diff --git a/MANUAL.txt b/MANUAL.txt index b9c4ef637..7bf74a8f9 100644 --- a/MANUAL.txt +++ b/MANUAL.txt @@ -3093,6 +3093,13 @@ output format. Some aspects of [Pandoc's Markdown citation syntax](#citations) are also accepted in `org` input. +#### Extension: `element_citations` #### + +In the `jats` output formats, this causes reference items to +be replaced with `` elements. These +elements are not influenced by CSL styles, but all information +on the item is included in tags. + #### Extension: `ntb` #### In the `context` output format this enables the use of [Natural Tables diff --git a/pandoc.cabal b/pandoc.cabal index 0d63cbe35..07feb10dd 100644 --- a/pandoc.cabal +++ b/pandoc.cabal @@ -638,6 +638,7 @@ library Text.Pandoc.Readers.Metadata, Text.Pandoc.Readers.Roff, Text.Pandoc.Writers.Docx.StyleMap, + Text.Pandoc.Writers.JATS.References, Text.Pandoc.Writers.JATS.Table, Text.Pandoc.Writers.JATS.Types, Text.Pandoc.Writers.LaTeX.Caption, diff --git a/src/Text/Pandoc/Extensions.hs b/src/Text/Pandoc/Extensions.hs index 39c2a0489..7aa32c52c 100644 --- a/src/Text/Pandoc/Extensions.hs +++ b/src/Text/Pandoc/Extensions.hs @@ -88,6 +88,7 @@ data Extension = -- does not affect readers/writers directly; it causes -- the eastAsianLineBreakFilter to be applied after -- parsing, in Text.Pandoc.App.convertWithOpts. + | Ext_element_citations -- ^ Use element-citation elements for JATS citations | Ext_emoji -- ^ Support emoji like :smile: | Ext_empty_paragraphs -- ^ Allow empty paragraphs | Ext_epub_html_exts -- ^ Recognise the EPUB extended version of HTML @@ -412,6 +413,11 @@ getDefaultExtensions "textile" = extensionsFromList Ext_smart, Ext_raw_html, Ext_auto_identifiers] +getDefaultExtensions "jats" = extensionsFromList + [Ext_auto_identifiers] +getDefaultExtensions "jats_archiving" = getDefaultExtensions "jats" +getDefaultExtensions "jats_publishing" = getDefaultExtensions "jats" +getDefaultExtensions "jats_articleauthoring" = getDefaultExtensions "jats" getDefaultExtensions "opml" = pandocExtensions -- affects notes getDefaultExtensions _ = extensionsFromList [Ext_auto_identifiers] @@ -554,6 +560,14 @@ getAllExtensions f = universalExtensions <> getAll f , Ext_smart , Ext_raw_tex ] + getAll "jats" = + extensionsFromList + [ Ext_auto_identifiers + , Ext_element_citations + ] + getAll "jats_archiving" = getAll "jats" + getAll "jats_publishing" = getAll "jats" + getAll "jats_articleauthoring" = getAll "jats" getAll "opml" = allMarkdownExtensions -- affects notes getAll "twiki" = autoIdExtensions <> extensionsFromList diff --git a/src/Text/Pandoc/Writers/JATS.hs b/src/Text/Pandoc/Writers/JATS.hs index c75d40745..a9369db7a 100644 --- a/src/Text/Pandoc/Writers/JATS.hs +++ b/src/Text/Pandoc/Writers/JATS.hs @@ -29,6 +29,7 @@ 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) @@ -40,6 +41,7 @@ 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 @@ -71,15 +73,19 @@ writeJATS = writeJatsArchiving -- | Convert a @'Pandoc'@ document to JATS. writeJats :: PandocMonad m => JATSTagSet -> WriterOptions -> Pandoc -> m Text -writeJats tagSet opts d = - runReaderT (evalStateT (docToJATS opts d) initialState) - environment - where initialState = JATSState { jatsNotes = [] } - environment = JATSEnv +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 @@ -258,7 +264,10 @@ blockToJATS opts (Div (ident,_,_) [Para lst]) | "ref-" `T.isPrefixOf` ident = inTagsSimple "mixed-citation" <$> inlinesToJATS opts lst blockToJATS opts (Div ("refs",_,_) xs) = do - contents <- blocksToJATS opts xs + 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 diff --git a/src/Text/Pandoc/Writers/JATS/References.hs b/src/Text/Pandoc/Writers/JATS/References.hs new file mode 100644 index 000000000..4ee7eb9dd --- /dev/null +++ b/src/Text/Pandoc/Writers/JATS/References.hs @@ -0,0 +1,160 @@ +{-# LANGUAGE LambdaCase #-} +{-# LANGUAGE OverloadedStrings #-} +{- | + Module : Text.Pandoc.Writers.JATS.References + Copyright : © 2021 Albert Krewinkel + License : GNU GPL, version 2 or above + + Maintainer : Albert Krewinkel + Stability : alpha + Portability : portable + +Creation of a bibliography list using @@ elements in +reference items. +-} +module Text.Pandoc.Writers.JATS.References + ( referencesToJATS + , referenceToJATS + ) where + +import Citeproc.Pandoc () +import Citeproc.Types + ( Date (..), DateParts (..), ItemId (..), Name (..), Reference (..) + , Val (..) , lookupVariable, valToText + ) +import Data.Text (Text) +import Text.DocLayout (Doc, empty, isEmpty, literal, vcat) +import Text.Pandoc.Class.PandocMonad (PandocMonad) +import Text.Pandoc.Builder (Inlines) +import Text.Pandoc.Options (WriterOptions) +import Text.Pandoc.Shared (tshow) +import Text.Pandoc.Writers.JATS.Types +import Text.Pandoc.XML (inTags) +import qualified Data.Text as T + +referencesToJATS :: PandocMonad m + => WriterOptions + -> [Reference Inlines] + -> JATS m (Doc Text) +referencesToJATS opts = + fmap (inTags True "ref-list" [] . vcat) . mapM (referenceToJATS opts) + +referenceToJATS :: PandocMonad m + => WriterOptions + -> Reference Inlines + -> JATS m (Doc Text) +referenceToJATS _opts ref = do + let refType = referenceType ref + let pubType = [("publication-type", refType) | not (T.null refType)] + let wrap = inTags True "ref" [("id", "ref-" <> unItemId (referenceId ref))] + . inTags True "element-citation" pubType + return . wrap . vcat $ + [ authors + , "title" `varInTag` + if refType == "book" + then "source" + else "article-title" + , if refType == "book" + then empty + else "container-title" `varInTag` "source" + , editors + , "publisher" `varInTag` "publisher-name" + , "publisher-place" `varInTag` "publisher-loc" + , yearTag + , accessed + , "volume" `varInTag` "volume" + , "issue" `varInTag` "issue" + , "page-first" `varInTag` "fpage" + , "page-last" `varInTag` "lpage" + , "pages" `varInTag` "page-range" + , "ISBN" `varInTag` "isbn" + , "ISSN" `varInTag` "issn" + , varInTagWith "doi" "pub-id" [("pub-id-type", "doi")] + , varInTagWith "pmid" "pub-id" [("pub-id-type", "pmid")] + ] + where + varInTag var tagName = varInTagWith var tagName [] + + varInTagWith var tagName tagAttribs = + case lookupVariable var ref >>= valToText of + Nothing -> mempty + Just val -> inTags' tagName tagAttribs $ literal val + + authors = case lookupVariable "author" ref of + Just (NamesVal names) -> + inTags True "person-group" [("person-group-type", "author")] . vcat $ + map toNameElements names + _ -> empty + + editors = case lookupVariable "editor" ref of + Just (NamesVal names) -> + inTags True "person-group" [("person-group-type", "editor")] . vcat $ + map toNameElements names + _ -> empty + + yearTag = + case lookupVariable "issued" ref of + Just (DateVal date) -> toDateElements date + _ -> empty + + accessed = + case lookupVariable "accessed" ref of + Just (DateVal d) -> inTags' "date-in-citation" + [("content-type", "access-date")] + (toDateElements d) + _ -> empty + +toDateElements :: Date -> Doc Text +toDateElements date = + case dateParts date of + dp@(DateParts (y:m:d:_)):_ -> yearElement y dp <> + monthElement m <> + dayElement d + dp@(DateParts (y:m:_)):_ -> yearElement y dp <> monthElement m + dp@(DateParts (y:_)):_ -> yearElement y dp + _ -> empty + +yearElement :: Int -> DateParts -> Doc Text +yearElement year dp = + inTags' "year" [("iso-8601-date", iso8601 dp)] $ literal (fourDigits year) + +monthElement :: Int -> Doc Text +monthElement month = inTags' "month" [] . literal $ twoDigits month + +dayElement :: Int -> Doc Text +dayElement day = inTags' "day" [] . literal $ twoDigits day + +iso8601 :: DateParts -> Text +iso8601 = T.intercalate "-" . \case + DateParts (y:m:d:_) -> [fourDigits y, twoDigits m, twoDigits d] + DateParts (y:m:_) -> [fourDigits y, twoDigits m] + DateParts (y:_) -> [fourDigits y] + _ -> [] + +twoDigits :: Int -> Text +twoDigits n = T.takeEnd 2 $ '0' `T.cons` tshow n + +fourDigits :: Int -> Text +fourDigits n = T.takeEnd 4 $ "000" <> tshow n + +toNameElements :: Name -> Doc Text +toNameElements name = + if not (isEmpty nameTags) + then inTags' "name" [] nameTags + else nameLiteral name `inNameTag` "string-name" + where + inNameTag val tag = maybe empty (inTags' tag [] . literal) val + surnamePrefix = maybe mempty (`T.snoc` ' ') $ + nameNonDroppingParticle name + givenSuffix = maybe mempty (T.cons ' ') $ + nameDroppingParticle name + nameTags = mconcat + [ ((surnamePrefix <>) <$> nameFamily name) `inNameTag` "surname" + , ((<> givenSuffix) <$> nameGiven name) `inNameTag` "given-names" + , nameSuffix name `inNameTag` "suffix" + ] + +-- | Put the supplied contents between start and end tags of tagType, +-- with specified attributes. +inTags' :: Text -> [(Text, Text)] -> Doc Text -> Doc Text +inTags' = inTags False diff --git a/src/Text/Pandoc/Writers/JATS/Types.hs b/src/Text/Pandoc/Writers/JATS/Types.hs index 54ed4a8bd..6fdddc0b5 100644 --- a/src/Text/Pandoc/Writers/JATS/Types.hs +++ b/src/Text/Pandoc/Writers/JATS/Types.hs @@ -17,11 +17,12 @@ module Text.Pandoc.Writers.JATS.Types ) where +import Citeproc.Types (Reference) import Control.Monad.Reader (ReaderT) import Control.Monad.State (StateT) import Data.Text (Text) import Text.DocLayout (Doc) -import Text.Pandoc.Definition (Block, Inline) +import Text.Pandoc.Builder (Block, Inline, Inlines) import Text.Pandoc.Options (WriterOptions) -- | JATS tag set variant @@ -40,6 +41,7 @@ data JATSEnv m = JATSEnv { jatsTagSet :: JATSTagSet , jatsInlinesWriter :: WriterOptions -> [Inline] -> JATS m (Doc Text) , jatsBlockWriter :: WriterOptions -> Block -> JATS m (Doc Text) + , jatsReferences :: [Reference Inlines] } -- | JATS writer type diff --git a/test/command/7042.md b/test/command/7042.md new file mode 100644 index 000000000..de0294da3 --- /dev/null +++ b/test/command/7042.md @@ -0,0 +1,146 @@ +``` +% pandoc -f markdown -t jats_publishing+element_citations --citeproc -s +--- +nocite: "[@*]" +references: +- author: + - family: Jane + given: Doe + container-title: Public Library of Tests + id: year-month + issued: 1999-08 + title: Year and month + type: article-journal +- accessed: 1999-01-22 + author: + - family: Negidius + given: Numerius + container-title: Public Library of Tests + id: access-date + issued: 1911-10-03 + title: Entry with access date + type: article-journal +- author: + - family: Beethoven + given: Ludwig + dropping-particle: van + - family: Bray + given: Jan + non-dropping-particle: de + container-title: Public Library of Tests + id: name-particles + issued: 1820 + title: Name particles, dropping and non-dropping + type: article-journal +- author: + - 宮水 三葉 + - 立花 瀧 + title: Big Book of Tests + id: book-with-japanese-authors + issued: 2016 + type: book +- author: + - family: Watson + given: J. D. + - family: Crick + given: F. H. C. + container-title: Nature + doi: '10.1038/171737a0' + id: full-journal-article-entry + issue: 4356 + issued: '1953-04-01' + pages: 737-738 + pmid: 13054692 + title: 'Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid' + type: article-journal + volume: 171 +... +^D + + +
+ + + + + + + + + + + + + + + + + + + + + + + JaneDoe + + Year and month + Public Library of Tests + 199908 + + + + + + NegidiusNumerius + + Entry with access date + Public Library of Tests + 19111003 + 19990122 + + + + + + BeethovenLudwig van + de BrayJan + + Name particles, dropping and non-dropping + Public Library of Tests + 1820 + + + + + + 宮水 三葉 + 立花 瀧 + + Big Book of Tests + 2016 + + + + + + WatsonJ. D. + CrickF. H. C. + + Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid + Nature + 19530401 + 171 + 4356 + 737 + 737-738 + 10.1038/171737a0 + 13054692 + + + + + +
+ +```