{-# LANGUAGE ScopedTypeVariables #-}
{-# LANGUAGE TupleSections #-}
{-# LANGUAGE OverloadedStrings #-}
{- |
   Module      : Text.Pandoc.Readers.JATS
   Copyright   : Copyright (C) 2017-2020 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 Control.Monad.State.Strict ( StateT(runStateT), gets, modify )
import Control.Monad (forM_,  when, unless, MonadPlus(mplus))
import Control.Monad.Except (throwError)
import Text.Pandoc.Error (PandocError(..))
import Data.Char (isDigit, isSpace)
import Data.Default
import Data.Generics
import Data.List (foldl', intersperse)
import qualified Data.Map as Map
import Data.Maybe (maybeToList, fromMaybe, catMaybes)
import Data.Text (Text)
import qualified Data.Text as T
import qualified Data.Text.Lazy as TL
import Text.Pandoc.XML (lookupEntity)
import Text.Pandoc.Builder
import Text.Pandoc.Class.PandocMonad (PandocMonad)
import Text.Pandoc.Options
import Text.Pandoc.Shared (safeRead, extractSpaces)
import Text.Pandoc.Walk (walk)
import Text.Pandoc.XML.Light
import Text.TeXMath (readMathML, writeTeX)
import qualified Data.Set as S (fromList, member)
import Data.Set ((\\))
import Text.Pandoc.Sources (ToSources(..), sourcesToText)

type JATS m = StateT JATSState m

data JATSState = JATSState{ JATSState -> Int
jatsSectionLevel :: Int
                          , JATSState -> QuoteType
jatsQuoteType    :: QuoteType
                          , JATSState -> Meta
jatsMeta         :: Meta
                          , JATSState -> Bool
jatsBook         :: Bool
                          , JATSState -> Map Text Blocks
jatsFootnotes    :: Map.Map Text Blocks
                          , JATSState -> [Content]
jatsContent      :: [Content]
                          , JATSState -> Bool
jatsInFigure     :: Bool
                          } deriving Int -> JATSState -> ShowS
[JATSState] -> ShowS
JATSState -> String
(Int -> JATSState -> ShowS)
-> (JATSState -> String)
-> ([JATSState] -> ShowS)
-> Show JATSState
forall a.
(Int -> a -> ShowS) -> (a -> String) -> ([a] -> ShowS) -> Show a
$cshowsPrec :: Int -> JATSState -> ShowS
showsPrec :: Int -> JATSState -> ShowS
$cshow :: JATSState -> String
show :: JATSState -> String
$cshowList :: [JATSState] -> ShowS
showList :: [JATSState] -> ShowS
Show

instance Default JATSState where
  def :: JATSState
def = JATSState{ jatsSectionLevel :: Int
jatsSectionLevel = Int
0
                 , jatsQuoteType :: QuoteType
jatsQuoteType = QuoteType
DoubleQuote
                 , jatsMeta :: Meta
jatsMeta = Meta
forall a. Monoid a => a
mempty
                 , jatsBook :: Bool
jatsBook = Bool
False
                 , jatsFootnotes :: Map Text Blocks
jatsFootnotes = Map Text Blocks
forall a. Monoid a => a
mempty
                 , jatsContent :: [Content]
jatsContent = []
                 , jatsInFigure :: Bool
jatsInFigure = Bool
False }


readJATS :: (PandocMonad m, ToSources a)
         => ReaderOptions
         -> a
         -> m Pandoc
readJATS :: forall (m :: * -> *) a.
(PandocMonad m, ToSources a) =>
ReaderOptions -> a -> m Pandoc
readJATS ReaderOptions
_ a
inp = do
  let sources :: Sources
sources = a -> Sources
forall a. ToSources a => a -> Sources
toSources a
inp
  [Content]
tree <- (Text -> m [Content])
-> ([Content] -> m [Content])
-> Either Text [Content]
-> m [Content]
forall a c b. (a -> c) -> (b -> c) -> Either a b -> c
either (PandocError -> m [Content]
forall a. PandocError -> m a
forall e (m :: * -> *) a. MonadError e m => e -> m a
throwError (PandocError -> m [Content])
-> (Text -> PandocError) -> Text -> m [Content]
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Text -> Text -> PandocError
PandocXMLError Text
"") [Content] -> m [Content]
forall a. a -> m a
forall (m :: * -> *) a. Monad m => a -> m a
return (Either Text [Content] -> m [Content])
-> Either Text [Content] -> m [Content]
forall a b. (a -> b) -> a -> b
$
            Text -> Either Text [Content]
parseXMLContents (Text -> Text
TL.fromStrict (Text -> Text) -> (Sources -> Text) -> Sources -> Text
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Sources -> Text
sourcesToText (Sources -> Text) -> Sources -> Text
forall a b. (a -> b) -> a -> b
$ Sources
sources)
  ([Blocks]
bs, JATSState
st') <- (StateT JATSState m [Blocks]
 -> JATSState -> m ([Blocks], JATSState))
-> JATSState
-> StateT JATSState m [Blocks]
-> m ([Blocks], JATSState)
forall a b c. (a -> b -> c) -> b -> a -> c
flip StateT JATSState m [Blocks] -> JATSState -> m ([Blocks], JATSState)
forall s (m :: * -> *) a. StateT s m a -> s -> m (a, s)
runStateT (JATSState
forall a. Default a => a
def{ jatsContent :: [Content]
jatsContent = [Content]
tree }) (StateT JATSState m [Blocks] -> m ([Blocks], JATSState))
-> StateT JATSState m [Blocks] -> m ([Blocks], JATSState)
forall a b. (a -> b) -> a -> b
$ (Content -> StateT JATSState m Blocks)
-> [Content] -> StateT JATSState m [Blocks]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
forall (m :: * -> *) a b. Monad m => (a -> m b) -> [a] -> m [b]
mapM Content -> StateT JATSState m Blocks
forall (m :: * -> *). PandocMonad m => Content -> JATS m Blocks
parseBlock [Content]
tree
  let footnotes :: Map Text Blocks
footnotes = JATSState -> Map Text Blocks
jatsFootnotes JATSState
st'
  let blockList :: [Block]
blockList = Blocks -> [Block]
forall a. Many a -> [a]
toList (Blocks -> [Block]) -> Blocks -> [Block]
forall a b. (a -> b) -> a -> b
$ [Blocks] -> Blocks
forall a. Monoid a => [a] -> a
mconcat [Blocks]
bs
  let linkToFootnotes :: Inline -> Inline
      linkToFootnotes :: Inline -> Inline
linkToFootnotes link' :: Inline
link'@(Link Attr
_attr [Inline]
_txt (Text
href, Text
_title)) =
        case Text -> Maybe (Char, Text)
T.uncons Text
href of
          Just (Char
'#', Text
rid) -> case Text -> Map Text Blocks -> Maybe Blocks
forall k a. Ord k => k -> Map k a -> Maybe a
Map.lookup Text
rid Map Text Blocks
footnotes of
                               Just Blocks
footnote -> [Block] -> Inline
Note (Blocks -> [Block]
forall a. Many a -> [a]
toList Blocks
footnote)
                               Maybe Blocks
Nothing       -> Inline
link'
          Maybe (Char, Text)
_               -> Inline
link'
      linkToFootnotes Inline
inline = Inline
inline
  Pandoc -> m Pandoc
forall a. a -> m a
forall (m :: * -> *) a. Monad m => a -> m a
return (Pandoc -> m Pandoc) -> Pandoc -> m Pandoc
forall a b. (a -> b) -> a -> b
$ Meta -> [Block] -> Pandoc
Pandoc (JATSState -> Meta
jatsMeta JATSState
st') ((Inline -> Inline) -> [Block] -> [Block]
forall a b. Walkable a b => (a -> a) -> b -> b
walk Inline -> Inline
linkToFootnotes [Block]
blockList)

-- convenience function to get an attribute value, defaulting to ""
attrValue :: Text -> Element -> Text
attrValue :: Text -> Element -> Text
attrValue Text
attr =
  Text -> Maybe Text -> Text
forall a. a -> Maybe a -> a
fromMaybe Text
"" (Maybe Text -> Text) -> (Element -> Maybe Text) -> Element -> Text
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Text -> Element -> Maybe Text
maybeAttrValue Text
attr

maybeAttrValue :: Text -> Element -> Maybe Text
maybeAttrValue :: Text -> Element -> Maybe Text
maybeAttrValue Text
attr Element
elt =
  (QName -> Bool) -> [Attr] -> Maybe Text
lookupAttrBy (\QName
x -> QName -> Text
qName QName
x Text -> Text -> Bool
forall a. Eq a => a -> a -> Bool
== Text
attr) (Element -> [Attr]
elAttribs Element
elt)

-- convenience function
named :: Text -> Element -> Bool
named :: Text -> Element -> Bool
named Text
s Element
e = QName -> Text
qName (Element -> QName
elName Element
e) Text -> Text -> Bool
forall a. Eq a => a -> a -> Bool
== Text
s

--

addMeta :: PandocMonad m => ToMetaValue a => Text -> a -> JATS m ()
addMeta :: forall (m :: * -> *) a.
(PandocMonad m, ToMetaValue a) =>
Text -> a -> JATS m ()
addMeta Text
field a
val = (JATSState -> JATSState) -> StateT JATSState m ()
forall s (m :: * -> *). MonadState s m => (s -> s) -> m ()
modify (Text -> a -> JATSState -> JATSState
forall a b. (HasMeta a, ToMetaValue b) => Text -> b -> a -> a
forall b. ToMetaValue b => Text -> b -> JATSState -> JATSState
setMeta Text
field a
val)

instance HasMeta JATSState where
  setMeta :: forall b. ToMetaValue b => Text -> b -> JATSState -> JATSState
setMeta Text
field b
v JATSState
s =  JATSState
s {jatsMeta :: Meta
jatsMeta = Text -> b -> Meta -> Meta
forall a b. (HasMeta a, ToMetaValue b) => Text -> b -> a -> a
forall b. ToMetaValue b => Text -> b -> Meta -> Meta
setMeta Text
field b
v (JATSState -> Meta
jatsMeta JATSState
s)}
  deleteMeta :: Text -> JATSState -> JATSState
deleteMeta Text
field JATSState
s = JATSState
s {jatsMeta :: Meta
jatsMeta = Text -> Meta -> Meta
forall a. HasMeta a => Text -> a -> a
deleteMeta Text
field (JATSState -> Meta
jatsMeta JATSState
s)}

isBlockElement :: Content -> Bool
isBlockElement :: Content -> Bool
isBlockElement (Elem Element
e) = QName -> Text
qName (Element -> QName
elName Element
e) Text -> Set Text -> Bool
forall a. Ord a => a -> Set a -> Bool
`S.member` Set Text
blocktags
  where blocktags :: Set Text
blocktags = [Text] -> Set Text
forall a. Ord a => [a] -> Set a
S.fromList ([Text]
paragraphLevel [Text] -> [Text] -> [Text]
forall a. [a] -> [a] -> [a]
++ [Text]
lists [Text] -> [Text] -> [Text]
forall a. [a] -> [a] -> [a]
++ [Text]
mathML [Text] -> [Text] -> [Text]
forall a. [a] -> [a] -> [a]
++ [Text]
other) Set Text -> Set Text -> Set Text
forall a. Ord a => Set a -> Set a -> Set a
\\ [Text] -> Set Text
forall a. Ord a => [a] -> Set a
S.fromList [Text]
inlinetags
        paragraphLevel :: [Text]
paragraphLevel = [Text
"address", Text
"array", Text
"boxed-text", Text
"chem-struct-wrap",
            Text
"code", Text
"fig", Text
"fig-group", Text
"graphic", Text
"media", Text
"preformat",
            Text
"supplementary-material", Text
"table-wrap", Text
"table-wrap-group",
            Text
"alternatives", Text
"disp-formula", Text
"disp-formula-group"]
        lists :: [Text]
lists = [Text
"def-list", Text
"list"]
        mathML :: [Text]
mathML = [Text
"tex-math", Text
"mml:math"]
        other :: [Text]
other = [Text
"p", Text
"related-article", Text
"related-object", Text
"ack", Text
"disp-quote",
            Text
"speech", Text
"statement", Text
"verse-group", Text
"x"]
        inlinetags :: [Text]
inlinetags = [Text
"email", Text
"ext-link", Text
"uri", Text
"inline-supplementary-material",
            Text
"related-article", Text
"related-object", Text
"hr", Text
"bold", Text
"fixed-case",
            Text
"italic", Text
"monospace", Text
"overline", Text
"overline-start", Text
"overline-end",
            Text
"roman", Text
"sans-serif", Text
"sc", Text
"strike", Text
"underline", Text
"underline-start",
            Text
"underline-end", Text
"ruby", Text
"alternatives", Text
"inline-graphic", Text
"private-char",
            Text
"chem-struct", Text
"inline-formula", Text
"tex-math", Text
"mml:math", Text
"abbrev",
            Text
"milestone-end", Text
"milestone-start", Text
"named-content", Text
"styled-content",
            Text
"fn", Text
"target", Text
"xref", Text
"sub", Text
"sup", Text
"x", Text
"address", Text
"array",
            Text
"boxed-text", Text
"chem-struct-wrap", Text
"code", Text
"fig", Text
"fig-group", Text
"graphic",
            Text
"media", Text
"preformat", Text
"supplementary-material", Text
"table-wrap",
            Text
"table-wrap-group", Text
"disp-formula", Text
"disp-formula-group",
            Text
"citation-alternatives", Text
"element-citation", Text
"mixed-citation",
            Text
"nlm-citation", Text
"award-id", Text
"funding-source", Text
"open-access",
            Text
"def-list", Text
"list", Text
"ack", Text
"disp-quote", Text
"speech", Text
"statement",
            Text
"verse-group"]
isBlockElement Content
_ = Bool
False

-- Trim leading and trailing newline characters
trimNl :: Text -> Text
trimNl :: Text -> Text
trimNl = (Char -> Bool) -> Text -> Text
T.dropAround (Char -> Char -> Bool
forall a. Eq a => a -> a -> Bool
== Char
'\n')

-- function that is used by both graphic (in parseBlock)
-- and inline-graphic (in parseInline)
getGraphic :: PandocMonad m
           => Maybe (Inlines, Text) -> Element -> JATS m Inlines
getGraphic :: forall (m :: * -> *).
PandocMonad m =>
Maybe (Inlines, Text) -> Element -> JATS m Inlines
getGraphic Maybe (Inlines, Text)
mbfigdata Element
e = do
  let atVal :: Text -> Text
atVal Text
a = Text -> Element -> Text
attrValue Text
a Element
e
      (Text
ident, Text
title, Inlines
capt) =
         case Maybe (Inlines, Text)
mbfigdata of
           Just (Inlines
capt', Text
i) -> (Text
i, Text
"fig:" Text -> Text -> Text
forall a. Semigroup a => a -> a -> a
<> Text -> Text
atVal Text
"title", Inlines
capt')
           Maybe (Inlines, Text)
Nothing        -> (Text -> Text
atVal Text
"id", Text -> Text
atVal Text
"title",
                              Text -> Inlines
text (Text -> Text
atVal Text
"alt-text"))
      attr :: (Text, [Text], [a])
attr = (Text
ident, Text -> [Text]
T.words (Text -> [Text]) -> Text -> [Text]
forall a b. (a -> b) -> a -> b
$ Text -> Text
atVal Text
"role", [])
      imageUrl :: Text
imageUrl = Text -> Text
atVal Text
"href"
  Inlines -> JATS m Inlines
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return (Inlines -> JATS m Inlines) -> Inlines -> JATS m Inlines
forall a b. (a -> b) -> a -> b
$ Attr -> Text -> Text -> Inlines -> Inlines
imageWith Attr
forall {a}. (Text, [Text], [a])
attr Text
imageUrl Text
title Inlines
capt

getBlocks :: PandocMonad m => Element -> JATS m Blocks
getBlocks :: forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks Element
e =  [Blocks] -> Blocks
forall a. Monoid a => [a] -> a
mconcat ([Blocks] -> Blocks)
-> StateT JATSState m [Blocks] -> StateT JATSState m Blocks
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$>
                 (Content -> StateT JATSState m Blocks)
-> [Content] -> StateT JATSState m [Blocks]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
forall (m :: * -> *) a b. Monad m => (a -> m b) -> [a] -> m [b]
mapM Content -> StateT JATSState m Blocks
forall (m :: * -> *). PandocMonad m => Content -> JATS m Blocks
parseBlock (Element -> [Content]
elContent Element
e)


parseBlock :: PandocMonad m => Content -> JATS m Blocks
parseBlock :: forall (m :: * -> *). PandocMonad m => Content -> JATS m Blocks
parseBlock (Text (CData CDataKind
CDataRaw Text
_ Maybe Line
_)) = Blocks -> StateT JATSState m Blocks
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return Blocks
forall a. Monoid a => a
mempty -- DOCTYPE
parseBlock (Text (CData CDataKind
_ Text
s Maybe Line
_)) = if (Char -> Bool) -> Text -> Bool
T.all Char -> Bool
isSpace Text
s
                                     then Blocks -> StateT JATSState m Blocks
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return Blocks
forall a. Monoid a => a
mempty
                                     else Blocks -> StateT JATSState m Blocks
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return (Blocks -> StateT JATSState m Blocks)
-> Blocks -> StateT JATSState m Blocks
forall a b. (a -> b) -> a -> b
$ Inlines -> Blocks
plain (Inlines -> Blocks) -> Inlines -> Blocks
forall a b. (a -> b) -> a -> b
$ Inlines -> Inlines
trimInlines (Inlines -> Inlines) -> Inlines -> Inlines
forall a b. (a -> b) -> a -> b
$ Text -> Inlines
text Text
s
parseBlock (CRef Text
x) = Blocks -> StateT JATSState m Blocks
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return (Blocks -> StateT JATSState m Blocks)
-> Blocks -> StateT JATSState m Blocks
forall a b. (a -> b) -> a -> b
$ Inlines -> Blocks
plain (Inlines -> Blocks) -> Inlines -> Blocks
forall a b. (a -> b) -> a -> b
$ Text -> Inlines
str (Text -> Inlines) -> Text -> Inlines
forall a b. (a -> b) -> a -> b
$ Text -> Text
T.toUpper Text
x
parseBlock (Elem Element
e) =
  case QName -> Text
qName (Element -> QName
elName Element
e) of
        Text
"p" -> (Inlines -> Blocks) -> [Content] -> StateT JATSState m Blocks
forall {m :: * -> *}.
PandocMonad m =>
(Inlines -> Blocks) -> [Content] -> StateT JATSState m Blocks
parseMixed Inlines -> Blocks
para (Element -> [Content]
elContent Element
e)
        Text
"code" -> StateT JATSState m Blocks
codeBlockWithLang
        Text
"preformat" -> StateT JATSState m Blocks
codeBlockWithLang
        Text
"disp-quote" -> StateT JATSState m Blocks
parseBlockquote
        Text
"list" -> case Text -> Element -> Text
attrValue Text
"list-type" Element
e of
                    Text
"bullet" -> [Blocks] -> Blocks
bulletList ([Blocks] -> Blocks)
-> StateT JATSState m [Blocks] -> StateT JATSState m Blocks
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> StateT JATSState m [Blocks]
listitems
                    Text
listType -> do
                      let start :: Int
start = Int -> Maybe Int -> Int
forall a. a -> Maybe a -> a
fromMaybe Int
1 (Maybe Int -> Int) -> Maybe Int -> Int
forall a b. (a -> b) -> a -> b
$
                                  ((Element -> Bool) -> Element -> Maybe Element
filterElement (Text -> Element -> Bool
named Text
"list-item") Element
e
                                               Maybe Element -> (Element -> Maybe Element) -> Maybe Element
forall a b. Maybe a -> (a -> Maybe b) -> Maybe b
forall (m :: * -> *) a b. Monad m => m a -> (a -> m b) -> m b
>>= (Element -> Bool) -> Element -> Maybe Element
filterElement (Text -> Element -> Bool
named Text
"label"))
                                   Maybe Element -> (Element -> Maybe Int) -> Maybe Int
forall a b. Maybe a -> (a -> Maybe b) -> Maybe b
forall (m :: * -> *) a b. Monad m => m a -> (a -> m b) -> m b
>>= Text -> Maybe Int
forall (m :: * -> *) a. (MonadPlus m, Read a) => Text -> m a
safeRead (Text -> Maybe Int) -> (Element -> Text) -> Element -> Maybe Int
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Element -> Text
textContent
                      ListAttributes -> [Blocks] -> Blocks
orderedListWith (Int
start, Text -> ListNumberStyle
forall {a}. (Eq a, IsString a) => a -> ListNumberStyle
parseListStyleType Text
listType, ListNumberDelim
DefaultDelim)
                        ([Blocks] -> Blocks)
-> StateT JATSState m [Blocks] -> StateT JATSState m Blocks
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> StateT JATSState m [Blocks]
listitems
        Text
"def-list" -> [(Inlines, [Blocks])] -> Blocks
definitionList ([(Inlines, [Blocks])] -> Blocks)
-> StateT JATSState m [(Inlines, [Blocks])]
-> StateT JATSState m Blocks
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> StateT JATSState m [(Inlines, [Blocks])]
deflistitems
        Text
"sec" -> (JATSState -> Int) -> StateT JATSState m Int
forall s (m :: * -> *) a. MonadState s m => (s -> a) -> m a
gets JATSState -> Int
jatsSectionLevel StateT JATSState m Int
-> (Int -> StateT JATSState m Blocks) -> StateT JATSState m Blocks
forall a b.
StateT JATSState m a
-> (a -> StateT JATSState m b) -> StateT JATSState m b
forall (m :: * -> *) a b. Monad m => m a -> (a -> m b) -> m b
>>= Int -> StateT JATSState m Blocks
forall {m :: * -> *}.
PandocMonad m =>
Int -> StateT JATSState m Blocks
sect (Int -> StateT JATSState m Blocks)
-> (Int -> Int) -> Int -> StateT JATSState m Blocks
forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Int -> Int -> Int
forall a. Num a => a -> a -> a
+Int
1)
        Text
"graphic" -> Inlines -> Blocks
para (Inlines -> Blocks)
-> StateT JATSState m Inlines -> StateT JATSState m Blocks
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Maybe (Inlines, Text) -> Element -> StateT JATSState m Inlines
forall (m :: * -> *).
PandocMonad m =>
Maybe (Inlines, Text) -> Element -> JATS m Inlines
getGraphic Maybe (Inlines, Text)
forall a. Maybe a
Nothing Element
e
        Text
"journal-meta" -> Element -> StateT JATSState m Blocks
forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
parseMetadata Element
e
        Text
"article-meta" -> Element -> StateT JATSState m Blocks
forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
parseMetadata Element
e
        Text
"custom-meta" -> Element -> StateT JATSState m Blocks
forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
parseMetadata Element
e
        Text
"title" -> Blocks -> StateT JATSState m Blocks
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return Blocks
forall a. Monoid a => a
mempty -- processed by header
        Text
"label" -> Blocks -> StateT JATSState m Blocks
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return Blocks
forall a. Monoid a => a
mempty -- processed by header
        Text
"table" -> StateT JATSState m Blocks
parseTable
        Text
"fig" -> StateT JATSState m Blocks
parseFigure
        Text
"fig-group" -> Attr -> Blocks -> Blocks
divWith (Text -> Element -> Text
attrValue Text
"id" Element
e, [Text
"fig-group"], [])
                          (Blocks -> Blocks)
-> StateT JATSState m Blocks -> StateT JATSState m Blocks
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Element -> StateT JATSState m Blocks
forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks Element
e
        Text
"table-wrap" -> Attr -> Blocks -> Blocks
divWith (Text -> Element -> Text
attrValue Text
"id" Element
e, [Text
"table-wrap"], [])
                          (Blocks -> Blocks)
-> StateT JATSState m Blocks -> StateT JATSState m Blocks
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Element -> StateT JATSState m Blocks
forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks Element
e
        Text
"caption" -> do
          Bool
inFigure <- (JATSState -> Bool) -> StateT JATSState m Bool
forall s (m :: * -> *) a. MonadState s m => (s -> a) -> m a
gets JATSState -> Bool
jatsInFigure
          if Bool
inFigure -- handled by parseFigure
             then Blocks -> StateT JATSState m Blocks
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return Blocks
forall a. Monoid a => a
mempty
             else Attr -> Blocks -> Blocks
divWith (Text -> Element -> Text
attrValue Text
"id" Element
e, [Text
"caption"], []) (Blocks -> Blocks)
-> StateT JATSState m Blocks -> StateT JATSState m Blocks
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Int -> StateT JATSState m Blocks
forall {m :: * -> *}.
PandocMonad m =>
Int -> StateT JATSState m Blocks
sect Int
6
        Text
"fn-group" -> StateT JATSState m Blocks
parseFootnoteGroup
        Text
"ref-list" -> Element -> StateT JATSState m Blocks
forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
parseRefList Element
e
        Text
"?xml"  -> Blocks -> StateT JATSState m Blocks
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return Blocks
forall a. Monoid a => a
mempty
        Text
_       -> Element -> StateT JATSState m Blocks
forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks Element
e
   where parseMixed :: (Inlines -> Blocks) -> [Content] -> StateT JATSState m Blocks
parseMixed Inlines -> Blocks
container [Content]
conts = do
           let ([Content]
ils,[Content]
rest) = (Content -> Bool) -> [Content] -> ([Content], [Content])
forall a. (a -> Bool) -> [a] -> ([a], [a])
break Content -> Bool
isBlockElement [Content]
conts
           Inlines
ils' <- Inlines -> Inlines
trimInlines (Inlines -> Inlines)
-> ([Inlines] -> Inlines) -> [Inlines] -> Inlines
forall b c a. (b -> c) -> (a -> b) -> a -> c
. [Inlines] -> Inlines
forall a. Monoid a => [a] -> a
mconcat ([Inlines] -> Inlines)
-> StateT JATSState m [Inlines] -> StateT JATSState m Inlines
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> (Content -> StateT JATSState m Inlines)
-> [Content] -> StateT JATSState m [Inlines]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
forall (m :: * -> *) a b. Monad m => (a -> m b) -> [a] -> m [b]
mapM Content -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Content -> JATS m Inlines
parseInline [Content]
ils
           let p :: Blocks
p = if Inlines
ils' Inlines -> Inlines -> Bool
forall a. Eq a => a -> a -> Bool
== Inlines
forall a. Monoid a => a
mempty then Blocks
forall a. Monoid a => a
mempty else Inlines -> Blocks
container Inlines
ils'
           case [Content]
rest of
                 []     -> Blocks -> StateT JATSState m Blocks
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return Blocks
p
                 (Content
r:[Content]
rs) -> do
                    Blocks
b <- Content -> StateT JATSState m Blocks
forall (m :: * -> *). PandocMonad m => Content -> JATS m Blocks
parseBlock Content
r
                    Blocks
x <- (Inlines -> Blocks) -> [Content] -> StateT JATSState m Blocks
parseMixed Inlines -> Blocks
container [Content]
rs
                    Blocks -> StateT JATSState m Blocks
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return (Blocks -> StateT JATSState m Blocks)
-> Blocks -> StateT JATSState m Blocks
forall a b. (a -> b) -> a -> b
$ Blocks
p Blocks -> Blocks -> Blocks
forall a. Semigroup a => a -> a -> a
<> Blocks
b Blocks -> Blocks -> Blocks
forall a. Semigroup a => a -> a -> a
<> Blocks
x
         codeBlockWithLang :: StateT JATSState m Blocks
codeBlockWithLang = do
           let classes' :: [Text]
classes' = case Text -> Element -> Text
attrValue Text
"language" Element
e of
                                Text
"" -> []
                                Text
x  -> [Text
x]
           Blocks -> StateT JATSState m Blocks
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return (Blocks -> StateT JATSState m Blocks)
-> Blocks -> StateT JATSState m Blocks
forall a b. (a -> b) -> a -> b
$ Attr -> Text -> Blocks
codeBlockWith (Text -> Element -> Text
attrValue Text
"id" Element
e, [Text]
classes', [])
                  (Text -> Blocks) -> Text -> Blocks
forall a b. (a -> b) -> a -> b
$ Text -> Text
trimNl (Text -> Text) -> Text -> Text
forall a b. (a -> b) -> a -> b
$ Element -> Text
strContentRecursive Element
e
         parseBlockquote :: StateT JATSState m Blocks
parseBlockquote = do
            Blocks
attrib <- case (Element -> Bool) -> Element -> Maybe Element
filterChild (Text -> Element -> Bool
named Text
"attribution") Element
e of
                             Maybe Element
Nothing  -> Blocks -> StateT JATSState m Blocks
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return Blocks
forall a. Monoid a => a
mempty
                             Just Element
z   -> Inlines -> Blocks
para (Inlines -> Blocks)
-> ([Inlines] -> Inlines) -> [Inlines] -> Blocks
forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text -> Inlines
str Text
"— " Inlines -> Inlines -> Inlines
forall a. Semigroup a => a -> a -> a
<>) (Inlines -> Inlines)
-> ([Inlines] -> Inlines) -> [Inlines] -> Inlines
forall b c a. (b -> c) -> (a -> b) -> a -> c
. [Inlines] -> Inlines
forall a. Monoid a => [a] -> a
mconcat
                                         ([Inlines] -> Blocks)
-> StateT JATSState m [Inlines] -> StateT JATSState m Blocks
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$>
                                              (Content -> StateT JATSState m Inlines)
-> [Content] -> StateT JATSState m [Inlines]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
forall (m :: * -> *) a b. Monad m => (a -> m b) -> [a] -> m [b]
mapM Content -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Content -> JATS m Inlines
parseInline (Element -> [Content]
elContent Element
z)
            Blocks
contents <- Element -> StateT JATSState m Blocks
forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks Element
e
            Blocks -> StateT JATSState m Blocks
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return (Blocks -> StateT JATSState m Blocks)
-> Blocks -> StateT JATSState m Blocks
forall a b. (a -> b) -> a -> b
$ Blocks -> Blocks
blockQuote (Blocks
contents Blocks -> Blocks -> Blocks
forall a. Semigroup a => a -> a -> a
<> Blocks
attrib)
         parseListStyleType :: a -> ListNumberStyle
parseListStyleType a
"roman-lower" = ListNumberStyle
LowerRoman
         parseListStyleType a
"roman-upper" = ListNumberStyle
UpperRoman
         parseListStyleType a
"alpha-lower" = ListNumberStyle
LowerAlpha
         parseListStyleType a
"alpha-upper" = ListNumberStyle
UpperAlpha
         parseListStyleType a
_             = ListNumberStyle
DefaultStyle
         listitems :: StateT JATSState m [Blocks]
listitems = (Element -> StateT JATSState m Blocks)
-> [Element] -> StateT JATSState m [Blocks]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
forall (m :: * -> *) a b. Monad m => (a -> m b) -> [a] -> m [b]
mapM Element -> StateT JATSState m Blocks
forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks ([Element] -> StateT JATSState m [Blocks])
-> [Element] -> StateT JATSState m [Blocks]
forall a b. (a -> b) -> a -> b
$ (Element -> Bool) -> Element -> [Element]
filterChildren (Text -> Element -> Bool
named Text
"list-item") Element
e
         deflistitems :: StateT JATSState m [(Inlines, [Blocks])]
deflistitems = (Element -> StateT JATSState m (Inlines, [Blocks]))
-> [Element] -> StateT JATSState m [(Inlines, [Blocks])]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
forall (m :: * -> *) a b. Monad m => (a -> m b) -> [a] -> m [b]
mapM Element -> StateT JATSState m (Inlines, [Blocks])
forall {m :: * -> *}.
PandocMonad m =>
Element -> StateT JATSState m (Inlines, [Blocks])
parseVarListEntry ([Element] -> StateT JATSState m [(Inlines, [Blocks])])
-> [Element] -> StateT JATSState m [(Inlines, [Blocks])]
forall a b. (a -> b) -> a -> b
$ (Element -> Bool) -> Element -> [Element]
filterChildren
                     (Text -> Element -> Bool
named Text
"def-item") Element
e
         parseVarListEntry :: Element -> StateT JATSState m (Inlines, [Blocks])
parseVarListEntry Element
e' = do
                     let terms :: [Element]
terms = (Element -> Bool) -> Element -> [Element]
filterChildren (Text -> Element -> Bool
named Text
"term") Element
e'
                     let items :: [Element]
items = (Element -> Bool) -> Element -> [Element]
filterChildren (Text -> Element -> Bool
named Text
"def") Element
e'
                     [Inlines]
terms' <- (Element -> StateT JATSState m Inlines)
-> [Element] -> StateT JATSState m [Inlines]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
forall (m :: * -> *) a b. Monad m => (a -> m b) -> [a] -> m [b]
mapM Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines [Element]
terms
                     [Blocks]
items' <- (Element -> StateT JATSState m Blocks)
-> [Element] -> StateT JATSState m [Blocks]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
forall (m :: * -> *) a b. Monad m => (a -> m b) -> [a] -> m [b]
mapM Element -> StateT JATSState m Blocks
forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks [Element]
items
                     (Inlines, [Blocks]) -> StateT JATSState m (Inlines, [Blocks])
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return ([Inlines] -> Inlines
forall a. Monoid a => [a] -> a
mconcat ([Inlines] -> Inlines) -> [Inlines] -> Inlines
forall a b. (a -> b) -> a -> b
$ Inlines -> [Inlines] -> [Inlines]
forall a. a -> [a] -> [a]
intersperse (Text -> Inlines
str Text
"; ") [Inlines]
terms', [Blocks]
items')
         parseFigure :: StateT JATSState m Blocks
parseFigure = do
           (JATSState -> JATSState) -> StateT JATSState m ()
forall s (m :: * -> *). MonadState s m => (s -> s) -> m ()
modify ((JATSState -> JATSState) -> StateT JATSState m ())
-> (JATSState -> JATSState) -> StateT JATSState m ()
forall a b. (a -> b) -> a -> b
$ \JATSState
st -> JATSState
st{ jatsInFigure :: Bool
jatsInFigure = Bool
True }
           Inlines
capt <- case (Element -> Bool) -> Element -> Maybe Element
filterChild (Text -> Element -> Bool
named Text
"caption") Element
e of
                     Just Element
t  -> [Inlines] -> Inlines
forall a. Monoid a => [a] -> a
mconcat ([Inlines] -> Inlines)
-> ([Inlines] -> [Inlines]) -> [Inlines] -> Inlines
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Inlines -> [Inlines] -> [Inlines]
forall a. a -> [a] -> [a]
intersperse Inlines
linebreak ([Inlines] -> Inlines)
-> StateT JATSState m [Inlines] -> StateT JATSState m Inlines
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$>
                                (Element -> StateT JATSState m Inlines)
-> [Element] -> StateT JATSState m [Inlines]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
forall (m :: * -> *) a b. Monad m => (a -> m b) -> [a] -> m [b]
mapM Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines ((Element -> Bool) -> Element -> [Element]
filterChildren (Bool -> Element -> Bool
forall a b. a -> b -> a
const Bool
True) Element
t)
                     Maybe Element
Nothing -> Inlines -> StateT JATSState m Inlines
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return Inlines
forall a. Monoid a => a
mempty
           Blocks
contents <- Element -> StateT JATSState m Blocks
forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks Element
e
           (JATSState -> JATSState) -> StateT JATSState m ()
forall s (m :: * -> *). MonadState s m => (s -> s) -> m ()
modify ((JATSState -> JATSState) -> StateT JATSState m ())
-> (JATSState -> JATSState) -> StateT JATSState m ()
forall a b. (a -> b) -> a -> b
$ \JATSState
st -> JATSState
st{ jatsInFigure :: Bool
jatsInFigure = Bool
False }
           Blocks -> StateT JATSState m Blocks
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return (Blocks -> StateT JATSState m Blocks)
-> Blocks -> StateT JATSState m Blocks
forall a b. (a -> b) -> a -> b
$ Attr -> Caption -> Blocks -> Blocks
figureWith
             (Text -> Element -> Text
attrValue Text
"id" Element
e, [], [])
             (Blocks -> Caption
simpleCaption (Blocks -> Caption) -> Blocks -> Caption
forall a b. (a -> b) -> a -> b
$ Inlines -> Blocks
plain Inlines
capt)
             Blocks
contents
         parseFootnoteGroup :: StateT JATSState m Blocks
parseFootnoteGroup = do
           [Element]
-> (Element -> StateT JATSState m ()) -> StateT JATSState m ()
forall (t :: * -> *) (m :: * -> *) a b.
(Foldable t, Monad m) =>
t a -> (a -> m b) -> m ()
forM_ ((Element -> Bool) -> Element -> [Element]
filterChildren (Text -> Element -> Bool
named Text
"fn") Element
e) ((Element -> StateT JATSState m ()) -> StateT JATSState m ())
-> (Element -> StateT JATSState m ()) -> StateT JATSState m ()
forall a b. (a -> b) -> a -> b
$ \Element
fn -> do
             let id' :: Text
id' = Text -> Element -> Text
attrValue Text
"id" Element
fn
             Blocks
contents <- Element -> StateT JATSState m Blocks
forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks Element
fn
             (JATSState -> JATSState) -> StateT JATSState m ()
forall s (m :: * -> *). MonadState s m => (s -> s) -> m ()
modify ((JATSState -> JATSState) -> StateT JATSState m ())
-> (JATSState -> JATSState) -> StateT JATSState m ()
forall a b. (a -> b) -> a -> b
$ \JATSState
st ->
               JATSState
st { jatsFootnotes :: Map Text Blocks
jatsFootnotes = Text -> Blocks -> Map Text Blocks -> Map Text Blocks
forall k a. Ord k => k -> a -> Map k a -> Map k a
Map.insert Text
id' Blocks
contents (JATSState -> Map Text Blocks
jatsFootnotes JATSState
st) }
           Blocks -> StateT JATSState m Blocks
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return Blocks
forall a. Monoid a => a
mempty

         parseTable :: StateT JATSState m Blocks
parseTable = do
                      let isCaption :: Element -> Bool
isCaption Element
x = Text -> Element -> Bool
named Text
"title" Element
x Bool -> Bool -> Bool
|| Text -> Element -> Bool
named Text
"caption" Element
x
                      Inlines
capt <- case (Element -> Bool) -> Element -> Maybe Element
filterChild Element -> Bool
isCaption Element
e of
                                    Just Element
t  -> Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
t
                                    Maybe Element
Nothing -> Inlines -> StateT JATSState m Inlines
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return Inlines
forall a. Monoid a => a
mempty
                      let e' :: Element
e' = Element -> Maybe Element -> Element
forall a. a -> Maybe a -> a
fromMaybe Element
e (Maybe Element -> Element) -> Maybe Element -> Element
forall a b. (a -> b) -> a -> b
$ (Element -> Bool) -> Element -> Maybe Element
filterChild (Text -> Element -> Bool
named Text
"tgroup") Element
e
                      let isColspec :: Element -> Bool
isColspec Element
x = Text -> Element -> Bool
named Text
"colspec" Element
x Bool -> Bool -> Bool
|| Text -> Element -> Bool
named Text
"col" Element
x
                      let colspecs :: [Element]
colspecs = case (Element -> Bool) -> Element -> Maybe Element
filterChild (Text -> Element -> Bool
named Text
"colgroup") Element
e' of
                                           Just Element
c -> (Element -> Bool) -> Element -> [Element]
filterChildren Element -> Bool
isColspec Element
c
                                           Maybe Element
_      -> (Element -> Bool) -> Element -> [Element]
filterChildren Element -> Bool
isColspec Element
e'
                      let isRow :: Element -> Bool
isRow Element
x = Text -> Element -> Bool
named Text
"row" Element
x Bool -> Bool -> Bool
|| Text -> Element -> Bool
named Text
"tr" Element
x
                      [Blocks]
headrows <- case (Element -> Bool) -> Element -> Maybe Element
filterChild (Text -> Element -> Bool
named Text
"thead") Element
e' of
                                       Just Element
h  -> case (Element -> Bool) -> Element -> Maybe Element
filterChild Element -> Bool
isRow Element
h of
                                                       Just Element
x  -> Element -> StateT JATSState m [Blocks]
parseRow Element
x
                                                       Maybe Element
Nothing -> [Blocks] -> StateT JATSState m [Blocks]
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return []
                                       Maybe Element
Nothing -> [Blocks] -> StateT JATSState m [Blocks]
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return []
                      [[Blocks]]
bodyrows <- case (Element -> Bool) -> Element -> Maybe Element
filterChild (Text -> Element -> Bool
named Text
"tbody") Element
e' of
                                       Just Element
b  -> (Element -> StateT JATSState m [Blocks])
-> [Element] -> StateT JATSState m [[Blocks]]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
forall (m :: * -> *) a b. Monad m => (a -> m b) -> [a] -> m [b]
mapM Element -> StateT JATSState m [Blocks]
parseRow
                                                  ([Element] -> StateT JATSState m [[Blocks]])
-> [Element] -> StateT JATSState m [[Blocks]]
forall a b. (a -> b) -> a -> b
$ (Element -> Bool) -> Element -> [Element]
filterChildren Element -> Bool
isRow Element
b
                                       Maybe Element
Nothing -> (Element -> StateT JATSState m [Blocks])
-> [Element] -> StateT JATSState m [[Blocks]]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
forall (m :: * -> *) a b. Monad m => (a -> m b) -> [a] -> m [b]
mapM Element -> StateT JATSState m [Blocks]
parseRow
                                                  ([Element] -> StateT JATSState m [[Blocks]])
-> [Element] -> StateT JATSState m [[Blocks]]
forall a b. (a -> b) -> a -> b
$ (Element -> Bool) -> Element -> [Element]
filterChildren Element -> Bool
isRow Element
e'
                      let toAlignment :: Element -> Alignment
toAlignment Element
c = case QName -> Element -> Maybe Text
findAttr (Text -> QName
unqual Text
"align") Element
c of
                                                Just Text
"left"   -> Alignment
AlignLeft
                                                Just Text
"right"  -> Alignment
AlignRight
                                                Just Text
"center" -> Alignment
AlignCenter
                                                Maybe Text
_             -> Alignment
AlignDefault
                      let toWidth :: Element -> Maybe b
toWidth Element
c = do
                            Text
w <- QName -> Element -> Maybe Text
findAttr (Text -> QName
unqual Text
"colwidth") Element
c
                            b
n <- Text -> Maybe b
forall (m :: * -> *) a. (MonadPlus m, Read a) => Text -> m a
safeRead (Text -> Maybe b) -> Text -> Maybe b
forall a b. (a -> b) -> a -> b
$ Text
"0" Text -> Text -> Text
forall a. Semigroup a => a -> a -> a
<> (Char -> Bool) -> Text -> Text
T.filter (\Char
x -> Char -> Bool
isDigit Char
x Bool -> Bool -> Bool
|| Char
x Char -> Char -> Bool
forall a. Eq a => a -> a -> Bool
== Char
'.') Text
w
                            if b
n b -> b -> Bool
forall a. Ord a => a -> a -> Bool
> b
0 then b -> Maybe b
forall a. a -> Maybe a
Just b
n else Maybe b
forall a. Maybe a
Nothing
                      let numrows :: Int
numrows = (Int -> Int -> Int) -> Int -> [Int] -> Int
forall b a. (b -> a -> b) -> b -> [a] -> b
forall (t :: * -> *) b a.
Foldable t =>
(b -> a -> b) -> b -> t a -> b
foldl' Int -> Int -> Int
forall a. Ord a => a -> a -> a
max Int
0 ([Int] -> Int) -> [Int] -> Int
forall a b. (a -> b) -> a -> b
$ ([Blocks] -> Int) -> [[Blocks]] -> [Int]
forall a b. (a -> b) -> [a] -> [b]
map [Blocks] -> Int
forall a. [a] -> Int
forall (t :: * -> *) a. Foldable t => t a -> Int
length [[Blocks]]
bodyrows
                      let aligns :: [Alignment]
aligns = case [Element]
colspecs of
                                     [] -> Int -> Alignment -> [Alignment]
forall a. Int -> a -> [a]
replicate Int
numrows Alignment
AlignDefault
                                     [Element]
cs -> (Element -> Alignment) -> [Element] -> [Alignment]
forall a b. (a -> b) -> [a] -> [b]
map Element -> Alignment
toAlignment [Element]
cs
                      let widths :: [ColWidth]
widths = case [Element]
colspecs of
                                     [] -> Int -> ColWidth -> [ColWidth]
forall a. Int -> a -> [a]
replicate Int
numrows ColWidth
ColWidthDefault
                                     [Element]
cs -> let ws :: [Maybe Double]
ws = (Element -> Maybe Double) -> [Element] -> [Maybe Double]
forall a b. (a -> b) -> [a] -> [b]
map Element -> Maybe Double
forall {b}. (Read b, Ord b, Num b) => Element -> Maybe b
toWidth [Element]
cs
                                           in case [Maybe Double] -> Maybe [Double]
forall (t :: * -> *) (m :: * -> *) a.
(Traversable t, Monad m) =>
t (m a) -> m (t a)
forall (m :: * -> *) a. Monad m => [m a] -> m [a]
sequence [Maybe Double]
ws of
                                                Just [Double]
ws' -> let tot :: Double
tot = [Double] -> Double
forall a. Num a => [a] -> a
forall (t :: * -> *) a. (Foldable t, Num a) => t a -> a
sum [Double]
ws'
                                                            in  Double -> ColWidth
ColWidth (Double -> ColWidth) -> (Double -> Double) -> Double -> ColWidth
forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Double -> Double -> Double
forall a. Fractional a => a -> a -> a
/ Double
tot) (Double -> ColWidth) -> [Double] -> [ColWidth]
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> [Double]
ws'
                                                Maybe [Double]
Nothing  -> Int -> ColWidth -> [ColWidth]
forall a. Int -> a -> [a]
replicate Int
numrows ColWidth
ColWidthDefault
                      let toRow :: [Blocks] -> Row
toRow = Attr -> [Cell] -> Row
Row Attr
nullAttr ([Cell] -> Row) -> ([Blocks] -> [Cell]) -> [Blocks] -> Row
forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Blocks -> Cell) -> [Blocks] -> [Cell]
forall a b. (a -> b) -> [a] -> [b]
map Blocks -> Cell
simpleCell
                          toHeaderRow :: [Blocks] -> [Row]
toHeaderRow [Blocks]
l = [[Blocks] -> Row
toRow [Blocks]
l | Bool -> Bool
not ([Blocks] -> Bool
forall a. [a] -> Bool
forall (t :: * -> *) a. Foldable t => t a -> Bool
null [Blocks]
l)]
                      Blocks -> StateT JATSState m Blocks
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return (Blocks -> StateT JATSState m Blocks)
-> Blocks -> StateT JATSState m Blocks
forall a b. (a -> b) -> a -> b
$ Caption
-> [ColSpec] -> TableHead -> [TableBody] -> TableFoot -> Blocks
table (Blocks -> Caption
simpleCaption (Blocks -> Caption) -> Blocks -> Caption
forall a b. (a -> b) -> a -> b
$ Inlines -> Blocks
plain Inlines
capt)
                                     ([Alignment] -> [ColWidth] -> [ColSpec]
forall a b. [a] -> [b] -> [(a, b)]
zip [Alignment]
aligns [ColWidth]
widths)
                                     (Attr -> [Row] -> TableHead
TableHead Attr
nullAttr ([Row] -> TableHead) -> [Row] -> TableHead
forall a b. (a -> b) -> a -> b
$ [Blocks] -> [Row]
toHeaderRow [Blocks]
headrows)
                                     [Attr -> RowHeadColumns -> [Row] -> [Row] -> TableBody
TableBody Attr
nullAttr RowHeadColumns
0 [] ([Row] -> TableBody) -> [Row] -> TableBody
forall a b. (a -> b) -> a -> b
$ ([Blocks] -> Row) -> [[Blocks]] -> [Row]
forall a b. (a -> b) -> [a] -> [b]
map [Blocks] -> Row
toRow [[Blocks]]
bodyrows]
                                     (Attr -> [Row] -> TableFoot
TableFoot Attr
nullAttr [])
         isEntry :: Element -> Bool
isEntry Element
x  = Text -> Element -> Bool
named Text
"entry" Element
x Bool -> Bool -> Bool
|| Text -> Element -> Bool
named Text
"td" Element
x Bool -> Bool -> Bool
|| Text -> Element -> Bool
named Text
"th" Element
x
         parseRow :: Element -> StateT JATSState m [Blocks]
parseRow = (Element -> StateT JATSState m Blocks)
-> [Element] -> StateT JATSState m [Blocks]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
forall (m :: * -> *) a b. Monad m => (a -> m b) -> [a] -> m [b]
mapM ((Inlines -> Blocks) -> [Content] -> StateT JATSState m Blocks
forall {m :: * -> *}.
PandocMonad m =>
(Inlines -> Blocks) -> [Content] -> StateT JATSState m Blocks
parseMixed Inlines -> Blocks
plain ([Content] -> StateT JATSState m Blocks)
-> (Element -> [Content]) -> Element -> StateT JATSState m Blocks
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Element -> [Content]
elContent) ([Element] -> StateT JATSState m [Blocks])
-> (Element -> [Element]) -> Element -> StateT JATSState m [Blocks]
forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Element -> Bool) -> Element -> [Element]
filterChildren Element -> Bool
isEntry
         sect :: Int -> StateT JATSState m Blocks
sect Int
n = do Bool
isbook <- (JATSState -> Bool) -> StateT JATSState m Bool
forall s (m :: * -> *) a. MonadState s m => (s -> a) -> m a
gets JATSState -> Bool
jatsBook
                     let n' :: Int
n' = if Bool
isbook Bool -> Bool -> Bool
|| Int
n Int -> Int -> Bool
forall a. Eq a => a -> a -> Bool
== Int
0 then Int
n Int -> Int -> Int
forall a. Num a => a -> a -> a
+ Int
1 else Int
n
                     Inlines
labelText <- case (Element -> Bool) -> Element -> Maybe Element
filterChild (Text -> Element -> Bool
named Text
"label") Element
e of
                                    Just Element
t -> (Inlines -> Inlines -> Inlines
forall a. Semigroup a => a -> a -> a
<> (Inlines
"." Inlines -> Inlines -> Inlines
forall a. Semigroup a => a -> a -> a
<> Inlines
space)) (Inlines -> Inlines)
-> StateT JATSState m Inlines -> StateT JATSState m Inlines
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$>
                                              Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
t
                                    Maybe Element
Nothing -> Inlines -> StateT JATSState m Inlines
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return Inlines
forall a. Monoid a => a
mempty
                     Inlines
headerText <- case (Element -> Bool) -> Element -> Maybe Element
filterChild (Text -> Element -> Bool
named Text
"title") Element
e Maybe Element -> Maybe Element -> Maybe Element
forall a. Maybe a -> Maybe a -> Maybe a
forall (m :: * -> *) a. MonadPlus m => m a -> m a -> m a
`mplus`
                                        ((Element -> Bool) -> Element -> Maybe Element
filterChild (Text -> Element -> Bool
named Text
"info") Element
e Maybe Element -> (Element -> Maybe Element) -> Maybe Element
forall a b. Maybe a -> (a -> Maybe b) -> Maybe b
forall (m :: * -> *) a b. Monad m => m a -> (a -> m b) -> m b
>>=
                                            (Element -> Bool) -> Element -> Maybe Element
filterChild (Text -> Element -> Bool
named Text
"title")) of
                                      Just Element
t  -> (Inlines
labelText Inlines -> Inlines -> Inlines
forall a. Semigroup a => a -> a -> a
<>) (Inlines -> Inlines)
-> StateT JATSState m Inlines -> StateT JATSState m Inlines
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$>
                                                  Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
t
                                      Maybe Element
Nothing -> Inlines -> StateT JATSState m Inlines
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return Inlines
forall a. Monoid a => a
mempty
                     Int
oldN <- (JATSState -> Int) -> StateT JATSState m Int
forall s (m :: * -> *) a. MonadState s m => (s -> a) -> m a
gets JATSState -> Int
jatsSectionLevel
                     (JATSState -> JATSState) -> StateT JATSState m ()
forall s (m :: * -> *). MonadState s m => (s -> s) -> m ()
modify ((JATSState -> JATSState) -> StateT JATSState m ())
-> (JATSState -> JATSState) -> StateT JATSState m ()
forall a b. (a -> b) -> a -> b
$ \JATSState
st -> JATSState
st{ jatsSectionLevel :: Int
jatsSectionLevel = Int
n }
                     Blocks
b <- Element -> StateT JATSState m Blocks
forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks Element
e
                     let ident :: Text
ident = Text -> Element -> Text
attrValue Text
"id" Element
e
                     (JATSState -> JATSState) -> StateT JATSState m ()
forall s (m :: * -> *). MonadState s m => (s -> s) -> m ()
modify ((JATSState -> JATSState) -> StateT JATSState m ())
-> (JATSState -> JATSState) -> StateT JATSState m ()
forall a b. (a -> b) -> a -> b
$ \JATSState
st -> JATSState
st{ jatsSectionLevel :: Int
jatsSectionLevel = Int
oldN }
                     Blocks -> StateT JATSState m Blocks
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return (Blocks -> StateT JATSState m Blocks)
-> Blocks -> StateT JATSState m Blocks
forall a b. (a -> b) -> a -> b
$ Attr -> Int -> Inlines -> Blocks
headerWith (Text
ident,[],[]) Int
n' Inlines
headerText Blocks -> Blocks -> Blocks
forall a. Semigroup a => a -> a -> a
<> Blocks
b

getInlines :: PandocMonad m => Element -> JATS m Inlines
getInlines :: forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
e' = Inlines -> Inlines
trimInlines (Inlines -> Inlines)
-> ([Inlines] -> Inlines) -> [Inlines] -> Inlines
forall b c a. (b -> c) -> (a -> b) -> a -> c
. [Inlines] -> Inlines
forall a. Monoid a => [a] -> a
mconcat ([Inlines] -> Inlines)
-> StateT JATSState m [Inlines] -> StateT JATSState m Inlines
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$>
                 (Content -> StateT JATSState m Inlines)
-> [Content] -> StateT JATSState m [Inlines]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
forall (m :: * -> *) a b. Monad m => (a -> m b) -> [a] -> m [b]
mapM Content -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Content -> JATS m Inlines
parseInline (Element -> [Content]
elContent Element
e')

parseMetadata :: PandocMonad m => Element -> JATS m Blocks
parseMetadata :: forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
parseMetadata Element
e = do
  Element -> JATS m ()
forall (m :: * -> *). PandocMonad m => Element -> JATS m ()
getTitle Element
e
  Element -> JATS m ()
forall (m :: * -> *). PandocMonad m => Element -> JATS m ()
getAuthors Element
e
  Element -> JATS m ()
forall (m :: * -> *). PandocMonad m => Element -> JATS m ()
getAffiliations Element
e
  Element -> JATS m ()
forall (m :: * -> *). PandocMonad m => Element -> JATS m ()
getAbstract Element
e
  Element -> JATS m ()
forall (m :: * -> *). PandocMonad m => Element -> JATS m ()
getPubDate Element
e
  Blocks -> JATS m Blocks
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return Blocks
forall a. Monoid a => a
mempty

getTitle :: PandocMonad m => Element -> JATS m ()
getTitle :: forall (m :: * -> *). PandocMonad m => Element -> JATS m ()
getTitle Element
e = do
  Inlines
tit <-  case (Element -> Bool) -> Element -> Maybe Element
filterElement (Text -> Element -> Bool
named Text
"article-title") Element
e of
               Just Element
s  -> Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
s
               Maybe Element
Nothing -> Inlines -> StateT JATSState m Inlines
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return Inlines
forall a. Monoid a => a
mempty
  Inlines
subtit <-  case (Element -> Bool) -> Element -> Maybe Element
filterElement (Text -> Element -> Bool
named Text
"subtitle") Element
e of
               Just Element
s  -> (Text -> Inlines
text Text
": " Inlines -> Inlines -> Inlines
forall a. Semigroup a => a -> a -> a
<>) (Inlines -> Inlines)
-> StateT JATSState m Inlines -> StateT JATSState m Inlines
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$>
                           Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
s
               Maybe Element
Nothing -> Inlines -> StateT JATSState m Inlines
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return Inlines
forall a. Monoid a => a
mempty
  Bool -> JATS m () -> JATS m ()
forall (f :: * -> *). Applicative f => Bool -> f () -> f ()
when (Inlines
tit Inlines -> Inlines -> Bool
forall a. Eq a => a -> a -> Bool
/= Inlines
forall a. Monoid a => a
mempty) (JATS m () -> JATS m ()) -> JATS m () -> JATS m ()
forall a b. (a -> b) -> a -> b
$ Text -> Inlines -> JATS m ()
forall (m :: * -> *) a.
(PandocMonad m, ToMetaValue a) =>
Text -> a -> JATS m ()
addMeta Text
"title" Inlines
tit
  Bool -> JATS m () -> JATS m ()
forall (f :: * -> *). Applicative f => Bool -> f () -> f ()
when (Inlines
subtit Inlines -> Inlines -> Bool
forall a. Eq a => a -> a -> Bool
/= Inlines
forall a. Monoid a => a
mempty) (JATS m () -> JATS m ()) -> JATS m () -> JATS m ()
forall a b. (a -> b) -> a -> b
$ Text -> Inlines -> JATS m ()
forall (m :: * -> *) a.
(PandocMonad m, ToMetaValue a) =>
Text -> a -> JATS m ()
addMeta Text
"subtitle" Inlines
subtit

getAuthors :: PandocMonad m => Element -> JATS m ()
getAuthors :: forall (m :: * -> *). PandocMonad m => Element -> JATS m ()
getAuthors Element
e = do
  [Inlines]
authors <- (Element -> StateT JATSState m Inlines)
-> [Element] -> StateT JATSState m [Inlines]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
forall (m :: * -> *) a b. Monad m => (a -> m b) -> [a] -> m [b]
mapM Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getContrib ([Element] -> StateT JATSState m [Inlines])
-> [Element] -> StateT JATSState m [Inlines]
forall a b. (a -> b) -> a -> b
$ (Element -> Bool) -> Element -> [Element]
filterElements
              (\Element
x -> Text -> Element -> Bool
named Text
"contrib" Element
x Bool -> Bool -> Bool
&&
                     Text -> Element -> Text
attrValue Text
"contrib-type" Element
x Text -> Text -> Bool
forall a. Eq a => a -> a -> Bool
== Text
"author") Element
e
  [Inlines]
authorNotes <- (Element -> StateT JATSState m Inlines)
-> [Element] -> StateT JATSState m [Inlines]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
forall (m :: * -> *) a b. Monad m => (a -> m b) -> [a] -> m [b]
mapM Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines ([Element] -> StateT JATSState m [Inlines])
-> [Element] -> StateT JATSState m [Inlines]
forall a b. (a -> b) -> a -> b
$ (Element -> Bool) -> Element -> [Element]
filterElements (Text -> Element -> Bool
named Text
"author-notes") Element
e
  let authors' :: [Inlines]
authors' = case ([Inlines] -> [Inlines]
forall a. [a] -> [a]
reverse [Inlines]
authors, [Inlines]
authorNotes) of
                   ([], [Inlines]
_)    -> []
                   ([Inlines]
_, [])    -> [Inlines]
authors
                   (Inlines
a:[Inlines]
as, [Inlines]
ns) -> [Inlines] -> [Inlines]
forall a. [a] -> [a]
reverse [Inlines]
as [Inlines] -> [Inlines] -> [Inlines]
forall a. [a] -> [a] -> [a]
++ [Inlines
a Inlines -> Inlines -> Inlines
forall a. Semigroup a => a -> a -> a
<> [Inlines] -> Inlines
forall a. Monoid a => [a] -> a
mconcat [Inlines]
ns]
  Bool -> JATS m () -> JATS m ()
forall (f :: * -> *). Applicative f => Bool -> f () -> f ()
unless ([Inlines] -> Bool
forall a. [a] -> Bool
forall (t :: * -> *) a. Foldable t => t a -> Bool
null [Inlines]
authors) (JATS m () -> JATS m ()) -> JATS m () -> JATS m ()
forall a b. (a -> b) -> a -> b
$ Text -> [Inlines] -> JATS m ()
forall (m :: * -> *) a.
(PandocMonad m, ToMetaValue a) =>
Text -> a -> JATS m ()
addMeta Text
"author" [Inlines]
authors'

getAffiliations :: PandocMonad m => Element -> JATS m ()
getAffiliations :: forall (m :: * -> *). PandocMonad m => Element -> JATS m ()
getAffiliations Element
x = do
  [Inlines]
affs <- (Element -> StateT JATSState m Inlines)
-> [Element] -> StateT JATSState m [Inlines]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
forall (m :: * -> *) a b. Monad m => (a -> m b) -> [a] -> m [b]
mapM Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines ([Element] -> StateT JATSState m [Inlines])
-> [Element] -> StateT JATSState m [Inlines]
forall a b. (a -> b) -> a -> b
$ (Element -> Bool) -> Element -> [Element]
filterChildren (Text -> Element -> Bool
named Text
"aff") Element
x
  Bool -> JATS m () -> JATS m ()
forall (f :: * -> *). Applicative f => Bool -> f () -> f ()
unless ([Inlines] -> Bool
forall a. [a] -> Bool
forall (t :: * -> *) a. Foldable t => t a -> Bool
null [Inlines]
affs) (JATS m () -> JATS m ()) -> JATS m () -> JATS m ()
forall a b. (a -> b) -> a -> b
$ Text -> [Inlines] -> JATS m ()
forall (m :: * -> *) a.
(PandocMonad m, ToMetaValue a) =>
Text -> a -> JATS m ()
addMeta Text
"institute" [Inlines]
affs

getAbstract :: PandocMonad m => Element -> JATS m ()
getAbstract :: forall (m :: * -> *). PandocMonad m => Element -> JATS m ()
getAbstract Element
e =
  case (Element -> Bool) -> Element -> Maybe Element
filterElement (Text -> Element -> Bool
named Text
"abstract") Element
e of
    Just Element
s -> do
      Blocks
blks <- Element -> JATS m Blocks
forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks Element
s
      Text -> Blocks -> JATS m ()
forall (m :: * -> *) a.
(PandocMonad m, ToMetaValue a) =>
Text -> a -> JATS m ()
addMeta Text
"abstract" Blocks
blks
    Maybe Element
Nothing -> () -> JATS m ()
forall a. a -> StateT JATSState m a
forall (f :: * -> *) a. Applicative f => a -> f a
pure ()

getPubDate :: PandocMonad m => Element -> JATS m ()
getPubDate :: forall (m :: * -> *). PandocMonad m => Element -> JATS m ()
getPubDate Element
e =
  case (Element -> Bool) -> Element -> Maybe Element
filterElement (Text -> Element -> Bool
named Text
"pub-date") Element
e of
    Just Element
d -> do
      case Text -> Element -> Maybe Text
maybeAttrValue Text
"iso-8601-date" Element
d of
        Just Text
isod -> Text -> Inlines -> JATS m ()
forall (m :: * -> *) a.
(PandocMonad m, ToMetaValue a) =>
Text -> a -> JATS m ()
addMeta Text
"date" (Text -> Inlines
text Text
isod)
        Maybe Text
Nothing -> do
          let yr :: Maybe Text
yr = Element -> Text
strContent (Element -> Text) -> Maybe Element -> Maybe Text
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> (Element -> Bool) -> Element -> Maybe Element
filterElement (Text -> Element -> Bool
named Text
"year") Element
d
          let mon :: Maybe Text
mon = Element -> Text
strContent (Element -> Text) -> Maybe Element -> Maybe Text
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> (Element -> Bool) -> Element -> Maybe Element
filterElement (Text -> Element -> Bool
named Text
"month") Element
d
          let day :: Maybe Text
day = Element -> Text
strContent (Element -> Text) -> Maybe Element -> Maybe Text
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> (Element -> Bool) -> Element -> Maybe Element
filterElement (Text -> Element -> Bool
named Text
"day") Element
d
          Text -> Inlines -> JATS m ()
forall (m :: * -> *) a.
(PandocMonad m, ToMetaValue a) =>
Text -> a -> JATS m ()
addMeta Text
"date" (Inlines -> JATS m ()) -> Inlines -> JATS m ()
forall a b. (a -> b) -> a -> b
$ Text -> Inlines
text (Text -> Inlines) -> Text -> Inlines
forall a b. (a -> b) -> a -> b
$ Text -> [Text] -> Text
T.intercalate Text
"-" ([Text] -> Text) -> [Text] -> Text
forall a b. (a -> b) -> a -> b
$ [Maybe Text] -> [Text]
forall a. [Maybe a] -> [a]
catMaybes [Maybe Text
yr, Maybe Text
mon, Maybe Text
day]
    Maybe Element
Nothing -> () -> JATS m ()
forall a. a -> StateT JATSState m a
forall (f :: * -> *) a. Applicative f => a -> f a
pure ()

getContrib :: PandocMonad m => Element -> JATS m Inlines
getContrib :: forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getContrib Element
x = do
  Inlines
given <- JATS m Inlines
-> (Element -> JATS m Inlines) -> Maybe Element -> JATS m Inlines
forall b a. b -> (a -> b) -> Maybe a -> b
maybe (Inlines -> JATS m Inlines
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return Inlines
forall a. Monoid a => a
mempty) Element -> JATS m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines
            (Maybe Element -> JATS m Inlines)
-> Maybe Element -> JATS m Inlines
forall a b. (a -> b) -> a -> b
$ (Element -> Bool) -> Element -> Maybe Element
filterElement (Text -> Element -> Bool
named Text
"given-names") Element
x
  Inlines
family <- JATS m Inlines
-> (Element -> JATS m Inlines) -> Maybe Element -> JATS m Inlines
forall b a. b -> (a -> b) -> Maybe a -> b
maybe (Inlines -> JATS m Inlines
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return Inlines
forall a. Monoid a => a
mempty) Element -> JATS m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines
            (Maybe Element -> JATS m Inlines)
-> Maybe Element -> JATS m Inlines
forall a b. (a -> b) -> a -> b
$ (Element -> Bool) -> Element -> Maybe Element
filterElement (Text -> Element -> Bool
named Text
"surname") Element
x
  if Inlines
given Inlines -> Inlines -> Bool
forall a. Eq a => a -> a -> Bool
== Inlines
forall a. Monoid a => a
mempty Bool -> Bool -> Bool
&& Inlines
family Inlines -> Inlines -> Bool
forall a. Eq a => a -> a -> Bool
== Inlines
forall a. Monoid a => a
mempty
     then Inlines -> JATS m Inlines
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return Inlines
forall a. Monoid a => a
mempty
     else if Inlines
given Inlines -> Inlines -> Bool
forall a. Eq a => a -> a -> Bool
== Inlines
forall a. Monoid a => a
mempty Bool -> Bool -> Bool
|| Inlines
family Inlines -> Inlines -> Bool
forall a. Eq a => a -> a -> Bool
== Inlines
forall a. Monoid a => a
mempty
          then Inlines -> JATS m Inlines
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return (Inlines -> JATS m Inlines) -> Inlines -> JATS m Inlines
forall a b. (a -> b) -> a -> b
$ Inlines
given Inlines -> Inlines -> Inlines
forall a. Semigroup a => a -> a -> a
<> Inlines
family
          else Inlines -> JATS m Inlines
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return (Inlines -> JATS m Inlines) -> Inlines -> JATS m Inlines
forall a b. (a -> b) -> a -> b
$ Inlines
given Inlines -> Inlines -> Inlines
forall a. Semigroup a => a -> a -> a
<> Inlines
space Inlines -> Inlines -> Inlines
forall a. Semigroup a => a -> a -> a
<> Inlines
family

parseRefList :: PandocMonad m => Element -> JATS m Blocks
parseRefList :: forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
parseRefList Element
e = do
  [Map Text MetaValue]
refs <- (Element -> StateT JATSState m (Map Text MetaValue))
-> [Element] -> StateT JATSState m [Map Text MetaValue]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
forall (m :: * -> *) a b. Monad m => (a -> m b) -> [a] -> m [b]
mapM Element -> StateT JATSState m (Map Text MetaValue)
forall (m :: * -> *).
PandocMonad m =>
Element -> JATS m (Map Text MetaValue)
parseRef ([Element] -> StateT JATSState m [Map Text MetaValue])
-> [Element] -> StateT JATSState m [Map Text MetaValue]
forall a b. (a -> b) -> a -> b
$ (Element -> Bool) -> Element -> [Element]
filterChildren (Text -> Element -> Bool
named Text
"ref") Element
e
  Text -> [Map Text MetaValue] -> JATS m ()
forall (m :: * -> *) a.
(PandocMonad m, ToMetaValue a) =>
Text -> a -> JATS m ()
addMeta Text
"references" [Map Text MetaValue]
refs
  Blocks -> JATS m Blocks
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return Blocks
forall a. Monoid a => a
mempty

parseRef :: PandocMonad m
         => Element -> JATS m (Map.Map Text MetaValue)
parseRef :: forall (m :: * -> *).
PandocMonad m =>
Element -> JATS m (Map Text MetaValue)
parseRef Element
e = do
  let combineWithDash :: Inlines -> Inlines -> Inlines
combineWithDash Inlines
x Inlines
y = Inlines
x Inlines -> Inlines -> Inlines
forall a. Semigroup a => a -> a -> a
<> Text -> Inlines
text Text
"-" Inlines -> Inlines -> Inlines
forall a. Semigroup a => a -> a -> a
<> Inlines
y
  let getName :: Element -> StateT JATSState m MetaValue
getName Element
nm = do
        Inlines
given <- StateT JATSState m Inlines
-> (Element -> StateT JATSState m Inlines)
-> Maybe Element
-> StateT JATSState m Inlines
forall b a. b -> (a -> b) -> Maybe a -> b
maybe (Inlines -> StateT JATSState m Inlines
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return Inlines
forall a. Monoid a => a
mempty) Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines
                  (Maybe Element -> StateT JATSState m Inlines)
-> Maybe Element -> StateT JATSState m Inlines
forall a b. (a -> b) -> a -> b
$ (Element -> Bool) -> Element -> Maybe Element
filterChild (Text -> Element -> Bool
named Text
"given-names") Element
nm
        Inlines
family <- StateT JATSState m Inlines
-> (Element -> StateT JATSState m Inlines)
-> Maybe Element
-> StateT JATSState m Inlines
forall b a. b -> (a -> b) -> Maybe a -> b
maybe (Inlines -> StateT JATSState m Inlines
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return Inlines
forall a. Monoid a => a
mempty) Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines
                  (Maybe Element -> StateT JATSState m Inlines)
-> Maybe Element -> StateT JATSState m Inlines
forall a b. (a -> b) -> a -> b
$ (Element -> Bool) -> Element -> Maybe Element
filterChild (Text -> Element -> Bool
named Text
"surname") Element
nm
        MetaValue -> StateT JATSState m MetaValue
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return (MetaValue -> StateT JATSState m MetaValue)
-> MetaValue -> StateT JATSState m MetaValue
forall a b. (a -> b) -> a -> b
$ Map Text Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue (Map Text Inlines -> MetaValue) -> Map Text Inlines -> MetaValue
forall a b. (a -> b) -> a -> b
$ [(Text, Inlines)] -> Map Text Inlines
forall k a. Ord k => [(k, a)] -> Map k a
Map.fromList [
            (Text
"given" :: Text, Inlines
given)
          , (Text
"family", Inlines
family)
          ]
  let refElement :: PandocMonad m
                 => Element -> Element -> JATS m (Maybe (Text, MetaValue))
      refElement :: forall (m :: * -> *).
PandocMonad m =>
Element -> Element -> JATS m (Maybe (Text, MetaValue))
refElement Element
c Element
el =
        case QName -> Text
qName (Element -> QName
elName Element
el) of
          Text
"article-title" -> (Text, MetaValue) -> Maybe (Text, MetaValue)
forall a. a -> Maybe a
Just ((Text, MetaValue) -> Maybe (Text, MetaValue))
-> (Inlines -> (Text, MetaValue))
-> Inlines
-> Maybe (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"title",) (MetaValue -> (Text, MetaValue))
-> (Inlines -> MetaValue) -> Inlines -> (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue (Inlines -> Maybe (Text, MetaValue))
-> StateT JATSState m Inlines -> JATS m (Maybe (Text, MetaValue))
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el
          Text
"source" ->
            case (Element -> Bool) -> Element -> Maybe Element
filterChild (Text -> Element -> Bool
named Text
"article-title") Element
c of
              Just Element
_ -> (Text, MetaValue) -> Maybe (Text, MetaValue)
forall a. a -> Maybe a
Just ((Text, MetaValue) -> Maybe (Text, MetaValue))
-> (Inlines -> (Text, MetaValue))
-> Inlines
-> Maybe (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"container-title",) (MetaValue -> (Text, MetaValue))
-> (Inlines -> MetaValue) -> Inlines -> (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue (Inlines -> Maybe (Text, MetaValue))
-> StateT JATSState m Inlines -> JATS m (Maybe (Text, MetaValue))
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el
              Maybe Element
Nothing -> (Text, MetaValue) -> Maybe (Text, MetaValue)
forall a. a -> Maybe a
Just ((Text, MetaValue) -> Maybe (Text, MetaValue))
-> (Inlines -> (Text, MetaValue))
-> Inlines
-> Maybe (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"title",) (MetaValue -> (Text, MetaValue))
-> (Inlines -> MetaValue) -> Inlines -> (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue (Inlines -> Maybe (Text, MetaValue))
-> StateT JATSState m Inlines -> JATS m (Maybe (Text, MetaValue))
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el
          Text
"label" -> (Text, MetaValue) -> Maybe (Text, MetaValue)
forall a. a -> Maybe a
Just ((Text, MetaValue) -> Maybe (Text, MetaValue))
-> (Inlines -> (Text, MetaValue))
-> Inlines
-> Maybe (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"citation-label",) (MetaValue -> (Text, MetaValue))
-> (Inlines -> MetaValue) -> Inlines -> (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue (Inlines -> Maybe (Text, MetaValue))
-> StateT JATSState m Inlines -> JATS m (Maybe (Text, MetaValue))
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el
          Text
"year" -> case (Element -> Bool) -> Element -> Maybe Element
filterChild (Text -> Element -> Bool
named Text
"month") Element
c of
                      Just Element
m -> (Text, MetaValue) -> Maybe (Text, MetaValue)
forall a. a -> Maybe a
Just ((Text, MetaValue) -> Maybe (Text, MetaValue))
-> (Inlines -> (Text, MetaValue))
-> Inlines
-> Maybe (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"issued",) (MetaValue -> (Text, MetaValue))
-> (Inlines -> MetaValue) -> Inlines -> (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue (Inlines -> Maybe (Text, MetaValue))
-> StateT JATSState m Inlines -> JATS m (Maybe (Text, MetaValue))
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$>
                                 (Inlines -> Inlines -> Inlines
combineWithDash
                                    (Inlines -> Inlines -> Inlines)
-> StateT JATSState m Inlines
-> StateT JATSState m (Inlines -> Inlines)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el StateT JATSState m (Inlines -> Inlines)
-> StateT JATSState m Inlines -> StateT JATSState m Inlines
forall a b.
StateT JATSState m (a -> b)
-> StateT JATSState m a -> StateT JATSState m b
forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
m)
                      Maybe Element
Nothing -> (Text, MetaValue) -> Maybe (Text, MetaValue)
forall a. a -> Maybe a
Just ((Text, MetaValue) -> Maybe (Text, MetaValue))
-> (Inlines -> (Text, MetaValue))
-> Inlines
-> Maybe (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"issued",) (MetaValue -> (Text, MetaValue))
-> (Inlines -> MetaValue) -> Inlines -> (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue (Inlines -> Maybe (Text, MetaValue))
-> StateT JATSState m Inlines -> JATS m (Maybe (Text, MetaValue))
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el
          Text
"volume" -> (Text, MetaValue) -> Maybe (Text, MetaValue)
forall a. a -> Maybe a
Just ((Text, MetaValue) -> Maybe (Text, MetaValue))
-> (Inlines -> (Text, MetaValue))
-> Inlines
-> Maybe (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"volume",) (MetaValue -> (Text, MetaValue))
-> (Inlines -> MetaValue) -> Inlines -> (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue (Inlines -> Maybe (Text, MetaValue))
-> StateT JATSState m Inlines -> JATS m (Maybe (Text, MetaValue))
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el
          Text
"issue" -> (Text, MetaValue) -> Maybe (Text, MetaValue)
forall a. a -> Maybe a
Just ((Text, MetaValue) -> Maybe (Text, MetaValue))
-> (Inlines -> (Text, MetaValue))
-> Inlines
-> Maybe (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"issue",) (MetaValue -> (Text, MetaValue))
-> (Inlines -> MetaValue) -> Inlines -> (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue (Inlines -> Maybe (Text, MetaValue))
-> StateT JATSState m Inlines -> JATS m (Maybe (Text, MetaValue))
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el
          Text
"isbn" -> (Text, MetaValue) -> Maybe (Text, MetaValue)
forall a. a -> Maybe a
Just ((Text, MetaValue) -> Maybe (Text, MetaValue))
-> (Inlines -> (Text, MetaValue))
-> Inlines
-> Maybe (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"ISBN",) (MetaValue -> (Text, MetaValue))
-> (Inlines -> MetaValue) -> Inlines -> (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue (Inlines -> Maybe (Text, MetaValue))
-> StateT JATSState m Inlines -> JATS m (Maybe (Text, MetaValue))
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el
          Text
"issn" -> (Text, MetaValue) -> Maybe (Text, MetaValue)
forall a. a -> Maybe a
Just ((Text, MetaValue) -> Maybe (Text, MetaValue))
-> (Inlines -> (Text, MetaValue))
-> Inlines
-> Maybe (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"ISSN",) (MetaValue -> (Text, MetaValue))
-> (Inlines -> MetaValue) -> Inlines -> (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue (Inlines -> Maybe (Text, MetaValue))
-> StateT JATSState m Inlines -> JATS m (Maybe (Text, MetaValue))
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el
          Text
"uri" -> (Text, MetaValue) -> Maybe (Text, MetaValue)
forall a. a -> Maybe a
Just ((Text, MetaValue) -> Maybe (Text, MetaValue))
-> (Inlines -> (Text, MetaValue))
-> Inlines
-> Maybe (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"url",) (MetaValue -> (Text, MetaValue))
-> (Inlines -> MetaValue) -> Inlines -> (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue (Inlines -> Maybe (Text, MetaValue))
-> StateT JATSState m Inlines -> JATS m (Maybe (Text, MetaValue))
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el
          Text
"fpage" ->
            case (Element -> Bool) -> Element -> Maybe Element
filterChild (Text -> Element -> Bool
named Text
"lpage") Element
c of
              Just Element
lp -> (Text, MetaValue) -> Maybe (Text, MetaValue)
forall a. a -> Maybe a
Just ((Text, MetaValue) -> Maybe (Text, MetaValue))
-> (Inlines -> (Text, MetaValue))
-> Inlines
-> Maybe (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"page",) (MetaValue -> (Text, MetaValue))
-> (Inlines -> MetaValue) -> Inlines -> (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue (Inlines -> Maybe (Text, MetaValue))
-> StateT JATSState m Inlines -> JATS m (Maybe (Text, MetaValue))
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$>
                          (Inlines -> Inlines -> Inlines
combineWithDash (Inlines -> Inlines -> Inlines)
-> StateT JATSState m Inlines
-> StateT JATSState m (Inlines -> Inlines)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el StateT JATSState m (Inlines -> Inlines)
-> StateT JATSState m Inlines -> StateT JATSState m Inlines
forall a b.
StateT JATSState m (a -> b)
-> StateT JATSState m a -> StateT JATSState m b
forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
lp)
              Maybe Element
Nothing -> (Text, MetaValue) -> Maybe (Text, MetaValue)
forall a. a -> Maybe a
Just ((Text, MetaValue) -> Maybe (Text, MetaValue))
-> (Inlines -> (Text, MetaValue))
-> Inlines
-> Maybe (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"page-first",) (MetaValue -> (Text, MetaValue))
-> (Inlines -> MetaValue) -> Inlines -> (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue (Inlines -> Maybe (Text, MetaValue))
-> StateT JATSState m Inlines -> JATS m (Maybe (Text, MetaValue))
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el
          Text
"publisher-name" -> (Text, MetaValue) -> Maybe (Text, MetaValue)
forall a. a -> Maybe a
Just ((Text, MetaValue) -> Maybe (Text, MetaValue))
-> (Inlines -> (Text, MetaValue))
-> Inlines
-> Maybe (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"publisher",) (MetaValue -> (Text, MetaValue))
-> (Inlines -> MetaValue) -> Inlines -> (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue (Inlines -> Maybe (Text, MetaValue))
-> StateT JATSState m Inlines -> JATS m (Maybe (Text, MetaValue))
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el
          Text
"publisher-loc" -> (Text, MetaValue) -> Maybe (Text, MetaValue)
forall a. a -> Maybe a
Just ((Text, MetaValue) -> Maybe (Text, MetaValue))
-> (Inlines -> (Text, MetaValue))
-> Inlines
-> Maybe (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"publisher-place",) (MetaValue -> (Text, MetaValue))
-> (Inlines -> MetaValue) -> Inlines -> (Text, MetaValue)
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue
                                (Inlines -> Maybe (Text, MetaValue))
-> StateT JATSState m Inlines -> JATS m (Maybe (Text, MetaValue))
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el
          Text
"edition" -> Maybe (Text, MetaValue) -> JATS m (Maybe (Text, MetaValue))
forall a. a -> StateT JATSState m a
forall (f :: * -> *) a. Applicative f => a -> f a
pure (Maybe (Text, MetaValue) -> JATS m (Maybe (Text, MetaValue)))
-> Maybe (Text, MetaValue) -> JATS m (Maybe (Text, MetaValue))
forall a b. (a -> b) -> a -> b
$ (Text, MetaValue) -> Maybe (Text, MetaValue)
forall a. a -> Maybe a
Just (Text
"edition",
                               Text -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue (Text -> MetaValue) -> (Text -> Text) -> Text -> MetaValue
forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Char -> Bool) -> Text -> Text
T.filter Char -> Bool
isDigit (Text -> MetaValue) -> Text -> MetaValue
forall a b. (a -> b) -> a -> b
$ Element -> Text
strContent Element
el)
          Text
"person-group" -> do [MetaValue]
names <- (Element -> StateT JATSState m MetaValue)
-> [Element] -> StateT JATSState m [MetaValue]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
forall (m :: * -> *) a b. Monad m => (a -> m b) -> [a] -> m [b]
mapM Element -> StateT JATSState m MetaValue
forall {m :: * -> *}.
PandocMonad m =>
Element -> StateT JATSState m MetaValue
getName
                                            ((Element -> Bool) -> Element -> [Element]
filterChildren (Text -> Element -> Bool
named Text
"name") Element
el)
                               Maybe (Text, MetaValue) -> JATS m (Maybe (Text, MetaValue))
forall a. a -> StateT JATSState m a
forall (f :: * -> *) a. Applicative f => a -> f a
pure (Maybe (Text, MetaValue) -> JATS m (Maybe (Text, MetaValue)))
-> Maybe (Text, MetaValue) -> JATS m (Maybe (Text, MetaValue))
forall a b. (a -> b) -> a -> b
$ (Text, MetaValue) -> Maybe (Text, MetaValue)
forall a. a -> Maybe a
Just (Text -> Element -> Text
attrValue Text
"person-group-type" Element
el,
                                            [MetaValue] -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue [MetaValue]
names)
          Text
"pub-id" -> case Text -> Element -> Text
attrValue Text
"pub-id-type" Element
el of
                         Text
"doi"  -> Maybe (Text, MetaValue) -> JATS m (Maybe (Text, MetaValue))
forall a. a -> StateT JATSState m a
forall (f :: * -> *) a. Applicative f => a -> f a
pure (Maybe (Text, MetaValue) -> JATS m (Maybe (Text, MetaValue)))
-> Maybe (Text, MetaValue) -> JATS m (Maybe (Text, MetaValue))
forall a b. (a -> b) -> a -> b
$ (Text, MetaValue) -> Maybe (Text, MetaValue)
forall a. a -> Maybe a
Just (Text
"DOI",  Text -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue (Text -> MetaValue) -> Text -> MetaValue
forall a b. (a -> b) -> a -> b
$ Element -> Text
strContent Element
el)
                         Text
"pmid" -> Maybe (Text, MetaValue) -> JATS m (Maybe (Text, MetaValue))
forall a. a -> StateT JATSState m a
forall (f :: * -> *) a. Applicative f => a -> f a
pure (Maybe (Text, MetaValue) -> JATS m (Maybe (Text, MetaValue)))
-> Maybe (Text, MetaValue) -> JATS m (Maybe (Text, MetaValue))
forall a b. (a -> b) -> a -> b
$ (Text, MetaValue) -> Maybe (Text, MetaValue)
forall a. a -> Maybe a
Just (Text
"PMID", Text -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue (Text -> MetaValue) -> Text -> MetaValue
forall a b. (a -> b) -> a -> b
$ Element -> Text
strContent Element
el)
                         Text
_      -> Maybe (Text, MetaValue) -> JATS m (Maybe (Text, MetaValue))
forall a. a -> StateT JATSState m a
forall (f :: * -> *) a. Applicative f => a -> f a
pure Maybe (Text, MetaValue)
forall a. Maybe a
Nothing
          Text
"object-id" -> case Text -> Element -> Text
attrValue Text
"pub-id-type" Element
el of
                         Text
"doi"  -> Maybe (Text, MetaValue) -> JATS m (Maybe (Text, MetaValue))
forall a. a -> StateT JATSState m a
forall (f :: * -> *) a. Applicative f => a -> f a
pure (Maybe (Text, MetaValue) -> JATS m (Maybe (Text, MetaValue)))
-> Maybe (Text, MetaValue) -> JATS m (Maybe (Text, MetaValue))
forall a b. (a -> b) -> a -> b
$ (Text, MetaValue) -> Maybe (Text, MetaValue)
forall a. a -> Maybe a
Just (Text
"DOI",  Text -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue (Text -> MetaValue) -> Text -> MetaValue
forall a b. (a -> b) -> a -> b
$ Element -> Text
strContent Element
el)
                         Text
"pmid" -> Maybe (Text, MetaValue) -> JATS m (Maybe (Text, MetaValue))
forall a. a -> StateT JATSState m a
forall (f :: * -> *) a. Applicative f => a -> f a
pure (Maybe (Text, MetaValue) -> JATS m (Maybe (Text, MetaValue)))
-> Maybe (Text, MetaValue) -> JATS m (Maybe (Text, MetaValue))
forall a b. (a -> b) -> a -> b
$ (Text, MetaValue) -> Maybe (Text, MetaValue)
forall a. a -> Maybe a
Just (Text
"PMID", Text -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue (Text -> MetaValue) -> Text -> MetaValue
forall a b. (a -> b) -> a -> b
$ Element -> Text
strContent Element
el)
                         Text
_      -> Maybe (Text, MetaValue) -> JATS m (Maybe (Text, MetaValue))
forall a. a -> StateT JATSState m a
forall (f :: * -> *) a. Applicative f => a -> f a
pure Maybe (Text, MetaValue)
forall a. Maybe a
Nothing


          Text
_ -> Maybe (Text, MetaValue) -> JATS m (Maybe (Text, MetaValue))
forall a. a -> StateT JATSState m a
forall (f :: * -> *) a. Applicative f => a -> f a
pure Maybe (Text, MetaValue)
forall a. Maybe a
Nothing
  [(Text, MetaValue)]
refVariables <-
    case (Element -> Bool) -> Element -> Maybe Element
filterChild (Text -> Element -> Bool
named Text
"element-citation") Element
e of
      Just Element
c -> ((Text
"type", Text -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue (Text -> MetaValue) -> Text -> MetaValue
forall a b. (a -> b) -> a -> b
$ case Text -> Element -> Text
attrValue Text
"publication-type" Element
c of
                            Text
"journal" -> Text
"article-journal"
                            Text
x -> Text
x) (Text, MetaValue) -> [(Text, MetaValue)] -> [(Text, MetaValue)]
forall a. a -> [a] -> [a]
:) ([(Text, MetaValue)] -> [(Text, MetaValue)])
-> ([Maybe (Text, MetaValue)] -> [(Text, MetaValue)])
-> [Maybe (Text, MetaValue)]
-> [(Text, MetaValue)]
forall b c a. (b -> c) -> (a -> b) -> a -> c
.
                  [Maybe (Text, MetaValue)] -> [(Text, MetaValue)]
forall a. [Maybe a] -> [a]
catMaybes ([Maybe (Text, MetaValue)] -> [(Text, MetaValue)])
-> StateT JATSState m [Maybe (Text, MetaValue)]
-> StateT JATSState m [(Text, MetaValue)]
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> (Element -> StateT JATSState m (Maybe (Text, MetaValue)))
-> [Element] -> StateT JATSState m [Maybe (Text, MetaValue)]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
forall (m :: * -> *) a b. Monad m => (a -> m b) -> [a] -> m [b]
mapM (Element -> Element -> StateT JATSState m (Maybe (Text, MetaValue))
forall (m :: * -> *).
PandocMonad m =>
Element -> Element -> JATS m (Maybe (Text, MetaValue))
refElement Element
c) (Element -> [Element]
elChildren Element
c)
      Maybe Element
Nothing -> [(Text, MetaValue)] -> StateT JATSState m [(Text, MetaValue)]
forall a. a -> StateT JATSState m a
forall (f :: * -> *) a. Applicative f => a -> f a
pure []   -- TODO handle mixed-citation
  -- allows round-tripping, since JATS writer puts ref- in front of citation ids:
  let stripPref :: Text -> Text
stripPref Text
t = Text -> Maybe Text -> Text
forall a. a -> Maybe a -> a
fromMaybe Text
t (Maybe Text -> Text) -> Maybe Text -> Text
forall a b. (a -> b) -> a -> b
$ Text -> Text -> Maybe Text
T.stripPrefix Text
"ref-" Text
t
  Map Text MetaValue -> JATS m (Map Text MetaValue)
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return (Map Text MetaValue -> JATS m (Map Text MetaValue))
-> Map Text MetaValue -> JATS m (Map Text MetaValue)
forall a b. (a -> b) -> a -> b
$ [(Text, MetaValue)] -> Map Text MetaValue
forall k a. Ord k => [(k, a)] -> Map k a
Map.fromList ((Text
"id", Text -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue (Text -> MetaValue) -> Text -> MetaValue
forall a b. (a -> b) -> a -> b
$ Text -> Text
stripPref (Text -> Text) -> Text -> Text
forall a b. (a -> b) -> a -> b
$ Text -> Element -> Text
attrValue Text
"id" Element
e)
                        (Text, MetaValue) -> [(Text, MetaValue)] -> [(Text, MetaValue)]
forall a. a -> [a] -> [a]
: [(Text, MetaValue)]
refVariables)

textContent :: Element -> Text
textContent :: Element -> Text
textContent = Element -> Text
strContent

strContentRecursive :: Element -> Text
strContentRecursive :: Element -> Text
strContentRecursive = Element -> Text
strContent (Element -> Text) -> (Element -> Element) -> Element -> Text
forall b c a. (b -> c) -> (a -> b) -> a -> c
.
  (\Element
e' -> Element
e'{ elContent :: [Content]
elContent = (Content -> Content) -> [Content] -> [Content]
forall a b. (a -> b) -> [a] -> [b]
map Content -> Content
elementToStr ([Content] -> [Content]) -> [Content] -> [Content]
forall a b. (a -> b) -> a -> b
$ Element -> [Content]
elContent Element
e' })

elementToStr :: Content -> Content
elementToStr :: Content -> Content
elementToStr (Elem Element
e') = CData -> Content
Text (CData -> Content) -> CData -> Content
forall a b. (a -> b) -> a -> b
$ CDataKind -> Text -> Maybe Line -> CData
CData CDataKind
CDataText (Element -> Text
strContentRecursive Element
e') Maybe Line
forall a. Maybe a
Nothing
elementToStr Content
x = Content
x

parseInline :: PandocMonad m => Content -> JATS m Inlines
parseInline :: forall (m :: * -> *). PandocMonad m => Content -> JATS m Inlines
parseInline (Text (CData CDataKind
_ Text
s Maybe Line
_)) = Inlines -> StateT JATSState m Inlines
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return (Inlines -> StateT JATSState m Inlines)
-> Inlines -> StateT JATSState m Inlines
forall a b. (a -> b) -> a -> b
$ Text -> Inlines
text Text
s
parseInline (CRef Text
ref) = Inlines -> StateT JATSState m Inlines
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return (Inlines -> StateT JATSState m Inlines)
-> Inlines -> StateT JATSState m Inlines
forall a b. (a -> b) -> a -> b
$ Inlines -> (Text -> Inlines) -> Maybe Text -> Inlines
forall b a. b -> (a -> b) -> Maybe a -> b
maybe (Text -> Inlines
text (Text -> Inlines) -> Text -> Inlines
forall a b. (a -> b) -> a -> b
$ Text -> Text
T.toUpper Text
ref) Text -> Inlines
text
                                (Maybe Text -> Inlines) -> Maybe Text -> Inlines
forall a b. (a -> b) -> a -> b
$ Text -> Maybe Text
lookupEntity Text
ref
parseInline (Elem Element
e) =
  case QName -> Text
qName (Element -> QName
elName Element
e) of
        Text
"italic" -> (Inlines -> Inlines) -> StateT JATSState m Inlines
forall {m :: * -> *}.
PandocMonad m =>
(Inlines -> Inlines) -> StateT JATSState m Inlines
innerInlines Inlines -> Inlines
emph
        Text
"bold" -> (Inlines -> Inlines) -> StateT JATSState m Inlines
forall {m :: * -> *}.
PandocMonad m =>
(Inlines -> Inlines) -> StateT JATSState m Inlines
innerInlines Inlines -> Inlines
strong
        Text
"strike" -> (Inlines -> Inlines) -> StateT JATSState m Inlines
forall {m :: * -> *}.
PandocMonad m =>
(Inlines -> Inlines) -> StateT JATSState m Inlines
innerInlines Inlines -> Inlines
strikeout
        Text
"sub" -> (Inlines -> Inlines) -> StateT JATSState m Inlines
forall {m :: * -> *}.
PandocMonad m =>
(Inlines -> Inlines) -> StateT JATSState m Inlines
innerInlines Inlines -> Inlines
subscript
        Text
"sup" -> (Inlines -> Inlines) -> StateT JATSState m Inlines
forall {m :: * -> *}.
PandocMonad m =>
(Inlines -> Inlines) -> StateT JATSState m Inlines
innerInlines Inlines -> Inlines
superscript
        Text
"underline" -> (Inlines -> Inlines) -> StateT JATSState m Inlines
forall {m :: * -> *}.
PandocMonad m =>
(Inlines -> Inlines) -> StateT JATSState m Inlines
innerInlines Inlines -> Inlines
underline
        Text
"break" -> Inlines -> StateT JATSState m Inlines
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return Inlines
linebreak
        Text
"sc" -> (Inlines -> Inlines) -> StateT JATSState m Inlines
forall {m :: * -> *}.
PandocMonad m =>
(Inlines -> Inlines) -> StateT JATSState m Inlines
innerInlines Inlines -> Inlines
smallcaps

        Text
"code" -> StateT JATSState m Inlines
codeWithLang
        Text
"monospace" -> StateT JATSState m Inlines
codeWithLang

        Text
"inline-graphic" -> Maybe (Inlines, Text) -> Element -> StateT JATSState m Inlines
forall (m :: * -> *).
PandocMonad m =>
Maybe (Inlines, Text) -> Element -> JATS m Inlines
getGraphic Maybe (Inlines, Text)
forall a. Maybe a
Nothing Element
e
        Text
"disp-quote" -> do
            QuoteType
qt <- (JATSState -> QuoteType) -> StateT JATSState m QuoteType
forall s (m :: * -> *) a. MonadState s m => (s -> a) -> m a
gets JATSState -> QuoteType
jatsQuoteType
            let qt' :: QuoteType
qt' = if QuoteType
qt QuoteType -> QuoteType -> Bool
forall a. Eq a => a -> a -> Bool
== QuoteType
SingleQuote then QuoteType
DoubleQuote else QuoteType
SingleQuote
            (JATSState -> JATSState) -> StateT JATSState m ()
forall s (m :: * -> *). MonadState s m => (s -> s) -> m ()
modify ((JATSState -> JATSState) -> StateT JATSState m ())
-> (JATSState -> JATSState) -> StateT JATSState m ()
forall a b. (a -> b) -> a -> b
$ \JATSState
st -> JATSState
st{ jatsQuoteType :: QuoteType
jatsQuoteType = QuoteType
qt' }
            Inlines
contents <- (Inlines -> Inlines) -> StateT JATSState m Inlines
forall {m :: * -> *}.
PandocMonad m =>
(Inlines -> Inlines) -> StateT JATSState m Inlines
innerInlines Inlines -> Inlines
forall a. a -> a
id
            (JATSState -> JATSState) -> StateT JATSState m ()
forall s (m :: * -> *). MonadState s m => (s -> s) -> m ()
modify ((JATSState -> JATSState) -> StateT JATSState m ())
-> (JATSState -> JATSState) -> StateT JATSState m ()
forall a b. (a -> b) -> a -> b
$ \JATSState
st -> JATSState
st{ jatsQuoteType :: QuoteType
jatsQuoteType = QuoteType
qt }
            Inlines -> StateT JATSState m Inlines
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return (Inlines -> StateT JATSState m Inlines)
-> Inlines -> StateT JATSState m Inlines
forall a b. (a -> b) -> a -> b
$ if QuoteType
qt QuoteType -> QuoteType -> Bool
forall a. Eq a => a -> a -> Bool
== QuoteType
SingleQuote
                        then Inlines -> Inlines
singleQuoted Inlines
contents
                        else Inlines -> Inlines
doubleQuoted Inlines
contents

        Text
"xref" -> do
            Inlines
ils <- (Inlines -> Inlines) -> StateT JATSState m Inlines
forall {m :: * -> *}.
PandocMonad m =>
(Inlines -> Inlines) -> StateT JATSState m Inlines
innerInlines Inlines -> Inlines
forall a. a -> a
id
            let rid :: Text
rid = Text -> Element -> Text
attrValue Text
"rid" Element
e
            let rids :: [Text]
rids = Text -> [Text]
T.words Text
rid
            let refType :: Maybe (Text, Text)
refType = (Text
"ref-type",) (Text -> (Text, Text)) -> Maybe Text -> Maybe (Text, Text)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Text -> Element -> Maybe Text
maybeAttrValue Text
"ref-type" Element
e
            let attr :: (Text, [a], [(Text, Text)])
attr = (Text -> Element -> Text
attrValue Text
"id" Element
e, [], Maybe (Text, Text) -> [(Text, Text)]
forall a. Maybe a -> [a]
maybeToList Maybe (Text, Text)
refType)
            Inlines -> StateT JATSState m Inlines
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return (Inlines -> StateT JATSState m Inlines)
-> Inlines -> StateT JATSState m Inlines
forall a b. (a -> b) -> a -> b
$ if Maybe (Text, Text)
refType Maybe (Text, Text) -> Maybe (Text, Text) -> Bool
forall a. Eq a => a -> a -> Bool
== (Text, Text) -> Maybe (Text, Text)
forall a. a -> Maybe a
Just (Text
"ref-type",Text
"bibr")
                        then [Citation] -> Inlines -> Inlines
cite
                             ((Text -> Citation) -> [Text] -> [Citation]
forall a b. (a -> b) -> [a] -> [b]
map (\Text
id' ->
                               let id'' :: Text
id'' = Text -> Maybe Text -> Text
forall a. a -> Maybe a -> a
fromMaybe Text
id' (Maybe Text -> Text) -> Maybe Text -> Text
forall a b. (a -> b) -> a -> b
$
                                           Text -> Text -> Maybe Text
T.stripPrefix Text
"ref-" Text
id'
                                 in Citation { citationId :: Text
citationId = Text
id''
                                             , citationPrefix :: [Inline]
citationPrefix = []
                                             , citationSuffix :: [Inline]
citationSuffix = []
                                             , citationMode :: CitationMode
citationMode = CitationMode
NormalCitation
                                             , citationNoteNum :: Int
citationNoteNum = Int
0
                                             , citationHash :: Int
citationHash = Int
0}) [Text]
rids)
                             Inlines
ils
                        else Attr -> Text -> Text -> Inlines -> Inlines
linkWith Attr
forall {a}. (Text, [a], [(Text, Text)])
attr (Text
"#" Text -> Text -> Text
forall a. Semigroup a => a -> a -> a
<> Text
rid) Text
"" Inlines
ils
        Text
"ext-link" -> do
             Inlines
ils <- (Inlines -> Inlines) -> StateT JATSState m Inlines
forall {m :: * -> *}.
PandocMonad m =>
(Inlines -> Inlines) -> StateT JATSState m Inlines
innerInlines Inlines -> Inlines
forall a. a -> a
id
             let title :: Text
title = Text -> Maybe Text -> Text
forall a. a -> Maybe a -> a
fromMaybe Text
"" (Maybe Text -> Text) -> Maybe Text -> Text
forall a b. (a -> b) -> a -> b
$ QName -> Element -> Maybe Text
findAttr (Text -> Maybe Text -> Maybe Text -> QName
QName Text
"title" (Text -> Maybe Text
forall a. a -> Maybe a
Just Text
"http://www.w3.org/1999/xlink") Maybe Text
forall a. Maybe a
Nothing) Element
e
             let href :: Text
href = case QName -> Element -> Maybe Text
findAttr (Text -> Maybe Text -> Maybe Text -> QName
QName Text
"href" (Text -> Maybe Text
forall a. a -> Maybe a
Just Text
"http://www.w3.org/1999/xlink") Maybe Text
forall a. Maybe a
Nothing) Element
e of
                               Just Text
h -> Text
h
                               Maybe Text
_      -> Text
"#" Text -> Text -> Text
forall a. Semigroup a => a -> a -> a
<> Text -> Element -> Text
attrValue Text
"rid" Element
e
             let ils' :: Inlines
ils' = if Inlines
ils Inlines -> Inlines -> Bool
forall a. Eq a => a -> a -> Bool
== Inlines
forall a. Monoid a => a
mempty then Text -> Inlines
str Text
href else Inlines
ils
             let attr :: (Text, [a], [a])
attr = (Text -> Element -> Text
attrValue Text
"id" Element
e, [], [])
             Inlines -> StateT JATSState m Inlines
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return (Inlines -> StateT JATSState m Inlines)
-> Inlines -> StateT JATSState m Inlines
forall a b. (a -> b) -> a -> b
$ Attr -> Text -> Text -> Inlines -> Inlines
linkWith Attr
forall {a} {a}. (Text, [a], [a])
attr Text
href Text
title Inlines
ils'

        Text
"disp-formula" -> (Text -> Inlines) -> StateT JATSState m Inlines
forall {m :: * -> *} {b}. (Monad m, Monoid b) => (Text -> b) -> m b
formula Text -> Inlines
displayMath
        Text
"inline-formula" -> (Text -> Inlines) -> StateT JATSState m Inlines
forall {m :: * -> *} {b}. (Monad m, Monoid b) => (Text -> b) -> m b
formula Text -> Inlines
math
        Text
"math" | QName -> Maybe Text
qURI (Element -> QName
elName Element
e) Maybe Text -> Maybe Text -> Bool
forall a. Eq a => a -> a -> Bool
== Text -> Maybe Text
forall a. a -> Maybe a
Just Text
"http://www.w3.org/1998/Math/MathML"
                   -> Inlines -> StateT JATSState m Inlines
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return (Inlines -> StateT JATSState m Inlines)
-> (Text -> Inlines) -> Text -> StateT JATSState m Inlines
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Text -> Inlines
math (Text -> StateT JATSState m Inlines)
-> Text -> StateT JATSState m Inlines
forall a b. (a -> b) -> a -> b
$ Element -> Text
mathML Element
e
        Text
"tex-math" -> Inlines -> StateT JATSState m Inlines
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return (Inlines -> StateT JATSState m Inlines)
-> (Text -> Inlines) -> Text -> StateT JATSState m Inlines
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Text -> Inlines
math (Text -> StateT JATSState m Inlines)
-> Text -> StateT JATSState m Inlines
forall a b. (a -> b) -> a -> b
$ Element -> Text
textContent Element
e

        Text
"email" -> Inlines -> StateT JATSState m Inlines
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return (Inlines -> StateT JATSState m Inlines)
-> Inlines -> StateT JATSState m Inlines
forall a b. (a -> b) -> a -> b
$ Text -> Text -> Inlines -> Inlines
link (Text
"mailto:" Text -> Text -> Text
forall a. Semigroup a => a -> a -> a
<> Element -> Text
textContent Element
e) Text
""
                          (Inlines -> Inlines) -> Inlines -> Inlines
forall a b. (a -> b) -> a -> b
$ Text -> Inlines
str (Text -> Inlines) -> Text -> Inlines
forall a b. (a -> b) -> a -> b
$ Element -> Text
textContent Element
e
        Text
"uri" -> Inlines -> StateT JATSState m Inlines
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return (Inlines -> StateT JATSState m Inlines)
-> Inlines -> StateT JATSState m Inlines
forall a b. (a -> b) -> a -> b
$ Text -> Text -> Inlines -> Inlines
link (Element -> Text
textContent Element
e) Text
"" (Inlines -> Inlines) -> Inlines -> Inlines
forall a b. (a -> b) -> a -> b
$ Text -> Inlines
str (Text -> Inlines) -> Text -> Inlines
forall a b. (a -> b) -> a -> b
$ Element -> Text
textContent Element
e
        Text
"fn" -> Blocks -> Inlines
note (Blocks -> Inlines) -> ([Blocks] -> Blocks) -> [Blocks] -> Inlines
forall b c a. (b -> c) -> (a -> b) -> a -> c
. [Blocks] -> Blocks
forall a. Monoid a => [a] -> a
mconcat ([Blocks] -> Inlines)
-> StateT JATSState m [Blocks] -> StateT JATSState m Inlines
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$>
                         (Content -> StateT JATSState m Blocks)
-> [Content] -> StateT JATSState m [Blocks]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
forall (m :: * -> *) a b. Monad m => (a -> m b) -> [a] -> m [b]
mapM Content -> StateT JATSState m Blocks
forall (m :: * -> *). PandocMonad m => Content -> JATS m Blocks
parseBlock (Element -> [Content]
elContent Element
e)
        Text
_          -> (Inlines -> Inlines) -> StateT JATSState m Inlines
forall {m :: * -> *}.
PandocMonad m =>
(Inlines -> Inlines) -> StateT JATSState m Inlines
innerInlines Inlines -> Inlines
forall a. a -> a
id
   where innerInlines :: (Inlines -> Inlines) -> StateT JATSState m Inlines
innerInlines Inlines -> Inlines
f = (Inlines -> Inlines) -> Inlines -> Inlines
extractSpaces Inlines -> Inlines
f (Inlines -> Inlines)
-> ([Inlines] -> Inlines) -> [Inlines] -> Inlines
forall b c a. (b -> c) -> (a -> b) -> a -> c
. [Inlines] -> Inlines
forall a. Monoid a => [a] -> a
mconcat ([Inlines] -> Inlines)
-> StateT JATSState m [Inlines] -> StateT JATSState m Inlines
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$>
                          (Content -> StateT JATSState m Inlines)
-> [Content] -> StateT JATSState m [Inlines]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
forall (m :: * -> *) a b. Monad m => (a -> m b) -> [a] -> m [b]
mapM Content -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Content -> JATS m Inlines
parseInline (Element -> [Content]
elContent Element
e)
         mathML :: Element -> Text
mathML Element
x =
            case Text -> Either Text [Exp]
readMathML (Text -> Either Text [Exp])
-> (Element -> Text) -> Element -> Either Text [Exp]
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Element -> Text
showElement (Element -> Either Text [Exp]) -> Element -> Either Text [Exp]
forall a b. (a -> b) -> a -> b
$ (forall a. Data a => a -> a) -> forall a. Data a => a -> a
everywhere ((QName -> QName) -> a -> a
forall a b. (Typeable a, Typeable b) => (b -> b) -> a -> a
mkT QName -> QName
removePrefix) Element
x of
                Left Text
_ -> Text
forall a. Monoid a => a
mempty
                Right [Exp]
m -> [Exp] -> Text
writeTeX [Exp]
m
         formula :: (Text -> b) -> m b
formula Text -> b
constructor = do
            let whereToLook :: Element
whereToLook = Element -> Maybe Element -> Element
forall a. a -> Maybe a -> a
fromMaybe Element
e (Maybe Element -> Element) -> Maybe Element -> Element
forall a b. (a -> b) -> a -> b
$ (Element -> Bool) -> Element -> Maybe Element
filterElement (Text -> Element -> Bool
named Text
"alternatives") Element
e
                texMaths :: [Text]
texMaths = (Element -> Text) -> [Element] -> [Text]
forall a b. (a -> b) -> [a] -> [b]
map Element -> Text
textContent ([Element] -> [Text]) -> [Element] -> [Text]
forall a b. (a -> b) -> a -> b
$
                            (Element -> Bool) -> Element -> [Element]
filterChildren (Text -> Element -> Bool
named  Text
"tex-math") Element
whereToLook
                mathMLs :: [Text]
mathMLs = (Element -> Text) -> [Element] -> [Text]
forall a b. (a -> b) -> [a] -> [b]
map Element -> Text
mathML ([Element] -> [Text]) -> [Element] -> [Text]
forall a b. (a -> b) -> a -> b
$
                            (Element -> Bool) -> Element -> [Element]
filterChildren Element -> Bool
isMathML Element
whereToLook
            b -> m b
forall a. a -> m a
forall (m :: * -> *) a. Monad m => a -> m a
return (b -> m b) -> ([Text] -> b) -> [Text] -> m b
forall b c a. (b -> c) -> (a -> b) -> a -> c
. [b] -> b
forall a. Monoid a => [a] -> a
mconcat ([b] -> b) -> ([Text] -> [b]) -> [Text] -> b
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Int -> [b] -> [b]
forall a. Int -> [a] -> [a]
take Int
1 ([b] -> [b]) -> ([Text] -> [b]) -> [Text] -> [b]
forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text -> b) -> [Text] -> [b]
forall a b. (a -> b) -> [a] -> [b]
map Text -> b
constructor ([Text] -> m b) -> [Text] -> m b
forall a b. (a -> b) -> a -> b
$ [Text]
texMaths [Text] -> [Text] -> [Text]
forall a. [a] -> [a] -> [a]
++ [Text]
mathMLs

         isMathML :: Element -> Bool
isMathML Element
x = QName -> Text
qName (Element -> QName
elName Element
x) Text -> Text -> Bool
forall a. Eq a => a -> a -> Bool
== Text
"math" Bool -> Bool -> Bool
&&
                      QName -> Maybe Text
qURI  (Element -> QName
elName Element
x) Maybe Text -> Maybe Text -> Bool
forall a. Eq a => a -> a -> Bool
==
                                      Text -> Maybe Text
forall a. a -> Maybe a
Just Text
"http://www.w3.org/1998/Math/MathML"
         removePrefix :: QName -> QName
removePrefix QName
elname = QName
elname { qPrefix :: Maybe Text
qPrefix = Maybe Text
forall a. Maybe a
Nothing }
         codeWithLang :: StateT JATSState m Inlines
codeWithLang = do
           let classes' :: [Text]
classes' = case Text -> Element -> Text
attrValue Text
"language" Element
e of
                               Text
"" -> []
                               Text
l  -> [Text
l]
           Inlines -> StateT JATSState m Inlines
forall a. a -> StateT JATSState m a
forall (m :: * -> *) a. Monad m => a -> m a
return (Inlines -> StateT JATSState m Inlines)
-> Inlines -> StateT JATSState m Inlines
forall a b. (a -> b) -> a -> b
$ Attr -> Text -> Inlines
codeWith (Text -> Element -> Text
attrValue Text
"id" Element
e,[Text]
classes',[]) (Text -> Inlines) -> Text -> Inlines
forall a b. (a -> b) -> a -> b
$ Element -> Text
strContentRecursive Element
e