Merge branch 'dev' into testing

package.json

 {
     "name": "Gargantext",
-    "version": "0.0.6.9.9.3.3",
+    "version": "0.0.6.9.9.5",
     "scripts": {
         "generate-purs-packages-nix": "./nix/generate-purs-packages.nix",
         "generate-psc-packages-nix": "./nix/generate-packages-json.bash",

spago.dhall

@@ -33,6 +33,7 @@ to generate this file without the comments in this block.
   , "dom-simple"
   , "effect"
   , "either"
+  , "enums"
   , "exceptions"
   , "ffi-simple"
   , "foldable-traversable"

src/Gargantext/Components/Annotation/Field.purs

@@ -13,18 +13,18 @@ module Gargantext.Components.Annotation.Field where
 
 import Gargantext.Prelude
 
-import DOM.Simple.Event as DE
 import Data.Array as A
 import Data.List (List(..), (:))
 import Data.Maybe (Maybe(..), maybe)
 import Data.String.Common (joinWith)
 import Data.Tuple (Tuple(..), snd)
 import Data.Tuple.Nested ((/\))
+import DOM.Simple.Event as DE
 import Effect (Effect)
 import Gargantext.Components.Annotation.Menu (annotationMenu, AnnotationMenu)
 import Gargantext.Components.Annotation.Types (MenuType(..), ModeType(..), termClass)
 import Gargantext.Core.NgramsTable.Functions (findNgramTermList, highlightNgrams, normNgram)
-import Gargantext.Core.NgramsTable.Types (NgramsTable, NgramsTerm)
+import Gargantext.Core.NgramsTable.Types (NgramsTable, NgramsTerm(..))
 import Gargantext.Types (CTabNgramType(..), TermList)
 import Gargantext.Utils.Reactix as R2
 import Gargantext.Utils.Selection as Sel
@@ -35,7 +35,7 @@ import Record as Record
 import Toestand as T
 
 here :: R2.Here
-here = R2.here "Gargantext.Components.Annotation.AnnotatedField"
+here = R2.here "Gargantext.Components.Annotation.Field"
 
 -- @NOTE #386: add parameter "type" ("Authors", "Terms")
 type Props =
@@ -52,7 +52,6 @@ type MouseEvent = E.SyntheticEvent DE.MouseEvent
 
 annotatedField :: R2.Leaf Props
 annotatedField = R2.leaf annotatedFieldCpt
-
 annotatedFieldCpt :: R.Component Props
 annotatedFieldCpt = here.component "annotatedField" cpt where
   cpt props _ = do
@@ -71,7 +70,6 @@ type InnerProps =
 
 annotatedFieldInner :: R2.Leaf InnerProps
 annotatedFieldInner = R2.leaf annotatedFieldInnerCpt
-
 annotatedFieldInnerCpt :: R.Component InnerProps
 annotatedFieldInnerCpt = here.component "annotatedFieldInner" cpt where
   cpt { menuRef
@@ -159,16 +157,16 @@ onAnnotationSelect
     s <- Sel.getSelection
     case s of
       Just sel -> do
-        case Sel.selectionToString sel of
-          "" -> hideMenu { menuRef, redrawMenu }
+        case (normNgram CTabTerms $ Sel.selectionToString sel) of
+          NormNgramsTerm "" -> hideMenu { menuRef, redrawMenu }
           sel' -> do
             showMenu { event
-                    , getList: findNgramTermList ngrams
-                    , menuRef
-                    , menuType: NewNgram
-                    , ngram: normNgram CTabTerms sel'
-                    , redrawMenu
-                    , setTermList }
+                     , getList: findNgramTermList ngrams
+                     , menuRef
+                     , menuType: NewNgram
+                     , ngram: sel'  -- normNgram CTabTerms sel'
+                     , redrawMenu
+                     , setTermList }
       Nothing -> hideMenu { menuRef, redrawMenu }
 
 onAnnotationSelect
@@ -241,7 +239,6 @@ type RunProps =
 
 annotateRun :: R2.Leaf RunProps
 annotateRun = R2.leaf annotatedRunCpt
-
 annotatedRunCpt :: R.Component RunProps
 annotatedRunCpt = here.component "annotatedRun" cpt where
   cpt { list, onSelect, text } _ = pure $ case list of

src/Gargantext/Components/Annotation/Menu.purs

@@ -36,7 +36,6 @@ type AnnotationMenu =
 
 annotationMenu :: R2.Leaf Props
 annotationMenu = R2.leaf annotationMenuCpt
-
 annotationMenuCpt :: R.Component Props
 annotationMenuCpt = here.component "main" cpt where
   cpt { menuRef } _ = do

src/Gargantext/Components/Category.purs

@@ -4,6 +4,7 @@ module Gargantext.Components.Category where
 import Gargantext.Prelude
 
 import Data.Array as A
+import Data.Enum (fromEnum)
 import Data.Generic.Rep (class Generic)
 import Data.Map as Map
 import Data.Maybe (Maybe(..), fromMaybe)
@@ -12,8 +13,8 @@ import Effect.Aff (launchAff_)
 import Effect.Class (liftEffect)
 import Gargantext.Components.Bootstrap as B
 import Gargantext.Components.Bootstrap.Types (Variant(..))
-import Gargantext.Components.Category.Types (Category(..), Star(..), cat2score, categories, clickAgain, decodeStar, star2score, stars)
-import Gargantext.Components.DocsTable.Types (DocumentsView(..), LocalCategories, LocalUserScore)
+import Gargantext.Components.Category.Types (Category(..), Star(..), cat2score, cat2star, categories, categoryNextState, decodeCategory, stars)
+import Gargantext.Components.DocsTable.Types (DocumentsView(..), LocalCategories)
 import Gargantext.Components.GraphQL.Context (NodeContext)
 import Gargantext.Components.GraphQL.Endpoints (getNodeContext, updateNodeContextCategory)
 import Gargantext.Config.REST (AffRESTError, RESTError(..))
@@ -36,9 +37,9 @@ type RatingProps =
   ( chartReload        :: T2.ReloadS
   , nodeId             :: NodeID
   , row                :: DocumentsView
-  , score              :: Star
+  , score              :: Category
   , session            :: Session
-  , setLocalCategories :: R.Setter LocalUserScore
+  -- , setLocalCategories :: R.Setter LocalCategories
   )
 
 rating :: R2.Component RatingProps
@@ -50,11 +51,11 @@ ratingCpt = here.component "rating" cpt where
       , row: DocumentsView r
       , score
       , session
-      , setLocalCategories
+      -- , setLocalCategories
       } _ = do
     pure $ renderRatingSimple { docId: r._id
                               , corpusId: nodeId
-                              , category: star2score score
+                              , category: score
                               , session } []
 
     -- -- | Behaviors
@@ -86,14 +87,17 @@ ratingCpt = here.component "rating" cpt where
     --     , className: ratingClassName score s
     --     }
 
-ratingIcon Star_0 Star_0  = "recycle"
+ratingIcon :: Category -> Star -> String
+ratingIcon Trash  Star_0  = "recycle"
 ratingIcon _      Star_0  = "trash"
-ratingIcon c      s       = star2score c < star2score s ? "star-o" $ "star"
+ratingIcon c      s       = fromEnum (cat2star c) < fromEnum s ? "star-o" $ "star"
 
+ratingVariant :: Star -> Star -> Variant
 ratingVariant Star_0 Star_0 = Dark
 ratingVariant _      Star_0 = Dark
 ratingVariant _      _      = Dark
 
+ratingClassName :: Star -> Star -> String
 ratingClassName Star_0 Star_0 = "rating-group__action"
 ratingClassName _      Star_0 = "rating-group__action"
 ratingClassName _      _      = "rating-group__star"
@@ -118,10 +122,12 @@ ratingSimpleLoaderCpt = here.component "ratingSimpleLoader" cpt where
     useLoader { errorHandler
               , loader: loadDocumentContext session
               , path: { docId, corpusId }
-              , render: \{ nc_category } -> renderRatingSimple { docId
-                                                               , corpusId
-                                                               , category: fromMaybe 0 nc_category
-                                                               , session } [] }
+              , render: \{ nc_category } -> do
+                  let category = fromMaybe UnRead $ decodeCategory <$> nc_category
+                  renderRatingSimple { docId
+                                     , corpusId
+                                     , category
+                                     , session } [] }
     where
       errorHandler err = do
         here.warn2 "[pageLayout] RESTError" err
@@ -139,7 +145,7 @@ loadDocumentContext session { docId, corpusId } = getNodeContext session docId c
 type RenderRatingSimpleProps =
   ( docId    :: NodeID
   , corpusId :: NodeID
-  , category :: Int
+  , category :: Category
   , session  :: Session )
 
 renderRatingSimple :: R2.Component RenderRatingSimpleProps
@@ -151,17 +157,17 @@ renderRatingSimpleCpt = here.component "renderRatingSimple" cpt where
       , category
       , session
       } _ = do
-    score <- T.useBox $ decodeStar category
+    categoryS <- T.useBox category
 
     pure $ ratingSimple { docId
                         , corpusId
-                        , score
+                        , category: categoryS
                         , session } []
 
 type RatingSimpleProps =
   ( docId    :: NodeID
   , corpusId :: NodeID
-  , score    :: T.Box Star
+  , category :: T.Box Category
   , session  :: Session )
 
 ratingSimple :: R2.Component RatingSimpleProps
@@ -170,19 +176,21 @@ ratingSimpleCpt :: R.Component RatingSimpleProps
 ratingSimpleCpt = here.component "ratingSimple" cpt where
   cpt { docId
       , corpusId
-      , score
+      , category
       , session
       } _ = do
-    score' <- T.useLive T.unequal score
+    category' <- T.useLive T.unequal category
+    let star' = cat2star category'
 
     let
       onClick c _ = do
-        let c' = score' == c ? clickAgain c $ c
+        -- let c' = score' == c ? clickAgain c $ c
+        let c' = categoryNextState category' c
 
         -- setLocalCategories $ Map.insert r._id c'
         launchAff_ do
-          _ <- updateNodeContextCategory session docId corpusId $ star2score c'
-          liftEffect $ T.write_ c' score
+          _ <- updateNodeContextCategory session docId corpusId $ cat2score c'
+          liftEffect $ T.write_ c' category
           pure unit
 
     pure $
@@ -190,17 +198,17 @@ ratingSimpleCpt = here.component "ratingSimple" cpt where
       { className: "rating-group" } $
       stars <#> \s ->
         B.iconButton
-        { name: ratingIcon score' s
+        { name: ratingIcon category' s
         , callback: onClick s
         , overlay: false
-        , variant: ratingVariant score' s
-        , className: ratingClassName score' s
+        , variant: ratingVariant star' s
+        , className: ratingClassName star' s
         }
 
 
 newtype RatingQuery =
   RatingQuery { nodeIds :: Array Int
-              , rating  :: Star
+              , rating  :: Category
               }
 derive instance Generic RatingQuery _
 instance JSON.WriteForeign RatingQuery where
@@ -267,6 +275,9 @@ icon cat b = btn b $ "fa fa-" <> (color $ size b $ icon' cat b)
     icon' Favorite false = "heart-o"
     icon' Favorite true = "heart"
 
+    icon' ToCite false = "quote-left-o"
+    icon' ToCite true = "quote-left"
+
     size :: Boolean -> String -> String
     size true  s = s <> " btn-lg"
     size false s = s <> " btn-sm"

src/Gargantext/Components/Category/Types.purs

 module Gargantext.Components.Category.Types where
 
-import Data.Generic.Rep (class Generic)
+import Data.Bounded.Generic (genericTop, genericBottom)
+import Data.Enum (class Enum, class BoundedEnum, succ, pred, fromEnum, toEnumWithDefaults)
+import Data.Enum.Generic (genericPred, genericSucc, genericCardinality, genericFromEnum, genericToEnum)
 import Data.Eq.Generic (genericEq)
+import Data.Generic.Rep (class Generic)
+import Data.Maybe (fromMaybe)
+import Data.Ord.Generic (genericCompare)
 import Data.Show.Generic (genericShow)
 import Simple.JSON as JSON
 
 import Gargantext.Prelude
 
 ------------------------------------------------------------------------
-data Star = Star_0 | Star_1 | Star_2 | Star_3 | Star_4
-
-stars :: Array Star
-stars = [Star_0, Star_1, Star_2, Star_3, Star_4]
-
-derive instance Generic Star _
-instance Show Star where show = genericShow
-instance Eq Star where eq = genericEq
-instance JSON.ReadForeign Star where
-  readImpl f = do
-    inst <- JSON.readImpl f
-    pure $ decodeStar inst
-instance JSON.WriteForeign Star where writeImpl = JSON.writeImpl <<< star2score
-
-decodeStar :: Int -> Star
-decodeStar 0 = Star_0
-decodeStar 1 = Star_1
-decodeStar 2 = Star_2
-decodeStar 3 = Star_3
-decodeStar 4 = Star_4
-decodeStar _ = Star_4
-
-star2score :: Star -> Int
-star2score Star_0 = 0
-star2score Star_1 = 1
-star2score Star_2 = 2
-star2score Star_3 = 3
-star2score Star_4 = 4
-
-
-clickAgain :: Star -> Star
-clickAgain Star_0 = Star_1
-clickAgain s      = decodeStar (star2score s - 1)
-
-
-------------------------------------------------------------------------
-data Category = Trash | UnRead | Checked | Topic | Favorite
+data Category = Trash | UnRead | Checked | Topic | Favorite | ToCite
+{-
+- `UnRead` is assigned initially for new docs
+- After reading a doc, `Checked` should be assigned automatically
+- Both `Trash` and `UnRead` map to 0 stars in the doc list
+-}
 
 categories :: Array Category
-categories = [Trash, UnRead, Checked, Topic, Favorite]
+categories = [Trash, UnRead, Checked, Topic, Favorite, ToCite]
 
 derive instance Generic Category _
+instance Ord Category where compare = genericCompare
+instance Enum Category where
+  pred = genericPred
+  succ = genericSucc
+instance Bounded Category where
+  bottom = genericBottom
+  top = genericTop
+instance BoundedEnum Category where
+  cardinality = genericCardinality
+  fromEnum = genericFromEnum
+  toEnum = genericToEnum
 instance Show Category where show = genericShow
 instance Eq Category where eq = genericEq
 instance JSON.ReadForeign Category where
@@ -58,26 +43,79 @@ instance JSON.ReadForeign Category where
     pure $ decodeCategory inst
 instance JSON.WriteForeign Category where writeImpl = JSON.writeImpl <<< cat2score
 
+catSucc :: Category -> Category
+catSucc c = fromMaybe ToCite $ succ c
+
+catPred :: Category -> Category
+catPred c = fromMaybe Trash $ pred c
+
+clickAgain :: Category -> Category
+clickAgain _     = UnRead
+
+
+-- | `categoryNextState :: current -> clicked -> new State`
+categoryNextState :: Category -> Star -> Category
+categoryNextState Trash Star_0 = UnRead
+categoryNextState _     Star_0 = Trash
+categoryNextState current clicked =
+  if (cat2star current) == clicked then
+    clickAgain current
+  else
+    star2catSimple clicked
+
 favCategory :: Category -> Category
 favCategory Favorite = Topic
 favCategory _        = Favorite
 
 trashCategory :: Category -> Category
-trashCategory _     = Trash
--- TODO: ?
---trashCategory Trash = UnRead
+trashCategory = const Trash
 
 decodeCategory :: Int -> Category
-decodeCategory 0 = Trash
-decodeCategory 1 = UnRead
-decodeCategory 2 = Checked
-decodeCategory 3 = Topic
-decodeCategory 4 = Favorite
-decodeCategory _ = UnRead
+decodeCategory = toEnumWithDefaults UnRead UnRead
 
 cat2score :: Category -> Int
-cat2score Trash    = 0
-cat2score UnRead   = 1
-cat2score Checked  = 2
-cat2score Topic    = 3
-cat2score Favorite = 4
+cat2score = fromEnum
+
+------------------------------------------------------------------------
+-- | This is just a helper to visualize categories.
+data Star = Star_0 | Star_1 | Star_2 | Star_3 | Star_4
+
+stars :: Array Star
+stars = [Star_0, Star_1, Star_2, Star_3, Star_4]
+
+derive instance Generic Star _
+instance Show Star where show = genericShow
+instance Eq Star where eq = genericEq
+instance Ord Star where compare = genericCompare
+instance Enum Star where
+  pred = genericPred
+  succ = genericSucc
+instance Bounded Star where
+  bottom = genericBottom
+  top = genericTop
+instance BoundedEnum Star where
+  cardinality = genericCardinality
+  fromEnum = genericFromEnum
+  toEnum = genericToEnum
+
+
+
+cat2star :: Category -> Star
+cat2star Trash    = Star_0
+cat2star UnRead   = Star_0
+cat2star Checked  = Star_1
+cat2star Topic    = Star_2
+cat2star Favorite = Star_3
+cat2star ToCite   = Star_4
+
+-- | This is a "reverse" of `cat2star`
+star2catSimple :: Star -> Category
+star2catSimple Star_0 = UnRead
+star2catSimple Star_1 = Checked
+star2catSimple Star_2 = Topic
+star2catSimple Star_3 = Favorite
+star2catSimple Star_4 = ToCite
+
+markCategoryChecked :: Category -> Category
+markCategoryChecked UnRead = Checked
+markCategoryChecked s = s

src/Gargantext/Components/DocsTable/Types.purs

@@ -7,14 +7,14 @@ import Data.Generic.Rep (class Generic)
 import Data.Map (Map)
 import Data.Maybe (Maybe(..), fromMaybe)
 import Data.Tuple (Tuple(..))
-import Gargantext.Components.Category.Types (Category, Star(..), decodeStar)
+import Gargantext.Components.Category.Types (Category(..), Star(..), decodeCategory)
 import Simple.JSON as JSON
 
 data Action
   = MarkCategory Int Category
 
 type DocumentsViewT =
-  ( category   :: Star
+  ( category   :: Category
   , date       :: Int
   , ngramCount :: Maybe Int
   , score      :: Maybe Int
@@ -65,8 +65,8 @@ type ResponseT =
   , score :: Maybe Int
   , title :: String )
 newtype Response = Response
-  { cid        :: Int
-  , category :: Star
+  { cid      :: Int
+  , category :: Category
   | ResponseT
   }
 
@@ -74,7 +74,7 @@ instance JSON.ReadForeign Response where
   readImpl f = do
     { category, id, hyperdata, ngramCount, score, title } :: { category :: Int, id :: Int | ResponseT } <- JSON.readImpl f
     --pure $ Response { category: decodeCategory category, cid, hyperdata, ngramCount, score, title }
-    pure $ Response { category: decodeStar category
+    pure $ Response { category: decodeCategory category
                     , cid: id
                     , hyperdata
                     , ngramCount
@@ -110,7 +110,7 @@ sampleData' = DocumentsView { _id : 1
                             , date : 2010
                             , title : "title"
                             , source : Just "source"
-                            , category : Star_1
+                            , category : UnRead
                             , ngramCount : Just 1
                             , score: Just 1 }
 
@@ -121,7 +121,7 @@ sampleData = map (\(Tuple t s) -> DocumentsView { _id : 1
                                                 , date : 2017
                                                 , title: t
                                                 , source: Just s
-                                                , category : Star_1
+                                                , category : UnRead
                                                 , ngramCount : Just 10
                                                 , score: Just 1 }) sampleDocuments
 

src/Gargantext/Components/Document/Layout.purs

@@ -16,7 +16,6 @@ import Gargantext.Components.AutoUpdate (autoUpdate)
 import Gargantext.Components.Bootstrap as B
 import Gargantext.Components.Bootstrap.Types (ComponentStatus(..), SpinnerTheme(..))
 import Gargantext.Components.Category (ratingSimpleLoader)
-import Gargantext.Components.Category.Types (decodeStar)
 import Gargantext.Components.Document.Types (DocPath, Document(..), LoadedData, initialState)
 import Gargantext.Components.NgramsTable.AutoSync (useAutoSync)
 import Gargantext.Components.Node (NodePoly(..))

src/Gargantext/Components/FacetsTable.purs

@@ -395,6 +395,7 @@ pageCpt = here.component "page" cpt
         wrapColElts = const identity
         -- TODO: how to interprete other scores?
         gi Trash = "fa fa-star-empty"
+        gi UnRead = "fa fa-star-empty"
         gi _ = "fa fa-star"
 
         documentUrl id { listId, nodeId } =

src/Gargantext/Components/Forest/Tree/Node/Action/Search/Types.purs

@@ -8,7 +8,6 @@ import Data.Maybe (Maybe(..), fromMaybe, maybe)
 import Data.Newtype (class Newtype)
 import Data.Set (Set)
 import Data.Set as Set
-import Data.String as String
 import Data.Tuple (Tuple)
 import Data.Tuple.Nested ((/\))
 import Gargantext.Components.GraphQL.IMT as GQLIMT
@@ -23,21 +22,18 @@ import Simple.JSON as JSON
 import URI.Extra.QueryPairs as QP
 import URI.Query as Q
 
-type Search = { databases :: Database
-              , datafield :: Maybe DataField
-              , url       :: String
-              , lang      :: Maybe Lang
-              , node_id   :: Maybe Int
-              , term      :: String
-              , years     :: Array String
+type Search = { databases    :: Database
+              , datafield    :: Maybe DataField
+              , url          :: String
+              , lang         :: Maybe Lang
+              , node_id      :: Maybe Int
+              , term         :: String
+              , years        :: Array String
               }
 
 isIsTex_Advanced :: Maybe DataField -> Boolean
 isIsTex_Advanced ( Just
-          ( External
-            ( Just ( IsTex_Advanced)
-            )
-          )
+          ( External ( IsTex_Advanced) )
         ) = true
 isIsTex_Advanced _ = false
 
@@ -51,13 +47,13 @@ class Doc a where
 
 dataFields :: Array DataField
 dataFields = [ {- Gargantext
-             , -} External Nothing
+             , -} External Empty
              , Web
              -- , Files
              ]
 
 data DataField = Gargantext
-               | External (Maybe Database)
+               | External Database
                | Web
                | Files
 
@@ -74,9 +70,9 @@ instance Doc DataField where
   doc Files        = "Zip files with formats.."
 derive instance Eq DataField
 instance JSON.WriteForeign DataField where
-  writeImpl (External (Just db)) = JSON.writeImpl $ "External " <> show db
-  writeImpl Web = JSON.writeImpl $ "Web"
-  writeImpl f = JSON.writeImpl $ show f
+  writeImpl (External db) = JSON.writeImpl { tag: "External"
+                                           , contents: JSON.writeImpl db }
+  writeImpl f = JSON.writeImpl $ JSON.writeImpl { tag: show f }
 
 ----------------------------------------
 data DataOriginApi = InternalOrigin { api :: Database }
@@ -91,23 +87,23 @@ instance JSON.WriteForeign DataOriginApi where
   writeImpl (ExternalOrigin { api }) = JSON.writeImpl { api }
 
 datafield2dataOriginApi :: DataField -> DataOriginApi
-datafield2dataOriginApi (External (Just a)) = ExternalOrigin { api : a }
-datafield2dataOriginApi _                   = InternalOrigin { api : IsTex } -- TODO fixme 
+datafield2dataOriginApi (External a) = ExternalOrigin { api : a }
+datafield2dataOriginApi _            = InternalOrigin { api : IsTex } -- TODO fixme
 
 ------------------------------------------------------------------------
 -- | Database search specifications
 
 datafield2database :: DataField -> Database
-datafield2database (External (Just x)) = x
-datafield2database _                   = Empty
+datafield2database (External x) = x
+datafield2database _            = Empty
 
 allDatabases :: Array Database
 allDatabases = [ Empty
-               , PubMed
-               , Arxiv
+               , PubMed { api_key: Nothing }
+               -- , Arxiv
                , HAL Nothing
                , IsTex
-               , IsTex_Advanced
+               -- , IsTex_Advanced
                -- , Isidore
                --, Web
                --, News
@@ -116,7 +112,7 @@ allDatabases = [ Empty
 
 data Database = All_Databases
               | Empty
-              | PubMed
+              | PubMed { api_key :: Maybe String }
               | Arxiv
               | HAL (Maybe Org)
               | IsTex
@@ -127,7 +123,7 @@ data Database = All_Databases
 derive instance Generic Database _
 instance Show Database where
   show All_Databases  = "All Databases"
-  show PubMed         = "PubMed"
+  show (PubMed _)     = "PubMed"
   show Arxiv          = "Arxiv"
   show (HAL _)        = "HAL"
   show IsTex          = "IsTex"
@@ -139,7 +135,7 @@ instance Show Database where
 
 instance Doc Database where
   doc All_Databases  = "All databases"
-  doc PubMed         = "All Medical publications"
+  doc (PubMed _)     = "All Medical publications"
   doc Arxiv          = "Arxiv"
   doc (HAL _)        = "All open science (archives ouvertes)"
   doc IsTex          = "All Elsevier enriched by CNRS/INIST"
@@ -149,22 +145,46 @@ instance Doc Database where
 --  doc News        = "Web filtered by News"
 --  doc SocialNetworks = "Web filtered by MicroBlogs"
 
-instance Read Database where
-  read :: String -> Maybe Database
-  read "All Databases"  = Just All_Databases
-  read "PubMed"         = Just PubMed
-  read "Arxiv"          = Just Arxiv
-  read "HAL"            = Just $ HAL Nothing
-  read "Isidore"        = Just Isidore
-  read "IsTex"          = Just IsTex
-  read "IsTex_Advanced" = Just IsTex_Advanced
-  -- read "Web"    = Just Web
-  -- read "News"   = Just News
-  -- read "Social Networks" = Just SocialNetworks
-  read _        = Nothing
+-- instance Read Database where
+--   read :: String -> Maybe Database
+--   read "All Databases"  = Just All_Databases
+--   read "PubMed"         = Just PubMed
+--   read "Arxiv"          = Just Arxiv
+--   read "HAL"            = Just $ HAL Nothing
+--   read "Isidore"        = Just Isidore
+--   read "IsTex"          = Just IsTex
+--   read "IsTex_Advanced" = Just IsTex_Advanced
+--   -- read "Web"    = Just Web
+--   -- read "News"   = Just News
+--   -- read "Social Networks" = Just SocialNetworks
+--   read _        = Nothing
+
+dbToInputValue :: Database -> String
+dbToInputValue All_Databases  = "all_databases"
+dbToInputValue (PubMed _)     = "pubmed"
+dbToInputValue Arxiv          = "arxiv"
+dbToInputValue (HAL _)        = "hal"
+dbToInputValue IsTex          = "istex"
+dbToInputValue IsTex_Advanced = "istex_advanced"
+dbToInputValue Isidore        = "isidore"
+dbToInputValue Empty          = "empty"
+
+dbFromInputValue :: String -> Maybe Database
+dbFromInputValue "all_databases"  = Just All_Databases
+dbFromInputValue "pubmed"         = Just (PubMed { api_key: Nothing})
+dbFromInputValue "arxiv"          = Just Arxiv
+dbFromInputValue "hal"            = Just (HAL Nothing)
+dbFromInputValue "istex"          = Just IsTex
+dbFromInputValue "istex_advanced" = Just IsTex_Advanced
+dbFromInputValue "isidore"        = Just Isidore
+dbFromInputValue "empty"          = Just Empty
+dbFromInputValue _                = Nothing
 
 derive instance Eq Database
-instance JSON.WriteForeign Database where writeImpl = JSON.writeImpl <<< show
+instance JSON.WriteForeign Database where
+  writeImpl (PubMed { api_key }) = JSON.writeImpl { tag: "PubMed"
+                                                  , _api_key: api_key }
+  writeImpl f = JSON.writeImpl { tag: show f }
 
 ------------------------------------------------------------------------
 -- | Organization specifications
@@ -234,16 +254,17 @@ instance Show SearchOrder where
 ------------------------------------------------------------------------
 
 newtype SearchQuery = SearchQuery
-  { query     :: String
-  , databases :: Database
-  , datafield :: Maybe DataField
-  , files_id  :: Array String
-  , lang      :: Maybe Lang
-  , limit     :: Maybe Int
-  , node_id   :: Maybe Int
-  , offset    :: Maybe Int
-  , order     :: Maybe SearchOrder
-  , selection :: ListSelection.Selection
+  { query        :: String
+  , databases    :: Database
+  , datafield    :: Maybe DataField
+  , files_id     :: Array String
+  , lang         :: Maybe Lang
+  , limit        :: Maybe Int
+  , node_id      :: Maybe Int
+  , offset       :: Maybe Int
+  , order        :: Maybe SearchOrder
+  , pubmedAPIKey :: Maybe String
+  , selection    :: ListSelection.Selection
   }
 derive instance Generic SearchQuery _
 derive instance Newtype SearchQuery _
@@ -260,27 +281,29 @@ instance GT.ToQuery SearchQuery where
           pair k = maybe [] $ \v ->
             [ QP.keyFromString k /\ Just (QP.valueFromString $ show v) ]
 instance JSON.WriteForeign SearchQuery where
-  writeImpl (SearchQuery { databases, datafield, lang, node_id, query, selection }) =
+  writeImpl (SearchQuery { databases, datafield, lang, node_id, pubmedAPIKey, query, selection }) =
     JSON.writeImpl { query: query -- String.replace (String.Pattern "\"") (String.Replacement "\\\"") query
                    , databases
                    , datafield
                    , lang: maybe "EN" show lang
                    , node_id: fromMaybe 0 node_id
                    , flowListWith: selection
+                   , pubmedAPIKey
                    }
 
 defaultSearchQuery :: SearchQuery
 defaultSearchQuery = SearchQuery
-  { query     : ""
-  , databases : Empty
-  , datafield : Nothing
-  , files_id  : []
-  , lang      : Nothing
-  , limit     : Nothing
-  , node_id   : Nothing
-  , offset    : Nothing
-  , order     : Nothing
-  , selection : ListSelection.NoList -- MyListsFirst
+  { query        : ""
+  , databases    : Empty
+  , datafield    : Nothing
+  , files_id     : []
+  , lang         : Nothing
+  , limit        : Nothing
+  , node_id      : Nothing
+  , offset       : Nothing
+  , order        : Nothing
+  , pubmedAPIKey : Nothing
+  , selection    : ListSelection.NoList -- MyListsFirst
   }
 
 performSearch :: Session -> Int -> SearchQuery -> AffRESTError GT.AsyncTaskWithType

src/Gargantext/Components/Forest/Tree/Node/Action/Upload.purs

@@ -156,6 +156,7 @@ uploadFileViewWithLangsCpt = here.component "uploadFileViewWithLangs" cpt
                 [ formChoiceSafe { items: [ CSV
                                           , CSV_HAL
                                           , WOS
+                                          , JSON
                                           -- , Iramuteq
                                           ]
                                  , default: CSV
@@ -585,7 +586,7 @@ uploadFile { contents, fileFormat, lang, fileType, id, nodeType, mName, selectio
                      , Tuple "_wjf_name"       mName
                  ]
     csvBodyParams = [ Tuple "_wtf_data"       (Just contents)
-                    , Tuple "_wtf_filetype"   (Just $ show NodeList)
+                    , Tuple "_wtf_filetype"   (Just $ show fileType)
                     , Tuple "_wtf_fileformat" (Just $ show fileFormat)
                     , Tuple "_wf_lang"        (Just $ show lang)
                     , Tuple "_wtf_name" mName

src/Gargantext/Components/GraphQL.purs

@@ -14,7 +14,7 @@ import Gargantext.Components.GraphQL.Contact (AnnuaireContact)
 import Gargantext.Components.GraphQL.Context as GQLCTX
 import Gargantext.Components.GraphQL.IMT as GQLIMT
 import Gargantext.Components.GraphQL.NLP as GQLNLP
-import Gargantext.Components.GraphQL.Node (Node)
+import Gargantext.Components.GraphQL.Node as GQLNode
 import Gargantext.Components.GraphQL.Tree (TreeFirstLevel)
 import Gargantext.Components.GraphQL.User (User, UserInfo, UserInfoM)
 import Gargantext.Components.GraphQL.Team (Team, TeamDeleteM)
@@ -78,8 +78,9 @@ type Schema
     , contexts_for_ngrams :: { corpus_id :: Int, ngrams_terms :: Array String } ==> Array GQLCTX.Context
     , imt_schools :: {} ==> Array GQLIMT.School
     , languages :: {} ==> Array GQLNLP.Language
-    , node_parent :: { node_id :: Int, parent_type :: String } ==> Array Node  -- TODO: parent_type :: NodeType
-    , nodes :: { node_id :: Int } ==> Array Node
+    , node_parent :: { node_id :: Int, parent_type :: String } ==> Array GQLNode.Node  -- TODO: parent_type :: NodeType
+    , nodes :: { node_id :: Int } ==> Array GQLNode.Node
+    , nodes_corpus :: { corpus_id :: Int } ==> Array GQLNode.Corpus
     , user_infos :: { user_id :: Int } ==> Array UserInfo
     , users :: { user_id :: Int } ==> Array User
     , team :: { team_node_id :: Int } ==> Team

src/Gargantext/Components/GraphQL/Endpoints.purs

@@ -14,7 +14,7 @@ import Gargantext.Components.GraphQL.Contact (AnnuaireContact, annuaireContactQu
 import Gargantext.Components.GraphQL.Context as GQLCTX
 import Gargantext.Components.GraphQL.IMT as GQLIMT
 import Gargantext.Components.GraphQL.NLP as GQLNLP
-import Gargantext.Components.GraphQL.Node (Node, nodeParentQuery, nodesQuery)
+import Gargantext.Components.GraphQL.Node (Corpus, Node, nodeParentQuery, nodesQuery, nodesCorpusQuery)
 import Gargantext.Components.GraphQL.Team (Team, teamQuery)
 import Gargantext.Components.GraphQL.Tree (TreeFirstLevel, treeFirstLevelQuery)
 import Gargantext.Components.GraphQL.User (UserInfo, userInfoQuery)
@@ -46,6 +46,15 @@ getNode session nodeId = do
     Nothing -> Left (CustomError $ "node with id" <> show nodeId <>" not found")
     Just node -> Right node
 
+getNodeCorpus :: Session -> Int -> AffRESTError Corpus
+getNodeCorpus session corpusId = do
+  { nodes_corpus } <- queryGql session "get nodes corpus" $
+                      nodesCorpusQuery `withVars` { id: corpusId }
+  liftEffect $ here.log2 "[getNodesCorpus] nodes_corpus" nodes_corpus
+  pure $ case A.head nodes_corpus of
+    Nothing -> Left (CustomError $ "corpus with id" <> show corpusId <>" not found")
+    Just corpus -> Right corpus
+
 getNodeParent :: Session -> Int -> NodeType -> Aff (Array Node)
 getNodeParent session nodeId parentType = do
   { node_parent } <- queryGql session "get node parent" $

src/Gargantext/Components/GraphQL/Node.purs

@@ -2,18 +2,35 @@ module Gargantext.Components.GraphQL.Node where
 
 import Gargantext.Prelude
 
+import Data.Maybe (Maybe)
 import GraphQL.Client.Args (Args, (=>>))
 import GraphQL.Client.Variable (Var(..))
 import Gargantext.Utils.GraphQL as GGQL
 import Type.Proxy (Proxy(..))
 
 
+type Corpus
+  = { id           :: Int
+    , name         :: String
+    , parent_id    :: Int
+    , pubmedAPIKey :: Maybe String
+    , type_id      :: Int }
+
 type Node
   = { id        :: Int
     , name      :: String
     , parent_id :: Int
     , type_id   :: Int }
 
+type NodesCorpusQuery =
+  { nodes_corpus :: Args
+             { corpus_id :: Var "id" Int }
+             { id :: Unit
+             , name :: Unit
+             , parent_id :: Unit
+             , pubmedAPIKey :: Unit
+             , type_id :: Unit } }
+
 type NodesQuery =
   { nodes :: Args
        { node_id :: Var "id" Int }
@@ -27,6 +44,11 @@ nodesQuery = { nodes: { node_id: Var :: _ "id" Int } =>>
                GGQL.getFieldsStandard (Proxy :: _ Node)
              }
 
+nodesCorpusQuery :: NodesCorpusQuery
+nodesCorpusQuery = { nodes_corpus: { corpus_id: Var :: _ "id" Int } =>>
+               GGQL.getFieldsStandard (Proxy :: _ Corpus)
+             }
+
 nodeParentQuery = { node_parent: { node_id: Var :: _ "id" Int
                                  , parent_type: Var :: _ "parent_type" String } =>>  -- TODO parent_type :: NodeType
                     GGQL.getFieldsStandard (Proxy :: _ Node)

src/Gargantext/Components/NgramsTable.purs

@@ -13,6 +13,7 @@ import Gargantext.Prelude
 import Data.Array as A
 import Data.Array as Array
 import Data.Either (Either(..))
+import Data.Foldable (any)
 import Data.FunctorWithIndex (mapWithIndex)
 import Data.Lens (to, view, (.~), (^.), (^?))
 import Data.Lens.At (at)
@@ -47,7 +48,7 @@ import Gargantext.Components.Table.Types (Params, orderByToGTOrderBy)
 import Gargantext.Components.Table.Types as TT
 import Gargantext.Config.REST (AffRESTError, RESTError, logRESTError)
 import Gargantext.Core.NgramsTable.Functions (addNewNgramA, applyNgramsPatches, chartsAfterSync, commitPatch, convOrderBy, coreDispatch, filterTermSize, ngramsRepoElementToNgramsElement, normNgram, patchSetFromMap, singletonNgramsTablePatch, tablePatchHasNgrams, toVersioned)
-import Gargantext.Core.NgramsTable.Types (Action(..), CoreAction(..), State, Dispatch, NgramsActionRef, NgramsClick, NgramsElement(..), NgramsPatch(..), NgramsTable, NgramsTablePatch(..), NgramsTerm(..), PageParams, PatchMap(..), Versioned(..), VersionedNgramsTable, VersionedWithCountNgramsTable, _NgramsElement, _NgramsRepoElement, _NgramsTable, _children, _list, _ngrams, _ngrams_repo_elements, _ngrams_scores, _occurrences, _root, applyPatchSet, ngramsTermText, replace)
+import Gargantext.Core.NgramsTable.Types (Action(..), CoreAction(..), State, Dispatch, NgramsActionRef, NgramsClick, NgramsElement(..), NgramsPatch(..), NgramsRepoElement(..), NgramsTable, NgramsTablePatch(..), NgramsTerm(..), PageParams, PatchMap(..), Versioned(..), VersionedNgramsTable, VersionedWithCountNgramsTable, _NgramsElement, _NgramsRepoElement, _NgramsTable, _children, _list, _ngrams, _ngrams_repo_elements, _ngrams_scores, _occurrences, _root, applyPatchSet, ngramsTermText, replace)
 import Gargantext.Hooks.Loader (useLoaderBox)
 import Gargantext.Routes (SessionRoute(..)) as Routes
 import Gargantext.Sessions (Session, get)
@@ -525,7 +526,11 @@ loadedNgramsTableBodyCpt = here.component "loadedNgramsTableBody" cpt where
         exactMatches :: Boolean
         exactMatches = not $ Seq.null $ Seq.filter fltr nres
           where
-            fltr (Tuple ng _) = queryExactMatchesLabel searchQuery (ngramsTermText ng)
+            -- | Match either ngrams term or its children with the
+            -- | `queryExactMatchesLabel` function.
+            fltr :: Tuple NgramsTerm NgramsRepoElement -> Boolean
+            fltr (Tuple ng (NgramsRepoElement { children })) =
+              any (queryExactMatchesLabel searchQuery) $ (Set.map ngramsTermText $ Set.insert ng children)
         rowsFilter :: NgramsElement -> Maybe NgramsElement
         rowsFilter ngramsElement =
           if displayRow { ngramsElement

src/Gargantext/Components/TopBar.purs

@@ -177,7 +177,7 @@ divDropdownLeftCpt = here.component "divDropdownLeft" cpt
       ]
       , -----------------------------------------------------------
       [ LiNav { title : "Chat"
-              , href  : "https://chat.iscpif.fr/channel/gargantext"
+              , href  : "https://webchat.oftc.net/?channels=#gargantext"
               , icon  : "fa fa-rocket"
               , text  : "Chat"
               }