Merge branch 'dev' into dev-test

package.yaml

@@ -49,6 +49,7 @@ library:
   - Gargantext.API.Admin.Types
   - Gargantext.API.Prelude
   - Gargantext.Core
+  - Gargantext.Core.Methods.Distances
   - Gargantext.Core.Types
   - Gargantext.Core.Types.Individu
   - Gargantext.Core.Types.Main
@@ -67,6 +68,8 @@ library:
   - Gargantext.Prelude
   - Gargantext.Prelude.Crypto.Pass.User
   - Gargantext.Prelude.GargDB
+  - Gargantext.Prelude.Crypto.Hash
+  - Gargantext.Prelude.Utils
   - Gargantext.Core.Text
   - Gargantext.Core.Text.Context
   - Gargantext.Core.Text.Corpus.Parsers
@@ -88,6 +91,8 @@ library:
   - Gargantext.Core.Text.Terms.WithList
   - Gargantext.Core.Text.Flow
   - Gargantext.Core.Viz.Graph
+  - Gargantext.Core.Viz.Graph.Tools
+  - Gargantext.Core.Viz.Graph.Tools.IGraph
   - Gargantext.Core.Viz.Graph.Index
   - Gargantext.Core.Viz.AdaptativePhylo
   - Gargantext.Core.Viz.Phylo.PhyloMaker
@@ -431,6 +436,7 @@ tests:
      - parsec
      - duckling
      - text
+     - unordered-containers
 #  garg-doctest:
 #    main: Main.hs
 #    source-dirs: src-doctest

src-test/Graph/Clustering.hs

+
+{-|
+Module      : Graph.Clustering
+Description : Basic tests to avoid quick regression
+Copyright   : (c) CNRS, 2017-Present
+License     : AGPL + CECILL v3
+Maintainer  : team@gargantext.org
+Stability   : experimental
+Portability : POSIX
+
+-}
+
+
+module Graph.Clustering where
+
+import Gargantext.API.Ngrams.Types (NgramsTerm(..))
+import Gargantext.Core.Viz.Graph (Graph(..))
+import Gargantext.Core.Viz.Graph.Tools (doDistanceMap)
+import Gargantext.Core.Viz.Graph.Tools.IGraph (spinglass)
+import Gargantext.Prelude
+import Test.Hspec
+import Data.HashMap.Strict (HashMap)
+import qualified Data.HashMap.Strict as HashMap
+import qualified Data.List as List
+import Gargantext.Core.Viz.Graph.Tools (PartitionMethod(..))
+import Gargantext.Core.Viz.Graph.Tools.IGraph (spinglass)
+import Gargantext.Core.Methods.Distances (Distance(..))
+
+myCooc :: HashMap (NgramsTerm, NgramsTerm) Int
+myCooc = HashMap.fromList [((NgramsTerm {unNgramsTerm = "gev au"},NgramsTerm {unNgramsTerm = "sqrt"}),12),((NgramsTerm {unNgramsTerm = "au"},NgramsTerm {unNgramsTerm = "data"}),8),((NgramsTerm {unNgramsTerm = "centralities"},NgramsTerm {unNgramsTerm = "transverse momentum"}),6),((NgramsTerm {unNgramsTerm = "au"},NgramsTerm {unNgramsTerm = "gev au"}),7),((NgramsTerm {unNgramsTerm = "d"},NgramsTerm {unNgramsTerm = "rhic"}),13),((NgramsTerm {unNgramsTerm = "p"},NgramsTerm {unNgramsTerm = "sqrt"}),27),((NgramsTerm {unNgramsTerm = "pi ^"},NgramsTerm {unNgramsTerm = "s"}),8),((NgramsTerm {unNgramsTerm = "gev"},NgramsTerm {unNgramsTerm = "p"}),27),((NgramsTerm {unNgramsTerm = "central au"},NgramsTerm {unNgramsTerm = "s"}),10),((NgramsTerm {unNgramsTerm = "au"},NgramsTerm {unNgramsTerm = "relativistic heavy ion collider"}),5),((NgramsTerm {unNgramsTerm = "eta"},NgramsTerm {unNgramsTerm = "gev"}),9),((NgramsTerm {unNgramsTerm = "phi"},NgramsTerm {unNgramsTerm = "transverse momentum"}),3),((NgramsTerm {unNgramsTerm = "centralities"},NgramsTerm {unNgramsTerm = "hadrons"}),4),((NgramsTerm {unNgramsTerm = "data"},NgramsTerm {unNgramsTerm = "gev"}),9),((NgramsTerm {unNgramsTerm = "d"},NgramsTerm {unNgramsTerm = "gev/c"}),3),((NgramsTerm {unNgramsTerm = "gev"},NgramsTerm {unNgramsTerm = "nn"}),80),((NgramsTerm {unNgramsTerm = "p"},NgramsTerm {unNgramsTerm = "particle"}),3),((NgramsTerm {unNgramsTerm = "au collisions"},NgramsTerm {unNgramsTerm = "p collisions"}),6),((NgramsTerm {unNgramsTerm = "nn"},NgramsTerm {unNgramsTerm = "sqrt"}),88),((NgramsTerm {unNgramsTerm = "centrality dependence"},NgramsTerm {unNgramsTerm = "gev/c"}),5),((NgramsTerm {unNgramsTerm = "gev"},NgramsTerm {unNgramsTerm = "gev au"}),5),((NgramsTerm {unNgramsTerm = "central au"},NgramsTerm {unNgramsTerm = "p_t"}),5),((NgramsTerm {unNgramsTerm = "relativistic heavy ion collider"},NgramsTerm {unNgramsTerm = "sqrt"}),10),((NgramsTerm {unNgramsTerm = "rhic"},NgramsTerm {unNgramsTerm = "s_nn"}),12),((NgramsTerm {unNgramsTerm = "au"},NgramsTerm {unNgramsTerm = "p"}),21),((NgramsTerm {unNgramsTerm = "data"},NgramsTerm {unNgramsTerm = "sqrt"}),6),((NgramsTerm {unNgramsTerm = "au-au collisions"},NgramsTerm {unNgramsTerm = "gev"}),12),((NgramsTerm {unNgramsTerm = "gev"},NgramsTerm {unNgramsTerm = "relativistic heavy ion collider"}),8),((NgramsTerm {unNgramsTerm = "centrality dependence"},NgramsTerm {unNgramsTerm = "rhic"}),3),((NgramsTerm {unNgramsTerm = "au"},NgramsTerm {unNgramsTerm = "eta"}),4),((NgramsTerm {unNgramsTerm = "eta"},NgramsTerm {unNgramsTerm = "sqrt"}),9),((NgramsTerm {unNgramsTerm = "nn"},NgramsTerm {unNgramsTerm = "particle"}),8),((NgramsTerm {unNgramsTerm = "au-au collisions"},NgramsTerm {unNgramsTerm = "sqrt"}),10),((NgramsTerm {unNgramsTerm = "gev/c"},NgramsTerm {unNgramsTerm = "s_nn"}),12),((NgramsTerm {unNgramsTerm = "data"},NgramsTerm {unNgramsTerm = "particle"}),4),((NgramsTerm {unNgramsTerm = "central au"},NgramsTerm {unNgramsTerm = "phenix experiment"}),4),((NgramsTerm {unNgramsTerm = "au"},NgramsTerm {unNgramsTerm = "nn"}),65),((NgramsTerm {unNgramsTerm = "mid-rapidity"},NgramsTerm {unNgramsTerm = "number"}),3),((NgramsTerm {unNgramsTerm = "p_t"},NgramsTerm {unNgramsTerm = "s_nn"}),11),((NgramsTerm {unNgramsTerm = "d"},NgramsTerm {unNgramsTerm = "not found"}),7),((NgramsTerm {unNgramsTerm = "d"},NgramsTerm {unNgramsTerm = "number"}),4),((NgramsTerm {unNgramsTerm = "nn"},NgramsTerm {unNgramsTerm = "pi ^"}),7),((NgramsTerm {unNgramsTerm = "hadrons"},NgramsTerm {unNgramsTerm = "spectra"}),3),((NgramsTerm {unNgramsTerm = "d"},NgramsTerm {unNgramsTerm = "s"}),9),((NgramsTerm {unNgramsTerm = "second part"},NgramsTerm {unNgramsTerm = "thesis"}),4),((NgramsTerm {unNgramsTerm = "eta"},NgramsTerm {unNgramsTerm = "pi ^"}),5),((NgramsTerm {unNgramsTerm = "midrapidity"},NgramsTerm {unNgramsTerm = "p collisions"}),3),((NgramsTerm {unNgramsTerm = "phenix experiment"},NgramsTerm {unNgramsTerm = "s_nn"}),13),((NgramsTerm {unNgramsTerm = "number"},NgramsTerm {unNgramsTerm = "s_nn"}),5),((NgramsTerm {unNgramsTerm = "nuclear modification factors"},NgramsTerm {unNgramsTerm = "p collisions"}),3),((NgramsTerm {unNgramsTerm = "centrality dependence"},NgramsTerm {unNgramsTerm = "number"}),4),((NgramsTerm {unNgramsTerm = "centrality dependence"},NgramsTerm {unNgramsTerm = "s"}),8),((NgramsTerm {unNgramsTerm = "mid-rapidity"},NgramsTerm {unNgramsTerm = "p"}),6),((NgramsTerm {unNgramsTerm = "lambda"},NgramsTerm {unNgramsTerm = "rhic"}),4),((NgramsTerm {unNgramsTerm = "p"},NgramsTerm {unNgramsTerm = "pi ^"}),13),((NgramsTerm {unNgramsTerm = "lambda"},NgramsTerm {unNgramsTerm = "p"}),3),((NgramsTerm {unNgramsTerm = "gev au"},NgramsTerm {unNgramsTerm = "pi ^"}),3),((NgramsTerm {unNgramsTerm = "central au"},NgramsTerm {unNgramsTerm = "nn"}),10),((NgramsTerm {unNgramsTerm = "gev/c"},NgramsTerm {unNgramsTerm = "mid-rapidity"}),7),((NgramsTerm {unNgramsTerm = "d"},NgramsTerm {unNgramsTerm = "p_t"}),3),((NgramsTerm {unNgramsTerm = "au collisions"},NgramsTerm {unNgramsTerm = "yields"}),7),((NgramsTerm {unNgramsTerm = "d"},NgramsTerm {unNgramsTerm = "phenix experiment"}),9),((NgramsTerm {unNgramsTerm = "mid-rapidity"},NgramsTerm {unNgramsTerm = "rhic"}),7),((NgramsTerm {unNgramsTerm = "central au"},NgramsTerm {unNgramsTerm = "gev/c"}),6),((NgramsTerm {unNgramsTerm = "data"},NgramsTerm {unNgramsTerm = "pi ^"}),4),((NgramsTerm {unNgramsTerm = "au collisions"},NgramsTerm {unNgramsTerm = "central collisions"}),3),((NgramsTerm {unNgramsTerm = "centrality dependence"},NgramsTerm {unNgramsTerm = "not found"}),7),((NgramsTerm {unNgramsTerm = "s"},NgramsTerm {unNgramsTerm = "s_nn"}),7),((NgramsTerm {unNgramsTerm = "centrality dependence"},NgramsTerm {unNgramsTerm = "phenix experiment"}),5),((NgramsTerm {unNgramsTerm = "data"},NgramsTerm {unNgramsTerm = "energy"}),3),((NgramsTerm {unNgramsTerm = "ratio"},NgramsTerm {unNgramsTerm = "s"}),4),((NgramsTerm {unNgramsTerm = "function"},NgramsTerm {unNgramsTerm = "nn"}),6),((NgramsTerm {unNgramsTerm = "energy"},NgramsTerm {unNgramsTerm = "p"}),4),((NgramsTerm {unNgramsTerm = "au collisions"},NgramsTerm {unNgramsTerm = "number"}),11),((NgramsTerm {unNgramsTerm = "p"},NgramsTerm {unNgramsTerm = "spectra"}),5),((NgramsTerm {unNgramsTerm = "central collisions"},NgramsTerm {unNgramsTerm = "s_nn"}),3),((NgramsTerm {unNgramsTerm = "gev/c"},NgramsTerm {unNgramsTerm = "nuclear modification factors"}),4),((NgramsTerm {unNgramsTerm = "energy"},NgramsTerm {unNgramsTerm = "nn"}),6),((NgramsTerm {unNgramsTerm = "measurements"},NgramsTerm {unNgramsTerm = "phenix experiment"}),8),((NgramsTerm {unNgramsTerm = "centralities"},NgramsTerm {unNgramsTerm = "not found"}),3),((NgramsTerm {unNgramsTerm = "mid-rapidity"},NgramsTerm {unNgramsTerm = "p collisions"}),3),((NgramsTerm {unNgramsTerm = "measurements"},NgramsTerm {unNgramsTerm = "not found"}),15),((NgramsTerm {unNgramsTerm = "centralities"},NgramsTerm {unNgramsTerm = "phenix experiment"}),9),((NgramsTerm {unNgramsTerm = "s_nn"},NgramsTerm {unNgramsTerm = "yields"}),3),((NgramsTerm {unNgramsTerm = "centralities"},NgramsTerm {unNgramsTerm = "s"}),14),((NgramsTerm {unNgramsTerm = "measurements"},NgramsTerm {unNgramsTerm = "s"}),18),((NgramsTerm {unNgramsTerm = "not found"},NgramsTerm {unNgramsTerm = "phi"}),4),((NgramsTerm {unNgramsTerm = "d"},NgramsTerm {unNgramsTerm = "yields"}),3),((NgramsTerm {unNgramsTerm = "nuclear modification factors"},NgramsTerm {unNgramsTerm = "rhic"}),5),((NgramsTerm {unNgramsTerm = "function"},NgramsTerm {unNgramsTerm = "gev au"}),3),((NgramsTerm {unNgramsTerm = "phenix experiment"},NgramsTerm {unNgramsTerm = "phi"}),3),((NgramsTerm {unNgramsTerm = "phi"},NgramsTerm {unNgramsTerm = "s"}),9),((NgramsTerm {unNgramsTerm = "gev/c"},NgramsTerm {unNgramsTerm = "midrapidity"}),4),((NgramsTerm {unNgramsTerm = "data"},NgramsTerm {unNgramsTerm = "function"}),6),((NgramsTerm {unNgramsTerm = "relativistic heavy ion collider"},NgramsTerm {unNgramsTerm = 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"spectra"},NgramsTerm {unNgramsTerm = "suppression"}),3),((NgramsTerm {unNgramsTerm = "au"},NgramsTerm {unNgramsTerm = "mid-rapidity"}),12),((NgramsTerm {unNgramsTerm = "nn"},NgramsTerm {unNgramsTerm = "s"}),89),((NgramsTerm {unNgramsTerm = "measurements"},NgramsTerm {unNgramsTerm = "spectra"}),5),((NgramsTerm {unNgramsTerm = "lambda"},NgramsTerm {unNgramsTerm = "sqrt"}),7),((NgramsTerm {unNgramsTerm = "nn"},NgramsTerm {unNgramsTerm = "phenix experiment"}),9),((NgramsTerm {unNgramsTerm = "nn"},NgramsTerm {unNgramsTerm = "number"}),9),((NgramsTerm {unNgramsTerm = "central au"},NgramsTerm {unNgramsTerm = "gev"}),10),((NgramsTerm {unNgramsTerm = "eta"},NgramsTerm {unNgramsTerm = "s"}),7),((NgramsTerm {unNgramsTerm = "gev au"},NgramsTerm {unNgramsTerm = "not found"}),7),((NgramsTerm {unNgramsTerm = "au collisions"},NgramsTerm {unNgramsTerm = "midrapidity"}),7),((NgramsTerm {unNgramsTerm = "data"},NgramsTerm {unNgramsTerm = "phenix experiment"}),3),((NgramsTerm {unNgramsTerm = "data"},NgramsTerm {unNgramsTerm = "s"}),5),((NgramsTerm {unNgramsTerm = "gev"},NgramsTerm {unNgramsTerm = "lambda"}),5),((NgramsTerm {unNgramsTerm = "p"},NgramsTerm {unNgramsTerm = "s"}),22),((NgramsTerm {unNgramsTerm = "au-au collisions"},NgramsTerm {unNgramsTerm = "not found"}),8),((NgramsTerm {unNgramsTerm = "p"},NgramsTerm {unNgramsTerm = "phenix experiment"}),13),((NgramsTerm {unNgramsTerm = "gev au"},NgramsTerm {unNgramsTerm = "s"}),8),((NgramsTerm {unNgramsTerm = "gev"},NgramsTerm {unNgramsTerm = "mid-rapidity"}),15),((NgramsTerm {unNgramsTerm = "au"},NgramsTerm {unNgramsTerm = "energy"}),8),((NgramsTerm {unNgramsTerm = "mid-rapidity"},NgramsTerm {unNgramsTerm = "ratio"}),3),((NgramsTerm {unNgramsTerm = "function"},NgramsTerm {unNgramsTerm = "particle"}),6),((NgramsTerm {unNgramsTerm = "au"},NgramsTerm {unNgramsTerm = "function"}),13),((NgramsTerm {unNgramsTerm = "energy"},NgramsTerm {unNgramsTerm = "particle"}),4),((NgramsTerm {unNgramsTerm = "measurements"},NgramsTerm {unNgramsTerm = "pi ^"}),8),((NgramsTerm {unNgramsTerm = "gev/c"},NgramsTerm {unNgramsTerm = "yields"}),5),((NgramsTerm {unNgramsTerm = "centralities"},NgramsTerm {unNgramsTerm = "pi ^"}),5),((NgramsTerm {unNgramsTerm = "gev"},NgramsTerm {unNgramsTerm = "spectra"}),7),((NgramsTerm {unNgramsTerm = "au collisions"},NgramsTerm {unNgramsTerm = "mid-rapidity"}),13),((NgramsTerm {unNgramsTerm = "au collisions"},NgramsTerm {unNgramsTerm = "lambda"}),5),((NgramsTerm {unNgramsTerm = "function"},NgramsTerm {unNgramsTerm = "gev"}),14),((NgramsTerm {unNgramsTerm = "central au"},NgramsTerm {unNgramsTerm = "centralities"}),5),((NgramsTerm {unNgramsTerm = "rhic"},NgramsTerm {unNgramsTerm = "yields"}),4),((NgramsTerm {unNgramsTerm = "number"},NgramsTerm {unNgramsTerm = "p collisions"}),3),((NgramsTerm {unNgramsTerm = "function"},NgramsTerm {unNgramsTerm = "sqrt"}),12),((NgramsTerm {unNgramsTerm = "mid-rapidity"},NgramsTerm {unNgramsTerm = "phi"}),3),((NgramsTerm {unNgramsTerm = "spectra"},NgramsTerm {unNgramsTerm = "sqrt"}),10),((NgramsTerm {unNgramsTerm = "pi ^"},NgramsTerm {unNgramsTerm = "suppression"}),3),((NgramsTerm {unNgramsTerm = "not found"},NgramsTerm {unNgramsTerm = "p collisions"}),6),((NgramsTerm {unNgramsTerm = "energy"},NgramsTerm {unNgramsTerm = "sqrt"}),10),((NgramsTerm {unNgramsTerm = "energy"},NgramsTerm {unNgramsTerm = "gev"}),9),((NgramsTerm {unNgramsTerm = "central collisions"},NgramsTerm {unNgramsTerm = "gev/c"}),4),((NgramsTerm {unNgramsTerm = "hadrons"},NgramsTerm {unNgramsTerm = "number"}),3),((NgramsTerm {unNgramsTerm = "au"},NgramsTerm {unNgramsTerm = "spectra"}),9),((NgramsTerm {unNgramsTerm = "central au"},NgramsTerm {unNgramsTerm = "suppression"}),4),((NgramsTerm {unNgramsTerm = "au collisions"},NgramsTerm {unNgramsTerm = "gev/c"}),18),((NgramsTerm {unNgramsTerm = "phi"},NgramsTerm {unNgramsTerm = "rhic"}),3),((NgramsTerm {unNgramsTerm = "function"},NgramsTerm {unNgramsTerm = "phenix experiment"}),9),((NgramsTerm {unNgramsTerm = "elliptic flow"},NgramsTerm {unNgramsTerm = "measurements"}),3),((NgramsTerm {unNgramsTerm = "function"},NgramsTerm {unNgramsTerm = "s"}),5),((NgramsTerm {unNgramsTerm = "au collisions"},NgramsTerm {unNgramsTerm = "gev au"}),12),((NgramsTerm {unNgramsTerm = "au collisions"},NgramsTerm {unNgramsTerm = "elliptic flow"}),10),((NgramsTerm {unNgramsTerm = "p"},NgramsTerm {unNgramsTerm = "suppression"}),5),((NgramsTerm {unNgramsTerm = "gev/c"},NgramsTerm {unNgramsTerm = "measurements"}),11),((NgramsTerm {unNgramsTerm = "au"},NgramsTerm {unNgramsTerm = "p collisions"}),11),((NgramsTerm {unNgramsTerm = "centralities"},NgramsTerm {unNgramsTerm = "eta"}),4),((NgramsTerm {unNgramsTerm = "gev"},NgramsTerm {unNgramsTerm = "transverse momentum"}),14),((NgramsTerm {unNgramsTerm = "gev"},NgramsTerm {unNgramsTerm = "hadrons"}),11),((NgramsTerm {unNgramsTerm = "function"},NgramsTerm {unNgramsTerm = "number"}),3),((NgramsTerm {unNgramsTerm = "energy"},NgramsTerm {unNgramsTerm = "s"}),7),((NgramsTerm {unNgramsTerm = "au collisions"},NgramsTerm {unNgramsTerm = "data"}),6),((NgramsTerm {unNgramsTerm = "measurements"},NgramsTerm {unNgramsTerm = "relativistic heavy ion collider"}),7),((NgramsTerm {unNgramsTerm = "au collisions"},NgramsTerm {unNgramsTerm = "nn"}),67),((NgramsTerm {unNgramsTerm = "ratio"},NgramsTerm {unNgramsTerm = "rhic"}),4),((NgramsTerm {unNgramsTerm = "sqrt"},NgramsTerm {unNgramsTerm = "transverse momentum"}),13),((NgramsTerm {unNgramsTerm = "hadrons"},NgramsTerm {unNgramsTerm = "sqrt"}),11),((NgramsTerm {unNgramsTerm = "p collisions"},NgramsTerm {unNgramsTerm = "sqrt"}),16),((NgramsTerm {unNgramsTerm = "function"},NgramsTerm {unNgramsTerm = "p_t"}),6),((NgramsTerm {unNgramsTerm = "centralities"},NgramsTerm {unNgramsTerm = "p"}),10),((NgramsTerm {unNgramsTerm = "measurements"},NgramsTerm {unNgramsTerm = "p"}),14),((NgramsTerm {unNgramsTerm = "centralities"},NgramsTerm {unNgramsTerm = "rhic"}),6),((NgramsTerm {unNgramsTerm = "gev"},NgramsTerm {unNgramsTerm = "p collisions"}),15),((NgramsTerm {unNgramsTerm = "measurements"},NgramsTerm {unNgramsTerm = "rhic"}),15),((NgramsTerm {unNgramsTerm = "au"},NgramsTerm {unNgramsTerm = "transverse momentum"}),7),((NgramsTerm {unNgramsTerm = "au"},NgramsTerm {unNgramsTerm = "hadrons"}),8),((NgramsTerm {unNgramsTerm = "nn"},NgramsTerm {unNgramsTerm = "suppression"}),6)]
+
+
+
+test :: IO ()
+test = hspec $ do
+  describe "Cross" $ do
+    let
+      (distanceMap,_,_) = doDistanceMap Conditional 0 myCooc
+    it "Partition test" $ do
+      partitions <- spinglass 1 distanceMap
+      let
+        result = List.length partitions > 1
+      shouldBe True result
+

src-test/Graph/Distance.hs

@@ -17,6 +17,7 @@ module Graph.Distance where
 
 import Test.Hspec
 
+{-
 import Gargantext.Core.Methods.Matrix.Accelerate.Utils (cross', matrix)
 import Gargantext.Prelude
 
@@ -26,4 +27,4 @@ test = hspec $ do
     let result = cross' $ matrix 3 ([1,1..] :: [Double])
     it "compare" $ do
       shouldBe result (matrix 3 ([2,2..] :: [Double]))
-
+-}

src-test/Main.hs

@@ -14,10 +14,11 @@ import Gargantext.Core (Lang(..))
 --import qualified Ngrams.Lang.Fr as Fr
 --import qualified Ngrams.Lang as Lang
 import qualified Ngrams.Lang.Occurrences as Occ
-import qualified Ngrams.Metrics as Metrics
-import qualified Parsers.Date as PD
-import qualified Graph.Distance as GD
-import qualified Utils.Crypto as Crypto
+import qualified Ngrams.Metrics          as Metrics
+import qualified Parsers.Date            as PD
+-- import qualified Graph.Distance          as GD
+import qualified Graph.Clustering        as Graph
+import qualified Utils.Crypto            as Crypto
 
 main :: IO ()
 main = do
@@ -25,6 +26,7 @@ main = do
 --    Lang.ngramsExtractionTest FR
 --    Lang.ngramsExtractionTest EN
 --    Metrics.main
-    PD.testFromRFC3339
+  Graph.test 
+  PD.testFromRFC3339
 --    GD.test
-    Crypto.test
+  Crypto.test

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

@@ -168,6 +168,7 @@ computeGraph cId d nt repo = do
   saveAsFileDebug "debug/my-cooc" myCooc
 
   graph <- liftBase $ cooc2graphWith Spinglass d 0 myCooc
+  saveAsFileDebug "debug/graph" graph
   pure graph
 
 
@@ -289,3 +290,9 @@ getGraphGexf :: UserId
 getGraphGexf uId nId = do
   HyperdataGraphAPI { _hyperdataAPIGraph = graph } <- getGraph uId nId
   pure $ addHeader "attachment; filename=graph.gexf" graph
+
+
+
+
+
+

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

@@ -110,14 +110,13 @@ filterByNeighbours threshold distanceMap = filteredMap
                            in List.take (round threshold) selected
                       ) indexes                 
 
-cooc2graphWith' :: ToComId a
-               => Partitions a
-               -> Distance
+
+doDistanceMap :: Distance
                -> Threshold
                -> HashMap (NgramsTerm, NgramsTerm) Int
-               -> IO Graph
-cooc2graphWith' doPartitions distance threshold myCooc = do
-  let
+               -> (Map (Int,Int) Double, Map (Index, Index) Int, Map NgramsTerm Index)
+doDistanceMap distance threshold myCooc = (distanceMap, myCooc', ti)
+  where
     -- TODO remove below
     theMatrix = Map.fromList
               $ HashMap.toList myCooc
@@ -135,8 +134,8 @@ cooc2graphWith' doPartitions distance threshold myCooc = do
 
     similarities = measure distance matCooc
     links = round (let n :: Double = fromIntegral tiSize in n * log n)
-    distanceMap = Map.fromList
-                $ List.take links
+
+    distanceMap = Map.fromList  $ List.take links
                 $ List.sortOn snd
                 $ Map.toList
                 $ case distance of
@@ -144,6 +143,16 @@ cooc2graphWith' doPartitions distance threshold myCooc = do
                     Distributional -> Map.filter (> 0)
                 $ mat2map similarities
 
+cooc2graphWith' :: ToComId a
+               => Partitions a
+               -> Distance
+               -> Threshold
+               -> HashMap (NgramsTerm, NgramsTerm) Int
+               -> IO Graph
+cooc2graphWith' doPartitions distance threshold myCooc = do
+  let
+    (distanceMap, myCooc', ti) = doDistanceMap distance threshold myCooc
+
     nodesApprox :: Int
     nodesApprox = n'
       where
@@ -151,15 +160,10 @@ cooc2graphWith' doPartitions distance threshold myCooc = do
         n' = Set.size $ Set.fromList $ as <> bs
     ClustersParams rivers _level = clustersParams nodesApprox
 
-  saveAsFileDebug "debug/the-matrix" theMatrix
-  saveAsFileDebug "debug/my-cooc-prime" myCooc'
-  saveAsFileDebug "debug/mat-cooc" matCooc
-  saveAsFileDebug "debug/similarities" similarities
-  saveAsFileDebug "debug/links" links
+{- | Debug
   saveAsFileDebug "debug/distanceMap" distanceMap
-  saveAsFileDebug "debug/nodesApprox" nodesApprox
-
   printDebug "similarities" similarities
+-}
 
   -- partitions <- if (Map.size distanceMap > 0)
   --     then doPartitions distanceMap
@@ -177,48 +181,6 @@ cooc2graphWith' doPartitions distance threshold myCooc = do
                     myCooc' bridgeness' confluence' partitions
 
 
-
--- cooc2graph :: Distance
---            -> Threshold
---            -> (Map (Text, Text) Int)
---            -> IO Graph
--- cooc2graph distance threshold myCooc = do
---   printDebug "cooc2graph" distance
---   let
---     -- TODO remove below
---     theMatrix = Map.fromList $ HashMap.toList myCooc
---     (ti, _) = createIndices theMatrix
---     myCooc' = toIndex ti theMatrix
---     matCooc = map2mat 0 (Map.size ti)
---             $ Map.filterWithKey (\(a,b) _ -> a /= b) 
---             $ Map.filter (> 1) myCooc'
---     distanceMat = measure distance matCooc
---     distanceMap = Map.filter (> threshold) $ mat2map distanceMat
-
---     nodesApprox :: Int
---     nodesApprox = n'
---       where
---         (as, bs) = List.unzip $ Map.keys distanceMap
---         n' = Set.size $ Set.fromList $ as <> bs
---     ClustersParams rivers _level = clustersParams nodesApprox
-
---   printDebug "Start" ("partitions" :: Text)
---   partitions <- if (Map.size distanceMap > 0)
---       -- then iLouvainMap 100 10 distanceMap
---       -- then hLouvain distanceMap
---       then doPartitions distanceMap
---       else panic "Text.Flow: DistanceMap is empty"
---   printDebug "End" ("partitions" :: Text)
-
---   let
---     -- bridgeness' = distanceMap
---     bridgeness' = trace ("Rivers: " <> show rivers)
---                 $ bridgeness rivers partitions distanceMap
---     confluence' = confluence (Map.keys bridgeness') 3 True False
-
---   pure $ data2graph (Map.toList $ Map.mapKeys unNgramsTerm ti)
---                     myCooc' bridgeness' confluence' partitions
-
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
 data ClustersParams = ClustersParams { bridgness :: Double

src/Gargantext/Prelude.hs

@@ -82,14 +82,18 @@ import qualified Data.List     as L hiding (head, sum)
 import qualified Data.Map      as M
 import qualified Data.Set      as Set
 import qualified Data.Vector   as V
-
+import System.FilePath.Posix (takeDirectory)
+import System.Directory (createDirectoryIfMissing)
 
 printDebug :: (Show a, MonadBase IO m) => [Char] -> a -> m ()
 printDebug msg x = liftBase . putStrLn $ msg <> " " <> show x
 -- printDebug _ _ = pure ()
 
 saveAsFileDebug :: (Show a, MonadBase IO m) => [Char] -> a -> m ()
-saveAsFileDebug fname x = liftBase . Protolude.writeFile fname $ pack $ show x
+saveAsFileDebug fname x = do
+  let dir = takeDirectory fname
+  _ <- liftBase $ createDirectoryIfMissing True dir
+  liftBase . Protolude.writeFile fname $ pack $ show x
 
 
 -- | splitEvery n == chunkAlong n n