Modify JATS reader to handle BITS too (#9138)

Add provision for title-group, book, book-part-wrapper, book-meta,
book-part-meta, book-title, book-title-group, index, toc, legend,
title, collection-meta

12 files changed, 1217 insertions, 14 deletions

diff --git a/src/Text/Pandoc/Readers/JATS.hs b/src/Text/Pandoc/Readers/JATS.hs
index 6cadef306..781c10953 100644
--- a/src/Text/Pandoc/Readers/JATS.hs
+++ b/src/Text/Pandoc/Readers/JATS.hs
@@ -163,8 +163,10 @@ parseBlock (CRef x) = return $ plain $ str $ T.toUpper x
 parseBlock (Elem e) = do
   sectionLevel <- gets jatsSectionLevel
   let parseBlockWithHeader = wrapWithHeader (sectionLevel+1) (getBlocks e)
-
+  
   case qName (elName e) of
+        "book" -> parseBook
+        "book-part-wrapper" -> parseBook
         "p" -> parseMixed para (elContent e)
         "code" -> codeBlockWithLang
         "preformat" -> codeBlockWithLang
@@ -201,6 +203,7 @@ parseBlock (Elem e) = do
         "article-meta" -> parseMetadata e
         "custom-meta" -> parseMetadata e
         "processing-meta" -> return mempty
+        "book-meta" -> parseMetadata e
         "title" -> return mempty -- processed by header
         "label" -> return mempty -- processed by header
         "table" -> parseTable
@@ -223,6 +226,19 @@ parseBlock (Elem e) = do
                             then blockFormula displayMath e
                             else divWith (attrValue "id" e, ["disp-formula"], [])
                                     <$> getBlocks e
+        "index" -> parseBlockWithHeader
+        "index-div" -> parseBlockWithHeader
+        "index-group" -> parseBlockWithHeader
+        "index-title-group" -> return mempty -- handled by index and index-div
+        "toc" -> parseBlockWithHeader
+        "toc-div" -> parseBlockWithHeader
+        "toc-entry" -> parseBlockWithHeader
+        "toc-group" -> parseBlockWithHeader
+        "toc-title-group" -> return mempty -- handled by toc 
+        "legend" -> parseBlockWithHeader
+        "dedication" -> parseBlockWithHeader
+        "foreword" -> parseBlockWithHeader
+        "preface" -> parseBlockWithHeader
         "?xml"  -> return mempty
         _       -> getBlocks e
    where parseMixed container conts = do
@@ -368,19 +384,35 @@ parseBlock (Elem e) = do
          parseElement = filterChildren isEntry
          wrapWithHeader n mBlocks = do
                       isBook <- gets jatsBook
-                      let n' = if isBook || n == 0 then n + 1 else n
+                      let n' = case (filterChild (named "title") e >>= maybeAttrValue "display-as") of
+                                  Just t -> read $ T.unpack t 
+                                  Nothing -> if isBook || n == 0 then n + 1 else n  
                       headerText <- case filterChild (named "title") e of
-                                        Just t  -> getInlines t
-                                        Nothing -> return mempty
+                                       Just t  -> case maybeAttrValue "supress" t of
+                                                     Just s -> if s == "no" 
+                                                                 then getInlines t 
+                                                                 else return mempty
+                                                     Nothing -> getInlines t
+                                       Nothing -> do
+                                           let name = qName (elName e)
+                                           if (name == "dedication" || name == "foreword" || name == "preface") 
+                                             then return $ str $ T.toTitle name
+                                             else case filterChild (named "index-title-group") e >>= filterChild (named "title") of
+                                                     Just i -> getInlines i
+                                                     Nothing -> case filterChild (named "toc-title-group") e >>= filterChild (named "title") of
+                                                                   Just t -> getInlines t
+                                                                   Nothing -> return mempty
                       oldN <- gets jatsSectionLevel
                       modify $ \st -> st{ jatsSectionLevel = n }
                       blocks <- mBlocks
                       let ident = attrValue "id" e
                       modify $ \st -> st{ jatsSectionLevel = oldN }
-                      return $ (if
-                        headerText == mempty
-                      then mempty
-                      else headerWith (ident,[],[]) n' headerText) <> blocks
+                      return $ (if headerText == mempty 
+                                  then mempty 
+                                  else headerWith (ident,[],[]) n' headerText) <> blocks
+         parseBook = do 
+           modify $ \st -> st{ jatsBook = True }
+           getBlocks e
 
 getInlines :: PandocMonad m => Element -> JATS m Inlines
 getInlines e' = trimInlines . mconcat <$>
@@ -388,16 +420,17 @@ getInlines e' = trimInlines . mconcat <$>
 
 parseMetadata :: PandocMonad m => Element -> JATS m Blocks
 parseMetadata e = do
-  getTitle e
-  getAuthors e
+  isBook <- gets jatsBook
+  if isBook then getBookTitle e else getArticleTitle e 
+  if isBook then getBookAuthors e else getArticleAuthors e
   getAffiliations e
   getAbstract e
   getPubDate e
   getPermissions e
   return mempty
 
-getTitle :: PandocMonad m => Element -> JATS m ()
-getTitle e = do
+getArticleTitle :: PandocMonad m => Element -> JATS m ()
+getArticleTitle e = do
   tit <-  case filterElement (named "article-title") e of
                Just s  -> getInlines s
                Nothing -> return mempty
@@ -408,8 +441,21 @@ getTitle e = do
   when (tit /= mempty) $ addMeta "title" tit
   when (subtit /= mempty) $ addMeta "subtitle" subtit
 
-getAuthors :: PandocMonad m => Element -> JATS m ()
-getAuthors e = do
+
+getBookTitle :: PandocMonad m => Element -> JATS m ()
+getBookTitle e = do
+  tit <-  case (filterElement (named "book-title-group") e >>= filterElement (named "book-title")) of
+               Just s  -> getInlines s
+               Nothing -> return mempty
+  subtit <-  case (filterElement (named "book-title-group") e >>= filterElement (named "subtitle")) of
+               Just s  -> (text ": " <>) <$>
+                           getInlines s
+               Nothing -> return mempty
+  when (tit /= mempty) $ addMeta "title" tit
+  when (subtit /= mempty) $ addMeta "subtitle" subtit
+
+getArticleAuthors :: PandocMonad m => Element -> JATS m ()
+getArticleAuthors e = do
   authors <- mapM getContrib $ filterElements
               (\x -> named "contrib" x &&
                      attrValue "contrib-type" x == "author") e
@@ -420,6 +466,18 @@ getAuthors e = do
                    (a:as, ns) -> reverse as ++ [a <> mconcat ns]
   unless (null authors) $ addMeta "author" authors'
 
+getBookAuthors :: PandocMonad m => Element -> JATS m ()
+getBookAuthors e = do
+  authors <- mapM getContrib $ filterElements (\x -> named "contrib-group" x) e
+              >>= filterElements (\x -> named "contrib" x &&
+                     attrValue "contrib-type" x == "author")
+  authorNotes <- mapM getInlines $ filterElements (named "author-notes") e
+  let authors' = case (reverse authors, authorNotes) of
+                   ([], _)    -> []
+                   (_, [])    -> authors
+                   (a:as, ns) -> reverse as ++ [a <> mconcat ns]
+  unless (null authors) $ addMeta "author" authors'
+
 getAffiliations :: PandocMonad m => Element -> JATS m ()
 getAffiliations x = do
   affs <- mapM getInlines $ filterChildren (named "aff") x
diff --git a/test/command/8867.md b/test/command/8867.md
new file mode 100644
index 000000000..f5a5a901f
--- /dev/null
+++ b/test/command/8867.md
@@ -0,0 +1,49 @@
+```
+% pandoc -f jats -t native -s
+<article-meta>
+      <title-group>
+        <article-title></article-title>
+      </title-group>
+      <permissions>
+        <copyright-statement>© 2023, Ellerman et al</copyright-statement>
+        <copyright-year>2023</copyright-year>
+        <copyright-holder>Ellerman et al</copyright-holder>
+        <license license-type="open-access">
+          <ali:license_ref xmlns:ali="http://www.niso.org/schemas/ali/1.0/">https://creativecommons.org/licenses/by/4.0/</ali:license_ref>
+          <license-p>This document is distributed under a Creative Commons Attribution 4.0 International license.</license-p>
+        </license>
+      </permissions>
+</article-meta>
+^D
+Pandoc
+  Meta
+    { unMeta =
+        fromList
+          [ ( "copyright"
+            , MetaMap
+                (fromList
+                   [ ( "holder" , MetaString "Ellerman et al" )
+                   , ( "statement"
+                     , MetaString "\169 2023, Ellerman et al"
+                     )
+                   , ( "year" , MetaString "2023" )
+                   ])
+            )
+          , ( "license"
+            , MetaMap
+                (fromList
+                   [ ( "link"
+                     , MetaString
+                         "https://creativecommons.org/licenses/by/4.0/"
+                     )
+                   , ( "text"
+                     , MetaString
+                         "This document is distributed under a Creative Commons Attribution 4.0 International license."
+                     )
+                   , ( "type" , MetaString "open-access" )
+                   ])
+            )
+          ]
+    }
+  []
+```
\ No newline at end of file
diff --git a/test/command/bits-book-meta.md b/test/command/bits-book-meta.md
new file mode 100644
index 000000000..53a64c7d7
--- /dev/null
+++ b/test/command/bits-book-meta.md
@@ -0,0 +1,104 @@
+```
+% pandoc -f jats -t native -s
+<book>
+    <book-meta>
+		<book-id book-id-type="publisher">handbook-648</book-id>
+  		<book-title-group>
+   			<book-title>The NCBI Handbook</book-title>
+  		</book-title-group>
+  		<contrib-group>
+   			<contrib contrib-type="author">
+    			<name><surname>McEntyre</surname>
+     			<given-names>Jo</given-names></name>
+    			<xref ref-type="aff" rid="bid.m.1"/>
+   			</contrib>
+   			<contrib contrib-type="editor">
+    			<name><surname>Ostell</surname>
+     			<given-names>Jim</given-names></name>
+    			<xref ref-type="aff" rid="bid.m.1"/>
+   			</contrib>
+  		</contrib-group>
+  		<aff id="bid.m.1">
+   			<institution>National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health</institution>, <addr-line>Bethesda, MD 20892-6510</addr-line>
+  		</aff>
+  		<pub-date iso-8601-date="2002-11">
+   			<month>11</month>
+   			<year>2002</year>
+  		</pub-date>
+  		<publisher>
+   			<publisher-name>National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health</publisher-name>
+   			<publisher-loc>Bethesda, MD</publisher-loc>
+  		</publisher>
+  		<edition>1</edition>
+  		<counts>
+   			<book-fig-count count="98"/>
+   			<book-table-count count="40"/>
+   			<book-equation-count count="0"/>
+   			<book-ref-count count="115"/>
+   			<book-page-count count="532"/>
+   			<book-word-count count="149852"/>
+  		</counts>
+ 	</book-meta>
+</book>
+^D
+Pandoc
+  Meta
+    { unMeta =
+        fromList
+          [ ( "author"
+            , MetaList
+                [ MetaInlines [ Str "Jo" , Space , Str "McEntyre" ] ]
+            )
+          , ( "date" , MetaInlines [ Str "2002-11" ] )
+          , ( "institute"
+            , MetaList
+                [ MetaInlines
+                    [ Str "National"
+                    , Space
+                    , Str "Center"
+                    , Space
+                    , Str "for"
+                    , Space
+                    , Str "Biotechnology"
+                    , Space
+                    , Str "Information"
+                    , Space
+                    , Str "(NCBI),"
+                    , Space
+                    , Str "National"
+                    , Space
+                    , Str "Library"
+                    , Space
+                    , Str "of"
+                    , Space
+                    , Str "Medicine,"
+                    , Space
+                    , Str "National"
+                    , Space
+                    , Str "Institutes"
+                    , Space
+                    , Str "of"
+                    , Space
+                    , Str "Health,"
+                    , Space
+                    , Str "Bethesda,"
+                    , Space
+                    , Str "MD"
+                    , Space
+                    , Str "20892-6510"
+                    ]
+                ]
+            )
+          , ( "title"
+            , MetaInlines
+                [ Str "The"
+                , Space
+                , Str "NCBI"
+                , Space
+                , Str "Handbook"
+                ]
+            )
+          ]
+    }
+  []
+```
\ No newline at end of file
diff --git a/test/command/bits-book-part-wrapper-meta.md b/test/command/bits-book-part-wrapper-meta.md
new file mode 100644
index 000000000..33f932068
--- /dev/null
+++ b/test/command/bits-book-part-wrapper-meta.md
@@ -0,0 +1,95 @@
+```
+% pandoc -f jats -t native -s
+<book-part-wrapper 
+  dtd-version="2.1"
+  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xmlns:xi="http://www.w3.org/2001/XInclude"
+  xmlns:mml="http://www.w3.org/1998/Math/MathML"
+  xmlns:xlink="http://www.w3.org/1999/xlink">
+
+ <collection-meta>
+  <title-group>
+   <title>Balisage Series on Markup Technologies</title>
+  </title-group>
+ 
+  <abstract>
+   <p>The <italic>Balisage Series on Markup Technologies</italic> 
+    is an occasional series...</p>
+  </abstract>
+ </collection-meta>
+
+ <book-meta>
+  <book-title-group>
+   <book-title>Proceedings of Balisage: The Markup Conference 
+    2013</book-title>
+  </book-title-group>
+ 
+  <abstract>
+   <p>Balisage is a peer-reviewed conference...</p></abstract>
+ 
+ </book-meta>
+</book-part-wrapper>
+^D
+Pandoc
+  Meta
+    { unMeta =
+        fromList
+          [ ( "abstract"
+            , MetaBlocks
+                [ Para
+                    [ Str "Balisage"
+                    , Space
+                    , Str "is"
+                    , Space
+                    , Str "a"
+                    , Space
+                    , Str "peer-reviewed"
+                    , Space
+                    , Str "conference..."
+                    ]
+                ]
+            )
+          , ( "title"
+            , MetaInlines
+                [ Str "Proceedings"
+                , Space
+                , Str "of"
+                , Space
+                , Str "Balisage:"
+                , Space
+                , Str "The"
+                , Space
+                , Str "Markup"
+                , Space
+                , Str "Conference"
+                , SoftBreak
+                , Str "2013"
+                ]
+            )
+          ]
+    }
+  [ Para
+      [ Str "The"
+      , Space
+      , Emph
+          [ Str "Balisage"
+          , Space
+          , Str "Series"
+          , Space
+          , Str "on"
+          , Space
+          , Str "Markup"
+          , Space
+          , Str "Technologies"
+          ]
+      , SoftBreak
+      , Str "is"
+      , Space
+      , Str "an"
+      , Space
+      , Str "occasional"
+      , Space
+      , Str "series..."
+      ]
+  ]
+```
\ No newline at end of file
diff --git a/test/command/bits-book-part-wrapper.md b/test/command/bits-book-part-wrapper.md
new file mode 100644
index 000000000..206ad951c
--- /dev/null
+++ b/test/command/bits-book-part-wrapper.md
@@ -0,0 +1,149 @@
+```
+% pandoc -f jats -t native
+<book-part-wrapper 
+  dtd-version="2.1"
+  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xmlns:xi="http://www.w3.org/2001/XInclude"
+  xmlns:mml="http://www.w3.org/1998/Math/MathML"
+  xmlns:xlink="http://www.w3.org/1999/xlink">
+
+ <collection-meta>
+  <title-group>
+   <title>Balisage Series on Markup Technologies</title>
+  </title-group>
+ 
+  <abstract>
+   <p>The <italic>Balisage Series on Markup Technologies</italic> 
+    is an occasional series...</p>
+  </abstract>
+ </collection-meta>
+
+ <book-meta>
+  <book-title-group>
+   <book-title>Proceedings of Balisage: The Markup Conference 
+    2013</book-title>
+  </book-title-group>
+ 
+  <abstract>
+   <p>Balisage is a peer-reviewed conference...</p></abstract>
+ 
+ </book-meta>
+
+ <book-part id="bid.1" book-part-type="part">
+   			<book-part-meta>
+    			<title-group>
+     				<label>Part 1</label>
+     				<title>The Databases</title>
+    			</title-group>
+   			</book-part-meta>
+   			<body>
+    			<sec id="bid.3">
+     				<title>History</title>
+     				<p>Initially, GenBank was built and maintained at Los Alamos 
+      				National Laboratory.</p>
+    			</sec>
+   			</body>
+   			<back>
+                <title>Back matter of book part</title>
+  				<ref-list>
+   					<title>References</title>
+   					<ref id="bid.41">
+    					<label>1</label>
+    					<element-citation>
+     						<person-group>
+      							<string-name>
+									<surname>Olson</surname>
+       								<given-names>M</given-names>
+								</string-name>
+      							<string-name>
+									<surname>Hood</surname>
+       								<given-names>L</given-names>
+								</string-name>
+      							<string-name>
+									<surname>Cantor</surname>
+       								<given-names>C</given-names>
+								</string-name>
+      							<string-name>
+									<surname>Botstein</surname>
+       								<given-names>D</given-names>
+								</string-name>
+     						</person-group>
+     						<article-title>A common language for physical mapping of the human genome</article-title>
+     						<source>Science</source>
+     						<year iso-8601-date="1989">1989</year>
+     						<volume>245</volume>
+     						<issue>4925</issue>
+     						<fpage>1434</fpage>
+     						<lpage>1435</lpage>
+     						<pub-id pub-id-type="pmid">2781285</pub-id>
+    					</element-citation>
+   					</ref>
+  				</ref-list>
+ 			</back>
+  	</book-part>
+</book-part-wrapper>
+^D
+[ Para
+    [ Str "The"
+    , Space
+    , Emph
+        [ Str "Balisage"
+        , Space
+        , Str "Series"
+        , Space
+        , Str "on"
+        , Space
+        , Str "Markup"
+        , Space
+        , Str "Technologies"
+        ]
+    , SoftBreak
+    , Str "is"
+    , Space
+    , Str "an"
+    , Space
+    , Str "occasional"
+    , Space
+    , Str "series..."
+    ]
+, Header 2 ( "bid.3" , [] , [] ) [ Str "History" ]
+, Para
+    [ Str "Initially,"
+    , Space
+    , Str "GenBank"
+    , Space
+    , Str "was"
+    , Space
+    , Str "built"
+    , Space
+    , Str "and"
+    , Space
+    , Str "maintained"
+    , Space
+    , Str "at"
+    , Space
+    , Str "Los"
+    , Space
+    , Str "Alamos"
+    , SoftBreak
+    , Str "National"
+    , Space
+    , Str "Laboratory."
+    ]
+, Header
+    2
+    ( "" , [] , [] )
+    [ Str "Back"
+    , Space
+    , Str "matter"
+    , Space
+    , Str "of"
+    , Space
+    , Str "book"
+    , Space
+    , Str "part"
+    ]
+, Header 1 ( "" , [] , [] ) [ Str "References" ]
+, Div ( "refs" , [] , [] ) []
+]
+```
\ No newline at end of file
diff --git a/test/command/bits-book.md b/test/command/bits-book.md
new file mode 100644
index 000000000..6515d35ee
--- /dev/null
+++ b/test/command/bits-book.md
@@ -0,0 +1,186 @@
+```
+% pandoc -f jats -t native
+<book dtd-version="2.1" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mml="http://www.w3.org/1998/Math/MathML">
+ 	<front-matter>
+  		<front-matter-part>
+   			<book-part-meta>
+    			<title-group>
+     				<title>About this book</title>
+    			</title-group>
+   			</book-part-meta>
+   			<named-book-part-body>
+    			<sec sec-type="miscinfo">
+     				<title>The NCBI Handbook</title>
+     				<p>Bioinformatics consists of a computational approach
+      				to biomedical information management and analysis.</p>
+    			</sec>
+   			</named-book-part-body>
+  		</front-matter-part>
+ 	</front-matter>
+ 	<book-body>
+  		<book-part id="bid.1" book-part-type="part">
+   			<book-part-meta>
+    			<title-group>
+     				<label>Part 1</label>
+     				<title>The Databases</title>
+    			</title-group>
+   			</book-part-meta>
+   			<body>
+    			<sec id="bid.3">
+     				<title>History</title>
+     				<p>Initially, GenBank was built and maintained at Los Alamos 
+      				National Laboratory.</p>
+    			</sec>
+   			</body>
+   			<back>
+                <title>Back matter of book part</title>
+  				<ref-list>
+   					<title>References</title>
+   					<ref id="bid.41">
+    					<label>1</label>
+    					<element-citation>
+     						<person-group>
+      							<string-name>
+									<surname>Olson</surname>
+       								<given-names>M</given-names>
+								</string-name>
+      							<string-name>
+									<surname>Hood</surname>
+       								<given-names>L</given-names>
+								</string-name>
+      							<string-name>
+									<surname>Cantor</surname>
+       								<given-names>C</given-names>
+								</string-name>
+      							<string-name>
+									<surname>Botstein</surname>
+       								<given-names>D</given-names>
+								</string-name>
+     						</person-group>
+     						<article-title>A common language for physical mapping of the human genome</article-title>
+     						<source>Science</source>
+     						<year iso-8601-date="1989">1989</year>
+     						<volume>245</volume>
+     						<issue>4925</issue>
+     						<fpage>1434</fpage>
+     						<lpage>1435</lpage>
+     						<pub-id pub-id-type="pmid">2781285</pub-id>
+    					</element-citation>
+   					</ref>
+  				</ref-list>
+ 			</back>
+  		</book-part>
+ 	</book-body>
+ 	<book-back>
+  		<ack id="bid.394">
+   		<title>Acknowledgments</title>
+   		<p>We gratefully acknowledge the work of Vladimir Soussov,
+    	as well as the entire NCBI Entrez team...</p>
+  		</ack>
+ 	</book-back>
+</book>
+^D
+[ Header
+    2
+    ( "" , [] , [] )
+    [ Str "The" , Space , Str "NCBI" , Space , Str "Handbook" ]
+, Para
+    [ Str "Bioinformatics"
+    , Space
+    , Str "consists"
+    , Space
+    , Str "of"
+    , Space
+    , Str "a"
+    , Space
+    , Str "computational"
+    , Space
+    , Str "approach"
+    , SoftBreak
+    , Str "to"
+    , Space
+    , Str "biomedical"
+    , Space
+    , Str "information"
+    , Space
+    , Str "management"
+    , Space
+    , Str "and"
+    , Space
+    , Str "analysis."
+    ]
+, Header 2 ( "bid.3" , [] , [] ) [ Str "History" ]
+, Para
+    [ Str "Initially,"
+    , Space
+    , Str "GenBank"
+    , Space
+    , Str "was"
+    , Space
+    , Str "built"
+    , Space
+    , Str "and"
+    , Space
+    , Str "maintained"
+    , Space
+    , Str "at"
+    , Space
+    , Str "Los"
+    , Space
+    , Str "Alamos"
+    , SoftBreak
+    , Str "National"
+    , Space
+    , Str "Laboratory."
+    ]
+, Header
+    2
+    ( "" , [] , [] )
+    [ Str "Back"
+    , Space
+    , Str "matter"
+    , Space
+    , Str "of"
+    , Space
+    , Str "book"
+    , Space
+    , Str "part"
+    ]
+, Header 1 ( "" , [] , [] ) [ Str "References" ]
+, Div ( "refs" , [] , [] ) []
+, Header 2 ( "bid.394" , [] , [] ) [ Str "Acknowledgments" ]
+, Para
+    [ Str "We"
+    , Space
+    , Str "gratefully"
+    , Space
+    , Str "acknowledge"
+    , Space
+    , Str "the"
+    , Space
+    , Str "work"
+    , Space
+    , Str "of"
+    , Space
+    , Str "Vladimir"
+    , Space
+    , Str "Soussov,"
+    , SoftBreak
+    , Str "as"
+    , Space
+    , Str "well"
+    , Space
+    , Str "as"
+    , Space
+    , Str "the"
+    , Space
+    , Str "entire"
+    , Space
+    , Str "NCBI"
+    , Space
+    , Str "Entrez"
+    , Space
+    , Str "team..."
+    ]
+]
+```
\ No newline at end of file
diff --git a/test/command/bits-index-elements.md b/test/command/bits-index-elements.md
new file mode 100644
index 000000000..6ba03cc38
--- /dev/null
+++ b/test/command/bits-index-elements.md
@@ -0,0 +1,83 @@
+```
+% pandoc -f jats -t native
+<index-group>
+	<index-title-group>
+		<title>Index group</title>
+	</index-title-group>
+	<p>Content of index group</p>
+	<index>
+		<index-title-group>
+			<title>Index</title>
+		</index-title-group>
+		<p>Content of index</p>
+  		<index-div>
+   			<index-title-group>
+    			<title>N</title>
+   			</index-title-group>
+   			<p>Content of index div</p>
+   			<index-entry>
+    			<term>Navy</term>
+    			<x>.</x>
+    			<see-entry>Armed forces</see-entry>
+    			<x>.</x>
+   			</index-entry>
+   			<index-entry>
+    			<term>Necessary and proper clause, congressional power</term>
+   			</index-entry>
+   			<index-entry>
+    			<term>Newsgathering as commerce</term>
+   			</index-entry>
+  		</index-div>
+	</index>
+</index-group>
+^D
+[ Header
+    1 ( "" , [] , [] ) [ Str "Index" , Space , Str "group" ]
+, Para
+    [ Str "Content"
+    , Space
+    , Str "of"
+    , Space
+    , Str "index"
+    , Space
+    , Str "group"
+    ]
+, Header 2 ( "" , [] , [] ) [ Str "Index" ]
+, Para
+    [ Str "Content" , Space , Str "of" , Space , Str "index" ]
+, Header 3 ( "" , [] , [] ) [ Str "N" ]
+, Para
+    [ Str "Content"
+    , Space
+    , Str "of"
+    , Space
+    , Str "index"
+    , Space
+    , Str "div"
+    ]
+, Plain [ Str "Navy" ]
+, Plain [ Str "." ]
+, Plain [ Str "Armed" , Space , Str "forces" ]
+, Plain [ Str "." ]
+, Plain
+    [ Str "Necessary"
+    , Space
+    , Str "and"
+    , Space
+    , Str "proper"
+    , Space
+    , Str "clause,"
+    , Space
+    , Str "congressional"
+    , Space
+    , Str "power"
+    ]
+, Plain
+    [ Str "Newsgathering"
+    , Space
+    , Str "as"
+    , Space
+    , Str "commerce"
+    ]
+]
+```
\ No newline at end of file
diff --git a/test/command/bits-legend.md b/test/command/bits-legend.md
new file mode 100644
index 000000000..0217e68fe
--- /dev/null
+++ b/test/command/bits-legend.md
@@ -0,0 +1,45 @@
+```
+% pandoc -f jats -t native
+<fig id="fig_A.1" orientation="portrait">
+ <label>Figure A.1</label>
+ <caption>
+  <title>Field of Application</title>
+ </caption>
+ <legend>
+  <title>Key</title>
+  <def-list>
+   <def-item>
+    <term>I</term>
+    <def><p>input</p></def>
+   </def-item>
+   <def-item>
+    <term>O</term>
+    <def><p>output</p></def>
+   </def-item>
+   ...
+  </def-list>
+ </legend>
+ <graphic xlink:href="1234"/>
+</fig>
+^D
+[ Figure
+    ( "fig_A.1" , [] , [] )
+    (Caption
+       Nothing
+       [ Plain
+           [ Str "Field"
+           , Space
+           , Str "of"
+           , Space
+           , Str "Application"
+           ]
+       ])
+    [ Header 1 ( "" , [] , [] ) [ Str "Key" ]
+    , DefinitionList
+        [ ( [ Str "I" ] , [ [ Para [ Str "input" ] ] ] )
+        , ( [ Str "O" ] , [ [ Para [ Str "output" ] ] ] )
+        ]
+    , Para [ Image ( "" , [] , [] ) [] ( "1234" , "" ) ]
+    ]
+]
+```
\ No newline at end of file
diff --git a/test/command/bits-named-boook-parts.md b/test/command/bits-named-boook-parts.md
new file mode 100644
index 000000000..8a879423e
--- /dev/null
+++ b/test/command/bits-named-boook-parts.md
@@ -0,0 +1,68 @@
+```
+% pandoc -f jats -t native
+<dedication>
+	<named-book-part-body>
+		<p>This is the dedication text.</p>
+	</named-book-part-body>
+</dedication>
+^D
+[ Header 1 ( "" , [] , [] ) [ Str "Dedication" ]
+, Para
+    [ Str "This"
+    , Space
+    , Str "is"
+    , Space
+    , Str "the"
+    , Space
+    , Str "dedication"
+    , Space
+    , Str "text."
+    ]
+]
+```
+
+```
+% pandoc -f jats -t native
+<foreword>
+	<named-book-part-body>
+		<p>This is the foreword text.</p>
+	</named-book-part-body>
+</foreword>
+^D
+[ Header 1 ( "" , [] , [] ) [ Str "Foreword" ]
+, Para
+    [ Str "This"
+    , Space
+    , Str "is"
+    , Space
+    , Str "the"
+    , Space
+    , Str "foreword"
+    , Space
+    , Str "text."
+    ]
+]
+```
+
+```
+% pandoc -f jats -t native
+<preface>
+	<named-book-part-body>
+		<p>This is the preface text.</p>
+	</named-book-part-body>
+</preface>
+^D
+[ Header 1 ( "" , [] , [] ) [ Str "Preface" ]
+, Para
+    [ Str "This"
+    , Space
+    , Str "is"
+    , Space
+    , Str "the"
+    , Space
+    , Str "preface"
+    , Space
+    , Str "text."
+    ]
+]
+```
\ No newline at end of file
diff --git a/test/command/bits-title-display-as.md b/test/command/bits-title-display-as.md
new file mode 100644
index 000000000..88bec9bc0
--- /dev/null
+++ b/test/command/bits-title-display-as.md
@@ -0,0 +1,175 @@
+```
+% pandoc -f jats -t native
+<sec>
+	<title>THE EUROPEAN UNION  EXPLAINED</title>
+</sec>
+^D
+[ Header
+    1
+    ( "" , [] , [] )
+    [ Str "THE"
+    , Space
+    , Str "EUROPEAN"
+    , Space
+    , Str "UNION"
+    , Space
+    , Str "EXPLAINED"
+    ]
+]
+```
+
+```
+% pandoc -f jats -t native
+<sec>
+	<title display-as="3">THE EUROPEAN UNION  EXPLAINED</title>
+</sec>
+^D
+[ Header
+    3
+    ( "" , [] , [] )
+    [ Str "THE"
+    , Space
+    , Str "EUROPEAN"
+    , Space
+    , Str "UNION"
+    , Space
+    , Str "EXPLAINED"
+    ]
+]
+```
+
+```
+% pandoc -f jats -t native
+<body>
+	<sec>
+		<title>The European Parliament</title>
+		<p>Members of the European Parliament (MEPs) are directly elected by EU citizens.</p>
+		<sec>
+		    <title display-as="3">Composition of the European Parliament</title>
+			<p>The seats in the European Parliament are allocated among the Member States.</p>
+		</sec>
+        <sec>
+            <title>Composition of the European Parliament - II </title>
+            <p>Most MEPs are associated with a national political party in their home country.</p>
+		</sec>
+    </sec>
+</body>
+^D
+[ Header
+    1
+    ( "" , [] , [] )
+    [ Str "The"
+    , Space
+    , Str "European"
+    , Space
+    , Str "Parliament"
+    ]
+, Para
+    [ Str "Members"
+    , Space
+    , Str "of"
+    , Space
+    , Str "the"
+    , Space
+    , Str "European"
+    , Space
+    , Str "Parliament"
+    , Space
+    , Str "(MEPs)"
+    , Space
+    , Str "are"
+    , Space
+    , Str "directly"
+    , Space
+    , Str "elected"
+    , Space
+    , Str "by"
+    , Space
+    , Str "EU"
+    , Space
+    , Str "citizens."
+    ]
+, Header
+    3
+    ( "" , [] , [] )
+    [ Str "Composition"
+    , Space
+    , Str "of"
+    , Space
+    , Str "the"
+    , Space
+    , Str "European"
+    , Space
+    , Str "Parliament"
+    ]
+, Para
+    [ Str "The"
+    , Space
+    , Str "seats"
+    , Space
+    , Str "in"
+    , Space
+    , Str "the"
+    , Space
+    , Str "European"
+    , Space
+    , Str "Parliament"
+    , Space
+    , Str "are"
+    , Space
+    , Str "allocated"
+    , Space
+    , Str "among"
+    , Space
+    , Str "the"
+    , Space
+    , Str "Member"
+    , Space
+    , Str "States."
+    ]
+, Header
+    2
+    ( "" , [] , [] )
+    [ Str "Composition"
+    , Space
+    , Str "of"
+    , Space
+    , Str "the"
+    , Space
+    , Str "European"
+    , Space
+    , Str "Parliament"
+    , Space
+    , Str "-"
+    , Space
+    , Str "II"
+    ]
+, Para
+    [ Str "Most"
+    , Space
+    , Str "MEPs"
+    , Space
+    , Str "are"
+    , Space
+    , Str "associated"
+    , Space
+    , Str "with"
+    , Space
+    , Str "a"
+    , Space
+    , Str "national"
+    , Space
+    , Str "political"
+    , Space
+    , Str "party"
+    , Space
+    , Str "in"
+    , Space
+    , Str "their"
+    , Space
+    , Str "home"
+    , Space
+    , Str "country."
+    ]
+]
+```
\ No newline at end of file
diff --git a/test/command/bits-title-supress.md b/test/command/bits-title-supress.md
new file mode 100644
index 000000000..e30841e10
--- /dev/null
+++ b/test/command/bits-title-supress.md
@@ -0,0 +1,122 @@
+```
+% pandoc -f jats -t native
+<sec>
+	<title>The European Parliament</title>
+	<p>Members of the European Parliament (MEPs) are directly elected by EU citizens.</p>
+</sec>
+^D
+[ Header
+    1
+    ( "" , [] , [] )
+    [ Str "The"
+    , Space
+    , Str "European"
+    , Space
+    , Str "Parliament"
+    ]
+, Para
+    [ Str "Members"
+    , Space
+    , Str "of"
+    , Space
+    , Str "the"
+    , Space
+    , Str "European"
+    , Space
+    , Str "Parliament"
+    , Space
+    , Str "(MEPs)"
+    , Space
+    , Str "are"
+    , Space
+    , Str "directly"
+    , Space
+    , Str "elected"
+    , Space
+    , Str "by"
+    , Space
+    , Str "EU"
+    , Space
+    , Str "citizens."
+    ]
+]
+```
+
+```
+% pandoc -f jats -t native
+<sec>
+	<title supress="no">The European Parliament</title>
+	<p>Members of the European Parliament (MEPs) are directly elected by EU citizens.</p>
+</sec>
+^D
+[ Header
+    1
+    ( "" , [] , [] )
+    [ Str "The"
+    , Space
+    , Str "European"
+    , Space
+    , Str "Parliament"
+    ]
+, Para
+    [ Str "Members"
+    , Space
+    , Str "of"
+    , Space
+    , Str "the"
+    , Space
+    , Str "European"
+    , Space
+    , Str "Parliament"
+    , Space
+    , Str "(MEPs)"
+    , Space
+    , Str "are"
+    , Space
+    , Str "directly"
+    , Space
+    , Str "elected"
+    , Space
+    , Str "by"
+    , Space
+    , Str "EU"
+    , Space
+    , Str "citizens."
+    ]
+]
+```
+
+```
+% pandoc -f jats -t native
+<sec>
+	<title supress="yes">The European Parliament</title>
+	<p>Members of the European Parliament (MEPs) are directly elected by EU citizens.</p>
+</sec>
+^D
+[ Para
+    [ Str "Members"
+    , Space
+    , Str "of"
+    , Space
+    , Str "the"
+    , Space
+    , Str "European"
+    , Space
+    , Str "Parliament"
+    , Space
+    , Str "(MEPs)"
+    , Space
+    , Str "are"
+    , Space
+    , Str "directly"
+    , Space
+    , Str "elected"
+    , Space
+    , Str "by"
+    , Space
+    , Str "EU"
+    , Space
+    , Str "citizens."
+    ]
+]
+```
\ No newline at end of file
diff --git a/test/command/bits-toc-elements.md b/test/command/bits-toc-elements.md
new file mode 100644
index 000000000..415a255e1
--- /dev/null
+++ b/test/command/bits-toc-elements.md
@@ -0,0 +1,69 @@
+```
+% pandoc -f jats -t native
+<toc-group>
+	<toc-title-group>
+		<title>TOC group</title>
+	</toc-title-group>
+	<p>Content of toc group</p>
+	<toc>
+		<toc-title-group>
+			<title>TOC</title>
+		</toc-title-group>
+		<p>Content of TOC</p>
+  		<toc-div content-type="sections">
+   			<toc-title-group>
+                <title>Mental Health Services</title>
+            </toc-title-group>
+            <toc-entry>
+                <label>Section 1</label>
+                <title>Introduction</title>
+                <nav-pointer rid="tc3"/>
+            </toc-entry>
+            <toc-entry>
+                <label>Section 2</label>
+                <title>Mental Health of the Population</title>
+                <nav-pointer rid="tc4"/>
+            </toc-entry>
+  		</toc-div>
+	</toc>
+</toc-group>
+^D
+[ Header
+    1 ( "" , [] , [] ) [ Str "TOC" , Space , Str "group" ]
+, Para
+    [ Str "Content"
+    , Space
+    , Str "of"
+    , Space
+    , Str "toc"
+    , Space
+    , Str "group"
+    ]
+, Header 2 ( "" , [] , [] ) [ Str "TOC" ]
+, Para
+    [ Str "Content" , Space , Str "of" , Space , Str "TOC" ]
+, Header
+    3
+    ( "" , [] , [] )
+    [ Str "Mental"
+    , Space
+    , Str "Health"
+    , Space
+    , Str "Services"
+    ]
+, Header 4 ( "" , [] , [] ) [ Str "Introduction" ]
+, Header
+    4
+    ( "" , [] , [] )
+    [ Str "Mental"
+    , Space
+    , Str "Health"
+    , Space
+    , Str "of"
+    , Space
+    , Str "the"
+    , Space
+    , Str "Population"
+    ]
+]
+```
\ No newline at end of file