Removed some more dead code

src/Gargantext/API/EKG.hs

@@ -16,16 +16,8 @@ Portability : POSIX
 
 module Gargantext.API.EKG where
 
-import Data.HashMap.Strict as HM
 import Data.Text as T
-import Data.Text.IO as T
-import Data.Time.Clock.POSIX (getPOSIXTime)
-import Network.Wai (Middleware)
-import Protolude
 import Servant
-import Servant.Auth (Auth)
-import Servant.Ekg (HasEndpoint, getEndpoint, enumerateEndpoints, monitorEndpoints)
-import System.Metrics
 import System.Metrics.Json qualified as J
 
 -- Mimics https://github.com/tibbe/ekg/blob/master/System/Remote/Snap.hs#L98
@@ -37,26 +29,3 @@ type EkgAPI =
        ) :<|>
        Raw
     )
-
-ekgServer :: FilePath -> Store -> Server EkgAPI
-ekgServer assetsDir store = (getAll :<|> getOne) :<|> serveDirectoryFileServer assetsDir
-
-  where getAll = J.Sample <$> liftIO (sampleAll store)
-        getOne segments = do
-          let metric = T.intercalate "." segments
-          metrics <- liftIO (sampleAll store)
-          maybe (liftIO (T.putStrLn "not found boohoo") >> throwError err404) (return . J.Value) (HM.lookup metric metrics)
-
-newEkgStore :: HasEndpoint api => Proxy api -> IO (Store, Middleware)
-newEkgStore api = do
-  s <- newStore
-  registerGcMetrics s
-  registerCounter "ekg.server_timestamp_ms" getTimeMs s -- used by UI
-  mid <- monitorEndpoints api s
-  pure (s, mid)
-
-  where getTimeMs = (round . (* 1000)) `fmap` getPOSIXTime
-
-instance HasEndpoint api => HasEndpoint (Auth xs a :> api) where
-    getEndpoint        _ = getEndpoint        (Proxy :: Proxy api)
-    enumerateEndpoints _ = enumerateEndpoints (Proxy :: Proxy api)

src/Gargantext/API/GraphQL/Node.hs

@@ -14,8 +14,7 @@ Portability : POSIX
 
 module Gargantext.API.GraphQL.Node where
 
-import Data.Aeson ( Result(..), Value(..) )
-import Data.Aeson.KeyMap qualified as KM
+import Data.Aeson ( Value(..) )
 import Data.Morpheus.Types ( GQLType )
 import Gargantext.API.Admin.Auth.Types ( AuthenticatedUser )
 import Gargantext.API.Auth.PolicyCheck ( nodeReadChecks, AccessPolicyManager )
@@ -28,7 +27,6 @@ import Gargantext.Database.Prelude (IsDBEnvExtra)  -- , JSONB)
 import Gargantext.Database.Query.Table.Node (getClosestChildrenByType, getClosestParentIdByType, getNode)
 import Gargantext.Database.Schema.Node qualified as N
 import Gargantext.Prelude
-import PUBMED.Types qualified as PUBMED
 
 data Corpus = Corpus
   { id           :: Int
@@ -145,12 +143,3 @@ toCorpus N.Node { .. } = Corpus { id = NN.unNodeId _node_id
                                 , name = _node_name
                                 , parent_id = NN.unNodeId <$> _node_parent_id
                                 , type_id = _node_typename }
-
-pubmedAPIKeyFromValue :: Value -> Maybe PUBMED.APIKey
-pubmedAPIKeyFromValue (Object kv) =
-  case KM.lookup "pubmed_api_key" kv of
-    Nothing -> Nothing
-    Just v  -> case fromJSON v of
-      Error _    -> Nothing
-      Success v' -> Just v'
-pubmedAPIKeyFromValue _           = Nothing

src/Gargantext/API/Job.hs

@@ -16,7 +16,6 @@ module Gargantext.API.Job (
   , jobLogAddMore
   , jobLogFailures
   , jobLogFailTotal
-  , jobLogEvt
   , jobLogFailTotalWithMessage
   , RemainingSteps(..)
   , addErrorEvent
@@ -84,6 +83,3 @@ jobLogFailTotal (JobLog { _scst_succeeded = mSucc
 
 jobLogFailTotalWithMessage :: ToHumanFriendlyError e => e -> JobLog -> JobLog
 jobLogFailTotalWithMessage message jl = addErrorEvent message $ jobLogFailTotal jl
-
-jobLogEvt :: JobLog -> ScraperEvent -> JobLog
-jobLogEvt jl evt = over (scst_events . _Just) (\evts -> (evt:evts)) jl

src/Gargantext/API/Ngrams.hs

@@ -105,53 +105,6 @@ import Text.Collate qualified as Unicode
 
 
 
-{-
--- TODO sequences of modifications (Patchs)
-type NgramsIdPatch = Patch NgramsId NgramsPatch
-
-ngramsPatch :: Int -> NgramsPatch
-ngramsPatch n = NgramsPatch (DM.fromList [(1, StopTerm)]) (Set.fromList [n]) Set.empty
-
-toEdit :: NgramsId -> NgramsPatch -> Edit NgramsId NgramsPatch
-toEdit n p = Edit n p
-ngramsIdPatch :: Patch NgramsId NgramsPatch
-ngramsIdPatch = fromList $ catMaybes $ reverse [ replace (1::NgramsId) (Just $ ngramsPatch 1) Nothing
-                                       , replace (1::NgramsId) Nothing (Just $ ngramsPatch 2)
-                                       , replace (2::NgramsId) Nothing (Just $ ngramsPatch 2)
-                                       ]
-
--- applyPatchBack :: Patch -> IO Patch
--- isEmptyPatch = Map.all (\x -> Set.isEmpty (add_children x) && Set.isEmpty ... )
--}
-------------------------------------------------------------------------
-------------------------------------------------------------------------
-------------------------------------------------------------------------
-
-{-
--- TODO: Replace.old is ignored which means that if the current list
--- `MapTerm` and that the patch is `Replace CandidateTerm StopTerm` then
--- the list is going to be `StopTerm` while it should keep `MapTerm`.
--- However this should not happen in non conflicting situations.
-mkListsUpdate :: NgramsType -> NgramsTablePatch -> [(NgramsTypeId, NgramsTerm, ListTypeId)]
-mkListsUpdate nt patches =
-  [ (ngramsTypeId nt, ng, listTypeId lt)
-  | (ng, patch) <- patches ^.. ntp_ngrams_patches . ifolded . withIndex
-  , lt <- patch ^.. patch_list . new
-  ]
-
-mkChildrenGroups :: (PatchSet NgramsTerm -> Set NgramsTerm)
-                 -> NgramsType
-                 -> NgramsTablePatch
-                 -> [(NgramsTypeId, NgramsParent, NgramsChild)]
-mkChildrenGroups addOrRem nt patches =
-  [ (ngramsTypeId nt, parent, child)
-  | (parent, patch) <- patches ^.. ntp_ngrams_patches . ifolded . withIndex
-  , child <- patch ^.. patch_children . to addOrRem . folded
-  ]
--}
-
-------------------------------------------------------------------------
-
 saveNodeStory :: ( MonadReader env m, MonadBase IO m, HasNodeStoryImmediateSaver env )
               => NodeId -> ArchiveList -> m ()
 saveNodeStory nId a = do
@@ -183,34 +136,6 @@ insertNewOnly :: a -> Maybe b -> a
 insertNewOnly m = maybe m (const $ errorTrace "insertNewOnly: impossible")
   -- TODO error handling
 
-{- unused
--- TODO refactor with putListNgrams
-copyListNgrams :: RepoCmdM env err m
-               => NodeId -> NodeId -> NgramsType
-               -> m ()
-copyListNgrams srcListId dstListId ngramsType = do
-  var <- view repoVar
-  liftBase $ modifyMVar_ var $
-    pure . (r_state . at ngramsType %~ (Just . f . something))
-  saveNodeStory
-  where
-    f :: Map NodeId NgramsTableMap -> Map NodeId NgramsTableMap
-    f m = m & at dstListId %~ insertNewOnly (m ^. at srcListId)
-
--- TODO refactor with putListNgrams
--- The list must be non-empty!
--- The added ngrams must be non-existent!
-addListNgrams :: RepoCmdM env err m
-              => NodeId -> NgramsType
-              -> [NgramsElement] -> m ()
-addListNgrams listId ngramsType nes = do
-  var <- view repoVar
-  liftBase $ modifyMVar_ var $
-    pure . (r_state . at ngramsType . _Just . at listId . _Just <>~ m)
-  saveNodeStory
-  where
-    m = Map.fromList $ (\n -> (n ^. ne_ngrams, n)) <$> nes
--}
 
 -- | TODO: incr the Version number
 -- && should use patch
@@ -227,18 +152,6 @@ setListNgrams listId ngramsType ns = do
                                               Nothing -> Just ns
                                               Just ns' -> Just $ ns <> ns')
   saveNodeStory listId a'
-  -- liftBase $ atomically $ do
-  --   nls <- readTVar var
-  --   writeTVar var $
-  --     ( unNodeStory
-  --       . at listId . _Just
-  --       . a_state
-  --       . at ngramsType
-  --       %~ (\mns' -> case mns' of
-  --              Nothing -> Just ns
-  --              Just ns' -> Just $ ns <> ns')
-  --     ) nls
-  -- saveNodeStory
 
 
 newNgramsFromNgramsStatePatch :: NgramsStatePatch' -> [Ngrams]
@@ -260,24 +173,10 @@ commitStatePatch :: ( HasNodeStory env err m
                  ->    Versioned NgramsStatePatch'
                  -> m (Versioned NgramsStatePatch')
 commitStatePatch listId (Versioned _p_version p) = do
-  -- printDebug "[commitStatePatch]" listId
   a <- getNodeStory listId
   archiveSaver <- view hasNodeArchiveStoryImmediateSaver
-  -- ns <- liftBase $ atomically $ readTVar var
   let
-    -- a = ns ^. unNodeStory . at listId . non initArchive
-    -- apply patches from version p_version to a ^. a_version
-    -- TODO Check this
-    --q = mconcat $ take (a ^. a_version - p_version) (a ^. a_history)
     q = mconcat $ a ^. a_history
-
-  --printDebug "[commitStatePatch] transformWith" (p,q)
-  -- let tws s = case s of
-  --       (Mod p) -> "Mod"
-  --       _ -> "Rpl"
-  -- printDebug "[commitStatePatch] transformWith" (tws $ p ^. _NgramsPatch, tws $ q ^. _NgramsPatch)
-
-  let
     (p', q') = transformWith ngramsStatePatchConflictResolution p q
     a' = a & a_version +~ 1
            & a_state   %~ act p'