[FEAT] from CSV file added

app/Main.hs

@@ -4,10 +4,13 @@ module Main where
 
 import Data.Set as Set
 import Data.String.Conversions (cs)
+import System.Environment (getArgs)
 import Data.Text (Text)
+import Graph.BAC.Clustering
 import Graph.BAC.ProxemyOptim
 import Graph.BAC.ProxemyOptim
 import Graph.FGL
+import Graph.Tools.Import
 import Prelude (String)
 import Protolude
 import qualified Data.IntMap                       as Dict
@@ -15,15 +18,16 @@ import qualified Data.List as List
 import qualified Eigen.Matrix as Matrix
 import qualified Eigen.SparseMatrix as SMatrix
 import qualified Prelude as Prelude
+import qualified Data.Graph.Inductive.PatriciaTree as DGIP
 
 
 main :: IO ()
 main = do
-  m <- randomAdjacency
+  fp <- getArgs
+  (m,g) <- case fp of
+    []    -> getUnlabGraph Random
+    [fp'] -> getUnlabGraph (WithFile fp')
+
   let
-    g :: Graph () ()
-    g = mkGraphUfromEdges
-      $ List.map (\(x,y,_) -> (x,y))
-      $ SMatrix.toList m
-    result = withG g (identity  . (clusteringOptim 3 Conf))
+    result = withG g (parts  . (clusteringOptim 3 Conf))
   print (result)

app/Main2.hs

-{-# LANGUAGE NoImplicitPrelude   #-}
-
-module Main2 where
-
-import Graph.Tools
-import Graph.BAC.Clustering
-import System.Environment (getArgs)
-import Protolude
-
-
-main :: IO ()
-main = do
-  [fp]    <- getArgs
-  graph <- readFileGraph TestGraph fp
-  print (clusterGraph 3 graph)
-
-  
-

gargantext-graph.cabal

@@ -4,7 +4,7 @@ cabal-version: 1.12
 --
 -- see: https://github.com/sol/hpack
 --
--- hash: 4cecc6b992a2dda8a33d66136d8ffcda1eb4fcfed9fb2a21df529821278d524d
+-- hash: c963b0693d31715c24d7005b13eb4c408cd00c23009b3e68b6dbf329a47db200
 
 name:           gargantext-graph
 version:        0.1.0.0
@@ -37,7 +37,10 @@ library
       Graph.BAC.Types
       Graph.FGL
       Graph.IGraph
-      Graph.Tools
+      Graph.Tools.CSV
+      Graph.Tools.Import
+      Graph.Tools.Random
+      Graph.Types
   other-modules:
       Paths_gargantext_graph
   hs-source-dirs:
@@ -68,12 +71,11 @@ library
 executable gargantext-graph-exe
   main-is: Main.hs
   other-modules:
-      Main2
       Paths_gargantext_graph
   hs-source-dirs:
       app
   default-extensions: DataKinds FlexibleInstances OverloadedStrings
-  ghc-options: -O2 -threaded -rtsopts -with-rtsopts=-N -fprof-auto
+  ghc-options: -O2 -threaded -rtsopts -with-rtsopts=-N -fprof-auto -Wmissing-signatures -Wcompat
   build-depends:
       accelerate
     , accelerate-arithmetic

package.yaml

@@ -58,8 +58,8 @@ executables:
     - -rtsopts
     - -with-rtsopts=-N
     - -fprof-auto
-      # - -Wmissing-signatures
-      # - -Wcompat
+    - -Wmissing-signatures
+    - -Wcompat
     dependencies:
     - gargantext-graph
 

run

 #!/bin/bash
 
-#~/.local/bin/gargantext-graph-exe $1 +RTS -p # -sstderr
-time ~/.local/bin/gargantext-graph-exe +RTS -p # -sstderr
+~/.local/bin/gargantext-graph-exe $1 +RTS -p # -sstderr
+#time ~/.local/bin/gargantext-graph-exe +RTS -p # -sstderr

src/Graph/BAC/ProxemyOptim.hs

@@ -44,6 +44,7 @@ import Eigen.Matrix (sum)
 import Eigen.SparseMatrix (SparseMatrix, SparseMatrixXd, (!), toMatrix)
 import GHC.TypeLits (KnownNat, Nat, SomeNat(SomeNat), type(+), natVal, sameNat, someNatVal)
 import Graph.FGL
+import Graph.Types
 import Prelude (String, readLn)
 import Protolude hiding (sum, natVal)
 import qualified Eigen.Matrix as DenseMatrix
@@ -91,7 +92,6 @@ type Length      = Int
 
 -- | A finite Graph is a Graph whose number of Nodes is a KnownNat
 data FiniteGraph (n :: Nat) a b = FiniteGraph (Graph a b)
-type Graph a b = DGI.Gr a b
 
 data Clustering a = ClusteringIs { parts :: !(Dict (Set a))
                                  , index :: !(Dict Int)
@@ -124,13 +124,9 @@ type ProxemyMatrix    n = MatrixD n
 type ConfluenceMatrix n = MatrixD n
 type ModularityMatrix n = MatrixD n
 
-type MatrixD          n = DenseMatrix.Matrix n n Double
-type MatrixS          n = SparseMatrix n n Double
-
 data SimilarityMatrix n = SimConf !(ConfluenceMatrix n)
                         | SimMod  !(ModularityMatrix n)
 
-type Dict = IntMap
 
 -----
 adjacent :: KnownNat n
@@ -445,25 +441,4 @@ sumWith dir f m = VS.fromList
             somme m' = map (sum . SMatrix.toMatrix) m'
 
 --------------------------------------------
--- | Random Matrix && Graph
--- TODO random matrix of any size for the tests
-
-randomMatrix :: IO (MatrixD 100)
-randomMatrix = DMatrix.random
-
-{-
-matrix2graph :: forall   n
-              . (KnownNat n)
-             => MatrixS n
-             -> FiniteGraph n () ()
-matrix2graph m = withG (mkGraphUfromEdges $ map (\(x,y,_) -> (x,y)) $ SMatrix.toList m)
-                       identity
--}
 
-randomAdjacency :: IO (MatrixS 100)
-randomAdjacency = do
-  m1 <- randomMatrix
-  m2 <- randomMatrix
-  pure $ SMatrix.fromMatrix
-       $ DMatrix.imap (\i j v -> if i < j && v > 0.9 then 1 else 0)
-       $ DMatrix.mul m1 m2

src/Graph/FGL.hs

-{-| Module      : Gargantext.Core.Viz.Graph.DGI
+{-| Module      : Graph.FGL
 Description : DGI main functions used in Garg
 Copyright   : (c) CNRS, 2017-Present
 License     : AGPL + CECILL v3
@@ -6,7 +6,9 @@ Maintainer  : team@gargantext.org
 Stability   : experimental
 Portability : POSIX
 
-Main DGI funs/types to ease portability with IGraph.
+This is supposed to be the main Graph funs/types of the library.
+
+Includes some tools to ease portability with IGraph.
 
 -}
 
@@ -17,49 +19,50 @@ Main DGI funs/types to ease portability with IGraph.
 module Graph.FGL where
 
 import Protolude
-import Graph.Tools (uniq)
+import Graph.Types
+import Graph.Tools.CSV (uniq)
 import qualified Data.List                         as List
-import qualified Data.IntMap                       as IntMap
+import qualified Data.IntMap                       as Dict
 import qualified Data.Set                          as Set
+import qualified Data.Graph.Inductive              as Graph
 import qualified Data.Graph.Inductive              as DGI
 import qualified Data.Graph.Inductive.PatriciaTree as DGIP
 import qualified Data.Map                          as Map
 ------------------------------------------------------------------
 ------------------------------------------------------------------
 -- | Main Types
-type Node = DGI.Node -- Int
-type Edge = DGI.Edge -- (Int, Int)
+type Node = Graph.Node -- Int
+type Edge = Graph.Edge -- (Int, Int)
 
 ------------------------------------------------------------------
 -- | Main Functions
-mkGraph :: [Node] -> [Edge] -> DGIP.Gr () ()
-mkGraph = DGI.mkUGraph
+mkGraph :: [Graph.Node] -> [Graph.Edge] -> Graph () ()
+mkGraph = Graph.mkUGraph
 
-neighbors :: DGIP.Gr a b -> Node -> [Node]
-neighbors = DGI.neighbors
+neighbors :: Graph a b -> Graph.Node -> [Graph.Node]
+neighbors = Graph.neighbors
 
 -- TODO optimize
-edges :: DGI.DynGraph gr => gr a b -> [Edge]
-edges g = uniq        $ DGI.edges g
-
+edges :: Graph.DynGraph gr => gr a b -> [Graph.Edge]
+edges g = uniq $ Graph.edges g
 
-nodes :: DGIP.Gr a b -> [Node]
-nodes = DGI.nodes
+nodes :: Graph a b -> [Graph.Node]
+nodes = Graph.nodes
 
 ------------------------------------------------------------------------
 -- | Graph Tools
-filterNeighbors :: DGIP.Gr a b -> Node -> [Node]
+filterNeighbors :: Graph a b -> Graph.Node -> [Graph.Node]
 filterNeighbors g n = List.nub $ neighbors g n
 
 -- Q: why not D.G.I.deg ? (Int as result)
-degree :: (DGI.DynGraph gr, Num weight) => gr a weight -> Node -> weight
+degree :: (Graph.DynGraph gr, Num weight) => gr a weight -> Node -> weight
 degree g n = sum
-           $ IntMap.elems
-           $ IntMap.fromListWith (+)
+           $ Dict.elems
+           $ Dict.fromListWith (+)
            $ map swap
-           $ DGI.lneighbors g n
+           $ Graph.lneighbors g n
 
-vcount :: DGIP.Gr a b -> Double
+vcount :: Graph a b -> Double
 vcount = fromIntegral . Set.size . Set.fromList . nodes
 
 
@@ -73,29 +76,29 @@ ecount = sum
 -- | HyperGraph
 
 {- TODO ?
-fromHypergraph :: IntMap (Set Node) -> DGI.Gr a Int -> DGI.Gr () ()
+fromHypergraph :: Dict (Set Node) -> DGI.Gr a Int -> DGI.Gr () ()
 fromHypergraph = undefined
 -}
 ------------------------------------------------------------------------
 toHypergraph ::  (Num b, Ord b, Fractional b, Monoid a, Ord a)
-             => IntMap (Set Node)
+             => Dict (Set Node)
              -> DGIP.Gr a b
              -> DGIP.Gr a b
 toHypergraph m g = toHypergraph' m g fromIntegral
 
 
 toHypergraph' :: (Num b, Ord b, Fractional b, Monoid a, Ord a)
-              => IntMap (Set Node)
-              -> DGIP.Gr a b
+              => Dict (Set Node)
+              -> Graph a b
               -> (Int -> b)
-              -> DGIP.Gr a b
-toHypergraph' m g f = DGI.mkGraph ns es
+              -> Graph a b
+toHypergraph' m g f = Graph.mkGraph ns es
   where
-    vs = IntMap.toList m
+    vs = Dict.toList m
     ns = map (\(n,ns) -> (n, List.foldl' (\m l -> m <> l) mempty
                              $ catMaybes
                              $ Set.toList
-                             $ Set.map (DGI.lab g) ns
+                             $ Set.map (Graph.lab g) ns
                         )
              ) vs
     es = selfNodes <> nbors
@@ -111,56 +114,61 @@ toHypergraph' m g f = DGI.mkGraph ns es
 
 type ClusterId = Int
 weightedNeighbors :: (Num b, Ord b)
-                   => IntMap ClusterId
-                   -> DGIP.Gr a b
+                   => Dict ClusterId
+                   -> Graph a b
                    -> (Node, Set Node)
                    -> [(Node,Node,b)]
 weightedNeighbors m g (n,ns) = catMaybes
-                             $ map (\(n',w) -> (,,) <$> Just n <*> IntMap.lookup n' m <*> Just w)
-                             $ IntMap.toList
+                             $ map (\(n',w) -> (,,) <$> Just n <*> Dict.lookup n' m <*> Just w)
+                             $ Dict.toList
                              $ hasNeighbors g ns
   {- TODO inverse 
     where
-      withEdge x y w = (,,) <$> Just n <*> IntMap.lookup n' m <*> Just w)
+      withEdge x y w = (,,) <$> Just n <*> Dict.lookup n' m <*> Just w)
   -}
 
-invIntMap :: IntMap (Set Node) -> IntMap ClusterId
-invIntMap m = IntMap.fromList
+invIntMap :: Dict (Set Node) -> Dict ClusterId
+invIntMap m = Dict.fromList
             $ List.concat
             $ map swp
-            $ IntMap.toList m
+            $ Dict.toList m
   where
     swp (n, ns) = List.zip (Set.toList ns) (cycle [n])
-------------------------------------------------------------------------
+
 ------------------------------------------------------------------------
 ------------------------------------------------------------------------
 class HasNeighbors a where
   hasNeighbors :: (Num b, Ord b, Ord a)
-                => DGIP.Gr a' b -> a -> IntMap b
+                => Graph a' b -> a -> Dict b
 
 instance HasNeighbors Node where
-  hasNeighbors g n = IntMap.fromListWith (+)
+  hasNeighbors g n = Dict.fromListWith (+)
                     $ map swap
-                    $ DGI.lneighbors g n
+                    $ Graph.lneighbors g n
 
 instance HasNeighbors (Set Node) where
-  hasNeighbors g s0 = Set.foldl' (\m k -> IntMap.delete k m) (intMap g s0) s0
-    where
-      intMap :: (Num b, Ord b, HasNeighbors c, Ord c)
-           => DGIP.Gr a b -> Set c -> IntMap b
-      intMap g s = IntMap.unionsWith (+)
+  hasNeighbors g s0 = Set.foldl' (\m k -> Dict.delete k m) (toDict g s0) s0
+
+
+
+toDict :: (Num b, Ord b, HasNeighbors c, Ord c)
+       => DGIP.Gr a b -> Set c -> Dict b
+toDict g s = Dict.unionsWith (+)
            $ Set.map (hasNeighbors g) s
 
 ------------------------------------------------------------------------
 -- | Tools
-hasWeight :: DGIP.Gr a b -> Set Node -> (Int -> b) -> b
+hasWeight :: Graph a b -> Set Node -> (Int -> b) -> b
 hasWeight g ns f = f
                  $ List.length
                  $ edges
-                 $ DGI.subgraph (Set.toList ns) g
+                 $ Graph.subgraph (Set.toList ns) g
+
+------------------------------------------------------------------------
+
 
 ------------------------------------------------------------------------
-mkGraphUfromEdges :: [(Int, Int)] -> DGIP.Gr () ()
+mkGraphUfromEdges :: [(Int, Int)] -> Graph () ()
 mkGraphUfromEdges es = mkGraph ns es
   where
     ns = List.nub (a <> b)
@@ -168,7 +176,7 @@ mkGraphUfromEdges es = mkGraph ns es
         (a, b) = List.unzip es
 
 
-mkLGraphfromEdges :: [(Int, Int, Double)] -> DGIP.Gr () Double
+mkLGraphfromEdges :: [(Int, Int, Double)] -> Graph () Double
 mkLGraphfromEdges es = DGI.mkGraph ns es
   where
     ns = List.zip (List.nub (a <> b)) (List.cycle [()])

src/Graph/Tools.hs

-{-| Module      : Graph.Tools
-Description :
-Copyright   : (c) CNRS, Alexandre Delanoë
-License     : AGPL + CECILL v3
-Maintainer  : alexandre+dev@delanoe.org
-Stability   : experimental
-Portability : POSIX
-
-
--}
-
-{-# LANGUAGE ConstraintKinds #-}
-{-# LANGUAGE InstanceSigs    #-}
-{-# LANGUAGE NoImplicitPrelude       #-}
-
-
-module Graph.Tools where
-
-import Data.Csv
-import Data.Text (pack, splitOn, unpack)
-import Data.Vector hiding (map, uniq)
-import Prelude (read)
-import Protolude
-import qualified Data.Map                          as Map
-import qualified Data.ByteString.Lazy              as BL
-import qualified Data.Graph.Inductive              as DGI
-import qualified Data.Graph.Inductive.PatriciaTree as DGIP
-import qualified Data.List                         as List
-import qualified Data.Set                          as Set
-import qualified Data.Vector                       as Vector
-
-------------------------------------------------------------------------
-uniq :: [DGI.Edge] -> [DGI.Edge]
-uniq ns = Set.toList
-        $ Set.fromList
-        $ map (\(n1,n2)
-                -> if n1 <= n2
-                      then (n1,n2)
-                      else (n2,n1)
-              ) ns
-
-
-uniq' :: [(Int,Int,Double)] -> [(Int,Int,Double)]
-uniq' ns = map (\(n1,n2) -> (n1,n2,1))
-         $ Map.keys
-         $ Map.fromListWith (+)
-         $ map (\(n1,n2,w)
-                  -> if n1 <= n2
-                        then ((n1,n2), w)
-                        else ((n2,n1), w)
-                ) ns
-
-------------------------------------------------------------------------
-
-data FileGraph = CillexGraph | TestGraph
-
-readFileGraph :: FileGraph -> FilePath -> IO (DGIP.Gr [Text] Double)
-readFileGraph CillexGraph fp = toGraph <$> snd <$> readFileCsvCillex fp
-readFileGraph TestGraph   fp = toGraph <$> snd <$> readFileCsvTest   fp
-
-
-toGraph :: ToNode a => Vector a -> (DGIP.Gr [Text] Double)
-toGraph vs = DGI.mkGraph ns (uniq' $ List.concat es)
-  where
-    (ns,es) = List.unzip
-            $ Vector.toList
-            $ Vector.map toNode vs
-
-------------------------------------------------------------------------
-class ToNode a where
-  toNode :: a -> ((Int, [Text]), [(Int,Int,Double)])
-
-instance ToNode CillexCsv
-  where
-    toNode :: CillexCsv -> ((Int, [Text]), [(Int,Int,Double)])
-    toNode (CillexCsv n v _ _ l) = (ln, es)
-      where
-        ln = (n, [l])
-        es = List.zip3 (cycle [n]) ns (cycle [1])
-        ns = map (read . unpack) $ splitOn "," v
-
-instance ToNode TestCsv
-  where
-    toNode :: TestCsv -> ((Int, [Text]), [(Int,Int,Double)])
-    toNode (TestCsv n v l) = (ln, es)
-      where
-        ln = (n, map show [l])
-        es = List.zip3 (cycle [n]) ns (cycle [1])
-        ns = map (read . unpack) $ splitOn "," v
-
-------------------------------------------------------------------------
-readFileCsvCillex :: FilePath -> IO (Header, Vector CillexCsv)
-readFileCsvCillex = fmap readWith . BL.readFile
-
-readFileCsvTest :: FilePath -> IO (Header, Vector TestCsv)
-readFileCsvTest = fmap readWith . BL.readFile
-
-csvDecodeOptions :: DecodeOptions
-csvDecodeOptions = defaultDecodeOptions {decDelimiter = delimiter}
-  where
-    delimiter :: Word8
-    delimiter = fromIntegral $ ord ','
-
-readWith :: FromNamedRecord a => BL.ByteString -> (Header, Vector a)
-readWith bs = case decodeByNameWith csvDecodeOptions bs of
-      Left e        -> panic (pack e)
-      Right csvDocs -> csvDocs
-
-------------------------------------------------------------------------
-data TestCsv =
-  TestCsv { rc_node    :: Int
-          , rc_voisins :: Text
-          , rc_id      :: Double
-          }
-    deriving (Show)
-
-instance FromNamedRecord TestCsv where
-  parseNamedRecord r = TestCsv <$> r .: "@node: #id_pdg"
-                               <*> r .: "%+voisins"
-                               <*> r .: "label"
-------------------------------------------------------------------------
-data CillexCsv =
-  CillexCsv { node    :: Int
-            , voisins :: Text
-            , id      :: Double
-            , lemme   :: Text
-            , label   :: Text
-            }
-    deriving (Show)
-
-instance FromNamedRecord CillexCsv where
-  parseNamedRecord r = CillexCsv <$> r .: "@node: #id_pdg"
-                                 <*> r .: "%+voisins"
-                                 <*> r .: "id"
-                                 <*> r .: "lemme"
-                                 <*> r .: "label"
-
-{-
-cillexCsvHeader =
-  header [ "@node: #id_pdg"
-         , "%+voisins"
-         , "id"
-         , "lemme"
-         , "label"
-         ]
-
--}
-