Re: [ANN] org-bibtex.el --- convert between Org headings and bibtex entries

["Thomas S. Dye" <tsd@tsdye.com>]

Hi Eric,

After tests on a variety of bibtex entries, using both point before  
the entry and selecting an entry, I can't reproduce the problem I had  
late the other night with org-bibtex-read/write.  Perhaps it was user  
error :(

Also, thanks for the text file patch.  My mail client and git am don't  
seem to cooperate.

I have a library session scheduled next week and am looking forward to  
taking my reading notes, including bibtex entries, entirely with Org- 
mode.

All the best,
Tom

On Apr 21, 2011, at 11:06 AM, Eric Schulte wrote:

> "Thomas S. Dye" <tsd@tsdye.com> writes:
>
>> Hi Eric,
>>
>> On Apr 20, 2011, at 9:00 AM, Eric Schulte wrote:
>>
>>> Hi Tom,
>>>
>>> "Thomas S. Dye" <tsd@tsdye.com> writes:
>>>
>>>> Hi Eric,
>>>>
>>>> This could be very useful and a significant enhancement to Org-mode
>>>> for note taking.  With it, library time can be spent almost  
>>>> entirely
>>>> within Org-mode, capturing bibliographic information and taking
>>>> reading notes.  It feels like the right level of functionality--
>>>> lightweight and easy to use, with lots of prompting material.
>>>>
>>>
>>> Thanks, I hope so.
>>>
>>>>
>>>> I created an entry with org-bibtex-create and then another with  
>>>> org-
>>>> bibtex-read/write.  When I ran org-bibtex, only the second entry  
>>>> was
>>>> exported.  Also, the org-bibtex-read/write process mangled the  
>>>> bibtex
>>>> entry a bit, so the resulting .bib file wasn't useful.  Note the
>>>> addition of {} around the publisher and year, and the truncation of
>>>> multi-line entries.
>>>>
>>>
>>> I /believe/ I have fixed this issue.  I am now using pre-existing
>>> bibtex
>>> functions for reading in entries, and for cleaning up entries
>>> written by
>>> org-bibtex.
>>>
>>
>> The org-bibtex-read/write process doesn't work on the example I sent.
>> The read appears to work (though I can't find a buffer *org-bibtex-
>> entries* afterwards), but the write inserts the headline asterisk  
>> then
>> fails with progn: Wrong type argument: char-or-string-p, nil.
>>
>
> Hmm, I can't re-create this error, the read and write work for me...
>
> Are you placing the point immediately before the bibtex entry before
> calling org-bibtex-read?
>
> After calling the read, does the `*org-bibtex-entries*' variable  
> appear
> to hold the information for the bibtex entry?
>
> Could you set `debug-on-error' to t, and then send me the entire error
> backtrace so I could see where this is going wrong?
>
>>
>>>>
>>>> Can I suggest some changes?
>>>>
>>>> 1) In our multi-user environment, where several authors are
>>>> contributing to a master bibtex file, we depend on the key  
>>>> generating
>>>> algorithm of bibtex-mode to help weed out duplicate entries.   This
>>>> isn't 100% effective, but it catches lots of duplicates and saves  
>>>> us
>>>> time.  Would it be possible to lift this mechanism and use it in  
>>>> org-
>>>> bibtex to generate the CUSTOM_ID?
>>>>
>>>
>>> I've added a new variable `org-bibtex-autogen-keys' which when set  
>>> to
>>> t will result in auto-generated keys being used instead of prompting
>>> the user to input such keys.
>>>
>>
>> Beautiful!
>>
>>>>
>>>> 2) It might be better to use the (generated) key as the Org  
>>>> headline,
>>>> instead of the title.  Titles can be longer than I find comfortable
>>>> for an Org-mode headline, whereas keys are usually about the right
>>>> length.
>>>>
>>>
>>> Hmm, I would tend to disagree here, but I think it may be a matter  
>>> of
>>> taste.  Note that if you include a TITLE property in a headline then
>>> it will be used instead of the contents of the headline, leaving you
>>> free to put whatever information you want into the headline.  I've
>>> just updated the headline creation so that it will create such a
>>> title property as well as using the title as the headline, leaving
>>> you free to subsequently change the headline.
>>>
>>
>> That sounds right to me.  Thanks.
>>
>>>>
>>>> 3) org-bibtex-cite seems like a natural next step, especially if it
>>>> offers a list of keys in the Org-mode buffer.
>>>>
>>>
>>> Meaning a function to allow tab-completion on keys...  I could see
>>> this
>>> being useful but I would imagine that the bib entries would  
>>> generally
>>> not live in the same buffer as the Org-mode text... rather I'd think
>>> some sort of global registry would be preferable.
>>>
>>
>> I guess it depends on how one uses the software.  The use I envision
>> is for note taking while doing background reading for a project.
>> First, enter a reference with org-bibtex-create, then take notes  
>> while
>> reading, and finally write a summary that might later be used in the
>> project document.  At this stage, org-bibtex hasn't been called, so
>> the only place the key is present is in the Org-mode buffer.
>> Inserting a reference then involves jumping back to the headline,
>> opening the properties drawer, selecting the value of CUSTOM_ID,
>> navigating back to the reference point and pasting in the key.  A
>> function that collects keys and then presents them in a list like the
>> one used to choose TYPE would make this process very easy.
>>
>> Do you mind my asking what your workflow is with org-bibtex?
>>
>
> Currently I'm just using org-bibtex to collect all of my scattered
> reading notes into a single monolithic .org file, but I anticipate
> dumping out .bib files from here when writing in the future.
>
> I do see how an automated method of collecting bibtex keys, and then
> offering a tab-completing insertion could be useful... I'll make a  
> note
> to this effect in my task file for org-bibtex.
>
> Best -- Eric
>
>>
>> All the best,
>> Tom
>>> Thanks for the suggestions, bug reports, and examples!
>>>
>>> Please do let me know if any of these issues remain -- Eric
>>>
>>>>
>>>> Here are the details of my test run:
>>>>
>>>> Existing bibtex entry:
>>>>
>>>> @Book{tuggle94:_cultur_resour_naval_air_station_barber_point,
>>>> author =    {H. David Tuggle and M. J. Tomonari-Tuggle and
>>>>                 D. Colt Denfeld},
>>>> title =        {Cultural Resources of Naval Air Station, Barbers
>>>>                 Point: Summary, Assessment, and Inventory Research
>>>>                 Design: Task 1b: Archaeological Research Services
>>>>                 for the Proposed Cleanup, Disposal, and Reuse of
>>>>                 Naval Air Station, Barbers Point, O`ahu, Hawai`i},
>>>> publisher =    iarii,
>>>> year =         1994,
>>>> series =    {Prepared for Belt Collins Hawaii},
>>>> address =   {Honolulu},
>>>> month =     {December}}
>>>>
>>>> Org-mode tree:
>>>>
>>>>
>>>> * Schulte bibtex
>>>>
>>>> ** A journal title
>>>>  :PROPERTIES:
>>>>  :type:     article
>>>>  :AUTHOR:   A. N. Author
>>>>  :JOURNAL:  Journal of Statistical Software
>>>>  :YEAR:     1998
>>>>  :CUSTOM_ID: author_10:article
>>>>  :END:
>>>>
>>>> ** {Cultural Resources of Naval Air Station, Barbers
>>>>  :PROPERTIES:
>>>>  :TYPE:     book
>>>>  :CUSTOM_ID: tuggle94:_cultur_resour_naval_air_station_barber_point
>>>>  :MONTH:    December}
>>>>  :ADDRESS:  Honolulu
>>>>  :SERIES:   Prepared for Belt Collins Hawaii
>>>>  :YEAR:     1994
>>>>  :PUBLISHER: iarii
>>>>  :AUTHOR:   {H. David Tuggle and M. J. Tomonari-Tuggle and
>>>>  :END:
>>>>
>>>> Org-bibtex output:
>>>>
>>>> @book{tuggle94:_cultur_resour_naval_air_station_barber_point,
>>>> author={{H. David Tuggle and M. J. Tomonari-Tuggle and},
>>>> title={{Cultural Resources of Naval Air Station, Barbers},
>>>> publisher={iarii},
>>>> year={1994},
>>>> series={Prepared for Belt Collins Hawaii},
>>>> address={Honolulu},
>>>> month={December}}
>>>> }
>>>>
>>>> hth,
>>>> Tom
>>>>
>>>> On Apr 19, 2011, at 1:52 PM, Eric Schulte wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> In an attempt to organize my reading notes, I've written the
>>>>> following
>>>>> tool which allows both for exporting Org-mode headlines with  
>>>>> bibtex
>>>>> meta-data to bibtex entries, and for reading existing bibtex  
>>>>> entries
>>>>> into Org-mode headings.
>>>>>
>>>>> One nice feature of these functions is the ability to check that  
>>>>> all
>>>>> required fields are present in a given headline based on the  
>>>>> bibtex
>>>>> type
>>>>> (e.g., :article, :inproceedings), and prompt for missing fields.
>>>>>
>>>>> See the top of the elisp file for more usage information.
>>>>> https://github.com/eschulte/org-bibtex/blob/master/org-bibtex.el
>>>>>
>>>>> Cheers -- Eric
>>>>>
>>>>> -- 
>>>>> Eric Schulte
>>>>> http://cs.unm.edu/~eschulte/
>>>>>
>>>>
>>>>
>>>
>>> -- 
>>> Eric Schulte
>>> http://cs.unm.edu/~eschulte/
>>
>>
>
> -- 
> Eric Schulte
> http://cs.unm.edu/~eschulte/