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 {-# LANGUAGE NoImplicitPrelude #-}
  13 {-# LANGUAGE OverloadedStrings #-}
  14
  15 module Gargantext.Text.Corpus.API.Pubmed
  16     where
  17
  18 import Data.Maybe
  19 import Data.Text (Text)
  20 import qualified Data.Text as Text
  21
  22 import Gargantext.Prelude
  23 import Gargantext.Core (Lang(..))
  24 import Gargantext.Database.Admin.Types.Hyperdata (HyperdataDocument(..))
  25
  26 import qualified PUBMED as PubMed
  27 import qualified PUBMED.Parser as PubMedDoc
  28
  29
  30 type Query = Text
  31 type Limit = PubMed.Limit
  32
  33 get :: Query -> Maybe Limit -> IO [HyperdataDocument]
  34 get q l = either (\e -> panic $ "CRAWL: PubMed" <> e) (map (toDoc EN)) <$> PubMed.getMetadataWith q l
  35
  36 toDoc :: Lang -> PubMedDoc.PubMed -> HyperdataDocument
  37 toDoc l (PubMedDoc.PubMed (PubMedDoc.PubMedArticle t j as aus)
  38                     (PubMedDoc.PubMedDate a y m d)
  39           ) = HyperdataDocument (Just "PubMed")
  40                                  Nothing
  41                                  Nothing
  42                                  Nothing
  43                                  Nothing
  44                                  Nothing
  45                                  t
  46                                  (authors aus)
  47                                  Nothing
  48                                  j
  49                                  (abstract as)
  50                                  (Just $ Text.pack $ show a)
  51                                  (Just $ fromIntegral y)
  52                                  (Just m)
  53                                  (Just d)
  54                                  Nothing
  55                                  Nothing
  56                                  Nothing
  57                                  (Just $ (Text.pack . show) l)
  58       where
  59         authors :: Maybe [PubMedDoc.Author] -> Maybe Text
  60         authors aus' = case aus' of
  61             Nothing -> Nothing
  62             Just au -> Just $ (Text.intercalate ", ") $ catMaybes $ map PubMedDoc.foreName au
  63
  64         abstract :: Maybe [Text] -> Maybe Text
  65         abstract as' = fmap (Text.intercalate ", ") as'
  66