{-# LANGUAGE ScopedTypeVariables #-} {-# LANGUAGE FlexibleContexts #-} {-# LANGUAGE StrictData #-} {-# LANGUAGE MultiParamTypeClasses #-} {-# LANGUAGE FlexibleInstances #-} {-# LANGUAGE OverloadedStrings #-} module Text.Pandoc.Citeproc ( processCitations ) where import Citeproc import Citeproc.Pandoc () import Text.Pandoc.Citeproc.Locator (parseLocator) import Text.Pandoc.Citeproc.CslJson (cslJsonToReferences) import Text.Pandoc.Citeproc.BibTeX (readBibtexString, Variant(..)) import Text.Pandoc.Citeproc.MetaValue (metaValueToReference, metaValueToText) import Text.Pandoc.Readers.Markdown (yamlToRefs) import Text.Pandoc.Class (setResourcePath, getResourcePath, getUserDataDir) import qualified Text.Pandoc.BCP47 as BCP47 import Data.ByteString (ByteString) import qualified Data.ByteString.Lazy as L import Text.Pandoc.Definition as Pandoc import Text.Pandoc.Walk import Text.Pandoc.Builder as B import Text.Pandoc (PandocMonad(..), PandocError(..), readDataFile, ReaderOptions(..), pandocExtensions, report, LogMessage(..), fetchItem) import Text.Pandoc.Shared (stringify, ordNub, blocksToInlines, tshow) import qualified Text.Pandoc.UTF8 as UTF8 import Data.Aeson (eitherDecode) import Data.Default import Data.Ord () import qualified Data.Map as M import qualified Data.Set as Set import Data.Char (isPunctuation, isUpper) import Data.Text (Text) import qualified Data.Text as T import Control.Monad.State import qualified Data.Sequence as Seq import qualified Data.Foldable as Foldable import System.FilePath import Control.Applicative import Control.Monad.Except import Data.Maybe (mapMaybe, fromMaybe) import Safe (lastMay, initSafe) -- import Debug.Trace as Trace (trace, traceShowId) processCitations :: PandocMonad m => Pandoc -> m Pandoc processCitations (Pandoc meta bs) = do let cslfile = (lookupMeta "csl" meta <|> lookupMeta "citation-style" meta) >>= metaValueToText let getFile defaultExtension fp = do oldRp <- getResourcePath mbUdd <- getUserDataDir setResourcePath $ oldRp ++ maybe [] (\u -> [u <> "/csl", u <> "/csl/dependent"]) mbUdd let fp' = if T.any (=='.') fp || "data:" `T.isPrefixOf` fp then fp else fp <> defaultExtension (result, _) <- fetchItem fp' setResourcePath oldRp return result let getCslDefault = readDataFile "default.csl" cslContents <- UTF8.toText <$> maybe getCslDefault (getFile ".csl") cslfile let abbrevFile = lookupMeta "citation-abbreviations" meta >>= metaValueToText mbAbbrevs <- case abbrevFile of Nothing -> return Nothing Just fp -> do rawAbbr <- getFile ".json" fp case eitherDecode (L.fromStrict rawAbbr) of Left err -> throwError $ PandocCiteprocError $ CiteprocParseError $ "Could not parse abbreviations file " <> fp <> "\n" <> T.pack err Right abbr -> return $ Just abbr let getParentStyle url = do -- first, try to retrieve the style locally, then use HTTP. let basename = T.takeWhileEnd (/='/') url UTF8.toText <$> catchError (getFile ".csl" basename) (\_ -> fst <$> fetchItem url) styleRes <- Citeproc.parseStyle getParentStyle cslContents style <- case styleRes of Left err -> throwError $ PandocAppError $ prettyCiteprocError err Right style -> return style{ styleAbbreviations = mbAbbrevs } mblang <- maybe (return Nothing) bcp47LangToIETF ((lookupMeta "lang" meta <|> lookupMeta "locale" meta) >>= metaValueToText) let locale = Citeproc.mergeLocales mblang style let getCiteId (Cite cs _) = Set.fromList $ map B.citationId cs getCiteId _ = mempty let metanocites = lookupMeta "nocite" meta let meta' = deleteMeta "nocite" meta let nocites = maybe mempty (query getCiteId) metanocites let citeIds = query getCiteId (Pandoc meta bs) let idpred = if "*" `Set.member` nocites then const True else (`Set.member` citeIds) let inlineRefs = case lookupMeta "references" meta of Just (MetaList rs) -> mapMaybe metaValueToReference rs _ -> [] externalRefs <- case lookupMeta "bibliography" meta of Just (MetaList xs) -> mconcat <$> mapM (getRefsFromBib locale idpred) (mapMaybe metaValueToText xs) Just x -> case metaValueToText x of Just fp -> getRefsFromBib locale idpred fp Nothing -> return [] Nothing -> return [] let refs = map (linkifyVariables . legacyDateRanges) (inlineRefs ++ externalRefs) let otherIdsMap = foldr (\ref m -> case T.words . extractText <$> M.lookup "other-ids" (referenceVariables ref) of Nothing -> m Just ids -> foldr (\id' -> M.insert id' (referenceId ref)) m ids) M.empty refs -- TODO: issue warning if no refs defined let citations = getCitations locale otherIdsMap $ Pandoc meta' bs let linkCites = maybe False truish $ lookupMeta "link-citations" meta let opts = defaultCiteprocOptions{ linkCitations = linkCites } let result = Citeproc.citeproc opts style (localeLanguage locale) refs citations mapM_ (report . CiteprocWarning) (resultWarnings result) let sopts = styleOptions style let classes = "references" : -- TODO remove this or keep for compatibility? "csl-bib-body" : ["hanging-indent" | styleHangingIndent sopts] let refkvs = (case styleEntrySpacing sopts of Just es | es > 0 -> (("entry-spacing",T.pack $ show es):) _ -> id) . (case styleLineSpacing sopts of Just ls | ls > 1 -> (("line-spacing",T.pack $ show ls):) _ -> id) $ [] let bibs = mconcat $ map (\(ident, out) -> B.divWith ("ref-" <> ident,["csl-entry"],[]) . B.para . walk (convertQuotes locale) . insertSpace $ out) (resultBibliography result) let moveNotes = maybe True truish $ lookupMeta "notes-after-punctuation" meta let cits = map (walk fixLinks . walk (convertQuotes locale)) $ resultCitations result let fixQuotes = case localePunctuationInQuote locale of Just True -> B.toList . movePunctuationInsideQuotes . B.fromList _ -> id let Pandoc meta'' bs' = maybe id (setMeta "nocite") metanocites . walk (map capitalizeNoteCitation . fixQuotes . mvPunct moveNotes locale) . walk deNote . evalState (walkM insertResolvedCitations $ Pandoc meta' bs) $ cits return $ Pandoc meta'' $ insertRefs refkvs classes meta'' (walk fixLinks $ B.toList bibs) bs' -- If we have a span.csl-left-margin followed by span.csl-right-inline, -- we insert a space. This ensures that they will be separated by a space, -- even in formats that don't have special handling for the display spans. insertSpace :: Inlines -> Inlines insertSpace ils = case Seq.viewl (unMany ils) of (Span ("",["csl-left-margin"],[]) xs) Seq.:< rest -> case Seq.lookup 0 rest of Just (Span ("",["csl-right-inline"],[]) _) -> Many $ Span ("",["csl-left-margin"],[]) (xs ++ case lastMay xs of Just Space -> [] _ -> [Space]) Seq.<| rest _ -> ils _ -> ils getRefsFromBib :: PandocMonad m => Locale -> (Text -> Bool) -> Text -> m [Reference Inlines] getRefsFromBib locale idpred fp = do (raw, _) <- fetchItem fp case formatFromExtension (T.unpack fp) of Just f -> getRefs locale f idpred (Just fp) raw Nothing -> throwError $ PandocAppError $ "Could not determine bibliography format for " <> fp getRefs :: PandocMonad m => Locale -> BibFormat -> (Text -> Bool) -> Maybe Text -> ByteString -> m [Reference Inlines] getRefs locale format idpred mbfp raw = do let err' = throwError . PandocBibliographyError (fromMaybe mempty mbfp) case format of Format_bibtex -> either (err' . tshow) return . readBibtexString Bibtex locale idpred . UTF8.toText $ raw Format_biblatex -> either (err' . tshow) return . readBibtexString Biblatex locale idpred . UTF8.toText $ raw Format_json -> either (err' . T.pack) (return . filter (idpred . unItemId . referenceId)) . cslJsonToReferences $ raw Format_yaml -> do rs <- yamlToRefs idpred def{ readerExtensions = pandocExtensions } (T.unpack <$> mbfp) (L.fromStrict raw) return $ mapMaybe metaValueToReference rs -- localized quotes convertQuotes :: Locale -> Inline -> Inline convertQuotes locale (Quoted qt ils) = case (M.lookup openterm terms, M.lookup closeterm terms) of (Just ((_,oq):_), Just ((_,cq):_)) -> Span ("",[],[]) (Str oq : ils ++ [Str cq]) _ -> Quoted qt ils where terms = localeTerms locale openterm = case qt of DoubleQuote -> "open-quote" SingleQuote -> "open-inner-quote" closeterm = case qt of DoubleQuote -> "close-quote" SingleQuote -> "close-inner-quote" convertQuotes _ x = x -- assumes we walk in same order as query insertResolvedCitations :: Inline -> State [Inlines] Inline insertResolvedCitations (Cite cs ils) = do resolved <- get case resolved of [] -> return (Cite cs ils) (x:xs) -> do put xs return $ Cite cs (B.toList x) insertResolvedCitations x = return x getCitations :: Locale -> M.Map Text ItemId -> Pandoc -> [Citeproc.Citation Inlines] getCitations locale otherIdsMap = Foldable.toList . query getCitation where getCitation (Cite cs _fallback) = Seq.singleton $ Citeproc.Citation { Citeproc.citationId = Nothing , Citeproc.citationNoteNumber = case cs of [] -> Nothing (Pandoc.Citation{ Pandoc.citationNoteNum = n }: _) | n > 0 -> Just n | otherwise -> Nothing , Citeproc.citationItems = fromPandocCitations locale otherIdsMap cs } getCitation _ = mempty fromPandocCitations :: Locale -> M.Map Text ItemId -> [Pandoc.Citation] -> [CitationItem Inlines] fromPandocCitations locale otherIdsMap = concatMap go where go c = let (loclab, suffix) = parseLocator locale (citationSuffix c) (mblab, mbloc) = case loclab of Just (loc, lab) -> (Just loc, Just lab) Nothing -> (Nothing, Nothing) cit = CitationItem { citationItemId = fromMaybe (ItemId $ Pandoc.citationId c) (M.lookup (Pandoc.citationId c) otherIdsMap) , citationItemLabel = mblab , citationItemLocator = mbloc , citationItemType = NormalCite , citationItemPrefix = case citationPrefix c of [] -> Nothing ils -> Just $ B.fromList ils <> B.space , citationItemSuffix = case suffix of [] -> Nothing ils -> Just $ B.fromList ils } in if Pandoc.citationId c == "*" then [] else case citationMode c of AuthorInText -> [ cit{ citationItemType = AuthorOnly , citationItemSuffix = Nothing } , cit{ citationItemType = Citeproc.SuppressAuthor , citationItemPrefix = Nothing } ] NormalCitation -> [ cit ] Pandoc.SuppressAuthor -> [ cit{ citationItemType = Citeproc.SuppressAuthor } ] data BibFormat = Format_biblatex | Format_bibtex | Format_json | Format_yaml deriving (Show, Eq, Ord) formatFromExtension :: FilePath -> Maybe BibFormat formatFromExtension fp = case dropWhile (== '.') $ takeExtension fp of "biblatex" -> Just Format_biblatex "bibtex" -> Just Format_bibtex "bib" -> Just Format_biblatex "json" -> Just Format_json "yaml" -> Just Format_yaml _ -> Nothing isNote :: Inline -> Bool isNote (Note _) = True isNote (Cite _ [Note _]) = True -- the following allows citation styles that are "in-text" but use superscript -- references to be treated as if they are "notes" for the purposes of moving -- the citations after trailing punctuation (see ): isNote (Cite _ [Superscript _]) = True isNote _ = False isSpacy :: Inline -> Bool isSpacy Space = True isSpacy SoftBreak = True isSpacy _ = False mvPunct :: Bool -> Locale -> [Inline] -> [Inline] mvPunct moveNotes locale (x : xs) | isSpacy x = x : mvPunct moveNotes locale xs -- 'x [^1],' -> 'x,[^1]' mvPunct moveNotes locale (q : s : x : ys) | isSpacy s , isNote x = let spunct = T.takeWhile isPunctuation $ stringify ys in if moveNotes then if T.null spunct then q : x : mvPunct moveNotes locale ys else q : Str spunct : x : mvPunct moveNotes locale (B.toList (dropTextWhile isPunctuation (B.fromList ys))) else q : x : mvPunct moveNotes locale ys -- 'x[^1],' -> 'x,[^1]' mvPunct moveNotes locale (Cite cs ils : ys) | not (null ils) , isNote (last ils) , startWithPunct ys , moveNotes = let s = stringify ys spunct = T.takeWhile isPunctuation s in Cite cs (init ils ++ [Str spunct | not (endWithPunct False (init ils))] ++ [last ils]) : mvPunct moveNotes locale (B.toList (dropTextWhile isPunctuation (B.fromList ys))) mvPunct moveNotes locale (s : x : ys) | isSpacy s, isNote x = x : mvPunct moveNotes locale ys mvPunct moveNotes locale (s : x@(Cite _ (Superscript _ : _)) : ys) | isSpacy s = x : mvPunct moveNotes locale ys mvPunct moveNotes locale (Cite cs ils : Str "." : ys) | "." `T.isSuffixOf` (stringify ils) = Cite cs ils : mvPunct moveNotes locale ys mvPunct moveNotes locale (x:xs) = x : mvPunct moveNotes locale xs mvPunct _ _ [] = [] -- move https://doi.org etc. prefix inside link text (#6723): fixLinks :: [Inline] -> [Inline] fixLinks (Str t : Link attr [Str u1] (u2,tit) : xs) | t <> u1 == u2 = Link attr [Str (t <> u1)] (u2,tit) : fixLinks xs fixLinks (x:xs) = x : fixLinks xs fixLinks [] = [] endWithPunct :: Bool -> [Inline] -> Bool endWithPunct _ [] = False endWithPunct onlyFinal xs@(_:_) = case reverse (T.unpack $ stringify xs) of [] -> True -- covers .), .", etc.: (d:c:_) | isPunctuation d && not onlyFinal && isEndPunct c -> True (c:_) | isEndPunct c -> True | otherwise -> False where isEndPunct c = c `elem` (".,;:!?" :: String) startWithPunct :: [Inline] -> Bool startWithPunct ils = case T.uncons (stringify ils) of Just (c,_) -> c `elem` (".,;:!?" :: [Char]) Nothing -> False truish :: MetaValue -> Bool truish (MetaBool t) = t truish (MetaString s) = isYesValue (T.toLower s) truish (MetaInlines ils) = isYesValue (T.toLower (stringify ils)) truish (MetaBlocks [Plain ils]) = isYesValue (T.toLower (stringify ils)) truish _ = False isYesValue :: Text -> Bool isYesValue "t" = True isYesValue "true" = True isYesValue "yes" = True isYesValue _ = False -- if document contains a Div with id="refs", insert -- references as its contents. Otherwise, insert references -- at the end of the document in a Div with id="refs" insertRefs :: [(Text,Text)] -> [Text] -> Meta -> [Block] -> [Block] -> [Block] insertRefs _ _ _ [] bs = bs insertRefs refkvs refclasses meta refs bs = if isRefRemove meta then bs else case runState (walkM go bs) False of (bs', True) -> bs' (_, False) -> case refTitle meta of Nothing -> case reverse bs of Header lev (id',classes,kvs) ys : xs -> reverse xs ++ [Header lev (id',addUnNumbered classes,kvs) ys, Div ("refs",refclasses,refkvs) refs] _ -> bs ++ [refDiv] Just ils -> bs ++ [Header 1 ("bibliography", ["unnumbered"], []) ils, refDiv] where refDiv = Div ("refs", refclasses, refkvs) refs addUnNumbered cs = "unnumbered" : [c | c <- cs, c /= "unnumbered"] go :: Block -> State Bool Block go (Div ("refs",cs,kvs) xs) = do put True -- refHeader isn't used if you have an explicit references div let cs' = ordNub $ cs ++ refclasses return $ Div ("refs",cs',kvs) (xs ++ refs) go x = return x refTitle :: Meta -> Maybe [Inline] refTitle meta = case lookupMeta "reference-section-title" meta of Just (MetaString s) -> Just [Str s] Just (MetaInlines ils) -> Just ils Just (MetaBlocks [Plain ils]) -> Just ils Just (MetaBlocks [Para ils]) -> Just ils _ -> Nothing isRefRemove :: Meta -> Bool isRefRemove meta = maybe False truish $ lookupMeta "suppress-bibliography" meta legacyDateRanges :: Reference Inlines -> Reference Inlines legacyDateRanges ref = ref{ referenceVariables = M.map go $ referenceVariables ref } where go (DateVal d) | null (dateParts d) , Just lit <- dateLiteral d = case T.splitOn "_" lit of [x,y] -> case Citeproc.rawDateEDTF (x <> "/" <> y) of Just d' -> DateVal d' Nothing -> DateVal d _ -> DateVal d go x = x linkifyVariables :: Reference Inlines -> Reference Inlines linkifyVariables ref = ref{ referenceVariables = M.mapWithKey go $ referenceVariables ref } where go "URL" x = tolink "https://" x go "DOI" x = tolink "https://doi.org/" (fixShortDOI x) go "ISBN" x = tolink "https://worldcat.org/isbn/" x go "PMID" x = tolink "https://www.ncbi.nlm.nih.gov/pubmed/" x go "PMCID" x = tolink "https://www.ncbi.nlm.nih.gov/pmc/articles/" x go _ x = x fixShortDOI x = let x' = extractText x in if "10/" `T.isPrefixOf` x' then TextVal $ T.drop 3 x' -- see http://shortdoi.org else TextVal x' tolink pref x = let x' = extractText x x'' = if "://" `T.isInfixOf` x' then x' else pref <> x' in FancyVal (B.link x'' "" (B.str x')) extractText :: Val Inlines -> Text extractText (TextVal x) = x extractText (FancyVal x) = toText x extractText (NumVal n) = T.pack (show n) extractText _ = mempty capitalizeNoteCitation :: Inline -> Inline capitalizeNoteCitation (Cite cs [Note [Para ils]]) = Cite cs [Note [Para $ B.toList $ addTextCase Nothing CapitalizeFirst $ B.fromList ils]] capitalizeNoteCitation x = x deNote :: [Inline] -> [Inline] deNote [] = [] deNote (Note bs:rest) = Note (walk go bs) : deNote rest where go [] = [] go (Cite (c:cs) ils : zs) | citationMode c == AuthorInText = Cite (c:cs) (concatMap (noteAfterComma (needsPeriod zs)) ils) : go zs | otherwise = Cite (c:cs) (concatMap noteInParens ils) : go zs go (x:xs) = x : go xs needsPeriod [] = True needsPeriod (Str t:_) = case T.uncons t of Nothing -> False Just (c,_) -> isUpper c needsPeriod (Space:zs) = needsPeriod zs needsPeriod _ = False noteInParens (Note bs') = Space : Str "(" : removeFinalPeriod (blocksToInlines bs') ++ [Str ")"] noteInParens x = [x] noteAfterComma needsPer (Note bs') = Str "," : Space : (if needsPer then id else removeFinalPeriod) (blocksToInlines bs') noteAfterComma _ x = [x] deNote (x:xs) = x : deNote xs -- Note: we can't use dropTextWhileEnd indiscriminately, -- because this would remove the final period on abbreviations like Ibid. -- But it turns out that when the note citation ends with Ibid. -- (or Ed. etc.), the last inline will be Str "" as a result of -- the punctuation-fixing mechanism that removes the double '.'. removeFinalPeriod :: [Inline] -> [Inline] removeFinalPeriod ils = case lastMay ils of Just (Span attr ils') -> initSafe ils ++ [Span attr (removeFinalPeriod ils')] Just (Emph ils') -> initSafe ils ++ [Emph (removeFinalPeriod ils')] Just (Strong ils') -> initSafe ils ++ [Strong (removeFinalPeriod ils')] Just (SmallCaps ils') -> initSafe ils ++ [SmallCaps (removeFinalPeriod ils')] Just (Str t) | T.takeEnd 1 t == "." -> initSafe ils ++ [Str (T.dropEnd 1 t)] | isRightQuote (T.takeEnd 1 t) -> removeFinalPeriod (initSafe ils ++ [Str tInit | not (T.null tInit)]) ++ [Str tEnd] where tEnd = T.takeEnd 1 t tInit = T.dropEnd 1 t _ -> ils where isRightQuote "\8221" = True isRightQuote "\8217" = True isRightQuote "\187" = True isRightQuote _ = False bcp47LangToIETF :: PandocMonad m => Text -> m (Maybe Lang) bcp47LangToIETF bcplang = case BCP47.parseBCP47 bcplang of Left _ -> do report $ InvalidLang bcplang return Nothing Right lang -> return $ Just $ Lang (BCP47.langLanguage lang) (if T.null (BCP47.langRegion lang) then Nothing else Just (BCP47.langRegion lang))