ebib configuration for org-bibtex

ebib configuration for org-bibtex

[Thomas S. Dye]

Aloha all,

I'm trying, partially successfully, to configure org-bibtex so it mimics
some useful features of ebib.  In particular, I'm wanting to add several
optional fields that ebib uses.


I have this in .emacs:

#+begin_src emacs-lisp :tangle yes
  (dolist (type org-bibtex-types)
    (push :url (cdr (assoc :optional (cdr type))))
    (push :annote (cdr (assoc :optional (cdr type))))
    (push :abstract (cdr (assoc :optional (cdr type))))
    (push :keywords (cdr (assoc :optional (cdr type))))
    (push :file (cdr (assoc :optional (cdr type))))
)

  (push (cons :url "A URL for the reference") org-bibtex-fields)
  (push (cons :annote "Annotation is typically not exported") org-bibtex-fields)
  (push (cons :abstract "Abstract for annotated bibliography") org-bibtex-fields)
  (push (cons :keywords "Keywords for sorting with ebib") org-bibtex-fields)
  (push (cons :file "A local file path used by ebib to open the
  reference in an appropriate application") org-bibtex-fields)
#+end_src

Most of it works fine, but the optional :file field doesn't respect its
argument.  So, the following entry in the Org-mode file:

** Active Documents with Org-mode
   :PROPERTIES:
   :TITLE:    Active Documents with Org-mode
   :TYPE:     article
   :AUTHOR:   Eric Schulte and Dan Davison
   :JOURNAL:  Computing in Science and Engineering
   :YEAR:     2011
   :VOLUME:   13
   :NUMBER:   3
   :PAGES:    2--9
   :MONTH:    May/June
   :URL:      http://www.cs.unm.edu/~eschulte/data/CISE-13-3-SciProg.pdf
   :FILE:     Schulte-Davison-Babel.pdf
   :CUSTOM_ID: schulte11:_activ_docum_org
   :END:

is exported with org-bibtex like this:

@article{schulte11:_activ_docum_org,
  author =       {Eric Schulte and Dan Davison},
  title =        {Active Documents with Org-mode},
  journal =      {Computing in Science and Engineering},
  year =         2011,
  file =         {/Users/dk/Public/projects/916-rr/rr.org},
  url =
  {http://www.cs.unm.edu/~eschulte/data/CISE-13-3-SciProg.pdf},
  volume =       13,
  number =       3,
  pages =        {2--9},
  month =        {May/June}
}

Pressing f in ebib now just takes me back to the Org-mode file, rather
than launching a pdf reader on my local copy of the article.

Any ideas how I can achieve my goal?

All the best,
Tom
-- 
Thomas S. Dye
http://www.tsdye.com

Re: ebib configuration for org-bibtex

[Eric Schulte]

tsd@tsdye.com (Thomas S. Dye) writes:

> Aloha all,
>
> I'm trying, partially successfully, to configure org-bibtex so it mimics
> some useful features of ebib.  In particular, I'm wanting to add several
> optional fields that ebib uses.
>
>
> I have this in .emacs:
>
> #+begin_src emacs-lisp :tangle yes
>   (dolist (type org-bibtex-types)
>     (push :url (cdr (assoc :optional (cdr type))))
>     (push :annote (cdr (assoc :optional (cdr type))))
>     (push :abstract (cdr (assoc :optional (cdr type))))
>     (push :keywords (cdr (assoc :optional (cdr type))))
>     (push :file (cdr (assoc :optional (cdr type))))
> )
>
>   (push (cons :url "A URL for the reference") org-bibtex-fields)
>   (push (cons :annote "Annotation is typically not exported") org-bibtex-fields)
>   (push (cons :abstract "Abstract for annotated bibliography") org-bibtex-fields)
>   (push (cons :keywords "Keywords for sorting with ebib") org-bibtex-fields)
>   (push (cons :file "A local file path used by ebib to open the
>   reference in an appropriate application") org-bibtex-fields)
> #+end_src
>
> Most of it works fine, but the optional :file field doesn't respect its
> argument.  So, the following entry in the Org-mode file:
>

Hi Tom,

The :file property is treated in a special manner when Org-mode resolves
properties (notice it is an element of the `org-special-properties'
variable).  I've just pushed up a change which temporarily removes :file
from this list while resolving bibtex entries.  This change should fix
your reported problem -- please let me know if it doesn't.  If any other
elements of `org-special-properties' seem likely to cause problems we
can temporarily remove them as well.

Best -- Eric

>
> ** Active Documents with Org-mode
>    :PROPERTIES:
>    :TITLE:    Active Documents with Org-mode
>    :TYPE:     article
>    :AUTHOR:   Eric Schulte and Dan Davison
>    :JOURNAL:  Computing in Science and Engineering
>    :YEAR:     2011
>    :VOLUME:   13
>    :NUMBER:   3
>    :PAGES:    2--9
>    :MONTH:    May/June
>    :URL:      http://www.cs.unm.edu/~eschulte/data/CISE-13-3-SciProg.pdf
>    :FILE:     Schulte-Davison-Babel.pdf
>    :CUSTOM_ID: schulte11:_activ_docum_org
>    :END:
>
> is exported with org-bibtex like this:
>
> @article{schulte11:_activ_docum_org,
>   author =       {Eric Schulte and Dan Davison},
>   title =        {Active Documents with Org-mode},
>   journal =      {Computing in Science and Engineering},
>   year =         2011,
>   file =         {/Users/dk/Public/projects/916-rr/rr.org},
>   url =
>   {http://www.cs.unm.edu/~eschulte/data/CISE-13-3-SciProg.pdf},
>   volume =       13,
>   number =       3,
>   pages =        {2--9},
>   month =        {May/June}
> }
>
> Pressing f in ebib now just takes me back to the Org-mode file, rather
> than launching a pdf reader on my local copy of the article.
>
> Any ideas how I can achieve my goal?
>
> All the best,
> Tom

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/

Re: ebib configuration for org-bibtex

[Thomas S. Dye]

Eric Schulte <schulte.eric@gmail.com> writes:

> tsd@tsdye.com (Thomas S. Dye) writes:
>
>> Aloha all,
>>
>> I'm trying, partially successfully, to configure org-bibtex so it mimics
>> some useful features of ebib.  In particular, I'm wanting to add several
>> optional fields that ebib uses.
>>
>>
>> I have this in .emacs:
>>
>> #+begin_src emacs-lisp :tangle yes
>>   (dolist (type org-bibtex-types)
>>     (push :url (cdr (assoc :optional (cdr type))))
>>     (push :annote (cdr (assoc :optional (cdr type))))
>>     (push :abstract (cdr (assoc :optional (cdr type))))
>>     (push :keywords (cdr (assoc :optional (cdr type))))
>>     (push :file (cdr (assoc :optional (cdr type))))
>> )
>>
>>   (push (cons :url "A URL for the reference") org-bibtex-fields)
>>   (push (cons :annote "Annotation is typically not exported") org-bibtex-fields)
>>   (push (cons :abstract "Abstract for annotated bibliography") org-bibtex-fields)
>>   (push (cons :keywords "Keywords for sorting with ebib") org-bibtex-fields)
>>   (push (cons :file "A local file path used by ebib to open the
>>   reference in an appropriate application") org-bibtex-fields)
>> #+end_src
>>
>> Most of it works fine, but the optional :file field doesn't respect its
>> argument.  So, the following entry in the Org-mode file:
>>
>
> Hi Tom,
>
> The :file property is treated in a special manner when Org-mode resolves
> properties (notice it is an element of the `org-special-properties'
> variable).  I've just pushed up a change which temporarily removes :file
> from this list while resolving bibtex entries.  This change should fix
> your reported problem -- please let me know if it doesn't.  If any other
> elements of `org-special-properties' seem likely to cause problems we
> can temporarily remove them as well.
>
> Best -- Eric
>

Hi Eric,

I looked up org-special-properties:

org-special-properties is a variable defined in `org.el'.
Its value is 
("TODO" "TAGS" "ALLTAGS" "DEADLINE" "SCHEDULED" "CLOCK" "CLOSED" "PRIORITY" "TIMESTAMP" "TIMESTAMP_IA" "BLOCKED" "FILE" "CLOCKSUM")

It looks to me as if FILE is the only one likely to play mischief with
bib files.

Thanks for the fix, which works as expected here.

All the best,
Tom

-- 
Thomas S. Dye
http://www.tsdye.com

Re: ebib configuration for org-bibtex

[Thomas S. Dye]

Eric Schulte <schulte.eric@gmail.com> writes:

> tsd@tsdye.com (Thomas S. Dye) writes:
>
>> Aloha all,
>>
>> I'm trying, partially successfully, to configure org-bibtex so it mimics
>> some useful features of ebib.  In particular, I'm wanting to add several
>> optional fields that ebib uses.
>>
>>
>> I have this in .emacs:
>>
>> #+begin_src emacs-lisp :tangle yes
>>   (dolist (type org-bibtex-types)
>>     (push :url (cdr (assoc :optional (cdr type))))
>>     (push :annote (cdr (assoc :optional (cdr type))))
>>     (push :abstract (cdr (assoc :optional (cdr type))))
>>     (push :keywords (cdr (assoc :optional (cdr type))))
>>     (push :file (cdr (assoc :optional (cdr type))))
>> )
>>
>>   (push (cons :url "A URL for the reference") org-bibtex-fields)
>>   (push (cons :annote "Annotation is typically not exported") org-bibtex-fields)
>>   (push (cons :abstract "Abstract for annotated bibliography") org-bibtex-fields)
>>   (push (cons :keywords "Keywords for sorting with ebib") org-bibtex-fields)
>>   (push (cons :file "A local file path used by ebib to open the
>>   reference in an appropriate application") org-bibtex-fields)
>> #+end_src
>>
>> Most of it works fine, but the optional :file field doesn't respect its
>> argument.  So, the following entry in the Org-mode file:
>>
>
> Hi Tom,
>
> The :file property is treated in a special manner when Org-mode resolves
> properties (notice it is an element of the `org-special-properties'
> variable).  I've just pushed up a change which temporarily removes :file
> from this list while resolving bibtex entries.  This change should fix
> your reported problem -- please let me know if it doesn't.  If any other
> elements of `org-special-properties' seem likely to cause problems we
> can temporarily remove them as well.
>
> Best -- Eric

Hi Eric,

I think this fix is causing some mischief.  In the Org-mode file where
a :FILE: property is set to preza-thesis.pdf R source code blocks
misbehave, as follows:

#+source: land-sale-plot
#+begin_src R :var y=sales
  str(y)
#+end_src

#+results: land-sale-plot
[[file:preza-thesis.pdf]]

All the best,
Tom

>
>>
>> ** Active Documents with Org-mode
>>    :PROPERTIES:
>>    :TITLE:    Active Documents with Org-mode
>>    :TYPE:     article
>>    :AUTHOR:   Eric Schulte and Dan Davison
>>    :JOURNAL:  Computing in Science and Engineering
>>    :YEAR:     2011
>>    :VOLUME:   13
>>    :NUMBER:   3
>>    :PAGES:    2--9
>>    :MONTH:    May/June
>>    :URL:      http://www.cs.unm.edu/~eschulte/data/CISE-13-3-SciProg.pdf
>>    :FILE:     Schulte-Davison-Babel.pdf
>>    :CUSTOM_ID: schulte11:_activ_docum_org
>>    :END:
>>
>> is exported with org-bibtex like this:
>>
>> @article{schulte11:_activ_docum_org,
>>   author =       {Eric Schulte and Dan Davison},
>>   title =        {Active Documents with Org-mode},
>>   journal =      {Computing in Science and Engineering},
>>   year =         2011,
>>   file =         {/Users/dk/Public/projects/916-rr/rr.org},
>>   url =
>>   {http://www.cs.unm.edu/~eschulte/data/CISE-13-3-SciProg.pdf},
>>   volume =       13,
>>   number =       3,
>>   pages =        {2--9},
>>   month =        {May/June}
>> }
>>
>> Pressing f in ebib now just takes me back to the Org-mode file, rather
>> than launching a pdf reader on my local copy of the article.
>>
>> Any ideas how I can achieve my goal?
>>
>> All the best,
>> Tom

-- 
Thomas S. Dye
http://www.tsdye.com

Re: ebib configuration for org-bibtex

[Bastien]

Hi Thomas,

tsd@tsdye.com (Thomas S. Dye) writes:

>> The :file property is treated in a special manner when Org-mode resolves
>> properties (notice it is an element of the `org-special-properties'
>> variable).  I've just pushed up a change which temporarily removes :file
>> from this list while resolving bibtex entries.  This change should fix
>> your reported problem -- please let me know if it doesn't.  If any other
>> elements of `org-special-properties' seem likely to cause problems we
>> can temporarily remove them as well.
>>
>> Best -- Eric
>
> Hi Eric,
>
> I think this fix is causing some mischief.

I reverted this commit -- let's wait Eric is back and can fix this with
a better solution.

Thanks,

-- 
 Bastien

Re: ebib configuration for org-bibtex

[Thomas S. Dye]

Bastien <bzg@altern.org> writes:

> Hi Thomas,
>
> tsd@tsdye.com (Thomas S. Dye) writes:
>
>>> The :file property is treated in a special manner when Org-mode resolves
>>> properties (notice it is an element of the `org-special-properties'
>>> variable).  I've just pushed up a change which temporarily removes :file
>>> from this list while resolving bibtex entries.  This change should fix
>>> your reported problem -- please let me know if it doesn't.  If any other
>>> elements of `org-special-properties' seem likely to cause problems we
>>> can temporarily remove them as well.
>>>
>>> Best -- Eric
>>
>> Hi Eric,
>>
>> I think this fix is causing some mischief.
>
> I reverted this commit -- let's wait Eric is back and can fix this with
> a better solution.
>
> Thanks,

Aloha Bastien,

It appears I was wrong about this.  I get the same behavior after the
reversion.  

This is something I haven't seen before.  I'll try to track down the
problem.

All the best,
Tom

-- 
Thomas S. Dye
http://www.tsdye.com

Re: ebib configuration for org-bibtex

[Bastien]

Hi Eric,

Bastien <bzg@altern.org> writes:

>> I think this fix is causing some mischief.
>
> I reverted this commit -- let's wait Eric is back and can fix this with
> a better solution.

Eric -- just making sure this is under your radar.  

I reverted your fix because it was not answering Thomas' problem, 
but it looks like your fix is right anyway, though not addressing
the issue at hand.   Could you have another look?

Thanks in advance!

-- 
 Bastien

Re: ebib configuration for org-bibtex

[Eric Schulte]

Bastien <bzg@altern.org> writes:

> Hi Eric,
>
> Bastien <bzg@altern.org> writes:
>
>>> I think this fix is causing some mischief.
>>
>> I reverted this commit -- let's wait Eric is back and can fix this with
>> a better solution.
>
> Eric -- just making sure this is under your radar.  
>

Thanks, I had lost track of the end of this thread.

>
> I reverted your fix because it was not answering Thomas' problem,
> but it looks like your fix is right anyway, though not addressing
> the issue at hand.   Could you have another look?
>

I've just reverted your reversion :).  I'll take a look at Toms problem
(which does appear to be separate) separately.

Thanks -- Eric

>
> Thanks in advance!

Re: ebib configuration for org-bibtex

[Eric Schulte]

[-- Attachment #1: Type: text/plain, Size: 2654 bytes --]

tsd@tsdye.com (Thomas S. Dye) writes:

> Eric Schulte <schulte.eric@gmail.com> writes:
>
>> tsd@tsdye.com (Thomas S. Dye) writes:
>>
>>> Aloha all,
>>>
>>> I'm trying, partially successfully, to configure org-bibtex so it mimics
>>> some useful features of ebib.  In particular, I'm wanting to add several
>>> optional fields that ebib uses.
>>>
>>>
>>> I have this in .emacs:
>>>
>>> #+begin_src emacs-lisp :tangle yes
>>>   (dolist (type org-bibtex-types)
>>>     (push :url (cdr (assoc :optional (cdr type))))
>>>     (push :annote (cdr (assoc :optional (cdr type))))
>>>     (push :abstract (cdr (assoc :optional (cdr type))))
>>>     (push :keywords (cdr (assoc :optional (cdr type))))
>>>     (push :file (cdr (assoc :optional (cdr type))))
>>> )
>>>
>>>   (push (cons :url "A URL for the reference") org-bibtex-fields)
>>>   (push (cons :annote "Annotation is typically not exported") org-bibtex-fields)
>>>   (push (cons :abstract "Abstract for annotated bibliography") org-bibtex-fields)
>>>   (push (cons :keywords "Keywords for sorting with ebib") org-bibtex-fields)
>>>   (push (cons :file "A local file path used by ebib to open the
>>>   reference in an appropriate application") org-bibtex-fields)
>>> #+end_src
>>>
>>> Most of it works fine, but the optional :file field doesn't respect its
>>> argument.  So, the following entry in the Org-mode file:
>>>
>>
>> Hi Tom,
>>
>> The :file property is treated in a special manner when Org-mode resolves
>> properties (notice it is an element of the `org-special-properties'
>> variable).  I've just pushed up a change which temporarily removes :file
>> from this list while resolving bibtex entries.  This change should fix
>> your reported problem -- please let me know if it doesn't.  If any other
>> elements of `org-special-properties' seem likely to cause problems we
>> can temporarily remove them as well.
>>
>> Best -- Eric
>
> Hi Eric,
>
> I think this fix is causing some mischief.  In the Org-mode file where
> a :FILE: property is set to preza-thesis.pdf R source code blocks
> misbehave, as follows:
>
> #+source: land-sale-plot
> #+begin_src R :var y=sales
>   str(y)
> #+end_src
>
> #+results: land-sale-plot
> [[file:preza-thesis.pdf]]
>

Hi Tom,

Are you still experiencing the problem mentioned above?  I'm unable to
reproduce it locally.  If so, would you mind trying to recreate the
problem with an emacs session launched using "emacs -Q" to see if the
cause lies somewhere in your personal configuration?

I *do* have a file header argument for code blocks inside of subtrees
which explicitly specify a file property (which can be easily checked
using C-c C-v I), e.g.,


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: w-file-header.org --]
[-- Type: text/x-org, Size: 530 bytes --]

** inheriting the file property
   :PROPERTIES:
   :FILE: something.png
   :END:

#+begin_src ditaa
   +-----------------------------+
   |                             |
   |    +-----+                  |
   |    |     |   +---------+    |
   |    |     |   |         |    |
   |    +-----+   |         |    |
   |              |         |    |
   |   file       |         |    |
   | inheritance  +---------+    |
   |                             |
   +-----------------------------+
#+end_src

#+results:
[[file:something.png]]

[-- Attachment #3: Type: text/plain, Size: 131 bytes --]


However when I do not specify such a FILE property, then no :file entry
is present in the code blocks parameters.

Thanks -- Eric

Re: ebib configuration for org-bibtex

[Thomas S. Dye]

Eric Schulte <schulte.eric@gmail.com> writes:

> tsd@tsdye.com (Thomas S. Dye) writes:
>
>> Eric Schulte <schulte.eric@gmail.com> writes:
>>
>>> tsd@tsdye.com (Thomas S. Dye) writes:
>>>
>>>> Aloha all,
>>>>
>>>> I'm trying, partially successfully, to configure org-bibtex so it mimics
>>>> some useful features of ebib.  In particular, I'm wanting to add several
>>>> optional fields that ebib uses.
>>>>
>>>>
>>>> I have this in .emacs:
>>>>
>>>> #+begin_src emacs-lisp :tangle yes
>>>>   (dolist (type org-bibtex-types)
>>>>     (push :url (cdr (assoc :optional (cdr type))))
>>>>     (push :annote (cdr (assoc :optional (cdr type))))
>>>>     (push :abstract (cdr (assoc :optional (cdr type))))
>>>>     (push :keywords (cdr (assoc :optional (cdr type))))
>>>>     (push :file (cdr (assoc :optional (cdr type))))
>>>> )
>>>>
>>>>   (push (cons :url "A URL for the reference") org-bibtex-fields)
>>>>   (push (cons :annote "Annotation is typically not exported") org-bibtex-fields)
>>>>   (push (cons :abstract "Abstract for annotated bibliography") org-bibtex-fields)
>>>>   (push (cons :keywords "Keywords for sorting with ebib") org-bibtex-fields)
>>>>   (push (cons :file "A local file path used by ebib to open the
>>>>   reference in an appropriate application") org-bibtex-fields)
>>>> #+end_src
>>>>
>>>> Most of it works fine, but the optional :file field doesn't respect its
>>>> argument.  So, the following entry in the Org-mode file:
>>>>
>>>
>>> Hi Tom,
>>>
>>> The :file property is treated in a special manner when Org-mode resolves
>>> properties (notice it is an element of the `org-special-properties'
>>> variable).  I've just pushed up a change which temporarily removes :file
>>> from this list while resolving bibtex entries.  This change should fix
>>> your reported problem -- please let me know if it doesn't.  If any other
>>> elements of `org-special-properties' seem likely to cause problems we
>>> can temporarily remove them as well.
>>>
>>> Best -- Eric
>>
>> Hi Eric,
>>
>> I think this fix is causing some mischief.  In the Org-mode file where
>> a :FILE: property is set to preza-thesis.pdf R source code blocks
>> misbehave, as follows:
>>
>> #+source: land-sale-plot
>> #+begin_src R :var y=sales
>>   str(y)
>> #+end_src
>>
>> #+results: land-sale-plot
>> [[file:preza-thesis.pdf]]
>>
>
> Hi Tom,
>
> Are you still experiencing the problem mentioned above?  I'm unable to
> reproduce it locally.  If so, would you mind trying to recreate the
> problem with an emacs session launched using "emacs -Q" to see if the
> cause lies somewhere in your personal configuration?
>
> I *do* have a file header argument for code blocks inside of subtrees
> which explicitly specify a file property (which can be easily checked
> using C-c C-v I), e.g.,
>
>
> ** inheriting the file property
>    :PROPERTIES:
>    :FILE: something.png
>    :END:
>
> #+begin_src ditaa
>    +-----------------------------+
>    |                             |
>    |    +-----+                  |
>    |    |     |   +---------+    |
>    |    |     |   |         |    |
>    |    +-----+   |         |    |
>    |              |         |    |
>    |   file       |         |    |
>    | inheritance  +---------+    |
>    |                             |
>    +-----------------------------+
> #+end_src
>
> #+results:
> [[file:something.png]]
>
>
> However when I do not specify such a FILE property, then no :file entry
> is present in the code blocks parameters.
>
> Thanks -- Eric

Hi Eric,

I think the confusion leading to my messages has been the cause of some
mischief.  Apologies for that.

The change you implemented to let the :FILE: property work correctly
with ebib does what it is supposed to do.  It does not cause the
"mischief" that I was experiencing.  AFAICT, your re-reversion of the
code back into Org-mode was the correct action.

I ran into the problem when I tried to include in my reading notes an R
graphic for some newly reported data.  The R source block was
immediately below the bibliographic subheading with the :FILE: property.
Babel saw the :FILE: property for the bibliographic subheading and
applied that to the R code block, as I now believe it is supposed to do.
My confusion came from the fact that I didn't recognize at the time that
Babel sees the :FILE: property for the bibliographic subheading the same
way it sees the :FILE: property for any other heading.  When I move the
R code away from the bibliographic subheading it all works as expected,
as you note.

Again, sorry for my noise, and thanks for your fix for the ebib
integration.

All the best,
Tom

-- 
T.S. Dye & Colleagues, Archaeologists
735 Bishop St, Suite 315, Honolulu, HI 96813
Tel: 808-529-0866, Fax: 808-529-0884
http://www.tsdye.com