update mcp

Author: geemi725

chapter_3/agent_mcp_example.ipynb

@@ -85,18 +85,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "b3c72322",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "✅ API key helper ready.\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import os\n",
     "from dotenv import load_dotenv\n",
@@ -133,18 +125,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": null,
    "id": "5032d7ac",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "✅ bio_tools_server.py written to disk.\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "server_code = '''\n",
     "#!/usr/bin/env python\n",
@@ -321,72 +305,52 @@
     "  \n",
     "Do **not** run this in a notebook cell with `!` — it blocks the kernel and no other cells will run.\n",
     "\n",
-    "**4.** Wait a few seconds until cloudflared prints a line like:\n",
+    "**4.** Wait a few seconds until cloudflared prints a line like. Read through the terminal logs to identify the correct URL.\n",
     "```\n",
     "https://abc-def-123.trycloudflare.com\n",
     "```\n",
-    "Copy that URL, paste it into the cell below, and run it.\n"
+    "Copy that URL, paste it into the cell below, and run it. \n",
+    "\n",
+    "Do not close the terminal as we want to keep the Cloudflare tunnel open.\n"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "id": "e4e0f7ca",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "1.27.0\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# Paste your cloudflared URL here (e.g. https://xxxx.trycloudflare.com)\n",
     "tunnel_url = \" https://xxxx.trycloudflare.com\""
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
+   "cell_type": "markdown",
    "id": "c91457af",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "✅ MCP URL set: https://difficulty-ages-stuck-corrections.trycloudflare.com/mcp\n"
-     ]
-    }
-   ],
    "source": [
-    "mcp_url = tunnel_url.rstrip(\"/\") + \"/mcp\"\n",
-    "mcp_server_config = {\"type\": \"url\", \"url\": mcp_url, \"name\": \"bio_tools\"}\n",
-    "print(f\"✅ MCP URL set: {mcp_url}\")"
+    "Now let's make sure if we can connect to the MCP server"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": null,
    "id": "695692ff",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "HTTP 400 — tunnel is up but server rejected the request (this is OK)\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import urllib.request\n",
+    "\n",
+    "mcp_url = tunnel_url.rstrip(\"/\") + \"/mcp\"\n",
+    "mcp_server_config = {\"type\": \"url\", \"url\": mcp_url, \"name\": \"bio_tools\"}\n",
+    "print(f\"✅ MCP URL set: {mcp_url}\")\n",
+    "\n",
     "req = urllib.request.Request(\n",
     "    mcp_server_config[\"url\"],\n",
     "    headers={\"Accept\": \"application/json, text/event-stream\"}\n",
     ")\n",
+    "\n",
     "try:\n",
     "    with urllib.request.urlopen(req, timeout=10) as r:\n",
     "        print(f\"✅ Reachable: HTTP {r.status}\")\n",
@@ -415,18 +379,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 30,
+   "execution_count": null,
    "id": "61810bd4",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Anthropic client ready.\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "from anthropic import Anthropic\n",
     "\n",
@@ -510,22 +466,7 @@
    "execution_count": null,
    "id": "6f726632",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "🧪 Question: \n",
-      "I'm studying the role of EGFR in non-small-cell lung cancer.\n",
-      "Here is a fragment of its amino acid sequence:\n",
-      "\n",
-      "MRPSGTAGAA...\n",
-      "\n",
-      "────────────────────────────────────────────────────────────\n",
-      "I'll analyze this EGFR fragment in two parallel ways: computing its biophysical properties from the sequence, and pulling together its biological/disease context. Then I'll synthesize drug discovery hypotheses."
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "egfr_sequence_fragment = (\n",
     "    \"MRPSGTAGAALLALLAALCPASRALEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYVQRNYDLSFLKTIQ\"\n",