[search] implement per-user api key for pubmed search

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

@@ -3,6 +3,7 @@ module Gargantext.Components.Forest.Tree.Node.Action.Search.SearchField where
 import Gargantext.Prelude
 
 import Data.Array as A
+import Data.Either (Either(..))
 import Data.Maybe (Maybe(..), maybe, fromMaybe)
 import Data.Newtype (over)
 import Data.Nullable (null)
@@ -15,8 +16,8 @@ import Effect (Effect)
 import Effect.Aff (launchAff_)
 import Effect.Class (liftEffect)
 import Gargantext.Components.Forest.Tree.Node.Action.Search.Frame (searchIframes)
-import Gargantext.Components.Forest.Tree.Node.Action.Search.Types (DataField(..), Database(..), IMT_org(..), Org(..), SearchQuery(..), allOrgs, dataFields, defaultSearchQuery, doc, performSearch, datafield2database, Search)
-import Gargantext.Components.GraphQL.Endpoints (getIMTSchools)
+import Gargantext.Components.Forest.Tree.Node.Action.Search.Types (DataField(..), Database(..), IMT_org(..), Org(..), SearchQuery(..), allOrgs, dataFields, defaultSearchQuery, doc, performSearch, datafield2database, Search, dbFromInputValue, dbToInputValue)
+import Gargantext.Components.GraphQL.Endpoints (getIMTSchools, getNodeCorpus)
 import Gargantext.Components.GraphQL.IMT as GQLIMT
 import Gargantext.Components.InputWithEnter (inputWithEnter)
 import Gargantext.Components.Lang (Lang(..))
@@ -37,8 +38,8 @@ here :: R2.Here
 here = R2.here "Gargantext.Components.Forest.Tree.Node.Action.Search.SearchField"
 
 defaultSearch :: Search
-defaultSearch = { databases: Empty
-                , datafield: Nothing
+defaultSearch = { databases    : Empty
+                , datafield    : Nothing
                 , node_id      : Nothing
                 , lang         : Nothing
                 , term         : ""
@@ -180,28 +181,19 @@ isExternal _ = false
 
 isArxiv :: Maybe DataField -> Boolean
 isArxiv (Just
-        ( External
-          ( Just Arxiv
-          )
-        )
+         ( External Arxiv )
         )   = true
 isArxiv _ = false
 
 isHAL :: Maybe DataField -> Boolean
 isHAL (Just
-        ( External
-          ( Just (HAL _ )
-          )
-        )
+       ( External (HAL _ ) )
       ) = true
 isHAL _ = false
 
 isIsTex :: Maybe DataField -> Boolean
 isIsTex ( Just
-          ( External
-            ( Just ( IsTex)
-            )
-          )
+          ( External ( IsTex ) )
         ) = true
 isIsTex _ = false
 
@@ -209,11 +201,8 @@ isIsTex _ = false
 isIMT :: Maybe DataField -> Boolean
 isIMT ( Just
         ( External
-          ( Just
           ( HAL
-              ( Just ( IMT _)
-              )
-            )
+            ( Just ( IMT _) )
           )
         )
       ) = true
@@ -222,24 +211,24 @@ isIMT _ = false
 isCNRS :: Maybe DataField -> Boolean
 isCNRS ( Just
          ( External
-          ( Just
            ( HAL
-              ( Just ( CNRS _)
-              )
-            )
+             ( Just ( CNRS _) )
            )
          )
       ) = true
 isCNRS _ = false
 
+isPubmed :: Maybe DataField -> Boolean
+isPubmed ( Just
+           ( External ( PubMed _ ) )
+         ) = true
+isPubmed _ = false
+
 needsLang :: Maybe DataField -> Boolean
 needsLang (Just Gargantext) = true
 needsLang (Just Web)        = true
 needsLang ( Just
-            ( External
-              ( Just (HAL _)
-              )
-            )
+            ( External (HAL _) )
           ) = true
 needsLang _                 = false
 
@@ -247,20 +236,18 @@ needsLang _                 = false
 isIn :: IMT_org -> Maybe DataField -> Boolean
 isIn org ( Just
            ( External
-             ( Just
              ( HAL
                ( Just
                  ( IMT imtOrgs )
                )
              )
            )
-           )
          ) = Set.member org imtOrgs
 isIn _ _ = false
 
 updateFilter :: IMT_org -> Array IMT_org -> Maybe DataField -> Maybe DataField
-updateFilter org allIMTorgs (Just (External (Just (HAL (Just (IMT imtOrgs)))))) =
- (Just (External (Just (HAL (Just $ IMT imtOrgs')))))
+updateFilter org allIMTorgs (Just (External (HAL (Just (IMT imtOrgs))))) =
+ Just $ External $ HAL $ Just $ IMT imtOrgs'
   where
     imtOrgs' = if Set.member org imtOrgs
                   then
@@ -272,7 +259,7 @@ updateFilter org allIMTorgs (Just (External (Just (HAL (Just (IMT imtOrgs))))))
                        then Set.fromFoldable allIMTorgs
                        else Set.insert org imtOrgs
 
-updateFilter org allIMTorgs _ = (Just (External (Just (HAL (Just (IMT imtOrgs'))))))
+updateFilter org allIMTorgs _ = (Just (External (HAL (Just (IMT imtOrgs')))))
   where
     imtOrgs' = if org == All_IMT
                   then Set.fromFoldable allIMTorgs
@@ -346,6 +333,7 @@ dataFieldNavCpt = here.component "dataFieldNav" cpt
 type DatabaseInputProps = (
     databases :: Array Database
   , search    :: T.Box Search
+  , session   :: Session
   )
 
 databaseInput :: R2.Component DatabaseInputProps
@@ -354,21 +342,35 @@ databaseInputCpt :: R.Component DatabaseInputProps
 databaseInputCpt = here.component "databaseInput" cpt
   where
     cpt { databases
-        , search } _ = do
+        , search
+        , session } _ = do
       search' <- T.useLive T.unequal search
 
       let db = case search'.datafield of
-            (Just (External (Just x))) -> Just x
+            (Just (External x)) -> Just x
             _                   -> Nothing
 
           liItem :: Database -> R.Element
           liItem  db' = H.option { className : "text-primary center"
-                                 , value: show db' } [ H.text (show db') ]
+                                 , value: dbToInputValue db' } [ H.text (show db') ]
 
           change e = do
-            let value = read $ R.unsafeEventValue e
-            T.modify_ (_ { datafield = Just $ External value
-                         , databases = fromMaybe Empty value
+            let value = dbFromInputValue $ R.unsafeEventValue e
+            -- TODO Fetch pubmed api key
+            launchAff_ $ do
+              updatedValue <- case value of
+                Just (PubMed _) ->
+                  case search'.node_id of
+                       Just nodeId -> do
+                         eCorpus <- getNodeCorpus session nodeId
+                         case eCorpus of
+                           Left _err -> pure $ PubMed { api_key: Nothing }
+                           Right c   -> pure $ PubMed { api_key: c.pubmedAPIKey }
+                       Nothing -> pure $ PubMed { api_key: Nothing }
+                _ -> pure $ fromMaybe Empty value
+
+              liftEffect $ T.modify_ (_ { datafield = Just $ External updatedValue
+                                        , databases = updatedValue
                                         }) search
 
       pure $
@@ -384,6 +386,40 @@ databaseInputCpt = here.component "databaseInput" cpt
     defaultValue datafield = show $ maybe Empty datafield2database datafield
 
 
+type PubmedInputProps = (
+    search :: T.Box Search
+  , session :: Session
+  )
+
+pubmedInput :: R2.Component PubmedInputProps
+pubmedInput = R.createElement pubmedInputCpt
+pubmedInputCpt :: R.Component PubmedInputProps
+pubmedInputCpt = here.component "pubmedInput" cpt where
+  cpt { search, session } _ = do
+    search' <- T.useLive T.unequal search
+
+    case search'.datafield of
+      Just (External (PubMed p@{ api_key })) ->
+        -- TODO Fetch current API key
+        pure $
+          H.div { className: "form-group" }
+            [ H.div { className: "text-primary center" } [ H.text "Pubmed API key" ]
+            , H.input { className: "form-control"
+                      , defaultValue: fromMaybe "" api_key
+                      , on: { blur: modifyPubmedAPIKey search p
+                            , change: modifyPubmedAPIKey search p
+                            , input: modifyPubmedAPIKey search p } } ]
+      _ -> pure $ H.div {} []
+    where
+      modifyPubmedAPIKey search p e = do
+        let val = R.unsafeEventValue e
+        let mVal = case val of
+              "" -> Nothing
+              s  -> Just s
+        T.modify_ (\s ->
+                    s { datafield = Just (External (PubMed p { api_key = mVal })) }) search
+
+
 type OrgInputProps =
   ( orgs :: Array Org
   | ComponentProps)
@@ -396,7 +432,7 @@ orgInputCpt = here.component "orgInput" cpt
     cpt { orgs, search } _ = do
       let change e = do
             let value = R.unsafeEventValue e
-            T.modify_ (_ { datafield = Just $ External $ Just $ HAL $ read value }) search
+            T.modify_ (_ { datafield = Just $ External $ HAL $ read value }) search
 
       pure $ H.div { className: "form-group" }
         [ H.div {className: "text-primary center"} [H.text "filter with organization: "]
@@ -438,13 +474,18 @@ datafieldInputCpt :: R.Component DatafieldInputProps
 datafieldInputCpt = here.component "datafieldInput" cpt where
   cpt { databases, langs, search, session } _ = do
     search' <- T.useLive T.unequal search
+    datafield <- T.useFocused (_.datafield) (\a b -> b { datafield = a }) search
     iframeRef <- R.useRef null
 
     pure $ H.div {}
       [ dataFieldNav { search } []
 
       , if isExternal search'.datafield
-        then databaseInput { databases, search } []
+        then databaseInput { databases, search, session } []
+        else H.div {} []
+
+      , if isPubmed search'.datafield
+        then pubmedInput { search, session } []
         else H.div {} []
 
       , if isHAL search'.datafield
@@ -594,23 +635,26 @@ searchQuery selection { datafield: Nothing, term } =
                                           , selection = selection }) defaultSearchQuery
 -- TODO Simplify both HAL Nothing and HAL (Just IMT) cases
 searchQuery selection { databases
-                      , datafield: datafield@(Just (External (Just (HAL Nothing))))
+                      , datafield: datafield@(Just (External (HAL Nothing)))
                       , lang
                       , term
                       , node_id
-                      , years } = over SearchQuery (_ { databases = databases
+                      , years } =
+  over SearchQuery (_ { databases = databases
                       , datafield = datafield
                       , lang      = lang
                       , node_id   = node_id
                       , query     = queryHAL term Nothing lang years
                       , selection = selection
                       }) defaultSearchQuery
+
 searchQuery selection { databases
-                      , datafield: datafield@(Just (External (Just (HAL (Just (IMT imtOrgs))))))
+                      , datafield: datafield@(Just (External (HAL (Just (IMT imtOrgs)))))
                       , lang
                       , term
                       , node_id
-                      , years } = over SearchQuery (_ { databases = databases
+                      , years } =
+  over SearchQuery (_ { databases = databases
                       , datafield = datafield
                       , lang      = lang
                       , node_id   = node_id

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
@@ -34,10 +33,7 @@ type Search = { databases :: Database
 
 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 }
@@ -91,19 +87,19 @@ instance JSON.WriteForeign DataOriginApi where
   writeImpl (ExternalOrigin { api }) = JSON.writeImpl { api }
 
 datafield2dataOriginApi :: DataField -> DataOriginApi
-datafield2dataOriginApi (External (Just a)) = ExternalOrigin { api : a }
+datafield2dataOriginApi (External a) = ExternalOrigin { api : a }
 datafield2dataOriginApi _            = InternalOrigin { api : IsTex } -- TODO fixme
 
 ------------------------------------------------------------------------
 -- | Database search specifications
 
 datafield2database :: DataField -> Database
-datafield2database (External (Just x)) = x
+datafield2database (External x) = x
 datafield2database _            = Empty
 
 allDatabases :: Array Database
 allDatabases = [ Empty
-               , PubMed
+               , PubMed { api_key: Nothing }
                , Arxiv
                , HAL Nothing
                , IsTex
@@ -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
@@ -243,6 +263,7 @@ newtype SearchQuery = SearchQuery
   , node_id      :: Maybe Int
   , offset       :: Maybe Int
   , order        :: Maybe SearchOrder
+  , pubmedAPIKey :: Maybe String
   , selection    :: ListSelection.Selection
   }
 derive instance Generic SearchQuery _
@@ -260,13 +281,14 @@ 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
@@ -280,6 +302,7 @@ defaultSearchQuery = SearchQuery
   , node_id      : Nothing
   , offset       : Nothing
   , order        : Nothing
+  , pubmedAPIKey : Nothing
   , selection    : ListSelection.NoList -- MyListsFirst
   }
 

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)