Support Istex

gargantext.cabal

@@ -85,8 +85,9 @@ library
       Gargantext.Core.Text.Corpus.API.Arxiv
       Gargantext.Core.Text.Corpus.API.EPO
       Gargantext.Core.Text.Corpus.API.Isidore
-      Gargantext.Core.Text.Corpus.API.Pubmed
+      Gargantext.Core.Text.Corpus.API.Istex
       Gargantext.Core.Text.Corpus.API.OpenAlex
+      Gargantext.Core.Text.Corpus.API.Pubmed
       Gargantext.Core.Text.Corpus.Query
       Gargantext.Core.Text.Corpus.Parsers
       Gargantext.Core.Text.Corpus.Parsers.CSV
@@ -230,7 +231,6 @@ library
       Gargantext.Core.Statistics
       Gargantext.Core.Text.Convert
       Gargantext.Core.Text.Corpus.API.Hal
-      Gargantext.Core.Text.Corpus.API.Istex
       Gargantext.Core.Text.Corpus.Parsers.Book
       Gargantext.Core.Text.Corpus.Parsers.Date.Attoparsec
       Gargantext.Core.Text.Corpus.Parsers.FrameWrite

src/Gargantext/Core/Text/Corpus/API.hs

@@ -63,17 +63,18 @@ get externalAPI la q mPubmedAPIKey epoAuthKey epoAPIUrl limit = do
       OpenAlex ->
         first ExternalAPIError <$> OpenAlex.get (fromMaybe "" Nothing {- email -}) q (toISO639 la) limit
       Arxiv    -> runExceptT $ do
-        corpusQuery <- ExceptT (pure parse_query)
-        ExceptT $ fmap Right (Arxiv.get la corpusQuery limit)
+        corpusQuery <- parse_query
+        ExceptT $ first ExternalAPIError <$> (Arxiv.get la corpusQuery limit)
       HAL      ->
         first ExternalAPIError <$> HAL.getC (toISO639 la) (Corpus.getRawQuery q) (Corpus.getLimit <$> limit)
-      IsTex   -> do
-        docs <- ISTEX.get la (Corpus.getRawQuery q) (Corpus.getLimit <$> limit)
-        pure $ Right (Just $ fromIntegral $ length docs, yieldMany docs)
+      IsTex   -> runExceptT $ do
+        corpusQuery <- parse_query
+        ExceptT $ first ExternalAPIError <$> ISTEX.get la corpusQuery limit
       Isidore -> runExceptT $ do
-        corpusQuery <- ExceptT (pure parse_query)
+        corpusQuery <- parse_query
         ExceptT $ first ExternalAPIError <$> ISIDORE.get la limit corpusQuery Nothing
       EPO -> do
         first ExternalAPIError <$> EPO.get epoAuthKey epoAPIUrl q (toISO639EN la) limit
   where
-    parse_query = first (InvalidInputQuery q . T.pack) $ Corpus.parseQuery q
+    parse_query :: ExceptT GetCorpusError IO Corpus.Query
+    parse_query = ExceptT $ pure $ first (InvalidInputQuery q . T.pack) $ Corpus.parseQuery q

src/Gargantext/Core/Text/Corpus/API/Arxiv.hs

@@ -20,6 +20,8 @@ module Gargantext.Core.Text.Corpus.API.Arxiv
 
 import Arxiv qualified as Arxiv
 import Conduit
+import Data.Either
+import Data.Maybe
 import Data.Text (unpack)
 import Data.Text qualified as Text
 import Gargantext.Core (Lang(..))
@@ -28,7 +30,7 @@ import Gargantext.Core.Types (Term(..))
 import Gargantext.Database.Admin.Types.Hyperdata (HyperdataDocument(..))
 import Gargantext.Prelude hiding (get)
 import Network.Api.Arxiv qualified as Ax
-
+import Servant.Client (ClientError)
 
 -- | Converts a Gargantext's generic boolean query into an Arxiv Query.
 convertQuery :: Corpus.Query -> Ax.Query
@@ -75,13 +77,13 @@ convertQuery q = mkQuery (interpretQuery q transformAST)
 get :: Lang
     -> Corpus.Query
     -> Maybe Corpus.Limit
-    -> IO (Maybe Integer, ConduitT () HyperdataDocument IO ())
+    -> IO (Either ClientError (Maybe Integer, ConduitT () HyperdataDocument IO ()))
 get la (convertQuery -> query) (fmap getLimit -> limit) = do
   (cnt, resC) <- case limit of
     Nothing  -> Arxiv.searchAxv' query
     (Just l) -> do (cnt, res) <- Arxiv.searchAxv' query
                    pure (cnt, res .| takeC l)
-  pure $ (Just $ fromIntegral cnt, resC .| mapC (toDoc la))
+  pure $ Right $ (Just $ fromIntegral cnt, resC .| mapC (toDoc la))
 
 toDoc :: Lang -> Arxiv.Result -> HyperdataDocument
 toDoc l (Arxiv.Result { abstract

src/Gargantext/Core/Text/Corpus/API/Isidore.hs

@@ -46,7 +46,7 @@ newtype IsidoreQuery = IsidoreQuery { _IsidoreQuery :: [EscapeItem] }
   deriving stock (Show, Eq)
   deriving newtype (Semigroup, Monoid)
 
--- | Returns an /url encoded/ query ready to be sent to pubmed.
+-- | Returns an /url encoded/ query ready to be sent to Isidore.
 getIsidoreQuery :: IsidoreQuery -> Text
 getIsidoreQuery (IsidoreQuery items) =
   Text.replace "q=" "" . TE.decodeUtf8 . renderQueryPartialEscape False $ [

src/Gargantext/Core/Text/Corpus/API/Istex.hs

@@ -9,24 +9,94 @@ Portability : POSIX
 
 -}
 
+{-# LANGUAGE DerivingStrategies #-}
+{-# LANGUAGE ViewPatterns       #-}
+
 
 module Gargantext.Core.Text.Corpus.API.Istex
+    ( get
+
+      -- * Internal API for testing
+    , getIstexQuery
+    , IstexQuery(..)
+    , convertQuery
+    )
     where
 
-import Data.List qualified as List
+import Data.ByteString.Char8 qualified as C8
+import Data.Conduit
+import Data.Conduit.Combinators (yieldMany)
+import Data.Maybe
+import Data.Monoid
+import Data.Semigroup
 import Data.Text qualified as Text
+import Data.Text.Encoding qualified as TE
 import Gargantext.Core (Lang(..))
 import Gargantext.Core.Text.Corpus.Parsers.JSON.Istex (toDoc)
+import Gargantext.Core.Text.Corpus.Query as Corpus
+import Gargantext.Core.Types (Term(..))
 import Gargantext.Database.Admin.Types.Hyperdata (HyperdataDocument(..))
-import Gargantext.Prelude
+import Gargantext.Prelude hiding (get)
 import ISTEX qualified as ISTEX
 import ISTEX.Client qualified as ISTEX
+import Network.HTTP.Types.URI (EscapeItem(..), renderQueryPartialEscape)
+import Servant.Client
+
+languageToQuery :: Lang -> C8.ByteString
+languageToQuery la =
+  "language:" <> case la of
+    FR -> "fre"
+    _  -> "eng" -- FIXME -- we should support all the languages.
+
+newtype IstexQuery = IstexQuery { _IstexQuery :: [EscapeItem] }
+  deriving stock (Show, Eq)
+  deriving newtype (Semigroup, Monoid)
+
+-- | Returns an /url encoded/ query ready to be sent to Istex.
+getIstexQuery :: Lang -> IstexQuery -> Text
+getIstexQuery lang (IstexQuery items) =
+  Text.replace "q=" "" . TE.decodeUtf8 . renderQueryPartialEscape False $ [
+    ("q", langItems <> items)
+    ]
+  where
+    langItems :: [EscapeItem]
+    langItems = [QN (languageToQuery lang), QN "+AND+"]
 
-type Query = Text
-type MaxResults = Maybe Int
+convertQuery :: Corpus.Query -> IstexQuery
+convertQuery q = IstexQuery (interpretQuery q transformAST)
+  where
+    transformAST :: BoolExpr Term -> [EscapeItem]
+    transformAST ast = case ast of
+      BAnd sub (BConst (Negative term))
+        -- The second term become positive, so that it can be translated.
+        -> (transformAST sub) <> [QN "+AND+NOT+"] <> transformAST (BConst (Positive term))
+      BAnd term1 (BNot term2)
+        -> transformAST term1 <> [QN "+AND+NOT+"] <> transformAST term2
+      BAnd sub1 sub2
+        -> transformAST sub1 <> [QN "+AND+"] <> transformAST sub2
+      BOr sub1 sub2
+        -> transformAST sub1 <> [QN "+OR+"] <> transformAST sub2
+      BNot (BConst (Negative term))
+        -> transformAST (BConst (Positive term)) -- double negation
+      BNot sub
+        -> [QN "NOT+"] <> transformAST sub
+      -- BTrue cannot happen is the query parser doesn't support parsing 'TRUE' alone.
+      BTrue
+        -> mempty
+      -- BTrue cannot happen is the query parser doesn't support parsing 'FALSE' alone.
+      BFalse
+        -> mempty
+      -- Maps the positive terms to contain 'abstract:'
+      BConst (Positive (Term term))
+        -> [QN "abstract:", QE (TE.encodeUtf8 term)]
+      BConst (Negative sub)
+        -> [QN "NOT+"] <> transformAST (BConst (Positive sub))
 
-get :: Lang -> Query -> MaxResults -> IO [HyperdataDocument]
-get la query' maxResults = do
+get :: Lang
+    -> Corpus.Query
+    -> Maybe Corpus.Limit
+    -> IO (Either ClientError (Maybe Integer, ConduitT () HyperdataDocument IO ()))
+get la (convertQuery -> query) maxResults = do
   --printDebug "[Istex.get] calling getMetadataScrollProgress for la" la
   --printDebug "[Istex.get] calling getMetadataScrollProgress for q" q
   --printDebug "[Istex.get] calling getMetadataScrollProgress for ml" ml
@@ -36,30 +106,15 @@ get la query' maxResults = do
   -- TODO check if abstract is in query already if not add like below
   -- eDocs <- ISTEX.getMetadataScroll (q <> " abstract:*")  "1m" Nothing 0  --(fromIntegral <$> ml)
   -- eDocs <- ISTEX.getMetadataScroll q "1m" Nothing 0  --(fromIntegral <$> ml)
-
-  let query = case (List.length $ Text.splitOn ":" query') == 1 of
-        -- True case means users is entering default search of IsTex
-        -- In that case we need to enrich his query with 2 parameters
-        -- First expected language: user has to define it in GTXT
-        -- Second : query in abstract
-        True  -> ("language:"<> lang la) <> " AND abstract:"<>query'
-            where
-              lang FR = "fre"
-              lang _  = "eng"
-
-        False -> query'
-        -- Complex queries of IsTex needs parameters using ":" so we leave the query as it is
-        -- in that case we suppose user is knowing what s.he is doing
-
-  eDocs <- ISTEX.getMetadataWith query maxResults
+  eDocs <- ISTEX.getMetadataWith (getIstexQuery la query) (getLimit <$> maxResults)
   -- printDebug "[Istex.get] will print length" (0 :: Int)
   case eDocs of
-    Left _ -> pure ()
-    Right (ISTEX.Documents { _documents_hits }) -> printDebug "[Istex.get] length docs" $ length _documents_hits
+    Left err -> pure $ Left err
+    Right docs@(ISTEX.Documents { _documents_hits }) -> do
+      printDebug "[Istex.get] length docs" $ length _documents_hits
   --ISTEX.getMetadataScrollProgress q ((\_ -> pack $ "1m") <$> ml) Nothing progress errorHandler
-  case eDocs of
-    Left err -> panic . Text.pack . show $ err
-    Right docs -> toDoc' la docs
+      docs' <- toDoc' la docs
+      pure $ Right (Just $ fromIntegral $ length docs', yieldMany docs')
   --pure $ either (panic . pack . show) (toDoc' la) eDocs
 --  where
 --    progress (ISTEX.ScrollResponse { _scroll_documents = ISTEX.Documents { _documents_hits }}) =

test/Test/Core/Text/Corpus/Query.hs

@@ -18,6 +18,7 @@ import qualified Data.Text as T
 import qualified Gargantext.Core.Text.Corpus.API.Arxiv as Arxiv
 import qualified Gargantext.Core.Text.Corpus.API.Pubmed as Pubmed
 import qualified Gargantext.Core.Text.Corpus.API.Isidore as Isidore
+import qualified Gargantext.Core.Text.Corpus.API.Istex   as Istex
 import qualified Network.Api.Arxiv as Arxiv
 
 import Test.Tasty
@@ -77,6 +78,14 @@ tests = withResource pubmedSettings (const (pure ())) $ \getPubmedKey ->
     , testCase "It supports '\"Haskell\" AND \"Idris\"'" testIsidore03
     , testCase "It supports 'A OR B'" testIsidore04
     ]
+  , testGroup "Istex expression converter" [
+      testCase "It supports 'A'" testIstex01
+    , testCase "It supports '-A'" testIstex02_01
+    , testCase "It supports 'NOT A'" testIstex02_02
+    , testCase "It supports 'NOT (NOT A)'" testIstex02_03
+    , testCase "It supports '\"Haskell\" AND \"Idris\"'" testIstex03
+    , testCase "It supports 'A OR B'" testIstex04
+    ]
   , testGroup "PUBMED real queries (skipped if PUBMED_API_KEY env var not set)" [
       testCase "It searches for \"Covid\"" (testPubMedCovid_01 getPubmedKey)
     , testCase "It searches for \"Covid\" AND \"Alzheimer\"" (testPubMedCovid_02 getPubmedKey)
@@ -92,6 +101,11 @@ tests = withResource pubmedSettings (const (pure ())) $ \getPubmedKey ->
       testCase "It searches for \"chicken pox\"" (testIsidoreRealWorld_01 getPubmedKey)
     , testCase "It searches for \"Dante\" AND \"Petrarca\"" (testIsidoreRealWorld_02 getPubmedKey)
     ]
+  -- .. ditto for Istex
+  , testGroup "Istex real queries (skipped if PUBMED_API_KEY env var not set)" [
+      testCase "It searches for \"brain\"" (testIstexRealWorld_01 getPubmedKey)
+    , testCase "It searches for \"brain\" AND NOT \"neural\"" (testIstexRealWorld_02 getPubmedKey)
+    ]
   ]
 
 -- | Checks that the 'RawQuery' can be translated into the expected 'BoolExpr' form,
@@ -286,6 +300,32 @@ testIsidore04 :: Assertion
 testIsidore04 = withValidQuery "A OR B" $ \q ->
   Isidore.getIsidoreQuery (Isidore.convertQuery q) @?= "A+OR+B"
 
+--
+-- Istex tests
+--
+
+testIstex01 :: Assertion
+testIstex01 = withValidQuery "A" $ \q ->
+  assertBool ("Query not converted into expression: " <> show @(BoolExpr Term) (fromCNF $ getQuery q))
+             (Istex.getIstexQuery EN (Istex.convertQuery q) == "language:eng+AND+abstract:A")
+
+testIstex02_01 :: Assertion
+testIstex02_01 = withValidQuery "-A" $ \q -> Istex.getIstexQuery EN (Istex.convertQuery q) @?= "language:eng+AND+NOT+abstract:A"
+
+testIstex02_02 :: Assertion
+testIstex02_02 = withValidQuery "NOT A" $ \q -> Istex.getIstexQuery EN (Istex.convertQuery q) @?= "language:eng+AND+NOT+abstract:A"
+
+testIstex02_03 :: Assertion
+testIstex02_03 = withValidQuery "NOT (NOT A)" $ \q -> Istex.getIstexQuery EN (Istex.convertQuery q) @?= "language:eng+AND+abstract:A"
+
+testIstex03 :: Assertion
+testIstex03 = withValidQuery "\"Haskell\" AND \"Idris\"" $ \q ->
+  Istex.getIstexQuery FR (Istex.convertQuery q) @?= "language:fre+AND+abstract:Haskell+AND+abstract:Idris"
+
+testIstex04 :: Assertion
+testIstex04 = withValidQuery "A OR B" $ \q ->
+  Istex.getIstexQuery EN (Istex.convertQuery q) @?= "language:eng+AND+abstract:A+OR+abstract:B"
+
 --
 -- Integration tests against the real services
 --
@@ -327,7 +367,10 @@ testArxivRealWorld_01 getPubmedKey = do
   case mb_key of
     Nothing -> pure ()
     Just _  -> withValidQuery "\"Haskell\"" $ \query -> do
-      (_, cnd) <- Arxiv.get EN query (Just 1)
+      res <- Arxiv.get EN query (Just 1)
+      case res of
+        Left err -> fail (show err)
+        Right (_, cnd) -> do
           hyperDocs <- sourceToList cnd
           case hyperDocs of
             []    -> fail "No documents found."
@@ -339,7 +382,10 @@ testArxivRealWorld_02 getPubmedKey = do
   case mb_key of
     Nothing -> pure ()
     Just _  -> withValidQuery "\"Haskell\" AND \"Agda\"" $ \query -> do
-      (_, cnd) <- Arxiv.get EN query (Just 1)
+      res <- Arxiv.get EN query (Just 1)
+      case res of
+        Left err -> fail (show err)
+        Right (_, cnd) -> do
           hyperDocs <- sourceToList cnd
           case hyperDocs of
             []    -> fail "No documents found."
@@ -379,3 +425,38 @@ testIsidoreRealWorld_02 getPubmedKey = do
           case hyperDocs of
             []    -> fail "No documents found."
             (x:_) -> isJust (_hd_title x) @?= True
+
+--
+-- Istex integration tests
+--
+
+testIstexRealWorld_01 :: IO (Maybe PubmedApiKey) -> Assertion
+testIstexRealWorld_01 getPubmedKey = do
+  mb_key <- getPubmedKey
+  case mb_key of
+    Nothing -> pure ()
+    Just _  -> withValidQuery "\"brain\"" $ \query -> do
+      res <- Istex.get EN query (Just 1)
+      case res of
+        Left err -> fail (show err)
+        Right (_, cnd) -> do
+          hyperDocs <- sourceToList cnd
+          case hyperDocs of
+            []    -> fail "No documents found."
+            (x:_) -> assertBool ("found: " <> show (_hd_title x))
+                                (maybe False (T.isInfixOf "brain") (_hd_title x))
+
+testIstexRealWorld_02 :: IO (Maybe PubmedApiKey) -> Assertion
+testIstexRealWorld_02 getPubmedKey = do
+  mb_key <- getPubmedKey
+  case mb_key of
+    Nothing -> pure ()
+    Just _  -> withValidQuery "\"brain\" AND NOT \"neural\"" $ \query -> do
+      res <- Istex.get EN query (Just 1)
+      case res of
+        Left err -> fail (show err)
+        Right (_, cnd) -> do
+          hyperDocs <- sourceToList cnd
+          case hyperDocs of
+            []    -> fail "No documents found."
+            (x:_) -> isJust (_hd_title x) @?= True