{-# 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
import Data.Char (isDigit, isSpace, toUpper)
import Data.Default
import Data.Generics
import Data.List (foldl', intersperse)
import qualified Data.Map as Map
import Data.Maybe (maybeToList, fromMaybe)
import Data.Text (Text)
import qualified Data.Text as T
import Text.HTML.TagSoup.Entity (lookupEntity)
import Text.Pandoc.Builder
import Text.Pandoc.Class.PandocMonad (PandocMonad)
import Text.Pandoc.Options
import Text.Pandoc.Shared (crFilter, safeRead, extractSpaces)
import Text.TeXMath (readMathML, writeTeX)
import Text.XML.Light
import qualified Data.Set as S (fromList, member)
import Data.Set ((\\))

type JATS m = StateT JATSState m

data JATSState = JATSState{ JATSState -> Int
jatsSectionLevel :: Int
                          , JATSState -> QuoteType
jatsQuoteType    :: QuoteType
                          , JATSState -> Meta
jatsMeta         :: Meta
                          , JATSState -> Bool
jatsBook         :: Bool
                          , JATSState -> [Content]
jatsContent      :: [Content]
                          } 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
showList :: [JATSState] -> ShowS
$cshowList :: [JATSState] -> ShowS
show :: JATSState -> String
$cshow :: JATSState -> String
showsPrec :: Int -> JATSState -> ShowS
$cshowsPrec :: Int -> JATSState -> ShowS
Show

instance Default JATSState where
  def :: JATSState
def = JATSState :: Int -> QuoteType -> Meta -> Bool -> [Content] -> JATSState
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
                 , jatsContent :: [Content]
jatsContent = [] }


readJATS :: PandocMonad m => ReaderOptions -> Text -> m Pandoc
readJATS :: ReaderOptions -> Text -> m Pandoc
readJATS ReaderOptions
_ Text
inp = do
  let tree :: [Content]
tree = [Content] -> [Content]
normalizeTree ([Content] -> [Content])
-> (String -> [Content]) -> String -> [Content]
forall b c a. (b -> c) -> (a -> b) -> a -> c
. String -> [Content]
forall s. XmlSource s => s -> [Content]
parseXML
               (String -> [Content]) -> String -> [Content]
forall a b. (a -> b) -> a -> b
$ Text -> String
T.unpack (Text -> String) -> Text -> String
forall a b. (a -> b) -> a -> b
$ Text -> Text
crFilter Text
inp
  ([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)
mapM Content -> StateT JATSState m Blocks
forall (m :: * -> *). PandocMonad m => Content -> JATS m Blocks
parseBlock [Content]
tree
  Pandoc -> m Pandoc
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') (Blocks -> [Block]
forall a. Many a -> [a]
toList (Blocks -> [Block]) -> ([Blocks] -> Blocks) -> [Blocks] -> [Block]
forall b c a. (b -> c) -> (a -> b) -> a -> c
. [Blocks] -> Blocks
forall a. Monoid a => [a] -> a
mconcat ([Blocks] -> [Block]) -> [Blocks] -> [Block]
forall a b. (a -> b) -> a -> b
$ [Blocks]
bs)

-- normalize input, consolidating adjacent Text and CRef elements
normalizeTree :: [Content] -> [Content]
normalizeTree :: [Content] -> [Content]
normalizeTree = (forall a. Data a => a -> a) -> forall a. Data a => a -> a
everywhere (([Content] -> [Content]) -> a -> a
forall a b. (Typeable a, Typeable b) => (b -> b) -> a -> a
mkT [Content] -> [Content]
go)
  where go :: [Content] -> [Content]
        go :: [Content] -> [Content]
go (Text (CData CDataKind
CDataRaw String
_ Maybe Line
_):[Content]
xs) = [Content]
xs
        go (Text (CData CDataKind
CDataText String
s1 Maybe Line
z):Text (CData CDataKind
CDataText String
s2 Maybe Line
_):[Content]
xs) =
           CData -> Content
Text (CDataKind -> String -> Maybe Line -> CData
CData CDataKind
CDataText (String
s1 String -> ShowS
forall a. [a] -> [a] -> [a]
++ String
s2) Maybe Line
z)Content -> [Content] -> [Content]
forall a. a -> [a] -> [a]
:[Content]
xs
        go (Text (CData CDataKind
CDataText String
s1 Maybe Line
z):CRef String
r:[Content]
xs) =
           CData -> Content
Text (CDataKind -> String -> Maybe Line -> CData
CData CDataKind
CDataText (String
s1 String -> ShowS
forall a. [a] -> [a] -> [a]
++ ShowS
convertEntity String
r) Maybe Line
z)Content -> [Content] -> [Content]
forall a. a -> [a] -> [a]
:[Content]
xs
        go (CRef String
r:Text (CData CDataKind
CDataText String
s1 Maybe Line
z):[Content]
xs) =
             CData -> Content
Text (CDataKind -> String -> Maybe Line -> CData
CData CDataKind
CDataText (ShowS
convertEntity String
r String -> ShowS
forall a. [a] -> [a] -> [a]
++ String
s1) Maybe Line
z)Content -> [Content] -> [Content]
forall a. a -> [a] -> [a]
:[Content]
xs
        go (CRef String
r1:CRef String
r2:[Content]
xs) =
             CData -> Content
Text (CDataKind -> String -> Maybe Line -> CData
CData CDataKind
CDataText (ShowS
convertEntity String
r1 String -> ShowS
forall a. [a] -> [a] -> [a]
++ ShowS
convertEntity String
r2) Maybe Line
forall a. Maybe a
Nothing)Content -> [Content] -> [Content]
forall a. a -> [a] -> [a]
:[Content]
xs
        go [Content]
xs = [Content]
xs

convertEntity :: String -> String
convertEntity :: ShowS
convertEntity String
e = String -> Maybe String -> String
forall a. a -> Maybe a -> a
Data.Maybe.fromMaybe ((Char -> Char) -> ShowS
forall a b. (a -> b) -> [a] -> [b]
map Char -> Char
toUpper String
e) (String -> Maybe String
lookupEntity String
e)

-- convenience function to get an attribute value, defaulting to ""
attrValue :: String -> Element -> Text
attrValue :: String -> Element -> Text
attrValue String
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
. String -> Element -> Maybe Text
maybeAttrValue String
attr

maybeAttrValue :: String -> Element -> Maybe Text
maybeAttrValue :: String -> Element -> Maybe Text
maybeAttrValue String
attr Element
elt =
  String -> Text
T.pack (String -> Text) -> Maybe String -> Maybe Text
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> (QName -> Bool) -> [Attr] -> Maybe String
lookupAttrBy (\QName
x -> QName -> String
qName QName
x String -> String -> Bool
forall a. Eq a => a -> a -> Bool
== String
attr) (Element -> [Attr]
elAttribs Element
elt)

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

--

addMeta :: PandocMonad m => ToMetaValue a => Text -> a -> JATS m ()
addMeta :: Text -> a -> JATS m ()
addMeta Text
field a
val = (JATSState -> JATSState) -> JATS 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
setMeta Text
field a
val)

instance HasMeta JATSState where
  setMeta :: 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
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 -> String
qName (Element -> QName
elName Element
e) String -> Set String -> Bool
forall a. Ord a => a -> Set a -> Bool
`S.member` Set String
blocktags
  where blocktags :: Set String
blocktags = [String] -> Set String
forall a. Ord a => [a] -> Set a
S.fromList ([String]
paragraphLevel [String] -> [String] -> [String]
forall a. [a] -> [a] -> [a]
++ [String]
lists [String] -> [String] -> [String]
forall a. [a] -> [a] -> [a]
++ [String]
mathML [String] -> [String] -> [String]
forall a. [a] -> [a] -> [a]
++ [String]
other) Set String -> Set String -> Set String
forall a. Ord a => Set a -> Set a -> Set a
\\ [String] -> Set String
forall a. Ord a => [a] -> Set a
S.fromList [String]
inlinetags
        paragraphLevel :: [String]
paragraphLevel = [String
"address", String
"array", String
"boxed-text", String
"chem-struct-wrap",
            String
"code", String
"fig", String
"fig-group", String
"graphic", String
"media", String
"preformat",
            String
"supplementary-material", String
"table-wrap", String
"table-wrap-group",
            String
"alternatives", String
"disp-formula", String
"disp-formula-group"]
        lists :: [String]
lists = [String
"def-list", String
"list"]
        mathML :: [String]
mathML = [String
"tex-math", String
"mml:math"]
        other :: [String]
other = [String
"p", String
"related-article", String
"related-object", String
"ack", String
"disp-quote",
            String
"speech", String
"statement", String
"verse-group", String
"x"]
        inlinetags :: [String]
inlinetags = [String
"email", String
"ext-link", String
"uri", String
"inline-supplementary-material",
            String
"related-article", String
"related-object", String
"hr", String
"bold", String
"fixed-case",
            String
"italic", String
"monospace", String
"overline", String
"overline-start", String
"overline-end",
            String
"roman", String
"sans-serif", String
"sc", String
"strike", String
"underline", String
"underline-start",
            String
"underline-end", String
"ruby", String
"alternatives", String
"inline-graphic", String
"private-char",
            String
"chem-struct", String
"inline-formula", String
"tex-math", String
"mml:math", String
"abbrev",
            String
"milestone-end", String
"milestone-start", String
"named-content", String
"styled-content",
            String
"fn", String
"target", String
"xref", String
"sub", String
"sup", String
"x", String
"address", String
"array",
            String
"boxed-text", String
"chem-struct-wrap", String
"code", String
"fig", String
"fig-group", String
"graphic",
            String
"media", String
"preformat", String
"supplementary-material", String
"table-wrap",
            String
"table-wrap-group", String
"disp-formula", String
"disp-formula-group",
            String
"citation-alternatives", String
"element-citation", String
"mixed-citation",
            String
"nlm-citation", String
"award-id", String
"funding-source", String
"open-access",
            String
"def-list", String
"list", String
"ack", String
"disp-quote", String
"speech", String
"statement",
            String
"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 :: Maybe (Inlines, Text) -> Element -> JATS m Inlines
getGraphic Maybe (Inlines, Text)
mbfigdata Element
e = do
  let atVal :: String -> Text
atVal String
a = String -> Element -> Text
attrValue String
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
<> String -> Text
atVal String
"title", Inlines
capt')
           Maybe (Inlines, Text)
Nothing        -> (String -> Text
atVal String
"id", String -> Text
atVal String
"title",
                              Text -> Inlines
text (String -> Text
atVal String
"alt-text"))
      attr :: (Text, [Text], [a])
attr = (Text
ident, Text -> [Text]
T.words (Text -> [Text]) -> Text -> [Text]
forall a b. (a -> b) -> a -> b
$ String -> Text
atVal String
"role", [])
      imageUrl :: Text
imageUrl = String -> Text
atVal String
"href"
  Inlines -> JATS m Inlines
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 :: Element -> JATS m Blocks
getBlocks Element
e =  [Blocks] -> Blocks
forall a. Monoid a => [a] -> a
mconcat ([Blocks] -> Blocks)
-> StateT JATSState m [Blocks] -> JATS m Blocks
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$>
                 (Content -> JATS m Blocks)
-> [Content] -> StateT JATSState m [Blocks]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM Content -> JATS m Blocks
forall (m :: * -> *). PandocMonad m => Content -> JATS m Blocks
parseBlock (Element -> [Content]
elContent Element
e)


parseBlock :: PandocMonad m => Content -> JATS m Blocks
parseBlock :: Content -> JATS m Blocks
parseBlock (Text (CData CDataKind
CDataRaw String
_ Maybe Line
_)) = Blocks -> JATS m Blocks
forall (m :: * -> *) a. Monad m => a -> m a
return Blocks
forall a. Monoid a => a
mempty -- DOCTYPE
parseBlock (Text (CData CDataKind
_ String
s Maybe Line
_)) = if (Char -> Bool) -> String -> Bool
forall (t :: * -> *) a. Foldable t => (a -> Bool) -> t a -> Bool
all Char -> Bool
isSpace String
s
                                     then Blocks -> JATS m Blocks
forall (m :: * -> *) a. Monad m => a -> m a
return Blocks
forall a. Monoid a => a
mempty
                                     else Blocks -> JATS m Blocks
forall (m :: * -> *) a. Monad m => a -> m a
return (Blocks -> JATS m Blocks) -> Blocks -> JATS 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 -> Inlines) -> Text -> Inlines
forall a b. (a -> b) -> a -> b
$ String -> Text
T.pack String
s
parseBlock (CRef String
x) = Blocks -> JATS m Blocks
forall (m :: * -> *) a. Monad m => a -> m a
return (Blocks -> JATS m Blocks) -> Blocks -> JATS 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 -> Text) -> Text -> Text
forall a b. (a -> b) -> a -> b
$ String -> Text
T.pack String
x
parseBlock (Elem Element
e) =
  case QName -> String
qName (Element -> QName
elName Element
e) of
        String
"p" -> (Inlines -> Blocks) -> [Content] -> JATS m Blocks
forall (m :: * -> *).
PandocMonad m =>
(Inlines -> Blocks) -> [Content] -> StateT JATSState m Blocks
parseMixed Inlines -> Blocks
para (Element -> [Content]
elContent Element
e)
        String
"code" -> JATS m Blocks
codeBlockWithLang
        String
"preformat" -> JATS m Blocks
codeBlockWithLang
        String
"disp-quote" -> JATS m Blocks
parseBlockquote
        String
"list" -> case String -> Element -> Text
attrValue String
"list-type" Element
e of
                    Text
"bullet" -> [Blocks] -> Blocks
bulletList ([Blocks] -> Blocks)
-> StateT JATSState m [Blocks] -> JATS 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 (String -> Element -> Bool
named String
"list-item") Element
e
                                               Maybe Element -> (Element -> Maybe Element) -> Maybe Element
forall (m :: * -> *) a b. Monad m => m a -> (a -> m b) -> m b
>>= (Element -> Bool) -> Element -> Maybe Element
filterElement (String -> Element -> Bool
named String
"label"))
                                   Maybe Element -> (Element -> Maybe Int) -> Maybe Int
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] -> JATS m Blocks
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> StateT JATSState m [Blocks]
listitems
        String
"def-list" -> [(Inlines, [Blocks])] -> Blocks
definitionList ([(Inlines, [Blocks])] -> Blocks)
-> StateT JATSState m [(Inlines, [Blocks])] -> JATS m Blocks
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> StateT JATSState m [(Inlines, [Blocks])]
deflistitems
        String
"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 -> JATS m Blocks) -> JATS m Blocks
forall (m :: * -> *) a b. Monad m => m a -> (a -> m b) -> m b
>>= Int -> JATS m Blocks
forall (m :: * -> *).
PandocMonad m =>
Int -> StateT JATSState m Blocks
sect (Int -> JATS m Blocks) -> (Int -> Int) -> Int -> JATS m Blocks
forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Int -> Int -> Int
forall a. Num a => a -> a -> a
+Int
1)
        String
"graphic" -> Inlines -> Blocks
para (Inlines -> Blocks) -> StateT JATSState m Inlines -> JATS m Blocks
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Maybe (Inlines, Text) -> Element -> StateT JATSState m Inlines
forall (m :: * -> *).
PandocMonad m =>
Maybe (Inlines, Text) -> Element -> JATS m Inlines
getGraphic Maybe (Inlines, Text)
forall a. Maybe a
Nothing Element
e
        String
"journal-meta" -> Element -> JATS m Blocks
forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
parseMetadata Element
e
        String
"article-meta" -> Element -> JATS m Blocks
forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
parseMetadata Element
e
        String
"custom-meta" -> Element -> JATS m Blocks
forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
parseMetadata Element
e
        String
"title" -> Blocks -> JATS m Blocks
forall (m :: * -> *) a. Monad m => a -> m a
return Blocks
forall a. Monoid a => a
mempty -- processed by header
        String
"label" -> Blocks -> JATS m Blocks
forall (m :: * -> *) a. Monad m => a -> m a
return Blocks
forall a. Monoid a => a
mempty -- processed by header
        String
"table" -> JATS m Blocks
parseTable
        String
"fig" -> JATS m Blocks
parseFigure
        String
"fig-group" -> Attr -> Blocks -> Blocks
divWith (String -> Element -> Text
attrValue String
"id" Element
e, [Text
"fig-group"], [])
                          (Blocks -> Blocks) -> JATS m Blocks -> JATS m Blocks
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Element -> JATS m Blocks
forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks Element
e
        String
"table-wrap" -> Attr -> Blocks -> Blocks
divWith (String -> Element -> Text
attrValue String
"id" Element
e, [Text
"table-wrap"], [])
                          (Blocks -> Blocks) -> JATS m Blocks -> JATS m Blocks
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Element -> JATS m Blocks
forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks Element
e
        String
"caption" -> Attr -> Blocks -> Blocks
divWith (String -> Element -> Text
attrValue String
"id" Element
e, [Text
"caption"], []) (Blocks -> Blocks) -> JATS m Blocks -> JATS m Blocks
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Int -> JATS m Blocks
forall (m :: * -> *).
PandocMonad m =>
Int -> StateT JATSState m Blocks
sect Int
6
        String
"ref-list" -> Element -> JATS m Blocks
forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
parseRefList Element
e
        String
"?xml"  -> Blocks -> JATS m Blocks
forall (m :: * -> *) a. Monad m => a -> m a
return Blocks
forall a. Monoid a => a
mempty
        String
_       -> Element -> JATS 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)
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 (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 (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 :: JATS m Blocks
codeBlockWithLang = do
           let classes' :: [Text]
classes' = case String -> Element -> Text
attrValue String
"language" Element
e of
                                Text
"" -> []
                                Text
x  -> [Text
x]
           Blocks -> JATS m Blocks
forall (m :: * -> *) a. Monad m => a -> m a
return (Blocks -> JATS m Blocks) -> Blocks -> JATS m Blocks
forall a b. (a -> b) -> a -> b
$ Attr -> Text -> Blocks
codeBlockWith (String -> Element -> Text
attrValue String
"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
textContentRecursive Element
e
         parseBlockquote :: JATS m Blocks
parseBlockquote = do
            Blocks
attrib <- case (Element -> Bool) -> Element -> Maybe Element
filterChild (String -> Element -> Bool
named String
"attribution") Element
e of
                             Maybe Element
Nothing  -> Blocks -> JATS m Blocks
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] -> JATS 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)
mapM Content -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Content -> JATS m Inlines
parseInline (Element -> [Content]
elContent Element
z)
            Blocks
contents <- Element -> JATS m Blocks
forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks Element
e
            Blocks -> JATS m Blocks
forall (m :: * -> *) a. Monad m => a -> m a
return (Blocks -> JATS m Blocks) -> Blocks -> JATS 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 -> JATS m Blocks)
-> [Element] -> StateT JATSState m [Blocks]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM Element -> JATS 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 (String -> Element -> Bool
named String
"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)
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
                     (String -> Element -> Bool
named String
"def-item") Element
e
         parseVarListEntry :: Element -> StateT JATSState m (Inlines, [Blocks])
parseVarListEntry Element
e' = do
                     let terms :: [Element]
terms = (Element -> Bool) -> Element -> [Element]
filterChildren (String -> Element -> Bool
named String
"term") Element
e'
                     let items :: [Element]
items = (Element -> Bool) -> Element -> [Element]
filterChildren (String -> Element -> Bool
named String
"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)
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)
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 (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 :: JATS m Blocks
parseFigure =
           -- if a simple caption and single graphic, we emit a standard
           -- implicit figure.  otherwise, we emit a div with the contents
           case (Element -> Bool) -> Element -> [Element]
filterChildren (String -> Element -> Bool
named String
"graphic") Element
e of
                  [Element
g] -> do
                         Inlines
capt <- case (Element -> Bool) -> Element -> Maybe Element
filterChild (String -> Element -> Bool
named String
"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)
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 (m :: * -> *) a. Monad m => a -> m a
return Inlines
forall a. Monoid a => a
mempty
                         Inlines
img <- Maybe (Inlines, Text) -> Element -> StateT JATSState m Inlines
forall (m :: * -> *).
PandocMonad m =>
Maybe (Inlines, Text) -> Element -> JATS m Inlines
getGraphic ((Inlines, Text) -> Maybe (Inlines, Text)
forall a. a -> Maybe a
Just (Inlines
capt, String -> Element -> Text
attrValue String
"id" Element
e)) Element
g
                         Blocks -> JATS m Blocks
forall (m :: * -> *) a. Monad m => a -> m a
return (Blocks -> JATS m Blocks) -> Blocks -> JATS m Blocks
forall a b. (a -> b) -> a -> b
$ Inlines -> Blocks
para Inlines
img
                  [Element]
_   -> Attr -> Blocks -> Blocks
divWith (String -> Element -> Text
attrValue String
"id" Element
e, [Text
"fig"], []) (Blocks -> Blocks) -> JATS m Blocks -> JATS m Blocks
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Element -> JATS m Blocks
forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks Element
e
         parseTable :: JATS m Blocks
parseTable = do
                      let isCaption :: Element -> Bool
isCaption Element
x = String -> Element -> Bool
named String
"title" Element
x Bool -> Bool -> Bool
|| String -> Element -> Bool
named String
"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 (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 (String -> Element -> Bool
named String
"tgroup") Element
e
                      let isColspec :: Element -> Bool
isColspec Element
x = String -> Element -> Bool
named String
"colspec" Element
x Bool -> Bool -> Bool
|| String -> Element -> Bool
named String
"col" Element
x
                      let colspecs :: [Element]
colspecs = case (Element -> Bool) -> Element -> Maybe Element
filterChild (String -> Element -> Bool
named String
"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 = String -> Element -> Bool
named String
"row" Element
x Bool -> Bool -> Bool
|| String -> Element -> Bool
named String
"tr" Element
x
                      [Blocks]
headrows <- case (Element -> Bool) -> Element -> Maybe Element
filterChild (String -> Element -> Bool
named String
"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 (m :: * -> *) a. Monad m => a -> m a
return []
                                       Maybe Element
Nothing -> [Blocks] -> StateT JATSState m [Blocks]
forall (m :: * -> *) a. Monad m => a -> m a
return []
                      [[Blocks]]
bodyrows <- case (Element -> Bool) -> Element -> Maybe Element
filterChild (String -> Element -> Bool
named String
"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)
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)
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 String
findAttr (String -> QName
unqual String
"align") Element
c of
                                                Just String
"left"   -> Alignment
AlignLeft
                                                Just String
"right"  -> Alignment
AlignRight
                                                Just String
"center" -> Alignment
AlignCenter
                                                Maybe String
_             -> Alignment
AlignDefault
                      let toWidth :: Element -> Maybe b
toWidth Element
c = do
                            Text
w <- QName -> Element -> Maybe Text
findAttrText (String -> QName
unqual String
"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 (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 (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)
sequence [Maybe Double]
ws of
                                                Just [Double]
ws' -> let tot :: Double
tot = [Double] -> Double
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 (t :: * -> *) a. Foldable t => t a -> Bool
null [Blocks]
l)]
                      Blocks -> JATS m Blocks
forall (m :: * -> *) a. Monad m => a -> m a
return (Blocks -> JATS m Blocks) -> Blocks -> JATS 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  = String -> Element -> Bool
named String
"entry" Element
x Bool -> Bool -> Bool
|| String -> Element -> Bool
named String
"td" Element
x Bool -> Bool -> Bool
|| String -> Element -> Bool
named String
"th" Element
x
         parseRow :: Element -> StateT JATSState m [Blocks]
parseRow = (Element -> JATS m Blocks)
-> [Element] -> StateT JATSState m [Blocks]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM ((Inlines -> Blocks) -> [Content] -> JATS m Blocks
forall (m :: * -> *).
PandocMonad m =>
(Inlines -> Blocks) -> [Content] -> StateT JATSState m Blocks
parseMixed Inlines -> Blocks
plain ([Content] -> JATS m Blocks)
-> (Element -> [Content]) -> Element -> JATS 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 (String -> Element -> Bool
named String
"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
<$>
                                              Element -> StateT JATSState m Inlines
forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
t
                                    Maybe Element
Nothing -> Inlines -> StateT JATSState m Inlines
forall (m :: * -> *) a. Monad m => a -> m a
return Inlines
forall a. Monoid a => a
mempty
                     Inlines
headerText <- case (Element -> Bool) -> Element -> Maybe Element
filterChild (String -> Element -> Bool
named String
"title") Element
e Maybe Element -> Maybe Element -> Maybe Element
forall (m :: * -> *) a. MonadPlus m => m a -> m a -> m a
`mplus`
                                        ((Element -> Bool) -> Element -> Maybe Element
filterChild (String -> Element -> Bool
named String
"info") Element
e Maybe Element -> (Element -> Maybe Element) -> Maybe Element
forall (m :: * -> *) a b. Monad m => m a -> (a -> m b) -> m b
>>=
                                            (Element -> Bool) -> Element -> Maybe Element
filterChild (String -> Element -> Bool
named String
"title")) of
                                      Just Element
t  -> (Inlines
labelText Inlines -> Inlines -> Inlines
forall a. Semigroup a => a -> a -> a
<>) (Inlines -> Inlines)
-> StateT JATSState m Inlines -> StateT JATSState m Inlines
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$>
                                                  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 (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 = String -> Element -> Text
attrValue String
"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 (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 :: 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] -> JATS m Inlines
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$>
                 (Content -> JATS m Inlines)
-> [Content] -> StateT JATSState m [Inlines]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM Content -> JATS m Inlines
forall (m :: * -> *). PandocMonad m => Content -> JATS m Inlines
parseInline (Element -> [Content]
elContent Element
e')

parseMetadata :: PandocMonad m => Element -> JATS m Blocks
parseMetadata :: 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
  Blocks -> JATS m Blocks
forall (m :: * -> *) a. Monad m => a -> m a
return Blocks
forall a. Monoid a => a
mempty

getTitle :: PandocMonad m => Element -> JATS m ()
getTitle :: Element -> JATS m ()
getTitle Element
e = do
  Inlines
tit <-  case (Element -> Bool) -> Element -> Maybe Element
filterElement (String -> Element -> Bool
named String
"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 (m :: * -> *) a. Monad m => a -> m a
return Inlines
forall a. Monoid a => a
mempty
  Inlines
subtit <-  case (Element -> Bool) -> Element -> Maybe Element
filterElement (String -> Element -> Bool
named String
"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 (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 :: 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)
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 -> String -> Element -> Bool
named String
"contrib" Element
x Bool -> Bool -> Bool
&&
                     String -> Element -> Text
attrValue String
"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)
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 (String -> Element -> Bool
named String
"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 (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 :: 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)
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 (String -> Element -> Bool
named String
"aff") Element
x
  Bool -> JATS m () -> JATS m ()
forall (f :: * -> *). Applicative f => Bool -> f () -> f ()
unless ([Inlines] -> 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 :: Element -> JATS m ()
getAbstract Element
e =
  case (Element -> Bool) -> Element -> Maybe Element
filterElement (String -> Element -> Bool
named String
"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 (f :: * -> *) a. Applicative f => a -> f a
pure ()

getContrib :: PandocMonad m => Element -> JATS m Inlines
getContrib :: 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 (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 (String -> Element -> Bool
named String
"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 (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 (String -> Element -> Bool
named String
"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 (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 (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 (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 :: 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)
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 (String -> Element -> Bool
named String
"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 (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 :: Element -> JATS m (Map Text MetaValue)
parseRef Element
e = do
  let refId :: Inlines
refId = Text -> Inlines
text (Text -> Inlines) -> Text -> Inlines
forall a b. (a -> b) -> a -> b
$ String -> Element -> Text
attrValue String
"id" Element
e
  let getInlineText :: String -> Element -> StateT JATSState m Inlines
getInlineText String
n = 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 (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)
-> (Element -> Maybe Element)
-> Element
-> StateT JATSState m Inlines
forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Element -> Bool) -> Element -> Maybe Element
filterChild (String -> Element -> Bool
named String
n)
  case (Element -> Bool) -> Element -> Maybe Element
filterChild (String -> Element -> Bool
named String
"element-citation") Element
e of
       Just Element
c  -> do
         let refType :: Inlines
refType = Text -> Inlines
text (Text -> Inlines) -> Text -> Inlines
forall a b. (a -> b) -> a -> b
$
               case String -> Element -> Text
attrValue String
"publication-type" Element
c of
                  Text
"journal" -> Text
"article-journal"
                  Text
x -> Text
x
         (Inlines
refTitle, Inlines
refContainerTitle) <- do
           Inlines
t <- String -> Element -> StateT JATSState m Inlines
forall (m :: * -> *).
PandocMonad m =>
String -> Element -> StateT JATSState m Inlines
getInlineText String
"article-title" Element
c
           Inlines
ct <- String -> Element -> StateT JATSState m Inlines
forall (m :: * -> *).
PandocMonad m =>
String -> Element -> StateT JATSState m Inlines
getInlineText String
"source" Element
c
           if Inlines
t Inlines -> Inlines -> Bool
forall a. Eq a => a -> a -> Bool
== Inlines
forall a. Monoid a => a
mempty
              then (Inlines, Inlines) -> StateT JATSState m (Inlines, Inlines)
forall (m :: * -> *) a. Monad m => a -> m a
return (Inlines
ct, Inlines
forall a. Monoid a => a
mempty)
              else (Inlines, Inlines) -> StateT JATSState m (Inlines, Inlines)
forall (m :: * -> *) a. Monad m => a -> m a
return (Inlines
t, Inlines
ct)
         Inlines
refLabel <- String -> Element -> StateT JATSState m Inlines
forall (m :: * -> *).
PandocMonad m =>
String -> Element -> StateT JATSState m Inlines
getInlineText String
"label" Element
c
         Inlines
refYear <- String -> Element -> StateT JATSState m Inlines
forall (m :: * -> *).
PandocMonad m =>
String -> Element -> StateT JATSState m Inlines
getInlineText String
"year" Element
c
         Inlines
refVolume <- String -> Element -> StateT JATSState m Inlines
forall (m :: * -> *).
PandocMonad m =>
String -> Element -> StateT JATSState m Inlines
getInlineText String
"volume" Element
c
         Inlines
refFirstPage <- String -> Element -> StateT JATSState m Inlines
forall (m :: * -> *).
PandocMonad m =>
String -> Element -> StateT JATSState m Inlines
getInlineText String
"fpage" Element
c
         Inlines
refLastPage <- String -> Element -> StateT JATSState m Inlines
forall (m :: * -> *).
PandocMonad m =>
String -> Element -> StateT JATSState m Inlines
getInlineText String
"lpage" Element
c
         Inlines
refPublisher <- String -> Element -> StateT JATSState m Inlines
forall (m :: * -> *).
PandocMonad m =>
String -> Element -> StateT JATSState m Inlines
getInlineText String
"publisher-name" Element
c
         Inlines
refPublisherPlace <- String -> Element -> StateT JATSState m Inlines
forall (m :: * -> *).
PandocMonad m =>
String -> Element -> StateT JATSState m Inlines
getInlineText String
"publisher-loc" Element
c
         let refPages :: Inlines
refPages = Inlines
refFirstPage Inlines -> Inlines -> Inlines
forall a. Semigroup a => a -> a -> a
<> (if Inlines
refLastPage Inlines -> Inlines -> Bool
forall a. Eq a => a -> a -> Bool
== Inlines
forall a. Monoid a => a
mempty
                                            then Inlines
forall a. Monoid a => a
mempty
                                            else Text -> Inlines
text Text
"\x2013" Inlines -> Inlines -> Inlines
forall a. Semigroup a => a -> a -> a
<> Inlines
refLastPage)
         let personGroups' :: [Element]
personGroups' = (Element -> Bool) -> Element -> [Element]
filterChildren (String -> Element -> Bool
named String
"person-group") Element
c
         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 (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 (String -> Element -> Bool
named String
"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 (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 (String -> Element -> Bool
named String
"surname") Element
nm
               MetaValue -> StateT JATSState m MetaValue
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)
                 ]
         [(Text, MetaValue)]
personGroups <- (Element -> StateT JATSState m (Text, MetaValue))
-> [Element] -> StateT JATSState m [(Text, MetaValue)]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM (\Element
pg ->
                                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)
mapM Element -> StateT JATSState m MetaValue
forall (m :: * -> *).
PandocMonad m =>
Element -> StateT JATSState m MetaValue
getName
                                            ((Element -> Bool) -> Element -> [Element]
filterChildren (String -> Element -> Bool
named String
"name") Element
pg)
                                   (Text, MetaValue) -> StateT JATSState m (Text, MetaValue)
forall (m :: * -> *) a. Monad m => a -> m a
return (String -> Element -> Text
attrValue String
"person-group-type" Element
pg,
                                           [MetaValue] -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue [MetaValue]
names))
                         [Element]
personGroups'
         Map Text MetaValue -> JATS m (Map Text MetaValue)
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, MetaValue)] -> Map Text MetaValue)
-> [(Text, MetaValue)] -> Map Text MetaValue
forall a b. (a -> b) -> a -> b
$
           [ (Text
"id" :: Text, Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue Inlines
refId)
           , (Text
"type", Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue Inlines
refType)
           , (Text
"title", Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue Inlines
refTitle)
           , (Text
"container-title", Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue Inlines
refContainerTitle)
           , (Text
"publisher", Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue Inlines
refPublisher)
           , (Text
"publisher-place", Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue Inlines
refPublisherPlace)
           , (Text
"title", Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue Inlines
refTitle)
           , (Text
"issued", 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
"year" :: Text, Inlines
refYear)
                          ])
           , (Text
"volume", Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue Inlines
refVolume)
           , (Text
"page", Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue Inlines
refPages)
           , (Text
"citation-label", Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue Inlines
refLabel)
           ] [(Text, MetaValue)] -> [(Text, MetaValue)] -> [(Text, MetaValue)]
forall a. [a] -> [a] -> [a]
++ [(Text, MetaValue)]
personGroups
       Maybe Element
Nothing -> Map Text MetaValue -> JATS m (Map Text MetaValue)
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 -> Map Text MetaValue
forall k a. Ord k => k -> a -> Map k a -> Map k a
Map.insert Text
"id" (Inlines -> MetaValue
forall a. ToMetaValue a => a -> MetaValue
toMetaValue Inlines
refId) Map Text MetaValue
forall a. Monoid a => a
mempty
       -- TODO handle mixed-citation

findAttrText :: QName -> Element -> Maybe Text
findAttrText :: QName -> Element -> Maybe Text
findAttrText QName
x = (String -> Text) -> Maybe String -> Maybe Text
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
fmap String -> Text
T.pack (Maybe String -> Maybe Text)
-> (Element -> Maybe String) -> Element -> Maybe Text
forall b c a. (b -> c) -> (a -> b) -> a -> c
. QName -> Element -> Maybe String
findAttr QName
x

textContent :: Element -> Text
textContent :: Element -> Text
textContent = String -> Text
T.pack (String -> Text) -> (Element -> String) -> Element -> Text
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Element -> String
strContent

textContentRecursive :: Element -> Text
textContentRecursive :: Element -> Text
textContentRecursive = String -> Text
T.pack (String -> Text) -> (Element -> String) -> Element -> Text
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Element -> String
strContentRecursive

strContentRecursive :: Element -> String
strContentRecursive :: Element -> String
strContentRecursive = Element -> String
strContent (Element -> String) -> (Element -> Element) -> Element -> String
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 -> String -> Maybe Line -> CData
CData CDataKind
CDataText (Element -> String
strContentRecursive Element
e') Maybe Line
forall a. Maybe a
Nothing
elementToStr Content
x = Content
x

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

        String
"code" -> JATS m Inlines
codeWithLang
        String
"monospace" -> JATS m Inlines
codeWithLang

        String
"inline-graphic" -> Maybe (Inlines, Text) -> Element -> JATS m Inlines
forall (m :: * -> *).
PandocMonad m =>
Maybe (Inlines, Text) -> Element -> JATS m Inlines
getGraphic Maybe (Inlines, Text)
forall a. Maybe a
Nothing Element
e
        String
"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) -> JATS 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 -> JATS m Inlines
forall (m :: * -> *) a. Monad m => a -> m a
return (Inlines -> JATS m Inlines) -> Inlines -> JATS 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

        String
"xref" -> do
            Inlines
ils <- (Inlines -> Inlines) -> JATS m Inlines
forall (m :: * -> *).
PandocMonad m =>
(Inlines -> Inlines) -> StateT JATSState m Inlines
innerInlines Inlines -> Inlines
forall a. a -> a
id
            let rid :: Text
rid = String -> Element -> Text
attrValue String
"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
<$> String -> Element -> Maybe Text
maybeAttrValue String
"ref-type" Element
e
            let attr :: (Text, [a], [(Text, Text)])
attr = (String -> Element -> Text
attrValue String
"id" Element
e, [], Maybe (Text, Text) -> [(Text, Text)]
forall a. Maybe a -> [a]
maybeToList Maybe (Text, Text)
refType)
            Inlines -> JATS m Inlines
forall (m :: * -> *) a. Monad m => a -> m a
return (Inlines -> JATS m Inlines) -> Inlines -> JATS 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' ->
                                     Citation :: Text
-> [Inline] -> [Inline] -> CitationMode -> Int -> Int -> Citation
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
        String
"ext-link" -> do
             Inlines
ils <- (Inlines -> Inlines) -> JATS 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
findAttrText (String -> Maybe String -> Maybe String -> QName
QName String
"title" (String -> Maybe String
forall a. a -> Maybe a
Just String
"http://www.w3.org/1999/xlink") Maybe String
forall a. Maybe a
Nothing) Element
e
             let href :: Text
href = case QName -> Element -> Maybe String
findAttr (String -> Maybe String -> Maybe String -> QName
QName String
"href" (String -> Maybe String
forall a. a -> Maybe a
Just String
"http://www.w3.org/1999/xlink") Maybe String
forall a. Maybe a
Nothing) Element
e of
                               Just String
h -> String -> Text
T.pack String
h
                               Maybe String
_      -> Text
"#" Text -> Text -> Text
forall a. Semigroup a => a -> a -> a
<> String -> Element -> Text
attrValue String
"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 = (String -> Element -> Text
attrValue String
"id" Element
e, [], [])
             Inlines -> JATS m Inlines
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
linkWith Attr
forall a a. (Text, [a], [a])
attr Text
href Text
title Inlines
ils'

        String
"disp-formula" -> (Text -> Inlines) -> JATS m Inlines
forall (m :: * -> *) a. (Monad m, Monoid a) => (Text -> a) -> m a
formula Text -> Inlines
displayMath
        String
"inline-formula" -> (Text -> Inlines) -> JATS m Inlines
forall (m :: * -> *) a. (Monad m, Monoid a) => (Text -> a) -> m a
formula Text -> Inlines
math
        String
"math" | QName -> Maybe String
qPrefix (Element -> QName
elName Element
e) Maybe String -> Maybe String -> Bool
forall a. Eq a => a -> a -> Bool
== String -> Maybe String
forall a. a -> Maybe a
Just String
"mml" -> Inlines -> JATS m Inlines
forall (m :: * -> *) a. Monad m => a -> m a
return (Inlines -> JATS m Inlines)
-> (Text -> Inlines) -> Text -> JATS m Inlines
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Text -> Inlines
math (Text -> JATS m Inlines) -> Text -> JATS m Inlines
forall a b. (a -> b) -> a -> b
$ Element -> Text
mathML Element
e
        String
"tex-math" -> Inlines -> JATS m Inlines
forall (m :: * -> *) a. Monad m => a -> m a
return (Inlines -> JATS m Inlines)
-> (Text -> Inlines) -> Text -> JATS m Inlines
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Text -> Inlines
math (Text -> JATS m Inlines) -> Text -> JATS m Inlines
forall a b. (a -> b) -> a -> b
$ Element -> Text
textContent Element
e

        String
"email" -> Inlines -> JATS m Inlines
forall (m :: * -> *) a. Monad m => a -> m a
return (Inlines -> JATS m Inlines) -> Inlines -> JATS 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
        String
"uri" -> Inlines -> JATS m Inlines
forall (m :: * -> *) a. Monad m => a -> m a
return (Inlines -> JATS m Inlines) -> Inlines -> JATS 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
        String
"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] -> JATS m Inlines
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$>
                         (Content -> StateT JATSState m Blocks)
-> [Content] -> StateT JATSState m [Blocks]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM Content -> StateT JATSState m Blocks
forall (m :: * -> *). PandocMonad m => Content -> JATS m Blocks
parseBlock (Element -> [Content]
elContent Element
e)
        String
_          -> (Inlines -> Inlines) -> JATS m Inlines
forall (m :: * -> *).
PandocMonad m =>
(Inlines -> Inlines) -> StateT JATSState m Inlines
innerInlines Inlines -> Inlines
forall a. a -> a
id
   where innerInlines :: (Inlines -> Inlines) -> StateT JATSState m Inlines
innerInlines Inlines -> Inlines
f = (Inlines -> Inlines) -> Inlines -> Inlines
extractSpaces Inlines -> Inlines
f (Inlines -> Inlines)
-> ([Inlines] -> Inlines) -> [Inlines] -> Inlines
forall b c a. (b -> c) -> (a -> b) -> a -> c
. [Inlines] -> Inlines
forall a. Monoid a => [a] -> a
mconcat ([Inlines] -> Inlines)
-> StateT JATSState m [Inlines] -> StateT JATSState m Inlines
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$>
                          (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)
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
. String -> Text
T.pack (String -> Text) -> (Element -> String) -> Element -> Text
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Element -> String
showElement (Element -> Either Text [Exp]) -> Element -> Either Text [Exp]
forall a b. (a -> b) -> a -> b
$ (forall a. Data a => a -> a) -> Element -> Element
(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 -> a) -> m a
formula Text -> a
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 (String -> Element -> Bool
named String
"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 (String -> Element -> Bool
named  String
"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
            a -> m a
forall (m :: * -> *) a. Monad m => a -> m a
return (a -> m a) -> ([Text] -> a) -> [Text] -> m a
forall b c a. (b -> c) -> (a -> b) -> a -> c
. [a] -> a
forall a. Monoid a => [a] -> a
mconcat ([a] -> a) -> ([Text] -> [a]) -> [Text] -> a
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Int -> [a] -> [a]
forall a. Int -> [a] -> [a]
take Int
1 ([a] -> [a]) -> ([Text] -> [a]) -> [Text] -> [a]
forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text -> a) -> [Text] -> [a]
forall a b. (a -> b) -> [a] -> [b]
map Text -> a
constructor ([Text] -> m a) -> [Text] -> m a
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 -> String
qName   (Element -> QName
elName Element
x) String -> String -> Bool
forall a. Eq a => a -> a -> Bool
== String
"math" Bool -> Bool -> Bool
&&
                      QName -> Maybe String
qPrefix (Element -> QName
elName Element
x) Maybe String -> Maybe String -> Bool
forall a. Eq a => a -> a -> Bool
== String -> Maybe String
forall a. a -> Maybe a
Just String
"mml"
         removePrefix :: QName -> QName
removePrefix QName
elname = QName
elname { qPrefix :: Maybe String
qPrefix = Maybe String
forall a. Maybe a
Nothing }
         codeWithLang :: JATS m Inlines
codeWithLang = do
           let classes' :: [Text]
classes' = case String -> Element -> Text
attrValue String
"language" Element
e of
                               Text
"" -> []
                               Text
l  -> [Text
l]
           Inlines -> JATS m Inlines
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 -> Inlines
codeWith (String -> Element -> Text
attrValue String
"id" Element
e,[Text]
classes',[]) (Text -> Inlines) -> Text -> Inlines
forall a b. (a -> b) -> a -> b
$ Element -> Text
textContentRecursive Element
e