Merge remote-tracking branch 'origin/fix-confluence-indices-bugs' into dev

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

@@ -128,7 +128,6 @@ recomputeGraph :: FlowCmdM env err m
                -> Bool
                -> m Graph
 recomputeGraph _uId nId method maybeDistance maybeStrength force = do
-  printDebug "recomputeGraph begins" (nId, method)
   nodeGraph <- getNodeWith nId (Proxy :: Proxy HyperdataGraph)
   let
     graph  = nodeGraph ^. node_hyperdata . hyperdataGraph
@@ -150,22 +149,15 @@ recomputeGraph _uId nId method maybeDistance maybeStrength force = do
 
   mcId <- getClosestParentIdByType nId NodeCorpus
   let cId = maybe (panic "[G.V.G.API] Node has no parent") identity mcId
-  printDebug "recomputeGraph corpus" cId
 
   listId  <- defaultList cId
-  printDebug "recomputeGraph list" listId
   repo <- getRepo [listId]
   let v   = repo ^. unNodeStory . at listId . _Just . a_version
-  printDebug "recomputeGraph got repo, version: " v
 
   let computeG mt = do
-        printDebug "about to run computeGraph" ()
-        g <- computeGraph cId method similarity strength NgramsTerms repo
-        seq g $ printDebug "graph computed" ()
+        !g <- computeGraph cId method similarity strength NgramsTerms repo
         let g' = set graph_metadata mt g
-        seq g' $ printDebug "computed graph with new metadata" ()
-        nentries <- updateHyperdata nId (HyperdataGraph (Just g') camera)
-        printDebug "graph hyperdata updated" ("entries" :: [Char], nentries)
+        _nentries <- updateHyperdata nId (HyperdataGraph (Just g') camera)
         pure g'
 
   case graph of
@@ -189,11 +181,8 @@ computeGraph :: FlowCmdM env err m
              -> NodeListStory
              -> m Graph
 computeGraph cId method d strength nt repo = do
-  printDebug "computeGraph" (cId, method, nt)
   lId  <- defaultList cId
-  printDebug "computeGraph got list id: " lId
   lIds <- selectNodesWithUsername NodeList userMaster
-  printDebug "computeGraph got nodes with username: " userMaster
   let ngs = filterListWithRoot [MapTerm]
           $ mapTermListRoot [lId] nt repo
 
@@ -201,10 +190,8 @@ computeGraph cId method d strength nt repo = do
          <$> getCoocByNgrams (Diagonal True)
          <$> groupNodesByNgrams ngs
          <$> getContextsByNgramsOnlyUser cId (lIds <> [lId]) nt (HashMap.keys ngs)
-  printDebug "computeGraph got coocs" (HashMap.size myCooc)
 
   graph <- liftBase $ cooc2graphWith method d 0 strength myCooc
-  printDebug "computeGraph got graph" ()
 
   --listNgrams <- getListNgrams [lId] nt
   --let graph' = mergeGraphNgrams graph (Just listNgrams)
@@ -265,7 +252,7 @@ graphRecompute u n logStatus = do
                    , _scst_remaining = Just 1
                    , _scst_events    = Just []
                    }
-  _g <- trace (show u) $ recomputeGraph u n Spinglass Nothing Nothing False
+  _g <- recomputeGraph u n Spinglass Nothing Nothing False
   pure  JobLog { _scst_succeeded = Just 1
                , _scst_failed    = Just 0
                , _scst_remaining = Just 0

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

@@ -9,13 +9,11 @@ Portability : POSIX
 
 -}
 
-{-# LANGUAGE ScopedTypeVariables #-}
+{-# LANGUAGE BangPatterns, ScopedTypeVariables #-}
 
 module Gargantext.Core.Viz.Graph.Tools
   where
 
-import Debug.Trace
-
 import Data.Aeson
 import Data.HashMap.Strict (HashMap)
 import Data.Map (Map)
@@ -26,7 +24,6 @@ import GHC.Generics (Generic)
 import Gargantext.API.Ngrams.Types (NgramsTerm(..))
 import Gargantext.Core.Methods.Distances (Distance(..), measure)
 import Gargantext.Core.Methods.Distances.Conditional (conditional)
--- import Gargantext.Core.Methods.Graph.BAC.Proxemy (confluence)
 import Gargantext.Core.Statistics
 import Gargantext.Core.Viz.Graph
 import Gargantext.Core.Viz.Graph.Bridgeness (bridgeness, Partitions, ToComId(..))
@@ -110,7 +107,7 @@ cooc2graphWith' :: ToComId a
                -> IO Graph
 cooc2graphWith' doPartitions distance threshold strength myCooc = do
   let (distanceMap, diag, ti) = doDistanceMap distance threshold strength myCooc
-  distanceMap `seq` trace "distanceMap OK" diag `seq` trace "diag OK" ti `seq` printDebug "ti done" ()
+  distanceMap `seq` diag `seq` ti `seq` return ()
 
 --{- -- Debug
   -- saveAsFileDebug "/tmp/distanceMap" distanceMap
@@ -124,21 +121,15 @@ cooc2graphWith' doPartitions distance threshold strength myCooc = do
                                 , "Maybe you should add more Map Terms in your list"
                                 , "Tutorial: link todo"
                                 ]
-  partitions `seq` printDebug "partitions done" ()
+  length partitions `seq` return ()
   let
     nodesApprox :: Int
     nodesApprox = n'
       where
         (as, bs) = List.unzip $ Map.keys distanceMap
         n' = Set.size $ Set.fromList $ as <> bs
-    bridgeness' = bridgeness (fromIntegral nodesApprox) partitions distanceMap
-    -- indices of bridgeness seem to start at 1, while computeConfluences
-    -- expects 0-based indexing.
-    -- ks = map (\(a, b) -> (a-1, b-1)) (Map.keys bridgeness')
-    confluence' = Map.empty -- Map.mapKeys (\(a, b) -> (a+1, b+1)) $ BAC.computeConfluences 3 ks True
-               -- confluence (Map.keys bridgeness') 3 True False
-  seq bridgeness' $ printDebug "bridgeness OK" ()
-  seq confluence' $ printDebug "confluence OK" ()
+    !bridgeness' = bridgeness (fromIntegral nodesApprox) partitions distanceMap
+    !confluence' = BAC.computeConfluences 3 (Map.keys bridgeness') True
   pure $ data2graph ti diag bridgeness' confluence' partitions
 
 type Reverse = Bool
@@ -161,21 +152,21 @@ doDistanceMap Distributional threshold strength myCooc = (distanceMap, toIndex t
     (ti, _it) = createIndices theMatrix
     tiSize  = Map.size ti
 
-    similarities = (\m -> m `seq` trace "measure done" m)
-                 $ (\m -> m `seq` trace "map2mat done" (measure Distributional m))
-                 $ (\m -> m `seq` trace "toIndex done" (map2mat Square 0 tiSize m))
-                 $ theMatrix `seq` trace "theMatrix done" (toIndex ti theMatrix)
+    similarities = (\m -> m `seq` m)
+                 $ (\m -> m `seq` measure Distributional m)
+                 $ (\m -> m `seq` map2mat Square 0 tiSize m)
+                 $ theMatrix `seq` toIndex ti theMatrix
 
     links = round (let n :: Double = fromIntegral tiSize in n * (log n)^(2::Int))
 
-    distanceMap = Map.fromList . trace "fromList" identity
+    distanceMap = Map.fromList
                 $ List.take links
                 $ (if strength == Weak then List.reverse else identity)
                 $ List.sortOn snd
                 $ Map.toList
                 $ edgesFilter
-                $ (\m -> m `seq` trace "map2map done" (Map.filter (> threshold) m))
-                $ similarities `seq` mat2map (trace "similarities done" similarities)
+                $ (\m -> m `seq` Map.filter (> threshold) m)
+                $ similarities `seq` mat2map similarities
 
 doDistanceMap Conditional threshold strength myCooc = (distanceMap, toIndex ti myCooc', ti)
   where

stack.yaml

@@ -35,7 +35,7 @@ extra-deps:
 - git: https://gitlab.iscpif.fr/gargantext/haskell-gargantext-prelude.git
   commit: 08096a4913572cf22762fa77613340207ec6d9fd
 - git: https://gitlab.iscpif.fr/gargantext/gargantext-graph.git
-  commit: 642b9ec7ffa59a5db7b2ec7b24436e07309dc097
+  commit: 588e104fe7593210956610cab0041fd16584a4ce
   # Data Mining Libs
 - git: https://github.com/delanoe/data-time-segment.git
   commit: 10a416b9f6c443866b36479c3441ebb3bcdeb7ef