mirror of
https://github.com/jgm/pandoc.git
synced 2026-08-24 17:26:32 +00:00
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
This commit is contained in:
@@ -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
|
||||
|
||||
@@ -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" )
|
||||
])
|
||||
)
|
||||
]
|
||||
}
|
||||
[]
|
||||
```
|
||||
@@ -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"
|
||||
]
|
||||
)
|
||||
]
|
||||
}
|
||||
[]
|
||||
```
|
||||
@@ -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..."
|
||||
]
|
||||
]
|
||||
```
|
||||
@@ -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" , [] , [] ) []
|
||||
]
|
||||
```
|
||||
@@ -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..."
|
||||
]
|
||||
]
|
||||
```
|
||||
@@ -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"
|
||||
]
|
||||
]
|
||||
```
|
||||
@@ -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" , "" ) ]
|
||||
]
|
||||
]
|
||||
```
|
||||
@@ -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."
|
||||
]
|
||||
]
|
||||
```
|
||||
@@ -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."
|
||||
]
|
||||
]
|
||||
```
|
||||
@@ -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."
|
||||
]
|
||||
]
|
||||
```
|
||||
@@ -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"
|
||||
]
|
||||
]
|
||||
```
|
||||
Reference in New Issue
Block a user