Merge branch 'abstract-parser-fix' of ssh://gitlab.iscpif.fr:20022/cgenie/pubmed

app/Main.hs

@@ -4,4 +4,4 @@ import PUBMED (getMetadataWith)
 
 
 main :: IO ()
-main = getMetadataWith "bisphenol" (Just 100) >>= print
+main = getMetadataWith "bisphenol" Nothing (Just 100) >>= print

crawlerPubMed.cabal

@@ -28,6 +28,7 @@ library
       PUBMED
       PUBMED.Client
       PUBMED.Parser
+      PUBMED.Test
   other-modules:
       Paths_crawlerPubMed
   hs-source-dirs:
@@ -46,6 +47,7 @@ library
     , data-time-segment
     , either
     , exceptions
+    , ghc
     , http-client
     , http-client-tls
     , http-media
@@ -78,6 +80,7 @@ executable crawlerPubMed-exe
     , data-time-segment
     , either
     , exceptions
+    , ghc
     , http-client
     , http-client-tls
     , http-media
@@ -113,6 +116,7 @@ test-suite crawlerPubMed-test
     , data-time-segment
     , either
     , exceptions
+    , ghc
     , http-client
     , http-client-tls
     , http-media

package.yaml

@@ -33,6 +33,7 @@ dependencies:
 - data-time-segment
 - either
 - exceptions
+- ghc
 - http-client
 - http-client-tls
 - http-media

src/PUBMED.hs

 module PUBMED where
 
+import Conduit
 import Control.Applicative
 import Data.Attoparsec.ByteString
 import Data.Attoparsec.ByteString.Char8 (anyChar)
 import Data.ByteString.Char8 (pack)
 import Data.ByteString.Lazy (ByteString)
+import Data.Maybe (fromMaybe)
 import Data.Text (Text)
 import Network.HTTP.Client (newManager)
 import Network.HTTP.Client.TLS (tlsManagerSettings)
 import PUBMED.Client
 import PUBMED.Parser
 import Prelude hiding (takeWhile)
-import Servant.Client (runClientM, mkClientEnv, BaseUrl(..), Scheme(..))
+import Servant.Client (runClientM, mkClientEnv, BaseUrl(..), ClientEnv, ClientError, Scheme(..))
 import qualified Data.ByteString.Lazy as LBS
 import qualified Data.List as List
 import qualified Data.Text as T
@@ -25,14 +27,43 @@ pmSearchPath = "entrez/eutils"
 pmPort :: Int
 pmPort = 443
 
+batchSize :: Int
+batchSize = 2000
+
+defaultEnv :: IO ClientEnv
 defaultEnv = do
   manager' <- newManager tlsManagerSettings
   pure $ mkClientEnv manager' $ BaseUrl Https pmHost pmPort pmSearchPath
 
 -- | API main function
-getMetadataWith :: Text -> Maybe Limit -> IO (Either Text [PubMed])
+getMetadataWith :: Text -> Maybe Integer -> Maybe Limit -> IO (Either Text [PubMed])
 getMetadataWith = runSimpleFindPubmedAbstractRequest
 
+getMetadataWithC :: Text -> Maybe Limit -> IO (Either ClientError (Maybe Integer, ConduitT () PubMed IO ()))
+getMetadataWithC query limit = do
+  env <- defaultEnv
+  -- First, estimate the total number of documents
+  eRes <- runClientM (search (Just query) Nothing (Just 1)) env
+  pure $ get' env query limit batchSize <$> eRes
+  where
+    get' :: ClientEnv -> Text -> Maybe Limit -> Int -> BsXml -> (Maybe Integer, ConduitT () PubMed IO ())
+    get' env q l perPage (BsXml res) =
+      ( Just numResults
+      , yieldMany [0..]
+        .| takeC (fromInteger numPages)
+        .| concatMapMC (getPage env q perPage))
+      where
+        numResults = fromMaybe 0 $ parseDocCount $ TL.fromStrict $ TE.decodeUtf8 $ LBS.toStrict res
+        numPages = numResults `div` (fromIntegral perPage) + 1
+
+    getPage :: ClientEnv -> Text -> Int -> Int -> IO [PubMed]
+    getPage env q perPage pageNum = do
+      let offset = fromIntegral $ pageNum * perPage
+      eDocs <- runSimpleFindPubmedAbstractRequest q (Just offset) (Just $ fromIntegral pageNum)
+      pure $ case eDocs of
+        Left err -> []
+        Right docs -> docs
+  
 -- | TODO this parser need at least one subs at the end
 -- (use endOfInput)
 removeSub :: Parser ByteString
@@ -57,6 +88,7 @@ type Limit = Integer
 
 runMultipleFPAR :: [Integer]
                 -> IO (Either Text [PubMed])
+runMultipleFPAR [] = pure $ Right []
 runMultipleFPAR ids = List.foldl1' concat'
                    <$> mapM runSimpleFetchPubmedAbstractRequest (by 300 ids)
   where
@@ -90,18 +122,18 @@ runSimpleFetchPubmedAbstractRequest ids = do
 --                                                pure []) :: XmlException -> IO [PubMed])
 --          Right <$> pure parsed
 
-runSimpleFindPubmedAbstractRequest :: Text -> Maybe Limit -> IO (Either Text [PubMed])
-runSimpleFindPubmedAbstractRequest query limit =  do
-  eDocIds <- searchDocIds query limit
+runSimpleFindPubmedAbstractRequest :: Text -> Maybe Integer -> Maybe Limit -> IO (Either Text [PubMed])
+runSimpleFindPubmedAbstractRequest query offset limit =  do
+  eDocIds <- searchDocIds query offset limit
   case eDocIds of
     Left err -> pure $ Left err
     Right docIds -> runMultipleFPAR docIds
 
-searchDocIds :: Text -> Maybe Limit -> IO (Either Text [Integer])
-searchDocIds query limit = do
+searchDocIds :: Text -> Maybe Integer -> Maybe Limit -> IO (Either Text [Integer])
+searchDocIds query offset limit = do
   env <- defaultEnv
   res <- runClientM
-    (search (Just query) limit)
+    (search (Just query) offset limit)
     env
   case res of
     (Left err) -> pure (Left $ T.pack $ show err)

src/PUBMED/Client.hs

@@ -23,6 +23,7 @@ type PUBMEDAPI =
 --  :> QueryParam "db" DB
 -- not mandatory since the base db is pubmed
   :> QueryParam "term" T.Text
+  :> QueryParam "retstart" Integer
   :> QueryParam "retmax" Integer
   :> Get '[BsXml] BsXml
   :<|>
@@ -35,7 +36,7 @@ type PUBMEDAPI =
 pubmedApi :: Proxy PUBMEDAPI
 pubmedApi = Proxy
 
-search :: Maybe T.Text -> Maybe Integer -> ClientM BsXml
+search :: Maybe T.Text -> Maybe Integer -> Maybe Integer -> ClientM BsXml
 
 fetch :: Maybe T.Text
   -> Maybe T.Text

src/PUBMED/Parser.hs

@@ -2,8 +2,8 @@
 
 module PUBMED.Parser where
 
-import Control.Lens ((^?), (^.), (^..), only, to, ix, prism', Prism')
-import Data.Maybe (catMaybes)
+import Control.Lens ((^?), (^.), (^..), only, to, ix, prism', Prism', Traversal')
+import Data.Maybe (catMaybes, fromMaybe)
 import Data.Time (UTCTime(..))
 import Data.Time.Segment (jour)
 import Prelude hiding (head)
@@ -12,6 +12,8 @@ import qualified Data.ByteString.Lazy as DBL
 import qualified Data.Text as T
 import qualified Data.Text.Lazy as TL
 import qualified Data.Text.Lazy.IO as TLIO
+import Panic (panic)
+import qualified Text.Read as TR
 import qualified Text.Taggy.Lens as TTL
 
 namedEl name = TTL.elements . TTL.named (only name) 
@@ -23,12 +25,19 @@ contentWithChildren = prism' NodeContent $ \case { NodeContent c -> Just c
 deepContent = TTL.children . traverse . contentWithChildren
 
 parseDocIds :: TL.Text -> [Integer]
-parseDocIds txt = map (\s -> read (T.unpack s) :: Integer) parsed
+parseDocIds txt = map parseId parsed
   where
     parsed = txt ^.. TTL.html . TTL.allNamed (only "eSearchResult") . namedEl "IdList" . namedEl "Id" . TTL.contents
+    parseId s = case (TR.readMaybe (T.unpack s) :: Maybe Integer) of
+      Nothing -> panic $ "Can't read doc id from: " <> (T.unpack s)
+      Just cnt -> cnt
+
+parseDocCount :: TL.Text -> Maybe Integer
+parseDocCount txt = TR.readMaybe $ T.unpack $ txt ^. TTL.html . TTL.allNamed (only "eSearchResult") . namedEl "Count" . TTL.contents
 
 data PubMed =
-     PubMed { pubmed_article :: PubMedArticle
+  PubMed { pubmed_id      :: Int
+         , pubmed_article :: PubMedArticle
          , pubmed_date    :: PubMedDate
          } deriving Show
 
@@ -63,19 +72,26 @@ parsePubMed :: TL.Text -> [PubMed]
 parsePubMed txt = catMaybes $ txt ^.. pubmedArticle . to pubMed
   where
     pubmedArticle = TTL.html . TTL.allNamed (only "PubmedArticleSet") . TTL.allNamed (only "PubmedArticle")
-    pubMed el = PubMed <$> el ^? article . to pubMedArticle
+    pubMed el = PubMed <$> el ^? articleId . to pubMedId
+                       <*> el ^? article . to pubMedArticle
                        <*> el ^? pubDate . to pubMedDate
       where
-        article = namedEl "MedlineCitation" . namedEl "Article"
+        medline :: Traversal' TTL.Element TTL.Element
+        medline = namedEl "MedlineCitation"
+        article = medline . namedEl "Article"
+        articleId = medline . namedEl "PMID"
         pubDate = namedEl "PubmedData" . namedEl "History" . namedEl "PubMedPubDate" . TTL.attributed (ix "PubStatus" . only "pubmed")
+    pubMedId el = case (TR.readMaybe $ T.unpack $ el ^. TTL.contents) of
+      Nothing -> panic $ "Cannot parse id: " <> (T.unpack $ el ^. TTL.contents)
+      Just id -> id
     pubMedDate el = PubMedDate { pubmedDate_date = jour y m d
                                , pubmedDate_year = y
                                , pubmedDate_month = m
                                , pubmedDate_day = d }
       where
-        y = read $ T.unpack $ el ^. namedEl "Year" . TTL.contents
-        m = read $ T.unpack $ el ^. namedEl "Month" . TTL.contents
-        d = read $ T.unpack $ el ^. namedEl "Day" . TTL.contents
+        y = fromMaybe 1 $ TR.readMaybe $ T.unpack $ el ^. namedEl "Year" . TTL.contents
+        m = fromMaybe 1 $ TR.readMaybe $ T.unpack $ el ^. namedEl "Month" . TTL.contents
+        d = fromMaybe 1 $ TR.readMaybe $ T.unpack $ el ^. namedEl "Day" . TTL.contents
     pubMedArticle el = PubMedArticle { pubmed_title = Just $ el ^. title
                                      , pubmed_journal = el ^? journalTitle
                                      , pubmed_abstract = el ^.. abstract