Barebone but buggy prototype

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

@@ -146,7 +146,7 @@ addToCorpusWithQuery user cid (WithQuery { _wq_query = q
       let db = datafield2origin datafield
       -- mPubmedAPIKey <- getUserPubmedAPIKey user
       -- printDebug "[addToCorpusWithQuery] mPubmedAPIKey" mPubmedAPIKey
-      eTxt <- getDataText db (Multi l) q maybeLimit
+      eTxt <- getDataText cid db (Multi l) q maybeLimit
 
       -- printDebug "[G.A.N.C.New] lTxts" lTxts
       case eTxt of

src/Gargantext/API/Node/Update.hs

@@ -57,12 +57,10 @@ import Gargantext.System.Logging.Types (LogLevel(..))
 import Gargantext.Utils.Jobs.Monad (MonadJobStatus(..))
 import Gargantext.Utils.UTCTime (timeMeasured)
 import HAL qualified
+import HAL.Types qualified as HAL
 import Servant.Server.Generic (AsServerT)
-import Data.Conduit
-import Data.Conduit.List hiding (mapM_)
 import Gargantext.Core
 import Gargantext.Core.Text.Corpus.API.Hal (toDoc')
-import Conduit (mapMC)
 import Gargantext.Database.Admin.Types.Hyperdata.Corpus (HyperdataCorpus)
 
 ------------------------------------------------------------------------
@@ -234,21 +232,19 @@ fetchHALDocuments :: ( IsDBCmd env err m
                      , MonadLogger m
                      , MonadCatch m
                      )
-                  => Maybe CorpusId
+                  => CorpusId
                   -> Maybe ISO639.ISO639_1
                   -> Text
                   -> Int
                   -> Int
                   -> m ()
-fetchHALDocuments Nothing _query _lang _offset _limit = do
-  $(logLocM) ERROR $ "fetchHALDocuments failed because no corpusId was provided."
-fetchHALDocuments (Just corpusId) lang query offset limit = do
-  docs_e <- liftBase $ HAL.getMetadataWithOptsC HAL.defaultHalOptions [query] (Just offset) (Just $ fromIntegral limit) lang
+fetchHALDocuments corpusId lang query offset limit = do
+  docs_e <- liftBase $ HAL.getMetadataWith [query] (Just offset) (Just $ fromIntegral limit) lang
   case docs_e of
     Left err -> do
       $(logLocM) ERROR $ T.pack (show err)
-    Right (_len, docsC) -> do
-      docs <- liftBase $ runConduit $ (docsC .| mapMC (toDoc' lang) .| consume)
+    Right HAL.Response{HAL._docs} -> do
+      docs <- mapM (liftBase . toDoc' lang) _docs
       -- FIXME(adn) How can we pass the TermType correctly in a serialised fashion?
       void $ addDocumentsToHyperCorpus @_ @_ @_ @_ @HyperdataCorpus Nothing (Mono $ fromISOLang lang) corpusId docs
 

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

@@ -38,6 +38,7 @@ import Gargantext.Prelude hiding (get)
 import Gargantext.Utils.Jobs.Error
 import Servant.Client (ClientError)
 import Gargantext.Database.Action.Flow.Types
+import Gargantext.Core.Types (CorpusId)
 
 data GetCorpusError
   = -- | We couldn't parse the user input query into something meaningful.
@@ -54,7 +55,8 @@ instance ToHumanFriendlyError GetCorpusError where
       "There was a network problem while contacting the " <> T.pack (show api) <> " API provider. Please try again later or contact your network administrator."
 
 -- | Get External API metadata main function
-get :: ExternalAPIs
+get :: CorpusId
+    -> ExternalAPIs
     -> Lang
     -- ^ A user-selected language in which documents needs to be retrieved.
     -- If the provider doesn't support the search filtered by language, or if the language
@@ -64,7 +66,7 @@ get :: ExternalAPIs
     -> Maybe Corpus.Limit
     -- -> IO [HyperdataDocument]
     -> IO (Either GetCorpusError (ResultsCount, DataProducer IO HyperdataDocument))
-get externalAPI lang q epoAPIUrl limit = do
+get corpusId externalAPI lang q epoAPIUrl limit = do
   -- For PUBMED, HAL, IsTex, Isidore and OpenAlex, we want to send the query as-it.
   -- For Arxiv we parse the query into a structured boolean query we submit over.
   case externalAPI of
@@ -80,7 +82,7 @@ get externalAPI lang q epoAPIUrl limit = do
         -- let's create a data producer that spins out separate jobs, and process batches
         -- of 25 documents at the time.
         first (ExternalAPIError externalAPI) <$>
-          HAL.getDataProducer (Just $ toISO639 lang) (Corpus.getRawQuery q) (Corpus.getLimit <$> limit)
+          HAL.getDataProducer corpusId (Just $ toISO639 lang) (Corpus.getRawQuery q) (Corpus.getLimit <$> limit)
       IsTex    -> do
         docs <- ISTEX.get lang (Corpus.getRawQuery q) (Corpus.getLimit <$> limit)
         pure $ Right $ toConduitProducer (Just $ fromIntegral $ length docs, yieldMany docs)

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

@@ -27,8 +27,8 @@ import HAL qualified
 import HAL.Doc.Document qualified as HAL
 import HAL.Types qualified as HAL
 import Servant.Client (ClientError (..))
-import System.IO.Error (userError)
 import Gargantext.Core.Worker.Jobs.Types (FetchDocumentsHALPayload(..), Job (..))
+import Gargantext.Core.Types (CorpusId)
 
 get :: Maybe ISO639.ISO639_1 -> Text -> Maybe Int -> IO [HyperdataDocument]
 get la q ml = do
@@ -74,26 +74,25 @@ toDoc' la (HAL.Document { .. }) = do
 -- A Simple ExceptT to make working with network requests a bit more pleasant.
 type HALMonad a = ExceptT ClientError IO a
 
-getDataProducer :: Maybe ISO639.ISO639_1
+getDataProducer :: CorpusId
+                -> Maybe ISO639.ISO639_1
                 -> Text
                 -> Maybe Int
                 -> IO (Either ClientError (ResultsCount, DataProducer IO HyperdataDocument))
-getDataProducer la q _mb_limit = runExceptT $ do
+getDataProducer corpusId la q _mb_limit = runExceptT $ do
   -- First of all, make a trivial query to fetch the full number of documents. Then, split the
   -- total requests into suitable batches and turn them into Jobs.
-  (mb_docs, _) <- ExceptT $ HAL.getMetadataWithC [q] (Just 0) (Just 1) la
-  case mb_docs of
-    Nothing -> throwError $ ConnectionError (toException $ userError "impossible, hal didn't return numDocs in the response.")
-    Just total -> do
+  total <- ExceptT $ HAL.countResultsOpts' (HAL.defaultHalOptions { HAL._hco_batchSize = 1 }) q la
+  putStrLn $ "Found " <> show total <> " documents matching the query."++""
   let (batches,finalBatchSize) = (fromInteger total) `divMod` halBatchSize
-      pure (ResultsCount total, DataAsyncBatchProducer $ mkBatches batches finalBatchSize 0)
+  pure (ResultsCount total, DataAsyncBatchProducer $ mkBatches (max 0 batches) finalBatchSize 0)
   where
-    mkBatches 1 finalBatchSize offset =
-      [FetchDocumentsHAL (FetchDocumentsHALPayload Nothing q la offset finalBatchSize)]
+    mkBatches 0 finalBatchSize offset =
+      [FetchDocumentsHAL (FetchDocumentsHALPayload corpusId q la offset finalBatchSize)]
     mkBatches curBatch finalBatchSize offset =
-      FetchDocumentsHAL (FetchDocumentsHALPayload Nothing q la offset halBatchSize)
+      FetchDocumentsHAL (FetchDocumentsHALPayload corpusId q la offset halBatchSize)
       : mkBatches (curBatch - 1) finalBatchSize (offset + halBatchSize)
 
 -- | The size of a single batch.
 halBatchSize :: Int
-halBatchSize = 500
+halBatchSize = 100

src/Gargantext/Core/Worker/Jobs/Types.hs

@@ -37,7 +37,7 @@ import qualified Data.LanguageCodes as ISO639
 
 data FetchDocumentsHALPayload
   = FetchDocumentsHALPayload
-  { _fdhp_corpus_id   :: Maybe CorpusId
+  { _fdhp_corpus_id   :: CorpusId
   , _fdhp_query       :: Text
   , _fdhp_lang        :: Maybe ISO639.ISO639_1
   , _fdhp_offset      :: Int
@@ -345,4 +345,4 @@ getWorkerMNodeId (UpdateNode { _un_node_id }) = Just _un_node_id
 getWorkerMNodeId (UploadDocument { _ud_node_id }) = Just _ud_node_id
 getWorkerMNodeId (ImportRemoteDocuments (ImportRemoteDocumentsPayload _ _ corpusId _ _)) = Just corpusId
 getWorkerMNodeId (ImportRemoteTerms (ImportRemoteTermsPayload listId _)) = Just listId
-getWorkerMNodeId (FetchDocumentsHAL (FetchDocumentsHALPayload{_fdhp_corpus_id})) = _fdhp_corpus_id
+getWorkerMNodeId (FetchDocumentsHAL (FetchDocumentsHALPayload{_fdhp_corpus_id})) = Just _fdhp_corpus_id

src/Gargantext/Database/Action/Flow.hs

@@ -98,7 +98,7 @@ import Gargantext.Database.Action.Search (searchDocInDatabase)
 import Gargantext.Database.Admin.Types.Hyperdata.Contact ( HyperdataContact )
 import Gargantext.Database.Admin.Types.Hyperdata.Corpus ( HyperdataAnnuaire, HyperdataCorpus(_hc_lang) )
 import Gargantext.Database.Admin.Types.Hyperdata.Document ( ToHyperdataDocument(toHyperdataDocument), HyperdataDocument )
-import Gargantext.Database.Admin.Types.Node hiding (ERROR, DEBUG) -- (HyperdataDocument(..), NodeType(..), NodeId, UserId, ListId, CorpusId, RootId, MasterCorpusId, MasterUserId)
+import Gargantext.Database.Admin.Types.Node hiding (INFO, ERROR, DEBUG) -- (HyperdataDocument(..), NodeType(..), NodeId, UserId, ListId, CorpusId, RootId, MasterCorpusId, MasterUserId)
 import Gargantext.Database.Prelude
 import Gargantext.Database.Query.Table.ContextNodeNgrams2 ( ContextNodeNgrams2Poly(..), insertContextNodeNgrams2 )
 import Gargantext.Database.Query.Table.Node ( MkCorpus, insertDefaultNodeIfNotExists, getOrMkList, getNodeWith )
@@ -112,7 +112,7 @@ import Gargantext.Database.Schema.Ngrams ( indexNgrams, NgramsId )
 import Gargantext.Database.Schema.Node
 import Gargantext.Database.Types
 import Gargantext.Prelude hiding (catch, onException, to)
-import Gargantext.System.Logging ( logLocM, LogLevel(DEBUG, ERROR), MonadLogger )
+import Gargantext.System.Logging ( logLocM, LogLevel(DEBUG, INFO, ERROR), MonadLogger )
 import Gargantext.Utils.Jobs.Monad ( JobHandle, MonadJobStatus(..), markFailureNoErr )
 import Servant.Client.Core (ClientError)
 
@@ -147,16 +147,17 @@ printDataProducer = \case
 
 -- TODO use the split parameter in config file
 getDataText :: (HasNodeError err)
-            => DataOrigin
+            => CorpusId
+            -> DataOrigin
             -> TermType Lang
             -> API.RawQuery
             -> Maybe API.Limit
             -> DBCmdWithEnv env err (Either API.GetCorpusError (DataText IO))
-getDataText (ExternalOrigin api) la q li = do
+getDataText corpusId (ExternalOrigin api) la q li = do
   cfg <- view hasConfig
-  eRes <- liftBase $ API.get api (_tt_lang la) q (_ac_epo_api_url $ _gc_apis cfg) li
+  eRes <- liftBase $ API.get corpusId api (_tt_lang la) q (_ac_epo_api_url $ _gc_apis cfg) li
   pure $ uncurry DataNew <$> eRes
-getDataText (InternalOrigin _) la q _li = do
+getDataText _ (InternalOrigin _) la q _li = do
   cfg <- view hasConfig
   runDBTx $ do
     (_masterUserId, _masterRootId, cId) <- getOrMkRootWithCorpus cfg MkCorpusUserMaster (Nothing :: Maybe HyperdataCorpus)
@@ -164,13 +165,14 @@ getDataText (InternalOrigin _) la q _li = do
     pure $ Right $ DataOld ids
 
 getDataText_Debug :: (HasNodeError err)
-                  => DataOrigin
+                  => CorpusId
+                  -> DataOrigin
                   -> TermType Lang
                   -> API.RawQuery
                   -> Maybe API.Limit
                   -> DBCmdWithEnv env err ()
-getDataText_Debug a l q li = do
-  result <- getDataText a l q li
+getDataText_Debug cid a l q li = do
+  result <- getDataText cid a l q li
   case result of
     Left  err -> liftBase $ putText $ show err
     Right res -> liftBase $ printDataText res
@@ -381,7 +383,9 @@ runDataProducer jobHandle processData = \case
       ]
 
   DataAsyncBatchProducer jobs
-    -> forM_ jobs sendJob
+    -> do
+      addMoreSteps (fromIntegral $ length jobs) jobHandle
+      forM_ jobs sendJob
 
 -- | Given a list of corpus documents and a 'NodeId' identifying the 'CorpusId', adds
 -- the given documents to the corpus. Returns the Ids of the inserted documents.
@@ -400,6 +404,7 @@ addDocumentsToHyperCorpus :: ( IsDBCmd env err m
                              -> [document]
                              -> m [DocId]
 addDocumentsToHyperCorpus mb_hyper la corpusId docs = do
+  $(logLocM) INFO $ "Adding " <> T.pack (show $ length docs) <> " to the hyper corpus " <> T.pack (show corpusId)
   cfg <- view hasConfig
   nlp <- view (nlpServerGet $ _tt_lang la)
   -- First extract all the ngrams for the input documents via the nlp server,