Merge remote-tracking branch 'upstream/master' into oai_pmh_ingestors

Author: eilmiv

.github/workflows/codeql-analysis.yml

@@ -42,7 +42,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v3
+      uses: github/codeql-action/init@v4
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -53,7 +53,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v3
+      uses: github/codeql-action/autobuild@v4
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 https://git.io/JvXDl
@@ -67,4 +67,4 @@ jobs:
     #   make release
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v3
+      uses: github/codeql-action/analyze@v4

.github/workflows/deployment-checks.yml

@@ -12,17 +12,32 @@ jobs:
       DB_PASSWORD: password
       SECRET_BASE_KEY: test_key
       RAILS_ENV: production
+    services:
+      postgres:
+        image: postgres
+        env:
+          POSTGRES_DB: ${{ env.DB_NAME }}
+          POSTGRES_USER: ${{ env.DB_USER }}
+          POSTGRES_PASSWORD: ${{ env.DB_PASSWORD }}
+        ports:
+          - 5432:5432
+        options: >-
+          --health-cmd "pg_isready"
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+      redis:
+        image: redis
+        options: >-
+          --health-cmd "redis-cli ping"
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        ports:
+          - 6379:6379
     steps:
-      - uses: harmon758/postgresql-action@v1
-        with:
-          postgresql db: ${DB_NAME}
-          postgresql user: ${DB_USER}
-          postgresql password: ${DB_PASSWORD}
-        name: Set up database
-
       - uses: actions/checkout@v4
         name: Set up Ruby
-
       - uses: ruby/setup-ruby@v1
         with:
           bundler-cache: true

.github/workflows/test.yml

@@ -12,23 +12,35 @@ jobs:
       DB_PASSWORD: password
       SECRET_BASE_KEY: test_key
       RAILS_ENV: test
-      REDIS_TEST_URL: redis://localhost:6456/0
+      REDIS_TEST_URL: redis://localhost:6379/0
+    services:
+      postgres:
+        image: postgres
+        env:
+          POSTGRES_DB: ${{ env.DB_NAME }}
+          POSTGRES_USER: ${{ env.DB_USER }}
+          POSTGRES_PASSWORD: ${{ env.DB_PASSWORD }}
+        ports:
+          - 5432:5432
+        options: >-
+          --health-cmd "pg_isready"
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+      redis:
+        image: redis
+        options: >-
+          --health-cmd "redis-cli ping"
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        ports:
+          - 6379:6379
     steps:
       - name: Install system dependencies
         run: |
           sudo apt-get update
           sudo apt-get install imagemagick
-      - name: Set up database
-        uses: harmon758/postgresql-action@v1
-        with:
-          postgresql db: ${DB_NAME}
-          postgresql user: ${DB_USER}
-          postgresql password: ${DB_PASSWORD}
-      - name: Set up Redis
-        uses: supercharge/redis-github-action@1.5.0
-        with:
-          redis-version: 6
-          redis-port: 6456
       - name: Check out code
         uses: actions/checkout@v4
       - name: Install Ruby & gems

Gemfile.lock

@@ -233,7 +233,8 @@ GEM
     http-accept (1.7.0)
     http-cookie (1.0.5)
       domain_name (~> 0.5)
-    httparty (0.21.0)
+    httparty (0.24.0)
+      csv
       mini_mime (>= 1.0.0)
       multi_xml (>= 0.5.2)
     i18n (1.14.7)
@@ -376,7 +377,8 @@ GEM
       railties (>= 3.0)
     msgpack (1.7.2)
     multi_json (1.17.0)
-    multi_xml (0.6.0)
+    multi_xml (0.8.0)
+      bigdecimal (>= 3.1, < 5)
     multipart-post (2.4.1)
     nested_form (0.3.2)
     net-http (0.6.0)
@@ -778,7 +780,7 @@ GEM
     unf_ext (0.0.8.2)
     unicode-display_width (2.4.2)
     unicode-types (1.10.0)
-    uri (1.0.3)
+    uri (1.0.4)
     useragent (0.16.11)
     validate_email (0.1.6)
       activemodel (>= 3.0)

app/assets/images/ORCID-iD_icon_unauth_vector.svg

@@ -17,7 +17,6 @@
 //= require bootstrap-tab-history
 //= require cytoscape
 //= require cytoscape-panzoom
-//= require jscolor
 //= require jquery.simplecolorpicker.js
 //= require split
 //= require handlebars.runtime
@@ -41,36 +40,41 @@
 //= require ol
 //= require ol-geocoder
 
-function redirect_to_sort_url(){
-    url = new URL(window.location.href);
-    url.searchParams.set(
-        "sort",
-        $("#sort").find(":selected").val()
-    );
-    window.location.replace(url.toString());
-}
-
-function redirect_with_updated_search(param, paramVal) {
-    url = new URL(window.location.href);
-    // special case for empty range types
-    if (param == 'start' && paramVal == '/') {
-        url.searchParams.delete(param);
-    } else {
-        url.searchParams.set(param, paramVal);
-    }
-    window.location.replace(url.toString());
-}
+const Index = {
+    applySorting: function () {
+        Index.setParam("sort", $("#sort").val());
+    },
 
-function reposition_tiles(container, tileClass){
-    var $container = $("." + container);
+    applyPerPage: function () {
+        Index.setParam("per_page", $("#per_page").val());
+    },
 
-    $container.imagesLoaded(function () {
-        $container.masonry({
-            // options...
-            itemSelector: "." + tileClass,
-            columnWidth: 20
+    applyDateParam: function (param, value) {
+        const url = new URL(window.location.href);
+        if (param === 'start' && value === '/') {
+            url.searchParams.delete(param);
+        } else {
+            url.searchParams.set(param, value);
+        }
+        window.location.replace(url.toString());
+    },
+
+    setParam: function (param, value) {
+        const url = new URL(window.location.href);
+        url.searchParams.set(param, value);
+        window.location.replace(url.toString());
+    },
+
+    repositionTiles(containerSelector, itemSelector) {
+        const container = $(containerSelector);
+        container.imagesLoaded(function () {
+            container.masonry({
+                // options...
+                itemSelector: itemSelector,
+                columnWidth: 20
+            });
         });
-    });
+    }
 }
 
 // Perform an ajax request to load the calendar and replace the contents
@@ -152,7 +156,7 @@ document.addEventListener("turbolinks:load", function(e) {
     $('a[data-toggle="tab"]').on('shown.bs.tab', function (e) {
         addTabToFilters(e.target.href.split('#').pop());
         // and reposition masonry tiles
-        reposition_tiles('masonry', 'masonry-brick');
+        Index.repositionTiles('.masonry', '.masonry-brick');
     });
 
     // Manually trigger bootstrap tab history (we should probably remove the dependency and reimplement in a turbolink-compatible way)
@@ -168,12 +172,14 @@ document.addEventListener("turbolinks:load", function(e) {
 
     // Masonry
     $(".nav-tabs a").on("shown.bs.tab", function(e) {
-        reposition_tiles('masonry', 'masonry-brick');
+        Index.repositionTiles('.masonry', '.masonry-brick');
     });
+
     $(window).on("orientationchange", function() {
-        reposition_tiles("masonry", "masonry-brick");
+        Index.repositionTiles('.masonry', '.masonry-brick');
     });
-    reposition_tiles("masonry", "masonry-brick");
+
+    Index.repositionTiles('.masonry', '.masonry-brick');
 
     new Clipboard(".clipboard-btn");
 

app/assets/images/ORCID-iD_icon_vector.svg

@@ -192,9 +192,9 @@ var Workflows = {
             $('#node-modal-form-title').val(data.name);
             $('#node-modal-form-description').val(data.description);
             if (data.color) {
-                $('#node-modal-form-colour')[0].jscolor.fromString(data.color);
+                $('#node-modal-form-colour').val(data.color);
             } else if (data.parent) {
-                $('#node-modal-form-colour')[0].jscolor.fromString(cy.$('#' + data.parent).data('color'));
+                $('#node-modal-form-colour').val(cy.$('#' + data.parent).data('color'));
             }
             $('#node-modal-form-parent-id').val(data.parent);
             $('#node-modal-form-x').val(position.x);
@@ -211,7 +211,7 @@ var Workflows = {
                     description: $('#node-modal-form-description').val(),
                     html_description: MarkdownIt.render($('#node-modal-form-description').val()),
                     color: $('#node-modal-form-colour').val(),
-                    font_color: $('#node-modal-form-colour').css("color"),
+                    font_color: Workflows.getTextColor($('#node-modal-form-colour').val()),
                     parent: $('#node-modal-form-parent-id').val(),
                     associatedResources: Workflows.associatedResources.fetch(),
                     ontologyTerms: Workflows.ontologyTerms.fetch()
@@ -470,6 +470,21 @@ var Workflows = {
                 );
             }
         }
+    },
+    getTextColor: function (hex) {
+        // Remove the leading '#', if present
+        hex = hex.replace('#', '');
+
+        // Parse r, g, b values
+        const r = parseInt(hex.substring(0, 2), 16);
+        const g = parseInt(hex.substring(2, 4), 16);
+        const b = parseInt(hex.substring(4, 6), 16);
+
+        // Calculate perceived brightness (luminance)
+        const brightness = (0.299 * r) + (0.587 * g) + (0.114 * b);
+
+        // Threshold of ~186 is a common practical cutoff
+        return brightness > 186 ? '#000000' : '#FFFFFF';
     }
 };
 
@@ -621,7 +636,6 @@ document.addEventListener("turbolinks:load", function() {
             // Initialize
             Workflows.cancelState();
             Workflows.history.initialize();
-            jscolor.installByClassName('jscolor');
         } else {
             // Hiding/revealing of child nodes
             if(hideChildNodes) {

app/assets/javascripts/application.js

@@ -18,7 +18,32 @@
 @import "font-awesome-sprockets";
 @import "font-awesome";
 @import "mixins/mixins";
-@import "*";
+
+// Local
+@import "about";
+@import "account";
+@import "activities";
+@import "autocomplete";
+@import "bootstrap-tweaks";
+@import "collaborations";
+@import "collection";
+@import "curators";
+@import "events";
+@import "external-resources";
+@import "footer";
+@import "forms";
+@import "headers";
+@import "helpers";
+@import "home";
+@import "icons";
+@import "learning-paths";
+@import "masonry";
+@import "nodes";
+@import "showcase";
+@import "toggle";
+@import "workflows";
+
+// Vendor
 @import "cytoscape-panzoom";
 @import "jquery.simplecolorpicker";
 @import "eonasdan-bootstrap-datetimepicker";
@@ -393,10 +418,21 @@ ul.unstyled {
 }
 
 .search-results-count {
-  margin-right: 5px;
+  margin-right: 1em;
   display: inline-block
 }
 
+.search-results-per-page {
+  display: inline-block;
+
+  select {
+    border: none;
+    padding: 0;
+    background: transparent;
+    border-bottom: 1px dashed $text-color;
+  }
+}
+
 .index-display-options {
   margin: 5px 0;
 }
@@ -1047,4 +1083,30 @@ td.day .calendar-text {
       top: 0;
     }
   }
-}
+}
+
+.theme-selector {
+  display: flex;
+  gap: 10px;
+}
+
+.theme-select-option {
+  flex-grow: 1;
+  label {
+    border: 5px solid;
+    padding: 10px 20px;
+    border-radius: 5px;
+    display: block;
+
+    hr {
+      border-width: 10px;
+    }
+  }
+}
+.btn-oidc-only {
+  font-size: 36px;
+  padding: 4px;
+  margin: 12px 10px;
+  display: flex;
+  justify-content: center;
+}