[ngrams] refactor PubMed DB type (to include Maybe APIKey)

src/Gargantext/API/Admin/Orchestrator/Types.hs

@@ -25,6 +25,7 @@ import Gargantext.Core.Types (TODO(..))
 import Gargantext.Core.Utils.Aeson (jsonOptions)
 import Gargantext.Core.Utils.Prefix (dropPrefixT)
 import Gargantext.Prelude
+import PUBMED.Types qualified as PUBMED
 import Test.QuickCheck (elements)
 import Test.QuickCheck.Arbitrary
 
@@ -32,13 +33,13 @@ import Test.QuickCheck.Arbitrary
 -- | Main Types
 -- TODO IsidoreAuth
 data ExternalAPIs = OpenAlex
-                  | PubMed
+                  | PubMed (Maybe PUBMED.APIKey)
                   | Arxiv
                   | HAL
                   | IsTex
                   | Isidore
                   | EPO
-  deriving (Show, Eq, Generic, Enum, Bounded)
+  deriving (Show, Eq, Generic)
 
 
 -- | Main Instances
@@ -46,11 +47,18 @@ instance FromJSON ExternalAPIs
 instance ToJSON ExternalAPIs
 
 externalAPIs :: [ExternalAPIs]
-externalAPIs = [minBound .. maxBound]
+externalAPIs =
+  [ OpenAlex
+  , PubMed Nothing
+  , Arxiv
+  , HAL
+  , IsTex
+  , Isidore
+  , EPO ]
 
 instance Arbitrary ExternalAPIs
   where
-    arbitrary = arbitraryBoundedEnum
+    arbitrary = elements externalAPIs
 
 instance ToSchema ExternalAPIs where
   declareNamedSchema = genericDeclareNamedSchemaUnrestricted defaultSchemaOptions

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

@@ -159,7 +159,6 @@ addToCorpusWithQuery user cid (WithQuery { _wq_query = q
                                          , _wq_datafield = datafield
                                          , _wq_lang = l
                                          , _wq_flowListWith = flw
-                                         , _wq_pubmedAPIKey = mPubmedAPIKey
                                          , .. }) maybeLimit jobHandle = do
   -- TODO ...
   $(logLocM) DEBUG $ "[addToCorpusWithQuery] (cid, dbs) " <> show (cid, dbs)
@@ -194,7 +193,7 @@ addToCorpusWithQuery user cid (WithQuery { _wq_query = q
       let db = database2origin dbs
       -- mPubmedAPIKey <- getUserPubmedAPIKey user
       -- printDebug "[addToCorpusWithQuery] mPubmedAPIKey" mPubmedAPIKey
-      eTxt <- getDataText db (Multi l) q mPubmedAPIKey mEPOAuthKey maybeLimit
+      eTxt <- getDataText db (Multi l) q mEPOAuthKey maybeLimit
 
       -- printDebug "[G.A.N.C.New] lTxts" lTxts
       case eTxt of

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

@@ -22,30 +22,31 @@ import Gargantext.API.Admin.Orchestrator.Types qualified as Types
 import Gargantext.Core.Utils.Prefix (unPrefix)
 import Gargantext.Database.Action.Flow.Types (DataOrigin(..))
 import Gargantext.Prelude
+import PUBMED.Types qualified as PUBMED
 
 data Database = Empty
               | OpenAlex
-              | PubMed
+              | PubMed (Maybe PUBMED.APIKey)
               | Arxiv
               | HAL
               | IsTex
               | Isidore
               | EPO
-  deriving (Eq, Show, Generic, Enum, Bounded)
+  deriving (Eq, Show, Generic)
 
 deriveJSON (unPrefix "") ''Database
 instance ToSchema Database where
   declareNamedSchema = genericDeclareNamedSchemaUnrestricted defaultSchemaOptions
 
 database2origin :: Database -> DataOrigin
-database2origin Empty    = InternalOrigin Types.IsTex
-database2origin OpenAlex = ExternalOrigin Types.OpenAlex
-database2origin PubMed   = ExternalOrigin Types.PubMed
-database2origin Arxiv    = ExternalOrigin Types.Arxiv
-database2origin HAL      = ExternalOrigin Types.HAL
-database2origin IsTex    = ExternalOrigin Types.IsTex
-database2origin Isidore  = ExternalOrigin Types.Isidore
-database2origin EPO      = ExternalOrigin Types.EPO
+database2origin Empty      = InternalOrigin Types.IsTex
+database2origin OpenAlex   = ExternalOrigin Types.OpenAlex
+database2origin (PubMed k) = ExternalOrigin (Types.PubMed k)
+database2origin Arxiv      = ExternalOrigin Types.Arxiv
+database2origin HAL        = ExternalOrigin Types.HAL
+database2origin IsTex      = ExternalOrigin Types.IsTex
+database2origin Isidore    = ExternalOrigin Types.Isidore
+database2origin EPO        = ExternalOrigin Types.EPO
 
 ------------------------------------------------------------------------
 data Datafield = Gargantext

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

@@ -36,7 +36,6 @@ import Gargantext.Core.Text.Corpus.Query qualified as Corpus
 import Gargantext.Database.Admin.Types.Hyperdata.Document (HyperdataDocument(..))
 import Gargantext.Prelude hiding (get)
 import Gargantext.Utils.Jobs.Error
-import PUBMED.Types qualified as PUBMED
 import Servant.Client (ClientError)
 
 data GetCorpusError
@@ -60,17 +59,16 @@ get :: ExternalAPIs
     -- If the provider doesn't support the search filtered by language, or if the language
     -- is not important, the frontend will simply send 'EN' to the backend.
     -> Corpus.RawQuery
-    -> Maybe PUBMED.APIKey
     -> Maybe EPO.AuthKey
     -> Text
     -> Maybe Corpus.Limit
     -- -> IO [HyperdataDocument]
     -> IO (Either GetCorpusError (Maybe Integer, ConduitT () HyperdataDocument IO ()))
-get externalAPI lang q mPubmedAPIKey epoAuthKey epoAPIUrl limit = do
+get externalAPI lang q epoAuthKey epoAPIUrl limit = do
   -- 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   ->
+      PubMed mPubmedAPIKey  ->
         first (ExternalAPIError externalAPI) <$> PUBMED.get (fromMaybe "" mPubmedAPIKey) q limit
       OpenAlex ->
         first (ExternalAPIError externalAPI) <$> OpenAlex.get (fromMaybe "" Nothing {- email -}) q (Just $ toISO639 lang) limit

src/Gargantext/Database/Action/Flow.hs

@@ -20,7 +20,7 @@ Portability : POSIX
 {-# LANGUAGE InstanceSigs            #-}
 {-# LANGUAGE ScopedTypeVariables     #-}
 {-# LANGUAGE TemplateHaskell         #-}
-{-# LANGUAGE TypeApplications  #-}
+{-# LANGUAGE TypeApplications        #-}
 {-# LANGUAGE TypeOperators           #-}
 
 module Gargantext.Database.Action.Flow -- (flowDatabase, ngrams2list)
@@ -34,9 +34,7 @@ module Gargantext.Database.Action.Flow -- (flowDatabase, ngrams2list)
   , flowCorpus
   , flowCorpusUser
   , flowAnnuaire
-  , insertMasterDocs
   , buildSocialList
-  , saveDocNgramsWith
   , addDocumentsToHyperCorpus
 
   , reIndexWith
@@ -109,7 +107,6 @@ import Gargantext.Database.Schema.Node (node_hyperdata)
 import Gargantext.Prelude hiding (to)
 import Gargantext.System.Logging ( logLocM, LogLevel(DEBUG), MonadLogger )
 import Gargantext.Utils.Jobs.Monad ( JobHandle, MonadJobStatus(..) )
-import PUBMED.Types qualified as PUBMED
 
 ------------------------------------------------------------------------
 -- Imports for upgrade function
@@ -129,20 +126,20 @@ printDataText (DataNew (maybeInt, conduitData)) = do
   res <- C.runConduit (conduitData .| CL.consume)
   putText $ show (maybeInt, res)
 
+
 -- TODO use the split parameter in config file
 getDataText :: (HasNodeError err)
             => DataOrigin
             -> TermType Lang
             -> API.RawQuery
-            -> Maybe PUBMED.APIKey
             -> Maybe EPO.AuthKey
             -> Maybe API.Limit
             -> DBCmdWithEnv env err (Either API.GetCorpusError DataText)
-getDataText (ExternalOrigin api) la q mPubmedAPIKey mAuthKey li = do
+getDataText (ExternalOrigin api) la q mAuthKey li = do
   cfg <- view hasConfig
-  eRes <- liftBase $ API.get api (_tt_lang la) q mPubmedAPIKey mAuthKey (_ac_epo_api_url $ _gc_apis cfg) li
+  eRes <- liftBase $ API.get api (_tt_lang la) q mAuthKey (_ac_epo_api_url $ _gc_apis cfg) li
   pure $ DataNew <$> eRes
-getDataText (InternalOrigin _) la q _ _ _li = do
+getDataText (InternalOrigin _) la q _ _li = do
   (_masterUserId, _masterRootId, cId) <- getOrMkRootWithCorpus MkCorpusUserMaster (Nothing :: Maybe HyperdataCorpus)
   ids <-  map fst <$> searchDocInDatabase cId (stem (_tt_lang la) GargPorterAlgorithm $ API.getRawQuery q)
   pure $ Right $ DataOld ids
@@ -154,7 +151,7 @@ getDataText_Debug :: (HasNodeError err)
                   -> Maybe API.Limit
                   -> DBCmdWithEnv env err ()
 getDataText_Debug a l q li = do
-  result <- getDataText a l q Nothing Nothing li
+  result <- getDataText a l q Nothing li
   case result of
     Left  err -> liftBase $ putText $ show err
     Right res -> liftBase $ printDataText res
@@ -443,6 +440,7 @@ insertMasterDocs ncs c lang hs  =  do
   -- _cooc <- insertDefaultNode NodeListCooc lId masterUserId
   pure $ map contextId2NodeId ids'
 
+
 saveDocNgramsWith :: (IsDBCmd env err m)
                   => ListId
                   -> HashMap.HashMap ExtractedNgrams (Map NgramsType (Map NodeId (TermsWeight, TermsCount)))