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

   1 {-|
   2 Module      : Gargantext.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.Text.Corpus.API.Pubmed
  14     where
  15
  16 import Data.Maybe
  17 import Data.Text (Text)
  18 import Gargantext.Prelude
  19 import Gargantext.Core (Lang(..))
  20 import Gargantext.Database.Admin.Types.Node (HyperdataDocument(..))
  21 import qualified Data.Text as Text
  22
  23 import qualified PUBMED as PubMed
  24 import qualified PUBMED.Parser as PubMedDoc
  25
  26
  27 type Query = Text
  28 type Limit = PubMed.Limit
  29
  30 get :: Query -> Maybe Limit -> IO [HyperdataDocument]
  31 get q l = either (\e -> panic $ "CRAWL: PubMed" <> e) (map (toDoc EN)) <$> PubMed.getMetadataWith q l
  32
  33 toDoc :: Lang -> PubMedDoc.PubMed -> HyperdataDocument
  34 toDoc l (PubMedDoc.PubMed (PubMedDoc.PubMedArticle t j as aus)
  35                     (PubMedDoc.PubMedDate a y m d)
  36           ) = HyperdataDocument (Just "PubMed")
  37                                  Nothing
  38                                  Nothing
  39                                  Nothing
  40                                  Nothing
  41                                  Nothing
  42                                  t
  43                                  (authors aus)
  44                                  Nothing
  45                                  j
  46                                  (abstract as)
  47                                  (Just $ Text.pack $ show a)
  48                                  (Just $ fromIntegral y)
  49                                  (Just m)
  50                                  (Just d)
  51                                  Nothing
  52                                  Nothing
  53                                  Nothing
  54                                  (Just $ (Text.pack . show) l)
  55       where
  56         authors :: Maybe [PubMedDoc.Author] -> Maybe Text
  57         authors aus' = case aus' of
  58             Nothing -> Nothing
  59             Just au -> Just $ (Text.intercalate ", ") $ catMaybes $ map PubMedDoc.foreName au
  60
  61         abstract :: Maybe [Text] -> Maybe Text
  62         abstract as' = fmap (Text.intercalate ", ") as'
  63