Re: citeproc-org and org-ref 3

[John Kitchin]

I have seen this happen at times, and I think it is style and maybe
browser dependent.

Could you send me a small example (including the csl file you use) that
I could look at?


Joseph Vidal-Rosset <joseph@vidal-rosset.net> writes:

> Hi John,
>
> A detail about exporting with org-ref 3 in html when the csl style is
> for numeric references. With org-ref 2 + citeproc-org, I got this:
>
> [1] R. Descartes, Meditations on First Philosophy: with Selections from
> the Objections and Replies. Oxford: OUP Oxford, 2008.
>
> (see the references here :
> https://www.vidal-rosset.net/descartess_first_proof_of_gods_existence_in_first-order_logic.html
> )
>
> With org-ref 3, with apparently any numeric style, I get this:
>
> [1]
> R. Descartes, Meditations on First Philosophy: with Selections from the
> Objections and Replies. Oxford: OUP Oxford, 2008.
>
> I mean that each bibliographical reference is below its number link, and
> it is not very nice. I wonder about the reason of this difference of
> output, and a possible solution.
>
> Best wishes,
>
> Jo.
>
> Le 02/12/2021 à 18:35, John Kitchin a écrit :
>> Glad to hear it is working again for you! Best wishes,
>>
>> Joseph Vidal-Rosset <joseph@vidal-rosset.net> writes:
>>
>>> Dear all,
>>>
>>>
>>> I just succeeded in solving my problem.
>>>
>>> l-210-235 of myblogexporter.el, I changed the code for:
>>>
>>> (defun org-export-head-export-headers (directory-name backend)
>>>     "Exports each heading to directory-name using backend"
>>>     (if (equal backend "html")
>>>         (org-export-head--run-on-each-heading
>>>          #'(lambda ()
>>>              (org-set-property
>>>               "EXPORT_FILE_NAME"
>>>               (concat directory-name (org-export-head--escaped-headline)))
>>>              (deactivate-mark)
>>>              (let ((org-export-before-parsing-hook
>>> '(org-ref-csl-preprocess-buffer)))
>>>                   (cl-letf (((symbol-function 'org-export-get-reference)
>>> (symbol-function 'org-export-get-reference-custom)))
>>>                     (if org-export-head-click-toc-h2
>>>                         (cl-letf ((
>>>                                    ;(symbol-function 'org-html-toc)
>>>                                    (symbol-function
>>> 'org-export-head--custom-toc)))
>>>                           (org-html-export-to-html nil t)))))
>>>              (set-buffer-modified-p t)) "-noexport-noreexport"))
>>>     (if (equal backend "pdf")
>>>         (org-export-head--run-on-each-heading
>>>          #'(lambda ()
>>>              (org-set-property
>>>               "EXPORT_FILE_NAME"
>>>               (concat directory-name (org-export-head--escaped-headline)))
>>>              (deactivate-mark)
>>>              (org-latex-export-to-pdf nil t)
>>>              (set-buffer-modified-p t)) "-noexport-noreexport")))
>>>
>>> and it works with org-ref 3.
>>>
>>> Best wishes,  I attach myblogexporter.el
>>>
>>> Jo.
>>>
>>> Le 02/12/2021 à 14:17, Joseph Vidal-Rosset a écrit :
>>>> Dear John (cc. Ivan),
>>>>
>>>> First, thanks for your help and for your patience, that's very kind of you.
>>>>
>>>> The good news is that indeed, org-ref 3 exports nicely the  html
>>>> bibliography with my CSL file, it works well with your org file and your
>>>> bibliography. My error was simple: I did not use the specific org-ref
>>>> keys but the ordinary h-o keys.. A stupid mistake.
>>>>
>>>> The bad news is that this new function for exporting with org-ref 3 is
>>>> not included in org-export-head, a nice org mode to blog exporter, made
>>>> by Ivan Tadeu Ferreira Antunes Filho, which converts each header to a
>>>> different file, I find this exporter very convenient. I had no problem
>>>> with this org-ref 2 to use this blog-exporter, but it org-ref 3 is
>>>> unfortunately not still adapted to its use. Nevertheless, I believe that
>>>> it should be possible to find the lines to include this function
>>>> (let  ((org-export-before-parsing-hook '(org-ref-csl-preprocess-buffer)))
>>>>        (org-open-file  (org-html-export-to-html)))
>>>> in org-export-head. I tried, but without success, because I am simply
>>>> not expert enough. I see the best, that is to export both with org-ref 3
>>>> (i.e. "r h") and org-export-head, but I am unable to code it.
>>>>
>>>> No doubt that it should be for you and Ivan a piece of cake, but please
>>>> do it only if you think that it is interesting and if you find the time
>>>> to do it.
>>>>
>>>> Best wishes,
>>>>
>>>> Jo.
>>>>
>>>> PS in attachment, myblogexporter.el in my ~/.emacs.d/personal  (usual
>>>> path with Prelude Emacs).
>>>>
>>>> Le 01/12/2021 à 23:16, John Kitchin a écrit :
>>>>>
>>>>> Joseph Vidal-Rosset <joseph@vidal-rosset.net> writes:
>>>>>
>>>>>> Dear Andras,
>>>>>>
>>>>>> You are very probably right. I will have a look on this entry in my
>>>>>> default bibliography file.
>>>>>>
>>>>>> The code
>>>>>>
>>>>>> (let  ((org-export-before-parsing-hook '(org-ref-csl-preprocess-buffer)))
>>>>>>            (org-open-file  (org-html-export-to-html)))
>>>>>>
>>>>>> put in .emacs.d/personal/preload/myorgexport.el
>>>>>>
>>>>> This code should not go in your init file. It is executed each time, and
>>>>> not what you want. I usually put it a src block at the end in a section
>>>>> tagged noexport and run it from there.
>>>>>
>>>>> Alternatively, if this is the only preprocessing you do, I think you can
>>>>> do C-c C-e rh to export to html (this runs the org-ref html exporter.
>>>>>
>>>>> Finally, if you really want something in your init file it should be
>>>>> like this:
>>>>>
>>>>> (defun my-html ()
>>>>>      (interactive)
>>>>>      (let  ((org-export-before-parsing-hook 
>>>>> '(org-ref-csl-preprocess-buffer)))
>>>>>        (org-open-file  (org-html-export-to-html))))
>>>>>
>>>>> and then later you run it with M-x my-html
>>>>>
>>>>>
>>>>>> provokes the request of opening a html file, when emacs --daemon is
>>>>>> started; therefore I conclude that it should not be used as I did...
>>>>>>
>>>>>> Anyway, every  tentative  to export in a bibliography in html fails at
>>>>>> the moment, even with a new bibliography file...  :(
>>>>>
>>>>> See of the one at
>>>>> https://github.com/jkitchin/org-ref/blob/master/examples/basic-csl.org
>>>>> works. The bib file is in
>>>>> https://github.com/jkitchin/org-ref/blob/master/org-ref.bib.
>>>>>
>>>>>
>>>>>
>>>>>>
>>>>>> Best wishes,
>>>>>>
>>>>>> Le 01/12/2021 à 17:33, András Simonyi a écrit :
>>>>>>> Dear Joseph,
>>>>>>>
>>>>>>> based on the error message there seems to be a problem with the
>>>>>>> 'curley-nil-on-bennet-spinoz' bibliography entry, is it possible that
>>>>>>> it contains a 'year = nil' row? If yes then I don't think that is
>>>>>>> well-formed, at least citeproc-el cannot currently parse it. Anyhow,
>>>>>>> apparently I need to improve/add citeproc-el error messages about
>>>>>>> bib(la)tex parsing, because several parsing problems have surfaced
>>>>>>> lately and the current error messages aren't helpful at all.
>>>>>>>
>>>>>>> best wishes,
>>>>>>> András
>>>>>>>
>>>>>>> On Wed, 1 Dec 2021 at 16:50, Joseph Vidal-Rosset
>>>>>>> <joseph@vidal-rosset.net> wrote:
>>>>>>>>
>>>>>>>> Dear John,
>>>>>>>>
>>>>>>>> I must say that to export references in html with org-ref 3, I meet a
>>>>>>>> lot of problems (with LaTeX, it's fine).
>>>>>>>>
>>>>>>>> I am using prelude emacs and  GNU Emacs 29.0.50 .
>>>>>>>>
>>>>>>>> Starting emacs --daemon, the code
>>>>>>>>
>>>>>>>> (let  ((org-export-before-parsing-hook 
>>>>>>>> '(org-ref-csl-preprocess-buffer)))
>>>>>>>>          (org-open-file  (org-html-export-to-html)))
>>>>>>>>
>>>>>>>> in my setup provokes this unwanting effect:
>>>>>>>>
>>>>>>>> [Prelude] Loading personal configuration files in
>>>>>>>> /home/joseph/.emacs.d/personal/preload...
>>>>>>>> Loading /home/joseph/.emacs.d/personal/preload/myorgexport.el 
>>>>>>>> (source)...
>>>>>>>> Output file:
>>>>>>>>
>>>>>>>> and with Enter :
>>>>>>>>
>>>>>>>> [Prelude] Loading personal configuration files in
>>>>>>>> /home/joseph/.emacs.d/personal/preload...
>>>>>>>> Loading /home/joseph/.emacs.d/personal/preload/myorgexport.el 
>>>>>>>> (source)...
>>>>>>>> Output file:
>>>>>>>> Warning (initialization): An error occurred while loading
>>>>>>>> ‘/home/joseph/.emacs.d/init.el’:
>>>>>>>>
>>>>>>>> Wrong type argument: stringp, nil
>>>>>>>>
>>>>>>>> To ensure normal operation, you should investigate and remove the
>>>>>>>> cause of the error in your initialization file.  Start Emacs with
>>>>>>>> the ‘--debug-init’ option to view a complete error backtrace. Disable
>>>>>>>> showing Disable logging
>>>>>>>> Starting Emacs daemon.
>>>>>>>>
>>>>>>>> With --debug-init, I get:
>>>>>>>>
>>>>>>>> Debugger entered--Lisp error: (wrong-type-argument stringp nil)
>>>>>>>>        string-to-number(nil)
>>>>>>>>        citeproc-bt--to-csl-date("nil" nil)
>>>>>>>>        citeproc-blt-entry-to-csl((("Url" .
>>>>>>>> "http://dx.doi.org/10.1163/9789004246638_005";) ("Doi" .
>>>>>>>> "10.1163/9789004246638_005") ("Date_added" . "Mon May 16 19:09:37 
>>>>>>>> 2016")
>>>>>>>> ("Booktitle" . "Spinoza: Issues and Directions") ("Series" . "Spinoza:
>>>>>>>> Issues and Directions") ("Year" . "nil") ("Publisher" . "Brill Academic
>>>>>>>> Publishers") ("Pages" . "39-52") ("Author" . "Edwin Curley") ("Title" .
>>>>>>>> "ON BENNETTS SPINOZA: THE ISSUE OF TELEOLOGY") ("=type=" . "InBook")
>>>>>>>> ("=key=" . "curley-nil-on-bennet-spinoz")) nil nil)
>>>>>>>>        #f(compiled-function (key entry) #<bytecode
>>>>>>>> -0x7fcb46b5c8e80b3>)("curley-nil-on-bennet-spinoz" (("Url" .
>>>>>>>> "http://dx.doi.org/10.1163/9789004246638_005";) ("Doi" .
>>>>>>>> "10.1163/9789004246638_005") ("Date_added" . "Mon May 16 19:09:37 
>>>>>>>> 2016")
>>>>>>>> ("Booktitle" . "Spinoza: Issues and Directions") ("Series" . "Spinoza:
>>>>>>>> Issues and Directions") ("Year" . "nil") ("Publisher" . "Brill Academic
>>>>>>>> Publishers") ("Pages" . "39-52") ("Author" . "Edwin Curley") ("Title" .
>>>>>>>> "ON BENNETTS SPINOZA: THE ISSUE OF TELEOLOGY") ("=type=" . "InBook")
>>>>>>>> ("=key=" . "curley-nil-on-bennet-spinoz")))
>>>>>>>>        maphash(#f(compiled-function (key entry) #<bytecode
>>>>>>>> -0x7fcb46b5c8e80b3>) #<hash-table equal 665/730 0x156f8acb26b7>)
>>>>>>>>        
>>>>>>>> citeproc-hash-itemgetter-from-any(("~/Dropbox/Orgzly/reforg.bib"))
>>>>>>>>        org-ref-process-buffer(html)
>>>>>>>>        org-ref-csl-preprocess-buffer(html)
>>>>>>>>        run-hook-with-args(org-ref-csl-preprocess-buffer html)
>>>>>>>>        org-export-as(html nil nil nil (:output-file "~/test.html"))
>>>>>>>>        org-export-to-file(html "~/test.html" nil nil nil nil nil)
>>>>>>>>        org-html-export-to-html()
>>>>>>>>        (org-open-file (org-html-export-to-html))
>>>>>>>>        (let ((org-export-before-parsing-hook
>>>>>>>> '(org-ref-csl-preprocess-buffer))) (org-open-file
>>>>>>>> (org-html-export-to-html)))
>>>>>>>>        eval-buffer(#<buffer  *load*-634240> nil
>>>>>>>> "/home/joseph/.emacs.d/personal/preload/myorgexport..." nil t)  ;
>>>>>>>> Reading at buffer position 3196
>>>>>>>>
>>>>>>>> load-with-code-conversion("/home/joseph/.emacs.d/personal/preload/myorgexport..."
>>>>>>>> "/home/joseph/.emacs.d/personal/preload/myorgexport..." nil nil)
>>>>>>>>        load("/home/joseph/.emacs.d/personal/preload/myorgexport...")
>>>>>>>>        mapc(load 
>>>>>>>> ("/home/joseph/.emacs.d/personal/preload/myorgexport..."))
>>>>>>>>        (progn (message "[Prelude] Loading personal configuration files 
>>>>>>>> in
>>>>>>>> ..." prelude-personal-preload-dir) (mapc 'load (directory-files
>>>>>>>> prelude-personal-preload-dir 't "^[^#.].*el$")))
>>>>>>>>        (if (file-exists-p prelude-personal-preload-dir) (progn (message
>>>>>>>> "[Prelude] Loading personal configuration files in ..."
>>>>>>>> prelude-personal-preload-dir) (mapc 'load (directory-files
>>>>>>>> prelude-personal-preload-dir 't "^[^#.].*el$"))))
>>>>>>>>        eval-buffer(#<buffer  *load*> nil 
>>>>>>>> "/home/joseph/.emacs.d/init.el" nil
>>>>>>>> t)  ; Reading at buffer position 4489
>>>>>>>>        load-with-code-conversion("/home/joseph/.emacs.d/init.el"
>>>>>>>> "/home/joseph/.emacs.d/init.el" t t)
>>>>>>>>        load("/home/joseph/.emacs.d/init" noerror nomessage)
>>>>>>>>        startup--load-user-init-file(#f(compiled-function () #<bytecode
>>>>>>>> 0xec639179d6199fa>) #f(compiled-function () #<bytecode
>>>>>>>> -0x1f3c686ddc0dc635>) t)
>>>>>>>>        command-line()
>>>>>>>>        normal-top-level()
>>>>>>>>
>>>>>>>> It's too complicated for me.
>>>>>>>> org-ref version 2 with citeproc-org by Andras worked well, but now I am
>>>>>>>> afraid that to downgrade to org-ref 2 is not necessarily the best
>>>>>>>> solution. I am lost.
>>>>>>>>
>>>>>>>> Best wishes, and thanks for your help.
>>>>>>>>
>>>>>>>> Jo.
>>>>>>>>
>>>>>>>>
>>>>>>>> Le 30/11/2021 à 18:31, John Kitchin a écrit :
>>>>>>>>> See https://www.youtube.com/watch?v=rRR-5NSpKyE
>>>>>>>>> <https://www.youtube.com/watch?v=rRR-5NSpKyE> for an overview of what 
>>>>>>>>> to
>>>>>>>>> do. basically you need a csl file that provides the style you want, 
>>>>>>>>> and
>>>>>>>>> you specify it like this in the org file or in default settings. You 
>>>>>>>>> may
>>>>>>>>> also need a locale file if you are not blogging in english.
>>>>>>>>>
>>>>>>>>> #+csl-style: apa-5th-edition.csl
>>>>>>>>>
>>>>>>>>> #+csl-locale: en-US
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> You can find a basic example org file for html export with CSL at
>>>>>>>>> https://github.com/jkitchin/org-ref/blob/master/examples/basic-csl.org
>>>>>>>>> <https://github.com/jkitchin/org-ref/blob/master/examples/basic-csl.org>
>>>>>>>>>
>>>>>>>>> Here is a minimal way to export your blog file I suppose.
>>>>>>>>>
>>>>>>>>> (let  ((org-export-before-parsing-hook 
>>>>>>>>> '(org-ref-csl-preprocess-buffer)))
>>>>>>>>>        (org-open-file  (org-html-export-to-html)))
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 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 <http://kitchingroup.cheme.cmu.edu>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Tue, Nov 30, 2021 at 12:16 PM András Simonyi
>>>>>>>>> <andras.simonyi@gmail.com <mailto:andras.simonyi@gmail.com>> wrote:
>>>>>>>>>
>>>>>>>>>         Dear Joseph,
>>>>>>>>>
>>>>>>>>>         unfortunately, my note on the `citeproc-org` page has become 
>>>>>>>>> kind of
>>>>>>>>>         misleading and has to be updated because org-ref didn't 
>>>>>>>>> switch to the
>>>>>>>>>         new org-cite citation syntax after all, although this was the 
>>>>>>>>> plan for
>>>>>>>>>         a while. I think if you wish to use org-ref 3 then you should 
>>>>>>>>> simply
>>>>>>>>>         remove citeproc-org entirely -- if I understand correctly the 
>>>>>>>>> latest
>>>>>>>>>         version of org-ref supports the old syntax as well and is 
>>>>>>>>> capable of
>>>>>>>>>         CSL-based export (among others) on its own.
>>>>>>>>>
>>>>>>>>>         best regards,
>>>>>>>>>         András
>>>>>>>>>
>>>>>>>>>         On Tue, 30 Nov 2021 at 18:00, Joseph Vidal-Rosset
>>>>>>>>>         <joseph@vidal-rosset.net <mailto:joseph@vidal-rosset.net>> 
>>>>>>>>> wrote:
>>>>>>>>>          >
>>>>>>>>>          >
>>>>>>>>>          > Dear John, and dear Andras,
>>>>>>>>>          >
>>>>>>>>>          > Having updated my org-ref to the last version, I see that 
>>>>>>>>> the html
>>>>>>>>>          > export of bibliography does not work any longer for my 
>>>>>>>>> blog.
>>>>>>>>>          >
>>>>>>>>>          > Reading Andras's note here
>>>>>>>>>          > https://github.com/andras-simonyi/citeproc-org
>>>>>>>>>         <https://github.com/andras-simonyi/citeproc-org>
>>>>>>>>>          > I confess that I am lost.
>>>>>>>>>          >
>>>>>>>>>          > What have I to do to not waste too much time with this 
>>>>>>>>> problem?
>>>>>>>>>          >
>>>>>>>>>          > Best wishes,
>>>>>>>>>          >
>>>>>>>>>          > Jo.
>>>>>>>>>          >
>>>>>>>>>
>>>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Professor John Kitchin
>>>>> Doherty Hall A207F
>>>>> Department of Chemical Engineering
>>>>> Carnegie Mellon University
>>>>> Pittsburgh, PA 15213
>>>>> 412-268-7803
>>>>> @johnkitchin
>>>>> http://kitchingroup.cheme.cmu.edu
>>>>> Pronouns: he/him/his
>>>>>
>>>
>>> [2. text/x-emacs-lisp; myblogexporter.el]...
>>
>>
>> --
>> Professor John Kitchin
>> Doherty Hall A207F
>> Department of Chemical Engineering
>> Carnegie Mellon University
>> Pittsburgh, PA 15213
>> 412-268-7803
>> @johnkitchin
>> http://kitchingroup.cheme.cmu.edu
>> Pronouns: he/him/his
>>


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