Merge branch 'dev' into 698-dev-ws-host-fix

.gitlab-ci.yml

 # Fixing the nixos image saves CI time so it doesn't have to pull new
 #image every time (nixos/nix updates quite often).
 # image: nixos/nix:latest
-image: nixos/nix:2.22.0
+image: nixos/nix:2.24.8
 
 #before_script:
   #- nix-env -iA nixpkgs.nix nixpkgs.cacert
@@ -32,6 +32,7 @@ compile:
       - .spago/
     
   script:
+    - nix --extra-experimental-features "nix-command flakes" run .#ci
     - nix --extra-experimental-features "nix-command flakes" run .#compile
 
 test:
@@ -46,6 +47,7 @@ test:
       - .spago/
     
   script:
+    - nix --extra-experimental-features "nix-command flakes" run .#compile
     - nix --extra-experimental-features "nix-command flakes" run .#test-ps
     
     - nix-collect-garbage --delete-older-than 14d

bin/install

@@ -8,5 +8,11 @@
 # nix-shell --show-trace --option build-fallback true --run 'bun install'
 # nix-shell --show-trace --option build-fallback true --run fix-bun
 # nix-shell --show-trace --option build-fallback true --run build
-#nix run .#install
+nix run .#install
 nix run .#build
+nix run .#build-css
+# nix-shell --run "npm run css-default-theme"
+# nix-shell --run "npm run css-dark-theme"
+# nix-shell --run "npm run css-herbie-theme"
+# nix-shell --run "npm run css-monotony-theme"
+# nix-shell --run "npm run css-greyson-theme"

default.nix

-with (import <nixpkgs> {});
-let
-  nodejs-with-packages = with nodePackages; [
-    bower
-    yarn
-  ]; in
-stdenv.mkDerivation rec {
-  name = "env";
-  env = buildEnv {
-    name = name;
-    paths = buildInputs;
-  };
-  buildInputs = [
-    nodejs-with-packages
-    yarn
-    yarn2nix
-  ];
-  builder = builtins.toFile "builder.sh" ''
-    source $stdenv/setup
-    touch $out
-  '';
-}

flake.lock

@@ -21,11 +21,11 @@
         "systems": "systems"
       },
       "locked": {
-        "lastModified": 1710146030,
-        "narHash": "sha256-SZ5L6eA7HJ/nmkzGG7/ISclqe6oZdOZTNoesiInkXPQ=",
+        "lastModified": 1726560853,
+        "narHash": "sha256-X6rJYSESBVr3hBoH0WbKE5KvhPU5bloyZ2L4K60/fPQ=",
         "owner": "numtide",
         "repo": "flake-utils",
-        "rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a",
+        "rev": "c1dfcf08411b08f6b8615f7d8971a2bfa81d5e8a",
         "type": "github"
       },
       "original": {
@@ -36,15 +36,16 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1701282334,
-        "narHash": "sha256-MxCVrXY6v4QmfTwIysjjaX0XUhqBbxTWWB4HXtDYsdk=",
+        "lastModified": 1717179513,
+        "narHash": "sha256-vboIEwIQojofItm2xGCdZCzW96U85l9nDW3ifMuAIdM=",
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "057f9aecfb71c4437d2b27d3323df7f93c010b7e",
+        "rev": "63dacb46bf939521bdc93981b4cbb7ecb58427a0",
         "type": "github"
       },
       "original": {
         "owner": "NixOS",
+        "ref": "24.05",
         "repo": "nixpkgs",
         "type": "github"
       }
@@ -58,11 +59,11 @@
         "slimlock": "slimlock"
       },
       "locked": {
-        "lastModified": 1720786645,
-        "narHash": "sha256-eiuWqQ9xTA2E76XDg13TQBecnLV1g+ahdauC0FYSD7U=",
+        "lastModified": 1727269424,
+        "narHash": "sha256-uoVjAkKbuJSA7++kyBjxLozICDdukZ+Mjj5Z/K5qMak=",
         "owner": "thomashoneyman",
         "repo": "purescript-overlay",
-        "rev": "c46925ec09fdf54b5bb4ba38b40e19918d3be7be",
+        "rev": "5a28abe663758634b1e5ca7053e08af62fd3be80",
         "type": "github"
       },
       "original": {

flake.nix

@@ -3,7 +3,7 @@
 
   inputs.flake-utils.url = "github:numtide/flake-utils";
 
-  inputs.nixpkgs.url = "github:NixOS/nixpkgs";
+  inputs.nixpkgs.url = "github:NixOS/nixpkgs?ref=24.05";
 
   inputs.purescript-overlay = {
     url = "github:thomashoneyman/purescript-overlay";
@@ -24,6 +24,7 @@
           spago-bin.spago-0_93_37
           #purescript
           #spago-unstable
+          esbuild
           nodejs
           nodePackages.npm
         ];
@@ -59,13 +60,37 @@
       in
         {
           packages = rec {
+            ci = pkgs.writeShellApplication {
+              name = "install";
+              runtimeInputs = dependencies;
+              text = ''
+              set -e
+
+              echo "Installing JS Dependencies (CI)"
+              # https://docs.npmjs.com/cli/v9/commands/npm-ci
+              npm ci
+              '';
+            };
+            install = pkgs.writeShellApplication {
+              name = "install";
+              runtimeInputs = dependencies;
+              text = ''
+              set -e
+
+              echo "Installing JS Dependencies"
+              npm install
+              # https://docs.npmjs.com/cli/v9/commands/npm-ci
+              #npm ci
+              #npm/bin/npm install --dev
+              '';
+            };
             compile = pkgs.writeShellApplication {
               name = "compile";
               runtimeInputs = dependencies;
               text = ''
               set -e
 
-              echo "Installing JS Dependencies"
+              #echo "Installing JS Dependencies"
               #npm install
               # https://docs.npmjs.com/cli/v9/commands/npm-ci
               #npm ci

package.json

 {
   "name": "Gargantext",
-  "version": "0.0.7.2.8",
+  "version": "0.0.7.3.1",
   "scripts": {
     "build": "spago build",
     "bundle": "spago bundle --module Main --outfile dist/bundle.min.js --minify --source-maps",
-    "css": "$npm_execpath css-themes",
-    "css-themes": "$npm_execpath css-default-theme && $npm_execpath css-dark-theme && $npm_execpath css-darkster-theme && $npm_execpath css-greyson-theme && $npm_execpath css-herbie-theme && $npm_execpath css-monotony-theme",
+    "css": "$npm_execpath run css-themes",
+    "css-themes": "$npm_execpath run css-default-theme && $npm_execpath run css-dark-theme && $npm_execpath run css-darkster-theme && $npm_execpath run css-greyson-theme && $npm_execpath run css-herbie-theme && $npm_execpath run css-monotony-theme",
     "css-default-theme": "sass src/sass/themes/default.scss:dist/styles/bootstrap-default.css",
     "css-dark-theme": "cp node_modules/bootstrap-dark/src/bootstrap-dark.css dist/styles/bootstrap-dark.css",
     "css-darkster-theme": "sass src/sass/themes/darkster.scss:dist/styles/bootstrap-darkster.css",

spago.lock

@@ -82,6 +82,7 @@ workspace:
         - unordered-collections: ">=3.1.0 <4.0.0"
         - unsafe-coerce: ">=6.0.0 <7.0.0"
         - uri: ">=9.0.0 <10.0.0"
+        - url-validator
         - uuid: ">=9.0.0 <10.0.0"
         - validation: ">=6.0.0 <7.0.0"
         - var
@@ -228,6 +229,7 @@ workspace:
         - unsafe-coerce
         - unsafe-reference
         - uri
+        - url-validator
         - uuid
         - validation
         - var
@@ -768,6 +770,9 @@ workspace:
     tuples-native:
       git: https://github.com/garganscript/purescript-tuples-native.git
       ref: v2.3.0-spago-next
+    url-validator:
+      git: https://github.com/bbarker/purescript-url-validator
+      ref: master
     var:
       git: https://github.com/garganscript/purescript-var
       ref: v3.0.1-spago-next
@@ -2295,6 +2300,15 @@ packages:
       - these
       - transformers
       - unfoldable
+  url-validator:
+    type: git
+    url: https://github.com/bbarker/purescript-url-validator
+    rev: 3514fc80cc277c44dc5b5bd30898f4a866bf6795
+    dependencies:
+      - either
+      - maybe
+      - prelude
+      - strings
   uuid:
     type: registry
     version: 9.0.0

spago.yaml

@@ -37,6 +37,11 @@ workspace:
       git: https://github.com/garganscript/purescript-websocket-simple
       ref: v3.0.2-spago-next
 
+    # other external packages
+    url-validator:
+      git: https://github.com/bbarker/purescript-url-validator
+      ref: master
+
     # for tests
     spec-discovery:
       git: https://github.com/purescript-spec/purescript-spec-discovery.git
@@ -125,6 +130,7 @@ package:
     - unordered-collections: ">=3.1.0 <4.0.0"
     - unsafe-coerce: ">=6.0.0 <7.0.0"
     - uri: ">=9.0.0 <10.0.0"
+    - url-validator
     - uuid: ">=9.0.0 <10.0.0"
     - validation: ">=6.0.0 <7.0.0"
     - var

src/Gargantext/Components/Document/Layout.purs

@@ -22,6 +22,7 @@ import Gargantext.Components.NgramsTable.AutoSync (useAutoSync)
 import Gargantext.Components.Node (NodePoly(..))
 import Gargantext.Core.NgramsTable.Functions (addNewNgramA, applyNgramsPatches, coreDispatch, findNgramRoot, setTermListA, computeCache)
 import Gargantext.Core.NgramsTable.Types (CoreAction(..), NgramsTerm, Versioned(..), replace)
+import Gargantext.Hooks.LinkHandler (useLinkHandler)
 import Gargantext.Hooks.Loader (useLoader)
 import Gargantext.Sessions (Session)
 import Gargantext.Utils as U
@@ -29,6 +30,7 @@ import Gargantext.Utils.Reactix as R2
 import Reactix as R
 import Reactix.DOM.HTML as H
 import Record as Record
+import Text.URL.Validate as TUV
 import Toestand as T
 
 -------------------------------------------------------------------------
@@ -91,6 +93,8 @@ layoutWithContextNgramsCpt = here.component "layoutWithContextNgrams" cpt where
     -- | States
     -- |
 
+    { goToURLInNewTab } <- useLinkHandler
+
     contextNgramsS <- T.useBox contextNgrams
     contextNgrams' <- T.useLive T.unequal contextNgramsS
 
@@ -282,83 +286,131 @@ layoutWithContextNgramsCpt = here.component "layoutWithContextNgrams" cpt where
             [
               annotate doc.title
             ]
-          -- ,
-          --   btnSeeMore "title"
           ]
+        ,
+          H.hr {}
         ,
           R2.fromMaybe doc.authors \authors ->
 
             H.div
-            { className: "document-layout__authors justify-content-space-between" }
+            { className: "document-layout__hdata justify-content-space-between" }
             [
               B.div'
-              { className: "document-layout__authors__label" }
+              { className: "document-layout__hdata__label" }
               "Authors"
             ,
-              H.div
-              { className: "document-layout__authors__content w-100" -- <> collapsibleClasses
+              B.div'
+              { className: "document-layout__hdata__content w-100"
               , id: getIdName "authors" }
-              [
-                -- @NOTE #386: annotate for "Authors" ngrams list
-                annotate (Just authors)
-              ]
-            -- ,
-            --   btnSeeMore "authors"
+              authors
             ]
         ,
           R2.fromMaybe doc.source \source ->
 
             H.div
-            { className: "document-layout__source justify-content-space-between" }
+            { className: "document-layout__hdata justify-content-space-between" }
             [
               B.div'
-              { className: "document-layout__source__label" }
+              { className: "document-layout__hdata__label" }
               "Source"
             ,
               B.div'
-              { className: "document-layout__source__content w-100" -- <> collapsibleClasses
+              { className: "document-layout__hdata__content w-100"
               , id: getIdName "sources" }
               source
-            -- ,
-            --   btnSeeMore "sources"
             ]
         ,
             H.div
-            { className: "document-layout__date" }
+            { className: "document-layout__hdata" }
             [
               B.div'
-              { className: "document-layout__date__label" }
+              { className: "document-layout__hdata__label" }
               "Date"
             ,
               B.div'
-              { className: "document-layout__date__content" }
+              { className: "document-layout__hdata__content" }
               (publicationDate $ Document doc)
             ]
-
-        ,  R2.fromMaybe doc.institutes \institutes ->
+        ,  
+          R2.fromMaybe doc.institutes \institutes ->
 
             H.div
-            { className: "document-layout__institutes justify-content-space-between" }
+            { className: "document-layout__hdata justify-content-space-between" }
             [
               B.div'
-              { className: "document-layout__institutes__label" }
+              { className: "document-layout__hdata__label" }
               "Institutes"
             ,
-              H.div
-              { className: "document-layout__institutes__content w-100" -- <> collapsibleClasses
+              B.div'
+              { className: "document-layout__hdata__content w-100"
               , id: getIdName "institutes" }
-              [
-                annotate (Just institutes)
-              ]
+              institutes
             -- ,
             --   btnSeeMore "institutes"
             ]
+        ,
+          R2.fromMaybe doc.doi \doi ->
 
-        , case path.mCorpusId of
-            Nothing -> H.div {} []
-            Just corpusId -> ratingSimpleLoader { docId: path.nodeId
-                                                , corpusId
-                                                , session: path.session  } []
+            H.div
+            { className: "document-layout__hdata justify-content-space-between" }
+            [
+              H.div
+              { className: "document-layout__hdata__label" }
+              [
+                R2.acronym { title: "Digital object identifier" } [ H.text "DOI" ]
+              ]
+            ,
+              H.div
+              { className: "document-layout__hdata__content w-100"
+              , id: getIdName "doi" }
+              [
+                if (TUV.validateURL doi) then
+                  H.a {classname: "", on: { click: goToURLInNewTab $ doi }} 
+                  [ 
+                    H.text doi 
+                  , H.i { className: "fa fa-external-link mx-1 small" } []
+                  ]
+                else
+                  H.text doi
+              ]
+            ]
+        ,
+          R2.fromMaybe doc.bdd \bdd ->
+
+            H.div
+            { className: "document-layout__hdata justify-content-space-between" }
+            [
+              B.div'
+              { className: "document-layout__hdata__label" }
+              "Data source"
+            ,
+              B.div'
+              { className: "document-layout__hdata__content w-100"
+              , id: getIdName "bdd" }
+              bdd
+            ]
+        , 
+          H.div
+            { className: "document-layout__hdata" }
+            [
+              B.div'
+              { className: "document-layout__hdata__label" }
+              "Tag"
+            , 
+              case path.mCorpusId of
+                Nothing -> H.div {} []
+                Just corpusId -> ratingSimpleLoader { docId: path.nodeId
+                                                    , corpusId
+                                                    , session: path.session  } []
+            ]
+
+        -- , case path.mCorpusId of
+        --     Nothing -> H.div {} []
+        --     Just corpusId -> ratingSimpleLoader { docId: path.nodeId
+        --                                         , corpusId
+        --                                         , session: path.session  } []
+        ,
+          H.hr {}
         ,
           R2.when hasAbstract $
 
@@ -390,19 +442,5 @@ publicationDate (Document {publication_year: Just py, publication_month: Nothing
 publicationDate (Document {publication_year: Just py, publication_month: Just pm, publication_day: Nothing}) = (U.zeroPad 2 py) <> "-" <> (U.zeroPad 2 pm)
 publicationDate (Document {publication_year: Just py, publication_month: Just pm, publication_day: Just pd}) = (U.zeroPad 2 py) <> "-" <> (U.zeroPad 2 pm) <> "-" <> (U.zeroPad 2 pd)
 
-
--- btnSeeMore :: String -> R.Element
--- btnSeeMore idStr =
---   H.a { role: "button"
---   , className: "collapsed btn-seemore text-primary"
---   , data: { toggle: "collapse" }
---   , aria: { expanded: false, controls: getIdName idStr }
---   , href: "#" <> getIdName idStr
---   }
---   [ H.text "" ]
-
 getIdName :: String -> String
 getIdName str = "annotated-field-expand__" <> str
-
--- collapsibleClasses :: String
--- collapsibleClasses = " annotated-field-expand collapse"

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

@@ -88,7 +88,7 @@ actionDownloadNodeList = R.createElement actionDownloadNodeListCpt
 actionDownloadNodeListCpt :: R.Component ActionDownload
 actionDownloadNodeListCpt = here.component "actionDownloadNodeList" cpt where
   cpt { id, session } _ = do
-    downloadFormat <- T.useBox NL_JSON_ZIP
+    downloadFormat <- T.useBox NL_JSON
     downloadFormat' <- T.useLive T.unequal downloadFormat
 
     pure $

src/Gargantext/Components/InputWithAutocomplete.purs

@@ -78,6 +78,7 @@ inputWithAutocompleteCpt = here.component "inputWithAutocomplete" cpt
                   , on: { focus: onFocus completions state'
                         , input: onInput completions
                         , change: onInput completions
+                        , keyDown: onInputKeyDown inputRef
                         , keyUp: onInputKeyUp inputRef
                         , blur: onBlur completions containerRef
                         }
@@ -140,7 +141,16 @@ inputWithAutocompleteCpt = here.component "inputWithAutocomplete" cpt
                 R2.blur input
                 pure false
           else
-            pure $ false
+            pure false
+
+        onInputKeyDown :: R.Ref (Nullable DOM.Element) -> DE.KeyboardEvent -> Effect Boolean
+        onInputKeyDown _ e = do
+          if DE.key e == "Enter" then do
+            R2.preventDefault e
+            R2.stopPropagation e
+            pure false
+          else
+            pure false
 
 ---------------------------------------------------------
 

src/Gargantext/Components/NgramsTable.purs

@@ -664,7 +664,7 @@ ngramsTableOrderWith orderBy =
 
 -- This is used to *decorate* the Select header with the checkbox.
 wrapColElts scProps _         (TT.ColumnName "Select") = const [NTSC.selectionCheckbox scProps]
-wrapColElts _       scoreType (TT.ColumnName "Score")  = (_ <> [H.text (" (" <> show scoreType <> ")")])
+wrapColElts _       scoreType (TT.ColumnName "Score")  = (_ <> [H.text (" (occurrences)")])
 wrapColElts _       _         _                        = identity
 
 type MkDispatchProps =

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

@@ -119,5 +119,5 @@ nodeCpt = R2.hereComponent here "node" hCpt where
                   ]
               _ -> H.p
                 { className: "text-center pt-10" }
-                [ H.text "Phylo not generated yet, please update the node settings to see your phylonometry." ]
+                [ H.text "Phylo not generated yet, please update the node settings to see your phylomemy." ]
       }

src/Gargantext/Components/PhyloExplorer/Resources.js

@@ -2062,7 +2062,9 @@ function setGroup(g, xScale, yScale, wScale) {
         fdt    = lines[i].fdt,
         roles  = lines[i].role,
         terms  = mergeLists(words,fdt,roles),
-        toSpan = (acc, w) => acc + "<tspan fdt=" + w[1]
+        toSpan = (acc, w, index) => {
+          let separator = index < terms.length - 1 ? "<tspan class='separator'> | </tspan>" : "";
+          return acc + "<tspan fdt=" + w[1]
                                  + " class='term fdt-" + w[1] + " " + "g-" + g.gId + findRole(w[2]) + "'"
                                  + " gy=" + yScale(g.to)
                                  + " gx=" + xScale(g.x)
@@ -2071,7 +2073,9 @@ function setGroup(g, xScale, yScale, wScale) {
                                  + " gid=" + g.gId
                                  + " bid=" + g.bId
                                  + " from="   + (g.to).getFullYear()
-                                 + ">" + w[0] + "</tspan>";
+                                 + ">" + w[0] + "</tspan>"
+                                 + separator;
+        };
 
     panel
         .append("text")

src/Gargantext/Components/Table.purs

@@ -761,8 +761,8 @@ tableCpt = here.component "table" cpt
             cs =
               wrapColElts c $
               case state.orderBy of
-                Just (ASC d)  | c == d -> [lnk (Just (DESC c)) "ASC " , lnk Nothing (columnName c)]
-                Just (DESC d) | c == d -> [lnk (Just (ASC  c)) "DESC ", lnk Nothing (columnName c)]
+                Just (ASC d)  | c == d -> [lnk (Just (DESC c)) ("ASC " <> (columnName c))]
+                Just (DESC d) | c == d -> [lnk (Just (ASC  c)) ("DESC " <> (columnName c))]
                 _ -> [lnk (Just (ASC c)) (columnName c)]
       pure $ container
         { pageSizeControl: sizeDD { params }

src/Gargantext/Utils/Reactix.purs

@@ -229,6 +229,9 @@ named = flip $ defineProperty "name"
 overState :: forall t. (t -> t) -> R.State t -> Effect Unit
 overState f (_state /\ setState) = setState f
 
+acronym :: ElemFactory
+acronym = createDOM "acronym"
+
 small :: ElemFactory
 small = createDOM "small"
 

src/sass/_legacy/_document.sass

@@ -15,7 +15,7 @@ $document-container-width: 780px
     justify-content: space-between
     padding: $card-spacer-y $card-spacer-x
     border-bottom: 1px solid $border-color
-    margin-bottom: $card-spacer-y
+    // margin-bottom: $card-spacer-y
 
   &__main-controls
     display: flex
@@ -57,41 +57,25 @@ $document-container-width: 780px
     font-weight: bold
     line-height: 1.4
     word-wrap: break-word
-    margin-bottom: space-x(3)
+    // margin-bottom: space-x(3)
     font-family: $headings-font-family
 
-  &__authors
-    display: flex
-    margin-bottom: space-x(0.5)
-
-    &__label
-      font-weight: bold
-      flex-basis: $label-column-size
-      flex-shrink: 0
-      font-size: 15px
-
-    &__content
-      line-height: 1.2
-      color: $gray-800
-
-  &__source,
-  &__institutes,
-  &__date
+  &__hdata
     display: flex
     margin-bottom: space-x(0.5)
+    line-height: 1.3em
+    font-size: 15px
 
     &__label
       font-weight: bold
       flex-basis: $label-column-size
       flex-shrink: 0
-      font-size: 15px
 
     &__content
-      font-size: 15px
       color: $gray-600
 
   &__abstract
-    margin-top: space-x(4)
+    margin-top: space-x(3)
     margin-bottom: space-x(3)
 
     &__content

src/sass/_legacy/_phylo.scss

@@ -209,7 +209,10 @@ $decreasing-color: #11638F;
   .term:hover {
     font-weight: bold;
   }
-
+  .separator {
+    fill: $graph-heading-color;
+  }
+  
   // .term-unfocus {
   //   fill: #A9A9A9;
   // }