Merge pull request #7042 from tarleb/jats-element-citations

JATS writer: use element citations

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