Merge remote-tracking branch 'origin/580-dev-phylo-params' into dev

src/Gargantext/Components/Nodes/Corpus/Phylo.purs

@@ -92,13 +92,14 @@ nodeCpt = R2.hereComponent here "node" hCpt where
             ]
           ]
       , defaultSlot:
-          R2.fromMaybe state' \(PhyloSet { corpusId, listId, phyloData }) ->
+          R2.fromMaybe state' \(PhyloSet { corpusId, listId, phyloData, phyloConfig}) ->
 
             let
               state_ :: Record PhyloStore.State
               state_ =
                 -- Data
                 { phyloData
+                , phyloConfig
                 , corpusId
                 , listId
                 , phyloId: nodeId

src/Gargantext/Components/PhyloExplorer/JSON.purs

@@ -3,6 +3,11 @@ module Gargantext.Components.PhyloExplorer.JSON
   , GraphData(..)
   , NodeData(..), RawObject(..)
   , EdgeData(..), RawEdge(..)
+  , Cluster(..), PhyloLabel(..)
+  , Sort(..), Synchrony(..)
+  , SeaElevation(..), PhyloSimilarity(..)
+  , TimeUnit(..), ConfigData(..)
+  , Quality(..)
   ) where
 
 import Gargantext.Prelude
@@ -26,6 +31,17 @@ newtype PhyloJSON = PhyloJSON
       , strict            :: Boolean
       | GraphData
       }
+  , pd_config         :: 
+      { clique            :: Cluster
+      , exportLabel       :: Array PhyloLabel
+      , exportSort        :: Sort
+      , phyloSynchrony    :: Synchrony
+      , phyloQuality      :: Quality
+      , seaElevation      :: SeaElevation
+      , similarity        :: PhyloSimilarity
+      , timeUnit          :: TimeUnit
+      | ConfigData
+      }
   }
 
 derive instance Generic PhyloJSON _
@@ -184,3 +200,157 @@ derive instance Eq RawEdge
 instance Show RawEdge where show = genericShow
 instance JSON.ReadForeign RawEdge where
   readImpl f = GR.to <$> untaggedSumRep f
+
+--------------------------------------------------
+
+type ConfigData =
+  ( corpusPath    :: String
+  , defaultMode   :: Boolean
+  , findAncestors :: Boolean
+  , listParser    :: String
+  , listPath      :: String
+  , outputPath    :: String
+  , phyloName     :: String
+  , phyloScale    :: Int
+  )
+
+data Cluster 
+  = Fis
+    { _fis_support :: Int
+    , _fis_size    :: Int 
+    }
+  | MaxClique
+    { _mcl_size      :: Int
+    , _mcl_threshold :: Number
+    , _mcl_filter    :: String 
+    }
+
+derive instance Generic Cluster _
+derive instance Eq Cluster 
+instance Show Cluster  where show = genericShow
+instance JSON.ReadForeign Cluster where
+  readImpl f = GR.to <$> untaggedSumRep f
+
+data PhyloLabel 
+  = BranchLabel
+    { _branch_labelTagger :: String
+    , _branch_labelSize   :: Int 
+    }
+  | GroupLabel
+    { _group_labelTagger  :: String
+    , _group_labelSize    :: Int 
+    }
+
+derive instance Generic PhyloLabel _
+derive instance Eq PhyloLabel 
+instance Show PhyloLabel  where show = genericShow
+instance JSON.ReadForeign PhyloLabel  where
+  readImpl f = GR.to <$> untaggedSumRep f
+
+data Sort = ByBirthDate { _sort_order :: String } | ByHierarchy {_sort_order :: String }
+
+derive instance Generic Sort _
+derive instance Eq Sort 
+instance Show Sort  where show = genericShow
+instance JSON.ReadForeign Sort  where
+  readImpl f = GR.to <$> untaggedSumRep f
+
+data Synchrony 
+  = ByProximityThreshold
+    { _bpt_threshold   :: Number
+    , _bpt_sensibility :: Number
+    , _bpt_scope       :: String
+    , _bpt_strategy    :: String
+    }
+  | ByProximityDistribution
+    { _bpd_sensibility :: Number
+    , _bpd_strategy    :: String
+    }
+
+derive instance Generic Synchrony _
+derive instance Eq Synchrony  
+instance Show Synchrony where show = genericShow
+instance JSON.ReadForeign Synchrony where
+  readImpl f = GR.to <$> untaggedSumRep f
+
+
+data SeaElevation 
+  = Constante
+    { _cons_start :: Number
+    , _cons_gap   :: Number
+    }
+  | Adaptative
+    { _adap_steps :: Number }
+  | Evolving
+    { _evol_neighborhood :: Boolean }
+
+derive instance Generic SeaElevation _
+derive instance Eq SeaElevation  
+instance Show SeaElevation where show = genericShow
+instance JSON.ReadForeign SeaElevation where
+  readImpl f = GR.to <$> untaggedSumRep f
+
+data PhyloSimilarity 
+  = WeightedLogJaccard
+    { _wlj_sensibility     :: Number
+    , _wlj_minSharedNgrams :: Int
+    }
+  | WeightedLogSim
+    { _wls_sensibility     :: Number
+    , _wls_minSharedNgrams :: Int
+    }
+  | Hamming
+    { _hmg_sensibility     :: Number
+    , _hmg_minSharedNgrams :: Int
+    }
+
+derive instance Generic PhyloSimilarity _
+derive instance Eq PhyloSimilarity  
+instance Show PhyloSimilarity where show = genericShow
+instance JSON.ReadForeign PhyloSimilarity where
+  readImpl f = GR.to <$> untaggedSumRep f
+
+data TimeUnit 
+  = Epoch
+    { _epoch_period :: Int
+    , _epoch_step   :: Int
+    , _epoch_matchingFrame :: Int
+    }
+  | Year
+    { _year_period :: Int
+    , _year_step   :: Int
+    , _year_matchingFrame :: Int
+    }
+  | Month
+    { _month_period :: Int
+    , _month_step   :: Int
+    , _month_matchingFrame :: Int
+    }
+  | Week
+    { _week_period :: Int
+    , _week_step   :: Int
+    , _week_matchingFrame :: Int
+    }
+  | Day
+    { _day_period :: Int
+    , _day_step   :: Int
+    , _day_matchingFrame :: Int
+    }
+
+derive instance Generic TimeUnit _
+derive instance Eq TimeUnit  
+instance Show TimeUnit where show = genericShow
+instance JSON.ReadForeign TimeUnit where
+  readImpl f = GR.to <$> untaggedSumRep f
+
+data Quality 
+  = Quality 
+    { _qua_granularity :: Number
+    , _qua_minBranch   :: Int 
+    }
+
+derive instance Generic Quality _
+derive instance Eq Quality 
+instance Show Quality where show = genericShow
+instance JSON.ReadForeign Quality where
+  readImpl f = GR.to <$> untaggedSumRep f

src/Gargantext/Components/PhyloExplorer/Sidebar/DetailsTab.purs

@@ -4,8 +4,9 @@ module Gargantext.Components.PhyloExplorer.DetailsTab
 
 import Gargantext.Prelude
 
+import Gargantext.Components.PhyloExplorer.JSON (Cluster(..), TimeUnit(..))
 import Gargantext.Components.PhyloExplorer.Store as PhyloStore
-import Gargantext.Components.PhyloExplorer.Types (PhyloData(..))
+import Gargantext.Components.PhyloExplorer.Types (PhyloConfig(..), PhyloData(..))
 import Gargantext.Utils (nbsp)
 import Gargantext.Utils.Reactix as R2
 import Reactix as R
@@ -26,6 +27,7 @@ detailsTabCpt = here.component "" cpt where
     store <- PhyloStore.use
 
     (PhyloData o) <- R2.useLive' store.phyloData
+    (PhyloConfig c) <- R2.useLive' store.phyloConfig
 
     -- | Render
     -- |
@@ -66,6 +68,20 @@ detailsTabCpt = here.component "" cpt where
         [
           H.text "How the phylomemy was built?"
         ]
+      ,
+        H.hr 
+        { className: "phylo-details-tab__delimiter" }
+      , 
+        -- Phylo params
+        H.ul
+        { className: "phylo-details-tab__counter" }
+        [ detailsTimeUnit c.timeUnit
+        , detailsParams c.levelOfObservation "Level of observation"
+        , detailsClique c.clique 
+        , detailsParams c.proximity "Proximity"
+        , detailsParams c.synchrony "Synchrony"
+        , detailsParams c.minBranch "Minimum Branch Size"
+        ]
       ]
 
 detailsCount :: Int -> String -> R.Element
@@ -85,3 +101,30 @@ detailsCount value label =
       H.text $ nbsp 1 <> label
     ]
   ]
+
+detailsParams :: forall a. (Show a) => a -> String -> R.Element
+detailsParams value label = 
+  H.li {} [ H.text $ label <> ": " <> show value ]
+
+detailsClique :: Cluster -> R.Element
+detailsClique c =
+  H.li {} [ H.text $ "Cluster algo: " <> parseClique c]
+  where
+    parseClique (Fis { _fis_support, _fis_size }) = "FIS. Support: " <> show _fis_support <> ". Size: " <> show _fis_size
+    parseClique (MaxClique { _mcl_size, _mcl_threshold, _mcl_filter}) =
+      "MaxClique. Size: " <> show _mcl_size <> ". Threshhold: " <> show _mcl_threshold <> ". Filter: " <> _mcl_filter
+
+detailsTimeUnit :: TimeUnit -> R.Element
+detailsTimeUnit t =
+  H.li {} [ H.text $ "Time unit: " <> parseTimeUnit t]
+  where
+    parseTimeUnit (Epoch {_epoch_period, _epoch_step, _epoch_matchingFrame}) = 
+      "Epoch. Period: " <> show _epoch_period <> ". Step: " <> show _epoch_step <>". Matching frame: " <> show _epoch_matchingFrame
+    parseTimeUnit (Year {_year_period, _year_step, _year_matchingFrame}) = 
+      "Year. Period: " <> show _year_period <> ". Step: " <> show _year_step <>". Matching frame: " <> show _year_matchingFrame
+    parseTimeUnit (Month {_month_period, _month_step, _month_matchingFrame}) = 
+      "Month. Period: " <> show _month_period <> ". Step: " <> show _month_step <>". Matching frame: " <> show _month_matchingFrame
+    parseTimeUnit (Week {_week_period, _week_step, _week_matchingFrame}) = 
+      "Week. Period: " <> show _week_period <> ". Step: " <> show _week_step <>". Matching frame: " <> show _week_matchingFrame
+    parseTimeUnit (Day {_day_period, _day_step, _day_matchingFrame}) = 
+      "Day. Period: " <> show _day_period <> ". Step: " <> show _day_step <>". Matching frame: " <> show _day_matchingFrame

src/Gargantext/Components/PhyloExplorer/Store.purs

@@ -11,7 +11,7 @@ module Gargantext.Components.PhyloExplorer.Store
 import Gargantext.Prelude
 
 import Data.Maybe (Maybe(..))
-import Gargantext.Components.PhyloExplorer.Types (CorpusId, DisplayView(..), ExtractedCount, ExtractedTerm, FrameDoc, PhyloData, Source, TabView(..), Term, ListId, defaultCacheParams)
+import Gargantext.Components.PhyloExplorer.Types (CorpusId, DisplayView(..), ExtractedCount, ExtractedTerm, FrameDoc, ListId, PhyloConfig, PhyloData, Source, TabView(..), Term, defaultCacheParams)
 import Gargantext.Types (NodeID, SidePanelState(..))
 import Gargantext.Utils (getter)
 import Gargantext.Utils.Reactix as R2
@@ -26,6 +26,7 @@ here = R2.here "Gargantext.Components.GraphExplorer.Store"
 type Store =
   -- Data
   ( phyloData           :: T.Box PhyloData
+  , phyloConfig         :: T.Box PhyloConfig
   , phyloId             :: T.Box NodeID
   , corpusId            :: T.Box CorpusId
   , listId              :: T.Box ListId
@@ -55,6 +56,7 @@ type Store =
 type State =
   -- Data
   ( phyloData           :: PhyloData
+  , phyloConfig         :: PhyloConfig
   , phyloId             :: NodeID
   , corpusId            :: CorpusId
   , listId              :: ListId

src/Gargantext/Components/PhyloExplorer/Types.purs

@@ -2,6 +2,7 @@ module Gargantext.Components.PhyloExplorer.Types
   ( PhyloSet(..), parseToPhyloSet
   , CorpusId, ListId, DocId
   , PhyloData(..)
+  , PhyloConfig(..)
   , Branch(..), Period(..), Group(..)
   , Link(..), AncestorLink(..), BranchLink(..)
   , Term(..)
@@ -19,8 +20,8 @@ import Gargantext.Prelude
 
 import Data.Array as Array
 import Data.Date as Date
-import Data.Generic.Rep (class Generic)
 import Data.FunctorWithIndex (mapWithIndex)
+import Data.Generic.Rep (class Generic)
 import Data.Int as Int
 import Data.Maybe (Maybe(..), maybe)
 import Data.Newtype (class Newtype)
@@ -30,7 +31,7 @@ import Data.String as String
 import Data.String.Extra (camelCase)
 import Data.Tuple as Tuple
 import Data.Tuple.Nested ((/\))
-import Gargantext.Components.PhyloExplorer.JSON (PhyloJSON(..), RawEdge(..), RawObject(..))
+import Gargantext.Components.PhyloExplorer.JSON (Cluster, PhyloJSON(..), PhyloSimilarity(..), Quality(..), RawEdge(..), RawObject(..), Synchrony(..), TimeUnit)
 import Simple.JSON as JSON
 
 -- @NOTE #219: PureScript Date or stick to JavaScript foreign?
@@ -45,9 +46,10 @@ type DocId    = Int
 ------------------------------------------------------------------
 
 data PhyloSet = PhyloSet
-  { corpusId  :: CorpusId
-  , listId    :: ListId
-  , phyloData :: PhyloData
+  { corpusId    :: CorpusId
+  , listId      :: ListId
+  , phyloData   :: PhyloData
+  , phyloConfig :: PhyloConfig
   }
 
 derive instance Generic PhyloSet _
@@ -78,11 +80,20 @@ parseToPhyloSet (PhyloJSON o) = PhyloSet
       , timeScale     : p.phyloTimeScale
       , weighted      : getGlobalWeightedValue groups
       }
+    , phyloConfig : PhyloConfig
+      { clique: c.clique
+      , timeUnit: c.timeUnit
+      , synchrony: parseSynchrony c.phyloSynchrony
+      , proximity: parseSimilarity c.similarity
+      , minBranch: parseQualityToMinBranch c.phyloQuality
+      , levelOfObservation: parseQualityToLevelOfObservation c.phyloQuality
+      }
   }
 
   where
     p             = o.pd_data
-
+    c             = o.pd_config
+  
     epochTS       = p.phyloTimeScale == "epoch"
 
     ancestorLinks = parseAncestorLinks p.edges
@@ -120,6 +131,36 @@ instance Show PhyloData where show = genericShow
 
 -----------------------------------------------------------
 
+data PhyloConfig = PhyloConfig
+  { clique :: Cluster
+  , timeUnit :: TimeUnit
+  , synchrony :: Number
+  , proximity :: Number
+  , minBranch :: Int
+  , levelOfObservation :: Number
+  }
+
+derive instance Generic PhyloConfig _  
+derive instance Eq PhyloConfig
+instance Show PhyloConfig where show = genericShow
+
+parseSynchrony :: Synchrony -> Number
+parseSynchrony (ByProximityThreshold { _bpt_threshold }) =  _bpt_threshold
+parseSynchrony (ByProximityDistribution { _bpd_sensibility }) = _bpd_sensibility
+
+parseSimilarity :: PhyloSimilarity -> Number
+parseSimilarity (WeightedLogJaccard { _wlj_sensibility }) = _wlj_sensibility
+parseSimilarity (WeightedLogSim { _wls_sensibility }) = _wls_sensibility
+parseSimilarity (Hamming { _hmg_sensibility }) = _hmg_sensibility
+
+parseQualityToMinBranch :: Quality -> Int
+parseQualityToMinBranch (Quality { _qua_minBranch }) = _qua_minBranch
+
+parseQualityToLevelOfObservation :: Quality -> Number
+parseQualityToLevelOfObservation (Quality { _qua_granularity }) = _qua_granularity
+
+-----------------------------------------------------------
+
 newtype Branch = Branch
   { bId     :: Int
   , gvid    :: Int