From e87b54dcad5e37133bc0f4cfc8039e9fd0dd1b4e Mon Sep 17 00:00:00 2001 From: John MacFarlane Date: Thu, 16 May 2019 21:39:03 -0700 Subject: JATS writer: properly handle footnotes. "Best Practice: When footnotes are grouped at the end of an article, wrap them in a `` and use an `` 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 | 52 ++++++++++++++++++++++++----------------- 3 files changed, 56 insertions(+), 31 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

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")) =?> "\n\ - \ Header 1<fn>\n\ - \ <p>note</p>\n\ - \ </fn>\n\ + \ Header 1<xref ref-type=\"fn\" rid=\"fn1\">1</xref>\n\ \" , "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: \$ \\ \> \[ \{ Footnotes -

Here is a footnote reference, +

Here is a footnote reference,1 and + another.2 This should + not be a footnote reference, because it contains a + space.[^my note] Here is an inline + note.3

+ +

Notes can go in quotes.4

+ + + +

And in list items.5

+ + +

This paragraph should not be part of the note, as it is not indented.

+ + + + +

Here is the footnote. It can go anywhere after the footnote reference. It need not be placed at the end of the document.

- and another. + +

Here’s the long note. This one contains multiple blocks.

Subsequent blocks are indented to show that they belong to the footnote (as with list items).

{ <code> }

If you want, you can indent every line, but you can also be lazy and just indent the first line of each block.

- This should not be a footnote reference, because it - contains a space.[^my note] Here is an inline note. + +

This is easier to type. Inline notes may contain links and ] verbatim characters, as well as [bracketed text].

-

- -

Notes can go in quotes. -

In quote.

-

- - - -

And in list items. -

In list.

-

- - -

This paragraph should not be part of the note, as it is not indented.

- - - + + +

In quote.

+ + +

In list.

+ + -- cgit v1.2.3