[refactor] some more imports refactoring

gargantext.cabal

@@ -160,7 +160,6 @@ library
       Gargantext.Core.Types.Phylo
       Gargantext.Core.Utils
       Gargantext.Core.Utils.Prefix
-      Gargantext.Core.Viz.Graph
       Gargantext.Core.Viz.Graph.Index
       Gargantext.Core.Viz.Graph.Tools
       Gargantext.Core.Viz.Graph.Tools.IGraph
@@ -327,6 +326,7 @@ library
       Gargantext.Core.Utils.DateUtils
       Gargantext.Core.Viz
       Gargantext.Core.Viz.Chart
+      Gargantext.Core.Viz.Graph
       Gargantext.Core.Viz.Graph.API
       Gargantext.Core.Viz.Graph.Bridgeness
       Gargantext.Core.Viz.Graph.FGL

src/Gargantext/API/Ngrams/Tools.hs

@@ -47,7 +47,6 @@ import Gargantext.Core.NodeStory (ArchiveList, HasNodeStory, NodeListStory, a_hi
 import Gargantext.Core.Types (ListType(..), NodeId, ListId)
 import Gargantext.Database.Action.Metrics.NgramsByContext (getOccByNgramsOnlyFast)
 import Gargantext.Database.Query.Table.Ngrams qualified as TableNgrams
-import Gargantext.Database.Query.Table.Node.Error (HasNodeError)
 import Gargantext.Database.Schema.Ngrams (NgramsType)
 import Gargantext.Prelude hiding ((%))
 import Gargantext.Prelude.Clock (hasTime, getTime)
@@ -68,7 +67,7 @@ getRepo listIds = do
 
 
 getNodeStory :: HasNodeStory env err m
-           => ListId -> m ArchiveList
+             => ListId -> m ArchiveList
 getNodeStory l = do
   f <- getNodeListStory
   liftBase $ f l
@@ -118,10 +117,10 @@ getListNgrams nodeIds ngramsType = listNgramsFromRepo nodeIds ngramsType
                                  <$> getRepo nodeIds
 
 
-getTermsWith :: (HasNodeStory env err m, Eq a, Hashable a)
-          => (NgramsTerm -> a) -> [ListId]
-          -> NgramsType -> Set ListType
-          -> m (HashMap a [a])
+getTermsWith :: (HasNodeStory env err m, Hashable a)
+             => (NgramsTerm -> a) -> [ListId]
+             -> NgramsType -> Set ListType
+             -> m (HashMap a [a])
 getTermsWith f ls ngt lts  = HM.fromListWith (<>)
                       <$> map toTreeWith
                       <$> HM.toList
@@ -256,8 +255,7 @@ dumpJsonTableMap fpath nodeId ngramsType = do
 -- | Helper function to set scores on an `NgramsTable`.
 setNgramsTableScores :: forall env err m t.
                         ( Each t t NgramsElement NgramsElement
-                        , HasNodeStory env err m
-                        , HasNodeError err )
+                        , HasNodeStory env err m )
                      => NodeId
                      -> ListId
                      -> TableNgrams.NgramsType

src/Gargantext/API/Node/Update.hs

@@ -31,8 +31,7 @@ import Gargantext.Core.Methods.Similarities (GraphMetric(..))
 import Gargantext.Core.NodeStory (HasNodeStory)
 import Gargantext.Core.Types.Main (ListType(..))
 import Gargantext.Core.Viz.Graph.API (recomputeGraph)
-import Gargantext.Core.Viz.Graph.Tools (PartitionMethod(..), BridgenessMethod(..))
-import Gargantext.Core.Viz.Graph.Types (Strength)
+import Gargantext.Core.Viz.Graph.Types (PartitionMethod(..), BridgenessMethod(..), Strength)
 import Gargantext.Core.Viz.Phylo (PhyloSubConfigAPI(..), subConfigAPI2config)
 import Gargantext.Core.Viz.Phylo.API.Tools (flowPhyloAPI)
 import Gargantext.Database.Action.Flow (reIndexWith)

src/Gargantext/Core/Methods/Graph/MaxClique.hs

@@ -50,7 +50,7 @@ def fast_maximal_cliques(g):
 
 
 module Gargantext.Core.Methods.Graph.MaxClique
-  where
+where
 
 import Data.Graph.Inductive hiding (Graph, neighbors, subgraph, (&))
 import Data.List (nub)
@@ -59,7 +59,8 @@ import Data.Set (fromList, isSubsetOf)
 import Gargantext.Core.Methods.Similarities (Similarity)
 import Gargantext.Core.Viz.Graph.FGL (Graph_Undirected, degree, neighbors, mkGraphUfromEdges)
 import Gargantext.Core.Viz.Graph.Index (createIndices, toIndex)
-import Gargantext.Core.Viz.Graph.Tools (cooc2graph',cooc2graph'', Threshold)
+import Gargantext.Core.Viz.Graph.Tools (cooc2graph',cooc2graph'')
+import Gargantext.Core.Viz.Graph.Types (Threshold)
 import Gargantext.Core.Viz.Phylo
 import Gargantext.Prelude
 

src/Gargantext/Core/Viz/Chart.hs

@@ -17,6 +17,7 @@ module Gargantext.Core.Viz.Chart
 import Data.HashMap.Strict qualified as HashMap
 import Data.List qualified as List
 import Data.Map.Strict (toList)
+import Data.Set qualified as Set
 import Data.Vector qualified as V
 import Gargantext.API.Ngrams.NgramsTree
 import Gargantext.API.Ngrams.Tools
@@ -34,7 +35,6 @@ import Gargantext.Database.Query.Table.NodeContext (selectDocsDates)
 import Gargantext.Database.Schema.Ngrams
 import Gargantext.Database.Schema.Node
 import Gargantext.Prelude hiding (toList)
-import qualified Data.Set            as Set
 
 
 histoData :: CorpusId -> DBCmd err Histo

src/Gargantext/Core/Viz/Graph.hs

@@ -9,18 +9,22 @@ Portability : POSIX
 
 -}
 
-{-# LANGUAGE TemplateHaskell      #-}
-
 module Gargantext.Core.Viz.Graph
-  where
+  ( -- REPL utilities
+    graphV3ToGraph
+  , graphV3ToGraphWithFiles
+  , mergeGraphNgrams
+  , readGraphFromJson
+  )
+where
 
 import Data.Aeson qualified as DA
 import Data.ByteString.Lazy as DBL (readFile, writeFile)
 import Data.HashMap.Strict (HashMap, lookup)
 import Data.Text qualified as Text
 import Gargantext.API.Ngrams.Types (NgramsTerm(..), NgramsRepoElement(..), mSetToList)
-import Gargantext.Core.Viz.Graph.Types
-import Gargantext.Database.Admin.Types.Hyperdata.Prelude
+import Gargantext.Core.Viz.Graph.Types (Attributes(..), AttributesV3(..), Edge(..), EdgeV3(..), Graph(..), GraphV3(..), Node(..), NodeV3(..), graph_nodes)
+import Gargantext.Database.Admin.Types.Hyperdata.Prelude (set)
 import Gargantext.Database.Schema.Ngrams (NgramsType(..))
 import Gargantext.Prelude
 import Text.Read qualified as Text

src/Gargantext/Core/Viz/Graph/API.hs

@@ -16,7 +16,7 @@ Portability : POSIX
 {-# LANGUAGE TypeOperators     #-}
 
 module Gargantext.Core.Viz.Graph.API
-  where
+where
 
 import Control.Lens (set, (^.), _Just, (^?), at)
 import Data.Aeson
@@ -31,9 +31,9 @@ import Gargantext.API.Prelude (GargM, GargServer)
 import Gargantext.Core.Methods.Similarities (Similarity(..), GraphMetric(..), withMetric)
 import Gargantext.Core.NodeStory (HasNodeStory, NodeListStory, a_version, unNodeStory)
 import Gargantext.Core.Types.Main (ListType(MapTerm))
-import Gargantext.Core.Viz.Graph.GEXF ()
-import Gargantext.Core.Viz.Graph.Tools -- (cooc2graph)
-import Gargantext.Core.Viz.Graph.Types (Graph, GraphMetadata(..), HyperdataGraph(..), HyperdataGraphAPI(..), LegendField(..), ListForGraph(..), MultiPartite(..), Partite(..), Strength(Strong), hyperdataGraph, gm_edgesStrength, gm_list, gm_metric, gm_startForceAtlas, graph_metadata, hyperdataCamera, lfg_version)
+import Gargantext.Core.Viz.Graph.GEXF ()  -- MimeRender instances
+import Gargantext.Core.Viz.Graph.Tools (cooc2graphWith)
+import Gargantext.Core.Viz.Graph.Types (BridgenessMethod(..), Graph, GraphMetadata(..), HyperdataGraph(..), HyperdataGraphAPI(..), LegendField(..), ListForGraph(..), MultiPartite(..), Partite(..), PartitionMethod(..), Strength(Strong), hyperdataGraph, gm_edgesStrength, gm_list, gm_metric, gm_startForceAtlas, graph_metadata, hyperdataCamera, lfg_version)
 import Gargantext.Database.Action.Metrics.NgramsByContext (getContextsByNgramsOnlyUser)
 import Gargantext.Database.Action.Node (mkNodeWithParent)
 import Gargantext.Database.Admin.Config (userMaster)

src/Gargantext/Core/Viz/Graph/Tools.hs

@@ -14,61 +14,41 @@ Portability : POSIX
 {-# LANGUAGE BangPatterns, ScopedTypeVariables #-}
 
 module Gargantext.Core.Viz.Graph.Tools
-  where
+  ( cooc2graph'
+  , cooc2graph''
+  , cooc2graphWith
+  , doSimilarityMap )
+where
 
-import Data.Aeson
 import Data.HashMap.Strict (HashMap)
 import Data.HashMap.Strict qualified as HashMap
 import Data.HashSet qualified as HashSet
 import Data.List qualified as List
 import Data.Map.Strict qualified as Map
 import Data.Set qualified as Set
-import Data.Swagger hiding (items)
 import Data.Text qualified as Text
 import Data.Vector.Storable qualified as Vec
 import Gargantext.API.Ngrams.Types (NgramsTerm(..))
 import Gargantext.Core.Methods.Similarities (Similarity(..), measure)
-import Gargantext.Core.Statistics
+import Gargantext.Core.Statistics (Dimension(..), pcaReduceTo)
 import Gargantext.Core.Viz.Graph.Bridgeness (bridgeness, Bridgeness(..), Partitions, nodeId2comId, {-recursiveClustering,-} recursiveClustering', setNodes2clusterNodes)
 import Gargantext.Core.Viz.Graph.Index (createIndices, toIndex, map2mat, mat2map, Index, MatrixShape(..))
-import Gargantext.Core.Viz.Graph.Tools.IGraph (mkGraphUfromEdges, spinglass, spinglass')
+import Gargantext.Core.Viz.Graph.Tools.IGraph (spinglass, spinglass')
 import Gargantext.Core.Viz.Graph.Tools.Infomap (infomap)
-import Gargantext.Core.Viz.Graph.Types (Attributes(..), Edge(..), Graph(..), MultiPartite(..), Node(..), Partite(..), Strength(..))
+import Gargantext.Core.Viz.Graph.Types (Attributes(..), BridgenessMethod(..), Edge(..), Graph(..), Layout(..), MultiPartite(..), Node(..), Occurrences, Partite(..), PartitionMethod(..), Strength(..), Threshold)
 import Gargantext.Core.Viz.Graph.Utils (edgesFilter, nodesFilter)
 import Gargantext.Database.Schema.Ngrams (NgramsType(..))
 import Gargantext.Prelude
 import Graph.BAC.ProxemyOptim qualified as BAC
 import Graph.Types (ClusterNode)
-import IGraph qualified as Igraph
-import IGraph.Algorithms.Layout qualified as Layout
-import IGraph.Random -- (Gen(..))
-import Test.QuickCheck (elements)
-import Test.QuickCheck.Arbitrary
-
-data PartitionMethod = Spinglass | Confluence | Infomap
-    deriving (Generic, Eq, Ord, Enum, Bounded, Show)
-instance FromJSON  PartitionMethod
-instance ToJSON    PartitionMethod
-instance ToSchema  PartitionMethod
-instance Arbitrary PartitionMethod where
-  arbitrary = elements [ minBound .. maxBound ]
-
-data BridgenessMethod = BridgenessMethod_Basic | BridgenessMethod_Advanced
-    deriving (Generic, Eq, Ord, Enum, Bounded, Show)
-instance FromJSON  BridgenessMethod
-instance ToJSON    BridgenessMethod
-instance ToSchema  BridgenessMethod
-instance Arbitrary BridgenessMethod where
-  arbitrary = elements [ minBound .. maxBound ]
 
 
 -------------------------------------------------------------
-defaultClustering :: Map (Int, Int) Double -> IO [ClusterNode]
--- defaultClustering x = pure $ BAC.defaultClustering x
-defaultClustering x = spinglass 1 x
+-- defaultClustering :: Map (Int, Int) Double -> IO [ClusterNode]
+-- -- defaultClustering x = pure $ BAC.defaultClustering x
+-- defaultClustering x = spinglass 1 x
 
 -------------------------------------------------------------
-type Threshold = Double
 
 cooc2graph' :: Ord t => Similarity
                      -> Double
@@ -156,8 +136,6 @@ cooc2graphWith' _doPartitions _bridgenessMethod multi similarity@Distributional
 
 
 
-type Reverse = Bool
-
 doSimilarityMap :: Similarity
               -> Threshold
               -> Strength
@@ -220,7 +198,6 @@ doSimilarityMap distriType threshold strength myCooc = (distanceMap, toIndex ti
 
 ----------------------------------------------------------
 -- | From data to Graph
-type Occurrences      = Int
 
 nodeTypeWith :: MultiPartite -> NgramsTerm -> NgramsType
 nodeTypeWith (MultiPartite (Partite s1 t1) (Partite _s2 t2)) t =
@@ -283,13 +260,11 @@ data2graph multi labels' occurences bridge conf partitions =
 
 ------------------------------------------------------------------------
 
-data Layout = KamadaKawai | ACP | ForceAtlas
 
-
-setCoord' :: (Int -> (Double, Double)) -> (Int, Node) -> Node
-setCoord' f (i,n) = n { node_x_coord = x, node_y_coord = y }
-  where
-    (x,y) = f i
+-- setCoord' :: (Int -> (Double, Double)) -> (Int, Node) -> Node
+-- setCoord' f (i,n) = n { node_x_coord = x, node_y_coord = y }
+--   where
+--     (x,y) = f i
 
 
 -- | ACP
@@ -334,16 +309,16 @@ getCoord ACP labels m n = to2d $ maybe (panic "Graph.Tools no coordinate") ident
     toVec n' ns' m'' = (n', Vec.fromList $ map (\n'' -> maybe 0 identity $ Map.lookup (n',n'') m'') ns')
 ------------------------------------------------------------------------
 
--- | KamadaKawai Layout
--- TODO TEST: check labels, nodeId and coordinates
-layout :: Map (Int, Int) Double -> Int -> Gen -> (Double, Double)
-layout m n gen = maybe (panic "") identity $ Map.lookup n $ coord
-  where
-    coord :: (Map Int (Double,Double))
-    coord = Map.fromList $ List.zip (Igraph.nodes g) $ (Layout.layout g p gen)
-    --p = Layout.defaultLGL
-    p = Layout.kamadaKawai
-    g = mkGraphUfromEdges $ map fst $ List.filter (\e -> snd e > 0) $ Map.toList m
+-- -- | KamadaKawai Layout
+-- -- TODO TEST: check labels, nodeId and coordinates
+-- layout :: Map (Int, Int) Double -> Int -> Gen -> (Double, Double)
+-- layout m n gen = maybe (panic "") identity $ Map.lookup n $ coord
+--   where
+--     coord :: (Map Int (Double,Double))
+--     coord = Map.fromList $ List.zip (Igraph.nodes g) $ (Layout.layout g p gen)
+--     --p = Layout.defaultLGL
+--     p = Layout.kamadaKawai
+--     g = mkGraphUfromEdges $ map fst $ List.filter (\e -> snd e > 0) $ Map.toList m
 
 -----------------------------------------------------------------------------
 -- MISC Tools

src/Gargantext/Core/Viz/Graph/Tools/IGraph.hs

@@ -13,50 +13,51 @@ Reference:
 -}
 
 module Gargantext.Core.Viz.Graph.Tools.IGraph
-  where
-
-import Data.Serialize
+  ( spinglass
+  , spinglass' )
+where
+
+import Data.List qualified as List
+import Data.Map.Strict qualified as Map
+import Data.Serialize (Serialize)
+import Data.Set qualified as Set
 import Data.Singletons (SingI)
-import Gargantext.Core.Viz.Graph.Index
+import Gargantext.Core.Viz.Graph.Index (createIndices, toIndex)
+import Gargantext.Prelude
 import Graph.Types (ClusterNode(..))
 import IGraph hiding (mkGraph, neighbors, edges, nodes, Node, Graph)
-import Protolude
-import Gargantext.Prelude (saveAsFileDebug)
-import qualified Data.List                   as List
-import qualified Data.Map.Strict             as Map
-import qualified IGraph                      as IG
-import qualified IGraph.Algorithms.Clique    as IG
-import qualified IGraph.Algorithms.Community as IG
-import qualified IGraph.Algorithms.Structure as IG
-import qualified IGraph.Random               as IG
-import qualified Data.Set                    as Set
+import IGraph qualified as IG
+import IGraph.Algorithms.Community qualified as IG
+import IGraph.Algorithms.Structure qualified as IG
+import IGraph.Random qualified as IG
+-- import IGraph.Algorithms.Clique qualified as IG
 
 ------------------------------------------------------------------
 -- | Main Types
 type Graph_Undirected = IG.Graph 'U () ()
-type Graph_Directed   = IG.Graph 'D () ()
+-- type Graph_Directed   = IG.Graph 'D () ()
 
-type Node  = IG.Node
-type Graph = IG.Graph
+-- type Node  = IG.Node
+-- type Graph = IG.Graph
 
 ------------------------------------------------------------------
 -- | Main Graph management Functions
-neighbors :: IG.Graph d v e -> IG.Node -> [IG.Node]
-neighbors = IG.neighbors
+-- neighbors :: IG.Graph d v e -> IG.Node -> [IG.Node]
+-- neighbors = IG.neighbors
 
-edges :: IG.Graph d v e -> [Edge]
-edges = IG.edges
+-- edges :: IG.Graph d v e -> [Edge]
+-- edges = IG.edges
 
-nodes :: IG.Graph d v e -> [IG.Node]
-nodes = IG.nodes
+-- nodes :: IG.Graph d v e -> [IG.Node]
+-- nodes = IG.nodes
 
 ------------------------------------------------------------------
 -- | Partitions
-maximalCliques :: IG.Graph d v e -> [[Int]]
-maximalCliques g = IG.maximalCliques g (min',max')
-  where
-    min' = 0
-    max' = 0
+-- maximalCliques :: IG.Graph d v e -> [[Int]]
+-- maximalCliques g = IG.maximalCliques g (min',max')
+--   where
+--     min' = 0
+--     max' = 0
 
 ------------------------------------------------------------------
 type Seed = Int

src/Gargantext/Core/Viz/Graph/Types.hs

@@ -246,6 +246,30 @@ instance FromField HyperdataGraphAPI
 
 
 
+data PartitionMethod = Spinglass | Confluence | Infomap
+    deriving (Generic, Eq, Ord, Enum, Bounded, Show)
+instance FromJSON  PartitionMethod
+instance ToJSON    PartitionMethod
+instance ToSchema  PartitionMethod
+instance Arbitrary PartitionMethod where
+  arbitrary = elements [ minBound .. maxBound ]
+
+data BridgenessMethod = BridgenessMethod_Basic | BridgenessMethod_Advanced
+    deriving (Generic, Eq, Ord, Enum, Bounded, Show)
+instance FromJSON  BridgenessMethod
+instance ToJSON    BridgenessMethod
+instance ToSchema  BridgenessMethod
+instance Arbitrary BridgenessMethod where
+  arbitrary = elements [ minBound .. maxBound ]
+
+
+
+data Layout = KamadaKawai | ACP | ForceAtlas
+
+type Occurrences      = Int
+type Threshold = Double
+type Reverse = Bool
+
 
 ---------------------- defaults
 

src/Gargantext/Database/Action/Flow.hs

@@ -282,8 +282,7 @@ addDocumentsToHyperCorpus ncs mb_hyper la corpusId docs = do
 
 ------------------------------------------------------------------------
 
-flowCorpusUser :: ( HasNodeError err
-                  , HasValidationError err
+flowCorpusUser :: ( HasValidationError err
                   , HasNLPServer env
                   , HasTreeError err
                   , HasNodeStory env err m

src/Gargantext/Database/Action/Flow/Utils.hs

@@ -73,7 +73,8 @@ import Gargantext.Prelude
 import Gargantext.Prelude.Crypto.Hash (Hash)
 
 
-createNodes :: ( DbCmd' env err m, HasNodeError err
+createNodes :: ( DbCmd' env err m
+               , HasNodeError err
                , MkCorpus c
                )
             => User
@@ -156,9 +157,7 @@ docNgrams lang nt ts doc =
         
 -- TODO Type NodeDocumentUnicised
 insertDocs :: ( DbCmd' env err m
-              -- , FlowCorpus a
               , FlowInsertDB a
-              , HasNodeError err
               )
               => UserId
               -> CorpusId
@@ -210,8 +209,7 @@ insertMasterDocs ncs c lang hs  =  do
 
 
 
-buildSocialList :: ( HasNodeError err
-                   , HasValidationError err
+buildSocialList :: ( HasValidationError err
                    , HasNLPServer env
                    , HasTreeError err
                    , HasNodeStory env err m
@@ -294,9 +292,7 @@ toInserted =
 
 
 
-documentIdWithNgrams :: HasNodeError err
-                     => (a
-                     -> DBCmd err (HashMap.HashMap b (Map NgramsType Int, TermsCount)))
+documentIdWithNgrams :: (a -> DBCmd err (HashMap.HashMap b (Map NgramsType Int, TermsCount)))
                      -> [Indexed NodeId a]
                      -> DBCmd err [DocumentIdWithNgrams a b]
 documentIdWithNgrams f = traverse toDocumentIdWithNgrams

test/Test/Graph/Clustering.hs

@@ -17,7 +17,6 @@ import Data.HashMap.Strict qualified as HashMap
 import Data.List qualified as List
 import Gargantext.API.Ngrams.Types (NgramsTerm(..))
 import Gargantext.Core.Methods.Similarities (Similarity(..))
--- import Gargantext.Core.Viz.Graph
 import Gargantext.Core.Viz.Graph.Tools (doSimilarityMap)
 import Gargantext.Core.Viz.Graph.Tools.IGraph (spinglass)
 import Gargantext.Core.Viz.Graph.Types

test/Test/Ngrams/Query/PaginationCorpus.hs

+{-|
+Module      : Test.Ngrams.Query.PaginationCorpus
+Description : Tests
+Copyright   : (c) CNRS, 2024-Present
+License     : AGPL + CECILL v3
+Maintainer  : team@gargantext.org
+Stability   : experimental
+Portability : POSIX
+
+-}
+
 {-# LANGUAGE ScopedTypeVariables #-}
+
 module Test.Ngrams.Query.PaginationCorpus where
 
 import           Prelude
 
 import           Data.Aeson
 import           Data.Map.Strict (Map)
-import           Gargantext.API.Ngrams
 import           Gargantext.API.Ngrams.Types
 import           Gargantext.Core.Types.Main
 import           Gargantext.Database.Admin.Types.Node