{-# LANGUAGE ScopedTypeVariables #-}
{-# LANGUAGE OverloadedStrings #-}
{-# LANGUAGE ViewPatterns #-}
module Text.Pandoc.Writers.JATS
( writeJATS
, writeJatsArchiving
, writeJatsPublishing
, writeJatsArticleAuthoring
) where
import Control.Monad.Reader
import Control.Monad.State
import Data.Generics (everywhere, mkT)
import Data.List (partition)
import qualified Data.Map as M
import Data.Maybe (fromMaybe)
import Data.Time (toGregorian, Day, parseTimeM, defaultTimeLocale, formatTime)
import qualified Data.Text as T
import Data.Text (Text)
import Text.Pandoc.Class.PandocMonad (PandocMonad, report)
import Text.Pandoc.Definition
import Text.Pandoc.Highlighting (languages, languagesByExtension)
import Text.Pandoc.Logging
import Text.Pandoc.MIME (getMimeType)
import Text.Pandoc.Walk (walk)
import Text.Pandoc.Options
import Text.DocLayout
import Text.Pandoc.Shared
import Text.Pandoc.Templates (renderTemplate)
import Text.DocTemplates (Context(..), Val(..))
import Text.Pandoc.Writers.Math
import Text.Pandoc.Writers.Shared
import Text.Pandoc.XML
import Text.TeXMath
import qualified Text.XML.Light as Xml
data JATSTagSet
= TagSetArchiving
| TagSetPublishing
| TagSetArticleAuthoring
deriving (Eq)
newtype JATSState = JATSState
{ jatsNotes :: [(Int, Doc Text)] }
type JATS a = StateT JATSState (ReaderT JATSTagSet a)
writeJatsArchiving :: PandocMonad m => WriterOptions -> Pandoc -> m Text
writeJatsArchiving = writeJats TagSetArchiving
writeJatsPublishing :: PandocMonad m => WriterOptions -> Pandoc -> m Text
writeJatsPublishing = writeJats TagSetPublishing
writeJatsArticleAuthoring :: PandocMonad m => WriterOptions -> Pandoc -> m Text
writeJatsArticleAuthoring = writeJats TagSetArticleAuthoring
writeJATS :: PandocMonad m => WriterOptions -> Pandoc -> m Text
writeJATS = writeJatsArchiving
writeJats :: PandocMonad m => JATSTagSet -> WriterOptions -> Pandoc -> m Text
writeJats tagSet opts d =
runReaderT (evalStateT (docToJATS opts d)
(JATSState{ jatsNotes = [] }))
tagSet
docToJATS :: PandocMonad m => WriterOptions -> Pandoc -> JATS m Text
docToJATS opts (Pandoc meta blocks) = do
let isBackBlock (Div ("refs",_,_) _) = True
isBackBlock _ = False
let (backblocks, bodyblocks) = partition isBackBlock blocks
let startLvl = case writerTopLevelDivision opts of
TopLevelPart -> -1
TopLevelChapter -> 0
TopLevelSection -> 1
TopLevelDefault -> 1
let fromBlocks = blocksToJATS opts . makeSections False (Just startLvl)
let colwidth = if writerWrapText opts == WrapAuto
then Just $ writerColumns opts
else Nothing
metadata <- metaToContext opts
fromBlocks
(fmap chomp . inlinesToJATS opts)
meta
main <- fromBlocks bodyblocks
notes <- reverse . map snd <$> gets jatsNotes
backs <- fromBlocks backblocks
tagSet <- ask
let fns = if null notes || tagSet == TagSetArticleAuthoring
then mempty
else inTagsIndented "fn-group" $ vcat notes
let back = backs $$ fns
let date =
case getField "date" metadata of
Nothing -> NullVal
Just (SimpleVal (x :: Doc Text)) ->
case parseDate (render Nothing x) of
Nothing -> NullVal
Just day ->
let (y,m,d) = toGregorian day
in MapVal . Context $ M.fromList
[("year" :: Text, SimpleVal $ text $ show y)
,("month", SimpleVal $ text $ show m)
,("day", SimpleVal $ text $ show d)
,("iso-8601", SimpleVal $ text $
formatTime defaultTimeLocale "%F" day)
]
Just x -> x
let context = defField "body" main
$ defField "back" back
$ resetField "date" date
$ defField "mathml" (case writerHTMLMathMethod opts of
MathML -> True
_ -> False) metadata
return $ render colwidth $
(if writerPreferAscii opts then fmap toEntities else id) $
case writerTemplate opts of
Nothing -> main
Just tpl -> renderTemplate tpl context
blocksToJATS :: PandocMonad m => WriterOptions -> [Block] -> JATS m (Doc Text)
blocksToJATS = wrappedBlocksToJATS (const False)
wrappedBlocksToJATS :: PandocMonad m
=> (Block -> Bool)
-> WriterOptions
-> [Block]
-> JATS m (Doc Text)
wrappedBlocksToJATS needsWrap opts =
fmap vcat . mapM wrappedBlockToJATS
where
wrappedBlockToJATS b = do
inner <- blockToJATS opts b
return $
if needsWrap b
then inTags True "p" [("specific-use","wrapper")] inner
else inner
plainToPara :: Block -> Block
plainToPara (Plain x) = Para x
plainToPara x = x
deflistItemsToJATS :: PandocMonad m
=> WriterOptions -> [([Inline],[[Block]])] -> JATS m (Doc Text)
deflistItemsToJATS opts items =
vcat <$> mapM (uncurry (deflistItemToJATS opts)) items
deflistItemToJATS :: PandocMonad m
=> WriterOptions -> [Inline] -> [[Block]] -> JATS m (Doc Text)
deflistItemToJATS opts term defs = do
term' <- inlinesToJATS opts term
def' <- wrappedBlocksToJATS (not . isPara)
opts $ concatMap (walk demoteHeaderAndRefs .
map plainToPara) defs
return $ inTagsIndented "def-item" $
inTagsSimple "term" term' $$
inTagsIndented "def" def'
listItemsToJATS :: PandocMonad m
=> WriterOptions -> Maybe [Text] -> [[Block]] -> JATS m (Doc Text)
listItemsToJATS opts markers items =
case markers of
Nothing -> vcat <$> mapM (listItemToJATS opts Nothing) items
Just ms -> vcat <$> zipWithM (listItemToJATS opts) (map Just ms) items
listItemToJATS :: PandocMonad m
=> WriterOptions -> Maybe Text -> [Block] -> JATS m (Doc Text)
listItemToJATS opts mbmarker item = do
contents <- wrappedBlocksToJATS (not . isParaOrList) opts
(walk demoteHeaderAndRefs item)
return $ inTagsIndented "list-item" $
maybe empty (\lbl -> inTagsSimple "label" (text $ T.unpack lbl)) mbmarker
$$ contents
imageMimeType :: Text -> [(Text, Text)] -> (Text, Text)
imageMimeType src kvs =
let mbMT = getMimeType (T.unpack src)
maintype = fromMaybe "image" $
lookup "mimetype" kvs `mplus`
(T.takeWhile (/='/') <$> mbMT)
subtype = fromMaybe "" $
lookup "mime-subtype" kvs `mplus`
((T.drop 1 . T.dropWhile (/='/')) <$> mbMT)
in (maintype, subtype)
languageFor :: [Text] -> Text
languageFor classes =
case langs of
(l:_) -> escapeStringForXML l
[] -> ""
where isLang l = T.toLower l `elem` map T.toLower languages
langsFrom s = if isLang s
then [s]
else languagesByExtension . T.toLower $ s
langs = concatMap langsFrom classes
codeAttr :: Attr -> (Text, [(Text, Text)])
codeAttr (ident,classes,kvs) = (lang, attr)
where
attr = [("id",ident) | not (T.null ident)] ++
[("language",lang) | not (T.null lang)] ++
[(k,v) | (k,v) <- kvs, k `elem` ["code-type",
"code-version", "executable",
"language-version", "orientation",
"platforms", "position", "specific-use"]]
lang = languageFor classes
blockToJATS :: PandocMonad m => WriterOptions -> Block -> JATS m (Doc Text)
blockToJATS _ Null = return empty
blockToJATS opts (Div (id',"section":_,kvs) (Header _lvl _ ils : xs)) = do
let idAttr = [("id", writerIdentifierPrefix opts <> id') | not (T.null id')]
let otherAttrs = ["sec-type", "specific-use"]
let attribs = idAttr ++ [(k,v) | (k,v) <- kvs, k `elem` otherAttrs]
title' <- inlinesToJATS opts ils
contents <- blocksToJATS opts xs
return $ inTags True "sec" attribs $
inTagsSimple "title" title' $$ contents
blockToJATS opts (Div (T.stripPrefix "ref-" -> Just _,_,_) [Para lst]) =
inlinesToJATS opts lst
blockToJATS opts (Div ("refs",_,_) xs) = do
contents <- blocksToJATS opts xs
return $ inTagsIndented "ref-list" contents
blockToJATS opts (Div (ident,[cls],kvs) bs) | cls `elem` ["fig", "caption", "table-wrap"] = do
contents <- blocksToJATS opts bs
let attr = [("id", ident) | not (T.null ident)] ++
[("xml:lang",l) | ("lang",l) <- kvs] ++
[(k,v) | (k,v) <- kvs, k `elem` ["specific-use",
"content-type", "orientation", "position"]]
return $ inTags True cls attr contents
blockToJATS opts (Div (ident,_,kvs) bs) = do
contents <- blocksToJATS opts bs
let attr = [("id", ident) | not (T.null ident)] ++
[("xml:lang",l) | ("lang",l) <- kvs] ++
[(k,v) | (k,v) <- kvs, k `elem` ["specific-use",
"content-type", "orientation", "position"]]
return $ inTags True "boxed-text" attr contents
blockToJATS opts (Header _ _ title) = do
title' <- inlinesToJATS opts title
return $ inTagsSimple "title" title'
blockToJATS opts (Plain lst) = blockToJATS opts (Para lst)
blockToJATS opts (Para [Image (ident,_,kvs) txt
(src,T.stripPrefix "fig:" -> Just tit)]) = do
alt <- inlinesToJATS opts txt
let (maintype, subtype) = imageMimeType src kvs
let capt = if null txt
then empty
else inTagsSimple "caption" $ inTagsSimple "p" alt
let attr = [("id", ident) | not (T.null ident)] ++
[(k,v) | (k,v) <- kvs, k `elem` ["fig-type", "orientation",
"position", "specific-use"]]
let graphicattr = [("mimetype",maintype),
("mime-subtype",subtype),
("xlink:href",src),
("xlink:title",tit)]
return $ inTags True "fig" attr $
capt $$ selfClosingTag "graphic" graphicattr
blockToJATS _ (Para [Image (ident,_,kvs) _ (src, tit)]) = do
let (maintype, subtype) = imageMimeType src kvs
let attr = [("id", ident) | not (T.null ident)] ++
[("mimetype", maintype),
("mime-subtype", subtype),
("xlink:href", src)] ++
[("xlink:title", tit) | not (T.null tit)] ++
[(k,v) | (k,v) <- kvs, k `elem` ["baseline-shift",
"content-type", "specific-use", "xlink:actuate",
"xlink:href", "xlink:role", "xlink:show",
"xlink:type"]]
return $ selfClosingTag "graphic" attr
blockToJATS opts (Para lst) =
inTagsSimple "p" <$> inlinesToJATS opts lst
blockToJATS opts (LineBlock lns) =
blockToJATS opts $ linesToPara lns
blockToJATS opts (BlockQuote blocks) = do
tagSet <- ask
let blocksToJats' = if tagSet == TagSetArticleAuthoring
then wrappedBlocksToJATS (not . isPara)
else blocksToJATS
inTagsIndented "disp-quote" <$> blocksToJats' opts blocks
blockToJATS _ (CodeBlock a str) = return $
inTags False tag attr (flush (text (T.unpack $ escapeStringForXML str)))
where (lang, attr) = codeAttr a
tag = if T.null lang then "preformat" else "code"
blockToJATS _ (BulletList []) = return empty
blockToJATS opts (BulletList lst) =
inTags True "list" [("list-type", "bullet")] <$>
listItemsToJATS opts Nothing lst
blockToJATS _ (OrderedList _ []) = return empty
blockToJATS opts (OrderedList (start, numstyle, delimstyle) items) = do
tagSet <- ask
let listType =
if tagSet == TagSetArticleAuthoring
then "order"
else case numstyle of
DefaultStyle -> "order"
Decimal -> "order"
Example -> "order"
UpperAlpha -> "alpha-upper"
LowerAlpha -> "alpha-lower"
UpperRoman -> "roman-upper"
LowerRoman -> "roman-lower"
let simpleList = start == 1 && (delimstyle == DefaultDelim ||
delimstyle == Period)
let markers = if simpleList
then Nothing
else Just $
orderedListMarkers (start, numstyle, delimstyle)
inTags True "list" [("list-type", listType)] <$>
listItemsToJATS opts markers items
blockToJATS opts (DefinitionList lst) =
inTags True "def-list" [] <$> deflistItemsToJATS opts lst
blockToJATS _ b@(RawBlock f str)
| f == "jats" = return $ text $ T.unpack str
| otherwise = do
report $ BlockNotRendered b
return empty
blockToJATS _ HorizontalRule = return empty
blockToJATS opts (Table [] aligns widths headers rows) = do
let percent w = tshow (truncate (100*w) :: Integer) <> "*"
let coltags = vcat $ zipWith (\w al -> selfClosingTag "col"
([("width", percent w) | w > 0] ++
[("align", alignmentToText al)])) widths aligns
thead <- if all null headers
then return empty
else inTagsIndented "thead" <$> tableRowToJATS opts True headers
tbody <- (inTagsIndented "tbody" . vcat) <$>
mapM (tableRowToJATS opts False) rows
return $ inTags True "table" [] $ coltags $$ thead $$ tbody
blockToJATS opts (Table caption aligns widths headers rows) = do
captionDoc <- inTagsIndented "caption" <$> blockToJATS opts (Para caption)
tbl <- blockToJATS opts (Table [] aligns widths headers rows)
return $ inTags True "table-wrap" [] $ captionDoc $$ tbl
alignmentToText :: Alignment -> Text
alignmentToText alignment = case alignment of
AlignLeft -> "left"
AlignRight -> "right"
AlignCenter -> "center"
AlignDefault -> "left"
tableRowToJATS :: PandocMonad m
=> WriterOptions
-> Bool
-> [[Block]]
-> JATS m (Doc Text)
tableRowToJATS opts isHeader cols =
(inTagsIndented "tr" . vcat) <$> mapM (tableItemToJATS opts isHeader) cols
tableItemToJATS :: PandocMonad m
=> WriterOptions
-> Bool
-> [Block]
-> JATS m (Doc Text)
tableItemToJATS opts isHeader [Plain item] =
inTags False (if isHeader then "th" else "td") [] <$>
inlinesToJATS opts item
tableItemToJATS opts isHeader item =
(inTags False (if isHeader then "th" else "td") [] . vcat) <$>
mapM (blockToJATS opts) item
inlinesToJATS :: PandocMonad m => WriterOptions -> [Inline] -> JATS m (Doc Text)
inlinesToJATS opts lst = hcat <$> mapM (inlineToJATS opts) (fixCitations lst)
where
fixCitations [] = []
fixCitations (x:xs) | needsFixing x =
x : Str (stringify ys) : fixCitations zs
where
needsFixing (RawInline (Format "jats") z) =
"<pub-id pub-id-type=" `T.isPrefixOf` z
needsFixing _ = False
isRawInline RawInline{} = True
isRawInline _ = False
(ys,zs) = break isRawInline xs
fixCitations (x:xs) = x : fixCitations xs
inlineToJATS :: PandocMonad m => WriterOptions -> Inline -> JATS m (Doc Text)
inlineToJATS _ (Str str) = return $ text $ T.unpack $ escapeStringForXML str
inlineToJATS opts (Emph lst) =
inTagsSimple "italic" <$> inlinesToJATS opts lst
inlineToJATS opts (Strong lst) =
inTagsSimple "bold" <$> inlinesToJATS opts lst
inlineToJATS opts (Strikeout lst) =
inTagsSimple "strike" <$> inlinesToJATS opts lst
inlineToJATS opts (Superscript lst) =
inTagsSimple "sup" <$> inlinesToJATS opts lst
inlineToJATS opts (Subscript lst) =
inTagsSimple "sub" <$> inlinesToJATS opts lst
inlineToJATS opts (SmallCaps lst) =
inTagsSimple "sc" <$> inlinesToJATS opts lst
inlineToJATS opts (Quoted SingleQuote lst) = do
contents <- inlinesToJATS opts lst
return $ char '‘' <> contents <> char '’'
inlineToJATS opts (Quoted DoubleQuote lst) = do
contents <- inlinesToJATS opts lst
return $ char '“' <> contents <> char '”'
inlineToJATS _ (Code a str) =
return $ inTags False tag attr $ literal (escapeStringForXML str)
where (lang, attr) = codeAttr a
tag = if T.null lang then "monospace" else "code"
inlineToJATS _ il@(RawInline f x)
| f == "jats" = return $ literal x
| otherwise = do
report $ InlineNotRendered il
return empty
inlineToJATS _ LineBreak = return cr
inlineToJATS _ Space = return space
inlineToJATS opts SoftBreak
| writerWrapText opts == WrapPreserve = return cr
| otherwise = return space
inlineToJATS opts (Note contents) = do
tagSet <- ask
if tagSet == TagSetArticleAuthoring
then inTagsIndented "fn" <$> wrappedBlocksToJATS (not . isPara) opts contents
else do
notes <- gets jatsNotes
let notenum = case notes of
(n, _):_ -> n + 1
[] -> 1
thenote <- inTags True "fn" [("id","fn" <> tshow notenum)]
<$> wrappedBlocksToJATS (not . isPara) opts
(walk demoteHeaderAndRefs contents)
modify $ \st -> st{ jatsNotes = (notenum, thenote) : notes }
return $ inTags False "xref" [("ref-type", "fn"),
("rid", "fn" <> tshow notenum)]
$ text (show notenum)
inlineToJATS opts (Cite _ lst) =
inlinesToJATS opts lst
inlineToJATS opts (Span ("",_,[]) ils) = inlinesToJATS opts ils
inlineToJATS opts (Span (ident,_,kvs) ils) = do
contents <- inlinesToJATS opts ils
let attr = [("id",ident) | not (T.null ident)] ++
[("xml:lang",l) | ("lang",l) <- kvs] ++
[(k,v) | (k,v) <- kvs
, k `elem` ["content-type", "rationale",
"rid", "specific-use"]]
return $ selfClosingTag "milestone-start" attr <> contents <>
selfClosingTag "milestone-end" []
inlineToJATS _ (Math t str) = do
let addPref (Xml.Attr q v)
| Xml.qName q == "xmlns" = Xml.Attr q{ Xml.qName = "xmlns:mml" } v
| otherwise = Xml.Attr q v
let fixNS' e = e{ Xml.elName =
(Xml.elName e){ Xml.qPrefix = Just "mml" } }
let fixNS = everywhere (mkT fixNS') .
(\e -> e{ Xml.elAttribs = map addPref (Xml.elAttribs e) })
let conf = Xml.useShortEmptyTags (const False) Xml.defaultConfigPP
res <- convertMath writeMathML t str
let tagtype = case t of
DisplayMath -> "disp-formula"
InlineMath -> "inline-formula"
let rawtex = text "<![CDATA[" <> literal str <> text "]]>"
let texMath = inTagsSimple "tex-math" rawtex
tagSet <- ask
return . inTagsSimple tagtype $
case res of
Right r -> let mathMl = text (Xml.ppcElement conf $ fixNS r)
in if tagSet == TagSetArticleAuthoring
then mathMl
else inTagsSimple "alternatives" $
cr <> texMath $$ mathMl
Left _ -> if tagSet /= TagSetArticleAuthoring
then texMath
else rawtex
inlineToJATS _ (Link _attr [Str t] (T.stripPrefix "mailto:" -> Just email, _))
| escapeURI t == email =
return $ inTagsSimple "email" $ literal (escapeStringForXML email)
inlineToJATS opts (Link (ident,_,kvs) txt (T.uncons -> Just ('#', src), _)) = do
let attr = [("id", ident) | not (T.null ident)] ++
[("alt", stringify txt) | not (null txt)] ++
[("rid", src)] ++
[(k,v) | (k,v) <- kvs, k `elem` ["ref-type", "specific-use"]]
if null txt
then return $ selfClosingTag "xref" attr
else do
contents <- inlinesToJATS opts txt
return $ inTags False "xref" attr contents
inlineToJATS opts (Link (ident,_,kvs) txt (src, tit)) = do
let attr = [("id", ident) | not (T.null ident)] ++
[("ext-link-type", "uri"),
("xlink:href", src)] ++
[("xlink:title", tit) | not (T.null tit)] ++
[(k,v) | (k,v) <- kvs, k `elem` ["assigning-authority",
"specific-use", "xlink:actuate",
"xlink:role", "xlink:show",
"xlink:type"]]
contents <- inlinesToJATS opts txt
return $ inTags False "ext-link" attr contents
inlineToJATS _ (Image (ident,_,kvs) _ (src, tit)) = do
let mbMT = getMimeType (T.unpack src)
let maintype = fromMaybe "image" $
lookup "mimetype" kvs `mplus`
(T.takeWhile (/='/') <$> mbMT)
let subtype = fromMaybe "" $
lookup "mime-subtype" kvs `mplus`
((T.drop 1 . T.dropWhile (/='/')) <$> mbMT)
let attr = [("id", ident) | not (T.null ident)] ++
[("mimetype", maintype),
("mime-subtype", subtype),
("xlink:href", src)] ++
[("xlink:title", tit) | not (T.null tit)] ++
[(k,v) | (k,v) <- kvs, k `elem` ["baseline-shift",
"content-type", "specific-use", "xlink:actuate",
"xlink:href", "xlink:role", "xlink:show",
"xlink:type"]]
return $ selfClosingTag "inline-graphic" attr
isParaOrList :: Block -> Bool
isParaOrList Para{} = True
isParaOrList Plain{} = True
isParaOrList BulletList{} = True
isParaOrList OrderedList{} = True
isParaOrList DefinitionList{} = True
isParaOrList _ = False
isPara :: Block -> Bool
isPara Para{} = True
isPara Plain{} = True
isPara _ = False
demoteHeaderAndRefs :: Block -> Block
demoteHeaderAndRefs (Header _ _ ils) = Para ils
demoteHeaderAndRefs (Div ("refs",cls,kvs) bs) =
Div ("",cls,kvs) bs
demoteHeaderAndRefs x = x
parseDate :: Text -> Maybe Day
parseDate s = msum (map (\fs -> parsetimeWith fs $ T.unpack s) formats) :: Maybe Day
where parsetimeWith = parseTimeM True defaultTimeLocale
formats = ["%x","%m/%d/%Y", "%D","%F", "%d %b %Y",
"%e %B %Y", "%b. %e, %Y", "%B %e, %Y",
"%Y%m%d", "%Y%m", "%Y"]