Re: citeproc-org and org-ref 3

[Joseph Vidal-Rosset]

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
>

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