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