fix

bin/gargantext-phylo/Main.hs

@@ -89,7 +89,7 @@ main = do
   
   let patterns = buildPatterns termList
 
-  let corpusParsed = map ( (\(y,t) -> Document y (filter (\e -> e /= "") t)) . filterTerms patterns) corpus
+  let corpusParsed = map ( (\(y,t) -> Document y t) . filterTerms patterns) corpus
 
   let query = PhyloQueryBuild "cultural_evolution" "Test" 5 3 defaultFis [] [] defaultWeightedLogJaccard 3 defaultRelatedComponents
 
@@ -97,15 +97,15 @@ main = do
 
   let foundations = DL.nub $ DL.concat $ map _pat_terms patterns
 
-  let phylo = toPhylo query corpusParsed foundations tree
+  -- let phylo = toPhylo query corpusParsed foundations tree
 
-  let queryView = PhyloQueryView 2 Merge False 1 [BranchAge] [defaultSmallBranch] [BranchPeakFreq,GroupLabelCooc] (Just (ByBranchAge,Asc)) Json Flat True
+  -- let queryView = PhyloQueryView 2 Merge False 1 [BranchAge] [defaultSmallBranch] [BranchPeakFreq,GroupLabelCooc] (Just (ByBranchAge,Asc)) Json Flat True
 
-  let view = toPhyloView queryView phylo
+  -- let view = toPhyloView queryView phylo
 
     -- TODO Phylo here
-  P.writeFile outputPath $ dotToString $ viewToDot view 
-  -- L.writeFile outputPath $ encode corpusParsed
+  -- P.writeFile outputPath $ dotToString $ viewToDot view 
+  L.writeFile outputPath $ encode corpusParsed
 
 
 

src/Gargantext/Viz/Phylo.hs

@@ -307,12 +307,7 @@ data Metric = BranchAge deriving (Generic, Show, Eq, Read)
 
 
 -- | Tagger constructors
-<<<<<<< HEAD
-data Tagger = BranchPeakFreq | GroupLabelCooc | GroupDynamics deriving (Show)
-=======
-data Tagger = BranchLabelFreq | GroupLabelCooc | GroupDynamics
-  deriving (Generic, Show, Read)
->>>>>>> dev
+data Tagger = BranchPeakFreq | GroupLabelCooc | GroupDynamics deriving (Show,Generic,Read)
 
 
 --------------
@@ -354,7 +349,7 @@ data PhyloQueryBuild = PhyloQueryBuild
     } deriving (Generic, Show, Eq)
 
 -- | To choose the Phylo edge you want to export : --> <-- <--> <=>
-data Filiation = Ascendant | Descendant | Merge | Complete deriving (Generic, Show)
+data Filiation = Ascendant | Descendant | Merge | Complete deriving (Generic, Show, Read)
 data EdgeType  = PeriodEdge | LevelEdge deriving (Generic, Show, Eq)
 
 -------------------
@@ -407,6 +402,7 @@ data PhyloNode = PhyloNode
 
 
 data ExportMode = Json | Dot | Svg
+  deriving (Generic, Show, Read)
 data DisplayMode = Flat | Nested
   deriving (Generic, Show, Read)
 

src/Gargantext/Viz/Phylo/API.hs

@@ -66,6 +66,7 @@ type GetPhylo =  QueryParam "listId"      ListId
               :> QueryParam "taggers"    [Tagger]
               :> QueryParam "sort"       Sort
               :> QueryParam "order"      Order
+              :> QueryParam "export"    ExportMode
               :> QueryParam "display"    DisplayMode
               :> QueryParam "verbose"     Bool
               :> Get '[JSON] PhyloView
@@ -74,11 +75,11 @@ type GetPhylo =  QueryParam "listId"      ListId
 -- Add real text processing
 -- Fix Filter parameters
 getPhylo :: PhyloId -> GargServer GetPhylo
-getPhylo _phyloId _lId l f b l' ms x y z ts s o d b' = do
+getPhylo _phyloId _lId l f b l' ms x y z ts s o e d b' = do
   let
     fs' = maybe (Just []) (\p -> Just [p]) $ SmallBranch <$> (SBParams <$> x <*> y <*> z)
     so  = (,) <$> s <*> o
-    q = initPhyloQueryView l f b l' ms fs' ts so d b'
+    q = initPhyloQueryView l f b l' ms fs' ts so e d b'
   -- | TODO remove phylo for real data here
   pure (toPhyloView  q phylo)
 
@@ -143,7 +144,7 @@ instance ToSchema PhyloGroup
 instance ToSchema PhyloLevel
 instance ToSchema PhyloNode
 instance ToSchema PhyloParam
-instance ToSchema PhyloPeaks
+instance ToSchema PhyloRoots
 instance ToSchema PhyloPeriod
 instance ToSchema PhyloQueryBuild
 instance ToSchema PhyloView
@@ -174,6 +175,12 @@ instance FromHttpApiData DisplayMode
     parseUrlPiece = readTextData
 
 
+instance ToParamSchema   ExportMode
+instance FromHttpApiData ExportMode
+  where
+    parseUrlPiece = readTextData    
+
+
 instance FromHttpApiData Sort
   where
     parseUrlPiece = readTextData

src/Gargantext/Viz/Phylo/Tools.hs

@@ -713,11 +713,8 @@ initWeightedLogJaccard (def 0 -> thr) (def 0.01 -> sens) = WLJParams thr sens
 -- | To initialize a PhyloQueryBuild from given and default parameters
 initPhyloQueryBuild :: Text -> Text -> Maybe Int -> Maybe Int -> Maybe Cluster -> Maybe [Metric] -> Maybe [Filter] -> Maybe Proximity -> Maybe Level -> Maybe Cluster -> PhyloQueryBuild
 initPhyloQueryBuild name desc (def 5 -> grain) (def 3 -> steps) (def defaultFis -> cluster) (def [] -> metrics) (def [] -> filters)
-  (def defaultWeightedLogJaccard -> matching') (def 2 -> nthLevel) (def defaultRelatedComponents -> nthCluster) =
-    PhyloQueryBuild name' desc' grain steps cluster metrics filters matching' nthLevel nthCluster
-      where
-        name' = maybe "Phylo Title" identity name
-        desc' = maybe "Phylo Desc"  identity desc
+  (def defaultWeightedLogJaccard -> matching) (def 2 -> nthLevel) (def defaultRelatedComponents -> nthCluster) =
+    PhyloQueryBuild name desc grain steps cluster metrics filters matching nthLevel nthCluster
 
 
 

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

@@ -138,19 +138,6 @@ addChildNodes shouldDo lvl lvlMin vb fl p v =
 
 
 -- | To transform a PhyloQuery into a PhyloView
-toPhyloView' :: Maybe Level
-                      -> Maybe Filiation
-                      -> Maybe Bool
-                      -> Maybe Level
-                      -> Maybe [Metric]
-                      -> Maybe [Filter]
-                      -> Maybe [Tagger]
-                      -> Maybe (Sort, Order)
-                      -> Maybe DisplayMode
-                      -> Maybe Bool
-                      -> PhyloQueryView
-toPhyloView' = initPhyloQueryView
-
 toPhyloView :: PhyloQueryView -> Phylo -> PhyloView
 toPhyloView q p = processDisplay (q ^. qv_display) (q ^. qv_export)
                 $ processSort    (q ^. qv_sort   ) p