Merge branch 'dev' into 341-dev-websockets

CHANGELOG.md

+## Version 0.0.7.1.5.2
+
+* [BACK][FIX] Order 2 small corpus
+* [FRONT][FIX][[Tree focus] Temporary HOTFIX: comment the forced focus (forest open nodes) for performances reason (#669)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/669)
+
+## Version 0.0.7.1.5.1
+
+* [FRONT][ADMIN] Dev Spago Config
+* [FRONT][FIX][[Phylo] On the exported SVG file: fix the background color behind the label (#668)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/668)
+
+## Version 0.0.7.1.5
+
+* [FRONT][ADM][Upgrade PureScript to 0.15.11 (#605)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/605)
+* [FRONT][FIX][For graph controls, add a debounce timer (#651)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/651)
+* [FRONT][FEAT][Export the phylo in JSON and dot format (#643)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/643)
+* [BACK][FIX][[Node Phylo] Export the phylo in JSON and dot format (#337)](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/337)
+* [BACK][FIX][Consider integrating Servant named routes (#271)](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/271)
+
+## Version 0.0.7.1.4
+
+* [FRONT][FIX][Search Term in Graph Explorer: spaces (#655)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/655)
+* [FRONT][ADMIN] Dev Spago next upgrade
+
 ## Version 0.0.7.1.3
 
 * [FRONT][FIX][[Tree (Node Graph)] (Update: remove it) - The "resync" picto no longer launch a reload - It should open the dialog box on the graph reload form confirmation (#644)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/644)

bin/metrics/metrics

+#!/bin/bash
+
+
+for f in bin/metrics/histo/*sql ; do
+  ./bin/psql gargantext.ini < $f
+done
+

devops/nix/config

+#!/bin/bash
+
+mkdir -p ~/.config/nix/
+echo "experimental-features = nix-command flakes" > ~/.config/nix/nix.conf
+
+

gargantext.cabal

@@ -5,7 +5,7 @@ cabal-version: 3.4
 -- see: https://github.com/sol/hpack
 
 name:           gargantext
-version: 0.0.7.1.3
+version: 0.0.7.1.5.2
 synopsis:       Search, map, share
 description:    Please see README.md
 category:       Data
@@ -134,9 +134,29 @@ library
       Gargantext.API.Node.File
       Gargantext.API.Node.Share
       Gargantext.API.Node.ShareURL
+      Gargantext.API.Node.Types
       Gargantext.API.Node.Update
       Gargantext.API.Prelude
       Gargantext.API.Routes
+      Gargantext.API.Routes.Named
+      Gargantext.API.Routes.Named.Contact
+      Gargantext.API.Routes.Named.Context
+      Gargantext.API.Routes.Named.Corpus
+      Gargantext.API.Routes.Named.Count
+      Gargantext.API.Routes.Named.Document
+      Gargantext.API.Routes.Named.File
+      Gargantext.API.Routes.Named.FrameCalc
+      Gargantext.API.Routes.Named.List
+      Gargantext.API.Routes.Named.Metrics
+      Gargantext.API.Routes.Named.Node
+      Gargantext.API.Routes.Named.Private
+      Gargantext.API.Routes.Named.Public
+      Gargantext.API.Routes.Named.Search
+      Gargantext.API.Routes.Named.Share
+      Gargantext.API.Routes.Named.Table
+      Gargantext.API.Routes.Named.Tree
+      Gargantext.API.Routes.Named.Viz
+      Gargantext.API.Routes.Types
       Gargantext.API.WebSockets
       Gargantext.Core
       Gargantext.Core.AsyncUpdates
@@ -281,12 +301,13 @@ library
       Gargantext.API.Node.Corpus.Searx
       Gargantext.API.Node.Document.Export
       Gargantext.API.Node.Document.Export.Types
+      Gargantext.API.Node.Phylo.Export
+      Gargantext.API.Node.Phylo.Export.Types
       Gargantext.API.Node.DocumentUpload
       Gargantext.API.Node.DocumentsFromWriteNodes
       Gargantext.API.Node.FrameCalcUpload
       Gargantext.API.Node.Get
       Gargantext.API.Node.New
-      Gargantext.API.Node.Types
       Gargantext.API.Public
       Gargantext.API.Search
       Gargantext.API.Server

src/Gargantext/API/Count.hs

@@ -16,8 +16,22 @@ Count API part of Gargantext.
 {-# LANGUAGE TypeOperators      #-}
 {-# LANGUAGE DeriveAnyClass     #-}
 
-module Gargantext.API.Count
-      where
+module Gargantext.API.Count (
+    CountAPI
+  , Scraper(..)
+  , QueryBool(..)
+  , Query(..)
+  , Message(..)
+  , Code
+  , Error
+  , Errors
+  , Counts(..)
+  , Count(..)
+
+  -- * functions
+  , count
+  , scrapers
+  ) where
 
 import Data.Swagger ( ToSchema(..), genericDeclareNamedSchema )
 import Data.Text (pack)

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

+{-# LANGUAGE TypeOperators #-}
 {-|
 Module      : Gargantext.API.Node.Corpus.Export
 Description : Corpus export
@@ -41,7 +42,14 @@ import Gargantext.Database.Query.Table.NodeContext (selectDocNodes)
 import Gargantext.Database.Schema.Context (_context_id)
 import Gargantext.Prelude hiding (hash)
 import Gargantext.Prelude.Crypto.Hash (hash)
-import Servant (Headers, Header, addHeader)
+import Servant (Headers, Header, addHeader, Summary, (:>), JSON, Get, QueryParam)
+
+--------------------------------------------------
+type API = Summary "Corpus Export"
+            :> "export"
+            :> QueryParam "listId"     ListId
+            :> QueryParam "ngramsType" NgramsType
+            :> Get '[JSON] (Headers '[Servant.Header "Content-Disposition" Text] Corpus)
 
 --------------------------------------------------
 -- | Hashes are ordered by Set

src/Gargantext/API/Node/Corpus/Export/Types.hs

@@ -18,8 +18,7 @@ import Data.Swagger ( ToSchema(..), genericDeclareNamedSchema, ToParamSchema(..)
 import Data.Text (Text)
 import GHC.Generics (Generic)
 import Gargantext.API.Node.Document.Export.Types qualified as DocumentExport
-import Gargantext.Core.Text.Ngrams (NgramsType(..))
-import Gargantext.Core.Types ( ListId, TODO )
+import Gargantext.Core.Types ( TODO )
 import Gargantext.Core.Utils.Prefix (unPrefix, unPrefixSwagger)
 import Servant
 
@@ -37,11 +36,4 @@ instance ToSchema Corpus where
 -------
 instance ToParamSchema Corpus where
   toParamSchema _ = toParamSchema (Proxy :: Proxy TODO)
---------------------------------------------------
-type API = Summary "Corpus Export"
-            :> "export"
-            :> QueryParam "listId"     ListId
-            :> QueryParam "ngramsType" NgramsType
-            :> Get '[JSON] (Headers '[Servant.Header "Content-Disposition" Text] Corpus)
-
 $(deriveJSON (unPrefix "_c_") ''Corpus)

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

@@ -22,10 +22,9 @@ module Gargantext.API.Node.Corpus.New
 
 import Conduit
 import Control.Lens ( view, non )
-import Data.Aeson ( genericParseJSON, genericToJSON )
 import Data.ByteString.Base64 qualified as BSB64
 import Data.Conduit.Internal (zipSources)
-import Data.Swagger ( ToSchema(..), genericDeclareNamedSchema )
+import Data.Swagger ( ToSchema(..) )
 import Data.Text qualified as T
 import Data.Text.Encoding qualified as TE
 import EPO.API.Client.Types qualified as EPO
@@ -34,17 +33,16 @@ import Gargantext.API.Admin.Types (HasSettings)
 import Gargantext.API.Ngrams (commitStatePatch, Versioned(..))
 import Gargantext.API.Node.Corpus.New.Types ( FileFormat(..), FileType(..) )
 import Gargantext.API.Node.Corpus.Searx ( triggerSearxSearch )
-import Gargantext.API.Node.Corpus.Types ( Database, Datafield(Web), database2origin )
+import Gargantext.API.Node.Corpus.Types ( Datafield(Web), database2origin )
 import Gargantext.API.Node.Corpus.Update (addLanguageToCorpus)
 import Gargantext.API.Node.Types
-import Gargantext.Core (Lang(..), withDefaultLanguage, defaultLanguage)
+import Gargantext.Core (withDefaultLanguage, defaultLanguage)
 import Gargantext.Core.NodeStory (HasNodeStoryImmediateSaver, HasNodeArchiveStoryImmediateSaver, currentVersion, NgramsStatePatch')
 import Gargantext.API.Admin.Orchestrator.Types qualified as API
 import Gargantext.Core.Text.Corpus.Query qualified as API
 import Gargantext.Core.Text.Corpus.Parsers qualified as Parser (FileType(..), parseFormatC, _ParseFormatError)
-import Gargantext.Core.Text.List.Social (FlowSocialListWith(..))
 import Gargantext.Core.Types.Individu (User(..))
-import Gargantext.Core.Utils.Prefix (unPrefix, unPrefixSwagger)
+import Gargantext.Core.Utils.Prefix (unPrefix)
 import Gargantext.Database.Action.Flow (flowCorpus, getDataText, flowDataText, TermType(..){-, allDataOrigins-})
 import Gargantext.Database.Action.Flow.Types (FlowCmdM)
 import Gargantext.Database.Action.Mail (sendMail)
@@ -64,7 +62,6 @@ import Gargantext.Prelude.Config (gc_max_docs_parsers)
 import Gargantext.System.Logging ( logLocM, LogLevel(..) )
 import Gargantext.Utils.Jobs.Monad (JobHandle, MonadJobStatus(..))
 import Servant ( JSON, type (:>), FormUrlEncoded, Capture, Summary )
-import Servant.Job.Utils (jsonOptions)
 import Test.QuickCheck.Arbitrary (Arbitrary(..))
 
 ------------------------------------------------------------------------
@@ -136,41 +133,6 @@ info :: ApiInfo
 info = ApiInfo API.externalAPIs
 
 ------------------------------------------------------------------------
-------------------------------------------------------------------------
-data WithQuery = WithQuery
-  { _wq_query        :: !API.RawQuery
-  , _wq_databases    :: !Database
-  , _wq_datafield    :: !(Maybe Datafield)
-  , _wq_lang         :: !Lang
-  , _wq_node_id      :: !Int
-  , _wq_flowListWith :: !FlowSocialListWith
-  , _wq_pubmedAPIKey :: !(Maybe Text)
-  , _wq_epoAPIUser   :: !(Maybe Text)
-  , _wq_epoAPIToken  :: !(Maybe Text)
-  }
-  deriving (Show, Eq, Generic)
-
-makeLenses ''WithQuery
-instance FromJSON WithQuery where
-  parseJSON = genericParseJSON $ jsonOptions "_wq_"
-instance ToJSON WithQuery where
-  toJSON = genericToJSON $ jsonOptions "_wq_"
-instance ToSchema WithQuery where
-  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_wq_")
-
-instance Arbitrary WithQuery where
-  arbitrary = WithQuery <$> arbitrary
-                        <*> arbitrary
-                        <*> arbitrary
-                        <*> arbitrary
-                        <*> arbitrary
-                        <*> arbitrary
-                        <*> arbitrary
-                        <*> arbitrary
-                        <*> arbitrary
-
-------------------------------------------------------------------------
-
 type AddWithQuery = Summary "Add with Query to corpus endpoint"
    :> "corpus"
      :> Capture "corpus_id" CorpusId

src/Gargantext/API/Node/Phylo/Export.hs

+{-|
+Module      : Gargantext.API.Node.Phylo.Export
+Description : Phylo export
+Copyright   : (c) CNRS, 2017-Present
+License     : AGPL + CECILL v3
+Maintainer  : team@gargantext.org
+Stability   : experimental
+Portability : POSIX
+-}
+
+module Gargantext.API.Node.Phylo.Export
+  where
+
+import Data.Aeson
+import Data.Text qualified as T
+import Gargantext.API.Node.Phylo.Export.Types
+import Gargantext.API.Prelude (GargNoServer, GargServer)
+import Gargantext.Core.Viz.Phylo.API.Tools
+import Gargantext.Core.Viz.Phylo.Example (phyloCleopatre)
+import Gargantext.Database.Admin.Types.Node (PhyloId, NodeId,)
+import Gargantext.Prelude
+import Servant
+
+api :: NodeId
+    -- ^ The ID of the target user
+    -> PhyloId
+    -> GargServer API
+api userNodeId dId = getPhyloJson userNodeId dId 
+                :<|> getPhyloDot userNodeId dId
+
+getPhyloJson  :: NodeId
+                -- ^ The ID of the target user
+              -> PhyloId
+              -> GargNoServer (Headers '[Header "Content-Disposition" T.Text] Value)
+getPhyloJson _ pId = do
+  maybePhyloData <- getPhyloData pId
+  let phyloData = fromMaybe phyloCleopatre maybePhyloData
+  phyloJson <- liftBase $ phylo2dot2json phyloData
+  pure $ addHeader (T.concat [ "attachment; filename="
+                                          , "GarganText_Phylo-"
+                                          , T.pack (show pId)
+                                          , ".json" ])
+                                          phyloJson
+
+
+getPhyloDot :: NodeId
+            -> PhyloId
+            -> GargNoServer (Headers '[Header "Content-Disposition" T.Text] T.Text)
+getPhyloDot _ pId = do
+  maybePhyloData <- getPhyloData pId
+  let phyloData = fromMaybe phyloCleopatre maybePhyloData
+  phyloDot <- liftBase $ phylo2dot phyloData
+  pure $ addHeader (T.concat [ "attachment; filename="
+                                          , "GarganText_Phylo-"
+                                          , T.pack (show pId)
+                                          , ".dot" ])
+                                          phyloDot
\ No newline at end of file

src/Gargantext/API/Node/Phylo/Export/Types.hs

+{-|
+Module      : Gargantext.API.Node.Phylo.Export.Types
+Description : Types for Gargantext.API.Node.Phylo.Export
+Copyright   : (c) CNRS, 2017-Present
+License     : AGPL + CECILL v3
+Maintainer  : team@gargantext.org
+Stability   : experimental
+Portability : POSIX
+-}
+
+{-# LANGUAGE TemplateHaskell #-}
+{-# LANGUAGE TypeOperators   #-}
+
+module Gargantext.API.Node.Phylo.Export.Types where
+
+import Data.Aeson
+import Data.Aeson.TH (deriveJSON)
+-- import Data.Csv (DefaultOrdered(..), ToNamedRecord(..), (.=), header, namedRecord)
+import Data.Swagger ( genericDeclareNamedSchema, ToParamSchema(..), ToSchema(..) )
+-- import Data.Text qualified as T
+-- import Data.Text.Encoding qualified as TE
+import Gargantext.Core.Types ( Node, TODO )
+import Gargantext.Core.Utils.Prefix (unPrefix, unPrefixSwagger)
+import Gargantext.Database.Admin.Types.Hyperdata.Phylo ( HyperdataPhylo(..) )
+import Gargantext.Database.Admin.Types.Node (PhyloId)
+-- import Gargantext.Database.Schema.Node (NodePoly(..))
+-- import Gargantext.Utils.Servant (ZIP)
+-- import Gargantext.Utils.Zip (zipContentsPure)
+import Protolude
+import Servant ((:>), (:<|>), Get, Header, Headers(..), JSON, Summary) --, PlainText, MimeRender(..)
+
+
+-- | Phylo Export
+data PhyloExport =
+  PhyloExport { _pe_phylos    :: [Phylo]
+              , _pe_garg_version :: Text
+              } deriving (Generic)
+
+data PhyloExportDOT =
+  PhyloExportDOT  { _ped_dexp   :: PhyloExport
+                  , _ped_doc_id :: PhyloId 
+                  } deriving (Generic)
+
+data PhyloExportJSON = 
+  PhyloExportJSON { _pej_pexp     :: PhyloExport
+                  , _pej_phy_id   :: PhyloId
+                  } deriving (Generic)
+    
+    
+data Phylo =
+  Phylo { _p_phylo    :: Node HyperdataPhylo
+        , _p_hash     :: Hash
+        } deriving (Generic)
+
+--instance Read Phylo where
+--  read "" = panic "not implemented"
+-- instance DefaultOrdered Phylo where
+--   headerOrder _ = header ["Publication Day"
+--                          , "Publication Month"
+--                          , "Publication Year"
+--                          , "Authors"
+--                          , "Title"
+--                          , "Source"
+--                          , "Abstract"]
+-- instance ToNamedRecord Phylo where
+--   toNamedRecord (Phylo { _p_phylo = Node { .. }}) =
+--     namedRecord
+--     [ "Publication Day" .= _hd_publication_day _node_hyperdata
+--     , "Publication Month" .= _hd_publication_month _node_hyperdata
+--     , "Publication Year" .= _hd_publication_year _node_hyperdata
+--     , "Authors" .= _hd_authors _node_hyperdata
+--     , "Title" .= _hd_title _node_hyperdata
+--     , "Source" .= (TE.encodeUtf8 <$> _hd_source _node_hyperdata)
+--     , "Abstract" .= (TE.encodeUtf8 <$> _hd_abstract _node_hyperdata) ]
+
+
+type Hash = Text
+-------
+instance ToSchema PhyloExport where
+  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_pe_")
+
+instance ToSchema PhyloExportDOT where
+  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_ped_")
+  
+instance ToSchema Phylo where
+  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_p_")
+
+
+-------
+instance ToParamSchema PhyloExport where
+  toParamSchema _ = toParamSchema (Proxy :: Proxy TODO)
+
+instance ToParamSchema PhyloExportDOT where
+  toParamSchema _ = toParamSchema (Proxy :: Proxy TODO)
+
+instance ToParamSchema Phylo where
+  toParamSchema _ = toParamSchema (Proxy :: Proxy TODO)
+
+--------------------------------------------------
+type API = Summary "Phylo Export"
+            :> "export"
+            :> ( "json"
+                 :> Get '[JSON] (Headers '[Servant.Header "Content-Disposition" Text] Value)
+               :<|> "dot"
+                 :> Get '[JSON] (Headers '[Servant.Header "Content-Disposition" Text] Text)
+                )
+
+-- type API = Summary "Phylo Export"
+--             :> "export"
+--                  :> Get '[JSON,DOT] (Headers '[Servant.Header "Content-Disposition" Text] Value)
+
+
+
+
+$(deriveJSON (unPrefix "_p_") ''Phylo)
+$(deriveJSON (unPrefix "_pe_") ''PhyloExport)
+
+
+------
+
+-- Needs to be here because of deriveJSON TH above
+
+-- pedFileName :: PhyloExportDOT -> Text
+-- pedFileName (PhyloExportDOT { .. }) = "GarganText_DocsList-" <> show _ped_doc_id <> ".dot"
+    
+-- instance MimeRender ZIP PhyloExportDOT where
+--   mimeRender _ dexpz@(PhyloExportDOT { .. }) =
+--     zipContentsPure (T.unpack $ pedFileName dexpz) (encode _ped_dexp)

src/Gargantext/API/Node/Types.hs

@@ -19,12 +19,15 @@ import Data.ByteString.Base64 qualified as BSB64
 import Data.Swagger
 import Data.Text qualified as T
 import Gargantext.API.Node.Corpus.New.Types (FileType, FileFormat)
+import Gargantext.API.Node.Corpus.Types
 import Gargantext.Core (Lang(..))
+import Gargantext.Core.Text.Corpus.Query qualified as API
 import Gargantext.Core.Text.List.Social (FlowSocialListWith)
 import Gargantext.Core.Utils.Prefix (unPrefixSwagger)
 import Gargantext.Database.GargDB qualified as GargDB
 import Gargantext.Prelude
 import Servant.Job.Utils (jsonOptions)
+import Test.QuickCheck
 import Web.FormUrlEncoded          (FromForm, ToForm)
 
 -------------------------------------------------------
@@ -77,3 +80,36 @@ instance GargDB.SaveFile NewWithFile where
 
 --instance GargDB.ReadFile NewWithFile where
 --  readFile' = TIO.readFile
+
+data WithQuery = WithQuery
+  { _wq_query        :: !API.RawQuery
+  , _wq_databases    :: !Database
+  , _wq_datafield    :: !(Maybe Datafield)
+  , _wq_lang         :: !Lang
+  , _wq_node_id      :: !Int
+  , _wq_flowListWith :: !FlowSocialListWith
+  , _wq_pubmedAPIKey :: !(Maybe Text)
+  , _wq_epoAPIUser   :: !(Maybe Text)
+  , _wq_epoAPIToken  :: !(Maybe Text)
+  }
+  deriving (Show, Eq, Generic)
+
+makeLenses ''WithQuery
+instance FromJSON WithQuery where
+  parseJSON = genericParseJSON $ jsonOptions "_wq_"
+instance ToJSON WithQuery where
+  toJSON = genericToJSON $ jsonOptions "_wq_"
+instance ToSchema WithQuery where
+  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_wq_")
+
+instance Arbitrary WithQuery where
+  arbitrary = WithQuery <$> arbitrary
+                        <*> arbitrary
+                        <*> arbitrary
+                        <*> arbitrary
+                        <*> arbitrary
+                        <*> arbitrary
+                        <*> arbitrary
+                        <*> arbitrary
+                        <*> arbitrary
+

src/Gargantext/API/Routes.hs

@@ -16,6 +16,7 @@ Portability : POSIX
 {-# LANGUAGE TypeOperators        #-}
 {-# LANGUAGE TypeApplications     #-}
 {-# LANGUAGE UndecidableInstances #-}
+{-# OPTIONS_GHC -fno-warn-orphans #-} -- instance HasSwagger (WithCustomErrorScheme GargAPI)
 
 module Gargantext.API.Routes
       where
@@ -30,7 +31,6 @@ import Gargantext.API.Admin.FrontEnd (FrontEndAPI)
 import Gargantext.API.Auth.PolicyCheck
 import Gargantext.API.Context
 import Gargantext.API.Count  (CountAPI, count, Query)
-import Gargantext.API.Errors (GargErrorScheme (..))
 import Gargantext.API.Errors.Types
 import Gargantext.API.GraphQL qualified as GraphQL
 import Gargantext.API.Members (MembersAPI, members)
@@ -40,13 +40,15 @@ import Gargantext.API.Node
 import Gargantext.API.Node.Contact qualified as Contact
 import Gargantext.API.Node.Corpus.Annuaire qualified as Annuaire
 import Gargantext.API.Node.Corpus.Export qualified as CorpusExport
-import Gargantext.API.Node.Corpus.Export.Types qualified as CorpusExport
 import Gargantext.API.Node.Corpus.New qualified as New
 import Gargantext.API.Node.Document.Export qualified as DocumentExport
 import Gargantext.API.Node.Document.Export.Types qualified as DocumentExport
+import Gargantext.API.Node.Phylo.Export qualified as PhyloExport
+import Gargantext.API.Node.Phylo.Export.Types qualified as PhyloExport
 import Gargantext.API.Node.ShareURL qualified as ShareURL
 import Gargantext.API.Prelude
 import Gargantext.API.Public qualified as Public
+import Gargantext.API.Routes.Types
 import Gargantext.API.WebSockets qualified as WebSockets
 import Gargantext.Core.Types.Individu (User(..))
 import Gargantext.Core.Viz.Graph.API
@@ -56,40 +58,17 @@ import Gargantext.Database.Prelude (HasConfig(..))
 import Gargantext.Prelude
 import Gargantext.Prelude.Config (gc_max_docs_scrapers)
 import Gargantext.Utils.Jobs (serveJobsAPI, MonadJobStatus(..))
-import Network.Wai (requestHeaders)
 import Servant
 import Servant.Auth as SA
 import Servant.Auth.Swagger ()
-import Servant.Ekg
-import Servant.Server.Internal.Delayed
-import Servant.Server.Internal.DelayedIO
 import Servant.Swagger
 import Servant.Swagger.UI
 
-data WithCustomErrorScheme a
-
-instance (HasServer subApi ctx) => HasServer (WithCustomErrorScheme subApi) ctx where
-  type ServerT (WithCustomErrorScheme subApi) m = GargErrorScheme -> ServerT subApi m
-  hoistServerWithContext _ pc nt s = hoistServerWithContext (Proxy :: Proxy subApi) pc nt . s
-  route Proxy ctx d = route (Proxy :: Proxy subApi) ctx (d `addHeaderCheck` getErrorScheme)
-    where
-      getErrorScheme :: DelayedIO GargErrorScheme
-      getErrorScheme = withRequest $ \rq -> do
-        let hdrs = requestHeaders rq
-            in case L.lookup "X-Garg-Error-Scheme" hdrs of
-                 Nothing     -> pure GES_old
-                 Just "new"  -> pure GES_new
-                 Just _      -> pure GES_old
+type GargAPI = MkGargAPI (GargAPIVersion GargAPI')
 
 instance HasSwagger (WithCustomErrorScheme GargAPI) where
     toSwagger _ = toSwagger (Proxy :: Proxy GargAPI)
 
-instance HasEndpoint sub => HasEndpoint (WithCustomErrorScheme sub) where
-  getEndpoint _ = getEndpoint (Proxy :: Proxy sub)
-  enumerateEndpoints _ = enumerateEndpoints (Proxy :: Proxy sub)
-
-type GargAPI = MkGargAPI (GargAPIVersion GargAPI')
-
 type MkGargAPI sub = "api" :> Summary "API " :> sub
 --- | TODO          :<|> Summary "Latest API" :> GargAPI'
 
@@ -182,6 +161,9 @@ type GargPrivateAPI' =
            :<|> "texts"    :> Capture "node_id" DocId
                            :> DocumentExport.API
 
+           :<|> "phylo"     :> Capture "node_id" DocId
+                            :> PhyloExport.API
+
         -- :<|> "counts" :> Stream GET NewLineFraming '[JSON] Count :> CountAPI
             -- TODO-SECURITY
            :<|> "count"    :> Summary "Count endpoint"
@@ -197,6 +179,10 @@ type GargPrivateAPI' =
                            :> Capture "graph_id" NodeId
                            :> GraphAPI
 
+          --  :<|> "phylo"    :> Summary "Phylo endpoint"
+          --                  :> Capture "pylo_id" NodeId
+          --                  :> 
+
            -- TODO move to NodeAPI?
            -- Tree endpoint
            :<|> "tree"    :> Summary "Tree endpoint"
@@ -283,6 +269,8 @@ serverPrivateGargAPI' authenticatedUser@(AuthenticatedUser userNodeId userId)
 
      :<|> DocumentExport.api userNodeId
 
+     :<|> PhyloExport.api userNodeId
+
      :<|> count -- TODO: undefined
 
      -- :<|> withAccess (Proxy :: Proxy (Search.API Search.SearchResult)) Proxy uid

src/Gargantext/API/Routes/Named.hs

+
+{-# LANGUAGE TypeOperators #-}
+{-# LANGUAGE DeriveGeneric #-}
+
+module Gargantext.API.Routes.Named where
+
+import Data.Text (Text)
+import GHC.Generics
+import Gargantext.API.Admin.Auth (ForgotPasswordAsyncParams)
+import Gargantext.API.Admin.Auth.Types
+import Gargantext.API.Admin.Orchestrator.Types
+import Gargantext.API.Routes.Named.Public
+import Gargantext.API.Routes.Named.Private
+import Servant.API ((:>), (:-), JSON, ReqBody, Post, Get, QueryParam)
+import Servant.API.Description (Summary)
+import Servant.API.NamedRoutes
+
+type GargAPI = NamedRoutes (MkGargAPI (GargAPIVersion GargAPI'))
+
+
+data MkGargAPI sub mode = MkGargAPI
+  { mkGargAPI :: mode :- "api" :> Summary "API " :> NamedRoutes sub
+  } deriving Generic
+
+
+data GargAPIVersion sub mode = GargAPIVersion
+  { gargAPIVersion :: mode :- "v1.0" :> Summary "Garg API Version " :> NamedRoutes sub
+  } deriving Generic
+
+
+data GargAPI' mode = GargAPI'
+  { gargAuthAPI                :: mode :- NamedRoutes AuthAPI
+  , gargForgotPasswordAPI      :: mode :- "forgot-password" :> NamedRoutes ForgotPasswordAPI
+  , gargForgotPasswordAsyncAPI :: mode :- "async" :> "forgot-password" :> NamedRoutes ForgotPasswordAsyncAPI
+  , gargVersionAPI             :: mode :- NamedRoutes GargVersion
+  , gargPrivateAPI             :: mode :- NamedRoutes GargPrivateAPI
+  , gargPublicAPI              :: mode :- "public" :> NamedRoutes GargPublicAPI
+  } deriving Generic
+
+
+data AuthAPI mode = AuthAPI
+  { authEp :: mode :- "auth"  :> Summary "AUTH API"
+                              :> ReqBody '[JSON] AuthRequest
+                              :> Post    '[JSON] AuthResponse
+  } deriving Generic
+
+
+data ForgotPasswordAPI mode = ForgotPasswordAPI
+  { forgotPasswordPostEp :: mode :- Summary "Forgot password POST API"
+                                 :> ReqBody '[JSON] ForgotPasswordRequest
+                                 :> Post '[JSON] ForgotPasswordResponse
+  , forgotPasswordGetEp  :: mode :- Summary "Forgot password GET API"
+                                 :> QueryParam "uuid" Text
+                                 :> Get '[JSON] ForgotPasswordGet
+  } deriving Generic
+
+
+data ForgotPasswordAsyncAPI mode = ForgotPasswordAsyncAPI
+  { forgotPasswordAsyncEp :: mode :- Summary "Forgot password asnc"
+                                  :> AsyncJobs JobLog '[JSON] ForgotPasswordAsyncParams JobLog
+  } deriving Generic
+
+
+data GargVersion mode = GargVersion
+  { gargVersionEp :: "version" :> Summary "Backend version" :> Get '[JSON] Text
+  } deriving Generic

src/Gargantext/API/Routes/Named/Contact.hs

+{-# LANGUAGE TypeOperators #-}
+{-# LANGUAGE DeriveGeneric #-}
+module Gargantext.API.Routes.Named.Contact (
+  -- * Routes types
+    ContactAPI(..)
+  , ContactAsyncAPI(..)
+
+  -- * API types (appears in the routes)
+  , AddContactParams(..)
+  ) where
+
+
+import Data.Text (Text)
+import GHC.Generics
+import Gargantext.API.Admin.Orchestrator.Types
+import Gargantext.API.Routes.Named.Node (NodeNodeAPI(..))
+import Gargantext.Database.Admin.Types.Hyperdata.Contact
+import Gargantext.Database.Admin.Types.Node
+import Servant
+
+
+data ContactAPI mode = ContactAPI
+  { contactAsyncAPI :: mode :- "contact" :> Summary "Contact endpoint" :> NamedRoutes ContactAsyncAPI
+  , getContactEp    :: mode :- Capture "contact_id" NodeId :> NamedRoutes (NodeNodeAPI HyperdataContact)
+  } deriving Generic
+
+
+newtype ContactAsyncAPI mode = ContactAsyncAPI
+  { addContactAsyncEp :: mode :- AsyncJobs JobLog '[JSON] AddContactParams JobLog
+  } deriving Generic
+
+
+data AddContactParams = AddContactParams         { firstname :: !Text, lastname :: !Text }
+                      | AddContactParamsAdvanced { firstname :: !Text
+                                                 , lastname  :: !Text
+                                                 -- TODO add others fields
+                                                 }
+    deriving Generic

src/Gargantext/API/Routes/Named/Context.hs

+{-# LANGUAGE TypeOperators #-}
+{-# LANGUAGE DeriveGeneric #-}
+
+module Gargantext.API.Routes.Named.Context where
+
+import GHC.Generics
+import Gargantext.Database.Admin.Types.Node
+import Servant
+
+data ContextAPI mode a = ContextAPI
+  { getNodeEp :: mode :- Get '[JSON] (Node a)
+  } deriving Generic

src/Gargantext/API/Routes/Named/Corpus.hs

+{-# LANGUAGE TypeOperators #-}
+{-# LANGUAGE DeriveGeneric #-}
+module Gargantext.API.Routes.Named.Corpus (
+  -- * Routes types
+    CorpusExportAPI(..)
+  , AddWithForm(..)
+  , AddWithQuery(..)
+  ) where
+
+import Data.Text (Text)
+import GHC.Generics
+import Gargantext.API.Admin.Orchestrator.Types
+import Gargantext.API.Node.Corpus.Annuaire hiding (AddWithForm)
+import Gargantext.API.Node.Corpus.Export.Types
+import Gargantext.API.Node.Types
+import Gargantext.Core.Text.Ngrams (NgramsType(..))
+import Gargantext.Database.Admin.Types.Node
+import Servant
+
+--------------------------------------------------
+newtype CorpusExportAPI mode = CorpusExportAPI
+  { corpusExportEp :: mode :- Summary "Corpus Export"
+                           :> "export"
+                           :> QueryParam "listId"     ListId
+                           :> QueryParam "ngramsType" NgramsType
+                           :> Get '[JSON] (Headers '[Servant.Header "Content-Disposition" Text] Corpus)
+  } deriving Generic
+
+newtype AddWithForm mode = AddWithForm
+  { addWithFormEp :: mode :- Summary "Add with FormUrlEncoded to annuaire endpoint"
+                          :> "annuaire"
+                          :> Capture "annuaire_id" AnnuaireId
+                          :> "add"
+                          :> "form"
+                          :> "async"
+                          :> AsyncJobs JobLog '[FormUrlEncoded] AnnuaireWithForm JobLog
+  } deriving Generic
+
+
+newtype AddWithQuery mode = AddWithQuery
+  { addWithQueryEp :: mode :- Summary "Add with Query to corpus endpoint"
+                           :> "corpus"
+                           :> Capture "corpus_id" CorpusId
+                           :> "query"
+                           :> AsyncJobs JobLog '[JSON] WithQuery JobLog
+  } deriving Generic

src/Gargantext/API/Routes/Named/Count.hs

+{-# LANGUAGE TypeOperators #-}
+{-# LANGUAGE DeriveGeneric #-}
+module Gargantext.API.Routes.Named.Count (
+  -- * Routes types
+    CountAPI(..)
+
+  -- * Re-exports
+  , module X
+  ) where
+
+import GHC.Generics
+import Servant
+import Gargantext.API.Count as X hiding (CountAPI)
+
+
+newtype CountAPI mode = CountAPI
+  { postCountsEp :: mode :- Post '[JSON] X.Counts
+  } deriving Generic

src/Gargantext/API/Routes/Named/Document.hs

+{-# LANGUAGE DeriveGeneric   #-}
+{-# LANGUAGE TemplateHaskell #-}
+{-# LANGUAGE TypeOperators   #-}
+module Gargantext.API.Routes.Named.Document (
+  -- * Routes types
+    DocumentsFromWriteNodesAPI(..)
+  , DocumentUploadAPI(..)
+  , DocumentExportAPI(..)
+
+  -- * API types
+  , Params(..)
+  , DocumentUpload(..)
+
+  -- * functions and lenses
+  , du_title
+  , du_sources
+  , du_language
+  , du_date
+  , du_authors
+  , du_abstract
+  ) where
+
+import Control.Lens
+import Data.Aeson
+import Data.Swagger hiding (fieldLabelModifier)
+import Data.Text (Text)
+import GHC.Generics
+import Gargantext.API.Admin.Orchestrator.Types
+import Gargantext.API.Node.Document.Export.Types
+import Gargantext.Core
+import Gargantext.Core.Text.List.Social
+import Gargantext.Core.Utils.Prefix
+import Gargantext.Utils.Servant (ZIP)
+import Prelude
+import Servant
+
+newtype DocumentExportAPI mode = DocumentExportAPI
+  { documentExportAPI ::
+      mode :- Summary "Document Export"
+           :> "export"
+           :> ( "json"
+                :> Get '[JSON] (Headers '[Servant.Header "Content-Disposition" Text] DocumentExport)
+              :<|> "json.zip"
+                :> Get '[ZIP] (Headers '[Servant.Header "Content-Disposition" Text] DocumentExportZIP)
+              :<|> "csv"
+                :> Get '[PlainText] (Headers '[Servant.Header "Content-Disposition" Text] Text) )
+  } deriving Generic
+
+newtype DocumentsFromWriteNodesAPI mode = DocumentsFromWriteNodesAPI
+  { docFromWriteNodesEp :: mode :- Summary " Documents from Write nodes."
+                                :> AsyncJobs JobLog '[JSON] Params JobLog
+  } deriving Generic
+
+
+newtype DocumentUploadAPI mode = DocumentUploadAPI
+  { uploadDocAsyncEp :: mode :- Summary " Document upload"
+                             :> "document"
+                             :> "upload"
+                             :> "async"
+                             :> AsyncJobs JobLog '[JSON] DocumentUpload JobLog
+  } deriving Generic
+
+
+data Params = Params
+  { id         :: Int
+  , paragraphs :: Text
+  , lang       :: Lang
+  , selection  :: FlowSocialListWith
+  }
+  deriving (Generic, Show)
+
+
+data DocumentUpload = DocumentUpload
+  { _du_abstract :: Text
+  , _du_authors  :: Text
+  , _du_sources  :: Text
+  , _du_title    :: Text
+  , _du_date     :: Text
+  , _du_language :: Text
+  }
+  deriving Generic
+
+
+--
+-- instances
+--
+
+instance FromJSON Params where
+  parseJSON = genericParseJSON defaultOptions
+
+instance ToJSON Params where
+  toJSON = genericToJSON defaultOptions
+
+instance ToSchema Params
+
+$(makeLenses ''DocumentUpload)
+
+instance ToSchema DocumentUpload
+
+instance FromJSON DocumentUpload
+  where
+    parseJSON = genericParseJSON
+            ( defaultOptions { sumEncoding = ObjectWithSingleField
+                            , fieldLabelModifier = unCapitalize . dropPrefix "_du_"
+                            , omitNothingFields = True
+                            }
+            )
+
+instance ToJSON DocumentUpload
+  where
+    toJSON = genericToJSON
+           ( defaultOptions { sumEncoding = ObjectWithSingleField
+                            , fieldLabelModifier = unCapitalize . dropPrefix "_du_"
+                            , omitNothingFields = True
+                            }
+           )
+

src/Gargantext/API/Routes/Named/File.hs

+{-# LANGUAGE DeriveGeneric #-}
+{-# LANGUAGE TypeOperators #-}
+module Gargantext.API.Routes.Named.File (
+  -- * Routes types
+    FileAPI(..)
+  , FileAsyncAPI(..)
+  ) where
+
+import Data.Text (Text)
+import GHC.Generics
+import Gargantext.API.Admin.Orchestrator.Types
+import Gargantext.API.Node.File
+import Gargantext.API.Node.Types
+import Servant
+
+data FileAPI mode = FileAPI
+  { fileDownloadEp :: mode :- Summary "File download"
+                           :> "download"
+                           :> Get '[RESPONSE] (Headers '[Servant.Header "Content-Type" Text] BSResponse)
+  } deriving Generic
+
+
+data FileAsyncAPI mode = FileAsyncAPI
+  { addFileAsyncEp :: mode :- Summary "File Async Api"
+                           :> "file"
+                           :> "add"
+                           :> AsyncJobs JobLog '[FormUrlEncoded] NewWithFile JobLog
+  } deriving Generic
+

src/Gargantext/API/Routes/Named/FrameCalc.hs

+{-# LANGUAGE TypeOperators #-}
+{-# LANGUAGE DeriveGeneric #-}
+
+module Gargantext.API.Routes.Named.FrameCalc where
+
+import Servant
+import GHC.Generics
+import Gargantext.API.Node.FrameCalcUpload (FrameCalcUpload)
+import Gargantext.API.Admin.Orchestrator.Types
+
+data FrameCalcAPI mode = FrameCalcAPI
+  { frameCalcUploadEp :: mode :- Summary " FrameCalc upload"
+                              :> "add"
+                              :> "framecalc"
+                              :> "async"
+                              :> AsyncJobs JobLog '[JSON] FrameCalcUpload JobLog
+  } deriving Generic
+

src/Gargantext/API/Routes/Named/List.hs

+{-# LANGUAGE TypeOperators #-}
+{-# LANGUAGE DeriveGeneric #-}
+module Gargantext.API.Routes.Named.List where
+
+import Data.Text (Text)
+import GHC.Generics
+import Gargantext.API.Admin.Orchestrator.Types
+import Gargantext.API.Ngrams.List.Types
+import Gargantext.API.Ngrams.Types
+import Gargantext.API.Types (HTML)
+import Gargantext.Database.Admin.Types.Node
+import Gargantext.Utils.Servant qualified as GUS
+import Servant
+
+newtype GETAPI mode = GETAPI
+  { getListEp :: mode :- Summary "Get List"
+                      :> "lists"
+                      :> Capture "listId" ListId
+                      :> ( "json"
+                           :> Get '[JSON, HTML] (Headers '[Header "Content-Disposition" Text] NgramsList)
+                         :<|>  "json.zip"
+                           :> Get '[GUS.ZIP] (Headers '[Header "Content-Disposition" Text] NgramsListZIP)
+                         :<|> "csv"
+                           :> Get '[GUS.CSV] (Headers '[Header "Content-Disposition" Text] NgramsTableMap) )
+  } deriving Generic
+
+
+newtype JSONAPI mode = JSONAPI
+  { updateListJSONEp :: mode :- Summary "Update List"
+                             :> "lists"
+                             :> Capture "listId" ListId
+                             :> "add"
+                             :> "form"
+                             :> "async"
+                             :> AsyncJobs JobLog '[FormUrlEncoded] WithJsonFile JobLog
+  } deriving Generic
+
+
+newtype CSVAPI mode = CSVAPI
+  { updateListCSVEp :: mode :- Summary "Update List (legacy v3 CSV)"
+                            :> "lists"
+                            :> Capture "listId" ListId
+                            :> "csv"
+                            :> "add"
+                            :> "form"
+                            :> "async"
+                            :> AsyncJobs JobLog '[FormUrlEncoded] WithTextFile JobLog
+  } deriving Generic

src/Gargantext/API/Routes/Named/Metrics.hs

+{-# LANGUAGE TypeOperators #-}
+{-# LANGUAGE DeriveGeneric #-}
+module Gargantext.API.Routes.Named.Metrics (
+  -- * Routes types
+
+    TreeAPI(..)
+  , ScatterAPI(..)
+  , ChartAPI(..)
+  , PieAPI(..)
+  ) where
+
+import Data.Text (Text)
+import Data.Time
+import Data.Vector
+import GHC.Generics
+import Gargantext.API.HashedResponse
+import Gargantext.API.Ngrams.NgramsTree
+import Gargantext.API.Ngrams.Types
+import Gargantext.Core.Types.Main
+import Gargantext.Core.Types.Query (Limit)
+import Gargantext.Core.Viz.Types
+import Gargantext.Database.Admin.Types.Metrics
+import Gargantext.Database.Admin.Types.Node
+import Servant
+
+
+data TreeAPI mode = TreeAPI
+  { treeChartEp       :: mode :- Summary " Tree API"
+                              :> QueryParam "from" UTCTime
+                              :> QueryParam "to"   UTCTime
+                              :> QueryParam  "list"       ListId
+                              :> QueryParamR "ngramsType" TabType
+                              :> QueryParamR "listType"   ListType
+                              :> Get '[JSON] (HashedResponse (ChartMetrics (Vector NgramsTree)))
+  , treeChartUpdateEp :: mode :- Summary "Tree Chart update"
+                              :> QueryParam  "list"       ListId
+                              :> QueryParamR "ngramsType" TabType
+                              :> QueryParamR "listType"   ListType
+                              :> Post '[JSON] ()
+  , treeHashEp        :: mode :- "hash"
+                              :> Summary "Tree Hash"
+                              :> QueryParam  "list"       ListId
+                              :> QueryParamR "ngramsType" TabType
+                              :> QueryParamR "listType"   ListType
+                              :> Get '[JSON] Text
+  } deriving Generic
+
+
+data ScatterAPI mode = ScatterAPI
+  { sepGenEp :: mode :- Summary "SepGen IncExc metrics"
+                     :> QueryParam  "list"       ListId
+                     :> QueryParamR "ngramsType" TabType
+                     :> QueryParam  "limit"      Limit
+                     :> Get '[JSON] (HashedResponse Metrics)
+  , scatterUpdateEp :: mode :- Summary "Scatter update"
+                            :> QueryParam  "list"       ListId
+                            :> QueryParamR "ngramsType" TabType
+                            :> QueryParam  "limit"      Limit
+                            :> Post '[JSON] ()
+  , scatterHashEp :: mode :- "hash"
+                          :> Summary "Scatter Hash"
+                          :> QueryParam  "list"       ListId
+                          :> QueryParamR "ngramsType" TabType
+                          :> Get '[JSON] Text
+  } deriving Generic
+
+
+data PieAPI mode = PieAPI
+  { getPieChartEp :: mode :- Summary "Pie Chart"
+                          :> QueryParam "from" UTCTime
+                          :> QueryParam "to"   UTCTime
+                          :> QueryParam  "list"       ListId
+                          :> QueryParamR "ngramsType" TabType
+                          :> Get '[JSON] (HashedResponse (ChartMetrics Histo))
+  , pieChartUpdateEp :: mode :- Summary "Pie Chart update"
+                             :> QueryParam  "list"       ListId
+                             :> QueryParamR "ngramsType" TabType
+                             :> QueryParam  "limit"      Limit
+                             :> Post '[JSON] ()
+  , pieHashEp :: mode :- "hash"
+                      :> Summary "Pie Hash"
+                      :> QueryParam  "list"       ListId
+                      :> QueryParamR "ngramsType" TabType
+                      :> Get '[JSON] Text
+  } deriving Generic
+
+
+data ChartAPI mode = ChartAPI
+  { getChartEp :: mode :- Summary " Chart API"
+                       :> QueryParam "from" UTCTime
+                       :> QueryParam "to"   UTCTime
+                       :> QueryParam  "list"       ListId
+                       :> QueryParamR "ngramsType" TabType
+                       :> Get '[JSON] (HashedResponse (ChartMetrics Histo))
+  , updateChartEp :: mode :- Summary "Chart update"
+                          :> QueryParam  "list"       ListId
+                          :> QueryParamR "ngramsType" TabType
+                          :> QueryParam  "limit"      Limit
+                          :> Post '[JSON] ()
+  , chartHashEp :: mode :- "hash"
+                        :> Summary "Chart Hash"
+                        :> QueryParam  "list"       ListId
+                        :> QueryParamR "ngramsType" TabType
+                        :> Get '[JSON] Text
+  } deriving Generic
+

src/Gargantext/API/Routes/Named/Private.hs

+
+{-# LANGUAGE TypeOperators #-}
+{-# LANGUAGE DeriveGeneric #-}
+
+module Gargantext.API.Routes.Named.Private (
+  -- * Routes types
+    GargPrivateAPI
+  , GargPrivateAPI'(..)
+  , GargAdminAPI(..)
+  , NodeEndpoint(..)
+  , MembersAPI(..)
+  ) where
+
+import Data.Text (Text)
+import GHC.Generics
+import Gargantext.API.Admin.Auth.Types
+import Gargantext.API.Auth.PolicyCheck
+import Gargantext.API.Routes.Named.Contact
+import Gargantext.API.Routes.Named.Context
+import Gargantext.API.Routes.Named.Corpus
+import Gargantext.API.Routes.Named.Count
+import Gargantext.API.Routes.Named.Document
+import Gargantext.API.Routes.Named.Metrics
+import Gargantext.API.Routes.Named.Node
+import Gargantext.API.Routes.Named.List qualified as List
+import Gargantext.API.Routes.Named.Share
+import Gargantext.API.Routes.Named.Tree
+import Gargantext.API.Routes.Named.Table
+import Gargantext.API.Routes.Named.Viz
+import Gargantext.Database.Admin.Types.Hyperdata.Any
+import Gargantext.Database.Admin.Types.Hyperdata.Corpus
+import Gargantext.Database.Admin.Types.Node
+import Servant.API
+import Servant.Auth qualified as SA
+
+
+type MkProtectedAPI private = SA.Auth '[SA.JWT, SA.Cookie] AuthenticatedUser :> private
+
+
+newtype GargPrivateAPI mode = GargPrivateAPI
+  { mkPrivateAPI :: mode :- MkProtectedAPI (NamedRoutes GargPrivateAPI')
+  } deriving Generic
+
+
+data GargPrivateAPI' mode = GargPrivateAPI'
+  { gargAdminAPI :: mode :- NamedRoutes GargAdminAPI
+  , nodeEp       :: mode :- NamedRoutes NodeEndpoint
+  , contextEp    :: mode :- "context"  :> Summary "Node endpoint"
+                                       :> Capture "node_id" ContextId
+                                       :> NamedRoutes (ContextAPI HyperdataAny)
+  , corpusNodeAPI :: mode :- "corpus"  :> Summary "Corpus endpoint"
+                                       :> Capture "corpus_id" CorpusId
+                                       :> NamedRoutes (NodeAPI HyperdataCorpus)
+  , corpusNodeNodeAPI :: mode :- "corpus" :> Summary "Corpus endpoint"
+                                          :> Capture "node1_id" NodeId
+                                          :> "document"
+                                          :> Capture "node2_id" NodeId
+                                          :> NamedRoutes (NodeNodeAPI HyperdataAny)
+  , corpusExportAPI :: mode :- "corpus" :> Capture "node_id" CorpusId
+                                        :> NamedRoutes CorpusExportAPI
+  , annuaireEp :: mode :- "annuaire" :> Summary "Annuaire endpoint"
+                                     :> Capture "annuaire_id" AnnuaireId
+                                     :> NamedRoutes (NodeAPI HyperdataAnnuaire)
+  , contactAPI :: mode :- "annuaire" :> Summary "Contact endpoint"
+                                     :> Capture "annuaire_id" NodeId
+                                     :> NamedRoutes ContactAPI
+  , tableNgramsAPI :: mode :- "document" :> Summary "Document endpoint"
+                                         :> Capture "doc_id" DocId
+                                         :> "ngrams"
+                                         :> NamedRoutes TableNgramsAPI
+  , documentExportAPI :: mode :- "texts" :> Capture "node_id" DocId
+                                         :> NamedRoutes DocumentExportAPI
+  , countAPI :: mode :- "count" :> Summary "Count endpoint"
+                                :> ReqBody '[JSON] Query
+                                :> NamedRoutes CountAPI
+  , graphAPI :: mode :- "graph" :> Summary "Graph endpoint"
+                                :> Capture "graph_id" NodeId
+                                :> NamedRoutes GraphAPI
+  , treeAPI :: mode :- "tree" :> Summary "Tree endpoint"
+                              :> Capture "tree_id" NodeId
+                              :> PolicyChecked (NamedRoutes TreeAPI)
+  , treeFlatAPI :: mode :- "treeflat" :> Summary "Flat tree endpoint"
+                                      :> Capture "tree_id" NodeId
+                                      :> NamedRoutes TreeFlatAPI
+  , membersAPI     :: mode :- "members" :> Summary "Team node members" :> NamedRoutes MembersAPI
+  , addWithFormEp  :: mode :- NamedRoutes AddWithForm
+  , addWithQueryEp :: mode :- NamedRoutes AddWithQuery
+  , listGetAPI     :: mode :- NamedRoutes List.GETAPI
+  , listJsonAPI    :: mode :- NamedRoutes List.JSONAPI
+  , listCsvAPI     :: mode :- NamedRoutes List.CSVAPI
+  , shareUrlEp     :: mode :- "shareurl" :> NamedRoutes ShareURL
+  } deriving Generic
+
+
+data GargAdminAPI mode = GargAdminAPI
+  { rootsEp       :: mode :- "user"  :> Summary "First user endpoint" :> NamedRoutes Roots
+  , adminNodesAPI :: mode :- "nodes" :> Summary "Nodes endpoint"
+                                     :> ReqBody '[JSON] [NodeId]
+                                     :> NamedRoutes NodesAPI
+  } deriving Generic
+
+
+data NodeEndpoint mode = NodeEndpoint
+  { nodeEndpointAPI :: mode :- "node" :> Summary "Node endpoint"
+                                      :> Capture "node_id" NodeId
+                                      :> NamedRoutes (NodeAPI HyperdataAny)
+  } deriving Generic
+
+
+data MembersAPI mode = MembersAPI
+  { getMembersEp :: mode :- Get '[JSON] [Text]
+  }
+

src/Gargantext/API/Routes/Named/Public.hs

+{-# LANGUAGE DeriveGeneric #-}
+{-# LANGUAGE TypeOperators #-}
+module Gargantext.API.Routes.Named.Public where
+
+import GHC.Generics
+import Gargantext.API.Public qualified as Public
+import Gargantext.API.Routes.Named.File
+import Gargantext.Database.Admin.Types.Node ( NodeId )
+import Servant.API
+
+data GargPublicAPI mode = GargPublicAPI
+  { publicHomeAPI :: mode :- NamedRoutes HomeAPI
+  , publicNodeAPI :: mode :- NamedRoutes NodeAPI
+  } deriving Generic
+
+data HomeAPI mode = HomeAPI
+  { homeEp :: mode :- Summary "Public Home API" :> Get '[JSON] [Public.PublicData]
+  } deriving Generic
+
+data NodeAPI mode = NodeAPI
+  { nodeEp :: mode :- Summary "Public Node API" :> Capture "node" NodeId :> "file" :> NamedRoutes FileAPI
+  } deriving Generic

src/Gargantext/API/Routes/Named/Search.hs

+{-# LANGUAGE TypeOperators #-}
+{-# LANGUAGE DeriveGeneric #-}
+module Gargantext.API.Routes.Named.Search (
+  -- * Routes types
+    SearchAPI(..)
+
+  -- * API types (appears in the routes)
+  , SearchType(..)
+  , SearchQuery(..)
+  , SearchResult(..)
+  , SearchResultTypes(..)
+  ) where
+
+
+import Data.Aeson
+import Data.Swagger
+import Data.Text (Text)
+import GHC.Generics
+import Gargantext.Core.Text.Corpus.Query (RawQuery (..))
+import Gargantext.Core.Types.Query (Limit, Offset)
+import Gargantext.Core.Types.Search
+import Gargantext.Core.Utils.Prefix (unPrefixSwagger)
+import Gargantext.Database.Query.Facet
+import Prelude
+import Servant
+import Test.QuickCheck
+
+
+-- TODO-ACCESS: CanSearch? or is it part of CanGetNode
+-- TODO-EVENTS: No event, this is a read-only query.
+data SearchAPI results mode = SearchAPI
+  { searchEp :: mode :- Summary "Search endpoint"
+                     :> ReqBody '[JSON] SearchQuery
+                     :> QueryParam "offset" Offset
+                     :> QueryParam "limit"  Limit
+                     :> QueryParam "order"  OrderBy
+                     :> Post '[JSON] results
+  } deriving Generic
+
+
+data SearchType = SearchDoc | SearchContact | SearchDocWithNgrams
+  deriving Generic
+
+
+data SearchQuery = SearchQuery
+  { query    :: !RawQuery
+  , expected :: !SearchType
+  } deriving Generic
+
+
+newtype SearchResult =
+  SearchResult { result :: SearchResultTypes }
+    deriving Generic
+
+
+data SearchResultTypes =
+    SearchResultDoc { docs     :: ![Row] }
+  | SearchResultContact  { contacts :: ![Row] }
+  | SearchNoResult      { message  :: !Text }
+  deriving Generic
+
+
+--
+-- instances
+--
+
+instance FromJSON SearchResult where
+  parseJSON = genericParseJSON defaultOptions
+
+instance ToJSON SearchResult where
+  toJSON = genericToJSON defaultOptions
+
+instance ToSchema SearchResult
+
+instance Arbitrary SearchResult where
+  arbitrary = SearchResult <$> arbitrary
+
+instance FromJSON SearchResultTypes where
+  parseJSON = genericParseJSON (defaultOptions { sumEncoding = defaultTaggedObject })
+
+instance ToJSON SearchResultTypes where
+  toJSON = genericToJSON (defaultOptions { sumEncoding = defaultTaggedObject })
+
+instance Arbitrary SearchResultTypes where
+  arbitrary = do
+    srd <- SearchResultDoc     <$> arbitrary
+    src <- SearchResultContact <$> arbitrary
+    srn <- pure $ SearchNoResult "No result because.."
+    elements [srd, src, srn]
+
+instance ToSchema SearchResultTypes where
+  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
+
+instance FromJSON SearchQuery where
+  parseJSON = genericParseJSON defaultOptions
+
+instance ToJSON SearchQuery where
+  toJSON = genericToJSON defaultOptions
+
+instance ToSchema SearchQuery
+
+instance Arbitrary SearchQuery where
+  arbitrary = elements [SearchQuery (RawQuery "electrodes") SearchDoc]
+
+instance FromJSON SearchType where
+  parseJSON = genericParseJSON (defaultOptions { sumEncoding = ObjectWithSingleField })
+
+instance ToJSON SearchType where
+  toJSON = genericToJSON (defaultOptions { sumEncoding = ObjectWithSingleField })
+
+instance ToSchema SearchType
+
+instance Arbitrary SearchType where
+  arbitrary = elements [SearchDoc, SearchContact]

src/Gargantext/API/Routes/Named/Share.hs

+{-# LANGUAGE TypeOperators #-}
+{-# LANGUAGE DeriveGeneric #-}
+
+module Gargantext.API.Routes.Named.Share (
+  -- * Routes types
+    ShareNode(..)
+  , Unpublish(..)
+  , ShareURL(..)
+
+  -- * API types (which appears in the routes)
+  , ShareNodeParams(..)
+  ) where
+
+import Data.Aeson
+import Data.Swagger
+import Data.Text (Text)
+import GHC.Generics
+import Gargantext.Database.Admin.Types.Node
+import Gargantext.Utils.Aeson qualified as GUA
+import Prelude
+import Servant
+import Test.QuickCheck
+
+newtype ShareURL mode = ShareURL
+  { shareUrlEp :: mode :- Summary "Fetch URL for sharing a node"
+                       :> QueryParam "type" NodeType
+                       :> QueryParam "id" NodeId
+                       :> Get '[JSON] Text
+  } deriving Generic
+
+
+newtype ShareNode mode = ShareNode
+  { shareNodeEp :: mode :- Summary " Share Node with username"
+                        :> ReqBody '[JSON] ShareNodeParams
+                        :> Post    '[JSON] Int
+  } deriving Generic
+
+
+newtype Unpublish mode = Unpublish
+  { unpublishEp :: mode :- Summary " Unpublish Node" :> Capture "node_id" NodeId :> Put '[JSON] Int
+  } deriving Generic
+
+--
+-- API Types
+--
+data ShareNodeParams = ShareTeamParams   { username :: Text  }
+                     | SharePublicParams { node_id  :: NodeId }
+  deriving (Generic)
+
+--
+-- Instances
+--
+
+-- TODO unPrefix "pn_" FromJSON, ToJSON, ToSchema, adapt frontend.
+instance FromJSON  ShareNodeParams where
+  parseJSON = genericParseJSON (defaultOptions { sumEncoding = GUA.defaultTaggedObject })
+instance ToJSON    ShareNodeParams where
+  toJSON = genericToJSON (defaultOptions { sumEncoding = GUA.defaultTaggedObject })
+instance ToSchema  ShareNodeParams
+instance Arbitrary ShareNodeParams where
+  arbitrary = elements [ ShareTeamParams "user1"
+                       , SharePublicParams (UnsafeMkNodeId 1)
+                       ]

src/Gargantext/API/Routes/Named/Table.hs

+{-# LANGUAGE DeriveGeneric   #-}
+{-# LANGUAGE TemplateHaskell #-}
+{-# LANGUAGE TypeOperators   #-}
+
+module Gargantext.API.Routes.Named.Table (
+  -- * Routes types
+    TableAPI(..)
+  , TableNgramsAPI(..)
+  , TableNgramsApiGet(..)
+  , TableNgramsApiPut(..)
+  , RecomputeScoresNgramsApiGet(..)
+  , TableNgramsApiGetVersion(..)
+  , TableNgramsAsyncAPI(..)
+
+  -- * API types (appears in the routes)
+
+  , TableQuery(..)
+  , FacetTableResult
+  ) where
+
+import Data.Aeson.TH
+import Data.Swagger
+import Data.Text (Text)
+import GHC.Generics
+import Gargantext.API.Admin.Orchestrator.Types
+import Gargantext.API.HashedResponse
+import Gargantext.API.Ngrams.Types (TabType(..), UpdateTableNgramsCharts, Version, QueryParamR, Versioned, VersionedWithCount, NgramsTable, NgramsTablePatch)
+import Gargantext.Core.Text.Corpus.Query (RawQuery)
+import Gargantext.Core.Types (TableResult(..))
+import Gargantext.Core.Types.Main (ListType)
+import Gargantext.Core.Types.Query
+import Gargantext.Core.Utils.Prefix (unPrefix, unPrefixSwagger)
+import Gargantext.Database.Admin.Types.Node (ListId)
+import Gargantext.Database.Query.Facet.Types
+import Prelude
+import Servant
+import Test.QuickCheck
+
+
+data TableAPI mode = TableAPI
+  { getTableEp   :: mode :- Summary "Table API"
+                         :> QueryParam "tabType" TabType
+                         :> QueryParam "limit" Limit
+                         :> QueryParam "offset" Offset
+                         :> QueryParam "orderBy" OrderBy
+                         :> QueryParam "query" RawQuery
+                         :> QueryParam "year" Text
+                         :> Get    '[JSON] (HashedResponse FacetTableResult)
+  , postTableEp :: mode :- Summary "Table API (POST)"
+                        :> ReqBody '[JSON] TableQuery
+                        :> Post    '[JSON] FacetTableResult
+  , hashTableEp :: mode :- "hash"
+                        :> Summary "Hash Table"
+                        :> QueryParam "tabType" TabType
+                        :> Get '[JSON] Text
+  } deriving Generic
+
+
+data TableNgramsAPI mode = TableNgramsAPI
+  { tableNgramsGetAPI       :: mode :- NamedRoutes TableNgramsApiGet
+  , tableNgramsPutAPI       :: mode :- NamedRoutes TableNgramsApiPut
+  , recomputeScoresEp       :: mode :- NamedRoutes RecomputeScoresNgramsApiGet
+  , tableNgramsGetVersionEp :: mode :- "version" :> NamedRoutes TableNgramsApiGetVersion
+  , tableNgramsAsyncAPI     :: mode :- NamedRoutes TableNgramsAsyncAPI
+  } deriving Generic
+
+
+data TableNgramsApiGet mode = TableNgramsApiGet
+  { getNgramsTableEp :: mode :- Summary " Table Ngrams API Get"
+                             :> QueryParamR "ngramsType"  TabType
+                             :> QueryParamR "list"        ListId
+                             :> QueryParamR "limit"       Limit
+                             :> QueryParam  "offset"      Offset
+                             :> QueryParam  "listType"    ListType
+                             :> QueryParam  "minTermSize" MinSize
+                             :> QueryParam  "maxTermSize" MaxSize
+                             :> QueryParam  "orderBy"     OrderBy
+                             :> QueryParam  "search"      Text
+                             :> Get    '[JSON] (VersionedWithCount NgramsTable)
+  } deriving Generic
+
+
+data TableNgramsApiPut mode = TableNgramsApiPut
+  { putNgramsTableEp :: mode :- Summary " Table Ngrams API Change"
+                             :> QueryParamR "ngramsType" TabType
+                             :> QueryParamR "list"       ListId
+                             :> ReqBody '[JSON] (Versioned NgramsTablePatch)
+                             :> Put     '[JSON] (Versioned NgramsTablePatch)
+  } deriving Generic
+
+
+data RecomputeScoresNgramsApiGet mode = RecomputeScoresNgramsApiGet
+  { recomputeNgramsEp :: mode :- Summary " Recompute scores for ngrams table"
+                              :> QueryParamR "ngramsType"  TabType
+                              :> QueryParamR "list"        ListId
+                              :> "recompute" :> Post '[JSON] Int
+  } deriving Generic
+
+
+data TableNgramsApiGetVersion mode = TableNgramsApiGetVersion
+  { getTableNgramsVersion :: mode :- Summary " Table Ngrams API Get Version"
+                                  :> QueryParamR "ngramsType"  TabType
+                                  :> QueryParamR "list"        ListId
+                                  :> Get    '[JSON] Version
+  } deriving Generic
+
+
+data TableNgramsAsyncAPI mode = TableNgramsAsyncAPI
+  { updateTableNgramsChartsEp :: mode :- Summary "Table Ngrams Async API"
+                                      :> "async"
+                                      :> "charts"
+                                      :> "update"
+                                      :> AsyncJobs JobLog '[JSON] UpdateTableNgramsCharts JobLog
+  } deriving Generic
+
+
+data TableQuery = TableQuery
+  { tq_offset       :: Offset
+  , tq_limit        :: Limit
+  , tq_orderBy      :: OrderBy
+  , tq_view         :: TabType
+  , tq_query        :: RawQuery
+  } deriving Generic
+
+type FacetTableResult = TableResult FacetDoc
+
+--
+-- instances
+--
+
+$(deriveJSON (unPrefix "tq_") ''TableQuery)
+
+instance ToSchema TableQuery where
+  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "tq_")
+
+instance Arbitrary TableQuery where
+  arbitrary = elements [TableQuery { tq_offset = 0
+                                   , tq_limit = 10
+                                   , tq_orderBy = DateAsc
+                                   , tq_view = Docs
+                                   , tq_query = "electrodes" }]

src/Gargantext/API/Routes/Named/Tree.hs

+{-# LANGUAGE TypeOperators #-}
+{-# LANGUAGE DeriveGeneric #-}
+
+module Gargantext.API.Routes.Named.Tree (
+  -- * Routes types
+    NodeTreeAPI(..)
+  , TreeFlatAPI(..)
+  ) where
+
+import Data.Text (Text)
+import GHC.Generics
+import Gargantext.Core.Types.Main
+import Gargantext.Database.Admin.Types.Node
+import Servant
+
+data NodeTreeAPI mode = NodeTreeAPI
+  { nodeTreeEp   :: mode :- QueryParams "type" NodeType :> Get '[JSON] (Tree NodeTree)
+  , firstLevelEp :: mode :- "first-level" :> QueryParams "type" NodeType :> Get '[JSON] (Tree NodeTree)
+  } deriving Generic
+
+
+data TreeFlatAPI mode = TreeFlatAPI
+  { getNodesEp :: mode :- QueryParams "type" NodeType :> QueryParam "query" Text :> Get '[JSON] [NodeTree]
+  } deriving Generic

src/Gargantext/API/Routes/Named/Viz.hs

+{-# LANGUAGE TypeOperators #-}
+{-# LANGUAGE DeriveGeneric #-}
+
+module Gargantext.API.Routes.Named.Viz (
+  -- * Routes types
+    PhyloAPI(..)
+  , GetPhylo(..)
+  , PostPhylo(..)
+  , GraphAPI(..)
+  , GraphAsyncAPI(..)
+  , GraphVersionsAPI(..)
+
+  -- * API types (appears in the routes)
+  , PhyloData(..)
+  , GraphVersions(..)
+  ) where
+
+import Data.Aeson
+import Data.Swagger
+import Data.Text (Text)
+import GHC.Generics
+import Gargantext.API.Admin.Orchestrator.Types ( JobLog )
+import Gargantext.Core.Types
+import Gargantext.Core.Types.Phylo
+import Gargantext.Core.Viz.Graph.Types
+import Gargantext.Core.Viz.LegacyPhylo (Level)
+import Gargantext.Core.Viz.Phylo
+import Gargantext.Core.Viz.Phylo.Legacy.LegacyMain (MinSizeBranch)
+import Prelude
+import Servant
+import Servant.Job.Async (AsyncJobsAPI)
+import Servant.XML.Conduit (XML)
+import Test.QuickCheck
+
+
+data PhyloAPI mode = PhyloAPI
+  { getPhyloEp  :: mode :- Summary "Phylo API" :> NamedRoutes GetPhylo
+  , postPhyloEp :: mode :- NamedRoutes PostPhylo
+  } deriving Generic
+
+
+newtype GetPhylo mode = GetPhylo
+  { getPhyloDataEp :: mode :- QueryParam "listId"      ListId
+                           :> QueryParam "level"       Level
+                           :> QueryParam "minSizeBranch" MinSizeBranch
+                           :> Get '[JSON] PhyloData
+  } deriving Generic
+
+
+newtype PostPhylo mode = PostPhylo
+  { postPhyloByListIdEp :: mode :- QueryParam "listId" ListId :> (Post '[JSON] NodeId)
+  } deriving Generic
+
+
+data GraphAPI mode = GraphAPI
+  { getGraphEp       :: mode :- Get '[JSON] HyperdataGraphAPI
+  , getGraphAsyncEp  :: mode :- "async" :> NamedRoutes GraphAsyncAPI
+  , cloneGraphEp     :: mode :- "clone" :> ReqBody '[JSON] HyperdataGraphAPI :> Post '[JSON] NodeId
+  , gexfEp           :: mode :- "gexf" :> Get '[XML] (Headers '[Servant.Header "Content-Disposition" Text] Graph)
+  , graphVersionsAPI :: mode :- "versions" :> NamedRoutes GraphVersionsAPI
+  } deriving Generic
+
+
+newtype GraphAsyncAPI mode = GraphAsyncAPI
+  { recomputeGraphEp :: mode :- Summary "Recompute graph"
+                             :> "recompute"
+                             :> AsyncJobsAPI JobLog () JobLog
+  } deriving Generic
+
+
+data GraphVersionsAPI mode = GraphVersionsAPI
+  { getGraphVersionsEp :: mode :- Summary "Graph versions" :> Get '[JSON] GraphVersions
+  , recomputeGraphVersionEp :: mode :- Summary "Recompute graph version" :> Post '[JSON] Graph
+  } deriving Generic
+
+
+data PhyloData = PhyloData { pd_corpusId :: NodeId
+                           , pd_listId   :: NodeId
+                           , pd_data     :: GraphData
+                           , pd_config   :: PhyloConfig
+                           }
+  deriving (Generic, Show, Eq)
+
+
+data GraphVersions = GraphVersions
+  { gv_graph :: Maybe Int
+  , gv_repo  :: Int
+  } deriving (Show, Generic)
+
+
+--
+-- instances
+--
+
+instance ToJSON PhyloData where
+  toJSON PhyloData{..} =
+    object [
+      "pd_corpusId" .= toJSON pd_corpusId
+    , "pd_listId"   .= toJSON pd_listId
+    , "pd_data"     .= toJSON pd_data
+    , "pd_config"   .= toJSON pd_config
+    ]
+
+instance FromJSON PhyloData where
+  parseJSON = withObject "PhyloData" $ \o -> do
+    pd_corpusId <- o .: "pd_corpusId"
+    pd_listId   <- o .: "pd_listId"
+    pd_data     <- o .: "pd_data"
+    pd_config   <- o .: "pd_config"
+    pure $ PhyloData{..}
+
+instance Arbitrary PhyloData where
+  arbitrary = PhyloData <$> arbitrary <*> arbitrary <*> arbitrary <*> arbitrary
+
+instance ToSchema PhyloData
+
+instance FromJSON GraphVersions
+
+instance ToJSON GraphVersions
+
+instance ToSchema GraphVersions
+

src/Gargantext/API/Routes/Types.hs

+{-# LANGUAGE TypeFamilies         #-}
+{-# LANGUAGE ScopedTypeVariables  #-}
+module Gargantext.API.Routes.Types where
+
+import Data.List qualified as L
+import Data.Proxy
+import Gargantext.API.Errors
+import Prelude
+import Servant.Ekg
+import Servant.Server
+import Servant.Server.Internal.DelayedIO
+import Servant.Server.Internal.Delayed
+import Network.Wai
+
+data WithCustomErrorScheme a
+
+instance (HasServer subApi ctx) => HasServer (WithCustomErrorScheme subApi) ctx where
+  type ServerT (WithCustomErrorScheme subApi) m = GargErrorScheme -> ServerT subApi m
+  hoistServerWithContext _ pc nt s = hoistServerWithContext (Proxy :: Proxy subApi) pc nt . s
+  route Proxy ctx d = route (Proxy :: Proxy subApi) ctx (d `addHeaderCheck` getErrorScheme)
+    where
+      getErrorScheme :: DelayedIO GargErrorScheme
+      getErrorScheme = withRequest $ \rq -> do
+        let hdrs = requestHeaders rq
+            in case L.lookup "X-Garg-Error-Scheme" hdrs of
+                 Nothing     -> pure GES_old
+                 Just "new"  -> pure GES_new
+                 Just _      -> pure GES_old
+
+instance HasEndpoint sub => HasEndpoint (WithCustomErrorScheme sub) where
+  getEndpoint _ = getEndpoint (Proxy :: Proxy sub)
+  enumerateEndpoints _ = enumerateEndpoints (Proxy :: Proxy sub)

src/Gargantext/Core/Methods/Similarities/Accelerate/Distributional.hs

@@ -204,7 +204,8 @@ logDistributional' n m' = trace ("logDistributional'") result
     -- m_{i,j} = 0 if n_{i,j} = 0 or i = j, 
     -- m_{i,j} = log(to * n_{i,j} / s_{i,j}) otherwise.
     mi = (.*) (matrixEye n)
-              (map (lift1 (\x -> let x' = x * to in cond (x' < 1) 0 (log x'))) ((./) m ss))
+              (map (lift1 (\x -> let x' = x * to in cond (x' < 0.5) 0 (log x'))) ((./) m ss))
+              -- (map (lift1 (\x -> let x' = x * to in cond (x' < 1) 0 (log x'))) ((./) m ss))
     -- mi_nnz :: Int
     -- mi_nnz = flip indexArray Z . run $
     --   foldAll (+) 0 $ map (\a -> ifThenElse (abs a < 10^(-6 :: Exp Int)) 0 1) mi

src/Gargantext/Core/Viz/Phylo/API/Tools.hs

@@ -76,7 +76,8 @@ phylo2dot2json phylo = do
         fileDot  = dirPath </> "phylo.dot"
         fileToJson = dirPath </> "output.json"
 
-    dotToFile fileFrom (toPhyloExport phylo)
+    phyloContent <- phylo2dot phylo
+    writeFile fileFrom phyloContent
 
     -- parsing a file can be done with:
     -- runParser' (Data.GraphViz.Parsing.parse :: Parse (Data.GraphViz.DotGraph Text)) $ TL.fromStrict f
@@ -91,6 +92,20 @@ phylo2dot2json phylo = do
       Just v  -> pure v
 
 
+phylo2dot :: Phylo -> IO Text
+phylo2dot phylo = do
+  withTempDirectory "/tmp" "phylo" $ \dirPath -> do
+    let fileFrom = dirPath </> "phyloFrom.dot"
+
+    dotToFile fileFrom (toPhyloExport phylo)
+
+    value <- readFile fileFrom
+
+    case value of
+      ""  -> panic "[G.C.V.Phylo.API.phylo2dot] Error no file"
+      _   -> pure value
+
+
 flowPhyloAPI :: (HasNodeStory env err m, HasNodeError err, MonadLogger m)
              => PhyloConfig -> CorpusId -> m Phylo
 flowPhyloAPI config cId = do

test/Test/Offline/JSON.hs

@@ -7,22 +7,22 @@
 module Test.Offline.JSON (tests) where
 
 import Data.Aeson
+import Data.ByteString qualified as B
+import Data.ByteString.Lazy.Char8 qualified as C8
 import Data.Either
 import Gargantext.API.Errors
 import Gargantext.API.Node.Corpus.New
 import Gargantext.API.Node.Corpus.Types
+import Gargantext.API.Node.Types
 import Gargantext.Core.Types.Phylo
 import Gargantext.Core.Viz.Phylo.API
+import Gargantext.Database.Admin.Types.Node
+import Paths_gargantext
 import Prelude
 import Test.Tasty
 import Test.Tasty.HUnit
 import Test.Tasty.QuickCheck
 import Text.RawString.QQ
-import qualified Data.ByteString as B
-import qualified Data.ByteString.Lazy.Char8 as C8
-
-import Paths_gargantext
-import Gargantext.Database.Admin.Types.Node
 
 jsonRoundtrip :: (Show a, FromJSON a, ToJSON a, Eq a) => a -> Property
 jsonRoundtrip a =