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
  11 -}
  12
  13 {-# LANGUAGE OverloadedStrings #-}
  14 {-# LANGUAGE NoImplicitPrelude #-}
  15
  16 module Gargantext.Text.Parsers.PubMed where
  17
  18
  19
  20 import Control.Monad (void)
  21 import Data.Conduit.List as CL hiding (catMaybes)
  22 import Control.Monad (join)
  23 import GHC.IO (FilePath)
  24 import Prelude (read, print)
  25 import Gargantext.Prelude
  26 import Control.Applicative ((<*))
  27 import Control.Monad.Catch (MonadThrow)
  28 import Data.Maybe (Maybe, catMaybes)
  29 import Data.Monoid (mconcat)
  30 import Text.XML.Stream.Parse
  31 import Data.Conduit (runConduit, (.|), ConduitT)
  32 import Data.Text (Text, unpack, concat)
  33 import Data.XML.Types (Event)
  34 import Data.ByteString (ByteString)
  35 import Data.Time.Segment (jour)
  36 import Data.Time (UTCTime(..))
  37 import qualified Data.ByteString.Lazy as DBL
  38 import Gargantext.Text.Parsers.Wikimedia
  39
  40
  41 data PubMedArticle =
  42      PubMedArticle { pubmed_title   :: Maybe Text
  43                    , pubmed_journal :: Maybe Text
  44                    , pubmed_abstract :: Maybe [Text]
  45                    , pubmed_date     :: UTCTime
  46                    , pubmed_year     :: Integer
  47                    , pubmed_month    :: Int
  48                    , pubmed_day      :: Int
  49                    }
  50      deriving (Show)
  51
  52 readPubMedFile :: FilePath -> IO ()
  53 readPubMedFile fp = do
  54   input <- DBL.readFile fp
  55   pubMedParser input
  56
  57
  58 pubMedParser :: DBL.ByteString -> IO ()
  59 pubMedParser bstring = runConduit $ parseLBS def bstring
  60                                  .| parseArticleSet
  61                                  .| CL.mapM_ print
  62
  63 --parseArticleSet :: MonadThrow m => ConduitT Event o m [PubMedArticle]
  64 parseArticleSet = do
  65   as <- force "force" $ tagIgnoreAttrs "PubmedArticleSet" $ manyYield parsePubMedArticle
  66   -- _ <- many $ ignoreAnyTreeContent
  67   return as
  68
  69 parsePubMedArticle :: MonadThrow m => ConduitT Event o m (Maybe PubMedArticle)
  70 parsePubMedArticle = do
  71   articles <- force "PubmedArticle" $ tagIgnoreAttrs "PubmedArticle" parsePubMedArticle'
  72   --_ <- many $ ignoreAnyTreeContent
  73   return articles
  74
  75 parsePubMedArticle' :: MonadThrow m => ConduitT Event o m (Maybe PubMedArticle)
  76 parsePubMedArticle' = do
  77   pubmed_article <- tagIgnoreAttrs "MedlineCitation" parseMedlineCitation
  78   --_ <- tagIgnoreAttrs "PubmedData" content
  79   _ <- many $ ignoreAnyTreeContent
  80   return pubmed_article
  81
  82 parseMedlineCitation :: MonadThrow m => ConduitT Event o m PubMedArticle
  83 parseMedlineCitation = do
  84   a <- force "article" $ manyTagsUntil "Article" parseArticle
  85   _ <- many $ ignoreAnyTreeContent
  86   return a
  87
  88 parseArticle :: MonadThrow m => ConduitT Event o m PubMedArticle
  89 parseArticle = do
  90   (journal,maybePubDate)  <- force "journal" $ manyTagsUntil "Journal" $ do
  91     maybePubDate' <- manyTagsUntil "JournalIssue" $ do
  92       maybePubDate'' <- manyTagsUntil "PubDate" $ do
  93         y <- tagIgnoreAttrs "Year"  content
  94         m <- tagIgnoreAttrs "Month" content
  95         d <- tagIgnoreAttrs "Day"   content
  96         return (y, m, d)
  97       return maybePubDate''
  98
  99     j <- manyTagsUntil "Title" content
 100     _ <- many $ ignoreAnyTreeContent
 101     return (j,join maybePubDate')
 102
 103   title    <- do
 104     t <- manyTagsUntil "ArticleTitle" content
 105     return t
 106
 107   abstracts <- do
 108     as <- manyTagsUntil "Abstract" $ many $ do
 109       txt <- tagIgnoreAttrs "AbstractText" $ do
 110         c <- content
 111         _ <- many $ ignoreAnyTreeContent
 112         return c
 113       _ <- many $ ignoreAnyTreeContent
 114       return txt
 115     return as
 116   -- TODO add authos
 117
 118   (year, month, day) <- case maybePubDate of
 119     Nothing -> force "ArticleDate" $ manyTagsUntil "ArticleDate" $ do
 120       y <- force "Year"  $ tagIgnoreAttrs "Year"  content
 121       m <- force "Month" $ tagIgnoreAttrs "Month" content
 122       d <- force "Day"   $ tagIgnoreAttrs "Day"   content
 123       return (read $ unpack y, read $ unpack m, read $ unpack d)
 124     Just (Just y, Just m, Just d)  -> return (read $ unpack "1", read $ unpack "3", read $ unpack "3")
 125     _ -> panic "error date"
 126
 127   _ <- many $ ignoreAnyTreeContent
 128   return $ PubMedArticle title journal abstracts (jour year month day) year month day
 129
 130
 131 pubMedData :: DBL.ByteString
 132 pubMedData = mconcat
 133   [ "<?xml version=\"1.0\"?>\n"
 134   , "<!DOCTYPE PubmedArticleSet PUBLIC \"-//NLM//DTD PubMedArticle, 1st June 2018//EN\" \"https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_180601.dtd\">\n"
 135   , "<PubmedArticleSet>\n"
 136   , "<PubmedArticle>\n"
 137   , " <MedlineCitation Status=\"Publisher\" Owner=\"NLM\">\n"
 138   , "        <PMID Version=\"1\">30357468</PMID>\n"
 139   , "        <DateRevised>\n"
 140   , "           <Year>2018</Year>\n"
 141   , "        </DateRevised>\n"
 142   , "        <Article PubModel=\"Print-Electronic\">\n"
 143   , "          <Journal>\n"
 144   , "            <ISSN IssnType=\"Electronic\">1432-1076</ISSN>\n"
 145   , "            <Title>European journal of pediatrics</Title>\n"
 146   , "          </Journal>\n"
 147   , "          <ArticleTitle>Title of the Article</ArticleTitle>\n"
 148   , "          <ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1007/s00431-018-3270-3</ELocationID>\n"
 149   , "          <Abstract>\n"
 150   , "              <AbstractText>Abstract Text.</AbstractText>\n"
 151   , "          </Abstract>\n"
 152   , "          <AuthorList>\n"
 153   , "          </AuthorList>\n"
 154   , "        </Article>\n"
 155   , " </MedlineCitation>\n"
 156   , " <PubmedData>\n"
 157   , "   <History>\n"
 158   , "   </History>\n"
 159   , " </PubmedData>\n"
 160   , "</PubmedArticle>\n"
 161   , "</PubmedArticleSet>\n"
 162   ]
 163
 164
 165