JATS writer: fix citations (#7018)

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

* JATS writer: fix citations

2 files changed, 23 insertions, 26 deletions

diff --git a/src/Text/Pandoc/App.hs b/src/Text/Pandoc/App.hs
index 725c76424..437af3257 100644
--- a/src/Text/Pandoc/App.hs
+++ b/src/Text/Pandoc/App.hs
@@ -50,10 +50,9 @@ import Text.Pandoc.App.Opt (Opt (..), LineEnding (..), defaultOpts,
 import Text.Pandoc.App.CommandLineOptions (parseOptions, options)
 import Text.Pandoc.App.OutputSettings (OutputSettings (..), optToOutputSettings)
 import Text.Pandoc.BCP47 (Lang (..), parseBCP47)
-import Text.Pandoc.Builder (setMeta)
 import Text.Pandoc.Filter (Filter (JSONFilter, LuaFilter), applyFilters)
 import Text.Pandoc.PDF (makePDF)
-import Text.Pandoc.SelfContained (makeDataURI, makeSelfContained)
+import Text.Pandoc.SelfContained (makeSelfContained)
 import Text.Pandoc.Shared (eastAsianLineBreakFilter, stripEmptyParagraphs,
          headerShift, isURI, tabFilter, uriPathToPath, filterIpynbOutput,
          defaultUserDataDirs, tshow, findM)
@@ -190,17 +189,6 @@ convertWithOpts opts = do
                     Nothing -> readDataFile "abbreviations"
                     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
            ""      -> setTranslations $ Lang "en" "" "US" []
            l       -> case parseBCP47 l of
@@ -286,7 +274,7 @@ convertWithOpts opts = do
                       then fillMediaBag
                       else return)
               >=> return . adjustMetadata (metadataFromFile <>)
-              >=> return . adjustMetadata (<> metadata)
+              >=> return . adjustMetadata (<> optMetadata opts)
               >=> applyTransforms transforms
               >=> applyFilters readerOpts filters [T.unpack format]
               >=> maybe return extractMedia (optExtractMedia opts)
diff --git a/src/Text/Pandoc/Writers/JATS.hs b/src/Text/Pandoc/Writers/JATS.hs
index e8d93b8d5..b2266d179 100644
--- a/src/Text/Pandoc/Writers/JATS.hs
+++ b/src/Text/Pandoc/Writers/JATS.hs
@@ -3,7 +3,7 @@
 {-# LANGUAGE ViewPatterns #-}
 {- |
    Module      : Text.Pandoc.Writers.JATS
-   Copyright   : Copyright (C) 2017-2021 John MacFarlane
+   Copyright   : 2017-2021 John MacFarlane
    License     : GNU GPL, version 2 or above
 
    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
 -- JATS varlistentrys.
 deflistItemsToJATS :: PandocMonad m
-                      => WriterOptions -> [([Inline],[[Block]])] -> JATS m (Doc Text)
+                   => WriterOptions
+                   -> [([Inline],[[Block]])] -> JATS m (Doc Text)
 deflistItemsToJATS opts items =
   vcat <$> mapM (uncurry (deflistItemToJATS opts)) items
 
 -- | Convert a term and a list of blocks into a JATS varlistentry.
 deflistItemToJATS :: PandocMonad m
-                     => WriterOptions -> [Inline] -> [[Block]] -> JATS m (Doc Text)
+                  => WriterOptions
+                  -> [Inline] -> [[Block]] -> JATS m (Doc Text)
 deflistItemToJATS opts term defs = do
   term' <- inlinesToJATS opts term
   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.
 listItemsToJATS :: PandocMonad m
-                => WriterOptions -> Maybe [Text] -> [[Block]] -> JATS m (Doc Text)
+                => WriterOptions
+                -> Maybe [Text] -> [[Block]] -> JATS m (Doc Text)
 listItemsToJATS opts markers items =
   case markers of
        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.
 listItemToJATS :: PandocMonad m
-               => WriterOptions -> Maybe Text -> [Block] -> JATS m (Doc Text)
+               => WriterOptions
+               -> Maybe Text -> [Block] -> JATS m (Doc Text)
 listItemToJATS opts mbmarker item = do
   contents <- wrappedBlocksToJATS (not . isParaOrList) opts
                  (walk demoteHeaderAndRefs item)
   return $ inTagsIndented "list-item" $
-           maybe empty (\lbl -> inTagsSimple "label" (text $ T.unpack lbl)) mbmarker
+           maybe empty (inTagsSimple "label" . text . T.unpack) mbmarker
            $$ contents
 
 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 $
       inTagsSimple "title" title' $$ contents
 -- 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
 blockToJATS opts (Div ("refs",_,_) xs) = do
   contents <- blocksToJATS opts xs
@@ -470,10 +476,13 @@ inlineToJATS _ (Link _attr [Str t] (T.stripPrefix "mailto:" -> Just email, _))
   | escapeURI t == email =
   return $ inTagsSimple "email" $ literal (escapeStringForXML email)
 inlineToJATS opts (Link (ident,_,kvs) txt (T.uncons -> Just ('#', src), _)) = do
-  let attr = [("id", ident) | not (T.null ident)] ++
-             [("alt", stringify txt) | not (null txt)] ++
-             [("rid", src)] ++
-             [(k,v) | (k,v) <- kvs, k `elem` ["ref-type", "specific-use"]]
+  let attr = mconcat
+             [ [("id", ident) | not (T.null ident)]
+             , [("alt", stringify txt) | not (null txt)]
+             , [("rid", src)]
+             , [(k,v) | (k,v) <- kvs, k `elem` ["ref-type", "specific-use"]]
+             , [("ref-type", "bibr") | "ref-" `T.isPrefixOf` src]
+             ]
   if null txt
      then return $ selfClosingTag "xref" attr
      else do
@@ -529,7 +538,7 @@ demoteHeaderAndRefs (Div ("refs",cls,kvs) bs) =
 demoteHeaderAndRefs x = x
 
 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
         formats = ["%x","%m/%d/%Y", "%D","%F", "%d %b %Y",
                     "%e %B %Y", "%b. %e, %Y", "%B %e, %Y",