[REBASE]

package.yaml

@@ -70,7 +70,7 @@ library:
   - Gargantext.API.Prelude
   - Gargantext.Core
   - Gargantext.Core.NodeStory
-  - Gargantext.Core.Methods.Distances
+  - Gargantext.Core.Methods.Similarities
   - Gargantext.Core.Types
   - Gargantext.Core.Types.Individu
   - Gargantext.Core.Types.Main

src/Gargantext/API/Ngrams/Tools.hs

@@ -187,11 +187,12 @@ getCoocByNgrams' f (Diagonal diag) m =
                                  <$> (fmap f $ HM.lookup t1 m)
                                  <*> (fmap f $ HM.lookup t2 m)
                )
-              | (t1,t2) <- if diag then
-                             [ (x,y) | x <- ks, y <- ks, x <= y] -- TODO if we keep a Data.Map here it might be
-                                                                 -- more efficient to enumerate all the y <= x.
-                           else
-                             listToCombi identity ks
+              | (t1,t2) <- if diag
+                              then [ (x,y) | x <- ks, y <- ks, x <= y]
+                                   -- TODO if we keep a Data.Map here it might be
+                                   -- more efficient to enumerate all the y <= x.
+                              else
+                                listToCombi identity ks
               ]
 
   where ks = HM.keys m

src/Gargantext/API/Node/Update.hs

@@ -27,7 +27,7 @@ import Gargantext.API.Admin.Types (HasSettings)
 import Gargantext.API.Ngrams.List (reIndexWith)
 --import Gargantext.API.Ngrams.Types (TabType(..))
 import Gargantext.API.Prelude (GargM, GargError, simuLogs)
-import Gargantext.Core.Methods.Distances (GraphMetric(..))
+import Gargantext.Core.Methods.Similarities (GraphMetric(..))
 import Gargantext.Core.Types.Main (ListType(..))
 import Gargantext.Core.Viz.Graph (Strength)
 import Gargantext.Core.Viz.Graph.API (recomputeGraph)

src/Gargantext/Core/Methods/Graph/MaxClique.hs

@@ -62,7 +62,7 @@ import Data.Set (fromList, toList, isSubsetOf)
 import Data.Graph.Inductive hiding (Graph, neighbors, subgraph, (&))
 import Gargantext.Core.Viz.Graph.FGL (Graph_Undirected, degree, neighbors, mkGraphUfromEdges)
 import Gargantext.Core.Viz.Graph.Tools (cooc2graph',cooc2graph'', Threshold)
-import Gargantext.Core.Methods.Distances (Distance)
+import Gargantext.Core.Methods.Similarities (Similarity)
 import Gargantext.Core.Viz.Graph.Index (createIndices, toIndex)
 import Gargantext.Core.Viz.Phylo
 -- import Debug.Trace (trace)
@@ -70,9 +70,9 @@ type Graph = Graph_Undirected
 type Neighbor = Node
 
 -- | getMaxCliques
--- TODO chose distance order
+-- TODO chose similarity order
 
-getMaxCliques :: Ord a => MaxCliqueFilter -> Distance -> Threshold -> Map (a, a) Int -> [[a]]
+getMaxCliques :: Ord a => MaxCliqueFilter -> Similarity -> Threshold -> Map (a, a) Int -> [[a]]
 getMaxCliques f d t m = map fromIndices $ getMaxCliques' t m'
   where
     m'          = toIndex to m

src/Gargantext/Core/Methods/Distances.hs → src/Gargantext/Core/Methods/Similarities.hs

 {-|
-Module      : Gargantext.Graph.Distances
-Description : Distance management tools
+Module      : Gargantext.Graph.Similarities
+Description : Similarity management tools
 Copyright   : (c) CNRS, 2017-Present
 License     : AGPL + CECILL v3
 Maintainer  : team@gargantext.org
@@ -11,32 +11,32 @@ Portability : POSIX
 
 {-# LANGUAGE Strict            #-}
 
-module Gargantext.Core.Methods.Distances
+module Gargantext.Core.Methods.Similarities
   where
 
 import Data.Aeson
 import Data.Array.Accelerate (Matrix)
 import Data.Swagger
 import GHC.Generics (Generic)
-import Gargantext.Core.Methods.Distances.Accelerate.Conditional (measureConditional)
-import Gargantext.Core.Methods.Distances.Accelerate.Distributional (logDistributional)
+import Gargantext.Core.Methods.Similarities.Accelerate.Conditional (measureConditional)
+import Gargantext.Core.Methods.Similarities.Accelerate.Distributional (logDistributional)
 import Gargantext.Prelude (Ord, Eq, Int, Double, Show)
 import Prelude (Enum, Bounded, minBound, maxBound)
 import Test.QuickCheck (elements)
 import Test.QuickCheck.Arbitrary
 
 ------------------------------------------------------------------------
-data Distance = Conditional | Distributional
+data Similarity = Conditional | Distributional
   deriving (Show, Eq)
 
-measure :: Distance -> Matrix Int -> Matrix Double
+measure :: Similarity -> Matrix Int -> Matrix Double
 measure Conditional    x = measureConditional x
 measure Distributional x = y
   where
     y = logDistributional x
 
 ------------------------------------------------------------------------
-withMetric :: GraphMetric -> Distance
+withMetric :: GraphMetric -> Similarity
 withMetric Order1 = Conditional
 withMetric Order2 = Distributional
 

src/Gargantext/Core/Methods/Distances/Accelerate/Conditional.hs → src/Gargantext/Core/Methods/Similarities/Accelerate/Conditional.hs

 {-|
-Module      : Gargantext.Core.Methods.Distances.Accelerate.Conditional
+Module      : Gargantext.Core.Methods.Similarities.Accelerate.Conditional
 Description : 
 Copyright   : (c) CNRS, 2017-Present
 License     : AGPL + CECILL v3
@@ -20,7 +20,7 @@ See Gargantext.Core.Methods.Graph.Accelerate)
 {-# LANGUAGE ScopedTypeVariables #-}
 {-# LANGUAGE ViewPatterns        #-}
 
-module Gargantext.Core.Methods.Distances.Accelerate.Conditional
+module Gargantext.Core.Methods.Similarities.Accelerate.Conditional
   where
 
 -- import qualified Data.Foldable as P (foldl1)
@@ -28,7 +28,7 @@ module Gargantext.Core.Methods.Distances.Accelerate.Conditional
 import Data.Array.Accelerate
 import Data.Array.Accelerate.Interpreter (run)
 import Gargantext.Core.Methods.Matrix.Accelerate.Utils
-import Gargantext.Core.Methods.Distances.Accelerate.SpeGen
+import Gargantext.Core.Methods.Similarities.Accelerate.SpeGen
 import qualified Gargantext.Prelude as P
 
 

src/Gargantext/Core/Methods/Distances/Accelerate/Distributional.hs → src/Gargantext/Core/Methods/Similarities/Accelerate/Distributional.hs

 {-|
-Module      : Gargantext.Core.Methods.Distances.Accelerate.Distributional
+Module      : Gargantext.Core.Methods.Similarities.Accelerate.Distributional
 Description :
 Copyright   : (c) CNRS, 2017-Present
 License     : AGPL + CECILL v3
@@ -8,7 +8,7 @@ Stability   : experimental
 Portability : POSIX
 
 
-* Distributional Distance metric
+* Distributional Similarity metric
 __Definition :__ Distributional metric is a relative metric which depends on the
 selected list, it represents structural equivalence of mutual information.
 
@@ -41,7 +41,7 @@ where $n_{ij}$ is the cooccurrence between term $i$ and term $j$
 {-# LANGUAGE ViewPatterns        #-}
 {-# LANGUAGE GADTs               #-}
 
-module Gargantext.Core.Methods.Distances.Accelerate.Distributional
+module Gargantext.Core.Methods.Similarities.Accelerate.Distributional
   where
 
 -- import qualified Data.Foldable as P (foldl1)

src/Gargantext/Core/Methods/Distances/Accelerate/SpeGen.hs → src/Gargantext/Core/Methods/Similarities/Accelerate/SpeGen.hs

 {-|
-Module      : Gargantext.Core.Methods.Distances.Accelerate.SpeGen
+Module      : Gargantext.Core.Methods.Similarities.Accelerate.SpeGen
 Description : 
 Copyright   : (c) CNRS, 2017-Present
 License     : AGPL + CECILL v3
@@ -20,7 +20,7 @@ See Gargantext.Core.Methods.Graph.Accelerate)
 {-# LANGUAGE ScopedTypeVariables #-}
 {-# LANGUAGE ViewPatterns        #-}
 
-module Gargantext.Core.Methods.Distances.Accelerate.SpeGen
+module Gargantext.Core.Methods.Similarities.Accelerate.SpeGen
   where
 
 -- import qualified Data.Foldable as P (foldl1)

src/Gargantext/Core/Methods/Distances/Conditional.hs → src/Gargantext/Core/Methods/Similarities/Conditional.hs

 {-|
-Module      : Gargantext.Core.Methods.Distances
+Module      : Gargantext.Core.Methods.Similarities
 Description : 
 Copyright   : (c) CNRS, 2017-Present
 License     : AGPL + CECILL v3
@@ -12,7 +12,7 @@ Motivation and definition of the @Conditional@ distance.
 
 {-# LANGUAGE BangPatterns      #-}
 {-# LANGUAGE Strict            #-}
-module Gargantext.Core.Methods.Distances.Conditional
+module Gargantext.Core.Methods.Similarities.Conditional
   where
 
 import Control.DeepSeq (NFData)

src/Gargantext/Core/Methods/Distances/Distributional.hs → src/Gargantext/Core/Methods/Similarities/Distributional.hs

 {-|
-Module      : Gargantext.Core.Methods.Distances.Distributional
+Module      : Gargantext.Core.Methods.Similarities.Distributional
 Description :
 Copyright   : (c) CNRS, 2017-Present
 License     : AGPL + CECILL v3
@@ -14,7 +14,7 @@ Motivation and definition of the @Distributional@ distance.
 {-# LANGUAGE Strict            #-}
 
 
-module Gargantext.Core.Methods.Distances.Distributional
+module Gargantext.Core.Methods.Similarities.Distributional
   where
 
 import Data.Matrix hiding (identity)

src/Gargantext/Core/Text/Metrics.hs

@@ -23,7 +23,7 @@ import Data.Map (Map)
 import Data.Monoid (Monoid, mempty)
 import Data.HashMap.Strict (HashMap)
 import Data.Semigroup (Semigroup)
-import Gargantext.Core.Methods.Distances.Accelerate.SpeGen
+import Gargantext.Core.Methods.Similarities.Accelerate.SpeGen
 import Gargantext.Core.Statistics (pcaReduceTo, Dimension(..))
 import Gargantext.Core.Viz.Graph.Index
 import Gargantext.Prelude

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

@@ -39,7 +39,7 @@ import Gargantext.Prelude
 -- starting as an API rexporting main functions of the great lib
 -- text-metrics of Mark Karpov
 
--- | Levenshtein Distance
+-- | Levenshtein Similarity
 -- In information theory, Linguistics and computer science, 
 -- the Levenshtein distance is a string metric for measuring 
 -- the difference between two sequences.
@@ -86,7 +86,7 @@ overlap = DTM.overlap
 jaccard :: Text -> Text -> Ratio Int
 jaccard = DTM.jaccard
 
--- | Hamming Distance
+-- | Hamming Similarity
 -- In information theory, the Hamming distance between two strings of
 -- equal length is the number of positions at which the corresponding
 -- symbols are different. In other words, it measures the minimum number of

src/Gargantext/Core/Viz/Graph.hs

@@ -25,7 +25,7 @@ import qualified Data.Text as T
 import qualified Text.Read as T
 
 import Gargantext.API.Ngrams.Types (NgramsTerm(..), NgramsRepoElement(..), mSetToList)
-import Gargantext.Core.Methods.Distances (GraphMetric)
+import Gargantext.Core.Methods.Similarities (GraphMetric)
 import Gargantext.Core.Types (ListId)
 import Gargantext.Database.Admin.Types.Hyperdata.Prelude
 import Gargantext.Database.Admin.Types.Node (NodeId)

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

@@ -27,7 +27,7 @@ import Gargantext.API.Admin.EnvTypes (GargJob(..), Env)
 import Gargantext.API.Admin.Orchestrator.Types
 import Gargantext.API.Ngrams.Tools
 import Gargantext.API.Prelude
-import Gargantext.Core.Methods.Distances (Distance(..), GraphMetric(..), withMetric)
+import Gargantext.Core.Methods.Similarities (Similarity(..), GraphMetric(..), withMetric)
 import Gargantext.Core.NodeStory
 import Gargantext.Core.Types.Main
 import Gargantext.Core.Viz.Graph
@@ -101,7 +101,7 @@ getGraph _uId nId = do
   listId <- defaultList cId
   repo <- getRepo [listId]
 
-  -- TODO Distance in Graph params
+  -- TODO Similarity in Graph params
   case graph of
     Nothing     -> do
         let defaultMetric          = Order1
@@ -129,16 +129,16 @@ recomputeGraph :: FlowCmdM env err m
                -> Maybe Strength
                -> Bool
                -> m Graph
-recomputeGraph _uId nId method maybeDistance maybeStrength force = do
+recomputeGraph _uId nId method maybeSimilarity maybeStrength force = do
   nodeGraph <- getNodeWith nId (Proxy :: Proxy HyperdataGraph)
   let
     graph  = nodeGraph ^. node_hyperdata . hyperdataGraph
     camera = nodeGraph ^. node_hyperdata . hyperdataCamera
     graphMetadata = graph ^? _Just . graph_metadata . _Just
     listVersion   = graph ^? _Just . graph_metadata . _Just . gm_list . lfg_version
-    graphMetric   = case maybeDistance of
+    graphMetric   = case maybeSimilarity of
                       Nothing -> graph ^? _Just . graph_metadata . _Just . gm_metric
-                      _       -> maybeDistance
+                      _       -> maybeSimilarity
     similarity = case graphMetric of
                    Nothing -> withMetric Order1
                    Just m  -> withMetric m
@@ -164,7 +164,7 @@ recomputeGraph _uId nId method maybeDistance maybeStrength force = do
 
   case graph of
     Nothing     -> do
-      mt     <- defaultGraphMetadata cId "Title" repo (fromMaybe Order1 maybeDistance) strength
+      mt     <- defaultGraphMetadata cId "Title" repo (fromMaybe Order1 maybeSimilarity) strength
       g <- computeG $ Just mt
       pure $ trace "[G.V.G.API.recomputeGraph] Graph empty, computed" g
     Just graph' -> if (listVersion == Just v) && (not force)
@@ -177,27 +177,24 @@ recomputeGraph _uId nId method maybeDistance maybeStrength force = do
 computeGraph :: FlowCmdM env err m
              => CorpusId
              -> PartitionMethod
-             -> Distance
+             -> Similarity
              -> Strength
              -> NgramsType
              -> NodeListStory
              -> m Graph
-computeGraph cId method d strength nt repo = do
-  lId  <- defaultList cId
+computeGraph corpusId method similarity strength nt repo = do
+  lId  <- defaultList corpusId
   lIds <- selectNodesWithUsername NodeList userMaster
   let ngs = filterListWithRoot [MapTerm]
           $ mapTermListRoot [lId] nt repo
 
-  !myCooc <- HashMap.filter (>1) -- Removing the hapax (ngrams with 1 cooc)
+             -- Removing the hapax (ngrams with 1 cooc)
+  !myCooc <- HashMap.filter (>1)
          <$> getCoocByNgrams (Diagonal True)
          <$> groupNodesByNgrams ngs
-         <$> getContextsByNgramsOnlyUser cId (lIds <> [lId]) nt (HashMap.keys ngs)
-
-  graph <- liftBase $ cooc2graphWith method d 0 strength myCooc
+         <$> getContextsByNgramsOnlyUser corpusId (lIds <> [lId]) nt (HashMap.keys ngs)
 
-  --listNgrams <- getListNgrams [lId] nt
-  --let graph' = mergeGraphNgrams graph (Just listNgrams)
-  -- saveAsFileDebug "/tmp/graphWithNodes" graph'
+  graph <- liftBase $ cooc2graphWith method similarity 0 strength myCooc
 
   pure graph
 

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

 {-|
-Module      : Gargantext.Graph.Distances.Utils
+Module      : Gargantext.Graph.Similarities.Utils
 Description : Tools to compute distances from Cooccurrences
 Copyright   : (c) CNRS, 2017-Present
 License     : AGPL + CECILL v3

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

@@ -22,8 +22,8 @@ import Data.Swagger hiding (items)
 import GHC.Float (sin, cos)
 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.Similarities (Similarity(..), measure)
+import Gargantext.Core.Methods.Similarities.Conditional (conditional)
 import Gargantext.Core.Statistics
 import Gargantext.Core.Viz.Graph
 import Gargantext.Core.Viz.Graph.Bridgeness (bridgeness, Partitions, ToComId(..))
@@ -65,7 +65,7 @@ defaultClustering x = spinglass 1 x
 type Threshold = Double
 
 
-cooc2graph' :: Ord t => Distance
+cooc2graph' :: Ord t => Similarity
                      -> Double
                      -> Map (t, t) Int
                      -> Map (Index, Index) Double
@@ -87,7 +87,7 @@ cooc2graph' distance threshold myCooc
 
 -- coocurrences graph computation
 cooc2graphWith :: PartitionMethod
-               -> Distance
+               -> Similarity
                -> Threshold
                -> Strength
                -> HashMap (NgramsTerm, NgramsTerm) Int
@@ -100,13 +100,13 @@ cooc2graphWith Infomap   = cooc2graphWith' (infomap "--silent --two-level -N2")
 
 cooc2graphWith' :: ToComId a
                => Partitions a
-               -> Distance
+               -> Similarity
                -> Threshold
                -> Strength
                -> HashMap (NgramsTerm, NgramsTerm) Int
                -> IO Graph
-cooc2graphWith' doPartitions distance threshold strength myCooc = do
-  let (distanceMap, diag, ti) = doDistanceMap distance threshold strength myCooc
+cooc2graphWith' doPartitions similarity threshold strength myCooc = do
+  let (distanceMap, diag, ti) = doSimilarityMap similarity threshold strength myCooc
   distanceMap `seq` diag `seq` ti `seq` return ()
 
 --{- -- Debug
@@ -134,7 +134,7 @@ cooc2graphWith' doPartitions distance threshold strength myCooc = do
 
 type Reverse = Bool
 
-doDistanceMap :: Distance
+doSimilarityMap :: Similarity
               -> Threshold
               -> Strength
               -> HashMap (NgramsTerm, NgramsTerm) Int
@@ -142,7 +142,7 @@ doDistanceMap :: Distance
                  , Map (Index, Index) Int
                  , Map NgramsTerm Index
                  )
-doDistanceMap Distributional threshold strength myCooc = (distanceMap, toIndex ti diag, ti)
+doSimilarityMap Distributional threshold strength myCooc = (distanceMap, toIndex ti diag, ti)
   where
     -- TODO remove below
     (diag, theMatrix) = Map.partitionWithKey (\(x,y) _ -> x == y)
@@ -168,7 +168,7 @@ doDistanceMap Distributional threshold strength myCooc = (distanceMap, toIndex t
                 $ (\m -> m `seq` Map.filter (> threshold) m)
                 $ similarities `seq` mat2map similarities
 
-doDistanceMap Conditional threshold strength myCooc = (distanceMap, toIndex ti myCooc', ti)
+doSimilarityMap Conditional threshold strength myCooc = (distanceMap, toIndex ti myCooc', ti)
   where
     myCooc' = Map.fromList $ HashMap.toList myCooc
     (ti, _it) = createIndices myCooc'
@@ -302,7 +302,7 @@ layout m n gen = maybe (panic "") identity $ Map.lookup n $ coord
 
 -----------------------------------------------------------------------------
 -- MISC Tools
-cooc2graph'' :: Ord t => Distance
+cooc2graph'' :: Ord t => Similarity
                       -> Double
                       -> Map (t, t) Int
                       -> Map (Index, Index) Double

src/Gargantext/Core/Viz/Phylo/PhyloMaker.hs

@@ -21,7 +21,7 @@ import Data.Vector (Vector)
 import Debug.Trace (trace)
 import Prelude (floor)
 
-import Gargantext.Core.Methods.Distances (Distance(Conditional))
+import Gargantext.Core.Methods.Similarities (Similarity(Conditional))
 import Gargantext.Core.Methods.Graph.MaxClique (getMaxCliques)
 import Gargantext.Core.Text.Context (TermList)
 import Gargantext.Core.Text.Metrics.FrequentItemSet (fisWithSizePolyMap, fisWithSizePolyMap', Size(..))

src/Gargantext/Core/Viz/Phylo/SynchronicClustering.hs

@@ -210,8 +210,8 @@ synchronicClustering phylo =
      in toNextScale phylo $ levelUpAncestors $ concat newBranches'
 
 
--- synchronicDistance :: Phylo -> Level -> String
--- synchronicDistance phylo lvl = 
+-- synchronicSimilarity :: Phylo -> Level -> String
+-- synchronicSimilarity phylo lvl = 
 --     foldl' (\acc branch -> 
 --              acc <> (foldl' (\acc' period ->
 --                               acc' <> let prox  = phyloProximity $ getConfig phylo