote:
> >>
> >> On 18 Mar 2008, at 3:26 PM, P Kishor wrote:
> >>
> >>> Hi folks,
> >>>
> >>> I have never had good experience importing data into another program
> >>> that I have exported from BibDesk. I love BibDesk for many of its
> >>> capabilities and flexibility, but it just doesn't fit my workflow
> >>> for
> >>> now. This, of course, is my failing, not BibDesk's. I just haven't
> >>> found a good workflow. More on that in another email; for now, the
> >>> BibDesk format --
> >>>
> >>> I exported my library, and tried to import it into Zotero, but the
> >>> import just wouldn't work, not with the entire library, not with a
> >>> few
> >>> records from the library, not even with one record from the library.
> >>>
> >>
> >>
> >> That is a problem of Zotero, as BibDesk export completely valid
> >> bibtex. Have you tried export as minimal bibtex?
> >
> > yes, even minimal bibtex failed. The only thing that succeeded was
> > bib2xml (MODS XML) and then into Zotero.
> >
>
>
> And have you tried turning off the template in the Files pref pane? It
> might be that they can't handle comments.
>
>
> >>
> >>
> >>> Eventually I used bib2xml [1] to convert to MODS XML, and then
> >>> imported that into Zotero. Of course, none of my attached (linked)
> >>> files came through.
> >>>
> >>> I tried the same with Sente. Fortunately, Sente was able to read the
> >>> BD export, but again, none of the attachments came through.
> >>>
> >>> When I open the .bib file, I don't see any human readable
> >>> information
> >>> for my linked file. I do see uuencoded kind of binary-to-text
> >>> gibberish. Here is an example --
> >>>
> >>> @article{Chapin_2004_aa,
> >>> Author = {Mac Chapin},
> >>> Date-Added = {2007-01-23 10:05:03 -0600},
> >>> Date-Modified = {2007-12-29 11:56:46 -0600},
> >>> Journal = {World Watch Magazine},
> >>> Local-Url =
> {file://localhost/Users/punkish/Documents/BibDesk/chapin-challenge_to_conservationists.pdf
> >>> },
> >>> Month = {11},
> >>> Title = {A Challenge to Conservationists},
> >>> Year = {2004},
> >>> Abstract = {As corporate and government money flow into the
> >>> three big
> >>> international organizations that dominate the "world's conservation
> >>> agenda," their programs have been marked by growing conflicts of
> >>> interest---and by a disturbing neglect of the indigenous peoples
> >>> whose land they are in business to protect.},
> >>> Bdsk-File-1 =
> >>>
> {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
> >>>
> FYTlNPYmplY3RfEEcuLi9Eb2N1bWVudHMvQmliRGVzay9DaGFwaW4vMjAwNC9BIENoYWxsZW5nZSB0byBDb25zZXJ2YXRpb25pc3QoYWEpLnBkZtIeHyYnoicjXE5TRGljdGlvbmFyeQAIABEAGgAfACkAMgA3ADoAPwBBAFMAXABiAGkAcAB4AIMAhQCIAIoAjACPAJEAkwCdAKoArwC3ALkCqQKuArcCwgLGAtQC2wLkAy4DMwM2AAAAAAAAAgEAAAAAAAAAKAAAAAAAAAAAAAAAAAAAA0M=}}
> >>>
> >>>
> >>> Of course, the double-quotes in the Abstract give rise to Tex errors
> >>> (" not allowed at top-level or some nonsense like that). Getting
> >>> back
> >>> to the location of the linked file, however, I might be missing
> >>> this,
> >>> but I can't see any helpful information. In the previous
> >>> generation of
> >>> BD, I had the "Local-Url" which very clearly stated that the file
> >>> was
> >>> at
> file://localhost/Users/punkish/Documents/BibDesk/chapin-challenge_to_conservationists.pdf
> >>> .
> >>> Of course, now with the new way of doing things, it is actually at
> >>> "~/Documents/BibDesk/Chapin/2004/A Challenge to
> >>> Conservationist(aa).pdf" but I don't see that information anywhere
> >>> in
> >>> the above record. Of course, it could be that gibberish, the value
> >>> of
> >>> "Bdsk-File-1" but this way is too opaque for me.
> >>>
> >>> Perhaps this is causing neither Zotero nor Sente to figure out where
> >>> the linked file is located. The Sente folks are being really nice
> >>> and
> >>> are helping me with "pre-sales support" trying to figure out how to
> >>> import this correctly, but I am now wondering about the logic of
> >>> such
> >>> a opaque way of storing things.
> >>>
> >>> How do I extract from the above record the location of my linked
> >>> file?
> >>>
> >>> [1] http://www.scripps.edu/~cdputnam/software/bibutils/bibutils.html
> >>>
> >>> --
> >>> Puneet Kishor http://punkish.eidesis.org/
> >>> Nelson Institute for Environmental Studies http://www.nelson.wisc.edu/
> >>> Open Source Geospatial Foundation (OSGeo) http://www.osgeo.org/
> >>
> >>
> >> These fields have been discussed on this list already several times.
> >> The Bdsk-File-* fields are opaque and specific to BibDesk (though we
> >> only use standard encodings and standard Cocoa and Carbon
> >> functionality, nothing truly custom), so no other program will be
> >> able
> >> to make sense out of it, unless they specifically add it. This allows
> >> much better and reliable tracking of files, as it is not restricted
> >> to
> >> the fragile relative or absolute path of the file.
> >
> > So, is there any way to re-construct the location of the linked file?
> > I don't have any issues with achieving better capability through the
> > use of BD-specific, Cocoa-specific encodings, as long as the encoded
> > information can be decoded upon export.
> >
>
>
> In BibDesk you can get it through copy/paste and AppleScript. You can
> also automatically synchronize a text field such as Local-Url with the
> first linked file using a script hook (there is one available on the
> Wiki).
I am assuming it is
http://bibdesk.sourceforge.net/scripts/LocalFileToLocal-UrlScriptHook.scpt
however, I am getting the following error --
An error has been encountered in accessing this page.
1. Server: bibdesk.sourceforge.net
2. URL path: /scripts/LocalFileToLocal-UrlScriptHook.scpt
3. Error notes: File does not exist:
/home/groups/b/bi/bibdesk/htdocs/scripts/LocalFileToLocal-UrlScriptHook.scpt
4. Error type: 404
5. Request method: GET
6. Request query string:
7. Time: 2008-03-18 09:23:16 PDT (1205857396)
> From the bibtex file, there is no way to reconstruct the path.
Hmmm... this is very worrying to *me* as it breaks down many other
potential tools. I routinely use Perl and its BibDesk modules to
access my library. The beauty of the .bib format is that it is plain
text, and all documented BibTex format. This divergence, that is also
irreversible without a fair bit of non-automate-able export sequence
of steps breaks all that.
I will continue trying to get the above mentioned script, and if that
works, I will consider rolling back to the BD version that was prior
to the current multi-attachment, Bdsk-file-? proprietary field
dependence. That was version 1.3.13 and earlier, no?
>
>
> > How does some other tool figure out where the linked file is stored?
> > That is the issue here, I guess.
> >
>
>
> They need to know how it is stored (which can be figured out from the
> source of BibDesk) and actually do it.
>
>
> > Many thanks for your assistance.
> >
> >
> >>
> >> Christiaan
> >>
>
--
Puneet Kishor http://punkish.eidesis.org/
Nelson Institute for Environmental Studies http://www.nelson.wisc.edu/
Open Source Geospatial Foundation (OSGeo) http://www.osgeo.org/
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