JATS writer: fix citations with PMID so they validate.

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

data/jats.csl

@@ -64,7 +64,7 @@
       <if type="book" match="any">
         <group prefix="{{jats}}&lt;source&gt;{{/jats}}" suffix="{{jats}}&lt;/source&gt;{{/jats}}">
 	        <text variable="title"/>
-				</group>			
+				</group>
 			</if>
       <else>
         <group prefix="{{jats}}&lt;article-title&gt;{{/jats}}" suffix="{{jats}}&lt;/article-title&gt;{{/jats}}">
@@ -90,8 +90,7 @@
     </choose>
     <choose>
       <if match="any" variable="PMID">
-        <group prefix="{{jats}}&lt;ext-link ext-link-type=&quot;pmid&quot; {{/jats}}" suffix="{{jats}}&lt;/ext-link&gt;{{/jats}}">
-          <text variable="PMID" prefix="{{jats}}xlink:href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/{{/jats}}" suffix="{{jats}}&quot; xlink:type=&quot;simple&quot;&gt;{{/jats}}"/>
+        <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>
@@ -202,4 +201,3 @@
     </layout>
   </bibliography>
 </style>
-

src/Text/Pandoc/Writers/JATS.hs

@@ -18,7 +18,7 @@ import Prelude
 import Control.Monad.Reader
 import Data.Char (toLower)
 import Data.Generics (everywhere, mkT)
-import Data.List (isSuffixOf, partition)
+import Data.List (isSuffixOf, partition, isPrefixOf)
 import Data.Maybe (fromMaybe)
 import Data.Text (Text)
 import Text.Pandoc.Class (PandocMonad, report)
@@ -322,11 +322,15 @@ inlinesToJATS :: PandocMonad m => WriterOptions -> [Inline] -> JATS m Doc
 inlinesToJATS opts lst = hcat <$> mapM (inlineToJATS opts) (fixCitations lst)
   where
    fixCitations [] = []
-   fixCitations (x@(RawInline (Format "jats") "<pub-id pub-id-type=\"doi\">") : xs) =
-     let isRawInline (RawInline{}) = True
-         isRawInline _             = False
-         (ys,zs)                   = break isRawInline xs
-         in x : Str (stringify ys) : fixCitations zs
+   fixCitations (x:xs) | needsFixing x =
+     x : Str (stringify ys) : fixCitations zs
+     where
+       needsFixing (RawInline (Format "jats") z) =
+           "<pub-id pub-id-type=" `isPrefixOf` z
+       needsFixing _             = False
+       isRawInline (RawInline{}) = True
+       isRawInline _             = False
+       (ys,zs)                   = break isRawInline xs
    fixCitations (x:xs) = x : fixCitations xs
 
 -- | Convert an inline element to JATS.