Cleanup

Removed some dead code, most notably the `Partition` and `PartitionMathod`
types which were not in actual use anywhere.
Also renamed some function arguments from single-/double-letter identifiers
to actual words.

src/Gargantext/API/Node/Update.hs

@@ -10,7 +10,6 @@ Portability : POSIX
 -}
 
 {-# LANGUAGE TypeApplications #-}
-{-# LANGUAGE TypeOperators    #-}
 
 module Gargantext.API.Node.Update
       where
@@ -64,11 +63,11 @@ updateNode :: (HasNodeStory env err m
            -> JobHandle m
            -> m ()
 updateNode nId (UpdateNodeParamsGraph
-                    (UpdateNodeConfigGraph metric partitionMethod bridgeMethod strength nt1 nt2)) jobHandle = do
+                    (UpdateNodeConfigGraph metric bridgeMethod strength nt1 nt2)) jobHandle = do
 
   markStarted 2 jobHandle
   -- printDebug "Computing graph: " method
-  _ <- recomputeGraph nId partitionMethod bridgeMethod (Just metric) (Just strength) nt1 nt2 True
+  _ <- recomputeGraph nId bridgeMethod (Just metric) (Just strength) nt1 nt2 True
   -- printDebug "Graph computed: " method
   markComplete jobHandle
 

src/Gargantext/API/Node/Update/Types.hs

@@ -5,7 +5,6 @@ import Data.Aeson
 import Data.Swagger ( ToSchema )
 import Gargantext.Core.Methods.Similarities (GraphMetric(..))
 import Gargantext.Core.Text.Ngrams (NgramsType)
-import Gargantext.Core.Viz.Graph.Tools (PartitionMethod(..))
 import Gargantext.Core.Viz.Graph.Types (BridgenessMethod, Strength)
 import Gargantext.Core.Viz.Phylo (PhyloSubConfigAPI(..))
 import Gargantext.Database.Admin.Types.Node ( NodeId, NodeType )
@@ -46,7 +45,6 @@ data Charts = Sources | Authors | Institutes | Ngrams | All
 
 ------------------------------------------------------------------------
 data UpdateNodeConfigGraph = UpdateNodeConfigGraph { methodGraphMetric        :: !GraphMetric
-                                                   , methodGraphClustering    :: !PartitionMethod
                                                    , methodGraphBridgeness    :: !BridgenessMethod
                                                    , methodGraphEdgesStrength :: !Strength
                                                    , methodGraphNodeType1     :: !NgramsType

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

@@ -71,10 +71,9 @@ getGraph nId = do
   case graph of
     Nothing     -> do
         let defaultMetric          = Order1
-        let defaultPartitionMethod = Spinglass
         let defaultEdgesStrength   = Strong
         let defaultBridgenessMethod = BridgenessBasic
-        graph' <- computeGraph cId defaultPartitionMethod defaultBridgenessMethod (withMetric defaultMetric) defaultEdgesStrength (NgramsTerms, NgramsTerms) repo
+        graph' <- computeGraph cId defaultBridgenessMethod (withMetric defaultMetric) defaultEdgesStrength (NgramsTerms, NgramsTerms) repo
         mt     <- defaultGraphMetadata cId listId "Title" repo defaultMetric defaultEdgesStrength
         let mt' = set gm_legend (generateLegend graph') mt
         let
@@ -91,7 +90,6 @@ getGraph nId = do
 --recomputeGraph :: UserId -> NodeId -> Maybe GraphMetric -> GargNoServer Graph
 recomputeGraph :: HasNodeStory env err m
                => NodeId
-               -> PartitionMethod
                -> BridgenessMethod
                -> Maybe GraphMetric
                -> Maybe Strength
@@ -99,7 +97,7 @@ recomputeGraph :: HasNodeStory env err m
                -> NgramsType
                -> Bool
                -> m Graph
-recomputeGraph nId partitionMethod bridgeMethod maybeSimilarity maybeStrength nt1 nt2 force' = do
+recomputeGraph nId bridgeMethod maybeSimilarity maybeStrength nt1 nt2 force' = do
   nodeGraph <- getNodeWith nId (Proxy :: Proxy HyperdataGraph)
   let
     graph  = nodeGraph ^. node_hyperdata . hyperdataGraph
@@ -127,7 +125,7 @@ recomputeGraph nId partitionMethod bridgeMethod maybeSimilarity maybeStrength nt
   let v   = repo ^. unNodeStory . at listId . _Just . a_version
 
   let computeG mt = do
-        !g <- computeGraph cId partitionMethod bridgeMethod similarity strength (nt1,nt2) repo
+        !g <- computeGraph cId bridgeMethod similarity strength (nt1,nt2) repo
         let mt' = set gm_legend (generateLegend g) mt
         let g' = set graph_metadata (Just mt') g
         _nentries <- updateHyperdata nId (HyperdataGraph (Just g') camera)
@@ -154,14 +152,13 @@ recomputeGraph nId partitionMethod bridgeMethod maybeSimilarity maybeStrength nt
 -- TODO remove repo
 computeGraph :: HasNodeError err
              => CorpusId
-             -> PartitionMethod
              -> BridgenessMethod
              -> Similarity
              -> Strength
              -> (NgramsType, NgramsType)
              -> NodeListStory
              -> DBCmd err Graph
-computeGraph corpusId partitionMethod bridgeMethod similarity strength (nt1,nt2) repo = do
+computeGraph corpusId bridgeMethod similarity strength (nt1,nt2) repo = do
   -- Getting the Node parameters
   lId  <- defaultList corpusId
   lIds <- selectNodesWithUsername NodeList userMaster
@@ -190,7 +187,7 @@ computeGraph corpusId partitionMethod bridgeMethod similarity strength (nt1,nt2)
 
   -- TODO MultiPartite Here
   liftBase
-        $ cooc2graphWith partitionMethod bridgeMethod (MultiPartite (Partite (HashMap.keysSet m1) nt1)
+        $ cooc2graphWith bridgeMethod (MultiPartite (Partite (HashMap.keysSet m1) nt1)
                                               (Partite (HashMap.keysSet m2) nt2)
                                               )
                                 similarity 0 strength myCooc
@@ -239,7 +236,7 @@ graphRecompute ::  (HasNodeStory env err m, MonadJobStatus m)
                -> m ()
 graphRecompute n jobHandle = do
   markStarted 1 jobHandle
-  _g <- recomputeGraph n Spinglass BridgenessBasic Nothing Nothing NgramsTerms NgramsTerms False
+  _g <- recomputeGraph n BridgenessBasic Nothing Nothing NgramsTerms NgramsTerms False
   markComplete jobHandle
 
 graphVersions :: (HasNodeStory env err m)
@@ -274,7 +271,7 @@ graphVersions u nId = do
 recomputeVersions :: HasNodeStory env err m
                   => NodeId
                   -> m Graph
-recomputeVersions nId = recomputeGraph nId Spinglass BridgenessBasic Nothing Nothing NgramsTerms NgramsTerms False
+recomputeVersions nId = recomputeGraph nId BridgenessBasic Nothing Nothing NgramsTerms NgramsTerms False
 
 ------------------------------------------------------------
 graphClone :: (HasNodeError err)

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

@@ -20,8 +20,6 @@ TODO use Map LouvainNodeId (Map LouvainNodeId)
 
 {-# OPTIONS_GHC -fno-warn-deprecations #-}
 
-{-# LANGUAGE BangPatterns #-}
-
 module Gargantext.Core.Viz.Graph.Bridgeness -- (bridgeness)
   where
 
@@ -33,7 +31,7 @@ import Data.Set qualified as Set
 import Data.Tuple.Extra qualified as Tuple
 import Gargantext.Core.Methods.Similarities (Similarity(..))
 import Gargantext.Core.Viz.Graph.Types (BridgenessMethod(..))
-import Gargantext.Prelude hiding (toList)
+import Gargantext.Prelude hiding (toList, filter)
 import Graph.Types (ClusterNode(..))
 ----------------------------------------------------------------------
 
@@ -113,13 +111,20 @@ bridgeness :: [[Set NodeId]]
            -> Similarity
            -> Map (NodeId, NodeId) Double
            -> Map (NodeId, NodeId) Double
-bridgeness sn method f sim m =
-  Map.unions $ [linksBetween] <> map (\s -> baseBridgeness (setNodes2clusterNodes s) method (if sim == Conditional then pi*f else f) m') sn
+bridgeness partitions method filter similarity m =
+  Map.unions $ [linksBetween] <>
+  map (\s -> baseBridgeness
+               (setNodes2clusterNodes s)
+               method
+               (if similarity == Conditional then pi*filter
+                                             else filter)
+               m'
+      ) partitions
     where
       (linksBetween, m') = Map.partitionWithKey (\(n1,n2) _v -> Map.lookup n1 mapNodeIdClusterId
                                                              /= Map.lookup n2 mapNodeIdClusterId
-                                                ) $ baseBridgeness clusters method f m
-      clusters = setNodes2clusterNodes (map Set.unions sn)
+                                                ) $ baseBridgeness clusters method filter m
+      clusters = setNodes2clusterNodes (map Set.unions partitions)
       mapNodeIdClusterId = clusterNodes2map clusters
 
 baseBridgeness :: [ClusterNode]
@@ -127,14 +132,14 @@ baseBridgeness :: [ClusterNode]
                -> Double
                -> Map (NodeId, NodeId) Double
                -> Map (NodeId, NodeId) Double
-baseBridgeness ns method b m = Map.fromList
+baseBridgeness partitions method filter m = Map.fromList
                       $ List.concat
                       $ Map.elems
                       $ (case method of
-                           BridgenessBasic -> filterComs (round b)
+                           BridgenessBasic -> filterComs (round filter)
                            BridgenessAdvanced -> filterComsAdvanced
                         )
-                      $ groupEdges (Map.fromList $ map nodeId2comId ns) m
+                      $ groupEdges (Map.fromList $ map nodeId2comId partitions) m
 
 
 groupEdges :: (Ord comId, Ord nodeId)
@@ -179,41 +184,3 @@ filterComsAdvanced m = Map.filter (not . null) $ mapWithKey filter' m
     filter' (c1,c2) xs
       | c1 == c2  = xs
       | otherwise = List.filter (\(_nn,v) -> v >= threshold) xs
-
---------------------------------------------------------------
--- Utils
-{--
-map2intMap :: Map (Int, Int) a -> IntMap (IntMap a)
-map2intMap m = IntMap.fromListWith (<>)
-             $ map (\((k1,k2), v) -> if k1 < k2
-                                   then (k1, IntMap.singleton k2 v)
-                                   else (k2, IntMap.singleton k1 v)
-                    )
-             $ Map.toList m
-
-look :: (Int,Int) -> IntMap (IntMap a) -> Maybe a
-look (k1,k2) m = if k1 < k2
-                    then case (IntMap.lookup k1 m) of
-                           Just m' -> IntMap.lookup k2 m'
-                           _       -> Nothing
-                    else look (k2,k1) m
-
-
-{-
-Compute the median of a list
-From:  https://hackage.haskell.org/package/dsp-0.2.5.1/docs/src/Numeric.Statistics.Median.html
-Compute the center of the list in a more lazy manner
-and thus halves memory requirement.
--}
-
-median :: (Ord a, Fractional a) => [a] -> a
-median [] = panic "medianFast: empty list has no median"
-median zs =
-   let recurse (x0:_)    (_:[])   = x0
-       recurse (x0:x1:_) (_:_:[]) = (x0+x1)/2
-       recurse (_:xs)    (_:_:ys) = recurse xs ys
-       recurse _ _  =
-          panic "median: this error cannot occur in the way 'recurse' is called"
-   in  recurse zs zs
-
--}

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

@@ -23,17 +23,15 @@ 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 ( ToSchema )
 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 ( pcaReduceTo, Dimension(Dimension) )
 import Gargantext.Core.Text.Ngrams (NgramsType(..))
-import Gargantext.Core.Viz.Graph.Bridgeness (bridgeness, Partitions, nodeId2comId, {-recursiveClustering,-} recursiveClustering', setNodes2clusterNodes)
+import Gargantext.Core.Viz.Graph.Bridgeness (bridgeness, 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.Infomap (infomap)
 import Gargantext.Core.Viz.Graph.Types (Attributes(..), BridgenessMethod, Edge(..), Graph(..), MultiPartite(..), Node(..), Partite(..), Strength(..), LegendField(..))
 import Gargantext.Core.Viz.Graph.Utils (edgesFilter, nodesFilter)
 import Gargantext.Prelude
@@ -42,16 +40,6 @@ import Graph.Types (ClusterNode)
 import IGraph qualified as Igraph
 import IGraph.Algorithms.Layout qualified as Layout
 import IGraph.Random ( Gen ) -- (Gen(..))
-import Test.QuickCheck (elements)
-import Test.QuickCheck.Arbitrary ( Arbitrary(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 ]
 
 
 -------------------------------------------------------------
@@ -82,33 +70,18 @@ cooc2graph' distance threshold myCooc
 
 
 -- coocurrences graph computation
-cooc2graphWith :: PartitionMethod
-               -> BridgenessMethod
-               -> MultiPartite
-               -> Similarity
-               -> Threshold
-               -> Strength
-               -> HashMap (NgramsTerm, NgramsTerm) Int
-               -> IO Graph
-cooc2graphWith Spinglass = cooc2graphWith' (spinglass 1)
-cooc2graphWith Confluence= cooc2graphWith' (\x -> pure $ BAC.defaultClustering x)
-cooc2graphWith Infomap   = cooc2graphWith' (infomap "-v -N2")
---cooc2graphWith Infomap   = cooc2graphWith' (infomap "--silent --two-level -N2")
-                        -- TODO: change these options, or make them configurable in UI?
-
-cooc2graphWith' :: Partitions
-                -> BridgenessMethod
+cooc2graphWith :: BridgenessMethod
                -> MultiPartite
                -> Similarity
                -> Threshold
                -> Strength
                -> HashMap (NgramsTerm, NgramsTerm) Int
                -> IO Graph
-cooc2graphWith' _doPartitions bridgenessMethod multi similarity threshold strength myCooc = do
+cooc2graphWith bridgenessMethod multi similarity threshold strength myCooc = do
   let (distanceMap, diag, ti) = doSimilarityMap similarity threshold strength myCooc
   distanceMap `seq` diag `seq` ti `seq` pure ()
 
-  partitions <- if (Map.size distanceMap > 0)
+  partitions <- if Map.size distanceMap > 0
       then recursiveClustering' (spinglass' 1) distanceMap
       else panic $ Text.unwords [ "I can not compute the graph you request"
                                 , "because either the quantity of documents"
@@ -126,27 +99,6 @@ cooc2graphWith' _doPartitions bridgenessMethod multi similarity threshold streng
 
   pure $ data2graph multi ti diag bridgeness' confluence' (setNodes2clusterNodes $ List.concat partitions)
 
-{-
-cooc2graphWith' _doPartitions _bridgenessMethod multi similarity@Distributional threshold strength myCooc = do
-  let (distanceMap, diag, ti) = doSimilarityMap similarity threshold strength myCooc
-  distanceMap `seq` diag `seq` ti `seq` pure ()
-
-  partitions <- if (Map.size distanceMap > 0)
-      then recursiveClustering (spinglass 1) distanceMap
-      else panic $ Text.unlines [ "[Gargantext.C.V.Graph.Tools] Similarity Matrix is empty"
-                                , "Maybe you should add more Map Terms in your list"
-                                , "Tutorial: TODO"
-                                ]
-  length partitions `seq` pure ()
-
-  let
-    !confluence' = BAC.computeConfluences 3 (Map.keys distanceMap) True
-    !bridgeness' = bridgeness (Bridgeness_Basic partitions 1.0) distanceMap
-
-  pure $ data2graph multi ti diag bridgeness' confluence' partitions
--}
-
-
 
 type Reverse = Bool