Merge pull request #4148 from stencila/jats-figures

fig, table-wrap & caption Divs for JATS writer

5 files changed, 160 insertions, 15 deletions

diff --git a/pandoc.cabal b/pandoc.cabal
index 0d05172d5..1bd24f4dd 100644
--- a/pandoc.cabal
+++ b/pandoc.cabal
@@ -636,6 +636,7 @@ test-suite test-pandoc
                   Tests.Writers.ConTeXt
                   Tests.Writers.Docbook
                   Tests.Writers.HTML
+                  Tests.Writers.JATS
                   Tests.Writers.Markdown
                   Tests.Writers.Org
                   Tests.Writers.Plain
diff --git a/src/Text/Pandoc/Writers/JATS.hs b/src/Text/Pandoc/Writers/JATS.hs
index 0ac37efba..8824eeb24 100644
--- a/src/Text/Pandoc/Writers/JATS.hs
+++ b/src/Text/Pandoc/Writers/JATS.hs
@@ -159,6 +159,17 @@ listItemToJATS opts mbmarker item = do
            maybe empty (\lbl -> inTagsIndented "label" (text lbl)) mbmarker
            $$ contents
 
+imageMimeType :: String -> [(String, String)] -> (String, String)
+imageMimeType src kvs =
+  let mbMT = getMimeType src
+      maintype = fromMaybe "image" $
+                  lookup "mimetype" kvs `mplus`
+                  (takeWhile (/='/') <$> mbMT)
+      subtype = fromMaybe "" $
+                  lookup "mime-subtype" kvs `mplus`
+                  ((drop 1 . dropWhile (/='/')) <$> mbMT)
+  in (maintype, subtype)
+
 -- | Convert a Pandoc block element to JATS.
 blockToJATS :: PandocMonad m => WriterOptions -> Block -> JATS m Doc
 blockToJATS _ Null = return empty
@@ -168,6 +179,13 @@ blockToJATS opts (Div ('r':'e':'f':'-':_,_,_) [Para lst]) =
 blockToJATS opts (Div ("refs",_,_) xs) = do
   contents <- blocksToJATS opts xs
   return $ inTagsIndented "ref-list" contents
+blockToJATS opts (Div (ident,[cls],kvs) bs) | cls `elem` ["fig", "caption", "table-wrap"] = do
+  contents <- blocksToJATS opts bs
+  let attr = [("id", ident) | not (null ident)] ++
+             [("xml:lang",l) | ("lang",l) <- kvs] ++
+             [(k,v) | (k,v) <- kvs, k `elem` ["specific-use",
+                 "content-type", "orientation", "position"]]
+  return $ inTags True cls attr contents
 blockToJATS opts (Div (ident,_,kvs) bs) = do
   contents <- blocksToJATS opts bs
   let attr = [("id", ident) | not (null ident)] ++
@@ -175,35 +193,40 @@ blockToJATS opts (Div (ident,_,kvs) bs) = do
              [(k,v) | (k,v) <- kvs, k `elem` ["specific-use",
                  "content-type", "orientation", "position"]]
   return $ inTags True "boxed-text" attr contents
-blockToJATS _ h@(Header{}) = do
-  -- should not occur after hierarchicalize, except inside lists/blockquotes
-  report $ BlockNotRendered h
-  return empty
+blockToJATS opts (Header _ _ title) = do
+  title' <- inlinesToJATS opts title
+  return $ inTagsSimple "title" title'
 -- No Plain, everything needs to be in a block-level tag
 blockToJATS opts (Plain lst) = blockToJATS opts (Para lst)
 -- title beginning with fig: indicates that the image is a figure
 blockToJATS opts (Para [Image (ident,_,kvs) txt
   (src,'f':'i':'g':':':tit)]) = do
   alt <- inlinesToJATS opts txt
+  let (maintype, subtype) = imageMimeType src kvs
   let capt = if null txt
                 then empty
                 else inTagsSimple "caption" alt
   let attr = [("id", ident) | not (null ident)] ++
              [(k,v) | (k,v) <- kvs, k `elem` ["fig-type", "orientation",
                                               "position", "specific-use"]]
-  let mbMT = getMimeType src
-  let maintype = fromMaybe "image" $
-                  lookup "mimetype" kvs `mplus`
-                  (takeWhile (/='/') <$> mbMT)
-  let subtype = fromMaybe "" $
-                  lookup "mime-subtype" kvs `mplus`
-                  ((drop 1 . dropWhile (/='/')) <$> mbMT)
   let graphicattr = [("mimetype",maintype),
-                     ("mime-subtype",drop 1 subtype),
+                     ("mime-subtype",subtype),
                      ("xlink:href",src),  -- do we need to URL escape this?
                      ("xlink:title",tit)]
   return $ inTags True "fig" attr $
               capt $$ selfClosingTag "graphic" graphicattr
+blockToJATS _ (Para [Image (ident,_,kvs) _ (src, tit)]) = do
+  let (maintype, subtype) = imageMimeType src kvs
+  let attr = [("id", ident) | not (null ident)] ++
+             [("mimetype", maintype),
+              ("mime-subtype", subtype),
+              ("xlink:href", src)] ++
+             [("xlink:title", tit) | not (null tit)] ++
+             [(k,v) | (k,v) <- kvs, k `elem` ["baseline-shift",
+                        "content-type", "specific-use", "xlink:actuate",
+                        "xlink:href", "xlink:role", "xlink:show",
+                        "xlink:type"]]
+  return $ selfClosingTag "graphic" attr
 blockToJATS opts (Para lst) =
   inTagsIndented "p" <$> inlinesToJATS opts lst
 blockToJATS opts (LineBlock lns) =
@@ -379,8 +402,8 @@ inlineToJATS _ (Link _attr [Str t] ('m':'a':'i':'l':'t':'o':':':email, _))
   return $ inTagsSimple "email" $ text (escapeStringForXML email)
 inlineToJATS opts (Link (ident,_,kvs) txt ('#':src, _)) = do
   let attr = [("id", ident) | not (null ident)] ++
-             [("alt", stringify txt),
-              ("rid", src)] ++
+             [("alt", stringify txt) | not (null txt)] ++
+             [("rid", src)] ++
              [(k,v) | (k,v) <- kvs, k `elem` ["ref-type", "specific-use"]]
   contents <- inlinesToJATS opts txt
   return $ inTags False "xref" attr contents
diff --git a/test/Tests/Writers/JATS.hs b/test/Tests/Writers/JATS.hs
new file mode 100644
index 000000000..cd4609849
--- /dev/null
+++ b/test/Tests/Writers/JATS.hs
@@ -0,0 +1,119 @@
+{-# LANGUAGE OverloadedStrings #-}
+module Tests.Writers.JATS (tests) where
+
+import Data.Text (unpack)
+import Test.Tasty
+import Tests.Helpers
+import Text.Pandoc
+import Text.Pandoc.Arbitrary ()
+import Text.Pandoc.Builder
+
+jats :: (ToPandoc a) => a -> String
+jats = unpack . purely (writeJATS def{ writerWrapText = WrapNone }) . toPandoc
+
+{-
+  "my test" =: X =?> Y
+
+is shorthand for
+
+  test jats "my test" $ X =?> Y
+
+which is in turn shorthand for
+
+  test jats "my test" (X,Y)
+-}
+
+infix 4 =:
+(=:) :: (ToString a, ToPandoc a)
+     => String -> (a, String) -> TestTree
+(=:) = test jats
+
+tests :: [TestTree]
+tests = [ testGroup "inline code"
+          [ "basic" =: code "@&" =?> "<p>\n  <monospace>@&amp;</monospace>\n</p>"
+          ]
+        , testGroup "images"
+          [ "basic" =:
+            image "/url" "title" mempty
+            =?> "<graphic mimetype=\"image\" mime-subtype=\"\" xlink:href=\"/url\" xlink:title=\"title\" />"
+          ]
+        , testGroup "inlines"
+          [ "Emphasis" =: emph ("emphasized")
+            =?> "<p>\n  <italic>emphasized</italic>\n</p>"
+          ]
+        , "bullet list" =: bulletList [ plain $ text "first"
+                                      , plain $ text "second"
+                                      , plain $ text "third"
+                                      ]
+            =?> "<list list-type=\"bullet\">\n\
+                \  <list-item>\n\
+                \    <p>\n\
+                \      first\n\
+                \    </p>\n\
+                \  </list-item>\n\
+                \  <list-item>\n\
+                \    <p>\n\
+                \      second\n\
+                \    </p>\n\
+                \  </list-item>\n\
+                \  <list-item>\n\
+                \    <p>\n\
+                \      third\n\
+                \    </p>\n\
+                \  </list-item>\n\
+                \</list>"
+        , testGroup "definition lists"
+          [ "with internal link" =: definitionList [(link "#go" "" (str "testing"),
+             [plain (text "hi there")])] =?>
+            "<def-list>\n\
+            \  <def-item>\n\
+            \    <term>\n\
+            \      <xref alt=\"testing\" rid=\"go\">testing</xref>\n\
+            \    </term>\n\
+            \    <def>\n\
+            \      <p>\n\
+            \        hi there\n\
+            \      </p>\n\
+            \    </def>\n\
+            \  </def-item>\n\
+            \</def-list>"
+          ]
+        , testGroup "math"
+          [ "escape |" =: para (math "\\sigma|_{\\{x\\}}") =?>
+            "<p>\n\
+            \  <inline-formula><alternatives>\n\
+            \  <tex-math><![CDATA[\\sigma|_{\\{x\\}}]]></tex-math>\n\
+            \  <mml:math display=\"inline\" xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"><mml:mrow><mml:mi>σ</mml:mi><mml:msub><mml:mo stretchy=\"false\" form=\"prefix\">|</mml:mo><mml:mrow><mml:mo stretchy=\"false\" form=\"prefix\">{</mml:mo><mml:mi>x</mml:mi><mml:mo stretchy=\"false\" form=\"postfix\">}</mml:mo></mml:mrow></mml:msub></mml:mrow></mml:math></alternatives></inline-formula>\n\
+            \</p>"
+          ]
+        , testGroup "headers"
+          [ "unnumbered header" =:
+            headerWith ("foo",["unnumbered"],[]) 1
+              (text "Header 1" <> note (plain $ text "note")) =?>
+            "<sec id=\"foo\">\n\
+            \  <title>Header 1<fn>\n\
+            \    <p>\n\
+            \      note\n\
+            \    </p>\n\
+            \  </fn></title>\n\
+            \</sec>"
+          , "unnumbered sub header" =:
+            headerWith ("foo",["unnumbered"],[]) 1
+              (text "Header")
+            <> headerWith ("foo",["unnumbered"],[]) 2
+              (text "Sub-Header") =?>
+            "<sec id=\"foo\">\n\
+            \  <title>Header</title>\n\
+            \  <sec id=\"foo\">\n\
+            \    <title>Sub-Header</title>\n\
+            \  </sec>\n\
+            \</sec>"
+          , "containing image" =:
+            header 1 (image "imgs/foo.jpg" "" (text "Alt text")) =?>
+            "<sec>\n\
+            \  <title><inline-graphic mimetype=\"image\" mime-subtype=\"jpeg\" xlink:href=\"imgs/foo.jpg\" /></title>\n\
+            \</sec>"
+          ]
+        ]
+
+
diff --git a/test/test-pandoc.hs b/test/test-pandoc.hs
index e1ce1bc70..123434411 100644
--- a/test/test-pandoc.hs
+++ b/test/test-pandoc.hs
@@ -25,6 +25,7 @@ import qualified Tests.Writers.Docbook
 import qualified Tests.Writers.Docx
 import qualified Tests.Writers.FB2
 import qualified Tests.Writers.HTML
+import qualified Tests.Writers.JATS
 import qualified Tests.Writers.LaTeX
 import qualified Tests.Writers.Markdown
 import qualified Tests.Writers.Muse
@@ -44,6 +45,7 @@ tests = testGroup "pandoc tests" [ Tests.Command.tests
           , testGroup "ConTeXt" Tests.Writers.ConTeXt.tests
           , testGroup "LaTeX" Tests.Writers.LaTeX.tests
           , testGroup "HTML" Tests.Writers.HTML.tests
+          , testGroup "JATS" Tests.Writers.JATS.tests
           , testGroup "Docbook" Tests.Writers.Docbook.tests
           , testGroup "Markdown" Tests.Writers.Markdown.tests
           , testGroup "Org" Tests.Writers.Org.tests
diff --git a/test/writer.jats b/test/writer.jats
index 0f52965bc..507e9f672 100644
--- a/test/writer.jats
+++ b/test/writer.jats
@@ -1379,7 +1379,7 @@ These should not be escaped:  \$ \\ \&gt; \[ \{</preformat>
   </p>
   <fig>
     <caption>lalune</caption>
-    <graphic mimetype="image" mime-subtype="peg" xlink:href="lalune.jpg" xlink:title="Voyage dans la Lune" />
+    <graphic mimetype="image" mime-subtype="jpeg" xlink:href="lalune.jpg" xlink:title="Voyage dans la Lune" />
   </fig>
   <p>
     Here is a movie