src/Gargantext/Core/Text/Corpus/API/Pubmed.hs

   1 {-|
   2 Module      : Gargantext.Core.Text.Corpus.API.Pubmed
   3 Description : Pubmed API connection
   4 Copyright   : (c) CNRS, 2017
   5 License     : AGPL + CECILL v3
   6 Maintainer  : team@gargantext.org
   7 Stability   : experimental
   8 Portability : POSIX
   9
  10 -}
  11
  12
  13 module Gargantext.Core.Text.Corpus.API.Pubmed
  14     where
  15
  16 import Data.Maybe
  17 import Data.Text (Text)
  18 import qualified Data.Text as Text
  19
  20 import Gargantext.Prelude
  21 import Gargantext.Core (Lang(..))
  22 import Gargantext.Database.Admin.Types.Hyperdata (HyperdataDocument(..))
  23
  24 import qualified PUBMED as PubMed
  25 import qualified PUBMED.Parser as PubMedDoc
  26
  27
  28 type Query = Text
  29 type Limit = PubMed.Limit
  30
  31 get :: Query -> Maybe Limit -> IO [HyperdataDocument]
  32 get q l = either (\e -> panic $ "CRAWL: PubMed" <> e) (map (toDoc EN)) <$> PubMed.getMetadataWith q l
  33
  34 toDoc :: Lang -> PubMedDoc.PubMed -> HyperdataDocument
  35 toDoc l (PubMedDoc.PubMed (PubMedDoc.PubMedArticle t j as aus)
  36                     (PubMedDoc.PubMedDate a y m d)
  37           ) = HyperdataDocument (Just "PubMed")
  38                                  Nothing
  39                                  Nothing
  40                                  Nothing
  41                                  Nothing
  42                                  Nothing
  43                                  t
  44                                  (authors aus)
  45                                  Nothing
  46                                  j
  47                                  (abstract as)
  48                                  (Just $ Text.pack $ show a)
  49                                  (Just $ fromIntegral y)
  50                                  (Just m)
  51                                  (Just d)
  52                                  Nothing
  53                                  Nothing
  54                                  Nothing
  55                                  (Just $ (Text.pack . show) l)
  56       where
  57         authors :: Maybe [PubMedDoc.Author] -> Maybe Text
  58         authors aus' = case aus' of
  59             Nothing -> Nothing
  60             Just au -> Just $ (Text.intercalate ", ") $ catMaybes $ map PubMedDoc.foreName au
  61
  62         abstract :: Maybe [Text] -> Maybe Text
  63         abstract as' = fmap (Text.intercalate ", ") as'
  64