Merge branch 'dev' into 238-dev-async-job-worker

CHANGELOG.md

+## Version 0.0.7.3.1
+
+* [FRONT][FIX][Cannot build the project on latest `dev` (#701)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/701)
+* [FRONT][FIX][Phylomemy  panel reload after first query (#674)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/674)
+* [BACK][FIX][Various test failures (#408)](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/408)
+* [BACK][FIX][Swagger documentation is down (#407)](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/407)
+* [BACK][ADMIN][Improve startup error from
+  `runDbCheck`](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/merge_requests/347)
+* [BACK][CLEAN] removing unused SQL function in schema.sql
+* [BACK][TESTS][Terms are calculated over all documents, even those in trash (#385)](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/385)
+
 ## Version 0.0.7.3 [/!\ Maintenance command inside]
 
 * [BACK][FIX][Upgrade to GHC 9.4.8][Switch from .ini to TOML? (#304)](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/304)

devops/postgres/schema.sql

@@ -404,35 +404,3 @@ FOR EACH ROW
 EXECUTE PROCEDURE check_node_stories_json();
 
 
-   CREATE OR REPLACE FUNCTION check_ngrams_json()
-    RETURNS TRIGGER AS $$
-    DECLARE
-      missing_ngrams_exist boolean;
-    BEGIN
-        WITH child_ngrams as
-          (SELECT jsonb_array_elements_text(ngrams_repo_element->'children') AS term
-           FROM node_stories
-           WHERE term = OLD.terms),
-          parent_ngrams AS
-          (SELECT ngrams_repo_element->>'root' AS term
-           FROM node_stories
-           WHERE term = OLD.terms),
-          child_parent_ngrams AS
-          (SELECT * FROM child_ngrams
-           UNION SELECT * FROM parent_ngrams)
-
-       SELECT EXISTS(SELECT * FROM child_parent_ngrams) INTO missing_ngrams_exist;
-
-       IF missing_ngrams_exist THEN
-          RAISE EXCEPTION 'ngrams are missing: %', row_to_json(OLD);
-       END IF;
-
-       RETURN OLD;
-    END;
-    $$ LANGUAGE plpgsql;
-
-  CREATE OR REPLACE TRIGGER check_ngrams_json_trg
-  AFTER DELETE
-  ON ngrams
-  FOR EACH ROW
-  EXECUTE PROCEDURE check_ngrams_json();

gargantext.cabal

@@ -5,7 +5,7 @@ cabal-version: 3.4
 -- see: https://github.com/sol/hpack
 
 name:           gargantext
-version: 0.0.7.3
+version: 0.0.7.3.1
 synopsis:       Search, map, share
 description:    Please see README.md
 category:       Data
@@ -34,6 +34,7 @@ data-files:
     ekg-assets/cross.png
     test-data/ngrams/GarganText_NgramsTerms-QuantumComputing.json
     test-data/ngrams/GarganText_DocsList-nodeId-177.json
+    test-data/ngrams/GarganText_NgramsTerms-nodeId-177.json
     test-data/ngrams/simple.json
     test-data/ngrams/simple.tsv
     test-data/phylo/bpa_phylo_test.json
@@ -255,6 +256,7 @@ library
       Gargantext.Database.Admin.Types.Hyperdata
       Gargantext.Database.Admin.Types.Hyperdata.Corpus
       Gargantext.Database.Admin.Types.Hyperdata.Document
+      Gargantext.Database.Admin.Types.Hyperdata.Folder
       Gargantext.Database.Admin.Types.Node
       Gargantext.Database.Prelude
       Gargantext.Database.Query.Facet
@@ -425,7 +427,6 @@ library
       Gargantext.Database.Admin.Types.Hyperdata.Dashboard
       Gargantext.Database.Admin.Types.Hyperdata.Default
       Gargantext.Database.Admin.Types.Hyperdata.File
-      Gargantext.Database.Admin.Types.Hyperdata.Folder
       Gargantext.Database.Admin.Types.Hyperdata.Frame
       Gargantext.Database.Admin.Types.Hyperdata.List
       Gargantext.Database.Admin.Types.Hyperdata.Model

hie.yaml

+cradle:
+  cabal:
+    - path: "./src"
+      component: "lib:gargantext"
+
+    - path: "./bin/gargantext-cli/Main.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/Admin.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/FileDiff.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/FilterTermsAndCooc.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/Import.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/Ini.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/Init.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/Invitations.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/ObfuscateDB.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/Parsers.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/Phylo.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/Phylo/Common.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/Phylo/Profile.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/Server/Routes.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/Types.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/CLI/Upgrade.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-cli/Paths_gargantext.hs"
+      component: "gargantext:exe:gargantext-cli"
+
+    - path: "./bin/gargantext-server/Main.hs"
+      component: "gargantext:exe:gargantext-server"
+
+    - path: "./bin/gargantext-server/Paths_gargantext.hs"
+      component: "gargantext:exe:gargantext-server"
+
+    - path: "./test"
+      component: "gargantext:test:garg-test-tasty"
+
+    - path: "./bin/gargantext-cli"
+      component: "gargantext:test:garg-test-tasty"
+
+    - path: "./test"
+      component: "gargantext:test:garg-test-hspec"
+
+    - path: "./bench/Main.hs"
+      component: "gargantext:bench:garg-bench"
+
+    - path: "./bench/Paths_gargantext.hs"
+      component: "gargantext:bench:garg-bench"

src/Gargantext/API.hs

@@ -92,12 +92,13 @@ startGargantext mode port sf@(SettingsFile settingsFile) = withLoggerHoisted mod
 
   where runDbCheck env = do
           r <- runExceptT (runReaderT DB.dbCheck env) `catch`
-            (\(_ :: SomeException) -> pure $ Right False)
+            (\(err :: SomeException) -> pure $ Left err)
           case r of
-            Right True -> pure ()
-            _ -> panicTrace $
-              "You must run 'gargantext-init " <> pack settingsFile <>
+            Right True  -> pure ()
+            Right False -> panicTrace $
+              "You must run 'gargantext-cli init " <> pack settingsFile <>
               "' before running gargantext-server (only the first time)."
+            Left err -> panicTrace $ "Unexpected exception:" <> show err
         oneHour = Clock.fromNanoSecs 3600_000_000_000
 
 portRouteInfo :: NotificationsConfig -> PortNumber -> MicroServicesProxyStatus -> IO ()

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

@@ -14,9 +14,10 @@ Portability : POSIX
 module Gargantext.Core.Viz.Graph.Types
   where
 
+import Data.Aeson (defaultOptions)
 import Data.HashSet (HashSet)
 import Data.HashSet qualified as HashSet
-import Data.Swagger (ToSchema(..), genericDeclareNamedSchema)
+import Data.Swagger (ToSchema(..), genericDeclareNamedSchema, defaultSchemaOptions)
 import Data.Text (pack)
 import Database.PostgreSQL.Simple.FromField (FromField(..))
 import Gargantext.API.Ngrams.Types (NgramsTerm)
@@ -245,9 +246,9 @@ instance FromField HyperdataGraphAPI
 
 data GraphLegendAPI = GraphLegendAPI [LegendField]
   deriving (Show, Generic)
-$(deriveJSON (unPrefix "_graphAPI") ''GraphLegendAPI)
+$(deriveJSON defaultOptions ''GraphLegendAPI)
 instance ToSchema GraphLegendAPI where
-  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_graphAPI")
+  declareNamedSchema = genericDeclareNamedSchema defaultSchemaOptions
 
 makeLenses ''GraphLegendAPI
 

test-data/ngrams/GarganText_DocsList-nodeId-177.json

@@ -58,5 +58,6 @@
       },
       "hash": ""
     }
-  ]
+  ],
+  "garg_version": "0.0.7.1.16"
 }

test-data/ngrams/GarganText_NgramsTerms-nodeId-177.json

+{ "NgramsTerms":{ "version":1 ,"data":{ "fortran":{"size":2,"list":"MapTerm","children":[]} } }
+}

test/Test/API/Routes.hs

@@ -8,24 +8,31 @@ module Test.API.Routes where
 import Data.Text.Encoding qualified as TE
 import Fmt (Builder, (+|), (|+))
 import Gargantext.API.Admin.Auth.Types (AuthRequest, AuthResponse, Token)
+import Gargantext.API.Admin.Orchestrator.Types (JobLog, asyncJobsAPI')
 import Gargantext.API.Errors
+import Gargantext.API.HashedResponse (HashedResponse)
 import Gargantext.API.Ngrams.Types ( NgramsTable, NgramsTablePatch, OrderBy, TabType, Versioned, VersionedWithCount )
 import Gargantext.API.Routes.Named
 import Gargantext.API.Routes.Named.Node
 import Gargantext.API.Routes.Named.Private hiding (tableNgramsAPI)
 import Gargantext.API.Routes.Named.Table
 import Gargantext.API.Types () -- MimeUnrender instances
-import Gargantext.Core.Types (ListId, NodeId)
+import Gargantext.Core.Text.Corpus.Query (RawQuery)
+import Gargantext.Core.Types (ListId, NodeId, NodeType, NodeTableResult)
 import Gargantext.Core.Types.Main (ListType)
 import Gargantext.Core.Types.Query (Limit, MaxSize, MinSize, Offset)
+import Gargantext.Database.Admin.Types.Hyperdata
+import Gargantext.Database.Query.Facet qualified as Facet
 import Gargantext.Prelude
 import Network.HTTP.Types qualified as H
 import Network.Wai.Handler.Warp (Port)
+import Servant ((:<|>)(..))
 import Servant.API.WebSocket qualified as WS
 import Servant.Auth.Client qualified as S
 import Servant.Client (ClientM)
 import Servant.Client.Core (RunClient, HasClient(..), Request)
 import Servant.Client.Generic ( genericClient, AsClientT )
+import Servant.Job.Async
 
 
 instance RunClient m => HasClient m WS.WebSocketPending where
@@ -47,6 +54,9 @@ mkUrl :: Port -> Builder -> ByteString
 mkUrl _port urlPiece =
   "/api/" +| curApi |+ urlPiece
 
+gqlUrl :: ByteString
+gqlUrl = "/gql"
+
 
 -- | The client for the full API. It also serves as a \"proof\" that our
 -- whole API has all the required instances to be used in a client.
@@ -64,19 +74,44 @@ auth_api = clientRoutes & apiWithCustomErrorScheme
                         & gargAuthAPI
                         & authEp
 
-table_ngrams_get_api :: Token
-                     -> NodeId
-                     -> TabType
-                     -> ListId
-                     -> Limit
-                     -> Maybe Offset
-                     -> Maybe ListType
-                     -> Maybe MinSize
-                     -> Maybe MaxSize
-                     -> Maybe OrderBy
-                     -> Maybe Text
-                     -> ClientM (VersionedWithCount NgramsTable)
-table_ngrams_get_api (toServantToken -> token) nodeId =
+toServantToken :: Token -> S.Token
+toServantToken = S.Token . TE.encodeUtf8
+
+update_node :: Token
+            -> NodeId
+            -> UpdateNodeParams
+            -> ClientM (JobStatus 'Safe JobLog)
+update_node (toServantToken -> token) nodeId params =
+  clientRoutes & apiWithCustomErrorScheme
+               & ($ GES_new)
+               & backendAPI
+               & backendAPI'
+               & mkBackEndAPI
+               & gargAPIVersion
+               & gargPrivateAPI
+               & mkPrivateAPI
+               & ($ token)
+               & nodeEp
+               & nodeEndpointAPI
+               & ($ nodeId)
+               & updateAPI
+               & updateNodeEp
+               & asyncJobsAPI'
+               & (\(_ :<|> submitForm :<|> _) -> submitForm (JobInput params Nothing))
+
+get_table_ngrams :: Token
+                 -> NodeId
+                 -> TabType
+                 -> ListId
+                 -> Limit
+                 -> Maybe Offset
+                 -> Maybe ListType
+                 -> Maybe MinSize
+                 -> Maybe MaxSize
+                 -> Maybe OrderBy
+                 -> Maybe Text
+                 -> ClientM (VersionedWithCount NgramsTable)
+get_table_ngrams (toServantToken -> token) nodeId =
   clientRoutes & apiWithCustomErrorScheme
                & ($ GES_new)
                & backendAPI
@@ -93,16 +128,13 @@ table_ngrams_get_api (toServantToken -> token) nodeId =
                & tableNgramsGetAPI
                & getNgramsTableEp
 
-toServantToken :: Token -> S.Token
-toServantToken = S.Token . TE.encodeUtf8
-
-table_ngrams_put_api :: Token
-                     -> NodeId
-                     -> TabType
-                     -> ListId
-                     -> Versioned NgramsTablePatch
-                     -> ClientM (Versioned NgramsTablePatch)
-table_ngrams_put_api (toServantToken -> token) nodeId =
+put_table_ngrams :: Token
+                 -> NodeId
+                 -> TabType
+                 -> ListId
+                 -> Versioned NgramsTablePatch
+                 -> ClientM (Versioned NgramsTablePatch)
+put_table_ngrams (toServantToken -> token) nodeId =
   clientRoutes & apiWithCustomErrorScheme
                & ($ GES_new)
                & backendAPI
@@ -118,3 +150,51 @@ table_ngrams_put_api (toServantToken -> token) nodeId =
                & tableNgramsAPI
                & tableNgramsPutAPI
                & putNgramsTableEp
+
+get_table :: Token
+          -> NodeId
+          -> Maybe TabType
+          -> Maybe Limit
+          -> Maybe Offset
+          -> Maybe Facet.OrderBy
+          -> Maybe RawQuery
+          -> Maybe Text
+          -> ClientM (HashedResponse FacetTableResult)
+get_table (toServantToken -> token) nodeId =
+  clientRoutes & apiWithCustomErrorScheme
+               & ($ GES_new)
+               & backendAPI
+               & backendAPI'
+               & mkBackEndAPI
+               & gargAPIVersion
+               & gargPrivateAPI
+               & mkPrivateAPI
+               & ($ token)
+               & nodeEp
+               & nodeEndpointAPI
+               & ($ nodeId)
+               & tableAPI
+               & getTableEp
+
+get_children :: Token
+             -> NodeId
+             -> Maybe NodeType
+             -> Maybe Offset
+             -> Maybe Limit
+             -> ClientM (NodeTableResult HyperdataAny)
+get_children (toServantToken -> token) nodeId =
+  clientRoutes & apiWithCustomErrorScheme
+               & ($ GES_new)
+               & backendAPI
+               & backendAPI'
+               & mkBackEndAPI
+               & gargAPIVersion
+               & gargPrivateAPI
+               & mkPrivateAPI
+               & ($ token)
+               & nodeEp
+               & nodeEndpointAPI
+               & ($ nodeId)
+               & childrenAPI
+               & summaryChildrenEp
+

test/Test/Utils.hs

@@ -7,33 +7,38 @@ module Test.Utils where
 
 import Control.Exception.Safe ()
 import Control.Monad ()
-import Data.Aeson qualified as JSON
 import Data.Aeson.KeyMap qualified as KM
+import Data.Aeson qualified as JSON
 import Data.ByteString.Char8 qualified as B
 import Data.ByteString.Lazy qualified as L
 import Data.Map.Strict qualified as Map
-import Data.Text qualified as T
 import Data.Text.Encoding qualified as TE
-import Data.Text.Lazy qualified as TL
 import Data.Text.Lazy.Encoding qualified as TLE
+import Data.Text.Lazy qualified as TL
+import Data.Text qualified as T
 import Data.TreeDiff
 import Fmt (Builder)
-import Gargantext.API.Routes.Types (xGargErrorScheme)
 import Gargantext.API.Admin.Auth.Types (AuthRequest(..), Token, authRes_token)
+import Gargantext.API.Admin.Orchestrator.Types
+import Gargantext.API.Routes.Types (xGargErrorScheme)
 import Gargantext.Core.Types.Individu (Username, GargPassword)
 import Gargantext.Prelude
 import Network.HTTP.Client (defaultManagerSettings, newManager)
-import Network.HTTP.Types (Header, Method, status200)
+import Network.HTTP.Client qualified as HTTP
 import Network.HTTP.Types.Header (hAccept, hAuthorization, hContentType)
+import Network.HTTP.Types (Header, Method, status200)
 import Network.Wai.Handler.Warp (Port)
 import Network.Wai.Test (SResponse(..))
 import Prelude qualified
-import Servant.Client (ClientEnv, baseUrlPort, mkClientEnv, parseBaseUrl, runClientM)
+import Servant.Client (ClientEnv, baseUrlPort, mkClientEnv, parseBaseUrl, runClientM, makeClientRequest, defaultMakeClientRequest)
+import Servant.Client.Core (BaseUrl)
+import Servant.Client.Core.Request qualified as Client
+import System.Environment (lookupEnv)
 import System.Timeout qualified as Timeout
 import Test.API.Routes (auth_api, mkUrl)
 import Test.Hspec.Expectations
-import Test.Hspec.Wai (MatchBody(..), WaiExpectation, WaiSession, request)
 import Test.Hspec.Wai.JSON (FromValue(..))
+import Test.Hspec.Wai (MatchBody(..), WaiExpectation, WaiSession, request)
 import Test.Hspec.Wai.Matcher (MatchHeader(..), ResponseMatcher(..), bodyEquals, formatHeader, match)
 import Test.Tasty.HUnit (Assertion, assertBool)
 import Test.Types
@@ -183,12 +188,27 @@ withValidLogin port ur pwd act = do
   case result of
     Left err  -> liftIO $ throwIO $ Prelude.userError (show err)
     Right res -> do
+      traceEnabled <- isJust <$> liftIO (lookupEnv "GARG_DEBUG_LOGS")
       let token = res ^. authRes_token
-      act clientEnv0 token
+      act (clientEnv0 { makeClientRequest = gargMkRequest traceEnabled }) token
+
+-- | Allows to enable/disable logging of the input 'Request' to check what the
+-- client is actually sending to the server.
+-- FIXME(adn) We cannot upgrade to servant-client 0.20 due to OpenAlex:
+-- https://gitlab.iscpif.fr/gargantext/crawlers/openalex/blob/main/src/OpenAlex/ServantClientLogging.hs#L24
+gargMkRequest :: Bool -> BaseUrl -> Client.Request -> HTTP.Request
+gargMkRequest traceEnabled bu clientRq =
+  let httpReq = defaultMakeClientRequest bu clientRq
+  in case traceEnabled of
+       True ->
+         traceShowId httpReq
+       False -> httpReq
 
 
 -- | Poll the given job URL every second until it finishes.
 -- Retries up to 60 times (i.e. for 1 minute, before giving up)
+-- /NOTE(adn)/: Check the content of the \"events\" logs as a stopgap
+-- measure for #390.
 pollUntilFinished :: HasCallStack
                   => Token
                   -> Port
@@ -208,7 +228,15 @@ pollUntilFinished tkn port mkUrlPiece = go 60
      | _jph_status h == "IsFailure"
      -> panicTrace $ "JobPollHandle contains a failure: " <> TE.decodeUtf8 (L.toStrict $ JSON.encode h)
      | otherwise
-     -> pure h
+     -> case any hasError (_jph_log h) of
+          True  -> panicTrace $ "JobPollHandle contains a failure: " <> TE.decodeUtf8 (L.toStrict $ JSON.encode h)
+          False -> pure h
+
+   -- FIXME(adn) This is wrong, errs should be >= 1.
+   hasError :: JobLog -> Bool
+   hasError JobLog{..} = case _scst_failed of
+     Nothing   -> False
+     Just errs -> errs > 1
 
 -- | Like HUnit's '@?=', but With a nicer error message in case the two entities are not equal.
 (@??=) :: (HasCallStack, ToExpr a, Eq a) => a -> a -> Assertion

test/Test/Utils/Jobs.hs

@@ -367,23 +367,30 @@ testMarkProgress = do
   myEnv <- newTestEnv
   -- evts  <- newTBQueueIO 7
   evts <- newTVarIO []
+  let expectedEvents = 7
   let getStatus hdl = do
         liftIO $ threadDelay 100_000
         st <- getLatestJobStatus hdl
         -- liftIO $ atomically $ writeTBQueue evts st
         liftIO $ atomically $ modifyTVar evts (\xs -> xs ++ [st])
-      readAllEvents = do  
+      readAllEvents = do
         -- We will get thread blocking if there is ANY error in the job
         -- Hence we assert the `readAllEvents` test doesn't take too long
-        mRet <- timeout 1_000_000 $ atomically $ do
+        mRet <- timeout 5_000_000 $ atomically $ do
           -- allEventsArrived <- isFullTBQueue evts
           evts' <- readTVar evts
           -- STM retry if things failed
           -- check allEventsArrived
-          check (length evts' == 7)
+          check (length evts' == expectedEvents)
           -- flushTBQueue evts
-          return evts'
-        return $ fromMaybe [] mRet
+          pure evts'
+        case mRet of
+          Nothing -> Prelude.fail $ "testMarkProgress: timeout exceeded, but didn't receive all 7 required events."
+          Just xs
+            | length xs == expectedEvents
+            -> pure xs
+            | otherwise
+            -> Prelude.fail $ "testMarkProgress: received some events, but they were not of the expected number (" <> show expectedEvents <> "): " <> show xs
 
   withJob_ myEnv $ \hdl _input -> do
     markStarted 10 hdl
@@ -410,6 +417,8 @@ testMarkProgress = do
     getStatus hdl
 
   evts' <- readAllEvents
+  -- This pattern match should never fail, because the precondition is
+  -- checked in 'readAllEvents'.
   let [jl0, jl1, jl2, jl3, jl4, jl5, jl6] = evts'
 
   -- Check the events are what we expect