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/SearchField.purs

@@ -36,12 +36,8 @@ here = R2.here "Gargantext.Components.Forest.Tree.Node.Action.Search.SearchField
 
 defaultSearch :: Search
 defaultSearch =
-  { databases: Empty
-  , datafield: Just (External Empty)
+  { datafield: External Empty
   , node_id: Nothing
-  , epoApiUser: Nothing
-  , epoApiToken: Nothing
-  , pubmedApiKey: Nothing
   , lang: Nothing
   , term: ""
   , url: ""
@@ -202,93 +198,73 @@ componentCNRSCpt = here.component "componentCNRS" cpt
       --, filterInput fi
       ]
 
-isExternal :: Maybe DataField -> Boolean
-isExternal (Just (External _)) = true
+isExternal :: DataField -> Boolean
+isExternal (External _) = true
 isExternal _ = false
 
-isArxiv :: Maybe DataField -> Boolean
-isArxiv
-  ( Just
-      (External Arxiv)
-  ) = true
+isArxiv :: DataField -> Boolean
+isArxiv (External Arxiv) = true
 isArxiv _ = false
 
-isHAL :: Maybe DataField -> Boolean
-isHAL
-  ( Just
-      (External (HAL _))
-  ) = true
+isHAL :: DataField -> Boolean
+isHAL (External (HAL _)) = true
 isHAL _ = false
 
-isIsTex :: Maybe DataField -> Boolean
-isIsTex
-  ( Just
-      (External (IsTex))
-  ) = true
+isIsTex :: DataField -> Boolean
+isIsTex (External (IsTex)) = true
 isIsTex _ = false
 
-isIMT :: Maybe DataField -> Boolean
+isIMT :: DataField -> Boolean
 isIMT
-  ( Just
-      ( External
-          ( HAL
-              (Just (IMT _))
-          )
+  ( External
+      ( HAL
+          (Just (IMT _))
       )
   ) = true
 isIMT _ = false
 
-isCNRS :: Maybe DataField -> Boolean
+isCNRS :: DataField -> Boolean
 isCNRS
-  ( Just
-      ( External
-          ( HAL
-              (Just (CNRS _))
-          )
+  ( External
+      ( HAL
+          (Just (CNRS _))
       )
   ) = true
 isCNRS _ = false
 
-isPubmed :: Maybe DataField -> Boolean
-isPubmed
-  ( Just
-      (External PubMed)
-  ) = true
+isPubmed :: DataField -> Boolean
+isPubmed (External (PubMed _)) = true
 isPubmed _ = false
 
-isEPO :: Maybe DataField -> Boolean
-isEPO
-  ( Just
-      (External EPO)
-  ) = true
+getPubmedAPIKey :: DataField -> Maybe String
+getPubmedAPIKey (External (PubMed mAPI)) = mAPI
+getPubmedAPIKey _ = Nothing
+
+isEPO :: DataField -> Boolean
+isEPO (External (EPO _ _)) = true
 isEPO _ = false
 
-needsLang :: Maybe DataField -> Boolean
-needsLang (Just Gargantext) = true
-needsLang (Just Web) = true
-needsLang
-  ( Just
-      (External (HAL _))
-  ) = true
+needsLang :: DataField -> Boolean
+needsLang Gargantext = true
+needsLang Web = true
+needsLang (External (HAL _)) = true
 needsLang _ = false
 
-isIn :: IMT_org -> Maybe DataField -> Boolean
+isIn :: IMT_org -> DataField -> Boolean
 isIn
   org
-  ( Just
-      ( External
-          ( HAL
-              ( Just
-                  (IMT imtOrgs)
-              )
+  ( External
+      ( 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 (HAL (Just (IMT imtOrgs))))) =
-  Just $ External $ HAL $ Just $ IMT imtOrgs'
+updateFilter :: IMT_org -> Array IMT_org -> DataField -> DataField
+updateFilter org allIMTorgs (External (HAL (Just (IMT imtOrgs)))) =
+  External $ HAL $ Just $ IMT imtOrgs'
   where
   imtOrgs' =
     if Set.member org imtOrgs then
@@ -297,7 +273,7 @@ updateFilter org allIMTorgs (Just (External (HAL (Just (IMT imtOrgs))))) =
     else if org == All_IMT then Set.fromFoldable allIMTorgs
     else Set.insert org imtOrgs
 
-updateFilter org allIMTorgs _ = (Just (External (HAL (Just (IMT imtOrgs')))))
+updateFilter org allIMTorgs _ = (External (HAL (Just (IMT imtOrgs'))))
   where
   imtOrgs' =
     if org == All_IMT then Set.fromFoldable allIMTorgs
@@ -350,8 +326,7 @@ dataFieldNavCpt = here.component "dataFieldNav" cpt
       [ H.div { className: "text-primary text-bold p-1" } [ H.text "Search options:" ]
       , H.div { className: "nav nav-tabs" } ((liItem search') <$> dataFields)
       , H.div { className: "center p-1" }
-          [ H.text
-              $ maybe "TODO: add Doc Instance" doc datafield
+          [ H.text $ doc datafield
           ]
       ]
     where
@@ -366,8 +341,7 @@ dataFieldNavCpt = here.component "dataFieldNav" cpt
         , on:
             { click: \_ -> T.modify_
                 ( _
-                    { datafield = Just df'
-                    , databases = datafield2database df'
+                    { datafield = df'
                     }
                 )
                 search
@@ -401,7 +375,7 @@ databaseInputCpt = here.component "databaseInput" cpt
 
     let
       db = case search'.datafield of
-        (Just (External x)) -> Just x
+        (External x) -> Just x
         _ -> Nothing
 
       dbInputValue = fromMaybe "" $ dbToInputValue <$> db
@@ -420,8 +394,7 @@ databaseInputCpt = here.component "databaseInput" cpt
 
         T.modify_
           ( _
-              { datafield = Just $ External updatedValue
-              , databases = updatedValue
+              { datafield = External updatedValue
               }
           )
           search
@@ -477,15 +450,16 @@ pubmedInputLoadedCpt = here.component "pubmedInputLoaded" cpt
     search' <- T.useLive T.unequal search
 
     R.useEffectOnce' $ do
-      when (search'.pubmedApiKey /= pubmedAPIKey) $ do
-        T.write_ (search' { pubmedApiKey = pubmedAPIKey }) search
+      when (getPubmedAPIKey search'.datafield /= pubmedAPIKey) $ do
+        T.modify_ (\s -> s { datafield = External $ PubMed pubmedAPIKey }) search
+    -- T.write_ (search' { pubmedApiKey = pubmedAPIKey }) search
 
     pure $
       H.div { className: "form-group p-1 m-0" }
         [ H.div { className: "text-primary center" } [ H.text "Pubmed API key" ]
         , H.input
             { className: "form-control"
-            , defaultValue: fromMaybe "" search'.pubmedApiKey
+            , defaultValue: fromMaybe "" pubmedAPIKey
             , on:
                 { blur: modifyPubmedAPIKey search
                 , change: modifyPubmedAPIKey search
@@ -502,7 +476,7 @@ pubmedInputLoadedCpt = here.component "pubmedInputLoaded" cpt
           s -> Just s
       T.modify_
         ( \s ->
-            s { pubmedApiKey = mVal }
+            s { datafield = External $ PubMed mVal }
         )
         searchS
 
@@ -537,6 +511,14 @@ type EPOInputLoadedProps =
   , search :: T.Box Search
   )
 
+searchEPOAPIUser :: Search -> Maybe String
+searchEPOAPIUser { datafield: External (EPO mAPIUser _) } = mAPIUser
+searchEPOAPIUser _ = Nothing
+
+searchEPOAPIToken :: Search -> Maybe String
+searchEPOAPIToken { datafield: External (EPO _ mAPIToken) } = mAPIToken
+searchEPOAPIToken _ = Nothing
+
 epoInputLoaded :: R2.Component EPOInputLoadedProps
 epoInputLoaded = R.createElement epoInputLoadedCpt
 
@@ -547,11 +529,10 @@ epoInputLoadedCpt = here.component "epoInputLoaded" cpt
     search' <- T.useLive T.unequal search
 
     R.useEffectOnce' $ do
-      when (search'.epoApiUser /= epoAPIUser || search'.epoApiToken /= epoAPIToken) $ do
+      when (searchEPOAPIUser search' /= epoAPIUser || searchEPOAPIToken search' /= epoAPIToken) $ do
         T.write_
           ( search'
-              { epoApiUser = epoAPIUser
-              , epoApiToken = epoAPIToken
+              { datafield = External (EPO epoAPIUser epoAPIToken)
               }
           )
           search
@@ -561,7 +542,7 @@ epoInputLoadedCpt = here.component "epoInputLoaded" cpt
         [ H.div { className: "text-primary center" } [ H.text "EPO API User" ]
         , H.input
             { className: "form-control"
-            , defaultValue: fromMaybe "" search'.epoApiUser
+            , defaultValue: fromMaybe "" $ searchEPOAPIUser search'
             , on:
                 { blur: modifyEPOAPIUser search
                 , change: modifyEPOAPIUser search
@@ -571,7 +552,7 @@ epoInputLoadedCpt = here.component "epoInputLoaded" cpt
         , H.div { className: "text-primary center" } [ H.text "EPO API Token" ]
         , H.input
             { className: "form-control"
-            , defaultValue: fromMaybe "" search'.epoApiToken
+            , defaultValue: fromMaybe "" $ searchEPOAPIToken search'
             , on:
                 { blur: modifyEPOAPIToken search
                 , change: modifyEPOAPIToken search
@@ -586,7 +567,7 @@ epoInputLoadedCpt = here.component "epoInputLoaded" cpt
         mVal = case val of
           "" -> Nothing
           s -> Just s
-      T.modify_ (\s -> s { epoApiUser = mVal }) searchS
+      T.modify_ (\s -> s { datafield = External (EPO mVal (searchEPOAPIToken s)) }) searchS
 
     modifyEPOAPIToken searchS e = do
       let val = R.unsafeEventValue e
@@ -594,7 +575,7 @@ epoInputLoadedCpt = here.component "epoInputLoaded" cpt
         mVal = case val of
           "" -> Nothing
           s -> Just s
-      T.modify_ (\s -> s { epoApiToken = mVal }) searchS
+      T.modify_ (\s -> s { datafield = External (EPO (searchEPOAPIUser s) mVal) }) searchS
 
 type OrgInputProps =
   ( orgs :: Array Org
@@ -611,7 +592,7 @@ orgInputCpt = here.component "orgInput" cpt
     let
       change e = do
         let value = R.unsafeEventValue e
-        T.modify_ (_ { datafield = Just $ External $ HAL $ read value }) search
+        T.modify_ (_ { datafield = External $ HAL $ read value }) search
 
     pure $ H.div { className: "form-group p-1 m-0" }
       [ H.div { className: "text-primary center" } [ H.text "filter with organization: " ]
@@ -685,7 +666,7 @@ datafieldInputCpt = here.component "datafieldInput" cpt
         else H.div {} []
 
       , if needsLang search'.datafield then
-          if search'.datafield == Just Web then
+          if search'.datafield == Web then
             langNav { langs: A.filter (\lang -> lang == FR) langs, search } []
           else
             langNav { langs, search } []
@@ -818,19 +799,10 @@ triggerSearch { onSearch, errors, session, selection, search } =
 --  modalShow "addCorpus"
 
 searchQuery :: ListSelection.Selection -> Search -> SearchQuery
-searchQuery selection { datafield: Nothing, term } =
-  over SearchQuery
-    ( _
-        { query = term
-        , selection = selection
-        }
-    )
-    defaultSearchQuery
 -- TODO Simplify both HAL Nothing and HAL (Just IMT) cases
 searchQuery
   selection
-  { databases
-  , datafield: datafield@(Just (External (HAL Nothing)))
+  { datafield: datafield@(External (HAL Nothing))
   , lang
   , node_id
   , term
@@ -838,8 +810,7 @@ searchQuery
   } =
   over SearchQuery
     ( _
-        { databases = databases
-        , datafield = datafield
+        { datafield = datafield
         , lang = lang
         , node_id = node_id
         , query = queryHAL term Nothing lang years
@@ -850,8 +821,7 @@ searchQuery
 
 searchQuery
   selection
-  { databases
-  , datafield: datafield@(Just (External (HAL (Just (IMT imtOrgs)))))
+  { datafield: datafield@(External (HAL (Just (IMT imtOrgs))))
   , lang
   , node_id
   , term
@@ -859,8 +829,7 @@ searchQuery
   } =
   over SearchQuery
     ( _
-        { databases = databases
-        , datafield = datafield
+        { datafield = datafield
         , lang = lang
         , node_id = node_id
         , query = queryHAL term (Just imtOrgs) lang years
@@ -868,55 +837,10 @@ searchQuery
         }
     )
     defaultSearchQuery
-searchQuery
-  selection
-  { databases
-  , datafield: datafield@(Just (External EPO))
-  , lang
-  , epoApiUser
-  , epoApiToken
-  , node_id
-  , term
-  } =
-  over SearchQuery
-    ( _
-        { databases = databases
-        , datafield = datafield
-        , lang = lang
-        , node_id = node_id
-        , epoAPIUser = epoApiUser
-        , epoAPIToken = epoApiToken
-        , query = term
-        , selection = selection
-        }
-    )
-    defaultSearchQuery
-searchQuery
-  selection
-  { databases
-  , datafield: datafield@(Just (External PubMed))
-  , lang
-  , pubmedApiKey
-  , node_id
-  , term
-  } =
-  over SearchQuery
-    ( _
-        { databases = databases
-        , datafield = datafield
-        , lang = lang
-        , node_id = node_id
-        , pubmedAPIKey = pubmedApiKey
-        , query = term
-        , selection = selection
-        }
-    )
-    defaultSearchQuery
-searchQuery selection { databases, datafield, lang, term, node_id } =
+searchQuery selection { datafield, lang, term, node_id } =
   over SearchQuery
     ( _
-        { databases = databases
-        , datafield = datafield
+        { datafield = datafield
         , lang = lang
         , node_id = node_id
         , query = term

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