Merge remote-tracking branch 'origin/dev-typeclasses-refactoring' into dev

src/Gargantext/API.hs

@@ -56,9 +56,9 @@ import Gargantext.API.Ngrams (saveNodeStoryImmediate)
 import Gargantext.API.Routes
 import Gargantext.API.Server (server)
 import Gargantext.Core.NodeStory
--- import Gargantext.Database.Prelude (Cmd)
--- import Gargantext.Database.Action.Metrics.NgramsByContext (refreshNgramsMaterialized)
+import Gargantext.Database.Prelude qualified as DB
 import Gargantext.Prelude hiding (putStrLn)
+import Gargantext.System.Logging
 import Network.HTTP.Types hiding (Query)
 import Network.Wai
 import Network.Wai.Handler.Warp hiding (defaultSettings)
@@ -66,10 +66,8 @@ import Network.Wai.Middleware.Cors
 import Network.Wai.Middleware.RequestLogger
 import Paths_gargantext (getDataDir)
 import Servant
+import System.Cron.Schedule qualified as Cron
 import System.FilePath
-import qualified Gargantext.Database.Prelude as DB
-import qualified System.Cron.Schedule as Cron
-import Gargantext.System.Logging
 
 -- | startGargantext takes as parameters port number and Ini file.
 startGargantext :: Mode -> PortNumber -> FilePath -> IO ()

src/Gargantext/API/Admin/Auth.hs

@@ -58,7 +58,7 @@ import Gargantext.Core.Mail.Types (mailSettings)
 import Gargantext.Core.Types.Individu (User(..), Username, GargPassword(..))
 import Gargantext.Database.Action.Flow.Types (FlowCmdM)
 import Gargantext.Database.Admin.Types.Node (NodeId(..))
-import Gargantext.Database.Prelude (Cmd', CmdM, CmdCommon)
+import Gargantext.Database.Prelude (Cmd', CmdCommon, DbCmd')
 import Gargantext.Database.Query.Table.User
 import Gargantext.Database.Query.Tree (isDescendantOf, isIn)
 import Gargantext.Database.Query.Tree.Root (getRoot)
@@ -79,7 +79,8 @@ import Gargantext.API.Auth.PolicyCheck
 
 -- | Main functions of authorization
 
-makeTokenForUser :: (HasSettings env, HasJoseError err)
+makeTokenForUser :: ( HasSettings env
+                    , HasJoseError err )
                  => NodeId -> Cmd' env err Token
 makeTokenForUser uid = do
   jwtS <- view $ settings . jwtSettings
@@ -88,10 +89,10 @@ makeTokenForUser uid = do
   either joseError (pure . toStrict . LE.decodeUtf8) e
   -- TODO not sure about the encoding...
 
-checkAuthRequest :: ( HasSettings env, CmdCommon env, HasJoseError err)
+checkAuthRequest :: ( HasSettings env, HasJoseError err, DbCmd' env err m )
                  => Username
                  -> GargPassword
-                 -> Cmd' env err CheckAuth
+                 -> m CheckAuth
 checkAuthRequest couldBeEmail (GargPassword p) = do
   -- Sometimes user put email instead of username
   -- hence we have to check before
@@ -113,8 +114,8 @@ checkAuthRequest couldBeEmail (GargPassword p) = do
               token <- makeTokenForUser uid
               pure $ Valid token uid userLight_id
 
-auth :: (HasSettings env, CmdCommon env, HasJoseError err)
-     => AuthRequest -> Cmd' env err AuthResponse
+auth :: (HasSettings env, HasJoseError err, DbCmd' env err m)
+     => AuthRequest -> m AuthResponse
 auth (AuthRequest u p) = do
   checkAuthRequest' <- checkAuthRequest u p
   case checkAuthRequest' of
@@ -135,7 +136,7 @@ authCheck _env (BasicAuthData login password) = pure $
   maybe Indefinite Authenticated $ TODO
 -}
 
-withAccessM :: (CmdM env err m, HasServerError err)
+withAccessM :: ( DbCmd' env err m )
             => AuthenticatedUser
             -> PathId
             -> m a
@@ -143,7 +144,6 @@ withAccessM :: (CmdM env err m, HasServerError err)
 withAccessM (AuthenticatedUser uId) (PathNode id) m = do
   d <- id `isDescendantOf` uId
   if d then m else m -- serverError err401
-
 withAccessM (AuthenticatedUser uId) (PathNodeNode cId docId) m = do
   _a <- isIn cId docId -- TODO use one query for all ?
   _d <- cId `isDescendantOf` uId

src/Gargantext/API/Context.hs

@@ -25,7 +25,7 @@ import Gargantext.API.Admin.Auth (withAccess)
 import Gargantext.API.Admin.Auth.Types (PathId(..), AuthenticatedUser)
 import Gargantext.API.Prelude
 import Gargantext.Database.Admin.Types.Node
-import Gargantext.Database.Prelude -- (Cmd, CmdM)
+import Gargantext.Database.Prelude (JSONB)
 import Gargantext.Database.Query.Table.Context
 
 -------------------------------------------------------------------

src/Gargantext/API/Dev.hs

@@ -14,22 +14,22 @@ module Gargantext.API.Dev where
 
 import Control.Exception (finally)
 import Control.Monad (fail)
-import Control.Monad.Reader (runReaderT)
 import Control.Monad.Except (runExceptT)
+import Control.Monad.Reader (runReaderT)
 import Gargantext.API.Admin.EnvTypes
 import Gargantext.API.Admin.Settings
 import Gargantext.API.Ngrams (saveNodeStoryImmediate)
 import Gargantext.API.Prelude
 import Gargantext.Core.NLP (nlpServerMap)
 import Gargantext.Core.NodeStory
-import Gargantext.Database.Prelude
+import Gargantext.Database.Prelude (Cmd', Cmd'', databaseParameters, runCmd)
 import Gargantext.Prelude
 import Gargantext.Prelude.Config (readConfig)
-import qualified Gargantext.Prelude.Mail as Mail
-import qualified Gargantext.Prelude.NLP as NLP
+import Gargantext.Prelude.Mail qualified as Mail
+import Gargantext.Prelude.NLP qualified as NLP
+import Gargantext.System.Logging
 import Servant
 import System.IO (FilePath)
-import Gargantext.System.Logging
 
 type IniPath  = FilePath
 -------------------------------------------------------------------

src/Gargantext/API/GraphQL/Context.hs

@@ -211,8 +211,8 @@ toHyperdataRowDocumentGQL hyperdata =
                                      }
     HyperdataRowContact { } -> Nothing
 
-updateNodeContextCategory :: ( CmdCommon env, HasSettings env) =>
-                             NodeContextCategoryMArgs -> GqlM' e env [Int]
+updateNodeContextCategory :: (CmdCommon env, HasSettings env)
+                          => NodeContextCategoryMArgs -> GqlM' e env [Int]
 updateNodeContextCategory NodeContextCategoryMArgs { context_id, node_id, category } = do
   _ <- lift $ DNC.updateNodeContextCategory (NodeId context_id) (NodeId node_id) category
 

src/Gargantext/API/GraphQL/PolicyCheck.hs

@@ -8,7 +8,7 @@ import Gargantext.API.Admin.Auth.Types
 import Gargantext.API.Auth.PolicyCheck
 import Gargantext.API.GraphQL.Types
 import Gargantext.API.Prelude
-import Gargantext.Database.Prelude
+import Gargantext.Database.Prelude (HasConnectionPool, HasConfig)
 
 withPolicy :: (HasConnectionPool env, HasConfig env)
            => AuthenticatedUser

src/Gargantext/API/GraphQL/User.hs

@@ -4,24 +4,21 @@
 module Gargantext.API.GraphQL.User where
 
 import Data.Maybe (listToMaybe)
-import Data.Morpheus.Types
-  ( GQLType
-  , lift
-  )
+import Data.Morpheus.Types ( GQLType , lift )
 import Data.Text (Text)
 import GHC.Generics (Generic)
+import Gargantext.API.Admin.Auth.Types
 import Gargantext.API.Admin.Types (HasSettings)
+import Gargantext.API.Auth.PolicyCheck
+import Gargantext.API.GraphQL.PolicyCheck
 import Gargantext.API.GraphQL.Types
+import Gargantext.Core.Types.Individu qualified as Individu
 import Gargantext.Database.Admin.Types.Hyperdata (HyperdataUser(..))
 import Gargantext.Database.Admin.Types.Node (NodeId(..))
 import Gargantext.Database.Prelude (CmdCommon)
+import Gargantext.Database.Query.Table.User qualified as DBUser
 import Gargantext.Database.Schema.User (UserLight(..))
 import Gargantext.Prelude
-import qualified Gargantext.Core.Types.Individu as Individu
-import qualified Gargantext.Database.Query.Table.User as DBUser
-import Gargantext.API.Admin.Auth.Types
-import Gargantext.API.Auth.PolicyCheck
-import Gargantext.API.GraphQL.PolicyCheck
 
 data User m = User
   { u_email     :: Text
@@ -54,9 +51,8 @@ resolveUsers autUser mgr UserArgs { user_id } = do
   withPolicy autUser mgr alwaysAllow $ dbUsers user_id
 
 -- | Inner function to fetch the user from DB.
-dbUsers
-  :: (CmdCommon env)
-  => Int -> GqlM e env [User (GqlM e env)]
+dbUsers :: (CmdCommon env)
+        => Int -> GqlM e env [User (GqlM e env)]
 dbUsers user_id = lift (map toUser <$> DBUser.getUsersWithId (Individu.RootId $ NodeId user_id))
 
 toUser

src/Gargantext/API/Metrics.hs

@@ -35,7 +35,7 @@ import Gargantext.Core.Viz.Types
 import Gargantext.Database.Admin.Types.Hyperdata (HyperdataList(..), hl_chart, hl_pie, hl_scatter, hl_tree)
 import Gargantext.Database.Admin.Types.Metrics (ChartMetrics(..), Metric(..), Metrics(..))
 import Gargantext.Database.Admin.Types.Node (NodeId)
-import Gargantext.Database.Prelude
+import Gargantext.Database.Prelude (DBCmd)
 import Gargantext.Database.Query.Table.Node (defaultList, getNodeWith)
 import Gargantext.Database.Query.Table.Node.Error (HasNodeError)
 import Gargantext.Database.Query.Table.Node.UpdateOpaleye (updateHyperdata)
@@ -185,12 +185,12 @@ getChart cId _start _end maybeListId tabType = do
 
   pure $ constructHashedResponse chart
 
-updateChart :: HasNodeError err =>
-  CorpusId
-  -> Maybe ListId
-  -> TabType
-  -> Maybe Limit
-  -> DBCmd err ()
+updateChart :: HasNodeError err
+            => CorpusId
+            -> Maybe ListId
+            -> TabType
+            -> Maybe Limit
+            -> DBCmd err ()
 updateChart cId maybeListId tabType maybeLimit = do
   listId <- case maybeListId of
     Just lid -> pure lid
@@ -202,12 +202,12 @@ updateChart cId maybeListId tabType maybeLimit = do
   _ <- updateChart' cId listId tabType maybeLimit
   pure ()
 
-updateChart' :: HasNodeError err =>
-  CorpusId
-  -> ListId
-  -> TabType
-  -> Maybe Limit
-  -> DBCmd err (ChartMetrics Histo)
+updateChart' :: HasNodeError err
+             => CorpusId
+             -> ListId
+             -> TabType
+             -> Maybe Limit
+             -> DBCmd err (ChartMetrics Histo)
 updateChart' cId listId tabType _maybeLimit = do
   node <- getNodeWith listId (Proxy :: Proxy HyperdataList)
   let hl = node ^. node_hyperdata
@@ -267,7 +267,7 @@ getPie cId _start _end maybeListId tabType = do
   chart <- case mChart of
     Just chart -> pure chart
     Nothing    -> do
-      updatePie' cId maybeListId tabType Nothing
+      updatePie' cId listId tabType Nothing
 
   pure $ constructHashedResponse chart
 
@@ -278,23 +278,23 @@ updatePie :: HasNodeStory env err m
           -> Maybe Limit
           -> m ()
 updatePie cId maybeListId tabType maybeLimit = do
+  listId <- case maybeListId of
+    Just lid -> pure lid
+    Nothing  -> defaultList cId
   printDebug "[updatePie] cId" cId
   printDebug "[updatePie] maybeListId" maybeListId
   printDebug "[updatePie] tabType" tabType
   printDebug "[updatePie] maybeLimit" maybeLimit
-  _ <- updatePie' cId maybeListId tabType maybeLimit
+  _ <- updatePie' cId listId tabType maybeLimit
   pure ()
 
 updatePie' :: (HasNodeStory env err m, HasNodeError err)
            => CorpusId
-           -> Maybe ListId
+           -> ListId
            -> TabType
            -> Maybe Limit
            -> m (ChartMetrics Histo)
-updatePie' cId maybeListId tabType _maybeLimit = do
-  listId <- case maybeListId of
-    Just lid -> pure lid
-    Nothing  -> defaultList cId
+updatePie' cId listId tabType _maybeLimit = do
   node <- getNodeWith listId (Proxy :: Proxy HyperdataList)
   let hl = node ^. node_hyperdata
       pieMap = hl ^. hl_pie

src/Gargantext/API/Ngrams/List.hs

@@ -16,12 +16,18 @@ Portability : POSIX
 module Gargantext.API.Ngrams.List
   where
 
+import Data.ByteString.Lazy qualified as BSL
+import Data.Csv qualified as Csv
 import Data.Either (Either(..))
 import Data.HashMap.Strict (HashMap)
+import Data.HashMap.Strict qualified as HashMap
 import Data.Map.Strict (Map, toList)
+import Data.Map.Strict qualified as Map
 import Data.Maybe (fromMaybe)
+import Data.Set qualified as Set
 import Data.Text (Text, concat, pack, splitOn)
 import Data.Vector (Vector)
+import Data.Vector qualified as Vec
 import Gargantext.API.Admin.EnvTypes (Env, GargJob(..))
 import Gargantext.API.Admin.Orchestrator.Types
 import Gargantext.API.Ngrams (setListNgrams)
@@ -34,25 +40,18 @@ import Gargantext.Core.NodeStory
 import Gargantext.Core.Types.Main (ListType(..))
 import Gargantext.Database.Action.Flow (reIndexWith)
 import Gargantext.Database.Action.Flow.Types (FlowCmdM)
--- import Gargantext.Database.Action.Metrics.NgramsByContext (refreshNgramsMaterialized)
 import Gargantext.Database.Admin.Types.Node
+import Gargantext.Database.Query.Table.Ngrams qualified as TableNgrams
 import Gargantext.Database.Query.Table.Node (getNode)
 import Gargantext.Database.Schema.Ngrams
 import Gargantext.Database.Schema.Node (_node_parent_id)
 import Gargantext.Database.Types (Indexed(..))
 import Gargantext.Prelude
 import Gargantext.Utils.Jobs (serveJobsAPI, MonadJobStatus(..))
+import Gargantext.Utils.Servant qualified as GUS
+import Prelude qualified
+import Protolude qualified as P
 import Servant
-import qualified Data.ByteString.Lazy as BSL
-import qualified Data.Csv as Csv
-import qualified Data.HashMap.Strict as HashMap
-import qualified Data.Map.Strict     as Map
-import qualified Data.Set            as Set
-import qualified Data.Vector         as Vec
-import qualified Gargantext.Database.Query.Table.Ngrams as TableNgrams
-import qualified Gargantext.Utils.Servant as GUS
-import qualified Prelude
-import qualified Protolude           as P
 ------------------------------------------------------------------------
 type GETAPI = Summary "Get List"
             :> "lists"
@@ -120,10 +119,10 @@ getCsv lId = do
 ------------------------------------------------------------------------
 -- TODO : purge list
 -- TODO talk
-setList :: FlowCmdM env err m
-    => ListId
-    -> NgramsList
-    -> m Bool
+setList :: HasNodeStory env err m
+        => ListId
+        -> NgramsList
+        -> m Bool
 setList l m  = do
   -- TODO check with Version for optim
   -- printDebug "New list as file" l
@@ -197,7 +196,7 @@ parseCsvData lst = Map.fromList $ conv <$> lst
                                              }
          )
 
-csvPost :: FlowCmdM env err m
+csvPost :: HasNodeStory env err m
         => ListId
         -> Text
         -> m (Either Text ())
@@ -236,7 +235,7 @@ csvPostAsync lId =
 
 
 -- | This is for debugging the CSV parser in the REPL
-importCsvFile :: FlowCmdM env err m
+importCsvFile :: (HasNodeStory env err m)
               => ListId -> P.FilePath -> m (Either Text ())
 importCsvFile lId fp = do
   contents <- liftBase $ P.readFile fp

src/Gargantext/API/Ngrams/Prelude.hs

@@ -36,7 +36,7 @@ import qualified Data.Text as Text
 
 ------------------------------------------------------------------------
 getNgramsList :: HasNodeStory env err m
-    => ListId -> m NgramsList
+              => ListId -> m NgramsList
 getNgramsList lId = fromList
        <$> zip ngramsTypes
        <$> mapM (getNgramsTableMap lId) ngramsTypes

src/Gargantext/API/Ngrams/Tools.hs

@@ -25,7 +25,7 @@ import Data.Validity
 import Gargantext.API.Ngrams.Types
 import Gargantext.Core.NodeStory
 import Gargantext.Core.Types (ListType(..), NodeId, NodeType(..), ListId)
-import Gargantext.Database.Prelude (CmdM, HasConnectionPool(..))
+import Gargantext.Database.Prelude (HasConnectionPool(..))
 import Gargantext.Database.Schema.Ngrams (NgramsType)
 import Gargantext.Prelude
 import qualified Data.HashMap.Strict as HM
@@ -229,7 +229,7 @@ getCoocByNgrams'' (Diagonal diag) (f1,f2) (m1,m2) =
 ------------------------------------------
 
 
-migrateFromDirToDb :: (CmdM env err m) -- , HasNodeStory env err m)
+migrateFromDirToDb :: (HasNodeStory env err m) -- , HasNodeStory env err m)
                    => m ()
 migrateFromDirToDb = do
   pool <- view connPool

src/Gargantext/API/Node.hs

@@ -37,12 +37,19 @@ import GHC.Generics (Generic)
 import Gargantext.API.Admin.Auth (withAccess, withPolicy)
 import Gargantext.API.Admin.Auth.Types (PathId(..), AuthenticatedUser (..))
 import Gargantext.API.Admin.EnvTypes
+import Gargantext.API.Auth.PolicyCheck
 import Gargantext.API.Metrics
 import Gargantext.API.Ngrams (TableNgramsApi, apiNgramsTableCorpus)
 import Gargantext.API.Ngrams.Types (TabType(..))
+import Gargantext.API.Node.DocumentUpload qualified as DocumentUpload
+import Gargantext.API.Node.DocumentsFromWriteNodes qualified as DocumentsFromWriteNodes
 import Gargantext.API.Node.File
+import Gargantext.API.Node.FrameCalcUpload qualified as FrameCalcUpload
 import Gargantext.API.Node.New
+import Gargantext.API.Node.Share qualified as Share
+import Gargantext.API.Node.Update qualified as Update
 import Gargantext.API.Prelude
+import Gargantext.API.Search qualified as Search
 import Gargantext.API.Table
 import Gargantext.Core.Types (NodeTableResult)
 import Gargantext.Core.Types.Individu (User(..))
@@ -50,15 +57,17 @@ import Gargantext.Core.Types.Main (Tree, NodeTree)
 import Gargantext.Core.Types.Query (Limit, Offset)
 import Gargantext.Core.Utils.Prefix (unPrefix)
 import Gargantext.Core.Viz.Phylo.API (PhyloAPI, phyloAPI)
+import Gargantext.Database.Action.Delete qualified as Action (deleteNode)
 import Gargantext.Database.Action.Flow.Pairing (pairing)
 import Gargantext.Database.Admin.Types.Hyperdata
 import Gargantext.Database.Admin.Types.Node
-import Gargantext.Database.Prelude -- (Cmd, CmdM)
+import Gargantext.Database.Prelude (Cmd, JSONB)
 import Gargantext.Database.Query.Facet (FacetDoc, OrderBy(..))
 import Gargantext.Database.Query.Table.Node
 import Gargantext.Database.Query.Table.Node.Children (getChildren)
 import Gargantext.Database.Query.Table.Node.Error (HasNodeError(..))
 import Gargantext.Database.Query.Table.Node.Update (Update(..), update)
+import Gargantext.Database.Query.Table.Node.Update qualified as U (update, Update(..))
 import Gargantext.Database.Query.Table.Node.UpdateOpaleye (updateHyperdata)
 import Gargantext.Database.Query.Table.NodeContext (nodeContextsCategory, nodeContextsScore)
 import Gargantext.Database.Query.Table.NodeNode
@@ -67,15 +76,6 @@ import Gargantext.Prelude
 import Servant
 import Test.QuickCheck (elements)
 import Test.QuickCheck.Arbitrary (Arbitrary, arbitrary)
-import qualified Gargantext.API.Node.DocumentUpload as DocumentUpload
-import qualified Gargantext.API.Node.DocumentsFromWriteNodes as DocumentsFromWriteNodes
-import qualified Gargantext.API.Node.FrameCalcUpload as FrameCalcUpload
-import qualified Gargantext.API.Node.Share  as Share
-import qualified Gargantext.API.Node.Update as Update
-import qualified Gargantext.API.Search as Search
-import qualified Gargantext.Database.Action.Delete as Action (deleteNode)
-import qualified Gargantext.Database.Query.Table.Node.Update as U (update, Update(..))
-import Gargantext.API.Auth.PolicyCheck
 
 
 -- | Admin NodesAPI

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

@@ -16,24 +16,21 @@ Main exports of Gargantext:
 module Gargantext.API.Node.Corpus.Export
   where
 
+import Data.HashMap.Strict qualified as HashMap
+import Data.List qualified as List
 import Data.Map.Strict (Map)
+import Data.Map.Strict qualified as Map
 import Data.Maybe (fromMaybe)
 import Data.Set (Set)
+import Data.Set qualified as Set
 import Data.Text (Text, pack)
-import qualified Data.List as List
-import qualified Data.Map.Strict as Map
-import qualified Data.Set as Set
-import qualified Data.HashMap.Strict as HashMap
-import Servant (Headers, Header, addHeader)
-
-import Gargantext.API.Node.Corpus.Export.Types
-import qualified Gargantext.API.Node.Document.Export.Types as DocumentExport
-import Gargantext.API.Ngrams.Types
 import Gargantext.API.Ngrams.Tools (filterListWithRoot, mapTermListRoot, getRepo)
+import Gargantext.API.Ngrams.Types
+import Gargantext.API.Node.Corpus.Export.Types
+import Gargantext.API.Node.Document.Export.Types qualified as DocumentExport
 import Gargantext.API.Prelude (GargNoServer)
-import Gargantext.Prelude.Crypto.Hash (hash)
-import Gargantext.Core.Types
 import Gargantext.Core.NodeStory
+import Gargantext.Core.Types
 import Gargantext.Database.Action.Metrics.NgramsByContext (getNgramsByContextOnlyUser)
 import Gargantext.Database.Admin.Config (userMaster)
 import Gargantext.Database.Admin.Types.Hyperdata (HyperdataDocument(..))
@@ -42,9 +39,11 @@ import Gargantext.Database.Query.Table.Node
 import Gargantext.Database.Query.Table.Node.Error (HasNodeError)
 import Gargantext.Database.Query.Table.Node.Select (selectNodesWithUsername)
 import Gargantext.Database.Query.Table.NodeContext (selectDocNodes)
-import Gargantext.Database.Schema.Ngrams (NgramsType(..))
 import Gargantext.Database.Schema.Context (_context_id, _context_hyperdata)
+import Gargantext.Database.Schema.Ngrams (NgramsType(..))
 import Gargantext.Prelude
+import Gargantext.Prelude.Crypto.Hash (hash)
+import Servant (Headers, Header, addHeader)
 
 --------------------------------------------------
 -- | Hashes are ordered by Set

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

@@ -32,7 +32,7 @@ import Servant.Swagger.Internal
 import Gargantext.API.Node.Corpus.New.Types
 import Gargantext.Core.Types (TODO)
 import Gargantext.Database.Admin.Types.Node
-import Gargantext.Database.Prelude -- (Cmd, CmdM)
+import Gargantext.Database.Prelude (Cmd)
 import Gargantext.Prelude
 import Gargantext.Prelude.Crypto.Hash (hash)
 

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

@@ -3,43 +3,46 @@
 module Gargantext.API.Node.Corpus.Searx where
 
 import Control.Lens (view)
+import Data.Aeson qualified as Aeson
 import Data.Aeson.TH (deriveJSON)
 import Data.Either (Either(..))
+import Data.HashMap.Strict qualified as HashMap
+import Data.Text qualified as T
+import Data.Text qualified as Text
 import Data.Time.Calendar (Day, toGregorian)
 import Data.Time.Format (defaultTimeLocale, formatTime, parseTimeM)
 import Data.Tuple.Select (sel1, sel2, sel3)
 import GHC.Generics (Generic)
 import Gargantext.Core (Lang(..))
-import Gargantext.Core.NLP (nlpServerGet)
+import Gargantext.Core.NLP (HasNLPServer, nlpServerGet)
+import Gargantext.Core.NodeStory (HasNodeStory)
+import Gargantext.Core.Text.Corpus.API qualified as API
 import Gargantext.Core.Text.List (buildNgramsLists)
 import Gargantext.Core.Text.List.Group.WithStem ({-StopSize(..),-} GroupParams(..))
 import Gargantext.Core.Text.Terms (TermType(..))
+import Gargantext.Core.Types (HasInvalidError)
 import Gargantext.Core.Types.Individu (User(..))
 import Gargantext.Core.Utils.Prefix (unPrefix)
 import Gargantext.Database.Action.Flow (addDocumentsToHyperCorpus) --, DataText(..))
 import Gargantext.Database.Action.Flow.List (flowList_DbRepo)
-import Gargantext.Database.Action.Flow.Types (FlowCmdM)
 import Gargantext.Database.Action.User (getUserId)
 import Gargantext.Database.Admin.Config (userMaster)
-import Gargantext.Database.Query.Table.Node (insertDefaultNodeIfNotExists)
 import Gargantext.Database.Admin.Types.Hyperdata.Corpus (HyperdataCorpus)
 import Gargantext.Database.Admin.Types.Hyperdata.Document (HyperdataDocument(..))
 import Gargantext.Database.Admin.Types.Node (CorpusId, ListId, NodeType(NodeTexts))
 import Gargantext.Database.Prelude (hasConfig)
-import Gargantext.Database.Query.Table.Node (defaultListMaybe, getOrMkList)
+import Gargantext.Database.Query.Table.Node (getOrMkList)
+import Gargantext.Database.Query.Table.Node (insertDefaultNodeIfNotExists)
+import Gargantext.Database.Query.Table.Node.Error (HasNodeError)
+import Gargantext.Database.Query.Tree.Error (HasTreeError)
 import Gargantext.Database.Query.Tree.Root (getOrMk_RootWithCorpus)
 import Gargantext.Prelude
 import Gargantext.Prelude.Config
 import Gargantext.Utils.Jobs (JobHandle, MonadJobStatus(..))
 import Network.HTTP.Client
 import Network.HTTP.Client.TLS
+import Prelude qualified
 import Protolude (catMaybes, encodeUtf8, rightToMaybe, Text, void)
-import qualified Data.Aeson as Aeson
-import qualified Data.HashMap.Strict as HashMap
-import qualified Data.Text as T
-import qualified Data.Text as Text
-import qualified Gargantext.Core.Text.Corpus.API as API
-import qualified Prelude
 
 langToSearx :: Lang -> Text
 langToSearx All = "en-US"
@@ -108,7 +111,12 @@ fetchSearxPage (FetchSearxParams { _fsp_language
   let dec = Aeson.eitherDecode $ responseBody res :: (Either Prelude.String SearxResponse)
   pure dec
 
-insertSearxResponse :: (MonadBase IO m, FlowCmdM env err m)
+insertSearxResponse :: ( MonadBase IO m
+                       , HasNodeStory env err m
+                       , HasNLPServer env
+                       , HasNodeError err
+                       , HasTreeError err
+                       , HasInvalidError err )
                     => User
                     -> CorpusId
                     -> ListId
@@ -145,13 +153,19 @@ insertSearxResponse user cId listId l (Right (SearxResponse { _srs_results })) =
   pure ()
 
 -- TODO Make an async task out of this?
-triggerSearxSearch :: (MonadBase IO m, FlowCmdM env err m, MonadJobStatus m)
-            => User
-            -> CorpusId
-            -> API.RawQuery
-            -> Lang
-            -> JobHandle m
-            -> m ()
+triggerSearxSearch :: ( MonadBase IO m
+                      , HasNodeStory env err m
+                      , HasNLPServer env
+                      , HasNodeError err
+                      , HasTreeError err
+                      , HasInvalidError err 
+                      , MonadJobStatus m )
+                   => User
+                   -> CorpusId
+                   -> API.RawQuery
+                   -> Lang
+                   -> JobHandle m
+                   -> m ()
 triggerSearxSearch user cId q l jobHandle = do
   userId <- getUserId user
 
@@ -167,12 +181,7 @@ triggerSearxSearch user cId q l jobHandle = do
   uId <- getUserId user
   let surl = _gc_frame_searx_url cfg
   -- printDebug "[triggerSearxSearch] surl" surl
-  mListId <- defaultListMaybe cId
-  listId <- case mListId of
-    Nothing -> do
-      listId <- getOrMkList cId uId
-      pure listId
-    Just listId -> pure listId
+  listId <- getOrMkList cId uId
 
   -- printDebug "[triggerSearxSearch] listId" listId
 

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

@@ -9,7 +9,7 @@ import Data.Proxy
 import Gargantext.Core
 import Gargantext.Database.Admin.Types.Hyperdata.Corpus
 import Gargantext.Database.Admin.Types.Node
-import Gargantext.Database.Prelude
+import Gargantext.Database.Prelude (DbCmd')
 import Gargantext.Database.Query.Table.Node
 import Gargantext.Database.Query.Table.Node.Error
 import Gargantext.Database.Query.Table.Node.UpdateOpaleye (updateHyperdata)

src/Gargantext/API/Node/New.hs

@@ -36,7 +36,7 @@ import Gargantext.API.Prelude
 import Gargantext.Database.Action.Flow.Types
 import Gargantext.Database.Action.Node
 import Gargantext.Database.Admin.Types.Node
-import Gargantext.Database.Prelude
+import Gargantext.Database.Prelude (Cmd)
 import Gargantext.Database.Query.Table.Node.Error (HasNodeError(..))
 import Gargantext.Database.Query.Table.Node.User
 import Gargantext.Database.Schema.Node

src/Gargantext/API/Node/Share.hs

@@ -27,7 +27,7 @@ import Gargantext.Database.Action.Share as DB (shareNodeWith, unPublish)
 import Gargantext.Database.Action.User
 import Gargantext.Database.Action.User.New
 import Gargantext.Database.Admin.Types.Node
-import Gargantext.Database.Prelude
+import Gargantext.Database.Prelude (CmdRandom)
 import Gargantext.Database.Query.Table.Node.Error (HasNodeError(..))
 import Gargantext.Database.Query.Tree (findNodesWithType)
 import Gargantext.Prelude

src/Gargantext/API/Prelude.hs

@@ -25,31 +25,31 @@ import Control.Exception (Exception)
 import Control.Lens (Prism', (#))
 import Control.Lens.TH (makePrisms)
 import Control.Monad (mapM_)
+import Control.Monad.Error.Class (MonadError(..))
 import Control.Monad.Except (ExceptT)
 import Control.Monad.Reader (ReaderT)
-import Control.Monad.Error.Class (MonadError(..))
 import Crypto.JOSE.Error as Jose
 import Data.Aeson.Types
-import qualified Data.Text as Text
 import Data.Typeable
 import Data.Validity
 import Gargantext.API.Admin.Orchestrator.Types
 import Gargantext.API.Admin.Types
+import Gargantext.Core.Mail.Types (HasMail)
 import Gargantext.Core.NLP (HasNLPServer)
 import Gargantext.Core.NodeStory
-import Gargantext.Core.Mail.Types (HasMail)
 import Gargantext.Core.Types
-import Gargantext.Database.Prelude
+import Gargantext.Database.Prelude (CmdM, CmdRandom, HasConnectionPool, HasConfig)
 import Gargantext.Database.Query.Table.Node.Error (NodeError(..), HasNodeError(..))
 import Gargantext.Database.Query.Tree
 import Gargantext.Prelude
-import           Gargantext.Utils.Jobs.Monad (MonadJobStatus(..), JobHandle)
-import qualified Gargantext.Utils.Jobs.Monad as Jobs
+import Gargantext.System.Logging
+import Gargantext.Utils.Jobs.Monad (MonadJobStatus(..), JobHandle)
+import Gargantext.Utils.Jobs.Monad qualified as Jobs
 import Servant
 import Servant.Job.Async
 import Servant.Job.Core (HasServerError(..), serverError)
-import qualified Servant.Job.Types as SJ
-import Gargantext.System.Logging
+import Servant.Job.Types qualified as SJ
+import qualified Data.Text as Text
 
 class HasJoseError e where
   _JoseError :: Prism' e Jose.Error

src/Gargantext/API/Public.hs

@@ -34,7 +34,7 @@ import qualified Data.Set as Set
 import Gargantext.API.Prelude
 import Gargantext.API.Node.File
 import Gargantext.Database.Query.Table.Node.Error (HasNodeError(..))
-import Gargantext.Database.Prelude
+import Gargantext.Database.Prelude (Cmd, DBCmd)
 import Gargantext.Database.Admin.Types.Hyperdata
 import Gargantext.Database.Admin.Types.Hyperdata.CorpusField
 import Gargantext.Database.Admin.Types.Node
@@ -79,7 +79,7 @@ api_node nId = do
 
 
 selectPublic :: HasNodeError err
-             => Cmd err [( Node HyperdataFolder, Maybe Int)]
+             => DBCmd err [( Node HyperdataFolder, Maybe Int)]
 selectPublic = selectPublicNodes
 
   -- For tests only

src/Gargantext/API/Table.hs

@@ -35,12 +35,8 @@ import Data.Aeson.TH (deriveJSON)
 import Data.Maybe
 import Data.Swagger
 import Data.Text (Text())
+import Data.Text qualified as T
 import GHC.Generics (Generic)
-import Prelude
-import Servant
-import Test.QuickCheck (elements)
-import Test.QuickCheck.Arbitrary (Arbitrary, arbitrary)
-
 import Gargantext.API.HashedResponse
 import Gargantext.API.Ngrams.Types (TabType(..))
 import Gargantext.API.Prelude (GargServer)
@@ -51,12 +47,15 @@ import Gargantext.Core.Utils.Prefix (unPrefix, unPrefixSwagger)
 import Gargantext.Database.Action.Learn (FavOrTrash(..), moreLike)
 import Gargantext.Database.Action.Search
 import Gargantext.Database.Admin.Types.Node hiding (ERROR, DEBUG)
-import Gargantext.Database.Prelude -- (Cmd, CmdM)
+import Gargantext.Database.Prelude (CmdM, DbCmd', DBCmd)
 import Gargantext.Database.Query.Facet (FacetDoc , runViewDocuments, runCountDocuments, OrderBy(..), runViewAuthorsDoc)
 import Gargantext.Database.Query.Table.Node.Error (HasNodeError)
 import Gargantext.Prelude
 import Gargantext.System.Logging
-import qualified Data.Text as T
+import Prelude
+import Servant
+import Test.QuickCheck (elements)
+import Test.QuickCheck.Arbitrary (Arbitrary, arbitrary)
 
 ------------------------------------------------------------------------
 
@@ -156,7 +155,7 @@ getTableHashApi cId tabType = do
   HashedResponse { hash = h } <- getTableApi cId tabType Nothing Nothing Nothing Nothing Nothing
   pure h
 
-searchInCorpus' :: (CmdM env err m, MonadLogger m)
+searchInCorpus' :: (DbCmd' env err m, MonadLogger m)
                 => CorpusId
                 -> Bool
                 -> RawQuery
@@ -185,7 +184,7 @@ getTable :: HasNodeError err
          -> Maybe OrderBy
          -> Maybe RawQuery
          -> Maybe Text
-         -> Cmd err FacetTableResult
+         -> DBCmd err FacetTableResult
 getTable cId ft o l order raw_query year = do
   docs      <- getTable' cId ft o l order query year
   docsCount <- runCountDocuments cId (ft == Just Trash) query year
@@ -201,7 +200,7 @@ getTable' :: HasNodeError err
           -> Maybe OrderBy
           -> Maybe Text
           -> Maybe Text
-          -> Cmd err [FacetDoc]
+          -> DBCmd err [FacetDoc]
 getTable' cId ft o l order query year =
   case ft of
     (Just Docs)      -> runViewDocuments cId False o l order query year
@@ -213,7 +212,7 @@ getTable' cId ft o l order query year =
 
 getPair :: ContactId -> Maybe TabType
          -> Maybe Offset  -> Maybe Limit
-         -> Maybe OrderBy -> Cmd err [FacetDoc]
+         -> Maybe OrderBy -> DBCmd err [FacetDoc]
 getPair cId ft o l order =
   case ft of
     (Just Docs)  -> runViewAuthorsDoc cId False o l order

src/Gargantext/Core/Mail.hs

@@ -14,16 +14,16 @@ module Gargantext.Core.Mail where
 import Control.Lens (view)
 import Control.Monad.Reader (MonadReader)
 import Control.Monad.Trans.Control (MonadBaseControl)
-import Network.URI.Encode (encodeText)
+import Data.List qualified as List
 import Data.Text (Text, unlines, splitOn)
 import Gargantext.Core.Types.Individu
+import Gargantext.Database.Prelude (HasConfig(..))
 import Gargantext.Database.Schema.User (UserLight(..))
 import Gargantext.Prelude
 import Gargantext.Prelude.Config (gc_url, gc_backend_name)
-import Gargantext.Database.Prelude
 import Gargantext.Prelude.Mail (gargMail, GargMail(..))
 import Gargantext.Prelude.Mail.Types (MailConfig)
-import qualified Data.List as List
+import Network.URI.Encode (encodeText)
 
 
 -- | Tool to put elsewhere

src/Gargantext/Core/NodeStoryFile.hs

@@ -23,7 +23,7 @@ import Control.Concurrent (MVar(), modifyMVar_, newMVar, readMVar, withMVar)
 import Control.Debounce (mkDebounce, defaultDebounceSettings, debounceFreq, debounceAction)
 import Gargantext.Core.NodeStory hiding (readNodeStoryEnv)
 import Gargantext.Core.Types (ListId, NodeId(..))
-import Gargantext.Database.Prelude (CmdM, hasConfig)
+import Gargantext.Database.Prelude (hasConfig)
 import Gargantext.Prelude
 import Gargantext.Prelude.Config (gc_repofilepath)
 import System.Directory (renameFile, createDirectoryIfMissing, doesFileExist, removeFile)
@@ -46,7 +46,7 @@ getRepo listIds = do
   -- v' <- liftBase $ readMVar v
   -- pure $ v'
 
-getRepoReadConfig :: (CmdM env err m)
+getRepoReadConfig :: (HasNodeStory env err m)
              => [ListId] -> m NodeListStory
 getRepoReadConfig listIds = do
   repoFP <- view $ hasConfig . gc_repofilepath

src/Gargantext/Core/Text/List.hs

@@ -18,14 +18,19 @@ module Gargantext.Core.Text.List
 
 import Control.Lens hiding (both) -- ((^.), view, over, set, (_1), (_2))
 import Data.HashMap.Strict (HashMap)
+import Data.HashMap.Strict qualified as HashMap
 import Data.HashSet (HashSet)
+import Data.HashSet qualified as HashSet
+import Data.List qualified as List
 import Data.Map.Strict (Map)
+import Data.Map.Strict qualified as Map
 import Data.Monoid (mempty)
 import Data.Ord (Down(..))
 import Data.Set (Set)
--- import Data.Text (Text)
+import Data.Set qualified as Set
 import Data.Tuple.Extra (both)
 import Gargantext.API.Ngrams.Types (NgramsElement, NgramsTerm(..))
+import Gargantext.Core.NLP (HasNLPServer)
 import Gargantext.Core.NodeStory
 import Gargantext.Core.Text (size)
 import Gargantext.Core.Text.List.Group
@@ -36,10 +41,11 @@ import Gargantext.Core.Text.List.Social.Prelude
 import Gargantext.Core.Text.Metrics (scored', Scored(..), scored_speExc, scored_genInc, normalizeGlobal, normalizeLocal, scored_terms)
 import Gargantext.Core.Types (ListType(..), MasterCorpusId, UserCorpusId)
 import Gargantext.Core.Types.Individu (User(..))
+import Gargantext.Data.HashMap.Strict.Utils qualified as HashMap
 import Gargantext.Database.Action.Metrics.NgramsByContext (getContextsByNgramsUser, getContextsByNgramsOnlyUser)
 import Gargantext.Database.Action.Metrics.TFICF (getTficf_withSample)
 import Gargantext.Database.Admin.Types.Node (NodeId)
-import Gargantext.Database.Prelude (CmdM)
+import Gargantext.Database.Prelude (DBCmd)
 import Gargantext.Database.Query.Table.Ngrams (text2ngrams)
 import Gargantext.Database.Query.Table.NgramsPostag (selectLems)
 import Gargantext.Database.Query.Table.Node (defaultList)
@@ -47,12 +53,6 @@ import Gargantext.Database.Query.Table.Node.Error (HasNodeError())
 import Gargantext.Database.Query.Tree.Error (HasTreeError)
 import Gargantext.Database.Schema.Ngrams (NgramsType(..), Ngrams(..))
 import Gargantext.Prelude
-import qualified Data.HashMap.Strict as HashMap
-import qualified Data.HashSet as HashSet
-import qualified Data.List    as List
-import qualified Data.Map.Strict as Map
-import qualified Data.Set     as Set
-import qualified Gargantext.Data.HashMap.Strict.Utils as HashMap
 
 {-
 -- TODO maybe useful for later
@@ -65,7 +65,7 @@ isStopTerm (StopSize n) x = Text.length x < n || any isStopChar (Text.unpack x)
 
 -- | TODO improve grouping functions of Authors, Sources, Institutes..
 buildNgramsLists :: ( HasNodeStory env err m
-                    , CmdM     env err m
+                    , HasNLPServer env
                     , HasTreeError err
                     , HasNodeError err
                     )
@@ -90,7 +90,7 @@ data MapListSize = MapListSize { unMapListSize :: !Int }
 data MaxListSize = MaxListSize { unMaxListSize :: !Int }
 
 buildNgramsOthersList :: ( HasNodeError err
-                         , CmdM     env err m
+                         , HasNLPServer env
                          , HasNodeStory env err m
                          , HasTreeError err
                          )
@@ -134,11 +134,9 @@ buildNgramsOthersList user uCid mfslw _groupParams (nt, MapListSize mapListSize,
 
 
 getGroupParams :: ( HasNodeError err
-                  , CmdM     env err m
-                  , HasNodeStory env err m
                   , HasTreeError err
                   )
-               => GroupParams -> HashSet Ngrams -> m GroupParams
+               => GroupParams -> HashSet Ngrams -> DBCmd err GroupParams
 getGroupParams gp@(GroupWithPosTag l nsc _m) ng = do
   !hashMap <- HashMap.fromList <$> selectLems l nsc (HashSet.toList ng)
   -- printDebug "hashMap" hashMap
@@ -148,7 +146,7 @@ getGroupParams gp _ = pure gp
 
 -- TODO use ListIds
 buildNgramsTermsList :: ( HasNodeError err
-                        , CmdM     env err m
+                        , HasNLPServer env
                         , HasNodeStory env err m
                         , HasTreeError err
                         )

src/Gargantext/Core/Text/List/Social.hs

@@ -17,29 +17,29 @@ import Control.Lens (view)
 import Control.Monad (mzero)
 import Data.Aeson
 import Data.HashMap.Strict (HashMap)
+import Data.List qualified as List
 import Data.Map.Strict (Map)
+import Data.Map.Strict qualified as Map
 import Data.Monoid (mconcat)
 import Data.Pool
 import Data.Swagger
+import Data.Text qualified as T
+import Data.Vector qualified as V
 import GHC.Generics
 import Gargantext.API.Ngrams.Types (NgramsTerm, NgramsPatch)
-import Gargantext.Core.NodeStory (HasNodeStory, getNodesArchiveHistory)
+import Gargantext.Core.NodeStory (getNodesArchiveHistory)
 import Gargantext.Core.Text.List.Social.Find (findListsId)
 import Gargantext.Core.Text.List.Social.Patch (addScorePatches)
 import Gargantext.Core.Text.List.Social.Prelude (FlowCont, FlowListScores)
 import Gargantext.Core.Types.Individu (User)
 import Gargantext.Database.Admin.Types.Node (ListId, NodeId(..))
-import Gargantext.Database.Prelude
+import Gargantext.Database.Prelude (DBCmd, connPool)
 import Gargantext.Database.Query.Table.Node.Error (HasNodeError)
 import Gargantext.Database.Query.Tree (NodeMode(Private), HasTreeError)
 import Gargantext.Database.Schema.Ngrams (NgramsType)
 import Gargantext.Prelude
 import Test.QuickCheck
 import Web.Internal.HttpApiData (ToHttpApiData, FromHttpApiData, parseUrlPiece, toUrlPiece)
-import qualified Data.List       as List
-import qualified Data.Map.Strict as Map
-import qualified Data.Text       as T
-import qualified Data.Vector     as V
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
 -- | Main parameters
@@ -116,84 +116,72 @@ keepAllParents _           = KeepAllParents True
 -}
 
 ------------------------------------------------------------------------
-flowSocialList :: ( HasNodeStory env err m
-                   , CmdM     env err m
-                   , HasNodeError err
-                   , HasTreeError err
-                   )
-                  => Maybe FlowSocialListWith
-                  -> User
-                  -> NgramsType
-                  -> FlowCont NgramsTerm FlowListScores
-                  -> m (FlowCont NgramsTerm FlowListScores)
+flowSocialList :: ( HasNodeError err
+                  , HasTreeError err
+                  )
+               => Maybe FlowSocialListWith
+               -> User
+               -> NgramsType
+               -> FlowCont NgramsTerm FlowListScores
+               -> DBCmd err (FlowCont NgramsTerm FlowListScores)
 flowSocialList Nothing u = flowSocialList' MySelfFirst u
 flowSocialList (Just (FlowSocialListWithPriority p))  u = flowSocialList' p u
 flowSocialList (Just (FlowSocialListWithLists    ls)) _ = getHistoryScores ls
 flowSocialList (Just (NoList _))                     _u = panic "[G.C.T.L.Social] Should not be executed"
 
-flowSocialList' :: ( HasNodeStory env err m
-                   , CmdM     env err m
-                   , HasNodeError err
+flowSocialList' :: ( HasNodeError err
                    , HasTreeError err
                    )
                   => FlowSocialListPriority
                   -> User -> NgramsType
                   -> FlowCont NgramsTerm FlowListScores
-                  -> m (FlowCont NgramsTerm FlowListScores)
+                  -> DBCmd err (FlowCont NgramsTerm FlowListScores)
 flowSocialList' flowPriority user nt flc =
   mconcat <$> mapM (flowSocialListByMode'   user nt flc)
                    (flowSocialListPriority flowPriority)
     where
 
-      flowSocialListByMode' :: ( HasNodeStory env err m
-                               , CmdM     env err m
-                               , HasNodeError err
+      flowSocialListByMode' :: ( HasNodeError err
                                , HasTreeError err
                                )
                             => User -> NgramsType
                             -> FlowCont NgramsTerm FlowListScores
                             -> NodeMode
-                            -> m (FlowCont NgramsTerm FlowListScores)
+                            -> DBCmd err (FlowCont NgramsTerm FlowListScores)
       flowSocialListByMode' user' nt' flc' mode =
             findListsId user' mode
         >>= flowSocialListByModeWith nt' flc'
 
 
-      flowSocialListByModeWith :: ( HasNodeStory env err m
-                                  , CmdM     env err m
-                                  , HasNodeError err
+      flowSocialListByModeWith :: ( HasNodeError err
                                   , HasTreeError err
                                   )
                                => NgramsType
                                -> FlowCont NgramsTerm FlowListScores
                                -> [ListId]
-                               -> m (FlowCont NgramsTerm FlowListScores)
+                               -> DBCmd err (FlowCont NgramsTerm FlowListScores)
       flowSocialListByModeWith nt'' flc'' listes =
         getHistoryScores listes nt'' flc''
 
 
 -----------------------------------------------------------------
-getHistoryScores :: ( HasNodeStory env err m
-                    , CmdM         env err m
-                    , HasNodeError     err
+getHistoryScores :: ( HasNodeError     err
                     , HasTreeError     err
                     )
                  => [ListId]
                  -> NgramsType
                  -> FlowCont NgramsTerm FlowListScores
-                 -> m (FlowCont NgramsTerm FlowListScores)
+                 -> DBCmd err (FlowCont NgramsTerm FlowListScores)
 getHistoryScores lists nt fl =
   addScorePatches nt lists fl <$> getHistory [nt] lists
 
 
-getHistory :: ( HasNodeStory env err m
-              , CmdM     env err m
-              , HasNodeError err
+getHistory :: ( HasNodeError err
               , HasTreeError err
               )
          => [NgramsType]
          -> [ListId]
-         -> m (Map ListId (Map NgramsType [HashMap NgramsTerm NgramsPatch]))
+         -> DBCmd err (Map ListId (Map NgramsType [HashMap NgramsTerm NgramsPatch]))
 getHistory types listsId = do
   pool <- view connPool
   nsp  <- liftBase $ withResource pool $ \c -> getNodesArchiveHistory c listsId

src/Gargantext/Core/Text/List/Social/Find.hs

@@ -17,7 +17,7 @@ import Control.Lens (view)
 import Gargantext.Core.Types.Individu
 import Gargantext.Database.Admin.Config
 import Gargantext.Database.Admin.Types.Node
-import Gargantext.Database.Prelude
+import Gargantext.Database.Prelude (DBCmd)
 import Gargantext.Database.Query.Table.Node.Error
 import Gargantext.Database.Query.Tree
 import Gargantext.Database.Query.Tree.Root (getRootId)
@@ -25,7 +25,7 @@ import Gargantext.Prelude
 
 ------------------------------------------------------------------------
 findListsId :: (HasNodeError err, HasTreeError err)
-            => User -> NodeMode -> Cmd err [NodeId]
+            => User -> NodeMode -> DBCmd err [NodeId]
 findListsId u mode = do
   rootId <- getRootId u
   ns <- map (view dt_nodeId) <$> filter ((== nodeTypeId NodeList) . (view dt_typeId))
@@ -40,7 +40,7 @@ findListsId u mode = do
 findNodes' :: (HasTreeError err, HasNodeError err)
           => RootId
           -> NodeMode
-          -> Cmd err [DbTreeNode]
+          -> DBCmd err [DbTreeNode]
 findNodes' r Private = do
   pv <- (findNodes r Private $ [NodeFolderPrivate]          <> commonNodes)
   sh <- (findNodes' r Shared)
@@ -52,3 +52,5 @@ findNodes' r PublicDirect = findNodes r Public  $ [NodeFolderPublic ]          <
 
 commonNodes:: [NodeType]
 commonNodes = [NodeFolder, NodeCorpus, NodeList, NodeFolderShared, NodeTeam]
+
+

src/Gargantext/Core/Viz/Chart.hs

@@ -25,7 +25,7 @@ import Gargantext.Core.NodeStory (HasNodeStory)
 import Gargantext.Core.Text.Metrics.Count (occurrencesWith)
 import Gargantext.Core.Types.Main
 import Gargantext.Database.Admin.Config
-import Gargantext.Database.Prelude
+import Gargantext.Database.Prelude (DBCmd)
 import Gargantext.Database.Query.Table.Node
 import Gargantext.Database.Query.Table.Node.Select
 import Gargantext.Database.Query.Table.NodeContext (selectDocsDates)

src/Gargantext/Core/Viz/Graph/API.hs

@@ -108,7 +108,7 @@ getGraph _uId nId = do
         let defaultEdgesStrength   = Strong
         let defaultBridgenessMethod = BridgenessMethod_Basic
         graph' <- computeGraph cId defaultPartitionMethod defaultBridgenessMethod (withMetric defaultMetric) defaultEdgesStrength (NgramsTerms, NgramsTerms) repo
-        mt     <- defaultGraphMetadata cId "Title" repo defaultMetric defaultEdgesStrength
+        mt     <- defaultGraphMetadata cId listId "Title" repo defaultMetric defaultEdgesStrength
         let
           graph'' = set graph_metadata (Just mt) graph'
           hg = HyperdataGraphAPI graph'' camera
@@ -167,7 +167,7 @@ recomputeGraph _uId nId partitionMethod bridgeMethod maybeSimilarity maybeStreng
 
   case graph of
     Nothing     -> do
-      mt     <- defaultGraphMetadata cId "Title" repo (fromMaybe Order1 maybeSimilarity) strength
+      mt     <- defaultGraphMetadata cId listId "Title" repo (fromMaybe Order1 maybeSimilarity) strength
       g <- computeG $ Just mt
       pure $ trace "[G.V.G.API.recomputeGraph] Graph empty, computed" g
     Just graph' -> if (listVersion == Just v) && (not force)
@@ -225,14 +225,13 @@ computeGraph corpusId partitionMethod bridgeMethod similarity strength (nt1,nt2)
 
 defaultGraphMetadata :: HasNodeError err
                      => CorpusId
+                     -> ListId
                      -> Text
                      -> NodeListStory
                      -> GraphMetric
                      -> Strength
                      -> DBCmd err GraphMetadata
-defaultGraphMetadata cId t repo gm str = do
-  lId  <- defaultList cId
-
+defaultGraphMetadata cId lId t repo gm str = do
   pure $ GraphMetadata { _gm_title         = t
                        , _gm_metric        = gm
                        , _gm_edgesStrength = Just str
@@ -282,11 +281,14 @@ type GraphVersionsAPI = Summary "Graph versions"
 
 graphVersionsAPI :: UserId -> NodeId -> GargServer GraphVersionsAPI
 graphVersionsAPI u n =
-           graphVersions 0 n
+           graphVersions u n
       :<|> recomputeVersions u n
 
-graphVersions :: Int -> NodeId -> GargNoServer GraphVersions
-graphVersions n nId = do
+graphVersions :: (HasNodeStory env err m)
+              => UserId
+              -> NodeId
+              -> m GraphVersions
+graphVersions u nId = do
   nodeGraph <- getNodeWith nId (Proxy :: Proxy HyperdataGraph)
   let
     graph =  nodeGraph
@@ -303,21 +305,14 @@ graphVersions n nId = do
   mcId <- getClosestParentIdByType nId NodeCorpus
   let cId = maybe (panic "[G.V.G.API] Node has no parent") identity mcId
 
-  maybeListId <- defaultListMaybe cId
-  case maybeListId of
-    Nothing     -> if n <= 2
-                      then graphVersions (n+1) cId
-                      else panic "[G.V.G.API] list not found after iterations"
-
-    Just listId -> do
-      repo <- getRepo [listId]
-      let v = repo ^. unNodeStory . at listId . _Just . a_version
-      -- printDebug "graphVersions" v
+  listId <- getOrMkList cId u
+  repo <- getRepo [listId]
+  let v = repo ^. unNodeStory . at listId . _Just . a_version
+  -- printDebug "graphVersions" v
 
-      pure $ GraphVersions { gv_graph = listVersion
-                           , gv_repo = v }
+  pure $ GraphVersions { gv_graph = listVersion
+                       , gv_repo = v }
 
---recomputeVersions :: UserId -> NodeId -> GargNoServer Graph
 recomputeVersions :: HasNodeStory env err m
                   => UserId
                   -> NodeId
@@ -325,10 +320,11 @@ recomputeVersions :: HasNodeStory env err m
 recomputeVersions uId nId = recomputeGraph uId nId Spinglass BridgenessMethod_Basic Nothing Nothing NgramsTerms NgramsTerms False
 
 ------------------------------------------------------------
-graphClone :: UserId
+graphClone :: HasNodeError err
+           => UserId
            -> NodeId
            -> HyperdataGraphAPI
-           -> GargNoServer NodeId
+           -> DBCmd err NodeId
 graphClone uId pId (HyperdataGraphAPI { _hyperdataAPIGraph = graph
                                       , _hyperdataAPICamera = camera }) = do
   let nodeType = NodeGraph

src/Gargantext/Core/Viz/Phylo/Legacy/LegacyMain.hs

@@ -16,42 +16,34 @@ Portability : POSIX
 module Gargantext.Core.Viz.Phylo.Legacy.LegacyMain
   where
 
--- import Data.GraphViz
--- import qualified Data.ByteString as DB
 import Control.Lens hiding (Level)
-import qualified Data.List as List
+import Data.HashMap.Strict qualified as HashMap
+import Data.List qualified as List
 import Data.Maybe
 import Data.Proxy
+import Data.Set qualified as Set
 import Data.Text (Text)
+import Data.Text qualified as Text
 import Debug.Trace (trace)
 import GHC.IO (FilePath)
 import Gargantext.API.Ngrams.Tools (getTermsWith)
 import Gargantext.API.Ngrams.Types
-import Gargantext.Database.Admin.Types.Node
+import Gargantext.Core (HasDBid, withDefaultLanguage)
+import Gargantext.Core.NodeStory (HasNodeStory)
 import Gargantext.Core.Text.Context (TermList)
 import Gargantext.Core.Text.Terms.WithList
-import Gargantext.Database.Query.Table.Node(defaultList, getNodeWith)
-import Gargantext.Prelude
-import Gargantext.Database.Action.Flow.Types
+import Gargantext.Core.Types
 import Gargantext.Core.Viz.LegacyPhylo hiding (Svg, Dot)
 import Gargantext.Database.Admin.Types.Hyperdata
+import Gargantext.Database.Query.Table.Node(defaultList, getNodeWith)
+import Gargantext.Database.Query.Table.NodeContext (selectDocs)
 import Gargantext.Database.Schema.Ngrams (NgramsType(..))
 import Gargantext.Database.Schema.Node
-import Gargantext.Database.Query.Table.NodeContext (selectDocs)
-import Gargantext.Core.Types
-import Gargantext.Core (HasDBid, withDefaultLanguage)
-
--- import Gargantext.Core.Viz.Phylo.LevelMaker (toPhylo)
--- import Gargantext.Core.Viz.Phylo.Tools
--- import Gargantext.Core.Viz.Phylo.View.Export
--- import Gargantext.Core.Viz.Phylo.View.ViewMaker    -- TODO Just Maker is fine
-import qualified Data.HashMap.Strict as HashMap
-import qualified Data.Set            as Set
-import qualified Data.Text           as Text
+import Gargantext.Prelude
 
 type MinSizeBranch = Int
 
-flowPhylo :: (FlowCmdM env err m, HasDBid NodeType)
+flowPhylo :: (HasNodeStory env err m, HasDBid NodeType)
           => CorpusId
           -> m Phylo
 flowPhylo cId = do

src/Gargantext/Database.hs

@@ -26,7 +26,7 @@ module Gargantext.Database ( module Gargantext.Database.Prelude
     where
 
 import Gargantext.Prelude
-import Gargantext.Database.Prelude -- (connectGargandb)
+import Gargantext.Database.Prelude (DBCmd) -- (connectGargandb)
 
 -- import Gargantext.Database.Schema.Node
 -- import Gargantext.Database.Query.Table.Node
@@ -36,11 +36,11 @@ import Gargantext.Database.Query.Table.NodeNode
 
 
 class InsertDB a where
-  insertDB :: a -> Cmd err Int
+  insertDB :: a -> DBCmd err Int
 
 {-
 class DeleteDB a where
-  deleteDB :: a -> Cmd err Int
+  deleteDB :: a -> DBCmd err Int
 -}
 
 instance InsertDB [NodeNode] where

src/Gargantext/Database/Action/Flow.hs

@@ -77,7 +77,7 @@ import Gargantext.Core (Lang(..), PosTagAlgo(..), NLPServerConfig)
 import Gargantext.Core (withDefaultLanguage)
 import Gargantext.Core.Ext.IMTUser (readFile_Annuaire)
 import Gargantext.Core.Flow.Types
-import Gargantext.Core.NLP (nlpServerGet)
+import Gargantext.Core.NLP (HasNLPServer, nlpServerGet)
 import Gargantext.Core.NodeStory (HasNodeStory)
 import Gargantext.Core.Text
 import Gargantext.Core.Text.Corpus.API qualified as API
@@ -88,7 +88,7 @@ import Gargantext.Core.Text.List.Social (FlowSocialListWith(..))
 import Gargantext.Core.Text.Terms
 import Gargantext.Core.Text.Terms.Mono.Stem.En (stemIt)
 import Gargantext.Core.Text.Terms.WithList (MatchedText, buildPatternsWith, termsInText)
-import Gargantext.Core.Types (POS(NP), TermsCount)
+import Gargantext.Core.Types (HasInvalidError, POS(NP), TermsCount)
 import Gargantext.Core.Types.Individu (User(..))
 import Gargantext.Core.Types.Main
 import Gargantext.Core.Types.Query (Limit)
@@ -103,7 +103,7 @@ import Gargantext.Database.Action.Search (searchDocInDatabase)
 import Gargantext.Database.Admin.Config (userMaster, corpusMasterName)
 import Gargantext.Database.Admin.Types.Hyperdata
 import Gargantext.Database.Admin.Types.Node hiding (DEBUG) -- (HyperdataDocument(..), NodeType(..), NodeId, UserId, ListId, CorpusId, RootId, MasterCorpusId, MasterUserId)
-import Gargantext.Database.Prelude
+import Gargantext.Database.Prelude (DbCmd', DBCmd)
 import Gargantext.Database.Query.Table.ContextNodeNgrams2
 import Gargantext.Database.Query.Table.Ngrams
 import Gargantext.Database.Query.Table.Node
@@ -127,7 +127,7 @@ import PUBMED.Types qualified as PUBMED
 ------------------------------------------------------------------------
 -- Imports for upgrade function
 import Gargantext.Database.Query.Tree.Root (getRootId)
-import Gargantext.Database.Query.Tree (findNodesId)
+import Gargantext.Database.Query.Tree (findNodesId, HasTreeError)
 
 ------------------------------------------------------------------------
 -- TODO use internal with API name (could be old data)
@@ -157,13 +157,13 @@ printDataText (DataNew (maybeInt, conduitData)) = do
   putText $ show (maybeInt, res)
 
 -- TODO use the split parameter in config file
-getDataText :: FlowCmdM env err m
+getDataText :: (HasNodeError err)
             => DataOrigin
             -> TermType Lang
             -> API.RawQuery
             -> Maybe PUBMED.APIKey
             -> Maybe API.Limit
-            -> m (Either API.GetCorpusError DataText)
+            -> DBCmd err (Either API.GetCorpusError DataText)
 getDataText (ExternalOrigin api) la q mPubmedAPIKey li = do
   eRes <- liftBase $ API.get api (_tt_lang la) q mPubmedAPIKey li
   pure $ DataNew <$> eRes
@@ -175,12 +175,12 @@ getDataText (InternalOrigin _) _la q _ _li = do
   ids <-  map fst <$> searchDocInDatabase cId (stemIt $ API.getRawQuery q)
   pure $ Right $ DataOld ids
 
-getDataText_Debug :: FlowCmdM env err m
-            => DataOrigin
-            -> TermType Lang
-            -> API.RawQuery
-            -> Maybe API.Limit
-            -> m ()
+getDataText_Debug :: (HasNodeError err)
+                  => DataOrigin
+                  -> TermType Lang
+                  -> API.RawQuery
+                  -> Maybe API.Limit
+                  -> DBCmd err ()
 getDataText_Debug a l q li = do
   result <- getDataText a l q Nothing li
   case result of
@@ -190,7 +190,12 @@ getDataText_Debug a l q li = do
 
 -------------------------------------------------------------------------------
 flowDataText :: forall env err m.
-                ( FlowCmdM env err m
+                ( DbCmd' env err m
+                , HasNodeStory env err m
+                , MonadLogger m
+                , HasNLPServer env
+                , HasTreeError err
+                , HasInvalidError err
                 , MonadJobStatus m
                 )
                 => User
@@ -214,7 +219,13 @@ flowDataText u (DataNew (mLen, txtC)) tt cid mfslw jobHandle = do
 
 ------------------------------------------------------------------------
 -- TODO use proxy
-flowAnnuaire :: (FlowCmdM env err m, MonadJobStatus m)
+flowAnnuaire :: ( DbCmd' env err m
+                , HasNodeStory env err m
+                , MonadLogger m
+                , HasNLPServer env
+                , HasTreeError err
+                , HasInvalidError err
+                , MonadJobStatus m )
              => User
              -> Either CorpusName [CorpusId]
              -> (TermType Lang)
@@ -227,7 +238,13 @@ flowAnnuaire u n l filePath jobHandle = do
   flow (Nothing :: Maybe HyperdataAnnuaire) u n l Nothing (fromIntegral $ length docs, yieldMany docs) jobHandle
 
 ------------------------------------------------------------------------
-flowCorpusFile :: (FlowCmdM env err m, MonadJobStatus m)
+flowCorpusFile :: ( DbCmd' env err m
+                  , HasNodeStory env err m
+                  , MonadLogger m
+                  , HasNLPServer env
+                  , HasTreeError err
+                  , HasInvalidError err
+                  , MonadJobStatus m )
            => User
            -> Either CorpusName [CorpusId]
            -> Limit -- Limit the number of docs (for dev purpose)
@@ -250,7 +267,14 @@ flowCorpusFile u n _l la ft ff fp mfslw jobHandle = do
 ------------------------------------------------------------------------
 -- | TODO improve the needed type to create/update a corpus
 -- (For now, Either is enough)
-flowCorpus :: (FlowCmdM env err m, FlowCorpus a, MonadJobStatus m)
+flowCorpus :: ( DbCmd' env err m
+              , HasNodeStory env err m
+              , MonadLogger m
+              , HasNLPServer env
+              , HasTreeError err
+              , HasInvalidError err
+              , FlowCorpus a
+              , MonadJobStatus m )
            => User
            -> Either CorpusName [CorpusId]
            -> TermType Lang
@@ -262,7 +286,12 @@ flowCorpus = flow (Nothing :: Maybe HyperdataCorpus)
 
 
 flow :: forall env err m a c.
-        ( FlowCmdM env err m
+        ( DbCmd' env err m
+        , HasNodeStory env err m
+        , MonadLogger m
+        , HasNLPServer env
+        , HasTreeError err
+        , HasInvalidError err
         , FlowCorpus a
         , MkCorpus c
         , MonadJobStatus m
@@ -338,7 +367,11 @@ createNodes user corpusName ctype = do
   pure (userId, userCorpusId, listId)
 
 
-flowCorpusUser :: ( FlowCmdM env err m
+flowCorpusUser :: ( HasNodeError err
+                  , HasInvalidError err
+                  , HasNLPServer env
+                  , HasTreeError err
+                  , HasNodeStory env err m
                   , MkCorpus c
                   )
                => Lang
@@ -589,7 +622,8 @@ instance HasText a => HasText (Node a)
 -- | TODO putelsewhere
 -- | Upgrade function
 -- Suppose all documents are English (this is the case actually)
-indexAllDocumentsWithPosTag :: FlowCmdM env err m
+indexAllDocumentsWithPosTag :: ( HasNodeStory env err m
+                               , HasNLPServer env )
                             => m ()
 indexAllDocumentsWithPosTag = do
   rootId    <- getRootId (UserName userMaster)
@@ -598,7 +632,8 @@ indexAllDocumentsWithPosTag = do
   _ <- mapM extractInsert (splitEvery 1000 docs)
   pure ()
 
-extractInsert :: FlowCmdM env err m
+extractInsert :: ( HasNodeStory env err m
+                 , HasNLPServer env )
               => [Node HyperdataDocument] -> m ()
 extractInsert docs = do
   let documentsWithId = map (\doc -> Indexed (doc ^. node_id) doc) docs

src/Gargantext/Database/Action/Flow/List.hs

@@ -17,27 +17,26 @@ Portability : POSIX
 module Gargantext.Database.Action.Flow.List
     where
 
+-- import Gargantext.Database.Query.Table.Node_NodeNgramsNodeNgrams
 import Control.Concurrent
 import Control.Lens ((^.), (+~), (%~), at, (.~), _Just)
 import Control.Monad.Reader
+import Data.List qualified as List
 import Data.Map.Strict (Map, toList)
+import Data.Map.Strict qualified as Map
+import Data.Map.Strict.Patch qualified as PM
 import Data.Text (Text)
 import Gargantext.API.Ngrams (saveNodeStory)
 import Gargantext.API.Ngrams.Tools (getNodeStoryVar)
 import Gargantext.API.Ngrams.Types
+import Gargantext.Core.NodeStory
 import Gargantext.Core.Types (HasInvalidError(..), assertValid)
 import Gargantext.Core.Types.Main (ListType(CandidateTerm))
-import Gargantext.Core.NodeStory
-import Gargantext.Database.Action.Flow.Types
 import Gargantext.Database.Admin.Types.Node
+import Gargantext.Database.Query.Table.Ngrams qualified as TableNgrams
 import Gargantext.Database.Query.Table.NodeNgrams (NodeNgramsPoly(..), NodeNgramsW, listInsertDb,{- getCgramsId -})
--- import Gargantext.Database.Query.Table.Node_NodeNgramsNodeNgrams
 import Gargantext.Database.Schema.Ngrams (NgramsType(..))
 import Gargantext.Prelude
-import qualified Data.List as List
-import qualified Data.Map.Strict as Map
-import qualified Data.Map.Strict.Patch as PM
-import qualified Gargantext.Database.Query.Table.Ngrams as TableNgrams
 
 -- FLOW LIST
 -- 1. select specific terms of the corpus when compared with others langs
@@ -82,10 +81,10 @@ flowList_Tficf' u m nt f = do
 
 
 ------------------------------------------------------------------------
-flowList_DbRepo :: FlowCmdM env err m
-         => ListId
-         -> Map NgramsType [NgramsElement]
-         -> m ListId
+flowList_DbRepo :: (HasInvalidError err, HasNodeStory env err m)
+                => ListId
+                -> Map NgramsType [NgramsElement]
+                -> m ListId
 flowList_DbRepo lId ngs = do
   -- printDebug "listId flowList" lId
   _mapCgramsId <- listInsertDb lId toNodeNgramsW (Map.toList ngs)
@@ -157,10 +156,10 @@ toNodeNgramsW' l'' ngs = [ NodeNgrams { _nng_id            = Nothing
                          ]
 
 
-listInsert :: FlowCmdM env err m
-             => ListId
-             -> Map NgramsType [NgramsElement]
-             -> m ()
+listInsert :: (HasInvalidError err, HasNodeStory env err m)
+           => ListId
+           -> Map NgramsType [NgramsElement]
+           -> m ()
 listInsert lId ngs = mapM_ (\(typeList, ngElmts)
                              -> putListNgrams lId typeList ngElmts) (toList ngs)
 

src/Gargantext/Database/Action/Flow/Pairing.hs

@@ -16,13 +16,18 @@ module Gargantext.Database.Action.Flow.Pairing
   -- (pairing)
     where
 
-import Debug.Trace (trace)
 import Control.Lens (_Just, (^.), view)
-import Data.Hashable (Hashable)
 import Data.HashMap.Strict (HashMap)
+import Data.HashMap.Strict qualified as HM
+import Data.HashMap.Strict qualified as HashMap
+import Data.Hashable (Hashable)
+import Data.List qualified as List
 import Data.Maybe (fromMaybe, catMaybes)
 import Data.Set (Set)
+import Data.Set qualified as Set
 import Data.Text (Text)
+import Data.Text qualified as Text
+import Debug.Trace (trace)
 import Gargantext.API.Ngrams.Tools
 import Gargantext.API.Ngrams.Types (NgramsTerm(..))
 import Gargantext.Core
@@ -42,16 +47,11 @@ import Gargantext.Database.Query.Table.Node.Error (HasNodeError)
 import Gargantext.Database.Query.Table.Node.Select (selectNodesWithUsername)
 import Gargantext.Database.Query.Table.NodeContext_NodeContext (insertNodeContext_NodeContext)
 import Gargantext.Database.Query.Table.NodeNode (insertNodeNode)
+import Gargantext.Database.Prelude (Cmd, runOpaQuery)
 import Gargantext.Database.Schema.Ngrams -- (NgramsType(..))
 import Gargantext.Database.Schema.Node
--- import Gargantext.Database.Schema.Context
-import qualified Data.HashMap.Strict as HM
 import Gargantext.Prelude hiding (sum)
 import Opaleye
-import qualified Data.HashMap.Strict as HashMap
-import qualified Data.List           as List
-import qualified Data.Set            as Set
-import qualified Data.Text           as Text
 
 -- | isPairedWith
 -- All NodeAnnuaire paired with a Corpus of NodeId nId:

src/Gargantext/Database/Action/Learn.hs

@@ -15,19 +15,19 @@ Portability : POSIX
 module Gargantext.Database.Action.Learn
   where
 
+import Data.List qualified as List
 import Data.Maybe
 import Data.Text (Text)
+import Data.Text qualified as Text
 import Gargantext.Core
+import Gargantext.Core.Text.Learn
 import Gargantext.Core.Types.Query (Offset, Limit(..))
 import Gargantext.Database.Admin.Types.Hyperdata
 import Gargantext.Database.Admin.Types.Node
+import Gargantext.Database.Prelude (DBCmd)
 import Gargantext.Database.Query.Facet
 import Gargantext.Database.Query.Table.Node.Error (HasNodeError)
-import Gargantext.Database.Prelude (Cmd)
 import Gargantext.Prelude
-import Gargantext.Core.Text.Learn
-import qualified Data.List as List
-import qualified Data.Text as Text
 
 data FavOrTrash = IsFav | IsTrash
   deriving (Eq)
@@ -35,14 +35,14 @@ data FavOrTrash = IsFav | IsTrash
 
 moreLike :: (HasDBid NodeType, HasNodeError err)
          => CorpusId   -> Maybe Offset -> Maybe Limit -> Maybe OrderBy
-         -> FavOrTrash -> Cmd err [FacetDoc]
+         -> FavOrTrash -> DBCmd err [FacetDoc]
 moreLike cId o _l order ft = do
   priors <- getPriors ft cId
   moreLikeWith cId o (Just 3) order ft priors
 
 ---------------------------------------------------------------------------
 getPriors :: (HasDBid NodeType, HasNodeError err)
-          => FavOrTrash -> CorpusId -> Cmd err (Events Bool)
+          => FavOrTrash -> CorpusId -> DBCmd err (Events Bool)
 getPriors ft cId = do
 
   docs_fav   <- filter (\(FacetDoc _ _ _ _ f _ _) -> f == Just 2)
@@ -60,7 +60,7 @@ getPriors ft cId = do
 
 moreLikeWith :: (HasDBid NodeType, HasNodeError err)
              => CorpusId   -> Maybe Offset -> Maybe Limit -> Maybe OrderBy
-             -> FavOrTrash -> Events Bool  -> Cmd err [FacetDoc]
+             -> FavOrTrash -> Events Bool  -> DBCmd err [FacetDoc]
 moreLikeWith cId o l order ft priors = do
 
   docs_test  <- filter (\(FacetDoc _ _ _ _ f _ _) -> f == Just 1)

src/Gargantext/Database/Action/Mail.hs

@@ -18,7 +18,7 @@ import Gargantext.Core.Mail (mail, MailModel(..))
 import Gargantext.Core.Mail.Types (mailSettings)
 import Gargantext.Core.Types.Individu (User(..))
 import Gargantext.Database.Action.User
-import Gargantext.Database.Prelude
+import Gargantext.Database.Prelude (CmdM)
 import Gargantext.Database.Query.Table.Node.Error (HasNodeError(..))
 import Gargantext.Database.Schema.User
 import Gargantext.Prelude

src/Gargantext/Database/Action/Metrics.hs

@@ -184,15 +184,13 @@ updateContextScore cId lId = do
 
 
 -- Used for scores in Doc Table
-getContextsNgramsScore :: --(FlowCmdM env err m)
-                          (HasNodeStory env err m)
+getContextsNgramsScore :: (HasNodeStory env err m)
                        => CorpusId -> ListId -> TabType -> ListType -> Maybe Limit
                        -> m (Map ContextId Int)
 getContextsNgramsScore cId lId tabType listType maybeLimit
  = Map.map Set.size <$> getContextsNgrams cId lId tabType listType maybeLimit
 
-getContextsNgrams :: --(FlowCmdM env err m)
-                     (HasNodeStory env err m)
+getContextsNgrams :: (HasNodeStory env err m)
                   => CorpusId -> ListId -> TabType -> ListType -> Maybe Limit
                   -> m (Map ContextId (Set NgramsTerm))
 getContextsNgrams cId lId tabType listType maybeLimit = do

src/Gargantext/Database/Action/Metrics/NgramsByContext.hs

@@ -249,11 +249,11 @@ queryNgramsOccurrencesOnlyByContextUser_withSample' = [sql|
 
 ------------------------------------------------------------------------
 getContextsByNgramsOnlyUser :: HasDBid NodeType
-                         => CorpusId
-                         -> [ListId]
-                         -> NgramsType
-                         -> [NgramsTerm]
-                         -> DBCmd err (HashMap NgramsTerm (Set NodeId))
+                            => CorpusId
+                            -> [ListId]
+                            -> NgramsType
+                            -> [NgramsTerm]
+                            -> DBCmd err (HashMap NgramsTerm (Set NodeId))
 getContextsByNgramsOnlyUser cId ls nt ngs =
      HM.unionsWith        (<>)
    . map (HM.fromListWith (<>)

src/Gargantext/Database/Action/Metrics/TFICF.hs

@@ -23,7 +23,7 @@ import Gargantext.Core
 import Gargantext.Core.Text.Metrics.TFICF
 import Gargantext.Database.Action.Metrics.NgramsByContext (getContextsByNgramsUser, {-getOccByNgramsOnlyFast,-} getOccByNgramsOnlyFast_withSample)
 import Gargantext.Database.Admin.Types.Node -- (ListId, CorpusId, NodeId)
-import Gargantext.Database.Prelude (Cmd)
+import Gargantext.Database.Prelude (DBCmd)
 import Gargantext.Database.Query.Table.NodeContext (selectCountDocs)
 import Gargantext.Database.Schema.Ngrams (NgramsType(..))
 import Gargantext.API.Ngrams.Types
@@ -58,10 +58,10 @@ getTficf cId mId nt = do
 -}
 
 getTficf_withSample :: HasDBid NodeType
-         => UserCorpusId
-         -> MasterCorpusId
-         -> NgramsType
-         -> Cmd err (HashMap NgramsTerm Double)
+                    => UserCorpusId
+                    -> MasterCorpusId
+                    -> NgramsType
+                    -> DBCmd err (HashMap NgramsTerm Double)
 getTficf_withSample cId mId nt = do
   mapTextDoubleLocal <- HM.filter (> 1)
      <$> HM.map (fromIntegral . Set.size)

src/Gargantext/Database/Action/Node.hs

@@ -30,7 +30,7 @@ import Gargantext.Database.Query.Table.Node.Error
 import Gargantext.Database.Query.Table.Node.UpdateOpaleye (updateHyperdata)
 import Gargantext.Prelude
 import Gargantext.Prelude.Crypto.Hash (hash)
-import Gargantext.Database.Prelude
+import Gargantext.Database.Prelude (DBCmd, HasConfig(..))
 import Control.Lens (view)
 import Gargantext.Prelude.Config (GargConfig(..))
 

src/Gargantext/Database/Action/Share.hs

@@ -25,17 +25,17 @@ import Gargantext.Database.Action.User (getUserId)
 import Gargantext.Database.Admin.Config (hasNodeType, isInNodeTypes)
 import Gargantext.Database.Admin.Types.Hyperdata (HyperdataAny(..))
 import Gargantext.Database.Admin.Types.Node
--- import Gargantext.Database.Query.Join (leftJoin3')
 import Gargantext.Database.Query.Table.Node (getNode, getNodesWith)
 import Gargantext.Database.Query.Table.Node.Error (HasNodeError, errorWith)
 import Gargantext.Database.Query.Table.NodeNode (deleteNodeNode, queryNodeNodeTable)
 import Gargantext.Database.Query.Table.User
 import Gargantext.Database.Query.Tree.Root (getRootId)
+import Gargantext.Database.Prelude (Cmd, runOpaQuery)
 import Gargantext.Database.Schema.Node
 import Gargantext.Prelude
 import Gargantext.Utils.Tuple (uncurryMaybe)
 import Opaleye hiding (not)
-import qualified Opaleye as O
+import Opaleye qualified as O
 
 -- | TODO move in PhyloConfig of Gargantext
 publicNodeTypes :: [NodeType]

src/Gargantext/Database/Action/TSQuery.hs

+{-|
+Module      : Gargantext.Database.Action.TSQuery
+Description :
+Copyright   : (c) CNRS, 2017-Present
+License     : AGPL + CECILL v3
+Maintainer  : team@gargantext.org
+Stability   : experimental
+Portability : POSIX
+
+Here is a longer description of this module, containing some
+commentary with @some markup@.
+-}
+
 module Gargantext.Database.Action.TSQuery where
 
 import Data.Aeson
@@ -8,11 +21,11 @@ import Data.Text (Text, words)
 import Database.PostgreSQL.Simple (Query)
 import Database.PostgreSQL.Simple.ToField
 import Gargantext.Core
+import Gargantext.Core.Text.Terms.Mono.Stem.En (stemIt)
 import Gargantext.Core.Types
 import Gargantext.Core.Types.Query (Limit, Offset)
-import Gargantext.Database.Prelude (Cmd, runPGSQuery)
+import Gargantext.Database.Prelude (DBCmd, runPGSQuery)
 import Gargantext.Prelude
-import Gargantext.Core.Text.Terms.Mono.Stem.En (stemIt)
 
 
 newtype TSQuery = UnsafeTSQuery [Text]
@@ -71,7 +84,7 @@ textSearchQuery = "SELECT n.id, n.hyperdata->'publication_year'     \
 textSearch :: HasDBid NodeType
            => TSQuery -> ParentId
            -> Limit -> Offset -> Order
-           -> Cmd err [(Int,Value,Value,Value, Value, Maybe Int)]
+           -> DBCmd err [(Int,Value,Value,Value, Value, Maybe Int)]
 textSearch q p l o ord = runPGSQuery textSearchQuery (q,p,p,typeId,ord,o,l)
   where
     typeId = toDBid NodeDocument

src/Gargantext/Database/Action/User/New.hs

@@ -29,7 +29,7 @@ import Gargantext.Core.Mail.Types (HasMail, mailSettings)
 import Gargantext.Core.Types.Individu
 import Gargantext.Database.Action.Flow (getOrMkRoot)
 import Gargantext.Database.Admin.Types.Node
-import Gargantext.Database.Prelude
+import Gargantext.Database.Prelude (Cmd, DBCmd, CmdM)
 import Gargantext.Database.Query.Table.Node.Error (HasNodeError(..), nodeError, NodeError(..))
 import Gargantext.Database.Query.Table.User
 import Gargantext.Prelude
@@ -135,12 +135,12 @@ _updateUsersPassword us = do
   pure 1
 
 ------------------------------------------------------------------------
-_rmUser :: HasNodeError err => User -> Cmd err Int64
+_rmUser :: HasNodeError err => User -> DBCmd err Int64
 _rmUser (UserName un) = deleteUsers [un]
 _rmUser _ = nodeError NotImplYet
 
 ------------------------------------------------------------------------
 -- TODO
-_rmUsers :: HasNodeError err => [User] -> Cmd err Int64
+_rmUsers :: HasNodeError err => [User] -> DBCmd err Int64
 _rmUsers [] = pure 0
 _rmUsers _  = undefined

src/Gargantext/Database/Prelude.hs

@@ -144,17 +144,15 @@ runCountOpaQuery q = do
   -- countRows is guaranteed to return a list with exactly one row so DL.head is safe here
   pure $ fromInt64ToInt $ DL.head counts
 
-formatPGSQuery :: PGS.ToRow a => PGS.Query -> a -> Cmd err DB.ByteString
+formatPGSQuery :: PGS.ToRow a => PGS.Query -> a -> DBCmd err DB.ByteString
 formatPGSQuery q a = mkCmd $ \conn -> PGS.formatQuery conn q a
 
 -- TODO use runPGSQueryDebug everywhere
-runPGSQuery' :: (PGS.ToRow a, PGS.FromRow b) => PGS.Query -> a -> Cmd err [b]
+runPGSQuery' :: (PGS.ToRow a, PGS.FromRow b) => PGS.Query -> a -> DBCmd err [b]
 runPGSQuery' q a = mkCmd $ \conn -> PGS.query conn q a
 
-runPGSQuery :: ( DbCmd' env err m
-               , PGS.FromRow r, PGS.ToRow q
-               )
-               => PGS.Query -> q -> m [r]
+runPGSQuery :: ( PGS.FromRow r, PGS.ToRow q )
+            => PGS.Query -> q -> DBCmd err [r]
 runPGSQuery q a = mkCmd $ \conn -> catch (PGS.query conn q a) (printError conn)
   where
     printError c (SomeException e) = do
@@ -179,10 +177,8 @@ runPGSQueryFold q initialState consume = mkCmd $ \conn -> catch (PGS.fold_ conn
 
 
 -- | TODO catch error
-runPGSQuery_ :: ( CmdM env err m
-               , PGS.FromRow r
-               )
-               => PGS.Query -> m [r]
+runPGSQuery_ :: ( PGS.FromRow r )
+             => PGS.Query -> DBCmd err [r]
 runPGSQuery_ q = mkCmd $ \conn -> catch (PGS.query_ conn q) printError
   where
     printError (SomeException e) = do
@@ -227,7 +223,7 @@ fromField' field mb = do
 printSqlOpa :: Default Unpackspec a a => Select a -> IO ()
 printSqlOpa = putStrLn . maybe "Empty query" identity . showSql
 
-dbCheck :: CmdM env err m => m Bool
+dbCheck :: DBCmd err Bool
 dbCheck = do
   r :: [PGS.Only Text] <- runPGSQuery_ "select username from public.auth_user"
   case r of

src/Gargantext/Database/Query/Facet.hs

@@ -43,7 +43,7 @@ import Data.Text qualified as T
 import Gargantext.Core
 import Gargantext.Core.Types
 import Gargantext.Core.Types.Query (Limit, Offset, IsTrash)
-import Gargantext.Database.Prelude
+import Gargantext.Database.Prelude (DBCmd, runCountOpaQuery, runOpaQuery)
 import Gargantext.Database.Query.Facet.Types
 import Gargantext.Database.Query.Filter
 import Gargantext.Database.Query.Table.Context
@@ -70,7 +70,7 @@ runViewAuthorsDoc :: HasDBid NodeType
                   -> Maybe Offset
                   -> Maybe Limit
                   -> Maybe OrderBy
-                  -> Cmd err [FacetDoc]
+                  -> DBCmd err [FacetDoc]
 runViewAuthorsDoc cId t o l order = runOpaQuery $ filterWith o l order $ viewAuthorsDoc cId t ntId
   where
     ntId = NodeDocument
@@ -125,11 +125,11 @@ runViewDocuments :: (HasDBid NodeType, HasNodeError err)
                  -> Maybe OrderBy
                  -> Maybe Text
                  -> Maybe Text
-                 -> Cmd err [FacetDoc]
+                 -> DBCmd err [FacetDoc]
 runViewDocuments cId t o l order query year = do
     listId <- defaultList cId
 
-    res <- runOpaQuery $ filterWith' o l order (sqlQuery listId) :: Cmd err [FacetDocAgg']
+    res <- runOpaQuery $ filterWith' o l order (sqlQuery listId) :: DBCmd err [FacetDocAgg']
     pure $ remapNgramsCount <$> res
   where
     sqlQuery lId = viewDocuments cId lId t (toDBid NodeDocument) query year
@@ -140,7 +140,7 @@ runViewDocuments cId t o l order query year = do
                , .. }
 
 runCountDocuments :: (HasDBid NodeType, HasNodeError err)
-                  => CorpusId -> IsTrash -> Maybe Text -> Maybe Text -> Cmd err Int
+                  => CorpusId -> IsTrash -> Maybe Text -> Maybe Text -> DBCmd err Int
 runCountDocuments cId t mQuery mYear = do
   listId <- defaultList cId
   runCountOpaQuery (sqlQuery listId)

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

@@ -25,7 +25,7 @@ import Gargantext.Core
 import Gargantext.Core.Types
 import Gargantext.Core.Types.Query (Limit, Offset)
 import Gargantext.Database.Admin.Types.Hyperdata
-import Gargantext.Database.Prelude
+import Gargantext.Database.Prelude (DBCmd, JSONB, runOpaQuery)
 import Gargantext.Database.Query.Filter (limit', offset')
 import Gargantext.Database.Query.Table.Node.Error
 import Gargantext.Database.Schema.Context
@@ -35,7 +35,7 @@ import Prelude            hiding (null, id, map, sum)
 
 
 getContextWith :: (HasNodeError err, JSONB a)
-            => ContextId -> proxy a -> Cmd err (Node a)
+            => ContextId -> proxy a -> DBCmd err (Node a)
 getContextWith nId _ = do
   maybeContext <- headMay <$> runOpaQuery (selectContext (pgNodeId nId))
   case maybeContext of
@@ -51,7 +51,7 @@ selectContext id' = proc () -> do
     restrict -< _context_id row .== id'
     returnA  -< row
 
-runGetContexts :: Select ContextRead -> Cmd err [Context HyperdataAny]
+runGetContexts :: Select ContextRead -> DBCmd err [Context HyperdataAny]
 runGetContexts = runOpaQuery
 
 ------------------------------------------------------------------------
@@ -84,11 +84,11 @@ selectContextsWith' parentId maybeContextType = proc () -> do
 
 
 ------------------------------------------------------------------------
-getDocumentsV3WithParentId :: HasDBid NodeType => NodeId -> Cmd err [Context HyperdataDocumentV3]
+getDocumentsV3WithParentId :: HasDBid NodeType => NodeId -> DBCmd err [Context HyperdataDocumentV3]
 getDocumentsV3WithParentId n = runOpaQuery $ selectContextsWith' n (Just NodeDocument)
 
 -- TODO: merge with getDocumentsWithParentId by having a class IsHyperdataDocument
-getDocumentsWithParentId :: HasDBid NodeType => NodeId -> Cmd err [Context HyperdataDocument]
+getDocumentsWithParentId :: HasDBid NodeType => NodeId -> DBCmd err [Context HyperdataDocument]
 getDocumentsWithParentId n = runOpaQuery $ selectContextsWith' n (Just NodeDocument)
 
 ------------------------------------------------------------------------
@@ -102,7 +102,8 @@ selectContextsWithParentID n = proc () -> do
 ------------------------------------------------------------------------
 -- | Example of use:
 -- runCmdReplEasy  (getNodesWithType NodeList (Proxy :: Proxy HyperdataList))
-getContextsWithType :: (HasNodeError err, JSONB a, HasDBid NodeType) => NodeType -> proxy a -> Cmd err [Context a]
+getContextsWithType :: (HasNodeError err, JSONB a, HasDBid NodeType)
+                    => NodeType -> proxy a -> DBCmd err [Context a]
 getContextsWithType nt _ = runOpaQuery $ selectContextsWithType nt
   where
     selectContextsWithType ::  HasDBid NodeType
@@ -112,7 +113,8 @@ getContextsWithType nt _ = runOpaQuery $ selectContextsWithType nt
         restrict -< tn .== (sqlInt4 $ toDBid nt')
         returnA -< row
 
-getContextsIdWithType :: (HasNodeError err, HasDBid NodeType) => NodeType -> Cmd err [ContextId]
+getContextsIdWithType :: (HasNodeError err, HasDBid NodeType)
+                      => NodeType -> DBCmd err [ContextId]
 getContextsIdWithType nt = do
   ns <- runOpaQuery $ selectContextsIdWithType nt
   pure (map NodeId ns)

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

@@ -28,7 +28,7 @@ import Data.HashMap.Strict (HashMap)
 import Data.Map.Strict (Map)
 import Data.Text (Text)
 import Gargantext.Core.Types
-import Gargantext.Database.Prelude (runOpaQuery, Cmd, formatPGSQuery, runPGSQuery, DBCmd)
+import Gargantext.Database.Prelude (runOpaQuery, formatPGSQuery, runPGSQuery, DBCmd)
 import Gargantext.Database.Query.Join (leftJoin3)
 import Gargantext.Database.Query.Table.ContextNodeNgrams2
 import Gargantext.Database.Query.Table.NodeNgrams (queryNodeNgramsTable)
@@ -45,7 +45,7 @@ import qualified Database.PostgreSQL.Simple as PGS
 queryNgramsTable :: Select NgramsRead
 queryNgramsTable = selectTable ngramsTable
 
-selectNgramsByDoc :: [ListId] -> DocId -> NgramsType -> Cmd err [Text]
+selectNgramsByDoc :: [ListId] -> DocId -> NgramsType -> DBCmd err [Text]
 selectNgramsByDoc lIds dId nt = runOpaQuery (query lIds dId nt)
   where
 
@@ -65,10 +65,10 @@ selectNgramsByDoc lIds dId nt = runOpaQuery (query lIds dId nt)
       returnA  -< ng^.ngrams_terms
 
 
-_postNgrams :: CorpusId -> DocId -> [Text] -> Cmd err Int
+_postNgrams :: CorpusId -> DocId -> [Text] -> DBCmd err Int
 _postNgrams = undefined
 
-_dbGetNgramsDb :: Cmd err [NgramsDB]
+_dbGetNgramsDb :: DBCmd err [NgramsDB]
 _dbGetNgramsDb = runOpaQuery queryNgramsTable
 
 
@@ -85,7 +85,7 @@ insertNgrams' ns = runPGSQuery queryInsertNgrams (PGS.Only $ Values fields ns)
   where
     fields = map (\t -> QualifiedIdentifier Nothing t) ["text", "int4"]
 
-_insertNgrams_Debug :: [(Text, Size)] -> Cmd err ByteString
+_insertNgrams_Debug :: [(Text, Size)] -> DBCmd err ByteString
 _insertNgrams_Debug ns = formatPGSQuery queryInsertNgrams (PGS.Only $ Values fields ns)
   where
     fields = map (\t -> QualifiedIdentifier Nothing t) ["text", "int4"]
@@ -111,13 +111,13 @@ queryInsertNgrams = [sql|
 
 
 --------------------------------------------------------------------------
-selectNgramsId :: [Text] -> Cmd err (Map NgramsId Text)
+selectNgramsId :: [Text] -> DBCmd err (Map NgramsId Text)
 selectNgramsId ns =
   if List.null ns
      then pure Map.empty
      else Map.fromList <$> map (\(Indexed i t) -> (i, t)) <$> (selectNgramsId' ns)
 
-selectNgramsId' :: [Text] -> Cmd err [Indexed Int Text]
+selectNgramsId' :: [Text] -> DBCmd err [Indexed Int Text]
 selectNgramsId' ns = runPGSQuery querySelectNgramsId ( PGS.Only
                                                      $ Values fields ns
                                                      )

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

@@ -24,7 +24,7 @@ import Data.Hashable (Hashable)
 import Data.Text (Text)
 import Gargantext.Core
 import Gargantext.Core.Types
-import Gargantext.Database.Prelude (Cmd, runPGSQuery, runPGSQuery_, DBCmd)
+import Gargantext.Database.Prelude (runPGSQuery, runPGSQuery_, DBCmd)
 import Gargantext.Database.Schema.Ngrams
 import Gargantext.Database.Schema.Prelude
 import Gargantext.Database.Query.Table.Ngrams
@@ -155,7 +155,7 @@ SELECT terms,id FROM ins_form_ret
 
 -- TODO add lang and postag algo
 -- TODO remove when form == lem in insert
-selectLems :: Lang -> NLPServerConfig -> [Ngrams] -> Cmd err [(Form, Lem)]
+selectLems :: Lang -> NLPServerConfig -> [Ngrams] -> DBCmd err [(Form, Lem)]
 selectLems l (NLPServerConfig { server }) ns = runPGSQuery querySelectLems (PGS.Only $ Values fields datas)
   where
     fields = map (\t -> QualifiedIdentifier Nothing t) ["int4","int4","text", "int4"]
@@ -180,7 +180,7 @@ querySelectLems = [sql|
   |]
 
 -- | Insert Table
-createTable_NgramsPostag :: Cmd err [Int]
+createTable_NgramsPostag :: DBCmd err [Int]
 createTable_NgramsPostag = map (\(PGS.Only a) -> a)
                         <$> runPGSQuery_ queryCreateTable
   where

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

@@ -25,22 +25,20 @@ import Control.Lens (set, view)
 import Data.Aeson
 import Data.Maybe (fromMaybe)
 import Data.Text (Text)
+import Database.PostgreSQL.Simple qualified as PGS
 import Database.PostgreSQL.Simple.SqlQQ (sql)
-import Opaleye hiding (FromField)
-import Prelude hiding (null, id, map, sum)
-
 import Gargantext.Core
 import Gargantext.Core.Types
 import Gargantext.Core.Types.Query (Limit, Offset)
 import Gargantext.Database.Admin.Types.Hyperdata
 import Gargantext.Database.Admin.Types.Hyperdata.Default
-import Gargantext.Database.Prelude
+import Gargantext.Database.Prelude (DBCmd, JSONB, mkCmd, runPGSQuery, runOpaQuery)
 import Gargantext.Database.Query.Filter (limit', offset')
 import Gargantext.Database.Query.Table.Node.Error
 import Gargantext.Database.Schema.Node
 import Gargantext.Prelude hiding (sum, head)
-
-import qualified Database.PostgreSQL.Simple as PGS
+import Opaleye hiding (FromField)
+import Prelude hiding (null, id, map, sum)
 
 
 queryNodeSearchTable :: Select NodeSearchRead

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

@@ -22,15 +22,11 @@ import Gargantext.Core
 import Gargantext.Core.Types
 import Gargantext.Core.Types.Query (Limit, Offset)
 import Gargantext.Database.Admin.Types.Hyperdata (HyperdataDocument, HyperdataContact)
-import Gargantext.Database.Prelude
+import Gargantext.Database.Prelude (DBCmd, JSONB, runCountOpaQuery, runOpaQuery)
 import Gargantext.Database.Query.Filter
-
-import Gargantext.Database.Schema.Node
-import Gargantext.Database.Schema.Context
-import Gargantext.Database.Schema.NodeContext
 import Gargantext.Database.Query.Table.NodeContext
-
-
+import Gargantext.Database.Schema.Context
+import Gargantext.Database.Schema.Node
 import Gargantext.Prelude
 import Opaleye
 

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

@@ -28,7 +28,7 @@ import Database.PostgreSQL.Simple.ToRow (ToRow(..))
 import Database.PostgreSQL.Simple.Types (Values(..), QualifiedIdentifier(..))
 import GHC.Generics (Generic)
 import Gargantext.Database.Admin.Types.Node
-import Gargantext.Database.Prelude (Cmd, runPGSQuery, formatPGSQuery, DBCmd)
+import Gargantext.Database.Prelude (runPGSQuery, formatPGSQuery, DBCmd)
 import Gargantext.Prelude
 
 ---------------------------------------------------------------------------
@@ -41,12 +41,12 @@ add pId ns = runPGSQuery queryAdd (Only $ Values fields inputData)
 
 -- | Adds a single document. Useful for debugging purposes, but
 -- not as efficient as adding documents in bulk via 'add'.
-add_one :: CorpusId -> ContextId -> Cmd err [Only Int]
+add_one :: CorpusId -> ContextId -> DBCmd err [Only Int]
 add_one pId ctxId = runPGSQuery queryAdd (Only $ Values fields [InputData pId ctxId])
   where
     fields    = map (\t-> QualifiedIdentifier Nothing t) inputSqlTypes
 
-add_debug :: CorpusId -> [ContextId] -> Cmd err ByteString
+add_debug :: CorpusId -> [ContextId] -> DBCmd err ByteString
 add_debug pId ns = formatPGSQuery queryAdd (Only $ Values fields inputData)
   where
     fields    = map (\t-> QualifiedIdentifier Nothing t) inputSqlTypes

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

@@ -16,16 +16,14 @@ module Gargantext.Database.Query.Table.Node.Select
   where
 
 import Control.Arrow (returnA)
-import Opaleye
-import Protolude
-
 import Gargantext.Core
 import Gargantext.Core.Types
 import Gargantext.Core.Types.Individu (Username)
-import Gargantext.Database.Prelude
-import Gargantext.Database.Schema.Node
-import Gargantext.Database.Schema.User
+import Gargantext.Database.Prelude (DBCmd, runOpaQuery)
 import Gargantext.Database.Query.Table.User
+import Gargantext.Database.Schema.Node
+import Opaleye
+import Protolude
 
 selectNodesWithUsername :: (HasDBid NodeType) => NodeType -> Username -> DBCmd err [NodeId]
 selectNodesWithUsername nt u = runOpaQuery $ proc () -> do

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

@@ -19,7 +19,7 @@ import Database.PostgreSQL.Simple
 
 import Gargantext.Prelude
 import Gargantext.Core.Types (Name)
-import Gargantext.Database.Prelude
+import Gargantext.Database.Prelude (DBCmd, runPGSQuery)
 import Gargantext.Database.Admin.Types.Node (NodeId, ParentId)
 
 -- import Data.ByteString
@@ -39,7 +39,7 @@ unOnly :: Only a -> a
 unOnly (Only a) = a
 
 -- TODO-ACCESS
-update :: Update -> Cmd err [Int]
+update :: Update -> DBCmd err [Int]
 update (Rename nId name) = map unOnly <$> runPGSQuery "UPDATE nodes SET name=? where id=? returning id"
                                            (DT.take 255 name,nId)
 update (Move nId pId)    = map unOnly <$> runPGSQuery "UPDATE nodes SET parent_id= ? where id=? returning id"

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

@@ -22,7 +22,7 @@ import Gargantext.Prelude
 import Gargantext.Database.Schema.Node
 import Gargantext.Database.Admin.Types.Hyperdata
 import Gargantext.Database.Admin.Types.Node
-import Gargantext.Database.Prelude (Cmd, mkCmd, DBCmd)
+import Gargantext.Database.Prelude (mkCmd, DBCmd)
 import Gargantext.Database.Query.Table.Node
 import Gargantext.Database.Query.Table.Node.Error
 
@@ -49,7 +49,7 @@ updateHyperdataQuery i h = seq h' $ {- trace "updateHyperdataQuery: encoded JSON
 updateNodesWithType :: ( HasNodeError err
                        , HasDBid NodeType
                        , HyperdataC a
-                       ) => NodeType -> proxy a -> (a -> a) -> Cmd err [Int64]
+                       ) => NodeType -> proxy a -> (a -> a) -> DBCmd err [Int64]
 updateNodesWithType nt p f = do
   ns <- getNodesWithType nt p
   mapM (\n -> updateHyperdata (_node_id n) (f $ _node_hyperdata n)) ns
@@ -61,7 +61,7 @@ updateNodeWithType :: ( HasNodeError err
                         -> NodeType
                         -> proxy a
                         -> (a -> a)
-                        -> Cmd err [Int64]
+                        -> DBCmd err [Int64]
 updateNodeWithType nId nt p f = do
   ns <- getNodeWithType nId nt p
   mapM (\n -> updateHyperdata (_node_id n) (f $ _node_hyperdata n)) ns
@@ -71,7 +71,7 @@ updateNodeWithType nId nt p f = do
 updateNodesWithType_ :: ( HasNodeError err
                         , HyperdataC a
                         , HasDBid NodeType
-                        ) => NodeType -> a -> Cmd err [Int64]
+                        ) => NodeType -> a -> DBCmd err [Int64]
 updateNodesWithType_ nt h = do
   ns <- getNodesIdWithType nt
   mapM (\n -> updateHyperdata n h) ns

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

@@ -17,14 +17,14 @@ import Gargantext.Core
 import Gargantext.Core.Types (Name)
 import Gargantext.Database.Admin.Types.Hyperdata (HyperdataUser(..), defaultHyperdataUser)
 import Gargantext.Database.Admin.Types.Node (Node, NodeId(..), UserId, NodeType(..), pgNodeId)
-import Gargantext.Database.Prelude -- (fromField', Cmd)
+import Gargantext.Database.Prelude (DBCmd, runOpaQuery)
 import Gargantext.Database.Query.Table.Node
 import Gargantext.Database.Schema.Node -- (Node(..))
 import Gargantext.Prelude
 import Opaleye (limit)
 
 
-getNodeUser :: NodeId -> Cmd err (Node HyperdataUser)
+getNodeUser :: NodeId -> DBCmd err (Node HyperdataUser)
 getNodeUser nId = do
     fromMaybe (panic $ "Node does not exist: " <> (cs $ show nId)) . headMay
              <$> runOpaQuery (limit 1 $ selectNode (pgNodeId nId))

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

@@ -46,25 +46,23 @@ module Gargantext.Database.Query.Table.NodeContext
 import Control.Arrow (returnA)
 import Control.Lens (view, (^.))
 import Data.Maybe (catMaybes)
-import Data.Time (UTCTime)
 import Data.Text (Text, splitOn)
+import Data.Time (UTCTime)
+import Database.PostgreSQL.Simple qualified as PGS (In(..), Query, Only(..))
 import Database.PostgreSQL.Simple.SqlQQ (sql)
 import Database.PostgreSQL.Simple.Types (Values(..), QualifiedIdentifier(..))
-import Opaleye
-import qualified Database.PostgreSQL.Simple as PGS (In(..), Query, Only(..))
-import qualified Opaleye as O
-
 import Gargantext.Core
 import Gargantext.Core.Types
--- import Gargantext.Core.Types.Search (HyperdataRow(..), toHyperdataRow)
 import Gargantext.Database.Admin.Types.Hyperdata
+import Gargantext.Database.Prelude (DBCmd, execPGSQuery, mkCmd, restrictMaybe, runCountOpaQuery, runPGSQuery, runOpaQuery)
 import Gargantext.Database.Query.Table.Node.Error (HasNodeError, NodeError(DoesNotExist), nodeError)
-import Gargantext.Database.Prelude
-import Gargantext.Prelude.Crypto.Hash (Hash)
 import Gargantext.Database.Schema.Context
 import Gargantext.Database.Schema.Node
 import Gargantext.Database.Schema.NodeContext
 import Gargantext.Prelude
+import Gargantext.Prelude.Crypto.Hash (Hash)
+import Opaleye
+import Opaleye qualified as O
 
 queryNodeContextTable :: Select NodeContextRead
 queryNodeContextTable = selectTable nodeContextTable

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

@@ -20,12 +20,12 @@ module Gargantext.Database.Query.Table.NodeContext_NodeContext
   where
 
 import Data.Text (Text)
+import Database.PostgreSQL.Simple qualified as PGS
 import Gargantext.Core.Types
-import Gargantext.Database.Prelude
+import Gargantext.Database.Prelude (DBCmd, runPGSQuery)
 import Gargantext.Database.Schema.NodeContext_NodeContext
 import Gargantext.Database.Schema.Prelude hiding (sum)
 import Gargantext.Prelude
-import qualified Database.PostgreSQL.Simple as PGS
 
 {-
 queryNodeContext_NodeContextTable :: Select NodeContext_NodeContextRead

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

@@ -26,20 +26,20 @@ module Gargantext.Database.Query.Table.NodeNgrams
   )
   where
 
+import Data.List qualified as List
 import Data.List.Extra (nubOrd)
 import Data.Map.Strict (Map)
+import Data.Map.Strict qualified as Map
 import Data.Maybe (fromMaybe)
 import Data.Text (Text)
+import Database.PostgreSQL.Simple qualified as PGS (Query, Only(..))
 import Gargantext.Core
 import Gargantext.Core.Types
-import Gargantext.Database.Prelude
+import Gargantext.Database.Prelude (DBCmd, runPGSQuery)
 import Gargantext.Database.Schema.Ngrams (NgramsType, ngramsTypeId, fromNgramsTypeId)
 import Gargantext.Database.Schema.NodeNgrams
 import Gargantext.Database.Schema.Prelude (Select, FromRow, sql, fromRow, toField, field, Values(..), QualifiedIdentifier(..), selectTable)
 import Gargantext.Prelude
-import qualified Data.List as List
-import qualified Data.Map.Strict as Map
-import qualified Database.PostgreSQL.Simple as PGS (Query, Only(..))
 
 
 queryNodeNgramsTable :: Select NodeNgramsRead
@@ -62,11 +62,9 @@ getCgramsId mapId nt t = case Map.lookup nt mapId of
   Just mapId' -> Map.lookup t mapId'
 
 
--- insertDb :: ListId -> Map NgramsType [NgramsElement] -> Cmd err [Result]
 listInsertDb :: Show a => ListId
              -> (ListId -> a -> [NodeNgramsW])
              -> a
-             -- -> Cmd err [Returning]
              -> DBCmd err (Map NgramsType (Map Text Int))
 listInsertDb l f ngs = Map.map Map.fromList
                     <$> Map.fromListWith (<>)

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

@@ -35,20 +35,20 @@ module Gargantext.Database.Query.Table.NodeNode
 
 import Control.Arrow (returnA)
 import Control.Lens ((^.), view)
-import Data.Text (Text, splitOn)
 import Data.Maybe (catMaybes)
+import Data.Text (Text, splitOn)
+import Database.PostgreSQL.Simple qualified as PGS
 import Database.PostgreSQL.Simple.SqlQQ (sql)
 import Database.PostgreSQL.Simple.Types (Values(..), QualifiedIdentifier(..))
 import Gargantext.Core
 import Gargantext.Core.Types
 import Gargantext.Database.Admin.Types.Hyperdata
-import Gargantext.Database.Prelude
+import Gargantext.Database.Prelude (DBCmd, mkCmd, runPGSQuery, runCountOpaQuery, runOpaQuery)
 import Gargantext.Database.Schema.Node
 import Gargantext.Database.Schema.NodeNode
 import Gargantext.Prelude
 import Opaleye
-import qualified Database.PostgreSQL.Simple as PGS
-import qualified Opaleye as O
+import Opaleye qualified as O
 
 queryNodeNodeTable :: Select NodeNodeRead
 queryNodeNodeTable = selectTable nodeNodeTable

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

@@ -23,7 +23,7 @@ module Gargantext.Database.Query.Table.NodeNodeNgrams
   where
 
 import Gargantext.Database.Admin.Types.Node (pgNodeId)
-import Gargantext.Database.Prelude (Cmd, mkCmd)
+import Gargantext.Database.Prelude (DBCmd, mkCmd)
 import Gargantext.Database.Schema.Ngrams (pgNgramsTypeId)
 import Gargantext.Database.Schema.NodeNodeNgrams
 import Gargantext.Database.Schema.Prelude
@@ -34,7 +34,7 @@ queryNodeNodeNgramsTable :: Query NodeNodeNgramsRead
 queryNodeNodeNgramsTable = selectTable nodeNodeNgramsTable
 
 -- | Insert utils
-insertNodeNodeNgrams :: [NodeNodeNgrams] -> Cmd err Int
+insertNodeNodeNgrams :: [NodeNodeNgrams] -> DBCmd err Int
 insertNodeNodeNgrams = insertNodeNodeNgramsW
                      . map (\(NodeNodeNgrams n1 n2 ng nt w) ->
                               NodeNodeNgrams (pgNodeId n1)
@@ -44,7 +44,7 @@ insertNodeNodeNgrams = insertNodeNodeNgramsW
                                              (sqlDouble w)
                                                   )
 
-insertNodeNodeNgramsW :: [NodeNodeNgramsWrite] -> Cmd err Int
+insertNodeNodeNgramsW :: [NodeNodeNgramsWrite] -> DBCmd err Int
 insertNodeNodeNgramsW nnnw =
   mkCmd $ \c -> fromIntegral <$> runInsert_ c insertNothing
     where

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

@@ -58,7 +58,7 @@ import Gargantext.Core.Types.Individu
 import qualified Gargantext.Prelude.Crypto.Auth as Auth
 import Gargantext.Database.Admin.Types.Hyperdata (HyperdataUser(..), hu_pubmed_api_key)
 import Gargantext.Database.Admin.Types.Node (NodeType(NodeUser), Node, NodeId(..), pgNodeId)
-import Gargantext.Database.Prelude
+import Gargantext.Database.Prelude (DBCmd, mkCmd, runOpaQuery)
 import Gargantext.Database.Query.Table.Node.UpdateOpaleye (updateNodeWithType)
 import Gargantext.Database.Schema.Node (NodeRead, node_hyperdata, queryNodeTable, node_id, node_user_id, node_typename)
 import Gargantext.Database.Schema.User
@@ -76,14 +76,14 @@ insertUsers us = mkCmd $ \c -> runInsert c insert
   where
     insert = Insert userTable us rCount Nothing
 
-deleteUsers :: [Username] -> Cmd err Int64
+deleteUsers :: [Username] -> DBCmd err Int64
 deleteUsers us = mkCmd $ \c -> runDelete_ c
                        $ Delete userTable
                                 (\user -> in_ (map sqlStrictText us) (user_username user))
                                 rCount
 
 -- Updates email or password only (for now)
-updateUserDB :: UserWrite -> Cmd err Int64
+updateUserDB :: UserWrite -> DBCmd err Int64
 updateUserDB us = mkCmd $ \c -> runUpdate_ c (updateUserQuery us)
   where
     updateUserQuery :: UserWrite -> Update Int64
@@ -119,7 +119,7 @@ toUserWrite (NewUser u m (Auth.PasswordHash p)) =
          , user_forgot_password_uuid = Nothing }
 
 ------------------------------------------------------------------
-getUsersWith :: Username -> Cmd err [UserLight]
+getUsersWith :: Username -> DBCmd err [UserLight]
 getUsersWith u = map toUserLight <$> runOpaQuery (selectUsersLightWith u)
 
 selectUsersLightWith :: Username -> Select UserRead
@@ -128,7 +128,7 @@ selectUsersLightWith u = proc () -> do
       restrict -< user_username row .== sqlStrictText u
       returnA  -< row
 
-getUsersWithEmail :: Text -> Cmd err [UserLight]
+getUsersWithEmail :: Text -> DBCmd err [UserLight]
 getUsersWithEmail e = map toUserLight <$> runOpaQuery (selectUsersLightWithEmail e)
 
 selectUsersLightWithEmail :: Text -> Select UserRead
@@ -137,7 +137,7 @@ selectUsersLightWithEmail e = proc () -> do
       restrict -< user_email row .== sqlStrictText e
       returnA  -< row
 
-getUsersWithForgotPasswordUUID :: UUID.UUID -> Cmd err [UserLight]
+getUsersWithForgotPasswordUUID :: UUID.UUID -> DBCmd err [UserLight]
 getUsersWithForgotPasswordUUID uuid = map toUserLight <$> runOpaQuery (selectUsersLightWithForgotPasswordUUID uuid)
 
 selectUsersLightWithForgotPasswordUUID :: UUID.UUID -> Select UserRead
@@ -173,7 +173,7 @@ queryUserTable = selectTable userTable
 
 ----------------------------------------------------------------------
 -- | Get hyperdata associated with user node.
-getUserHyperdata :: User -> Cmd err [HyperdataUser]
+getUserHyperdata :: User -> DBCmd err [HyperdataUser]
 getUserHyperdata (RootId uId) = do
   runOpaQuery (selectUserHyperdataWithId uId)
   where
@@ -195,7 +195,7 @@ getUserHyperdata _ = undefined
 
 
 -- | Same as `getUserHyperdata` but returns a `Node` type.
-getUserNodeHyperdata :: User -> Cmd err [Node HyperdataUser]
+getUserNodeHyperdata :: User -> DBCmd err [Node HyperdataUser]
 getUserNodeHyperdata (RootId uId) = do
   runOpaQuery (selectUserHyperdataWithId uId)
   where
@@ -215,14 +215,14 @@ getUserNodeHyperdata (UserDBId uId) = do
       returnA  -< row
 getUserNodeHyperdata _ = undefined
 
-getUsersWithHyperdata :: User -> Cmd err [(UserLight, HyperdataUser)]
+getUsersWithHyperdata :: User -> DBCmd err [(UserLight, HyperdataUser)]
 getUsersWithHyperdata i = do
   u <- getUsersWithId i
   h <- getUserHyperdata i
   -- printDebug "[getUsersWithHyperdata]" (u,h)
   pure $ zip u h
 
-getUsersWithNodeHyperdata :: User -> Cmd err [(UserLight, Node HyperdataUser)]
+getUsersWithNodeHyperdata :: User -> DBCmd err [(UserLight, Node HyperdataUser)]
 getUsersWithNodeHyperdata i = do
   u <- getUsersWithId i
   h <- getUserNodeHyperdata i
@@ -230,7 +230,7 @@ getUsersWithNodeHyperdata i = do
   pure $ zip u h
 
 
-updateUserEmail :: UserLight -> Cmd err Int64
+updateUserEmail :: UserLight -> DBCmd err Int64
 updateUserEmail (UserLight { .. }) = mkCmd $ \c -> runUpdate_ c updateUserQuery
   where
     updateUserQuery :: Update Int64
@@ -240,7 +240,7 @@ updateUserEmail (UserLight { .. }) = mkCmd $ \c -> runUpdate_ c updateUserQuery
       , uWhere      = (\row -> user_id row .== (sqlInt4 userLight_id))
       , uReturning  = rCount }
 
-updateUserPassword :: UserLight -> Cmd err Int64
+updateUserPassword :: UserLight -> DBCmd err Int64
 updateUserPassword (UserLight { userLight_password = GargPassword password, .. }) = mkCmd $ \c -> runUpdate_ c updateUserQuery
   where
     updateUserQuery :: Update Int64
@@ -250,7 +250,7 @@ updateUserPassword (UserLight { userLight_password = GargPassword password, .. }
       , uWhere      = \row -> user_id row .== sqlInt4 userLight_id
       , uReturning  = rCount }
 
-updateUserForgotPasswordUUID :: UserLight -> Cmd err Int64
+updateUserForgotPasswordUUID :: UserLight -> DBCmd err Int64
 updateUserForgotPasswordUUID (UserLight { .. }) = mkCmd $ \c -> runUpdate_ c updateUserQuery
   where
     pass = sqlStrictText $ fromMaybe "" userLight_forgot_password_uuid
@@ -261,7 +261,7 @@ updateUserForgotPasswordUUID (UserLight { .. }) = mkCmd $ \c -> runUpdate_ c upd
       , uWhere      = \row -> user_id row .== sqlInt4 userLight_id
       , uReturning  = rCount }
 
-getUserPubmedAPIKey :: User -> Cmd err (Maybe PUBMED.APIKey)
+getUserPubmedAPIKey :: User -> DBCmd err (Maybe PUBMED.APIKey)
 getUserPubmedAPIKey user = do
   hs <- getUserHyperdata user
   case hs of
@@ -269,7 +269,7 @@ getUserPubmedAPIKey user = do
     (x:_) -> pure $ _hu_pubmed_api_key x
 
 updateUserPubmedAPIKey :: (HasDBid NodeType, HasNodeError err)
-                        => User -> PUBMED.APIKey -> Cmd err Int64
+                        => User -> PUBMED.APIKey -> DBCmd err Int64
 updateUserPubmedAPIKey (RootId uId) apiKey = do
   _ <- updateNodeWithType uId NodeUser (Proxy :: Proxy HyperdataUser) (\h -> h & hu_pubmed_api_key ?~ apiKey)
   pure 1
@@ -303,7 +303,7 @@ getUser :: Username -> DBCmd err (Maybe UserLight)
 getUser u = userLightWithUsername u <$> usersLight
 
 ----------------------------------------------------------------------
-insertNewUsers :: [NewUser GargPassword] -> Cmd err Int64
+insertNewUsers :: [NewUser GargPassword] -> DBCmd err Int64
 insertNewUsers newUsers = do
   users' <- liftBase $ mapM toUserHash newUsers
   insertUsers $ map toUserWrite users'

src/Gargantext/Database/Query/Tree.hs

@@ -60,7 +60,7 @@ import Gargantext.Core.Types.Main (NodeTree(..), Tree(..))
 import Gargantext.Database.Admin.Config (fromNodeTypeId, nodeTypeId, fromNodeTypeId)
 import Gargantext.Database.Admin.Types.Hyperdata.Any (HyperdataAny)
 import Gargantext.Database.Admin.Types.Node
-import Gargantext.Database.Prelude (Cmd, runPGSQuery, DBCmd)
+import Gargantext.Database.Prelude (runPGSQuery, DBCmd)
 import Gargantext.Database.Query.Table.Node (getNodeWith)
 import Gargantext.Database.Query.Table.Node.Error (HasNodeError)
 import Gargantext.Database.Query.Table.NodeNode (getNodeNode)
@@ -89,7 +89,7 @@ tree :: (HasTreeError err, HasNodeError err)
      => TreeMode
      -> RootId
      -> [NodeType]
-     -> Cmd err (Tree NodeTree)
+     -> DBCmd err (Tree NodeTree)
 tree TreeBasic    = tree_basic
 tree TreeAdvanced = tree_advanced
 tree TreeFirstLevel = tree_first_level
@@ -100,7 +100,7 @@ tree TreeFirstLevel = tree_first_level
 tree_basic :: (HasTreeError err, HasNodeError err)
            => RootId
            -> [NodeType]
-           -> Cmd err (Tree NodeTree)
+           -> DBCmd err (Tree NodeTree)
 tree_basic r nodeTypes =
   (dbTree r nodeTypes <&> toTreeParent) >>= toTree
   -- Same as (but easier to read) :
@@ -110,7 +110,7 @@ tree_basic r nodeTypes =
 tree_advanced :: (HasTreeError err, HasNodeError err)
               => RootId
               -> [NodeType]
-              -> Cmd err (Tree NodeTree)
+              -> DBCmd err (Tree NodeTree)
 tree_advanced r nodeTypes = do
   -- let rPrefix s = "[tree_advanced] root = " <> show r <> " " <> s
   mainRoot    <- findNodes r Private nodeTypes
@@ -128,7 +128,7 @@ tree_advanced r nodeTypes = do
 tree_first_level :: (HasTreeError err, HasNodeError err)
                  => RootId
                  -> [NodeType]
-                 -> Cmd err (Tree NodeTree)
+                 -> DBCmd err (Tree NodeTree)
 tree_first_level r nodeTypes = do
   -- let rPrefix s = mconcat [ "[tree_first_level] root = "
   --                         , show r
@@ -151,7 +151,7 @@ tree_flat :: (HasTreeError err, HasNodeError err)
           => RootId
           -> [NodeType]
           -> Maybe Text
-          -> Cmd err [NodeTree]
+          -> DBCmd err [NodeTree]
 tree_flat r nodeTypes q = do
   mainRoot <- findNodes r Private nodeTypes
   publicRoots <- findNodes r Public nodeTypes
@@ -169,7 +169,7 @@ findNodes :: (HasTreeError err, HasNodeError err)
           => RootId
           -> NodeMode
           -> [NodeType]
-          -> Cmd err [DbTreeNode]
+          -> DBCmd err [DbTreeNode]
 findNodes r Private nt       = dbTree r nt
 findNodes r Shared  nt       = findShared r NodeFolderShared nt sharedTreeUpdate
 findNodes r SharedDirect  nt = findSharedDirect r NodeFolderShared nt sharedTreeUpdate
@@ -181,7 +181,7 @@ findNodes r PublicDirect  nt = findSharedDirect r NodeFolderPublic nt publicTree
 --   Queries the `nodes_nodes` table.
 findShared :: HasTreeError err
            => RootId -> NodeType -> [NodeType] -> UpdateTree err
-           -> Cmd err [DbTreeNode]
+           -> DBCmd err [DbTreeNode]
 findShared r nt nts fun = do
   foldersSharedId <- findNodesId r [nt]
   trees           <- mapM (updateTree nts fun) foldersSharedId
@@ -192,7 +192,7 @@ findShared r nt nts fun = do
 -- and get the tree for its parent.
 findSharedDirect :: (HasTreeError err, HasNodeError err)
                  => RootId -> NodeType -> [NodeType] -> UpdateTree err
-                 -> Cmd err [DbTreeNode]
+                 -> DBCmd err [DbTreeNode]
 findSharedDirect r nt nts fun = do
   -- let rPrefix s = mconcat [ "[findSharedDirect] r = "
   --                         , show r
@@ -214,11 +214,11 @@ findSharedDirect r nt nts fun = do
       pure $ concat trees
 
 
-type UpdateTree err = ParentId -> [NodeType] -> NodeId -> Cmd err [DbTreeNode]
+type UpdateTree err = ParentId -> [NodeType] -> NodeId -> DBCmd err [DbTreeNode]
 
 updateTree :: HasTreeError err
            => [NodeType] -> UpdateTree err -> RootId
-           -> Cmd err [DbTreeNode]
+           -> DBCmd err [DbTreeNode]
 updateTree nts fun r = do
   folders       <- getNodeNode r
   nodesSharedId <- mapM (fun r nts)
@@ -245,12 +245,12 @@ publicTreeUpdate p nt n = dbTree n nt
 
 
 -- | findNodesId returns all nodes matching nodeType but the root (Nodeuser)
-findNodesId :: RootId -> [NodeType] -> Cmd err [NodeId]
+findNodesId :: RootId -> [NodeType] -> DBCmd err [NodeId]
 findNodesId r nt = tail
                 <$> map _dt_nodeId
                 <$> dbTree r nt
 
-findNodesWithType :: RootId -> [NodeType] -> [NodeType] -> Cmd err [DbTreeNode]
+findNodesWithType :: RootId -> [NodeType] -> [NodeType] -> DBCmd err [DbTreeNode]
 findNodesWithType root target through =
   filter isInTarget <$> dbTree root through
     where
@@ -331,7 +331,7 @@ toSubtreeParent r ns = fromListWith (\a b -> nub $ a <> b) . map (\n -> (_dt_par
 -- | Main DB Tree function
 dbTree :: RootId
        -> [NodeType]
-       -> Cmd err [DbTreeNode]
+       -> DBCmd err [DbTreeNode]
 dbTree rootId nodeTypes = map (\(nId, tId, pId, n) -> DbTreeNode nId tId pId n)
   <$> runPGSQuery [sql|
     WITH RECURSIVE
@@ -383,7 +383,7 @@ isDescendantOf childId rootId = (== [Only True])
   |] (childId, rootId)
 
 -- TODO should we check the category?
-isIn :: NodeId -> DocId -> Cmd err Bool
+isIn :: NodeId -> DocId -> DBCmd err Bool
 isIn cId docId = ( == [Only True])
   <$> runPGSQuery [sql| SELECT COUNT(*) = 1
     FROM nodes_nodes nn
@@ -393,8 +393,8 @@ isIn cId docId = ( == [Only True])
 
 -- Recursive parents function to construct a breadcrumb
 recursiveParents :: NodeId
-       -> [NodeType]
-       -> Cmd err [DbTreeNode]
+                 -> [NodeType]
+                 -> DBCmd err [DbTreeNode]
 recursiveParents nodeId nodeTypes = map (\(nId, tId, pId, n) -> DbTreeNode nId tId pId n)
   <$> runPGSQuery [sql|
     WITH RECURSIVE recursiveParents AS

test/Test/Database/Types.hs

@@ -34,6 +34,7 @@ import Gargantext.API.Prelude
 import Gargantext.Core.Mail.Types (HasMail(..))
 import Gargantext.Core.NLP (HasNLPServer(..))
 import Gargantext.Database.Query.Table.Node.Error
+import Gargantext.Database.Prelude (HasConfig(..), HasConnectionPool(..))
 import Gargantext.Prelude.Config
 import Gargantext.Prelude.Mail.Types (MailConfig(..), LoginType(NoAuth))
 import Gargantext.System.Logging (HasLogger(..), Logger, MonadLogger(..))