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From: John Kitchin <jkitchin@andrew.cmu.edu>
To: "Bruce D'Arcus" <bdarcus@gmail.com>
Cc: org-mode-email <emacs-orgmode@gnu.org>
Subject: Re: [PATCH] oc-basic: Detect malformed bibtex bibliographies
Date: Wed, 20 Apr 2022 08:44:32 -0400	[thread overview]
Message-ID: <CAJ51ETp67jayCmpK2nYjD3t5a8OhJP8dKCFu9HW_bvqZB7Dz3A@mail.gmail.com> (raw)
In-Reply-To: <CAF-FPGMyU70+NaaLCkFsfL_r3Bmy=M+HqH=t4JNoyt1UVgNhuw@mail.gmail.com>

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I would see if you can cache the result and not do it more than needed; it
can add a performance issue on large files.

John

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



On Wed, Apr 20, 2022 at 8:39 AM Bruce D'Arcus <bdarcus@gmail.com> wrote:

> On Wed, Apr 20, 2022 at 8:28 AM Ihor Radchenko <yantar92@gmail.com> wrote:
> >
> > There is an edge case triggering infinite loop in oc-basic.
> >
> > It is caused by bibtex-map-entries (used in
> > org-cite-basic--parse-bibtex) when ran on a malformed bibtex buffer [1].
> >
> > The proposed patch validates the bibtex buffer before processing and
> > throws an error if issues are found.  `bibtex-validate` also
> > conveniently displays a list of errors with clickable links to
> > problematic lines.
> >
> > I believe that it is useful for the users to see such issues instead of,
> > say, failing silently on malformed bibliographies.
> >
> > WDYT?
>
> I haven't tested it, but this is an excellent idea!
>
> Bruce
>
> > Best,
> > Ihor
> >
> > [1] https://debbugs.gnu.org/cgi/bugreport.cgi?bug=55036
> >
> > * lisp/oc-basic.el (org-cite-basic--parse-bibtex): Validate the
> > bibliography before parsing.  Display list of issues if any (via
> > `bibtex-validate`).
> > (org-cite-basic--parse-bibliography): Set buffer file name needed by
> > `bibtex-validate`.  Empty the cache in case of error.
> > ---
> >  lisp/oc-basic.el | 38 ++++++++++++++++++++++++--------------
> >  1 file changed, 24 insertions(+), 14 deletions(-)
> >
> > diff --git a/lisp/oc-basic.el b/lisp/oc-basic.el
> > index 873986d07..79f7a4844 100644
> > --- a/lisp/oc-basic.el
> > +++ b/lisp/oc-basic.el
> > @@ -214,6 +214,10 @@ (defun org-cite-basic--parse-bibtex (dialect)
> >    (let ((entries (make-hash-table :test #'equal))
> >          (bibtex-sort-ignore-string-entries t))
> >      (bibtex-set-dialect dialect t)
> > +    ;; Throw an error if bibliography is malformed.
> > +    (unless (bibtex-validate)
> > +      (user-error "Malformed bibliography at %S"
> > +                  (or (buffer-file-name) (current-buffer))))
> >      (bibtex-map-entries
> >       (lambda (key &rest _)
> >         ;; Normalize entries: field names are turned into symbols
> > @@ -258,21 +262,27 @@ (defun org-cite-basic--parse-bibliography
> (&optional info)
> >              (when (or (org-file-has-changed-p file)
> >                        (not (gethash file
> org-cite-basic--file-id-cache)))
> >                (insert-file-contents file)
> > +              (setf (buffer-file-name) file)
> >                (puthash file (org-buffer-hash)
> org-cite-basic--file-id-cache))
> > -           (let* ((file-id (cons file (gethash file
> org-cite-basic--file-id-cache)))
> > -                   (entries
> > -                    (or (cdr (assoc file-id
> org-cite-basic--bibliography-cache))
> > -                        (let ((table
> > -                               (pcase (file-name-extension file)
> > -                                 ("json" (org-cite-basic--parse-json))
> > -                                 ("bib" (org-cite-basic--parse-bibtex
> 'biblatex))
> > -                                 ("bibtex"
> (org-cite-basic--parse-bibtex 'BibTeX))
> > -                                 (ext
> > -                                  (user-error "Unknown bibliography
> extension: %S"
> > -                                              ext)))))
> > -                          (push (cons file-id table)
> org-cite-basic--bibliography-cache)
> > -                          table))))
> > -              (push (cons file entries) results)))))
> > +            (unwind-protect
> > +                (condition-case nil
> > +                    (unwind-protect
> > +                       (let* ((file-id (cons file (gethash file
> org-cite-basic--file-id-cache)))
> > +                               (entries
> > +                                (or (cdr (assoc file-id
> org-cite-basic--bibliography-cache))
> > +                                    (let ((table
> > +                                           (pcase (file-name-extension
> file)
> > +                                             ("json"
> (org-cite-basic--parse-json))
> > +                                             ("bib"
> (org-cite-basic--parse-bibtex 'biblatex))
> > +                                             ("bibtex"
> (org-cite-basic--parse-bibtex 'BibTeX))
> > +                                             (ext
> > +                                              (user-error "Unknown
> bibliography extension: %S"
> > +                                                          ext)))))
> > +                                      (push (cons file-id table)
> org-cite-basic--bibliography-cache)
> > +                                      table))))
> > +                          (push (cons file entries) results))
> > +                      (setf (buffer-file-name) nil))
> > +                  (error (setq org-cite-basic--file-id-cache nil)))))))
> >        (when info (plist-put info :cite-basic/bibliography results))
> >        results)))
> >
> > --
> > 2.35.1
> >
> >
> >
> > --
> > Ihor Radchenko,
> > PhD,
> > Center for Advancing Materials Performance from the Nanoscale (CAMP-nano)
> > State Key Laboratory for Mechanical Behavior of Materials, Xi'an
> Jiaotong University, Xi'an, China
> > Email: yantar92@gmail.com, ihor_radchenko@alumni.sutd.edu.sg
> >
>
>

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  reply	other threads:[~2022-04-20 12:47 UTC|newest]

Thread overview: 4+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2022-04-20 12:28 Ihor Radchenko
2022-04-20 12:38 ` Bruce D'Arcus
2022-04-20 12:44   ` John Kitchin [this message]
2022-04-20 13:02     ` Ihor Radchenko

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