[louvain] experimental graphology louvain plugin usage

package.json

@@ -42,6 +42,7 @@
         "echarts-for-react": "^3.0.1",
         "esbuild": "^0.15.7",
         "graphology": "^0.25.1",
+        "graphology-communities-louvain": "^2.0.1",
         "graphology-layout-forceatlas2": "^0.9.2",
         "graphology-layout-noverlap": "^0.4.2",
         "graphology-operators": "^1.6.0",

src/Gargantext/Components/Forest/Tree/Node.purs

@@ -362,7 +362,7 @@ nodeSpanCpt = here.component "nodeSpan" cpt
           R2.when isSelected $
 
             H.div
-            { class: "mainleaf-selection-indicator" }
+            { className: "mainleaf-selection-indicator" }
             []
         ]
 

src/Gargantext/Components/GraphExplorer/Layout.purs

@@ -11,6 +11,7 @@ import Data.Maybe (Maybe(..), fromJust)
 import Data.Nullable (null, Nullable)
 import Data.Sequence as Seq
 import Data.Set as Set
+import Data.Traversable (traverse_)
 import Data.Tuple (Tuple(..))
 import Effect (Effect)
 import Gargantext.Components.App.Store as AppStore
@@ -26,11 +27,14 @@ import Gargantext.Components.GraphExplorer.Types (GraphSideDoc)
 import Gargantext.Components.GraphExplorer.Types as GET
 import Gargantext.Components.GraphExplorer.Utils as GEU
 import Gargantext.Config (defaultFrontends)
-import Gargantext.Data.Louvain as Louvain
+import Gargantext.Data.Louvain as DLouvain
 import Gargantext.Hooks.Session (useSession)
 import Gargantext.Hooks.Sigmax.ForceAtlas2 as ForceAtlas
+import Gargantext.Hooks.Sigmax.Graphology as Graphology
+import Gargantext.Hooks.Sigmax.Louvain as Louvain
 import Gargantext.Hooks.Sigmax.Noverlap as Noverlap
 import Gargantext.Hooks.Sigmax as Sigmax
+import Gargantext.Hooks.Sigmax.Sigma as SigmaxS
 import Gargantext.Hooks.Sigmax.Types as SigmaxT
 import Gargantext.Types as GT
 import Gargantext.Types as Types
@@ -241,7 +245,6 @@ graphViewCpt = R.memo' $ here.component "graphView" cpt where
     , removedNodeIds
     , selectedNodeIds
     , showEdges
-    , showLouvain
     , graph
     } <- GraphStore.use
 
@@ -251,27 +254,39 @@ graphViewCpt = R.memo' $ here.component "graphView" cpt where
     removedNodeIds'     <- R2.useLive' removedNodeIds
     selectedNodeIds'    <- R2.useLive' selectedNodeIds
     showEdges'          <- R2.useLive' showEdges
-    showLouvain'        <- R2.useLive' showLouvain
     graph'              <- R2.useLive' graph
 
     -- | Computed
     -- |
 
-    -- TODO Cache this?
-    let louvainGraph =
-          if showLouvain' then
-            let louvain = Louvain.louvain unit in
-            let cluster = Louvain.init louvain (SigmaxT.louvainNodes graph') (SigmaxT.louvainEdges graph') in
-            SigmaxT.louvainGraph graph' cluster
-          else
-            graph'
-
-    let transformedGraph = transformGraph louvainGraph { edgeConfluence'
-                                                        , edgeWeight'
-                                                        , nodeSize'
-                                                        , removedNodeIds'
-                                                        , selectedNodeIds'
-                                                        , showEdges' }
+    let transformParams = { edgeConfluence'
+                          , edgeWeight'
+                          , nodeSize'
+                          , removedNodeIds'
+                          , selectedNodeIds'
+                          , showEdges' }
+    -- let transformedGraph = transformGraph graph' transformParams
+    transformedGraphS <- T.useBox $ transformGraph graph' transformParams
+
+    -- todo Cache this?
+    R.useEffect' $ do
+      --let louvain = Louvain.louvain unit in
+      --let cluster = Louvain.init louvain (SigmaxT.louvainNodes graph') (SigmaxT.louvainEdges graph') in
+      --SigmaxT.louvainGraph graph' cluster
+      Sigmax.dependOnSigma (R.readRef sigmaRef) "[graphView (louvainGraph)] no sigma" $ \sigma -> do
+        newGraph <- Louvain.assignVisible (SigmaxS.graph sigma) {}
+        -- here.log2 "[graphView] newGraph" newGraph
+        -- here.log2 "[graphView] nodes" $ A.fromFoldable $ Graphology.nodes newGraph
+        let cluster = Louvain.cluster newGraph :: DLouvain.LouvainCluster
+        let lgraph = SigmaxT.louvainGraph graph' cluster :: SigmaxT.SGraph
+        --T.write_ (transformGraph lgraph transformParams) transformedGraphS
+        -- apply colors
+        -- traverse_ (\{ id, color } ->
+        --   Graphology.mergeNodeAttributes (SigmaxS.graph sigma) id { color }
+        -- ) (SigmaxT.graphNodes lgraph)
+        T.write_ lgraph transformedGraphS
+
+    transformedGraph <- R2.useLive' transformedGraphS
 
     -- R.useEffect' $ do
     --   let (SigmaxT.Graph { edges: e }) = transformedGraph
@@ -303,10 +318,12 @@ convert (GET.GraphData r) = Tuple r.metaData $ SigmaxT.Graph {nodes, edges}
     nodes = foldMapWithIndex nodeFn normalizedNodes
     nodeFn :: Int -> GEGT.Node -> Seq.Seq (Record SigmaxT.Node)
     nodeFn _i nn@(GEGT.Node n) =
+      let (GEGT.Cluster { clustDefault }) = n.attributes in
       Seq.singleton {
           borderColor: color
         , children: n.children
         , color : color
+        , community : clustDefault  -- for the communities-louvain graphology plugin
         , equilateral: { numPoints: 3 }
         , gargType
         , hidden : false

src/Gargantext/Components/GraphExplorer/Store.purs

@@ -50,7 +50,7 @@ type Store =
   , nodeSize                   :: T.Box Range.NumberRange
   , nodeSizeRange              :: T.Box Range.NumberRange
   , showEdges                  :: T.Box SigmaxT.ShowEdgesState
-  , showLouvain                :: T.Box Boolean
+  --, showLouvain                :: T.Box Boolean
   , labelSize                  :: T.Box Number
   , labelRenderedSizeThreshold :: T.Box Number
   , mouseSelectorSize          :: T.Box Number
@@ -84,7 +84,7 @@ type State =
   , nodeSize                   :: Range.NumberRange
   , nodeSizeRange              :: Range.NumberRange
   , showEdges                  :: SigmaxT.ShowEdgesState
-  , showLouvain                :: Boolean
+  --, showLouvain                :: Boolean
   , labelSize                  :: Number
   , labelRenderedSizeThreshold :: Number
   , mouseSelectorSize          :: Number
@@ -110,7 +110,7 @@ options ::
   , edgeConfluence             :: Range.NumberRange
   , graphStage                 :: GET.Stage
   , nodeSize                   :: Range.NumberRange
-  , showLouvain                :: Boolean
+  --, showLouvain                :: Boolean
   , showEdges                  :: SigmaxT.ShowEdgesState
   -- Terms update
   , removedNodeIds             :: SigmaxT.NodeIds
@@ -132,7 +132,7 @@ options =
   , edgeConfluence             : Range.Closed { min: 0.0, max: 1.0 }
   , graphStage                 : GET.Init
   , nodeSize                   : Range.Closed { min: 0.0, max: 100.0 }
-  , showLouvain                : false
+  --, showLouvain                : false
   , showEdges                  : SigmaxT.EShow
   -- Terms update
   , removedNodeIds             : Set.empty

src/Gargantext/Components/GraphExplorer/Toolbar/Buttons.purs

@@ -2,7 +2,7 @@ module Gargantext.Components.GraphExplorer.Toolbar.Buttons
   ( centerButton
   , cameraButton
   , edgesToggleButton
-  , louvainToggleButton
+  , louvainButton
   , pauseForceAtlasButton
   , pauseNoverlapButton
   , resetForceAtlasButton
@@ -157,27 +157,28 @@ edgesToggleButtonCpt = here.component "edgesToggleButton" cpt
 
 ------------------------------------------------------
 
-type LouvainToggleButtonProps =
+type LouvainButtonProps =
   ( forceAtlasState :: T.Box SigmaxTypes.ForceAtlasState
-  , state           :: T.Box Boolean
+  , graph           :: T.Box SigmaxTypes.SGraph
+  , sigmaRef        :: R.Ref Sigmax.Sigma
   )
 
-louvainToggleButton :: R2.Leaf LouvainToggleButtonProps
-louvainToggleButton = R2.leaf louvainToggleButtonCpt
-louvainToggleButtonCpt :: R.Component LouvainToggleButtonProps
-louvainToggleButtonCpt = here.component "louvainToggleButton" cpt
+louvainButton :: R2.Leaf LouvainButtonProps
+louvainButton = R2.leaf louvainButtonCpt
+louvainButtonCpt :: R.Component LouvainButtonProps
+louvainButtonCpt = here.component "louvainButton" cpt
   where
-    cpt { forceAtlasState, state } _ = do
-      state' <- R2.useLive' state
+    cpt { forceAtlasState, graph, sigmaRef } _ = do
+      graph' <- R2.useLive' graph
       forceAtlasState' <- R2.useLive' forceAtlasState
 
       pure $
         B.button
-        { callback: \_ -> T.modify_ (not) state
+        { callback: \_ -> do
+             pure unit
+
         , status: SigmaxTypes.forceAtlasComponentStatus forceAtlasState'
-        , variant: state' ?
-            ButtonVariant Secondary $
-            OutlinedButtonVariant Secondary
+        , variant: OutlinedButtonVariant Secondary
         }
         [ H.text "Louvain" ]
 

src/Gargantext/Components/GraphExplorer/Toolbar/Controls.purs

@@ -11,7 +11,7 @@ import Effect.Timer (setTimeout)
 import Gargantext.Components.Bootstrap as B
 import Gargantext.Components.GraphExplorer.Resources as Graph
 import Gargantext.Components.GraphExplorer.Store as GraphStore
-import Gargantext.Components.GraphExplorer.Toolbar.Buttons (centerButton, edgesToggleButton, louvainToggleButton, pauseForceAtlasButton, pauseNoverlapButton, multiSelectEnabledButton)
+import Gargantext.Components.GraphExplorer.Toolbar.Buttons (centerButton, edgesToggleButton, louvainButton, pauseForceAtlasButton, pauseNoverlapButton, multiSelectEnabledButton)
 import Gargantext.Components.GraphExplorer.Toolbar.RangeControl (edgeConfluenceControl, nodeSizeControl)
 import Gargantext.Components.GraphExplorer.Toolbar.SlideButton (labelSizeButton, labelRenderedSizeThresholdButton, mouseSelectorSizeSlider)
 import Gargantext.Components.GraphExplorer.Types as GET
@@ -63,7 +63,6 @@ controlsCpt = R.memo' $ here.component "controls" cpt where
     , nodeSizeRange
     , selectedNodeIds
     , showEdges
-    , showLouvain
     , showSidebar
     , sideTab
     } <- GraphStore.use
@@ -200,8 +199,9 @@ controlsCpt = R.memo' $ here.component "controls" cpt where
             ,
               gap
             ,
-              louvainToggleButton { forceAtlasState
-                                  , state: showLouvain }
+              louvainButton { forceAtlasState
+                            , graph
+                            , sigmaRef }
             ]
           ]
         ,

src/Gargantext/Hooks/Sigmax/Graphology.js

@@ -74,3 +74,7 @@ export function _filterEdges(g, fn) {
     return fn(attrs);
   })
 }
+
+export function _copy(g) {
+  return g.copy();
+}

src/Gargantext/Hooks/Sigmax/Graphology.purs

@@ -37,15 +37,17 @@ foreign import _updateEachEdgeAttributes :: EffectFn2 Graph (Record Types.Edge -
 foreign import _mapEdges :: forall a. Fn2 Graph (Record Types.Edge -> a) (Array a)
 foreign import _filterEdges :: Fn2 Graph (Record Types.Edge -> Boolean) (Array Types.EdgeId)
 
+foreign import _copy :: EffectFn1 Graph Graph
+
 
 newGraph :: Unit -> Effect Graph
 newGraph = runEffectFn1 _newGraph
 
-graphFromSigmaxGraph :: Types.Graph Types.Node Types.Edge -> Effect Graph
-graphFromSigmaxGraph (Types.Graph g) = do
+graphFromSigmaxGraph :: Types.SGraph -> Effect Graph
+graphFromSigmaxGraph g = do
   graph <- newGraph unit
-  _ <- traverse (addNode graph) g.nodes
-  _ <- traverse (addEdge graph) g.edges
+  _ <- traverse (addNode graph) $ Types.graphNodes g
+  _ <- traverse (addEdge graph) $ Types.graphEdges g
   pure graph
 
 addNode :: Graph -> Record Types.Node -> Effect String
@@ -86,6 +88,9 @@ updateEachEdgeAttributes = runEffectFn2 _updateEachEdgeAttributes
 filterEdges :: Graph -> (Record Types.Edge -> Boolean) -> Array Types.EdgeId
 filterEdges = runFn2 _filterEdges
 
+copy :: Graph -> Effect Graph
+copy = runEffectFn1 _copy
+
 -- TODO Maybe our use of this function (`updateWithGraph`) in code is
 -- too much. We convert Types.Graph into Graphology.Graph and then
 -- update Sigma.graph with this.

src/Gargantext/Hooks/Sigmax/Louvain.js

+'use strict';
+
+// https://graphology.github.io/standard-library/communities-louvain
+
+import louvain from 'graphology-communities-louvain';
+
+export function _assign(graph, options) {
+  louvain.assign(graph, {
+    getEdgeWeight: 'weight',
+    resolution: 2
+  });
+  return graph;
+}

src/Gargantext/Hooks/Sigmax/Louvain.purs

+module Gargantext.Hooks.Sigmax.Louvain where
+
+-- FFI for communities-louvain: https://graphology.github.io/standard-library/communities-louvain
+
+import Prelude
+
+import Data.Array as A
+import Data.Map as Map
+import Data.Sequence as Seq
+import Data.Set as Set
+import Data.Traversable (traverse)
+import Data.Tuple (Tuple(..))
+import Effect (Effect)
+import Effect.Timer (setTimeout)
+import Effect.Uncurried (EffectFn1, EffectFn2, EffectFn3, EffectFn4, runEffectFn1, runEffectFn2, runEffectFn3, runEffectFn4)
+import FFI.Simple ((..), (...), (.=))
+import Gargantext.Data.Louvain as DLouvain
+import Gargantext.Hooks.Sigmax.Graphology as Graphology
+import Gargantext.Hooks.Sigmax.Types as Types
+import Record as Record
+
+-- | Type representing the web worker.
+foreign import data LouvainLayout :: Type
+
+graph :: LouvainLayout -> Graphology.Graph
+graph s = s .. "graph" :: Graphology.Graph
+
+foreign import _assign :: forall settings. EffectFn2 Graphology.Graph settings Graphology.Graph
+
+assign :: forall settings. Graphology.Graph -> settings -> Effect Graphology.Graph
+assign = runEffectFn2 _assign
+
+assignVisible :: forall settings. Graphology.Graph -> settings -> Effect Graphology.Graph
+assignVisible g s = do
+  n <- Graphology.copy g
+  Graphology.updateGraphOnlyVisible n
+  assign n s
+
+-- \[{ id, community }] -> { id: community }
+cluster :: Graphology.Graph -> DLouvain.LouvainCluster
+cluster g = Map.fromFoldable $ (\{ id, community } -> Tuple id community) <$> (Graphology.nodes g)

src/Gargantext/Hooks/Sigmax/Types.purs

@@ -42,6 +42,7 @@ type Node = (
     borderColor :: String
   , children    :: Array String
   , color       :: String
+  , community   :: Int  -- this is filled in by the communities-louvain graphology plugin
   , equilateral :: { numPoints :: Int }
   , gargType    :: GT.Mode
   , hidden      :: Boolean
@@ -255,16 +256,14 @@ louvainNodes :: SGraph -> Array Louvain.Node
 louvainNodes g = Seq.toUnfoldable $ Seq.map _.id (graphNodes g)
 
 louvainGraph :: SGraph -> Louvain.LouvainCluster -> SGraph
-louvainGraph g cluster = Graph {nodes: newNodes, edges: newEdges}
+louvainGraph g cluster = Graph {nodes: newNodes, edges: graphEdges g}
   where
-    nodes = graphNodes g
-    edges = graphEdges g
-
-    newNodes = (nodeClusterColor cluster) <$> nodes
+    newNodes = (nodeClusterColor cluster) <$> (graphNodes g)
     nm = nodesMap newNodes
-    newEdges = (edgeClusterColor cluster nm) <$> edges
+    newEdges = (edgeClusterColor cluster nm) <$> (graphEdges g)
 
-edgeClusterColor cluster nm e = e { color = sourceNode.color, sourceNode = sourceNode, targetNode = targetNode }
+--edgeClusterColor _cluster nm e = e { color = sourceNode.color, sourceNode = sourceNode, targetNode = targetNode }
+edgeClusterColor _cluster nm e = e { color = sourceNode.color }
   where
     sourceNode = case Map.lookup e.source nm of
       Just sn -> sn

yarn.lock

@@ -5388,6 +5388,24 @@ graceful-fs@^4.1.2:
   resolved "https://registry.yarnpkg.com/graceful-fs/-/graceful-fs-4.2.6.tgz#ff040b2b0853b23c3d31027523706f1885d76bee"
   integrity sha512-nTnJ528pbqxYanhpDYsi4Rd8MAeaBA67+RZ10CM1m3bTAVFEDcd5AuA4a6W5YkGZ1iNXHzZz8T6TBKLeBuNriQ==
 
+graphology-communities-louvain@^2.0.1:
+  version "2.0.1"
+  resolved "https://registry.yarnpkg.com/graphology-communities-louvain/-/graphology-communities-louvain-2.0.1.tgz#56636700912b75d25c6906e5162743792f5f0893"
+  integrity sha512-JxEH8uxao6FcWp3UXNDJIRjU3pamzp9aqIWgpfAqWE66aPwHeBIB39YnqTgbe4baUJRdpbcp1u8jJiYvojHGIQ==
+  dependencies:
+    graphology-indices "^0.17.0"
+    graphology-utils "^2.4.4"
+    mnemonist "^0.39.0"
+    pandemonium "^2.3.0"
+
+graphology-indices@^0.17.0:
+  version "0.17.0"
+  resolved "https://registry.yarnpkg.com/graphology-indices/-/graphology-indices-0.17.0.tgz#b93ad32162ff8b09814547aedb101248f0fcbd2e"
+  integrity sha512-A7RXuKQvdqSWOpn7ZVQo4S33O0vCfPBnUSf7FwE0zNCasqwZVUaCXePuWo5HBpWw68KJcwObZDHpFk6HKH6MYQ==
+  dependencies:
+    graphology-utils "^2.4.2"
+    mnemonist "^0.39.0"
+
 graphology-layout-forceatlas2@^0.9.2:
   version "0.9.2"
   resolved "https://registry.yarnpkg.com/graphology-layout-forceatlas2/-/graphology-layout-forceatlas2-0.9.2.tgz#0f5986f55ef0d72162f23edd1837aa8dac69f20e"
@@ -5409,7 +5427,7 @@ graphology-operators@^1.6.0:
   dependencies:
     graphology-utils "^2.0.0"
 
-graphology-utils@^2.0.0, graphology-utils@^2.1.0, graphology-utils@^2.3.0, graphology-utils@^2.5.0:
+graphology-utils@^2.0.0, graphology-utils@^2.1.0, graphology-utils@^2.3.0, graphology-utils@^2.4.2, graphology-utils@^2.4.4, graphology-utils@^2.5.0:
   version "2.5.2"
   resolved "https://registry.yarnpkg.com/graphology-utils/-/graphology-utils-2.5.2.tgz#4d30d6e567d27c01f105e1494af816742e8d2440"
   integrity sha512-ckHg8MXrXJkOARk56ZaSCM1g1Wihe2d6iTmz1enGOz4W/l831MBCKSayeFQfowgF8wd+PQ4rlch/56Vs/VZLDQ==
@@ -7280,6 +7298,13 @@ mkdirp@^1.0.3, mkdirp@^1.0.4:
   resolved "https://registry.yarnpkg.com/mkdirp/-/mkdirp-1.0.4.tgz#3eb5ed62622756d79a5f0e2a221dfebad75c2f7e"
   integrity sha512-vVqVZQyf3WLx2Shd0qJ9xuvqgAyKPLAiqITEtqW0oIUjzo3PePDd6fW9iFz30ef7Ysp/oiWqbhszeGWW2T6Gzw==
 
+mnemonist@^0.39.0, mnemonist@^0.39.2:
+  version "0.39.5"
+  resolved "https://registry.yarnpkg.com/mnemonist/-/mnemonist-0.39.5.tgz#5850d9b30d1b2bc57cc8787e5caa40f6c3420477"
+  integrity sha512-FPUtkhtJ0efmEFGpU14x7jGbTB+s18LrzRL2KgoWz9YvcY3cPomz8tih01GbHwnGk/OmkOKfqd/RAQoc8Lm7DQ==
+  dependencies:
+    obliterator "^2.0.1"
+
 modify-values@^1.0.0:
   version "1.0.1"
   resolved "https://registry.yarnpkg.com/modify-values/-/modify-values-1.0.1.tgz#b3939fa605546474e3e3e3c63d64bd43b4ee6022"
@@ -7570,7 +7595,7 @@ object.pick@^1.3.0:
   dependencies:
     isobject "^3.0.1"
 
-obliterator@^2.0.2:
+obliterator@^2.0.1, obliterator@^2.0.2:
   version "2.0.4"
   resolved "https://registry.yarnpkg.com/obliterator/-/obliterator-2.0.4.tgz#fa650e019b2d075d745e44f1effeb13a2adbe816"
   integrity sha512-lgHwxlxV1qIg1Eap7LgIeoBWIMFibOjbrYPIPJZcI1mmGAI2m3lNYpK12Y+GBdPQ0U1hRwSord7GIaawz962qQ==
@@ -7769,6 +7794,13 @@ pako@~1.0.5:
   resolved "https://registry.yarnpkg.com/pako/-/pako-1.0.11.tgz#6c9599d340d54dfd3946380252a35705a6b992bf"
   integrity sha512-4hLB8Py4zZce5s4yd9XzopqwVv/yGNhV1Bl8NTmCq1763HeK2+EwVTv+leGeL13Dnh2wfbqowVPXCIO0z4taYw==
 
+pandemonium@^2.3.0:
+  version "2.4.1"
+  resolved "https://registry.yarnpkg.com/pandemonium/-/pandemonium-2.4.1.tgz#bd51ca72184c6ae135f9049a33c8605bfdb9574d"
+  integrity sha512-wRqjisUyiUfXowgm7MFH2rwJzKIr20rca5FsHXCMNm1W5YPP1hCtrZfgmQ62kP7OZ7Xt+cR858aB28lu5NX55g==
+  dependencies:
+    mnemonist "^0.39.2"
+
 parcel@^2.0.0-rc.0:
   version "2.0.0-rc.0"
   resolved "https://registry.yarnpkg.com/parcel/-/parcel-2.0.0-rc.0.tgz#862d5568f13ed4b7d762f792b23d4445f6fddaf2"