9dd2eef · typeable/pandoc

git.iko.soy/typeable/pandoc

JATS writer: fix citations with PMID so they validate.

Closes #5481. This includes an update to data/jats.csl.

commit9dd2eefded7879df85150484c0476410dd77a4f7 authorJohn MacFarlane <jgm@berkeley.edu> dateSat 4 May 2019, 08:45 (8 years ago) parentd73cb5f

2 files changed+12−10

compare with master

unifiedsplit

data/jats.csl+2−4 src/Text/Pandoc/Writers/JATS.hs+10−6

data/jats.csl+2−4

@@ -64,7 +64,7 @@

6464 <if type="book" match="any">

6565 <group prefix="{{jats}}<source>{{/jats}}" suffix="{{jats}}</source>{{/jats}}">

6666 <text variable="title"/>

67− </group>

67+ </group>

6868 </if>

6969 <else>

7070 <group prefix="{{jats}}<article-title>{{/jats}}" suffix="{{jats}}</article-title>{{/jats}}">

@@ -90,8 +90,7 @@

9090 </choose>

9191 <choose>

9292 <if match="any" variable="PMID">

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

94− <text variable="PMID" prefix="{{jats}}xlink:href="http://www.ncbi.nlm.nih.gov/pubmed/{{/jats}}" suffix="{{jats}}" xlink:type="simple">{{/jats}}"/>

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

9594 <text variable="PMID"/>

9695 </group>

9796 </if>

@@ -202,4 +201,3 @@

202201 </layout>

203202 </bibliography>

204203</style>

205−

src/Text/Pandoc/Writers/JATS.hs+10−6

@@ -18,7 +18,7 @@ import Prelude

1818import Control.Monad.Reader

1919import Data.Char (toLower)

2020import Data.Generics (everywhere, mkT)

21−import Data.List (isSuffixOf, partition)

21+import Data.List (isSuffixOf, partition, isPrefixOf)

2222import Data.Maybe (fromMaybe)

2323import Data.Text (Text)

2424import Text.Pandoc.Class (PandocMonad, report)

@@ -322,11 +322,15 @@ inlinesToJATS :: PandocMonad m => WriterOptions -> [Inline] -> JATS m Doc

322322inlinesToJATS opts lst = hcat <$> mapM (inlineToJATS opts) (fixCitations lst)

323323 where

324324 fixCitations [] = []

325− fixCitations (x@(RawInline (Format "jats") "<pub-id pub-id-type=\"doi\">") : xs) =

326− let isRawInline (RawInline{}) = True

327− isRawInline _ = False

328− (ys,zs) = break isRawInline xs

329− in x : Str (stringify ys) : fixCitations zs

325+ fixCitations (x:xs) | needsFixing x =

326+ x : Str (stringify ys) : fixCitations zs

327+ where

328+ needsFixing (RawInline (Format "jats") z) =

329+ "<pub-id pub-id-type=" `isPrefixOf` z

330+ needsFixing _ = False

331+ isRawInline (RawInline{}) = True

332+ isRawInline _ = False

333+ (ys,zs) = break isRawInline xs

330334 fixCitations (x:xs) = x : fixCitations xs

331335

332336-- | Convert an inline element to JATS.