[refactor] unify Database & ExternalIDs

These types are the same, except for Database.Empty

I managed to have backwards compatibility with the frontend format,
hence the frontend doesn't need any changes.

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

@@ -13,67 +13,41 @@ module Gargantext.API.Node.Corpus.Types where
 
 import Control.Lens ( (?~) )
 import Control.Monad.Fail (fail)
-import Data.Aeson ( Value(..), (.:), (.:?), (.=), withText, object, withObject )
-import Data.Aeson.Types (unexpected)
+import Data.Aeson ( Value(..), (.:), (.=), withText, object, withObject )
+import Data.Aeson.Types ( Parser )
 import Data.Swagger
 import Data.Text qualified as T
 import Gargantext.API.Admin.Orchestrator.Types qualified as Types
 import Gargantext.Database.Action.Flow.Types (DataOrigin(..))
 import Gargantext.Prelude
-import PUBMED.Types qualified as PUBMED
 
 type EPOAPIToken = Text
 type EPOAPIUser = Text
 
-data Database = Empty
-              | OpenAlex
-              | PubMed (Maybe PUBMED.APIKey)
-              | Arxiv
-              | HAL
-              | IsTex
-              | Isidore
-              | EPO (Maybe EPOAPIUser) (Maybe EPOAPIToken)
+data Database =
+    Empty
+  | DB Types.ExternalAPIs
   deriving (Eq, Show, Generic)
-
 instance FromJSON Database where
   parseJSON = withObject "Database" $ \o -> do
-    db <- o .: "db"
+    db <- o .: "db" :: Parser Text
     case db of
       "Empty" -> pure Empty
-      "OpenAlex" -> pure OpenAlex
-      "PubMed" -> do
-        mAPIKey <- o .:? "api_key"
-        pure $ PubMed mAPIKey
-      "Arxiv" -> pure Arxiv
-      "HAL" -> pure HAL
-      "IsTex" -> pure IsTex
-      "Isidore" -> pure Isidore
-      "EPO" -> do
-        mAPIUser <- o .:? "api_user"
-        mAPIToken <- o .:? "api_token"
-        pure $ EPO mAPIUser mAPIToken
-      s -> unexpected (String s)
+      _       -> do
+        eapi <- parseJSON (Object o) :: Parser Types.ExternalAPIs
+        pure $ DB eapi
 instance ToJSON Database where
-  toJSON (PubMed mAPIKey) = object [ "db" .= toJSON ("PubMed" :: Text)
-                                   , "api_key" .= toJSON mAPIKey ]
-  toJSON (EPO mAPIUser mAPIToken) = object [ "db" .= toJSON ("EPO" :: Text)
-                                           , "api_user" .= toJSON mAPIUser
-                                           , "api_token" .= toJSON mAPIToken ]
-  toJSON t = object [ "db" .= toJSON (show t :: Text) ]
+  toJSON Empty = object [ "db" .= (show Empty :: Text)]
+  toJSON (DB db) = toJSON db
 instance ToSchema Database where
   declareNamedSchema = genericDeclareNamedSchemaUnrestricted defaultSchemaOptions
 
+
 datafield2origin :: Datafield -> DataOrigin
-datafield2origin (External Empty)                    = InternalOrigin Types.IsTex
-datafield2origin (External OpenAlex)                 = ExternalOrigin Types.OpenAlex
-datafield2origin (External (PubMed mAPIKey))         = ExternalOrigin (Types.PubMed mAPIKey)
-datafield2origin (External Arxiv)                    = ExternalOrigin Types.Arxiv
-datafield2origin (External HAL)                      = ExternalOrigin Types.HAL
-datafield2origin (External IsTex)                    = ExternalOrigin Types.IsTex
-datafield2origin (External Isidore)                  = ExternalOrigin Types.Isidore
-datafield2origin (External (EPO mAPIUser mAPIToken)) = ExternalOrigin (Types.EPO mAPIUser mAPIToken)
--- | This isn't really used
-datafield2origin _                                   = InternalOrigin Types.IsTex
+datafield2origin (External Empty)   = InternalOrigin Types.IsTex
+datafield2origin (External (DB db)) = ExternalOrigin db
+-- -- | This isn't really used
+datafield2origin _                  = InternalOrigin Types.IsTex
 
 ------------------------------------------------------------------------
 data Datafield = Gargantext

src/Gargantext/Core/Worker.hs

@@ -156,11 +156,6 @@ notifyJobKilled env (W.State { name }) (Just bm) = do
 
 
 -- | Spawn a worker with PGMQ broker
--- TODO:
---  - reduce size of DB pool
---  - progress report via notifications
---  - I think there is no point to save job result, as usually there is none (we have side-effects only)
---  - replace Servant.Job to use workers instead of garg API threads
 withPGMQWorker :: HasWorkerBroker
                 => WorkerEnv
                 -> WorkerDefinition

test/Test/API/Setup.hs

@@ -185,7 +185,7 @@ dbEnvSetup ctx = do
   _ <- createAliceAndBob testEnv
 
   pure ctx
-
+  
 -- show the full exceptions during testing, rather than shallowing them under a generic
 -- "Something went wrong".
 showDebugExceptions :: SomeException -> Wai.Response

test/Test/Instances.hs

@@ -131,13 +131,7 @@ instance Arbitrary FileType where arbitrary = genericArbitrary
 
 instance Arbitrary CT.Database where
   arbitrary = oneof [ pure CT.Empty
-                    , pure CT.OpenAlex
-                    , CT.PubMed <$> arbitrary
-                    , pure CT.Arxiv
-                    , pure CT.HAL
-                    , pure CT.IsTex
-                    , pure CT.Isidore
-                    , CT.EPO <$> arbitrary <*> arbitrary ]
+                    , CT.DB <$> arbitrary ]
 instance Arbitrary Datafield where arbitrary = genericArbitrary
 
 instance Arbitrary WithQuery where arbitrary = genericArbitrary