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JATS writer: fix citations (#7018)

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* JATS writer: keep code lines at 80 chars or below

* JATS writer: fix citations
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11
COPYRIGHT
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@ -181,7 +181,7 @@ http://github.com/paulrouget/dzslides
Released under the Do What the Fuck You Want To Public License. Released under the Do What the Fuck You Want To Public License.
------------------------------------------------------------------------ ------------------------------------------------------------------------
Pandoc embeds a lua interpreter (via hslua). Pandoc embeds a Lua interpreter (via hslua).
Copyright © 1994–2020 Lua.org, PUC-Rio. Copyright © 1994–2020 Lua.org, PUC-Rio.
@ -203,12 +203,3 @@ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
------------------------------------------------------------------------
The template pandoc.jats is Copyright 2013--2015 Martin Fenner,
released under GPL version 2 or later.
The file data/jats.csl is derived from a csl file by Martin Fenner,
revised by Martin Paul Eve and then John MacFarlane.
"This work is licensed under a Creative Commons Attribution-ShareAlike 3.0
License. Originally by Martin Fenner."

203
data/jats.csl
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@ -1,203 +0,0 @@
<?xml version="1.0" encoding="utf-8"?>
<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" default-locale="en-US">
<info>
<title>Journal Article Tag Suite</title>
<title-short>JATS</title-short>
<id>http://www.zotero.org/styles/journal-article-tag-suite</id>
<link href="https://github.com/MartinPaulEve/JATS-CSL/blob/master/jats.csl" rel="self"/>
<link rel="documentation" href="http://jats.nlm.nih.gov/archiving/tag-library/1.0/index.html"/>
<author>
<name>Martin Paul Eve</name>
<email>martin@martineve.com</email>
</author>
<category citation-format="numeric"/>
<category field="medicine"/>
<category field="biology"/>
<summary>Use this style to generate bibliographic data in Journal Article Tagging Suite (JATS) 1.0 XML format</summary>
<updated>2014-06-21T17:41:26+00:00</updated>
<rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License. Originally by Martin Fenner.</rights>
</info>
<locale xml:lang="en">
<terms>
<term name="et-al">{{jats}}&lt;etal/&gt;{{/jats}}</term>
</terms>
</locale>
<macro name="citation-number">
<text variable="citation-number" prefix="{{jats}}id=&quot;ref-{{/jats}}" suffix="{{jats}}&quot;&gt;{{/jats}}"/>
</macro>
<macro name="author">
<names variable="author" delimiter=" ">
<name prefix="{{jats}}&lt;name&gt;{{/jats}}" suffix="{{jats}}&lt;/name&gt;{{/jats}}" name-as-sort-order="all" sort-separator=" ">
<name-part name="family" text-case="capitalize-first" prefix="{{jats}}&lt;surname&gt;{{/jats}}" suffix="{{jats}}&lt;/surname&gt;{{/jats}}"/>
<name-part name="given" text-case="capitalize-first" prefix="{{jats}}&lt;given-names&gt;{{/jats}}" suffix="{{jats}}&lt;/given-names&gt;{{/jats}}"/>
</name>
<substitute>
<names variable="editor"/>
</substitute>
</names>
</macro>
<macro name="editor" delimiter=" ">
<names variable="editor" prefix="{{jats}}&lt;person-group person-group-type=&quot;editor&quot;&gt;{{/jats}}" suffix="{{jats}}&lt;/person-group&gt;{{/jats}}">
<name prefix="{{jats}}&lt;name&gt;{{/jats}}" suffix="{{jats}}&lt;/name&gt;{{/jats}}" name-as-sort-order="all" sort-separator=" ">
<name-part name="family" text-case="capitalize-first" prefix="{{jats}}&lt;surname&gt;{{/jats}}" suffix="{{jats}}&lt;/surname&gt;{{/jats}}"/>
<name-part name="given" text-case="capitalize-first" prefix="{{jats}}&lt;given-names&gt;{{/jats}}" suffix="{{jats}}&lt;/given-names&gt;{{/jats}}"/>
</name>
<substitute>
<names variable="editor"/>
</substitute>
</names>
</macro>
<macro name="editor">
<group delimiter=": ">
<names variable="editor">
<name prefix="{{jats}}&lt;name&gt;{{/jats}}" suffix="{{jats}}&lt;/name&gt;{{/jats}}" name-as-sort-order="all" sort-separator="">
<name-part name="family" text-case="capitalize-first" prefix="{{jats}}&lt;surname&gt;{{/jats}}" suffix="{{jats}}&lt;/surname&gt;{{/jats}}"/>
<name-part name="given" text-case="capitalize-first" prefix="{{jats}}&lt;given-names&gt;{{/jats}}" suffix="{{jats}}&lt;given-names&gt;{{/jats}}"/>
</name>
</names>
</group>
</macro>
<macro name="title">
<choose>
<if type="book" match="any">
<group prefix="{{jats}}&lt;source&gt;{{/jats}}" suffix="{{jats}}&lt;/source&gt;{{/jats}}">
<text variable="title"/>
</group>
</if>
<else>
<group prefix="{{jats}}&lt;article-title&gt;{{/jats}}" suffix="{{jats}}&lt;/article-title&gt;{{/jats}}">
<text variable="title"/>
</group>
</else>
</choose>
</macro>
<macro name="container-title">
<text variable="container-title" form="short" prefix="{{jats}}&lt;source&gt;{{/jats}}" suffix="{{jats}}&lt;/source&gt;{{/jats}}"/>
</macro>
<macro name="publisher">
<text variable="publisher" prefix="{{jats}}&lt;publisher-name&gt;{{/jats}}" suffix="{{jats}}&lt;/publisher-name&gt;{{/jats}}"/>
<text variable="publisher-place" prefix="{{jats}}&lt;publisher-loc&gt;{{/jats}}" suffix="{{jats}}&lt;/publisher-loc&gt;{{/jats}}"/>
</macro>
<macro name="link">
<choose>
<if match="any" variable="DOI">
<group prefix="{{jats}}&lt;pub-id pub-id-type=&quot;doi&quot;&gt;{{/jats}}" suffix="{{jats}}&lt;/pub-id&gt;{{/jats}}">
<text variable="DOI"/>
</group>
</if>
</choose>
<choose>
<if match="any" variable="PMID">
<group prefix="{{jats}}&lt;pub-id pub-id-type=&quot;pmid&quot;&gt;{{/jats}}" suffix="{{jats}}&lt;/pub-id&gt;{{/jats}}">
<text variable="PMID"/>
</group>
</if>
</choose>
<choose>
<if variable="URL" match="any">
<text variable="URL" />
</if>
</choose>
</macro>
<macro name="date">
<choose>
<if type="article-journal article-magazine article-newspaper report patent book" match="any">
<group prefix="{{jats}}&lt;date&gt;{{/jats}}" suffix="{{jats}}&lt;/date&gt;{{/jats}}">
<date variable="issued">
<date-part name="day" form="numeric-leading-zeros" prefix="{{jats}}&lt;day&gt;{{/jats}}" suffix="{{jats}}&lt;/day&gt;{{/jats}}"/>
<date-part name="month" form="numeric-leading-zeros" prefix="{{jats}}&lt;month&gt;{{/jats}}" suffix="{{jats}}&lt;/month&gt;{{/jats}}"/>
<date-part name="year" prefix="{{jats}}&lt;year&gt;{{/jats}}" suffix="{{jats}}&lt;/year&gt;{{/jats}}"/>
</date>
</group>
</if>
<else>
<group prefix="{{jats}}&lt;date-in-citation content-type=&quot;access-date&quot;{{/jats}}" suffix="{{jats}}&lt;/date-in-citation&gt;{{/jats}}">
<date variable="accessed" prefix="{{jats}} iso-8601-date=&quot;{{/jats}}" suffix="{{jats}}&quot;&gt;{{/jats}}">
<date-part name="year"/>
<date-part name="month" form="numeric-leading-zeros" prefix="{{jats}}-{{/jats}}"/>
<date-part name="day" form="numeric-leading-zeros" prefix="{{jats}}-{{/jats}}"/>
</date>
<date variable="accessed">
<date-part name="day" prefix="{{jats}}&lt;day&gt;{{/jats}}" suffix="{{jats}}&lt;/day&gt;{{/jats}}"/>
<date-part name="month" form="numeric-leading-zeros" prefix="{{jats}}&lt;month&gt;{{/jats}}" suffix="{{jats}}&lt;/month&gt;{{/jats}}"/>
<date-part name="year" prefix="{{jats}}&lt;year&gt;{{/jats}}" suffix="{{jats}}&lt;/year&gt;{{/jats}}"/>
</date>
</group>
</else>
</choose>
</macro>
<macro name="location">
<choose>
<if type="article-journal article-magazine" match="any">
<text variable="volume" prefix="{{jats}}&lt;volume&gt;{{/jats}}" suffix="{{jats}}&lt;/volume&gt;{{/jats}}"/>
<text variable="issue" prefix="{{jats}}&lt;issue&gt;{{/jats}}" suffix="{{jats}}&lt;/issue&gt;{{/jats}}"/>
</if>
</choose>
<choose>
<if type="article-journal article-magazine article-newspaper chapter" match="any">
<text variable="page-first" prefix="{{jats}}&lt;fpage&gt;{{/jats}}" suffix="{{jats}}&lt;/fpage&gt;{{/jats}}"/>
</if>
</choose>
</macro>
<macro name="publication-type">
<group prefix="{{jats}} publication-type=&quot;{{/jats}}" suffix="{{jats}}&quot;&gt;{{/jats}}">
<choose>
<if type="article-journal article-magazine article-newspaper" match="any">
<text value="journal"/>
</if>
<else-if type="book" match="any">
<text value="book"/>
</else-if>
<else-if type="chapter" match="any">
<text value="bookchapter"/>
</else-if>
<else-if type="dataset" match="any">
<text value="dataset"/>
</else-if>
<else-if type="patent" match="any">
<text value="patent"/>
</else-if>
<else-if type="report" match="any">
<text value="report"/>
</else-if>
<else-if type="review" match="any">
<text value="review"/>
</else-if>
<else>
<text value="standard"/>
</else>
</choose>
</group>
</macro>
<citation collapse="citation-number">
<sort>
<key variable="citation-number"/>
</sort>
<layout delimiter=",">
<group prefix="{{jats}}&lt;xref ref-type=&quot;bibr&quot; rid=&quot;{{/jats}}" suffix="{{jats}}&lt;/xref&gt;{{/jats}}">
<text variable="citation-number" prefix="{{jats}}ref-{{/jats}}" suffix="{{jats}}&quot;&gt;{{/jats}}"/>
<text variable="citation-number"/>
</group>
</layout>
</citation>
<bibliography sort-separator="">
<layout>
<group prefix="{{jats}}&lt;ref {{/jats}}" suffix="{{jats}}&lt;/ref&gt;{{/jats}}">
<text macro="citation-number"/>
<group prefix="{{jats}}&lt;element-citation{{/jats}}" suffix="{{jats}}&lt;/element-citation&gt;{{/jats}}">
<text macro="publication-type"/>
<text macro="author" prefix="{{jats}}&lt;person-group person-group-type=&quot;author&quot;&gt;{{/jats}}" suffix="{{jats}}&lt;/person-group&gt;{{/jats}}"/>
<text macro="title" />
<text macro="container-title"/>
<text macro="editor"/>
<text macro="publisher"/>
<text macro="date"/>
<text macro="location"/>
<text macro="link"/>
</group>
</group>
</layout>
</bibliography>
</style>

2
pandoc.cabal
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@ -180,8 +180,6 @@ data-files:
data/pandoc.List.lua data/pandoc.List.lua
-- bash completion template -- bash completion template
data/bash_completion.tpl data/bash_completion.tpl
-- jats csl
data/jats.csl
-- citeproc -- citeproc
data/default.csl data/default.csl
citeproc/biblatex-localization/*.lbx.strings citeproc/biblatex-localization/*.lbx.strings

16
src/Text/Pandoc/App.hs
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@ -50,10 +50,9 @@ import Text.Pandoc.App.Opt (Opt (..), LineEnding (..), defaultOpts,
import Text.Pandoc.App.CommandLineOptions (parseOptions, options) import Text.Pandoc.App.CommandLineOptions (parseOptions, options)
import Text.Pandoc.App.OutputSettings (OutputSettings (..), optToOutputSettings) import Text.Pandoc.App.OutputSettings (OutputSettings (..), optToOutputSettings)
import Text.Pandoc.BCP47 (Lang (..), parseBCP47) import Text.Pandoc.BCP47 (Lang (..), parseBCP47)
import Text.Pandoc.Builder (setMeta)
import Text.Pandoc.Filter (Filter (JSONFilter, LuaFilter), applyFilters) import Text.Pandoc.Filter (Filter (JSONFilter, LuaFilter), applyFilters)
import Text.Pandoc.PDF (makePDF) import Text.Pandoc.PDF (makePDF)
import Text.Pandoc.SelfContained (makeDataURI, makeSelfContained) import Text.Pandoc.SelfContained (makeSelfContained)
import Text.Pandoc.Shared (eastAsianLineBreakFilter, stripEmptyParagraphs, import Text.Pandoc.Shared (eastAsianLineBreakFilter, stripEmptyParagraphs,
headerShift, isURI, tabFilter, uriPathToPath, filterIpynbOutput, headerShift, isURI, tabFilter, uriPathToPath, filterIpynbOutput,
defaultUserDataDirs, tshow, findM) defaultUserDataDirs, tshow, findM)
@ -190,17 +189,6 @@ convertWithOpts opts = do
Nothing -> readDataFile "abbreviations" Nothing -> readDataFile "abbreviations"
Just f -> readFileStrict f Just f -> readFileStrict f
metadata <- if format == "jats" &&
isNothing (lookupMeta "csl" (optMetadata opts)) &&
isNothing (lookupMeta "citation-style"
(optMetadata opts))
then do
jatsCSL <- readDataFile "jats.csl"
let jatsEncoded = makeDataURI
("application/xml", jatsCSL)
return $ setMeta "csl" jatsEncoded $ optMetadata opts
else return $ optMetadata opts
case lookupMetaString "lang" (optMetadata opts) of case lookupMetaString "lang" (optMetadata opts) of
"" -> setTranslations $ Lang "en" "" "US" [] "" -> setTranslations $ Lang "en" "" "US" []
l -> case parseBCP47 l of l -> case parseBCP47 l of
@ -286,7 +274,7 @@ convertWithOpts opts = do
then fillMediaBag then fillMediaBag
else return) else return)
>=> return . adjustMetadata (metadataFromFile <>) >=> return . adjustMetadata (metadataFromFile <>)
>=> return . adjustMetadata (<> metadata) >=> return . adjustMetadata (<> optMetadata opts)
>=> applyTransforms transforms >=> applyTransforms transforms
>=> applyFilters readerOpts filters [T.unpack format] >=> applyFilters readerOpts filters [T.unpack format]
>=> maybe return extractMedia (optExtractMedia opts) >=> maybe return extractMedia (optExtractMedia opts)

33
src/Text/Pandoc/Writers/JATS.hs
View file

@ -3,7 +3,7 @@
{-# LANGUAGE ViewPatterns #-} {-# LANGUAGE ViewPatterns #-}
{- | {- |
Module : Text.Pandoc.Writers.JATS Module : Text.Pandoc.Writers.JATS
Copyright : Copyright (C) 2017-2021 John MacFarlane Copyright : 2017-2021 John MacFarlane
License : GNU GPL, version 2 or above License : GNU GPL, version 2 or above
Maintainer : John MacFarlane <jgm@berkeley.edu> Maintainer : John MacFarlane <jgm@berkeley.edu>
@ -168,13 +168,15 @@ plainToPara x = x
-- | Convert a list of pairs of terms and definitions into a list of -- | Convert a list of pairs of terms and definitions into a list of
-- JATS varlistentrys. -- JATS varlistentrys.
deflistItemsToJATS :: PandocMonad m deflistItemsToJATS :: PandocMonad m
=> WriterOptions -> [([Inline],[[Block]])] -> JATS m (Doc Text) => WriterOptions
-> [([Inline],[[Block]])] -> JATS m (Doc Text)
deflistItemsToJATS opts items = deflistItemsToJATS opts items =
vcat <$> mapM (uncurry (deflistItemToJATS opts)) items vcat <$> mapM (uncurry (deflistItemToJATS opts)) items
-- | Convert a term and a list of blocks into a JATS varlistentry. -- | Convert a term and a list of blocks into a JATS varlistentry.
deflistItemToJATS :: PandocMonad m deflistItemToJATS :: PandocMonad m
=> WriterOptions -> [Inline] -> [[Block]] -> JATS m (Doc Text) => WriterOptions
-> [Inline] -> [[Block]] -> JATS m (Doc Text)
deflistItemToJATS opts term defs = do deflistItemToJATS opts term defs = do
term' <- inlinesToJATS opts term term' <- inlinesToJATS opts term
def' <- wrappedBlocksToJATS (not . isPara) def' <- wrappedBlocksToJATS (not . isPara)
@ -186,7 +188,8 @@ deflistItemToJATS opts term defs = do
-- | Convert a list of lists of blocks to a list of JATS list items. -- | Convert a list of lists of blocks to a list of JATS list items.
listItemsToJATS :: PandocMonad m listItemsToJATS :: PandocMonad m
=> WriterOptions -> Maybe [Text] -> [[Block]] -> JATS m (Doc Text) => WriterOptions
-> Maybe [Text] -> [[Block]] -> JATS m (Doc Text)
listItemsToJATS opts markers items = listItemsToJATS opts markers items =
case markers of case markers of
Nothing -> vcat <$> mapM (listItemToJATS opts Nothing) items Nothing -> vcat <$> mapM (listItemToJATS opts Nothing) items
@ -194,12 +197,13 @@ listItemsToJATS opts markers items =
-- | Convert a list of blocks into a JATS list item. -- | Convert a list of blocks into a JATS list item.
listItemToJATS :: PandocMonad m listItemToJATS :: PandocMonad m
=> WriterOptions -> Maybe Text -> [Block] -> JATS m (Doc Text) => WriterOptions
-> Maybe Text -> [Block] -> JATS m (Doc Text)
listItemToJATS opts mbmarker item = do listItemToJATS opts mbmarker item = do
contents <- wrappedBlocksToJATS (not . isParaOrList) opts contents <- wrappedBlocksToJATS (not . isParaOrList) opts
(walk demoteHeaderAndRefs item) (walk demoteHeaderAndRefs item)
return $ inTagsIndented "list-item" $ return $ inTagsIndented "list-item" $
maybe empty (\lbl -> inTagsSimple "label" (text $ T.unpack lbl)) mbmarker maybe empty (inTagsSimple "label" . text . T.unpack) mbmarker
$$ contents $$ contents
imageMimeType :: Text -> [(Text, Text)] -> (Text, Text) imageMimeType :: Text -> [(Text, Text)] -> (Text, Text)
@ -247,7 +251,9 @@ blockToJATS opts (Div (id',"section":_,kvs) (Header _lvl _ ils : xs)) = do
return $ inTags True "sec" attribs $ return $ inTags True "sec" attribs $
inTagsSimple "title" title' $$ contents inTagsSimple "title" title' $$ contents
-- Bibliography reference: -- Bibliography reference:
blockToJATS opts (Div (T.stripPrefix "ref-" -> Just _,_,_) [Para lst]) = blockToJATS opts (Div (ident,_,_) [Para lst]) | "ref-" `T.isPrefixOf` ident =
inTags True "ref" [("id", ident)] .
inTagsSimple "mixed-citation" <$>
inlinesToJATS opts lst inlinesToJATS opts lst
blockToJATS opts (Div ("refs",_,_) xs) = do blockToJATS opts (Div ("refs",_,_) xs) = do
contents <- blocksToJATS opts xs contents <- blocksToJATS opts xs
@ -470,10 +476,13 @@ inlineToJATS _ (Link _attr [Str t] (T.stripPrefix "mailto:" -> Just email, _))
| escapeURI t == email = | escapeURI t == email =
return $ inTagsSimple "email" $ literal (escapeStringForXML email) return $ inTagsSimple "email" $ literal (escapeStringForXML email)
inlineToJATS opts (Link (ident,_,kvs) txt (T.uncons -> Just ('#', src), _)) = do inlineToJATS opts (Link (ident,_,kvs) txt (T.uncons -> Just ('#', src), _)) = do
let attr = [("id", ident) | not (T.null ident)] ++ let attr = mconcat
[("alt", stringify txt) | not (null txt)] ++ [ [("id", ident) | not (T.null ident)]
[("rid", src)] ++ , [("alt", stringify txt) | not (null txt)]
[(k,v) | (k,v) <- kvs, k `elem` ["ref-type", "specific-use"]] , [("rid", src)]
, [(k,v) | (k,v) <- kvs, k `elem` ["ref-type", "specific-use"]]
, [("ref-type", "bibr") | "ref-" `T.isPrefixOf` src]
]
if null txt if null txt
then return $ selfClosingTag "xref" attr then return $ selfClosingTag "xref" attr
else do else do
@ -529,7 +538,7 @@ demoteHeaderAndRefs (Div ("refs",cls,kvs) bs) =
demoteHeaderAndRefs x = x demoteHeaderAndRefs x = x
parseDate :: Text -> Maybe Day parseDate :: Text -> Maybe Day
parseDate s = msum (map (\fs -> parsetimeWith fs $ T.unpack s) formats) :: Maybe Day parseDate s = msum (map (`parsetimeWith` T.unpack s) formats)
where parsetimeWith = parseTimeM True defaultTimeLocale where parsetimeWith = parseTimeM True defaultTimeLocale
formats = ["%x","%m/%d/%Y", "%D","%F", "%d %b %Y", formats = ["%x","%m/%d/%Y", "%D","%F", "%d %b %Y",
"%e %B %Y", "%b. %e, %Y", "%B %e, %Y", "%e %B %Y", "%b. %e, %Y", "%B %e, %Y",

48
test/command/7016.md Normal file
View file

@ -0,0 +1,48 @@
```
% pandoc --citeproc --to=jats_archiving --standalone
---
csl: command/apa.csl
references:
- id: doe
type: article
author:
- family: Doe
given: Jane
container-title: Proceedings of the Academy of Test Inputs
doi: 10.x/nope
issued: 2021
title: Another article
...
Blah [@doe].
^D
<?xml version="1.0" encoding="utf-8" ?>
<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.2 20190208//EN"
"JATS-archivearticle1.dtd">
<article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" dtd-version="1.2" article-type="other">
<front>
<journal-meta>
<journal-id></journal-id>
<journal-title-group>
</journal-title-group>
<issn></issn>
<publisher>
<publisher-name></publisher-name>
</publisher>
</journal-meta>
<article-meta>
</article-meta>
</front>
<body>
<p>Blah (Doe, 2021).</p>
</body>
<back>
<ref-list>
<ref id="ref-doe">
<mixed-citation>Doe, J. (2021). Another article. <italic>Proceedings
of the Academy of Test Inputs</italic>.
doi:<ext-link ext-link-type="uri" xlink:href="https://doi.org/10.x/nope">10.x/nope</ext-link></mixed-citation>
</ref>
</ref-list>
</back>
</article>
```