From mboxrd@z Thu Jan 1 00:00:00 1970 X-Msuck: nntp://news.gmane.io/gmane.text.pandoc/25112 Path: news.gmane.io!.POSTED.ciao.gmane.io!not-for-mail From: Gu Lu Newsgroups: gmane.text.pandoc Subject: Re: Converting Markdown to (Multi)Markdown but citations are getting expanded twice? Date: Tue, 5 May 2020 07:09:28 -0700 (PDT) Message-ID: <261c27ed-275a-4b07-9eab-d6b584bec482@googlegroups.com> References: <5041cd75-7c55-41ec-a8c6-ac28580a39ef@googlegroups.com> Reply-To: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_Part_612_121305770.1588687768667" Injection-Info: ciao.gmane.io; posting-host="ciao.gmane.io:159.69.161.202"; logging-data="116498"; mail-complaints-to="usenet@ciao.gmane.io" To: pandoc-discuss Original-X-From: pandoc-discuss+bncBCAJXENMVEBBBGXHYX2QKGQERBUOMXI-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org Tue May 05 16:09:35 2020 Return-path: Envelope-to: gtp-pandoc-discuss@m.gmane-mx.org Original-Received: from mail-oi1-f187.google.com ([209.85.167.187]) by ciao.gmane.io with esmtps (TLS1.3:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.92) (envelope-from ) id 1jVyGN-000UC6-7u for gtp-pandoc-discuss@m.gmane-mx.org; Tue, 05 May 2020 16:09:35 +0200 Original-Received: by mail-oi1-f187.google.com with SMTP id j84sf1585151oib.21 for ; Tue, 05 May 2020 07:09:35 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=googlegroups.com; s=20161025; h=sender:date:from:to:message-id:in-reply-to:references:subject :mime-version:x-original-sender:reply-to:precedence:mailing-list :list-id:list-post:list-help:list-archive:list-subscribe :list-unsubscribe; bh=Y5yMeztkGJGEZ3tWL9XeWXX4fdpjik9tz0BYAvAx5Do=; b=iy90iq7QUrsY+t9vIPde0X9vx1IbdKRIe3oJ5+u47hQLCk/TD76VrtrnkN5lS0lyPJ kVMiqu6FPlqzSA/SK2U3VYBXhY8bg/Pi1RVfFfep7m3qHQfXd/tzVHgNCAo8tjyxhFBc tg2SP+pPaTcADXuEEpUsS5xz6XLteermcBc6rmWezW14FEEui848lWHSYfvQju+IyPVV GkhLhvw93pCXpOvGBLODcTItboEsSPFP+WBRalTRaSdRjOhYa8zGyCZQdlbgclNQmhXK q4xTZShWu0yKSCTscAUUS4fc1LWC4hQ6zYC6Bi3EBxhw2SiMVWUAXq/fLj+hPXw8K6Lo 0QUA== DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=date:from:to:message-id:in-reply-to:references:subject:mime-version :x-original-sender:reply-to:precedence:mailing-list:list-id :list-post:list-help:list-archive:list-subscribe:list-unsubscribe; bh=Y5yMeztkGJGEZ3tWL9XeWXX4fdpjik9tz0BYAvAx5Do=; b=fPDz19ICx8SqR5fTAP2FZU14xhFabOjj7Oa3hzgrDzIlcc5S04vHJ3ZahN1oorDXEq WOvbkr9EE1/xNYvMcITwwNUgNDkRuyGVeh2XqKSsmvqYmRzINGeNLcL2MCGtygqtZUxF Gl1kahNAezTfRom5XwiUbo5Xz2qvFVP6KYaGO18Rzr+xk/ZAQS+GVVR8oz9NQQmNUXt9 nq22eqT/z32AvA0aD2LEMTrsjEYi/8uymIMaivoaQmi3AmLTQGToUpnWNIEr1PWdoLe2 00TjsaypaMGt42qykJdCIVCovjlsX7mqQddwtA7jeM6ObfiQGfxW9JyNYaEl+Tw0jnJc jMMw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=sender:x-gm-message-state:date:from:to:message-id:in-reply-to :references:subject:mime-version:x-original-sender:reply-to :precedence:mailing-list:list-id:x-spam-checked-in-group:list-post :list-help:list-archive:list-subscribe:list-unsubscribe; bh=Y5yMeztkGJGEZ3tWL9XeWXX4fdpjik9tz0BYAvAx5Do=; b=dsgS0ev/5EaAV5rpqtMpdV7HUcIa68nqL7/3gkRvD3sEIN94pyKCsdpVJ9cNMpGRap rJKhJeKITA/AhTNYP7cWTB8xeVKLa88Hiw85iTyLUmVl6TTCHaSPrD8rRliq8JRwODIC sO2EfAkPUyctA3mjDMD/3SXXtKPolRZ6XiSXY8sXxyh8waDrIGw/iJk+nFkNTFHsDK8o 1xMujDGXH5sL7a7GtBUEl1yLG6YIh+mhyiRY8JFoYDiMA4V7S1xBrAr9GlHMa8hNHUY1 srt2P2+qxFyt9e+ir2twVGe2asTW2JAX/bS60txJXhIhQAzeR8e5Wz2oXtoFeUtCbwg7 zdXw== Original-Sender: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org X-Gm-Message-State: AGi0PuYuDR+3ib57RpxJ5+xHwxx97WuTjnJLHF2/hPa01dkDYjVerdPH xU2uuOFKcBaoAKXqgJgWJFY= X-Google-Smtp-Source: APiQypIQ2Vk6+bCd0Q82WQgCL+coXlJZMJ2fNP687iYx/frFTNpttuTi8gUhKB4QTeDfNrSb/ZCSew== X-Received: by 2002:a9d:67c9:: with SMTP id c9mr2718209otn.334.1588687774216; Tue, 05 May 2020 07:09:34 -0700 (PDT) X-BeenThere: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org Original-Received: by 2002:a9d:6e97:: with SMTP id a23ls659286otr.2.gmail; Tue, 05 May 2020 07:09:30 -0700 (PDT) X-Received: by 2002:a9d:136:: with SMTP id 51mr2095124otu.331.1588687769328; Tue, 05 May 2020 07:09:29 -0700 (PDT) In-Reply-To: <5041cd75-7c55-41ec-a8c6-ac28580a39ef-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> X-Original-Sender: guill.louvel-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org Precedence: list Mailing-list: list pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org; contact pandoc-discuss+owners-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org List-ID: X-Google-Group-Id: 1007024079513 List-Post: , List-Help: , List-Archive: , List-Unsubscribe: , Xref: news.gmane.io gmane.text.pandoc:25112 Archived-At: ------=_Part_612_121305770.1588687768667 Content-Type: multipart/alternative; boundary="----=_Part_613_92356590.1588687768668" ------=_Part_613_92356590.1588687768668 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable This is because you are mixing footnotes and citations. *@deustachio_2003*= =20 is a text citation: it will be expanded into e.g. "(Deustachio 2003)" or=20 "[1]" depending on your citation style. It is equivalent to the latex=20 *\cite{deustachio_2003}* command. This is not to be confused with items in= =20 the bibliography. The bibliography will automatically be created at the end= =20 of the document, so no need to make it yourself using footnotes. Le mardi 5 mai 2020 13:40:31 UTC+2, Balaji a =C3=A9crit : > > Hello, > > I'm very new to using tools such as pandoc so it's very possible that thi= s=20 > is a case of mis-reading TFM, but hours of searching thru Stackoverflow a= nd=20 > other community posts have left me at a dead-end so I hope someone can he= lp=20 > me out. > > I'm trying to convert Markdown files that have BiBTeX style citations int= o=20 > Markdown again but expand the citation as a footnote. I've come close usi= ng=20 > the Chicago Manual of Style 17th edition CSL but am finding that the=20 > citation gets expanded twice. A minimal example below: > > Original Markdown file - cite.md: > Here is one reference citing the Reactome Project. [^1] > > [^1]: @deustachio_2003 > > > BiB file - cite.bib: > @article{deustachio_2003, title=3D{Pentose phosphate pathway}, volume=3D{= 5},=20 > DOI=3D{10.3180/react_1859.1}, journal=3D{Reactome - a curated knowledgeba= se=20 > of biological pathways}, author=3D{Deustachio, P}, year=3D{2003}, month= =3D{Mar}} > > Pandoc command: > pandoc cite.md --filter pandoc-citeproc -t markdown_mmd -o cite-new.md -- > bibliography=3Dcite.bib --csl=3Dchicago-full.csl > > Output file - cite-new.md: > Here is one reference citing the Reactome Project.[^1] > >
> >
> > Deustachio, P. =E2=80=9CPentose Phosphate Pathway.=E2=80=9D *Reactome - a= Curated > Knowledgebase of Biological Pathways* 5 (March 2003). > . > >
> >
> > [^1]: P Deustachio, =E2=80=9CPentose Phosphate Pathway,=E2=80=9D *Reactom= e - a Curated > Knowledgebase of Biological Pathways* 5 (March 2003), > > > I have not been able to figure out how to prevent the additional citation= =20 > in the
from appearing in the output Markdown file and would= =20 > appreciate any help in this regard! > > FWIW, this is using pandoc 2.9.2.1 on Windows. > --=20 You received this message because you are subscribed to the Google Groups "= pandoc-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an e= mail to pandoc-discuss+unsubscribe-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org To view this discussion on the web visit https://groups.google.com/d/msgid/= pandoc-discuss/261c27ed-275a-4b07-9eab-d6b584bec482%40googlegroups.com. ------=_Part_613_92356590.1588687768668 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
This is because you are mixing footnotes and citations. @deustachio_2003 is a tex= t citation: it will be expanded into e.g. "(Deustachio 2003)" or = "[1]" depending on your citation style. It is equivalent to the l= atex \cite{deustachio_2003} command. This is not to be confused with items in the bibliography. Th= e bibliography will automatically be created at the end of the document, so= no need to make it yourself using footnotes.

Le mardi 5 mai 2020 13= :40:31 UTC+2, Balaji a =C3=A9crit=C2=A0:
Hello,

I'm ver= y new to using tools such as pandoc so it's very possible that this is = a case of mis-reading TFM, but hours of searching thru Stackoverflow and ot= her community posts have left me at a dead-end so I hope someone can help m= e out.

I'm trying to convert Markdown files th= at have BiBTeX style citations into Markdown again but expand the citation = as a footnote. I've come close using the Chicago Manual of Style 17th e= dition CSL but am finding that the citation gets expanded twice. A minimal = example below:

Original Markdown file - cite.md:
Here is one reference citing t= he Reactome Project. = [^1]

[^= 1]: @deustachi= o_2003

<= br>BiB file - cite.bib:
@article{deustachio_2003, title=3D{Pentose phosphate pathway},= volume= =3D{5},= DOI=3D= {10.3180/react_1859.1= }, journal=3D{Reactome - a curated knowledgebase of biological pathways}, author=3D{Deustachio, P}, year=3D{2003}, month=3D{Mar}}

Pandoc command:
pandoc cite.md --filter pandoc-citeproc -t markdown_mmd -o cite-new<= span style=3D"color:#660">.md --bibliography=3Dcite.bib --csl<= span style=3D"color:#660">=3Dchicago-full= .csl

Output file - cite-new.md:
= Here is= one reference citing the Reactome Project.[^1]

<div id=3D<= span style=3D"color:#080">"refs" class= =3D"references hanging-indent"<= /span> markdown=3D"1">

<div id=3D"ref-deustachi= o_2003" markdown=3D"1">

Deustachio,= P. =E2=80=9C<= /span>Pentose = Phosphate Pathway.=E2=80=9D *Reactome - a Curated
Knowledgebase of Biological Pathways<= span style=3D"color:#660">* 5 (March 2003).
<https://doi.org/10.3180/react_1859.1>.

</div>

</div= >

[^1]: P <= span style=3D"color:#606">Deustachio, =E2=80=9C<= /span>Pentose = Phosphate Pathway,=E2=80=9D *Reactome - a Curated
=C2=A0 =C2=A0 Knowledgebase of Biolog= ical Pa= thways*= 5 (March 2003= ),
=C2=A0 = =C2=A0 <https://doi.org/10.3180/react_1859.1>

I have not b= een able to figure out how to prevent the additional citation in the <div></div> from appearing in the output Markdown file and would appreciate= any help in this regard!

FWIW, th= is is using pandoc 2.9.2.1 on Windows.

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