[EPO] patents works now

gargantext.cabal

@@ -79,6 +79,7 @@ library
       Gargantext.Core.Text.Context
       Gargantext.Core.Text.Corpus.API
       Gargantext.Core.Text.Corpus.API.Arxiv
+      Gargantext.Core.Text.Corpus.API.EPO
       Gargantext.Core.Text.Corpus.API.Pubmed
       Gargantext.Core.Text.Corpus.API.OpenAlex
       Gargantext.Core.Text.Corpus.Query
@@ -523,6 +524,7 @@ library
     , servant-blaze ^>= 0.9.1
     , servant-cassava ^>= 0.10.1
     , servant-client ^>= 0.18.3
+    , servant-client-core ^>= 0.18.3
     , servant-ekg ^>= 0.3.1
     , servant-flatten ^>= 0.2
     , servant-job >= 0.2.0.0

src/Gargantext/API/GraphQL.hs

@@ -82,6 +82,8 @@ data Mutation m
   = Mutation
     { update_user_info       :: GQLUserInfo.UserInfoMArgs -> m Int
     , update_user_pubmed_api_key :: GQLUser.UserPubmedAPIKeyMArgs -> m Int
+    , update_user_epo_api_user :: GQLUser.UserEPOAPIUserMArgs -> m Int
+    , update_user_epo_api_token :: GQLUser.UserEPOAPITokenMArgs -> m Int
     , delete_team_membership :: GQLTeam.TeamDeleteMArgs -> m [Int]
     , update_node_context_category :: GQLCTX.NodeContextCategoryMArgs -> m [Int]
     } deriving (Generic, GQLType)
@@ -127,6 +129,8 @@ rootResolver authenticatedUser policyManager =
                             , tree_branch         = GQLTree.resolveBreadcrumb }
     , mutationResolver = Mutation { update_user_info       = GQLUserInfo.updateUserInfo
                                   , update_user_pubmed_api_key = GQLUser.updateUserPubmedAPIKey
+                                  , update_user_epo_api_user = GQLUser.updateUserEPOAPIUser
+                                  , update_user_epo_api_token = GQLUser.updateUserEPOAPIToken
                                   , delete_team_membership = GQLTeam.deleteTeamMembership
                                   , update_node_context_category = GQLCTX.updateNodeContextCategory }
     , subscriptionResolver = Undefined }

src/Gargantext/API/GraphQL/User.hs

@@ -47,6 +47,18 @@ data UserPubmedAPIKeyMArgs
     , api_key  :: Text }
     deriving (Generic, GQLType)
 
+data UserEPOAPIUserMArgs
+  = UserEPOAPIUserMArgs
+    { user_id  :: Int
+    , api_user :: Text }
+    deriving (Generic, GQLType)
+
+data UserEPOAPITokenMArgs
+  = UserEPOAPITokenMArgs
+    { user_id   :: Int
+    , api_token :: Text }
+    deriving (Generic, GQLType)
+
 -- | Function to resolve user from a query.
 resolveUsers
   :: (CmdCommon env)
@@ -82,3 +94,17 @@ updateUserPubmedAPIKey UserPubmedAPIKeyMArgs { user_id, api_key } = do
   _ <- lift $ DBUser.updateUserPubmedAPIKey (Individu.RootId $ UnsafeMkNodeId user_id) api_key
 
   pure 1
+
+updateUserEPOAPIUser :: ( CmdCommon env, HasSettings env) =>
+                        UserEPOAPIUserMArgs -> GqlM' e env Int
+updateUserEPOAPIUser UserEPOAPIUserMArgs { user_id, api_user } = do
+  _ <- lift $ DBUser.updateUserEPOAPIUser (Individu.RootId $ UnsafeMkNodeId user_id) api_user
+
+  pure 1
+
+updateUserEPOAPIToken :: ( CmdCommon env, HasSettings env) =>
+                         UserEPOAPITokenMArgs -> GqlM' e env Int
+updateUserEPOAPIToken UserEPOAPITokenMArgs { user_id, api_token } = do
+  _ <- lift $ DBUser.updateUserEPOAPIToken (Individu.RootId $ UnsafeMkNodeId user_id) api_token
+
+  pure 1

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

@@ -31,6 +31,7 @@ import Data.Conduit.Internal (zipSources)
 import Data.Swagger
 import Data.Text qualified as T
 import Data.Text.Encoding qualified as TE
+import EPO.API.Client.Types qualified as EPO
 import Gargantext.API.Admin.Orchestrator.Types (JobLog(..), AsyncJobs)
 import Gargantext.API.Admin.Types (HasSettings)
 import Gargantext.API.Ngrams (commitStatePatch, Versioned(..))
@@ -144,6 +145,8 @@ data WithQuery = WithQuery
   , _wq_node_id      :: !Int
   , _wq_flowListWith :: !FlowSocialListWith
   , _wq_pubmedAPIKey :: !(Maybe Text)
+  , _wq_epoAPIUser   :: !(Maybe Text)
+  , _wq_epoAPIToken  :: !(Maybe Text)
   }
   deriving (Show, Eq, Generic)
 
@@ -163,6 +166,8 @@ instance Arbitrary WithQuery where
                         <*> arbitrary
                         <*> arbitrary
                         <*> arbitrary
+                        <*> arbitrary
+                        <*> arbitrary
 
 ------------------------------------------------------------------------
 
@@ -204,12 +209,16 @@ addToCorpusWithQuery user cid (WithQuery { _wq_query = q
                                          , _wq_datafield = datafield
                                          , _wq_lang = l
                                          , _wq_flowListWith = flw
-                                         , _wq_pubmedAPIKey = mPubmedAPIKey }) maybeLimit jobHandle = do
+                                         , _wq_pubmedAPIKey = mPubmedAPIKey
+                                         , .. }) maybeLimit jobHandle = do
   -- TODO ...
   $(logLocM) DEBUG $ T.pack $ "(cid, dbs) " <> show (cid, dbs)
   $(logLocM) DEBUG $ T.pack $ "datafield  " <> show datafield
   $(logLocM) DEBUG $ T.pack $ "flowListWith " <> show flw
 
+  let mEPOAuthKey = EPO.AuthKey <$> (EPO.User <$> _wq_epoAPIUser)
+                                <*> (EPO.Token <$> _wq_epoAPIToken)
+
   addLanguageToCorpus cid l
 
   case datafield of
@@ -233,7 +242,7 @@ addToCorpusWithQuery user cid (WithQuery { _wq_query = q
       let db = database2origin dbs
       -- mPubmedAPIKey <- getUserPubmedAPIKey user
       -- printDebug "[addToCorpusWithQuery] mPubmedAPIKey" mPubmedAPIKey
-      eTxt <- getDataText db (Multi l) q mPubmedAPIKey maybeLimit
+      eTxt <- getDataText db (Multi l) q mPubmedAPIKey mEPOAuthKey maybeLimit
 
       -- printDebug "[G.A.N.C.New] lTxts" lTxts
       case eTxt of

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

@@ -23,7 +23,7 @@ import Control.Monad.Except
 import Data.Text qualified as T
 import EPO.API.Client.Types qualified as EPO
 import Gargantext.API.Admin.Orchestrator.Types (ExternalAPIs(..), externalAPIs)
-import Gargantext.Core (Lang(..), toISO639)
+import Gargantext.Core (Lang(..), toISO639, toISO639EN)
 import Gargantext.Core.Text.Corpus.API.Arxiv qualified as Arxiv
 import Gargantext.Core.Text.Corpus.API.EPO qualified as EPO
 import Gargantext.Core.Text.Corpus.API.Hal qualified as HAL
@@ -53,7 +53,7 @@ get :: ExternalAPIs
     -> Maybe Corpus.Limit
     -- -> IO [HyperdataDocument]
     -> IO (Either GetCorpusError (Maybe Integer, ConduitT () HyperdataDocument IO ()))
-get externalAPI la q mPubmedAPIKey limit = do
+get externalAPI la q mPubmedAPIKey epoAuthKey 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
@@ -73,6 +73,6 @@ get externalAPI la q mPubmedAPIKey limit = do
         docs <- ISIDORE.get la (Corpus.getLimit <$> limit) (Just $ Corpus.getRawQuery q) Nothing
         pure $ Right (Just $ fromIntegral $ length docs, yieldMany docs)
       EPO -> do
-        first ExternalAPIError <$> EPO.get (fromMaybe "" Nothing {- email -}) q (toISO639 la) limit
+        first ExternalAPIError <$> EPO.get epoAuthKey q (toISO639EN la) limit
   where
     parse_query = first (InvalidInputQuery q . T.pack) $ Corpus.parseQuery q

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

+{-|
+Module      : Gargantext.Core.Text.Corpus.API.EPO
+Description : EPO (patents) API interface
+Copyright   : (c) CNRS, 2023
+License     : AGPL + CECILL v3
+Maintainer  : team@gargantext.org
+Stability   : experimental
+Portability : POSIX
+-}
+module Gargantext.Core.Text.Corpus.API.EPO where
+
+import Conduit
+import Data.LanguageCodes (ISO639_1)
+import Data.Map.Strict qualified as Map
+import Data.Text qualified as T
+import EPO.API.Client.Types qualified as EPO
+import EPO.API.Client.Implementation qualified as EPO
+import Gargantext.Core (iso639ToText)
+import Gargantext.Core.Text.Corpus.Query qualified as Corpus
+import Gargantext.Database.Admin.Types.Hyperdata (HyperdataDocument(..))
+import Network.URI (parseURI)
+import Protolude
+import Servant.Client.Core (ClientError(ConnectionError))
+
+
+get :: Maybe EPO.AuthKey
+    -> Corpus.RawQuery
+    -> ISO639_1
+    -> Maybe Corpus.Limit
+    -> IO (Either ClientError (Maybe Integer, ConduitT () HyperdataDocument IO ()))
+get Nothing _ _ _ = do
+  -- throwIO $ EPO.OtherError "AuthKey is required"
+  pure $ Left $ ConnectionError $ toException $ ErrorCall "AuthKey is required"
+get (Just authKey) q lang mLimit = do
+  let _limit = Corpus.getLimit $ fromMaybe 10000 mLimit
+  case parseURI "http://localhost:3000" of
+    Nothing -> pure $ Left $ ConnectionError $ toException $ ErrorCall "Cannot parse API URL"
+    Just apiUrl -> do
+      EPO.Paginated { .. } <- EPO.searchEPOAPI apiUrl authKey 1 20 (Corpus.getRawQuery q)
+      pure $ Right ( Just $ fromIntegral total, yieldMany items .| mapC (toDoc lang) )
+
+toDoc :: ISO639_1 -> EPO.HyperdataDocument -> HyperdataDocument
+toDoc lang (EPO.HyperdataDocument { .. }) =
+  HyperdataDocument { _hd_bdd = Just "EPO"
+                    , _hd_doi = Nothing
+                    , _hd_url = Nothing
+                    , _hd_uniqId = id
+                    , _hd_uniqIdBdd = id
+                    , _hd_page = Nothing
+                    , _hd_title = Map.lookup lang titles
+                    , _hd_authors = authors_
+                    , _hd_institutes = Nothing
+                    , _hd_source = Nothing
+                    , _hd_abstract = Map.lookup lang abstracts
+                    , _hd_publication_date = publication_date
+                    , _hd_publication_year = publication_year
+                    , _hd_publication_month = publication_month
+                    , _hd_publication_day = publication_day
+                    , _hd_publication_hour = Nothing
+                    , _hd_publication_minute = Nothing
+                    , _hd_publication_second = Nothing
+                    , _hd_language_iso2 = Just $ iso639ToText lang }
+
+  where
+    authors_ = if authors == []
+      then Nothing
+      else Just (T.intercalate ", " authors)
+  
+--   EPO.withAuthKey authKey $ \token -> do
+--     let range = EPO.Range { rBegin = 1, rEnd = limit }
+--     (len, docsC) <- EPO.searchPublishedDataWithFetchC token (Just $ Corpus.getRawQuery q) (Just range)
+--     pure (len, docsC .|
+--                takeC limit .|
+--                mapC (toDoc lang))
+
+-- toDoc :: ISO639_1 -> EPO.ExchangeDocument -> HyperdataDocument
+-- toDoc lang (EPO.ExchangeDocument { bibliographicData = EPO.BibliographicData { .. }
+--                                  , abstracts } ) =
+--   HyperdataDocument { _hd_bdd = Just "EPO"
+--                     , _hd_doi = Nothing
+--                     , _hd_url = Nothing
+--                     , _hd_uniqId = EPO.documentIdToText <$> (head documentIds)
+--                     , _hd_uniqIdBdd = EPO.documentIdToText <$> (head documentIds)
+--                     , _hd_page = Nothing
+--                     , _hd_title = Map.lookup lang inventionTitlesMap
+--                     , _hd_authors = authors parties
+--                     , _hd_institutes = Nothing
+--                     , _hd_source = Nothing
+--                     , _hd_abstract = Map.lookup lang abstractMap
+--                     , _hd_publication_date = T.pack <$> showGregorian <$> publicationDate
+--                     , _hd_publication_year = year
+--                     , _hd_publication_month = month
+--                     , _hd_publication_day = day
+--                     , _hd_publication_hour = Nothing
+--                     , _hd_publication_minute = Nothing
+--                     , _hd_publication_second = Nothing
+--                     , _hd_language_iso2 = Just $ iso639ToText lang }
+--       where
+--         authors :: EPO.Parties -> Maybe Text
+--         authors (EPO.Parties { inventors = Nothing }) = Nothing
+--         authors (EPO.Parties { inventors = Just EPO.Inventors { inventors } }) =
+--           Just $ T.intercalate ", " (getInventorName <$> inventors)
+
+--         getInventorName :: EPO.Inventor -> Text
+--         getInventorName (EPO.Inventor { inventorName = EPO.InventorName { name } }) = name
+
+--         abstractMap :: Map.Map ISO639_1 Text
+--         abstractMap = Map.fromList [(l, text) | (EPO.Abstract { lang = l, text }) <- abstracts]
+
+--         EPO.PublicationReferenceDet { documentIds } = publicationReference
+
+--         dates :: [Day]
+--         dates = catMaybes (EPO.date <$> documentIds)
+
+--         publicationDate :: Maybe Day
+--         publicationDate = head dates
+
+--         (year, month, day) = case publicationDate of
+--           Nothing -> (Nothing, Nothing, Nothing)
+--           Just pd -> let (y, m, d) = toGregorian pd in
+--             (Just $ fromIntegral y, Just m, Just d)
+
+--         inventionTitlesMap :: Map ISO639_1 Text
+--         inventionTitlesMap = Map.fromList [(l, text) | EPO.InventionTitle { lang = l, text } <- inventionTitles]

src/Gargantext/Database/Action/Flow.hs

@@ -69,6 +69,7 @@ import Data.Proxy
 import Data.Set qualified as Set
 import Data.Swagger
 import Data.Text qualified as T
+import EPO.API.Client.Types qualified as EPO
 import Gargantext.API.Ngrams.Tools (getTermsWith)
 import Gargantext.API.Ngrams.Types qualified as NT
 import Gargantext.Core (Lang(..), PosTagAlgo(..), NLPServerConfig)
@@ -160,12 +161,13 @@ getDataText :: (HasNodeError err)
             -> TermType Lang
             -> API.RawQuery
             -> Maybe PUBMED.APIKey
+            -> Maybe EPO.AuthKey
             -> Maybe API.Limit
             -> 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
+getDataText (ExternalOrigin api) la q mPubmedAPIKey mAuthKey li = do
+  eRes <- liftBase $ API.get api (_tt_lang la) q mPubmedAPIKey mAuthKey li
   pure $ DataNew <$> eRes
-getDataText (InternalOrigin _) _la q _ _li = do
+getDataText (InternalOrigin _) _la q _ _ _li = do
   (_masterUserId, _masterRootId, cId) <- getOrMk_RootWithCorpus
                                            (UserName userMaster)
                                            (Left "")
@@ -180,7 +182,7 @@ getDataText_Debug :: (HasNodeError err)
                   -> Maybe API.Limit
                   -> DBCmd err ()
 getDataText_Debug a l q li = do
-  result <- getDataText a l q Nothing li
+  result <- getDataText a l q Nothing Nothing li
   case result of
     Left  err -> liftBase $ putText $ show err
     Right res -> liftBase $ printDataText res

src/Gargantext/Database/Admin/Types/Hyperdata/User.hs

@@ -40,6 +40,8 @@ data HyperdataUser =
                    , _hu_shared         :: !(Maybe HyperdataContact)
                    , _hu_public         :: !(Maybe HyperdataPublic)
                    , _hu_pubmed_api_key :: !(Maybe PUBMED.APIKey)
+                   , _hu_epo_api_user   :: !(Maybe Text)
+                   , _hu_epo_api_token  :: !(Maybe Text)
                    } deriving (Eq, Show, Generic)
 
 instance GQLType HyperdataUser where
@@ -71,7 +73,9 @@ defaultHyperdataUser =
     { _hu_private        = Just defaultHyperdataPrivate
     , _hu_shared         = Just defaultHyperdataContact
     , _hu_public         = Just defaultHyperdataPublic
-    , _hu_pubmed_api_key = Nothing }
+    , _hu_pubmed_api_key = Nothing
+    , _hu_epo_api_user   = Nothing
+    , _hu_epo_api_token  = Nothing }
 
 defaultHyperdataPublic :: HyperdataPublic
 defaultHyperdataPublic = HyperdataPublic "pseudo" [1..10]
@@ -100,7 +104,12 @@ $(deriveJSON (unPrefix "_hpu_") ''HyperdataPublic)
 
 -- | Arbitrary instances
 instance Arbitrary HyperdataUser where
-  arbitrary = HyperdataUser <$> arbitrary <*> arbitrary <*> arbitrary <*> arbitrary
+  arbitrary = HyperdataUser <$> arbitrary
+                            <*> arbitrary
+                            <*> arbitrary
+                            <*> arbitrary
+                            <*> arbitrary
+                            <*> arbitrary
 
 instance Arbitrary HyperdataPrivate where
   arbitrary = pure defaultHyperdataPrivate

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

@@ -34,6 +34,8 @@ module Gargantext.Database.Query.Table.User
   , updateUserForgotPasswordUUID
   , getUserPubmedAPIKey
   , updateUserPubmedAPIKey
+  , updateUserEPOAPIUser
+  , updateUserEPOAPIToken
   , getUser
   , insertNewUsers
   , selectUsersLightWith
@@ -56,7 +58,7 @@ import Data.UUID qualified as UUID
 import Gargantext.Core (HasDBid)
 import Gargantext.Core.Types.Individu
 import Gargantext.Database.Admin.Config (nodeTypeId)
-import Gargantext.Database.Admin.Types.Hyperdata (HyperdataUser(..), hu_pubmed_api_key)
+import Gargantext.Database.Admin.Types.Hyperdata (HyperdataUser(..), hu_pubmed_api_key, hu_epo_api_user, hu_epo_api_token)
 import Gargantext.Database.Admin.Types.Node (NodeType(NodeUser), Node, NodeId(..), pgNodeId)
 import Gargantext.Database.Admin.Types.Node (UserId(..))
 import Gargantext.Database.Prelude
@@ -275,6 +277,21 @@ updateUserPubmedAPIKey (RootId uId) apiKey = do
   _ <- updateNodeWithType uId NodeUser (Proxy :: Proxy HyperdataUser) (\h -> h & hu_pubmed_api_key ?~ apiKey)
   pure 1
 updateUserPubmedAPIKey _ _ = undefined
+
+updateUserEPOAPIUser :: (HasDBid NodeType, HasNodeError err)
+                     => User -> Text -> DBCmd err Int64
+updateUserEPOAPIUser (RootId uId) apiUser = do
+  _ <- updateNodeWithType uId NodeUser (Proxy :: Proxy HyperdataUser) (\h -> h & hu_epo_api_user ?~ apiUser)
+  pure 1
+updateUserEPOAPIUser _ _ = undefined
+
+updateUserEPOAPIToken :: (HasDBid NodeType, HasNodeError err)
+                      => User -> Text -> DBCmd err Int64
+updateUserEPOAPIToken (RootId uId) apiToken = do
+  _ <- updateNodeWithType uId NodeUser (Proxy :: Proxy HyperdataUser) (\h -> h & hu_epo_api_token ?~ apiToken)
+  pure 1
+updateUserEPOAPIToken _ _ = undefined
+
 ------------------------------------------------------------------
 -- | Select User with some parameters
 -- Not optimized version