Upload 17 files

.gitignore

@@ -0,0 +1,52 @@
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# VS Code
+.vscode/
+
+# Environment
+.env
+.venv
+venv/
+ENV/
+
+# mypy
+.mypy_cache/
+
+# Logs
+*.log 

Dockerfile

@@ -1,32 +1,32 @@
-FROM python:3.10-slim
-
-ENV PYTHONUNBUFFERED=1
-ENV PIP_NO_CACHE_DIR=1
-ENV DEBIAN_FRONTEND=noninteractive
-ENV MCP_LOCAL=2
-
-RUN apt-get update && apt-get install -y \
-    build-essential \
-    git \
-    curl \
-    wget \
-    ca-certificates \
-    libglib2.0-0 \
-    libsm6 \
-    libxext6 \
-    libxrender-dev \
-    libopenbabel-dev \
-    python3-dev \
-    libboost-all-dev \
-    && rm -rf /var/lib/apt/lists/*
-
-WORKDIR /app
-
-COPY . /app
-
-RUN pip install --upgrade pip setuptools wheel build && \
-    pip install -r requirements.txt
-
-EXPOSE 7860
-
-CMD ["python", "app.py"]
+FROM python:3.10-slim
+
+WORKDIR /app
+
+# Install system dependencies
+RUN apt-get update && apt-get install -y \
+    libmagic1 \
+    && rm -rf /var/lib/apt/lists/*
+
+# Copy requirements first for better caching
+COPY requirements.txt .
+RUN pip install -r requirements.txt
+
+# Copy application files
+COPY main.py .
+COPY app.py .
+COPY utils.py .
+COPY schema.py .
+COPY mcp_context.json .
+
+# Copy test files
+COPY tests/ tests/
+
+# Create a test script
+RUN echo '#!/bin/bash\npytest -v "$@"' > /usr/local/bin/run-tests && \
+    chmod +x /usr/local/bin/run-tests
+
+# Expose port
+EXPOSE 7860
+
+# Run the integrated server
+CMD ["python", "app.py"]

LICENSE

@@ -1,27 +1,27 @@
-BSD 3-Clause License
-
-Copyright (c) 2023, Martin Buttenschoen
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-1. Redistributions of source code must retain the above copyright notice, this
-   list of conditions and the following disclaimer.
-2. Redistributions in binary form must reproduce the above copyright notice,
-   this list of conditions and the following disclaimer in the documentation
-   and/or other materials provided with the distribution.
-3. Neither the name of the copyright holder nor the names of its
-   contributors may be used to endorse or promote products derived from
-   this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+BSD 3-Clause License
+
+Copyright (c) 2023, Martin Buttenschoen
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -1,151 +1,252 @@
----
-title: Posebusters Wrapper MCP
-emoji: 😻
-colorFrom: gray
-colorTo: pink
-sdk: gradio
-sdk_version: 5.36.2
-app_file: app.py
-pinned: false
-license: bsd-3-clause
-short_description: 'Unofficial MCP for PoseBusters: validates ligand–protein'
----
-
-
-Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
-
-
-# 🧪 PoseBusters Wrapper MCP
-
-This Hugging Face Space provides an **MCP-compatible API wrapper** around [PoseBusters](https://github.com/maabuu/posebusters), a command-line tool for validating the **physical and chemical plausibility** of molecular docking poses.
-
-> **⚠️ Disclaimer**  
-> This project is unofficial and not affiliated with or endorsed by the original author of PoseBusters.
-
----
-
-## ✅ Features
-
-✅ **Supports molecular file uploads**  
-Accepts ligand files (`.sdf`) and protein structures (`.pdb`) via either:
-- a simple web interface (Gradio tab UI), or  
-- HTTP POST requests using `multipart/form-data`.
-
-🔁 **Redocking validation (optional)**  
-If a crystal ligand (`.sdf`) is provided, the API performs redocking validation by comparing it to the predicted ligand pose.
-
-⚙️ **Leverages the `bust` CLI from PoseBusters**  
-Internally, this wrapper uses the PoseBusters command-line tool to evaluate:
-- pose plausibility  
-- chemical validity  
-- geometry checks  
-
-📊 **Structured JSON responses**  
-The output follows the [Model Context Protocol (MCP)](https://modelcontextprotocol.io), making it easy to use results in:
-- UI panels  
-- workflows  
-- logic pipelines  
-
-🤖 **MCP-Compatible API (for use in AI workflows)**  
-
-This project is fully **MCP-compliant**, meaning it follows the [Model Context Protocol (MCP)](https://modelcontextprotocol.io), the standard for exposing tools in AI-driven workflows and UIs.
-
-- ✅ Exposes a valid `GET /mcp/context` for tool discovery and UI generation.
-- ✅ Accepts `POST /mcp/predict` with `multipart/form-data` for structured tool execution.
-- ✅ Returns results in structured JSON, ready for use in agents, chatbots, or pipelines.
-- ✅ When deployed on your own **Hugging Face Spaces**, it works as an **MCP server** that can be added to your toolset from the MCP badge.
-
-*🧠 What does this mean for you?*
-
-If you're using **VSCode with Hugging Face MCP**, **Claude**, or **any other MCP-compatible client**, you can:
-
-- 🔹 Add this tool directly from its Space card using the MCP badge.
-- 🔹 Interact with it using standard UI panels or programmatic workflows.
-- 🔹 Submit files like `.sdf` and `.pdb` and receive validated pose results.
-
-*Notes*
-
-- Although this app **does not use Gradio for serving**, it runs perfectly inside a **Gradio Space** or a Docker container, using `FastAPI` as its backend.
-- **You must set the environment variable `MCP_LOCAL=2`** to enable full MCP server behavior. This activates the `/mcp/context` and `/mcp/predict` endpoints.
-- It is **fully MCP-compatible** and **discoverable** once deployed with this variable.
-- You can host it on your own infrastructure, or push it to Spaces for instant integration into MCP-enabled environments.
----
-
-## 🤗 How to Use (in Hugging Face Space)
-
-👉 **Space UI**: [https://huggingface.co/spaces/lepanto1571/posebusters-wrapper-MCP](https://huggingface.co/spaces/lepanto1571/posebusters-wrapper-MCP)
-
-- Upload your `.sdf` ligand and `.pdb` protein files
-- (Optional) Add a `.sdf` with the ''true'' crystal ligand
-- Click on **Submit**
-- Results will appear in the interactive table
-
----
-
-## 🐳 Run Locally with Docker
-### 1. Clone the repository
-
-```bash
-git clone https://github.com/lepanto1571/posebusters-wrapper-MCP.git
-cd posebusters-wrapper-MCP
-```
-
-### 2. Build the Docker image
-
-```bash
-docker buildx build --load -t posebusters-wrapper-mcp .
-```
-### 3. Run the container
-
-```bash
-docker run -p 7860:7860 -e MCP_LOCAL=2 posebusters-wrapper-mcp
-```
-The server will start on http://localhost:7860.
-
----
-
-## ⚙️ How to Use the API (MCP-compatible)
-
-### 🔎 1. Discover API via MCP Context
-
-```bash
-curl -X GET http://localhost:7860/mcp/context
-```
-
-### 2. Run validation (ligand + protein)
-
-```bash
-curl -X POST http://localhost:7860/mcp/predict \
-  -F action=validate_pose \
-  -F ligand_path=@ligand.sdf \
-  -F protein_path=@protein.pdb
-```
-### 3. Run redocking validation (ligand + crystal + protein)
-
-```bash
-curl -X POST http://localhost:7860/mcp/predict \
-  -F action=redocking_validation \
-  -F ligand_path=@ligand.sdf \
-  -F protein_path=@protein.pdb \
-  -F crystal_path=@crystal.sdf
-```
-
----
-
-## 📚 Documentation & Citation
-### 📖 PoseBusters documentation:
-Full usage and command-line reference available at
-https://posebusters.readthedocs.io/en/latest
-
-### 🧾 Scientific paper:
-Martin Buttenschoen, Andreas Bender (2023). "PoseBusters: a consistency check for 3D protein–ligand binding poses".
-Read it on arXiv: https://arxiv.org/abs/2308.05777
-
-### 💡 If you use this wrapper or PoseBusters in your work, consider citing the original paper.
-
----
-
-## 📄 License and Credits
-This project uses [PoseBusters](https://github.com/maabuu/posebusters) by Martin Buttenschoen (© 2023) under the BSD 3-Clause License.  
-This service is **not affiliated with or endorsed by** the original author.
-
+---
+title: Posebusters Wrapper MCP
+emoji: 😻
+colorFrom: gray
+colorTo: pink
+sdk: gradio
+sdk_version: 5.36.2
+app_file: app.py
+pinned: false
+license: bsd-3-clause
+short_description: 'MCP wrapper for PoseBusters: validates ligand–protein struct'
+---
+
+Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
+
+
+# 🧪 PoseBusters MCP Wrapper
+
+This Hugging Face Space provides an **MCP-compatible API wrapper** around [PoseBusters](https://github.com/maabuu/posebusters), a command-line tool for validating the **physical and chemical plausibility** of molecular docking poses.
+
+> **⚠️ Disclaimer**  
+> This project is unofficial and not affiliated with or endorsed by the original author of PoseBusters.
+
+---
+
+## ✅ Features
+
+✅ **Supports molecular file uploads**  
+Accepts ligand files (`.sdf`) and protein structures (`.pdb`) via either:
+- a simple web interface (Gradio tab UI), or  
+- HTTP POST requests using `multipart/form-data`.
+
+🔁 **Redocking validation (optional)**  
+If a crystal ligand (`.sdf`) is provided, the API performs redocking validation by comparing it to the predicted ligand pose.
+
+⚙️ **Leverages the `bust` CLI from PoseBusters**  
+Internally, this wrapper uses the PoseBusters command-line tool to evaluate:
+- pose plausibility  
+- chemical validity  
+- geometry checks  
+
+📊 **Structured JSON responses**  
+The output follows the [Model Context Protocol (MCP)](https://modelcontextprotocol.io), making it easy to use results in:
+- UI panels  
+- workflows  
+- logic pipelines  
+
+🤖 **MCP-Compatible API (for use in AI workflows)**  
+
+This project is fully **MCP-compliant**, meaning it follows the [Model Context Protocol (MCP)](https://modelcontextprotocol.io), the standard for exposing tools in AI-driven workflows and UIs.
+
+- ✅ Exposes a valid `GET /mcp/context` for tool discovery and UI generation.
+- ✅ Accepts `POST /mcp/predict` with `multipart/form-data` for structured tool execution.
+- ✅ Returns results in structured JSON, ready for use in agents, chatbots, or pipelines.
+- ✅ When deployed on your own **Hugging Face Spaces**, it works as an **MCP server** that can be added to your toolset from the MCP badge.
+
+*🧠 What does this mean for you?*
+
+If you're using **VSCode with Hugging Face MCP**, **Claude**, or **any other MCP-compatible client**, you can:
+
+- 🔹 Add this tool directly from its Space card using the MCP badge.
+- 🔹 Interact with it using standard UI panels or programmatic workflows.
+- 🔹 Submit files like `.sdf` and `.pdb` and receive validated pose results.
+
+*Notes*
+
+- The app runs perfectly inside a **Gradio Space** or a Docker container, using `FastAPI` as its backend.
+- The app is **fully MCP-compatible** and **discoverable** once deployed.
+- You can host it on your own infrastructure, or push it to Spaces for instant integration into MCP-enabled environments.
+
+---
+
+## 🤗 How to Use (in Hugging Face Space)
+
+👉 **Space UI**: [https://huggingface.co/spaces/lepanto1571/posebusters-wrapper-MCP](https://huggingface.co/spaces/lepanto1571/posebusters-wrapper-MCP)
+
+- Upload your `.sdf` ligand and `.pdb` protein files
+- (Optional) Add a `.sdf` with the ''true'' crystal ligand
+- Click on **Submit**
+- Results will appear in the interactive table
+
+---
+
+## 🐳 Run Locally with Docker
+### 1. Clone the repository
+
+```bash
+git clone https://github.com/lepanto1571/posebusters-wrapper-MCP.git
+cd posebusters-wrapper-MCP
+```
+
+### 2. Build the Docker image
+
+```bash
+docker buildx build --load -t posebusters-wrapper-mcp .
+```
+### 3. Run the container
+
+```bash
+docker run -p 7860:7860 posebusters-wrapper-mcp
+```
+The server will start on http://localhost:7860.
+
+---
+
+## ⚙️ How to Use the API (MCP-compatible)
+
+### 🔎 1. Discover API via MCP Context
+
+```bash
+# Using curl
+curl -X GET http://localhost:7860/mcp/context
+
+# Using Python
+import requests
+response = requests.get("http://localhost:7860/mcp/context")
+context = response.json()
+```
+
+### 2. Run validation (ligand + protein)
+
+```bash
+# Using curl
+curl -X POST http://localhost:7860/mcp/predict \
+  -F action=validate_pose \
+  -F ligand_input=@ligand.sdf \
+  -F protein_input=@protein.pdb
+
+# Using Python
+import requests
+
+files = {
+    'ligand_input': ('ligand.sdf', open('ligand.sdf', 'rb')),
+    'protein_input': ('protein.pdb', open('protein.pdb', 'rb'))
+}
+data = {'action': 'validate_pose'}
+
+response = requests.post(
+    "http://localhost:7860/mcp/predict",
+    files=files,
+    data=data
+)
+results = response.json()
+```
+
+### 3. Run redocking validation (ligand + crystal + protein)
+
+```bash
+# Using curl
+curl -X POST http://localhost:7860/mcp/predict \
+  -F action=redocking_validation \
+  -F ligand_input=@ligand.sdf \
+  -F protein_input=@protein.pdb \
+  -F crystal_input=@crystal.sdf
+
+# Using Python
+import requests
+
+files = {
+    'ligand_input': ('ligand.sdf', open('ligand.sdf', 'rb')),
+    'protein_input': ('protein.pdb', open('protein.pdb', 'rb')),
+    'crystal_input': ('crystal.sdf', open('crystal.sdf', 'rb'))
+}
+data = {'action': 'redocking_validation'}
+
+response = requests.post(
+    "http://localhost:7860/mcp/predict",
+    files=files,
+    data=data
+)
+results = response.json()
+```
+
+### Response Format
+
+All responses follow the MCP standard format:
+
+```python
+{
+    "object_id": "validation_results",
+    "data": {
+        "columns": ["ligand_id", "status", "passed/total", "details"],
+        "rows": [
+            ["mol1", "✅", "8/8", "All tests passed"],
+            # ... more results
+        ]
+    }
+}
+```
+
+### Error Handling
+
+The API uses standard HTTP status codes:
+- 200: Success
+- 400: Invalid request (wrong file type, missing required files)
+- 500: Server error (validation failed, internal error)
+
+Error responses include detailed messages:
+```python
+{
+    "object_id": "validation_results",
+    "data": {
+        "columns": ["ligand_id", "status", "passed/total", "details"],
+        "rows": [
+            ["unknown", "❌", "0/0", "Detailed error message"]
+        ]
+    }
+}
+```
+
+## 🧪 Development and Testing
+
+### Running Tests
+
+Tests can be run directly using Docker:
+
+```bash
+# Run tests with verbose output
+docker run posebusters-wrapper-mcp pytest -v
+
+# Run tests with coverage report
+docker run posebusters-wrapper-mcp pytest --cov=. --cov-report=term-missing
+```
+
+### Validation
+
+The API uses JSON Schema validation for:
+- MCP Context (`/mcp/context`)
+- Prediction Responses (`/mcp/predict`)
+- File Types (MIME validation)
+
+Schema definitions are in `schema.py`.
+
+---
+
+## 📚 Documentation & Citation
+### 📖 PoseBusters documentation:
+Full usage and command-line reference available at
+https://posebusters.readthedocs.io/en/latest
+
+### 🧾 Scientific paper:
+Martin Buttenschoen, Andreas Bender (2023). "PoseBusters: a consistency check for 3D protein–ligand binding poses".
+Read it on arXiv: https://arxiv.org/abs/2308.05777
+
+### 💡 If you use this wrapper or PoseBusters in your work, consider citing the original paper.
+
+---
+
+## 📄 License and Credits
+This project uses [PoseBusters](https://github.com/maabuu/posebusters) by Martin Buttenschoen (© 2023) under the BSD 3-Clause License.  
+This service is **not affiliated with or endorsed by** the original author.
+

app.py

@@ -1,242 +1,182 @@
-import gradio as gr
-from fastapi import FastAPI, Request, UploadFile, File, Form
-from fastapi.responses import JSONResponse
-import pandas as pd
-import traceback
-import tempfile
-import subprocess
-import os
-import csv
-import base64
-import uvicorn
-
-app = FastAPI()
-latest_results = []
-
-
-def validate_files(ligand_file, protein_file, crystal_file=None):
-    if not ligand_file or not protein_file:
-        raise ValueError("Both ligand (.sdf) and protein (.pdb) files must be uploaded.")
-    ligand_path = ligand_file.name
-    protein_path = protein_file.name
-    crystal_path = crystal_file.name if crystal_file else None
-    return ligand_path, protein_path, crystal_path
-
-
-def format_results_to_mcp(csv_text: str, stderr_text: str = "", ligand_path: str = None) -> list:
-    rows = []
-    if not csv_text.strip():
-        ligand_id = os.path.basename(ligand_path) if ligand_path else "unknown"
-        if stderr_text.strip():
-            rows.append([
-                ligand_id,
-                "❌",
-                "0/0",
-                stderr_text.strip().splitlines()[0]
-            ])
-        else:
-            rows.append([
-                ligand_id,
-                "❌",
-                "0/0",
-                "PoseBusters output is empty."
-            ])
-        return rows
-
-    reader = csv.DictReader(csv_text.strip().splitlines())
-    for row in reader:
-        ligand_id = row.get("molecule", "?")
-        failed_tests = []
-        passed_n = 0
-        total_n = 0
-
-        for k, v in row.items():
-            if k in {"file", "molecule"}:
-                continue
-            if v == "True":
-                passed_n += 1
-                total_n += 1
-            elif v == "False":
-                failed_tests.append(k)
-                total_n += 1
-
-        rows.append([
-            ligand_id,
-            "✅" if not failed_tests else "❌",
-            f"{passed_n}/{total_n}",
-            ", ".join(failed_tests) if failed_tests else "All tests passed"
-        ])
-
-    return rows
-
-
-from fastapi import UploadFile, File, Form, Request
-from fastapi.responses import JSONResponse
-
-@app.post("/mcp/predict")
-async def predict(
-    action: str = Form(...),
-    ligand_path: UploadFile = File(None),
-    protein_path: UploadFile = File(None),
-    crystal_path: UploadFile = File(None),
-):
-    try:
-        if not ligand_path or not protein_path:
-            return JSONResponse(status_code=400, content={"error": "Missing ligand or protein file"})
-
-        async def save(upload, suffix):
-            with tempfile.NamedTemporaryFile(delete=False, suffix=suffix) as tmp:
-                tmp.write(await upload.read())
-                return tmp.name
-
-        ligand_file_path = await save(ligand_path, ".sdf")
-        protein_file_path = await save(protein_path, ".pdb")
-        crystal_file_path = await save(crystal_path, ".sdf") if crystal_path else None
-
-        if action == "validate_pose":
-            cmd = ["bust", ligand_file_path, "-p", protein_file_path, "--outfmt", "csv"]
-
-        elif action == "redocking_validation":
-            if not crystal_file_path:
-                return JSONResponse(status_code=400, content={"error": "Missing crystal ligand file"})
-            cmd = ["bust", ligand_file_path, "-l", crystal_file_path, "-p", protein_file_path, "--outfmt", "csv"]
-
-        else:
-            return JSONResponse(status_code=400, content={"error": f"Unknown action: {action}"})
-
-        result = subprocess.run(cmd, capture_output=True, text=True)
-        rows = format_results_to_mcp(result.stdout, result.stderr, ligand_file_path)
-
-        return {
-            "columns": ["ligand_id", "status", "passed/total", "details"],
-            "rows": rows
-        }
-
-    except Exception as e:
-        return {
-            "error": str(e),
-            "traceback": traceback.format_exc()
-        }
-
-
-
-def gradio_ui(ligand_file, protein_file, crystal_file=None):
-    try:
-        ligand_path, protein_path, crystal_path = validate_files(ligand_file, protein_file, crystal_file)
-
-        if crystal_path:
-            cmd = ["bust", ligand_path, "-l", crystal_path, "-p", protein_path, "--outfmt", "csv"]
-        else:
-            cmd = ["bust", ligand_path, "-p", protein_path, "--outfmt", "csv"]
-
-        result = subprocess.run(cmd, capture_output=True, text=True)
-
-        rows = format_results_to_mcp(result.stdout, result.stderr, ligand_path)
-
-        global latest_results
-        latest_results = rows
-
-        return {
-            "columns": ["ligand_id", "status", "passed/total", "details"],
-            "rows": rows
-        }
-
-    except Exception as e:
-        return {
-            "columns": ["ligand_id", "status", "passed/total", "details"],
-            "rows": [[os.path.basename(ligand_file.name), "❌", "0/0", str(e)]],
-            "error": str(e),
-            "traceback": traceback.format_exc()
-        }
-
-@app.get("/mcp/context")
-def get_mcp_context():
-    return {
-        "app": {
-            "id": "lepanto1571.wrapper.posebusters",
-            "name": "PoseBusters MCP wrapper",
-            "version": "0.5"
-        },
-        "windows": [
-            {
-                "id": "posebusters_view",
-                "title": "Validation Panel",
-                "view": {
-                    "type": "form",
-                    "objects": ["ligand_input", "protein_input", "crystal_input", "validation_results"]
-                }
-            }
-        ],
-        "objects": [
-            {"type": "file", "id": "ligand_input", "name": "Ligand file", "format": "sdf"},
-            {"type": "file", "id": "protein_input", "name": "Protein file", "format": "pdb"},
-            {"type": "file", "id": "crystal_input", "name": "Crystal ligand file (optional)", "format": "sdf", "optional": True},
-            {
-                "type": "table",
-                "id": "validation_results",
-                "columns": ["ligand_id", "status", "passed/total", "details"],
-                "rows": latest_results
-            }
-        ],
-        "actions": [
-            {
-                "name": "validate_pose",
-                "description": "Validate ligand–protein structure",
-                "parameters": {
-                    "ligand_path": "ligand_input",
-                    "protein_path": "protein_input"
-                }
-            },
-            {
-                "name": "redocking_validation",
-                "description": "Validate redocking using a reference ligand",
-                "parameters": {
-                    "ligand_path": "ligand_input",
-                    "crystal_path": "crystal_input",
-                    "protein_path": "protein_input"
-                }
-            }
-        ]
-    }
-
-import gradio.themes.base
-
-theme = gradio.themes.Base()
-
-iface = gr.Interface(
-    fn=gradio_ui,
-    inputs=[
-        gr.File(label="Ligand (.sdf)", type="filepath"),
-        gr.File(label="Protein (.pdb)", type="filepath"),
-        gr.File(label="Crystal Ligand (.sdf, optional)", type="filepath")
-    ],
-    outputs="json",
-    title="PoseBusters Wrapper MCP",
-    description="Free MCP-compatible API for validating ligand–protein structures using PoseBusters.",
-    theme=theme
-)
-
-context_button = gr.Interface(
-    fn=get_mcp_context,
-    inputs=[],
-    outputs="json",
-    title="MCP Context",
-    description="Returns the MCP context metadata for the app.",
-    theme=theme
-)
-
-demo = gr.TabbedInterface(
-    interface_list=[iface, context_button],
-    tab_names=["Validation", "MCP Context"],
-    theme=theme
-)
-
-def main():
-    if os.environ.get("MCP_LOCAL") == "2":
-        print("Running MCP server on 0.0.0.0:7860")
-        uvicorn.run(app, host="0.0.0.0", port=7860)
-    else:
-        demo.launch(server_name="0.0.0.0")
-
-if __name__ == "__main__":
-    main()
+# Standard library imports
+import os
+import io
+import asyncio
+from pathlib import Path
+from typing import Any, Dict, Optional
+from contextlib import contextmanager
+
+# Third-party imports
+import gradio as gr
+from fastapi import FastAPI, File, Form, UploadFile
+import uvicorn
+import json
+
+# Local imports
+from utils import validate_mime_type, format_results_to_mcp
+from main import predict, app as fastapi_app
+
+# Check if we're running in Hugging Face Spaces
+IS_HF_SPACE = os.getenv("SPACE_ID") is not None
+
+# Store the original working directory
+ORIGINAL_CWD = os.getcwd()
+
+@contextmanager
+def stable_cwd():
+    """Context manager to maintain a stable working directory."""
+    current_dir = os.getcwd()
+    try:
+        os.chdir(ORIGINAL_CWD)
+        yield
+    finally:
+        os.chdir(current_dir)
+
+# Get MCP context with proper path handling
+def get_mcp_context_wrapper() -> Dict[str, Any]:
+    """Wrapper around get_mcp_context that handles Spaces paths."""
+    try:
+        with stable_cwd():
+            # In Spaces, we know the file is in the root directory
+            if IS_HF_SPACE:
+                context_path = Path(ORIGINAL_CWD) / 'mcp_context.json'
+                if not context_path.exists():
+                    raise FileNotFoundError(f"MCP context file not found at {context_path}")
+                with open(context_path, 'r') as f:
+                    return json.load(f)
+            # Otherwise use the utility function that searches multiple locations
+            from utils import get_mcp_context
+            return get_mcp_context()
+    except Exception as e:
+        return {
+            "error": f"Failed to load MCP context: {str(e)}",
+            "app": {
+                "id": "lepanto1571.wrapper.posebusters",
+                "name": "PoseBusters MCP wrapper",
+                "version": "0.5"
+            }
+        }
+
+async def process_files(ligand_file, protein_file, crystal_file=None):
+    """Process uploaded files using the robust predict function from main.py."""
+    try:
+        with stable_cwd():
+            # Handle file uploads in a way that works in both environments
+            async def create_upload_file(file_obj) -> Optional[UploadFile]:
+                if file_obj is None:
+                    return None
+                
+                try:
+                    # Get the filename, handling both string paths and file-like objects
+                    if hasattr(file_obj, 'orig_name'):
+                        filename = file_obj.orig_name
+                    elif hasattr(file_obj, 'name'):
+                        filename = file_obj.name
+                    else:
+                        filename = str(file_obj)
+
+                    # Create a UploadFile object that works in both environments
+                    if hasattr(file_obj, 'read'):
+                        # File-like object (e.g. in Spaces or already open file)
+                        content = await file_obj.read() if asyncio.iscoroutinefunction(file_obj.read) else file_obj.read()
+                        if hasattr(file_obj, 'seek'):
+                            file_obj.seek(0)  # Reset file pointer for future reads
+                        file_like = io.BytesIO(content if isinstance(content, bytes) else content.encode('utf-8'))
+                        return UploadFile(
+                            file=file_like,
+                            filename=Path(filename).name
+                        )
+                    elif hasattr(file_obj, 'name') and os.path.exists(file_obj.name):
+                        # Local file path that exists
+                        return UploadFile(
+                            file=open(file_obj.name, "rb"),
+                            filename=Path(filename).name
+                        )
+                    else:
+                        raise ValueError(f"Unable to read file: {filename}")
+                        
+                except Exception as e:
+                    raise ValueError(f"Failed to process file {getattr(file_obj, 'name', str(file_obj))}: {str(e)}")
+
+            # Convert files to UploadFile objects
+            ligand_input = await create_upload_file(ligand_file)
+            protein_input = await create_upload_file(protein_file)
+            crystal_input = await create_upload_file(crystal_file)
+
+            if not ligand_input or not protein_input:
+                raise ValueError("Both ligand and protein files are required")
+
+            # Use the action based on whether crystal file is provided
+            action = "redocking_validation" if crystal_input else "validate_pose"
+
+            # Call the robust predict function
+            return await predict(
+                action=action,
+                ligand_input=ligand_input,
+                protein_input=protein_input,
+                crystal_input=crystal_input
+            )
+
+    except Exception as e:
+        return {
+            "object_id": "validation_results",
+            "data": {
+                "columns": ["ligand_id", "status", "passed/total", "details"],
+                "rows": [[
+                    Path(getattr(ligand_file, 'orig_name', 
+                          getattr(ligand_file, 'name', 'unknown'))).stem,
+                    "❌",
+                    "0/0",
+                    str(e)
+                ]]
+            }
+        }
+
+theme = gr.themes.Base()
+
+# Main validation interface
+validation_ui = gr.Interface(
+    fn=process_files,
+    inputs=[
+        gr.File(label="Ligand (.sdf)", type="filepath", file_count="single"),
+        gr.File(label="Protein (.pdb)", type="filepath", file_count="single"),
+        gr.File(label="Crystal Ligand (.sdf, optional)", type="filepath", file_count="single")
+    ],
+    outputs="json",
+    title="PoseBusters Validation",
+    description="Upload files to validate ligand–protein structures using PoseBusters.",
+    theme=theme,
+    cache_examples=False  # Disable caching to prevent file handle issues
+)
+
+# MCP Context viewer
+context_ui = gr.Interface(
+    fn=get_mcp_context_wrapper,
+    inputs=None,
+    outputs=gr.JSON(),
+    title="MCP Context",
+    description="View the MCP context metadata that defines this tool's capabilities.",
+    theme=theme,
+    cache_examples=False  # Disable caching to prevent file handle issues
+)
+
+# Combined interface
+demo = gr.TabbedInterface(
+    interface_list=[validation_ui, context_ui],
+    tab_names=["💊 Validation", "🔍 MCP Context"],
+    title="PoseBusters MCP Wrapper",
+    theme=theme
+)
+
+def main():
+    """Run the server based on environment."""
+    if IS_HF_SPACE:
+        # In Hugging Face Spaces, just run the Gradio app
+        demo.launch(server_name="0.0.0.0")
+    else:
+        # For local/Docker, mount Gradio into FastAPI and run the server
+        app = gr.mount_gradio_app(fastapi_app, demo, path="/")
+        uvicorn.run(app, host="0.0.0.0", port=7860)
+
+if __name__ == "__main__":
+    main()

data/1of6_ligand.sdf

@@ -0,0 +1,31 @@
+DTY
+     RDKit          3D
+
+ 13 13  0  0  1  0  0  0  0  0999 V2000
+   30.6770   -3.3700   50.5160 N   0  0  0  0  0  0  0  0  0  0  0  0
+   31.3780   -3.1310   49.2550 C   0  0  2  0  0  0  0  0  0  0  0  0
+   31.9670   -4.4050   48.6940 C   0  0  0  0  0  0  0  0  0  0  0  0
+   32.0170   -5.4920   49.3380 O   0  0  0  0  0  0  0  0  0  0  0  0
+   32.4890   -2.1160   49.5260 C   0  0  0  0  0  0  0  0  0  0  0  0
+   32.0300   -0.7150   49.8830 C   0  0  0  0  0  0  0  0  0  0  0  0
+   32.2930   -0.2240   51.1250 C   0  0  0  0  0  0  0  0  0  0  0  0
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+   31.8570    1.0320   51.4460 C   0  0  0  0  0  0  0  0  0  0  0  0
+   30.9070    1.3420   49.2730 C   0  0  0  0  0  0  0  0  0  0  0  0
+   31.2050    1.8270   50.5410 C   0  0  0  0  0  0  0  0  0  0  0  0
+   30.8150    2.9790   50.9180 O   0  0  0  0  0  0  0  0  0  0  0  0
+   32.3720   -4.3160   47.5370 O   0  0  0  0  0  0  0  0  0  0  0  0
+  2  1  1  1
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+  2  5  1  0
+  3  4  2  0
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+  5  6  1  0
+  6  7  2  0
+  6  8  1  0
+  7  9  1  0
+  8 10  2  0
+  9 11  2  0
+ 10 11  1  0
+ 11 12  1  0
+M  END

data/1of6_ligands.sdf

@@ -0,0 +1,256 @@
+DTY
+     RDKit          3D
+
+ 13 13  0  0  1  0  0  0  0  0999 V2000
+   30.2540   -2.5680   74.6470 N   0  0  0  0  0  0  0  0  0  0  0  0
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+   31.3690   -4.4990   76.1010 O   0  0  0  0  0  0  0  0  0  0  0  0
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+   27.2580   -2.4780   75.0340 C   0  0  0  0  0  0  0  0  0  0  0  0
+   26.8210   -1.4240   75.8630 C   0  0  0  0  0  0  0  0  0  0  0  0
+   26.7940   -2.4670   73.7230 C   0  0  0  0  0  0  0  0  0  0  0  0
+   25.8850   -0.4270   75.4190 C   0  0  0  0  0  0  0  0  0  0  0  0
+   25.9000   -1.4590   73.2560 C   0  0  0  0  0  0  0  0  0  0  0  0
+   25.4270   -0.3980   74.0850 C   0  0  0  0  0  0  0  0  0  0  0  0
+   24.6220    0.5320   73.6460 O   0  0  0  0  0  0  0  0  0  0  0  0
+   30.1990   -4.2930   77.8630 O   0  0  0  0  0  0  0  0  0  0  0  0
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+  6  8  1  0
+  7  9  1  0
+  8 10  2  0
+  9 11  2  0
+ 10 11  1  0
+ 11 12  1  0
+M  END
+$$$$
+DTY
+     RDKit          3D
+
+ 13 13  0  0  1  0  0  0  0  0999 V2000
+    9.9250   13.9750   69.7540 N   0  0  0  0  0  0  0  0  0  0  0  0
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+   12.8680   11.1570   72.5970 C   0  0  0  0  0  0  0  0  0  0  0  0
+   14.1380   11.5440   72.1180 C   0  0  0  0  0  0  0  0  0  0  0  0
+   15.1170   10.6980   72.1020 O   0  0  0  0  0  0  0  0  0  0  0  0
+    7.8390   14.5290   72.6020 O   0  0  0  0  0  0  0  0  0  0  0  0
+  2  1  1  6
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+  6  8  1  0
+  7  9  1  0
+  8 10  2  0
+  9 11  2  0
+ 10 11  1  0
+ 11 12  1  0
+M  END
+$$$$
+DTY
+     RDKit          3D
+
+ 13 13  0  0  1  0  0  0  0  0999 V2000
+   26.1300   22.5850   52.9470 N   0  0  0  0  0  0  0  0  0  0  0  0
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+   26.3460   16.4460   51.3140 O   0  0  0  0  0  0  0  0  0  0  0  0
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+  2  1  1  1
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+  2  5  1  0
+  3  4  2  0
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+  5  6  1  0
+  6  7  2  0
+  6  8  1  0
+  7  9  1  0
+  8 10  2  0
+  9 11  2  0
+ 10 11  1  0
+ 11 12  1  0
+M  END
+$$$$
+DTY
+     RDKit          3D
+
+ 13 13  0  0  1  0  0  0  0  0999 V2000
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+   85.2190   41.7490   47.7280 O   0  0  0  0  0  0  0  0  0  0  0  0
+  2  1  1  1
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+  6  8  1  0
+  7  9  1  0
+  8 10  2  0
+  9 11  2  0
+ 10 11  1  0
+ 11 12  1  0
+M  END
+$$$$
+DTY
+     RDKit          3D
+
+ 13 13  0  0  1  0  0  0  0  0999 V2000
+   64.2120   59.0260   71.4630 N   0  0  0  0  0  0  0  0  0  0  0  0
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+   68.6070   56.5980   73.2120 C   0  0  0  0  0  0  0  0  0  0  0  0
+   69.6140   55.8620   73.0710 O   0  0  0  0  0  0  0  0  0  0  0  0
+   62.3520   60.3180   72.6160 O   0  0  0  0  0  0  0  0  0  0  0  0
+  2  1  1  6
+  2  3  1  0
+  2  5  1  0
+  3  4  2  0
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+  5  6  1  0
+  6  7  2  0
+  6  8  1  0
+  7  9  1  0
+  8 10  2  0
+  9 11  2  0
+ 10 11  1  0
+ 11 12  1  0
+M  END
+$$$$
+DTY
+     RDKit          3D
+
+ 13 13  0  0  1  0  0  0  0  0999 V2000
+   85.3020   43.0320   73.7720 N   0  0  0  0  0  0  0  0  0  0  0  0
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+   80.8710   43.9700   72.9940 C   0  0  0  0  0  0  0  0  0  0  0  0
+   80.4220   44.9020   73.9230 C   0  0  0  0  0  0  0  0  0  0  0  0
+   79.4820   45.7400   73.6110 O   0  0  0  0  0  0  0  0  0  0  0  0
+   85.4920   41.1990   76.8520 O   0  0  0  0  0  0  0  0  0  0  0  0
+  2  1  1  6
+  2  3  1  0
+  2  5  1  0
+  3  4  2  0
+  3 13  1  0
+  5  6  1  0
+  6  7  2  0
+  6  8  1  0
+  7  9  1  0
+  8 10  2  0
+  9 11  2  0
+ 10 11  1  0
+ 11 12  1  0
+M  END
+$$$$
+DTY
+     RDKit          3D
+
+ 13 13  0  0  1  0  0  0  0  0999 V2000
+   30.6770   -3.3700   50.5160 N   0  0  0  0  0  0  0  0  0  0  0  0
+   31.3780   -3.1310   49.2550 C   0  0  2  0  0  0  0  0  0  0  0  0
+   31.9670   -4.4050   48.6940 C   0  0  0  0  0  0  0  0  0  0  0  0
+   32.0170   -5.4920   49.3380 O   0  0  0  0  0  0  0  0  0  0  0  0
+   32.4890   -2.1160   49.5260 C   0  0  0  0  0  0  0  0  0  0  0  0
+   32.0300   -0.7150   49.8830 C   0  0  0  0  0  0  0  0  0  0  0  0
+   32.2930   -0.2240   51.1250 C   0  0  0  0  0  0  0  0  0  0  0  0
+   31.3170    0.0570   48.9730 C   0  0  0  0  0  0  0  0  0  0  0  0
+   31.8570    1.0320   51.4460 C   0  0  0  0  0  0  0  0  0  0  0  0
+   30.9070    1.3420   49.2730 C   0  0  0  0  0  0  0  0  0  0  0  0
+   31.2050    1.8270   50.5410 C   0  0  0  0  0  0  0  0  0  0  0  0
+   30.8150    2.9790   50.9180 O   0  0  0  0  0  0  0  0  0  0  0  0
+   32.3720   -4.3160   47.5370 O   0  0  0  0  0  0  0  0  0  0  0  0
+  2  1  1  1
+  2  3  1  0
+  2  5  1  0
+  3  4  2  0
+  3 13  1  0
+  5  6  1  0
+  6  7  2  0
+  6  8  1  0
+  7  9  1  0
+  8 10  2  0
+  9 11  2  0
+ 10 11  1  0
+ 11 12  1  0
+M  END
+$$$$
+DTY
+     RDKit          3D
+
+ 13 13  0  0  1  0  0  0  0  0999 V2000
+   78.1870   69.1110   54.6720 N   0  0  0  0  0  0  0  0  0  0  0  0
+   78.4910   69.2750   53.2300 C   0  0  2  0  0  0  0  0  0  0  0  0
+   78.2650   70.7210   52.9630 C   0  0  0  0  0  0  0  0  0  0  0  0
+   77.6840   71.4160   53.7710 O   0  0  0  0  0  0  0  0  0  0  0  0
+   77.6090   68.4400   52.2900 C   0  0  0  0  0  0  0  0  0  0  0  0
+   77.8710   66.9670   52.3560 C   0  0  0  0  0  0  0  0  0  0  0  0
+   79.0090   66.4720   51.7490 C   0  0  0  0  0  0  0  0  0  0  0  0
+   77.0040   66.0680   53.0050 C   0  0  0  0  0  0  0  0  0  0  0  0
+   79.3270   65.1250   51.8140 C   0  0  0  0  0  0  0  0  0  0  0  0
+   77.3050   64.7110   53.0120 C   0  0  0  0  0  0  0  0  0  0  0  0
+   78.4750   64.2220   52.4400 C   0  0  0  0  0  0  0  0  0  0  0  0
+   78.7940   62.9710   52.5270 O   0  0  0  0  0  0  0  0  0  0  0  0
+   78.5830   71.2520   51.9460 O   0  0  0  0  0  0  0  0  0  0  0  0
+  2  1  1  1
+  2  3  1  0
+  2  5  1  0
+  3  4  2  0
+  3 13  1  0
+  5  6  1  0
+  6  7  2  0
+  6  8  1  0
+  7  9  1  0
+  8 10  2  0
+  9 11  2  0
+ 10 11  1  0
+ 11 12  1  0
+M  END
+$$$$

main.py

@@ -0,0 +1,170 @@
+# Standard library imports
+import os
+import subprocess
+import tempfile
+import traceback
+from pathlib import Path
+from typing import Dict, Any, Optional
+
+# Third-party imports
+import gradio as gr
+from fastapi import FastAPI, File, Form, UploadFile, HTTPException
+from fastapi.responses import JSONResponse
+from jsonschema import validate, ValidationError
+from schema import MCP_CONTEXT_SCHEMA, MCP_PREDICT_RESPONSE_SCHEMA
+
+# Local imports
+from utils import validate_mime_type, format_results_to_mcp, get_mcp_context, ALLOWED_MIME_TYPES
+
+app = FastAPI(title="PoseBusters MCP API")
+
+@app.post("/mcp/predict")
+async def predict(
+    action: str = Form(...),
+    ligand_input: UploadFile = File(...),
+    protein_input: UploadFile = File(...),
+    crystal_input: Optional[UploadFile] = File(None),
+) -> Dict[str, Any]:
+    """
+    MCP-compliant prediction endpoint.
+    Validates file types and runs PoseBusters validation.
+    Response is validated against MCP_PREDICT_RESPONSE_SCHEMA.
+    """
+    try:
+        # Validate MIME types
+        validate_mime_type(ligand_input, ".sdf")
+        validate_mime_type(protein_input, ".pdb")
+        if crystal_input:
+            validate_mime_type(crystal_input, ".sdf")
+
+        async def save_upload(upload: UploadFile, suffix: str) -> str:
+            """Safely save uploaded file with secure naming."""
+            with tempfile.NamedTemporaryFile(delete=False, suffix=suffix) as tmp:
+                content = await upload.read()
+                tmp.write(content)
+                return tmp.name
+
+        # Create a temporary directory for isolated execution
+        with tempfile.TemporaryDirectory() as tmpdir:
+            try:
+                # Save files in the temporary directory
+                ligand_path = await save_upload(ligand_input, ".sdf")
+                protein_path = await save_upload(protein_input, ".pdb")
+                crystal_path = await save_upload(crystal_input, ".sdf") if crystal_input else None
+
+                # Move to temporary directory
+                os.chdir(tmpdir)
+
+                if action == "validate_pose":
+                    cmd = ["bust", ligand_path, "-p", protein_path, "--outfmt", "csv"]
+                elif action == "redocking_validation":
+                    if not crystal_path:
+                        raise HTTPException(status_code=400, detail="Missing crystal ligand file")
+                    cmd = ["bust", ligand_path, "-l", crystal_path, "-p", protein_path, "--outfmt", "csv"]
+                else:
+                    raise HTTPException(status_code=400, detail=f"Unknown action: {action}")
+
+                # Use list form of subprocess.run to avoid shell injection
+                # Add timeout of 5 minutes
+                result = subprocess.run(
+                    cmd,
+                    capture_output=True,
+                    text=True,
+                    check=False,  # Don't raise on non-zero exit
+                    timeout=300  # 5 minutes timeout
+                )
+
+                response = format_results_to_mcp(
+                    result.stdout,
+                    result.stderr,
+                    Path(ligand_input.filename).stem
+                )
+                try:
+                    validate(instance=response, schema=MCP_PREDICT_RESPONSE_SCHEMA)
+                    return response
+                except ValidationError as e:
+                    return JSONResponse(
+                        status_code=500,
+                        content={
+                            "object_id": "validation_results",
+                            "data": {
+                                "columns": ["ligand_id", "status", "passed/total", "details"],
+                                "rows": [[
+                                    Path(ligand_input.filename).stem,
+                                    "❌",
+                                    "0/0",
+                                    f"Schema validation error: {str(e)}"
+                                ]]
+                            }
+                        }
+                    )
+
+            finally:
+                # Clean up temporary files
+                for path in [ligand_path, protein_path, crystal_path]:
+                    if path and os.path.exists(path):
+                        try:
+                            os.unlink(path)
+                        except OSError:
+                            pass
+
+    except subprocess.TimeoutExpired as e:
+        return JSONResponse(
+            status_code=500,
+            content={
+                "object_id": "validation_results",
+                "data": {
+                    "columns": ["ligand_id", "status", "passed/total", "details"],
+                    "rows": [[
+                        Path(ligand_input.filename).stem,
+                        "❌",
+                        "0/0",
+                        f"Process timed out after {e.timeout} seconds"
+                    ]]
+                }
+            }
+        )
+    except HTTPException:
+        raise
+    except Exception as e:
+        return JSONResponse(
+            status_code=500,
+            content={
+                "object_id": "validation_results",
+                "data": {
+                    "columns": ["ligand_id", "status", "passed/total", "details"],
+                    "rows": [[
+                        Path(ligand_input.filename).stem,
+                        "❌",
+                        "0/0",
+                        str(e)
+                    ]]
+                },
+                "error": str(e),
+                "traceback": traceback.format_exc()
+            }
+        )
+
+@app.get("/mcp/context")
+def context() -> Dict[str, Any]:
+    """
+    Return MCP context with empty initial validation results.
+    Response is validated against MCP_CONTEXT_SCHEMA.
+    """
+    try:
+        context = get_mcp_context()
+        validate(instance=context, schema=MCP_CONTEXT_SCHEMA)
+        return context
+    except ValidationError as e:
+        return JSONResponse(
+            status_code=500,
+            content={"error": f"Schema validation error: {str(e)}"}
+        )
+
+def main():
+    """Run the FastAPI server."""
+    import uvicorn
+    uvicorn.run(app, host="0.0.0.0", port=7860)
+
+if __name__ == "__main__":
+    main() 

mcp_context.json

@@ -1,63 +1,99 @@
-{
-  "app": {
-    "id": "lepanto1571.wrapper.posebusters",
-    "name": "PoseBusters MCP wrapper",
-    "version": "0.5"
-  },
-  "windows": [
-    {
-      "id": "posebusters_view",
-      "title": "Validation Panel",
-      "view": {
-        "type": "form",
-        "objects": ["ligand_input", "protein_input", "crystal_input", "validation_results"]
-      }
-    }
-  ],
-  "objects": [
-    {
-      "type": "file",
-      "id": "ligand_input",
-      "name": "Ligand file",
-      "format": "sdf"
-    },
-    {
-      "type": "file",
-      "id": "protein_input",
-      "name": "Protein file",
-      "format": "pdb"
-    },
-    {
-      "type": "file",
-      "id": "crystal_input",
-      "name": "Crystal ligand file (optional)",
-      "format": "sdf",
-      "optional": true
-    },
-    {
-      "type": "table",
-      "id": "validation_results",
-      "columns": ["ligand_id", "status", "passed/total", "details"],
-      "rows": []
-    }
-  ],
-  "actions": [
-    {
-      "name": "validate_pose",
-      "description": "Validate ligand–protein structure",
-      "parameters": {
-        "ligand_path": "ligand_input",
-        "protein_path": "protein_input"
-      }
-    },
-    {
-      "name": "redocking_validation",
-      "description": "Validate redocking using a reference ligand",
-      "parameters": {
-        "ligand_path": "ligand_input",
-        "protein_path": "protein_input",
-        "crystal_path": "crystal_input"
-      }
-    }
-  ]
-}
+{
+  "app": {
+    "id": "lepanto1571.wrapper.posebusters",
+    "name": "PoseBusters MCP wrapper",
+    "version": "0.5"
+  },
+  "windows": [
+    {
+      "id": "posebusters_view",
+      "title": "Validation Panel",
+      "view": {
+        "type": "form",
+        "objects": ["ligand_input", "protein_input", "crystal_input", "validation_results"]
+      }
+    }
+  ],
+  "objects": [
+    {
+      "type": "file",
+      "id": "ligand_input",
+      "name": "Ligand file",
+      "format": "sdf"
+    },
+    {
+      "type": "file",
+      "id": "protein_input",
+      "name": "Protein file",
+      "format": "pdb"
+    },
+    {
+      "type": "file",
+      "id": "crystal_input",
+      "name": "Crystal ligand file (optional)",
+      "format": "sdf",
+      "optional": true
+    },
+    {
+      "type": "table",
+      "id": "validation_results",
+      "name": "Validation Results",
+      "description": "Results of PoseBusters validation checks",
+      "columns": [
+        {
+          "id": "ligand_id",
+          "name": "Ligand ID",
+          "type": "string",
+          "description": "Identifier of the validated ligand"
+        },
+        {
+          "id": "status",
+          "name": "Status",
+          "type": "string",
+          "description": "Validation status (✅ for pass, ❌ for fail)",
+          "enum": ["✅", "❌"]
+        },
+        {
+          "id": "passed/total",
+          "name": "Tests Passed",
+          "type": "string",
+          "description": "Number of passed tests vs total tests (format: X/Y)"
+        },
+        {
+          "id": "details",
+          "name": "Details",
+          "type": "string",
+          "description": "List of failed tests or 'All tests passed'"
+        }
+      ],
+      "rows": []
+    }
+  ],
+  "actions": [
+    {
+      "name": "validate_pose",
+      "description": "Validate ligand–protein structure",
+      "parameters": {
+        "ligand_input": "ligand_input",
+        "protein_input": "protein_input"
+      },
+      "output": {
+        "object_id": "validation_results",
+        "type": "table"
+      }
+    },
+    {
+      "name": "redocking_validation",
+      "description": "Validate redocking using a reference ligand",
+      "parameters": {
+        "ligand_input": "ligand_input",
+        "crystal_input": "crystal_input",
+        "protein_input": "protein_input"
+      },
+      "output": {
+        "object_id": "validation_results",
+        "type": "table"
+      }
+    }
+  ]
+}

pytest.ini

@@ -0,0 +1,4 @@
+[pytest]
+testpaths = tests
+python_files = test_*.py
+addopts = -v --tb=short 

requirements.txt

@@ -1,6 +1,15 @@
-fastapi
-uvicorn
-gradio
-pandas
-rdkit-pypi
-posebusters
+fastapi>=0.109.0
+uvicorn>=0.27.0
+python-multipart>=0.0.6
+gradio>=4.8.0
+requests>=2.31.0
+pandas>=2.1.3
+rdkit-pypi
+posebusters
+python-magic>=0.4.27  # For MIME type validation
+jsonschema>=4.21.1
+
+# Testing dependencies
+pytest>=7.4.0
+pytest-cov>=4.1.0
+pytest-asyncio>=0.21.0  # For async test support

schema.py

@@ -0,0 +1,128 @@
+"""JSON Schema definitions for MCP context and responses."""
+
+MCP_CONTEXT_SCHEMA = {
+    "type": "object",
+    "required": ["app", "windows", "objects", "actions"],
+    "properties": {
+        "app": {
+            "type": "object",
+            "required": ["id", "name", "version"],
+            "properties": {
+                "id": {"type": "string"},
+                "name": {"type": "string"},
+                "version": {"type": "string"}
+            }
+        },
+        "windows": {
+            "type": "array",
+            "items": {
+                "type": "object",
+                "required": ["id", "title", "view"],
+                "properties": {
+                    "id": {"type": "string"},
+                    "title": {"type": "string"},
+                    "view": {
+                        "type": "object",
+                        "required": ["type", "objects"],
+                        "properties": {
+                            "type": {"type": "string", "enum": ["form"]},
+                            "objects": {
+                                "type": "array",
+                                "items": {"type": "string"}
+                            }
+                        }
+                    }
+                }
+            }
+        },
+        "objects": {
+            "type": "array",
+            "items": {
+                "type": "object",
+                "required": ["type", "id", "name"],
+                "properties": {
+                    "type": {"type": "string", "enum": ["file", "table"]},
+                    "id": {"type": "string"},
+                    "name": {"type": "string"},
+                    "format": {"type": "string"},
+                    "optional": {"type": "boolean"},
+                    "description": {"type": "string"},
+                    "columns": {
+                        "type": "array",
+                        "items": {
+                            "type": "object",
+                            "required": ["id", "name", "type", "description"],
+                            "properties": {
+                                "id": {"type": "string"},
+                                "name": {"type": "string"},
+                                "type": {"type": "string"},
+                                "description": {"type": "string"},
+                                "enum": {
+                                    "type": "array",
+                                    "items": {"type": "string"}
+                                }
+                            }
+                        }
+                    },
+                    "rows": {
+                        "type": "array",
+                        "items": {
+                            "type": "array",
+                            "items": {"type": "string"}
+                        }
+                    }
+                }
+            }
+        },
+        "actions": {
+            "type": "array",
+            "items": {
+                "type": "object",
+                "required": ["name", "description", "parameters", "output"],
+                "properties": {
+                    "name": {"type": "string"},
+                    "description": {"type": "string"},
+                    "parameters": {
+                        "type": "object",
+                        "additionalProperties": {"type": "string"}
+                    },
+                    "output": {
+                        "type": "object",
+                        "required": ["object_id", "type"],
+                        "properties": {
+                            "object_id": {"type": "string"},
+                            "type": {"type": "string"}
+                        }
+                    }
+                }
+            }
+        }
+    }
+}
+
+MCP_PREDICT_RESPONSE_SCHEMA = {
+    "type": "object",
+    "required": ["object_id", "data"],
+    "properties": {
+        "object_id": {"type": "string"},
+        "data": {
+            "type": "object",
+            "required": ["columns", "rows"],
+            "properties": {
+                "columns": {
+                    "type": "array",
+                    "items": {"type": "string"}
+                },
+                "rows": {
+                    "type": "array",
+                    "items": {
+                        "type": "array",
+                        "items": {"type": "string"}
+                    }
+                }
+            }
+        },
+        "error": {"type": "string"},
+        "traceback": {"type": "string"}
+    }
+} 

tests/conftest.py

@@ -0,0 +1,6 @@
+import os
+import sys
+
+# Add the parent directory to Python path so we can import app modules
+app_dir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+sys.path.insert(0, app_dir) 

tests/test_mcp.py

@@ -0,0 +1,101 @@
+"""Tests for MCP context and response validation."""
+import json
+import pytest
+from pathlib import Path
+from jsonschema import validate, ValidationError
+
+from schema import MCP_CONTEXT_SCHEMA, MCP_PREDICT_RESPONSE_SCHEMA
+from utils import format_results_to_mcp, get_mcp_context
+
+def test_mcp_context_schema():
+    """Test that the MCP context follows the schema."""
+    context = get_mcp_context()
+    validate(instance=context, schema=MCP_CONTEXT_SCHEMA)
+    
+    # Test required fields
+    assert "app" in context
+    assert "id" in context["app"]
+    assert "name" in context["app"]
+    assert "version" in context["app"]
+    
+    # Test windows configuration
+    assert "windows" in context
+    assert len(context["windows"]) > 0
+    assert "objects" in context["windows"][0]["view"]
+    
+    # Test objects configuration
+    assert "objects" in context
+    file_objects = [obj for obj in context["objects"] if obj["type"] == "file"]
+    assert len(file_objects) >= 2  # At least ligand and protein
+    
+    # Test actions configuration
+    assert "actions" in context
+    assert len(context["actions"]) >= 1
+    for action in context["actions"]:
+        assert "parameters" in action
+        assert "output" in action
+
+def test_mcp_response_format():
+    """Test that the MCP response formatter produces valid output."""
+    # Test successful case
+    csv_text = "molecule,test1,test2\nmol1,True,False\n"
+    response = format_results_to_mcp(csv_text, "", "mol1")
+    validate(instance=response, schema=MCP_PREDICT_RESPONSE_SCHEMA)
+    
+    assert response["object_id"] == "validation_results"
+    assert "columns" in response["data"]
+    assert "rows" in response["data"]
+    assert len(response["data"]["rows"]) == 1
+    
+    # Test error case
+    response = format_results_to_mcp("", "Error occurred", "mol1")
+    validate(instance=response, schema=MCP_PREDICT_RESPONSE_SCHEMA)
+    assert response["data"]["rows"][0][1] == "❌"  # Status should be fail
+
+def test_mcp_response_content():
+    """Test the content of MCP responses for different scenarios."""
+    # Test all tests passing
+    csv_text = "molecule,test1,test2\nmol1,True,True\n"
+    response = format_results_to_mcp(csv_text, "", "mol1")
+    row = response["data"]["rows"][0]
+    assert row[1] == "✅"  # Status
+    assert row[2] == "2/2"  # Passed/Total
+    assert row[3] == "All tests passed"  # Details
+    
+    # Test some tests failing
+    csv_text = "molecule,test1,test2,test3\nmol1,True,False,False\n"
+    response = format_results_to_mcp(csv_text, "", "mol1")
+    row = response["data"]["rows"][0]
+    assert row[1] == "❌"  # Status
+    assert row[2] == "1/3"  # Passed/Total
+    assert "test2" in row[3] and "test3" in row[3]  # Failed tests in details
+
+def test_invalid_mcp_context():
+    """Test that invalid MCP context raises ValidationError."""
+    invalid_context = {
+        "app": {"name": "Test"}  # Missing required fields
+    }
+    with pytest.raises(ValidationError):
+        validate(instance=invalid_context, schema=MCP_CONTEXT_SCHEMA)
+
+def test_invalid_mcp_response():
+    """Test that invalid MCP response raises ValidationError."""
+    invalid_response = {
+        "object_id": "validation_results",
+        "data": {
+            "columns": ["col1"],
+            "rows": [["too", "many", "columns"]]  # Inconsistent columns
+        }
+    }
+    
+    with pytest.raises(ValidationError) as exc_info:
+        # First validate that rows match column count
+        columns_count = len(invalid_response["data"]["columns"])
+        for row in invalid_response["data"]["rows"]:
+            if len(row) != columns_count:
+                raise ValidationError(f"Row length {len(row)} does not match columns length {columns_count}")
+                
+        # Then validate schema
+        validate(instance=invalid_response, schema=MCP_PREDICT_RESPONSE_SCHEMA)
+    
+    assert "Row length" in str(exc_info.value) 

utils.py

@@ -0,0 +1,112 @@
+"""Shared utilities for the PoseBusters MCP wrapper."""
+
+# Standard library imports
+import csv
+import mimetypes
+from pathlib import Path
+from typing import Any, Dict, List
+import json
+
+# Third-party imports
+from fastapi import UploadFile, HTTPException
+
+# Constants
+ALLOWED_MIME_TYPES = {
+    ".sdf": ["chemical/x-mdl-sdfile", "application/octet-stream", "text/plain"],
+    ".pdb": ["chemical/x-pdb", "application/octet-stream", "text/plain"]
+}
+
+def validate_mime_type(file: UploadFile, expected_ext: str) -> None:
+    """Validate file MIME type and extension."""
+    if not file.filename:
+        raise HTTPException(status_code=400, detail=f"Missing filename for {expected_ext} file")
+    
+    file_ext = Path(file.filename).suffix.lower()
+    if file_ext != expected_ext:
+        raise HTTPException(
+            status_code=400, 
+            detail=f"Invalid file extension. Expected {expected_ext}, got {file_ext}"
+        )
+    
+    content_type = file.content_type or mimetypes.guess_type(file.filename)[0] or "application/octet-stream"
+    if not content_type or content_type not in ALLOWED_MIME_TYPES[expected_ext]:
+        raise HTTPException(
+            status_code=400,
+            detail=f"Invalid MIME type for {expected_ext} file"
+        )
+
+def format_results_to_mcp(csv_text: str, stderr_text: str = "", ligand_id: str = "unknown") -> Dict[str, Any]:
+    """Format PoseBusters results to MCP standard output format."""
+    rows: List[List[str]] = []
+    
+    if not csv_text.strip():
+        error_msg = stderr_text.strip().splitlines()[0] if stderr_text.strip() else "PoseBusters output is empty."
+        rows.append([ligand_id, "❌", "0/0", error_msg])
+    else:
+        reader = csv.DictReader(csv_text.strip().splitlines())
+        for row in reader:
+            ligand_id = row.get("molecule", "?")
+            failed_tests = []
+            passed_n = total_n = 0
+
+            for k, v in row.items():
+                if k in {"file", "molecule"}:
+                    continue
+                if v == "True":
+                    passed_n += 1
+                    total_n += 1
+                elif v == "False":
+                    failed_tests.append(k)
+                    total_n += 1
+
+            rows.append([
+                ligand_id,
+                "✅" if not failed_tests else "❌",
+                f"{passed_n}/{total_n}",
+                ", ".join(failed_tests) if failed_tests else "All tests passed"
+            ])
+
+    # Create response
+    response = {
+        "object_id": "validation_results",
+        "data": {
+            "columns": ["ligand_id", "status", "passed/total", "details"],
+            "rows": rows
+        }
+    }
+
+    # Validate row lengths
+    expected_cols = len(response["data"]["columns"])
+    for row in response["data"]["rows"]:
+        if len(row) != expected_cols:
+            raise ValueError(f"Row length {len(row)} does not match columns length {expected_cols}")
+
+    return response
+
+def get_mcp_context() -> Dict[str, Any]:
+    """Return MCP context from the JSON file."""
+    try:
+        # Get the directory where the current file (utils.py) is located
+        current_dir = Path(__file__).parent
+        context_path = current_dir / 'mcp_context.json'
+        
+        # If not found in current directory, try the app root (for Spaces)
+        if not context_path.exists():
+            context_path = current_dir / '..' / 'mcp_context.json'
+            context_path = context_path.resolve()
+            
+        if not context_path.exists():
+            raise FileNotFoundError(f"MCP context file not found at {context_path}")
+            
+        with open(context_path, 'r') as f:
+            return json.load(f)
+    except FileNotFoundError as e:
+        raise HTTPException(
+            status_code=500,
+            detail=str(e)
+        )
+    except json.JSONDecodeError:
+        raise HTTPException(
+            status_code=500,
+            detail="Invalid MCP context JSON format"
+        )