68fa437 · typeable/pandoc

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JATS writer: fix citations (#7018)

68fa437Albert Krewinkel6 years ago

COPYRIGHT+1−10

compare with master

unifiedsplit

@@ -181,7 +181,7 @@ http://github.com/paulrouget/dzslides

181Released under the Do What the Fuck You Want To Public License.

182

183------------------------------------------------------------------------

184−Pandoc embeds a lua interpreter (via hslua).

184+Pandoc embeds a Lua interpreter (via hslua).

185

187

@@ -203,12 +203,3 @@ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE

203LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION

204OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION

205WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

206−

207−------------------------------------------------------------------------

209−released under GPL version 2 or later.

210−

211−The file data/jats.csl is derived from a csl file by Martin Fenner,

212−revised by Martin Paul Eve and then John MacFarlane.

213−"This work is licensed under a Creative Commons Attribution-ShareAlike 3.0

214−License. Originally by Martin Fenner."

data/jats.csldeleted−203

@@ -1,203 +0,0 @@

1−<?xml version="1.0" encoding="utf-8"?>

2−<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" default-locale="en-US">

3− <info>

4− <title>Journal Article Tag Suite</title>

5− <title-short>JATS</title-short>

6− <id>http://www.zotero.org/styles/journal-article-tag-suite</id>

7− <link href="https://github.com/MartinPaulEve/JATS-CSL/blob/master/jats.csl" rel="self"/>

8− <link rel="documentation" href="http://jats.nlm.nih.gov/archiving/tag-library/1.0/index.html"/>

9− <author>

10− <name>Martin Paul Eve</name>

11− <email>martin@martineve.com</email>

12− </author>

13− <category citation-format="numeric"/>

14− <category field="medicine"/>

15− <category field="biology"/>

16− <summary>Use this style to generate bibliographic data in Journal Article Tagging Suite (JATS) 1.0 XML format</summary>

17− <updated>2014-06-21T17:41:26+00:00</updated>

18− <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>

19− </info>

20− <locale xml:lang="en">

21− <terms>

22− <term name="et-al">{{jats}}<etal/>{{/jats}}</term>

23− </terms>

24− </locale>

25− <macro name="citation-number">

26− <text variable="citation-number" prefix="{{jats}}id="ref-{{/jats}}" suffix="{{jats}}">{{/jats}}"/>

27− </macro>

28− <macro name="author">

29− <names variable="author" delimiter=" ">

30− <name prefix="{{jats}}<name>{{/jats}}" suffix="{{jats}}</name>{{/jats}}" name-as-sort-order="all" sort-separator=" ">

31− <name-part name="family" text-case="capitalize-first" prefix="{{jats}}<surname>{{/jats}}" suffix="{{jats}}</surname>{{/jats}}"/>

32− <name-part name="given" text-case="capitalize-first" prefix="{{jats}}<given-names>{{/jats}}" suffix="{{jats}}</given-names>{{/jats}}"/>

33− </name>

34− <substitute>

35− <names variable="editor"/>

36− </substitute>

37− </names>

38− </macro>

39−

40− <macro name="editor" delimiter=" ">

41− <names variable="editor" prefix="{{jats}}<person-group person-group-type="editor">{{/jats}}" suffix="{{jats}}</person-group>{{/jats}}">

42− <name prefix="{{jats}}<name>{{/jats}}" suffix="{{jats}}</name>{{/jats}}" name-as-sort-order="all" sort-separator=" ">

43− <name-part name="family" text-case="capitalize-first" prefix="{{jats}}<surname>{{/jats}}" suffix="{{jats}}</surname>{{/jats}}"/>

44− <name-part name="given" text-case="capitalize-first" prefix="{{jats}}<given-names>{{/jats}}" suffix="{{jats}}</given-names>{{/jats}}"/>

45− </name>

46− <substitute>

47− <names variable="editor"/>

48− </substitute>

49− </names>

50− </macro>

51−

52− <macro name="editor">

53− <group delimiter=": ">

54− <names variable="editor">

55− <name prefix="{{jats}}<name>{{/jats}}" suffix="{{jats}}</name>{{/jats}}" name-as-sort-order="all" sort-separator="">

56− <name-part name="family" text-case="capitalize-first" prefix="{{jats}}<surname>{{/jats}}" suffix="{{jats}}</surname>{{/jats}}"/>

57− <name-part name="given" text-case="capitalize-first" prefix="{{jats}}<given-names>{{/jats}}" suffix="{{jats}}<given-names>{{/jats}}"/>

58− </name>

59− </names>

60− </group>

61− </macro>

62− <macro name="title">

63− <choose>

64− <if type="book" match="any">

65− <group prefix="{{jats}}<source>{{/jats}}" suffix="{{jats}}</source>{{/jats}}">

66− <text variable="title"/>

67− </group>

68− </if>

69− <else>

70− <group prefix="{{jats}}<article-title>{{/jats}}" suffix="{{jats}}</article-title>{{/jats}}">

71− <text variable="title"/>

72− </group>

73− </else>

74− </choose>

75− </macro>

76− <macro name="container-title">

77− <text variable="container-title" form="short" prefix="{{jats}}<source>{{/jats}}" suffix="{{jats}}</source>{{/jats}}"/>

78− </macro>

79− <macro name="publisher">

80− <text variable="publisher" prefix="{{jats}}<publisher-name>{{/jats}}" suffix="{{jats}}</publisher-name>{{/jats}}"/>

81− <text variable="publisher-place" prefix="{{jats}}<publisher-loc>{{/jats}}" suffix="{{jats}}</publisher-loc>{{/jats}}"/>

82− </macro>

83− <macro name="link">

84− <choose>

85− <if match="any" variable="DOI">

86− <group prefix="{{jats}}<pub-id pub-id-type="doi">{{/jats}}" suffix="{{jats}}</pub-id>{{/jats}}">

87− <text variable="DOI"/>

88− </group>

89− </if>

90− </choose>

91− <choose>

92− <if match="any" variable="PMID">

93− <group prefix="{{jats}}<pub-id pub-id-type="pmid">{{/jats}}" suffix="{{jats}}</pub-id>{{/jats}}">

94− <text variable="PMID"/>

95− </group>

96− </if>

97− </choose>

98− <choose>

99− <if variable="URL" match="any">

100− <text variable="URL" />

101− </if>

102− </choose>

103− </macro>

104− <macro name="date">

105− <choose>

106− <if type="article-journal article-magazine article-newspaper report patent book" match="any">

107− <group prefix="{{jats}}<date>{{/jats}}" suffix="{{jats}}</date>{{/jats}}">

108− <date variable="issued">

109− <date-part name="day" form="numeric-leading-zeros" prefix="{{jats}}<day>{{/jats}}" suffix="{{jats}}</day>{{/jats}}"/>

110− <date-part name="month" form="numeric-leading-zeros" prefix="{{jats}}<month>{{/jats}}" suffix="{{jats}}</month>{{/jats}}"/>

111− <date-part name="year" prefix="{{jats}}<year>{{/jats}}" suffix="{{jats}}</year>{{/jats}}"/>

112− </date>

113− </group>

114− </if>

115− <else>

116− <group prefix="{{jats}}<date-in-citation content-type="access-date"{{/jats}}" suffix="{{jats}}</date-in-citation>{{/jats}}">

117− <date variable="accessed" prefix="{{jats}} iso-8601-date="{{/jats}}" suffix="{{jats}}">{{/jats}}">

118− <date-part name="year"/>

119− <date-part name="month" form="numeric-leading-zeros" prefix="{{jats}}-{{/jats}}"/>

120− <date-part name="day" form="numeric-leading-zeros" prefix="{{jats}}-{{/jats}}"/>

121− </date>

122− <date variable="accessed">

123− <date-part name="day" prefix="{{jats}}<day>{{/jats}}" suffix="{{jats}}</day>{{/jats}}"/>

124− <date-part name="month" form="numeric-leading-zeros" prefix="{{jats}}<month>{{/jats}}" suffix="{{jats}}</month>{{/jats}}"/>

125− <date-part name="year" prefix="{{jats}}<year>{{/jats}}" suffix="{{jats}}</year>{{/jats}}"/>

126− </date>

127− </group>

128− </else>

129− </choose>

130− </macro>

131− <macro name="location">

132− <choose>

133− <if type="article-journal article-magazine" match="any">

134− <text variable="volume" prefix="{{jats}}<volume>{{/jats}}" suffix="{{jats}}</volume>{{/jats}}"/>

135− <text variable="issue" prefix="{{jats}}<issue>{{/jats}}" suffix="{{jats}}</issue>{{/jats}}"/>

136− </if>

137− </choose>

138− <choose>

139− <if type="article-journal article-magazine article-newspaper chapter" match="any">

140− <text variable="page-first" prefix="{{jats}}<fpage>{{/jats}}" suffix="{{jats}}</fpage>{{/jats}}"/>

141− </if>

142− </choose>

143− </macro>

144− <macro name="publication-type">

145− <group prefix="{{jats}} publication-type="{{/jats}}" suffix="{{jats}}">{{/jats}}">

146− <choose>

147− <if type="article-journal article-magazine article-newspaper" match="any">

148− <text value="journal"/>

149− </if>

150− <else-if type="book" match="any">

151− <text value="book"/>

152− </else-if>

153− <else-if type="chapter" match="any">

154− <text value="bookchapter"/>

155− </else-if>

156− <else-if type="dataset" match="any">

157− <text value="dataset"/>

158− </else-if>

159− <else-if type="patent" match="any">

160− <text value="patent"/>

161− </else-if>

162− <else-if type="report" match="any">

163− <text value="report"/>

164− </else-if>

165− <else-if type="review" match="any">

166− <text value="review"/>

167− </else-if>

168− <else>

169− <text value="standard"/>

170− </else>

171− </choose>

172− </group>

173− </macro>

174− <citation collapse="citation-number">

175− <sort>

176− <key variable="citation-number"/>

177− </sort>

178− <layout delimiter=",">

179− <group prefix="{{jats}}<xref ref-type="bibr" rid="{{/jats}}" suffix="{{jats}}</xref>{{/jats}}">

180− <text variable="citation-number" prefix="{{jats}}ref-{{/jats}}" suffix="{{jats}}">{{/jats}}"/>

181− <text variable="citation-number"/>

182− </group>

183− </layout>

184− </citation>

185− <bibliography sort-separator="">

186− <layout>

187− <group prefix="{{jats}}<ref {{/jats}}" suffix="{{jats}}</ref>{{/jats}}">

188− <text macro="citation-number"/>

189− <group prefix="{{jats}}<element-citation{{/jats}}" suffix="{{jats}}</element-citation>{{/jats}}">

190− <text macro="publication-type"/>

191− <text macro="author" prefix="{{jats}}<person-group person-group-type="author">{{/jats}}" suffix="{{jats}}</person-group>{{/jats}}"/>

192− <text macro="title" />

193− <text macro="container-title"/>

194− <text macro="editor"/>

195− <text macro="publisher"/>

196− <text macro="date"/>

197− <text macro="location"/>

198− <text macro="link"/>

199− </group>

200− </group>

201− </layout>

202− </bibliography>

203−</style>

pandoc.cabal−2

@@ -180,8 +180,6 @@ data-files:

180 data/pandoc.List.lua

181 -- bash completion template

182 data/bash_completion.tpl

183− -- jats csl

184− data/jats.csl

185 -- citeproc

183 -- citeproc

186 data/default.csl

184 data/default.csl

187 citeproc/biblatex-localization/*.lbx.strings

185 citeproc/biblatex-localization/*.lbx.strings

src/Text/Pandoc/App.hs+2−14

@@ -50,10 +50,9 @@ import Text.Pandoc.App.Opt (Opt (..), LineEnding (..), defaultOpts,

50import Text.Pandoc.App.CommandLineOptions (parseOptions, options)

51import Text.Pandoc.App.OutputSettings (OutputSettings (..), optToOutputSettings)

52import Text.Pandoc.BCP47 (Lang (..), parseBCP47)

53−import Text.Pandoc.Builder (setMeta)

54import Text.Pandoc.Filter (Filter (JSONFilter, LuaFilter), applyFilters)

53import Text.Pandoc.Filter (Filter (JSONFilter, LuaFilter), applyFilters)

55import Text.Pandoc.PDF (makePDF)

54import Text.Pandoc.PDF (makePDF)

56−import Text.Pandoc.SelfContained (makeDataURI, makeSelfContained)

55+import Text.Pandoc.SelfContained (makeSelfContained)

57import Text.Pandoc.Shared (eastAsianLineBreakFilter, stripEmptyParagraphs,

56import Text.Pandoc.Shared (eastAsianLineBreakFilter, stripEmptyParagraphs,

58 headerShift, isURI, tabFilter, uriPathToPath, filterIpynbOutput,

57 headerShift, isURI, tabFilter, uriPathToPath, filterIpynbOutput,

59 defaultUserDataDirs, tshow, findM)

58 defaultUserDataDirs, tshow, findM)

@@ -190,17 +189,6 @@ convertWithOpts opts = do

190 Nothing -> readDataFile "abbreviations"

189 Nothing -> readDataFile "abbreviations"

191 Just f -> readFileStrict f

190 Just f -> readFileStrict f

192

191

193− metadata <- if format == "jats" &&

194− isNothing (lookupMeta "csl" (optMetadata opts)) &&

195− isNothing (lookupMeta "citation-style"

196− (optMetadata opts))

197− then do

198− jatsCSL <- readDataFile "jats.csl"

199− let jatsEncoded = makeDataURI

200− ("application/xml", jatsCSL)

201− return $ setMeta "csl" jatsEncoded $ optMetadata opts

202− else return $ optMetadata opts

203−

204 case lookupMetaString "lang" (optMetadata opts) of

192 case lookupMetaString "lang" (optMetadata opts) of

205 "" -> setTranslations $ Lang "en" "" "US" []

193 "" -> setTranslations $ Lang "en" "" "US" []

206 l -> case parseBCP47 l of

194 l -> case parseBCP47 l of

@@ -286,7 +274,7 @@ convertWithOpts opts = do

286 then fillMediaBag

274 then fillMediaBag

287 else return)

275 else return)

288 >=> return . adjustMetadata (metadataFromFile <>)

276 >=> return . adjustMetadata (metadataFromFile <>)

289− >=> return . adjustMetadata (<> metadata)

277+ >=> return . adjustMetadata (<> optMetadata opts)

290 >=> applyTransforms transforms

278 >=> applyTransforms transforms

291 >=> applyFilters readerOpts filters [T.unpack format]

279 >=> applyFilters readerOpts filters [T.unpack format]

292 >=> maybe return extractMedia (optExtractMedia opts)

280 >=> maybe return extractMedia (optExtractMedia opts)

src/Text/Pandoc/Writers/JATS.hs+21−12

@@ -3,7 +3,7 @@

3{-# LANGUAGE ViewPatterns #-}

4{- |

5 Module : Text.Pandoc.Writers.JATS

6+ Copyright : 2017-2021 John MacFarlane

7 License : GNU GPL, version 2 or above

9 Maintainer : John MacFarlane <jgm@berkeley.edu>

@@ -168,13 +168,15 @@ plainToPara x = x

168-- | Convert a list of pairs of terms and definitions into a list of

169-- JATS varlistentrys.

170deflistItemsToJATS :: PandocMonad m

171+ => WriterOptions

171− => WriterOptions -> [([Inline],[[Block]])] -> JATS m (Doc Text)

172+ -> [([Inline],[[Block]])] -> JATS m (Doc Text)

172deflistItemsToJATS opts items =

173deflistItemsToJATS opts items =

173 vcat <$> mapM (uncurry (deflistItemToJATS opts)) items

174 vcat <$> mapM (uncurry (deflistItemToJATS opts)) items

174

175

175-- | Convert a term and a list of blocks into a JATS varlistentry.

176-- | Convert a term and a list of blocks into a JATS varlistentry.

176deflistItemToJATS :: PandocMonad m

177deflistItemToJATS :: PandocMonad m

178+ => WriterOptions

177− => WriterOptions -> [Inline] -> [[Block]] -> JATS m (Doc Text)

179+ -> [Inline] -> [[Block]] -> JATS m (Doc Text)

178deflistItemToJATS opts term defs = do

180deflistItemToJATS opts term defs = do

179 term' <- inlinesToJATS opts term

181 term' <- inlinesToJATS opts term

180 def' <- wrappedBlocksToJATS (not . isPara)

182 def' <- wrappedBlocksToJATS (not . isPara)

@@ -186,7 +188,8 @@ deflistItemToJATS opts term defs = do

186

188

187-- | Convert a list of lists of blocks to a list of JATS list items.

189-- | Convert a list of lists of blocks to a list of JATS list items.

188listItemsToJATS :: PandocMonad m

190listItemsToJATS :: PandocMonad m

191+ => WriterOptions

189− => WriterOptions -> Maybe [Text] -> [[Block]] -> JATS m (Doc Text)

192+ -> Maybe [Text] -> [[Block]] -> JATS m (Doc Text)

190listItemsToJATS opts markers items =

193listItemsToJATS opts markers items =

191 case markers of

194 case markers of

192 Nothing -> vcat <$> mapM (listItemToJATS opts Nothing) items

195 Nothing -> vcat <$> mapM (listItemToJATS opts Nothing) items

@@ -194,12 +197,13 @@ listItemsToJATS opts markers items =

194

197

195-- | Convert a list of blocks into a JATS list item.

198-- | Convert a list of blocks into a JATS list item.

196listItemToJATS :: PandocMonad m

199listItemToJATS :: PandocMonad m

200+ => WriterOptions

197− => WriterOptions -> Maybe Text -> [Block] -> JATS m (Doc Text)

201+ -> Maybe Text -> [Block] -> JATS m (Doc Text)

198listItemToJATS opts mbmarker item = do

202listItemToJATS opts mbmarker item = do

199 contents <- wrappedBlocksToJATS (not . isParaOrList) opts

203 contents <- wrappedBlocksToJATS (not . isParaOrList) opts

200 (walk demoteHeaderAndRefs item)

204 (walk demoteHeaderAndRefs item)

201 return $ inTagsIndented "list-item" $

205 return $ inTagsIndented "list-item" $

202− maybe empty (\lbl -> inTagsSimple "label" (text $ T.unpack lbl)) mbmarker

206+ maybe empty (inTagsSimple "label" . text . T.unpack) mbmarker

203 $$ contents

207 $$ contents

204

208

205imageMimeType :: Text -> [(Text, Text)] -> (Text, Text)

209imageMimeType :: Text -> [(Text, Text)] -> (Text, Text)

@@ -247,7 +251,9 @@ blockToJATS opts (Div (id',"section":_,kvs) (Header _lvl _ ils : xs)) = do

247 return $ inTags True "sec" attribs $

251 return $ inTags True "sec" attribs $

248 inTagsSimple "title" title' $$ contents

252 inTagsSimple "title" title' $$ contents

249-- Bibliography reference:

253-- Bibliography reference:

250−blockToJATS opts (Div (T.stripPrefix "ref-" -> Just _,_,_) [Para lst]) =

254+blockToJATS opts (Div (ident,_,_) [Para lst]) | "ref-" `T.isPrefixOf` ident =

255+ inTags True "ref" [("id", ident)] .

256+ inTagsSimple "mixed-citation" <$>

251 inlinesToJATS opts lst

257 inlinesToJATS opts lst

252blockToJATS opts (Div ("refs",_,_) xs) = do

258blockToJATS opts (Div ("refs",_,_) xs) = do

253 contents <- blocksToJATS opts xs

259 contents <- blocksToJATS opts xs

@@ -470,10 +476,13 @@ inlineToJATS _ (Link _attr [Str t] (T.stripPrefix "mailto:" -> Just email, _))

470 | escapeURI t == email =

476 | escapeURI t == email =

471 return $ inTagsSimple "email" $ literal (escapeStringForXML email)

477 return $ inTagsSimple "email" $ literal (escapeStringForXML email)

472inlineToJATS opts (Link (ident,_,kvs) txt (T.uncons -> Just ('#', src), _)) = do

478inlineToJATS opts (Link (ident,_,kvs) txt (T.uncons -> Just ('#', src), _)) = do

479+ let attr = mconcat

473− let attr = [("id", ident) | not (T.null ident)] ++

480+ [ [("id", ident) | not (T.null ident)]

474− [("alt", stringify txt) | not (null txt)] ++

481+ , [("alt", stringify txt) | not (null txt)]

475− [("rid", src)] ++

482+ , [("rid", src)]

476− [(k,v) | (k,v) <- kvs, k `elem` ["ref-type", "specific-use"]]

483+ , [(k,v) | (k,v) <- kvs, k `elem` ["ref-type", "specific-use"]]

484+ , [("ref-type", "bibr") | "ref-" `T.isPrefixOf` src]

485+ ]

477 if null txt

486 if null txt

478 then return $ selfClosingTag "xref" attr

487 then return $ selfClosingTag "xref" attr

479 else do

488 else do

@@ -529,7 +538,7 @@ demoteHeaderAndRefs (Div ("refs",cls,kvs) bs) =

529demoteHeaderAndRefs x = x

538demoteHeaderAndRefs x = x

530

539

531parseDate :: Text -> Maybe Day

540parseDate :: Text -> Maybe Day

532−parseDate s = msum (map (\fs -> parsetimeWith fs $ T.unpack s) formats) :: Maybe Day

541+parseDate s = msum (map (`parsetimeWith` T.unpack s) formats)

533 where parsetimeWith = parseTimeM True defaultTimeLocale

542 where parsetimeWith = parseTimeM True defaultTimeLocale

534 formats = ["%x","%m/%d/%Y", "%D","%F", "%d %b %Y",

543 formats = ["%x","%m/%d/%Y", "%D","%F", "%d %b %Y",

535 "%e %B %Y", "%b. %e, %Y", "%B %e, %Y",

544 "%e %B %Y", "%b. %e, %Y", "%B %e, %Y",

test/command/7016.mdnew file+48

@@ -0,0 +1,48 @@

1+```

2+% pandoc --citeproc --to=jats_archiving --standalone

3+---

4+csl: command/apa.csl

5+references:

6+- id: doe

7+ type: article

8+ author:

9+ - family: Doe

10+ given: Jane

11+ container-title: Proceedings of the Academy of Test Inputs

12+ doi: 10.x/nope

13+ issued: 2021

14+ title: Another article

15+...

16+Blah [@doe].

17+^D

18+<?xml version="1.0" encoding="utf-8" ?>

19+<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.2 20190208//EN"

20+ "JATS-archivearticle1.dtd">

21+<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">

22+<front>

23+<journal-meta>

24+<journal-id></journal-id>

25+<journal-title-group>

26+</journal-title-group>

27+<issn></issn>

28+<publisher>

29+<publisher-name></publisher-name>

30+</publisher>

31+</journal-meta>

32+<article-meta>

33+</article-meta>

34+</front>

35+<body>

36+<p>Blah (Doe, 2021).</p>

37+</body>

38+<back>

39+<ref-list>

40+ <ref id="ref-doe">

41+ <mixed-citation>Doe, J. (2021). Another article. <italic>Proceedings

42+ of the Academy of Test Inputs</italic>.

43+ doi:<ext-link ext-link-type="uri" xlink:href="https://doi.org/10.x/nope">10.x/nope</ext-link></mixed-citation>

44+ </ref>

45+</ref-list>

46+</back>

47+</article>

48+```