[FIX] Nodes with one edge only are removed now

bin/install

@@ -2,4 +2,11 @@
 
 #stack install --nix --profile --test --fast --no-install-ghc --skip-ghc-check
 
-env LANG=C.UTF-8 stack install --haddock --nix --test --no-install-ghc --skip-ghc-check --no-haddock-deps
+if [[ $1 == "dev" ]] ;
+  then
+    echo "DEV install"
+    env LANG=C.UTF-8 stack install --nix --no-install-ghc --skip-ghc-check --no-haddock-deps
+  else
+    echo "PROD install (with documentation)" 
+    env LANG=C.UTF-8 stack install --haddock --nix --test --no-install-ghc --skip-ghc-check --no-haddock-deps
+fi

gargantext.cabal

@@ -5,7 +5,7 @@ cabal-version: 1.12
 -- see: https://github.com/sol/hpack
 
 name:           gargantext
-version: 0.0.6.6
+version:        0.0.6.6
 synopsis:       Search, map, share
 description:    Please see README.md
 category:       Data

src/Gargantext/Core/Text/Metrics/Count.hs

@@ -26,6 +26,7 @@ Source : https://en.wikipedia.org/wiki/Type%E2%80%93token_distinction#Occurrence
 module Gargantext.Core.Text.Metrics.Count
   where
 
+import Debug.Trace (trace)
 import Data.Text (Text)
 import Control.Arrow (Arrow(..), (***))
 import qualified Data.List as List
@@ -143,8 +144,10 @@ occurrences = occurrencesOn _terms_stem
 occurrencesOn :: (Ord a, Ord b) => (a -> b) -> [a] -> Map b (Map a Int)
 occurrencesOn f = foldl' (\m a -> insertWith (unionWith (+)) (f a) (singleton a 1) m) empty
 
-occurrencesWith :: (Foldable list, Ord k, Num a) => (b -> k) -> list b -> Map k a
-occurrencesWith f xs = foldl' (\x y -> insertWith (+) (f y) 1 x) empty xs
+occurrencesWith :: (Foldable list, Ord k, Num a, Show k, Show a, Show (list b)) => (b -> k) -> list b -> Map k a
+occurrencesWith f xs = trace (show (xs,m))  m
+  where
+    m = foldl' (\x y -> insertWith (+) (f y) 1 x) empty xs
 
 -- TODO add groups and filter stops
 

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

@@ -30,7 +30,7 @@ import Gargantext.Core.Viz.Graph.Bridgeness (bridgeness, Partitions, ToComId(..)
 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.Utils (edgesFilter)
+import Gargantext.Core.Viz.Graph.Utils (edgesFilter, nodesFilter)
 import Gargantext.Prelude
 import Graph.Types (ClusterNode)
 import IGraph.Random -- (Gen(..))
@@ -172,9 +172,7 @@ doDistanceMap Conditional threshold strength myCooc = (distanceMap, toIndex ti m
   where
     myCooc' = Map.fromList $ HashMap.toList myCooc
     (ti, _it) = createIndices myCooc'
-
     links = round (let n :: Double = fromIntegral (Map.size ti) in n * log n)
-
     distanceMap = toIndex ti
                 $ Map.fromList
                 $ List.take links
@@ -216,16 +214,18 @@ data2graph labels' occurences bridge conf partitions = Graph { _graph_nodes = no
                      }
                )
             | (l, n) <- labels
-            , Set.member n nodesWithScores
+            , Set.member n toKeep
             ]
 
+    (bridge', toKeep) = nodesFilter (\v -> v > 1) bridge
+
     edges = [ Edge { edge_source = cs (show s)
                    , edge_target = cs (show t)
                    , edge_weight = weight
                    , edge_confluence = maybe 0 identity $ Map.lookup (s,t) conf
                    , edge_id     = cs (show i)
                    }
-            | (i, ((s,t), weight)) <- zip ([0..]::[Integer] ) $ Map.toList bridge
+            | (i, ((s,t), weight)) <- zip ([0..]::[Integer] ) $ Map.toList bridge'
             , s /= t
             , weight > 0
             ]
@@ -235,11 +235,6 @@ data2graph labels' occurences bridge conf partitions = Graph { _graph_nodes = no
 
     labels = Map.toList labels'
 
-    nodesWithScores = Set.fromList
-                     $ List.concat
-                     $ map (\((s,t),d) -> if d > 0 && s/=t then [s,t] else [])
-                     $ Map.toList bridge
-
 
 ------------------------------------------------------------------------
 
@@ -338,5 +333,3 @@ filterByNeighbours threshold distanceMap = filteredMap
                            in List.take (round threshold) selected
                       ) indexes
 
-
-

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

@@ -17,16 +17,19 @@ These functions are used for Vector.Matrix only.
 module Gargantext.Core.Viz.Graph.Utils
   where
 
+import Data.List (unzip)
 import Data.Map (Map)
 import Data.Matrix hiding (identity)
+import Data.Maybe (catMaybes)
+import Data.Set (Set)
 import Data.Vector (Vector)
-import qualified Data.List   as L
-import qualified Data.Map    as Map
+import Gargantext.Core.Text.Metrics.Count (occurrencesWith)
 import Gargantext.Prelude
-import Data.List (unzip)
-import qualified Data.Vector as V
-import Data.Maybe (catMaybes)
-import qualified Data.Set    as Set
+import qualified Data.List    as List
+import qualified Data.Map     as Map
+import qualified Data.Set     as Set
+import qualified Data.Vector  as Vector
+
 ------------------------------------------------------------------------
 -- | Some utils to build the matrix from cooccurrence results
 
@@ -42,13 +45,13 @@ type AxisId = Int
 
 -- Data.Vector.Additions
 dropAt :: Int -> Vector a -> Vector a
-dropAt n v = debut <> (V.tail fin)
+dropAt n v = debut <> (Vector.tail fin)
   where
-    debut = V.take n v
-    fin   = V.drop n v
+    debut = Vector.take n v
+    fin   = Vector.drop n v
 
 total :: Num a => Matrix a -> a
-total m = V.sum $ V.map (\c -> V.sum (getCol c m)) (V.enumFromTo 1 (nOf Col m))
+total m = Vector.sum $ Vector.map (\c -> Vector.sum (getCol c m)) (Vector.enumFromTo 1 (nOf Col m))
 
 nOf :: Axis -> Matrix a -> Int
 nOf Row = nrows
@@ -60,10 +63,10 @@ axis Row = getRow
 
 
 toListsWithIndex :: Matrix a ->  [((Int, Int), a)]
-toListsWithIndex m = concat' $ zip [1..] $ map (\c -> zip [1..] c) $ toLists m
+toListsWithIndex m = concat' $ zip [1..] $ List.map (\c -> zip [1..] c) $ toLists m
   where
     concat' :: [(Int, [(Int, a)])] -> [((Int, Int), a)]
-    concat' xs = L.concat $ map (\(x, ys) -> map (\(y, a) -> ((x,y), a)) ys ) xs
+    concat' xs = List.concat $ List.map (\(x, ys) -> List.map (\(y, a) -> ((x,y), a)) ys ) xs
 
 ------------------------------------------------------------------------
 -- Utils to manage Graphs
@@ -82,7 +85,19 @@ edgesFilter m = Map.fromList $ catMaybes results
     keys    = Set.toList $ Set.fromList (x <> y)
     (x,y)   = unzip $ Map.keys m
 
-
+nodesFilter :: (Show a, Show b, Ord a, Ord b, Num b) => (b -> Bool) -> Map (a,a) b -> (Map (a,a) b, Set a)
+nodesFilter f m = (m', toKeep) 
+  where
+    m' = Map.filterWithKey (\(a,b) _ -> Set.member a toKeep && Set.member b toKeep) m
+    toKeep = Set.fromList
+           $ Map.keys
+           $ Map.filter f
+           $ occurrencesWith identity
+           $ tupleConcat
+           $ List.unzip
+           $ Map.keys m
+    tupleConcat :: ([a],[a]) -> [a]
+    tupleConcat (a,b) = a <> b
 
 
 getMax :: Ord b

src/Gargantext/Database/Action/Metrics/TFICF.hs

@@ -57,7 +57,7 @@ getTficf cId mId nt = do
     ) mapTextDoubleLocal
 -}
 
-getTficf_withSample :: HasDBid NodeType 
+getTficf_withSample :: HasDBid NodeType
          => UserCorpusId
          -> MasterCorpusId
          -> NgramsType
@@ -68,7 +68,8 @@ getTficf_withSample cId mId nt = do
      <$> getContextsByNgramsUser cId nt
 
   countLocal  <- selectCountDocs cId
-  let countGlobal = countLocal * 10
+  let countGlobal = countLocal
+      -- * 10
 
   mapTextDoubleGlobal <- HM.map fromIntegral
                      <$> getOccByNgramsOnlyFast_withSample mId countGlobal nt

src/Gargantext/Database/Query/Table/Node/UpdateOpaleye.hs

@@ -38,7 +38,7 @@ updateHyperdataQuery i h = seq h' $ trace "updateHyperdataQuery: encoded JSON" $
    , uUpdateWith = updateEasy (\  (Node _ni _nh _nt _nu _np _nn _nd _h)
                                 -> trace "updating mate" $ Node _ni _nh _nt _nu _np _nn _nd h'
                               )
-   , uWhere      = (\row -> trace "uWhere" $ _node_id row .== pgNodeId i )
+   , uWhere      = (\row -> {-trace "uWhere" $-} _node_id row .== pgNodeId i )
    , uReturning  = rCount
    }
     where h' =  (sqlJSONB $ cs $ encode $ h)
@@ -65,5 +65,3 @@ updateNodesWithType_ nt h = do
   mapM (\n -> updateHyperdata n h) ns
 
 
-
-