JATS reader: improve handling of fn-group elements (#7914)

Footnotes in `<fn-group>` elements are collected and re-inserted into
the document as proper footnotes in the place where they are referenced.

Fixes: #6348

2 files changed, 65 insertions, 2 deletions

diff --git a/src/Text/Pandoc/Readers/JATS.hs b/src/Text/Pandoc/Readers/JATS.hs
index 37e0d13bc..03ed4a659 100644
--- a/src/Text/Pandoc/Readers/JATS.hs
+++ b/src/Text/Pandoc/Readers/JATS.hs
@@ -30,8 +30,9 @@ import Text.Pandoc.Builder
 import Text.Pandoc.Class.PandocMonad (PandocMonad)
 import Text.Pandoc.Options
 import Text.Pandoc.Shared (safeRead, extractSpaces)
-import Text.TeXMath (readMathML, writeTeX)
+import Text.Pandoc.Walk (walk)
 import Text.Pandoc.XML.Light
+import Text.TeXMath (readMathML, writeTeX)
 import qualified Data.Set as S (fromList, member)
 import Data.Set ((\\))
 import Text.Pandoc.Sources (ToSources(..), sourcesToText)
@@ -43,6 +44,7 @@ data JATSState = JATSState{ jatsSectionLevel :: Int
                           , jatsQuoteType    :: QuoteType
                           , jatsMeta         :: Meta
                           , jatsBook         :: Bool
+                          , jatsFootnotes    :: Map.Map Text Blocks
                           , jatsContent      :: [Content]
                           } deriving Show
 
@@ -51,6 +53,7 @@ instance Default JATSState where
                  , jatsQuoteType = DoubleQuote
                  , jatsMeta = mempty
                  , jatsBook = False
+                 , jatsFootnotes = mempty
                  , jatsContent = [] }
 
 
@@ -63,7 +66,17 @@ readJATS _ inp = do
   tree <- either (throwError . PandocXMLError "") return $
             parseXMLContents (TL.fromStrict . sourcesToText $ sources)
   (bs, st') <- flip runStateT (def{ jatsContent = tree }) $ mapM parseBlock tree
-  return $ Pandoc (jatsMeta st') (toList . mconcat $ bs)
+  let footnotes = jatsFootnotes st'
+  let blockList = toList $ mconcat bs
+  let linkToFootnotes :: Inline -> Inline
+      linkToFootnotes link'@(Link _attr _txt (href, _title)) =
+        case T.uncons href of
+          Just ('#', rid) -> case Map.lookup rid footnotes of
+                               Just footnote -> Note (toList footnote)
+                               Nothing       -> link'
+          _               -> link'
+      linkToFootnotes inline = inline
+  return $ Pandoc (jatsMeta st') (walk linkToFootnotes blockList)
 
 -- convenience function to get an attribute value, defaulting to ""
 attrValue :: Text -> Element -> Text
@@ -175,6 +188,7 @@ parseBlock (Elem e) =
         "table-wrap" -> divWith (attrValue "id" e, ["table-wrap"], [])
                           <$> getBlocks e
         "caption" -> divWith (attrValue "id" e, ["caption"], []) <$> sect 6
+        "fn-group" -> parseFootnoteGroup
         "ref-list" -> parseRefList e
         "?xml"  -> return mempty
         _       -> getBlocks e
@@ -239,6 +253,13 @@ parseBlock (Elem e) =
                           (attrValue "title" g)
 
                   _   -> divWith (attrValue "id" e, ["fig"], []) <$> getBlocks e
+         parseFootnoteGroup = do
+           forM_ (filterChildren (named "fn") e) $ \fn -> do
+             let id' = attrValue "id" fn
+             contents <- getBlocks fn
+             modify $ \st ->
+               st { jatsFootnotes = Map.insert id' contents (jatsFootnotes st) }
+           return mempty
 
          parseTable = do
                       let isCaption x = named "title" x || named "caption" x
diff --git a/test/command/6348.md b/test/command/6348.md
new file mode 100644
index 000000000..7f599e52e
--- /dev/null
+++ b/test/command/6348.md
@@ -0,0 +1,42 @@
+```
+% pandoc -f jats -t native
+<?xml version="1.0" encoding="utf-8"?>
+<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Publishing DTD v1.0 20120330//EN" "http://jats.nlm.nih.gov/publishing/1.0/JATS-journalpublishing1.dtd">
+<article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" dtd-version="1.0" article-type="research-article">
+  <front>
+    <journal-meta>
+      <journal-title-group>
+        <journal-title>Opinion Research</journal-title>
+      </journal-title-group>
+    </journal-meta>
+    <article-meta>
+      <title-group>
+        <article-title>Example article</article-title>
+      </title-group>
+    </article-meta>
+  </front>
+  <body>
+    <sec sec-type="results">
+      <title>Results</title>
+      <p>A University <xref ref-type="fn" rid="N0001">1</xref></p>
+    </sec>
+  </body>
+  <back>
+    <fn-group>
+      <fn id="N0001">
+        <p>footnote</p>
+      </fn>
+    </fn-group>
+  </back>
+</article>
+^D
+[ Header 1 ( "" , [] , [] ) [ Str "Results" ]
+, Para
+    [ Str "A"
+    , Space
+    , Str "University"
+    , Space
+    , Note [ Para [ Str "footnote" ] ]
+    ]
+]
+```