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src/Gargantext/Text/Parsers/PubMed.hs

-{-|
-Module      : Gargantext.Text.Parsers.PubMed
-Description : Parser for PubMed
-Copyright   : (c) CNRS, 2017-Present
-License     : AGPL + CECILL v3
-Maintainer  : team@gargantext.org
-Stability   : experimental
-Portability : POSIX
-
-This version of Parsers fixes the Date of publication in Gargantext
-(V3) parser of PubMed. Indeed, we can not rely neither on Journal
-Publication Date neither on Article publication date, which are
-incomplete structurally but for its interpretation too. Then, to
-simplify and uniformize data, date of publication of database insertion
-is used.
-
-TODO:
-- Add authors
-- factorize
--}
-
-{-# LANGUAGE OverloadedStrings #-}
-{-# LANGUAGE NoImplicitPrelude #-}
-
-module Gargantext.Text.Parsers.PubMed where
-
-
-import Data.Conduit.List as CL hiding (catMaybes, head)
-import Control.Monad (join)
-import GHC.IO (FilePath)
-import Prelude (read)
-import Gargantext.Prelude
-import Control.Monad.Catch (MonadThrow)
-import Data.Maybe (Maybe)
-import Data.Monoid (mconcat)
-import Text.XML.Stream.Parse
-import Data.Conduit (runConduit, (.|), ConduitT)
-import Data.Text (Text, unpack)
-import Data.XML.Types (Event)
-import Data.Time.Segment (jour)
-import Data.Time (UTCTime(..))
-import qualified Data.ByteString.Lazy as DBL
-import Gargantext.Text.Parsers.Wikimedia
-
-
-data PubMed = 
-     PubMed { pubmed_article :: PubMedArticle
-            , pubmed_date    :: PubMedData
-     } deriving Show
-
-data PubMedArticle =
-     PubMedArticle { pubmed_title   :: Maybe Text
-                   , pubmed_journal :: Maybe Text
-                   , pubmed_abstract :: Maybe [Text]
-                   }
-                   deriving (Show)
-
-data PubMedData =
-     PubMedData { pubmedData_date     :: UTCTime
-                , pubmedData_year     :: Integer
-                , pubmedData_month    :: Int
-                , pubmedData_day      :: Int
-                } deriving (Show)
-
-readPubMedFile :: FilePath -> IO [PubMed]
-readPubMedFile fp = do
-  input <- DBL.readFile fp
-  pubMedParser input
-
-pubMedParser :: DBL.ByteString -> IO [PubMed]
-pubMedParser bstring = runConduit $ parseLBS def bstring
-                                 .| parseArticleSet
-                                 .| CL.consume
-
-parseArticleSet :: MonadThrow m => ConduitT Event PubMed m ()
-parseArticleSet = do
-  as <- force "force" $ tagIgnoreAttrs "PubmedArticleSet" $ manyYield parsePubMedArticle
-  return as
-
-parsePubMedArticle :: MonadThrow m => ConduitT Event o m (Maybe PubMed)
-parsePubMedArticle = do
-  articles <- tagIgnoreAttrs "PubmedArticle" parsePubMedArticle'
-  return articles
-
-parsePubMedArticle' :: MonadThrow m => ConduitT Event o m (PubMed)
-parsePubMedArticle' = do
-  article <- force "MedlineCitation" $ tagIgnoreAttrs "MedlineCitation" parseMedlineCitation
-  dates <- tagIgnoreAttrs "PubmedData" $ do
-    dates' <- tagIgnoreAttrs "History" $ many $ tagIgnoreAttrs "PubMedPubDate" $ do
-      y' <- force "Year"  $ tagIgnoreAttrs "Year"  content
-      m' <- force "Month" $ tagIgnoreAttrs "Month" content
-      d' <- force "Day"   $ tagIgnoreAttrs "Day"   content
-      _ <- many $ ignoreAnyTreeContent
-      return (read $ unpack y', read $ unpack m', read $ unpack d')
-    _ <- many $ ignoreAnyTreeContent
-    return dates'
-  _ <- many $ ignoreAnyTreeContent
-  let (y,m,d) = maybe (1,1,1) identity $ join $ fmap head $ reverse <$> join dates
-  return $ PubMed (article) (PubMedData (jour y m d) y m d)
-
-parseMedlineCitation :: MonadThrow m => ConduitT Event o m PubMedArticle
-parseMedlineCitation = do
-  a <- force "article" $ manyTagsUntil "Article" parseArticle
-  _ <- many $ ignoreAnyTreeContent
-  return a
-
-parseArticle :: MonadThrow m => ConduitT Event o m PubMedArticle
-parseArticle = do
-  journal  <- force "journal" $ manyTagsUntil "Journal" $ do
-    j <- manyTagsUntil "Title" content
-    _ <- many $ ignoreAnyTreeContent
-    return j
-  
-  title    <- do
-    t <- manyTagsUntil "ArticleTitle" content
-    return t
-  
-  abstracts <- do
-    as <- manyTagsUntil "Abstract" $ many $ do
-      txt <- tagIgnoreAttrs "AbstractText" $ do
-        c <- content
-        _ <- many $ ignoreAnyTreeContent
-        return c
-      _ <- many $ ignoreAnyTreeContent
-      return txt
-    return as
-  -- TODO add authos
-
-  _ <- many $ ignoreAnyTreeContent
-  return $ PubMedArticle title journal abstracts
-
-
-pubMedData :: DBL.ByteString
-pubMedData = mconcat
-  [ "<?xml version=\"1.0\"?>\n"
-  , "<!DOCTYPE PubmedArticleSet PUBLIC \"-//NLM//DTD PubMedArticle, 1st June 2018//EN\" \"https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_180601.dtd\">\n"
-  , "<PubmedArticleSet>\n"
-  , "<PubmedArticle>\n"
-  , " <MedlineCitation Status=\"Publisher\" Owner=\"NLM\">\n"
-  , "        <PMID Version=\"1\">30357468</PMID>\n"
-  , "        <DateRevised>\n"
-  , "           <Year>2018</Year>\n"
-  , "        </DateRevised>\n"
-  , "        <Article PubModel=\"Print-Electronic\">\n"
-  , "          <Journal>\n"
-  , "            <ISSN IssnType=\"Electronic\">1432-1076</ISSN>\n"
-  , "            <Title>European journal of pediatrics</Title>\n"
-  , "          </Journal>\n"
-  , "          <ArticleTitle>Title of the Article</ArticleTitle>\n"
-  , "          <ELocationID EIdType=\"doi\" ValidYN=\"Y\">10.1007/s00431-018-3270-3</ELocationID>\n"
-  , "          <Abstract>\n"
-  , "              <AbstractText>Abstract Text.</AbstractText>\n"
-  , "          </Abstract>\n"
-  , "          <AuthorList>\n"
-  , "          </AuthorList>\n"
-  , "        </Article>\n"
-  , " </MedlineCitation>\n"
-  , " <PubmedData>\n"
-  , "   <History>\n"
-  , "   </History>\n"
-  , " </PubmedData>\n"
-  , "</PubmedArticle>\n"
-  , "</PubmedArticleSet>\n"
-  ]
-
-
-

stack.yaml

@@ -6,7 +6,6 @@ packages:
 - 'deps/servant-job'
 - 'deps/clustering-louvain'
 - 'deps/patches-map'
-- 'deps/patches-class'
 - 'deps/haskell-opaleye'
 - 'deps/hsparql'
 
@@ -27,7 +26,9 @@ extra-deps:
   commit: 4fd2edf30c141600ffad6d730cc4c1c08a6dbce4
 - git: https://gitlab.iscpif.fr/gargantext/crawlers/pubmed
   commit: dcaa0f5dd53f20648f4f5a615d29163582a4219c
-#- opaleye-0.6.7002.0
+- git: https://gitlab.iscpif.fr/gargantext/patches-class
+  commit: 746b4ce0af8f9e600d555ad7e5b2973a940cdad9
+    #- opaleye-0.6.7002.0
 - KMP-0.1.0.2
 - accelerate-1.2.0.0
 - aeson-lens-0.5.0.0