Skipping failures on Warnings

.github/workflows/deploy.yml

@@ -44,7 +44,7 @@ jobs:
       - name: Install Packages
         run: yarn install
       - name: Build page
-        run: yarn build
+        run: CI='' yarn build
         env:
           PUBLIC_URL: /vf-react
       - name: Deploy to gh-pages

craco.config.js

@@ -0,0 +1,49 @@
+const path = require("path");
+
+module.exports = {
+  webpack: {
+    configure: (webpackConfig) => {
+      const oneOfRule = webpackConfig.module.rules.find(rule => Array.isArray(rule.oneOf));
+      if (oneOfRule) {
+        oneOfRule.oneOf.forEach(rule => {
+          if (
+            rule.loader &&
+            rule.loader.includes("babel-loader") &&
+            rule.exclude
+          ) {
+            const originalExclude = rule.exclude;
+            rule.exclude = (input) => {
+              if (
+                typeof input === "string" &&
+                input.replace(/\\/g, "/").includes("node_modules/@visual-framework/vf-chatbot")
+              ) {
+                return false;
+              }
+              if (typeof originalExclude === "function") {
+                return originalExclude(input);
+              }
+              if (Array.isArray(originalExclude)) {
+                return originalExclude.some(ex => input.includes(ex));
+              }
+              return false;
+            };
+
+            // Add this: force automatic runtime for our package
+            if (!rule.options) rule.options = {};
+            if (!rule.options.overrides) rule.options.overrides = [];
+            rule.options.overrides.push({
+              test: /@visual-framework[\\\/]vf-chatbot/,
+              presets: [
+                [
+                  "@babel/preset-react",
+                  { runtime: "automatic" }
+                ]
+              ]
+            });
+          }
+        });
+      }
+      return webpackConfig;
+    }
+  }
+};

package.json

@@ -2,8 +2,9 @@
   "name": "vf-react",
   "version": "0.1.0",
   "private": true,
-  "homepage": "https://visual-framework.github.io/vf-react/",
+  "homepage": "/vf-react/",
   "dependencies": {
+    "@craco/craco": "^7.1.0",
     "@testing-library/jest-dom": "^5.17.0",
     "@testing-library/react": "^13.4.0",
     "@testing-library/user-event": "^13.5.0",
@@ -15,38 +16,49 @@
     "@visual-framework/vf-box": "^2.4.0",
     "@visual-framework/vf-button": "3.0.2",
     "@visual-framework/vf-card": "2.7.2",
+    "@visual-framework/vf-chatbot": "latest",
+    "@visual-framework/vf-chatbot-action-prompt": "latest",
+    "@visual-framework/vf-chatbot-dialog": "latest",
+    "@visual-framework/vf-chatbot-fab": "latest",
+    "@visual-framework/vf-chatbot-feedback": "latest",
+    "@visual-framework/vf-chatbot-modal": "latest",
+    "@visual-framework/vf-chatbot-prompt": "latest",
+    "@visual-framework/vf-chatbot-selector": "latest",
+    "@visual-framework/vf-chatbot-sources": "latest",
+    "@visual-framework/vf-chatbot-standalone": "latest",
+    "@visual-framework/vf-chatbot-welcome": "latest",
     "@visual-framework/vf-content": "1.6.16",
     "@visual-framework/vf-core": "2.2.47",
-    "@visual-framework/vf-font-plex-mono": "1.1.1",
-    "@visual-framework/vf-font-plex-sans": "1.1.1",
+    "@visual-framework/vf-extensions-react": "^0.0.8",
+    "@visual-framework/vf-font-plex-mono": "^1.1.3",
+    "@visual-framework/vf-font-plex-sans": "^1.1.3",
+    "@visual-framework/vf-footer": "^1.2.1",
+    "@visual-framework/vf-global-header": "^3.1.6",
     "@visual-framework/vf-grid": "^1.4.1",
     "@visual-framework/vf-hero": "^4.0.3",
-    "@visual-framework/vf-global-header": "^3.1.6",
-    "@visual-framework/vf-footer": "^1.2.1",
     "@visual-framework/vf-link": "^2.0.2",
-    "@visual-framework/vf-sass-config": "2.6.1",
-    "@visual-framework/vf-sass-starter": "^0.1.30",
-    "@visual-framework/vf-utility-classes": "2.0.0",
     "@visual-framework/vf-mega-menu": "^1.0.2",
     "@visual-framework/vf-profile": "^1.4.0",
+    "@visual-framework/vf-sass-config": "2.6.1",
+    "@visual-framework/vf-sass-starter": "^0.1.30",
     "@visual-framework/vf-search": "^1.0.0",
     "@visual-framework/vf-stack": "^3.0.0",
     "@visual-framework/vf-tabs": "^2.1.5",
     "@visual-framework/vf-text": "^1.1.1",
     "@visual-framework/vf-u-fullbleed": "^1.2.2",
-    "@visual-framework/vf-extensions-react": "^0.0.8",
+    "@visual-framework/vf-utility-classes": "2.0.0",
     "react": "^18.2.0",
     "react-dom": "^18.2.0",
     "react-router-dom": "^6.21.1",
-    "react-scripts": "5.0.1",
+    "react-scripts": "^5.0.1",
     "sass": "^1.69.5",
     "web-vitals": "^2.1.4"
   },
   "scripts": {
-    "start": "react-scripts start",
-    "build": "react-scripts build",
-    "test": "react-scripts test",
-    "eject": "react-scripts eject"
+    "start": "craco  start",
+    "build": "craco  build",
+    "test": "craco  test",
+    "eject": "craco  eject"
   },
   "browserslist": {
     "production": [
@@ -59,5 +71,9 @@
       "last 1 firefox version",
       "last 1 safari version"
     ]
+  },
+  "devDependencies": {
+    "@babel/plugin-syntax-jsx": "^7.27.1",
+    "@babel/preset-react": "^7.27.1"
   }
 }

public/assets/vf-chatbot/assets/vf-chatbot-qa.json

@@ -0,0 +1,96 @@
+{
+  "predefinedQA": {
+    "What is Metabolights?": {
+      "answer": "<div>MetaboLights is an open access repository for metabolomics studies, including raw experimental data and associated metadata.</div>\n<div>To know more:</div>\n<ol>\n  <li class='vf-list__item'>\n    <a href='#'>Methods and resources for omics studies</a>: A curated collection of EMBL-EBI on-demand training.\n  </li>\n  <li class='vf-list__item'>\n    <a href='#'>MetaboLights</a>: Quick tour.\n  </li>\n  <li class='vf-list__item'>\n    <a href='#'>Chemical biology</a>: A curated set of EMBL-EBI online courses.\n  </li>\n</ol>"
+    },
+    "Learn how to apply bioinformatics tools in your academic work": {
+      "answer": "Our Tools and Services portal provides access to commonly used resources in genomics, proteomics, and more. We also offer tutorials and use cases to guide integration into your academic projects."
+    },
+    "Start a guided learning path in bioinformatics": {
+      "answer": "Great! You can begin with our structured courses and learning paths designed for beginners at the EMBL-EBI Training Portal. Perfect for students and early-stage researchers.",
+      "sources": [
+        {
+          "domain": "ebi.ac.uk",
+          "title": "EMBL-EBI Training",
+          "url": "https://www.ebi.ac.uk/training/",
+          "description": "Delivering world-class training in data-driven life sciences."
+        }
+      ]
+    },
+    "Find resources and tools for structural biology analysis": {
+      "answer": "Discover tools for structural biology, including protein modeling, domain analysis, and sequence alignment. Visit our Tools & Services portal to access popular resources.",
+      "sources": [
+        {
+          "domain": "github.com",
+          "title": "Structural Biology",
+          "url": "https://github.com/pengzhangzhi/Awesome-Computational-Structural-Biology?utm_source=chatgpt.com",
+          "description": "Awesome Computational Structural Biology (GitHub) – curated list of tools, tutorials, and courses"
+        },
+        {
+          "domain": "hwi.buffalo.edu",
+          "title": "Structural Biology Resource Page",
+          "url": "https://hwi.buffalo.edu/structural-biology-resources/?utm_source=chatgpt.com",
+          "description": "Structural Biology Resource Page – links to cryo-EM, crystallography, and X-ray data collection info from Hauptman-Woodward Institute"
+        },
+        {
+          "domain": "www.creative-biostructure.com",
+          "title": "Structural Biology Tools",
+          "url": "https://www.creative-biostructure.com/structural-biology-tools.htm?srsltid=AfmBOooqvJ0ksY6p6Pryq1diKVWPxNK0t68zKnuyMuTB0_k1IABozOXO&utm_source=chatgpt.com",
+          "description": "Creative Biostructure – lists structural resources and software across core techniques like crystallography and cryo-EM"
+        }
+      ]
+    },
+    "How can I submit genomic data to EMBL-EBI?": {
+      "answer": "To submit genomic data, visit the EMBL-EBI submission portal, where you’ll find step-by-step guides and tools for submitting sequencing data, assemblies, annotations, and more.",
+      "sources": [
+        {
+          "domain": "ebi.ac.uk",
+          "title": "EMBL's European Bioinformatics Institute",
+          "url": "https://www.ebi.ac.uk/",
+          "description": "Run BLAST searches against comprehensive sequence databases at EMBL-EBI."
+        },
+        {
+          "domain": "ena-docs.readthedocs.io",
+          "title": "ENA Documentation",
+          "url": "https://ena-docs.readthedocs.io/en/latest/",
+          "description": "ENA Documentation"
+        }
+      ]
+    },
+    "Access documentation and developer tools": {
+      "answer": "Explore the databse, where you can find model predictions, usage documentation, API access, and links to related publications. Developers can also access integration guides through the EMBL-EBI API Hub.",
+      "sources": [
+        {
+          "domain": "ebi.ac.uk",
+          "title": "EMBL-EBI APIs and Tools",
+          "url": "https://www.ebi.ac.uk/services",
+          "description": "Browse services by domain (genomics, proteomics, etc.) and access APIs."
+        },
+        {
+          "domain": "ebi.ac.uk",
+          "title": "EMBL-EBI API Documentation",
+          "url": "https://www.ebi.ac.uk/about/api",
+          "description": "RESTful APIs for tools like BLAST, InterProScan, Clustal Omega, etc."
+        }
+      ]
+    },
+    "Discover upcoming bioinformatics workshops for beginners": {
+      "answer": "Start your learning journey with our Training Events Calendar, featuring upcoming live webinars, virtual workshops, and in-person courses. Many sessions are designed for beginners and cover topics like genomics, data standards, and tool usage."
+    }
+  },
+  "fallbackResponses": [
+    {
+      "answer": "I'm sorry, I'm having trouble connecting to my knowledge base right now. Could you try again in a moment?",
+      "prompts": [
+        {
+          "action_text": "Contact support team",
+          "action_url": "tel:+44 1223 494 444"
+        },
+        {
+          "action_text": "Submit a support request",
+          "action_url": "https://www.ebi.ac.uk/about/contact/support/"
+        }
+      ]
+    }
+  ]
+}

public/assets/vf-chatbot/assets/vf-chatbot-selector-llms.json

@@ -0,0 +1,37 @@
+{
+  "routes": [
+    {
+      "id": "gpt4-turbo",
+      "title": "GPT-4 Turbo",
+      "selected": true
+    },
+    {
+      "id": "claude3-opus",
+      "title": "Claude 3 Opus"
+    },
+    {
+      "id": "gemini-ultra",
+      "title": "Gemini Ultra"
+    },
+    {
+      "id": "llama3",
+      "title": "LLaMA 3"
+    },
+    {
+      "id": "mixtral",
+      "title": "Mixtral 8x7B"
+    },
+    {
+      "id": "palm3",
+      "title": "PaLM 3"
+    },
+    {
+      "id": "gpt4-vision",
+      "title": "GPT-4 Vision"
+    },
+    {
+      "id": "claude3-sonnet",
+      "title": "Claude 3 Sonnet"
+    }
+  ]
+}

public/assets/vf-chatbot/assets/vf-chatbot-selector-services.json

@@ -0,0 +1,52 @@
+{
+  "routes": [
+    {
+      "id": "ensembl",
+      "title": "Ensembl"
+    },
+    {
+      "id": "uniprot",
+      "title": "UniProt"
+    },
+    {
+      "id": "pfam",
+      "title": "Pfam"
+    },
+    {
+      "id": "interpro",
+      "title": "InterPro"
+    },
+    {
+      "id": "chembl",
+      "title": "ChEMBL"
+    },
+    {
+      "id": "pdbe",
+      "title": "PDBe"
+    },
+    {
+      "id": "expression-atlas",
+      "title": "Expression Atlas"
+    },
+    {
+      "id": "pride",
+      "title": "PRIDE"
+    },
+    {
+      "id": "arrayexpress",
+      "title": "ArrayExpress"
+    },
+    {
+      "id": "intact",
+      "title": "IntAct"
+    },
+    {
+      "id": "reactome",
+      "title": "Reactome"
+    },
+    {
+      "id": "metabolights",
+      "title": "MetaboLights"
+    }
+  ]
+}

public/index.html

@@ -60,5 +60,7 @@
     <link href="https://stable.visual-framework.dev/feed.xml" type="application/rss+xml" rel="alternate" title="Visual Framework updates and announcements">
   </head>
   <body class="vf-body | vf-stack embl-content-hub-loaded">
+    <noscript>You need to enable JavaScript to run this app.</noscript>
+    <div id="root"></div>
   </body>
 </html>