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
  32 -- | TODO put default pubmed query in gargantext.ini
  33 -- by default: 10K docs
  34 get :: Query -> Maybe Limit -> IO [HyperdataDocument]
  35 get q l = either (\e -> panic $ "CRAWL: PubMed" <> e) (map (toDoc EN))
  36         <$> PubMed.getMetadataWith q l
  37
  38 toDoc :: Lang -> PubMedDoc.PubMed -> HyperdataDocument
  39 toDoc l (PubMedDoc.PubMed (PubMedDoc.PubMedArticle t j as aus)
  40                     (PubMedDoc.PubMedDate a y m d)
  41           ) = HyperdataDocument (Just "PubMed")
  42                                  Nothing
  43                                  Nothing
  44                                  Nothing
  45                                  Nothing
  46                                  Nothing
  47                                  t
  48                                  (authors aus)
  49                                  (institutes aus)
  50                                  j
  51                                  (abstract as)
  52                                  (Just $ Text.pack $ show a)
  53                                  (Just $ fromIntegral y)
  54                                  (Just m)
  55                                  (Just d)
  56                                  Nothing
  57                                  Nothing
  58                                  Nothing
  59                                  (Just $ (Text.pack . show) l)
  60       where
  61         authors :: Maybe [PubMedDoc.Author] -> Maybe Text
  62         authors aus' = case aus' of
  63             Nothing -> Nothing
  64             Just au -> Just $ (Text.intercalate ", ")
  65                             $ catMaybes
  66                             $ map (\n -> PubMedDoc.foreName n <> Just " " <> PubMedDoc.lastName n) au
  67
  68         institutes :: Maybe [PubMedDoc.Author] -> Maybe Text
  69         institutes aus' = case aus' of
  70             Nothing -> Nothing
  71             Just au -> Just $ (Text.intercalate ", ")
  72                             $ (map (Text.replace ", " " - "))
  73                             $ catMaybes
  74                             $ map PubMedDoc.affiliation au
  75
  76
  77         abstract :: Maybe [Text] -> Maybe Text
  78         abstract as' = fmap (Text.intercalate ", ") as'
  79