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-rw-r--r--src/Text/Pandoc/Templates.hs1
-rw-r--r--src/Text/Pandoc/Writers.hs8
-rw-r--r--src/Text/Pandoc/Writers/JATS.hs140
3 files changed, 107 insertions, 42 deletions
diff --git a/src/Text/Pandoc/Templates.hs b/src/Text/Pandoc/Templates.hs
index f04a73b58..6444728ae 100644
--- a/src/Text/Pandoc/Templates.hs
+++ b/src/Text/Pandoc/Templates.hs
@@ -90,6 +90,7 @@ getDefaultTemplate writer = do
"docbook" -> getDefaultTemplate "docbook5"
"epub" -> getDefaultTemplate "epub3"
"beamer" -> getDefaultTemplate "latex"
+ "jats" -> getDefaultTemplate "jats_archiving"
"markdown_strict" -> getDefaultTemplate "markdown"
"multimarkdown" -> getDefaultTemplate "markdown"
"markdown_github" -> getDefaultTemplate "markdown"
diff --git a/src/Text/Pandoc/Writers.hs b/src/Text/Pandoc/Writers.hs
index 753972855..cdf3ca1c8 100644
--- a/src/Text/Pandoc/Writers.hs
+++ b/src/Text/Pandoc/Writers.hs
@@ -41,6 +41,9 @@ module Text.Pandoc.Writers
, writeHtml5String
, writeICML
, writeJATS
+ , writeJatsArchiving
+ , writeJatsArticleAuthoring
+ , writeJatsPublishing
, writeJSON
, writeJira
, writeLaTeX
@@ -146,7 +149,10 @@ writers = [
,("docbook" , TextWriter writeDocbook5)
,("docbook4" , TextWriter writeDocbook4)
,("docbook5" , TextWriter writeDocbook5)
- ,("jats" , TextWriter writeJATS)
+ ,("jats" , TextWriter writeJatsArchiving)
+ ,("jats_articleauthoring", TextWriter writeJatsArticleAuthoring)
+ ,("jats_publishing" , TextWriter writeJatsPublishing)
+ ,("jats_archiving" , TextWriter writeJatsArchiving)
,("jira" , TextWriter writeJira)
,("opml" , TextWriter writeOPML)
,("opendocument" , TextWriter writeOpenDocument)
diff --git a/src/Text/Pandoc/Writers/JATS.hs b/src/Text/Pandoc/Writers/JATS.hs
index ab95110bf..49ace4636 100644
--- a/src/Text/Pandoc/Writers/JATS.hs
+++ b/src/Text/Pandoc/Writers/JATS.hs
@@ -4,7 +4,7 @@
{-# LANGUAGE ViewPatterns #-}
{- |
Module : Text.Pandoc.Writers.JATS
- Copyright : Copyright (C) 2017-2019 John MacFarlane
+ Copyright : Copyright (C) 2017-2020 John MacFarlane
License : GNU GPL, version 2 or above
Maintainer : John MacFarlane <jgm@berkeley.edu>
@@ -15,7 +15,12 @@ Conversion of 'Pandoc' documents to JATS XML.
Reference:
https://jats.nlm.nih.gov/publishing/tag-library
-}
-module Text.Pandoc.Writers.JATS ( writeJATS ) where
+module Text.Pandoc.Writers.JATS
+ ( writeJATS
+ , writeJatsArchiving
+ , writeJatsPublishing
+ , writeJatsArticleAuthoring
+ ) where
import Prelude
import Control.Monad.Reader
import Control.Monad.State
@@ -43,19 +48,46 @@ import Text.Pandoc.XML
import Text.TeXMath
import qualified Text.XML.Light as Xml
-data JATSVersion = JATS1_1
- deriving (Eq, Show)
+-- | JATS tag set variant
+data JATSTagSet
+ = TagSetArchiving -- ^ Archiving and Interchange Tag Set
+ | TagSetPublishing -- ^ Journal Publishing Tag Set
+ | TagSetArticleAuthoring -- ^ Article Authoring Tag Set
+ deriving (Eq)
-data JATSState = JATSState
+-- | Internal state used by the writer.
+newtype JATSState = JATSState
{ jatsNotes :: [(Int, Doc Text)] }
-type JATS a = StateT JATSState (ReaderT JATSVersion a)
+-- | JATS writer type
+type JATS a = StateT JATSState (ReaderT JATSTagSet a)
+-- | 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 opts d =
+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)
- (JATSState{ jatsNotes = [] }))
- JATS1_1
+ (JATSState{ jatsNotes = [] }))
+ tagSet
-- | Convert Pandoc document to string in JATS format.
docToJATS :: PandocMonad m => WriterOptions -> Pandoc -> JATS m Text
@@ -80,7 +112,10 @@ docToJATS opts (Pandoc meta blocks) = do
main <- fromBlocks bodyblocks
notes <- reverse . map snd <$> gets jatsNotes
backs <- fromBlocks backblocks
- let fns = if null notes
+ tagSet <- ask
+ -- 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
@@ -116,6 +151,8 @@ docToJATS opts (Pandoc meta blocks) = do
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
@@ -275,8 +312,12 @@ blockToJATS opts (Para lst) =
inTagsSimple "p" <$> inlinesToJATS opts lst
blockToJATS opts (LineBlock lns) =
blockToJATS opts $ linesToPara lns
-blockToJATS opts (BlockQuote blocks) =
- inTagsIndented "disp-quote" <$> blocksToJATS opts blocks
+blockToJATS opts (BlockQuote blocks) = do
+ tagSet <- ask
+ 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
@@ -287,14 +328,20 @@ blockToJATS opts (BulletList lst) =
listItemsToJATS opts Nothing lst
blockToJATS _ (OrderedList _ []) = return empty
blockToJATS opts (OrderedList (start, numstyle, delimstyle) items) = do
- let listType = case numstyle of
- DefaultStyle -> "order"
- Decimal -> "order"
- Example -> "order"
- UpperAlpha -> "alpha-upper"
- LowerAlpha -> "alpha-lower"
- UpperRoman -> "roman-upper"
- LowerRoman -> "roman-lower"
+ tagSet <- ask
+ 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
@@ -407,17 +454,22 @@ inlineToJATS opts SoftBreak
| writerWrapText opts == WrapPreserve = return cr
| otherwise = return space
inlineToJATS opts (Note contents) = 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)
+ tagSet <- ask
+ -- 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
@@ -444,16 +496,22 @@ inlineToJATS _ (Math t str) = do
let tagtype = case t of
DisplayMath -> "disp-formula"
InlineMath -> "inline-formula"
- let rawtex = inTagsSimple "tex-math"
- $ text "<![CDATA[" <>
- literal str <>
- text "]]>"
- return $ inTagsSimple tagtype $
- case res of
- Right r -> inTagsSimple "alternatives" $
- cr <> rawtex $$
- text (Xml.ppcElement conf $ fixNS r)
- Left _ -> rawtex
+
+ let rawtex = text "<![CDATA[" <> literal str <> text "]]>"
+ let texMath = inTagsSimple "tex-math" rawtex
+
+ tagSet <- ask
+ 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)
generated by cgit v1.2.3 (git 2.39.1) at 2024-11-16 00:47:32 +0000