Headers

+$else$ +

+$endif$ + + +$if(journal.publisher-id)$ +$journal.publisher-id$ +$endif$ +$if(journal.nlm-ta)$ +$journal.nlm-ta$ +$endif$ +$if(journal.pmc)$ +$journal.pmc$ +$endif$ + +$if(journal.title)$ +$journal.title$ +$endif$ +$if(journal.abbrev-title)$ +$journal.abbrev-title$ +$endif$ + +$if(journal.pissn)$ +$journal.pissn$ +$endif$ +$if(journal.eissn)$ +$journal.eissn$ +$endif$ + +$journal.publisher-name$ +$if(journal.publisher-loc)$ +$journal.publisher-loc$ +$endif$ + + + +$if(article.publisher-id)$ +$article.publisher-id$ +$endif$ +$if(article.doi)$ +$article.doi$ +$endif$ +$if(article.pmid)$ +$article.pmid$ +$endif$ +$if(article.pmcid)$ +$article.pmcid$ +$endif$ +$if(article.art-access-id)$ +$article.art-access-id$ +$endif$ +$if(article.heading)$ + + +$article.heading$ + +$if(article.categories)$ + +$for(article.categories)$ +$article.categories$ +$endfor$ + +$endif$ + +$endif$ +$if(title)$ + +$title$ + +$endif$ +$if(author)$ + +$for(author)$ + +$if(author.orcid)$ +$author.orcid$ +$endif$ + +$if(author.surname)$ +$author.surname$ +$author.given-names$ +$else$ +$author$ +$endif$ + +$if(author.email)$ +$author.email$ +$endif$ +$if(author.aff-id)$ + +$endif$ +$if(author.cor-id)$ +^* +$endif$ + +$endfor$ + +$endif$ +$if(article.author-notes)$ + +$if(article.author-notes.corresp)$ +$for(article.author-notes.corresp)$ +* E-mail: $article.author-notes.corresp.email$ +$endfor$ +$endif$ +$if(article.author-notes.conflict)$ +

$article.author-notes.conflict$

+$endif$ +$if(article.author-notes.con)$ +

$article.author-notes.con$

+$endif$ + +$endif$ +$if(date)$ +$if(date.iso-8601)$ + +$else$ + +$endif$ +$if(date.day)$ +$pub-date.day$ +$endif$ +$if(date.month)$ +$pub-date.month$ +$endif$ +$if(date.year)$ +$pub-date.year$ +$else$ +$date$ +$endif$ + +$endif$ +$if(article.volume)$ +$article.volume$ +$endif$ +$if(article.issue)$ +$article.issue$ +$endif$ +$if(article.fpage)$ +$article.fpage$ +$endif$ +$if(article.lpage)$ +$article.lpage$ +$endif$ +$if(article.elocation-id)$ +$article.elocation-id$ +$endif$ +$if(history)$ + + +$endif$ +$if(copyright)$ + +$if(copyright.statement)$ +$copyright.statement$ +$endif$ +$if(copyright.year)$ +$copyright.year$ +$endif$ +$if(copyright.holder)$ +$copyright.holder$ +$endif$ +$if(copyright.text)$ + +$copyright.text$ + + +$endif$ +$endif$ +$if(tags)$ + +$for(tags)$ +$tags$ +$endfor$ + +$endif$ +$if(article.funding-statement)$ + +$article.funding-statement$ + +$endif$ + +$if(notes)$ +$notes$ +$endif$ + +$body$ +

diff --git a/pandoc.cabal b/pandoc.cabal index 592c308e3..596b52c44 100644 --- a/pandoc.cabal +++ b/pandoc.cabal @@ -41,6 +41,7 @@ Data-Files: data/templates/default.html5 data/templates/default.docbook4 data/templates/default.docbook5 + data/templates/default.jats data/templates/default.tei data/templates/default.beamer data/templates/default.opendocument -- cgit v1.2.3 From 831e1c5edd4703b6ab0953a79980e37ea1bee5dc Mon Sep 17 00:00:00 2001 From: John MacFarlane Date: Tue, 28 Mar 2017 09:51:30 +0200 Subject: Added JATS writer. * New module Text.Pandoc.Writer.JATS exporting writeJATS. * New output format `jats`. * Added tests. * Revised manual. --- MANUAL.txt | 12 +- pandoc.cabal | 3 + src/Text/Pandoc.hs | 3 + src/Text/Pandoc/Writers/JATS.hs | 429 ++++++++++++ test/Tests/Old.hs | 3 + test/tables.jats | 616 +++++++++++++++++ test/writer.jats | 1425 +++++++++++++++++++++++++++++++++++++++ 7 files changed, 2485 insertions(+), 6 deletions(-) create mode 100644 src/Text/Pandoc/Writers/JATS.hs create mode 100644 test/tables.jats create mode 100644 test/writer.jats diff --git a/MANUAL.txt b/MANUAL.txt index e11e57459..f0e951f75 100644 --- a/MANUAL.txt +++ b/MANUAL.txt @@ -291,9 +291,9 @@ General options (LaTeX), `beamer` (LaTeX beamer slide show), `context` (ConTeXt), `man` (groff man), `mediawiki` (MediaWiki markup), `dokuwiki` (DokuWiki markup), `zimwiki` (ZimWiki markup), - `textile` (Textile), `org` (Emacs Org mode), - `texinfo` (GNU Texinfo), `opml` (OPML), `docbook` or `docbook4` - (DocBook 4), `docbook5` (DocBook 5), `opendocument` (OpenDocument), + `textile` (Textile), `org` (Emacs Org mode), `texinfo` (GNU Texinfo), + `opml` (OPML), `docbook` or `docbook4` (DocBook 4), `docbook5` + (DocBook 5), `jats` (JATS XML), `opendocument` (OpenDocument), `odt` (OpenOffice text document), `docx` (Word docx), `haddock` (Haddock markup), `rtf` (rich text format), `epub2` (EPUB v2 book), `epub` or `epub3` (EPUB v3), `fb2` (FictionBook2 e-book), @@ -616,8 +616,8 @@ General writer options : Include an automatically generated table of contents (or, in the case of `latex`, `context`, `docx`, `rst`, or `ms`, an instruction to create one) in the output document. This - option has no effect on `man`, `docbook4`, `docbook5`, `slidy`, - `slideous`, `s5`, or `odt` output. + option has no effect on `man`, `docbook4`, `docbook5`, `jats`, + `slidy`, `slideous`, `s5`, or `odt` output. `--toc-depth=`*NUMBER* @@ -1000,7 +1000,7 @@ Math rendering in HTML `--mathml` -: Convert TeX math to [MathML] (in `docbook4`, `docbook5`, +: Convert TeX math to [MathML] (in `docbook4`, `docbook5`, `jats`, `html4` and `html5`). `--jsmath`[`=`*URL*] diff --git a/pandoc.cabal b/pandoc.cabal index 596b52c44..33694dec0 100644 --- a/pandoc.cabal +++ b/pandoc.cabal @@ -159,6 +159,7 @@ Extra-Source-Files: test/tables.context test/tables.docbook4 test/tables.docbook5 + test/tables.jats test/tables.dokuwiki test/tables.zimwiki test/tables.icml @@ -187,6 +188,7 @@ Extra-Source-Files: test/writer.context test/writer.docbook4 test/writer.docbook5 + test/writer.jats test/writer.html4 test/writer.html5 test/writer.man @@ -381,6 +383,7 @@ Library Text.Pandoc.Readers.EPUB, Text.Pandoc.Writers.Native, Text.Pandoc.Writers.Docbook, + Text.Pandoc.Writers.JATS, Text.Pandoc.Writers.OPML, Text.Pandoc.Writers.HTML, Text.Pandoc.Writers.ICML, diff --git a/src/Text/Pandoc.hs b/src/Text/Pandoc.hs index e77bc6d45..977ad1ab4 100644 --- a/src/Text/Pandoc.hs +++ b/src/Text/Pandoc.hs @@ -117,6 +117,7 @@ module Text.Pandoc , writeICML , writeDocbook4 , writeDocbook5 + , writeJATS , writeOPML , writeOpenDocument , writeMan @@ -182,6 +183,7 @@ import Text.Pandoc.Writers.CommonMark import Text.Pandoc.Writers.ConTeXt import Text.Pandoc.Writers.Custom import Text.Pandoc.Writers.Docbook +import Text.Pandoc.Writers.JATS import Text.Pandoc.Writers.Docx import Text.Pandoc.Writers.DokuWiki import Text.Pandoc.Writers.EPUB @@ -287,6 +289,7 @@ writers = [ ,("docbook" , StringWriter writeDocbook5) ,("docbook4" , StringWriter writeDocbook4) ,("docbook5" , StringWriter writeDocbook5) + ,("jats" , StringWriter writeJATS) ,("opml" , StringWriter writeOPML) ,("opendocument" , StringWriter writeOpenDocument) ,("latex" , StringWriter writeLaTeX) diff --git a/src/Text/Pandoc/Writers/JATS.hs b/src/Text/Pandoc/Writers/JATS.hs new file mode 100644 index 000000000..9aaba78e0 --- /dev/null +++ b/src/Text/Pandoc/Writers/JATS.hs @@ -0,0 +1,429 @@ +{-# LANGUAGE OverloadedStrings #-} +{-# LANGUAGE PatternGuards #-} +{- +Copyright (C) 2006-2015 John MacFarlane + +This program is free software; you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation; either version 2 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program; if not, write to the Free Software +Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +-} +{- | + Module : Text.Pandoc.Writers.JATS + Copyright : Copyright (C) 2017 John MacFarlane + License : GNU GPL, version 2 or above + + Maintainer : John MacFarlane + Stability : alpha + Portability : portable + +Conversion of 'Pandoc' documents to JATS XML. +Reference: +https://jats.nlm.nih.gov/publishing/tag-library/1.1d3/element/mml-math.html +-} +module Text.Pandoc.Writers.JATS ( writeJATS ) where +import Control.Monad.Reader +import Data.Char (toLower) +import Data.Generics (everywhere, mkT) +import Data.List (intercalate, isSuffixOf) +import Data.Maybe (fromMaybe) +import qualified Text.Pandoc.Builder as B +import Text.Pandoc.Class (PandocMonad, report) +import Text.Pandoc.Definition +import Text.Pandoc.Highlighting (languages, languagesByExtension) +import Text.Pandoc.Logging +import Text.Pandoc.Options +import Text.Pandoc.Pretty +import Text.Pandoc.Shared +import Text.Pandoc.Templates (renderTemplate') +import Text.Pandoc.Writers.Math +import Text.Pandoc.Writers.Shared +import Text.Pandoc.XML +import Text.Pandoc.MIME (getMimeType) +import Text.TeXMath +import qualified Text.XML.Light as Xml + +data JATSVersion = JATS1_1 + deriving (Eq, Show) + +type DB = ReaderT JATSVersion + +-- | Convert list of authors to a docbook section +authorToJATS :: PandocMonad m => WriterOptions -> [Inline] -> DB m B.Inlines +authorToJATS opts name' = do + name <- render Nothing <$> inlinesToJATS opts name' + let colwidth = if writerWrapText opts == WrapAuto + then Just $ writerColumns opts + else Nothing + return $ B.rawInline "docbook" $ render colwidth $ + if ',' `elem` name + then -- last name first + let (lastname, rest) = break (==',') name + firstname = triml rest in + inTagsSimple "firstname" (text $ escapeStringForXML firstname) <> + inTagsSimple "surname" (text $ escapeStringForXML lastname) + else -- last name last + let namewords = words name + lengthname = length namewords + (firstname, lastname) = case lengthname of + 0 -> ("","") + 1 -> ("", name) + n -> (intercalate " " (take (n-1) namewords), last namewords) + in inTagsSimple "firstname" (text $ escapeStringForXML firstname) $$ + inTagsSimple "surname" (text $ escapeStringForXML lastname) + +writeJATS :: PandocMonad m => WriterOptions -> Pandoc -> m String +writeJATS opts d = + runReaderT (docToJATS opts d) JATS1_1 + +-- | Convert Pandoc document to string in JATS format. +docToJATS :: PandocMonad m => WriterOptions -> Pandoc -> DB m String +docToJATS opts (Pandoc meta blocks) = do + let elements = hierarchicalize blocks + let colwidth = if writerWrapText opts == WrapAuto + then Just $ writerColumns opts + else Nothing + let render' = render colwidth + let opts' = if (maybe False (("/book>" `isSuffixOf`) . trimr) + (writerTemplate opts) && + TopLevelDefault == writerTopLevelDivision opts) + then opts{ writerTopLevelDivision = TopLevelChapter } + else opts + -- The numbering here follows LaTeX's internal numbering + let startLvl = case writerTopLevelDivision opts' of + TopLevelPart -> -1 + TopLevelChapter -> 0 + TopLevelSection -> 1 + TopLevelDefault -> 1 + auths' <- mapM (authorToJATS opts) $ docAuthors meta + let meta' = B.setMeta "author" auths' meta + metadata <- metaToJSON opts + (fmap (render colwidth . vcat) . + (mapM (elementToJATS opts' startLvl) . + hierarchicalize)) + (fmap (render colwidth) . inlinesToJATS opts') + meta' + main <- (render' . inTagsIndented "body" . vcat) <$> + (mapM (elementToJATS opts' startLvl) elements) + let context = defField "body" main + $ defField "mathml" (case writerHTMLMathMethod opts of + MathML -> True + _ -> False) + $ metadata + return $ case writerTemplate opts of + Nothing -> main + Just tpl -> renderTemplate' tpl context + +-- | Convert an Element to JATS. +elementToJATS :: PandocMonad m => WriterOptions -> Int -> Element -> DB m Doc +elementToJATS opts _ (Blk block) = blockToJATS opts block +elementToJATS opts lvl (Sec _ _num (id',_,kvs) title elements) = do + let idAttr = [("id", writerIdentifierPrefix opts ++ id') | not (null id')] + let otherAttrs = ["sec-type", "specific-use"] + let attribs = idAttr ++ [(k,v) | (k,v) <- kvs, k `elem` otherAttrs] + contents <- mapM (elementToJATS opts (lvl + 1)) elements + title' <- inlinesToJATS opts title + return $ inTags True "sec" attribs $ + inTagsSimple "title" title' $$ vcat contents + +-- | Convert a list of Pandoc blocks to JATS. +blocksToJATS :: PandocMonad m => WriterOptions -> [Block] -> DB m Doc +blocksToJATS opts = fmap vcat . mapM (blockToJATS opts) + +-- | Auxiliary function to convert Plain block to Para. +plainToPara :: Block -> Block +plainToPara (Plain x) = Para x +plainToPara x = x + +-- | Convert a list of pairs of terms and definitions into a list of +-- JATS varlistentrys. +deflistItemsToJATS :: PandocMonad m + => WriterOptions -> [([Inline],[[Block]])] -> DB m Doc +deflistItemsToJATS opts items = + vcat <$> mapM (\(term, defs) -> deflistItemToJATS opts term defs) items + +-- | Convert a term and a list of blocks into a JATS varlistentry. +deflistItemToJATS :: PandocMonad m + => WriterOptions -> [Inline] -> [[Block]] -> DB m Doc +deflistItemToJATS opts term defs = do + term' <- inlinesToJATS opts term + def' <- blocksToJATS opts $ concatMap (map plainToPara) defs + return $ inTagsIndented "def-item" $ + inTagsIndented "term" term' $$ + inTagsIndented "def" def' + +-- | Convert a list of lists of blocks to a list of JATS list items. +listItemsToJATS :: PandocMonad m + => WriterOptions -> (Maybe [String]) -> [[Block]] -> DB m Doc +listItemsToJATS opts markers items = + case markers of + Nothing -> vcat <$> mapM (listItemToJATS opts Nothing) items + Just ms -> vcat <$> zipWithM (listItemToJATS opts) (map Just ms) items + +-- | Convert a list of blocks into a JATS list item. +listItemToJATS :: PandocMonad m + => WriterOptions -> (Maybe String) -> [Block] -> DB m Doc +listItemToJATS opts mbmarker item = do + contents <- blocksToJATS opts item + return $ inTagsIndented "list-item" $ + maybe empty (\lbl -> inTagsIndented "label" (text lbl)) mbmarker + $$ contents + +-- | Convert a Pandoc block element to JATS. +blockToJATS :: PandocMonad m => WriterOptions -> Block -> DB m Doc +blockToJATS _ Null = return empty +-- Add ids to paragraphs in divs with ids - this is needed for +-- pandoc-citeproc to get link anchors in bibliographies: +blockToJATS opts (Div (ident,_,_) [Para lst]) = + let attribs = [("id", ident) | not (null ident)] in + inTags True "p" attribs <$> inlinesToJATS opts lst +blockToJATS opts (Div (ident,_,kvs) bs) = 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 "boxed-text" attr contents +blockToJATS _ (Header _ _ _) = + return empty -- should not occur after hierarchicalize +-- 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 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), + ("xlink:href",src), -- do we need to URL escape this? + ("xlink:title",tit)] + return $ inTags True "fig" attr $ + capt $$ selfClosingTag "graphic" graphicattr +blockToJATS opts (Para lst) = + inTagsIndented "p" <$> inlinesToJATS opts lst +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 $ + 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 +blockToJATS _ (BulletList []) = return empty +blockToJATS opts (BulletList lst) = do + inTags True "list" [("list-type", "bullet")] <$> + listItemsToJATS opts Nothing lst +blockToJATS _ (OrderedList _ []) = return empty +blockToJATS opts (OrderedList (start, numstyle, delimstyle) items) = do + let listType = case numstyle of + DefaultStyle -> "order" + Decimal -> "order" + Example -> "order" + UpperAlpha -> "alpha-upper" + LowerAlpha -> "alpha-lower" + UpperRoman -> "roman-upper" + LowerRoman -> "roman-lower" + let simpleList = start == 1 && (delimstyle == DefaultDelim || + delimstyle == Period) + let markers = if simpleList + then Nothing + else Just $ + orderedListMarkers (start, numstyle, delimstyle) + inTags True "list" [("list-type", listType)] <$> + listItemsToJATS opts markers items +blockToJATS opts (DefinitionList lst) = do + inTags True "def-list" [] <$> deflistItemsToJATS opts lst +blockToJATS _ b@(RawBlock f str) + | f == "jats" = return $ text str -- raw XML block + | otherwise = do + report $ BlockNotRendered b + return empty +blockToJATS _ HorizontalRule = return empty -- not semantic +blockToJATS opts (Table [] aligns widths headers rows) = do + let percent w = show (truncate (100*w) :: Integer) ++ "*" + let coltags = vcat $ zipWith (\w al -> selfClosingTag "col" + ([("width", percent w) | w > 0] ++ + [("align", alignmentToString al)])) widths aligns + thead <- if all null headers + then return empty + else inTagsIndented "thead" <$> tableRowToJATS opts True headers + tbody <- (inTagsIndented "tbody" . vcat) <$> + mapM (tableRowToJATS opts False) rows + return $ inTags True "table" [] $ coltags $$ thead $$ tbody +blockToJATS opts (Table caption aligns widths headers rows) = do + captionDoc <- inTagsIndented "caption" <$> blockToJATS opts (Para caption) + tbl <- blockToJATS opts (Table [] aligns widths headers rows) + return $ inTags True "table-wrap" [] $ captionDoc $$ tbl + +alignmentToString :: Alignment -> [Char] +alignmentToString alignment = case alignment of + AlignLeft -> "left" + AlignRight -> "right" + AlignCenter -> "center" + AlignDefault -> "left" + +tableRowToJATS :: PandocMonad m + => WriterOptions + -> Bool + -> [[Block]] + -> DB m Doc +tableRowToJATS opts isHeader cols = + (inTagsIndented "tr" . vcat) <$> mapM (tableItemToJATS opts isHeader) cols + +tableItemToJATS :: PandocMonad m + => WriterOptions + -> Bool + -> [Block] + -> DB m Doc +tableItemToJATS opts isHeader item = + (inTags True (if isHeader then "th" else "td") [] . vcat) <$> + mapM (blockToJATS opts) item + +-- | Convert a list of inline elements to JATS. +inlinesToJATS :: PandocMonad m => WriterOptions -> [Inline] -> DB m Doc +inlinesToJATS opts lst = hcat <$> mapM (inlineToJATS opts) lst + +-- | Convert an inline element to JATS. +inlineToJATS :: PandocMonad m => WriterOptions -> Inline -> DB m Doc +inlineToJATS _ (Str str) = return $ text $ escapeStringForXML str +inlineToJATS opts (Emph lst) = + inTagsSimple "italic" <$> inlinesToJATS opts lst +inlineToJATS opts (Strong lst) = + inTags False "bold" [("role", "strong")] <$> inlinesToJATS opts lst +inlineToJATS opts (Strikeout lst) = + inTagsSimple "strike" <$> inlinesToJATS opts lst +inlineToJATS opts (Superscript lst) = + inTagsSimple "sup" <$> inlinesToJATS opts lst +inlineToJATS opts (Subscript lst) = + inTagsSimple "sub" <$> inlinesToJATS opts lst +inlineToJATS opts (SmallCaps lst) = + inTags False "sc" [("role", "smallcaps")] <$> + inlinesToJATS opts lst +inlineToJATS opts (Quoted SingleQuote lst) = do + contents <- inlinesToJATS opts lst + return $ char '‘' <> contents <> char '’' +inlineToJATS opts (Quoted DoubleQuote lst) = do + contents <- inlinesToJATS opts lst + return $ char '“' <> contents <> char '”' +inlineToJATS _ (Code _ str) = + return $ inTagsSimple "monospace" $ text (escapeStringForXML str) +inlineToJATS _ il@(RawInline f x) + | f == "jats" = return $ text x + | otherwise = do + report $ InlineNotRendered il + return empty +inlineToJATS _ LineBreak = return $ selfClosingTag "break" [] +inlineToJATS _ Space = return space +inlineToJATS opts SoftBreak + | writerWrapText opts == WrapPreserve = return cr + | otherwise = return space +inlineToJATS opts (Note contents) = + -- TODO technically only

tags are allowed inside + inTagsIndented "fn" <$> blocksToJATS opts contents +inlineToJATS opts (Cite _ lst) = + -- TODO revisit this after examining the jats.csl pipeline + inlinesToJATS opts lst +inlineToJATS opts (Span ("",_,[]) ils) = inlinesToJATS opts ils +inlineToJATS opts (Span (ident,_,kvs) ils) = do + contents <- inlinesToJATS opts ils + let attr = [("id",ident) | not (null ident)] ++ + [("xml:lang",l) | ("lang",l) <- kvs] ++ + [(k,v) | (k,v) <- kvs + , k `elem` ["content-type", "rationale", + "rid", "specific-use"]] + return $ selfClosingTag "milestone-start" attr <> contents <> + selfClosingTag "milestone-end" [] +inlineToJATS _ (Math t str) = do + let addPref (Xml.Attr q v) + | Xml.qName q == "xmlns" = Xml.Attr q{ Xml.qName = "xmlns:mml" } v + | otherwise = Xml.Attr q v + let fixNS' e = e{ Xml.elName = + (Xml.elName e){ Xml.qPrefix = Just "mml" } } + let fixNS = everywhere (mkT fixNS') . + (\e -> e{ Xml.elAttribs = map addPref (Xml.elAttribs e) }) + let conf = Xml.useShortEmptyTags (const False) Xml.defaultConfigPP + res <- convertMath writeMathML t str + let tagtype = case t of + DisplayMath -> "disp-formula" + InlineMath -> "inline-formula" + return $ inTagsSimple tagtype $ + case res of + Right r -> text $ Xml.ppcElement conf + $ fixNS r + Left _ -> inTagsSimple "tex-math" + $ text " + text str <> + text "]]>" +inlineToJATS _ (Link _attr [Str t] ('m':'a':'i':'l':'t':'o':':':email, _)) + | escapeURI t == 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)] ++ + [(k,v) | (k,v) <- kvs, k `elem` ["ref-type", "specific-use"]] + contents <- inlinesToJATS opts txt + return $ inTags False "xref" attr contents +inlineToJATS opts (Link (ident,_,kvs) txt (src, tit)) = do + let attr = [("id", ident) | not (null ident)] ++ + [("ext-link-type", "uri"), + ("xlink:href", src)] ++ + [("xlink:title", tit) | not (null tit)] ++ + [(k,v) | (k,v) <- kvs, k `elem` ["assigning-authority", + "specific-use", "xlink:actuate", + "xlink:role", "xlink:show", + "xlink:type"]] + contents <- inlinesToJATS opts txt + return $ inTags False "ext-link" attr contents +inlineToJATS _ (Image (ident,_,kvs) _ (src, tit)) = do + 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 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 "inline-graphic" attr diff --git a/test/Tests/Old.hs b/test/Tests/Old.hs index 3c473792f..fceb776f7 100644 --- a/test/Tests/Old.hs +++ b/test/Tests/Old.hs @@ -77,6 +77,9 @@ tests = [ testGroup "markdown" , testGroup "docbook5" [ testGroup "writer" $ writerTests "docbook5" ] + , testGroup "jats" + [ testGroup "writer" $ writerTests "jats" + ] , testGroup "native" [ testGroup "writer" $ writerTests "native" , test "reader" ["-r", "native", "-w", "native", "-s"] diff --git a/test/tables.jats b/test/tables.jats new file mode 100644 index 000000000..11f543f17 --- /dev/null +++ b/test/tables.jats @@ -0,0 +1,616 @@ + +

+ Simple table with caption: +

+ + +

+ Demonstration of simple table syntax. +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + Right + +	+ + Left + +	+ + Center + +	+ + Default + +
+ + 12 + +	+ + 12 + +	+ + 12 + +	+ + 12 + +
+ + 123 + +	+ + 123 + +	+ + 123 + +	+ + 123 + +
+ + 1 + +	+ + 1 + +	+ + 1 + +	+ + 1 + +

+ +

+ Simple table without caption: +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + Right + +	+ + Left + +	+ + Center + +	+ + Default + +
+ + 12 + +	+ + 12 + +	+ + 12 + +	+ + 12 + +
+ + 123 + +	+ + 123 + +	+ + 123 + +	+ + 123 + +
+ + 1 + +	+ + 1 + +	+ + 1 + +	+ + 1 + +

+ Simple table indented two spaces: +

+ + +

+ Demonstration of simple table syntax. +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + Right + +	+ + Left + +	+ + Center + +	+ + Default + +
+ + 12 + +	+ + 12 + +	+ + 12 + +	+ + 12 + +
+ + 123 + +	+ + 123 + +	+ + 123 + +	+ + 123 + +
+ + 1 + +	+ + 1 + +	+ + 1 + +	+ + 1 + +

+ +

+ Multiline table with caption: +

+ + +

+ Here’s the caption. It may span multiple lines. +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + Centered Header + +	+ + Left Aligned + +	+ + Right Aligned + +	+ + Default aligned + +
+ + First + +	+ + row + +	+ + 12.0 + +	+ + Example of a row that spans multiple lines. + +
+ + Second + +	+ + row + +	+ + 5.0 + +	+ + Here’s another one. Note the blank line between rows. + +

+ +

+ Multiline table without caption: +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + Centered Header + +	+ + Left Aligned + +	+ + Right Aligned + +	+ + Default aligned + +
+ + First + +	+ + row + +	+ + 12.0 + +	+ + Example of a row that spans multiple lines. + +
+ + Second + +	+ + row + +	+ + 5.0 + +	+ + Here’s another one. Note the blank line between rows. + +

+ Table without column headers: +

+ + + + + + + + + + + + + + + + + + + + + + + + + +

+ + 12 + +	+ + 12 + +	+ + 12 + +	+ + 12 + +
+ + 123 + +	+ + 123 + +	+ + 123 + +	+ + 123 + +
+ + 1 + +	+ + 1 + +	+ + 1 + +	+ + 1 + +

+ Multiline table without column headers: +

+ + + + + + + + + + + + + + + + + + + +

+ + First + +	+ + row + +	+ + 12.0 + +	+ + Example of a row that spans multiple lines. + +
+ + Second + +	+ + row + +	+ + 5.0 + +	+ + Here’s another one. Note the blank line between rows. + +

+ diff --git a/test/writer.jats b/test/writer.jats new file mode 100644 index 000000000..1703de4aa --- /dev/null +++ b/test/writer.jats @@ -0,0 +1,1425 @@ + + +

+ + + + + + + + + + +Pandoc Test Suite + + +July 17, 2006 + + + + +

+ This is a set of tests for pandoc. Most of them are adapted from John + Gruber’s markdown test suite. +

+ + Headers + + Level 2 with an + <ext-link ext-link-type="uri" xlink:href="/url">embedded + link</ext-link> + + Level 3 with <italic>emphasis</italic> + + Level 4 + + Level 5 + + + + + + + Level 1 + + Level 2 with <italic>emphasis</italic> + + Level 3 +

+ with no blank line +

+ + + + Level 2 +

+ with no blank line +

+ + + + Paragraphs +

+ Here’s a regular paragraph. +

+ In Markdown 1.0.0 and earlier. Version 8. This line turns into a list + item. Because a hard-wrapped line in the middle of a paragraph looked + like a list item. +

+ Here’s one with a bullet. * criminey. +

+ There should be a hard line breakhere. +

+ + + Block Quotes +

+ E-mail style: +

+ +

+ This is a block quote. It is pretty short. +

+ + +

+ Code in a block quote: +

+ sub status { + print "working"; +} +

+ A list: +

+ + +

+ item one +

+ + +

+ item two +

+ + +

+ Nested block quotes: +

+ +

+ nested +

+ + +

+ nested +

+ + +

+ This should not be a block quote: 2 > 1. +

+ And a following paragraph. +

+ + + Code Blocks +

+ Code: +

+ ---- (should be four hyphens) + +sub status { + print "working"; +} + +this code block is indented by one tab +

+ And: +

+ this code block is indented by two tabs + +These should not be escaped: \$ \\ \> \[ \{ + + + Lists + + Unordered +

+ Asterisks tight: +

+ + +

+ asterisk 1 +

+ + +

+ asterisk 2 +

+ + +

+ asterisk 3 +

+ + +

+ Asterisks loose: +

+ + +

+ asterisk 1 +

+ + +

+ asterisk 2 +

+ + +

+ asterisk 3 +

+ + +

+ Pluses tight: +

+ + +

+ Plus 1 +

+ + +

+ Plus 2 +

+ + +

+ Plus 3 +

+ + +

+ Pluses loose: +

+ + +

+ Plus 1 +

+ + +

+ Plus 2 +

+ + +

+ Plus 3 +

+ + +

+ Minuses tight: +

+ + +

+ Minus 1 +

+ + +

+ Minus 2 +

+ + +

+ Minus 3 +

+ + +

+ Minuses loose: +

+ + +

+ Minus 1 +

+ + +

+ Minus 2 +

+ + +

+ Minus 3 +

+ + + + + Ordered +

+ Tight: +

+ + +

+ First +

+ + +

+ Second +

+ + +

+ Third +

+ + +

+ and: +

+ + +

+ One +

+ + +

+ Two +

+ + +

+ Three +

+ + +

+ Loose using tabs: +

+ + +

+ First +

+ + +

+ Second +

+ + +

+ Third +

+ + +

+ and using spaces: +

+ + +

+ One +

+ + +

+ Two +

+ + +

+ Three +

+ + +

+ Multiple paragraphs: +

+ + +

+ Item 1, graf one. +

+ Item 1. graf two. The quick brown fox jumped over the lazy dog’s + back. +

+ + +

+ Item 2. +

+ + +

+ Item 3. +

+ + + + + Nested + + +

+ Tab +

+ + +

+ Tab +

+ + +

+ Tab +

+ + + + + + +

+ Here’s another: +

+ + +

+ First +

+ + +

+ Second: +

+ + +

+ Fee +

+ + +

+ Fie +

+ + +

+ Foe +

+ + + + +

+ Third +

+ + +

+ Same thing but with paragraphs: +

+ + +

+ First +

+ + +

+ Second: +

+ + +

+ Fee +

+ + +

+ Fie +

+ + +

+ Foe +

+ + + + +

+ Third +

+ + + + + Tabs and spaces + + +

+ this is a list item indented with tabs +

+ + +

+ this is a list item indented with spaces +

+ + +

+ this is an example list item indented with tabs +

+ + +

+ this is an example list item indented with spaces +

+ + + + + + + Fancy list markers + + + + (2) + +

+ begins with 2 +

+ + + + (3) + +

+ and now 3 +

+ with a continuation +

+ + + + iv. + +

+ sublist with roman numerals, starting with 4 +

+ + + + v. + +

+ more items +

+ + + + (A) + +

+ a subsublist +

+ + + + (B) + +

+ a subsublist +

+ + + + + + +

+ Nesting: +

+ + +

+ Upper Alpha +

+ + +

+ Upper Roman. +

+ + + + (6) + +

+ Decimal start with 6 +

+ + + + c) + +

+ Lower alpha with paren +

+ + + + + + + + +

+ Autonumbering: +

+ + +

+ Autonumber. +

+ + +

+ More. +

+ + +

+ Nested. +

+ + + + +

+ Should not be a list item: +

+ M.A. 2007 +

+ B. Williams +

+ + + + Definition Lists +

+ Tight using spaces: +

+ + + + apple + + +

+ red fruit +

+ + + + + orange + + +

+ orange fruit +

+ + + + + banana + + +

+ yellow fruit +

+ + + +

+ Tight using tabs: +

+ + + + apple + + +

+ red fruit +

+ + + + + orange + + +

+ orange fruit +

+ + + + + banana + + +

+ yellow fruit +

+ + + +

+ Loose: +

+ + + + apple + + +

+ red fruit +

+ + + + + orange + + +

+ orange fruit +

+ + + + + banana + + +

+ yellow fruit +

+ + + +

+ Multiple blocks with italics: +

+ + + + apple + + +

+ red fruit +

+ contains seeds, crisp, pleasant to taste +

+ + + + + orange + + +

+ orange fruit +

+ { orange code block } + +

+ orange block quote +

+ + + + +

+ Multiple definitions, tight: +

+ + + + apple + + +

+ red fruit +

+ computer +

+ + + + + orange + + +

+ orange fruit +

+ bank +

+ + + +

+ Multiple definitions, loose: +

+ + + + apple + + +

+ red fruit +

+ computer +

+ + + + + orange + + +

+ orange fruit +

+ bank +

+ + + +

+ Blank line after term, indented marker, alternate markers: +

+ + + + apple + + +

+ red fruit +

+ computer +

+ + + + + orange + + +

+ orange fruit +

+ + +

+ sublist +

+ + +

+ sublist +

+ + + + + + + + HTML Blocks +

+ Simple block on one line: +

+ +

+ foo +

+ +

+ And nested without indentation: +

+ + +

+ foo +

+ + +

+ bar +

+ + +

+ Interpreted markdown in a table: +

+ This is emphasized +

+ And this is strong +

+ Here’s a simple block: +

+ foo +

+ This should be a code block, though: +

+ <div> + foo +</div> +

+ As should this: +

+ <div>foo</div> +

+ Now, nested: +

+ + + +

+ foo +

+ + + +

+ This should just be an HTML comment: +

+ Multiline: +

+ Code block: +

+  +

+ Just plain comment, with trailing spaces on the line: +

+ Code: +

+ <hr /> +

+ Hr’s: +

+ + + Inline Markup +

+ This is emphasized, and so is this. +

+ This is strong, and so is + this. +

+ An emphasized + link. +

+ This is strong and em. +

+ So is this word. +

+ This is strong and em. +

+ So is this word. +

+ This is code: >, $, + \, \$, + <html>. +

+ ~~This is strikeout.~~ +

+ Superscripts: a^bcd a^hello + a^hello there. +

+ Subscripts: H₂O, H₂₃O, H_{many of them}O. +

+ These should not be superscripts or subscripts, because of the unescaped + spaces: a^b c^d, a~b c~d. +

+ + + Smart quotes, ellipses, dashes +

+ “Hello,” said the spider. “‘Shelob’ is my name.” +

+ ‘A’, ‘B’, and ‘C’ are letters. +

+ ‘Oak,’ ‘elm,’ and ‘beech’ are names of trees. So is ‘pine.’ +

+ ‘He said, “I want to go.”’ Were you alive in the 70’s? +

+ Here is some quoted ‘code’ and a + “quoted + link”. +

+ Some dashes: one—two — three—four — five. +

+ Dashes between numbers: 5–7, 255–66, 1987–1999. +

+ Ellipses…and…and…. +

+ + + LaTeX + + +

+ + +

+ 2+2=4 +

+ + +

+ x∈y +

+ + +

+ α∧ω +

+ + +

+ 223 +

+ + +

+ p-Tree +

+ + +

+ Here’s some display math: + ddxf(x)=limh→0f(x+h)−f(x)h +

+ + +

+ Here’s one that has a line break in it: + α+ω×x2. +

+ + +

+ These shouldn’t be math: +

+ + +

+ To get the famous equation, write $e = mc^2$. +

+ + +

+ $22,000 is a lot of money. So is $34,000. (It + worked if “lot” is emphasized.) +

+ + +

+ Shoes ($20) and socks ($5). +

+ + +

+ Escaped $: $73 this should be + emphasized 23$. +

+ + +

+ Here’s a LaTeX table: +

+ + + Special Characters +

+ Here is some unicode: +

+ + +

+ I hat: Î +

+ + +

+ o umlaut: ö +

+ + +

+ section: § +

+ + +

+ set membership: ∈ +

+ + +

+ AT&T has an ampersand in their name. +

+ AT&T is another way to write it. +

+ This & that. +

+ 4 < 5. +

+ 6 > 5. +

+ Backslash: \ +

+ Backtick: ` +

+ Asterisk: * +

+ Underscore: _ +

+ Left brace: { +

+ Right brace: } +

+ Left bracket: [ +

+ Right bracket: ] +

+ Left paren: ( +

+ Right paren: ) +

+ Greater-than: > +

+ Hash: # +

+ Period: . +

+ Bang: ! +

+ Plus: + +

+ Minus: - +

+ + + Links + + Explicit +

+ Just a + URL. +

+ URL + and title. +

+ URL + and title +

+ with_underscore +

+ Email + link +

+ Empty. +

+ + + Reference +

+ Foo bar. +

+ With embedded + [brackets]. +

+ b by + itself should be a link. +

+ Indented + once. +

+ Indented + twice. +

+ Indented + thrice. +

+ This should [not][] be a link. +

+ [not]: /url +

+ Foo + bar. +

+ Foo + biz. +

+ + + With ampersands +

+ Here’s a + link + with an ampersand in the URL. +

+ Here’s a link with an amersand in the link text: + AT&T. +

+ Here’s an + inline + link. +

+ Here’s an + inline + link in pointy braces. +

+ + + Autolinks +

+ With an ampersand: + http://example.com/?foo=1&bar=2 +

+ + +

+ In a list? +

+ + +

+ http://example.com/ +

+ + +

+ It should. +

+ + +

+ An e-mail address: nobody@nowhere.net +

+ +

+ Blockquoted: + http://example.com/ +

+ +

+ Auto-links should not occur here: + <http://example.com/> +

+ or here: <http://example.com/> + + + + Images +

+ From “Voyage dans la Lune” by Georges Melies (1902): +

+ + lalune + + +

+ Here is a movie + + icon. +

+ + + Footnotes +

+ Here is a footnote reference, +

+ Here is the footnote. It can go anywhere after the footnote + reference. It need not be placed at the end of the document. +

+ and another. +

+ Here’s the long note. This one contains multiple blocks. +

+ Subsequent blocks are indented to show that they belong to the + footnote (as with list items). +

+ { <code> } +

+ If you want, you can indent every line, but you can also be lazy and + just indent the first line of each block. +

+ This should not be a footnote reference, because + it contains a space.[^my note] Here is an inline note. +

+ This is easier to type. Inline notes may contain + links + and ] verbatim characters, as well as + [bracketed text]. +

+ +

+ Notes can go in quotes. +

+ In quote. +

+ +

+ + + +

+ And in list items. +

+ In list. +

+ +

+ + +

+ This paragraph should not be part of the note, as it is not indented. +

+ + +

-- cgit v1.2.3