{-# 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)
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)
import Safe (headMay)
import Text.Printf (printf)

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
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{ jatsSectionLevel :: Int
jatsSectionLevel = Int
0
                 , jatsQuoteType :: QuoteType
jatsQuoteType = QuoteType
DoubleQuote
                 , jatsMeta :: Meta
jatsMeta = forall a. Monoid a => a
mempty
                 , jatsBook :: Bool
jatsBook = Bool
False
                 , jatsFootnotes :: Map Text Blocks
jatsFootnotes = 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 = forall a. ToSources a => a -> Sources
toSources a
inp
  [Content]
tree <- forall a c b. (a -> c) -> (b -> c) -> Either a b -> c
either (forall e (m :: * -> *) a. MonadError e m => e -> m a
throwError forall b c a. (b -> c) -> (a -> b) -> a -> c
. Text -> Text -> PandocError
PandocXMLError Text
"") forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$
            Text -> Either Text [Content]
parseXMLContents (Text -> Text
TL.fromStrict forall b c a. (b -> c) -> (a -> b) -> a -> c
. Sources -> Text
sourcesToText forall a b. (a -> b) -> a -> b
$ Sources
sources)
  ([Blocks]
bs, JATSState
st') <- forall a b c. (a -> b -> c) -> b -> a -> c
flip forall s (m :: * -> *) a. StateT s m a -> s -> m (a, s)
runStateT (forall a. Default a => a
def{ jatsContent :: [Content]
jatsContent = [Content]
tree }) forall a b. (a -> b) -> a -> b
$ forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM 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 = forall a. Many a -> [a]
toList forall a b. (a -> b) -> a -> b
$ 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 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 (forall a. Many a -> [a]
toList Blocks
footnote)
                               Maybe Blocks
Nothing       -> Inline
link'
          Maybe (Char, Text)
_               -> Inline
link'
      linkToFootnotes Inline
inline = Inline
inline
  forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ Meta -> [Block] -> Pandoc
Pandoc (JATSState -> Meta
jatsMeta JATSState
st') (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 =
  forall a. a -> Maybe a -> a
fromMaybe 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 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) 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 = forall s (m :: * -> *). MonadState s m => (s -> s) -> m ()
modify (forall a b. (HasMeta a, ToMetaValue b) => Text -> b -> a -> a
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 = 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 = 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) = case QName -> Text
qName (Element -> QName
elName Element
e) of
            Text
"disp-formula" -> if Element -> Bool
onlyOneChild Element
e
                                  then if Element -> Bool
hasFormulaChild Element
e
                                          then Bool
False
                                          else case (Element -> Bool) -> Element -> Maybe Element
filterChild (Text -> Element -> Bool
named Text
"alternatives") Element
e of
                                            Just Element
a -> if Element -> Bool
hasFormulaChild Element
a then Bool
False else Bool
True
                                            Maybe Element
Nothing -> Bool
True
                                  else Bool
True
            Text
"alternatives" -> if Element -> Bool
hasFormulaChild Element
e then Bool
False else Bool
True
            Text
_ -> QName -> Text
qName (Element -> QName
elName Element
e) forall a. Ord a => a -> Set a -> Bool
`S.member` Set Text
blocktags

  where blocktags :: Set Text
blocktags = forall a. Ord a => [a] -> Set a
S.fromList ([Text]
paragraphLevel forall a. [a] -> [a] -> [a]
++ [Text]
lists forall a. [a] -> [a] -> [a]
++ [Text]
formulae forall a. [a] -> [a] -> [a]
++ [Text]
other) forall a. Ord a => Set a -> Set a -> Set a
\\ forall a. Ord a => [a] -> Set a
S.fromList [Text]
canBeInline
        paragraphLevel :: [Text]
paragraphLevel = [Text
"address", Text
"answer", Text
"answer-set", Text
"array", Text
"boxed-text", Text
"chem-struct-wrap",
            Text
"code", Text
"explanation", Text
"fig", Text
"fig-group", Text
"graphic", Text
"media", Text
"preformat", Text
"question", Text
"question-wrap", Text
"question-wrap-group",
            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"]
        formulae :: [Text]
formulae = [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"]
        canBeInline :: [Text]
canBeInline = [Text
"tex-math", Text
"mml:math", Text
"related-object", Text
"x"]
        onlyOneChild :: Element -> Bool
onlyOneChild Element
x = forall (t :: * -> *) a. Foldable t => t a -> Int
length (Element -> [Element]
allChildren Element
x) forall a. Eq a => a -> a -> Bool
== Int
1
        allChildren :: Element -> [Element]
allChildren Element
x = (Element -> Bool) -> Element -> [Element]
filterChildren (forall a b. a -> b -> a
const Bool
True) Element
x

isBlockElement Content
_ = Bool
False

-- Trim leading and trailing newline characters
trimNl :: Text -> Text
trimNl :: Text -> Text
trimNl = (Char -> Bool) -> Text -> Text
T.dropAround (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:" 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 forall a b. (a -> b) -> a -> b
$ Text -> Text
atVal Text
"role", [])
      imageUrl :: Text
imageUrl = Text -> Text
atVal Text
"href"
  forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ Attr -> Text -> Text -> Inlines -> Inlines
imageWith 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 =  forall a. Monoid a => [a] -> a
mconcat forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$>
                 forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM 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
_)) = forall (m :: * -> *) a. Monad m => a -> m a
return 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 forall (m :: * -> *) a. Monad m => a -> m a
return forall a. Monoid a => a
mempty
                                     else forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ Inlines -> Blocks
plain forall a b. (a -> b) -> a -> b
$ Inlines -> Inlines
trimInlines forall a b. (a -> b) -> a -> b
$ Text -> Inlines
text Text
s
parseBlock (CRef Text
x) = forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ Inlines -> Blocks
plain forall a b. (a -> b) -> a -> b
$ Text -> Inlines
str forall a b. (a -> b) -> a -> b
$ Text -> Text
T.toUpper Text
x
parseBlock (Elem Element
e) = do
  Int
sectionLevel <- forall s (m :: * -> *) a. MonadState s m => (s -> a) -> m a
gets JATSState -> Int
jatsSectionLevel
  let parseBlockWithHeader :: StateT JATSState m Blocks
parseBlockWithHeader = forall {m :: * -> *}.
PandocMonad m =>
Int -> StateT JATSState m Blocks -> StateT JATSState m Blocks
wrapWithHeader (Int
sectionLevelforall a. Num a => a -> a -> a
+Int
1) (forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks Element
e)

  case QName -> Text
qName (Element -> QName
elName Element
e) of
        Text
"p" -> 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" -> forall {m :: * -> *}.
PandocMonad m =>
Int -> StateT JATSState m Blocks -> StateT JATSState m Blocks
wrapWithHeader (Int
sectionLevelforall a. Num a => a -> a -> a
+Int
1) StateT JATSState m Blocks
parseBlockquote
        Text
"list" ->  forall {m :: * -> *}.
PandocMonad m =>
Int -> StateT JATSState m Blocks -> StateT JATSState m Blocks
wrapWithHeader (Int
sectionLevelforall a. Num a => a -> a -> a
+Int
1) StateT JATSState m Blocks
parseList
        Text
"def-list" -> forall {m :: * -> *}.
PandocMonad m =>
Int -> StateT JATSState m Blocks -> StateT JATSState m Blocks
wrapWithHeader (Int
sectionLevelforall a. Num a => a -> a -> a
+Int
1) ([(Inlines, [Blocks])] -> Blocks
definitionList forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> StateT JATSState m [(Inlines, [Blocks])]
deflistitems)
        Text
"sec" -> StateT JATSState m Blocks
parseBlockWithHeader
        Text
"abstract" -> StateT JATSState m Blocks
parseBlockWithHeader
        Text
"ack" -> StateT JATSState m Blocks
parseBlockWithHeader
        Text
"answer" -> StateT JATSState m Blocks
parseBlockWithHeader
        Text
"answer-set" -> StateT JATSState m Blocks
parseBlockWithHeader
        Text
"app" -> StateT JATSState m Blocks
parseBlockWithHeader
        Text
"app-group" -> StateT JATSState m Blocks
parseBlockWithHeader
        Text
"author-comment" -> StateT JATSState m Blocks
parseBlockWithHeader
        Text
"author-notes" -> StateT JATSState m Blocks
parseBlockWithHeader
        Text
"back" -> StateT JATSState m Blocks
parseBlockWithHeader
        Text
"bio" -> StateT JATSState m Blocks
parseBlockWithHeader
        Text
"explanation" -> StateT JATSState m Blocks
parseBlockWithHeader
        Text
"glossary" -> StateT JATSState m Blocks
parseBlockWithHeader
        Text
"kwd-group" -> StateT JATSState m Blocks
parseBlockWithHeader
        Text
"list-item" -> StateT JATSState m Blocks
parseBlockWithHeader
        Text
"notes" -> StateT JATSState m Blocks
parseBlockWithHeader
        Text
"option" -> StateT JATSState m Blocks
parseBlockWithHeader
        Text
"question" -> StateT JATSState m Blocks
parseBlockWithHeader
        Text
"question-preamble" -> StateT JATSState m Blocks
parseBlockWithHeader
        Text
"question-wrap-group" -> StateT JATSState m Blocks
parseBlockWithHeader
        Text
"statement" -> StateT JATSState m Blocks
parseBlockWithHeader
        Text
"supplement" -> StateT JATSState m Blocks
parseBlockWithHeader
        Text
"table-wrap-foot" -> StateT JATSState m Blocks
parseBlockWithHeader
        Text
"trans-abstract" -> StateT JATSState m Blocks
parseBlockWithHeader
        Text
"verse-group" -> StateT JATSState m Blocks
parseBlockWithHeader
        Text
"graphic" -> Inlines -> Blocks
para forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> forall (m :: * -> *).
PandocMonad m =>
Maybe (Inlines, Text) -> Element -> JATS m Inlines
getGraphic forall a. Maybe a
Nothing Element
e
        Text
"journal-meta" -> forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
parseMetadata Element
e
        Text
"article-meta" -> forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
parseMetadata Element
e
        Text
"custom-meta" -> forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
parseMetadata Element
e
        Text
"processing-meta" -> forall (m :: * -> *) a. Monad m => a -> m a
return forall a. Monoid a => a
mempty
        Text
"title" -> forall (m :: * -> *) a. Monad m => a -> m a
return forall a. Monoid a => a
mempty -- processed by header
        Text
"label" -> forall (m :: * -> *) a. Monad m => a -> m a
return 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"], [])
                          forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks Element
e
        Text
"table-wrap" -> Attr -> Blocks -> Blocks
divWith (Text -> Element -> Text
attrValue Text
"id" Element
e, [Text
"table-wrap"], [])
                          forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks Element
e
        Text
"caption" -> do
          Bool
inFigure <- forall s (m :: * -> *) a. MonadState s m => (s -> a) -> m a
gets JATSState -> Bool
jatsInFigure
          if Bool
inFigure -- handled by parseFigure
             then forall (m :: * -> *) a. Monad m => a -> m a
return forall a. Monoid a => a
mempty
             else Attr -> Blocks -> Blocks
divWith (Text -> Element -> Text
attrValue Text
"id" Element
e, [Text
"caption"], []) forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> forall {m :: * -> *}.
PandocMonad m =>
Int -> StateT JATSState m Blocks -> StateT JATSState m Blocks
wrapWithHeader Int
6 (forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks Element
e)
        Text
"fn-group" -> StateT JATSState m Blocks
parseFootnoteGroup
        Text
"ref-list" -> forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
parseRefList Element
e
        Text
"alternatives" -> if Element -> Bool
hasFormulaChild Element
e
                            then forall (m :: * -> *).
PandocMonad m =>
(Text -> Inlines) -> Element -> JATS m Blocks
blockFormula Text -> Inlines
displayMath Element
e
                            else forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks Element
e
        Text
"disp-formula" -> if Element -> Bool
hasFormulaChild Element
e
                            then forall (m :: * -> *).
PandocMonad m =>
(Text -> Inlines) -> Element -> JATS m Blocks
blockFormula Text -> Inlines
displayMath Element
e
                            else Attr -> Blocks -> Blocks
divWith (Text -> Element -> Text
attrValue Text
"id" Element
e, [Text
"disp-formula"], [])
                                    forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks Element
e
        Text
"?xml"  -> forall (m :: * -> *) a. Monad m => a -> m a
return forall a. Monoid a => a
mempty
        Text
_       -> 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) = forall a. (a -> Bool) -> [a] -> ([a], [a])
break Content -> Bool
isBlockElement [Content]
conts
           Inlines
ils' <- Inlines -> Inlines
trimInlines forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. Monoid a => [a] -> a
mconcat forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM forall (m :: * -> *). PandocMonad m => Content -> JATS m Inlines
parseInline [Content]
ils
           let p :: Blocks
p = if Inlines
ils' forall a. Eq a => a -> a -> Bool
== forall a. Monoid a => a
mempty then forall a. Monoid a => a
mempty else Inlines -> Blocks
container Inlines
ils'
           case [Content]
rest of
                 []     -> forall (m :: * -> *) a. Monad m => a -> m a
return Blocks
p
                 (Content
r:[Content]
rs) -> do
                    Blocks
b <- 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
                    forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ Blocks
p forall a. Semigroup a => a -> a -> a
<> Blocks
b 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]
           forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ Attr -> Text -> Blocks
codeBlockWith (Text -> Element -> Text
attrValue Text
"id" Element
e, [Text]
classes', [])
                  forall a b. (a -> b) -> a -> b
$ Text -> Text
trimNl 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
"attrib") Element
e of
                             Maybe Element
Nothing  -> forall (m :: * -> *) a. Monad m => a -> m a
return forall a. Monoid a => a
mempty
                             Just Element
z   -> Inlines -> Blocks
para forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text -> Inlines
str Text
"— " forall a. Semigroup a => a -> a -> a
<>) forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. Monoid a => [a] -> a
mconcat
                                         forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$>
                                              forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM forall (m :: * -> *). PandocMonad m => Content -> JATS m Inlines
parseInline (Element -> [Content]
elContent Element
z)
            Blocks
contents <- forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks Element
e
            forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ Blocks -> Blocks
blockQuote (Blocks
contents forall a. Semigroup a => a -> a -> a
<> Blocks
attrib)
         parseList :: StateT JATSState m Blocks
parseList = do
            case Text -> Element -> Text
attrValue Text
"list-type" Element
e of
              Text
"bullet" -> [Blocks] -> Blocks
bulletList forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> StateT JATSState m [Blocks]
listitems
              Text
listType -> do
                let start :: Int
start =
                      forall a. a -> Maybe a -> a
fromMaybe Int
1 forall a b. (a -> b) -> a -> b
$
                        ( (Element -> Bool) -> Element -> Maybe Element
filterElement (Text -> Element -> Bool
named Text
"list-item") Element
e
                            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")
                        )
                          forall (m :: * -> *) a b. Monad m => m a -> (a -> m b) -> m b
>>= forall (m :: * -> *) a. (MonadPlus m, Read a) => Text -> m a
safeRead forall b c a. (b -> c) -> (a -> b) -> a -> c
. Element -> Text
textContent
                ListAttributes -> [Blocks] -> Blocks
orderedListWith (Int
start, forall {a}. (Eq a, IsString a) => a -> ListNumberStyle
parseListStyleType Text
listType, ListNumberDelim
DefaultDelim)
                  forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> StateT JATSState m [Blocks]
listitems
         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 = forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks 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 = forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM forall {m :: * -> *}.
PandocMonad m =>
Element -> StateT JATSState m (Inlines, [Blocks])
parseVarListEntry 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' <- forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines [Element]
terms
                     [Blocks]
items' <- forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks [Element]
items
                     forall (m :: * -> *) a. Monad m => a -> m a
return (forall a. Monoid a => [a] -> a
mconcat forall a b. (a -> b) -> a -> b
$ forall a. a -> [a] -> [a]
intersperse (Text -> Inlines
str Text
"; ") [Inlines]
terms', [Blocks]
items')
         parseFigure :: StateT JATSState m Blocks
parseFigure = do
           forall s (m :: * -> *). MonadState s m => (s -> s) -> m ()
modify 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  -> forall a. Monoid a => [a] -> a
mconcat forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. a -> [a] -> [a]
intersperse Inlines
linebreak forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$>
                                forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines ((Element -> Bool) -> Element -> [Element]
filterChildren (forall a b. a -> b -> a
const Bool
True) Element
t)
                     Maybe Element
Nothing -> forall (m :: * -> *) a. Monad m => a -> m a
return forall a. Monoid a => a
mempty
           Blocks
contents <- forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks Element
e
           forall s (m :: * -> *). MonadState s m => (s -> s) -> m ()
modify forall a b. (a -> b) -> a -> b
$ \JATSState
st -> JATSState
st{ jatsInFigure :: Bool
jatsInFigure = Bool
False }
           forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ Attr -> Caption -> Blocks -> Blocks
figureWith
             (Text -> Element -> Text
attrValue Text
"id" Element
e, [], [])
             (Blocks -> Caption
simpleCaption forall a b. (a -> b) -> a -> b
$ Inlines -> Blocks
plain Inlines
capt)
             Blocks
contents
         parseFootnoteGroup :: StateT JATSState m Blocks
parseFootnoteGroup = do
           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) forall a b. (a -> b) -> a -> b
$ \Element
fn -> do
             let id' :: Text
id' = Text -> Element -> Text
attrValue Text
"id" Element
fn
             Blocks
contents <- forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks Element
fn
             forall s (m :: * -> *). MonadState s m => (s -> s) -> m ()
modify forall a b. (a -> b) -> a -> b
$ \JATSState
st ->
               JATSState
st { jatsFootnotes :: Map Text Blocks
jatsFootnotes = 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) }
           forall (m :: * -> *) a. Monad m => a -> m a
return 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  -> forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
t
                                    Maybe Element
Nothing -> forall (m :: * -> *) a. Monad m => a -> m a
return forall a. Monoid a => a
mempty
                      let e' :: Element
e' = forall a. a -> Maybe a -> a
fromMaybe Element
e 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

                      let parseRows :: Element -> [[Element]]
parseRows Element
elementWithRows =
                            forall a b. (a -> b) -> [a] -> [b]
map Element -> [Element]
parseElement forall a b. (a -> b) -> a -> b
$ (Element -> Bool) -> Element -> [Element]
filterChildren Element -> Bool
isRow Element
elementWithRows

                      -- list of list of body cell elements
                      let multipleBodyRowElements :: [[[Element]]]
multipleBodyRowElements =
                            forall a b. (a -> b) -> [a] -> [b]
map Element -> [[Element]]
parseRows forall a b. (a -> b) -> a -> b
$ (Element -> Bool) -> Element -> [Element]
filterChildren (Text -> Element -> Bool
named Text
"tbody") Element
e'

                      -- list of list header cell elements
                      let headRowElements :: [[Element]]
headRowElements = forall b a. b -> (a -> b) -> Maybe a -> b
maybe [] Element -> [[Element]]
parseRows ((Element -> Bool) -> Element -> Maybe Element
filterChild (Text -> Element -> Bool
named Text
"thead") Element
e')

                      -- list of foot cell elements
                      let footRowElements :: [[Element]]
footRowElements = forall b a. b -> (a -> b) -> Maybe a -> b
maybe [] Element -> [[Element]]
parseRows ((Element -> Bool) -> Element -> Maybe Element
filterChild (Text -> Element -> Bool
named Text
"tfoot") 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 toColSpan :: Element -> a
toColSpan Element
element = forall a. a -> Maybe a -> a
fromMaybe a
1 forall a b. (a -> b) -> a -> b
$
                            QName -> Element -> Maybe Text
findAttr (Text -> QName
unqual Text
"colspan") Element
element forall (m :: * -> *) a b. Monad m => m a -> (a -> m b) -> m b
>>= forall (m :: * -> *) a. (MonadPlus m, Read a) => Text -> m a
safeRead
                      let toRowSpan :: Element -> a
toRowSpan Element
element =  forall a. a -> Maybe a -> a
fromMaybe a
1 forall a b. (a -> b) -> a -> b
$
                            QName -> Element -> Maybe Text
findAttr (Text -> QName
unqual Text
"rowspan") Element
element forall (m :: * -> *) a b. Monad m => m a -> (a -> m b) -> m b
>>= forall (m :: * -> *) a. (MonadPlus m, Read a) => Text -> m a
safeRead
                      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 <- forall (m :: * -> *) a. (MonadPlus m, Read a) => Text -> m a
safeRead forall a b. (a -> b) -> a -> b
$ Text
"0" 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 forall a. Eq a => a -> a -> Bool
== Char
'.') Text
w
                            if b
n forall a. Ord a => a -> a -> Bool
> b
0 then forall a. a -> Maybe a
Just b
n else forall a. Maybe a
Nothing
                      let firstBody :: [[Element]]
firstBody = forall a. a -> Maybe a -> a
fromMaybe [] (forall a. [a] -> Maybe a
headMay [[[Element]]]
multipleBodyRowElements)
                      let numrows :: Int
numrows = forall (t :: * -> *) b a.
Foldable t =>
(b -> a -> b) -> b -> t a -> b
foldl' forall a. Ord a => a -> a -> a
max Int
0 forall a b. (a -> b) -> a -> b
$ forall a b. (a -> b) -> [a] -> [b]
map forall (t :: * -> *) a. Foldable t => t a -> Int
length [[Element]]
firstBody
                      let aligns :: [Alignment]
aligns = case [Element]
colspecs of
                                     [] -> forall a. Int -> a -> [a]
replicate Int
numrows Alignment
AlignDefault
                                     [Element]
cs -> forall a b. (a -> b) -> [a] -> [b]
map Element -> Alignment
toAlignment [Element]
cs
                      let widths :: [ColWidth]
widths = case [Element]
colspecs of
                                     [] -> forall a. Int -> a -> [a]
replicate Int
numrows ColWidth
ColWidthDefault
                                     [Element]
cs -> let ws :: [Maybe Double]
ws = forall a b. (a -> b) -> [a] -> [b]
map forall {b}. (Read b, Ord b, Num b) => Element -> Maybe b
toWidth [Element]
cs
                                           in case 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 = forall (t :: * -> *) a. (Foldable t, Num a) => t a -> a
sum [Double]
ws'
                                                            in  Double -> ColWidth
ColWidth forall b c a. (b -> c) -> (a -> b) -> a -> c
. (forall a. Fractional a => a -> a -> a
/ Double
tot) forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> [Double]
ws'
                                                Maybe [Double]
Nothing  -> forall a. Int -> a -> [a]
replicate Int
numrows ColWidth
ColWidthDefault
                      let parseCell :: Element -> StateT JATSState m Blocks
parseCell = forall {m :: * -> *}.
PandocMonad m =>
(Inlines -> Blocks) -> [Content] -> StateT JATSState m Blocks
parseMixed Inlines -> Blocks
plain forall b c a. (b -> c) -> (a -> b) -> a -> c
. Element -> [Content]
elContent
                      let elementToCell :: Element -> StateT JATSState m Cell
elementToCell Element
element = Alignment -> RowSpan -> ColSpan -> Blocks -> Cell
cell
                            (Element -> Alignment
toAlignment Element
element)
                            (Int -> RowSpan
RowSpan forall a b. (a -> b) -> a -> b
$ forall {a}. (Num a, Read a) => Element -> a
toRowSpan Element
element)
                            (Int -> ColSpan
ColSpan forall a b. (a -> b) -> a -> b
$ forall {a}. (Num a, Read a) => Element -> a
toColSpan Element
element)
                            forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> (Element -> StateT JATSState m Blocks
parseCell Element
element)
                      let rowElementsToCells :: t Element -> StateT JATSState m (t Cell)
rowElementsToCells t Element
elements = forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM Element -> StateT JATSState m Cell
elementToCell t Element
elements
                      let toRow :: [Element] -> StateT JATSState m Row
toRow = forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
fmap (Attr -> [Cell] -> Row
Row Attr
nullAttr) forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall {t :: * -> *}.
Traversable t =>
t Element -> StateT JATSState m (t Cell)
rowElementsToCells
                          toRows :: t [Element] -> StateT JATSState m (t Row)
toRows t [Element]
elements = forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM [Element] -> StateT JATSState m Row
toRow t [Element]
elements

                      [Row]
headerRows <- forall {t :: * -> *}.
Traversable t =>
t [Element] -> StateT JATSState m (t Row)
toRows [[Element]]
headRowElements
                      [Row]
footerRows <- forall {t :: * -> *}.
Traversable t =>
t [Element] -> StateT JATSState m (t Row)
toRows [[Element]]
footRowElements
                      [[Row]]
bodyRows <- forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM forall {t :: * -> *}.
Traversable t =>
t [Element] -> StateT JATSState m (t Row)
toRows [[[Element]]]
multipleBodyRowElements

                      forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ Caption
-> [ColSpec] -> TableHead -> [TableBody] -> TableFoot -> Blocks
table (Blocks -> Caption
simpleCaption forall a b. (a -> b) -> a -> b
$ Inlines -> Blocks
plain Inlines
capt)
                                     (forall a b. [a] -> [b] -> [(a, b)]
zip [Alignment]
aligns [ColWidth]
widths)
                                     (Attr -> [Row] -> TableHead
TableHead Attr
nullAttr [Row]
headerRows)
                                     (forall a b. (a -> b) -> [a] -> [b]
map (Attr -> RowHeadColumns -> [Row] -> [Row] -> TableBody
TableBody Attr
nullAttr RowHeadColumns
0 []) [[Row]]
bodyRows)
                                     (Attr -> [Row] -> TableFoot
TableFoot Attr
nullAttr [Row]
footerRows)
         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
         parseElement :: Element -> [Element]
parseElement = (Element -> Bool) -> Element -> [Element]
filterChildren Element -> Bool
isEntry
         wrapWithHeader :: Int -> StateT JATSState m Blocks -> StateT JATSState m Blocks
wrapWithHeader Int
n StateT JATSState m Blocks
mBlocks = do
                      Bool
isBook <- 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 forall a. Eq a => a -> a -> Bool
== Int
0 then Int
n forall a. Num a => a -> a -> a
+ Int
1 else Int
n
                      Inlines
headerText <- case (Element -> Bool) -> Element -> Maybe Element
filterChild (Text -> Element -> Bool
named Text
"title") Element
e of
                                        Just Element
t  -> forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
t
                                        Maybe Element
Nothing -> forall (m :: * -> *) a. Monad m => a -> m a
return forall a. Monoid a => a
mempty
                      Int
oldN <- forall s (m :: * -> *) a. MonadState s m => (s -> a) -> m a
gets JATSState -> Int
jatsSectionLevel
                      forall s (m :: * -> *). MonadState s m => (s -> s) -> m ()
modify forall a b. (a -> b) -> a -> b
$ \JATSState
st -> JATSState
st{ jatsSectionLevel :: Int
jatsSectionLevel = Int
n }
                      Blocks
blocks <- StateT JATSState m Blocks
mBlocks
                      let ident :: Text
ident = Text -> Element -> Text
attrValue Text
"id" Element
e
                      forall s (m :: * -> *). MonadState s m => (s -> s) -> m ()
modify forall a b. (a -> b) -> a -> b
$ \JATSState
st -> JATSState
st{ jatsSectionLevel :: Int
jatsSectionLevel = Int
oldN }
                      forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ (if
                        Inlines
headerText forall a. Eq a => a -> a -> Bool
== forall a. Monoid a => a
mempty
                      then forall a. Monoid a => a
mempty
                      else Attr -> Int -> Inlines -> Blocks
headerWith (Text
ident,[],[]) Int
n' Inlines
headerText) forall a. Semigroup a => a -> a -> a
<> Blocks
blocks

getInlines :: PandocMonad m => Element -> JATS m Inlines
getInlines :: forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
e' = Inlines -> Inlines
trimInlines forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. Monoid a => [a] -> a
mconcat forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$>
                 forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM 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
  forall (m :: * -> *). PandocMonad m => Element -> JATS m ()
getTitle Element
e
  forall (m :: * -> *). PandocMonad m => Element -> JATS m ()
getAuthors Element
e
  forall (m :: * -> *). PandocMonad m => Element -> JATS m ()
getAffiliations Element
e
  forall (m :: * -> *). PandocMonad m => Element -> JATS m ()
getAbstract Element
e
  forall (m :: * -> *). PandocMonad m => Element -> JATS m ()
getPubDate Element
e
  forall (m :: * -> *). PandocMonad m => Element -> JATS m ()
getPermissions Element
e
  forall (m :: * -> *) a. Monad m => a -> m a
return 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  -> forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
s
               Maybe Element
Nothing -> forall (m :: * -> *) a. Monad m => a -> m a
return 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
": " forall a. Semigroup a => a -> a -> a
<>) forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$>
                           forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
s
               Maybe Element
Nothing -> forall (m :: * -> *) a. Monad m => a -> m a
return forall a. Monoid a => a
mempty
  forall (f :: * -> *). Applicative f => Bool -> f () -> f ()
when (Inlines
tit forall a. Eq a => a -> a -> Bool
/= forall a. Monoid a => a
mempty) forall a b. (a -> b) -> a -> b
$ forall (m :: * -> *) a.
(PandocMonad m, ToMetaValue a) =>
Text -> a -> JATS m ()
addMeta Text
"title" Inlines
tit
  forall (f :: * -> *). Applicative f => Bool -> f () -> f ()
when (Inlines
subtit forall a. Eq a => a -> a -> Bool
/= forall a. Monoid a => a
mempty) forall a b. (a -> b) -> a -> b
$ 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 <- forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getContrib 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 forall a. Eq a => a -> a -> Bool
== Text
"author") Element
e
  [Inlines]
authorNotes <- forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines 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 (forall a. [a] -> [a]
reverse [Inlines]
authors, [Inlines]
authorNotes) of
                   ([], [Inlines]
_)    -> []
                   ([Inlines]
_, [])    -> [Inlines]
authors
                   (Inlines
a:[Inlines]
as, [Inlines]
ns) -> forall a. [a] -> [a]
reverse [Inlines]
as forall a. [a] -> [a] -> [a]
++ [Inlines
a forall a. Semigroup a => a -> a -> a
<> forall a. Monoid a => [a] -> a
mconcat [Inlines]
ns]
  forall (f :: * -> *). Applicative f => Bool -> f () -> f ()
unless (forall (t :: * -> *) a. Foldable t => t a -> Bool
null [Inlines]
authors) forall a b. (a -> b) -> a -> b
$ 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 <- forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines forall a b. (a -> b) -> a -> b
$ (Element -> Bool) -> Element -> [Element]
filterChildren (Text -> Element -> Bool
named Text
"aff") Element
x
  forall (f :: * -> *). Applicative f => Bool -> f () -> f ()
unless (forall (t :: * -> *) a. Foldable t => t a -> Bool
null [Inlines]
affs) forall a b. (a -> b) -> a -> b
$ 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 <- forall (m :: * -> *). PandocMonad m => Element -> JATS m Blocks
getBlocks Element
s
      forall (m :: * -> *) a.
(PandocMonad m, ToMetaValue a) =>
Text -> a -> JATS m ()
addMeta Text
"abstract" Blocks
blks
    Maybe Element
Nothing -> 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 -> forall (m :: * -> *). PandocMonad m => Element -> JATS m Text
getDate Element
d forall (m :: * -> *) a b. Monad m => m a -> (a -> m b) -> m b
>>= forall (m :: * -> *) a.
(PandocMonad m, ToMetaValue a) =>
Text -> a -> JATS m ()
addMeta Text
"date" forall b c a. (b -> c) -> (a -> b) -> a -> c
. Text -> Inlines
text
    Maybe Element
Nothing -> forall (f :: * -> *) a. Applicative f => a -> f a
pure ()

-- extract a structured date and create an ISO-8901 string date from it
getDate :: PandocMonad m => Element -> JATS m Text
getDate :: forall (m :: * -> *). PandocMonad m => Element -> JATS m Text
getDate Element
e =
  case Text -> Element -> Maybe Text
maybeAttrValue Text
"iso-8601-date" Element
e of
    Just Text
isod -> forall (f :: * -> *) a. Applicative f => a -> f a
pure Text
isod
    Maybe Text
Nothing -> do
      let extractDate :: Element -> Maybe Int
          extractDate :: Element -> Maybe Int
extractDate = forall (m :: * -> *) a. (MonadPlus m, Read a) => Text -> m a
safeRead forall b c a. (b -> c) -> (a -> b) -> a -> c
. Element -> Text
strContent
      let yr :: Maybe Int
yr = (Element -> Bool) -> Element -> Maybe Element
filterElement (Text -> Element -> Bool
named Text
"year") Element
e forall (m :: * -> *) a b. Monad m => m a -> (a -> m b) -> m b
>>= Element -> Maybe Int
extractDate
      let mon :: Maybe Int
mon = (Element -> Bool) -> Element -> Maybe Element
filterElement (Text -> Element -> Bool
named Text
"month") Element
e forall (m :: * -> *) a b. Monad m => m a -> (a -> m b) -> m b
>>= Element -> Maybe Int
extractDate
      let day :: Maybe Int
day = (Element -> Bool) -> Element -> Maybe Element
filterElement (Text -> Element -> Bool
named Text
"day") Element
e forall (m :: * -> *) a b. Monad m => m a -> (a -> m b) -> m b
>>= Element -> Maybe Int
extractDate
      let stringDate :: Maybe Text
stringDate = Element -> Text
strContent forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> (Element -> Bool) -> Element -> Maybe Element
filterElement (Text -> Element -> Bool
named Text
"string-date") Element
e
      forall (f :: * -> *) a. Applicative f => a -> f a
pure forall a b. (a -> b) -> a -> b
$
        case (Maybe Int
yr, Maybe Int
mon, Maybe Int
day) of
          (Just Int
y, Just Int
m, Just Int
d) -> String -> Text
T.pack forall a b. (a -> b) -> a -> b
$ forall r. PrintfType r => String -> r
printf String
"%04d-%02d-%02d" Int
y Int
m Int
d
          (Just Int
y, Just Int
m, Maybe Int
Nothing) -> String -> Text
T.pack forall a b. (a -> b) -> a -> b
$ forall r. PrintfType r => String -> r
printf String
"%04d-%02d" Int
y Int
m
          (Just Int
y, Maybe Int
Nothing, Maybe Int
Nothing) -> String -> Text
T.pack forall a b. (a -> b) -> a -> b
$ forall r. PrintfType r => String -> r
printf String
"%04d" Int
y
          (Maybe Int, Maybe Int, Maybe Int)
_ -> forall a. a -> Maybe a -> a
fromMaybe forall a. Monoid a => a
mempty Maybe Text
stringDate

getPermissions :: PandocMonad m => Element -> JATS m ()
getPermissions :: forall (m :: * -> *). PandocMonad m => Element -> JATS m ()
getPermissions Element
e = do
  Map Text MetaValue
copyright <- forall (m :: * -> *).
PandocMonad m =>
Element -> JATS m (Map Text MetaValue)
getCopyright Element
e
  Map Text MetaValue
license <-  case (Element -> Bool) -> Element -> Maybe Element
filterElement (Text -> Element -> Bool
named Text
"license") Element
e of
               Just Element
s  -> forall (m :: * -> *).
PandocMonad m =>
Element -> JATS m (Map Text MetaValue)
getLicense Element
s
               Maybe Element
Nothing -> forall (m :: * -> *) a. Monad m => a -> m a
return forall a. Monoid a => a
mempty
  forall (f :: * -> *). Applicative f => Bool -> f () -> f ()
when (Map Text MetaValue
copyright forall a. Eq a => a -> a -> Bool
/= forall a. Monoid a => a
mempty) forall a b. (a -> b) -> a -> b
$ forall (m :: * -> *) a.
(PandocMonad m, ToMetaValue a) =>
Text -> a -> JATS m ()
addMeta Text
"copyright" Map Text MetaValue
copyright
  forall (f :: * -> *). Applicative f => Bool -> f () -> f ()
when (Map Text MetaValue
license forall a. Eq a => a -> a -> Bool
/= forall a. Monoid a => a
mempty) forall a b. (a -> b) -> a -> b
$ forall (m :: * -> *) a.
(PandocMonad m, ToMetaValue a) =>
Text -> a -> JATS m ()
addMeta Text
"license" Map Text MetaValue
license

getCopyright :: PandocMonad m => Element -> JATS m (Map.Map Text MetaValue)
getCopyright :: forall (m :: * -> *).
PandocMonad m =>
Element -> JATS m (Map Text MetaValue)
getCopyright Element
e = do
  let holder :: Maybe (Text, MetaValue)
holder = Element -> Text -> Text -> Maybe (Text, MetaValue)
metaElement Element
e Text
"copyright-holder" Text
"holder"
  let statement :: Maybe (Text, MetaValue)
statement = Element -> Text -> Text -> Maybe (Text, MetaValue)
metaElement Element
e Text
"copyright-statement" Text
"statement"
  let year :: Maybe (Text, MetaValue)
year = Element -> Text -> Text -> Maybe (Text, MetaValue)
metaElement Element
e Text
"copyright-year" Text
"year"
  forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ forall k a. Ord k => [(k, a)] -> Map k a
Map.fromList (forall a. [Maybe a] -> [a]
catMaybes forall a b. (a -> b) -> a -> b
$ [Maybe (Text, MetaValue)
holder, Maybe (Text, MetaValue)
statement, Maybe (Text, MetaValue)
year])

getLicense :: PandocMonad m => Element -> JATS m (Map.Map Text MetaValue)
getLicense :: forall (m :: * -> *).
PandocMonad m =>
Element -> JATS m (Map Text MetaValue)
getLicense Element
e = do
  let licenseType :: Maybe (Text, MetaValue)
licenseType = Element -> Text -> Text -> Maybe (Text, MetaValue)
metaAttribute Element
e Text
"license-type" Text
"type"
  let licenseLink :: Maybe (Text, MetaValue)
licenseLink = Element -> Text -> Maybe (Text, MetaValue)
metaElementAliRef Element
e Text
"link"
  let licenseText :: Maybe (Text, MetaValue)
licenseText = Element -> Text -> Text -> Maybe (Text, MetaValue)
metaElement Element
e Text
"license-p" Text
"text"
  forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ forall k a. Ord k => [(k, a)] -> Map k a
Map.fromList (forall a. [Maybe a] -> [a]
catMaybes forall a b. (a -> b) -> a -> b
$ [Maybe (Text, MetaValue)
licenseType, Maybe (Text, MetaValue)
licenseLink, Maybe (Text, MetaValue)
licenseText])

metaElement :: Element -> Text -> Text -> Maybe (Text, MetaValue)
metaElement :: Element -> Text -> Text -> Maybe (Text, MetaValue)
metaElement Element
e Text
child Text
key =
  case (Element -> Bool) -> Element -> Maybe Element
filterElement (Text -> Element -> Bool
named Text
child) Element
e of
    Just Element
content -> forall a. a -> Maybe a
Just (Text
key, forall a. ToMetaValue a => a -> MetaValue
toMetaValue forall a b. (a -> b) -> a -> b
$ Element -> Text
strContent Element
content)
    Maybe Element
Nothing -> forall a. Maybe a
Nothing

metaElementAliRef :: Element -> Text -> Maybe (Text, MetaValue)
metaElementAliRef :: Element -> Text -> Maybe (Text, MetaValue)
metaElementAliRef Element
e Text
key =
  case (Element -> Bool) -> Element -> Maybe Element
filterElement Element -> Bool
isAliLicenseRef Element
e of
    Just Element
content -> forall a. a -> Maybe a
Just (Text
key, forall a. ToMetaValue a => a -> MetaValue
toMetaValue forall a b. (a -> b) -> a -> b
$ Element -> Text
strContent Element
content)
    Maybe Element
Nothing -> forall a. Maybe a
Nothing

metaAttribute :: Element -> Text -> Text -> Maybe (Text, MetaValue)
metaAttribute :: Element -> Text -> Text -> Maybe (Text, MetaValue)
metaAttribute Element
e Text
attr Text
key =
  case Text -> Element -> Maybe Text
maybeAttrValue Text
attr Element
e of
    Just Text
content -> forall a. a -> Maybe a
Just (Text
key, forall a. ToMetaValue a => a -> MetaValue
toMetaValue Text
content)
    Maybe Text
Nothing -> forall a. Maybe a
Nothing

getContrib :: PandocMonad m => Element -> JATS m Inlines
getContrib :: forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getContrib Element
x = do
  Inlines
given <- forall b a. b -> (a -> b) -> Maybe a -> b
maybe (forall (m :: * -> *) a. Monad m => a -> m a
return forall a. Monoid a => a
mempty) forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines
            forall a b. (a -> b) -> a -> b
$ (Element -> Bool) -> Element -> Maybe Element
filterElement (Text -> Element -> Bool
named Text
"given-names") Element
x
  Inlines
family <- forall b a. b -> (a -> b) -> Maybe a -> b
maybe (forall (m :: * -> *) a. Monad m => a -> m a
return forall a. Monoid a => a
mempty) forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines
            forall a b. (a -> b) -> a -> b
$ (Element -> Bool) -> Element -> Maybe Element
filterElement (Text -> Element -> Bool
named Text
"surname") Element
x
  if Inlines
given forall a. Eq a => a -> a -> Bool
== forall a. Monoid a => a
mempty Bool -> Bool -> Bool
&& Inlines
family forall a. Eq a => a -> a -> Bool
== forall a. Monoid a => a
mempty
     then forall (m :: * -> *) a. Monad m => a -> m a
return forall a. Monoid a => a
mempty
     else if Inlines
given forall a. Eq a => a -> a -> Bool
== forall a. Monoid a => a
mempty Bool -> Bool -> Bool
|| Inlines
family forall a. Eq a => a -> a -> Bool
== forall a. Monoid a => a
mempty
          then forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ Inlines
given forall a. Semigroup a => a -> a -> a
<> Inlines
family
          else forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ Inlines
given forall a. Semigroup a => a -> a -> a
<> Inlines
space 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 <- forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM forall (m :: * -> *).
PandocMonad m =>
Element -> JATS m (Map Text MetaValue)
parseRef forall a b. (a -> b) -> a -> b
$ (Element -> Bool) -> Element -> [Element]
filterChildren (Text -> Element -> Bool
named Text
"ref") Element
e
  let mbtitle :: Maybe Element
mbtitle = (Element -> Bool) -> Element -> Maybe Element
filterChild (Text -> Element -> Bool
named Text
"title") Element
e
  Blocks
title <- case Maybe Element
mbtitle of
    Maybe Element
Nothing -> forall (f :: * -> *) a. Applicative f => a -> f a
pure forall a. Monoid a => a
mempty
    Just Element
te -> Int -> Inlines -> Blocks
header Int
1 forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> forall (m :: * -> *). PandocMonad m => Content -> JATS m Inlines
parseInline (Element -> Content
Elem Element
te)
  forall (m :: * -> *) a.
(PandocMonad m, ToMetaValue a) =>
Text -> a -> JATS m ()
addMeta Text
"references" [Map Text MetaValue]
refs
  forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ Blocks
title forall a. Semigroup a => a -> a -> a
<> Attr -> Blocks -> Blocks
divWith (Text
"refs",[],[]) 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 forall a. Semigroup a => a -> a -> a
<> Text -> Inlines
text Text
"-" forall a. Semigroup a => a -> a -> a
<> Inlines
y
  let getName :: Element -> StateT JATSState m MetaValue
getName Element
nm = do
        Inlines
given <- forall b a. b -> (a -> b) -> Maybe a -> b
maybe (forall (m :: * -> *) a. Monad m => a -> m a
return forall a. Monoid a => a
mempty) forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines
                  forall a b. (a -> b) -> a -> b
$ (Element -> Bool) -> Element -> Maybe Element
filterChild (Text -> Element -> Bool
named Text
"given-names") Element
nm
        Inlines
family <- forall b a. b -> (a -> b) -> Maybe a -> b
maybe (forall (m :: * -> *) a. Monad m => a -> m a
return forall a. Monoid a => a
mempty) forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines
                  forall a b. (a -> b) -> a -> b
$ (Element -> Bool) -> Element -> Maybe Element
filterChild (Text -> Element -> Bool
named Text
"surname") Element
nm
        forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ forall a. ToMetaValue a => a -> MetaValue
toMetaValue forall a b. (a -> b) -> a -> b
$ 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" -> forall a. a -> Maybe a
Just forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"title",) forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. ToMetaValue a => a -> MetaValue
toMetaValue forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el
          Text
"source" ->
            case (Element -> Bool) -> Element -> Maybe Element
filterChild (Text -> Element -> Bool
named Text
"article-title") Element
c of
              Just Element
_ -> forall a. a -> Maybe a
Just forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"container-title",) forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. ToMetaValue a => a -> MetaValue
toMetaValue forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el
              Maybe Element
Nothing -> forall a. a -> Maybe a
Just forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"title",) forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. ToMetaValue a => a -> MetaValue
toMetaValue forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el
          Text
"label" -> forall a. a -> Maybe a
Just forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"citation-label",) forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. ToMetaValue a => a -> MetaValue
toMetaValue forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> 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 -> forall a. a -> Maybe a
Just forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"issued",) forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. ToMetaValue a => a -> MetaValue
toMetaValue forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$>
                                 (Inlines -> Inlines -> Inlines
combineWithDash
                                    forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
m)
                      Maybe Element
Nothing -> forall a. a -> Maybe a
Just forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"issued",) forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. ToMetaValue a => a -> MetaValue
toMetaValue forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el
          Text
"volume" -> forall a. a -> Maybe a
Just forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"volume",) forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. ToMetaValue a => a -> MetaValue
toMetaValue forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el
          Text
"issue" -> forall a. a -> Maybe a
Just forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"issue",) forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. ToMetaValue a => a -> MetaValue
toMetaValue forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el
          Text
"isbn" -> forall a. a -> Maybe a
Just forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"ISBN",) forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. ToMetaValue a => a -> MetaValue
toMetaValue forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el
          Text
"issn" -> forall a. a -> Maybe a
Just forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"ISSN",) forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. ToMetaValue a => a -> MetaValue
toMetaValue forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el
          Text
"uri" -> forall a. a -> Maybe a
Just forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"url",) forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. ToMetaValue a => a -> MetaValue
toMetaValue forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> 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 -> forall a. a -> Maybe a
Just forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"page",) forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. ToMetaValue a => a -> MetaValue
toMetaValue forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$>
                          (Inlines -> Inlines -> Inlines
combineWithDash forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
lp)
              Maybe Element
Nothing -> forall a. a -> Maybe a
Just forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"page-first",) forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. ToMetaValue a => a -> MetaValue
toMetaValue forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el
          Text
"publisher-name" -> forall a. a -> Maybe a
Just forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"publisher",) forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. ToMetaValue a => a -> MetaValue
toMetaValue forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el
          Text
"publisher-loc" -> forall a. a -> Maybe a
Just forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Text
"publisher-place",) forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. ToMetaValue a => a -> MetaValue
toMetaValue
                                forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> forall (m :: * -> *). PandocMonad m => Element -> JATS m Inlines
getInlines Element
el
          Text
"edition" -> forall (f :: * -> *) a. Applicative f => a -> f a
pure forall a b. (a -> b) -> a -> b
$ forall a. a -> Maybe a
Just (Text
"edition",
                               forall a. ToMetaValue a => a -> MetaValue
toMetaValue forall b c a. (b -> c) -> (a -> b) -> a -> c
. (Char -> Bool) -> Text -> Text
T.filter Char -> Bool
isDigit forall a b. (a -> b) -> a -> b
$ Element -> Text
strContent Element
el)
          Text
"person-group" -> do [MetaValue]
names <- forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM forall {m :: * -> *}.
PandocMonad m =>
Element -> StateT JATSState m MetaValue
getName
                                            ((Element -> Bool) -> Element -> [Element]
filterChildren (Text -> Element -> Bool
named Text
"name") Element
el)
                               forall (f :: * -> *) a. Applicative f => a -> f a
pure forall a b. (a -> b) -> a -> b
$ forall a. a -> Maybe a
Just (Text -> Element -> Text
attrValue Text
"person-group-type" Element
el,
                                            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"  -> forall (f :: * -> *) a. Applicative f => a -> f a
pure forall a b. (a -> b) -> a -> b
$ forall a. a -> Maybe a
Just (Text
"DOI",  forall a. ToMetaValue a => a -> MetaValue
toMetaValue forall a b. (a -> b) -> a -> b
$ Element -> Text
strContent Element
el)
                         Text
"pmid" -> forall (f :: * -> *) a. Applicative f => a -> f a
pure forall a b. (a -> b) -> a -> b
$ forall a. a -> Maybe a
Just (Text
"PMID", forall a. ToMetaValue a => a -> MetaValue
toMetaValue forall a b. (a -> b) -> a -> b
$ Element -> Text
strContent Element
el)
                         Text
_      -> forall (f :: * -> *) a. Applicative f => a -> f a
pure forall a. Maybe a
Nothing
          Text
"object-id" -> case Text -> Element -> Text
attrValue Text
"pub-id-type" Element
el of
                         Text
"doi"  -> forall (f :: * -> *) a. Applicative f => a -> f a
pure forall a b. (a -> b) -> a -> b
$ forall a. a -> Maybe a
Just (Text
"DOI",  forall a. ToMetaValue a => a -> MetaValue
toMetaValue forall a b. (a -> b) -> a -> b
$ Element -> Text
strContent Element
el)
                         Text
"pmid" -> forall (f :: * -> *) a. Applicative f => a -> f a
pure forall a b. (a -> b) -> a -> b
$ forall a. a -> Maybe a
Just (Text
"PMID", forall a. ToMetaValue a => a -> MetaValue
toMetaValue forall a b. (a -> b) -> a -> b
$ Element -> Text
strContent Element
el)
                         Text
_      -> forall (f :: * -> *) a. Applicative f => a -> f a
pure forall a. Maybe a
Nothing


          Text
_ -> forall (f :: * -> *) a. Applicative f => a -> f a
pure 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", forall a. ToMetaValue a => a -> MetaValue
toMetaValue 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) forall a. a -> [a] -> [a]
:) forall b c a. (b -> c) -> (a -> b) -> a -> c
.
                  forall a. [Maybe a] -> [a]
catMaybes forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM (forall (m :: * -> *).
PandocMonad m =>
Element -> Element -> JATS m (Maybe (Text, MetaValue))
refElement Element
c) (Element -> [Element]
elChildren Element
c)
      Maybe Element
Nothing -> 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 = forall a. a -> Maybe a -> a
fromMaybe Text
t forall a b. (a -> b) -> a -> b
$ Text -> Text -> Maybe Text
T.stripPrefix Text
"ref-" Text
t
  forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ forall k a. Ord k => [(k, a)] -> Map k a
Map.fromList ((Text
"id", forall a. ToMetaValue a => a -> MetaValue
toMetaValue forall a b. (a -> b) -> a -> b
$ Text -> Text
stripPref forall a b. (a -> b) -> a -> b
$ Text -> Element -> Text
attrValue Text
"id" Element
e)
                        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 forall b c a. (b -> c) -> (a -> b) -> a -> c
.
  (\Element
e' -> Element
e'{ elContent :: [Content]
elContent = forall a b. (a -> b) -> [a] -> [b]
map Content -> Content
elementToStr 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 forall a b. (a -> b) -> a -> b
$ CDataKind -> Text -> Maybe Line -> CData
CData CDataKind
CDataText (Element -> Text
strContentRecursive Element
e') 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
_)) = forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ Text -> Inlines
text Text
s
parseInline (CRef Text
ref) = forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ forall b a. b -> (a -> b) -> Maybe a -> b
maybe (Text -> Inlines
text forall a b. (a -> b) -> a -> b
$ Text -> Text
T.toUpper Text
ref) Text -> Inlines
text
                                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" -> forall {m :: * -> *}.
PandocMonad m =>
(Inlines -> Inlines) -> StateT JATSState m Inlines
innerInlines Inlines -> Inlines
emph
        Text
"bold" -> forall {m :: * -> *}.
PandocMonad m =>
(Inlines -> Inlines) -> StateT JATSState m Inlines
innerInlines Inlines -> Inlines
strong
        Text
"strike" -> forall {m :: * -> *}.
PandocMonad m =>
(Inlines -> Inlines) -> StateT JATSState m Inlines
innerInlines Inlines -> Inlines
strikeout
        Text
"sub" -> forall {m :: * -> *}.
PandocMonad m =>
(Inlines -> Inlines) -> StateT JATSState m Inlines
innerInlines Inlines -> Inlines
subscript
        Text
"sup" -> forall {m :: * -> *}.
PandocMonad m =>
(Inlines -> Inlines) -> StateT JATSState m Inlines
innerInlines Inlines -> Inlines
superscript
        Text
"underline" -> forall {m :: * -> *}.
PandocMonad m =>
(Inlines -> Inlines) -> StateT JATSState m Inlines
innerInlines Inlines -> Inlines
underline
        Text
"break" -> forall (m :: * -> *) a. Monad m => a -> m a
return Inlines
linebreak
        Text
"sc" -> 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" -> forall (m :: * -> *).
PandocMonad m =>
Maybe (Inlines, Text) -> Element -> JATS m Inlines
getGraphic forall a. Maybe a
Nothing Element
e
        Text
"disp-quote" -> do
            QuoteType
qt <- forall s (m :: * -> *) a. MonadState s m => (s -> a) -> m a
gets JATSState -> QuoteType
jatsQuoteType
            let qt' :: QuoteType
qt' = if QuoteType
qt forall a. Eq a => a -> a -> Bool
== QuoteType
SingleQuote then QuoteType
DoubleQuote else QuoteType
SingleQuote
            forall s (m :: * -> *). MonadState s m => (s -> s) -> m ()
modify forall a b. (a -> b) -> a -> b
$ \JATSState
st -> JATSState
st{ jatsQuoteType :: QuoteType
jatsQuoteType = QuoteType
qt' }
            Inlines
contents <- forall {m :: * -> *}.
PandocMonad m =>
(Inlines -> Inlines) -> StateT JATSState m Inlines
innerInlines forall a. a -> a
id
            forall s (m :: * -> *). MonadState s m => (s -> s) -> m ()
modify forall a b. (a -> b) -> a -> b
$ \JATSState
st -> JATSState
st{ jatsQuoteType :: QuoteType
jatsQuoteType = QuoteType
qt }
            forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ if QuoteType
qt 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 <- forall {m :: * -> *}.
PandocMonad m =>
(Inlines -> Inlines) -> StateT JATSState m Inlines
innerInlines 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",) 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, [], forall a. Maybe a -> [a]
maybeToList Maybe (Text, Text)
refType)
            forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ if Maybe (Text, Text)
refType forall a. Eq a => a -> a -> Bool
== forall a. a -> Maybe a
Just (Text
"ref-type",Text
"bibr")
                        then [Citation] -> Inlines -> Inlines
cite
                             (forall a b. (a -> b) -> [a] -> [b]
map (\Text
id' ->
                               let id'' :: Text
id'' = forall a. a -> Maybe a -> a
fromMaybe Text
id' 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 forall {a}. (Text, [a], [(Text, Text)])
attr (Text
"#" forall a. Semigroup a => a -> a -> a
<> Text
rid) Text
"" Inlines
ils
        Text
"ext-link" -> do
             Inlines
ils <- forall {m :: * -> *}.
PandocMonad m =>
(Inlines -> Inlines) -> StateT JATSState m Inlines
innerInlines forall a. a -> a
id
             let title :: Text
title = forall a. a -> Maybe a -> a
fromMaybe Text
"" forall a b. (a -> b) -> a -> b
$ QName -> Element -> Maybe Text
findAttr (Text -> Maybe Text -> Maybe Text -> QName
QName Text
"title" (forall a. a -> Maybe a
Just Text
"http://www.w3.org/1999/xlink") 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" (forall a. a -> Maybe a
Just Text
"http://www.w3.org/1999/xlink") forall a. Maybe a
Nothing) Element
e of
                               Just Text
h -> Text
h
                               Maybe Text
_      -> Text
"#" forall a. Semigroup a => a -> a -> a
<> Text -> Element -> Text
attrValue Text
"rid" Element
e
             let ils' :: Inlines
ils' = if Inlines
ils forall a. Eq a => a -> a -> Bool
== 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, [], [])
             forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ Attr -> Text -> Text -> Inlines -> Inlines
linkWith forall {a} {a}. (Text, [a], [a])
attr Text
href Text
title Inlines
ils'

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

        Text
"email" -> forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ Text -> Text -> Inlines -> Inlines
link (Text
"mailto:" forall a. Semigroup a => a -> a -> a
<> Element -> Text
textContent Element
e) Text
""
                          forall a b. (a -> b) -> a -> b
$ Text -> Inlines
str forall a b. (a -> b) -> a -> b
$ Element -> Text
textContent Element
e
        Text
"uri" -> forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ Text -> Text -> Inlines -> Inlines
link (Element -> Text
textContent Element
e) Text
"" forall a b. (a -> b) -> a -> b
$ Text -> Inlines
str forall a b. (a -> b) -> a -> b
$ Element -> Text
textContent Element
e
        Text
"fn" -> Blocks -> Inlines
note forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. Monoid a => [a] -> a
mconcat forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$>
                         forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM forall (m :: * -> *). PandocMonad m => Content -> JATS m Blocks
parseBlock (Element -> [Content]
elContent Element
e)
        Text
_          -> forall {m :: * -> *}.
PandocMonad m =>
(Inlines -> Inlines) -> StateT JATSState m Inlines
innerInlines forall a. a -> a
id
   where innerInlines :: (Inlines -> Inlines) -> StateT JATSState m Inlines
innerInlines Inlines -> Inlines
f = (Inlines -> Inlines) -> Inlines -> Inlines
extractSpaces Inlines -> Inlines
f forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. Monoid a => [a] -> a
mconcat forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$>
                          forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM forall (m :: * -> *). PandocMonad m => Content -> JATS m Inlines
parseInline (Element -> [Content]
elContent Element
e)
         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]
           forall (m :: * -> *) a. Monad m => a -> m a
return forall a b. (a -> b) -> a -> b
$ Attr -> Text -> Inlines
codeWith (Text -> Element -> Text
attrValue Text
"id" Element
e,[Text]
classes',[]) forall a b. (a -> b) -> a -> b
$ Element -> Text
strContentRecursive Element
e

inlineFormula ::  PandocMonad m => (Text->Inlines) -> Element -> JATS m Inlines
inlineFormula :: forall (m :: * -> *).
PandocMonad m =>
(Text -> Inlines) -> Element -> JATS m Inlines
inlineFormula Text -> Inlines
constructor Element
e = do
            let whereToLook :: Element
whereToLook = forall a. a -> Maybe a -> a
fromMaybe Element
e forall a b. (a -> b) -> a -> b
$ (Element -> Bool) -> Element -> Maybe Element
filterElement (Text -> Element -> Bool
named Text
"alternatives") Element
e
                texMaths :: [Text]
texMaths = forall a b. (a -> b) -> [a] -> [b]
map Element -> Text
textContent forall a b. (a -> b) -> a -> b
$
                            (Element -> Bool) -> Element -> [Element]
filterChildren (Text -> Element -> Bool
named  Text
"tex-math") Element
whereToLook
                mathMLs :: [Text]
mathMLs = forall a b. (a -> b) -> [a] -> [b]
map Element -> Text
mathML forall a b. (a -> b) -> a -> b
$
                            (Element -> Bool) -> Element -> [Element]
filterChildren Element -> Bool
isMathML Element
whereToLook
            forall (m :: * -> *) a. Monad m => a -> m a
return forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. Monoid a => [a] -> a
mconcat forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. Int -> [a] -> [a]
take Int
1 forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a b. (a -> b) -> [a] -> [b]
map Text -> Inlines
constructor forall a b. (a -> b) -> a -> b
$ [Text]
texMaths forall a. [a] -> [a] -> [a]
++ [Text]
mathMLs

blockFormula ::  PandocMonad m => (Text->Inlines) -> Element -> JATS m Blocks
blockFormula :: forall (m :: * -> *).
PandocMonad m =>
(Text -> Inlines) -> Element -> JATS m Blocks
blockFormula Text -> Inlines
constructor Element
e = do
            let whereToLook :: Element
whereToLook = forall a. a -> Maybe a -> a
fromMaybe Element
e forall a b. (a -> b) -> a -> b
$ (Element -> Bool) -> Element -> Maybe Element
filterElement (Text -> Element -> Bool
named Text
"alternatives") Element
e
                texMaths :: [Text]
texMaths = forall a b. (a -> b) -> [a] -> [b]
map Element -> Text
textContent forall a b. (a -> b) -> a -> b
$
                            (Element -> Bool) -> Element -> [Element]
filterChildren (Text -> Element -> Bool
named  Text
"tex-math") Element
whereToLook
                mathMLs :: [Text]
mathMLs = forall a b. (a -> b) -> [a] -> [b]
map Element -> Text
mathML forall a b. (a -> b) -> a -> b
$
                            (Element -> Bool) -> Element -> [Element]
filterChildren Element -> Bool
isMathML Element
whereToLook
            forall (m :: * -> *) a. Monad m => a -> m a
return forall b c a. (b -> c) -> (a -> b) -> a -> c
. Inlines -> Blocks
para forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. [a] -> a
head forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a. Int -> [a] -> [a]
take Int
1 forall b c a. (b -> c) -> (a -> b) -> a -> c
. forall a b. (a -> b) -> [a] -> [b]
map Text -> Inlines
constructor forall a b. (a -> b) -> a -> b
$ [Text]
texMaths forall a. [a] -> [a] -> [a]
++ [Text]
mathMLs

mathML :: Element -> Text
mathML :: Element -> Text
mathML Element
x =
          case Text -> Either Text [Exp]
readMathML forall b c a. (b -> c) -> (a -> b) -> a -> c
. Element -> Text
showElement forall a b. (a -> b) -> a -> b
$ (forall a. Data a => a -> a) -> forall a. Data a => a -> a
everywhere (forall a b. (Typeable a, Typeable b) => (b -> b) -> a -> a
mkT QName -> QName
removePrefix) Element
x of
                Left Text
_ -> forall a. Monoid a => a
mempty
                Right [Exp]
m -> [Exp] -> Text
writeTeX [Exp]
m
          where removePrefix :: QName -> QName
removePrefix QName
elname = QName
elname { qPrefix :: Maybe Text
qPrefix = forall a. Maybe a
Nothing }

isMathML :: Element -> Bool
isMathML :: Element -> Bool
isMathML Element
x = QName -> Text
qName (Element -> QName
elName Element
x) forall a. Eq a => a -> a -> Bool
== Text
"math" Bool -> Bool -> Bool
&&
                      QName -> Maybe Text
qURI  (Element -> QName
elName Element
x) forall a. Eq a => a -> a -> Bool
==
                                      forall a. a -> Maybe a
Just Text
"http://www.w3.org/1998/Math/MathML"

formulaChildren :: Element -> [Element]
formulaChildren :: Element -> [Element]
formulaChildren Element
x = (Element -> Bool) -> Element -> [Element]
filterChildren Element -> Bool
isMathML Element
x forall a. [a] -> [a] -> [a]
++ (Element -> Bool) -> Element -> [Element]
filterChildren (Text -> Element -> Bool
named Text
"tex-math") Element
x

hasFormulaChild :: Element -> Bool
hasFormulaChild :: Element -> Bool
hasFormulaChild Element
x = forall (t :: * -> *) a. Foldable t => t a -> Int
length (Element -> [Element]
formulaChildren Element
x) forall a. Ord a => a -> a -> Bool
> Int
0

isAliLicenseRef :: Element -> Bool
isAliLicenseRef :: Element -> Bool
isAliLicenseRef Element
x = QName -> Text
qName (Element -> QName
elName Element
x) forall a. Eq a => a -> a -> Bool
== Text
"license_ref" Bool -> Bool -> Bool
&&
                      QName -> Maybe Text
qURI  (Element -> QName
elName Element
x) forall a. Eq a => a -> a -> Bool
==
                                      forall a. a -> Maybe a
Just Text
"http://www.niso.org/schemas/ali/1.0/"