From e87b54dcad5e37133bc0f4cfc8039e9fd0dd1b4e Mon Sep 17 00:00:00 2001
From: John MacFarlane <jgm@berkeley.edu>
Date: Thu, 16 May 2019 21:39:03 -0700
Subject: [PATCH] JATS writer: properly handle footnotes.
"Best Practice: When footnotes are grouped at the end of an article,
wrap them in a `<fn-group>` and use an `<xref>` element in the text, as
usual, to tie each footnote in the list to a particular location in the
text."
Closes #5511.
---
src/Text/Pandoc/Writers/JATS.hs | 31 +++++++++++++-----
test/Tests/Writers/JATS.hs | 4 +--
test/writer.jats | 56 +++++++++++++++++++--------------
3 files changed, 58 insertions(+), 33 deletions(-)
diff --git a/src/Text/Pandoc/Writers/JATS.hs b/src/Text/Pandoc/Writers/JATS.hs
index e2c4e1e72..25ef3b223 100644
--- a/src/Text/Pandoc/Writers/JATS.hs
+++ b/src/Text/Pandoc/Writers/JATS.hs
@@ -16,6 +16,7 @@ https://jats.nlm.nih.gov/publishing/tag-library
module Text.Pandoc.Writers.JATS ( writeJATS ) where
import Prelude
import Control.Monad.Reader
+import Control.Monad.State
import Data.Char (toLower)
import Data.Generics (everywhere, mkT)
import Data.List (isSuffixOf, partition, isPrefixOf)
@@ -39,11 +40,16 @@ import qualified Text.XML.Light as Xml
data JATSVersion = JATS1_1
deriving (Eq, Show)
-type JATS = ReaderT JATSVersion
+data JATSState = JATSState
+ { jatsNotes :: [(Int, Doc)] }
+
+type JATS a = StateT JATSState (ReaderT JATSVersion a)
writeJATS :: PandocMonad m => WriterOptions -> Pandoc -> m Text
writeJATS opts d =
- runReaderT (docToJATS opts d) JATS1_1
+ runReaderT (evalStateT (docToJATS opts d)
+ (JATSState{ jatsNotes = [] }))
+ JATS1_1
-- | Convert Pandoc document to string in JATS format.
docToJATS :: PandocMonad m => WriterOptions -> Pandoc -> JATS m Text
@@ -52,7 +58,7 @@ docToJATS opts (Pandoc meta blocks) = do
isBackBlock _ = False
let (backblocks, bodyblocks) = partition isBackBlock blocks
let elements = hierarchicalize bodyblocks
- let backElements = hierarchicalize backblocks
+ let backElements = hierarchicalize $ backblocks
let colwidth = if writerWrapText opts == WrapAuto
then Just $ writerColumns opts
else Nothing
@@ -77,8 +83,10 @@ docToJATS opts (Pandoc meta blocks) = do
meta
main <- (render' . vcat) <$>
mapM (elementToJATS opts' startLvl) elements
- back <- (render' . vcat) <$>
- mapM (elementToJATS opts' startLvl) backElements
+ notes <- reverse . map snd <$> gets jatsNotes
+ backs <- mapM (elementToJATS opts' startLvl) backElements
+ let fns = inTagsIndented "fn-group" $ vcat notes
+ let back = render' $ vcat backs $$ fns
let context = defField "body" main
$ defField "back" back
$ defField "mathml" (case writerHTMLMathMethod opts of
@@ -368,9 +376,18 @@ inlineToJATS _ Space = return space
inlineToJATS opts SoftBreak
| writerWrapText opts == WrapPreserve = return cr
| otherwise = return space
-inlineToJATS opts (Note contents) =
+inlineToJATS opts (Note contents) = do
-- TODO technically only <p> tags are allowed inside
- inTagsIndented "fn" <$> blocksToJATS opts contents
+ notes <- gets jatsNotes
+ let notenum = case notes of
+ (n, _):_ -> n + 1
+ [] -> 1
+ thenote <- inTags True "fn" [("id","fn" ++ show notenum)]
+ <$> blocksToJATS opts contents
+ modify $ \st -> st{ jatsNotes = (notenum, thenote) : notes }
+ return $ inTags False "xref" [("ref-type", "fn"),
+ ("rid", "fn" ++ show notenum)]
+ $ text (show notenum)
inlineToJATS opts (Cite _ lst) =
-- TODO revisit this after examining the jats.csl pipeline
inlinesToJATS opts lst
diff --git a/test/Tests/Writers/JATS.hs b/test/Tests/Writers/JATS.hs
index 669220eea..6de058701 100644
--- a/test/Tests/Writers/JATS.hs
+++ b/test/Tests/Writers/JATS.hs
@@ -86,9 +86,7 @@ tests = [ testGroup "inline code"
headerWith ("foo",["unnumbered"],[]) 1
(text "Header 1" <> note (plain $ text "note")) =?>
"<sec id=\"foo\">\n\
- \ <title>Header 1<fn>\n\
- \ <p>note</p>\n\
- \ </fn></title>\n\
+ \ <title>Header 1<xref ref-type=\"fn\" rid=\"fn1\">1</xref></title>\n\
\</sec>"
, "unnumbered sub header" =:
headerWith ("foo",["unnumbered"],[]) 1
diff --git a/test/writer.jats b/test/writer.jats
index a4d604607..99cb3230b 100644
--- a/test/writer.jats
+++ b/test/writer.jats
@@ -844,38 +844,48 @@ These should not be escaped: \$ \\ \> \[ \{</preformat>
</sec>
<sec id="footnotes">
<title>Footnotes</title>
- <p>Here is a footnote reference,<fn>
- <p>Here is the footnote. It can go anywhere after the footnote reference.
- It need not be placed at the end of the document.</p>
- </fn> and another.<fn>
- <p>Here’s the long note. This one contains multiple blocks.</p>
- <p>Subsequent blocks are indented to show that they belong to the footnote
- (as with list items).</p>
- <preformat> { <code> }</preformat>
- <p>If you want, you can indent every line, but you can also be lazy and
- just indent the first line of each block.</p>
- </fn> This should <italic>not</italic> be a footnote reference, because it
- contains a space.[^my note] Here is an inline note.<fn>
- <p>This is <italic>easier</italic> to type. Inline notes may contain
- <ext-link ext-link-type="uri" xlink:href="http://google.com">links</ext-link>
- and <monospace>]</monospace> verbatim characters, as well as [bracketed
- text].</p>
- </fn></p>
+ <p>Here is a footnote reference,<xref ref-type="fn" rid="fn1">1</xref> and
+ another.<xref ref-type="fn" rid="fn2">2</xref> This should
+ <italic>not</italic> be a footnote reference, because it contains a
+ space.[^my note] Here is an inline
+ note.<xref ref-type="fn" rid="fn3">3</xref></p>
<disp-quote>
- <p>Notes can go in quotes.<fn>
- <p>In quote.</p>
- </fn></p>
+ <p>Notes can go in quotes.<xref ref-type="fn" rid="fn4">4</xref></p>
</disp-quote>
<list list-type="order">
<list-item>
- <p>And in list items.<fn>
- <p>In list.</p>
- </fn></p>
+ <p>And in list items.<xref ref-type="fn" rid="fn5">5</xref></p>
</list-item>
</list>
<p>This paragraph should not be part of the note, as it is not indented.</p>
</sec>
</body>
<back>
+<fn-group>
+ <fn id="fn1">
+ <p>Here is the footnote. It can go anywhere after the footnote reference.
+ It need not be placed at the end of the document.</p>
+ </fn>
+ <fn id="fn2">
+ <p>Here’s the long note. This one contains multiple blocks.</p>
+ <p>Subsequent blocks are indented to show that they belong to the footnote
+ (as with list items).</p>
+ <preformat> { <code> }</preformat>
+ <p>If you want, you can indent every line, but you can also be lazy and
+ just indent the first line of each block.</p>
+ </fn>
+ <fn id="fn3">
+ <p>This is <italic>easier</italic> to type. Inline notes may contain
+ <ext-link ext-link-type="uri" xlink:href="http://google.com">links</ext-link>
+ and <monospace>]</monospace> verbatim characters, as well as [bracketed
+ text].</p>
+ </fn>
+ <fn id="fn4">
+ <p>In quote.</p>
+ </fn>
+ <fn id="fn5">
+ <p>In list.</p>
+ </fn>
+</fn-group>
</back>
</article>