Merge branch 'dev' into 294-dev-test

src/Gargantext/Components/FolderView.purs

@@ -48,6 +48,7 @@ type Props =
   , session :: Session
   , backFolder :: Boolean
   , tasks :: T.Box GAT.Storage
+  , reloadForest :: T.Box T2.Reload
   )
 
 data FolderStyle = FolderUp | FolderChild
@@ -57,12 +58,12 @@ folderView props = R.createElement folderViewCpt props []
 
 folderViewCpt :: R.Component Props
 folderViewCpt = here.component "folderViewCpt" cpt where
-  cpt {nodeId, session, backFolder, tasks} _ = do
+  cpt {nodeId, session, backFolder, tasks, reloadForest} _ = do
     setPopoverRef <- R.useRef Nothing
     reload <- T.useBox T2.newReload
     reload' <- T.useLive T.unequal reload
     useLoader { nodeId, session, reload: reload'} loadFolders $
-      \folders -> folderViewMain {folders, nodeId, session, backFolder, tasks, reload, setPopoverRef}
+      \folders -> folderViewMain {folders, nodeId, session, backFolder, tasks, reload, setPopoverRef, reloadForest}
 
 type FolderViewProps = 
   ( 
@@ -72,6 +73,7 @@ type FolderViewProps =
   , backFolder :: Boolean
   , tasks :: T.Box GAT.Storage
   , reload :: T.Box T2.Reload
+  , reloadForest :: T.Box T2.Reload
   , setPopoverRef :: R.Ref (Maybe (Boolean -> Effect Unit))
   )
 
@@ -80,11 +82,11 @@ folderViewMain props = R.createElement folderViewMainCpt props []
 
 folderViewMainCpt :: R.Component FolderViewProps
 folderViewMainCpt = here.component "folderViewMainCpt" cpt where
-  cpt {nodeId, session, backFolder, tasks, setPopoverRef, reload, folders: tree@(NTree (LNode {parent_id: parentId, nodeType}) (folders))} _ = do
+  cpt {nodeId, session, backFolder, tasks, setPopoverRef, reload, reloadForest, folders: tree@(NTree (LNode {parent_id: parentId, nodeType}) (folders))} _ = do
     let foldersS = A.sortBy sortFolders folders
     let backHome = isBackHome nodeType
     let parent = makeParentFolder parentId session backFolder backHome
-    let children = makeFolderElements foldersS {session, setPopoverRef, nodeId, tasks, reload}
+    let children = makeFolderElements foldersS {session, setPopoverRef, nodeId, tasks, reload, reloadForest}
 
     pure $ H.div {className: "fv folders"} $ parent <> children
 
@@ -98,7 +100,8 @@ folderViewMainCpt = here.component "folderViewMainCpt" cpt where
                                                           , setPopoverRef: props.setPopoverRef
                                                           , parentId: props.nodeId
                                                           , tasks: props.tasks
-                                                          , reload: props.reload} []
+                                                          , reload: props.reload
+                                                          , reloadForest: props.reloadForest} []
 
   makeParentFolder :: Maybe Int -> Session -> Boolean -> Boolean -> Array R.Element
   makeParentFolder (Just parentId) session _ _ =
@@ -159,6 +162,7 @@ type FolderProps =
   , parentId :: Int
   , tasks :: T.Box GAT.Storage
   , reload :: T.Box T2.Reload
+  , reloadForest :: T.Box T2.Reload
   | FolderSimpleProps
   )
 
@@ -167,9 +171,9 @@ folder = R.createElement folderCpt
 
 folderCpt :: R.Component FolderProps
 folderCpt = here.component "folderCpt" cpt where
-  cpt props@{style, text, nodeId, session, nodeType, setPopoverRef, parentId, tasks, reload} _ = do
+  cpt props@{style, text, nodeId, session, nodeType, setPopoverRef, parentId, tasks, reload, reloadForest} _ = do
     let sid = sessionId session
-    let dispatch a = performAction a {setPopoverRef, session, nodeId, parentId, tasks, reload}
+    let dispatch a = performAction a {setPopoverRef, session, nodeId, parentId, tasks, reload, reloadForest}
     popoverRef <- R.useRef null
 
     R.useEffect' $ do
@@ -253,6 +257,7 @@ type PerformActionProps =
   , parentId :: Int
   , tasks :: T.Box GAT.Storage
   , reload :: T.Box T2.Reload
+  , reloadForest :: T.Box T2.Reload
   )
 
 performAction :: Action -> Record PerformActionProps -> Aff Unit
@@ -280,6 +285,7 @@ performAction = performAction' where
 
   refreshFolders p = do 
     liftEffect $ T2.reload p.reload
+    liftEffect $ T2.reload p.reloadForest
     closePopover p
 
   deleteNode' nt p@{ nodeId: id, parentId: parent_id } = do

src/Gargantext/Components/Forest/Tree/Node/Settings.purs

@@ -185,6 +185,7 @@ settingsBox Corpus =
                                 , Dashboard
                                 , NodeFrameWrite
                                 , NodeFrameCalc
+                                , Phylo
                                 ]
                           , Link (linkParams Annuaire)
                           , Move moveParameters

src/Gargantext/Components/Graph.purs

@@ -302,22 +302,24 @@ sigmaSettings =
   }
   
 type ForceAtlas2Settings =
-  ( adjustSizes :: Boolean
-  , barnesHutOptimize :: Boolean
-  -- , barnesHutTheta :: Number
-  , edgeWeightInfluence :: Number
-  -- , fixedY  :: Boolean
-  , gravity :: Number
-  , iterationsPerRender :: Number
-  , linLogMode :: Boolean
+  ( adjustSizes                    :: Boolean
+  , barnesHutOptimize              :: Boolean
+  -- , barnesHutTheta              :: Number
+  , edgeWeightInfluence            :: Number
+  -- , fixedY                      :: Boolean
+  , gravity                        :: Number
+  , includeHiddenEdges             :: Boolean
+  , includeHiddenNodes             :: Boolean
+  , iterationsPerRender            :: Number
+  , linLogMode                     :: Boolean
   , outboundAttractionDistribution :: Boolean
-  , scalingRatio :: Number
-  , skipHidden :: Boolean
-  , slowDown :: Number
-  , startingIterations :: Number
-  , strongGravityMode :: Boolean
-  -- , timeout :: Number
-  -- , worker :: Boolean
+  , scalingRatio                   :: Number
+  , skipHidden                     :: Boolean
+  , slowDown                       :: Number
+  , startingIterations             :: Number
+  , strongGravityMode              :: Boolean
+  -- , timeout                     :: Number
+  -- , worker                      :: Boolean
   )
 
 forceAtlas2Settings :: {|ForceAtlas2Settings}
@@ -327,6 +329,8 @@ forceAtlas2Settings =
   , edgeWeightInfluence : 1.0
     -- fixedY : false
   , gravity : 0.01
+  , includeHiddenEdges: false
+  , includeHiddenNodes: true
   , iterationsPerRender : 50.0 -- 10.0
   , linLogMode : false  -- false
   , outboundAttractionDistribution: false

src/Gargantext/Components/GraphExplorer/Controls.purs

@@ -20,7 +20,7 @@ import Gargantext.Components.Graph as Graph
 import Gargantext.Components.GraphExplorer.Button (centerButton, cameraButton)
 import Gargantext.Components.GraphExplorer.RangeControl (edgeConfluenceControl, edgeWeightControl, nodeSizeControl)
 import Gargantext.Components.GraphExplorer.SlideButton (labelSizeButton, mouseSelectorSizeButton)
-import Gargantext.Components.GraphExplorer.ToggleButton (multiSelectEnabledButton, edgesToggleButton, louvainToggleButton, pauseForceAtlasButton)
+import Gargantext.Components.GraphExplorer.ToggleButton (multiSelectEnabledButton, edgesToggleButton, louvainToggleButton, pauseForceAtlasButton, resetForceAtlasButton)
 import Gargantext.Components.GraphExplorer.Sidebar.Types as GEST
 import Gargantext.Components.GraphExplorer.Types as GET
 import Gargantext.Hooks.Sigmax as Sigmax
@@ -108,11 +108,12 @@ controlsCpt = here.component "controls" cpt
           _          -> pure unit
 
       -- Handle case when FA is paused from outside events, eg. the automatic timer.
-      R.useEffect' $ Sigmax.handleForceAtlas2Pause sigmaRef forceAtlasState mFAPauseRef
+      R.useEffect' $ Sigmax.handleForceAtlas2Pause sigmaRef forceAtlasState mFAPauseRef Graph.forceAtlas2Settings
 
       -- Handle automatic edge hiding when FA is running (to prevent flickering).
-      R.useEffect2' sigmaRef forceAtlasState' $ do
-        T.modify_ (SigmaxT.forceAtlasEdgeState forceAtlasState') showEdges
+      -- TODO Commented temporarily: this breaks forceatlas rendering after reset
+      -- R.useEffect2' sigmaRef forceAtlasState' $ do
+      --   T.modify_ (SigmaxT.forceAtlasEdgeState forceAtlasState') showEdges
 
       -- Automatic opening of sidebar when a node is selected (but only first time).
       R.useEffect' $ do
@@ -162,6 +163,7 @@ controlsCpt = here.component "controls" cpt
                  [ RH.ul { className: "navbar-nav mx-auto" }
                    [ -- change type button (?)
                      navItem [ centerButton sigmaRef ]
+                   , navItem [ resetForceAtlasButton { forceAtlasState, sigmaRef } [] ]
                    , navItem [ pauseForceAtlasButton { state: forceAtlasState } [] ]
                    , navItem [ edgesToggleButton { state: showEdges } [] ]
                    , navItem [ louvainToggleButton { state: showLouvain } [] ]

src/Gargantext/Components/GraphExplorer/ToggleButton.purs

@@ -8,19 +8,22 @@ module Gargantext.Components.GraphExplorer.ToggleButton
   , multiSelectEnabledButton
   , sidebarToggleButton
   , pauseForceAtlasButton
+  , resetForceAtlasButton
   , treeToggleButton
   ) where
 
 import Prelude
 
 import Effect (Effect)
-import Reactix as R
-import Reactix.DOM.HTML as H
-import Toestand as T
-
+import Gargantext.Components.Graph as Graph
+import Gargantext.Hooks.Sigmax as Sigmax
+import Gargantext.Hooks.Sigmax.Sigma as Sigma
 import Gargantext.Hooks.Sigmax.Types as SigmaxTypes
 import Gargantext.Types as GT
 import Gargantext.Utils.Reactix as R2
+import Reactix as R
+import Reactix.DOM.HTML as H
+import Toestand as T
 
 here :: R2.Here
 here = R2.here "Gargantext.Components.GraphExplorer.ToggleButton"
@@ -156,9 +159,33 @@ pauseForceAtlasButtonCpt = here.component "forceAtlasToggleButton" cpt
     text SigmaxTypes.InitialStopped = "Start Force Atlas"
     text SigmaxTypes.Running = "Pause Force Atlas"
     text SigmaxTypes.Paused = "Start Force Atlas"
+    text SigmaxTypes.Killed = "Start Force Atlas"
 
     onClick state _ = T.modify_ SigmaxTypes.toggleForceAtlasState state
 
+type ResetForceAtlasProps = (
+    forceAtlasState :: T.Box SigmaxTypes.ForceAtlasState
+  , sigmaRef        :: R.Ref Sigmax.Sigma
+)
+
+resetForceAtlasButton :: R2.Component ResetForceAtlasProps
+resetForceAtlasButton = R.createElement resetForceAtlasButtonCpt
+resetForceAtlasButtonCpt :: R.Component ResetForceAtlasProps
+resetForceAtlasButtonCpt = here.component "resetForceAtlasToggleButton" cpt
+  where
+    cpt { forceAtlasState, sigmaRef } _ = do
+      pure $ H.button { className: "btn btn-outline-primary"
+                      , on: { click: onClick forceAtlasState sigmaRef }
+                      } [ R2.small {} [ H.text "Reset Force Atlas" ] ]
+
+    onClick forceAtlasState sigmaRef _ = do
+      -- TODO Sigma.killForceAtlas2 sigma
+      -- startForceAtlas2 sigma
+      Sigmax.dependOnSigma (R.readRef sigmaRef) "[resetForceAtlasButton] no sigma" $ \sigma -> do
+        Sigma.killForceAtlas2 sigma
+        Sigma.refreshForceAtlas sigma Graph.forceAtlas2Settings
+        T.write_ SigmaxTypes.Killed forceAtlasState
+
 type TreeToggleButtonProps = (
   state :: T.Box Boolean
 )

src/Gargantext/Components/Nodes/Corpus.purs

@@ -15,9 +15,9 @@ import Effect (Effect)
 import Effect.Aff (Aff, launchAff_, throwError)
 import Effect.Class (liftEffect)
 import Effect.Exception (error)
+import Gargantext.AsyncTasks as GAT
 import Gargantext.Components.CodeEditor as CE
 import Gargantext.Components.FolderView as FV
-import Gargantext.AsyncTasks as GAT
 import Gargantext.Components.InputWithEnter (inputWithEnter)
 import Gargantext.Components.Node (NodePoly(..), HyperdataList)
 import Gargantext.Components.Nodes.Corpus.Types (CorpusData, Hyperdata(..))
@@ -38,15 +38,15 @@ import Toestand as T
 here :: R2.Here
 here = R2.here "Gargantext.Components.Nodes.Corpus"
 
-type Props = ( nodeId  :: Int, session :: Session, tasks :: T.Box GAT.Storage )
+type Props = ( nodeId  :: Int, session :: Session, tasks :: T.Box GAT.Storage, reloadForest :: T2.ReloadS )
 
 corpusLayout :: R2.Leaf Props
 corpusLayout props = R.createElement corpusLayoutCpt props []
 
 corpusLayoutCpt :: R.Component Props
 corpusLayoutCpt = here.component "corpusLayout" cpt where
-  cpt { nodeId, session, tasks } _ = do
-    pure $ corpusLayoutMain { key, nodeId, session, tasks }
+  cpt { nodeId, session, tasks, reloadForest } _ = do
+    pure $ corpusLayoutMain { key, nodeId, session, tasks, reloadForest }
       where
         key = show (sessionId session) <> "-" <> show nodeId
 
@@ -55,6 +55,7 @@ type KeyProps =
   , key     :: String
   , session :: Session
   , tasks   :: T.Box GAT.Storage
+  , reloadForest :: T2.ReloadS
   )
 
 corpusLayoutMain :: R2.Leaf KeyProps
@@ -63,7 +64,7 @@ corpusLayoutMain props = R.createElement corpusLayoutMainCpt props []
 corpusLayoutMainCpt :: R.Component KeyProps
 corpusLayoutMainCpt = here.component "corpusLayoutMain" cpt
   where
-    cpt { nodeId, key, session, tasks } _ = do
+    cpt { nodeId, key, session, tasks, reloadForest } _ = do
       viewType <- T.useBox Folders
 
       pure $ H.div {} [
@@ -73,7 +74,7 @@ corpusLayoutMainCpt = here.component "corpusLayoutMain" cpt
           , H.div { className: "col-1" } [ FV.homeButton ]
           ]
         ]
-      , H.div {} [corpusLayoutSelection {state: viewType, key, session, nodeId, tasks}]
+      , H.div {} [corpusLayoutSelection {state: viewType, key, session, nodeId, tasks, reloadForest}]
       ]
 
 type SelectionProps = 
@@ -82,6 +83,7 @@ type SelectionProps =
   , session :: Session
   , state   :: T.Box ViewType
   , tasks   :: T.Box GAT.Storage
+  , reloadForest :: T2.ReloadS
   )
 
 corpusLayoutSelection :: R2.Leaf SelectionProps
@@ -89,14 +91,14 @@ corpusLayoutSelection props = R.createElement corpusLayoutSelectionCpt props []
 
 corpusLayoutSelectionCpt :: R.Component SelectionProps
 corpusLayoutSelectionCpt = here.component "corpusLayoutSelection" cpt where
-  cpt { nodeId, session, key, state, tasks} _ = do
+  cpt { nodeId, session, key, state, tasks, reloadForest} _ = do
     state' <- T.useLive T.unequal state
     viewType <- T.read state
 
-    pure $ renderContent viewType nodeId session key tasks
+    pure $ renderContent viewType nodeId session key tasks reloadForest
 
-  renderContent Folders nodeId session key tasks = FV.folderView { nodeId, session, backFolder: true, tasks }
-  renderContent Code nodeId session key tasks = corpusLayoutWithKey { key, nodeId, session }
+  renderContent Folders nodeId session key tasks reloadForest = FV.folderView { nodeId, session, backFolder: true, tasks, reloadForest }
+  renderContent Code nodeId session key tasks _ = corpusLayoutWithKey { key, nodeId, session }
 
 type CorpusKeyProps =
   ( nodeId  :: Int

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

+module Gargantext.Components.Nodes.Corpus.Phylo where
+
+import Gargantext.Prelude
+  ( pure, ($) )
+
+-- import Gargantext.Utils.Toestand as T2
+-- import Toestand as T
+import Data.Tuple.Nested ((/\))
+import Effect (Effect)
+import Gargantext.Sessions (Session)
+import Gargantext.Types (NodeID)
+import Gargantext.Utils.Reactix as R2
+import Reactix as R
+import Reactix.DOM.HTML as H
+
+here :: R2.Here
+here = R2.here "Gargantext.Components.Nodes.Corpus.Phylo"
+
+type Props = ( nodeId :: NodeID, session :: Session )
+
+phyloLayout :: R2.Component Props
+phyloLayout = R.createElement phyloLayoutCpt
+
+phyloLayoutCpt :: R.Component Props
+phyloLayoutCpt = here.component "phyloLayout" cpt where
+  cpt { nodeId, session } content = do
+    pure $  H.h1 {} [ H.text "Hello Phylo" ]

src/Gargantext/Components/Nodes/Home.purs

@@ -24,6 +24,7 @@ import Reactix as R
 import Reactix.DOM.HTML as H
 import Routing.Hash (setHash)
 import Toestand as T
+import Gargantext.Utils.Toestand as T2
 
 here :: R2.Here
 here = R2.here "Gargantext.Components.Nodes.Home"
@@ -59,6 +60,7 @@ type HomeProps s l =
   , sessions  :: s
   , showLogin :: l
   , tasks     :: T.Box GAT.Storage
+  , reloadForest :: T.Box T2.Reload
   )
 
 homeLayout :: forall s l. T.Read s Sessions => T.ReadWrite l Boolean
@@ -68,7 +70,7 @@ homeLayoutCpt :: forall s l. T.Read s Sessions => T.ReadWrite l Boolean
              => R.Component (HomeProps s l)
 homeLayoutCpt = here.component "homeLayout" cpt
   where
-    cpt { backend, lang, sessions, showLogin, tasks} _ = do
+    cpt { backend, lang, sessions, showLogin, tasks, reloadForest} _ = do
       backend' <- T.useLive T.unequal backend
       sessions' <- T.useLive T.unequal sessions
       let landingData = langLandingData lang
@@ -77,7 +79,7 @@ homeLayoutCpt = here.component "homeLayout" cpt
         [ H.div { className: "home-title container1" }
           [ jumboTitle landingData ]
         , H.div { className: "home-research-form container1" } [] -- TODO
-        , joinButtonOrTutorial tasks sessions' (click backend')
+        , joinButtonOrTutorial tasks reloadForest sessions' (click backend')
         , H.div { className: "home-public container1" }
           [ renderPublic { }
           , H.div { className:"col-12 d-flex justify-content-center" }
@@ -98,11 +100,11 @@ homeLayoutCpt = here.component "homeLayout" cpt
                   T.write_ true showLogin
             Just b -> T.write_ true showLogin
 
-joinButtonOrTutorial :: forall e. T.Box GAT.Storage -> Sessions -> (e -> Effect Unit) -> R.Element
-joinButtonOrTutorial tasks sessions click =
+joinButtonOrTutorial :: forall e. T.Box GAT.Storage -> T2.ReloadS -> Sessions -> (e -> Effect Unit) -> R.Element
+joinButtonOrTutorial tasks reloadForest sessions click =
   if Sessions.null sessions
   then joinButton click
-  else tutorial {tasks, sessions: Sessions.unSessions sessions}
+  else tutorial {tasks, reloadForest, sessions: Sessions.unSessions sessions}
      
 joinButton :: forall e. (e -> Effect Unit) -> R.Element
 joinButton click =
@@ -110,10 +112,10 @@ joinButton click =
   -- form { backend, sessions, visible }
   H.div { className: divClass
         , style: { paddingTop: "100px", paddingBottom: "100px" } }
-  [ H.button { className: buttonClass, title, on: { click } } [ H.text "Join" ] ] where
+        [ H.button { className: buttonClass, title, on: { click } } [ H.text "Log in" ] ] where
     title = "Connect to the server"
     divClass = "flex-space-around d-flex justify-content-center" 
-    buttonClass = "btn btn-primary my-2"
+    buttonClass = "btn btn-primary btn-lg btn-block"
 
 incompatible :: String
 incompatible =
@@ -134,9 +136,9 @@ data Tuto = Tuto { title :: String, id :: String, text  :: String }
 summary :: R.Element
 summary =
   H.div {}
-  [ H.h3 {} [ H.text "Tutorial summary"]
+  [ H.h3 {} [ H.text "Summary"]
   , H.ol {}
-    [ sum "Getting Started (beginners)" startTutos "alert-info"
+    [ sum "Getting Started for beginners" startTutos "alert-info"
     -- , sum "How to play (advanced users)?" playTutos "alert-warning"
     -- , sum "How to master (expert users)?" expertTutos "alert-danger"
     ]]
@@ -148,21 +150,20 @@ summary =
         , H.ol {} (map toSummary tutos) ] ]          
     toSummary (Tuto x) = H.li {} [ H.a {href: "#" <> x.id} [ H.text x.title ]]
 
-tutorial :: R2.Leaf (sessions :: Array Session, tasks :: T.Box GAT.Storage)
+tutorial :: R2.Leaf (sessions :: Array Session, tasks :: T.Box GAT.Storage, reloadForest :: T.Box T2.Reload)
 tutorial props = R.createElement tutorialCpt props []
 
-tutorialCpt :: R.Component (sessions :: Array Session, tasks:: T.Box GAT.Storage)
+tutorialCpt :: R.Component (sessions :: Array Session, tasks :: T.Box GAT.Storage, reloadForest :: T.Box T2.Reload)
 tutorialCpt = here.component "tutorial" cpt where
-  cpt {sessions, tasks} _ = do
+  cpt {sessions, tasks, reloadForest} _ = do
     let folders = makeFolders sessions
 
     pure $ H.div { className: "mx-auto container" }
       [ H.div {className: "d-flex justify-content-center"} [ H.table {} folders ]
-      , H.h1 {} [H.text "Welcome!"]
-      , H.h2 {} [H.text "For easy start, just watch the tutorials"]
-      , summary
-      , H.h3 {} [H.text "Tutorial resources"]
-      , section "How to start?" "alert-info" startTutos
+      -- , H.h1 {} [H.text "Tutorials"]
+      -- , summary
+      -- , H.h3 {} [H.text "Resources"]
+      -- , section "How to start?" "alert-info" startTutos
       -- , section "How to play?" "alert-warning" playTutos
       -- , section "How to master?" "alert-danger" expertTutos
       ]
@@ -178,11 +179,11 @@ tutorialCpt = here.component "tutorial" cpt where
         sessionToFolder session@(Session {treeId, username, backend: (Backend {name})}) = 
           H.tr {} [
             H.div { className: "d-flex justify-content-center" } [ H.text (username <> "@" <> name) ]
-          , H.div {} [ FV.folderView {session, tasks, nodeId: treeId, backFolder: false} ] ]
+          , H.div {} [ FV.folderView {session, tasks, reloadForest, nodeId: treeId, backFolder: false} ] ]
 
 startTutos :: Array Tuto
 startTutos =
-  [ Tuto { title: "The tree is your friend"
+  [ Tuto { title: "The tree to manage your data"
          , id: "0_tree.ogv"
          , text : "The tree enables you to control all your actions. The Tree has typed nodes. Each node has some attributes and some methods which depend on its type. This specific ergonomy helps the memorization of all the complexity of the GarganTexts' features: hence you do not need to remember all the documentation! Just remember these simple axioms, the Tree is built with parent-children relations of nodes which have specific attributes and methods. To get its methods and attributes, just click on the wheel near its name (for this feature, see advanced tutorial: how to play with GarganText)." }
   -- ,  Tuto { title : "Edit your profile"

src/Gargantext/Components/Router.purs

@@ -26,6 +26,7 @@ import Gargantext.Components.Nodes.Annuaire.User (userLayout)
 import Gargantext.Components.Nodes.Annuaire.User.Contact (contactLayout)
 import Gargantext.Components.Nodes.Corpus (corpusLayout)
 import Gargantext.Components.Nodes.Corpus.Dashboard (dashboardLayout)
+import Gargantext.Components.Nodes.Corpus.Phylo (phyloLayout)
 import Gargantext.Components.Nodes.Corpus.Document (documentMainLayout)
 import Gargantext.Components.Nodes.File (fileLayout)
 import Gargantext.Components.Nodes.Frame (frameLayout)
@@ -180,6 +181,7 @@ renderRouteCpt = here.component "renderRoute" cpt where
         GR.Lists s n              -> lists (sessionNodeProps s n) []
         GR.Login                  -> login' boxes
         GR.PGraphExplorer s g     -> graphExplorer (sessionNodeProps s g) []
+        GR.PhyloExplorer s g      -> phyloExplorer (sessionNodeProps s g) []
         GR.RouteFile s n          -> routeFile (sessionNodeProps s n) []
         GR.RouteFrameCalc  s n    -> routeFrame (Record.merge { nodeType: NodeFrameCalc } $ sessionNodeProps s n) []
         GR.RouteFrameCode  s n    -> routeFrame (Record.merge { nodeType: NodeFrameNotebook } $ sessionNodeProps s n) []
@@ -279,7 +281,7 @@ corpusCpt = here.component "corpus" cpt where
   cpt props@{ boxes, nodeId } _ = do
     let sessionProps = RE.pick props :: Record SessionProps
     pure $ authed (Record.merge { content: \session ->
-                                   corpusLayout { nodeId, session, tasks: boxes.tasks } } sessionProps) []
+                                   corpusLayout { nodeId, session, tasks: boxes.tasks, reloadForest: boxes.reloadForest } } sessionProps) []
 
 type CorpusDocumentProps =
   ( corpusId :: CorpusId
@@ -335,13 +337,24 @@ graphExplorerCpt = here.component "graphExplorer" cpt where
                                    GraphExplorer.explorerLayout { boxes
                                                                 , graphId: nodeId
                                                                 , session } [] } sessionProps) []
+phyloExplorer :: R2.Component SessionNodeProps
+phyloExplorer = R.createElement phyloExplorerCpt
+phyloExplorerCpt :: R.Component SessionNodeProps
+phyloExplorerCpt = here.component "phylo" cpt
+  where
+    cpt props@{ boxes, nodeId } _ = do
+      let sessionProps = RE.pick props :: Record SessionProps
+      pure $ authed (Record.merge { content: \session ->
+                                     phyloLayout { nodeId, session } [] } sessionProps) []
+
+
 
 home :: R2.Component Props
 home = R.createElement homeCpt
 homeCpt :: R.Component Props
 homeCpt = here.component "home" cpt where
-  cpt props@{ boxes: boxes@{ backend, sessions, showLogin, tasks } } _ = do
-    pure $ homeLayout { backend, lang: LL_EN, sessions, showLogin, tasks }
+  cpt props@{ boxes: boxes@{ backend, sessions, showLogin, tasks, reloadForest} } _ = do
+    pure $ homeLayout { backend, lang: LL_EN, sessions, showLogin, tasks, reloadForest }
 
 lists :: R2.Component SessionNodeProps
 lists = R.createElement listsCpt
@@ -410,7 +423,7 @@ teamCpt = here.component "team" cpt where
   cpt props@{ boxes, nodeId } _ = do
     let sessionProps = RE.pick props :: Record SessionProps
     pure $ authed (Record.merge { content: \session ->
-                                   corpusLayout { nodeId, session, tasks: boxes.tasks} } sessionProps) []
+                                   corpusLayout { nodeId, session, tasks: boxes.tasks, reloadForest: boxes.reloadForest } } sessionProps) []
 
 texts :: R2.Component SessionNodeProps
 texts = R.createElement textsCpt

src/Gargantext/Hooks/Sigmax.purs

@@ -113,28 +113,21 @@ dependOnContainer container notFoundMsg f = do
 -- | Effect for handling pausing FA via state changes.  We need this because
 -- | pausing can be done not only via buttons but also from the initial
 -- | setTimer.
---handleForceAtlasPause sigmaRef (toggled /\ setToggled) mFAPauseRef = do
-handleForceAtlas2Pause :: R.Ref Sigma -> T.Box ST.ForceAtlasState -> R.Ref (Maybe TimeoutId) -> Effect Unit
-handleForceAtlas2Pause sigmaRef forceAtlasState mFAPauseRef = do
+handleForceAtlas2Pause :: forall settings. R.Ref Sigma -> T.Box ST.ForceAtlasState -> R.Ref (Maybe TimeoutId) -> settings -> Effect Unit
+handleForceAtlas2Pause sigmaRef forceAtlasState mFAPauseRef settings = do
   let sigma = R.readRef sigmaRef
   toggled <- T.read forceAtlasState
   dependOnSigma sigma "[handleForceAtlas2Pause] sigma: Nothing" $ \s -> do
-    --log2 "[handleForceAtlas2Pause] mSigma: Just " s
-    --log2 "[handleForceAtlas2Pause] toggled: " toggled
     let isFARunning = Sigma.isForceAtlas2Running s
-    --log2 "[handleForceAtlas2Pause] isFARunning: " isFARunning
     case Tuple toggled isFARunning of
       Tuple ST.InitialRunning false -> do
-        -- hide edges during forceAtlas rendering, this prevents flickering
-        Sigma.restartForceAtlas2 s
+        Sigma.restartForceAtlas2 s settings
       Tuple ST.Running false -> do
-        -- hide edges during forceAtlas rendering, this prevents flickering
-        Sigma.restartForceAtlas2 s
+        Sigma.restartForceAtlas2 s settings
         case R.readRef mFAPauseRef of
           Nothing -> pure unit
           Just timeoutId -> clearTimeout timeoutId
       Tuple ST.Paused true -> do
-        -- restore edges state
         Sigma.stopForceAtlas2 s
       _ -> pure unit
 

src/Gargantext/Hooks/Sigmax/Sigma.purs

@@ -222,8 +222,8 @@ startForceAtlas2 :: forall settings. Sigma -> settings -> Effect Unit
 startForceAtlas2 s settings = pure $ s ... "startForceAtlas2" $ [ settings ]
 
 -- | Restart forceAtlas2 on a sigmajs instance.
-restartForceAtlas2 :: Sigma -> Effect Unit
-restartForceAtlas2 s = startForceAtlas2 s null
+restartForceAtlas2 :: forall settings. Sigma -> settings -> Effect Unit
+restartForceAtlas2 s settings = startForceAtlas2 s settings
 
 -- | Stop forceAtlas2 on a sigmajs instance.
 stopForceAtlas2 :: Sigma -> Effect Unit
@@ -239,14 +239,14 @@ isForceAtlas2Running s = s ... "isForceAtlas2Running" $ [] :: Boolean
 
 -- | Refresh forceAtlas2 (with a `setTimeout` hack as it seems it doesn't work
 -- | otherwise).
-refreshForceAtlas :: Sigma -> Effect Unit
-refreshForceAtlas s = do
+refreshForceAtlas :: forall settings. Sigma -> settings -> Effect Unit
+refreshForceAtlas s settings = do
   let isRunning = isForceAtlas2Running s
   if isRunning then
     pure unit
   else do
     _ <- setTimeout 100 $ do
-      restartForceAtlas2 s
+      restartForceAtlas2 s settings
       _ <- setTimeout 100 $
         stopForceAtlas2 s
       pure unit

src/Gargantext/Hooks/Sigmax/Sigmajs.js

@@ -4,14 +4,3 @@ exports.goToImpl = function(cam) {
     return cam.goTo(props);
   };
 };
-exports.pauseForceAtlas2 = function() {
-  var s = window.sigmaGargInstance;
-  if (s) {
-    if (s.isForceAtlas2Running()) {
-      s.stopForceAtlas2()
-    }
-    else {
-      s.startForceAtlas2()
-    }
-  }
-};

src/Gargantext/Hooks/Sigmax/Sigmajs.purs

@@ -103,8 +103,6 @@ foreign import goToImpl :: forall o. CameraInstance -> EffectFn1 { | o } CameraI
 goTo :: forall o. Optional o CameraProps => CameraInstance -> { | o } -> Effect CameraInstance
 goTo cam = runEffectFn1 (goToImpl cam)
 
-foreign import pauseForceAtlas2 :: Effect Unit
-
 type SigmaProps =
   ( renderer :: String
   , settings :: SigmaSettings

src/Gargantext/Hooks/Sigmax/Types.purs

@@ -157,7 +157,7 @@ eqGraph (Graph {nodes: n1, edges: e1}) (Graph {nodes: n2, edges: e2}) = (n1 == n
 -- however when graph is loaded initially, forceAtlas is running for a couple of
 -- seconds and then stops (unless the user alters this by clicking the toggle
 -- button).
-data ForceAtlasState = InitialRunning | InitialStopped | Running | Paused
+data ForceAtlasState = InitialRunning | InitialStopped | Running | Paused | Killed
 
 derive instance genericForceAtlasState :: Generic ForceAtlasState _
 instance eqForceAtlasState :: Eq ForceAtlasState where
@@ -168,6 +168,7 @@ toggleForceAtlasState InitialRunning = Paused
 toggleForceAtlasState InitialStopped = InitialRunning
 toggleForceAtlasState Running = Paused
 toggleForceAtlasState Paused = Running
+toggleForceAtlasState Killed = InitialRunning
 
 -- | Custom state for show edges. Normally it is EShow or EHide (show/hide
 -- | edges). However, edges are temporarily turned off when forceAtlas is
@@ -218,6 +219,8 @@ forceAtlasEdgeState Running EShow = ETempHiddenThenShow
 forceAtlasEdgeState Running es = es
 forceAtlasEdgeState Paused ETempHiddenThenShow = EShow
 forceAtlasEdgeState Paused es = es
+forceAtlasEdgeState Killed ETempHiddenThenShow = EShow
+forceAtlasEdgeState Killed es = es
 
 
 louvainEdges :: SGraph -> Array (Record Louvain.Edge)

src/Gargantext/Router.purs

@@ -24,6 +24,7 @@ router = oneOf
                         <*> (lit "document" *> int)
      , Dashboard      <$> (route "dashboard" *> sid) <*> int
      , PGraphExplorer <$> (route "graph"     *> sid) <*> int
+     , PhyloExplorer  <$> (route "phylo"     *> sid) <*> int
      , Texts          <$> (route "texts"     *> sid) <*> int
      , Lists          <$> (route "lists"     *> sid) <*> int
     , ContactPage     <$> (route "annuaire"  *> sid) <*> int

src/Gargantext/Routes.purs

@@ -24,6 +24,7 @@ data AppRoute
   | Lists          SessionId Int
   | Login
   | PGraphExplorer  SessionId Int
+  | PhyloExplorer   SessionId Int
   | RouteFile       SessionId Int
   | RouteFrameCalc  SessionId Int
   | RouteFrameCode  SessionId Int
@@ -70,6 +71,7 @@ instance showAppRoute :: Show AppRoute where
   show (Document    _ s i)      = "Document"       <> show i <> " (" <> show s <> ")"
   show (CorpusDocument s _ _ i) = "CorpusDocument" <> show i <> " (" <> show s <> ")"
   show (PGraphExplorer s i)     = "graphExplorer"  <> show i <> " (" <> show s <> ")"
+  show (PhyloExplorer  s i)     = "phyloExplorer"  <> show i <> " (" <> show s <> ")"
   show (Dashboard      s i)     = "Dashboard"      <> show i <> " (" <> show s <> ")"
   show (Texts          s i)     = "texts"          <> show i <> " (" <> show s <> ")"
   show (Lists          s i)     = "lists"          <> show i <> " (" <> show s <> ")"
@@ -95,6 +97,7 @@ appPath (Corpus s i)             = "corpus/"     <> show s <> "/" <> show i
 appPath (Document s l i)         = "list/"       <> show s <> "/" <> show l <> "/document/" <> show i
 appPath (Dashboard s i)          = "dashboard/"  <> show s <> "/" <> show i
 appPath (PGraphExplorer s i)     = "graph/"      <> show s <> "/" <> show i
+appPath (PhyloExplorer  s i)     = "phylo/"      <> show s <> "/" <> show i
 appPath (Texts s i)              = "texts/"      <> show s <> "/" <> show i
 appPath (Lists s i)              = "lists/"      <> show s <> "/" <> show i
 appPath (Annuaire s i)           = "annuaire/"   <> show s <> "/" <> show i
@@ -114,6 +117,7 @@ nodeTypeAppRoute GT.FolderPrivate s i  = Just $ FolderPrivate s i
 nodeTypeAppRoute GT.FolderPublic s i   = Just $ FolderPublic s i
 nodeTypeAppRoute GT.FolderShared s i   = Just $ FolderShared s i
 nodeTypeAppRoute GT.Graph s i          = Just $ PGraphExplorer s i
+nodeTypeAppRoute GT.Phylo s i          = Just $ PhyloExplorer  s i
 nodeTypeAppRoute GT.NodeContact s i    = Just $ Annuaire s i
 nodeTypeAppRoute GT.NodeFile s i       = Just $ RouteFile s i
 nodeTypeAppRoute GT.NodeList s i       = Just $ Lists s i