add a toPhylo function and the foundation of the Rest routes

src/Gargantext/Viz/Phylo.hs

@@ -43,6 +43,21 @@ import Gargantext.Core.Utils.Prefix (unPrefix)
 import Gargantext.Prelude
 
 ------------------------------------------------------------------------
+data PhyloQuery = PhyloQuery 
+    { _phyloQuery_phyloName  :: Text
+    , _phyloQuery_phyloDescription :: Text
+
+    , _phyloQuery_timeGrain  :: Int
+    , _phyloQuery_timeSteps  :: Int
+    
+    , _phyloQuery_fstCluster :: Clustering
+    , _phyloQuery_timeMatching :: Proximity
+    
+    , _phyloQuery_nthLevel :: Level
+    , _phyloQuery_nthCluster :: Clustering
+    } deriving (Show)
+
+
 data PhyloExport =
      PhyloExport { _phyloExport_param :: PhyloParam
                  , _phyloExport_data :: Phylo
@@ -53,6 +68,7 @@ data PhyloParam =
      PhyloParam { _phyloParam_version     :: Text -- Double ?
                 , _phyloParam_software    :: Software
                 , _phyloParam_params      :: Hash
+                , _phyloParam_query       :: Maybe PhyloQuery
      } deriving (Generic, Show)
 
 type Hash = Text
@@ -185,12 +201,21 @@ data PhyloError = LevelDoesNotExist
           deriving (Show)               
 
 
--- | A List of Proximity mesures or strategies 
-data Proximity  = WeightedLogJaccard | Hamming | FromPairs
--- | A List of Clustering methods 
-data Clustering  = Louvain | RelatedComponents
-
-data PairTo = Childs | Parents 
+-- | A List of Proximity methods names
+data ProximityName  = WeightedLogJaccard | Hamming | Filiation deriving (Show)
+-- | A List of Clustering methods names
+data ClusteringName = Louvain | RelatedComponents | FrequentItemSet deriving (Show)
+-- | A constructor for Proximities
+data Proximity = Proximity
+  { _proximity_name      :: ProximityName
+  , _proximity_params    :: Map Text Double
+  , _proximity_threshold :: Maybe Double } deriving (Show)
+-- | A constructor for Clustering
+data Clustering = Clustering
+  { _clustering_name       :: ClusteringName
+  , _clustering_params     :: Map Text Double
+  , _clustering_paramsBool :: Map Text Bool
+  , _clustering_proximity  :: Maybe Proximity } deriving (Show)
 
 ------------------------------------------------------------------------
 -- | To export a Phylo | --
@@ -261,8 +286,8 @@ data QueryFilter = QueryFilter
   }
 
 
--- | A PhyloQuery is the structured representation of a user query to be applied to a Phylo
-data PhyloQuery = PhyloQuery 
+-- | A PhyloQueryView is the structured representation of a user query to be applied to a Phylo
+data PhyloQueryView = PhyloQueryView 
   { _query_lvl    :: Level
 
   -- Does the PhyloGraph contain ascendant, descendant or a complete Filiation ?
@@ -300,11 +325,14 @@ makeLenses ''PhyloGroup
 makeLenses ''PhyloLevel
 makeLenses ''PhyloPeriod
 makeLenses ''PhyloView
-makeLenses ''PhyloQuery
+makeLenses ''PhyloQueryView
 makeLenses ''PhyloBranch
 makeLenses ''PhyloNode
 makeLenses ''PhyloEdge
+makeLenses ''Proximity
+makeLenses ''Clustering
 makeLenses ''QueryFilter
+makeLenses ''PhyloQuery
 
 -- | JSON instances 
 $(deriveJSON (unPrefix "_phylo_"       ) ''Phylo       ) 
@@ -314,6 +342,11 @@ $(deriveJSON (unPrefix "_phylo_group"  ) ''PhyloGroup  )
 -- 
 $(deriveJSON (unPrefix "_software_"    ) ''Software    )
 $(deriveJSON (unPrefix "_phyloParam_"  ) ''PhyloParam  )
+$(deriveJSON (unPrefix "_clustering_"  ) ''Clustering  )
+$(deriveJSON (unPrefix "_proximity_"   ) ''Proximity   )
+$(deriveJSON (unPrefix "") ''ProximityName )
+$(deriveJSON (unPrefix "") ''ClusteringName )
+$(deriveJSON (unPrefix "_phyloQuery_"  ) ''PhyloQuery  )
 $(deriveJSON (unPrefix "_phyloExport_" ) ''PhyloExport )
 
 -- | TODO XML instances

src/Gargantext/Viz/Phylo/Aggregates/Cluster.hs

@@ -17,6 +17,8 @@ Portability : POSIX
 module Gargantext.Viz.Phylo.Aggregates.Cluster
   where
 
+import Control.Lens     hiding (makeLenses, both, Level)
+
 import Data.List        (last,head,union,concat,null,nub,(++),init,tail,(!!))
 import Data.Map         (Map,elems,adjust,unionWith,intersectionWith)
 import Data.Set         (Set)
@@ -35,18 +37,18 @@ import qualified Data.Set    as Set
 
 
 -- | To apply a Clustering method to a PhyloGraph
-graphToClusters :: (Clustering,[Double]) -> GroupGraph -> [Cluster]
-graphToClusters (clust,param) (nodes,edges) = case clust of 
+graphToClusters :: Clustering -> GroupGraph -> [Cluster]
+graphToClusters clust (nodes,edges) = case clust ^. clustering_name of 
   Louvain           -> undefined -- louvain (nodes,edges)
   RelatedComponents -> relatedComp 0 (head nodes) (tail nodes,edges) [] []   
 
 
 -- | To transform a Phylo into Clusters of PhyloGroups at a given level
-phyloToClusters :: Level -> (Proximity,[Double]) -> (Clustering,[Double]) -> Phylo -> Map (Date,Date) [Cluster]
-phyloToClusters lvl (prox,param) (clus,param') p = Map.fromList 
+phyloToClusters :: Level -> Proximity -> Clustering -> Phylo -> Map (Date,Date) [Cluster]
+phyloToClusters lvl prox clus p = Map.fromList 
                                 $ zip (getPhyloPeriods p) 
-                                                       (map (\prd -> let graph = groupsToGraph (prox,param) (getGroupsWithFilters lvl prd p) p
+                                   (map (\prd -> let graph = groupsToGraph prox (getGroupsWithFilters lvl prd p) p
                                                  in if null (fst graph) 
                                                     then []
-                                                                        else graphToClusters (clus,param') graph) 
+                                                    else graphToClusters clus graph) 
                                    (getPhyloPeriods p))

src/Gargantext/Viz/Phylo/BranchMaker.hs

@@ -20,7 +20,7 @@ module Gargantext.Viz.Phylo.BranchMaker
 import Control.Lens     hiding (both, Level)
 
 import Data.List        (last,head,union,concat,null,nub,(++),init,tail,(!!))
-import Data.Map         (Map,elems,adjust,unionWith,intersectionWith)
+import Data.Map         (Map,elems,adjust,unionWith,intersectionWith,empty,(!))
 import Data.Set         (Set)
 import Data.Tuple       (fst, snd)
 
@@ -44,19 +44,19 @@ graphToBranches lvl (nodes,edges) p = concat
 
 
 -- | To transform a list of PhyloGroups into a PhyloGraph by using a given Proximity mesure
-groupsToGraph :: (Proximity,[Double]) -> [PhyloGroup] -> Phylo -> GroupGraph
-groupsToGraph (prox,param) groups p = (groups,edges)
+groupsToGraph :: Proximity -> [PhyloGroup] -> Phylo -> GroupGraph
+groupsToGraph prox groups p = (groups,edges)
   where 
     edges :: GroupEdges
-    edges = case prox of  
-      FromPairs          -> (nub . concat) $ map (\g -> (map (\g' -> ((g',g),1)) $ getGroupParents g p)
+    edges = case prox ^. proximity_name of  
+      Filiation          -> (nub . concat) $ map (\g -> (map (\g' -> ((g',g),1)) $ getGroupParents g p)
                                                         ++
                                                         (map (\g' -> ((g,g'),1)) $ getGroupChilds g p)) groups 
-      WeightedLogJaccard -> filter (\edge -> snd edge >= (param !! 0)) 
+      WeightedLogJaccard -> filter (\edge -> snd edge >= (fromJust (prox ^. proximity_threshold))) 
                           $ map (\(x,y) -> ((x,y), weightedLogJaccard 
-                                (param !! 1) (getGroupCooc x) 
+                                (getSensibility prox) (getGroupCooc x) 
                                 (unifySharedKeys (getGroupCooc x) (getGroupCooc y)))) $ listToDirectedCombi groups
-      Hamming            -> filter (\edge -> snd edge <= (param !! 0)) 
+      Hamming            -> filter (\edge -> snd edge <= (fromJust (prox ^. proximity_threshold))) 
                           $ map (\(x,y) -> ((x,y), hamming (getGroupCooc x) 
                                 (unifySharedKeys (getGroupCooc x) (getGroupCooc y)))) $ listToDirectedCombi groups                          
       _                  -> undefined 
@@ -72,5 +72,5 @@ setPhyloBranches lvl p = alterGroupWithLevel (\g -> let bIdx = (fst . head) $ fi
     bs = graphToBranches lvl graph p
     --------------------------------------
     graph :: GroupGraph
-    graph = groupsToGraph (FromPairs,[]) (getGroupsWithLevel lvl p) p
+    graph = groupsToGraph (Proximity Filiation empty Nothing) (getGroupsWithLevel lvl p) p
     --------------------------------------
\ No newline at end of file

src/Gargantext/Viz/Phylo/Example.hs

@@ -56,6 +56,7 @@ import Gargantext.Viz.Phylo.LevelMaker
 import Gargantext.Viz.Phylo.LinkMaker
 import Gargantext.Viz.Phylo.Metrics.Proximity
 import Gargantext.Viz.Phylo.Metrics.Clustering
+import Gargantext.Viz.Phylo.PhyloMaker
 import Gargantext.Viz.Phylo.Tools
 import Gargantext.Viz.Phylo.View.Display
 import Gargantext.Viz.Phylo.View.Filters
@@ -74,20 +75,43 @@ import qualified Data.Tuple  as Tuple
 import qualified Data.Vector as Vector
 
 
+------------------------------------------------------------------------
+-- | STEP 13 | -- Create a Phylo from a Rest request 
+
+
+phylo' :: Phylo
+phylo' = toPhylo phyloQuery corpus actants
+
+
+phyloQuery :: PhyloQuery
+phyloQuery = PhyloQuery "Cesar et Cleôpatre" "An example of Phylomemy (french without accent)"
+                        5 3
+                        (Clustering FrequentItemSet 
+                                    (singleton "supportInf" 1)
+                                    (Map.fromList [("filterFis",True),("emptyFis",False)])
+                                    Nothing)
+                        (Proximity  WeightedLogJaccard 
+                                    (singleton "sensibility" 0) (Just 0.01))
+                        2
+                        (Clustering RelatedComponents
+                                    empty empty
+                                    (Just (Proximity Filiation empty Nothing)))
+
+
 ------------------------------------------------------------------------
 -- | STEP 12 | -- Return a Phylo as a View for upcomming visiualization tasks 
 
 
 -- | To do : add a queryParser from an URL and then update the defaultQuery
-urlToQuery :: Text -> PhyloQuery
+urlToQuery :: Text -> PhyloQueryView
 urlToQuery url = defaultQuery 
               & query_metrics %~ (++ [BranchAge])
               & query_filters %~ (++ [QueryFilter LonelyBranch [2,2,1]])
               & query_taggers %~ (++ [BranchLabelFreq,GroupLabelCooc])
 
 
-defaultQuery :: PhyloQuery
-defaultQuery = PhyloQuery 3 Descendant False 1 [] [] [] (Just (ByBranchAge,Asc)) Flat True
+defaultQuery :: PhyloQueryView
+defaultQuery = PhyloQueryView 3 Descendant False 1 [] [] [] (Just (ByBranchAge,Asc)) Flat True
 
 
 urlQuery :: Text
@@ -107,16 +131,16 @@ phyloView = toPhyloView urlQuery phylo6
 
 
 phylo6 :: Phylo
-phylo6 = toNthLevel 6 (WeightedLogJaccard,[0.01,0]) (RelatedComponents, []) (WeightedLogJaccard,[0.01,0]) phylo3  
+phylo6 = toNthLevel 6 (Proximity WeightedLogJaccard (singleton "sensibility" 0) (Just 0.01)) (Clustering RelatedComponents empty empty (Just (Proximity Filiation empty Nothing)))  phylo3  
 
 
 phylo3 :: Phylo
 phylo3 = setPhyloBranches 3
-       $ interTempoMatching Childs  3 (WeightedLogJaccard,[0.01,0])
-       $ interTempoMatching Parents 3 (WeightedLogJaccard,[0.01,0]) 
+       $ interTempoMatching Descendant 3 (Proximity WeightedLogJaccard (singleton "sensibility" 0) (Just 0.01))
+       $ interTempoMatching Ascendant 3 (Proximity WeightedLogJaccard (singleton "sensibility" 0) (Just 0.01)) 
        $ setLevelLinks (2,3) 
        $ addPhyloLevel 3 
-          (phyloToClusters 2 (WeightedLogJaccard,[0.01,0]) (RelatedComponents, []) phyloBranch2) 
+          (phyloToClusters 2 (Proximity WeightedLogJaccard (singleton "sensibility" 0) (Just 0.01)) (Clustering RelatedComponents empty empty (Just (Proximity Filiation empty Nothing))) phyloBranch2) 
           phyloBranch2
 
 
@@ -128,11 +152,11 @@ phyloBranch2 = setPhyloBranches 2 phylo2_c
 
 
 phylo2_c :: Phylo
-phylo2_c = interTempoMatching Childs 2 (WeightedLogJaccard,[0.01,0]) phylo2_p
+phylo2_c = interTempoMatching Descendant 2 (Proximity WeightedLogJaccard (singleton "sensibility" 0) (Just 0.01)) phylo2_p
 
 
 phylo2_p :: Phylo
-phylo2_p = interTempoMatching Parents 2 (WeightedLogJaccard,[0.01,0]) phylo2_1_2
+phylo2_p = interTempoMatching Ascendant 2 (Proximity WeightedLogJaccard (singleton "sensibility" 0) (Just 0.01)) phylo2_1_2
 
 
 phylo2_1_2 :: Phylo
@@ -145,7 +169,7 @@ phylo2 = addPhyloLevel 2 phyloCluster phyloBranch1
 
 
 phyloCluster :: Map (Date,Date) [Cluster] 
-phyloCluster = phyloToClusters 1 (WeightedLogJaccard,[0.01,0]) (RelatedComponents, []) phyloBranch1
+phyloCluster = phyloToClusters 1 (Proximity WeightedLogJaccard (singleton "sensibility" 0) (Just 0.01)) (Clustering RelatedComponents empty empty (Just (Proximity Filiation empty Nothing))) phyloBranch1
 
 
 ------------------------------------------------------------------------
@@ -161,11 +185,11 @@ phyloBranch1 = setPhyloBranches 1 phylo1_c
 
 
 phylo1_c :: Phylo
-phylo1_c = interTempoMatching Childs 1 (WeightedLogJaccard,[0.01,0]) phylo1_p
+phylo1_c = interTempoMatching Descendant 1 (Proximity WeightedLogJaccard (singleton "sensibility" 0) (Just 0.01)) phylo1_p
 
 
 phylo1_p :: Phylo
-phylo1_p = interTempoMatching Parents 1 (WeightedLogJaccard,[0.01,0]) phylo1_0_1
+phylo1_p = interTempoMatching Ascendant 1 (Proximity WeightedLogJaccard (singleton "sensibility" 0) (Just 0.01)) phylo1_0_1
 
 
 ------------------------------------------------------------------------
@@ -245,3 +269,9 @@ actants = [ "Cleopatre"   , "Ptolemee", "Ptolemee-XIII", "Ptolemee-XIV"
 
 corpus :: [(Date, Text)]
 corpus = List.sortOn fst [ (-51,"Cleopatre règne sur l’egypte entre 51 et 30 av. J.-C. avec ses frères-epoux Ptolemee-XIII et Ptolemee-XIV, puis aux côtes du general romain Marc-Antoine. Elle est celèbre pour avoir ete la compagne de Jules Cesar puis d'Antoine, avec lesquels elle a eu plusieurs enfants. Partie prenante dans la guerre civile opposant Antoine à Octave, elle est vaincue à la bataille d'Actium en 31 av. J.-C. Sa defaite va permettre aux Romains de mener à bien la conquête de l’egypte, evenement qui marquera la fin de l'epoque hellenistique."), (-40,"Il existe relativement peu d'informations sur son sejour à Rome, au lendemain de l'assassinat de Cesar, ou sur la periode passee à Alexandrie durant l'absence d'Antoine, entre -40 et -37."), (-48,"L'historiographie antique lui est globalement defavorable car inspiree par son vainqueur, l'empereur Auguste, et par son entourage, dont l'interêt est de la noircir, afin d'en faire l'adversaire malfaisant de Rome et le mauvais genie d'Antoine. On observe par ailleurs que Cesar ne fait aucune mention de sa liaison avec elle dans les Commentaires sur la Guerre civile"), (-69,"Cleopatre est nee au cours de l'hiver -69/-686 probablement à Alexandrie."), (-48,"Pompee a en effet ete le protecteur de Ptolemee XII, le père de Cleopatre et de Ptolemee-XIII dont il se considère comme le tuteur."), (-48,"Ptolemee-XIII et Cleopatre auraient d'ailleurs aide Pompee par l'envoi d'une flotte de soixante navires."), (-48,"Mais le jeune roi Ptolemee-XIII et ses conseillers jugent sa cause perdue et pensent s'attirer les bonnes graces du vainqueur en le faisant assassiner à peine a-t-il pose le pied sur le sol egyptien, près de Peluse, le 30 juillet 48 av. J.-C., sous les yeux de son entourage."), (-48,"Cesar fait enterrer la tête de Pompee dans le bosquet de Nemesis en bordure du mur est de l'enceinte d'Alexandrie. Pour autant la mort de Pompee est une aubaine pour Cesar qui tente par ailleurs de profiter des querelles dynastiques pour annexer l’egypte."), (-48,"Il est difficile de se prononcer clairement sur les raisons qui ont pousse Cesar à s'attarder à Alexandrie. Il y a des raisons politiques, mais aussi des raisons plus sentimentales (Cleopatre ?). Il tente d'abord d'obtenir le remboursement de dettes que Ptolemee XII"), (-46,"Les deux souverains sont convoques par Cesar au palais royal d'Alexandrie. Ptolemee-XIII s'y rend après diverses tergiversations ainsi que Cleopatre."), (-47,"A Rome, Cleopatre epouse alors un autre de ses frères cadets, à Alexandrie, Ptolemee-XIV, sur l'injonction de Jules Cesar"), (-46,"Cesar a-t-il comme objectif de montrer ce qu'il en coûte de se revolter contre Rome en faisant figurer dans son triomphe la sœur de Cleopatre et de Ptolemee-XIV, Arsinoe, qui s'est fait reconnaître reine par les troupes de Ptolemee-XIII ?"), (-44,"Au debut de l'annee -44, Cesar est assassine par Brutus. Profitant de la situation confuse qui s'ensuit, Cleopatre quitte alors Rome à la mi-avril, faisant escale en Grèce. Elle parvient à Alexandrie en juillet -44."), (-44,"La guerre que se livrent les assassins de Cesar, Cassius et Brutus et ses heritiers, Octave et Marc-Antoine, oblige Cleopatre à des contorsions diplomatiques."), (-41,"Nous ignorons depuis quand Cleopatre, agee de 29 ans en -41, et Marc-Antoine, qui a une quarantaine d'annees, se connaissent. Marc-Antoine est l'un des officiers qui ont participe au retablissement de Ptolemee XII.  Il est plus vraisemblable qu'ils se soient frequentes lors du sejour à Rome de Cleopatre."), (-42,"Brutus tient la Grèce tandis que Cassius s'installe en Syrie. Le gouverneur de Cleopatre à Chypre, Serapion, vient en aide à Cassius."), (-42,"Cassius aurait envisage de s'emparer d'Alexandrie quand le 'debarquement' en Grèce d'Antoine et d'Octave l'oblige à renoncer à ses projets")]
+
+
+------------------------------------------------------------------------
+-- | From REST routes | -- Let's build a Phylomemy from scratch 
+
+

src/Gargantext/Viz/Phylo/LevelMaker.hs

@@ -23,11 +23,13 @@ import Data.Map                     (Map, (!), empty, restrictKeys, filterWithKe
 import Data.Set                     (Set)
 import Data.Text                    (Text, words)
 import Data.Tuple.Extra
+import Data.Vector                  (Vector)
 
 import Gargantext.Prelude                   hiding (head)
 import Gargantext.Viz.Phylo.Aggregates.Cluster
 import Gargantext.Viz.Phylo.Aggregates.Cooc
 import Gargantext.Viz.Phylo.Aggregates.Document
+import Gargantext.Viz.Phylo.Aggregates.Fis
 import Gargantext.Viz.Phylo
 import Gargantext.Viz.Phylo.Tools
 import Gargantext.Viz.Phylo.LinkMaker
@@ -37,6 +39,7 @@ import qualified Data.List   as List
 import qualified Data.Map    as Map
 import qualified Data.Set    as Set
 import qualified Data.Text   as Text
+import qualified Data.Vector as Vector
 
 
 -- | A typeClass for polymorphic PhyloLevel functions
@@ -141,6 +144,7 @@ toPhyloLevel lvl m p = alterPhyloPeriods
                                         ) period) p
 
 
+-- | To init a Phylo
 initPhylo :: Grain -> Step -> [(Date,Text)] -> [Ngrams] -> (Ngrams -> Ngrams) -> Phylo
 initPhylo g s c a f = addPhyloLevel 0 (corpusToDocs f c base) base
   where
@@ -151,18 +155,74 @@ initPhylo g s c a f = addPhyloLevel 0 (corpusToDocs f c base) base
 
 
 -- | To incrementally add new Levels to a Phylo by making all the linking and aggregation tasks 
-toNthLevel :: Level -> (Proximity,[Double]) -> (Clustering,[Double]) -> (Proximity,[Double]) -> Phylo -> Phylo
-toNthLevel lvlMax (prox,param1) (clus,param2) (prox',param3) p 
+toNthLevel :: Level -> Proximity -> Clustering -> Phylo -> Phylo
+toNthLevel lvlMax prox clus p 
   | lvl >= lvlMax = p
-  | otherwise     = toNthLevel lvlMax (prox,param1) (clus,param2) (prox',param3)
+  | otherwise     = toNthLevel lvlMax prox clus
                   $ setPhyloBranches (lvl + 1)                  
-                  $ interTempoMatching Childs  (lvl + 1) (prox',param3)
-                  $ interTempoMatching Parents (lvl + 1) (prox',param3)
+                  $ interTempoMatching Descendant  (lvl + 1) prox
+                  $ interTempoMatching Ascendant (lvl + 1) prox
                   $ setLevelLinks (lvl, lvl + 1)
                   $ addPhyloLevel (lvl + 1)
-                    (phyloToClusters lvl (prox,param1) (clus,param2) p) p
+                    (phyloToClusters lvl (fromJust $ clus ^. clustering_proximity) clus p) p
   where
     --------------------------------------
     lvl :: Level 
     lvl = getLastLevel p 
     --------------------------------------
+
+
+-- | To reconstruct the Level 1 of a Phylo based on a Clustering Methods
+toPhylo1 :: Clustering -> Proximity -> Map (Date, Date) [Document] -> Phylo -> Phylo
+toPhylo1 clst proxy d p = case getClusterName clst of 
+                FrequentItemSet -> setPhyloBranches 1
+                                 $ interTempoMatching Descendant 1 proxy
+                                 $ interTempoMatching Ascendant 1 proxy
+                                 $ setLevelLinks (0,1)
+                                 $ setLevelLinks (1,0)
+                                 $ addPhyloLevel 1 phyloFis p
+                  where 
+                    --------------------------------------
+                    phyloFis :: Map (Date, Date) [Fis]
+                    phyloFis = filterFisBySupport (getClusterParamBool clst "emptyFis") (round $ getClusterParam clst "supportInf") (filterFisByNested (docsToFis d))
+                    --------------------------------------
+
+                _               -> panic "[ERR][Viz.Phylo.PhyloMaker.toPhylo1] fst clustering not recognized"
+
+
+-- | To reconstruct the Level 0 of a Phylo
+toPhylo0 :: Map (Date, Date) [Document] -> Phylo -> Phylo 
+toPhylo0 d p = addPhyloLevel 0 d p
+
+
+-- | To reconstruct the Base of a Phylo
+toPhyloBase :: PhyloQuery -> [(Date, Text)] -> [Ngrams] -> Phylo 
+toPhyloBase q c a = initPhyloBase periods foundations
+  where 
+    --------------------------------------
+    periods :: [(Date,Date)] 
+    periods = initPeriods (getTimeGrain q) (getTimeSteps q) 
+            $ both fst (head c,last c)
+    --------------------------------------        
+    foundations :: Vector Ngrams
+    foundations = initFoundations a
+    --------------------------------------
+
+
+-- | To reconstruct a Phylomemy from a PhyloQuery, a Corpus and a list of actants 
+toPhylo :: PhyloQuery -> [(Date, Text)] -> [Ngrams] -> Phylo
+toPhylo q c a = toNthLevel (getNthLevel q) (getTimeMatching q) (getNthCluster q) phylo1
+  where
+    --------------------------------------
+    phylo1 :: Phylo
+    phylo1 = toPhylo1 (getFstCluster q) (getTimeMatching q) phyloDocs phylo0    
+    --------------------------------------
+    phylo0 :: Phylo
+    phylo0 = toPhylo0 phyloDocs phyloBase
+    -------------------------------------- 
+    phyloDocs :: Map (Date, Date) [Document]
+    phyloDocs = corpusToDocs groupNgramsWithTrees c phyloBase
+    -------------------------------------- 
+    phyloBase :: Phylo
+    phyloBase = toPhyloBase q c a
+    -------------------------------------- 
\ No newline at end of file

src/Gargantext/Viz/Phylo/LinkMaker.hs

@@ -19,7 +19,7 @@ module Gargantext.Viz.Phylo.LinkMaker
 
 import Control.Lens                 hiding (both, Level)
 import Data.List                    ((++), sort, concat, nub, words, zip, sortOn, head, null, tail, splitAt, (!!), elem)
-import Data.Map                     (Map)
+import Data.Map                     (Map,(!))
 import Data.Set                     (Set)
 import Data.Tuple.Extra
 
@@ -85,19 +85,19 @@ setLevelLinks (lvl,lvl') p = alterPhyloGroups (linkGroupsByLevel (lvl,lvl') p) p
 
 
 -- | To apply the corresponding proximity function based on a given Proximity
-getProximity :: (Proximity,[Double]) -> PhyloGroup -> PhyloGroup -> (PhyloGroupId, Double)
-getProximity (prox,param) g1 g2 = case prox of 
-  WeightedLogJaccard -> ((getGroupId g2),weightedLogJaccard (param !! 1) (getGroupCooc g1) (unifySharedKeys (getGroupCooc g2) (getGroupCooc g1)))
+getProximity :: Proximity -> PhyloGroup -> PhyloGroup -> (PhyloGroupId, Double)
+getProximity prox g1 g2 = case (prox ^. proximity_name) of 
+  WeightedLogJaccard -> ((getGroupId g2),weightedLogJaccard (getSensibility prox) (getGroupCooc g1) (unifySharedKeys (getGroupCooc g2) (getGroupCooc g1)))
   Hamming            -> ((getGroupId g2),hamming (getGroupCooc g1) (unifySharedKeys (getGroupCooc g2) (getGroupCooc g1)))
   _                  -> panic ("[ERR][Viz.Phylo.Example.getProximity] Proximity function not defined")
 
 
 -- | To get the next or previous PhyloPeriod based on a given PhyloPeriodId
-getNextPeriods :: PairTo -> PhyloPeriodId -> [PhyloPeriodId] -> [PhyloPeriodId] 
+getNextPeriods :: Filiation -> PhyloPeriodId -> [PhyloPeriodId] -> [PhyloPeriodId] 
 getNextPeriods to id l = case to of 
-    Childs  -> unNested id ((tail . snd) next) 
-    Parents -> unNested id ((reverse . fst) next)
-    _       -> panic ("[ERR][Viz.Phylo.Example.getNextPeriods] PairTo type not defined")
+    Descendant -> unNested id ((tail . snd) next) 
+    Ascendant  -> unNested id ((reverse . fst) next)
+    _          -> panic ("[ERR][Viz.Phylo.Example.getNextPeriods] Filiation type not defined")
     where 
       --------------------------------------
       next :: ([PhyloPeriodId], [PhyloPeriodId])
@@ -122,11 +122,11 @@ getNextPeriods to id l = case to of
 
 
 -- | To find the best set (max = 2) of Childs/Parents candidates based on a given Proximity mesure until a maximum depth (max = Period + 5 units )  
-findBestCandidates :: PairTo -> Int -> Int -> (Proximity,[Double]) -> PhyloGroup -> Phylo -> [(PhyloGroupId, Double)]
-findBestCandidates to depth max (prox,param) group p
+findBestCandidates :: Filiation -> Int -> Int -> Proximity -> PhyloGroup -> Phylo -> [(PhyloGroupId, Double)]
+findBestCandidates to depth max prox group p
   | depth > max || null next = [] 
   | (not . null) best = take 2 best
-  | otherwise = findBestCandidates to (depth + 1) max (prox,param) group p   
+  | otherwise = findBestCandidates to (depth + 1) max prox group p   
   where
     --------------------------------------
     next :: [PhyloPeriodId]
@@ -136,23 +136,23 @@ findBestCandidates to depth max (prox,param) group p
     candidates = getGroupsWithFilters (getGroupLevel group) (head next) p
     --------------------------------------
     scores :: [(PhyloGroupId, Double)]
-    scores = map (\group' -> getProximity (prox,param) group group') candidates
+    scores = map (\group' -> getProximity prox group group') candidates
     --------------------------------------
     best :: [(PhyloGroupId, Double)]
     best = reverse
          $ sortOn snd 
-         $ filter (\(id,score) -> case prox of 
-            WeightedLogJaccard -> score >= (param !! 0)
-            Hamming            -> score <= (param !! 0)) scores
+         $ filter (\(id,score) -> case (prox ^. proximity_name) of 
+            WeightedLogJaccard -> score >= fromJust (prox ^. proximity_threshold)
+            Hamming            -> score <= fromJust (prox ^. proximity_threshold)) scores
     --------------------------------------
 
 
 -- | To add a new list of Pointers into an existing Childs/Parents list of Pointers 
-makePair :: PairTo -> PhyloGroup -> [(PhyloGroupId, Double)] -> PhyloGroup
+makePair :: Filiation -> PhyloGroup -> [(PhyloGroupId, Double)] -> PhyloGroup
 makePair to group ids = case to of 
-    Childs  -> over (phylo_groupPeriodChilds) addPointers group
-    Parents -> over (phylo_groupPeriodParents) addPointers group
-    _       -> panic ("[ERR][Viz.Phylo.Example.makePair] PairTo type not defined")
+    Descendant  -> over (phylo_groupPeriodChilds) addPointers group
+    Ascendant   -> over (phylo_groupPeriodParents) addPointers group
+    _           -> panic ("[ERR][Viz.Phylo.Example.makePair] Filiation type not defined")
     where
       -------------------------------------- 
       addPointers :: [Pointer] -> [Pointer]
@@ -161,8 +161,8 @@ makePair to group ids = case to of
 
 
 -- | To pair all the Phylogroups of given PhyloLevel to their best Parents or Childs
-interTempoMatching :: PairTo -> Level -> (Proximity,[Double]) -> Phylo -> Phylo
-interTempoMatching to lvl (prox,param) p = alterPhyloGroups
+interTempoMatching :: Filiation -> Level -> Proximity -> Phylo -> Phylo
+interTempoMatching to lvl prox p = alterPhyloGroups
                                     (\groups -> 
                                       map (\group ->
                                             if (getGroupLevel group) == lvl
@@ -170,7 +170,7 @@ interTempoMatching to lvl (prox,param) p = alterPhyloGroups
                                               let
                                                 --------------------------------------
                                                 candidates :: [(PhyloGroupId, Double)] 
-                                                candidates = findBestCandidates to 1 5 (prox,param) group p
+                                                candidates = findBestCandidates to 1 5 prox group p
                                                 --------------------------------------
                                               in 
                                                 makePair to group candidates

src/Gargantext/Viz/Phylo/Tools.hs

@@ -20,7 +20,7 @@ module Gargantext.Viz.Phylo.Tools
 import Control.Lens         hiding (both, Level)
 import Data.List            (filter, intersect, (++), sort, null, head, tail, last, tails, delete, nub, concat, union, sortOn)
 import Data.Maybe           (mapMaybe)
-import Data.Map             (Map, mapKeys, member, elems, adjust)
+import Data.Map             (Map, mapKeys, member, elems, adjust, (!))
 import Data.Set             (Set)
 import Data.Text            (Text, toLower)
 import Data.Tuple.Extra
@@ -136,7 +136,31 @@ getBranchIdsWith lvl p = sortOn snd
 
 -- | To get the Meta value of a PhyloBranch 
 getBranchMeta :: Text -> PhyloBranch -> Double 
-getBranchMeta k b = (b ^. phylo_branchMeta) Map.! k
+getBranchMeta k b = (b ^. phylo_branchMeta) ! k
+
+
+-- | To get the Name of a Clustering Methods
+getClusterName :: Clustering -> ClusteringName
+getClusterName c = _clustering_name c
+
+
+-- | To get the params of a Clustering Methods
+getClusterParam :: Clustering -> Text -> Double
+getClusterParam c k = if (member k $ _clustering_params c)
+                      then (_clustering_params c) Map.! k
+                      else panic "[ERR][Viz.Phylo.Tools.getClusterParam] the key is not in params"
+
+
+-- | To get the boolean params of a Clustering Methods
+getClusterParamBool :: Clustering -> Text -> Bool
+getClusterParamBool c k = if (member k $ _clustering_paramsBool c)
+                      then (_clustering_paramsBool c) Map.! k
+                      else panic "[ERR][Viz.Phylo.Tools.getClusterParamBool] the key is not in paramsBool"
+
+
+-- | To get the first clustering method to apply to get the level 1 of a Phylo
+getFstCluster :: PhyloQuery -> Clustering
+getFstCluster q = q ^. phyloQuery_fstCluster
 
 
 -- | To get the foundations of a Phylo
@@ -355,6 +379,16 @@ getNodesInBranches v = filter (\n -> isJust $ n ^. phylo_nodeBranchId)
                      $ v ^. phylo_viewNodes
 
 
+-- | To get the cluster methods to apply to the Nths levels of a Phylo
+getNthCluster :: PhyloQuery -> Clustering
+getNthCluster q = q ^. phyloQuery_nthCluster
+
+
+-- | To get the Sup Level of a reconstruction of a Phylo from a PhyloQuery
+getNthLevel :: PhyloQuery -> Level
+getNthLevel q = q ^. phyloQuery_nthLevel
+
+
 -- | To get the PhylolevelId of a given PhyloLevel
 getPhyloLevelId :: PhyloLevel -> PhyloLevelId
 getPhyloLevelId = _phylo_levelId
@@ -376,6 +410,13 @@ getPhyloPeriodId :: PhyloPeriod -> PhyloPeriodId
 getPhyloPeriodId prd = _phylo_periodId prd 
 
 
+-- | To get the sensibility of a Proximity if it exists
+getSensibility :: Proximity -> Double
+getSensibility prox = if (member "sensibility" $ prox ^. proximity_params)
+                      then (prox ^. proximity_params) ! "sensibility"
+                      else panic "[ERR][Viz.Phylo.Tools.getSensibility] sensibility not in params"
+
+
 -- | To get the PhyloGroupId of the Source of a PhyloEdge 
 getSourceId :: PhyloEdge -> PhyloGroupId
 getSourceId e = e ^. phylo_edgeSource 
@@ -386,6 +427,21 @@ getTargetId :: PhyloEdge -> PhyloGroupId
 getTargetId e = e ^. phylo_edgeTarget
 
 
+-- | To get the Grain of the PhyloPeriods from a PhyloQuery
+getTimeGrain :: PhyloQuery -> Int
+getTimeGrain q = q ^. phyloQuery_timeGrain 
+
+
+-- | To get the intertemporal matching strategy to apply to a Phylo from a PhyloQuery
+getTimeMatching :: PhyloQuery -> Proximity
+getTimeMatching q = q ^. phyloQuery_timeMatching
+
+
+-- | To get the Steps of the PhyloPeriods from a PhyloQuery
+getTimeSteps :: PhyloQuery -> Int 
+getTimeSteps q = q ^. phyloQuery_timeSteps
+
+
 -- | To get all the PhyloBranchIds of a PhyloView
 getViewBranchIds :: PhyloView -> [PhyloBranchId]
 getViewBranchIds v = map getBranchId $ v ^. phylo_viewBranches

src/Gargantext/Viz/Phylo/View/ViewMaker.hs

@@ -125,7 +125,7 @@ addChildNodes shouldDo lvl lvlMin vb fl p v =
 
 
 -- | To transform a PhyloQuery into a PhyloView
-queryToView :: PhyloQuery -> Phylo -> PhyloView
+queryToView :: PhyloQueryView -> Phylo -> PhyloView
 queryToView q p = processDisplay (q ^. query_display)
                 $ processSort (q ^. query_sort) p
                 $ processTaggers (q ^. query_taggers) p
@@ -137,7 +137,7 @@ queryToView q p = processDisplay (q ^. query_display)
 
 -- | dirty params
 phyloParams :: PhyloParam
-phyloParams = PhyloParam "v0.1" (Software "Gargantext" "v4") ""
+phyloParams = PhyloParam "v0.1" (Software "Gargantext" "v4") "" Nothing
 
 
 -- | To do : effectively get the PhyloParams of a Phylo