Merge pull request #5 from genomoncology/server-hanging

Update package version to 0.1.1.
Add example scripts for MCP integration and Python SDK.
Update troubleshooting documentation for macOS.
Modify trial search example to remove --size argument.
Update dependencies in pyproject.toml.
Add script to run the MCP server.
Enable deptry checks on example scripts.

Author: imaurer

docs/troubleshooting/macos.md

@@ -23,7 +23,7 @@ You can run `biomcp` commands directly without a full installation using `uvx`.
   ```
 - Test a search command (e.g., trial search):
   ```bash
-  uvx --from biomcp-python biomcp trial search --condition NSCLC --size 1 | head -n 5
+  uvx --from biomcp-python biomcp trial search --condition NSCLC | head -n 5
   # Expected Output (NCT ID and Title will vary):
   # # Record 1
   # Nct Number: NCT0XXXXXXX

example_scripts/mcp_integration.py

@@ -0,0 +1,82 @@
+#!/usr/bin/env -S uv --quiet run --script
+# /// script
+# requires-python = ">=3.11"
+# dependencies = [
+#     "mcp",
+# ]
+# ///
+
+# Scripts to reproduce this page:
+# https://biomcp.org/mcp_integration/
+
+import asyncio
+
+from mcp.client.session import ClientSession
+from mcp.client.stdio import StdioServerParameters, stdio_client
+from mcp.types import TextContent
+
+
+async def check_server():
+    # Run with pypi package
+    # server_params = StdioServerParameters(
+    #     command="uvx",
+    #     args=["--from", "biomcp-python", "biomcp", "run"],
+    # )
+
+    # Run with local code
+    server_params = StdioServerParameters(
+        command="python",
+        args=["-m", "biomcp", "run"],
+    )
+
+    async with (
+        stdio_client(server_params) as (read, write),
+        ClientSession(read, write) as session,
+    ):
+        await session.initialize()
+
+        # list prompts
+        prompts = await session.list_prompts()
+        print("Available prompts:", prompts)
+
+        # list resources
+        resources = await session.list_resources()
+        print("Available resources:", resources)
+
+        # list tools
+        tool_result = await session.list_tools()
+        tools = tool_result.tools
+        print("Available tools:", tools)
+        assert len(tools) >= 9
+
+        # run tool
+        tool_name = "variant_details"
+        tool_args = {"variant_id": "rs113488022"}
+        result = await session.call_tool(tool_name, tool_args)
+        assert result.isError is False, f"Error: {result.content}"
+
+        # --- Assertions ---
+        # 1. Check the call was successful (not an error)
+        assert (
+            result.isError is False
+        ), f"Tool call resulted in error: {result.content}"
+
+        # 2. Check there is content
+        assert result.content is not None
+        assert len(result.content) >= 1
+
+        # 3. Check the type of the first content block
+        content_block = result.content[0]
+        assert isinstance(content_block, TextContent)
+
+        markdown_output = content_block.text
+        # print(markdown_output)
+        assert isinstance(markdown_output, str)
+        assert "rs113488022" in markdown_output
+        assert "BRAF" in markdown_output
+        assert "Pathogenic" in markdown_output
+        print(f"Successfully called tool '{tool_name}' with args {tool_args}")
+
+
+if __name__ == "__main__":
+    asyncio.run(check_server())

example_scripts/python_sdk.py

@@ -0,0 +1,108 @@
+#!/usr/bin/env -S uv --quiet run --script
+# /// script
+# requires-python = ">=3.11"
+# dependencies = [
+#     "biomcp-python",
+# ]
+# ///
+
+# Scripts to reproduce this page:
+# https://biomcp.org/python_sdk/
+
+import asyncio
+import json
+
+from biomcp.trials.search import (
+    RecruitingStatus,
+    TrialPhase,
+    TrialQuery,
+    search_trials,
+)
+from biomcp.variants.getter import get_variant
+from biomcp.variants.search import VariantQuery, search_variants
+
+
+async def find_pathogenic_tp53():
+    # noinspection PyTypeChecker
+    query = VariantQuery(gene="TP53", significance="pathogenic", size=5)
+    # Get results as Markdown (default)
+    json_output_str = await search_variants(query, output_json=True)
+    data = json.loads(json_output_str)
+    assert len(data) == 5
+    for item in data:
+        clinvar = item.get("clinvar")
+        for rcv in clinvar.get("rcv", []):
+            assert "pathogenic" in rcv["clinical_significance"].lower()
+
+
+async def get_braf_v600e_details():
+    variant_id = "chr7:g.140453136A>T"  # BRAF V600E variant
+
+    # Get results as JSON string
+    json_output_str = await get_variant(variant_id, output_json=True)
+    data = json.loads(json_output_str)
+
+    # Process the variant data
+    assert data, "No data returned for BRAF V600E variant"
+    variant = data[0]
+    clinvar = variant.get("clinvar", {})
+    cosmic = variant.get("cosmic", {})
+    docm = variant.get("docm", {})
+
+    # Verify key variant details
+    assert clinvar.get("gene", {}).get("symbol") == "BRAF"
+    assert clinvar.get("chrom") == "7"
+    assert clinvar.get("cytogenic") == "7q34"
+    assert cosmic.get("cosmic_id") == "COSM476"
+    assert docm.get("aa_change") == "p.V600E"
+
+    # Verify HGVS coding variants
+    hgvs_coding = clinvar.get("hgvs", {}).get("coding", [])
+    assert len(hgvs_coding) >= 13
+    assert "NM_004333.6:c.1799T>A" in hgvs_coding
+
+
+async def find_melanoma_trials():
+    query = TrialQuery(
+        conditions=["Melanoma"],
+        interventions=["Pembrolizumab"],
+        recruiting_status=RecruitingStatus.OPEN,
+        phase=TrialPhase.PHASE3,
+    )
+
+    # Get results as JSON string
+    json_output_str = await search_trials(query, output_json=True)
+    data = json.loads(json_output_str)
+
+    # Verify we got results
+    assert data, "No trials found"
+    assert len(data) >= 2, "Expected at least 2 melanoma trials"
+
+    # Verify first trial details (NCT05727904)
+    trial1 = data[0]
+    assert trial1["NCT Number"] == "NCT05727904"
+    assert "lifileucel" in trial1["Study Title"].lower()
+    assert trial1["Study Status"] == "RECRUITING"
+    assert trial1["Phases"] == "PHASE3"
+    assert int(trial1["Enrollment"]) == 670
+    assert "Melanoma" in trial1["Conditions"]
+    assert "Pembrolizumab" in trial1["Interventions"]
+
+    # Verify second trial details (NCT06697301)
+    trial2 = data[1]
+    assert trial2["NCT Number"] == "NCT06697301"
+    assert "EIK1001" in trial2["Study Title"]
+    assert trial2["Study Status"] == "RECRUITING"
+    assert "PHASE3" in trial2["Phases"]
+    assert int(trial2["Enrollment"]) == 740
+    assert trial2["Conditions"] == "Advanced Melanoma"
+
+
+def run():
+    asyncio.run(find_pathogenic_tp53())
+    asyncio.run(get_braf_v600e_details())
+    asyncio.run(find_melanoma_trials())
+
+
+if __name__ == "__main__":
+    run()

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "biomcp-python"
-version = "0.1.0"
+version = "0.1.1"
 description = "Biomedical Model Context Protocol Server"
 authors = [{ name = "Ian Maurer", email = "imaurer@gmail.com" }]
 readme = "README.md"
@@ -16,7 +16,6 @@ classifiers = [
     "Topic :: Software Development :: Libraries :: Python Modules",
 ]
 dependencies = [
-    "anyio>=4.8.0",
     "certifi>=2025.1.31",
     "diskcache>=5.6.3",
     "httpx>=0.28.1",
@@ -61,8 +60,6 @@ build-backend = "setuptools.build_meta"
 [tool.setuptools.package-data]
 biomcp = ["resources/*.md"]
 
-
-
 [project.scripts]
 biomcp = "biomcp.__main__:main"
 
@@ -164,3 +161,15 @@ omit = [
     "src/*/server.py",
     "src/*/http_client.py",
 ]
+
+[tool.deptry]
+exclude = [
+  "example_scripts/python_sdk.py",
+  "venv",
+  ".venv",
+  ".direnv",
+  "tests",
+  ".git",
+    "build",
+    "dist",
+]

src/biomcp/cli/server.py

@@ -1,7 +1,5 @@
-import signal
-import sys
+import asyncio
 
-import anyio
 import typer
 
 from .. import logger, mcp_app
@@ -13,19 +11,9 @@
 def run_server():
     """Run the BioMCP server with STDIO transport."""
 
-    # Use a simpler approach - just force exit on SIGINT
-    def handle_sigint(sig, frame):
-        typer.echo("\nShutting down server...")
-        sys.exit(0)
+    tools = asyncio.run(mcp_app.list_tools())
+    tools_str = ",".join(t.name for t in tools)
+    logger.info(f"Tools loaded: {tools_str}")
 
-    # Register only for SIGINT
-    signal.signal(signal.SIGINT, handle_sigint)
-
-    logger.info("Starting MCP server... (v0.0.1)")
-    try:
-        anyio.run(mcp_app.run_stdio_async)
-        logger.info("MCP server stopped gracefully.")
-        return 0
-    except Exception as e:
-        logger.error(f"Error running MCP server: {e}")
-        return 1
+    logger.info("Starting MCP server:")
+    mcp_app.run()