    {-# LANGUAGE NoImplicitPrelude #-}
    {-# LANGUAGE TupleSections #-}
    {-
    Copyright (C) 2017-2018 Hamish Mackenzie

    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.Readers.JATS
       Copyright   : Copyright (C) 2017-2018 Hamish Mackenzie
       License     : GNU GPL, version 2 or above

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

    Conversion of JATS XML to 'Pandoc' document.
    -}

    module Text.Pandoc.Readers.JATS ( readJATS ) where
    import Prelude
    import Control.Monad.State.Strict
    import Data.Char (isDigit, isSpace, toUpper)
    import Data.Default
    import Data.Generics
    import Data.List (foldl', intersperse)
    import qualified Data.Map as Map
    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
                              , jatsBook         :: Bool
                              , jatsFigureTitle  :: Inlines
                              , jatsContent      :: [Content]
                              } deriving Show

    instance Default JATSState where
      def = JATSState{ jatsSectionLevel = 0
                     , jatsQuoteType = DoubleQuote
                     , jatsMeta = mempty
                     , 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

    --

    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 <$> (filterElement (named "list-item") e
                                                   >>= filterElement (named "label")))
                                       >>= safeRead
                          orderedListWith (start, parseListStyleType listType, DefaultDelim)
                            <$> listitems
            "def-list" -> definitionList <$> deflistitems
            "sec" -> gets jatsSectionLevel >>= sect . (+1)
            "graphic" -> para <$> getGraphic e
            "journal-meta" -> parseMetadata e
            "article-meta" -> parseMetadata e
            "custom-meta" -> parseMetadata e
            "title" -> return mempty -- processed by header
            "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"], []) <$> sect 6
            "ref-list" -> parseRefList e
            "?xml"  -> return mempty
            _       -> getBlocks e
       where parseMixed container conts = do
               let (ils,rest) = break isBlockElement conts
               ils' <- (trimInlines . mconcat) <$> 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')
             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 = foldl' max 0 $ map length bodyrows
                          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

    getInlines :: PandocMonad m => Element -> JATS m Inlines
    getInlines e' = (trimInlines . mconcat) <$>
                     mapM parseInline (elContent e')

    parseMetadata :: PandocMonad m => Element -> JATS m Blocks
    parseMetadata e = do
      getTitle e
      getAuthors e
      getAffiliations e
      return mempty

    getTitle :: PandocMonad m => Element -> JATS m ()
    getTitle e = do
      tit <-  case filterElement (named "article-title") e of
                   Just s  -> getInlines s
                   Nothing -> return mempty
      subtit <-  case filterElement (named "subtitle") e of
                   Just s  -> (text ": " <>) <$>
                               getInlines s
                   Nothing -> return mempty
      when (tit /= mempty) $ addMeta "title" tit
      when (subtit /= mempty) $ addMeta "subtitle" subtit

    getAuthors :: PandocMonad m => Element -> JATS m ()
    getAuthors e = do
      authors <- mapM getContrib $ filterElements
                  (\x -> named "contrib" x &&
                         attrValue "contrib-type" x == "author") e
      authorNotes <- mapM getInlines $ filterElements (named "author-notes") e
      let authors' = case (reverse authors, authorNotes) of
                       ([], _)    -> []
                       (_, [])    -> authors
                       (a:as, ns) -> reverse as ++ [a <> mconcat ns]
      unless (null authors) $ addMeta "author" authors'

    getAffiliations :: PandocMonad m => Element -> JATS m ()
    getAffiliations x = do
      affs <- mapM getInlines $ filterChildren (named "aff") x
      unless (null affs) $ addMeta "institute" affs

    getContrib :: PandocMonad m => Element -> JATS m Inlines
    getContrib x = do
      given <- maybe (return mempty) getInlines
                $ filterElement (named "given-names") x
      family <- maybe (return mempty) getInlines
                $ filterElement (named "surname") x
      if given == mempty && family == mempty
         then return mempty
         else if given == mempty || family == mempty
              then return $ given <> family
              else return $ given <> space <> family

    parseRefList :: PandocMonad m => Element -> JATS m Blocks
    parseRefList e = do
      refs <- mapM parseRef $ filterChildren (named "ref") e
      addMeta "references" refs
      return mempty

    parseRef :: PandocMonad m
             => Element -> JATS m (Map.Map String MetaValue)
    parseRef e = do
      let refId = text $ attrValue "id" e
      let getInlineText n = maybe (return mempty) getInlines . filterChild (named n)
      case filterChild (named "element-citation") e of
           Just c  -> do
             let refType = text $
                   case attrValue "publication-type" c of
                      "journal" -> "article-journal"
                      x -> x
             (refTitle, refContainerTitle) <- do
               t <- getInlineText "article-title" c
               ct <- getInlineText "source" c
               if t == mempty
                  then return (ct, mempty)
                  else return (t, ct)
             refLabel <- getInlineText "label" c
             refYear <- getInlineText "year" c
             refVolume <- getInlineText "volume" c
             refFirstPage <- getInlineText "fpage" c
             refLastPage <- getInlineText "lpage" c
             refPublisher <- getInlineText "publisher-name" c
             refPublisherPlace <- getInlineText "publisher-loc" c
             let refPages = refFirstPage <> (if refLastPage == mempty
                                                then mempty
                                                else text "\x2013" <> refLastPage)
             let personGroups' = filterChildren (named "person-group") c
             let getName nm = do
                   given <- maybe (return mempty) getInlines
                             $ filterChild (named "given-names") nm
                   family <- maybe (return mempty) getInlines
                             $ filterChild (named "surname") nm
                   return $ toMetaValue $ Map.fromList [
                       ("given", given)
                     , ("family", family)
                     ]
             personGroups <- mapM (\pg ->
                                    do names <- mapM getName
                                                (filterChildren (named "name") pg)
                                       return (attrValue "person-group-type" pg,
                                               toMetaValue names))
                             personGroups'
             return $ Map.fromList $
               [ ("id", toMetaValue refId)
               , ("type", toMetaValue refType)
               , ("title", toMetaValue refTitle)
               , ("container-title", toMetaValue refContainerTitle)
               , ("publisher", toMetaValue refPublisher)
               , ("publisher-place", toMetaValue refPublisherPlace)
               , ("title", toMetaValue refTitle)
               , ("issued", toMetaValue
                            $ Map.fromList [
                                ("year", refYear)
                              ])
               , ("volume", toMetaValue refVolume)
               , ("page", toMetaValue refPages)
               , ("citation-label", toMetaValue refLabel)
               ] ++ personGroups
           Nothing -> return $ Map.insert "id" (toMetaValue refId) mempty
           -- TODO handle mixed-citation

    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 $ if refType == Just ("ref-type","bibr")
                            then cite [Citation{
                                             citationId = rid
                                           , citationPrefix = []
                                           , citationSuffix = []
                                           , citationMode = NormalCitation
                                           , citationNoteNum = 0
                                           , citationHash = 0}] ils
                            else 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) <$>
                             mapM parseBlock (elContent e)
            _          -> innerInlines
       where innerInlines = (trimInlines . mconcat) <$>
                              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