[Merge]

package.yaml

@@ -158,6 +158,7 @@ library:
   - full-text-search
   - fullstop
   - gargantext-prelude
+  - gargantext-graph >= 0.1.0.0
   - graphviz
   - hashable
   - haskell-igraph

src/Gargantext/Core/Mail.hs

@@ -64,7 +64,7 @@ email_to' (NewUser u m _) = (m,u)
 
 ------------------------------------------------------------------------
 bodyWith :: ServerAddress -> MailModel -> [Text]
-bodyWith server (Invitation u) = [ "Congratulation, you have been granted a beta user account to test the"
+bodyWith server (Invitation u) = [ "Congratulation, you have been granted a user account to test the"
                                  , "new GarganText platform!"
                                  ] <> (email_credentials server u)
 

src/Gargantext/Core/Text/Corpus/Parsers.hs

@@ -25,9 +25,8 @@ module Gargantext.Core.Text.Corpus.Parsers (FileFormat(..), clean, parseFile, cl
 
 import "zip" Codec.Archive.Zip (withArchive, getEntry, getEntries)
 import Control.Concurrent.Async as CCA (mapConcurrently)
-import Control.Monad (join, sequence)
-import Control.Monad.IO.Class (liftIO)
 import Data.Attoparsec.ByteString (parseOnly, Parser)
+import Control.Monad (join)
 import Data.Either(Either(..))
 import Data.Either.Extra (partitionEithers)
 import Data.List (concat, lookup)
@@ -98,13 +97,11 @@ parseFormat WOS bs = do
           $ [runParser'  WOS bs]
   pure $ Right docs
 parseFormat ZIP bs = do
-  path <- emptySystemTempFile "parsed.zip"
+  path <- emptySystemTempFile "parsed-zip"
   DB.writeFile path bs
-  withArchive path $ do
-    files <- DM.keys <$> getEntries
-    filesContents <- mapM getEntry files
-    ddocs <- liftIO $ mapM (parseFormat CsvGargV3) filesContents
-    pure $ concat <$> sequence ddocs
+  parsedZip <- withArchive path $ do
+    DM.keys <$> getEntries
+  pure $ Left $ "Not implemented for ZIP, parsedZip" <> show parsedZip
 parseFormat _ _ = undefined
 
 -- | Parse file into documents

src/Gargantext/Core/Text/Corpus/Parsers/Date.hs

@@ -119,7 +119,7 @@ getTimeValue rt = case head rt of
     Nothing
   Just x  -> case rval x of
     RVal Time t -> Just $ toJSON t
-    _  -> do 
+    _  -> do
       Nothing
 
 extractValue :: Maybe Value -> Maybe Text

src/Gargantext/Core/Text/Corpus/Parsers/Wikidata.hs

 {-|
 Module      : Gargantext.Core.Text.Corpus.Parsers.Wikidata
+<<<<<<< HEAD
 Description : To query Wikidata 
+=======
+Description : To query Wikidata
+>>>>>>> dev-clustering
 Copyright   : (c) CNRS, 2019-Present
 License     : AGPL + CECILL v3
 Maintainer  : team@gargantext.org
@@ -29,7 +33,7 @@ import Gargantext.Core.Text.Corpus.Parsers.Date (dateSplit)
 
 
 
-data WikiResult = WikiResult { _wr_cid         :: Maybe Text 
+data WikiResult = WikiResult { _wr_cid         :: Maybe Text
                              , _wr_title       :: Maybe Text
                              , _wr_url         :: Maybe Text
                              , _wr_yearStart   :: Maybe Text
@@ -48,10 +52,9 @@ wikidataGet n m = do
 
 wikiPageToDocument :: NumberOfSections -> WikiResult ->  IO HyperdataDocument
 wikiPageToDocument m wr = do
- 
   sections <- case wr ^. wr_url of
     Nothing -> pure []
-    Just  u -> crawlPage u 
+    Just  u -> crawlPage u
 
   let bdd    = Just "wikidata"
       doi    = Nothing
@@ -129,5 +132,3 @@ wikidataQuery n = List.unlines
       ,"       LIMIT " <> (cs $ show n)
       ]
 
-
-

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

@@ -24,7 +24,7 @@ import Data.Maybe (catMaybes)
 import Data.Ord (Down(..))
 import Gargantext.Prelude
 import qualified Data.Map as DM
-import Gargantext.Core.Viz.Graph.Tools.IGraph (ClusterNode(..))
+import Graph.Types (ClusterNode(..))
 
 ----------------------------------------------------------------------
 type Partitions a = Map (Int, Int) Double -> IO [a]

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

@@ -27,8 +27,10 @@ import Gargantext.Core.Statistics
 import Gargantext.Core.Viz.Graph
 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, ClusterNode)
+import Gargantext.Core.Viz.Graph.Tools.IGraph (mkGraphUfromEdges, spinglass)
 import Gargantext.Prelude
+import Graph.Types (ClusterNode)
+import qualified Graph.BAC.ProxemyOptim as BAC
 import IGraph.Random -- (Gen(..))
 import qualified Data.HashMap.Strict      as HashMap
 import qualified Data.List                as List
@@ -40,12 +42,10 @@ import qualified IGraph.Algorithms.Layout as Layout
 
 
 -------------------------------------------------------------
-
 defaultClustering :: Map (Int, Int) Double -> IO [ClusterNode]
-defaultClustering = spinglass 1
+defaultClustering x = pure $ BAC.defaultClustering x
 
 -------------------------------------------------------------
-
 type Threshold = Double
 
 cooc2graph' :: Ord t => Distance

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

@@ -20,6 +20,7 @@ import Data.Singletons (SingI)
 import IGraph hiding (mkGraph, neighbors, edges, nodes, Node, Graph)
 import Protolude
 import Gargantext.Core.Viz.Graph.Index
+import Graph.Types
 import qualified Data.List                   as List
 import qualified IGraph                      as IG
 import qualified IGraph.Algorithms.Clique    as IG
@@ -82,10 +83,6 @@ partitions_spinglass' s g = do
   IG.findCommunity g Nothing Nothing IG.spinglass gen
 
 
-data ClusterNode = ClusterNode { cl_node_id :: Int
-                               , cl_community_id :: Int
-                               }
-
 toClusterNode :: [[Int]] -> [ClusterNode]
 toClusterNode ns = List.concat
                  $ map (\(cId, ns') -> map (\n -> ClusterNode n cId) ns')

stack.yaml

@@ -4,7 +4,7 @@ flags: {}
 extra-package-dbs: []
 packages:
 - .
-#- 'deps/patches-class'
+  #- 'deps/gargantext-graph'
 #- 'deps/patches-map'
 #- 'deps/accelerate'
 #- 'deps/accelerate-utility'
@@ -30,6 +30,9 @@ extra-deps:
 - #git: https://gitlab.iscpif.fr/gargantext/haskell-gargantext-prelude.git
   git: https://gitlab.iscpif.fr/cgenie/haskell-gargantext-prelude.git
   commit: 35b09629a658fc16cc9ff63e7591e58511cd98a7
+  #git: ssh://git@gitlab.iscpif.fr:20022/gargantext/gargantext-graph.git
+- git: ssh://gitolite3@delanoe.org/gargantext-graph
+  commit: 294887a220460bd0c114638fff9ea53306cd2f18
   # Data Mining Libs
 - git: https://github.com/delanoe/data-time-segment.git
   commit: 10a416b9f6c443866b36479c3441ebb3bcdeb7ef
@@ -88,7 +91,18 @@ extra-deps:
 - git: https://github.com/rspeer/wikiparsec.git
   commit: 9637a82344bb70f7fa8f02e75db3c081ccd434ce
 
-  # Others dependencies (using stack resolver)
+  # Gargantext-graph
+- eigen-3.3.7.0@sha256:7c24a86426b238e02ba0ac2179cc44997518b443a13828ed7a791fe49a6dffa5,82060
+- git: https://github.com/alpmestan/sparse-linear.git
+  commit: bc6ca8058077b0b5702ea4b88bd4189cfcad267a
+  subdirs:
+    - sparse-linear
+- git: https://github.com/alpmestan/hmatrix.git
+  commit: b9fca8beee0f23c17a6b2001ec834d071709e6e7
+  subdirs:
+    - packages/base
+
+      # Others dependencies (using stack resolver)
 - constraints-extras-0.3.1.0@sha256:12016ebb91ad5ed2c82bf7e48c6bd6947d164d33c9dca5ac3965de1bb6c780c0,1777
 - KMP-0.2.0.0@sha256:6dfbac03ef00ebd9347234732cb86a40f62ab5a80c0cc6bedb8eb51766f7df28,2562
 - Unique-0.4.7.8@sha256:9661f45aa31dde119a2114566166ea38b011a45653337045ee4ced75636533c0,2067
@@ -122,3 +136,10 @@ extra-deps:
 - taggy-0.2.1@sha256:7bc55ddba178971dc6052163597f0445a0a2b5b0ca0e84ce651d53d722e3c265,4662
 
 - servant-ekg-0.3.1@sha256:19bd9dc3943983da8e79d6f607614c68faea4054fb889d508c8a2b67b6bdd448,2203
+
+
+# For the graph clustering
+ghc-options:
+  hmatrix: -O2 -fsimpl-tick-factor=10000 -fdicts-cheap -fdicts-strict -flate-dmd-anal  -fno-state-hack
+  sparse-linear: -O2 -fsimpl-tick-factor=10000 -fdicts-cheap -fdicts-strict -flate-dmd-anal  -fno-state-hack
+  gargantext-graph: -O2 -fsimpl-tick-factor=10000 -fdicts-cheap -fdicts-strict -flate-dmd-anal  -fno-state-hack