diff --git a/src/Gargantext/API/Admin/Orchestrator/Types.hs b/src/Gargantext/API/Admin/Orchestrator/Types.hs
index 8cdd98daeca4f540a9e51c1e05f51257f94763e2..e4c4c1bfebbded930f9f6f4efcdf2443a951ff7f 100644
--- a/src/Gargantext/API/Admin/Orchestrator/Types.hs
+++ b/src/Gargantext/API/Admin/Orchestrator/Types.hs
@@ -6,6 +6,7 @@ module Gargantext.API.Admin.Orchestrator.Types
where
import Control.Lens hiding (elements)
+import Control.Monad.Reader (MonadReader)
import Data.Aeson
import Data.Morpheus.Types
( GQLType
@@ -23,7 +24,9 @@ import Test.QuickCheck.Arbitrary
import qualified Gargantext.API.GraphQL.Utils as GQLU
import Gargantext.Core.Types (TODO(..))
+import Gargantext.Database.Prelude (HasConfig(..))
import Gargantext.Prelude
+import Gargantext.Prelude.Config (gc_pubmed_api_key)
------------------------------------------------------------------------
instance Arbitrary a => Arbitrary (JobStatus 'Safe a) where
@@ -34,24 +37,39 @@ instance Arbitrary a => Arbitrary (JobOutput a) where
-- | Main Types
-- TODO IsidoreAuth
-data ExternalAPIs = PubMed
+data ExternalAPIs = All
+ | PubMed { mAPIKey :: Maybe Text }
| Arxiv
| HAL
| IsTex
| Isidore
- deriving (Show, Eq, Generic, Enum, Bounded)
+ deriving (Show, Eq, Generic)
-- | Main Instances
instance FromJSON ExternalAPIs
instance ToJSON ExternalAPIs
-externalAPIs :: [ExternalAPIs]
-externalAPIs = [minBound .. maxBound]
+externalAPIs :: ( MonadReader env m
+ , HasConfig env) => m [ExternalAPIs]
+externalAPIs = do
+ pubmed_api_key <- view $ hasConfig . gc_pubmed_api_key
+
+ pure [ All
+ , PubMed { mAPIKey = Just pubmed_api_key }
+ , Arxiv
+ , HAL
+ , IsTex
+ , Isidore ]
instance Arbitrary ExternalAPIs
where
- arbitrary = arbitraryBoundedEnum
+ arbitrary = elements [ All
+ , PubMed { mAPIKey = Nothing }
+ , Arxiv
+ , HAL
+ , IsTex
+ , Isidore ]
instance ToSchema ExternalAPIs where
declareNamedSchema = genericDeclareNamedSchemaUnrestricted defaultSchemaOptions
diff --git a/src/Gargantext/API/Node/Corpus/New.hs b/src/Gargantext/API/Node/Corpus/New.hs
index 71cdcd7be8236253b64a481a79449183253d614e..39200c63d105c7601ebf24beb1304674524652bb 100644
--- a/src/Gargantext/API/Node/Corpus/New.hs
+++ b/src/Gargantext/API/Node/Corpus/New.hs
@@ -54,13 +54,13 @@ import Gargantext.Database.Action.Mail (sendMail)
import Gargantext.Database.Action.Node (mkNodeWithParent)
import Gargantext.Database.Action.User (getUserId)
import Gargantext.Database.Admin.Types.Hyperdata
-import Gargantext.Database.Admin.Types.Node (CorpusId, NodeType(..))
+import Gargantext.Database.Admin.Types.Node (CorpusId, NodeType(..), UserId)
import Gargantext.Database.Prelude (hasConfig)
import Gargantext.Database.Query.Table.Node (getNodeWith, updateCorpusPubmedAPIKey)
import Gargantext.Database.Query.Table.Node.UpdateOpaleye (updateHyperdata)
import Gargantext.Database.Schema.Node (node_hyperdata)
import Gargantext.Prelude
-import Gargantext.Prelude.Config (gc_max_docs_parsers, gc_pubmed_api_key)
+import Gargantext.Prelude.Config (gc_max_docs_parsers)
import Gargantext.Utils.Jobs (JobHandle, MonadJobStatus(..))
import qualified Gargantext.Core.Text.Corpus.API as API
import qualified Gargantext.Core.Text.Corpus.Parsers as Parser (FileType(..), parseFormatC)
@@ -131,8 +131,11 @@ deriveJSON (unPrefix "") 'ApiInfo
instance ToSchema ApiInfo
-info :: ApiInfo
-info = ApiInfo API.externalAPIs
+info :: FlowCmdM env err m => UserId -> m ApiInfo
+info _u = do
+ ext <- API.externalAPIs
+
+ pure $ ApiInfo ext
------------------------------------------------------------------------
------------------------------------------------------------------------
@@ -216,8 +219,7 @@ addToCorpusWithQuery user cid (WithQuery { _wq_query = q
_ -> do
case datafield of
- Just (External PubMed) -> do
- _api_key <- view $ hasConfig . gc_pubmed_api_key
+ Just (External (PubMed { _api_key })) -> do
printDebug "[addToCorpusWithQuery] pubmed api key" _api_key
_ <- updateCorpusPubmedAPIKey cid _api_key
pure ()
@@ -229,7 +231,7 @@ addToCorpusWithQuery user cid (WithQuery { _wq_query = q
-- if cid is corpus -> add to corpus
-- if cid is root -> create corpus in Private
-- printDebug "[G.A.N.C.New] getDataText with query" q
- let db = database2origin dbs
+ db <- database2origin dbs
eTxt <- getDataText db (Multi l) q maybeLimit
-- printDebug "[G.A.N.C.New] lTxts" lTxts
diff --git a/src/Gargantext/API/Node/Corpus/Types.hs b/src/Gargantext/API/Node/Corpus/Types.hs
index 368805f8c4bb52562b0ef8b823f58ea8b68868df..e4f90ac784bfea99daba387e3d6de218e75c9ac4 100644
--- a/src/Gargantext/API/Node/Corpus/Types.hs
+++ b/src/Gargantext/API/Node/Corpus/Types.hs
@@ -4,6 +4,7 @@ module Gargantext.API.Node.Corpus.Types where
import Control.Lens hiding (elements, Empty)
import Control.Monad.Fail (fail)
+import Control.Monad.Reader (MonadReader)
import Data.Aeson
import Data.Aeson.TH (deriveJSON)
import Data.Monoid (mempty)
@@ -11,35 +12,48 @@ import Data.Swagger
import GHC.Generics (Generic)
import Test.QuickCheck
import qualified Data.Text as T
+import qualified PUBMED.Types as PUBMED
import Gargantext.Prelude
import qualified Gargantext.API.Admin.Orchestrator.Types as Types
import Gargantext.Core.Utils.Prefix (unPrefix)
import Gargantext.Database.Action.Flow (DataOrigin(..))
+import Gargantext.Database.Prelude (HasConfig(..))
data Database = Empty
- | PubMed
+ | PubMed { _api_key :: Maybe PUBMED.APIKey }
| Arxiv
| HAL
| IsTex
| Isidore
- deriving (Eq, Show, Generic, Enum, Bounded)
+ deriving (Eq, Show, Generic)
+
+instance Arbitrary Database
+ where
+ arbitrary = elements [ Empty
+ , PubMed { _api_key = Nothing }
+ , Arxiv
+ , HAL
+ , IsTex
+ , Isidore ]
-instance Arbitrary Database where
- arbitrary = arbitraryBoundedEnum
deriveJSON (unPrefix "") ''Database
instance ToSchema Database where
declareNamedSchema = genericDeclareNamedSchemaUnrestricted defaultSchemaOptions
-database2origin :: Database -> DataOrigin
-database2origin Empty = InternalOrigin Types.IsTex
-database2origin PubMed = ExternalOrigin Types.PubMed
-database2origin Arxiv = ExternalOrigin Types.Arxiv
-database2origin HAL = ExternalOrigin Types.HAL
-database2origin IsTex = ExternalOrigin Types.IsTex
-database2origin Isidore = ExternalOrigin Types.Isidore
+database2origin :: ( MonadReader env m
+ , HasConfig env ) => Database -> m DataOrigin
+database2origin Empty = pure $ InternalOrigin Types.IsTex
+database2origin (PubMed { _api_key }) = do
+ -- pubmed_api_key <- view $ hasConfig . gc_pubmed_api_key
+
+ pure $ ExternalOrigin $ Types.PubMed { mAPIKey = _api_key }
+database2origin Arxiv = pure $ ExternalOrigin Types.Arxiv
+database2origin HAL = pure $ ExternalOrigin Types.HAL
+database2origin IsTex = pure $ ExternalOrigin Types.IsTex
+database2origin Isidore = pure $ ExternalOrigin Types.Isidore
------------------------------------------------------------------------
data Datafield = Gargantext
diff --git a/src/Gargantext/Core/Text/Corpus/API.hs b/src/Gargantext/Core/Text/Corpus/API.hs
index 1851fef618d023fe6fbdfaf37e5d2a6fdf557a4f..9548d92b2a9f929481390af1abb30290a4a915d3 100644
--- a/src/Gargantext/Core/Text/Corpus/API.hs
+++ b/src/Gargantext/Core/Text/Corpus/API.hs
@@ -19,7 +19,6 @@ module Gargantext.Core.Text.Corpus.API
) where
import Conduit
-import Control.Lens ((^.))
import Data.Bifunctor
import Data.Either (Either(..))
import Data.Maybe
@@ -28,7 +27,6 @@ import Gargantext.API.Admin.Orchestrator.Types (ExternalAPIs(..), externalAPIs)
import Gargantext.Core (Lang(..))
import Gargantext.Database.Admin.Types.Hyperdata (HyperdataDocument(..))
import Gargantext.Prelude
-import Gargantext.Prelude.Config (GargConfig, gc_pubmed_api_key)
import qualified Gargantext.Core.Text.Corpus.API.Arxiv as Arxiv
import qualified Gargantext.Core.Text.Corpus.API.Hal as HAL
import qualified Gargantext.Core.Text.Corpus.API.Isidore as ISIDORE
@@ -45,24 +43,33 @@ data GetCorpusError
deriving (Show, Eq)
-- | Get External API metadata main function
-get :: GargConfig
- -> ExternalAPIs
+get :: ExternalAPIs
-> Lang
-> Corpus.RawQuery
-> Maybe Corpus.Limit
-- -> IO [HyperdataDocument]
-> IO (Either GetCorpusError (Maybe Integer, ConduitT () HyperdataDocument IO ()))
-get cfg externalAPI la q limit = do
+get api la q limit =
case Corpus.parseQuery q of
Left err -> pure $ Left $ InvalidInputQuery q (T.pack err)
- Right corpusQuery -> case externalAPI of
- PubMed -> first ExternalAPIError <$>
- PUBMED.get (cfg ^. gc_pubmed_api_key) corpusQuery limit
- --docs <- PUBMED.get q default_limit -- EN only by default
- --pure (Just $ fromIntegral $ length docs, yieldMany docs)
- Arxiv -> Right <$> Arxiv.get la corpusQuery limit
- HAL -> first ExternalAPIError <$> HAL.getC la (Corpus.getRawQuery q) (Corpus.getLimit <$> limit)
- IsTex -> do docs <- ISTEX.get la (Corpus.getRawQuery q) (Corpus.getLimit <$> limit)
- pure $ Right (Just $ fromIntegral $ length docs, yieldMany docs)
- Isidore -> do docs <- ISIDORE.get la (Corpus.getLimit <$> limit) (Just $ Corpus.getRawQuery q) Nothing
- pure $ Right (Just $ fromIntegral $ length docs, yieldMany docs)
+ Right corpusQuery ->
+ case api of
+ PubMed { mAPIKey = mAPIKey } -> first ExternalAPIError <$>
+ PUBMED.get (fromMaybe "" mAPIKey) corpusQuery limit
+ --docs <- PUBMED.get q default_limit -- EN only by default
+ --pure (Just $ fromIntegral $ length docs, yieldMany docs)
+ Arxiv -> Right <$> Arxiv.get la corpusQuery limit
+ HAL -> first ExternalAPIError <$>
+ HAL.getC la (Corpus.getRawQuery q) (Corpus.getLimit <$> limit)
+ IsTex -> do
+ docs <- ISTEX.get la (Corpus.getRawQuery q) (Corpus.getLimit <$> limit)
+ pure $ Right (Just $ fromIntegral $ length docs, yieldMany docs)
+ Isidore -> do
+ docs <- ISIDORE.get la (Corpus.getLimit <$> limit) (Just $ Corpus.getRawQuery q) Nothing
+ pure $ Right (Just $ fromIntegral $ length docs, yieldMany docs)
+ externalApi ->
+ panic $ "[G.C.T.Corpus.API] This options are note taken into account: " <> (cs $ show externalApi)
+
+-- | Some Sugar for the documentation
+-- type Query = PUBMED.Query
+-- type Limit = PUBMED.Limit
diff --git a/src/Gargantext/Core/Text/Corpus/Query.hs b/src/Gargantext/Core/Text/Corpus/Query.hs
index 373d42942078e3daf8ef201c0d64ed3d24681c69..dfb67ad1cc7758464f857f8a734bac75c1eb2d5d 100644
--- a/src/Gargantext/Core/Text/Corpus/Query.hs
+++ b/src/Gargantext/Core/Text/Corpus/Query.hs
@@ -51,7 +51,7 @@ newtype Limit = Limit { getLimit :: Int }
-- | An opaque wrapper around a 'Query' type which can be parsed from a boolean
-- expression like (a AND b) OR c, and which can be interpreted in many ways
-- according to the particular service we are targeting.
-newtype Query = Query { getQuery :: (BoolExpr.CNF Term) }
+newtype Query = Query { getQuery :: BoolExpr.CNF Term }
deriving Show
interpretQuery :: Query -> (BoolExpr.BoolExpr Term -> ast) -> ast
diff --git a/src/Gargantext/Database/Action/Flow.hs b/src/Gargantext/Database/Action/Flow.hs
index 9fa6193de4e85a6467892c9ec4ad6774c09f9838..de1ea77924c0ee5d86e3b8ccd9e559a77b4209e3 100644
--- a/src/Gargantext/Database/Action/Flow.hs
+++ b/src/Gargantext/Database/Action/Flow.hs
@@ -50,6 +50,7 @@ module Gargantext.Database.Action.Flow -- (flowDatabase, ngrams2list)
import Conduit
import Control.Lens ((^.), view, _Just, makeLenses, over, traverse)
+import Control.Monad.Reader (MonadReader)
import Data.Aeson.TH (deriveJSON)
import Data.Conduit.Internal (zipSources)
import qualified Data.Conduit.List as CList
@@ -131,8 +132,13 @@ deriveJSON (unPrefix "_do_") ''DataOrigin
instance ToSchema DataOrigin where
declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_do_")
-allDataOrigins :: [DataOrigin]
-allDataOrigins = map InternalOrigin API.externalAPIs <> map ExternalOrigin API.externalAPIs
+allDataOrigins :: ( MonadReader env m
+ , HasConfig env) => m [DataOrigin]
+allDataOrigins = do
+ ext <- API.externalAPIs
+
+ pure $ map InternalOrigin ext
+ <> map ExternalOrigin ext
---------------
data DataText = DataOld ![NodeId]
@@ -154,8 +160,9 @@ getDataText :: FlowCmdM env err m
-> Maybe API.Limit
-> m (Either API.GetCorpusError DataText)
getDataText (ExternalOrigin api) la q li = do
- cfg <- view $ hasConfig
- eRes <- liftBase $ API.get cfg api (_tt_lang la) q li
+ -- cfg <- view $ hasConfig
+ -- DEPRECATED: Use apiKey per user instead (not the global one)
+ eRes <- liftBase $ API.get api (_tt_lang la) q li
pure $ DataNew <$> eRes
getDataText (InternalOrigin _) _la q _li = do
diff --git a/src/Gargantext/Database/Query/Table/Node.hs b/src/Gargantext/Database/Query/Table/Node.hs
index 8759c647ac4c0663cded8f2bc91192234af495ca..0d4aa9c96d636443d84b34f53b0dadb9f17af4ea 100644
--- a/src/Gargantext/Database/Query/Table/Node.hs
+++ b/src/Gargantext/Database/Query/Table/Node.hs
@@ -342,8 +342,8 @@ getCorpusPubmedAPIKey cId = do
|]
params = PGS.Only cId
-updateCorpusPubmedAPIKey :: NodeId -> PUBMED.APIKey -> Cmd err Int64
-updateCorpusPubmedAPIKey cId apiKey =
+updateCorpusPubmedAPIKey :: NodeId -> Maybe PUBMED.APIKey -> Cmd err Int64
+updateCorpusPubmedAPIKey cId mAPIKey =
execPGSQuery query params
where
query :: PGS.Query
@@ -352,7 +352,7 @@ updateCorpusPubmedAPIKey cId apiKey =
SET hyperdata = hyperdata || ?
WHERE id = ?
|]
- params = (encode $ object [ "pubmed_api_key" .= apiKey ], cId)
+ params = (encode $ object [ "pubmed_api_key" .= mAPIKey ], cId)
------------------------------------------------------------------------
-- TODO
-- currently this function removes the child relation