GNU bug report logs - #56475
28.1.50; bibtex-parse-entry disregards @string substitutions

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Ihor Radchenko <yantar92 <at> gmail.com>
To: bug-gnu-emacs <at> gnu.org
Subject: 28.1.50; bibtex-parse-entry disregards @string substitutions
Date: Sun, 10 Jul 2022 15:14:57 +0800

Consider the following bibliography:

@string{jgr="J. Geophys. Res."}
@article{chouet88,
journal=jgr,
author={Chouet, B.},
title={Resonance of a fluid-driven crack: [...]},
year={1988},
volume={93},
number={B5},
pages={4375-4400}}

With point at bol in "@article", running M-: (bibtex-parse-entry)
yields:

(("=type=" . "article") ("=key=" . "chouet88") ("journal" . "jgr")
("author" . "{Chouet, B.}") ("title" . "{Resonance of a fluid-driven
crack: [...]}") ("year" . "{1988}") ("volume" . "{93}") ("number" .
"{B5}") ("pages" . "{4375-4400}"))

Note the journal field value: ("journal" . "jgr")

Expected: ("journal" . "J. Geophys. Res.")

This bug report is originated from Org ML:
https://list.orgmode.org/orgmode/25288.4658.491916.790389 <at> gargle.gargle.HOWL/

Org currently relies on built-in bibtex.el to parse bibliography files.
However, the built-in parser does not appear to be complete.

Best,
Ihor

In GNU Emacs 28.1.50 (build 1, x86_64-pc-linux-gnu, cairo version 1.16.0)
 of 2022-05-26 built on localhost
Repository revision: a9f17ccce336ad5d384a6271f205a84141980019
Repository branch: emacs-28
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Memory information:
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Message #8 received at 56475 <at> debbugs.gnu.org (full text, mbox):

From: Lars Ingebrigtsen <larsi <at> gnus.org>
To: Ihor Radchenko <yantar92 <at> gmail.com>
Cc: 56475 <at> debbugs.gnu.org, Roland Winkler <winkler <at> gnu.org>
Subject: Re: bug#56475: 28.1.50; bibtex-parse-entry disregards @string
 substitutions
Date: Mon, 11 Jul 2022 12:16:56 +0200

Ihor Radchenko <yantar92 <at> gmail.com> writes:

> Org currently relies on built-in bibtex.el to parse bibliography files.
> However, the built-in parser does not appear to be complete.

Perhaps Roland has some comments; added to the CCs.

-- 
(domestic pets only, the antidote for overdose, milk.)
   bloggy blog: http://lars.ingebrigtsen.no

Message #11 received at 56475 <at> debbugs.gnu.org (full text, mbox):

From: Roland Winkler <winkler <at> gnu.org>
To: Lars Ingebrigtsen <larsi <at> gnus.org>
Cc: 56475 <at> debbugs.gnu.org, Ihor Radchenko <yantar92 <at> gmail.com>
Subject: Re: bug#56475: 28.1.50; bibtex-parse-entry disregards @string
 substitutions
Date: Mon, 11 Jul 2022 12:12:59 -0500

On Mon, Jul 11 2022, Lars Ingebrigtsen wrote:
> Ihor Radchenko <yantar92 <at> gmail.com> writes:
>
>> Org currently relies on built-in bibtex.el to parse bibliography files.
>> However, the built-in parser does not appear to be complete.
>
> Perhaps Roland has some comments; added to the CCs.

The arg CONTENT of bibtex-parse-entry is passed on to
bibtex-text-in-field-bounds that gives you a more complete description
of what it does.  So I believe binding bibtex-expand-strings to t while
calling bibtex-parse-entry with arg CONTENT non-nil should do the job.

The parser in bibtex.el goes through some effort to deal with BibTeX
constructs such as

    title = "Foo " # BAR # {Baz},

correctly.

Message #14 received at 56475 <at> debbugs.gnu.org (full text, mbox):

From: Roland Winkler <winkler <at> gnu.org>
To: Lars Ingebrigtsen <larsi <at> gnus.org>
Cc: 56475 <at> debbugs.gnu.org, Ihor Radchenko <yantar92 <at> gmail.com>
Subject: Re: bug#56475: 28.1.50; bibtex-parse-entry disregards @string
 substitutions
Date: Mon, 11 Jul 2022 12:29:18 -0500

On Mon, Jul 11 2022, Roland Winkler wrote:
> The arg CONTENT of bibtex-parse-entry is passed on to
> bibtex-text-in-field-bounds that gives you a more complete description
> of what it does.  So I believe binding bibtex-expand-strings to t while
> calling bibtex-parse-entry with arg CONTENT non-nil should do the job.

I should add: The code in bibtex.el that relies on this is bibtex-url,
which in turn relies on font-lock to activate clickable links in your
bib files.  Users may or may not want to expand strings for their rules
defined in bibtex-generate-url-list.

If I understand your issue correctly you probably want to let-bind the
user variable bibtex-expand-strings while calling bibtex-parse-entry so
that your code works irrespective of what users have chosen for
bibtex-expand-strings.

Message #17 received at 56475 <at> debbugs.gnu.org (full text, mbox):

From: Ihor Radchenko <yantar92 <at> gmail.com>
To: Roland Winkler <winkler <at> gnu.org>
Cc: Lars Ingebrigtsen <larsi <at> gnus.org>, 56475 <at> debbugs.gnu.org
Subject: Re: bug#56475: 28.1.50; bibtex-parse-entry disregards @string
 substitutions
Date: Tue, 12 Jul 2022 10:32:41 +0800

Roland Winkler <winkler <at> gnu.org> writes:

> If I understand your issue correctly you probably want to let-bind the
> user variable bibtex-expand-strings while calling bibtex-parse-entry so
> that your code works irrespective of what users have chosen for
> bibtex-expand-strings.

Thanks for the pointer!
I tried my reproducer by running
M-: (let ((bibtex-expand-strings t)) (bibtex-parse-entry))
instead of
M-: (bibtex-parse-entry)

Unfortunately, the journal field is still not substituted.

Best,
Ihor

Message #20 received at 56475 <at> debbugs.gnu.org (full text, mbox):

From: Roland Winkler <winkler <at> gnu.org>
To: Ihor Radchenko <yantar92 <at> gmail.com>
Cc: Lars Ingebrigtsen <larsi <at> gnus.org>, 56475 <at> debbugs.gnu.org
Subject: Re: bug#56475: 28.1.50; bibtex-parse-entry disregards @string
 substitutions
Date: Mon, 11 Jul 2022 23:14:58 -0500

On Tue, Jul 12 2022, Ihor Radchenko wrote:
> Roland Winkler <winkler <at> gnu.org> writes:
>
>> If I understand your issue correctly you probably want to let-bind the
>> user variable bibtex-expand-strings while calling bibtex-parse-entry so
>> that your code works irrespective of what users have chosen for
>> bibtex-expand-strings.
>
> Thanks for the pointer!
> I tried my reproducer by running
> M-: (let ((bibtex-expand-strings t)) (bibtex-parse-entry))
> instead of
> M-: (bibtex-parse-entry)
>
> Unfortunately, the journal field is still not substituted.

The variable bibtex-string-files tells bibtex.el where it can find the
string definitions (which are then stored in the variable
bibtex-strings).  This complements bibtex-files that tells bibtex.el
where it can find the BibTeX entries.  A command like
bibtex-search-entry searches the entries in the files in bibtex-files.

Message #23 received at 56475 <at> debbugs.gnu.org (full text, mbox):

From: Ihor Radchenko <yantar92 <at> gmail.com>
To: Roland Winkler <winkler <at> gnu.org>
Cc: Lars Ingebrigtsen <larsi <at> gnus.org>, 56475 <at> debbugs.gnu.org
Subject: Re: bug#56475: 28.1.50; bibtex-parse-entry disregards @string
 substitutions
Date: Tue, 12 Jul 2022 14:04:55 +0800

Roland Winkler <winkler <at> gnu.org> writes:

>> Thanks for the pointer!
>> I tried my reproducer by running
>> M-: (let ((bibtex-expand-strings t)) (bibtex-parse-entry))
>> instead of
>> M-: (bibtex-parse-entry)
>>
>> Unfortunately, the journal field is still not substituted.
>
> The variable bibtex-string-files tells bibtex.el where it can find the
> string definitions (which are then stored in the variable
> bibtex-strings).  This complements bibtex-files that tells bibtex.el
> where it can find the BibTeX entries.  A command like
> bibtex-search-entry searches the entries in the files in bibtex-files.

I am wondering why bibtex-string-files is not documented inside the
docstring of bibtex-expand-strings. Same for bibtex-expand-strings not
being documented in bibtex-parse-entry.

As for using bibtex-string-files in my specific scenario, I cannot make
it work as well.

I tried the following simple test:

M-: (let ((bibtex-string-files `(,(buffer-file-name))) (bibtex-expand-strings t)) (bibtex-parse-entry))

The journal field is still not handled: ("journal" . "jgr")

Also, note that bibtex-string-files cannot help with situations when the
BibTeX buffer does not have an associated file.

Best,
Ihor

Message #26 received at 56475 <at> debbugs.gnu.org (full text, mbox):

From: Roland Winkler <winkler <at> gnu.org>
To: Ihor Radchenko <yantar92 <at> gmail.com>
Cc: Lars Ingebrigtsen <larsi <at> gnus.org>, 56475 <at> debbugs.gnu.org
Subject: Re: bug#56475: 28.1.50; bibtex-parse-entry disregards @string
 substitutions
Date: Tue, 12 Jul 2022 10:31:19 -0500

On Tue, Jul 12 2022, Ihor Radchenko wrote:
> I am wondering why bibtex-string-files is not documented inside the
> docstring of bibtex-expand-strings. Same for bibtex-expand-strings not
> being documented in bibtex-parse-entry.

I believe the situation is the other way round: bibtex-files and
bibtex-string-files are basic user variables for bibtex-mode and have
been around for 30+ years (much longer than I support bibtex.el).
bibtex-expand-strings is a small add-on in this context.

> I tried the following simple test:
>
> M-: (let ((bibtex-string-files `(,(buffer-file-name)))
> (bibtex-expand-strings t)) (bibtex-parse-entry))
>
> The journal field is still not handled: ("journal" . "jgr")

Try

M-: (let ((bibtex-string-files `(,(buffer-file-name)))
(bibtex-expand-strings t)) (bibtex-parse-entry t))

> Also, note that bibtex-string-files cannot help with situations when
> the BibTeX buffer does not have an associated file.

When does this happen?  To the best of my knowledge, this has never been
an issue for users of bibtex.el.

Message #29 received at 56475 <at> debbugs.gnu.org (full text, mbox):

From: Ihor Radchenko <yantar92 <at> gmail.com>
To: Roland Winkler <winkler <at> gnu.org>
Cc: Lars Ingebrigtsen <larsi <at> gnus.org>, 56475 <at> debbugs.gnu.org
Subject: Re: bug#56475: 28.1.50; bibtex-parse-entry disregards @string
 substitutions
Date: Sun, 17 Jul 2022 16:34:02 +0800

Roland Winkler <winkler <at> gnu.org> writes:

> On Tue, Jul 12 2022, Ihor Radchenko wrote:
>> I am wondering why bibtex-string-files is not documented inside the
>> docstring of bibtex-expand-strings. Same for bibtex-expand-strings not
>> being documented in bibtex-parse-entry.
>
> I believe the situation is the other way round: bibtex-files and
> bibtex-string-files are basic user variables for bibtex-mode and have
> been around for 30+ years (much longer than I support bibtex.el).
> bibtex-expand-strings is a small add-on in this context.

I think that the main issue on my side is that I interact with bibtex.el
from API perspective without editing many actual .bib files. So, I was
mostly looking into parser API instead of user customizations.

If you start exploring bibtex.el from bibtex-parse-entry and its
docstring, it is not very easy to figure out that bibtex-string-files
and bibtex-expand-strings need to be set. They are not mentioned in the
docstring other than by common word "extract content" with "extract"
meaning being not very clear.

>> I tried the following simple test:
>>
>> M-: (let ((bibtex-string-files `(,(buffer-file-name)))
>> (bibtex-expand-strings t)) (bibtex-parse-entry))
>>
>> The journal field is still not handled: ("journal" . "jgr")
>
> Try
>
> M-: (let ((bibtex-string-files `(,(buffer-file-name)))
> (bibtex-expand-strings t)) (bibtex-parse-entry t))

Thanks! It works now.

>> Also, note that bibtex-string-files cannot help with situations when
>> the BibTeX buffer does not have an associated file.
>
> When does this happen?  To the best of my knowledge, this has never been
> an issue for users of bibtex.el.

It is more of a hypothetical scenario that might occur in future if Org
tries to support bibliographies provided inside .org files. Such
bibliographies will need to be converted to .bib files transiently and
might not need to be saved on disk.

In any case, it is not a concern you need to worry about now. AFAIU,
bibtex.el depends on .bib buffers having non-nil buffer-file-name in
multiple places.

Best,
Ihor

Message #32 received at 56475 <at> debbugs.gnu.org (full text, mbox):

From: Roland Winkler <winkler <at> gnu.org>
To: Ihor Radchenko <yantar92 <at> gmail.com>
Cc: Lars Ingebrigtsen <larsi <at> gnus.org>, 56475 <at> debbugs.gnu.org
Subject: Re: bug#56475: 28.1.50; bibtex-parse-entry disregards @string
 substitutions
Date: Sun, 17 Jul 2022 15:10:39 -0500

On Sun, Jul 17 2022, Ihor Radchenko wrote:
>>> Also, note that bibtex-string-files cannot help with situations when
>>> the BibTeX buffer does not have an associated file.
>>
>> When does this happen?  To the best of my knowledge, this has never been
>> an issue for users of bibtex.el.
>
> It is more of a hypothetical scenario that might occur in future if Org
> tries to support bibliographies provided inside .org files. Such
> bibliographies will need to be converted to .bib files transiently and
> might not need to be saved on disk.

This sounds to me like reinventing the wheel and a poor design choice.
BibTeX is a well-established bibliography format with a large ecosystem
[(La)TeX].  Also, publishers provide BibTeX records for their journal
articles.  (Occassionally I need to deal with records that have some
other database format like RIS.  Converting formats is always painful.)

From a practical perspective, BibTeX mode is built around the idea that
users may have a large bibliography database.  Something like 10,000
records is not exotic.  Then it is natural to split up these entries
among multiple files.  BibTeX mode and its API support this very nicely.
(I have many little helper functions in my emacs init file that use the
BibTeX mode API.  Maybe I should put some of these also into bibtex.el.)

What are the usage scenarios you have in mind for putting a bibliography
database into org mode that comes with its own database format?

Message #35 received at 56475 <at> debbugs.gnu.org (full text, mbox):

From: Ihor Radchenko <yantar92 <at> gmail.com>
To: Roland Winkler <winkler <at> gnu.org>
Cc: Lars Ingebrigtsen <larsi <at> gnus.org>, 56475 <at> debbugs.gnu.org
Subject: Re: bug#56475: 28.1.50; bibtex-parse-entry disregards @string
 substitutions
Date: Mon, 18 Jul 2022 12:07:09 +0800

[Message part 1 (text/plain, inline)]

Roland Winkler <winkler <at> gnu.org> writes:

>>> When does this happen?  To the best of my knowledge, this has never been
>>> an issue for users of bibtex.el.
>>
>> It is more of a hypothetical scenario that might occur in future if Org
>> tries to support bibliographies provided inside .org files. Such
>> bibliographies will need to be converted to .bib files transiently and
>> might not need to be saved on disk.
>
> This sounds to me like reinventing the wheel and a poor design choice.
> BibTeX is a well-established bibliography format with a large ecosystem
> [(La)TeX].  Also, publishers provide BibTeX records for their journal
> articles.  (Occassionally I need to deal with records that have some
> other database format like RIS.  Converting formats is always painful.)
> ...
> What are the usage scenarios you have in mind for putting a bibliography
> database into org mode that comes with its own database format?

Org mode provides transparent conversion between BibTeX and Org formats.

The advantages of keeping bibliography in Org involve the extra things
you can do with Org headlines compared to BibTeX records:

- You can keep the related notes together with the bibliographic record
  and make use of Org markup, including inline images, inline LaTeX
  formulas, and cross-links to other bibliographic records. An example of
  such record is in the attached screenshot.

[bibtex-note-example.png (image/png, inline)]

[Message part 3 (text/plain, inline)]

- You can convert such records to actionable tasks and schedule them
  using org-agenda. This integrates literature review process with task
  management capabilities of Org.

- You can easily search across the literature records while also
  indexing the records according to personal notes/tags/relevance to
  specific projects/etc

- You can visualize relations between literature records using packages
  like org-roam-ui: https://github.com/org-roam/org-roam-ui

- You can attach the literature PDFs/related data alongside with the
  literature record using org-attach mechanism

- You can put the bibliographic records together with notes inside the
  actual authored document, being able to review and search across the
  used literature. They can also be transparently exported to the
  required printable format like pdf/Tex/html/odt/etc

> From a practical perspective, BibTeX mode is built around the idea that
> users may have a large bibliography database.  Something like 10,000
> records is not exotic.  Then it is natural to split up these entries
> among multiple files.  BibTeX mode and its API support this very nicely.
> (I have many little helper functions in my emacs init file that use the
> BibTeX mode API.  Maybe I should put some of these also into bibtex.el.)

Sure. I am not saying that the current API is incorrect. It's just
geared towards specific kind of traditional workflow.

For the bibtex.el extension, I am pretty sure that people do want some
helper functions. Some Org-related projects are even using
alternative API-oriented implementations of BibTeX parsers:
https://github.com/joostkremers/parsebib You may find reading the
parsebib's readme useful to get an idea what people need. parsebib is at
least being used by https://github.com/andras-simonyi/citeproc-el that
is natively supported by Org mode's citation engine
(https://blog.tecosaur.com/tmio/2021-07-31-citations.html).

Best,
Ihor

Message #40 received at 56475-done <at> debbugs.gnu.org (full text, mbox):

From: Roland Winkler <winkler <at> gnu.org>
To: Ihor Radchenko <yantar92 <at> gmail.com>
Cc: Lars Ingebrigtsen <larsi <at> gnus.org>, 56475-done <at> debbugs.gnu.org
Subject: Re: bug#56475: 28.1.50; bibtex-parse-entry disregards @string
 substitutions
Date: Fri, 30 Dec 2022 00:37:30 -0600

On Mon, Jul 18 2022, Ihor Radchenko wrote:
> Sure. I am not saying that the current API is incorrect. It's just
> geared towards specific kind of traditional workflow.

Closing.

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