[PHYLO.API] Adding REST functions.

src/Gargantext/API/Node.hs

@@ -63,6 +63,8 @@ import Gargantext.API.Settings
 import Gargantext.Text.Metrics (Scored(..))
 import Gargantext.Viz.Graph hiding (Node)-- (Graph(_graph_metadata),LegendField(..), GraphMetadata(..),readGraphFromJson,defaultGraph)
 import Gargantext.Viz.Graph.Tools (cooc2graph)
+import Gargantext.Viz.Phylo.API (getPhylo)
+import Gargantext.Viz.Phylo hiding (Tree)
 import Servant
 import Test.QuickCheck (elements)
 import Test.QuickCheck.Arbitrary (Arbitrary, arbitrary)

src/Gargantext/Database/Types/Node.hs

@@ -82,7 +82,6 @@ instance Arbitrary NodeId where
   arbitrary = NodeId <$> arbitrary
 
 type ParentId = NodeId
-type GraphId  = NodeId
 type CorpusId = NodeId
 type ListId   = NodeId
 type DocumentId = NodeId
@@ -91,6 +90,8 @@ type RootId   = NodeId
 type MasterCorpusId = CorpusId
 type UserCorpusId   = CorpusId
 
+type GraphId  = NodeId
+type PhyloId  = NodeId
 type AnnuaireId = NodeId
 type ContactId  = NodeId
 

src/Gargantext/Viz/Phylo.hs

@@ -52,7 +52,7 @@ import Gargantext.Prelude
 data PhyloParam =
      PhyloParam { _phyloParam_version  :: Text -- Double ?
                 , _phyloParam_software :: Software
-                , _phyloParam_query    :: PhyloQuery
+                , _phyloParam_query    :: PhyloQueryBuild
      } deriving (Generic, Show, Eq)
 
 
@@ -326,7 +326,7 @@ data Order = Asc | Desc deriving (Show)
 
 
 -- | A Phyloquery describes a phylomemic reconstruction
-data PhyloQuery = PhyloQuery
+data PhyloQueryBuild = PhyloQueryBuild
     { _q_phyloTitle :: Text
     , _q_phyloDesc  :: Text
 
@@ -352,7 +352,6 @@ data PhyloQuery = PhyloQuery
 data Filiation = Ascendant | Descendant | Merge | Complete deriving (Show)
 data EdgeType  = PeriodEdge | LevelEdge deriving (Show)
 
-
 -------------------
 -- | PhyloView | --
 -------------------
@@ -360,39 +359,39 @@ data EdgeType  = PeriodEdge | LevelEdge deriving (Show)
 
 -- | A PhyloView is the output type of a Phylo
 data PhyloView = PhyloView
-  { _phylo_viewParam       :: PhyloParam
-  , _phylo_viewTitle       :: Text
-  , _phylo_viewDescription :: Text
-  , _phylo_viewFiliation   :: Filiation
-  , _phylo_viewMetrics     :: Map Text [Double]
-  , _phylo_viewBranches    :: [PhyloBranch]
-  , _phylo_viewNodes       :: [PhyloNode]
-  , _phylo_viewEdges       :: [PhyloEdge]
+  { _pv_param       :: PhyloParam
+  , _pv_title       :: Text
+  , _pv_description :: Text
+  , _pv_filiation   :: Filiation
+  , _pv_metrics     :: Map Text [Double]
+  , _pv_branches    :: [PhyloBranch]
+  , _pv_nodes       :: [PhyloNode]
+  , _pv_edges       :: [PhyloEdge]
   } deriving (Show)
 
 -- | A phyloview is made of PhyloBranches, edges and nodes
 data PhyloBranch = PhyloBranch
-  { _phylo_branchId      :: PhyloBranchId
-  , _phylo_branchLabel   :: Text
-  , _phylo_branchMetrics :: Map Text [Double]
+  { _pb_id      :: PhyloBranchId
+  , _pb_label   :: Text
+  , _pb_metrics :: Map Text [Double]
   } deriving (Show)
 
 data PhyloEdge = PhyloEdge
-  { _phylo_edgeSource :: PhyloGroupId
-  , _phylo_edgeTarget :: PhyloGroupId
-  , _phylo_edgeType   :: EdgeType
-  , _phylo_edgeWeight :: Weight
+  { _pe_source :: PhyloGroupId
+  , _pe_target :: PhyloGroupId
+  , _pe_type   :: EdgeType
+  , _pe_weight :: Weight
   } deriving (Show)
 
 data PhyloNode = PhyloNode
-  { _phylo_nodeId        :: PhyloGroupId
-  , _phylo_nodeBranchId  :: Maybe PhyloBranchId
-  , _phylo_nodeLabel     :: Text
-  , _phylo_nodeNgramsIdx :: [Int]
-  , _phylo_nodeNgrams    :: Maybe [Ngrams]
-  , _phylo_nodeMetrics      :: Map Text [Double]
-  , _phylo_nodeLevelParents :: Maybe [PhyloGroupId]
-  , _phylo_nodeLevelChilds  :: [PhyloNode]
+  { _pn_id        :: PhyloGroupId
+  , _pn_bid  :: Maybe PhyloBranchId
+  , _pn_label     :: Text
+  , _pn_idx :: [Int]
+  , _pn_ngrams    :: Maybe [Ngrams]
+  , _pn_metrics      :: Map Text [Double]
+  , _pn_parents :: Maybe [PhyloGroupId]
+  , _pn_childs  :: [PhyloNode]
   } deriving (Show)
 
 
@@ -448,7 +447,7 @@ makeLenses ''Proximity
 makeLenses ''Cluster
 makeLenses ''Filter
 --
-makeLenses ''PhyloQuery
+makeLenses ''PhyloQueryBuild
 makeLenses ''PhyloQueryView
 --
 makeLenses ''PhyloView
@@ -485,7 +484,14 @@ $(deriveJSON (unPrefix "_rc_" )      ''RCParams      )
 $(deriveJSON (unPrefix "_wlj_" )     ''WLJParams     )
 $(deriveJSON (unPrefix "_sb_" )      ''SBParams      )
 --
-$(deriveJSON (unPrefix "_q_" ) ''PhyloQuery )
+$(deriveJSON (unPrefix "_q_" )  ''PhyloQueryBuild  )
+$(deriveJSON (unPrefix "_pv_" ) ''PhyloView   )
+$(deriveJSON (unPrefix "_pb_" ) ''PhyloBranch )
+$(deriveJSON (unPrefix "_pe_" ) ''PhyloEdge   )
+$(deriveJSON (unPrefix "_pn_" ) ''PhyloNode   )
+
+$(deriveJSON defaultOptions ''Filiation )
+$(deriveJSON defaultOptions ''EdgeType  )
 
 
 ----------------------------

src/Gargantext/Viz/Phylo/Example.hs

@@ -81,7 +81,7 @@ phyloFromQuery :: Phylo
 phyloFromQuery = toPhylo (queryParser queryEx) corpus actants actantsTrees
 
 -- | To do : create a request handler and a query parser
-queryParser :: [Char] -> PhyloQuery
+queryParser :: [Char] -> PhyloQueryBuild
 queryParser _q = phyloQuery
 
 queryEx :: [Char]
@@ -94,8 +94,8 @@ queryEx = "title=Cesar et Cleôpatre"
           ++ "nthCluster=RelatedComponents"
           ++ "nthProximity=Filiation"
 
-phyloQuery :: PhyloQuery
-phyloQuery = PhyloQuery "Cesar et Cleôpatre" "An example of Phylomemy (french without accent)"
+phyloQuery :: PhyloQueryBuild
+phyloQuery = PhyloQueryBuild "Cesar et Cleôpatre" "An example of Phylomemy (french without accent)"
              5 3 defaultFis [] [] defaultWeightedLogJaccard 3 defaultRelatedComponents
 
 

src/Gargantext/Viz/Phylo/LevelMaker.hs

@@ -25,7 +25,7 @@ import Data.Map                     (Map, (!), empty, restrictKeys, filterWithKe
 import Data.Text (Text)
 import Data.Tuple.Extra
 import Data.Vector                  (Vector)
-import Gargantext.Prelude                   hiding (head)
+import Gargantext.Prelude           hiding (head)
 import Gargantext.Viz.Phylo
 import Gargantext.Viz.Phylo.Aggregates.Cluster
 import Gargantext.Viz.Phylo.Aggregates.Cooc
@@ -145,8 +145,8 @@ toNthLevel lvlMax prox clus p
   | lvl >= lvlMax = p
   | otherwise     = toNthLevel lvlMax prox clus
                   $ setPhyloBranches (lvl + 1)
-                  $ interTempoMatching Descendant  (lvl + 1) prox
-                  $ interTempoMatching Ascendant (lvl + 1) prox
+                  $ interTempoMatching Descendant (lvl + 1) prox
+                  $ interTempoMatching Ascendant  (lvl + 1) prox
                   $ setLevelLinks (lvl, lvl + 1)
                   $ addPhyloLevel (lvl + 1)
                     (phyloToClusters lvl (getProximity clus) clus p) p
@@ -162,7 +162,7 @@ toPhylo1 :: Cluster -> Proximity -> [Metric] -> [Filter] -> Map (Date, Date) [Do
 toPhylo1 clus prox metrics filters d p = case clus of
   Fis (FisParams k s) -> setPhyloBranches 1
                        $ interTempoMatching Descendant 1 prox
-                       $ interTempoMatching Ascendant 1 prox
+                       $ interTempoMatching Ascendant  1 prox
                        $ setLevelLinks (0,1)
                        $ setLevelLinks (1,0)
                        $ addPhyloLevel 1 phyloFis p
@@ -181,7 +181,7 @@ toPhylo0 d p = addPhyloLevel 0 d p
 
 
 -- | To reconstruct the Base of a Phylo
-toPhyloBase :: PhyloQuery -> PhyloParam -> [(Date, Text)] -> [Ngrams] -> [Tree Ngrams] -> Phylo
+toPhyloBase :: PhyloQueryBuild -> PhyloParam -> [(Date, Text)] -> [Ngrams] -> [Tree Ngrams] -> Phylo
 toPhyloBase q p c a ts = initPhyloBase periods foundations peaks p
   where
     --------------------------------------
@@ -197,8 +197,8 @@ toPhyloBase q p c a ts = initPhyloBase periods foundations peaks p
     --------------------------------------
 
 
--- | To reconstruct a Phylomemy from a PhyloQuery, a Corpus and a list of actants
-toPhylo :: PhyloQuery -> [(Date, Text)] -> [Ngrams] -> [Tree Ngrams] -> Phylo
+-- | To reconstruct a Phylomemy from a PhyloQueryBuild, a Corpus and a list of actants
+toPhylo :: PhyloQueryBuild -> [(Date, Text)] -> [Ngrams] -> [Tree Ngrams] -> Phylo
 toPhylo q c a ts = toNthLevel (getNthLevel q) (getInterTemporalMatching q) (getNthCluster q) phylo1
   where
     --------------------------------------

src/Gargantext/Viz/Phylo/Tools.hs

@@ -145,7 +145,7 @@ initPhyloBase :: [(Date, Date)] -> Vector Ngrams -> PhyloPeaks -> PhyloParam ->
 initPhyloBase pds fds pks prm = Phylo ((fst . head) pds, (snd . last) pds) fds pks (map (\pd -> initPhyloPeriod pd []) pds) prm
 
 -- | To init the param of a Phylo
-initPhyloParam :: Maybe Text -> Maybe Software -> Maybe PhyloQuery -> PhyloParam
+initPhyloParam :: Maybe Text -> Maybe Software -> Maybe PhyloQueryBuild -> PhyloParam
 initPhyloParam (def defaultPhyloVersion -> v) (def defaultSoftware -> s) (def defaultQuery -> q) = PhyloParam v s q
 
 -- | To get the foundations of a Phylo
@@ -495,14 +495,14 @@ getNeighbours directed g e = case directed of
 
 -- | To get the PhyloBranchId of PhyloNode if it exists
 getNodeBranchId :: PhyloNode -> PhyloBranchId
-getNodeBranchId n = case n ^. phylo_nodeBranchId of
+getNodeBranchId n = case n ^. pn_bid of
                      Nothing -> panic "[ERR][Viz.Phylo.Tools.getNodeBranchId] branchId not found"
                      Just i  -> i
 
 
 -- | To get the PhyloGroupId of a PhyloNode
 getNodeId :: PhyloNode -> PhyloGroupId
-getNodeId n = n ^. phylo_nodeId
+getNodeId n = n ^. pn_id
 
 
 -- | To get the Level of a PhyloNode
@@ -513,12 +513,12 @@ getNodeLevel n = (snd . fst) $ getNodeId n
 -- | To get the Parent Node of a PhyloNode in a PhyloView
 getNodeParent :: PhyloNode -> PhyloView -> [PhyloNode]
 getNodeParent n v = filter (\n' -> elem (getNodeId n') (getNodeParentsId n))
-                  $ v ^. phylo_viewNodes
+                  $ v ^. pv_nodes
 
 
 -- | To get the Parent Node id of a PhyloNode if it exists
 getNodeParentsId :: PhyloNode -> [PhyloGroupId]
-getNodeParentsId n = case n ^. phylo_nodeLevelParents of
+getNodeParentsId n = case n ^. pn_parents of
                     Nothing  -> panic "[ERR][Viz.Phylo.Tools.getNodeParentsId] node parent not found"
                     Just ids -> ids
 
@@ -536,18 +536,18 @@ getNodesByBranches v = zip bIds $ map (\id -> filter (\n -> (getNodeBranchId n)
 
 -- | To get a list of PhyloNodes owned by any PhyloBranches in a PhyloView
 getNodesInBranches :: PhyloView -> [PhyloNode]
-getNodesInBranches v = filter (\n -> isJust $ n ^. phylo_nodeBranchId)
-                     $ v ^. phylo_viewNodes
+getNodesInBranches v = filter (\n -> isJust $ n ^. pn_bid)
+                     $ v ^. pv_nodes
 
 
 -- | To get the PhyloGroupId of the Source of a PhyloEdge
 getSourceId :: PhyloEdge -> PhyloGroupId
-getSourceId e = e ^. phylo_edgeSource
+getSourceId e = e ^. pe_source
 
 
 -- | To get the PhyloGroupId of the Target of a PhyloEdge
 getTargetId :: PhyloEdge -> PhyloGroupId
-getTargetId e = e ^. phylo_edgeTarget
+getTargetId e = e ^. pe_target
 
 
 ---------------------
@@ -557,7 +557,7 @@ getTargetId e = e ^. phylo_edgeTarget
 
 -- | To get the PhyloBranchId of a PhyloBranch
 getBranchId :: PhyloBranch -> PhyloBranchId
-getBranchId b = b ^. phylo_branchId
+getBranchId b = b ^. pb_id
 
 
 -- | To get a list of PhyloBranchIds given a Level in a Phylo
@@ -569,12 +569,12 @@ getBranchIdsWith lvl p = sortOn snd
 
 -- | To get the Meta value of a PhyloBranch
 getBranchMeta :: Text -> PhyloBranch -> [Double]
-getBranchMeta k b = (b ^. phylo_branchMetrics) ! k
+getBranchMeta k b = (b ^. pb_metrics) ! k
 
 
 -- | To get all the PhyloBranchIds of a PhyloView
 getViewBranchIds :: PhyloView -> [PhyloBranchId]
-getViewBranchIds v = map getBranchId $ v ^. phylo_viewBranches
+getViewBranchIds v = map getBranchId $ v ^. pv_branches
 
 
 --------------------------------
@@ -582,47 +582,47 @@ getViewBranchIds v = map getBranchId $ v ^. phylo_viewBranches
 --------------------------------
 
 -- | To get the first clustering method to apply to get the contextual units of a Phylo
-getContextualUnit :: PhyloQuery -> Cluster
+getContextualUnit :: PhyloQueryBuild -> Cluster
 getContextualUnit q = q ^. q_contextualUnit
 
 
 -- | To get the metrics to apply to contextual units
-getContextualUnitMetrics :: PhyloQuery -> [Metric]
+getContextualUnitMetrics :: PhyloQueryBuild -> [Metric]
 getContextualUnitMetrics q = q ^. q_contextualUnitMetrics
 
 
 -- | To get the filters to apply to contextual units
-getContextualUnitFilters :: PhyloQuery -> [Filter]
+getContextualUnitFilters :: PhyloQueryBuild -> [Filter]
 getContextualUnitFilters q = q ^. q_contextualUnitFilters
 
 
 -- | To get the cluster methods to apply to the Nths levels of a Phylo
-getNthCluster :: PhyloQuery -> Cluster
+getNthCluster :: PhyloQueryBuild -> Cluster
 getNthCluster q = q ^. q_nthCluster
 
 
 -- | To get the Sup Level of a reconstruction of a Phylo from a PhyloQuery
-getNthLevel :: PhyloQuery -> Level
+getNthLevel :: PhyloQueryBuild -> Level
 getNthLevel q = q ^. q_nthLevel
 
 
 -- | To get the Grain of the PhyloPeriods from a PhyloQuery
-getPeriodGrain :: PhyloQuery -> Int
+getPeriodGrain :: PhyloQueryBuild -> Int
 getPeriodGrain q = q ^. q_periodGrain
 
 
 -- | To get the intertemporal matching strategy to apply to a Phylo from a PhyloQuery
-getInterTemporalMatching :: PhyloQuery -> Proximity
+getInterTemporalMatching :: PhyloQueryBuild -> Proximity
 getInterTemporalMatching q = q ^. q_interTemporalMatching
 
 
 -- | To get the Steps of the PhyloPeriods from a PhyloQuery
-getPeriodSteps :: PhyloQuery -> Int
+getPeriodSteps :: PhyloQueryBuild -> Int
 getPeriodSteps q = q ^. q_periodSteps
 
 
 --------------------------------------------------
--- | PhyloQuery & PhyloQueryView Constructors | --
+-- | PhyloQueryBuild & PhyloQueryView Constructors | --
 --------------------------------------------------
 
 
@@ -655,10 +655,10 @@ initWeightedLogJaccard (def 0 -> thr) (def 0.01 -> sens) = WLJParams thr sens
 
 
 -- | To initialize a PhyloQuery from given and default parameters
-initPhyloQuery :: Text -> Text -> Maybe Int -> Maybe Int -> Maybe Cluster -> Maybe [Metric] -> Maybe [Filter] -> Maybe Proximity -> Maybe Level -> Maybe Cluster -> PhyloQuery
+initPhyloQuery :: Text -> Text -> Maybe Int -> Maybe Int -> Maybe Cluster -> Maybe [Metric] -> Maybe [Filter] -> Maybe Proximity -> Maybe Level -> Maybe Cluster -> PhyloQueryBuild
 initPhyloQuery name desc (def 5 -> grain) (def 3 -> steps) (def defaultFis -> cluster) (def [] -> metrics) (def [] -> filters)
   (def defaultWeightedLogJaccard -> matching') (def 2 -> nthLevel) (def defaultRelatedComponents -> nthCluster) =
-    PhyloQuery name desc grain steps cluster metrics filters matching' nthLevel nthCluster
+    PhyloQueryBuild name desc grain steps cluster metrics filters matching' nthLevel nthCluster
 
 
 -- | To initialize a PhyloQueryView default parameters
@@ -706,7 +706,7 @@ defaultWeightedLogJaccard = WeightedLogJaccard (initWeightedLogJaccard Nothing N
 
 -- Queries
 
-defaultQuery :: PhyloQuery
+defaultQuery :: PhyloQueryBuild
 defaultQuery = initPhyloQuery "Cesar et Cleôpatre" "An example of Phylomemy (french without accent)"
                               Nothing Nothing Nothing Nothing Nothing Nothing Nothing Nothing
 

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

@@ -38,7 +38,7 @@ toNestedView ns ns'
       nested :: [PhyloNode]
       nested = foldl (\ns'' n -> let nIds' = getNodeParentsId n
                                 in map (\n' -> if elem (getNodeId n') nIds'
-                                               then n' & phylo_nodeLevelChilds %~ (++ [n])
+                                               then n' & pn_childs %~ (++ [n])
                                                else n') ns'') ns' ns
       --------------------------------------  
 
@@ -47,8 +47,8 @@ toNestedView ns ns'
 processDisplay :: DisplayMode -> PhyloView -> PhyloView
 processDisplay d v = case d of 
                      Flat   -> v
-                     Nested -> let ns  = sortOn getNodeLevel $ v ^. phylo_viewNodes
+                     Nested -> let ns  = sortOn getNodeLevel $ v ^. pv_nodes
                                    lvl = getNodeLevel $ head ns
-                               in v & phylo_viewNodes .~ toNestedView (filter (\n -> lvl == getNodeLevel n) ns)
+                               in v & pv_nodes .~ toNestedView (filter (\n -> lvl == getNodeLevel n) ns)
                                                                       (filter (\n -> lvl <  getNodeLevel n) ns) 
                      --_      -> panic "[ERR][Viz.Phylo.Example.processDisplay] display not found"

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

@@ -28,13 +28,13 @@ import Gargantext.Viz.Phylo.Tools
 
 -- | To clean a PhyloView list of Nodes, Edges, etc after having filtered its Branches
 cleanNodesEdges :: PhyloView -> PhyloView -> PhyloView
-cleanNodesEdges v v' = v' & phylo_viewNodes %~ (filter (\n -> not $ elem (getNodeId n) nIds))
-                          & phylo_viewNodes %~ (map (\n -> if isNothing (n ^. phylo_nodeLevelParents)
+cleanNodesEdges v v' = v' & pv_nodes %~ (filter (\n -> not $ elem (getNodeId n) nIds))
+                          & pv_nodes %~ (map (\n -> if isNothing (n ^. pn_parents)
                                                            then n
                                                            else if (not .null) $ (getNodeParentsId n) `intersect` nIds
-                                                                then n & phylo_nodeLevelParents .~ Nothing
+                                                                then n & pn_parents .~ Nothing
                                                                 else n ))
-                          & phylo_viewEdges %~ (filter (\e -> (not $ elem (getSourceId e) nIds)
+                          & pv_edges %~ (filter (\e -> (not $ elem (getSourceId e) nIds)
                                                            && (not $ elem (getTargetId e) nIds)))
   where
     --------------------------------------
@@ -54,9 +54,9 @@ filterSmallBranch inf sup min' prds v = cleanNodesEdges v v'
   where
     --------------------------------------
     v' :: PhyloView
-    v' = v & phylo_viewBranches %~ (filter (\b -> let ns = filter (\n -> (getBranchId b)  == (getNodeBranchId n))
-                                                         $ getNodesInBranches v
-                                                      prds' = nub $ map (\n -> (fst . fst) $ getNodeId n) ns
+    v' = v & pv_branches %~ (filter (\b -> let
+                                              ns = filter (\n -> (getBranchId b)  == (getNodeBranchId n)) $ getNodesInBranches v
+                                              prds' = nub $ map (\n -> (fst . fst) $ getNodeId n) ns
                                                   in not (isLone ns prds')))
     --------------------------------------
     isLone :: [PhyloNode] -> [PhyloPeriodId] -> Bool

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

@@ -29,10 +29,10 @@ import Gargantext.Viz.Phylo.Tools
 
 -- | To add a new meta Metric to a PhyloBranch
 addBranchMetrics :: PhyloBranchId -> Text -> Double -> PhyloView -> PhyloView
-addBranchMetrics id lbl val v = over (phylo_viewBranches
+addBranchMetrics id lbl val v = over (pv_branches
                                      . traverse)
                                     (\b -> if getBranchId b == id
-                                           then b & phylo_branchMetrics %~ insert lbl [val]
+                                           then b & pb_metrics %~ insert lbl [val]
                                            else b) v
 
 

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

@@ -27,7 +27,7 @@ import Gargantext.Viz.Phylo.Tools
 
 -- | To sort a PhyloView by Age
 sortBranchByAge :: Order -> PhyloView -> PhyloView
-sortBranchByAge o v = v & phylo_viewBranches %~ f
+sortBranchByAge o v = v & pv_branches %~ f
   where
     --------------------------------------
     f :: [PhyloBranch] -> [PhyloBranch] 

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

@@ -66,10 +66,10 @@ mostOccNgrams thr group = (nub . concat )
 
 -- | To alter the label of a PhyloBranch
 alterBranchLabel :: (PhyloBranchId,Text) -> PhyloView -> PhyloView
-alterBranchLabel (id,lbl) v = over (phylo_viewBranches
+alterBranchLabel (id,lbl) v = over (pv_branches
                                    . traverse)
                                    (\b -> if getBranchId b == id
-                                          then b & phylo_branchLabel .~ lbl
+                                          then b & pb_label .~ lbl
                                           else b) v
 
 
@@ -83,12 +83,12 @@ branchLabelFreq v thr p = foldl (\v' (id,lbl) -> alterBranchLabel (id,lbl) v') v
 
 -- | To set the label of a PhyloNode as the nth most coocurent terms of its PhyloNodes
 nodeLabelCooc :: PhyloView -> Int -> Phylo -> PhyloView
-nodeLabelCooc v thr p = over (phylo_viewNodes
+nodeLabelCooc v thr p = over (pv_nodes
                              . traverse)
                              (\n -> let lbl = ngramsToLabel (getPeaksLabels p)
                                             $ mostOccNgrams thr
                                             $ head $ getGroupsFromIds [getNodeId n] p
-                                    in n & phylo_nodeLabel .~ lbl) v
+                                    in n & pn_label .~ lbl) v
 
 
 -- | To process a sorted list of Taggers to a PhyloView

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

@@ -76,16 +76,16 @@ groupsToNodes isR isV ns gs = map (\g -> let idxs = getGroupNgrams g
 
 mergeEdges :: [PhyloEdge] -> [PhyloEdge] -> [PhyloEdge]
 mergeEdges lAsc lDes = elems
-                     $ unionWithKey (\_k vAsc vDes -> vDes & phylo_edgeWeight .~ (max (vAsc ^. phylo_edgeWeight) (vDes ^. phylo_edgeWeight))) mAsc mDes
+                     $ unionWithKey (\_k vAsc vDes -> vDes & pe_weight .~ (max (vAsc ^. pe_weight) (vDes ^. pe_weight))) mAsc mDes
   where
     --------------------------------------
     mAsc :: Map (PhyloGroupId,PhyloGroupId) PhyloEdge
     mAsc = fromList
-         $ zip (map (\e -> (e ^. phylo_edgeTarget,e ^. phylo_edgeSource)) lAsc) lAsc
+         $ zip (map (\e -> (e ^. pe_target,e ^. pe_source)) lAsc) lAsc
     --------------------------------------
     mDes :: Map (PhyloGroupId,PhyloGroupId) PhyloEdge
     mDes = fromList
-         $ zip (map (\e -> (e ^. phylo_edgeSource,e ^. phylo_edgeTarget)) lDes) lDes
+         $ zip (map (\e -> (e ^. pe_source,e ^. pe_target)) lDes) lDes
     --------------------------------------
 
 
@@ -117,11 +117,11 @@ addChildNodes shouldDo lvl lvlMin vb fl p v =
   if (not shouldDo) || (lvl == lvlMin)
   then v
   else addChildNodes shouldDo (lvl - 1) lvlMin vb fl p
-     $ v & phylo_viewBranches %~ (++ (phyloToBranches (lvl - 1) p))
-         & phylo_viewNodes %~ (++ (groupsToNodes False vb (getPeaksLabels p) gs'))
-         & phylo_viewEdges %~ (++ (groupsToEdges fl PeriodEdge gs'))
-         & phylo_viewEdges %~ (++ (groupsToEdges Descendant LevelEdge gs ))
-         & phylo_viewEdges %~ (++ (groupsToEdges Ascendant LevelEdge  gs'))
+     $ v & pv_branches %~ (++ (phyloToBranches (lvl - 1) p))
+         & pv_nodes %~ (++ (groupsToNodes False vb (getPeaksLabels p) gs'))
+         & pv_edges %~ (++ (groupsToEdges fl PeriodEdge gs'))
+         & pv_edges %~ (++ (groupsToEdges Descendant LevelEdge gs ))
+         & pv_edges %~ (++ (groupsToEdges Ascendant LevelEdge  gs'))
     where
       --------------------------------------
       gs :: [PhyloGroup]
@@ -135,7 +135,7 @@ addChildNodes shouldDo lvl lvlMin vb fl p v =
 -- | To transform a PhyloQuery into a PhyloView
 toPhyloView :: PhyloQueryView -> Phylo -> PhyloView
 toPhyloView q p = processDisplay (q ^. qv_display)
-                $ processSort (q ^. qv_sort) p
+                $ processSort    (q ^. qv_sort   ) p
                 $ processTaggers (q ^. qv_taggers) p
                 $ processFilters (q ^. qv_filters) p
                 $ processMetrics (q ^. qv_metrics) p