aboutsummaryrefslogtreecommitdiff
path: root/src/Text/Pandoc/Readers/JATS.hs
blob: 8158a4511d4b2abf5eb67646278a275abc33bcc0 (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
{-# LANGUAGE ExplicitForAll, TupleSections #-}
module Text.Pandoc.Readers.JATS ( readJATS ) where
import Control.Monad.State.Strict
import Data.Char (isDigit, isSpace, toUpper)
import Data.Default
import Data.Generics
import Data.List (intersperse)
import qualified Data.Map as Map
import Data.Maybe (maybeToList, fromMaybe)
import Data.Text (Text)
import qualified Data.Text as T
import Text.HTML.TagSoup.Entity (lookupEntity)
import Text.Pandoc.Builder
import Text.Pandoc.Class (PandocMonad)
import Text.Pandoc.Options
import Text.Pandoc.Shared (underlineSpan, crFilter, safeRead)
import Text.TeXMath (readMathML, writeTeX)
import Text.XML.Light
import qualified Data.Set as S (fromList, member)
import Data.Set ((\\))

type JATS m = StateT JATSState m

data JATSState = JATSState{ jatsSectionLevel :: Int
                          , jatsQuoteType    :: QuoteType
                          , jatsMeta         :: Meta
                          , jatsBook         :: Bool
                          , jatsFigureTitle  :: Inlines
                          , jatsContent      :: [Content]
                          } deriving Show

instance Default JATSState where
  def = JATSState{ jatsSectionLevel = 0
                 , jatsQuoteType = DoubleQuote
                 , jatsMeta = mempty
                 , jatsBook = False
                 , jatsFigureTitle = mempty
                 , jatsContent = [] }


readJATS :: PandocMonad m => ReaderOptions -> Text -> m Pandoc
readJATS _ inp = do
  let tree = normalizeTree . parseXML
               $ T.unpack $ crFilter inp
  (bs, st') <- flip runStateT (def{ jatsContent = tree }) $ mapM parseBlock tree
  return $ Pandoc (jatsMeta st') (toList . mconcat $ bs)

-- normalize input, consolidating adjacent Text and CRef elements
normalizeTree :: [Content] -> [Content]
normalizeTree = everywhere (mkT go)
  where go :: [Content] -> [Content]
        go (Text (CData CDataRaw _ _):xs) = xs
        go (Text (CData CDataText s1 z):Text (CData CDataText s2 _):xs) =
           Text (CData CDataText (s1 ++ s2) z):xs
        go (Text (CData CDataText s1 z):CRef r:xs) =
           Text (CData CDataText (s1 ++ convertEntity r) z):xs
        go (CRef r:Text (CData CDataText s1 z):xs) =
             Text (CData CDataText (convertEntity r ++ s1) z):xs
        go (CRef r1:CRef r2:xs) =
             Text (CData CDataText (convertEntity r1 ++ convertEntity r2) Nothing):xs
        go xs = xs

convertEntity :: String -> String
convertEntity e = Data.Maybe.fromMaybe (map toUpper e) (lookupEntity e)

-- convenience function to get an attribute value, defaulting to ""
attrValue :: String -> Element -> String
attrValue attr =
  fromMaybe "" . maybeAttrValue attr

maybeAttrValue :: String -> Element -> Maybe String
maybeAttrValue attr elt =
  lookupAttrBy (\x -> qName x == attr) (elAttribs elt)

-- convenience function
named :: String -> Element -> Bool
named s e = qName (elName e) == s

--

addMeta :: PandocMonad m => ToMetaValue a => String -> a -> JATS m ()
addMeta field val = modify (setMeta field val)

instance HasMeta JATSState where
  setMeta field v s =  s {jatsMeta = setMeta field v (jatsMeta s)}
  deleteMeta field s = s {jatsMeta = deleteMeta field (jatsMeta s)}

isBlockElement :: Content -> Bool
isBlockElement (Elem e) = qName (elName e) `S.member` blocktags
  where blocktags = S.fromList (paragraphLevel ++ lists ++ mathML ++ other) \\ S.fromList inlinetags
        paragraphLevel = ["address", "array", "boxed-text", "chem-struct-wrap",
            "code", "fig", "fig-group", "graphic", "media", "preformat",
            "supplementary-material", "table-wrap", "table-wrap-group",
            "alternatives", "disp-formula", "disp-formula-group"]
        lists = ["def-list", "list"]
        mathML = ["tex-math", "mml:math"]
        other = ["p", "related-article", "related-object", "ack", "disp-quote",
            "speech", "statement", "verse-group", "x"]
        inlinetags = ["email", "ext-link", "uri", "inline-supplementary-material",
            "related-article", "related-object", "hr", "bold", "fixed-case",
            "italic", "monospace", "overline", "overline-start", "overline-end",
            "roman", "sans-serif", "sc", "strike", "underline", "underline-start",
            "underline-end", "ruby", "alternatives", "inline-graphic", "private-char",
            "chem-struct", "inline-formula", "tex-math", "mml:math", "abbrev",
            "milestone-end", "milestone-start", "named-content", "styled-content",
            "fn", "target", "xref", "sub", "sup", "x", "address", "array",
            "boxed-text", "chem-struct-wrap", "code", "fig", "fig-group", "graphic",
            "media", "preformat", "supplementary-material", "table-wrap",
            "table-wrap-group", "disp-formula", "disp-formula-group",
            "citation-alternatives", "element-citation", "mixed-citation",
            "nlm-citation", "award-id", "funding-source", "open-access",
            "def-list", "list", "ack", "disp-quote", "speech", "statement",
            "verse-group"]
isBlockElement _ = False

-- Trim leading and trailing newline characters
trimNl :: String -> String
trimNl = reverse . go . reverse . go
  where go ('\n':xs) = xs
        go xs        = xs

-- function that is used by both graphic (in parseBlock)
-- and inline-graphic (in parseInline)
getGraphic :: PandocMonad m => Element -> JATS m Inlines
getGraphic e = do
  let atVal a = attrValue a e
      attr = (atVal "id", words $ atVal "role", [])
      imageUrl = atVal "href"
      captionOrLabel = case filterChild (\x -> named "caption" x
                                            || named "label" x) e of
                        Nothing -> return mempty
                        Just z  -> mconcat <$>
                                         mapM parseInline (elContent z)
  figTitle <- gets jatsFigureTitle
  let (caption, title) = if isNull figTitle
                            then (captionOrLabel, atVal "title")
                            else (return figTitle, "fig:")
  fmap (imageWith attr imageUrl title) caption

getBlocks :: PandocMonad m => Element -> JATS m Blocks
getBlocks e =  mconcat <$>
                 mapM parseBlock (elContent e)


parseBlock :: PandocMonad m => Content -> JATS m Blocks
parseBlock (Text (CData CDataRaw _ _)) = return mempty -- DOCTYPE
parseBlock (Text (CData _ s _)) = if all isSpace s
                                     then return mempty
                                     else return $ plain $ trimInlines $ text s
parseBlock (CRef x) = return $ plain $ str $ map toUpper x
parseBlock (Elem e) =
  case qName (elName e) of
        "p" -> parseMixed para (elContent e)
        "code" -> codeBlockWithLang
        "preformat" -> codeBlockWithLang
        "disp-quote" -> parseBlockquote
        "list" -> case attrValue "list-type" e of
                    "bullet" -> bulletList <$> listitems
                    listType -> do
                      let start = fromMaybe 1 $
                                  (strContent <$> (filterElement (named "list-item") e
                                               >>= filterElement (named "lable")))
                                   >>= safeRead
                      orderedListWith (start, parseListStyleType listType, DefaultDelim)
                        <$> listitems
        "def-list" -> definitionList <$> deflistitems
        "sec" -> gets jatsSectionLevel >>= sect . (+1)
        "graphic" -> para <$> getGraphic e
        "journal-meta" -> parseMetadata e
        "article-meta" -> parseMetadata e
        "custom-meta" -> parseMetadata e
        "title" -> return mempty -- processed by header
        "table" -> parseTable
        "fig" -> divWith (attrValue "id" e, ["fig"], []) <$> getBlocks e
        "table-wrap" -> divWith (attrValue "id" e, ["table-wrap"], []) <$> getBlocks e
        "caption" -> divWith (attrValue "id" e, ["caption"], []) <$> sect 6
        "ref-list" -> parseRefList e
        "?xml"  -> return mempty
        _       -> getBlocks e
   where parseMixed container conts = do
           let (ils,rest) = break isBlockElement conts
           ils' <- (trimInlines . mconcat) <$> mapM parseInline ils
           let p = if ils' == mempty then mempty else container ils'
           case rest of
                 []     -> return p
                 (r:rs) -> do
                    b <- parseBlock r
                    x <- parseMixed container rs
                    return $ p <> b <> x
         codeBlockWithLang = do
           let classes' = case attrValue "language" e of
                                "" -> []
                                x  -> [x]
           return $ codeBlockWith (attrValue "id" e, classes', [])
                  $ trimNl $ strContentRecursive e
         parseBlockquote = do
            attrib <- case filterChild (named "attribution") e of
                             Nothing  -> return mempty
                             Just z   -> (para . (str "— " <>) . mconcat)
                                         <$>
                                              mapM parseInline (elContent z)
            contents <- getBlocks e
            return $ blockQuote (contents <> attrib)
         parseListStyleType "roman-lower" = LowerRoman
         parseListStyleType "roman-upper" = UpperRoman
         parseListStyleType "alpha-lower" = LowerAlpha
         parseListStyleType "alpha-upper" = UpperAlpha
         parseListStyleType _             = DefaultStyle
         listitems = mapM getBlocks $ filterChildren (named "list-item") e
         deflistitems = mapM parseVarListEntry $ filterChildren
                     (named "def-item") e
         parseVarListEntry e' = do
                     let terms = filterChildren (named "term") e'
                     let items = filterChildren (named "def") e'
                     terms' <- mapM getInlines terms
                     items' <- mapM getBlocks items
                     return (mconcat $ intersperse (str "; ") terms', items')
         parseTable = do
                      let isCaption x = named "title" x || named "caption" x
                      caption <- case filterChild isCaption e of
                                       Just t  -> getInlines t
                                       Nothing -> return mempty
                      let e' = fromMaybe e $ filterChild (named "tgroup") e
                      let isColspec x = named "colspec" x || named "col" x
                      let colspecs = case filterChild (named "colgroup") e' of
                                           Just c -> filterChildren isColspec c
                                           _      -> filterChildren isColspec e'
                      let isRow x = named "row" x || named "tr" x
                      headrows <- case filterChild (named "thead") e' of
                                       Just h  -> case filterChild isRow h of
                                                       Just x  -> parseRow x
                                                       Nothing -> return []
                                       Nothing -> return []
                      bodyrows <- case filterChild (named "tbody") e' of
                                       Just b  -> mapM parseRow
                                                  $ filterChildren isRow b
                                       Nothing -> mapM parseRow
                                                  $ filterChildren isRow e'
                      let toAlignment c = case findAttr (unqual "align") c of
                                                Just "left"   -> AlignLeft
                                                Just "right"  -> AlignRight
                                                Just "center" -> AlignCenter
                                                _             -> AlignDefault
                      let toWidth c = case findAttr (unqual "colwidth") c of
                                                Just w -> fromMaybe 0
                                                   $ safeRead $ '0': filter (\x ->
                                                     isDigit x || x == '.') w
                                                Nothing -> 0 :: Double
                      let numrows = case bodyrows of
                                         [] -> 0
                                         xs -> maximum $ map length xs
                      let aligns = case colspecs of
                                     [] -> replicate numrows AlignDefault
                                     cs -> map toAlignment cs
                      let widths = case colspecs of
                                     []  -> replicate numrows 0
                                     cs  -> let ws = map toWidth cs
                                                tot = sum ws
                                            in  if all (> 0) ws
                                                   then map (/ tot) ws
                                                   else replicate numrows 0
                      let headrows' = if null headrows
                                         then replicate numrows mempty
                                         else headrows
                      return $ table caption (zip aligns widths)
                                 headrows' bodyrows
         isEntry x  = named "entry" x || named "td" x || named "th" x
         parseRow = mapM (parseMixed plain . elContent) . filterChildren isEntry
         sect n = do isbook <- gets jatsBook
                     let n' = if isbook || n == 0 then n + 1 else n
                     headerText <- case filterChild (named "title") e `mplus`
                                        (filterChild (named "info") e >>=
                                            filterChild (named "title")) of
                                      Just t  -> getInlines t
                                      Nothing -> return mempty
                     oldN <- gets jatsSectionLevel
                     modify $ \st -> st{ jatsSectionLevel = n }
                     b <- getBlocks e
                     let ident = attrValue "id" e
                     modify $ \st -> st{ jatsSectionLevel = oldN }
                     return $ headerWith (ident,[],[]) n' headerText <> b

getInlines :: PandocMonad m => Element -> JATS m Inlines
getInlines e' = (trimInlines . mconcat) <$>
                 mapM parseInline (elContent e')

parseMetadata :: PandocMonad m => Element -> JATS m Blocks
parseMetadata e = do
  getTitle e
  getAuthors e
  getAffiliations e
  return mempty

getTitle :: PandocMonad m => Element -> JATS m ()
getTitle e = do
  tit <-  case filterElement (named "article-title") e of
               Just s  -> getInlines s
               Nothing -> return mempty
  subtit <-  case filterElement (named "subtitle") e of
               Just s  -> (text ": " <>) <$>
                           getInlines s
               Nothing -> return mempty
  when (tit /= mempty) $ addMeta "title" tit
  when (subtit /= mempty) $ addMeta "subtitle" subtit

getAuthors :: PandocMonad m => Element -> JATS m ()
getAuthors e = do
  authors <- mapM getContrib $ filterElements
              (\x -> named "contrib" x &&
                     attrValue "contrib-type" x == "author") e
  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
  unless (null affs) $ addMeta "institute" affs

getContrib :: PandocMonad m => Element -> JATS m Inlines
getContrib x = do
  given <- maybe (return mempty) getInlines
            $ filterElement (named "given-names") x
  family <- maybe (return mempty) getInlines
            $ filterElement (named "surname") x
  if given == mempty && family == mempty
     then return mempty
     else if given == mempty || family == mempty
          then return $ given <> family
          else return $ given <> space <> family

parseRefList :: PandocMonad m => Element -> JATS m Blocks
parseRefList e = do
  refs <- mapM parseRef $ filterChildren (named "ref") e
  addMeta "references" refs
  return mempty

parseRef :: PandocMonad m
         => Element -> JATS m (Map.Map String MetaValue)
parseRef e = do
  let refId = text $ attrValue "id" e
  let getInlineText n = maybe (return mempty) getInlines . filterChild (named n)
  case filterChild (named "element-citation") e of
       Just c  -> do
         let refType = text $
               case attrValue "publication-type" c of
                  "journal" -> "article-journal"
                  x -> x
         (refTitle, refContainerTitle) <- do
           t <- getInlineText "article-title" c
           ct <- getInlineText "source" c
           if t == mempty
              then return (ct, mempty)
              else return (t, ct)
         refLabel <- getInlineText "label" c
         refYear <- getInlineText "year" c
         refVolume <- getInlineText "volume" c
         refFirstPage <- getInlineText "fpage" c
         refLastPage <- getInlineText "lpage" c
         refPublisher <- getInlineText "publisher-name" c
         refPublisherPlace <- getInlineText "publisher-loc" c
         let refPages = refFirstPage <> (if refLastPage == mempty
                                            then mempty
                                            else text "\x2013" <> refLastPage)
         let personGroups' = filterChildren (named "person-group") c
         let getName nm = do
               given <- maybe (return mempty) getInlines
                         $ filterChild (named "given-names") nm
               family <- maybe (return mempty) getInlines
                         $ filterChild (named "surname") nm
               return $ toMetaValue $ Map.fromList [
                   ("given", given)
                 , ("family", family)
                 ]
         personGroups <- mapM (\pg ->
                                do names <- mapM getName
                                            (filterChildren (named "name") pg)
                                   return (attrValue "person-group-type" pg,
                                           toMetaValue names))
                         personGroups'
         return $ Map.fromList $
           [ ("id", toMetaValue refId)
           , ("type", toMetaValue refType)
           , ("title", toMetaValue refTitle)
           , ("container-title", toMetaValue refContainerTitle)
           , ("publisher", toMetaValue refPublisher)
           , ("publisher-place", toMetaValue refPublisherPlace)
           , ("title", toMetaValue refTitle)
           , ("issued", toMetaValue
                        $ Map.fromList [
                            ("year", refYear)
                          ])
           , ("volume", toMetaValue refVolume)
           , ("page", toMetaValue refPages)
           , ("citation-label", toMetaValue refLabel)
           ] ++ personGroups
       Nothing -> return $ Map.insert "id" (toMetaValue refId) mempty
       -- TODO handle mixed-citation

strContentRecursive :: Element -> String
strContentRecursive = strContent .
  (\e' -> e'{ elContent = map elementToStr $ elContent e' })

elementToStr :: Content -> Content
elementToStr (Elem e') = Text $ CData CDataText (strContentRecursive e') Nothing
elementToStr x = x

parseInline :: PandocMonad m => Content -> JATS m Inlines
parseInline (Text (CData _ s _)) = return $ text s
parseInline (CRef ref) =
  return $ maybe (text $ map toUpper ref) text $ lookupEntity ref
parseInline (Elem e) =
  case qName (elName e) of
        "italic" -> emph <$> innerInlines
        "bold" -> strong <$> innerInlines
        "strike" -> strikeout <$> innerInlines
        "sub" -> subscript <$> innerInlines
        "sup" -> superscript <$> innerInlines
        "underline" -> underlineSpan <$> innerInlines
        "break" -> return linebreak
        "sc" -> smallcaps <$> innerInlines

        "code" -> codeWithLang
        "monospace" -> codeWithLang

        "inline-graphic" -> getGraphic e
        "disp-quote" -> do
            qt <- gets jatsQuoteType
            let qt' = if qt == SingleQuote then DoubleQuote else SingleQuote
            modify $ \st -> st{ jatsQuoteType = qt' }
            contents <- innerInlines
            modify $ \st -> st{ jatsQuoteType = qt }
            return $ if qt == SingleQuote
                        then singleQuoted contents
                        else doubleQuoted contents

        "xref" -> do
            ils <- innerInlines
            let rid = attrValue "rid" e
            let refType = ("ref-type",) <$> maybeAttrValue "ref-type" e
            let attr = (attrValue "id" e, [], maybeToList refType)
            return $ if refType == Just ("ref-type","bibr")
                        then cite [Citation{
                                         citationId = rid
                                       , citationPrefix = []
                                       , citationSuffix = []
                                       , citationMode = NormalCitation
                                       , citationNoteNum = 0
                                       , citationHash = 0}] ils
                        else linkWith attr ('#' : rid) "" ils
        "ext-link" -> do
             ils <- innerInlines
             let title = fromMaybe "" $ findAttr (QName "title" (Just "http://www.w3.org/1999/xlink") Nothing) e
             let href = case findAttr (QName "href" (Just "http://www.w3.org/1999/xlink") Nothing) e of
                               Just h -> h
                               _      -> '#' : attrValue "rid" e
             let ils' = if ils == mempty then str href else ils
             let attr = (attrValue "id" e, [], [])
             return $ linkWith attr href title ils'

        "disp-formula" -> formula displayMath
        "inline-formula" -> formula math
        "math" | qPrefix (elName e) == Just "mml" -> return . math $ mathML e
        "tex-math" -> return . math $ strContent e

        "email" -> return $ link ("mailto:" ++ strContent e) ""
                          $ str $ strContent e
        "uri" -> return $ link (strContent e) "" $ str $ strContent e
        "fn" -> (note . mconcat) <$>
                         mapM parseBlock (elContent e)
        _          -> innerInlines
   where innerInlines = (trimInlines . mconcat) <$>
                          mapM parseInline (elContent e)
         mathML x =
            case readMathML . showElement $ everywhere (mkT removePrefix) x of
                Left _ -> mempty
                Right m -> writeTeX m
         formula constructor = do
            let whereToLook = fromMaybe e $ filterElement (named "alternatives") e
                texMaths = map strContent $
                            filterChildren (named  "tex-math") whereToLook
                mathMLs = map mathML $
                            filterChildren isMathML whereToLook
            return . mconcat . take 1 . map constructor $ texMaths ++ mathMLs

         isMathML x = qName   (elName x) == "math" &&
                      qPrefix (elName x) == Just "mml"
         removePrefix elname = elname { qPrefix = Nothing }
         codeWithLang = do
           let classes' = case attrValue "language" e of
                               "" -> []
                               l  -> [l]
           return $ codeWith (attrValue "id" e,classes',[]) $ strContentRecursive e