    {-# LANGUAGE NoImplicitPrelude #-}
    {-# LANGUAGE OverloadedStrings #-}

    {-
    Copyright (C) 2006-2018 John MacFarlane <jgm@berkeley.edu>

    This program is free software; you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation; either version 2 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program; if not, write to the Free Software
    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
    -}
    {- |
       Module      : Text.Pandoc.Writers.JATS
       Copyright   : Copyright (C) 2017-2018 John MacFarlane
       License     : GNU GPL, version 2 or above

       Maintainer  : John MacFarlane <jgm@berkeley.edu>
       Stability   : alpha
       Portability : portable

    Conversion of 'Pandoc' documents to JATS XML.
    Reference:
    https://jats.nlm.nih.gov/publishing/tag-library
    -}
    module Text.Pandoc.Writers.JATS ( writeJATS ) where
    import Prelude
    import Control.Monad.Reader
    import Data.Char (toLower)
    import Data.Generics (everywhere, mkT)
    import Data.List (isSuffixOf, partition)
    import Data.Maybe (fromMaybe)
    import Data.Text (Text)
    import Text.Pandoc.Class (PandocMonad, report)
    import Text.Pandoc.Definition
    import Text.Pandoc.Highlighting (languages, languagesByExtension)
    import Text.Pandoc.Logging
    import Text.Pandoc.MIME (getMimeType)
    import Text.Pandoc.Options
    import Text.Pandoc.Pretty
    import Text.Pandoc.Shared
    import Text.Pandoc.Templates (renderTemplate')
    import Text.Pandoc.Writers.Math
    import Text.Pandoc.Writers.Shared
    import Text.Pandoc.XML
    import Text.TeXMath
    import qualified Text.XML.Light as Xml

    data JATSVersion = JATS1_1
         deriving (Eq, Show)

    type JATS = ReaderT JATSVersion

    writeJATS :: PandocMonad m => WriterOptions -> Pandoc -> m Text
    writeJATS opts d =
      runReaderT (docToJATS opts d) JATS1_1

    -- | Convert Pandoc document to string in JATS format.
    docToJATS :: PandocMonad m => WriterOptions -> Pandoc -> JATS m Text
    docToJATS opts (Pandoc meta blocks) = do
      let isBackBlock (Div ("refs",_,_) _) = True
          isBackBlock _                    = False
      let (backblocks, bodyblocks) = partition isBackBlock blocks
      let elements = hierarchicalize bodyblocks
      let backElements = hierarchicalize backblocks
      let colwidth = if writerWrapText opts == WrapAuto
                        then Just $ writerColumns opts
                        else Nothing
      let render'  :: Doc -> Text
          render'  = render colwidth
      let opts'    = if maybe False (("/book>" `isSuffixOf`) . trimr)
                                (writerTemplate opts) &&
                         TopLevelDefault == writerTopLevelDivision opts
                        then opts{ writerTopLevelDivision = TopLevelChapter }
                        else opts
      -- The numbering here follows LaTeX's internal numbering
      let startLvl = case writerTopLevelDivision opts' of
                       TopLevelPart    -> -1
                       TopLevelChapter -> 0
                       TopLevelSection -> 1
                       TopLevelDefault -> 1
      metadata <- metaToJSON opts
                     (fmap (render' . vcat) .
                              mapM (elementToJATS opts' startLvl) .
                                hierarchicalize)
                     (fmap render' . inlinesToJATS opts')
                     meta
      main <- (render' . vcat) <$>
                mapM (elementToJATS opts' startLvl) elements
      back <- (render' . vcat) <$>
                mapM (elementToJATS opts' startLvl) backElements
      let context = defField "body" main
                  $ defField "back" back
                  $ defField "mathml" (case writerHTMLMathMethod opts of
                                            MathML -> True
                                            _      -> False) metadata
      (if writerPreferAscii opts then toEntities else id) <$>
        case writerTemplate opts of
           Nothing  -> return main
           Just tpl -> renderTemplate' tpl context

    -- | Convert an Element to JATS.
    elementToJATS :: PandocMonad m => WriterOptions -> Int -> Element -> JATS m Doc
    elementToJATS opts _   (Blk block) = blockToJATS opts block
    elementToJATS opts lvl (Sec _ _num (id',_,kvs) title elements) = do
      let idAttr = [("id", writerIdentifierPrefix opts ++ id') | not (null id')]
      let otherAttrs = ["sec-type", "specific-use"]
      let attribs = idAttr ++ [(k,v) | (k,v) <- kvs, k `elem` otherAttrs]
      contents <- mapM (elementToJATS opts (lvl + 1)) elements
      title' <- inlinesToJATS opts title
      return $ inTags True "sec" attribs $
          inTagsSimple "title" title' $$ vcat contents

    -- | Convert a list of Pandoc blocks to JATS.
    blocksToJATS :: PandocMonad m => WriterOptions -> [Block] -> JATS m Doc
    blocksToJATS opts = fmap vcat . mapM (blockToJATS opts)

    -- | Auxiliary function to convert Plain block to Para.
    plainToPara :: Block -> Block
    plainToPara (Plain x) = Para x
    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
    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
    deflistItemToJATS opts term defs = do
      term' <- inlinesToJATS opts term
      def' <- blocksToJATS opts $ concatMap (map plainToPara) defs
      return $ inTagsIndented "def-item" $
          inTagsSimple "term" term' $$
          inTagsIndented "def" def'

    -- | Convert a list of lists of blocks to a list of JATS list items.
    listItemsToJATS :: PandocMonad m
                    => WriterOptions -> Maybe [String] -> [[Block]] -> JATS m Doc
    listItemsToJATS opts markers items =
      case markers of
           Nothing -> vcat <$> mapM (listItemToJATS opts Nothing) items
           Just ms -> vcat <$> zipWithM (listItemToJATS opts) (map Just ms) items

    -- | Convert a list of blocks into a JATS list item.
    listItemToJATS :: PandocMonad m
                   => WriterOptions -> Maybe String -> [Block] -> JATS m Doc
    listItemToJATS opts mbmarker item = do
      contents <- blocksToJATS opts item
      return $ inTagsIndented "list-item" $
               maybe empty (\lbl -> inTagsSimple "label" (text lbl)) mbmarker
               $$ contents

    imageMimeType :: String -> [(String, String)] -> (String, String)
    imageMimeType src kvs =
      let mbMT = getMimeType src
          maintype = fromMaybe "image" $
                      lookup "mimetype" kvs `mplus`
                      (takeWhile (/='/') <$> mbMT)
          subtype = fromMaybe "" $
                      lookup "mime-subtype" kvs `mplus`
                      ((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
    -- Bibliography reference:
    blockToJATS opts (Div ('r':'e':'f':'-':_,_,_) [Para lst]) =
      inlinesToJATS opts lst
    blockToJATS opts (Div ("refs",_,_) xs) = do
      contents <- blocksToJATS opts xs
      return $ inTagsIndented "ref-list" contents
    blockToJATS opts (Div (ident,[cls],kvs) bs) | cls `elem` ["fig", "caption", "table-wrap"] = do
      contents <- blocksToJATS opts bs
      let attr = [("id", ident) | not (null ident)] ++
                 [("xml:lang",l) | ("lang",l) <- kvs] ++
                 [(k,v) | (k,v) <- kvs, k `elem` ["specific-use",
                     "content-type", "orientation", "position"]]
      return $ inTags True cls attr contents
    blockToJATS opts (Div (ident,_,kvs) bs) = do
      contents <- blocksToJATS opts bs
      let attr = [("id", ident) | not (null ident)] ++
                 [("xml:lang",l) | ("lang",l) <- kvs] ++
                 [(k,v) | (k,v) <- kvs, k `elem` ["specific-use",
                     "content-type", "orientation", "position"]]
      return $ inTags True "boxed-text" attr contents
    blockToJATS opts (Header _ _ title) = do
      title' <- inlinesToJATS opts title
      return $ inTagsSimple "title" title'
    -- No Plain, everything needs to be in a block-level tag
    blockToJATS opts (Plain lst) = blockToJATS opts (Para lst)
    -- title beginning with fig: indicates that the image is a figure
    blockToJATS opts (Para [Image (ident,_,kvs) txt
      (src,'f':'i':'g':':':tit)]) = do
      alt <- inlinesToJATS opts txt
      let (maintype, subtype) = imageMimeType src kvs
      let capt = if null txt
                    then empty
                    else inTagsSimple "caption" alt
      let attr = [("id", ident) | not (null ident)] ++
                 [(k,v) | (k,v) <- kvs, k `elem` ["fig-type", "orientation",
                                                  "position", "specific-use"]]
      let graphicattr = [("mimetype",maintype),
                         ("mime-subtype",subtype),
                         ("xlink:href",src),  -- do we need to URL escape this?
                         ("xlink:title",tit)]
      return $ inTags True "fig" attr $
                  capt $$ selfClosingTag "graphic" graphicattr
    blockToJATS _ (Para [Image (ident,_,kvs) _ (src, tit)]) = do
      let (maintype, subtype) = imageMimeType src kvs
      let attr = [("id", ident) | not (null ident)] ++
                 [("mimetype", maintype),
                  ("mime-subtype", subtype),
                  ("xlink:href", src)] ++
                 [("xlink:title", tit) | not (null tit)] ++
                 [(k,v) | (k,v) <- kvs, k `elem` ["baseline-shift",
                            "content-type", "specific-use", "xlink:actuate",
                            "xlink:href", "xlink:role", "xlink:show",
                            "xlink:type"]]
      return $ selfClosingTag "graphic" attr
    blockToJATS opts (Para lst) =
      inTagsSimple "p" <$> inlinesToJATS opts lst
    blockToJATS opts (LineBlock lns) =
      blockToJATS opts $ linesToPara lns
    blockToJATS opts (BlockQuote blocks) =
      inTagsIndented "disp-quote" <$> blocksToJATS opts blocks
    blockToJATS _ (CodeBlock a str) = return $
      inTags False tag attr (flush (text (escapeStringForXML str)))
        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")] <$>
      listItemsToJATS opts Nothing lst
    blockToJATS _ (OrderedList _ []) = return empty
    blockToJATS opts (OrderedList (start, numstyle, delimstyle) items) = do
      let listType = case numstyle of
                           DefaultStyle -> "order"
                           Decimal      -> "order"
                           Example      -> "order"
                           UpperAlpha   -> "alpha-upper"
                           LowerAlpha   -> "alpha-lower"
                           UpperRoman   -> "roman-upper"
                           LowerRoman   -> "roman-lower"
      let simpleList = start == 1 && (delimstyle == DefaultDelim ||
                                      delimstyle == Period)
      let markers = if simpleList
                       then Nothing
                       else Just $
                              orderedListMarkers (start, numstyle, delimstyle)
      inTags True "list" [("list-type", listType)] <$>
        listItemsToJATS opts markers items
    blockToJATS opts (DefinitionList lst) =
      inTags True "def-list" [] <$> deflistItemsToJATS opts lst
    blockToJATS _ b@(RawBlock f str)
      | f == "jats"    = return $ text str -- raw XML block
      | otherwise      = do
          report $ BlockNotRendered b
          return empty
    blockToJATS _ HorizontalRule = return empty -- not semantic
    blockToJATS opts (Table [] aligns widths headers rows) = do
      let percent w    = show (truncate (100*w) :: Integer) ++ "*"
      let coltags = vcat $ zipWith (\w al -> selfClosingTag "col"
                           ([("width", percent w) | w > 0] ++
                            [("align", alignmentToString al)])) widths aligns
      thead <- if all null headers
                  then return empty
                  else inTagsIndented "thead" <$> tableRowToJATS opts True headers
      tbody <- (inTagsIndented "tbody" . vcat) <$>
                    mapM (tableRowToJATS opts False) rows
      return $ inTags True "table" [] $ coltags $$ thead $$ tbody
    blockToJATS opts (Table caption aligns widths headers rows) = do
      captionDoc <- inTagsIndented "caption" <$> blockToJATS opts (Para caption)
      tbl <- blockToJATS opts (Table [] aligns widths headers rows)
      return $ inTags True "table-wrap" [] $ captionDoc $$ tbl

    alignmentToString :: Alignment -> [Char]
    alignmentToString alignment = case alignment of
                                     AlignLeft    -> "left"
                                     AlignRight   -> "right"
                                     AlignCenter  -> "center"
                                     AlignDefault -> "left"

    tableRowToJATS :: PandocMonad m
                      => WriterOptions
                      -> Bool
                      -> [[Block]]
                      -> JATS m Doc
    tableRowToJATS opts isHeader cols =
      (inTagsIndented "tr" . vcat) <$> mapM (tableItemToJATS opts isHeader) cols

    tableItemToJATS :: PandocMonad m
                       => WriterOptions
                       -> Bool
                       -> [Block]
                       -> JATS m Doc
    tableItemToJATS opts isHeader [Plain item] =
      inTags False (if isHeader then "th" else "td") [] <$>
        inlinesToJATS opts item
    tableItemToJATS opts isHeader item =
      (inTags False (if isHeader then "th" else "td") [] . vcat) <$>
        mapM (blockToJATS opts) item

    -- | Convert a list of inline elements to JATS.
    inlinesToJATS :: PandocMonad m => WriterOptions -> [Inline] -> JATS m Doc
    inlinesToJATS opts lst = hcat <$> mapM (inlineToJATS opts) lst

    -- | Convert an inline element to JATS.
    inlineToJATS :: PandocMonad m => WriterOptions -> Inline -> JATS m Doc
    inlineToJATS _ (Str str) = return $ text $ escapeStringForXML str
    inlineToJATS opts (Emph lst) =
      inTagsSimple "italic" <$> inlinesToJATS opts lst
    inlineToJATS opts (Strong lst) =
      inTagsSimple "bold" <$> inlinesToJATS opts lst
    inlineToJATS opts (Strikeout lst) =
      inTagsSimple "strike" <$> inlinesToJATS opts lst
    inlineToJATS opts (Superscript lst) =
      inTagsSimple "sup" <$> inlinesToJATS opts lst
    inlineToJATS opts (Subscript lst) =
      inTagsSimple "sub" <$> inlinesToJATS opts lst
    inlineToJATS opts (SmallCaps lst) =
      inTagsSimple "sc" <$> inlinesToJATS opts lst
    inlineToJATS opts (Quoted SingleQuote lst) = do
      contents <- inlinesToJATS opts lst
      return $ char '‘' <> contents <> char '’'
    inlineToJATS opts (Quoted DoubleQuote lst) = do
      contents <- inlinesToJATS opts lst
      return $ char '“' <> contents <> char '”'
    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
          report $ InlineNotRendered il
          return empty
    inlineToJATS _ LineBreak = return $ selfClosingTag "break" []
    inlineToJATS _ Space = return space
    inlineToJATS opts SoftBreak
      | writerWrapText opts == WrapPreserve = return cr
      | otherwise = return space
    inlineToJATS opts (Note contents) =
      -- TODO technically only <p> tags are allowed inside
      inTagsIndented "fn" <$> blocksToJATS opts contents
    inlineToJATS opts (Cite _ lst) =
      -- TODO revisit this after examining the jats.csl pipeline
      inlinesToJATS opts lst
    inlineToJATS opts (Span ("",_,[]) ils) = inlinesToJATS opts ils
    inlineToJATS opts (Span (ident,_,kvs) ils) = do
      contents <- inlinesToJATS opts ils
      let attr = [("id",ident) | not (null ident)] ++
                 [("xml:lang",l) | ("lang",l) <- kvs] ++
                 [(k,v) | (k,v) <- kvs
                        ,  k `elem` ["content-type", "rationale",
                                     "rid", "specific-use"]]
      return $ selfClosingTag "milestone-start" attr <> contents <>
               selfClosingTag "milestone-end" []
    inlineToJATS _ (Math t str) = do
      let addPref (Xml.Attr q v)
             | Xml.qName q == "xmlns" = Xml.Attr q{ Xml.qName = "xmlns:mml" } v
             | otherwise = Xml.Attr q v
      let fixNS' e = e{ Xml.elName =
                             (Xml.elName e){ Xml.qPrefix = Just "mml" } }
      let fixNS = everywhere (mkT fixNS') .
                  (\e -> e{ Xml.elAttribs = map addPref (Xml.elAttribs e) })
      let conf = Xml.useShortEmptyTags (const False) Xml.defaultConfigPP
      res <- convertMath writeMathML t str
      let tagtype = case t of
                         DisplayMath -> "disp-formula"
                         InlineMath  -> "inline-formula"
      let rawtex = inTagsSimple "tex-math"
                                    $ text "<![CDATA[" <>
                                      text str <>
                                      text "]]>"
      return $ inTagsSimple tagtype $
                 case res of
                       Right r  -> inTagsSimple "alternatives" $
                                      cr <> rawtex $$
                                      text (Xml.ppcElement conf $ fixNS r)
                       Left _   -> rawtex
    inlineToJATS _ (Link _attr [Str t] ('m':'a':'i':'l':'t':'o':':':email, _))
      | escapeURI t == email =
      return $ inTagsSimple "email" $ text (escapeStringForXML email)
    inlineToJATS opts (Link (ident,_,kvs) txt ('#':src, _)) = do
      let attr = [("id", ident) | not (null ident)] ++
                 [("alt", stringify txt) | not (null txt)] ++
                 [("rid", src)] ++
                 [(k,v) | (k,v) <- kvs, k `elem` ["ref-type", "specific-use"]]
      if null txt
         then return $ selfClosingTag "xref" attr
         else do
            contents <- inlinesToJATS opts txt
            return $ inTags False "xref" attr contents
    inlineToJATS opts (Link (ident,_,kvs) txt (src, tit)) = do
      let attr = [("id", ident) | not (null ident)] ++
                 [("ext-link-type", "uri"),
                  ("xlink:href", src)] ++
                 [("xlink:title", tit) | not (null tit)] ++
                 [(k,v) | (k,v) <- kvs, k `elem` ["assigning-authority",
                                                  "specific-use", "xlink:actuate",
                                                  "xlink:role", "xlink:show",
                                                  "xlink:type"]]
      contents <- inlinesToJATS opts txt
      return $ inTags False "ext-link" attr contents
    inlineToJATS _ (Image (ident,_,kvs) _ (src, tit)) = do
      let mbMT = getMimeType src
      let maintype = fromMaybe "image" $
                      lookup "mimetype" kvs `mplus`
                      (takeWhile (/='/') <$> mbMT)
      let subtype = fromMaybe "" $
                      lookup "mime-subtype" kvs `mplus`
                      ((drop 1 . dropWhile (/='/')) <$> mbMT)
      let attr = [("id", ident) | not (null ident)] ++
                 [("mimetype", maintype),
                  ("mime-subtype", subtype),
                  ("xlink:href", src)] ++
                 [("xlink:title", tit) | not (null tit)] ++
                 [(k,v) | (k,v) <- kvs, k `elem` ["baseline-shift",
                            "content-type", "specific-use", "xlink:actuate",
                            "xlink:href", "xlink:role", "xlink:show",
                            "xlink:type"]]
      return $ selfClosingTag "inline-graphic" attr