[graph] some refactoring of Core.Viz.Graph

gargantext.cabal

 cabal-version: 1.12
 
--- This file has been generated from package.yaml by hpack version 0.35.1.
+-- This file has been generated from package.yaml by hpack version 0.34.7.
 --
 -- see: https://github.com/sol/hpack
 
 name:           gargantext
-version: 0.0.6.9.1
+version:        0.0.6.9.1
 synopsis:       Search, map, share
 description:    Please see README.md
 category:       Data
@@ -232,6 +232,7 @@ library
       Gargantext.Core.Viz.Graph.FGL
       Gargantext.Core.Viz.Graph.GEXF
       Gargantext.Core.Viz.Graph.Legend
+      Gargantext.Core.Viz.Graph.PatriciaTreeTypes
       Gargantext.Core.Viz.Graph.Tools.Infomap
       Gargantext.Core.Viz.Graph.Types
       Gargantext.Core.Viz.Graph.Utils

src/Gargantext/API/GraphQL/Context.hs

@@ -184,7 +184,7 @@ toHyperdataRowDocumentGQL hyperdata =
                                      , hrd_uniqId             = _hr_uniqId
                                      , hrd_uniqIdBdd          = _hr_uniqIdBdd
                                      }
-    HyperdataRowContact _ _ _ -> Nothing
+    HyperdataRowContact { } -> Nothing
 
 updateNodeContextCategory :: (HasConnectionPool env, HasConfig env, HasMail env, HasSettings env) =>
                              NodeContextCategoryMArgs -> GqlM' e env [Int]

src/Gargantext/API/Node/Update.hs

@@ -29,9 +29,9 @@ import Gargantext.API.Ngrams.List (reIndexWith)
 import Gargantext.API.Prelude (GargM, GargError, simuLogs)
 import Gargantext.Core.Methods.Similarities (GraphMetric(..))
 import Gargantext.Core.Types.Main (ListType(..))
-import Gargantext.Core.Viz.Graph (Strength)
 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.Phylo (PhyloSubConfig(..), subConfig2config)
 import Gargantext.Core.Viz.Phylo.API.Tools (flowPhyloAPI)
 import Gargantext.Database.Action.Flow.Pairing (pairing)

src/Gargantext/Core/Viz.hs

@@ -14,4 +14,3 @@ Vizualisation of text stats
 
 module Gargantext.Core.Viz
   where
-

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

@@ -30,9 +30,9 @@ import Gargantext.API.Prelude
 import Gargantext.Core.Methods.Similarities (Similarity(..), GraphMetric(..), withMetric)
 import Gargantext.Core.NodeStory
 import Gargantext.Core.Types.Main
-import Gargantext.Core.Viz.Graph
 import Gargantext.Core.Viz.Graph.GEXF ()
 import Gargantext.Core.Viz.Graph.Tools -- (cooc2graph)
+import Gargantext.Core.Viz.Graph.Types
 import Gargantext.Database.Action.Metrics.NgramsByContext (getContextsByNgramsOnlyUser)
 import Gargantext.Database.Action.Flow.Types (FlowCmdM)
 import Gargantext.Database.Action.Node (mkNodeWithParent)

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

@@ -19,18 +19,17 @@ module Gargantext.Core.Viz.Graph.GEXF
   where
 
 import Gargantext.Prelude
-import Gargantext.Core.Viz.Graph
 import qualified Data.HashMap.Lazy as HashMap
 import qualified Gargantext.Prelude as P
-import qualified Gargantext.Core.Viz.Graph as G
+import qualified Gargantext.Core.Viz.Graph.Types as G
 import qualified Xmlbf as Xmlbf
 import Prelude (error)
 
 -- Converts to GEXF format
 -- See https://gephi.org/gexf/format/
-instance Xmlbf.ToXml Graph where
-  toXml (Graph { _graph_nodes = graphNodes
-                , _graph_edges = graphEdges }) = root graphNodes graphEdges
+instance Xmlbf.ToXml G.Graph where
+  toXml (G.Graph { _graph_nodes = graphNodes
+                 , _graph_edges = graphEdges }) = root graphNodes graphEdges
     where
       root :: [G.Node] -> [G.Edge] -> [Xmlbf.Node]
       root gn ge =
@@ -77,5 +76,5 @@ instance Xmlbf.ToXml Graph where
 
 -- just to be able to derive a client for the entire gargantext API,
 -- we however want to avoid sollicitating this instance
-instance Xmlbf.FromXml Graph where
+instance Xmlbf.FromXml G.Graph where
   fromXml = error "FromXml Graph: not defined, just a placeholder"

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

+{-| Module      : Gargantext.Core.Viz.Graph.PatriciaTreeTypes
+Description :
+Copyright   : (c) CNRS, Alexandre Delanoë
+License     : AGPL + CECILL v3
+Maintainer  : contact@gargantext.org
+Stability   : experimental
+Portability : POSIX
+
+-}
+
+module Gargantext.Core.Viz.Graph.PatriciaTreeTypes where
+
+import qualified Data.Graph.Inductive.PatriciaTree as DGIP
+-- import Data.IntMap (IntMap)
+-- import qualified Eigen.Matrix as DenseMatrix
+-- import Eigen.SparseMatrix (SparseMatrix)
+
+--import qualified Data.Matrix.Sparse.Static    as Sparse
+-- import qualified Data.Vector.Unboxed          as VU
+-- import qualified Numeric.LinearAlgebra.Static as Dense
+import Protolude hiding (sum, natVal)
+
+-- | Main Types use in this libray
+
+type Dict = IntMap
+
+-- | Use the optimized version of Graph
+type Graph a b = DGIP.Gr a b
+
+-- | Type for Matrix computation optimizations (with Eigen)
+-- type MatrixD          n = Dense.L n n
+-- type MatrixS          n = Sparse.Matrix n n Double

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

@@ -25,11 +25,11 @@ import Gargantext.API.Ngrams.Types (NgramsTerm(..))
 import Gargantext.Core.Methods.Similarities (Similarity(..), measure)
 import Gargantext.Core.Methods.Similarities.Conditional (conditional)
 import Gargantext.Core.Statistics
-import Gargantext.Core.Viz.Graph
 import Gargantext.Core.Viz.Graph.Bridgeness (bridgeness, Bridgeness(..), Partitions, nodeId2comId)
 import Gargantext.Core.Viz.Graph.Index (createIndices, toIndex, map2mat, mat2map, Index, MatrixShape(..))
 import Gargantext.Core.Viz.Graph.Tools.IGraph (mkGraphUfromEdges, spinglass)
 import Gargantext.Core.Viz.Graph.Tools.Infomap (infomap)
+import Gargantext.Core.Viz.Graph.Types (Attributes(..), Edge(..), Graph(..), MultiPartite(..), Node(..), Partite(..), Strength(..))
 import Gargantext.Database.Schema.Ngrams (NgramsType(..))
 import Gargantext.Core.Viz.Graph.Utils (edgesFilter, nodesFilter)
 import Gargantext.Prelude
@@ -242,6 +242,7 @@ data2graph multi labels' occurences bridge conf partitions =
     (bridge', toKeep) = nodesFilter (\v -> v > 1) bridge
 
     edges = [ Edge { edge_source = cs (show s)
+                   , edge_hidden = Nothing
                    , edge_target = cs (show t)
                    , edge_weight = weight
                    , edge_confluence = maybe 0 identity $ Map.lookup (s,t) conf
@@ -340,7 +341,7 @@ cooc2graph'' distance threshold myCooc = neighbourMap
 -- Quentin
 filterByNeighbours :: Double -> Map (Index, Index) Double -> Map (Index, Index) Double
 filterByNeighbours threshold distanceMap = filteredMap
-  where 
+  where
     indexes :: [Index]
     indexes = List.nub $ List.concat $ map (\(idx,idx') -> [idx,idx'] ) $ Map.keys distanceMap
     filteredMap :: Map (Index, Index) Double
@@ -354,4 +355,3 @@ filterByNeighbours threshold distanceMap = filteredMap
                                        $ Map.filterWithKey (\(from,_) _ -> idx == from) distanceMap
                            in List.take (round threshold) selected
                       ) indexes
-

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

@@ -10,6 +10,7 @@ Portability : POSIX
 -}
 
 
+{-# OPTIONS_GHC -fno-warn-unused-imports #-}
 
 module Gargantext.Database.Admin.Types.Hyperdata
   ( module Gargantext.Database.Admin.Types.Hyperdata.Any
@@ -26,7 +27,7 @@ module Gargantext.Database.Admin.Types.Hyperdata
   , module Gargantext.Database.Admin.Types.Hyperdata.Texts
   , module Gargantext.Database.Admin.Types.Hyperdata.Phylo
   , module Gargantext.Database.Admin.Types.Hyperdata.User
-  , module Gargantext.Core.Viz.Graph
+  , module Gargantext.Core.Viz.Graph.Types
   )
   where
 
@@ -44,4 +45,4 @@ import Gargantext.Database.Admin.Types.Hyperdata.Prelude (Hyperdata)
 import Gargantext.Database.Admin.Types.Hyperdata.Texts
 import Gargantext.Database.Admin.Types.Hyperdata.Phylo
 import Gargantext.Database.Admin.Types.Hyperdata.User
-import Gargantext.Core.Viz.Graph (HyperdataGraph(..), defaultHyperdataGraph)
+import Gargantext.Core.Viz.Graph.Types (HyperdataGraph(..), defaultHyperdataGraph)

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

@@ -27,7 +27,7 @@ import Gargantext.Database.Admin.Types.Hyperdata.Prelude
 
 
 data DefaultHyperdata =
-    DefaultUser    HyperdataUser 
+    DefaultUser    HyperdataUser
   | DefaultContact HyperdataContact
 
   | DefaultCorpus    HyperdataCorpus

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

@@ -11,7 +11,7 @@ Portability : POSIX
 
 
 module Gargantext.Database.Admin.Types.Hyperdata.Prelude
-  ( module Control.Lens 
+  ( module Control.Lens
   , module Data.Aeson
   , module Data.Aeson.TH
   , module Data.Aeson.Types
@@ -66,8 +66,3 @@ data Chart =
 instance ToJSON Chart
 instance FromJSON Chart
 instance ToSchema Chart
-
-
-
-
-