Improve support for code language in JATS

4 files changed, 59 insertions, 21 deletions

diff --git a/src/Text/Pandoc/Readers/JATS.hs b/src/Text/Pandoc/Readers/JATS.hs
index fc71e9a51..851fbec35 100644
--- a/src/Text/Pandoc/Readers/JATS.hs
+++ b/src/Text/Pandoc/Readers/JATS.hs
@@ -15,6 +15,8 @@ import Text.Pandoc.Options
 import Text.Pandoc.Shared (underlineSpan, crFilter, safeRead)
 import Text.TeXMath (readMathML, writeTeX)
 import Text.XML.Light
+import qualified Data.Set as S (fromList, member)
+import Data.Set ((\\))
 
 type JATS m = StateT JATSState m
 
@@ -98,8 +100,8 @@ instance HasMeta JATSState where
   deleteMeta field s = s {jatsMeta = deleteMeta field (jatsMeta s)}
 
 isBlockElement :: Content -> Bool
-isBlockElement (Elem e) = qName (elName e) `elem` blocktags
-  where blocktags = paragraphLevel ++ lists ++ mathML ++ other
+isBlockElement (Elem e) = qName (elName e) `S.member` blocktags
+  where blocktags = S.fromList (paragraphLevel ++ lists ++ mathML ++ other) \\ S.fromList inlinetags
         paragraphLevel = ["address", "array", "boxed-text", "chem-struct-wrap",
             "code", "fig", "fig-group", "graphic", "media", "preformat",
             "supplementary-material", "table-wrap", "table-wrap-group",
@@ -108,6 +110,21 @@ isBlockElement (Elem e) = qName (elName e) `elem` blocktags
         mathML = ["tex-math", "mml:math"]
         other = ["p", "related-article", "related-object", "ack", "disp-quote",
             "speech", "statement", "verse-group", "x"]
+        inlinetags = ["email", "ext-link", "uri", "inline-supplementary-material",
+            "related-article", "related-object", "hr", "bold", "fixed-case",
+            "italic", "monospace", "overline", "overline-start", "overline-end",
+            "roman", "sans-serif", "sc", "strike", "underline", "underline-start",
+            "underline-end", "ruby", "alternatives", "inline-graphic", "private-char",
+            "chem-struct", "inline-formula", "tex-math", "mml:math", "abbrev",
+            "milestone-end", "milestone-start", "named-content", "styled-content",
+            "fn", "target", "xref", "sub", "sup", "x", "address", "array",
+            "boxed-text", "chem-struct-wrap", "code", "fig", "fig-group", "graphic",
+            "media", "preformat", "supplementary-material", "table-wrap",
+            "table-wrap-group", "disp-formula", "disp-formula-group",
+            "citation-alternatives", "element-citation", "mixed-citation",
+            "nlm-citation", "award-id", "funding-source", "open-access",
+            "def-list", "list", "ack", "disp-quote", "speech", "statement",
+            "verse-group"]
 isBlockElement _ = False
 
 -- Trim leading and trailing newline characters
diff --git a/src/Text/Pandoc/Writers/JATS.hs b/src/Text/Pandoc/Writers/JATS.hs
index 8824eeb24..8dda969d9 100644
--- a/src/Text/Pandoc/Writers/JATS.hs
+++ b/src/Text/Pandoc/Writers/JATS.hs
@@ -170,6 +170,28 @@ imageMimeType src kvs =
                   ((drop 1 . dropWhile (/='/')) <$> mbMT)
   in (maintype, subtype)
 
+languageFor :: [String] -> String
+languageFor classes =
+  case langs of
+     (l:_) -> escapeStringForXML l
+     []    -> ""
+    where isLang l    = map toLower l `elem` map (map toLower) languages
+          langsFrom s = if isLang s
+                           then [s]
+                           else languagesByExtension . map toLower $ s
+          langs       = concatMap langsFrom classes
+
+codeAttr :: Attr -> (String, [(String, String)])
+codeAttr (ident,classes,kvs) = (lang, attr)
+    where
+       attr = [("id",ident) | not (null ident)] ++
+              [("language",lang) | not (null lang)] ++
+              [(k,v) | (k,v) <- kvs, k `elem` ["code-type",
+                "code-version", "executable",
+                "language-version", "orientation",
+                    "platforms", "position", "specific-use"]]
+       lang  = languageFor classes
+
 -- | Convert a Pandoc block element to JATS.
 blockToJATS :: PandocMonad m => WriterOptions -> Block -> JATS m Doc
 blockToJATS _ Null = return empty
@@ -233,23 +255,10 @@ blockToJATS opts (LineBlock lns) =
   blockToJATS opts $ linesToPara lns
 blockToJATS opts (BlockQuote blocks) =
   inTagsIndented "disp-quote" <$> blocksToJATS opts blocks
-blockToJATS _ (CodeBlock (ident,classes,kvs) str) = return $
+blockToJATS _ (CodeBlock a str) = return $
   inTags False tag attr (flush (text (escapeStringForXML str)))
-    where attr  = [("id",ident) | not (null ident)] ++
-                  [("language",lang) | not (null lang)] ++
-                  [(k,v) | (k,v) <- kvs, k `elem` ["code-type",
-                    "code-version", "executable",
-                    "language-version", "orientation",
-                    "platforms", "position", "specific-use"]]
-          tag   = if null lang then "preformat" else "code"
-          lang  = case langs of
-                     (l:_) -> escapeStringForXML l
-                     []    -> ""
-          isLang l    = map toLower l `elem` map (map toLower) languages
-          langsFrom s = if isLang s
-                           then [s]
-                           else languagesByExtension . map toLower $ s
-          langs       = concatMap langsFrom classes
+    where (lang, attr) = codeAttr a
+          tag          = if null lang then "preformat" else "code"
 blockToJATS _ (BulletList []) = return empty
 blockToJATS opts (BulletList lst) =
   inTags True "list" [("list-type", "bullet")] <$>
@@ -346,8 +355,10 @@ inlineToJATS opts (Quoted SingleQuote lst) = do
 inlineToJATS opts (Quoted DoubleQuote lst) = do
   contents <- inlinesToJATS opts lst
   return $ char '“' <> contents <> char '”'
-inlineToJATS _ (Code _ str) =
-  return $ inTagsSimple "monospace" $ text (escapeStringForXML str)
+inlineToJATS _ (Code a str) =
+  return $ inTags False tag attr $ text (escapeStringForXML str)
+    where (lang, attr) = codeAttr a
+          tag          = if null lang then "monospace" else "code"
 inlineToJATS _ il@(RawInline f x)
   | f == "jats" = return $ text x
   | otherwise   = do
diff --git a/test/Tests/Readers/JATS.hs b/test/Tests/Readers/JATS.hs
index ed6317c71..5c7dfa77c 100644
--- a/test/Tests/Readers/JATS.hs
+++ b/test/Tests/Readers/JATS.hs
@@ -14,6 +14,11 @@ jats = purely $ readJATS def
 tests :: [TestTree]
 tests = [ testGroup "inline code"
           [ test jats "basic" $ "<p>\n  <monospace>@&amp;</monospace>\n</p>" =?> para (code "@&")
+          , test jats "lang" $ "<p>\n  <code language=\"c\">@&amp;</code>\n</p>" =?> para (codeWith ("", ["c"], []) "@&")
+          ]
+        , testGroup "block code"
+          [ test jats "basic" $ "<preformat>@&amp;</preformat>" =?> codeBlock "@&"
+          , test jats "lang" $ "<code language=\"c\">@&amp;</code>" =?> codeBlockWith ("", ["c"], []) "@&"
           ]
         , testGroup "images"
           [ test jats "basic" $ "<graphic mimetype=\"image\" mime-subtype=\"\" xlink:href=\"/url\" xlink:title=\"title\" />"
diff --git a/test/Tests/Writers/JATS.hs b/test/Tests/Writers/JATS.hs
index cd4609849..f14f1c229 100644
--- a/test/Tests/Writers/JATS.hs
+++ b/test/Tests/Writers/JATS.hs
@@ -31,6 +31,11 @@ infix 4 =:
 tests :: [TestTree]
 tests = [ testGroup "inline code"
           [ "basic" =: code "@&" =?> "<p>\n  <monospace>@&amp;</monospace>\n</p>"
+          , "lang" =: codeWith ("", ["c"], []) "@&" =?> "<p>\n  <code language=\"c\">@&amp;</code>\n</p>"
+          ]
+        , testGroup "block code"
+          [ "basic" =: codeBlock "@&" =?> "<preformat>@&amp;</preformat>"
+          , "lang" =: codeBlockWith ("", ["c"], []) "@&" =?> "<code language=\"c\">@&amp;</code>"
           ]
         , testGroup "images"
           [ "basic" =:
@@ -38,7 +43,7 @@ tests = [ testGroup "inline code"
             =?> "<graphic mimetype=\"image\" mime-subtype=\"\" xlink:href=\"/url\" xlink:title=\"title\" />"
           ]
         , testGroup "inlines"
-          [ "Emphasis" =: emph ("emphasized")
+          [ "Emphasis" =: emph "emphasized"
             =?> "<p>\n  <italic>emphasized</italic>\n</p>"
           ]
         , "bullet list" =: bulletList [ plain $ text "first"