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-rw-r--r--src/Text/Pandoc/Citeproc.hs39
-rw-r--r--src/Text/Pandoc/Extensions.hs14
-rw-r--r--src/Text/Pandoc/Writers/JATS.hs21
-rw-r--r--src/Text/Pandoc/Writers/JATS/References.hs160
-rw-r--r--src/Text/Pandoc/Writers/JATS/Types.hs4
5 files changed, 213 insertions, 25 deletions
diff --git a/src/Text/Pandoc/Citeproc.hs b/src/Text/Pandoc/Citeproc.hs
index 9649c6971..6658c8c0c 100644
--- a/src/Text/Pandoc/Citeproc.hs
+++ b/src/Text/Pandoc/Citeproc.hs
@@ -18,33 +18,36 @@ 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.Builder (Inlines, Many(..), deleteMeta, setMeta)
+import qualified Text.Pandoc.Builder as B
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.Class (PandocMonad(..), getResourcePath, getUserDataDir,
+ fetchItem, readDataFile, report, setResourcePath)
+import Text.Pandoc.Error (PandocError(..))
+import Text.Pandoc.Extensions (pandocExtensions)
+import Text.Pandoc.Logging (LogMessage(..))
+import Text.Pandoc.Options (ReaderOptions(..))
import Text.Pandoc.Shared (stringify, ordNub, blocksToInlines, tshow)
import qualified Text.Pandoc.UTF8 as UTF8
+import Text.Pandoc.Walk (query, walk, walkM)
+import Control.Applicative ((<|>))
+import Control.Monad.Except (catchError, throwError)
+import Control.Monad.State (State, evalState, get, put, runState)
import Data.Aeson (eitherDecode)
-import Data.Default
-import Data.Ord ()
+import Data.ByteString (ByteString)
+import qualified Data.ByteString.Lazy as L
+import Data.Char (isPunctuation, isUpper)
+import Data.Default (Default(def))
+import qualified Data.Foldable as Foldable
import qualified Data.Map as M
+import Data.Maybe (mapMaybe, fromMaybe)
+import Data.Ord ()
+import qualified Data.Sequence as Seq
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 System.FilePath (takeExtension)
import Safe (lastMay, initSafe)
-- import Debug.Trace as Trace (trace, traceShowId)
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 <tarleb@zeitkraut.de>
+ Stability : alpha
+ Portability : portable
+
+Creation of a bibliography list using @<element-citation>@ 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
generated by cgit v1.2.3 (git 2.39.1) at 2024-12-12 14:22:58 +0000