[STACK LTS] upgrade + external API deps.

package.yaml

@@ -30,7 +30,7 @@ library:
   - Gargantext.API.FrontEnd
   - Gargantext.API.Ngrams
   - Gargantext.API.Node
-  - Gargantext.API.Orchestrator
+    #  - Gargantext.API.Orchestrator
   - Gargantext.API.Search
   - Gargantext.API.Settings
   - Gargantext.Core
@@ -168,7 +168,7 @@ library:
   - servant-auth
   - servant-blaze
   - servant-client
-  - servant-job
+    #  - servant-job
   - servant-mock
   - servant-multipart
   - servant-server

src/Gargantext/API.hs

@@ -126,7 +126,7 @@ instance HasInvalidError GargError where
 instance HasTreeError GargError where
   _TreeError = _GargTreeError
 
-showAsServantErr :: Show a => a -> ServantErr
+showAsServantErr :: Show a => a -> ServerError
 showAsServantErr a = err500 { errBody = BL8.pack $ show a }
 
 fireWall :: Applicative f => Request -> FireWall -> f Bool

src/Gargantext/API/Ngrams.hs

@@ -56,7 +56,7 @@ import Data.Map.Strict (Map)
 import qualified Data.Set as Set
 import Control.Category ((>>>))
 import Control.Concurrent
-import Control.Lens (makeLenses, makePrisms, Getter, Iso', iso, from, (.~), (?=), (#), to, folded, {-withIndex, ifolded,-} view, use, (^.), (^..), (^?), (+~), (%~), (%=), sumOf, at, _Just, Each(..), itraverse_, both, forOf_, (%%~))
+import Control.Lens (makeLenses, makePrisms, Getter, Iso', iso, from, (.~), (?=), (#), to, folded, {-withIndex, ifolded,-} view, use, (^.), (^..), (^?), (+~), (%~), (%=), sumOf, at, _Just, Each(..), itraverse_, both, forOf_, (%%~), (?~))
 import Control.Monad.Error.Class (MonadError)
 import Control.Monad.Reader
 import Control.Monad.State
@@ -441,11 +441,11 @@ instance (Eq a, Arbitrary a) => Arbitrary (Replace a) where
     -- If they happen to be equal then the patch is Keep.
 
 instance ToSchema a => ToSchema (Replace a) where
-  declareNamedSchema (_ :: proxy (Replace a)) = do
+  declareNamedSchema (_ :: Proxy (Replace a)) = do
     -- TODO Keep constructor is not supported here.
     aSchema <- declareSchemaRef (Proxy :: Proxy a)
     return $ NamedSchema (Just "Replace") $ mempty
-      & type_ .~ SwaggerObject
+      & type_ ?~ SwaggerObject
       & properties .~
           InsOrdHashMap.fromList
           [ ("old", aSchema)

src/Gargantext/API/Settings.hs

@@ -46,7 +46,7 @@ import qualified Data.ByteString.Lazy as L
 
 import Servant
 import Servant.Client (BaseUrl, parseBaseUrl)
-import Servant.Job.Async (newJobEnv, defaultSettings)
+--import Servant.Job.Async (newJobEnv, defaultSettings)
 import Web.HttpApiData (parseUrlPiece)
 import qualified Jose.Jwk as Jose
 import qualified Jose.Jwa as Jose
@@ -60,7 +60,7 @@ import Control.Lens
 import Gargantext.Prelude
 import Gargantext.Database.Utils (databaseParameters, HasConnection(..), Cmd', runCmd)
 import Gargantext.API.Ngrams (NgramsRepo, HasRepoVar(..), HasRepoSaver(..), HasRepo(..), RepoEnv(..), r_version, saveRepo, initRepo, renv_var, renv_lock)
-import Gargantext.API.Orchestrator.Types
+--import Gargantext.API.Orchestrator.Types
 
 type PortNumber = Int
 
@@ -147,7 +147,7 @@ data Env = Env
   , _env_repo     :: !RepoEnv
   , _env_manager  :: !Manager
   , _env_self_url :: !BaseUrl
-  , _env_scrapers :: !ScrapersEnv
+  --, _env_scrapers :: !ScrapersEnv
   }
   deriving (Generic)
 
@@ -243,7 +243,7 @@ newEnv port file = do
   param    <- databaseParameters file
   conn     <- connect param
   repo     <- readRepoEnv
-  scrapers_env <- newJobEnv defaultSettings manager
+  --scrapers_env <- newJobEnv defaultSettings manager
   logger <- newStderrLoggerSet defaultBufSize
 
   pure $ Env
@@ -252,7 +252,7 @@ newEnv port file = do
     , _env_conn       = conn
     , _env_repo       = repo
     , _env_manager    = manager
-    , _env_scrapers   = scrapers_env
+    --, _env_scrapers   = scrapers_env
     , _env_self_url   = self_url
     }
 
@@ -305,7 +305,7 @@ withDevEnv iniPath k = do
 runCmdRepl :: Show err => Cmd' DevEnv err a -> IO a
 runCmdRepl f = withDevEnv "gargantext.ini" $ \env -> runCmdDev env f
 
-runCmdReplServantErr :: Cmd' DevEnv ServantErr a -> IO a
+runCmdReplServantErr :: Cmd' DevEnv ServerError a -> IO a
 runCmdReplServantErr = runCmdRepl
 
 -- Use only for dev
@@ -324,5 +324,5 @@ runCmdDevNoErr :: DevEnv -> Cmd' DevEnv () a -> IO a
 runCmdDevNoErr = runCmdDev
 
 -- Use only for dev
-runCmdDevServantErr :: DevEnv -> Cmd' DevEnv ServantErr a -> IO a
+runCmdDevServantErr :: DevEnv -> Cmd' DevEnv ServerError a -> IO a
 runCmdDevServantErr = runCmdDev

src/Gargantext/API/Utils.hs

+{-|
+Module      : Gargantext.API.Utils
+Description : Server API main Types
+Copyright   : (c) CNRS, 2017-Present
+License     : BSD3
+Maintainer  : team@gargantext.org
+Stability   : experimental
+Portability : POSIX
+
+Mainly copied from Servant.Job.Utils (Thanks)
+
+-}
+
+{-# LANGUAGE OverloadedStrings  #-}
+{-# LANGUAGE NoImplicitPrelude  #-}
+
+module Gargantext.API.Utils
+  where
+
+import Gargantext.Prelude
+import Data.Maybe (Maybe, fromMaybe)
+import Prelude (String)
+import qualified Data.Text as T
+import Data.Swagger
+import Data.Text (Text)
+
+
+
+swaggerOptions :: Text -> SchemaOptions
+swaggerOptions pref = defaultSchemaOptions
+  { Data.Swagger.fieldLabelModifier = modifier pref
+  , Data.Swagger.unwrapUnaryRecords = False
+  }
+
+
+modifier :: Text -> String -> String
+modifier pref field = T.unpack
+                    $ T.stripPrefix pref (T.pack field) ?! "Expecting prefix " <> T.unpack pref
+
+
+infixr 4 ?|
+
+-- Reverse infix form of "fromMaybe"
+(?|) :: Maybe a -> a -> a
+(?|) = flip fromMaybe
+
+infixr 4 ?!
+
+-- Reverse infix form of "fromJust" with a custom error message
+(?!) :: Maybe a -> String -> a
+(?!) ma' msg = ma' ?| panic (T.pack msg)

src/Gargantext/Text/Corpus/API.hs

@@ -55,7 +55,7 @@ type Query = Text
 type Limit = PubMed.Limit
 
 get :: ExternalAPIs -> Query -> Maybe Limit -> IO [HyperdataDocument]
-get PubMed q l = either (\e -> panic $ "CRAWL: PubMed" <> e) (map (toDoc EN)) <$> PubMed.crawler q l
+get PubMed q l = either (\e -> panic $ "CRAWL: PubMed" <> e) (map (toDoc EN)) <$> PubMed.getMetadataWith q l
 get _ _ _ = undefined
 
 toDoc :: Lang -> Doc.PubMed -> HyperdataDocument

src/Gargantext/Viz/Chart.hs

@@ -106,7 +106,7 @@ treeData cId nt lt = do
   pure $ toTree lt cs' m
 
 
-treeData' :: FlowCmdM env ServantErr m
+treeData' :: FlowCmdM env ServerError m
         => CorpusId -> NgramsType -> ListType
         -> m [MyTree]
 treeData' cId nt lt = do

src/Gargantext/Viz/Phylo/API.hs

@@ -29,6 +29,7 @@ import qualified Data.ByteString as DB
 import qualified Data.ByteString.Lazy as DBL
 import Data.Swagger
 import Gargantext.API.Types
+import Gargantext.API.Utils (swaggerOptions)
 import Gargantext.Database.Types.Node (PhyloId, ListId, CorpusId)
 import Gargantext.Database.Schema.Node (insertNodes, nodePhyloW, getNodePhylo)
 import Gargantext.Database.Types.Node -- (NodePhylo(..))
@@ -38,7 +39,6 @@ import Gargantext.Viz.Phylo.Main
 import Gargantext.Viz.Phylo.Example
 import Gargantext.API.Ngrams (TODO(..))
 import Servant
-import Servant.Job.Utils (swaggerOptions)
 import Test.QuickCheck (elements)
 import Test.QuickCheck.Arbitrary (Arbitrary, arbitrary)
 import Web.HttpApiData (parseUrlPiece, readTextData)

stack.yaml

-resolver: lts-12.26
+resolver: lts-14.1
 flags: {}
 extra-package-dbs: []
 packages:
@@ -22,14 +22,21 @@ extra-deps:
   commit: 3fe28b683aba5ddf05e3b5f8eced0bd05c5a29f9
 - git: https://github.com/robstewart57/rdf4h.git
   commit: 4fd2edf30c141600ffad6d730cc4c1c08a6dbce4
+    #
+    # External API connectin to get data
 - git: https://gitlab.iscpif.fr/gargantext/crawlers/pubmed.git
-  commit: ac4f8ecfb2e579041a350e4718bc6d4e7a832d92
+  commit: 01a6bf1e79cd5aef8628b240bbd47cb2a0864d5e
+- git: https://gitlab.iscpif.fr/gargantext/crawlers/istex.git
+  commit: daeae80365250c4bd539f0a65e271f9aa37f731f
 - git: https://gitlab.iscpif.fr/gargantext/crawlers/hal.git
-  commit: bf57642f6b66f554fdc0a38ac391cd8200dffcb3
+  commit: ef9e638c97788df251f50b71fcdd9551b87f12c5
+- git: https://gitlab.iscpif.fr/gargantext/crawlers/isidore.git
+  commit: 3db385e767d2100d8abe900833c6e7de3ac55e1b
+    #
 - git: https://gitlab.iscpif.fr/gargantext/patches-class
   commit: 746b4ce0af8f9e600d555ad7e5b2973a940cdad9
-- git: https://github.com/np/servant-job.git
-  commit: ac4227441bbca30c44235582b5ec31340c569021
+  #- git: https://github.com/np/servant-job.git
+  # commit: ac4227441bbca30c44235582b5ec31340c569021
 - git: https://gitlab.iscpif.fr/gargantext/clustering-louvain.git
   commit: 1c636112b151110408e7c5a28cec39e46657358e
 - git: https://github.com/np/patches-map
@@ -38,10 +45,8 @@ extra-deps:
   commit: 53385de076be09f728a1b58c035a18e9ff9bcfd6
 - git: https://github.com/delanoe/hsparql.git
   commit: 308c74b71a1abb0a91546fa57d353131248e3a7f
-- git: https://gitlab.iscpif.fr/gargantext/crawlers/isidore.git
-  commit: e39454101b53916e3082085ebfe922df695fc775
 - KMP-0.1.0.2
-- accelerate-1.2.0.0
+- accelerate-1.2.0.1
 - aeson-lens-0.5.0.0
 - deepseq-th-0.1.0.4
 - duckling-0.1.3.0
@@ -56,8 +61,9 @@ extra-deps:
 - json-stream-0.4.2.4  # Text.Parsers (JSON)
 - serialise-0.2.0.0
 - servant-flatten-0.2
-- servant-multipart-0.11.2
+  #- servant-multipart-0.11.2
 - stemmer-0.5.2
 - time-units-1.0.0
 - validity-0.9.0.0 # patches-{map,class}
-- directory-1.3.1.5  
+- directory-1.3.1.5
+- process-1.6.5.1@sha256:77a9afeb676357f67fe5cf1ad79aca0745fb6f7fb96b786d510af08f622643f6,2468