Send PUBMED the raw query from the frontend

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

@@ -19,14 +19,16 @@ module Gargantext.Core.Text.Corpus.API
   ) where
 
 import Conduit
+import Control.Monad.Except
 import Data.Bifunctor
 import Data.Either (Either(..))
 import Data.Maybe
-import qualified Data.Text as T
 import Gargantext.API.Admin.Orchestrator.Types (ExternalAPIs(..), externalAPIs)
 import Gargantext.Core (Lang(..), toISO639)
 import Gargantext.Database.Admin.Types.Hyperdata (HyperdataDocument(..))
 import Gargantext.Prelude
+import Servant.Client (ClientError)
+import qualified Data.Text as T
 import qualified Gargantext.Core.Text.Corpus.API.Arxiv   as Arxiv
 import qualified Gargantext.Core.Text.Corpus.API.Hal     as HAL
 import qualified Gargantext.Core.Text.Corpus.API.Isidore as ISIDORE
@@ -35,7 +37,6 @@ import qualified Gargantext.Core.Text.Corpus.API.OpenAlex as OpenAlex
 import qualified Gargantext.Core.Text.Corpus.API.Pubmed  as PUBMED
 import qualified Gargantext.Core.Text.Corpus.Query as Corpus
 import qualified PUBMED.Types as PUBMED
-import Servant.Client (ClientError)
 
 data GetCorpusError
   = -- | We couldn't parse the user input query into something meaningful.
@@ -53,18 +54,23 @@ get :: ExternalAPIs
     -- -> IO [HyperdataDocument]
     -> IO (Either GetCorpusError (Maybe Integer, ConduitT () HyperdataDocument IO ()))
 get externalAPI la q mPubmedAPIKey limit = do
-  case Corpus.parseQuery q of
-    Left err -> pure $ Left $ InvalidInputQuery q (T.pack err)
-    Right corpusQuery -> case externalAPI of
-      OpenAlex -> first ExternalAPIError <$>
-                    OpenAlex.get (fromMaybe "" Nothing {- email -}) q (toISO639 la) limit
-      PubMed -> first ExternalAPIError <$>
-                  PUBMED.get (fromMaybe "" mPubmedAPIKey) corpusQuery limit
-      --docs <- PUBMED.get   q default_limit -- EN only by default
-      --pure (Just $ fromIntegral $ length docs, yieldMany docs)
-      Arxiv   -> Right <$> Arxiv.get la corpusQuery limit
-      HAL     -> first ExternalAPIError <$> 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)
-      Isidore -> do docs <- ISIDORE.get la (Corpus.getLimit <$> limit) (Just $ Corpus.getRawQuery q) Nothing
-                    pure $ Right (Just $ fromIntegral $ length docs, yieldMany docs)
+  -- For PUBMED, HAL, IsTex, Isidore and OpenAlex, we want to send the query as-it.
+  -- For Arxiv we parse the query into a structured boolean query we submit over.
+  case externalAPI of
+      PubMed   ->
+        first ExternalAPIError <$> PUBMED.get (fromMaybe "" mPubmedAPIKey) q limit
+      OpenAlex ->
+        first ExternalAPIError <$> 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)
+      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)
+      Isidore  -> do
+        docs <- ISIDORE.get la (Corpus.getLimit <$> limit) (Just $ Corpus.getRawQuery q) Nothing
+        pure $ Right (Just $ fromIntegral $ length docs, yieldMany docs)
+  where
+    parse_query = first (InvalidInputQuery q . T.pack) $ Corpus.parseQuery q

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

@@ -45,6 +45,15 @@ import PUBMED.Types (Config(..))
 
 -- | A pubmed query.
 -- See: https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch
+-- The documentation for PUBMED says:
+-- Values for query keys may also be provided in term if they are preceeded by a
+-- '#' (%23 in the URL). While only one query_key parameter can be provided to ESearch,
+-- any number of query keys can be combined in term. Also, if query keys are provided in term,
+-- they can be combined with OR or NOT in addition to AND.
+-- Example:
+-- esearch.fcgi?db=pubmed&term=%231+AND+asthma&WebEnv=<webenv string>&usehistory=y
+--
+-- Therefore, we can pretty-print our 'Query' back into something that PubMed could understand.
 newtype ESearch = ESearch { _ESearch :: [EscapeItem] }
   deriving stock (Show, Eq)
   deriving newtype (Semigroup, Monoid)
@@ -87,21 +96,14 @@ convertQuery q = ESearch (interpretQuery q transformAST)
         -> [QN "NOT+", QE (TE.encodeUtf8 term)]
 
 get :: Text
-    -> Corpus.Query
+    -> Corpus.RawQuery
     -> Maybe Limit
     -> IO (Either ClientError (Maybe Integer, ConduitT () HyperdataDocument IO ()))
 get apiKey q l = do
-  -- The documentation for PUBMED says:
-  -- Values for query keys may also be provided in term if they are preceeded by a
-  -- '#' (%23 in the URL). While only one query_key parameter can be provided to ESearch,
-  -- any number of query keys can be combined in term. Also, if query keys are provided in term,
-  -- they can be combined with OR or NOT in addition to AND.
-  -- Example:
-  -- esearch.fcgi?db=pubmed&term=%231+AND+asthma&WebEnv=<webenv string>&usehistory=y
-  --
-  -- Therefore, we can pretty-print our 'Query' back into something that PubMed could understand.
+  -- NOTE(adinapoli): For now we do not interpret the PUBMED query into something
+  -- more structured, like an 'ESearch' term, but we could, in the future.
   eRes <- runReaderT PubMed.getMetadataWithC (Config { apiKey  = Just apiKey
-                                                     , query   = getESearch $ convertQuery q
+                                                     , query   = getRawQuery q
                                                      , perPage = Just 200
                                                      , mWebEnv = Nothing })
   let takeLimit = case l of

test/Core/Text/Corpus/Query.hs

@@ -226,7 +226,7 @@ testPubMedCovid_01 getPubmedKey = do
   case mb_key of
     Nothing -> pure ()
     Just k  -> withValidQuery "\"Covid\"" $ \query -> do
-      res <- Pubmed.get (_PubmedApiKey k) query (Just 1)
+      res <- Pubmed.get (_PubmedApiKey k) (renderQuery query) (Just 1)
       case res of
         Left err       -> fail (show err)
         Right (_, cnd) -> do
@@ -241,7 +241,7 @@ testPubMedCovid_02 getPubmedKey = do
   case mb_key of
     Nothing -> pure ()
     Just k  -> withValidQuery "\"Covid\" AND \"Alzheimer\"" $ \query -> do
-      res <- Pubmed.get (_PubmedApiKey k) query (Just 1)
+      res <- Pubmed.get (_PubmedApiKey k) (renderQuery query) (Just 1)
       case res of
         Left err       -> fail (show err)
         Right (_, cnd) -> do