src/Gargantext/Text/Parsers/PubMed.hs

   1 {-|
   2 Module      : Gargantext.Text.Parsers.PubMed
   3 Description : Parser for Wikimedia dump
   4 Copyright   : (c) CNRS, 2017-Present
   5 License     : AGPL + CECILL v3
   6 Maintainer  : team@gargantext.org
   7 Stability   : experimental
   8 Portability : POSIX
   9
  10 This version of Parsers fixes the Date of publication in Gargantext
  11 (V3) parser of PubMed. Indeed, we can not rely neither on Journal
  12 Publication Date neither on Article publication date, which are
  13 incomplete structurally but for its interpretation too. Then, to
  14 simplify and uniformize data, date of publication of database insertion
  15 is used.
  16
  17 TODO:
  18 - Add authors
  19 - factorize
  20 -}
  21
  22 {-# LANGUAGE OverloadedStrings #-}
  23 {-# LANGUAGE NoImplicitPrelude #-}
  24
  25 module Gargantext.Text.Parsers.PubMed where
  26
  27
  28 import Data.Conduit.List as CL hiding (catMaybes, head)
  29 import Control.Monad (join)
  30 import GHC.IO (FilePath)
  31 import Prelude (read)
  32 import Gargantext.Prelude
  33 import Control.Monad.Catch (MonadThrow)
  34 import Data.Maybe (Maybe)
  35 import Data.Monoid (mconcat)
  36 import Text.XML.Stream.Parse
  37 import Data.Conduit (runConduit, (.|), ConduitT)
  38 import Data.Text (Text, unpack)
  39 import Data.XML.Types (Event)
  40 import Data.Time.Segment (jour)
  41 import Data.Time (UTCTime(..))
  42 import qualified Data.ByteString.Lazy as DBL
  43 import Gargantext.Text.Parsers.Wikimedia
  44
  45
  46 data PubMed =
  47      PubMed { pubmed_article :: PubMedArticle
  48             , pubmed_date    :: PubMedData
  49      } deriving Show
  50
  51 data PubMedArticle =
  52      PubMedArticle { pubmed_title   :: Maybe Text
  53                    , pubmed_journal :: Maybe Text
  54                    , pubmed_abstract :: Maybe [Text]
  55                    }
  56                    deriving (Show)
  57
  58 data PubMedData =
  59      PubMedData { pubmedData_date     :: UTCTime
  60                 , pubmedData_year     :: Integer
  61                 , pubmedData_month    :: Int
  62                 , pubmedData_day      :: Int
  63                 } deriving (Show)
  64
  65 readPubMedFile :: FilePath -> IO [PubMed]
  66 readPubMedFile fp = do
  67   input <- DBL.readFile fp
  68   pubMedParser input
  69
  70 pubMedParser :: DBL.ByteString -> IO [PubMed]
  71 pubMedParser bstring = runConduit $ parseLBS def bstring
  72                                  .| parseArticleSet
  73                                  .| CL.consume
  74
  75 parseArticleSet :: MonadThrow m => ConduitT Event PubMed m ()
  76 parseArticleSet = do
  77   as <- force "force" $ tagIgnoreAttrs "PubmedArticleSet" $ manyYield parsePubMedArticle
  78   return as
  79
  80 parsePubMedArticle :: MonadThrow m => ConduitT Event o m (Maybe PubMed)
  81 parsePubMedArticle = do
  82   articles <- tagIgnoreAttrs "PubmedArticle" parsePubMedArticle'
  83   return articles
  84
  85 parsePubMedArticle' :: MonadThrow m => ConduitT Event o m (PubMed)
  86 parsePubMedArticle' = do
  87   article <- force "MedlineCitation" $ tagIgnoreAttrs "MedlineCitation" parseMedlineCitation
  88   dates <- tagIgnoreAttrs "PubmedData" $ do
  89     dates' <- tagIgnoreAttrs "History" $ many $ tagIgnoreAttrs "PubMedPubDate" $ do
  90       y' <- force "Year"  $ tagIgnoreAttrs "Year"  content
  91       m' <- force "Month" $ tagIgnoreAttrs "Month" content
  92       d' <- force "Day"   $ tagIgnoreAttrs "Day"   content
  93       _ <- many $ ignoreAnyTreeContent
  94       return (read $ unpack y', read $ unpack m', read $ unpack d')
  95     _ <- many $ ignoreAnyTreeContent
  96     return dates'
  97   _ <- many $ ignoreAnyTreeContent
  98   let (y,m,d) = maybe (1,1,1) identity $ join $ fmap head $ reverse <$> join dates
  99   return $ PubMed (article) (PubMedData (jour y m d) y m d)
 100
 101 parseMedlineCitation :: MonadThrow m => ConduitT Event o m PubMedArticle
 102 parseMedlineCitation = do
 103   a <- force "article" $ manyTagsUntil "Article" parseArticle
 104   _ <- many $ ignoreAnyTreeContent
 105   return a
 106
 107 parseArticle :: MonadThrow m => ConduitT Event o m PubMedArticle
 108 parseArticle = do
 109   journal  <- force "journal" $ manyTagsUntil "Journal" $ do
 110     j <- manyTagsUntil "Title" content
 111     _ <- many $ ignoreAnyTreeContent
 112     return j
 113
 114   title    <- do
 115     t <- manyTagsUntil "ArticleTitle" content
 116     return t
 117
 118   abstracts <- do
 119     as <- manyTagsUntil "Abstract" $ many $ do
 120       txt <- tagIgnoreAttrs "AbstractText" $ do
 121         c <- content
 122         _ <- many $ ignoreAnyTreeContent
 123         return c
 124       _ <- many $ ignoreAnyTreeContent
 125       return txt
 126     return as
 127   -- TODO add authos
 128
 129   _ <- many $ ignoreAnyTreeContent
 130   return $ PubMedArticle title journal abstracts
 131
 132
 133 pubMedData :: DBL.ByteString
 134 pubMedData = mconcat
 135   [ "<?xml version=\"1.0\"?>\n"
 136   , "<!DOCTYPE PubmedArticleSet PUBLIC \"-//NLM//DTD PubMedArticle, 1st June 2018//EN\" \"https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_180601.dtd\">\n"
 137   , "<PubmedArticleSet>\n"
 138   , "<PubmedArticle>\n"
 139   , " <MedlineCitation Status=\"Publisher\" Owner=\"NLM\">\n"
 140   , "        <PMID Version=\"1\">30357468</PMID>\n"
 141   , "        <DateRevised>\n"
 142   , "           <Year>2018</Year>\n"
 143   , "        </DateRevised>\n"
 144   , "        <Article PubModel=\"Print-Electronic\">\n"
 145   , "          <Journal>\n"
 146   , "            <ISSN IssnType=\"Electronic\">1432-1076</ISSN>\n"
 147   , "            <Title>European journal of pediatrics</Title>\n"
 148   , "          </Journal>\n"
 149   , "          <ArticleTitle>Title of the Article</ArticleTitle>\n"
 150   , "          <ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1007/s00431-018-3270-3</ELocationID>\n"
 151   , "          <Abstract>\n"
 152   , "              <AbstractText>Abstract Text.</AbstractText>\n"
 153   , "          </Abstract>\n"
 154   , "          <AuthorList>\n"
 155   , "          </AuthorList>\n"
 156   , "        </Article>\n"
 157   , " </MedlineCitation>\n"
 158   , " <PubmedData>\n"
 159   , "   <History>\n"
 160   , "   </History>\n"
 161   , " </PubmedData>\n"
 162   , "</PubmedArticle>\n"
 163   , "</PubmedArticleSet>\n"
 164   ]
 165
 166
 167