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 <bdar...@gmail.com> wrote: > On Wed, Apr 20, 2022 at 8:28 AM Ihor Radchenko <yanta...@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: yanta...@gmail.com, ihor_radche...@alumni.sutd.edu.sg > > > >
