reactome · heliamoh · Sep 17, 2025 · Sep 15, 2025 · Sep 15, 2025 · Sep 15, 2025
diff --git a/.chainlit/config.toml b/.chainlit/config.toml
@@ -74,7 +74,7 @@ github = "https://github.com/reactome/reactome_chatbot/issues"
 
 # Specify a Javascript file that can be used to customize the user interface.
 # The Javascript file can be served from the public directory.
-# custom_js = "/public/test.js"
+custom_js = "/public/custom.js"
 
 # Specify a custom meta image url.
 # custom_meta_image_url = "https://chainlit-cloud.s3.eu-west-3.amazonaws.com/logo/chainlit_banner.png"

diff --git a/.dockerignore b/.dockerignore
@@ -1,3 +1,4 @@
+data/
 embeddings/
 embeddings_bak/
 csv_files/

diff --git a/bin/chat-fastapi.py b/bin/chat-fastapi.py
@@ -288,15 +288,17 @@ async def landing_page():
     <body>
         <div class="container">
             <div class="logo">
-                <img src="https://reactome.org/templates/favourite/images/logo/logo.png" alt="Reactome Logo">
+                <a href="https://reactome.org" target="_blank">
+                    <img src="https://reactome.org/templates/favourite/images/logo/logo.png" alt="Reactome Logo">
+                </a>
             </div>
             <h1>Meet the React-to-Me AI Chatbot!</h1>
             <p class="centered-text">Your new guide to Reactome. Whether you're looking for specific genes and pathways or just browsing, our AI Chatbot is here to assist you!</p>
 
             <div class="button-container">
                 <a class="button" href="$CHAINLIT_URL/chat/guest/" target="_blank">Guest Access</a>
                 <a class="button" href="$CHAINLIT_URL/chat/personal/" target="_blank">Log In</a>
-                <a class="button feedback-button" href="https://forms.gle/Rvzb8EA73yZs7wd38" target="_blank">Feedback</a>
+                <a class="button feedback-button" href="mailto:help@reactome.org" target="_blank">Feedback</a>
             </div>
 
             <p class="left-justified">Choose <strong>Guest Access</strong> to try the chatbot out. <strong>Log In</strong> will give an increased query allowance and securely stores your chat history so you can save and continue conversations.</p>

diff --git a/chainlit.md b/chainlit.md
@@ -35,3 +35,10 @@ Explore pathways such as:
 
 Happy exploring with React-to-me!
 
+## _Disclaimer_
+
+_This chatbot uses large language model (LLM) technology to assist with questions about the Reactome Knowledgebase. Responses are generated automatically and may contain inaccuracies, outdated information or speculative language._
+
+_The information you provide may be retained in accordance with Reactome’s AI provider’s retention policy, which is located [here](https://openai.com/enterprise-privacy/). Do not share sensitive, personal or confidential information._
+
+_The chatbot does not substitute for expert curation or peer-reviewed sources and is not a suitable resource for clinical decisions. Users are responsible for validating any output before using it for research, publication, or medical decisions. Any use of this chatbot is subject to Reactome’s [disclaimer](https://reactome.org/about/disclaimer)._
diff --git a/config_default.yml b/config_default.yml
@@ -18,17 +18,11 @@ messages:
 
   welcome:
     message: |-
-      Welcome to {chat_profile}, your interactive chatbot for exploring Reactome!
+      Welcome to {chat_profile}, your interactive chatbot for exploring **[Reactome](https://reactome.org/)**!
       Ask me about biological pathways and processes.
     trigger:
       event: on_chat_start
 
-  survey_message:
-    message: |-
-      We hope you're enjoying your experience with React-to-me! We'd love to hear your feedback to make it even better. Please take a few minutes to fill out our [survey](https://forms.gle/Rvzb8EA73yZs7wd38).
-    trigger:
-      after_messages: 3
-
   demo-message:
     message: |-
       Hello!

diff --git a/public/custom.js b/public/custom.js
@@ -0,0 +1,64 @@
+/* 
+ * Replace the contents of the Chainlit watermark/footer
+ */
+(function () {
+  const CUSTOM_FOOTER_HTML = `
+    <div class="text-xs text-muted-foreground text-center">
+      <span>
+        <em>
+          <strong>Disclaimer:</strong>
+          Our chatbot uses AI to assist you.
+          Responses are generated automatically and may not always be accurate.
+          Do not share sensitive, personal or confidential information.
+          For more information, please click on the “Readme” icon at the top-right of this window.
+        </em>
+      </span>
+    </div>
+  `.trim();
+
+  const WATERMARK_SELECTOR = 'a.watermark';
+  const APPLIED_ATTR = 'data-custom-watermark';
+
+  function replaceFooterContents(root = document) {
+    const nodes = root instanceof Element
+      ? root.querySelectorAll(WATERMARK_SELECTOR)
+      : document.querySelectorAll(WATERMARK_SELECTOR);
+
+    nodes.forEach((el) => {
+      if (!(el instanceof HTMLElement)) return;
+      if (el.getAttribute(APPLIED_ATTR) === '1') return;
+
+      el.innerHTML = CUSTOM_FOOTER_HTML;
+
+      // disable the link behaviour
+      el.removeAttribute('href');
+      el.removeAttribute('target');
+      el.style.pointerEvents = 'none';
+
+      el.setAttribute(APPLIED_ATTR, '1');
+    });
+  }
+
+  // Initial run (in case the element is already present).
+  if (document.readyState === 'loading') {
+    document.addEventListener('DOMContentLoaded', () => replaceFooterContents(document));
+  } else {
+    replaceFooterContents(document);
+  }
+
+  // Re-apply on future UI updates (SPA re-renders).
+  const mo = new MutationObserver((mutations) => {
+    for (const m of mutations) {
+      for (const node of m.addedNodes) {
+        if (node instanceof Element) {
+          // If the watermark itself is added or its parent subtree changes, update.
+          if (node.matches?.(WATERMARK_SELECTOR) || node.querySelector?.(WATERMARK_SELECTOR)) {
+            replaceFooterContents(node);
+          }
+        }
+      }
+    }
+  });
+
+  mo.observe(document.documentElement, { childList: true, subtree: true });
+})();
diff --git a/public/elements/SearchResults.jsx b/public/elements/SearchResults.jsx
@@ -16,6 +16,7 @@ const SearchResults = () => {
                     <a
                         key={result.id}
                         href={result.url}
+                        target="_blank"
                         className="flex flex-col items-start gap-2 rounded-lg border p-3 text-left text-sm transition-all hover:bg-accent"
                     >
                         <div className="flex w-full flex-col gap-1">

diff --git a/public/favicon.ico b/public/favicon.ico
diff --git a/public/favicon.svg b/public/favicon.svg
diff --git a/src/util/embedding_environment.py b/src/util/embedding_environment.py
@@ -27,8 +27,11 @@ def get_dict(cls) -> dict[str, Path]:
         return cls._get().embeddings
 
     @classmethod
-    def get_dir(cls, key: str) -> Path:
-        return EM_ARCHIVE / cls._get().embeddings[key]
+    def get_dir(cls, key: str) -> Path | None:
+        if key in cls._get().embeddings:
+            return EM_ARCHIVE / cls._get().embeddings[key]
+        else:
+            return None
 
     @classmethod
     def get_model(cls, key: str) -> str: