Squashed commit of the following:

commit ea934d83
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Jan 14 06:59:11 2025 +0100

    [search] move EPO user/token into the datafield

commit b01a85eb
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Mon Jan 13 10:15:27 2025 +0100

    [search] search query json format fixes

    Related to haskell-gargantext#441

    Related to commmit
    haskell-gargantext@bc29319c

commit 3b50603a
Merge: a93e055b 2e43c474
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Fri Jan 10 12:04:36 2025 +0100

    Merge branch 'dev' into 204-ngrams-refactor-fixes

commit a93e055b
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Wed Jan 8 18:22:37 2025 +0100

    [search] pubmed constructor with api key

This commit has to be merged together with
haskell-gargantext!385 (03b33383)

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

@@ -55,7 +55,7 @@ searchIframesCpt = here.component "searchIframes" cpt
 
     pure $
       if isIsTex_Advanced search'.datafield then divIframe { frameSource: Istex, iframeRef, search } []
-      else if Just Web == search'.datafield then divIframe { frameSource: Searx, iframeRef, search } []
+      else if Web == search'.datafield then divIframe { frameSource: Searx, iframeRef, search } []
       else H.div {} []
 
 type IFrameProps =

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

@@ -2,6 +2,7 @@ module Gargantext.Components.Forest.Tree.Node.Action.Search.Types where
 
 import Gargantext.Prelude
 
+import Data.Array as A
 -- import Data.Bounded (class Bounded)
 import Data.Either (Either)
 -- import Data.Enum (class Enum, class BoundedEnum)
@@ -26,23 +27,16 @@ import URI.Extra.QueryPairs as QP
 import URI.Query as Q
 
 type Search =
-  { databases :: Database
-  , datafield :: Maybe DataField
+  { datafield :: DataField
   , url :: String
   , lang :: Maybe Lang
   , node_id :: Maybe Int
-  , epoApiUser :: Maybe String
-  , epoApiToken :: Maybe String
-  , pubmedApiKey :: Maybe String
   , term :: String
   , years :: Array String
   }
 
-isIsTex_Advanced :: Maybe DataField -> Boolean
-isIsTex_Advanced
-  ( Just
-      (External (IsTex_Advanced))
-  ) = true
+isIsTex_Advanced :: DataField -> Boolean
+isIsTex_Advanced (External (IsTex_Advanced)) = true
 isIsTex_Advanced _ = false
 
 ------------------------------------------------------------------------
@@ -81,7 +75,7 @@ instance Doc DataField where
 
 derive instance Eq DataField
 instance JSON.WriteForeign DataField where
-  writeImpl (External db) = JSON.writeImpl { "External": JSON.writeImpl $ show db }
+  writeImpl (External db) = JSON.writeImpl { "External": db }
   writeImpl Gargantext = JSON.writeImpl "Gargantext"
   writeImpl Web = JSON.writeImpl "Web"
   writeImpl Files = JSON.writeImpl "Files"
@@ -116,13 +110,13 @@ data Database
   = All_Databases
   | Empty
   | OpenAlex
-  | PubMed
+  | PubMed (Maybe String)
   | Arxiv
   | HAL (Maybe Org)
   | IsTex
   | IsTex_Advanced
   | Isidore
-  | EPO
+  | EPO (Maybe String) (Maybe String)
 
 --              | News
 --              | SocialNetworks
@@ -133,13 +127,13 @@ derive instance Generic Database _
 instance Show Database where
   show All_Databases = "All Databases"
   show OpenAlex = "OpenAlex"
-  show PubMed = "PubMed"
+  show (PubMed _) = "PubMed"
   show Arxiv = "Arxiv"
   show (HAL _) = "HAL"
   show IsTex = "IsTex"
   show IsTex_Advanced = "IsTex_Advanced"
   show Isidore = "Isidore"
-  show EPO = "EPO"
+  show (EPO _ _) = "EPO"
   show Empty = "Empty"
 
 --  show News   = "News"
@@ -148,13 +142,13 @@ instance Show Database where
 instance Doc Database where
   doc All_Databases = "All databases"
   doc OpenAlex = "OpenAlex db"
-  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"
   doc IsTex_Advanced = "IsTex advanced search"
   doc Isidore = "All (French) Social Sciences"
-  doc EPO = "European Patent Office"
+  doc (EPO _ _) = "European Patent Office"
   doc Empty = "Empty"
 
 --  doc News        = "Web filtered by News"
@@ -176,17 +170,24 @@ instance Doc Database where
 
 derive instance Eq Database
 instance JSON.WriteForeign Database where
-  writeImpl f = JSON.writeImpl $ show f
+  writeImpl (PubMed mAPIKey) = JSON.writeImpl { "db": "PubMed", "api_key": mAPIKey }
+  writeImpl (EPO mAPIUser mAPIToken) = JSON.writeImpl
+    { "db": "PubMed"
+    , "api_user": mAPIUser
+    , "api_token": mAPIToken
+    }
+  writeImpl (HAL mOrg) = JSON.writeImpl { "db": "HAL", "org": mOrg }
+  writeImpl d = JSON.writeImpl { "db": show d }
 
 allDatabases :: Array Database
 allDatabases =
   [ Empty
-  , PubMed
+  , PubMed Nothing
   , HAL Nothing
   , Arxiv
   , OpenAlex
   , IsTex
-  -- , EPO
+  -- , EPO Nothing Nothing
   --, IsTex_Advanced
   --, Isidore
   --, Web
@@ -197,25 +198,25 @@ allDatabases =
 dbToInputValue :: Database -> String
 dbToInputValue All_Databases = "all_databases"
 dbToInputValue OpenAlex = "openalex"
-dbToInputValue PubMed = "pubmed"
+dbToInputValue (PubMed _) = "pubmed"
 dbToInputValue Arxiv = "arxiv"
 dbToInputValue (HAL _) = "hal"
 dbToInputValue IsTex = "istex"
 dbToInputValue IsTex_Advanced = "istex_advanced"
 dbToInputValue Isidore = "isidore"
-dbToInputValue EPO = "epo"
+dbToInputValue (EPO _ _) = "epo"
 dbToInputValue Empty = "empty"
 
 dbFromInputValue :: String -> Maybe Database
 dbFromInputValue "all_databases" = Just All_Databases
 dbFromInputValue "openalex" = Just OpenAlex
-dbFromInputValue "pubmed" = Just PubMed
+dbFromInputValue "pubmed" = Just (PubMed 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 "epo" = Just EPO
+dbFromInputValue "epo" = Just (EPO Nothing Nothing)
 dbFromInputValue "empty" = Just Empty
 dbFromInputValue _ = Nothing
 
@@ -252,6 +253,9 @@ instance Read Org where
   read _ = Nothing
 
 derive instance Eq Org
+-- | NOTE: IMT_org list isn't really used here in JSON
+-- | encoding. Instead, for HAL, a special query is constructed in
+-- | SearchField (queryHAL function).
 instance JSON.WriteForeign Org where
   writeImpl = JSON.writeImpl <<< show
 
@@ -294,8 +298,7 @@ instance Show SearchOrder where
 
 newtype SearchQuery = SearchQuery
   { query :: String
-  , databases :: Database
-  , datafield :: Maybe DataField
+  , datafield :: DataField
   , files_id :: Array String
   , lang :: Maybe Lang
   , limit :: Maybe Int
@@ -304,7 +307,6 @@ newtype SearchQuery = SearchQuery
   , order :: Maybe SearchOrder
   , epoAPIUser :: Maybe String
   , epoAPIToken :: Maybe String
-  , pubmedAPIKey :: Maybe String
   , selection :: ListSelection.Selection
   }
 
@@ -329,34 +331,29 @@ instance GT.ToQuery SearchQuery where
 instance JSON.WriteForeign SearchQuery where
   writeImpl
     ( SearchQuery
-        { databases
-        , datafield
+        { datafield
         , lang
         , node_id
         , epoAPIUser
         , epoAPIToken
-        , 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
       , epoAPIUser
       , epoAPIToken
-      , pubmedAPIKey
       }
 
 defaultSearchQuery :: SearchQuery
 defaultSearchQuery = SearchQuery
   { query: ""
-  , databases: Empty
-  , datafield: Nothing
+  , datafield: External Empty
   , files_id: []
   , lang: Nothing
   , limit: Nothing
@@ -365,7 +362,6 @@ defaultSearchQuery = SearchQuery
   , order: Nothing
   , epoAPIUser: Nothing
   , epoAPIToken: Nothing
-  , pubmedAPIKey: Nothing
   , selection: ListSelection.NoList -- MyListsFirst
   }
 

src/Gargantext/Context/Progress.purs

@@ -68,8 +68,7 @@ asyncProgressCpt = R2.hereComponent here "asyncProgress" hCpt
 
         here.log "[onProgress] TODO: Implement status killed"
         if
-          GT.asyncTaskLogIsFinished atl ||
-            GT.asyncTaskLogIsError atl then do
+          GT.asyncTaskLogIsFinished atl then do
           handleErrorInAsyncTaskLog errors atl
           -- resetInterval intervalIdRef Nothing (pure unit)
           onFinish unit