org-ref: xxx-add-bibtex-entry with an org-capture like interface

org-ref: xxx-add-bibtex-entry with an org-capture like interface

[Daniele Nicolodi]

Hello John,

sorry for the cryptic subject but I was unable to come up with something
better.  I am revamping my workflow to take notes about articles I read
or that I save to be read later and I decided to explore if org-ref and
the related utility packages fit what I would like to be able to do.

org-ref offers quite a few very useful facilities, however, I would like
an interface to add new entries to the bibliography more similar to
org-capture: I would like to have a command that asks for an identifier
(for example a URL, a DOI, an arXiv id) and pops up a buffer with a
populated bibtex entry that can be verified and amended before being
appended to a bibtex file (for example add some keywords).

I think most of the building blocks are there, but before starting to
hack something together myself I wanted to check if this functionality
is already there and I missed it, and if it would be interesting to add
it to the functionality shipped with org-ref. Of course, any hint on how
to implement this effectively is greatly appreciated.

Thank you.

Cheers,
Dan

Re: org-ref: xxx-add-bibtex-entry with an org-capture like interface

[John Kitchin]

This is basically what doi-add-bibtex-entry does. There isn't one
function that does arxiv too, but there is arxiv-add-bibtex-entry. Those
are both commands in org-ref. These don't pop up a buffer for approval,
that is something you would have to build yourself.

There are many workflows people want, the one above works for me when I
am writing, and just want to add entries with minimal disruption. I
usually polish the entries later if needed. I can see a slower, approach
like you describe too.

Daniele Nicolodi <daniele@grinta.net> writes:

> Hello John,
>
> sorry for the cryptic subject but I was unable to come up with something
> better.  I am revamping my workflow to take notes about articles I read
> or that I save to be read later and I decided to explore if org-ref and
> the related utility packages fit what I would like to be able to do.
>
> org-ref offers quite a few very useful facilities, however, I would like
> an interface to add new entries to the bibliography more similar to
> org-capture: I would like to have a command that asks for an identifier
> (for example a URL, a DOI, an arXiv id) and pops up a buffer with a
> populated bibtex entry that can be verified and amended before being
> appended to a bibtex file (for example add some keywords).
>
> I think most of the building blocks are there, but before starting to
> hack something together myself I wanted to check if this functionality
> is already there and I missed it, and if it would be interesting to add
> it to the functionality shipped with org-ref. Of course, any hint on how
> to implement this effectively is greatly appreciated.
>
> Thank you.
>
> Cheers,
> Dan


--
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu

Re: org-ref: xxx-add-bibtex-entry with an org-capture like interface

[Alan Schmitt]

Hello,

On 2020-04-09 15:43, John Kitchin <jkitchin@andrew.cmu.edu> writes:

> This is basically what doi-add-bibtex-entry does. There isn't one
> function that does arxiv too, but there is arxiv-add-bibtex-entry. Those
> are both commands in org-ref. These don't pop up a buffer for approval,
> that is something you would have to build yourself.
>
> There are many workflows people want, the one above works for me when I
> am writing, and just want to add entries with minimal disruption. I
> usually polish the entries later if needed. I can see a slower, approach
> like you describe too.

There is also the biblio-lookup command (from biblio.el,
https://github.com/cpitclaudel/biblio.el) that might be useful for this.

Best,

Alan

Re: org-ref: xxx-add-bibtex-entry with an org-capture like interface

[Daniele Nicolodi]

On 09-04-2020 13:43, John Kitchin wrote:
> This is basically what doi-add-bibtex-entry does. There isn't one
> function that does arxiv too, but there is arxiv-add-bibtex-entry. Those
> are both commands in org-ref. These don't pop up a buffer for approval,
> that is something you would have to build yourself.
> 
> There are many workflows people want, the one above works for me when I
> am writing, and just want to add entries with minimal disruption. I
> usually polish the entries later if needed. I can see a slower, approach
> like you describe too.

Hello John,

I have been able to hack something combining org-capture and the utility
functions you mention that implements the workflow I described.

There is only one issue: doi-utils-insert-bibtex-entry-from-doi contains
a (save-buffer) call that does not play nicely when I call it on a
temporary buffer. Why is the (save-buffer) there?
doi-utils-insert-bibtex-entry-from-doi looks like an utility function,
thus I think it should not try to save the current buffer. What do you
think?

Thank you.

Cheers,
Dan

Re: org-ref: xxx-add-bibtex-entry with an org-capture like interface

[John Kitchin]

That function inserts into a bibtex file, and if you don't save it then
the new entry is not "findable", so it is somewhat critical to do that
in my mind. It could make sense to check if there is a file attached to
the buffer though, and only save in that case. That would preserve the
current behavior, and solve your problem I think. WDYT?

Daniele Nicolodi <daniele@grinta.net> writes:

> On 09-04-2020 13:43, John Kitchin wrote:
>> This is basically what doi-add-bibtex-entry does. There isn't one
>> function that does arxiv too, but there is arxiv-add-bibtex-entry. Those
>> are both commands in org-ref. These don't pop up a buffer for approval,
>> that is something you would have to build yourself.
>>
>> There are many workflows people want, the one above works for me when I
>> am writing, and just want to add entries with minimal disruption. I
>> usually polish the entries later if needed. I can see a slower, approach
>> like you describe too.
>
> Hello John,
>
> I have been able to hack something combining org-capture and the utility
> functions you mention that implements the workflow I described.
>
> There is only one issue: doi-utils-insert-bibtex-entry-from-doi contains
> a (save-buffer) call that does not play nicely when I call it on a
> temporary buffer. Why is the (save-buffer) there?
> doi-utils-insert-bibtex-entry-from-doi looks like an utility function,
> thus I think it should not try to save the current buffer. What do you
> think?
>
> Thank you.
>
> Cheers,
> Dan


--
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu