pandoc-3.0: src/Text/Pandoc/Readers/JATS.hs
{-# LANGUAGE ScopedTypeVariables #-}
{-# LANGUAGE TupleSections #-}
{-# LANGUAGE OverloadedStrings #-}
{- |
Module : Text.Pandoc.Readers.JATS
Copyright : Copyright (C) 2017-2020 Hamish Mackenzie
License : GNU GPL, version 2 or above
Maintainer : John MacFarlane <jgm@berkeley.edu>
Stability : alpha
Portability : portable
Conversion of JATS XML to 'Pandoc' document.
-}
module Text.Pandoc.Readers.JATS ( readJATS ) where
import Control.Monad.State.Strict ( StateT(runStateT), gets, modify )
import Control.Monad (forM_, when, unless, MonadPlus(mplus))
import Control.Monad.Except (throwError)
import Text.Pandoc.Error (PandocError(..))
import Data.Char (isDigit, isSpace)
import Data.Default
import Data.Generics
import Data.List (foldl', intersperse)
import qualified Data.Map as Map
import Data.Maybe (maybeToList, fromMaybe, catMaybes)
import Data.Text (Text)
import qualified Data.Text as T
import qualified Data.Text.Lazy as TL
import Text.Pandoc.XML (lookupEntity)
import Text.Pandoc.Builder
import Text.Pandoc.Class.PandocMonad (PandocMonad)
import Text.Pandoc.Options
import Text.Pandoc.Shared (safeRead, extractSpaces)
import Text.Pandoc.Walk (walk)
import Text.Pandoc.XML.Light
import Text.TeXMath (readMathML, writeTeX)
import qualified Data.Set as S (fromList, member)
import Data.Set ((\\))
import Text.Pandoc.Sources (ToSources(..), sourcesToText)
type JATS m = StateT JATSState m
data JATSState = JATSState{ jatsSectionLevel :: Int
, jatsQuoteType :: QuoteType
, jatsMeta :: Meta
, jatsBook :: Bool
, jatsFootnotes :: Map.Map Text Blocks
, jatsContent :: [Content]
} deriving Show
instance Default JATSState where
def = JATSState{ jatsSectionLevel = 0
, jatsQuoteType = DoubleQuote
, jatsMeta = mempty
, jatsBook = False
, jatsFootnotes = mempty
, jatsContent = [] }
readJATS :: (PandocMonad m, ToSources a)
=> ReaderOptions
-> a
-> m Pandoc
readJATS _ inp = do
let sources = toSources inp
tree <- either (throwError . PandocXMLError "") return $
parseXMLContents (TL.fromStrict . sourcesToText $ sources)
(bs, st') <- flip runStateT (def{ jatsContent = tree }) $ mapM parseBlock tree
let footnotes = jatsFootnotes st'
let blockList = toList $ mconcat bs
let linkToFootnotes :: Inline -> Inline
linkToFootnotes link'@(Link _attr _txt (href, _title)) =
case T.uncons href of
Just ('#', rid) -> case Map.lookup rid footnotes of
Just footnote -> Note (toList footnote)
Nothing -> link'
_ -> link'
linkToFootnotes inline = inline
return $ Pandoc (jatsMeta st') (walk linkToFootnotes blockList)
-- convenience function to get an attribute value, defaulting to ""
attrValue :: Text -> Element -> Text
attrValue attr =
fromMaybe "" . maybeAttrValue attr
maybeAttrValue :: Text -> Element -> Maybe Text
maybeAttrValue attr elt =
lookupAttrBy (\x -> qName x == attr) (elAttribs elt)
-- convenience function
named :: Text -> Element -> Bool
named s e = qName (elName e) == s
--
addMeta :: PandocMonad m => ToMetaValue a => Text -> a -> JATS m ()
addMeta field val = modify (setMeta field val)
instance HasMeta JATSState where
setMeta field v s = s {jatsMeta = setMeta field v (jatsMeta s)}
deleteMeta field s = s {jatsMeta = deleteMeta field (jatsMeta s)}
isBlockElement :: Content -> Bool
isBlockElement (Elem e) = qName (elName e) `S.member` blocktags
where blocktags = S.fromList (paragraphLevel ++ lists ++ mathML ++ other) \\ S.fromList inlinetags
paragraphLevel = ["address", "array", "boxed-text", "chem-struct-wrap",
"code", "fig", "fig-group", "graphic", "media", "preformat",
"supplementary-material", "table-wrap", "table-wrap-group",
"alternatives", "disp-formula", "disp-formula-group"]
lists = ["def-list", "list"]
mathML = ["tex-math", "mml:math"]
other = ["p", "related-article", "related-object", "ack", "disp-quote",
"speech", "statement", "verse-group", "x"]
inlinetags = ["email", "ext-link", "uri", "inline-supplementary-material",
"related-article", "related-object", "hr", "bold", "fixed-case",
"italic", "monospace", "overline", "overline-start", "overline-end",
"roman", "sans-serif", "sc", "strike", "underline", "underline-start",
"underline-end", "ruby", "alternatives", "inline-graphic", "private-char",
"chem-struct", "inline-formula", "tex-math", "mml:math", "abbrev",
"milestone-end", "milestone-start", "named-content", "styled-content",
"fn", "target", "xref", "sub", "sup", "x", "address", "array",
"boxed-text", "chem-struct-wrap", "code", "fig", "fig-group", "graphic",
"media", "preformat", "supplementary-material", "table-wrap",
"table-wrap-group", "disp-formula", "disp-formula-group",
"citation-alternatives", "element-citation", "mixed-citation",
"nlm-citation", "award-id", "funding-source", "open-access",
"def-list", "list", "ack", "disp-quote", "speech", "statement",
"verse-group"]
isBlockElement _ = False
-- Trim leading and trailing newline characters
trimNl :: Text -> Text
trimNl = T.dropAround (== '\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 mbfigdata e = do
let atVal a = attrValue a e
(ident, title, capt) =
case mbfigdata of
Just (capt', i) -> (i, "fig:" <> atVal "title", capt')
Nothing -> (atVal "id", atVal "title",
text (atVal "alt-text"))
attr = (ident, T.words $ atVal "role", [])
imageUrl = atVal "href"
return $ imageWith attr imageUrl title capt
getBlocks :: PandocMonad m => Element -> JATS m Blocks
getBlocks e = mconcat <$>
mapM parseBlock (elContent e)
parseBlock :: PandocMonad m => Content -> JATS m Blocks
parseBlock (Text (CData CDataRaw _ _)) = return mempty -- DOCTYPE
parseBlock (Text (CData _ s _)) = if T.all isSpace s
then return mempty
else return $ plain $ trimInlines $ text s
parseBlock (CRef x) = return $ plain $ str $ T.toUpper x
parseBlock (Elem e) =
case qName (elName e) of
"p" -> parseMixed para (elContent e)
"code" -> codeBlockWithLang
"preformat" -> codeBlockWithLang
"disp-quote" -> parseBlockquote
"list" -> case attrValue "list-type" e of
"bullet" -> bulletList <$> listitems
listType -> do
let start = fromMaybe 1 $
(filterElement (named "list-item") e
>>= filterElement (named "label"))
>>= safeRead . textContent
orderedListWith (start, parseListStyleType listType, DefaultDelim)
<$> listitems
"def-list" -> definitionList <$> deflistitems
"sec" -> gets jatsSectionLevel >>= sect . (+1)
"graphic" -> para <$> getGraphic Nothing e
"journal-meta" -> parseMetadata e
"article-meta" -> parseMetadata e
"custom-meta" -> parseMetadata e
"title" -> return mempty -- processed by header
"label" -> return mempty -- processed by header
"table" -> parseTable
"fig" -> parseFigure
"fig-group" -> divWith (attrValue "id" e, ["fig-group"], [])
<$> getBlocks e
"table-wrap" -> divWith (attrValue "id" e, ["table-wrap"], [])
<$> getBlocks e
"caption" -> divWith (attrValue "id" e, ["caption"], []) <$> sect 6
"fn-group" -> parseFootnoteGroup
"ref-list" -> parseRefList e
"?xml" -> return mempty
_ -> getBlocks e
where parseMixed container conts = do
let (ils,rest) = break isBlockElement conts
ils' <- trimInlines . mconcat <$> mapM parseInline ils
let p = if ils' == mempty then mempty else container ils'
case rest of
[] -> return p
(r:rs) -> do
b <- parseBlock r
x <- parseMixed container rs
return $ p <> b <> x
codeBlockWithLang = do
let classes' = case attrValue "language" e of
"" -> []
x -> [x]
return $ codeBlockWith (attrValue "id" e, classes', [])
$ trimNl $ strContentRecursive e
parseBlockquote = do
attrib <- case filterChild (named "attribution") e of
Nothing -> return mempty
Just z -> para . (str "— " <>) . mconcat
<$>
mapM parseInline (elContent z)
contents <- getBlocks e
return $ blockQuote (contents <> attrib)
parseListStyleType "roman-lower" = LowerRoman
parseListStyleType "roman-upper" = UpperRoman
parseListStyleType "alpha-lower" = LowerAlpha
parseListStyleType "alpha-upper" = UpperAlpha
parseListStyleType _ = DefaultStyle
listitems = mapM getBlocks $ filterChildren (named "list-item") e
deflistitems = mapM parseVarListEntry $ filterChildren
(named "def-item") e
parseVarListEntry e' = do
let terms = filterChildren (named "term") e'
let items = filterChildren (named "def") e'
terms' <- mapM getInlines terms
items' <- mapM getBlocks items
return (mconcat $ intersperse (str "; ") terms', items')
parseFigure = do
capt <- case filterChild (named "caption") e of
Just t -> mconcat . intersperse linebreak <$>
mapM getInlines (filterChildren (const True) t)
Nothing -> return mempty
contents <- getBlocks e
return $ figureWith
(attrValue "id" e, [], [])
(simpleCaption $ plain capt)
contents
parseFootnoteGroup = do
forM_ (filterChildren (named "fn") e) $ \fn -> do
let id' = attrValue "id" fn
contents <- getBlocks fn
modify $ \st ->
st { jatsFootnotes = Map.insert id' contents (jatsFootnotes st) }
return mempty
parseTable = do
let isCaption x = named "title" x || named "caption" x
capt <- case filterChild isCaption e of
Just t -> getInlines t
Nothing -> return mempty
let e' = fromMaybe e $ filterChild (named "tgroup") e
let isColspec x = named "colspec" x || named "col" x
let colspecs = case filterChild (named "colgroup") e' of
Just c -> filterChildren isColspec c
_ -> filterChildren isColspec e'
let isRow x = named "row" x || named "tr" x
headrows <- case filterChild (named "thead") e' of
Just h -> case filterChild isRow h of
Just x -> parseRow x
Nothing -> return []
Nothing -> return []
bodyrows <- case filterChild (named "tbody") e' of
Just b -> mapM parseRow
$ filterChildren isRow b
Nothing -> mapM parseRow
$ filterChildren isRow e'
let toAlignment c = case findAttr (unqual "align") c of
Just "left" -> AlignLeft
Just "right" -> AlignRight
Just "center" -> AlignCenter
_ -> AlignDefault
let toWidth c = do
w <- findAttr (unqual "colwidth") c
n <- safeRead $ "0" <> T.filter (\x -> isDigit x || x == '.') w
if n > 0 then Just n else Nothing
let numrows = foldl' max 0 $ map length bodyrows
let aligns = case colspecs of
[] -> replicate numrows AlignDefault
cs -> map toAlignment cs
let widths = case colspecs of
[] -> replicate numrows ColWidthDefault
cs -> let ws = map toWidth cs
in case sequence ws of
Just ws' -> let tot = sum ws'
in ColWidth . (/ tot) <$> ws'
Nothing -> replicate numrows ColWidthDefault
let toRow = Row nullAttr . map simpleCell
toHeaderRow l = [toRow l | not (null l)]
return $ table (simpleCaption $ plain capt)
(zip aligns widths)
(TableHead nullAttr $ toHeaderRow headrows)
[TableBody nullAttr 0 [] $ map toRow bodyrows]
(TableFoot nullAttr [])
isEntry x = named "entry" x || named "td" x || named "th" x
parseRow = mapM (parseMixed plain . elContent) . filterChildren isEntry
sect n = do isbook <- gets jatsBook
let n' = if isbook || n == 0 then n + 1 else n
labelText <- case filterChild (named "label") e of
Just t -> (<> ("." <> space)) <$>
getInlines t
Nothing -> return mempty
headerText <- case filterChild (named "title") e `mplus`
(filterChild (named "info") e >>=
filterChild (named "title")) of
Just t -> (labelText <>) <$>
getInlines t
Nothing -> return mempty
oldN <- gets jatsSectionLevel
modify $ \st -> st{ jatsSectionLevel = n }
b <- getBlocks e
let ident = attrValue "id" e
modify $ \st -> st{ jatsSectionLevel = oldN }
return $ headerWith (ident,[],[]) n' headerText <> b
getInlines :: PandocMonad m => Element -> JATS m Inlines
getInlines e' = trimInlines . mconcat <$>
mapM parseInline (elContent e')
parseMetadata :: PandocMonad m => Element -> JATS m Blocks
parseMetadata e = do
getTitle e
getAuthors e
getAffiliations e
getAbstract e
getPubDate e
return mempty
getTitle :: PandocMonad m => Element -> JATS m ()
getTitle e = do
tit <- case filterElement (named "article-title") e of
Just s -> getInlines s
Nothing -> return mempty
subtit <- case filterElement (named "subtitle") e of
Just s -> (text ": " <>) <$>
getInlines s
Nothing -> return mempty
when (tit /= mempty) $ addMeta "title" tit
when (subtit /= mempty) $ addMeta "subtitle" subtit
getAuthors :: PandocMonad m => Element -> JATS m ()
getAuthors e = do
authors <- mapM getContrib $ filterElements
(\x -> named "contrib" x &&
attrValue "contrib-type" x == "author") e
authorNotes <- mapM getInlines $ filterElements (named "author-notes") e
let authors' = case (reverse authors, authorNotes) of
([], _) -> []
(_, []) -> authors
(a:as, ns) -> reverse as ++ [a <> mconcat ns]
unless (null authors) $ addMeta "author" authors'
getAffiliations :: PandocMonad m => Element -> JATS m ()
getAffiliations x = do
affs <- mapM getInlines $ filterChildren (named "aff") x
unless (null affs) $ addMeta "institute" affs
getAbstract :: PandocMonad m => Element -> JATS m ()
getAbstract e =
case filterElement (named "abstract") e of
Just s -> do
blks <- getBlocks s
addMeta "abstract" blks
Nothing -> pure ()
getPubDate :: PandocMonad m => Element -> JATS m ()
getPubDate e =
case filterElement (named "pub-date") e of
Just d -> do
case maybeAttrValue "iso-8601-date" d of
Just isod -> addMeta "date" (text isod)
Nothing -> do
let yr = strContent <$> filterElement (named "year") d
let mon = strContent <$> filterElement (named "month") d
let day = strContent <$> filterElement (named "day") d
addMeta "date" $ text $ T.intercalate "-" $ catMaybes [yr, mon, day]
Nothing -> pure ()
getContrib :: PandocMonad m => Element -> JATS m Inlines
getContrib x = do
given <- maybe (return mempty) getInlines
$ filterElement (named "given-names") x
family <- maybe (return mempty) getInlines
$ filterElement (named "surname") x
if given == mempty && family == mempty
then return mempty
else if given == mempty || family == mempty
then return $ given <> family
else return $ given <> space <> family
parseRefList :: PandocMonad m => Element -> JATS m Blocks
parseRefList e = do
refs <- mapM parseRef $ filterChildren (named "ref") e
addMeta "references" refs
return mempty
parseRef :: PandocMonad m
=> Element -> JATS m (Map.Map Text MetaValue)
parseRef e = do
let combineWithDash x y = x <> text "-" <> y
let getName nm = do
given <- maybe (return mempty) getInlines
$ filterChild (named "given-names") nm
family <- maybe (return mempty) getInlines
$ filterChild (named "surname") nm
return $ toMetaValue $ Map.fromList [
("given" :: Text, given)
, ("family", family)
]
let refElement :: PandocMonad m
=> Element -> Element -> JATS m (Maybe (Text, MetaValue))
refElement c el =
case qName (elName el) of
"article-title" -> Just . ("title",) . toMetaValue <$> getInlines el
"source" ->
case filterChild (named "article-title") c of
Just _ -> Just . ("container-title",) . toMetaValue <$> getInlines el
Nothing -> Just . ("title",) . toMetaValue <$> getInlines el
"label" -> Just . ("citation-label",) . toMetaValue <$> getInlines el
"year" -> case filterChild (named "month") c of
Just m -> Just . ("issued",) . toMetaValue <$>
(combineWithDash
<$> getInlines el <*> getInlines m)
Nothing -> Just . ("issued",) . toMetaValue <$> getInlines el
"volume" -> Just . ("volume",) . toMetaValue <$> getInlines el
"issue" -> Just . ("issue",) . toMetaValue <$> getInlines el
"isbn" -> Just . ("ISBN",) . toMetaValue <$> getInlines el
"issn" -> Just . ("ISSN",) . toMetaValue <$> getInlines el
"uri" -> Just . ("url",) . toMetaValue <$> getInlines el
"fpage" ->
case filterChild (named "lpage") c of
Just lp -> Just . ("page",) . toMetaValue <$>
(combineWithDash <$> getInlines el <*> getInlines lp)
Nothing -> Just . ("page-first",) . toMetaValue <$> getInlines el
"publisher-name" -> Just . ("publisher",) . toMetaValue <$> getInlines el
"publisher-loc" -> Just . ("publisher-place",) . toMetaValue
<$> getInlines el
"edition" -> pure $ Just ("edition",
toMetaValue . T.filter isDigit $ strContent el)
"person-group" -> do names <- mapM getName
(filterChildren (named "name") el)
pure $ Just (attrValue "person-group-type" el,
toMetaValue names)
"pub-id" -> case attrValue "pub-id-type" el of
"doi" -> pure $ Just ("DOI", toMetaValue $ strContent el)
"pmid" -> pure $ Just ("PMID", toMetaValue $ strContent el)
_ -> pure Nothing
"object-id" -> case attrValue "pub-id-type" el of
"doi" -> pure $ Just ("DOI", toMetaValue $ strContent el)
"pmid" -> pure $ Just ("PMID", toMetaValue $ strContent el)
_ -> pure Nothing
_ -> pure Nothing
refVariables <-
case filterChild (named "element-citation") e of
Just c -> (("type", toMetaValue $ case attrValue "publication-type" c of
"journal" -> "article-journal"
x -> x) :) .
catMaybes <$> mapM (refElement c) (elChildren c)
Nothing -> pure [] -- TODO handle mixed-citation
-- allows round-tripping, since JATS writer puts ref- in front of citation ids:
let stripPref t = fromMaybe t $ T.stripPrefix "ref-" t
return $ Map.fromList (("id", toMetaValue $ stripPref $ attrValue "id" e)
: refVariables)
textContent :: Element -> Text
textContent = strContent
strContentRecursive :: Element -> Text
strContentRecursive = strContent .
(\e' -> e'{ elContent = map elementToStr $ elContent e' })
elementToStr :: Content -> Content
elementToStr (Elem e') = Text $ CData CDataText (strContentRecursive e') Nothing
elementToStr x = x
parseInline :: PandocMonad m => Content -> JATS m Inlines
parseInline (Text (CData _ s _)) = return $ text s
parseInline (CRef ref) = return $ maybe (text $ T.toUpper ref) text
$ lookupEntity ref
parseInline (Elem e) =
case qName (elName e) of
"italic" -> innerInlines emph
"bold" -> innerInlines strong
"strike" -> innerInlines strikeout
"sub" -> innerInlines subscript
"sup" -> innerInlines superscript
"underline" -> innerInlines underline
"break" -> return linebreak
"sc" -> innerInlines smallcaps
"code" -> codeWithLang
"monospace" -> codeWithLang
"inline-graphic" -> getGraphic Nothing e
"disp-quote" -> do
qt <- gets jatsQuoteType
let qt' = if qt == SingleQuote then DoubleQuote else SingleQuote
modify $ \st -> st{ jatsQuoteType = qt' }
contents <- innerInlines id
modify $ \st -> st{ jatsQuoteType = qt }
return $ if qt == SingleQuote
then singleQuoted contents
else doubleQuoted contents
"xref" -> do
ils <- innerInlines id
let rid = attrValue "rid" e
let rids = T.words rid
let refType = ("ref-type",) <$> maybeAttrValue "ref-type" e
let attr = (attrValue "id" e, [], maybeToList refType)
return $ if refType == Just ("ref-type","bibr")
then cite
(map (\id' ->
let id'' = fromMaybe id' $
T.stripPrefix "ref-" id'
in Citation { citationId = id''
, citationPrefix = []
, citationSuffix = []
, citationMode = NormalCitation
, citationNoteNum = 0
, citationHash = 0}) rids)
ils
else linkWith attr ("#" <> rid) "" ils
"ext-link" -> do
ils <- innerInlines id
let title = fromMaybe "" $ findAttr (QName "title" (Just "http://www.w3.org/1999/xlink") Nothing) e
let href = case findAttr (QName "href" (Just "http://www.w3.org/1999/xlink") Nothing) e of
Just h -> h
_ -> "#" <> attrValue "rid" e
let ils' = if ils == mempty then str href else ils
let attr = (attrValue "id" e, [], [])
return $ linkWith attr href title ils'
"disp-formula" -> formula displayMath
"inline-formula" -> formula math
"math" | qURI (elName e) == Just "http://www.w3.org/1998/Math/MathML"
-> return . math $ mathML e
"tex-math" -> return . math $ textContent e
"email" -> return $ link ("mailto:" <> textContent e) ""
$ str $ textContent e
"uri" -> return $ link (textContent e) "" $ str $ textContent e
"fn" -> note . mconcat <$>
mapM parseBlock (elContent e)
_ -> innerInlines id
where innerInlines f = extractSpaces f . mconcat <$>
mapM parseInline (elContent e)
mathML x =
case readMathML . showElement $ everywhere (mkT removePrefix) x of
Left _ -> mempty
Right m -> writeTeX m
formula constructor = do
let whereToLook = fromMaybe e $ filterElement (named "alternatives") e
texMaths = map textContent $
filterChildren (named "tex-math") whereToLook
mathMLs = map mathML $
filterChildren isMathML whereToLook
return . mconcat . take 1 . map constructor $ texMaths ++ mathMLs
isMathML x = qName (elName x) == "math" &&
qURI (elName x) ==
Just "http://www.w3.org/1998/Math/MathML"
removePrefix elname = elname { qPrefix = Nothing }
codeWithLang = do
let classes' = case attrValue "language" e of
"" -> []
l -> [l]
return $ codeWith (attrValue "id" e,classes',[]) $ strContentRecursive e