Issue with bibliography while exporting with org mode 9.5

[lazzalazza]

Hi,

I get a "Wrong type argument, stringp, ("/path/to/bibliography.bib")" error every time I try to export via pandoc: as a result, I am not able to export anymore.

I have already written to the org mode mantainers but apparently the problem is upstream and has to do rather with this package specifically...

Here's the backtrace of the error:

Debugger entered--Lisp error: (wrong-type-argument stringp ("/Users/test/Dropbox/ciao.bib" "/Dropbox/Standard/Bibliografia/bibliografia_gener..."))
split-string(("/Users/test/Dropbox/ciao.bib" "/Dropbox/Standard/Bibliografia/bibliografia_gener...") "\n")
#f(compiled-function (it) #<bytecode 0x1a35aa0a79e6febf>)((bibliography . :bibliography))

• org-pandoc-template(#("#+bibliography: ciao.bib\n\n* Firs..." 28 43 (:parent (headline (:raw-value "First paragraph" :begin 43 :end 86 :pre-blank 0 :contents-begin 62 :contents-end 85 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 43 ...) (section ... ...))) 44 59 (:parent (paragraph (:begin 62 :end 85 :contents-begin 62 :contents-end 85 :post-blank 0 :post-affiliated 62 :parent ...) #("Text text text." 0 15 ...) (footnote-reference ...) #("\n" 0 1 ...)))) (:export-options nil :back-end #s(org-export-backend :name pandoc :parent org :transcoders ((latex-environment . org-pandoc-latex-environ) (link . org-pandoc-link) (table . org-pandoc-table) (template . org-pandoc-template) (paragraph . org-pandoc-paragraph) (src-block . org-pandoc-src-block)) :options ((:pandoc-options "PANDOC_OPTIONS" nil nil space) (:pandoc-extensions "PANDOC_EXTENSIONS" nil nil space) (:pandoc-metadata "PANDOC_METADATA" nil nil space) (:pandoc-variables "PANDOC_VARIABLES" nil nil space) (:epub-chapter-level "EPUB_CHAPTER_LEVEL" nil nil t) (:epub-cover-image "EPUB_COVER" nil nil t) (:epub-stylesheet "EPUB_STYLESHEET" nil nil t) (:epub-embed-font "EPUB_EMBED_FONT" nil nil newline) (:epub-meta "EPUB_META" nil nil newline) (:epub-css "EPUB_CSS" nil nil newline) (:epub-rights "EPUB_RIGHTS" nil nil newline) (:bibliography "BIBLIOGRAPHY")) :filters nil :blocks nil :menu (112 "export via pandoc" (... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...))) :translate-alist ((latex-environment . org-pandoc-latex-environ) (link . org-pandoc-link) (table . org-pandoc-table) (template . org-pandoc-template) (paragraph . org-pandoc-paragraph) (src-block . org-pandoc-src-block) (babel-call . org-org-identity) (bold . org-org-identity) (center-block . org-org-identity) (clock . org-org-identity) (code . org-org-identity) (diary-sexp . org-org-identity) (drawer . org-org-identity) (dynamic-block . org-org-identity) (entity . org-org-identity) (example-block . org-org-identity) (export-block . org-org-export-block) (fixed-width . org-org-identity) (footnote-definition . ignore) (footnote-reference . org-org-identity) (headline . org-org-headline) (horizontal-rule . org-org-identity) (inline-babel-call . org-org-identity) (inline-src-block . org-org-identity) (inlinetask . org-org-identity) (italic . org-org-identity) (item . org-org-identity) (keyword . org-org-keyword) (latex-environment . org-org-identity) (latex-fragment . org-org-identity) (line-break . org-org-identity) (link . org-org-link) ...) :exported-data #<hash-table eq 17/4001 0x1ff11ec3ad5f> :input-buffer "prova.org" :input-file "/Users/test/Dropbox/prova.org" :pandoc-options nil :pandoc-extensions nil :pandoc-metadata nil :pandoc-variables nil :epub-chapter-level nil :epub-cover-image nil :epub-stylesheet nil :epub-embed-font nil :epub-meta nil :epub-css nil ...))
  org-export-as(pandoc nil nil nil (:output-file "prova.tmpPDzJxT.org"))
  org-export-to-file(pandoc "prova.tmpPDzJxT.org" nil nil nil nil nil #f(compiled-function (f) #<bytecode 0xb0002599e44c2eb>))
  org-pandoc-export(docx nil nil nil nil nil 0)
  org-pandoc-export-to-docx-and-open(nil nil nil nil)
  org-export-dispatch(nil)
  funcall-interactively(org-export-dispatch nil)
  command-execute(org-export-dispatch)

Thank you so much,

Andrea.

[a-fent]

Thank you for the report. With Org 9.5 having in-built citation support, the way the BIBLIOGRAPHY option is handled is now incompatible between org and pandoc. There are multiple ways citations could be handled (by org-mode itself, by pandoc, or by the latex processor). I need to work out which are possible and how to support them. There are also some changes needed in pandoc to catch up: jgm/pandoc#7329

I have it on top of my list on the maintained fork of ox-pandoc. Feel free to comment there.

For now, you'll either have to use Org 9.4 or use Org 9.5 with the built-in export backends, not ox-pandoc.

[lazzalazza]

@a-fent Thank you so much for your reply and for your effort: ox-pandoc is such an amazing package and I can't wait to see it fully working again!

[lazzalazza]

PS. I have played a little with the code and tryed feeding the split-string function with (nth 0 value), to see if I could temporarily patch the problem... It didn't work. The bibliography item was not recognized and simply printed as a link in the output file (a .docx in my case).

[a-fent]

Yes, there are a few things that need to be changed in option handling and processing. I have got as far as having ox-pandoc pass through the bibliography if on 9.5, so it will let Org mode handle citations. So you can use "basic" or "biblatex" (for example) and have it work.

It's on a branch if you want to try it. https://github.com/emacsorphanage/ox-pandoc/tree/citations-org9.5

[lazzalazza]

Thanks! Sorry, when you say "you can use "basic" or "biblatex" (for example) and have it work", what do you refer to exactly? I have tried the code, it doesn't give me any problem while exporting, but the result is not formatted (i still get a link that says "cite:&bibliographyitem" in my .docx file). Probably this was meant to be, being this an early stage of development of the branch...

[a-fent]

Thank you, I appreciate you taking the time to try it out.

I should have been clearer: I meant that if you put a #+CITE_EXPORT header in the document, Org 9.5+ should process the citations in the way described in the Org manual

However I have only tried the biblatex and basic processors. If you are exporting to docx you probably will want to use the CSL exporter.

[lazzalazza]

No, thank you! I had already set the value of org-cite-export-processors: (setq org-cite-export-processors '((beamer biblatex) (latex biblatex) (t csl "~/Dropbox/Standard/Modelli/andrea.csl"))) so – if I am not wrong – it should have worked in the first place, shouldn’t it?

…

Il giorno 17 nov 2021, alle ore 15:17, Alex Fenton ***@***.***> ha scritto: Thank you, I appreciate you taking the time to try it out. I should have been clearer: I meant that if you put a #+CITE_EXPORT header in the document, Org 9.5+ should process the citations in the way described in the Org manual <https://orgmode.org/manual/Citation-export-processors.html#Citation-export-processors> However I have only tried the biblatex and basic processors. If you are exporting to docx you probably will want to use the CSL exporter. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#85 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AONRCSKP3S4UBH77KIASY53UMO2OVANCNFSM5HWEUJJQ>. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[a-fent]

Not 100% sure, I haven't worked that much yet with the new citation system. But looks right. My test document sets it in the org-mode header line. #+CITE_EXPORT: biblatex which produces an \autocite (IIRC).

[lazzalazza]

Hi! Is there any update on the treatment of org 9.5 citations? I see that a new release appeared on MELPA in the meanwhile, but the exporting of citations via csl still seems impossible. Am I doing anything wrong or the development is still on its way? Thank you so much!

[a-fent]

Please could you post a minimal example at the thread emacsorphanage#1 together with any error messages?

It should work in theory, but it's still experimental and more reports on the CSL export in particular would help.

[lazzalazza]

Sure, I just did it! Thanks!

…

Il giorno 1 dic 2021, alle ore 08:11, Alex Fenton ***@***.***> ha scritto: Please could you post a minimal example at the thread emacsorphanage#1 <emacsorphanage#1> together with any error messages? It should work in theory, but it's still experimental and more reports on the CSL export in particular would help. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#85 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AONRCSKS3IMUHBBANDBE4YDUOXDCBANCNFSM5HWEUJJQ>. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.