Merge branch '111-dev-refactor-text-corpus-api-with-conduit-alp' of...

Merge branch '111-dev-refactor-text-corpus-api-with-conduit-alp' of ssh://gitlab.iscpif.fr:20022/gargantext/haskell-gargantext into dev

bin/gargantext-import/Main.hs

@@ -17,10 +17,11 @@ module Main where
 
 import Control.Exception (finally)
 import Data.Either
+import Data.Maybe (Maybe(..))
 import Data.Text (Text)
-import Prelude (read)
 import System.Environment (getArgs)
 import qualified Data.Text as Text
+import Text.Read (readMaybe)
 
 import Gargantext.API.Dev (withDevEnv, runCmdDev)
 import Gargantext.API.Admin.EnvTypes (DevEnv(..))
@@ -46,11 +47,14 @@ main = do
     --tt = (Unsupervised EN 6 0 Nothing)
     tt = (Multi EN)
     format = CsvGargV3 -- CsvHal --WOS
+    limit' = case (readMaybe limit :: Maybe Int) of
+      Nothing -> panic $ "Cannot read limit: " <> (Text.pack limit)
+      Just l  -> l
     corpus :: forall m. FlowCmdM DevEnv GargError m => m CorpusId
-    corpus = flowCorpusFile (UserName $ cs user) (Left (cs name :: Text)) (read limit :: Int) tt  format corpusPath Nothing (\_ -> pure ())
+    corpus = flowCorpusFile (UserName $ cs user) (Left (cs name :: Text)) limit' tt  format corpusPath Nothing (\_ -> pure ())
 
     corpusCsvHal :: forall m. FlowCmdM DevEnv GargError m => m CorpusId
-    corpusCsvHal = flowCorpusFile (UserName $ cs user) (Left (cs name :: Text)) (read limit :: Int) tt CsvHal corpusPath Nothing (\_ -> pure ())
+    corpusCsvHal = flowCorpusFile (UserName $ cs user) (Left (cs name :: Text)) limit' tt CsvHal corpusPath Nothing (\_ -> pure ())
 
     annuaire :: forall m. FlowCmdM DevEnv GargError m => m CorpusId
     annuaire = flowAnnuaire (UserName $ cs user) (Left "Annuaire") (Multi EN) corpusPath (\_ -> pure ())

src/Gargantext/API/Node/Contact.hs

@@ -22,6 +22,7 @@ Portability : POSIX
 module Gargantext.API.Node.Contact
       where
 
+import Conduit
 import Data.Aeson
 import Data.Either (Either(Right))
 import Data.Maybe (Maybe(..))
@@ -93,7 +94,7 @@ addContact u nId (AddContactParams fn ln) logStatus = do
                    , _scst_remaining = Just 1
                    , _scst_events    = Just []
                    }
-  _ <- flow (Nothing :: Maybe HyperdataAnnuaire) u (Right [nId]) (Multi EN) Nothing [[hyperdataContact fn ln]] logStatus
+  _ <- flow (Nothing :: Maybe HyperdataAnnuaire) u (Right [nId]) (Multi EN) Nothing (Just 1, yield $ hyperdataContact fn ln) logStatus
 
   pure  JobLog { _scst_succeeded = Just 2
                , _scst_failed    = Just 0

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

@@ -18,6 +18,8 @@ New corpus means either:
 module Gargantext.API.Node.Corpus.New
       where
 
+
+import Conduit
 import Control.Lens hiding (elements, Empty)
 import Data.Aeson
 import Data.Aeson.TH (deriveJSON)
@@ -39,7 +41,7 @@ import Gargantext.Prelude
 
 import Gargantext.API.Admin.Orchestrator.Types (JobLog(..), AsyncJobs, ScraperEvent(..), scst_events)
 import Gargantext.API.Admin.Types (HasSettings)
-import Gargantext.API.Job (jobLogSuccess, jobLogFailTotal, jobLogFailTotalWithMessage)
+import Gargantext.API.Job (addEvent, jobLogSuccess, jobLogFailTotal, jobLogFailTotalWithMessage)
 import Gargantext.API.Node.Corpus.New.File
 import Gargantext.API.Node.Corpus.Searx
 import Gargantext.API.Node.Corpus.Types
@@ -213,15 +215,20 @@ addToCorpusWithQuery user cid (WithQuery { _wq_query = q
       -- TODO if cid is folder -> create Corpus
       --      if cid is corpus -> add to corpus
       --      if cid is root   -> create corpus in Private
-      txts <- mapM (\db -> getDataText db (Multi l) q maybeLimit) [database2origin dbs]
-  
-      logStatus JobLog { _scst_succeeded = Just 2
+      eTxts <- mapM (\db -> getDataText db (Multi l) q maybeLimit) [database2origin dbs]
+      let lTxts = lefts eTxts
+      case lTxts of
+        [] -> do
+          let txts = rights eTxts
+          -- TODO Sum lenghts of each txt elements
+          logStatus $ JobLog { _scst_succeeded = Just 2
                              , _scst_failed    = Just 0
                              , _scst_remaining = Just $ 1 + length txts
                              , _scst_events    = Just []
                              }
 
-      cids <- mapM (\txt -> flowDataText user txt (Multi l) cid Nothing logStatus) txts
+          cids <- mapM (\txt -> do
+                           flowDataText user txt (Multi l) cid Nothing logStatus) txts
           printDebug "corpus id" cids
           printDebug "sending email" ("xxxxxxxxxxxxxxxxxxxxx" :: Text)
           sendMail user
@@ -232,6 +239,14 @@ addToCorpusWithQuery user cid (WithQuery { _wq_query = q
                       , _scst_events    = Just []
                       }
         
+        (err:_) -> do
+          pure $ addEvent "ERROR" (T.pack $ show err) $
+            JobLog { _scst_succeeded = Just 2
+                   , _scst_failed    = Just 1
+                   , _scst_remaining = Just 0
+                   , _scst_events    = Just []
+                   }
+
 
 type AddWithForm = Summary "Add with FormUrlEncoded to corpus endpoint"
    :> "corpus"
@@ -268,15 +283,16 @@ addToCorpusWithForm user cid (NewWithForm ft d l _n) logStatus jobLog = do
         _   -> cs d
   eDocs <- liftBase $ parse data'
   case eDocs of
-    Right docs' -> do
+    Right docs -> do
       -- TODO Add progress (jobStatus) update for docs - this is a
       -- long action
+
       limit' <- view $ hasConfig . gc_max_docs_parsers
       let limit = fromIntegral limit'
-      if length docs' > limit then do
-        printDebug "[addToCorpusWithForm] number of docs exceeds the limit" (show $ length docs')
+      if length docs > limit then do
+        printDebug "[addToCorpusWithForm] number of docs exceeds the limit" (show $ length docs)
         let panicMsg' = [ "[addToCorpusWithForm] number of docs ("
-                        , show $ length docs'
+                        , show $ length docs
                         , ") exceeds the MAX_DOCS_PARSERS limit ("
                         , show limit
                         , ")" ]
@@ -285,7 +301,6 @@ addToCorpusWithForm user cid (NewWithForm ft d l _n) logStatus jobLog = do
         panic panicMsg
       else
         pure ()
-      let docs = splitEvery 500 $ take limit docs'
 
       printDebug "Parsing corpus finished : " cid
       logStatus jobLog2
@@ -296,7 +311,8 @@ addToCorpusWithForm user cid (NewWithForm ft d l _n) logStatus jobLog = do
                           (Right [cid])
                           (Multi $ fromMaybe EN l)
                           Nothing
-                          (map (map toHyperdataDocument) docs)
+                          (Just $ fromIntegral $ length docs, yieldMany docs .| mapC toHyperdataDocument)
+                          --(map (map toHyperdataDocument) docs)
                           logStatus
 
       printDebug "Extraction finished   : " cid

src/Gargantext/API/Node/DocumentsFromWriteNodes.hs

@@ -16,6 +16,7 @@ Portability : POSIX
 module Gargantext.API.Node.DocumentsFromWriteNodes
       where
 
+import Conduit
 import Control.Lens ((^.))
 import Data.Aeson
 import Data.Either (Either(..), rights)
@@ -100,7 +101,7 @@ documentsFromWriteNodes uId nId _p logStatus = do
   let parsedE = (\(node, contents) -> hyperdataDocumentFromFrameWrite (node ^. node_hyperdata, contents)) <$> frameWritesWithContents
   let parsed = rights parsedE
 
-  _ <- flowDataText (RootId (NodeId uId)) (DataNew [parsed]) (Multi EN) cId Nothing logStatus
+  _ <- flowDataText (RootId (NodeId uId)) (DataNew (Just $ fromIntegral $ length parsed, yieldMany parsed)) (Multi EN) cId Nothing logStatus
 
   pure $ jobLogSuccess jobLog
 ------------------------------------------------------------------------

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

@@ -18,6 +18,8 @@ module Gargantext.Core.Text.Corpus.API
   )
     where
 
+import Conduit
+import Data.Either (Either(..))
 import Data.Maybe
 import Gargantext.API.Admin.Orchestrator.Types (ExternalAPIs(..), externalAPIs)
 import Gargantext.Core (Lang(..))
@@ -27,6 +29,7 @@ import qualified Gargantext.Core.Text.Corpus.API.Hal     as HAL
 import qualified Gargantext.Core.Text.Corpus.API.Isidore as ISIDORE
 import qualified Gargantext.Core.Text.Corpus.API.Istex   as ISTEX
 import qualified Gargantext.Core.Text.Corpus.API.Pubmed  as PUBMED
+import Servant.Client (ClientError)
 
 -- | TODO put in gargantext.init
 default_limit :: Maybe Integer
@@ -37,11 +40,18 @@ get :: ExternalAPIs
     -> Lang
     -> Query
     -> Maybe Limit
-    -> IO [HyperdataDocument]
-get PubMed  _la q _l = PUBMED.get   q default_limit -- EN only by default
-get HAL      la q _l = HAL.get   la q default_limit
-get IsTex    la q _l = ISTEX.get la q default_limit
-get Isidore  la q _l = ISIDORE.get la (fromIntegral <$> default_limit) (Just q) Nothing
+    -- -> IO [HyperdataDocument]
+    -> IO (Either ClientError (Maybe Integer, ConduitT () HyperdataDocument IO ()))
+get PubMed  _la q _l = PUBMED.get q Nothing
+  --docs <- PUBMED.get   q default_limit -- EN only by default
+  --pure (Just $ fromIntegral $ length docs, yieldMany docs)
+get HAL      la q _l = HAL.getC  la q Nothing
+get IsTex    la q _l = do
+  docs <- ISTEX.get la q default_limit
+  pure $ Right (Just $ fromIntegral $ length docs, yieldMany docs)
+get Isidore  la q _l = do
+  docs <- ISIDORE.get la (fromIntegral <$> default_limit) (Just q) Nothing
+  pure $ Right (Just $ fromIntegral $ length docs, yieldMany docs)
 get _        _  _ _ = undefined
 
 -- | Some Sugar for the documentation

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

@@ -12,8 +12,11 @@ Portability : POSIX
 module Gargantext.Core.Text.Corpus.API.Hal
     where
 
+import Conduit
+import Data.Either
 import Data.Maybe
 import Data.Text (Text, pack, intercalate)
+import Servant.Client (ClientError)
 
 import Gargantext.Core (Lang(..))
 import Gargantext.Database.Admin.Types.Hyperdata (HyperdataDocument(..))
@@ -25,8 +28,16 @@ import qualified HAL.Doc.Corpus as HAL
 
 get :: Lang -> Text -> Maybe Integer -> IO [HyperdataDocument]
 get la q ml = do
-  docs <- HAL.getMetadataWith q (Just 0) (fromIntegral <$> ml)
-  either (panic . pack . show) (\d -> mapM (toDoc' la) $ HAL._docs d) docs
+  eDocs <- HAL.getMetadataWith q (Just 0) ml
+  either (panic . pack . show) (\d -> mapM (toDoc' la) $ HAL._docs d) eDocs
+
+getC :: Lang -> Text -> Maybe Integer -> IO (Either ClientError (Maybe Integer, ConduitT () HyperdataDocument IO ()))
+getC la q ml = do
+  eRes <- HAL.getMetadataWithC q (Just 0) ml
+  pure $ (\(len, docsC) -> (len, docsC .| mapMC (toDoc' la))) <$> eRes
+--  case eRes of
+--    Left err -> panic $ pack $ show err
+--    Right (len, docsC) -> pure (len, docsC .| mapMC (toDoc' la))
 
 toDoc' :: Lang -> HAL.Corpus -> IO HyperdataDocument
 toDoc' la (HAL.Corpus i t ab d s aus affs struct_id) = do

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

@@ -13,9 +13,12 @@ Portability : POSIX
 module Gargantext.Core.Text.Corpus.API.Pubmed
     where
 
+import Conduit
+import Data.Either (Either)
 import Data.Maybe
 import Data.Text (Text)
 import qualified Data.Text as Text
+import Servant.Client (ClientError)
 
 import Gargantext.Prelude
 import Gargantext.Core (Lang(..))
@@ -31,17 +34,21 @@ type Limit = PubMed.Limit
 
 -- | TODO put default pubmed query in gargantext.ini
 -- by default: 10K docs
-get :: Query -> Maybe Limit -> IO [HyperdataDocument]
-get q l = either (\e -> panic $ "CRAWL: PubMed" <> e) (map (toDoc EN))
-        <$> PubMed.getMetadataWith q l
+get :: Query -> Maybe Limit -> IO (Either ClientError (Maybe Integer, ConduitT () HyperdataDocument IO ()))
+get q l = do
+  eRes <- PubMed.getMetadataWithC q l
+  pure $ (\(len, docsC) -> (len, docsC .| mapC (toDoc EN))) <$> eRes
+  --either (\e -> panic $ "CRAWL: PubMed" <> e) (map (toDoc EN))
+  --      <$> PubMed.getMetadataWithC q l
 
 toDoc :: Lang -> PubMedDoc.PubMed -> HyperdataDocument
-toDoc l (PubMedDoc.PubMed (PubMedDoc.PubMedArticle t j as aus)
-                    (PubMedDoc.PubMedDate a y m d)
+toDoc l (PubMedDoc.PubMed { pubmed_id
+                          , pubmed_article = PubMedDoc.PubMedArticle t j as aus
+                          , pubmed_date = PubMedDoc.PubMedDate a y m d }
           ) = HyperdataDocument { _hd_bdd = Just "PubMed"
                                 , _hd_doi = Nothing
                                 , _hd_url = Nothing
-                                , _hd_uniqId = Nothing
+                                , _hd_uniqId = Just $ Text.pack $ show pubmed_id
                                 , _hd_uniqIdBdd = Nothing
                                 , _hd_page = Nothing
                                 , _hd_title = t

src/Gargantext/Core/Types/Main.hs

@@ -34,7 +34,7 @@ import Gargantext.Prelude
 import Servant.API (FromHttpApiData(..), ToHttpApiData(..))
 import Test.QuickCheck (elements)
 import Test.QuickCheck.Arbitrary (Arbitrary, arbitrary)
-import Text.Read (read)
+import Text.Read (readMaybe)
 
 type CorpusName = Text
 ------------------------------------------------------------------------
@@ -74,7 +74,11 @@ instance Semigroup ListType
 
 
 instance FromHttpApiData ListType where
-  parseUrlPiece = Right . read . unpack
+  parseUrlPiece s = Right s'
+    where
+      s' = case (readMaybe $ unpack s) of
+        Nothing -> panic $ "Cannot read url piece: " <> s
+        Just s'' -> s''
 instance ToHttpApiData ListType where
   toUrlPiece = pack . show
 

src/Gargantext/Database/Action/Flow.hs

@@ -46,8 +46,10 @@ module Gargantext.Database.Action.Flow -- (flowDatabase, ngrams2list)
   )
     where
 
+import Conduit
 import Control.Lens ((^.), view, _Just, makeLenses)
 import Data.Aeson.TH (deriveJSON)
+import Data.Conduit.Internal (zipSources)
 import Data.Either
 import Data.HashMap.Strict (HashMap)
 import Data.Hashable (Hashable)
@@ -60,6 +62,7 @@ import qualified Data.Text as T
 import Data.Traversable (traverse)
 import Data.Tuple.Extra (first, second)
 import GHC.Generics (Generic)
+import Servant.Client (ClientError)
 import System.FilePath (FilePath)
 import qualified Data.HashMap.Strict as HashMap
 import qualified Gargantext.Data.HashMap.Strict.Utils as HashMap
@@ -103,6 +106,7 @@ import Gargantext.Prelude
 import Gargantext.Prelude.Crypto.Hash (Hash)
 import qualified Gargantext.Core.Text.Corpus.API as API
 import qualified Gargantext.Database.Query.Table.Node.Document.Add  as Doc  (add)
+import qualified Prelude as Prelude
 
 ------------------------------------------------------------------------
 -- Imports for upgrade function
@@ -127,7 +131,8 @@ allDataOrigins = map InternalOrigin API.externalAPIs
 
 ---------------
 data DataText = DataOld ![NodeId]
-              | DataNew ![[HyperdataDocument]]
+              | DataNew !(Maybe Integer, ConduitT () HyperdataDocument IO ())
+              -- | DataNew ![[HyperdataDocument]]
 
 -- TODO use the split parameter in config file
 getDataText :: FlowCmdM env err m
@@ -135,10 +140,10 @@ getDataText :: FlowCmdM env err m
             -> TermType Lang
             -> API.Query
             -> Maybe API.Limit
-            -> m DataText
-getDataText (ExternalOrigin api) la q li = liftBase $ DataNew
-                                  <$> splitEvery 500
-                                  <$> API.get api (_tt_lang la) q li
+            -> m (Either ClientError DataText)
+getDataText (ExternalOrigin api) la q li = liftBase $ do
+  eRes <- API.get api (_tt_lang la) q li
+  pure $ DataNew <$> eRes
 
 getDataText (InternalOrigin _) _la q _li = do
   (_masterUserId, _masterRootId, cId) <- getOrMk_RootWithCorpus
@@ -146,10 +151,11 @@ getDataText (InternalOrigin _) _la q _li = do
                                            (Left "")
                                            (Nothing :: Maybe HyperdataCorpus)
   ids <-  map fst <$> searchDocInDatabase cId (stemIt q)
-  pure $ DataOld ids
+  pure $ Right $ DataOld ids
 
 -------------------------------------------------------------------------------
-flowDataText :: ( FlowCmdM env err m
+flowDataText :: forall env err m.
+                ( FlowCmdM env err m
                 )
                 => User
                 -> DataText
@@ -161,7 +167,8 @@ flowDataText :: ( FlowCmdM env err m
 flowDataText u (DataOld ids) tt cid mfslw _ = flowCorpusUser (_tt_lang tt) u (Right [cid]) corpusType ids mfslw
   where
     corpusType = (Nothing :: Maybe HyperdataCorpus)
-flowDataText u (DataNew txt) tt cid mfslw logStatus = flowCorpus u (Right [cid]) tt mfslw txt logStatus
+flowDataText u (DataNew (mLen, txtC)) tt cid mfslw logStatus =
+  flowCorpus u (Right [cid]) tt mfslw (mLen, (transPipe liftBase txtC)) logStatus
 
 ------------------------------------------------------------------------
 -- TODO use proxy
@@ -173,8 +180,9 @@ flowAnnuaire :: (FlowCmdM env err m)
              -> (JobLog -> m ())
              -> m AnnuaireId
 flowAnnuaire u n l filePath logStatus = do
-  docs <- liftBase $ (( splitEvery 500 <$> readFile_Annuaire filePath) :: IO [[HyperdataContact]])
-  flow (Nothing :: Maybe HyperdataAnnuaire) u n l Nothing docs logStatus
+  -- TODO Conduit for file
+  docs <- liftBase $ ((readFile_Annuaire filePath) :: IO [HyperdataContact])
+  flow (Nothing :: Maybe HyperdataAnnuaire) u n l Nothing (Just $ fromIntegral $ length docs, yieldMany docs) logStatus
 
 ------------------------------------------------------------------------
 flowCorpusFile :: (FlowCmdM env err m)
@@ -185,12 +193,13 @@ flowCorpusFile :: (FlowCmdM env err m)
            -> Maybe FlowSocialListWith
            -> (JobLog -> m ())
            -> m CorpusId
-flowCorpusFile u n l la ff fp mfslw logStatus = do
+flowCorpusFile u n _l la ff fp mfslw logStatus = do
   eParsed <- liftBase $ parseFile ff fp
   case eParsed of
     Right parsed -> do
-      let docs = splitEvery 500 $ take l parsed
-      flowCorpus u n la mfslw (map (map toHyperdataDocument) docs) logStatus
+      flowCorpus u n la mfslw (Just $ fromIntegral $ length parsed, yieldMany parsed .| mapC toHyperdataDocument) logStatus
+      --let docs = splitEvery 500 $ take l parsed
+      --flowCorpus u n la mfslw (yieldMany $ map (map toHyperdataDocument) docs) logStatus
     Left e       -> panic $ "Error: " <> (T.pack e)
 
 ------------------------------------------------------------------------
@@ -201,13 +210,14 @@ flowCorpus :: (FlowCmdM env err m, FlowCorpus a)
            -> Either CorpusName [CorpusId]
            -> TermType Lang
            -> Maybe FlowSocialListWith
-           -> [[a]]
+           -> (Maybe Integer, ConduitT () a m ())
            -> (JobLog -> m ())
            -> m CorpusId
 flowCorpus = flow (Nothing :: Maybe HyperdataCorpus)
 
 
-flow :: ( FlowCmdM env err m
+flow :: forall env err m a c.
+        ( FlowCmdM env err m
         , FlowCorpus a
         , MkCorpus c
         )
@@ -216,22 +226,39 @@ flow :: ( FlowCmdM env err m
         -> Either CorpusName [CorpusId]
         -> TermType Lang
         -> Maybe FlowSocialListWith
-        -> [[a]]
+        -> (Maybe Integer, ConduitT () a m ())
         -> (JobLog -> m ())
         -> m CorpusId
-flow c u cn la mfslw docs logStatus = do
+flow c u cn la mfslw (mLength, docsC) logStatus = do
   -- TODO if public insertMasterDocs else insertUserDocs
-  ids <- traverse (\(idx, doc) -> do
-                      id <- insertMasterDocs c la doc
-                      logStatus JobLog { _scst_succeeded = Just $ 1 + idx
+  ids <- runConduit $
+      zipSources (yieldMany [1..]) docsC
+      .| mapMC insertDoc
+      .| sinkList
+--  ids <- traverse (\(idx, doc) -> do
+--                      id <- insertMasterDocs c la doc
+--                      logStatus JobLog { _scst_succeeded = Just $ 1 + idx
+--                                       , _scst_failed    = Just 0
+--                                       , _scst_remaining = Just $ length docs - idx
+--                                       , _scst_events    = Just []
+--                                       }
+--                      pure id
+--                  ) (zip [1..] docs)
+  flowCorpusUser (la ^. tt_lang) u cn c ids mfslw
+
+  where
+    insertDoc :: (Integer, a) -> m NodeId
+    insertDoc (idx, doc) = do
+      id <- insertMasterDocs c la [doc]
+      case mLength of
+        Nothing -> pure ()
+        Just len -> do
+          logStatus JobLog { _scst_succeeded = Just $ fromIntegral $ 1 + idx
                            , _scst_failed    = Just 0
-                                       , _scst_remaining = Just $ length docs - idx
+                           , _scst_remaining = Just $ fromIntegral $ len - idx
                            , _scst_events    = Just []
                            }
-                      pure id
-                  ) (zip [1..] docs)
-  flowCorpusUser (la ^. tt_lang) u cn c (concat ids) mfslw
-
+      pure $ Prelude.head id
       
 
 
@@ -250,7 +277,7 @@ flowCorpusUser l user corpusName ctype ids mfslw = do
   -- User Flow
   (userId, _rootId, userCorpusId) <- getOrMk_RootWithCorpus user corpusName ctype
   -- NodeTexts is first
-  _tId <- insertDefaultNode NodeTexts userCorpusId userId
+  _tId <- insertDefaultNodeIfNotExists NodeTexts userCorpusId userId
   -- printDebug "NodeTexts: " tId
 
   -- NodeList is second
@@ -276,8 +303,8 @@ flowCorpusUser l user corpusName ctype ids mfslw = do
   -- _ <- insertOccsUpdates userCorpusId mastListId
   -- printDebug "userListId" userListId
   -- User Graph Flow
-  _ <- insertDefaultNode NodeDashboard userCorpusId userId
-  _ <- insertDefaultNode NodeGraph     userCorpusId userId
+  _ <- insertDefaultNodeIfNotExists NodeDashboard userCorpusId userId
+  _ <- insertDefaultNodeIfNotExists NodeGraph     userCorpusId userId
   --_ <- mkPhylo  userCorpusId userId
   -- Annuaire Flow
   -- _ <- mkAnnuaire  rootUserId userId
@@ -322,7 +349,7 @@ saveDocNgramsWith :: ( FlowCmdM env err m)
                   -> m ()
 saveDocNgramsWith lId mapNgramsDocs' = do
   terms2id <- insertExtractedNgrams $ HashMap.keys mapNgramsDocs'
-  printDebug "terms2id" terms2id
+  --printDebug "terms2id" terms2id
 
   let mapNgramsDocs = HashMap.mapKeys extracted2ngrams mapNgramsDocs'
 
@@ -331,7 +358,7 @@ saveDocNgramsWith lId mapNgramsDocs' = do
                $ map (first _ngramsTerms . second Map.keys)
                $ HashMap.toList mapNgramsDocs
 
-  printDebug "saveDocNgramsWith" mapCgramsId
+  --printDebug "saveDocNgramsWith" mapCgramsId
   -- insertDocNgrams
   _return <- insertContextNodeNgrams2
            $ catMaybes [ ContextNodeNgrams2 <$> Just nId
@@ -504,5 +531,3 @@ extractInsert docs = do
                     documentsWithId
   _ <- insertExtractedNgrams $ HashMap.keys mapNgramsDocs'
   pure ()
-
-

src/Gargantext/Database/Prelude.hs

@@ -24,7 +24,7 @@ import Data.ByteString.Char8 (hPutStrLn)
 import Data.Either.Extra (Either)
 import Data.Pool (Pool, withResource)
 import Data.Profunctor.Product.Default (Default)
-import Data.Text (unpack, Text)
+import Data.Text (pack, unpack, Text)
 import Data.Word (Word16)
 import Database.PostgreSQL.Simple (Connection, connect)
 import Database.PostgreSQL.Simple.FromField ( Conversion, ResultError(ConversionFailed), fromField, returnError)
@@ -36,7 +36,7 @@ import Opaleye (Unpackspec, showSql, FromFields, Select, runSelect, SqlJsonb, De
 import Opaleye.Aggregate (countRows)
 import System.IO (FilePath)
 import System.IO (stderr)
-import Text.Read (read)
+import Text.Read (readMaybe)
 import qualified Data.ByteString      as DB
 import qualified Data.List as DL
 import qualified Database.PostgreSQL.Simple as PGS
@@ -176,9 +176,13 @@ databaseParameters :: FilePath -> IO PGS.ConnectInfo
 databaseParameters fp = do
   ini <- readIniFile' fp
   let val' key = unpack $ val ini "database" key
+  let dbPortRaw = val' "DB_PORT"
+  let dbPort = case (readMaybe dbPortRaw :: Maybe Word16) of
+        Nothing -> panic $ "DB_PORT incorrect: " <> (pack dbPortRaw)
+        Just d  -> d
 
   pure $ PGS.ConnectInfo { PGS.connectHost     = val' "DB_HOST"
-                         , PGS.connectPort     = read (val' "DB_PORT") :: Word16
+                         , PGS.connectPort     = dbPort
                          , PGS.connectUser     = val' "DB_USER"
                          , PGS.connectPassword = val' "DB_PASS"
                          , PGS.connectDatabase = val' "DB_NAME"

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

@@ -255,6 +255,14 @@ insertDefaultNode :: HasDBid NodeType
                   => NodeType -> ParentId -> UserId -> Cmd err [NodeId]
 insertDefaultNode nt p u = insertNode nt Nothing Nothing p u
 
+insertDefaultNodeIfNotExists :: HasDBid NodeType
+                             => NodeType -> ParentId -> UserId -> Cmd err [NodeId]
+insertDefaultNodeIfNotExists nt p u = do
+  children <- getChildrenByType p nt
+  case children of
+    [] -> insertDefaultNode nt p u
+    xs -> pure xs
+
 insertNode :: HasDBid NodeType
            => NodeType -> Maybe Name -> Maybe DefaultHyperdata -> ParentId -> UserId -> Cmd err [NodeId]
 insertNode nt n h p u = insertNodesR [nodeW nt n h p u]

stack.yaml

@@ -69,11 +69,11 @@ extra-deps:
 
   # External Data API connectors
 - git: https://gitlab.iscpif.fr/gargantext/crawlers/pubmed.git
-  commit: 9cdba6423decad5acfacb0f274212fd8723ce734
+  commit: bfbdc993675ec647af400f2491a17468f2c4e045
 - git: https://gitlab.iscpif.fr/gargantext/crawlers/istex.git
   commit: daeae80365250c4bd539f0a65e271f9aa37f731f
 - git: https://gitlab.iscpif.fr/gargantext/crawlers/hal.git
-  commit: 020f5f9b308f5c23c925aedf5fb11f8b4728fb19
+  commit: 2fc233399af29ead31d4020c445810721435d2e6
 - git: https://gitlab.iscpif.fr/gargantext/crawlers/isidore.git
   commit: 3db385e767d2100d8abe900833c6e7de3ac55e1b