Merge pull request #4177 from stencila/jats-xml-reader

Add Basic JATS reader based on DocBook reader
2017-12-21 23:16:03 -07:00 · 2017-12-21 23:16:03 -07:00 · af04881655
commit af04881655
parent 32f9dbbae5 d853571397
10 changed files with 2761 additions and 20 deletions
--- a/pandoc.cabal
+++ b/pandoc.cabal
@ -212,6 +212,7 @@ extra-source-files:
                 test/creole-reader.txt
                 test/creole-reader.native
                 test/rst-reader.rst
+                 test/jats-reader.xml
                 test/s5-basic.html
                 test/s5-fancy.html
                 test/s5-fragment.html
@ -434,6 +435,7 @@ library
                   Text.Pandoc.Readers.RST,
                   Text.Pandoc.Readers.Org,
                   Text.Pandoc.Readers.DocBook,
+                   Text.Pandoc.Readers.JATS,
                   Text.Pandoc.Readers.OPML,
                   Text.Pandoc.Readers.Textile,
                   Text.Pandoc.Readers.Native,
@ -623,6 +625,7 @@ test-suite test-pandoc
                  Tests.Shared
                  Tests.Readers.LaTeX
                  Tests.Readers.HTML
+                  Tests.Readers.JATS
                  Tests.Readers.Markdown
                  Tests.Readers.Org
                  Tests.Readers.RST
--- a/src/Text/Pandoc/Readers.hs
+++ b/src/Text/Pandoc/Readers.hs
@ -52,6 +52,7 @@ module Text.Pandoc.Readers
  , readOrg
  , readLaTeX
  , readHtml
+  , readJATS
  , readTextile
  , readDocBook
  , readOPML
@ -84,7 +85,8 @@ import Text.Pandoc.Readers.DocBook
 import Text.Pandoc.Readers.Docx
 import Text.Pandoc.Readers.EPUB
 import Text.Pandoc.Readers.Haddock
-import Text.Pandoc.Readers.HTML
+import Text.Pandoc.Readers.HTML (readHtml)
+import Text.Pandoc.Readers.JATS (readJATS)
 import Text.Pandoc.Readers.LaTeX
 import Text.Pandoc.Readers.Markdown
 import Text.Pandoc.Readers.MediaWiki
@ -129,6 +131,7 @@ readers = [ ("native"       , TextReader readNative)
           ,("org"          , TextReader readOrg)
           ,("textile"      , TextReader readTextile) -- TODO : textile+lhs
           ,("html"         , TextReader readHtml)
+           ,("jats"         , TextReader readJATS)
           ,("latex"        , TextReader readLaTeX)
           ,("haddock"      , TextReader readHaddock)
           ,("twiki"        , TextReader readTWiki)
--- a/src/Text/Pandoc/Readers/JATS.hs
+++ b/src/Text/Pandoc/Readers/JATS.hs
@ -0,0 +1,404 @@
+{-# LANGUAGE ExplicitForAll, TupleSections #-}
+module Text.Pandoc.Readers.JATS ( readJATS ) where
+import Control.Monad.State.Strict
+import Data.Char (isDigit, isSpace, toUpper)
+import Data.Default
+import Data.Generics
+import Data.List (intersperse)
+import Data.Maybe (maybeToList, fromMaybe)
+import Data.Text (Text)
+import qualified Data.Text as T
+import Text.HTML.TagSoup.Entity (lookupEntity)
+import Text.Pandoc.Builder
+import Text.Pandoc.Class (PandocMonad)
+import Text.Pandoc.Options
+import Text.Pandoc.Shared (underlineSpan, crFilter, safeRead)
+import Text.TeXMath (readMathML, writeTeX)
+import Text.XML.Light
+import qualified Data.Set as S (fromList, member)
+import Data.Set ((\\))
+
+type JATS m = StateT JATSState m
+
+data JATSState = JATSState{ jatsSectionLevel :: Int
+                          , jatsQuoteType    :: QuoteType
+                          , jatsMeta         :: Meta
+                          , jatsAcceptsMeta  :: Bool
+                          , jatsBook         :: Bool
+                          , jatsFigureTitle  :: Inlines
+                          , jatsContent      :: [Content]
+                          } deriving Show
+
+instance Default JATSState where
+  def = JATSState{ jatsSectionLevel = 0
+                 , jatsQuoteType = DoubleQuote
+                 , jatsMeta = mempty
+                 , jatsAcceptsMeta = False
+                 , jatsBook = False
+                 , jatsFigureTitle = mempty
+                 , jatsContent = [] }
+
+
+readJATS :: PandocMonad m => ReaderOptions -> Text -> m Pandoc
+readJATS _ inp = do
+  let tree = normalizeTree . parseXML
+               $ T.unpack $ crFilter inp
+  (bs, st') <- flip runStateT (def{ jatsContent = tree }) $ mapM parseBlock tree
+  return $ Pandoc (jatsMeta st') (toList . mconcat $ bs)
+
+-- normalize input, consolidating adjacent Text and CRef elements
+normalizeTree :: [Content] -> [Content]
+normalizeTree = everywhere (mkT go)
+  where go :: [Content] -> [Content]
+        go (Text (CData CDataRaw _ _):xs) = xs
+        go (Text (CData CDataText s1 z):Text (CData CDataText s2 _):xs) =
+           Text (CData CDataText (s1 ++ s2) z):xs
+        go (Text (CData CDataText s1 z):CRef r:xs) =
+           Text (CData CDataText (s1 ++ convertEntity r) z):xs
+        go (CRef r:Text (CData CDataText s1 z):xs) =
+             Text (CData CDataText (convertEntity r ++ s1) z):xs
+        go (CRef r1:CRef r2:xs) =
+             Text (CData CDataText (convertEntity r1 ++ convertEntity r2) Nothing):xs
+        go xs = xs
+
+convertEntity :: String -> String
+convertEntity e = Data.Maybe.fromMaybe (map toUpper e) (lookupEntity e)
+
+-- convenience function to get an attribute value, defaulting to ""
+attrValue :: String -> Element -> String
+attrValue attr =
+  fromMaybe "" . maybeAttrValue attr
+
+maybeAttrValue :: String -> Element -> Maybe String
+maybeAttrValue attr elt =
+  lookupAttrBy (\x -> qName x == attr) (elAttribs elt)
+
+-- convenience function
+named :: String -> Element -> Bool
+named s e = qName (elName e) == s
+
+--
+
+acceptingMetadata :: PandocMonad m => JATS m a -> JATS m a
+acceptingMetadata p = do
+  modify (\s -> s { jatsAcceptsMeta = True } )
+  res <- p
+  modify (\s -> s { jatsAcceptsMeta = False })
+  return res
+
+checkInMeta :: (PandocMonad m, Monoid a) => JATS m () -> JATS m a
+checkInMeta p = do
+  accepts <- jatsAcceptsMeta <$> get
+  when accepts p
+  return mempty
+
+addMeta :: PandocMonad m => ToMetaValue a => String -> a -> JATS m ()
+addMeta field val = modify (setMeta field val)
+
+instance HasMeta JATSState where
+  setMeta field v s =  s {jatsMeta = setMeta field v (jatsMeta s)}
+  deleteMeta field s = s {jatsMeta = deleteMeta field (jatsMeta s)}
+
+isBlockElement :: Content -> Bool
+isBlockElement (Elem e) = qName (elName e) `S.member` blocktags
+  where blocktags = S.fromList (paragraphLevel ++ lists ++ mathML ++ other) \\ S.fromList inlinetags
+        paragraphLevel = ["address", "array", "boxed-text", "chem-struct-wrap",
+            "code", "fig", "fig-group", "graphic", "media", "preformat",
+            "supplementary-material", "table-wrap", "table-wrap-group",
+            "alternatives", "disp-formula", "disp-formula-group"]
+        lists = ["def-list", "list"]
+        mathML = ["tex-math", "mml:math"]
+        other = ["p", "related-article", "related-object", "ack", "disp-quote",
+            "speech", "statement", "verse-group", "x"]
+        inlinetags = ["email", "ext-link", "uri", "inline-supplementary-material",
+            "related-article", "related-object", "hr", "bold", "fixed-case",
+            "italic", "monospace", "overline", "overline-start", "overline-end",
+            "roman", "sans-serif", "sc", "strike", "underline", "underline-start",
+            "underline-end", "ruby", "alternatives", "inline-graphic", "private-char",
+            "chem-struct", "inline-formula", "tex-math", "mml:math", "abbrev",
+            "milestone-end", "milestone-start", "named-content", "styled-content",
+            "fn", "target", "xref", "sub", "sup", "x", "address", "array",
+            "boxed-text", "chem-struct-wrap", "code", "fig", "fig-group", "graphic",
+            "media", "preformat", "supplementary-material", "table-wrap",
+            "table-wrap-group", "disp-formula", "disp-formula-group",
+            "citation-alternatives", "element-citation", "mixed-citation",
+            "nlm-citation", "award-id", "funding-source", "open-access",
+            "def-list", "list", "ack", "disp-quote", "speech", "statement",
+            "verse-group"]
+isBlockElement _ = False
+
+-- Trim leading and trailing newline characters
+trimNl :: String -> String
+trimNl = reverse . go . reverse . go
+  where go ('\n':xs) = xs
+        go xs        = xs
+
+-- function that is used by both graphic (in parseBlock)
+-- and inline-graphic (in parseInline)
+getGraphic :: PandocMonad m => Element -> JATS m Inlines
+getGraphic e = do
+  let atVal a = attrValue a e
+      attr = (atVal "id", words $ atVal "role", [])
+      imageUrl = atVal "href"
+      captionOrLabel = case filterChild (\x -> named "caption" x
+                                            || named "label" x) e of
+                        Nothing -> return mempty
+                        Just z  -> mconcat <$>
+                                         mapM parseInline (elContent z)
+  figTitle <- gets jatsFigureTitle
+  let (caption, title) = if isNull figTitle
+                            then (captionOrLabel, atVal "title")
+                            else (return figTitle, "fig:")
+  fmap (imageWith attr imageUrl title) caption
+
+getBlocks :: PandocMonad m => Element -> JATS m Blocks
+getBlocks e =  mconcat <$>
+                 mapM parseBlock (elContent e)
+
+
+parseBlock :: PandocMonad m => Content -> JATS m Blocks
+parseBlock (Text (CData CDataRaw _ _)) = return mempty -- DOCTYPE
+parseBlock (Text (CData _ s _)) = if all isSpace s
+                                     then return mempty
+                                     else return $ plain $ trimInlines $ text s
+parseBlock (CRef x) = return $ plain $ str $ map toUpper x
+parseBlock (Elem e) =
+  case qName (elName e) of
+        "p" -> parseMixed para (elContent e)
+        "code" -> codeBlockWithLang
+        "preformat" -> codeBlockWithLang
+        "disp-quote" -> parseBlockquote
+        "list" -> case attrValue "list-type" e of
+                    "bullet" -> bulletList <$> listitems
+                    listType -> do
+                      let start = fromMaybe 1 $
+                                  (strContent <$> (filterElement (named "list-item") e
+                                               >>= filterElement (named "lable")))
+                                   >>= safeRead
+                      orderedListWith (start, parseListStyleType listType, DefaultDelim)
+                        <$> listitems
+        "def-list" -> definitionList <$> deflistitems
+        "sec" -> gets jatsSectionLevel >>= sect . (+1)
+        "title" -> return mempty
+        "title-group" -> checkInMeta getTitle
+        "graphic" -> para <$> getGraphic e
+        "journal-meta" -> metaBlock
+        "article-meta" -> metaBlock
+        "custom-meta" -> metaBlock
+        "table" -> parseTable
+        "fig" -> divWith (attrValue "id" e, ["fig"], []) <$> getBlocks e
+        "table-wrap" -> divWith (attrValue "id" e, ["table-wrap"], []) <$> getBlocks e
+        "caption" -> divWith (attrValue "id" e, ["caption"], []) <$> sect 6
+        "ref-list" -> divWith ("refs", [], []) <$> getBlocks e
+        "ref" -> divWith ("ref-" <> attrValue "id" e, [], []) <$> getBlocks e
+        "?xml"  -> return mempty
+        _       -> getBlocks e
+   where parseMixed container conts = do
+           let (ils,rest) = break isBlockElement conts
+           ils' <- (trimInlines . mconcat) <$> mapM parseInline ils
+           let p = if ils' == mempty then mempty else container ils'
+           case rest of
+                 []     -> return p
+                 (r:rs) -> do
+                    b <- parseBlock r
+                    x <- parseMixed container rs
+                    return $ p <> b <> x
+         codeBlockWithLang = do
+           let classes' = case attrValue "language" e of
+                                "" -> []
+                                x  -> [x]
+           return $ codeBlockWith (attrValue "id" e, classes', [])
+                  $ trimNl $ strContentRecursive e
+         parseBlockquote = do
+            attrib <- case filterChild (named "attribution") e of
+                             Nothing  -> return mempty
+                             Just z   -> (para . (str "— " <>) . mconcat)
+                                         <$>
+                                              mapM parseInline (elContent z)
+            contents <- getBlocks e
+            return $ blockQuote (contents <> attrib)
+         parseListStyleType "roman-lower" = LowerRoman
+         parseListStyleType "roman-upper" = UpperRoman
+         parseListStyleType "alpha-lower" = LowerAlpha
+         parseListStyleType "alpha-upper" = UpperAlpha
+         parseListStyleType _             = DefaultStyle
+         listitems = mapM getBlocks $ filterChildren (named "list-item") e
+         deflistitems = mapM parseVarListEntry $ filterChildren
+                     (named "def-item") e
+         parseVarListEntry e' = do
+                     let terms = filterChildren (named "term") e'
+                     let items = filterChildren (named "def") e'
+                     terms' <- mapM getInlines terms
+                     items' <- mapM getBlocks items
+                     return (mconcat $ intersperse (str "; ") terms', items')
+         getTitle =  do
+                     tit <-  case filterChild (named "article-title") e of
+                                  Just s  -> getInlines s
+                                  Nothing -> return mempty
+                     subtit <-  case filterChild (named "subtitle") e of
+                                  Just s  -> (text ": " <>) <$>
+                                              getInlines s
+                                  Nothing -> return mempty
+                     addMeta "title" (tit <> subtit)
+
+         parseTable = do
+                      let isCaption x = named "title" x || named "caption" x
+                      caption <- case filterChild isCaption e of
+                                       Just t  -> getInlines t
+                                       Nothing -> return mempty
+                      let e' = fromMaybe e $ filterChild (named "tgroup") e
+                      let isColspec x = named "colspec" x || named "col" x
+                      let colspecs = case filterChild (named "colgroup") e' of
+                                           Just c -> filterChildren isColspec c
+                                           _      -> filterChildren isColspec e'
+                      let isRow x = named "row" x || named "tr" x
+                      headrows <- case filterChild (named "thead") e' of
+                                       Just h  -> case filterChild isRow h of
+                                                       Just x  -> parseRow x
+                                                       Nothing -> return []
+                                       Nothing -> return []
+                      bodyrows <- case filterChild (named "tbody") e' of
+                                       Just b  -> mapM parseRow
+                                                  $ filterChildren isRow b
+                                       Nothing -> mapM parseRow
+                                                  $ filterChildren isRow e'
+                      let toAlignment c = case findAttr (unqual "align") c of
+                                                Just "left"   -> AlignLeft
+                                                Just "right"  -> AlignRight
+                                                Just "center" -> AlignCenter
+                                                _             -> AlignDefault
+                      let toWidth c = case findAttr (unqual "colwidth") c of
+                                                Just w -> fromMaybe 0
+                                                   $ safeRead $ '0': filter (\x ->
+                                                     isDigit x || x == '.') w
+                                                Nothing -> 0 :: Double
+                      let numrows = case bodyrows of
+                                         [] -> 0
+                                         xs -> maximum $ map length xs
+                      let aligns = case colspecs of
+                                     [] -> replicate numrows AlignDefault
+                                     cs -> map toAlignment cs
+                      let widths = case colspecs of
+                                     []  -> replicate numrows 0
+                                     cs  -> let ws = map toWidth cs
+                                                tot = sum ws
+                                            in  if all (> 0) ws
+                                                   then map (/ tot) ws
+                                                   else replicate numrows 0
+                      let headrows' = if null headrows
+                                         then replicate numrows mempty
+                                         else headrows
+                      return $ table caption (zip aligns widths)
+                                 headrows' bodyrows
+         isEntry x  = named "entry" x || named "td" x || named "th" x
+         parseRow = mapM (parseMixed plain . elContent) . filterChildren isEntry
+         sect n = do isbook <- gets jatsBook
+                     let n' = if isbook || n == 0 then n + 1 else n
+                     headerText <- case filterChild (named "title") e `mplus`
+                                        (filterChild (named "info") e >>=
+                                            filterChild (named "title")) of
+                                      Just t  -> getInlines t
+                                      Nothing -> return mempty
+                     oldN <- gets jatsSectionLevel
+                     modify $ \st -> st{ jatsSectionLevel = n }
+                     b <- getBlocks e
+                     let ident = attrValue "id" e
+                     modify $ \st -> st{ jatsSectionLevel = oldN }
+                     return $ headerWith (ident,[],[]) n' headerText <> b
+--         lineItems = mapM getInlines $ filterChildren (named "line") e
+         metaBlock = acceptingMetadata (getBlocks e) >> return mempty
+
+getInlines :: PandocMonad m => Element -> JATS m Inlines
+getInlines e' = (trimInlines . mconcat) <$>
+                 mapM parseInline (elContent e')
+
+strContentRecursive :: Element -> String
+strContentRecursive = strContent .
+  (\e' -> e'{ elContent = map elementToStr $ elContent e' })
+
+elementToStr :: Content -> Content
+elementToStr (Elem e') = Text $ CData CDataText (strContentRecursive e') Nothing
+elementToStr x = x
+
+parseInline :: PandocMonad m => Content -> JATS m Inlines
+parseInline (Text (CData _ s _)) = return $ text s
+parseInline (CRef ref) =
+  return $ maybe (text $ map toUpper ref) text $ lookupEntity ref
+parseInline (Elem e) =
+  case qName (elName e) of
+        "italic" -> emph <$> innerInlines
+        "bold" -> strong <$> innerInlines
+        "strike" -> strikeout <$> innerInlines
+        "sub" -> subscript <$> innerInlines
+        "sup" -> superscript <$> innerInlines
+        "underline" -> underlineSpan <$> innerInlines
+        "break" -> return linebreak
+        "sc" -> smallcaps <$> innerInlines
+
+        "code" -> codeWithLang
+        "monospace" -> codeWithLang
+
+        "inline-graphic" -> getGraphic e
+        "disp-quote" -> do
+            qt <- gets jatsQuoteType
+            let qt' = if qt == SingleQuote then DoubleQuote else SingleQuote
+            modify $ \st -> st{ jatsQuoteType = qt' }
+            contents <- innerInlines
+            modify $ \st -> st{ jatsQuoteType = qt }
+            return $ if qt == SingleQuote
+                        then singleQuoted contents
+                        else doubleQuoted contents
+
+        "xref" -> do
+            ils <- innerInlines
+            let rid = attrValue "rid" e
+            let refType = ("ref-type",) <$> maybeAttrValue "ref-type" e
+            let attr = (attrValue "id" e, [], maybeToList refType)
+            return $ linkWith attr ('#' : rid) "" ils
+        "ext-link" -> do
+             ils <- innerInlines
+             let title = fromMaybe "" $ findAttr (QName "title" (Just "http://www.w3.org/1999/xlink") Nothing) e
+             let href = case findAttr (QName "href" (Just "http://www.w3.org/1999/xlink") Nothing) e of
+                               Just h -> h
+                               _      -> '#' : attrValue "rid" e
+             let ils' = if ils == mempty then str href else ils
+             let attr = (attrValue "id" e, [], [])
+             return $ linkWith attr href title ils'
+
+        "disp-formula" -> formula displayMath
+        "inline-formula" -> formula math
+        "math" | qPrefix (elName e) == Just "mml" -> return . math $ mathML e
+        "tex-math" -> return . math $ strContent e
+
+        "email" -> return $ link ("mailto:" ++ strContent e) ""
+                          $ str $ strContent e
+        "uri" -> return $ link (strContent e) "" $ str $ strContent e
+        "fn" -> (note . mconcat) <$>
+                         mapM parseBlock (elContent e)
+        -- Note: this isn't a real docbook tag; it's what we convert
+        -- <?asciidor-br?> to in handleInstructions, above.  A kludge to
+        -- work around xml-light's inability to parse an instruction.
+        _          -> innerInlines
+   where innerInlines = (trimInlines . mconcat) <$>
+                          mapM parseInline (elContent e)
+         mathML x =
+            case readMathML . showElement $ everywhere (mkT removePrefix) x of
+                Left _ -> mempty
+                Right m -> writeTeX m
+         formula constructor = do
+            let whereToLook = fromMaybe e $ filterElement (named "alternatives") e
+                texMaths = map strContent $
+                            filterChildren (named  "tex-math") whereToLook
+                mathMLs = map mathML $
+                            filterChildren isMathML whereToLook
+            return . mconcat . take 1 . map constructor $ texMaths ++ mathMLs
+
+         isMathML x = qName   (elName x) == "math" &&
+                      qPrefix (elName x) == Just "mml"
+         removePrefix elname = elname { qPrefix = Nothing }
+         codeWithLang = do
+           let classes' = case attrValue "language" e of
+                               "" -> []
+                               l  -> [l]
+           return $ codeWith (attrValue "id" e,classes',[]) $ strContentRecursive e
+
--- a/src/Text/Pandoc/Writers/JATS.hs
+++ b/src/Text/Pandoc/Writers/JATS.hs
@ -170,6 +170,28 @@ imageMimeType src kvs =
                  ((drop 1 . dropWhile (/='/')) <$> mbMT)
  in (maintype, subtype)

+languageFor :: [String] -> String
+languageFor classes =
+  case langs of
+     (l:_) -> escapeStringForXML l
+     []    -> ""
+    where isLang l    = map toLower l `elem` map (map toLower) languages
+          langsFrom s = if isLang s
+                           then [s]
+                           else languagesByExtension . map toLower $ s
+          langs       = concatMap langsFrom classes
+
+codeAttr :: Attr -> (String, [(String, String)])
+codeAttr (ident,classes,kvs) = (lang, attr)
+    where
+       attr = [("id",ident) | not (null ident)] ++
+              [("language",lang) | not (null lang)] ++
+              [(k,v) | (k,v) <- kvs, k `elem` ["code-type",
+                "code-version", "executable",
+                "language-version", "orientation",
+                    "platforms", "position", "specific-use"]]
+       lang  = languageFor classes
+
 -- | Convert a Pandoc block element to JATS.
 blockToJATS :: PandocMonad m => WriterOptions -> Block -> JATS m Doc
 blockToJATS _ Null = return empty
@ -233,23 +255,10 @@ blockToJATS opts (LineBlock lns) =
  blockToJATS opts $ linesToPara lns
 blockToJATS opts (BlockQuote blocks) =
  inTagsIndented "disp-quote" <$> blocksToJATS opts blocks
-blockToJATS _ (CodeBlock (ident,classes,kvs) str) = return $
+blockToJATS _ (CodeBlock a str) = return $
  inTags False tag attr (flush (text (escapeStringForXML str)))
-    where attr  = [("id",ident) | not (null ident)] ++
-                  [("language",lang) | not (null lang)] ++
-                  [(k,v) | (k,v) <- kvs, k `elem` ["code-type",
-                    "code-version", "executable",
-                    "language-version", "orientation",
-                    "platforms", "position", "specific-use"]]
-          tag   = if null lang then "preformat" else "code"
-          lang  = case langs of
-                     (l:_) -> escapeStringForXML l
-                     []    -> ""
-          isLang l    = map toLower l `elem` map (map toLower) languages
-          langsFrom s = if isLang s
-                           then [s]
-                           else languagesByExtension . map toLower $ s
-          langs       = concatMap langsFrom classes
+    where (lang, attr) = codeAttr a
+          tag          = if null lang then "preformat" else "code"
 blockToJATS _ (BulletList []) = return empty
 blockToJATS opts (BulletList lst) =
  inTags True "list" [("list-type", "bullet")] <$>
@ -349,8 +358,10 @@ inlineToJATS opts (Quoted SingleQuote lst) = do
 inlineToJATS opts (Quoted DoubleQuote lst) = do
  contents <- inlinesToJATS opts lst
  return $ char '“' <> contents <> char '”'
-inlineToJATS _ (Code _ str) =
-  return $ inTagsSimple "monospace" $ text (escapeStringForXML str)
+inlineToJATS _ (Code a str) =
+  return $ inTags False tag attr $ text (escapeStringForXML str)
+    where (lang, attr) = codeAttr a
+          tag          = if null lang then "monospace" else "code"
 inlineToJATS _ il@(RawInline f x)
  | f == "jats" = return $ text x
  | otherwise   = do
--- a/test/Tests/Old.hs
+++ b/test/Tests/Old.hs
@ -79,6 +79,8 @@ tests = [ testGroup "markdown"
          ]
        , testGroup "jats"
          [ testGroup "writer" $ writerTests "jats"
+          , test "reader" ["-r", "jats", "-w", "native", "-s"]
+            "jats-reader.xml" "jats-reader.native"
          ]
        , testGroup "native"
          [ testGroup "writer" $ writerTests "native"
--- a/test/Tests/Readers/JATS.hs
+++ b/test/Tests/Readers/JATS.hs
@ -0,0 +1,116 @@
+{-# LANGUAGE OverloadedStrings #-}
+module Tests.Readers.JATS (tests) where
+
+import Data.Text (Text)
+import Test.Tasty
+import Tests.Helpers
+import Text.Pandoc
+import Text.Pandoc.Arbitrary ()
+import Text.Pandoc.Builder
+
+jats :: Text -> Pandoc
+jats = purely $ readJATS def
+
+tests :: [TestTree]
+tests = [ testGroup "inline code"
+          [ test jats "basic" $ "<p>\n  <monospace>@&amp;</monospace>\n</p>" =?> para (code "@&")
+          , test jats "lang" $ "<p>\n  <code language=\"c\">@&amp;</code>\n</p>" =?> para (codeWith ("", ["c"], []) "@&")
+          ]
+        , testGroup "block code"
+          [ test jats "basic" $ "<preformat>@&amp;</preformat>" =?> codeBlock "@&"
+          , test jats "lang" $ "<code language=\"c\">@&amp;</code>" =?> codeBlockWith ("", ["c"], []) "@&"
+          ]
+        , testGroup "images"
+          [ test jats "basic" $ "<graphic mimetype=\"image\" mime-subtype=\"\" xlink:href=\"/url\" xlink:title=\"title\" />"
+            =?> para (image "/url" "title" mempty)
+          ]
+        , test jats "bullet list" $
+                            "<list list-type=\"bullet\">\n\
+                            \  <list-item>\n\
+                            \    <p>\n\
+                            \      first\n\
+                            \    </p>\n\
+                            \  </list-item>\n\
+                            \  <list-item>\n\
+                            \    <p>\n\
+                            \      second\n\
+                            \    </p>\n\
+                            \  </list-item>\n\
+                            \  <list-item>\n\
+                            \    <p>\n\
+                            \      third\n\
+                            \    </p>\n\
+                            \  </list-item>\n\
+                            \</list>"
+                =?> bulletList [ para $ text "first"
+                               , para $ text "second"
+                               , para $ text "third"
+                               ]
+        , testGroup "definition lists"
+          [ test jats "with internal link" $
+            "<def-list>\n\
+            \  <def-item>\n\
+            \    <term>\n\
+            \      <xref alt=\"testing\" rid=\"go\">testing</xref>\n\
+            \    </term>\n\
+            \    <def>\n\
+            \      <p>\n\
+            \        hi there\n\
+            \      </p>\n\
+            \    </def>\n\
+            \  </def-item>\n\
+            \</def-list>"
+            =?> definitionList [(link "#go" "" (str "testing"),
+                [para (text "hi there")])]
+          ]
+        , testGroup "math"
+          [ test jats "escape |" $
+            "<p>\n\
+            \  <inline-formula><alternatives>\n\
+            \  <tex-math><![CDATA[\\sigma|_{\\{x\\}}]]></tex-math>\n\
+            \  <mml:math display=\"inline\" xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"><mml:mrow><mml:mi>σ</mml:mi><mml:msub><mml:mo stretchy=\"false\" form=\"prefix\">|</mml:mo><mml:mrow><mml:mo stretchy=\"false\" form=\"prefix\">{</mml:mo><mml:mi>x</mml:mi><mml:mo stretchy=\"false\" form=\"postfix\">}</mml:mo></mml:mrow></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>\n\
+            \</p>"
+            =?> para (math "\\sigma|_{\\{x\\}}")
+          , test jats "tex-math only" $
+            "<p>\n\
+            \  <inline-formula><alternatives>\n\
+            \  <tex-math><![CDATA[\\sigma|_{\\{x\\}}]]></tex-math>\n\
+            \</p>"
+            =?> para (math "\\sigma|_{\\{x\\}}")
+          , test jats "math ml only" $
+            "<p>\n\
+            \  <inline-formula><alternatives>\n\
+            \  <mml:math display=\"inline\" xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"><mml:mrow><mml:mi>σ</mml:mi><mml:msub><mml:mo stretchy=\"false\" form=\"prefix\">|</mml:mo><mml:mrow><mml:mo stretchy=\"false\" form=\"prefix\">{</mml:mo><mml:mi>x</mml:mi><mml:mo stretchy=\"false\" form=\"postfix\">}</mml:mo></mml:mrow></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>\n\
+            \</p>"
+            =?> para (math "\\sigma|_{\\{ x\\}}")
+          ]
+        , testGroup "headers"
+-- TODO fix footnotes in headers
+--          [ test jats "unnumbered header" $
+--            "<sec>\n\
+--            \  <title>Header 1<fn>\n\
+--            \    <p>\n\
+--            \      note\n\
+--            \    </p>\n\
+--            \  </fn></title>\n\
+--            \</sec>"
+--            =?> header 1
+--                (text "Header 1" <> note (plain $ text "note"))
+          [ test jats "unnumbered sub header" $
+            "<sec id=\"foo\">\n\
+            \  <title>Header</title>\n\
+            \  <sec id=\"foo2\">\n\
+            \    <title>Sub-Header</title>\n\
+            \  </sec>\n\
+            \</sec>"
+            =?> headerWith ("foo", [], []) 1
+                  (text "Header")
+                <> headerWith  ("foo2", [], []) 2
+                  (text "Sub-Header")
+          , test jats "containing image" $
+            "<sec>\n\
+            \  <title><inline-graphic mimetype=\"image\" mime-subtype=\"jpeg\" xlink:href=\"imgs/foo.jpg\" /></title>\n\
+            \</sec>"
+            =?> header 1 (image "imgs/foo.jpg" "" mempty)
+          ]
+        ]
--- a/test/Tests/Writers/JATS.hs
+++ b/test/Tests/Writers/JATS.hs
@ -31,6 +31,11 @@ infix 4 =:
 tests :: [TestTree]
 tests = [ testGroup "inline code"
          [ "basic" =: code "@&" =?> "<p>\n  <monospace>@&amp;</monospace>\n</p>"
+          , "lang" =: codeWith ("", ["c"], []) "@&" =?> "<p>\n  <code language=\"c\">@&amp;</code>\n</p>"
+          ]
+        , testGroup "block code"
+          [ "basic" =: codeBlock "@&" =?> "<preformat>@&amp;</preformat>"
+          , "lang" =: codeBlockWith ("", ["c"], []) "@&" =?> "<code language=\"c\">@&amp;</code>"
          ]
        , testGroup "images"
          [ "basic" =:
@ -38,7 +43,7 @@ tests = [ testGroup "inline code"
            =?> "<graphic mimetype=\"image\" mime-subtype=\"\" xlink:href=\"/url\" xlink:title=\"title\" />"
          ]
        , testGroup "inlines"
-          [ "Emphasis" =: emph ("emphasized")
+          [ "Emphasis" =: emph "emphasized"
            =?> "<p>\n  <italic>emphasized</italic>\n</p>"
          ]
        , "bullet list" =: bulletList [ plain $ text "first"
--- a/test/jats-reader.native
+++ b/test/jats-reader.native
@ -0,0 +1,422 @@
+Pandoc (Meta {unMeta = fromList [("title",MetaInlines [Str "Pandoc",Space,Str "Test",Space,Str "Suite"])]})
+[Para [Str "This",Space,Str "is",Space,Str "a",Space,Str "set",Space,Str "of",Space,Str "tests",Space,Str "for",Space,Str "pandoc.",Space,Str "Most",Space,Str "of",Space,Str "them",Space,Str "are",Space,Str "adapted",Space,Str "from",Space,Str "John",SoftBreak,Str "Gruber's",Space,Str "markdown",Space,Str "test",Space,Str "suite."]
+,Header 1 ("headers",[],[]) [Str "Headers"]
+,Header 2 ("level-2-with-an-embedded-link",[],[]) [Str "Level",Space,Str "2",Space,Str "with",Space,Str "an",SoftBreak,Link ("",[],[]) [Str "embedded",SoftBreak,Str "link"] ("/url","")]
+,Header 3 ("level-3-with-emphasis",[],[]) [Str "Level",Space,Str "3",Space,Str "with",Space,Emph [Str "emphasis"]]
+,Header 4 ("level-4",[],[]) [Str "Level",Space,Str "4"]
+,Header 5 ("level-5",[],[]) [Str "Level",Space,Str "5"]
+,Header 1 ("level-1",[],[]) [Str "Level",Space,Str "1"]
+,Header 2 ("level-2-with-emphasis",[],[]) [Str "Level",Space,Str "2",Space,Str "with",Space,Emph [Str "emphasis"]]
+,Header 3 ("level-3",[],[]) [Str "Level",Space,Str "3"]
+,Para [Str "with",Space,Str "no",Space,Str "blank",Space,Str "line"]
+,Header 2 ("level-2",[],[]) [Str "Level",Space,Str "2"]
+,Para [Str "with",Space,Str "no",Space,Str "blank",Space,Str "line"]
+,Header 1 ("paragraphs",[],[]) [Str "Paragraphs"]
+,Para [Str "Here's",Space,Str "a",Space,Str "regular",Space,Str "paragraph."]
+,Para [Str "In",Space,Str "Markdown",Space,Str "1.0.0",Space,Str "and",Space,Str "earlier.",Space,Str "Version",Space,Str "8.",Space,Str "This",Space,Str "line",Space,Str "turns",Space,Str "into",Space,Str "a",SoftBreak,Str "list",Space,Str "item.",Space,Str "Because",Space,Str "a",Space,Str "hard-wrapped",Space,Str "line",Space,Str "in",Space,Str "the",Space,Str "middle",Space,Str "of",Space,Str "a",Space,Str "paragraph",SoftBreak,Str "looked",Space,Str "like",Space,Str "a",Space,Str "list",Space,Str "item."]
+,Para [Str "Here's",Space,Str "one",Space,Str "with",Space,Str "a",Space,Str "bullet.",Space,Str "*",Space,Str "criminey."]
+,Para [Str "There",Space,Str "should",Space,Str "be",Space,Str "a",Space,Str "hard",Space,Str "line",Space,Str "break",LineBreak,Str "here."]
+,Header 1 ("block-quotes",[],[]) [Str "Block",Space,Str "Quotes"]
+,Para [Str "E-mail",Space,Str "style:"]
+,BlockQuote
+ [Para [Str "This",Space,Str "is",Space,Str "a",Space,Str "block",Space,Str "quote.",Space,Str "It",Space,Str "is",Space,Str "pretty",Space,Str "short."]]
+,BlockQuote
+ [Para [Str "Code",Space,Str "in",Space,Str "a",Space,Str "block",Space,Str "quote:"]
+ ,CodeBlock ("",[],[]) "sub status {\n    print \"working\";\n}"
+ ,Para [Str "A",Space,Str "list:"]
+ ,OrderedList (1,DefaultStyle,DefaultDelim)
+  [[Para [Str "item",Space,Str "one"]]
+  ,[Para [Str "item",Space,Str "two"]]]
+ ,Para [Str "Nested",Space,Str "block",Space,Str "quotes:"]
+ ,BlockQuote
+  [Para [Str "nested"]]
+ ,BlockQuote
+  [Para [Str "nested"]]]
+,Para [Str "This",Space,Str "should",Space,Str "not",Space,Str "be",Space,Str "a",Space,Str "block",Space,Str "quote:",Space,Str "2",Space,Str ">",Space,Str "1."]
+,Para [Str "Box-style:"]
+,BlockQuote
+ [Para [Str "Example:"]
+ ,CodeBlock ("",[],[]) "sub status {\n    print \"working\";\n}"]
+,BlockQuote
+ [OrderedList (1,DefaultStyle,DefaultDelim)
+  [[Para [Str "do",Space,Str "laundry"]]
+  ,[Para [Str "take",Space,Str "out",Space,Str "the",Space,Str "trash"]]]]
+,Para [Str "Here's",Space,Str "a",Space,Str "nested",Space,Str "one:"]
+,BlockQuote
+ [Para [Str "Joe",Space,Str "said:"]
+ ,BlockQuote
+  [Para [Str "Don't",Space,Str "quote",Space,Str "me."]]]
+,Para [Str "And",Space,Str "a",Space,Str "following",Space,Str "paragraph."]
+,Header 1 ("code-blocks",[],[]) [Str "Code",Space,Str "Blocks"]
+,Para [Str "Code:"]
+,CodeBlock ("",[],[]) "---- (should be four hyphens)\n\nsub status {\n    print \"working\";\n}\n\nthis code block is indented by one tab"
+,Para [Str "And:"]
+,CodeBlock ("",[],[]) "    this code block is indented by two tabs\n\nThese should not be escaped:  \\$ \\\\ \\> \\[ \\{"
+,Header 1 ("lists",[],[]) [Str "Lists"]
+,Header 2 ("unordered",[],[]) [Str "Unordered"]
+,Para [Str "Asterisks",Space,Str "tight:"]
+,BulletList
+ [[Para [Str "asterisk",Space,Str "1"]]
+ ,[Para [Str "asterisk",Space,Str "2"]]
+ ,[Para [Str "asterisk",Space,Str "3"]]]
+,Para [Str "Asterisks",Space,Str "loose:"]
+,BulletList
+ [[Para [Str "asterisk",Space,Str "1"]]
+ ,[Para [Str "asterisk",Space,Str "2"]]
+ ,[Para [Str "asterisk",Space,Str "3"]]]
+,Para [Str "Pluses",Space,Str "tight:"]
+,BulletList
+ [[Para [Str "Plus",Space,Str "1"]]
+ ,[Para [Str "Plus",Space,Str "2"]]
+ ,[Para [Str "Plus",Space,Str "3"]]]
+,Para [Str "Pluses",Space,Str "loose:"]
+,BulletList
+ [[Para [Str "Plus",Space,Str "1"]]
+ ,[Para [Str "Plus",Space,Str "2"]]
+ ,[Para [Str "Plus",Space,Str "3"]]]
+,Para [Str "Minuses",Space,Str "tight:"]
+,BulletList
+ [[Para [Str "Minus",Space,Str "1"]]
+ ,[Para [Str "Minus",Space,Str "2"]]
+ ,[Para [Str "Minus",Space,Str "3"]]]
+,Para [Str "Minuses",Space,Str "loose:"]
+,BulletList
+ [[Para [Str "Minus",Space,Str "1"]]
+ ,[Para [Str "Minus",Space,Str "2"]]
+ ,[Para [Str "Minus",Space,Str "3"]]]
+,Header 2 ("ordered",[],[]) [Str "Ordered"]
+,Para [Str "Tight:"]
+,OrderedList (1,DefaultStyle,DefaultDelim)
+ [[Para [Str "First"]]
+ ,[Para [Str "Second"]]
+ ,[Para [Str "Third"]]]
+,Para [Str "and:"]
+,OrderedList (1,DefaultStyle,DefaultDelim)
+ [[Para [Str "One"]]
+ ,[Para [Str "Two"]]
+ ,[Para [Str "Three"]]]
+,Para [Str "Loose",Space,Str "using",Space,Str "tabs:"]
+,OrderedList (1,DefaultStyle,DefaultDelim)
+ [[Para [Str "First"]]
+ ,[Para [Str "Second"]]
+ ,[Para [Str "Third"]]]
+,Para [Str "and",Space,Str "using",Space,Str "spaces:"]
+,OrderedList (1,DefaultStyle,DefaultDelim)
+ [[Para [Str "One"]]
+ ,[Para [Str "Two"]]
+ ,[Para [Str "Three"]]]
+,Para [Str "Multiple",Space,Str "paragraphs:"]
+,OrderedList (1,DefaultStyle,DefaultDelim)
+ [[Para [Str "Item",Space,Str "1,",Space,Str "graf",Space,Str "one."]
+  ,Para [Str "Item",Space,Str "1.",Space,Str "graf",Space,Str "two.",Space,Str "The",Space,Str "quick",Space,Str "brown",Space,Str "fox",Space,Str "jumped",Space,Str "over",Space,Str "the",Space,Str "lazy",SoftBreak,Str "dog's",Space,Str "back."]]
+ ,[Para [Str "Item",Space,Str "2."]]
+ ,[Para [Str "Item",Space,Str "3."]]]
+,Para [Str "List",Space,Str "styles:"]
+,OrderedList (1,DefaultStyle,DefaultDelim)
+ []
+,OrderedList (1,LowerRoman,DefaultDelim)
+ []
+,Header 2 ("nested",[],[]) [Str "Nested"]
+,BulletList
+ [[Para [Str "Tab"]
+  ,BulletList
+   [[Para [Str "Tab"]
+    ,BulletList
+     [[Para [Str "Tab"]]]]]]]
+,Para [Str "Here's",Space,Str "another:"]
+,OrderedList (1,DefaultStyle,DefaultDelim)
+ [[Para [Str "First"]]
+ ,[Para [Str "Second:"]
+  ,BulletList
+   [[Para [Str "Fee"]]
+   ,[Para [Str "Fie"]]
+   ,[Para [Str "Foe"]]]]
+ ,[Para [Str "Third"]]]
+,Para [Str "Same",Space,Str "thing",Space,Str "but",Space,Str "with",Space,Str "paragraphs:"]
+,OrderedList (1,DefaultStyle,DefaultDelim)
+ [[Para [Str "First"]]
+ ,[Para [Str "Second:"]
+  ,BulletList
+   [[Para [Str "Fee"]]
+   ,[Para [Str "Fie"]]
+   ,[Para [Str "Foe"]]]]
+ ,[Para [Str "Third"]]]
+,Header 2 ("tabs-and-spaces",[],[]) [Str "Tabs",Space,Str "and",Space,Str "spaces"]
+,BulletList
+ [[Para [Str "this",Space,Str "is",Space,Str "a",Space,Str "list",Space,Str "item",Space,Str "indented",Space,Str "with",Space,Str "tabs"]]
+ ,[Para [Str "this",Space,Str "is",Space,Str "a",Space,Str "list",Space,Str "item",Space,Str "indented",Space,Str "with",Space,Str "spaces"]
+  ,BulletList
+   [[Para [Str "this",Space,Str "is",Space,Str "an",Space,Str "example",Space,Str "list",Space,Str "item",Space,Str "indented",Space,Str "with",Space,Str "tabs"]]
+   ,[Para [Str "this",Space,Str "is",Space,Str "an",Space,Str "example",Space,Str "list",Space,Str "item",Space,Str "indented",Space,Str "with",Space,Str "spaces"]]]]]
+,Header 2 ("fancy-list-markers",[],[]) [Str "Fancy",Space,Str "list",Space,Str "markers"]
+,Para [Str "Autonumbering:"]
+,OrderedList (1,DefaultStyle,DefaultDelim)
+ [[Para [Str "Autonumber."]]
+ ,[Para [Str "More."]
+  ,OrderedList (1,DefaultStyle,DefaultDelim)
+   [[Para [Str "Nested."]]]]]
+,Header 2 ("definition",[],[]) [Str "Definition"]
+,DefinitionList
+ [([Str "Violin"],
+   [[Para [Str "Stringed",Space,Str "musical",Space,Str "instrument."]
+    ,Para [Str "Torture",Space,Str "device."]]])
+ ,([Str "Cello",LineBreak,Str "Violoncello"],
+   [[Para [Str "Low-voiced",Space,Str "stringed",Space,Str "instrument."]]])]
+,Header 1 ("inline-markup",[],[]) [Str "Inline",Space,Str "Markup"]
+,Para [Str "This",Space,Str "is",Space,Emph [Str "emphasized"],Str ",",Space,Str "and",Space,Str "so",Space,Emph [Str "is",SoftBreak,Str "this"],Str "."]
+,Para [Str "This",Space,Str "is",Space,Strong [Str "strong"],Str ",",Space,Str "and",Space,Str "so",SoftBreak,Strong [Str "is",Space,Str "this"],Str "."]
+,Para [Str "Empty",Space,Strong [],Space,Str "and",Space,Emph [],Str "."]
+,Para [Str "An",SoftBreak,Emph [Link ("",[],[]) [Str "emphasized",SoftBreak,Str "link"] ("/url","")],Str "."]
+,Para [Strong [Emph [Str "This",Space,Str "is",Space,Str "strong",Space,Str "and",Space,Str "em."]]]
+,Para [Str "So",Space,Str "is",Space,Strong [Emph [Str "this"]],Space,Str "word."]
+,Para [Strong [Emph [Str "This",Space,Str "is",Space,Str "strong",Space,Str "and",Space,Str "em."]]]
+,Para [Str "So",Space,Str "is",Space,Strong [Emph [Str "this"]],Space,Str "word."]
+,Para [Str "This",Space,Str "is",Space,Str "code:",Space,Code ("",[],[]) ">",Str ",",Space,Code ("",[],[]) "$",Str ",",SoftBreak,Code ("",[],[]) "\\",Str ",",Space,Code ("",[],[]) "\\$",Str ",",SoftBreak,Code ("",[],[]) "<html>",Str "."]
+,Para [Str "This",Space,Str "is",Space,SmallCaps [Str "small",Space,Str "caps"],Str "."]
+,Para [Str "These",Space,Str "are",Space,Str "all",Space,Str "underlined:",Space,Str "foo",Space,Str "and",Space,Str "bar."]
+,Para [Str "These",Space,Str "are",Space,Str "all",Space,Str "strikethrough:",Space,Strikeout [Str "foo"],Str ",",SoftBreak,Strikeout [Str "bar"],Str ",",Space,Str "and",Space,Strikeout [Str "baz"],Str "."]
+,Header 1 ("smart-quotes-ellipses-dashes",[],[]) [Str "Smart",Space,Str "quotes,",Space,Str "ellipses,",Space,Str "dashes"]
+,Para [Str "\"Hello,\"",Space,Str "said",Space,Str "the",Space,Str "spider.",Space,Str "\"'Shelob'",Space,Str "is",Space,Str "my",Space,Str "name.\""]
+,Para [Str "'A',",Space,Str "'B',",Space,Str "and",Space,Str "'C'",Space,Str "are",Space,Str "letters."]
+,Para [Str "'Oak,'",Space,Str "'elm,'",Space,Str "and",Space,Str "'beech'",Space,Str "are",Space,Str "names",Space,Str "of",Space,Str "trees.",Space,Str "So",Space,Str "is",Space,Str "'pine.'"]
+,Para [Str "'He",Space,Str "said,",Space,Str "\"I",Space,Str "want",Space,Str "to",Space,Str "go.\"'",Space,Str "Were",Space,Str "you",Space,Str "alive",Space,Str "in",Space,Str "the",Space,Str "70's?"]
+,Para [Str "Here",Space,Str "is",Space,Str "some",Space,Str "quoted",Space,Str "'",Code ("",[],[]) "code",Str "'",Space,Str "and",Space,Str "a",SoftBreak,Str "\"",Link ("",[],[]) [Str "quoted",SoftBreak,Str "link"] ("http://example.com/?foo=1&bar=2",""),Str "\"."]
+,Para [Str "Some",Space,Str "dashes:",Space,Str "one---two",Space,Str "---",Space,Str "three--four",Space,Str "--",Space,Str "five."]
+,Para [Str "Dashes",Space,Str "between",Space,Str "numbers:",Space,Str "5-7,",Space,Str "255-66,",Space,Str "1987-1999."]
+,Para [Str "Ellipses...and.",Space,Str ".",Space,Str ".and",Space,Str ".",Space,Str ".",Space,Str ".",Space,Str "."]
+,Header 1 ("latex",[],[]) [Str "LaTeX"]
+,BulletList
+ [[Para [Str "\\cite[22-23]{smith.1899}"]]
+ ,[Para [Str "\\doublespacing"]]
+ ,[Para [Str "$2+2=4$"]]
+ ,[Para [Str "$x",Space,Str "\\in",Space,Str "y$"]]
+ ,[Para [Str "$\\alpha",Space,Str "\\wedge",Space,Str "\\omega$"]]
+ ,[Para [Str "$223$"]]
+ ,[Para [Str "$p$-Tree"]]
+ ,[Para [Str "$\\frac{d}{dx}f(x)=\\lim_{h\\to",Space,Str "0}\\frac{f(x+h)-f(x)}{h}$"]]
+ ,[Para [Str "Here's",Space,Str "one",Space,Str "that",Space,Str "has",Space,Str "a",Space,Str "line",Space,Str "break",Space,Str "in",Space,Str "it:",Space,Str "$\\alpha",Space,Str "+",Space,Str "\\omega",Space,Str "\\times",SoftBreak,Str "x^2$."]]]
+,Para [Str "These",Space,Str "shouldn't",Space,Str "be",Space,Str "math:"]
+,BulletList
+ [[Para [Str "To",Space,Str "get",Space,Str "the",Space,Str "famous",Space,Str "equation,",Space,Str "write",SoftBreak,Code ("",[],[]) "$e = mc^2$",Str "."]]
+ ,[Para [Str "$22,000",Space,Str "is",Space,Str "a",Space,Emph [Str "lot"],Space,Str "of",Space,Str "money.",Space,Str "So",Space,Str "is",Space,Str "$34,000.",Space,Str "(It",SoftBreak,Str "worked",Space,Str "if",Space,Str "\"lot\"",Space,Str "is",Space,Str "emphasized.)"]]
+ ,[Para [Str "Escaped",Space,Code ("",[],[]) "$",Str ":",Space,Str "$73",Space,Emph [Str "this",Space,Str "should",Space,Str "be",SoftBreak,Str "emphasized"],Space,Str "23$."]]]
+,Para [Str "Here's",Space,Str "a",Space,Str "LaTeX",Space,Str "table:"]
+,Para [Str "\\begin{tabular}{|l|l|}\\hline",Space,Str "Animal",Space,Str "&",Space,Str "Number",Space,Str "\\\\",Space,Str "\\hline",Space,Str "Dog",Space,Str "&",SoftBreak,Str "2",Space,Str "\\\\",Space,Str "Cat",Space,Str "&",Space,Str "1",Space,Str "\\\\",Space,Str "\\hline",Space,Str "\\end{tabular}"]
+,Header 1 ("special-characters",[],[]) [Str "Special",Space,Str "Characters"]
+,Para [Str "Here",Space,Str "is",Space,Str "some",Space,Str "unicode:"]
+,BulletList
+ [[Para [Str "I",Space,Str "hat:",Space,Str "\206"]]
+ ,[Para [Str "o",Space,Str "umlaut:",Space,Str "\246"]]
+ ,[Para [Str "section:",Space,Str "\167"]]
+ ,[Para [Str "set",Space,Str "membership:",Space,Str "elem"]]
+ ,[Para [Str "copyright:",Space,Str "\169"]]]
+,Para [Str "AT&T",Space,Str "has",Space,Str "an",Space,Str "ampersand",Space,Str "in",Space,Str "their",Space,Str "name."]
+,Para [Str "AT&T",Space,Str "is",Space,Str "another",Space,Str "way",Space,Str "to",Space,Str "write",Space,Str "it."]
+,Para [Str "This",Space,Str "&",Space,Str "that."]
+,Para [Str "4",Space,Str "<",Space,Str "5."]
+,Para [Str "6",Space,Str ">",Space,Str "5."]
+,Para [Str "Backslash:",Space,Str "\\"]
+,Para [Str "Backtick:",Space,Str "`"]
+,Para [Str "Asterisk:",Space,Str "*"]
+,Para [Str "Underscore:",Space,Str "_"]
+,Para [Str "Left",Space,Str "brace:",Space,Str "{"]
+,Para [Str "Right",Space,Str "brace:",Space,Str "}"]
+,Para [Str "Left",Space,Str "bracket:",Space,Str "["]
+,Para [Str "Right",Space,Str "bracket:",Space,Str "]"]
+,Para [Str "Left",Space,Str "paren:",Space,Str "("]
+,Para [Str "Right",Space,Str "paren:",Space,Str ")"]
+,Para [Str "Greater-than:",Space,Str ">"]
+,Para [Str "Hash:",Space,Str "#"]
+,Para [Str "Period:",Space,Str "."]
+,Para [Str "Bang:",Space,Str "!"]
+,Para [Str "Plus:",Space,Str "+"]
+,Para [Str "Minus:",Space,Str "-"]
+,Header 1 ("links",[],[]) [Str "Links"]
+,Header 2 ("explicit",[],[]) [Str "Explicit"]
+,Para [Str "Just",Space,Str "a",SoftBreak,Link ("",[],[]) [Str "URL"] ("/url/",""),Str "."]
+,Para [Link ("",[],[]) [Str "URL",SoftBreak,Str "and",Space,Str "title"] ("/url/","title"),Str "."]
+,Para [Link ("",[],[]) [Str "URL",SoftBreak,Str "and",Space,Str "title"] ("/url/","title preceded by two spaces"),Str "."]
+,Para [Link ("",[],[]) [Str "URL",SoftBreak,Str "and",Space,Str "title"] ("/url/","title preceded by a tab"),Str "."]
+,Para [Link ("",[],[]) [Str "URL",SoftBreak,Str "and",Space,Str "title"] ("/url/","title with \"quotes\" in it")]
+,Para [Link ("",[],[]) [Str "URL",SoftBreak,Str "and",Space,Str "title"] ("/url/","title with single quotes")]
+,Para [Str "Email",Space,Str "link",Space,Str "(nobody",Space,Str "[at]",Space,Str "nowhere.net)"]
+,Para [Link ("",[],[]) [Str "Empty"] ("",""),Str "."]
+,Header 2 ("reference",[],[]) [Str "Reference"]
+,Para [Str "Foo",SoftBreak,Link ("",[],[]) [Str "bar"] ("/url/",""),Str "."]
+,Para [Str "Foo",SoftBreak,Link ("",[],[]) [Str "bar"] ("/url/",""),Str "."]
+,Para [Str "Foo",SoftBreak,Link ("",[],[]) [Str "bar"] ("/url/",""),Str "."]
+,Para [Str "With",Space,Link ("",[],[]) [Str "embedded",SoftBreak,Str "[brackets]"] ("/url/",""),Str "."]
+,Para [Link ("",[],[]) [Str "b"] ("/url/",""),Space,Str "by",SoftBreak,Str "itself",Space,Str "should",Space,Str "be",Space,Str "a",Space,Str "link."]
+,Para [Str "Indented",SoftBreak,Link ("",[],[]) [Str "once"] ("/url",""),Str "."]
+,Para [Str "Indented",SoftBreak,Link ("",[],[]) [Str "twice"] ("/url",""),Str "."]
+,Para [Str "Indented",SoftBreak,Link ("",[],[]) [Str "thrice"] ("/url",""),Str "."]
+,Para [Str "This",Space,Str "should",Space,Str "[not]",Space,Str "be",Space,Str "a",Space,Str "link."]
+,CodeBlock ("",[],[]) "[not]: /url"
+,Para [Str "Foo",SoftBreak,Link ("",[],[]) [Str "bar"] ("/url/","Title with \"quotes\" inside"),Str "."]
+,Para [Str "Foo",SoftBreak,Link ("",[],[]) [Str "biz"] ("/url/","Title with \"quote\" inside"),Str "."]
+,Header 2 ("with-ampersands",[],[]) [Str "With",Space,Str "ampersands"]
+,Para [Str "Here's",Space,Str "a",SoftBreak,Link ("",[],[]) [Str "link",SoftBreak,Str "with",Space,Str "an",Space,Str "ampersand",Space,Str "in",Space,Str "the",Space,Str "URL"] ("http://example.com/?foo=1&bar=2",""),Str "."]
+,Para [Str "Here's",Space,Str "a",Space,Str "link",Space,Str "with",Space,Str "an",Space,Str "amersand",Space,Str "in",Space,Str "the",Space,Str "link",Space,Str "text:",SoftBreak,Link ("",[],[]) [Str "AT&T"] ("http://att.com/","AT&T"),Str "."]
+,Para [Str "Here's",Space,Str "an",SoftBreak,Link ("",[],[]) [Str "inline",SoftBreak,Str "link"] ("/script?foo=1&bar=2",""),Str "."]
+,Para [Str "Here's",Space,Str "an",SoftBreak,Link ("",[],[]) [Str "inline",SoftBreak,Str "link",Space,Str "in",Space,Str "pointy",Space,Str "braces"] ("/script?foo=1&bar=2",""),Str "."]
+,Header 2 ("autolinks",[],[]) [Str "Autolinks"]
+,Para [Str "With",Space,Str "an",Space,Str "ampersand:",SoftBreak,Link ("",[],[]) [Str "http://example.com/?foo=1&bar=2"] ("http://example.com/?foo=1&bar=2","")]
+,BulletList
+ [[Para [Str "In",Space,Str "a",Space,Str "list?"]]
+ ,[Para [Link ("",[],[]) [Str "http://example.com/"] ("http://example.com/","")]]
+ ,[Para [Str "It",Space,Str "should."]]]
+,Para [Str "An",Space,Str "e-mail",Space,Str "address:",Space,Str "nobody",Space,Str "[at]",Space,Str "nowhere.net"]
+,BlockQuote
+ [Para [Str "Blockquoted:",SoftBreak,Link ("",[],[]) [Str "http://example.com/"] ("http://example.com/","")]]
+,Para [Str "Auto-links",Space,Str "should",Space,Str "not",Space,Str "occur",Space,Str "here:",SoftBreak,Code ("",[],[]) "<http://example.com/>"]
+,CodeBlock ("",[],[]) "or here: <http://example.com/>"
+,Header 1 ("images",[],[]) [Str "Images"]
+,Para [Str "From",Space,Str "\"Voyage",Space,Str "dans",Space,Str "la",Space,Str "Lune\"",Space,Str "by",Space,Str "Georges",Space,Str "Melies",Space,Str "(1902):"]
+,Para [Image ("",[],[]) [] ("lalune.jpg","Voyage dans la Lune")]
+,Para [Str "Here",Space,Str "is",Space,Str "a",Space,Str "movie",SoftBreak,Image ("",[],[]) [] ("movie.jpg",""),SoftBreak,Str "icon."]
+,Header 1 ("footnotes",[],[]) [Str "Footnotes"]
+,Para [Str "Here",Space,Str "is",Space,Str "a",Space,Str "footnote",Space,Str "reference",Link ("",[],[]) [Str "(1)"] ("#note_1",""),Str ",",SoftBreak,Str "and",SoftBreak,Str "another",Link ("",[],[]) [Str "(longnote)"] ("#note_longnote",""),Str ".",SoftBreak,Str "This",Space,Str "should",Space,Emph [Str "not"],Space,Str "be",Space,Str "a",Space,Str "footnote",Space,Str "reference,",Space,Str "because",Space,Str "it",SoftBreak,Str "contains",Space,Str "a",Space,Str "space^(my",Space,Str "note)."]
+,Para [Link ("",[],[]) [Str "(1)"] ("#ref_1",""),Space,Str "Here",Space,Str "is",Space,Str "the",Space,Str "footnote.",Space,Str "It",Space,Str "can",SoftBreak,Str "go",Space,Str "anywhere",Space,Str "in",Space,Str "the",Space,Str "document,",Space,Str "not",Space,Str "just",Space,Str "at",Space,Str "the",Space,Str "end."]
+,Para [Link ("",[],[]) [Str "(longnote)"] ("#ref_longnote",""),Space,Str "Here's",SoftBreak,Str "the",Space,Str "other",Space,Str "note.",Space,Str "This",Space,Str "one",Space,Str "contains",Space,Str "multiple",Space,Str "blocks."]
+,Para [Str "Caret",Space,Str "characters",Space,Str "are",Space,Str "used",Space,Str "to",Space,Str "indicate",Space,Str "that",Space,Str "the",Space,Str "blocks",Space,Str "all",Space,Str "belong",Space,Str "to",SoftBreak,Str "a",Space,Str "single",Space,Str "footnote",Space,Str "(as",Space,Str "with",Space,Str "block",Space,Str "quotes)."]
+,CodeBlock ("",[],[]) "  { <code> }"
+,Para [Str "If",Space,Str "you",Space,Str "want,",Space,Str "you",Space,Str "can",Space,Str "use",Space,Str "a",Space,Str "caret",Space,Str "at",Space,Str "the",Space,Str "beginning",Space,Str "of",Space,Str "every",Space,Str "line,",Space,Str "as",SoftBreak,Str "with",Space,Str "blockquotes,",Space,Str "but",Space,Str "all",Space,Str "that",Space,Str "you",Space,Str "need",Space,Str "is",Space,Str "a",Space,Str "caret",Space,Str "at",Space,Str "the",Space,Str "beginning",SoftBreak,Str "of",Space,Str "the",Space,Str "first",Space,Str "line",Space,Str "of",Space,Str "the",Space,Str "block",Space,Str "and",Space,Str "any",Space,Str "preceding",Space,Str "blank",Space,Str "lines."]
+,Para [Str "text",Space,Emph [Str "Leading",Space,Str "space"]]
+,Para [Emph [Str "Trailing",Space,Str "space"],Space,Str "text"]
+,Para [Str "text",Space,Emph [Str "Leading",Space,Str "spaces"]]
+,Para [Emph [Str "Trailing",Space,Str "spaces"],Space,Str "text"]
+,Header 1 ("tables",[],[]) [Str "Tables"]
+,Header 2 ("tables-with-headers",[],[]) [Str "Tables",Space,Str "with",Space,Str "Headers"]
+,Table [] [AlignLeft,AlignLeft,AlignLeft] [0.0,0.0,0.0]
+ [[Para [Str "X"]]
+ ,[Para [Str "Y"]]
+ ,[Para [Str "Z"]]]
+ [[[Para [Str "1"]]
+  ,[Para [Str "2"]]
+  ,[Para [Str "3"]]]
+ ,[[Para [Str "4"]]
+  ,[Para [Str "5"]]
+  ,[Para [Str "6"]]]]
+,Table [] [AlignLeft,AlignLeft,AlignLeft] [0.0,0.0,0.0]
+ [[Para [Str "X"]]
+ ,[Para [Str "Y"]]
+ ,[Para [Str "Z"]]]
+ [[[Para [Str "1"]]
+  ,[Para [Str "2"]]
+  ,[Para [Str "3"]]]
+ ,[[Para [Str "4"]]
+  ,[Para [Str "5"]]
+  ,[Para [Str "6"]]]]
+,Table [] [AlignLeft,AlignLeft,AlignLeft] [0.0,0.0,0.0]
+ [[Para [Str "X"]]
+ ,[Para [Str "Y"]]
+ ,[Para [Str "Z"]]]
+ [[[Para [Str "1"]]
+  ,[Para [Str "2"]]
+  ,[Para [Str "3"]]]
+ ,[[Para [Str "4"]]
+  ,[Para [Str "5"]]
+  ,[Para [Str "6"]]]]
+,Table [] [AlignLeft,AlignLeft,AlignLeft] [0.0,0.0,0.0]
+ [[Para [Str "X"]]
+ ,[Para [Str "Y"]]
+ ,[Para [Str "Z"]]]
+ [[[Para [Str "1"]]
+  ,[Para [Str "2"]]
+  ,[Para [Str "3"]]]
+ ,[[Para [Str "4"]]
+  ,[Para [Str "5"]]
+  ,[Para [Str "6"]]]]
+,Table [] [AlignLeft,AlignLeft,AlignLeft] [0.0,0.0,0.0]
+ [[Para [Str "X"]]
+ ,[Para [Str "Y"]]
+ ,[Para [Str "Z"]]]
+ [[[Para [Str "1"]]
+  ,[Para [Str "2"]]
+  ,[Para [Str "3"]]]
+ ,[[Para [Str "4"]]
+  ,[Para [Str "5"]]
+  ,[Para [Str "6"]]]]
+,Table [] [AlignLeft,AlignLeft,AlignLeft] [0.0,0.0,0.0]
+ [[Para [Str "X"]]
+ ,[Para [Str "Y"]]
+ ,[Para [Str "Z"]]]
+ [[[Para [Str "1"]]
+  ,[Para [Str "2"]]
+  ,[Para [Str "3"]]]
+ ,[[Para [Str "4"]]
+  ,[Para [Str "5"]]
+  ,[Para [Str "6"]]]]
+,Table [] [AlignLeft,AlignLeft,AlignLeft] [0.0,0.0,0.0]
+ [[Para [Str "X"]]
+ ,[Para [Str "Y"]]
+ ,[Para [Str "Z"]]]
+ [[[Para [Str "1"]]
+  ,[Para [Str "2"]]
+  ,[Para [Str "3"]]]
+ ,[[Para [Str "4"]]
+  ,[Para [Str "5"]]
+  ,[Para [Str "6"]]]]
+,Table [] [AlignLeft,AlignLeft,AlignLeft] [0.0,0.0,0.0]
+ [[Para [Str "X"]]
+ ,[Para [Str "Y"]]
+ ,[Para [Str "Z"]]]
+ [[[Para [Str "1"]]
+  ,[Para [Str "2"]]
+  ,[Para [Str "3"]]]
+ ,[[Para [Str "4"]]
+  ,[Para [Str "5"]]
+  ,[Para [Str "6"]]]]
+,Table [] [AlignLeft,AlignLeft,AlignLeft] [0.0,0.0,0.0]
+ [[Para [Str "X"]]
+ ,[Para [Str "Y"]]
+ ,[Para [Str "Z"]]]
+ [[[Para [Str "1"]]
+  ,[Para [Str "2"]]
+  ,[Para [Str "3"]]]
+ ,[[Para [Str "4"]]
+  ,[Para [Str "5"]]
+  ,[Para [Str "6"]]]]
+,Header 2 ("tables-without-headers",[],[]) [Str "Tables",Space,Str "without",Space,Str "Headers"]
+,Table [] [AlignLeft,AlignLeft,AlignLeft] [0.0,0.0,0.0]
+ [[]
+ ,[]
+ ,[]]
+ [[[Para [Str "1"]]
+  ,[Para [Str "2"]]
+  ,[Para [Str "3"]]]
+ ,[[Para [Str "4"]]
+  ,[Para [Str "5"]]
+  ,[Para [Str "6"]]]]
+,Table [] [AlignLeft,AlignLeft,AlignLeft] [0.0,0.0,0.0]
+ [[]
+ ,[]
+ ,[]]
+ [[[Para [Str "1"]]
+  ,[Para [Str "2"]]
+  ,[Para [Str "3"]]]
+ ,[[Para [Str "4"]]
+  ,[Para [Str "5"]]
+  ,[Para [Str "6"]]]]
+,Table [] [AlignLeft,AlignLeft,AlignLeft] [0.0,0.0,0.0]
+ [[]
+ ,[]
+ ,[]]
+ [[[Para [Str "1"]]
+  ,[Para [Str "2"]]
+  ,[Para [Str "3"]]]
+ ,[[Para [Str "4"]]
+  ,[Para [Str "5"]]
+  ,[Para [Str "6"]]]]
+,Table [] [AlignLeft,AlignLeft,AlignLeft] [0.0,0.0,0.0]
+ [[]
+ ,[]
+ ,[]]
+ [[[Para [Str "1"]]
+  ,[Para [Str "2"]]
+  ,[Para [Str "3"]]]
+ ,[[Para [Str "4"]]
+  ,[Para [Str "5"]]
+  ,[Para [Str "6"]]]]
+,Header 2 ("empty-tables",[],[]) [Str "Empty",Space,Str "Tables"]
+,Para [Str "This",Space,Str "section",Space,Str "should",Space,Str "be",Space,Str "empty."]]
--- a/test/jats-reader.xml
+++ b/test/jats-reader.xml
--- a/test/test-pandoc.hs
+++ b/test/test-pandoc.hs
@ -11,6 +11,7 @@ import qualified Tests.Readers.Creole
 import qualified Tests.Readers.Docx
 import qualified Tests.Readers.EPUB
 import qualified Tests.Readers.HTML
+import qualified Tests.Readers.JATS
 import qualified Tests.Readers.LaTeX
 import qualified Tests.Readers.Markdown
 import qualified Tests.Readers.Muse
@ -61,6 +62,7 @@ tests = testGroup "pandoc tests" [ Tests.Command.tests
          [ testGroup "LaTeX" Tests.Readers.LaTeX.tests
          , testGroup "Markdown" Tests.Readers.Markdown.tests
          , testGroup "HTML" Tests.Readers.HTML.tests
+          , testGroup "JATS" Tests.Readers.JATS.tests
          , testGroup "Org" Tests.Readers.Org.tests
          , testGroup "RST" Tests.Readers.RST.tests
          , testGroup "Docx" Tests.Readers.Docx.tests