Try the hotfix

src/Gargantext/API/Node/Corpus/New.hs

@@ -56,7 +56,7 @@ import Gargantext.Database.Action.User (getUserId)
 import Gargantext.Database.Admin.Types.Hyperdata
 import Gargantext.Database.Admin.Types.Node (CorpusId, NodeType(..))
 import Gargantext.Database.Prelude (hasConfig)
-import Gargantext.Database.Query.Table.Node (getNodeWith)
+import Gargantext.Database.Query.Table.Node (getNodeWith, updateCorpusPubmedAPIKey)
 import Gargantext.Database.Query.Table.Node.UpdateOpaleye (updateHyperdata)
 import Gargantext.Database.Schema.Node (node_hyperdata)
 import Gargantext.Prelude
@@ -208,10 +208,10 @@ addToCorpusWithQuery user cid (WithQuery { _wq_query = q
 
     _ -> do
       case datafield of
-         Just (External PubMed) -> do
+         Just (External (Just PubMed)) -> do
            _api_key <- view $ hasConfig . gc_pubmed_api_key
            printDebug "[addToCorpusWithQuery] pubmed api key" _api_key
-           _ <- updateCorpusPubmedAPIKey cid _api_key
+           _ <- updateCorpusPubmedAPIKey cid (Just _api_key)
            pure ()
          _ -> pure ()
       markStarted 3 jobHandle

src/Gargantext/API/Node/Corpus/Types.hs

@@ -4,7 +4,6 @@ module Gargantext.API.Node.Corpus.Types where
 
 import Control.Lens hiding (elements, Empty)
 import Control.Monad.Fail (fail)
-import Control.Monad.Reader (MonadReader)
 import Data.Aeson
 import Data.Aeson.TH (deriveJSON)
 import Data.Monoid (mempty)

src/Gargantext/Database/Query/Table/Node.hs

@@ -29,6 +29,7 @@ import Data.Text (Text)
 import Database.PostgreSQL.Simple.SqlQQ (sql)
 import Opaleye hiding (FromField)
 import Prelude hiding (null, id, map, sum)
+import qualified PUBMED.Types as PUBMED
 
 import Gargantext.Core
 import Gargantext.Core.Types
@@ -327,6 +328,32 @@ insertNodesWithParent pid ns = insertNodes (set node_parent_id (pgNodeId <$> pid
 
 insertNodesWithParentR :: Maybe ParentId -> [NodeWrite] -> Cmd err [NodeId]
 insertNodesWithParentR pid ns = insertNodesR (set node_parent_id (pgNodeId <$> pid) <$> ns)
+
+getCorpusPubmedAPIKey :: NodeId -> Cmd err (Maybe PUBMED.APIKey)
+getCorpusPubmedAPIKey cId = do
+  res <- runPGSQuery query params
+  pure $ (\(PGS.Only apiKey) -> apiKey) <$> head res
+  where
+    query :: PGS.Query
+    query = [sql|
+                SELECT hyperdata -> 'pubmed_api_key'
+                FROM nodes
+                WHERE id = ?
+            |]
+    params = PGS.Only cId
+
+updateCorpusPubmedAPIKey :: NodeId -> Maybe PUBMED.APIKey -> Cmd err Int64
+updateCorpusPubmedAPIKey cId mAPIKey =
+  execPGSQuery query params
+  where
+    query :: PGS.Query
+    query = [sql|
+                UPDATE nodes
+                SET hyperdata = hyperdata || ?
+                WHERE id = ?
+            |]
+    params = (encode $ object [ "pubmed_api_key" .= mAPIKey ], cId)
+
 ------------------------------------------------------------------------
 -- TODO
 -- currently this function removes the child relation