src/Gargantext/Core/Text/Corpus/Parsers/CSV.hs

   1 {-|
   2 Module      : Gargantext.Core.Text.Corpus.Parsers.CSV
   3 Description :
   4 Copyright   : (c) CNRS, 2017-Present
   5 License     : AGPL + CECILL v3
   6 Maintainer  : team@gargantext.org
   7 Stability   : experimental
   8 Portability : POSIX
   9
  10 CSV parser for Gargantext corpus files.
  11
  12 -}
  13
  14
  15 module Gargantext.Core.Text.Corpus.Parsers.CSV where
  16
  17 import Conduit
  18 import Control.Applicative
  19 import qualified Data.ByteString      as BS
  20 import qualified Data.ByteString.Lazy as BL
  21 import Data.Char (ord)
  22 import Data.Csv
  23 import Data.Either (Either(..))
  24 import Data.Maybe (fromMaybe)
  25 import Data.Text (Text, pack, length, intercalate)
  26 import Data.Time.Segment (jour)
  27 import qualified Data.Vector          as V
  28 import Data.Vector (Vector)
  29 import GHC.IO (FilePath)
  30 import GHC.Word (Word8)
  31
  32 import qualified Prelude
  33
  34 import Gargantext.Database.Admin.Types.Hyperdata (HyperdataDocument(..))
  35 import Gargantext.Prelude hiding (length)
  36 import Gargantext.Core.Text
  37 import Gargantext.Core.Text.Context
  38
  39 ---------------------------------------------------------------
  40 headerCsvGargV3 :: Header
  41 headerCsvGargV3 =
  42   header [ "title"
  43          , "source"
  44          , "publication_year"
  45          , "publication_month"
  46          , "publication_day"
  47          , "abstract"
  48          , "authors"
  49          ]
  50 ---------------------------------------------------------------
  51 data CsvGargV3 = CsvGargV3
  52     { d_docId             :: !Int
  53     , d_title             :: !Text
  54     , d_source            :: !Text
  55     , d_publication_year  :: !Int
  56     , d_publication_month :: !Int
  57     , d_publication_day   :: !Int
  58     , d_abstract          :: !Text
  59     , d_authors           :: !Text
  60     }
  61     deriving (Show)
  62 ---------------------------------------------------------------
  63 -- | Doc 2 HyperdataDocument
  64 toDoc :: CsvGargV3 -> HyperdataDocument
  65 toDoc (CsvGargV3 did dt _ dpy dpm dpd dab dau) =
  66   HyperdataDocument { _hd_bdd = Just "CSV"
  67                     , _hd_doi = Just . pack . show $ did
  68                     , _hd_url = Nothing
  69                     , _hd_uniqId = Nothing
  70                     , _hd_uniqIdBdd = Nothing
  71                     , _hd_page = Nothing
  72                     , _hd_title = Just dt
  73                     , _hd_authors = Nothing
  74                     , _hd_institutes = Just dau
  75                     , _hd_source = Just dab
  76                     , _hd_abstract = Nothing
  77                     , _hd_publication_date = Nothing
  78                     , _hd_publication_year = Just dpy
  79                     , _hd_publication_month = Just dpm
  80                     , _hd_publication_day = Just dpd
  81                     , _hd_publication_hour = Nothing
  82                     , _hd_publication_minute = Nothing
  83                     , _hd_publication_second = Nothing
  84                     , _hd_language_iso2 = Nothing }
  85
  86 ---------------------------------------------------------------
  87 -- | Types Conversions
  88 toDocs :: Vector CsvDoc -> [CsvGargV3]
  89 toDocs v = V.toList
  90          $ V.zipWith (\nId (CsvDoc { .. }) -- (CsvDoc t s mPy pm pd abst auth)
  91                        -> CsvGargV3 { d_docId = nId
  92                                     , d_title = csv_title
  93                                     , d_source = csv_source
  94                                     , d_publication_year = fromMIntOrDec defaultYear csv_publication_year
  95                                     , d_publication_month = fromMaybe defaultMonth csv_publication_month
  96                                     , d_publication_day = fromMaybe defaultDay csv_publication_day
  97                                     , d_abstract = csv_abstract
  98                                     , d_authors = csv_authors })
  99                        (V.enumFromN 1 (V.length v'')) v''
 100           where
 101             v'' = V.foldl (\v' sep -> V.concatMap (splitDoc (docsSize v') sep) v') v seps
 102             seps= (V.fromList [Paragraphs 1, Sentences 3, Chars 3])
 103
 104 ---------------------------------------------------------------
 105 fromDocs :: Vector CsvGargV3 -> Vector CsvDoc
 106 fromDocs docs = V.map fromDocs' docs
 107   where
 108     fromDocs' (CsvGargV3 { .. }) = CsvDoc { csv_title = d_title
 109                                           , csv_source = d_source
 110                                           , csv_publication_year = Just $ IntOrDec d_publication_year
 111                                           , csv_publication_month = Just d_publication_month
 112                                           , csv_publication_day = Just d_publication_day
 113                                           , csv_abstract = d_abstract
 114                                           , csv_authors = d_authors }
 115
 116 ---------------------------------------------------------------
 117 -- | Split a document in its context
 118 -- TODO adapt the size of the paragraph according to the corpus average
 119 splitDoc :: Mean -> SplitContext -> CsvDoc -> Vector CsvDoc
 120 splitDoc m splt doc = let docSize = (length $ csv_abstract doc) in
 121                           if docSize > 1000
 122                             then
 123                               if (mod (round m) docSize) >= 10
 124                                 then
 125                                   splitDoc' splt doc
 126                                 else
 127                                   V.fromList [doc]
 128                             else
 129                               V.fromList [doc]
 130   where
 131     splitDoc' :: SplitContext -> CsvDoc -> Vector CsvDoc
 132     splitDoc' contextSize (CsvDoc { .. }) = V.fromList $ [firstDoc] <> nextDocs
 133         where
 134           firstDoc = CsvDoc { csv_abstract = firstAbstract, .. }
 135           firstAbstract = head' "splitDoc'1" abstracts
 136
 137           nextDocs = map (\txt -> CsvDoc { csv_title = head' "splitDoc'2" $ sentences txt
 138                                          , csv_abstract = unsentences $ tail' "splitDoc'1" $ sentences txt
 139                                          , .. }
 140                           ) (tail' "splitDoc'2" abstracts)
 141
 142           abstracts    = (splitBy $ contextSize) csv_abstract
 143
 144 ---------------------------------------------------------------
 145 ---------------------------------------------------------------
 146 type Mean = Double
 147
 148 docsSize :: Vector CsvDoc -> Mean
 149 docsSize csvDoc = mean ls
 150   where
 151     ls = V.toList $ V.map (fromIntegral . length . csv_abstract) csvDoc
 152
 153
 154 ---------------------------------------------------------------
 155 newtype IntOrDec = IntOrDec Int
 156   deriving (Show, Eq, Read)
 157 unIntOrDec :: IntOrDec -> Int
 158 unIntOrDec (IntOrDec i) = i
 159 instance FromField IntOrDec where
 160   parseField s = case runParser (parseField s :: Parser Int) of
 161     Left _err -> IntOrDec <$> Prelude.floor <$> (parseField s :: Parser Double)
 162     Right n   -> pure $ IntOrDec n
 163 instance ToField IntOrDec where
 164   toField (IntOrDec i) = toField i
 165
 166 fromMIntOrDec :: Int -> Maybe IntOrDec -> Int
 167 fromMIntOrDec default' mVal = unIntOrDec $ fromMaybe (IntOrDec default') mVal
 168 defaultYear :: Int
 169 defaultYear = 1973
 170 defaultMonth :: Int
 171 defaultMonth = 1
 172 defaultDay :: Int
 173 defaultDay = 1
 174
 175 data CsvDoc = CsvDoc
 176     { csv_title             :: !Text
 177     , csv_source            :: !Text
 178     , csv_publication_year  :: !(Maybe IntOrDec)
 179     , csv_publication_month :: !(Maybe Int)
 180     , csv_publication_day   :: !(Maybe Int)
 181     , csv_abstract          :: !Text
 182     , csv_authors           :: !Text
 183     }
 184     deriving (Show)
 185
 186 instance FromNamedRecord CsvDoc where
 187   parseNamedRecord r = do
 188     csv_title <- r .: "title" <|> r .: "Title"
 189     csv_source <- r .: "source" <|> r .: "Source"
 190     csv_publication_year <- r .: "publication_year" <|> r .: "Publication Year"
 191     csv_publication_month <- r .: "publication_month" <|> r .: "Publication Month"
 192     csv_publication_day <- r .: "publication_day" <|> r .: "Publication Day"
 193     csv_abstract <- r .: "abstract" <|> r .: "Abstract"
 194     csv_authors <- r .: "authors" <|> r .: "Authors"
 195     pure $ CsvDoc { .. }
 196
 197 instance ToNamedRecord CsvDoc where
 198   toNamedRecord (CsvDoc{ .. }) =
 199     namedRecord [ "title"             .= csv_title
 200                 , "source"            .= csv_source
 201                 , "publication_year"  .= csv_publication_year
 202                 , "publication_month" .= csv_publication_month
 203                 , "publication_day"   .= csv_publication_day
 204                 , "abstract"          .= csv_abstract
 205                 , "authors"           .= csv_authors
 206                 ]
 207
 208 hyperdataDocument2csvDoc :: HyperdataDocument -> CsvDoc
 209 hyperdataDocument2csvDoc h = CsvDoc { csv_title = m $ _hd_title h
 210                                     , csv_source = m $ _hd_source h
 211                                     , csv_publication_year = Just $ IntOrDec $ mI $ _hd_publication_year h
 212                                     , csv_publication_month = Just $ mI $ _hd_publication_month h
 213                                     , csv_publication_day = Just $ mI $ _hd_publication_day   h
 214                                     , csv_abstract = m $ _hd_abstract h
 215                                     , csv_authors = m $ _hd_authors h }
 216
 217   where
 218     m = maybe "" identity
 219     mI = maybe 0 identity
 220
 221
 222 data Delimiter = Tab | Comma
 223
 224 csvDecodeOptions :: Delimiter -> DecodeOptions
 225 csvDecodeOptions d = defaultDecodeOptions {decDelimiter = delimiter d}
 226
 227 csvEncodeOptions :: Delimiter -> EncodeOptions
 228 csvEncodeOptions d = defaultEncodeOptions {encDelimiter = delimiter d}
 229
 230 delimiter :: Delimiter -> Word8
 231 delimiter Tab   = fromIntegral $ ord '\t'
 232 delimiter Comma = fromIntegral $ ord ','
 233 ------------------------------------------------------------------------
 234 ------------------------------------------------------------------------
 235 readCsvOn' :: [CsvDoc -> Text] -> FilePath -> IO (Either Prelude.String [Text])
 236 readCsvOn' fields fp = do
 237   r <- readFile fp
 238   pure $ ( V.toList
 239           . V.map (\l -> intercalate (pack " ") $ map (\field -> field l) fields)
 240           . snd ) <$> r
 241
 242 ------------------------------------------------------------------------
 243
 244 readFileLazy :: (FromNamedRecord a) => proxy a -> Delimiter -> FilePath -> IO (Either Prelude.String (Header, Vector a))
 245 readFileLazy d f = fmap (readByteStringLazy d f) . BL.readFile
 246
 247 readFileStrict :: (FromNamedRecord a)
 248                => proxy a
 249                -> Delimiter
 250                -> FilePath
 251                -> IO (Either Prelude.String (Header, Vector a))
 252 readFileStrict d f = fmap (readByteStringStrict d f) . BS.readFile
 253
 254 readByteStringLazy :: (FromNamedRecord a)
 255                    => proxy a
 256                    -> Delimiter
 257                    -> BL.ByteString
 258                    -> Either Prelude.String (Header, Vector a)
 259 readByteStringLazy _f d bs = decodeByNameWith (csvDecodeOptions d) bs
 260
 261 readByteStringStrict :: (FromNamedRecord a)
 262                      => proxy a
 263                      -> Delimiter
 264                      -> BS.ByteString
 265                      -> Either Prelude.String (Header, Vector a)
 266 readByteStringStrict d ff = (readByteStringLazy d ff) . BL.fromStrict
 267
 268 ------------------------------------------------------------------------
 269 -- | TODO use readFileLazy
 270 readFile :: FilePath -> IO (Either Prelude.String (Header, Vector CsvDoc))
 271 readFile fp = do
 272   result <- fmap (readCsvLazyBS Comma) $ BL.readFile fp
 273   case result of
 274     Left _err -> fmap (readCsvLazyBS Tab) $ BL.readFile fp
 275     Right res -> pure $ Right res
 276
 277
 278
 279 -- | TODO use readByteStringLazy
 280 readCsvLazyBS :: Delimiter -> BL.ByteString -> Either Prelude.String (Header, Vector CsvDoc)
 281 readCsvLazyBS d bs = decodeByNameWith (csvDecodeOptions d) bs
 282
 283 ------------------------------------------------------------------------
 284 -- | TODO use readFileLazy
 285 readCsvHal :: FilePath -> IO (Either Prelude.String (Header, Vector CsvHal))
 286 readCsvHal = fmap readCsvHalLazyBS . BL.readFile
 287
 288 -- | TODO use readByteStringLazy
 289 readCsvHalLazyBS :: BL.ByteString -> Either Prelude.String (Header, Vector CsvHal)
 290 readCsvHalLazyBS bs = decodeByNameWith (csvDecodeOptions Tab) bs
 291
 292 readCsvHalBSStrict :: BS.ByteString -> Either Prelude.String (Header, Vector CsvHal)
 293 readCsvHalBSStrict = readCsvHalLazyBS . BL.fromStrict
 294
 295 ------------------------------------------------------------------------
 296 writeFile :: FilePath -> (Header, Vector CsvDoc) -> IO ()
 297 writeFile fp (h, vs) = BL.writeFile fp $
 298                       encodeByNameWith (csvEncodeOptions Tab) h (V.toList vs)
 299
 300 writeDocs2Csv :: FilePath -> [HyperdataDocument] -> IO ()
 301 writeDocs2Csv fp hs = BL.writeFile fp $ hyperdataDocument2csv hs
 302
 303 hyperdataDocument2csv :: [HyperdataDocument] -> BL.ByteString
 304 hyperdataDocument2csv hs = encodeByNameWith (csvEncodeOptions Tab) headerCsvGargV3 (map hyperdataDocument2csvDoc hs)
 305
 306 ------------------------------------------------------------------------
 307 -- Hal Format
 308 data CsvHal = CsvHal
 309     { csvHal_title  :: !Text
 310     , csvHal_source :: !Text
 311     , csvHal_publication_year  :: !Integer
 312     , csvHal_publication_month :: !Int
 313     , csvHal_publication_day   :: !Int
 314     , csvHal_abstract          :: !Text
 315     , csvHal_authors           :: !Text
 316
 317     , csvHal_url               :: !Text
 318     , csvHal_isbn_s            :: !Text
 319     , csvHal_issue_s           :: !Text
 320     , csvHal_journalPublisher_s:: !Text
 321     , csvHal_language_s        :: !Text
 322
 323     , csvHal_doiId_s           :: !Text
 324     , csvHal_authId_i          :: !Text
 325     , csvHal_instStructId_i    :: !Text
 326     , csvHal_deptStructId_i    :: !Text
 327     , csvHal_labStructId_i     :: !Text
 328
 329     , csvHal_rteamStructId_i   :: !Text
 330     , csvHal_docType_s         :: !Text
 331     }
 332     deriving (Show)
 333
 334 instance FromNamedRecord CsvHal where
 335   parseNamedRecord r = do
 336     csvHal_title <- r .: "title"
 337     csvHal_source <- r .: "source"
 338     csvHal_publication_year <- r .: "publication_year"
 339     csvHal_publication_month <- r .: "publication_month"
 340     csvHal_publication_day <- r .: "publication_day"
 341     csvHal_abstract <- r .: "abstract"
 342     csvHal_authors <- r .: "authors"
 343     csvHal_url <- r .: "url"
 344     csvHal_isbn_s <- r .: "isbn_s"
 345     csvHal_issue_s <- r .: "issue_s"
 346     csvHal_journalPublisher_s <- r .: "journalPublisher_s"
 347     csvHal_language_s <- r .: "language_s"
 348     csvHal_doiId_s <- r .: "doiId_s"
 349     csvHal_authId_i <- r .: "authId_i"
 350     csvHal_instStructId_i <- r .: "instStructId_i"
 351     csvHal_deptStructId_i <- r .: "deptStructId_i"
 352     csvHal_labStructId_i <- r .: "labStructId_i"
 353     csvHal_rteamStructId_i <- r .: "rteamStructId_i"
 354     csvHal_docType_s <- r .: "docType_s"
 355     pure $ CsvHal { .. }
 356
 357 instance ToNamedRecord CsvHal where
 358   --toNamedRecord (CsvHal t s py  pm pd abst aut  url isbn iss j lang  doi auth inst dept lab team doct) =
 359   toNamedRecord (CsvHal { .. }) =
 360     namedRecord [ "title"  .= csvHal_title
 361                 , "source" .= csvHal_source
 362
 363                 , "publication_year"  .= csvHal_publication_year
 364                 , "publication_month" .= csvHal_publication_month
 365                 , "publication_day"   .= csvHal_publication_day
 366
 367                 , "abstract"          .= csvHal_abstract
 368                 , "authors"           .= csvHal_authors
 369
 370                 , "url"                .= csvHal_url
 371                 , "isbn_s"             .= csvHal_isbn_s
 372                 , "issue_s"            .= csvHal_issue_s
 373                 , "journalPublisher_s" .= csvHal_journalPublisher_s
 374                 , "language_s"         .= csvHal_language_s
 375
 376                 , "doiId_s"            .= csvHal_doiId_s
 377                 , "authId_i"           .= csvHal_authId_i
 378                 , "instStructId_i"     .= csvHal_instStructId_i
 379                 , "deptStructId_i"     .= csvHal_deptStructId_i
 380                 , "labStructId_i"      .= csvHal_labStructId_i
 381
 382                 , "rteamStructId_i"    .= csvHal_rteamStructId_i
 383                 , "docType_s"          .= csvHal_docType_s
 384                ]
 385
 386 csvHal2doc :: CsvHal -> HyperdataDocument
 387 csvHal2doc (CsvHal { .. }) =
 388   HyperdataDocument { _hd_bdd = Just "CsvHal"
 389                     , _hd_doi = Just csvHal_doiId_s
 390                     , _hd_url = Just csvHal_url
 391                     , _hd_uniqId = Nothing
 392                     , _hd_uniqIdBdd = Nothing
 393                     , _hd_page = Nothing
 394                     , _hd_title = Just csvHal_title
 395                     , _hd_authors = Just csvHal_authors
 396                     , _hd_institutes = Just csvHal_instStructId_i
 397                     , _hd_source = Just csvHal_source
 398                     , _hd_abstract = Just csvHal_abstract
 399                     , _hd_publication_date = Just $ pack . show $ jour csvHal_publication_year
 400                                                                       csvHal_publication_month
 401                                                                       csvHal_publication_day
 402                     , _hd_publication_year = Just $ fromIntegral csvHal_publication_year
 403                     , _hd_publication_month = Just csvHal_publication_month
 404                     , _hd_publication_day = Just csvHal_publication_day
 405                     , _hd_publication_hour = Nothing
 406                     , _hd_publication_minute = Nothing
 407                     , _hd_publication_second = Nothing
 408                     , _hd_language_iso2 = Nothing }
 409
 410
 411 csv2doc :: CsvDoc -> HyperdataDocument
 412 csv2doc (CsvDoc { .. })
 413   = HyperdataDocument { _hd_bdd = Just "CsvHal"
 414                       , _hd_doi = Nothing
 415                       , _hd_url = Nothing
 416                       , _hd_uniqId = Nothing
 417                       , _hd_uniqIdBdd = Nothing
 418                       , _hd_page = Nothing
 419                       , _hd_title = Just csv_title
 420                       , _hd_authors = Just csv_authors
 421                       , _hd_institutes = Nothing
 422                       , _hd_source = Just csv_source
 423                       , _hd_abstract = Just csv_abstract
 424                       , _hd_publication_date = Just $ pack . show $ jour (fromIntegral pubYear)
 425                                                                          pubMonth
 426                                                                          pubDay
 427                       , _hd_publication_year = Just pubYear
 428                       , _hd_publication_month = Just pubMonth
 429                       , _hd_publication_day = Just pubDay
 430                       , _hd_publication_hour = Nothing
 431                       , _hd_publication_minute = Nothing
 432                       , _hd_publication_second = Nothing
 433                       , _hd_language_iso2 = Nothing }
 434   where
 435     pubYear = fromMIntOrDec defaultYear csv_publication_year
 436     pubMonth = fromMaybe defaultMonth csv_publication_month
 437     pubDay = fromMaybe defaultDay csv_publication_day
 438
 439 ------------------------------------------------------------------------
 440 parseHal :: FilePath -> IO (Either Prelude.String [HyperdataDocument])
 441 parseHal fp = do
 442   r <- readCsvHal fp
 443   pure $ (V.toList . V.map csvHal2doc . snd) <$> r
 444
 445 parseHal' :: BL.ByteString -> Either Prelude.String [HyperdataDocument]
 446 parseHal' bs = (V.toList . V.map csvHal2doc . snd) <$> readCsvHalLazyBS bs
 447
 448 ------------------------------------------------------------------------
 449
 450 parseCsv :: FilePath -> IO (Either Prelude.String [HyperdataDocument])
 451 parseCsv fp = fmap (V.toList . V.map csv2doc . snd) <$> readFile fp
 452
 453 {-
 454 parseCsv' ::  BL.ByteString -> Either Prelude.String [HyperdataDocument]
 455 parseCsv' bs = (V.toList . V.map csv2doc . snd) <$> readCsvLazyBS Comma bs
 456 -}
 457
 458 parseCsv' :: BL.ByteString -> Either Prelude.String [HyperdataDocument]
 459 parseCsv' bs = do
 460   let
 461     result = case readCsvLazyBS Comma bs of
 462       Left  _err -> readCsvLazyBS Tab bs
 463       Right res -> Right res
 464   (V.toList . V.map csv2doc . snd) <$> result
 465
 466 parseCsvC :: BL.ByteString
 467           -> Either Prelude.String (Maybe Integer, ConduitT () HyperdataDocument Identity ())
 468 parseCsvC bs = do
 469   let
 470     result = case readCsvLazyBS Comma bs of
 471       Left  _err -> readCsvLazyBS Tab bs
 472       Right res -> Right res
 473   case result of
 474     Left err -> Left err
 475     Right r -> Right $ (Just $ Prelude.fromIntegral $ Prelude.length $ snd r, (yieldMany $ snd r) .| mapC csv2doc)
 476
 477 ------------------------------------------------------------------------
 478 -- Csv v3 weighted for phylo
 479
 480 data Csv' = Csv'
 481       { csv'_title             :: !Text
 482       , csv'_source            :: !Text
 483       , csv'_publication_year  :: !Int
 484       , csv'_publication_month :: !Int
 485       , csv'_publication_day   :: !Int
 486       , csv'_abstract          :: !Text
 487       , csv'_authors           :: !Text
 488       , csv'_weight            :: !Double } deriving (Show)
 489
 490
 491 instance FromNamedRecord Csv' where
 492   parseNamedRecord r = do
 493     csv'_title <- r .: "title"
 494     csv'_source <- r .: "source"
 495     csv'_publication_year <- r .: "publication_year"
 496     csv'_publication_month <- r .: "publication_month"
 497     csv'_publication_day <- r .: "publication_day"
 498     csv'_abstract <- r .: "abstract"
 499     csv'_authors <- r .: "authors"
 500     csv'_weight <- r .: "weight"
 501     pure $ Csv' { .. }
 502
 503 readWeightedCsv :: FilePath -> IO (Header, Vector Csv')
 504 readWeightedCsv fp =
 505   fmap (\bs ->
 506     case decodeByNameWith (csvDecodeOptions Tab) bs of
 507       Left e       -> panic (pack e)
 508       Right corpus -> corpus
 509     ) $ BL.readFile fp