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|
{-# LANGUAGE ScopedTypeVariables #-}
{-# LANGUAGE OverloadedStrings #-}
{-# LANGUAGE ViewPatterns #-}
{- |
Module : Text.Pandoc.Writers.JATS
Copyright : 2017-2021 John MacFarlane
License : GNU GPL, version 2 or above
Maintainer : John MacFarlane <jgm@berkeley.edu>
Stability : alpha
Portability : portable
Conversion of 'Pandoc' documents to JATS XML.
Reference:
https://jats.nlm.nih.gov/publishing/tag-library
-}
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.Citeproc (getReferences)
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.JATS.References (referencesToJATS)
import Text.Pandoc.Writers.JATS.Table (tableToJATS)
import Text.Pandoc.Writers.JATS.Types
import Text.Pandoc.Writers.Math
import Text.Pandoc.Writers.Shared
import Text.Pandoc.XML
import Text.TeXMath
import qualified Text.Pandoc.Writers.AnnotatedTable as Ann
import qualified Text.XML.Light as Xml
-- | Convert a @'Pandoc'@ document to JATS (Archiving and Interchange
-- Tag Set.)
writeJatsArchiving :: PandocMonad m => WriterOptions -> Pandoc -> m Text
writeJatsArchiving = writeJats TagSetArchiving
-- | Convert a @'Pandoc'@ document to JATS (Journal Publishing Tag Set.)
writeJatsPublishing :: PandocMonad m => WriterOptions -> Pandoc -> m Text
writeJatsPublishing = writeJats TagSetPublishing
-- | Convert a @'Pandoc'@ document to JATS (Archiving and Interchange
-- Tag Set.)
writeJatsArticleAuthoring :: PandocMonad m => WriterOptions -> Pandoc -> m Text
writeJatsArticleAuthoring = writeJats TagSetArticleAuthoring
-- | Alias for @'writeJatsArchiving'@. This function exists for backwards
-- compatibility, but will be deprecated in the future. Use
-- @'writeJatsArchiving'@ instead.
writeJATS :: PandocMonad m => WriterOptions -> Pandoc -> m Text
writeJATS = writeJatsArchiving
-- | Convert a @'Pandoc'@ document to JATS.
writeJats :: PandocMonad m => JATSTagSet -> WriterOptions -> Pandoc -> m Text
writeJats tagSet opts d = do
refs <- if extensionEnabled Ext_element_citations $ writerExtensions opts
then getReferences Nothing d
else pure []
let environment = JATSEnv
{ jatsTagSet = tagSet
, jatsInlinesWriter = inlinesToJATS
, jatsBlockWriter = blockToJATS
, jatsReferences = refs
}
let initialState = JATSState { jatsNotes = [] }
runReaderT (evalStateT (docToJATS opts d) initialState)
environment
-- | Convert Pandoc document to string in JATS format.
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
-- The numbering here follows LaTeX's internal numbering
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 <- gets (reverse . map snd . jatsNotes)
backs <- fromBlocks backblocks
tagSet <- asks jatsTagSet
-- In the "Article Authoring" tag set, occurrence of fn-group elements
-- is restricted to table footers. Footnotes have to be placed inline.
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
-- | Convert a list of Pandoc blocks to JATS.
blocksToJATS :: PandocMonad m => WriterOptions -> [Block] -> JATS m (Doc Text)
blocksToJATS = wrappedBlocksToJATS (const False)
-- | Like @'blocksToJATS'@, but wraps top-level blocks into a @<p>@
-- element if the @needsWrap@ predicate evaluates to @True@.
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 || isBlockQuote b -- see #7041
then inTags True "p" [("specific-use","wrapper")] inner
else inner
isBlockQuote (BlockQuote _) = True
isBlockQuote _ = False
-- | Auxiliary function to convert Plain block to Para.
plainToPara :: Block -> Block
plainToPara (Plain x) = Para x
plainToPara x = x
-- | Convert a list of pairs of terms and definitions into a list of
-- JATS varlistentrys.
deflistItemsToJATS :: PandocMonad m
=> WriterOptions
-> [([Inline],[[Block]])] -> JATS m (Doc Text)
deflistItemsToJATS opts items =
vcat <$> mapM (uncurry (deflistItemToJATS opts)) items
-- | Convert a term and a list of blocks into a JATS varlistentry.
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'
-- | Convert a list of lists of blocks to a list of JATS list items.
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
-- | Convert a list of blocks into a JATS list item.
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 (inTagsSimple "label" . text . T.unpack) mbmarker
$$ contents
imageMimeType :: Text -> [(Text, Text)] -> (Text, Text)
imageMimeType src kvs =
let mbMT = getMimeType (T.unpack src)
maintype = fromMaybe "image" $
lookup "mimetype" kvs `mplus`
(T.takeWhile (/='/') <$> mbMT)
subtype = fromMaybe "" $
lookup "mime-subtype" kvs `mplus`
(T.drop 1 . T.dropWhile (/='/') <$> mbMT)
in (maintype, subtype)
languageFor :: [Text] -> Text
languageFor classes =
case langs of
(l:_) -> escapeStringForXML l
[] -> ""
where isLang l = T.toLower l `elem` map T.toLower languages
langsFrom s = if isLang s
then [s]
else languagesByExtension . T.toLower $ s
langs = concatMap langsFrom classes
codeAttr :: Attr -> (Text, [(Text, Text)])
codeAttr (ident,classes,kvs) = (lang, attr)
where
attr = [("id", escapeNCName ident) | not (T.null ident)] ++
[("language",lang) | not (T.null lang)] ++
[(k,v) | (k,v) <- kvs, k `elem` ["code-type",
"code-version", "executable",
"language-version", "orientation",
"platforms", "position", "specific-use"]]
lang = languageFor classes
-- | Convert a Pandoc block element to JATS.
blockToJATS :: PandocMonad m => WriterOptions -> Block -> JATS m (Doc Text)
blockToJATS _ Null = return empty
blockToJATS opts (Div (id',"section":_,kvs) (Header _lvl _ ils : xs)) = do
let idAttr = [ ("id", writerIdentifierPrefix opts <> escapeNCName id')
| not (T.null id')]
let otherAttrs = ["sec-type", "specific-use"]
let attribs = idAttr ++ [(k,v) | (k,v) <- kvs, k `elem` otherAttrs]
title' <- inlinesToJATS opts ils
contents <- blocksToJATS opts xs
return $ inTags True "sec" attribs $
inTagsSimple "title" title' $$ contents
-- Bibliography reference:
blockToJATS opts (Div (ident,_,_) [Para lst]) | "ref-" `T.isPrefixOf` ident =
inTags True "ref" [("id", escapeNCName ident)] .
inTagsSimple "mixed-citation" <$>
inlinesToJATS opts lst
blockToJATS opts (Div ("refs",_,_) xs) = do
refs <- asks jatsReferences
contents <- if null refs
then blocksToJATS opts xs
else referencesToJATS opts refs
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", escapeNCName 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", escapeNCName 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'
-- No Plain, everything needs to be in a block-level tag
blockToJATS opts (Plain lst) = blockToJATS opts (Para lst)
-- title beginning with fig: indicates that the image is a figure
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", escapeNCName 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), -- do we need to URL escape this?
("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", escapeNCName 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 <- asks jatsTagSet
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 <- asks jatsTagSet
let listType =
-- The Article Authoring tag set doesn't allow a more specific
-- @list-type@ attribute than "order".
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 -- raw XML block
| otherwise = do
report $ BlockNotRendered b
return empty
blockToJATS _ HorizontalRule = return empty -- not semantic
blockToJATS opts (Table attr caption colspecs thead tbody tfoot) =
tableToJATS opts (Ann.toTable attr caption colspecs thead tbody tfoot)
-- | Convert a list of inline elements to JATS.
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
-- | Convert an inline element to JATS.
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 (Underline lst) =
inTagsSimple "underline" <$> 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 -- not allowed as child of p
-- see https://jats.nlm.nih.gov/publishing/tag-library/1.2/element/break.html
inlineToJATS _ Space = return space
inlineToJATS opts SoftBreak
| writerWrapText opts == WrapPreserve = return cr
| otherwise = return space
inlineToJATS opts (Note contents) = do
tagSet <- asks jatsTagSet
-- Footnotes must occur inline when using the Article Authoring tag set.
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) =
-- TODO revisit this after examining the jats.csl pipeline
inlinesToJATS opts lst
inlineToJATS opts (Span ("",_,[]) ils) = inlinesToJATS opts ils
inlineToJATS opts (Span (ident,_,kvs) ils) = do
contents <- inlinesToJATS opts ils
let attr = [("id", escapeNCName 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 <- asks jatsTagSet
return . inTagsSimple tagtype $
case res of
Right r -> let mathMl = text (Xml.ppcElement conf $ fixNS r)
-- tex-math is unsupported in Article Authoring tag set
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 = mconcat
[ [("id", escapeNCName ident) | not (T.null ident)]
, [("alt", stringify txt) | not (null txt)]
, [("rid", escapeNCName src)]
, [(k,v) | (k,v) <- kvs, k `elem` ["ref-type", "specific-use"]]
, [("ref-type", "bibr") | "ref-" `T.isPrefixOf` src]
]
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", escapeNCName 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", escapeNCName 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 (`parsetimeWith` T.unpack s) formats)
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"]
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