Merge branch 'dev' into 571-dev-node-corpus-api-search-fixes-take-2

CHANGELOG.md

+## Version 0.0.6.9.9.6.7
+
+* [FRONT][FIX][Node Corpus / API search (#571)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/571)
+* [BACK][FIX] PhyloTypes
+* [FRONT][FIX][[Node Doc] Annotation: select/add ngram to map terms doesn't seems to sync in frontend render (#563)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/563)
+* [FRONT][FIX][[Graph] Rearrange the graph toolbar (#567)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/567)
+
 ## Version 0.0.6.9.9.6.6
 
 * [BACK|FRONT][WARNING] Button to launch API corpus is broken for now

bin/gargantext-phylo/Main.hs

@@ -21,7 +21,7 @@ import Control.Concurrent.Async (mapConcurrently)
 import Crypto.Hash.SHA256 (hash)
 import Data.Aeson
 import Data.Either (Either(..), fromRight)
-import Data.List  (concat, nub, isSuffixOf)
+import Data.List  (concat, nub, isSuffixOf,sort,tail)
 import Data.List.Split
 import Data.Maybe (fromMaybe)
 import Data.String (String)
@@ -39,7 +39,7 @@ import Gargantext.Core.Viz.Phylo
 import Gargantext.Core.Viz.Phylo.API.Tools
 import Gargantext.Core.Viz.Phylo.PhyloExport (toPhyloExport, dotToFile)
 import Gargantext.Core.Viz.Phylo.PhyloMaker  (toPhylo, toPhyloWithoutLink)
-import Gargantext.Core.Viz.Phylo.PhyloTools  (printIOMsg, printIOComment, setConfig)
+import Gargantext.Core.Viz.Phylo.PhyloTools  (printIOMsg, printIOComment, setConfig, toPeriods, getTimePeriod, getTimeStep)
 import Gargantext.Database.Admin.Types.Hyperdata (HyperdataDocument(..))
 import Gargantext.Database.Schema.Ngrams (NgramsType(..))
 import Gargantext.Prelude
@@ -89,7 +89,7 @@ wosToDocs limit patterns time path = do
                                       (fromIntegral $ fromJust $ _hd_publication_year d)
                                       (fromJust $ _hd_publication_month d)
                                       (fromJust $ _hd_publication_day d) time)
-                                    (termsInText patterns $ title <> " " <> abstr) Nothing [])
+                                    (termsInText patterns $ title <> " " <> abstr) Nothing [] time)
         <$> concat
         <$> mapConcurrently (\file ->
               filter (\d -> (isJust $ _hd_publication_year d)
@@ -109,6 +109,7 @@ csvToDocs parser patterns time path =
                                        (termsInText patterns $ (csv_title row) <> " " <> (csv_abstract row))
                                        Nothing
                                        []
+                                       time
                      ) <$> snd <$> either (\err -> panic $ cs $ "CSV error" <> (show err)) identity <$> Csv.readCSVFile path
     Csv' limit -> Vector.toList
       <$> Vector.take limit
@@ -117,18 +118,35 @@ csvToDocs parser patterns time path =
                                        (termsInText patterns $ (csv'_title row) <> " " <> (csv'_abstract row))
                                        (Just $ csv'_weight row)
                                        (map (T.strip . pack) $ splitOn ";" (unpack $ (csv'_source row)))
+                                       time
                      ) <$> snd <$> Csv.readWeightedCsv path
 
 
 -- To parse a file into a list of Document
-fileToDocs' :: CorpusParser -> FilePath -> TimeUnit -> TermList -> IO [Document]
-fileToDocs' parser path time lst = do
+fileToDocsAdvanced :: CorpusParser -> FilePath -> TimeUnit -> TermList -> IO [Document]
+fileToDocsAdvanced parser path time lst = do
   let patterns = buildPatterns lst
   case parser of
       Wos limit  -> wosToDocs limit  patterns time path
       Csv  _     -> csvToDocs parser patterns time path
       Csv' _     -> csvToDocs parser patterns time path
 
+fileToDocsDefault :: CorpusParser -> FilePath -> [TimeUnit] -> TermList -> IO [Document]
+fileToDocsDefault parser path timeUnits lst = 
+  if length timeUnits > 0
+    then
+      do 
+        let timeUnit = (head' "fileToDocsDefault" timeUnits)
+        docs <- fileToDocsAdvanced parser path timeUnit lst  
+        let periods = toPeriods (sort $ nub $ map date docs) (getTimePeriod timeUnit) (getTimeStep timeUnit)
+        if (length periods < 3)
+         then fileToDocsDefault parser path (tail timeUnits) lst
+         else pure docs
+    else panic "this corpus is incompatible with the phylomemy reconstruction"
+
+-- on passe à passer la time unit dans la conf envoyé au phyloMaker
+-- dans le phyloMaker si default est true alors dans le setDefault ou pense à utiliser la TimeUnit de la conf 
+
 
 ---------------
 -- | Label | --
@@ -251,7 +269,11 @@ main = do
 
             printIOMsg "Parse the corpus"
             mapList <-  fileToList (listParser config) (listPath config)
-            corpus  <- fileToDocs' (corpusParser config) (corpusPath config) (timeUnit config) mapList
+
+            corpus  <- if (defaultMode config)
+                        then fileToDocsDefault (corpusParser config) (corpusPath config) [Year 3 1 5,Month 3 1 5,Week 4 2 5] mapList
+                        else fileToDocsAdvanced (corpusParser config) (corpusPath config) (timeUnit config)  mapList
+            
             printIOComment (show (length corpus) <> " parsed docs from the corpus")
 
             printIOComment (show (length $ nub $ concat $ map text corpus) <> " Size ngs_coterms")

gargantext.cabal

@@ -5,7 +5,7 @@ cabal-version: 1.12
 -- see: https://github.com/sol/hpack
 
 name:           gargantext
-version: 0.0.6.9.9.6.6
+version:        0.0.6.9.9.6.7
 synopsis:       Search, map, share
 description:    Please see README.md
 category:       Data
@@ -26,6 +26,8 @@ data-files:
     ekg-assets/chart_line_add.png
     ekg-assets/cross.png
     test-data/ngrams/GarganText_NgramsTerms-QuantumComputing.json
+    test-data/phylo/bpa_phylo_test.json
+    test-data/phylo/open_science.json
 
 library
   exposed-modules:
@@ -81,6 +83,7 @@ library
       Gargantext.Core.Types.Individu
       Gargantext.Core.Types.Main
       Gargantext.Core.Types.Query
+      Gargantext.Core.Types.Phylo
       Gargantext.Core.Utils
       Gargantext.Core.Utils.Prefix
       Gargantext.Core.Viz.Graph
@@ -235,7 +238,6 @@ library
       Gargantext.Core.Text.Terms.Multi.PosTagging
       Gargantext.Core.Text.Terms.Multi.PosTagging.Types
       Gargantext.Core.Text.Upload
-      Gargantext.Core.Types.Phylo
       Gargantext.Core.Types.Search
       Gargantext.Core.Utils.DateUtils
       Gargantext.Core.Viz

package.yaml

@@ -6,7 +6,7 @@ name: gargantext
 #         | | | +-----  Layers * : New versions with API additions
 #         | | | | +---  Layers * : New versions without API breaking changes
 #         | | | | |
-version: '0.0.6.9.9.6.6'
+version: '0.0.6.9.9.6.7'
 synopsis: Search, map, share
 description: Please see README.md
 category: Data
@@ -45,6 +45,8 @@ data-files:
   - ekg-assets/chart_line_add.png
   - ekg-assets/cross.png
   - test-data/ngrams/GarganText_NgramsTerms-QuantumComputing.json
+  - test-data/phylo/bpa_phylo_test.json
+  - test-data/phylo/open_science.json
 library:
   source-dirs: src
   ghc-options:
@@ -109,6 +111,7 @@ library:
   - Gargantext.Core.Types.Individu
   - Gargantext.Core.Types.Main
   - Gargantext.Core.Types.Query
+  - Gargantext.Core.Types.Phylo
   - Gargantext.Core.Utils
   - Gargantext.Core.Utils.Prefix
   - Gargantext.Core.Viz.Graph

src-test/Offline/JSON.hs

@@ -9,16 +9,21 @@ import Data.Aeson
 import Data.Either
 import Gargantext.API.Node.Corpus.New
 import Gargantext.API.Node.Corpus.Types
+import Gargantext.Core.Types.Phylo
 import Gargantext.Core.Viz.Phylo.API
 import Prelude
 import Test.Tasty
 import Test.Tasty.HUnit
 import Test.Tasty.QuickCheck
 import Text.RawString.QQ
+import qualified Data.ByteString as B
 import qualified Data.ByteString.Lazy.Char8 as C8
 
+import Paths_gargantext
+
 jsonRoundtrip :: (Show a, FromJSON a, ToJSON a, Eq a) => a -> Property
-jsonRoundtrip a = eitherDecode (encode a) === Right a
+jsonRoundtrip a =
+  counterexample ("Parsed JSON: " <> C8.unpack (encode a)) $ eitherDecode (encode a) === Right a
 
 tests :: TestTree
 tests = testGroup "JSON" [
@@ -26,7 +31,14 @@ tests = testGroup "JSON" [
   , testProperty "WithQuery roundtrips" (jsonRoundtrip @WithQuery)
   , testCase "WithQuery frontend compliance" testWithQueryFrontend
   , testGroup "Phylo" [
-    testProperty "PhyloData" (jsonRoundtrip @PhyloData)
+    testProperty "PeriodToNode"  (jsonRoundtrip @PeriodToNodeData)
+  , testProperty "GraphData"     (jsonRoundtrip @GraphData)
+  , testProperty "GraphDataData" (jsonRoundtrip @GraphDataData)
+  , testProperty "ObjectData"    (jsonRoundtrip @ObjectData)
+  , testProperty "PhyloData"     (jsonRoundtrip @PhyloData)
+  , testProperty "LayerData"     (jsonRoundtrip @LayerData)
+  , testCase "can parse bpa_phylo_test.json" testParseBpaPhylo
+  , testCase "can parse open_science.json" testOpenSciencePhylo
   ]
   ]
 
@@ -40,3 +52,19 @@ testWithQueryFrontend = do
 -- instances, this test would fail, and we will be notified.
 cannedWithQueryPayload :: String
 cannedWithQueryPayload = [r| {"query":"Haskell","node_id":138,"lang":"EN","flowListWith":{"type":"MyListsFirst"},"datafield":"External Arxiv","databases":"Arxiv"} |]
+
+testParseBpaPhylo :: Assertion
+testParseBpaPhylo = do
+  pth      <- getDataFileName "test-data/phylo/bpa_phylo_test.json"
+  jsonBlob <- B.readFile pth
+  case eitherDecodeStrict' @GraphData jsonBlob of
+    Left err    -> error err
+    Right _     -> pure ()
+
+testOpenSciencePhylo :: Assertion
+testOpenSciencePhylo = do
+  pth      <- getDataFileName "test-data/phylo/open_science.json"
+  jsonBlob <- B.readFile pth
+  case eitherDecodeStrict' @PhyloData jsonBlob of
+    Left err    -> error err
+    Right _     -> pure ()

src/Gargantext/Core/Viz/Phylo.hs

@@ -135,7 +135,7 @@ data TimeUnit =
       { _day_period :: Int
       , _day_step   :: Int
       , _day_matchingFrame :: Int }
-      deriving (Show,Generic,Eq)
+      deriving (Show,Generic,Eq,NFData)
 
 instance ToSchema TimeUnit where
   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
@@ -227,7 +227,7 @@ defaultConfig =
             , phyloScale     = 2
             , similarity     = WeightedLogJaccard 0.5 1
             , seaElevation   = Constante 0.1 0.1
-            , defaultMode    = True
+            , defaultMode    = False
             , findAncestors  = False
             , phyloSynchrony = ByProximityThreshold 0.5 0 AllBranches MergeAllGroups
             , phyloQuality   = Quality 0.5 1
@@ -355,6 +355,7 @@ data Document = Document
       , text    :: [Ngrams]
       , weight  :: Maybe Double
       , sources :: [Text]
+      , docTime :: TimeUnit
       } deriving (Eq,Show,Generic,NFData)
 
 
@@ -372,6 +373,7 @@ data PhyloFoundations = PhyloFoundations
 data PhyloCounts = PhyloCounts
       { coocByDate    :: !(Map Date Cooc)
       , docsByDate    :: !(Map Date Double)
+      , rootsCountByDate :: !(Map Date (Map Int Double))
       , rootsCount    :: !(Map Int  Double)
       , rootsFreq     :: !(Map Int  Double)
       , lastRootsFreq :: !(Map Int  Double)
@@ -487,8 +489,10 @@ data PhyloGroup =
                  , _phylo_groupSources  :: [Int]
                  , _phylo_groupNgrams   :: [Int]
                  , _phylo_groupCooc     :: !(Cooc)
+                 , _phylo_groupDensity  :: Double
                  , _phylo_groupBranchId :: PhyloBranchId
                  , _phylo_groupMeta     :: Map Text [Double]
+                 , _phylo_groupRootsCount    :: Map Int Double
                  , _phylo_groupScaleParents  :: [Pointer]
                  , _phylo_groupScaleChilds   :: [Pointer]
                  , _phylo_groupPeriodParents :: [Pointer]

src/Gargantext/Core/Viz/Phylo/API/Tools.hs

@@ -91,7 +91,9 @@ flowPhyloAPI config cId = do
   corpus <- corpusIdtoDocuments (timeUnit config) cId
   let phyloWithCliques = toPhyloWithoutLink corpus config
   -- writePhylo phyloWithCliquesFile phyloWithCliques
-  pure $ toPhylo (setConfig config phyloWithCliques)
+  printDebug "PhyloConfig old: " config
+
+  pure $ toPhylo $ setConfig config phyloWithCliques
 
 --------------------------------------------------------------------
 corpusIdtoDocuments :: TimeUnit -> CorpusId -> GargNoServer [Document]
@@ -120,7 +122,7 @@ toPhyloDocs patterns time d =
                                       (fromIntegral $ fromMaybe 1 $ _hd_publication_year d)
                                       (fromMaybe 1 $ _hd_publication_month d)
                                       (fromMaybe 1 $ _hd_publication_day d) time)
-                                    (termsInText' patterns $ title <> " " <> abstr) Nothing []
+                                    (termsInText' patterns $ title <> " " <> abstr) Nothing [] time
 
 
 
@@ -138,7 +140,7 @@ context2phyloDocument timeUnit context (ngs_terms, ngs_sources) = do
     text'    = maybe [] toText $ Map.lookup contextId ngs_terms
     sources' = maybe [] toText $ Map.lookup contextId ngs_sources
 
-  pure $ Document date date' text' Nothing sources'
+  pure $ Document date date' text' Nothing sources' (Year 3 1 5)
 
 
 -- TODO better default date and log the errors to improve data quality

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

@@ -111,6 +111,7 @@ docs = map (\(d,t)
                 (filter (\n -> isRoots n (foundations ^. foundations_roots)) $ monoTexts t) 
                 Nothing
                 []
+                (Year 3 1 5)
             ) corpus
 
 

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

@@ -143,29 +143,27 @@ periodToDotNode prd prd' =
 groupToDotNode :: Vector Ngrams -> PhyloGroup -> Int -> Dot DotId
 groupToDotNode fdt g bId =
     node (groupIdToDotId $ getGroupId g)
-    ( [ FontName "Arial"
-      , Shape Square
-      , penWidth 4
-      , toLabel (groupToTable fdt g) ]
-      <> [ toAttr "nodeType" "group"
-         , toAttr "gid" (groupIdToDotId $ getGroupId g)
-         , toAttr "from" (pack $ show (fst $ g ^. phylo_groupPeriod))
-         , toAttr "to"   (pack $ show (snd $ g ^. phylo_groupPeriod))
-         , toAttr "strFrom" (pack $ show (fst $ g ^. phylo_groupPeriod'))
-         , toAttr "strTo"   (pack $ show (snd $ g ^. phylo_groupPeriod'))
-         , toAttr "branchId" (pack $ unwords (init $ map show $ snd $ g ^. phylo_groupBranchId))
-         , toAttr "bId" (pack $ show bId)
-         , toAttr "support" (pack $ show (g ^. phylo_groupSupport))
-         , toAttr "weight" (pack $ show (g ^. phylo_groupWeight))
-         , toAttr "source" (pack $ show (nub $ g ^. phylo_groupSources))
-         , toAttr "sourceFull" (pack $ show (g ^. phylo_groupSources))
-         , toAttr "lbl" (pack $ show (ngramsToLabel fdt (g ^. phylo_groupNgrams)))
-         , toAttr "foundation" (pack $ show (idxToLabel (g ^. phylo_groupNgrams)))
-         , toAttr "role" (pack $ show (idxToLabel' ((g ^. phylo_groupMeta) ! "dynamics")))
-         , toAttr "frequence" (pack $ show (idxToLabel' ((g ^. phylo_groupMeta) ! "frequence")))
-         , toAttr "seaLvl" (pack $ show ((g ^. phylo_groupMeta) ! "seaLevels"))
-         ])
-
+                     ([FontName "Arial", Shape Square, penWidth 4,  toLabel (groupToTable fdt g)]
+                      <> [ toAttr "nodeType" "group"
+                         , toAttr "gid" (groupIdToDotId $ getGroupId g)
+                         , toAttr "from" (pack $ show (fst $ g ^. phylo_groupPeriod))
+                         , toAttr "to"   (pack $ show (snd $ g ^. phylo_groupPeriod))
+                         , toAttr "strFrom" (pack $ show (fst $ g ^. phylo_groupPeriod'))
+                         , toAttr "strTo"   (pack $ show (snd $ g ^. phylo_groupPeriod'))
+                         , toAttr "branchId" (pack $ unwords (init $ map show $ snd $ g ^. phylo_groupBranchId))
+                         , toAttr "bId" (pack $ show bId)
+                         , toAttr "support" (pack $ show (g ^. phylo_groupSupport))
+                         , toAttr "weight" (pack $ show (g ^. phylo_groupWeight))
+                         , toAttr "source" (pack $ show (nub $ g ^. phylo_groupSources))
+                         , toAttr "sourceFull" (pack $ show (g ^. phylo_groupSources))
+                         , toAttr "density" (pack $ show (g ^. phylo_groupDensity))
+                         , toAttr "cooc" (pack $ show (g ^. phylo_groupCooc))
+                         , toAttr "lbl" (pack $ show (ngramsToLabel fdt (g ^. phylo_groupNgrams)))
+                         , toAttr "foundation" (pack $ show (idxToLabel (g ^. phylo_groupNgrams)))
+                         , toAttr "role" (pack $ show (idxToLabel' ((g ^. phylo_groupMeta) ! "dynamics")))
+                         , toAttr "frequence" (pack $ show (idxToLabel' ((g ^. phylo_groupMeta) ! "frequence")))
+                         , toAttr "seaLvl" (pack $ show ((g ^. phylo_groupMeta) ! "seaLevels"))
+                         ])
 
 toDotEdge' :: DotId -> DotId -> [Char] -> [Char] -> EdgeType -> Dot DotId
 toDotEdge' source target thr w edgeType = edge source target
@@ -447,8 +445,10 @@ branchDating export =
                                       else acc ) [] $ export ^. export_groups
             periods = nub groups
             birth = fst $ head' "birth" groups
-            age   = (snd $ last' "age"  groups) - birth
+            death = snd $ last' "death" groups
+            age   = death - birth
         in b & branch_meta %~ insert "birth" [fromIntegral birth]
+             & branch_meta %~ insert "death" [fromIntegral death]
              & branch_meta %~ insert "age"   [fromIntegral age]
              & branch_meta %~ insert "size"  [fromIntegral $ length periods] ) export
 

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

@@ -34,6 +34,7 @@ import Gargantext.Core.Viz.Phylo.TemporalMatching (toPhyloQuality, temporalMatch
 import Gargantext.Prelude
 
 import qualified Data.Set as Set
+import qualified Data.Map as Map
 import qualified Data.List as List
 import qualified Data.Vector as Vector
 
@@ -191,7 +192,7 @@ findSeaLadder phylo = case getSeaElevation phylo of
                    in acc ++ (concat pairs')
                ) [] $ keys $ phylo ^. phylo_periods
 
-appendGroups :: (a -> Period -> (Text,Text) -> Scale -> Int -> [Cooc] -> PhyloGroup) -> Scale -> Map (Date,Date) [a] -> Phylo -> Phylo
+appendGroups :: (a -> Period -> (Text,Text) -> Scale -> Int -> [Cooc] ->  Map Int Double -> PhyloGroup) -> Scale -> Map (Date,Date) [a] -> Phylo -> Phylo
 appendGroups f lvl m phylo =  trace ("\n" <> "-- | Append " <> show (length $ concat $ elems m) <> " groups to Level " <> show (lvl) <> "\n")
     $ over ( phylo_periods
            .  traverse
@@ -206,23 +207,28 @@ appendGroups f lvl m phylo =  trace ("\n" <> "-- | Append " <> show (length $ co
                               & phylo_scaleGroups .~ (fromList $ foldl (\groups obj ->
                                     groups ++ [ (((pId,lvl),length groups)
                                               , f obj pId pId' lvl (length groups)
-                                                  (elems $ restrictKeys (getCoocByDate phylo) $ periodsToYears [pId]))
+                                                  -- select the cooc of the periods
+                                                  (elems $ restrictKeys (getCoocByDate phylo) $ periodsToYears [pId])
+                                                  -- select and merge the roots count of the periods
+                                                  (foldl (\acc count -> unionWith (+) acc count) empty 
+                                                    $ elems $ restrictKeys (getRootsCountByDate phylo) $ periodsToYears [pId]))
                                               ] ) [] phyloCUnit)
                          else
                             phyloLvl )
            phylo
 
 
-clusterToGroup :: Clustering -> Period -> (Text,Text) -> Scale ->  Int -> [Cooc] -> PhyloGroup
-clusterToGroup fis pId pId' lvl idx coocs = PhyloGroup pId pId' lvl idx ""
+clusterToGroup :: Clustering -> Period -> (Text,Text) -> Scale ->  Int -> [Cooc] -> Map Int Double -> PhyloGroup
+clusterToGroup fis pId pId' lvl idx coocs rootsCount = PhyloGroup pId pId' lvl idx ""
                    (fis ^. clustering_support )
                    (fis ^. clustering_visWeighting)
                    (fis ^. clustering_visFiltering)
                    (fis ^. clustering_roots)
                    (ngramsToCooc (fis ^. clustering_roots) coocs)
+                   (ngramsToDensity (fis ^. clustering_roots) coocs rootsCount)
                    (1,[0]) -- branchid (lvl,[path in the branching tree])
                    (fromList [("breaks",[0]),("seaLevels",[0])])
-                   [] [] [] [] [] [] []
+                   rootsCount [] [] [] [] [] [] []
 
 
 -----------------------
@@ -446,6 +452,16 @@ docsToTermCount docs roots = fromList
 
 
 
+docsToTimeTermCount :: [Document] -> Vector Ngrams  -> (Map Date (Map Int Double))
+docsToTimeTermCount docs roots = 
+    let docs' = Map.map (\l -> fromList $ map (\lst -> (head' "docsToTimeTermCount" lst, fromIntegral $ length lst))
+                             $ group $ sort l)
+              $ fromListWith (++)
+              $ map (\d -> (date d, nub $ ngramsToIdx (text d) roots)) docs
+        time  = fromList $ map (\t -> (t,Map.empty)) $ toTimeScale (keys docs') 1
+     in unionWith (Map.union) time docs'
+
+
 docsToLastTermFreq :: Int -> [Document] -> Vector Ngrams -> Map Int Double
 docsToLastTermFreq n docs fdt =
   let last   = take n $ reverse $ sort $ map date docs
@@ -472,15 +488,15 @@ initPhyloScales lvlMax pId =
     fromList $ map (\lvl -> ((pId,lvl),PhyloScale pId ("","") lvl empty)) [1..lvlMax]
 
 
-setDefault :: PhyloConfig -> PhyloConfig
-setDefault conf = conf {
+setDefault :: PhyloConfig -> TimeUnit -> PhyloConfig
+setDefault conf timeScale = conf { 
                     phyloScale = 2,
                     similarity = WeightedLogJaccard 0.5 2,
                     findAncestors = True,
                     phyloSynchrony = ByProximityThreshold 0.6 0 SiblingBranches MergeAllGroups,
                     phyloQuality = Quality 0.5 3,
-                    timeUnit = Year 3 1 3,
-                    clique = MaxClique 5 30 ByNeighbours,
+                    timeUnit = timeScale,
+                    clique = Fis 3 5,
                     exportLabel = [BranchLabel MostEmergentTfIdf 2, GroupLabel MostEmergentInclusive 2],
                     exportSort = ByHierarchy Desc,
                     exportFilter = [ByBranchSize 3]
@@ -492,18 +508,21 @@ setDefault conf = conf {
 initPhylo :: [Document] -> PhyloConfig -> Phylo
 initPhylo docs conf =
     let roots = Vector.fromList $ nub $ concat $ map text docs
+        timeScale = head' "initPhylo" $ map docTime docs
         foundations = PhyloFoundations roots empty
         docsSources = PhyloSources (Vector.fromList $ nub $ concat $ map sources docs)
         docsCounts  = PhyloCounts (docsToTimeScaleCooc docs (foundations ^. foundations_roots))
                              (docsToTimeScaleNb docs)
+                             (docsToTimeTermCount docs (foundations ^. foundations_roots))
                              (docsToTermCount docs (foundations ^. foundations_roots))
                              (docsToTermFreq docs (foundations ^. foundations_roots))
-                             (docsToLastTermFreq (getTimePeriod $ timeUnit conf) docs (foundations ^. foundations_roots))
+                             (docsToLastTermFreq (getTimePeriod timeScale) docs (foundations ^. foundations_roots))
         params = if (defaultMode conf)
-                 then defaultPhyloParam { _phyloParam_config = setDefault conf }
+                 then defaultPhyloParam { _phyloParam_config = setDefault conf timeScale }
                  else defaultPhyloParam { _phyloParam_config = conf }
-        periods = toPeriods (sort $ nub $ map date docs) (getTimePeriod $ timeUnit conf) (getTimeStep $ timeUnit conf)
+        periods = toPeriods (sort $ nub $ map date docs) (getTimePeriod timeScale) (getTimeStep timeScale)
     in trace ("\n" <> "-- | Init a phylo out of " <> show(length docs) <> " docs \n")
+       $ trace ("\n" <> "-- | lambda " <> show(_qua_granularity $ phyloQuality $ _phyloParam_config params)) 
        $ Phylo foundations
                docsSources
                docsCounts
@@ -511,4 +530,4 @@ initPhylo docs conf =
                params
                (fromList $ map (\prd -> (prd, PhyloPeriod prd ("","") (initPhyloScales 1 prd))) periods)
                0
-               (_qua_granularity $ phyloQuality $ conf)
+               (_qua_granularity $ phyloQuality $ _phyloParam_config params)

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

@@ -14,7 +14,7 @@ module Gargantext.Core.Viz.Phylo.PhyloTools where
 
 import Control.Lens hiding (Level)
 import Data.List (sort, concat, null, union, (++), tails, sortOn, nub, init, tail, iterate, transpose, partition, tails, nubBy, group, notElem, (!!))
-import Data.Map (Map, elems, fromList, unionWith, keys, member, (!), filterWithKey, fromListWith, empty, restrictKeys)
+import Data.Map (Map, elems, fromList, findWithDefault, unionWith, keys, member, (!), filterWithKey, fromListWith, empty, restrictKeys)
 import Data.Set (Set, disjoint)
 import Data.String (String)
 import Data.Text (Text,unpack)
@@ -313,6 +313,27 @@ ngramsToCooc ngrams coocs =
     in  filterWithKey (\k _ -> elem k pairs) cooc
 
 
+-----------------
+-- | Density | --
+-----------------
+
+
+-- | To build the density of a phylogroup
+-- density is defined in Callon M, Courtial JP, Laville F (1991) Co-word analysis as a tool for describing 
+-- the network of interaction between basic and technological research: The case of polymer chemistry. 
+-- Scientometric 22: 155–205.
+ngramsToDensity :: [Int] -> [Cooc] -> (Map Int Double) -> Double
+ngramsToDensity ngrams coocs rootsCount =
+    let cooc  = foldl (\acc cooc' -> sumCooc acc cooc') empty coocs
+        pairs = listToCombi' ngrams
+        density = map (\(i,j) -> 
+            let nij = findWithDefault 0 (i,j) cooc
+             in (nij * nij) / ((rootsCount ! i) * (rootsCount ! j))) pairs
+    in (sum density) / (fromIntegral $ length ngrams)
+
+
+
+
 ------------------
 -- | Defaults | --
 ------------------
@@ -458,6 +479,9 @@ getPeriodIds phylo = sortOn fst
                    $ keys
                    $ phylo ^. phylo_periods
 
+getLastDate :: Phylo -> Date
+getLastDate phylo = snd $ last' "lastDate" $ getPeriodIds phylo
+
 getLevelParentId :: PhyloGroup -> PhyloGroupId
 getLevelParentId g = fst $ head' "getLevelParentId" $ g ^. phylo_groupScaleParents
 
@@ -495,7 +519,7 @@ getConfig :: Phylo -> PhyloConfig
 getConfig phylo = (phylo ^. phylo_param) ^. phyloParam_config
 
 getLevel :: Phylo -> Double
-getLevel phylo = _phylo_level phylo
+getLevel phylo = (phyloQuality (getConfig phylo)) ^. qua_granularity
 
 getLadder :: Phylo -> [Double]
 getLadder phylo = phylo ^. phylo_seaLadder
@@ -503,6 +527,9 @@ getLadder phylo = phylo ^. phylo_seaLadder
 getCoocByDate :: Phylo -> Map Date Cooc
 getCoocByDate phylo = coocByDate (phylo ^. phylo_counts)
 
+getRootsCountByDate :: Phylo -> Map Date (Map Int Double)
+getRootsCountByDate phylo = rootsCountByDate (phylo ^. phylo_counts)    
+
 getDocsByDate :: Phylo -> Map Date Double
 getDocsByDate phylo = docsByDate (phylo ^. phylo_counts)
 

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

@@ -16,7 +16,7 @@ import Control.Lens hiding (Level)
 import Control.Monad (sequence)
 import Control.Parallel.Strategies (parList, rdeepseq, using)
 import Data.List ((++), null, intersect, nub, concat, sort, sortOn, groupBy)
-import Data.Map  (Map, fromList, fromListWith, foldlWithKey, (!), insert, empty, restrictKeys, elems, mapWithKey, member)
+import Data.Map  (Map, fromList, fromListWith, foldlWithKey, (!), insert, empty, restrictKeys, elems, mapWithKey, member, unionWith)
 import Gargantext.Core.Viz.Phylo
 import Gargantext.Core.Viz.Phylo.PhyloExport (processDynamics)
 import Gargantext.Core.Viz.Phylo.PhyloTools
@@ -32,6 +32,7 @@ import qualified Data.Map as Map
 mergeGroups :: [Cooc] -> PhyloGroupId -> Map PhyloGroupId PhyloGroupId -> [PhyloGroup] -> PhyloGroup
 mergeGroups coocs id mapIds childs = 
     let ngrams = (sort . nub . concat) $ map _phylo_groupNgrams childs
+        counts = foldl (\acc count -> unionWith (+) acc count) empty $ map _phylo_groupRootsCount childs
     in PhyloGroup (fst $ fst id) (_phylo_groupPeriod' $ head' "mergeGroups" childs)
                   (snd $ fst id) (snd id) ""
                   (sum $ map _phylo_groupSupport childs) 
@@ -40,8 +41,12 @@ mergeGroups coocs id mapIds childs =
                   (concat $ map _phylo_groupSources childs) 
                   ngrams
                   (ngramsToCooc ngrams coocs) 
+                  (ngramsToDensity ngrams coocs counts)
+                  -- todo add density here
                   ((snd $ fst id),bId)
-                  (mergeMeta bId childs) [] (map (\g -> (getGroupId g, 1)) childs)
+                  (mergeMeta bId childs)
+                  counts 
+                  [] (map (\g -> (getGroupId g, 1)) childs)
                   (updatePointers $ concat $ map _phylo_groupPeriodParents childs)
                   (updatePointers $ concat $ map _phylo_groupPeriodChilds  childs)
                   (mergeAncestors $ concat $ map _phylo_groupAncestors childs)