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From: "Bruce D'Arcus" <bdarcus@gmail.com>
To: org-mode-email <emacs-orgmode@gnu.org>
Subject: Re: [PATCH] oc-basic: Detect malformed bibtex bibliographies
Date: Wed, 20 Apr 2022 08:38:27 -0400	[thread overview]
Message-ID: <CAF-FPGMyU70+NaaLCkFsfL_r3Bmy=M+HqH=t4JNoyt1UVgNhuw@mail.gmail.com> (raw)
In-Reply-To: <bc8e6b99805af23c77020c3ce2d3f2495f420dad.1650457377.git.yantar92@gmail.com>

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
>


  reply	other threads:[~2022-04-20 12:39 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 [this message]
2022-04-20 12:44   ` John Kitchin
2022-04-20 13:02     ` Ihor Radchenko

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