nexotype-mcp 0.1.0__tar.gz

nexotype_mcp-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: nexotype-mcp
+Version: 0.1.0
+Summary: Nexotype MCP Server — biomedical knowledge graph for drug discovery, genomics, and market intelligence
+Keywords: mcp,nexotype,biotech,drug-discovery,knowledge-graph,genomics,ai,claude,llm
+Author: Robert Radoslav
+Author-email: Robert Radoslav <43938206+rbtrsv@users.noreply.github.com>
+License-Expression: MIT
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: click>=8.3.2
+Requires-Dist: fastmcp>=3.2.3
+Requires-Dist: httpx>=0.28.1
+Requires-Python: >=3.12
+Project-URL: Documentation, https://www.nexotype.com
+Project-URL: Homepage, https://www.nexotype.com
+Project-URL: PyPI, https://pypi.org/project/nexotype-mcp/
+Description-Content-Type: text/markdown
+
+# Nexotype MCP Server
+
+AI-powered biomedical knowledge graph for drug discovery, genomics, and market intelligence.
+
+Connect your AI tools to the Nexotype platform and query the biomedical knowledge graph through conversation.
+
+## Installation
+
+```bash
+pip install nexotype-mcp
+```
+
+Or with uv:
+
+```bash
+uv tool install nexotype-mcp
+```
+
+Already installed? Update:
+
+```bash
+pip install --upgrade nexotype-mcp
+```
+
+## Authentication
+
+```bash
+nexotype-cli login
+```
+
+Enter your email and password. Credentials are stored securely at `~/.nexotype/credentials.json` (chmod 600).
+
+## Configure Your AI Client
+
+### Claude Desktop
+
+Edit `~/Library/Application Support/Claude/claude_desktop_config.json` (macOS) or `%APPDATA%\Claude\claude_desktop_config.json` (Windows):
+
+```json
+{
+  "mcpServers": {
+    "nexotype": {
+      "command": "nexotype-mcp"
+    }
+  }
+}
+```
+
+### Claude Code
+
+```bash
+claude mcp add nexotype -- nexotype-mcp
+```
+
+### VS Code / Cursor
+
+Add to your MCP settings:
+
+```json
+{
+  "nexotype": {
+    "command": "nexotype-mcp"
+  }
+}
+```
+
+Restart the application after saving.
+
+## Tools (28)
+
+### Graph Intelligence (6 tools)
+
+| Tool | Description |
+|------|-------------|
+| `explore_network` | N-hop neighborhood of any entity |
+| `find_path` | Shortest path between two entities |
+| `find_similar` | Entities sharing the most relationships |
+| `company_deep_dive` | Full portfolio of a pharma/biotech company |
+| `drug_discovery` | Targets, pathways, indications for a drug |
+| `competitive_landscape` | All drugs and companies targeting a protein |
+
+### AI Query (1 tool)
+
+| Tool | Description |
+|------|-------------|
+| `ask_knowledge_graph` | Natural language question → grounded answer from graph |
+
+### Search & Browse (2 tools)
+
+| Tool | Description |
+|------|-------------|
+| `search_entities` | List entities of any of the 61 types |
+| `get_entity` | Full details for a specific entity |
+
+### Context (3 tools)
+
+| Tool | Description |
+|------|-------------|
+| `get_permissions` | Check subscription tier and domain access |
+| `list_subjects` | List available biological subjects |
+| `set_subject` | Set active subject for personalization tools |
+
+### Personalized Health (10 tools)
+
+| Tool | Description |
+|------|-------------|
+| `get_user_profile` | Personal info linked to the subject |
+| `list_user_variants` | Detected genomic variants |
+| `list_biomarker_readings` | Time-series health data |
+| `create_biomarker_reading` | Log a new biomarker measurement |
+| `list_treatment_logs` | Intervention history |
+| `create_treatment_log` | Log a new treatment |
+| `list_pathway_scores` | Pathway health scores |
+| `list_recommendations` | Personalized treatment suggestions |
+| `upload_genomic_file` | Upload VCF/23andMe file for analysis |
+| `get_processing_status` | Check genomic file processing progress |
+
+### Commercial Intelligence (6 tools)
+
+| Tool | Description |
+|------|-------------|
+| `list_market_organizations` | Pharma/biotech companies |
+| `get_market_organization` | Full company details |
+| `list_patents` | Patent filings and status |
+| `list_development_pipelines` | Clinical trial phases |
+| `list_regulatory_approvals` | FDA/EMA approvals |
+| `list_licensing_agreements` | Commercial partnerships |
+
+## Example Queries
+
+```
+"What drugs target EGFR and are in Phase III?"
+"Show me Novo Nordisk's full portfolio"
+"What variants are associated with Alzheimer's risk?"
+"Compare GLP-1 receptor agonists across companies"
+"Who else is targeting mTOR?"
+"List all therapeutic peptides in the database"
+"What are my detected genomic variants?"
+```
+
+## CLI Commands
+
+| Command | Description |
+|---------|-------------|
+| `nexotype-cli login` | Authenticate with email/password |
+| `nexotype-cli logout` | Delete stored credentials |
+| `nexotype-cli status` | Show current auth status |
+
+## Environment Variables
+
+| Variable | Default | Description |
+|----------|---------|-------------|
+| `NEXOTYPE_API_URL` | `http://localhost:8000` | API server URL |

nexotype_mcp-0.1.0/README.md

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+# Nexotype MCP Server
+
+AI-powered biomedical knowledge graph for drug discovery, genomics, and market intelligence.
+
+Connect your AI tools to the Nexotype platform and query the biomedical knowledge graph through conversation.
+
+## Installation
+
+```bash
+pip install nexotype-mcp
+```
+
+Or with uv:
+
+```bash
+uv tool install nexotype-mcp
+```
+
+Already installed? Update:
+
+```bash
+pip install --upgrade nexotype-mcp
+```
+
+## Authentication
+
+```bash
+nexotype-cli login
+```
+
+Enter your email and password. Credentials are stored securely at `~/.nexotype/credentials.json` (chmod 600).
+
+## Configure Your AI Client
+
+### Claude Desktop
+
+Edit `~/Library/Application Support/Claude/claude_desktop_config.json` (macOS) or `%APPDATA%\Claude\claude_desktop_config.json` (Windows):
+
+```json
+{
+  "mcpServers": {
+    "nexotype": {
+      "command": "nexotype-mcp"
+    }
+  }
+}
+```
+
+### Claude Code
+
+```bash
+claude mcp add nexotype -- nexotype-mcp
+```
+
+### VS Code / Cursor
+
+Add to your MCP settings:
+
+```json
+{
+  "nexotype": {
+    "command": "nexotype-mcp"
+  }
+}
+```
+
+Restart the application after saving.
+
+## Tools (28)
+
+### Graph Intelligence (6 tools)
+
+| Tool | Description |
+|------|-------------|
+| `explore_network` | N-hop neighborhood of any entity |
+| `find_path` | Shortest path between two entities |
+| `find_similar` | Entities sharing the most relationships |
+| `company_deep_dive` | Full portfolio of a pharma/biotech company |
+| `drug_discovery` | Targets, pathways, indications for a drug |
+| `competitive_landscape` | All drugs and companies targeting a protein |
+
+### AI Query (1 tool)
+
+| Tool | Description |
+|------|-------------|
+| `ask_knowledge_graph` | Natural language question → grounded answer from graph |
+
+### Search & Browse (2 tools)
+
+| Tool | Description |
+|------|-------------|
+| `search_entities` | List entities of any of the 61 types |
+| `get_entity` | Full details for a specific entity |
+
+### Context (3 tools)
+
+| Tool | Description |
+|------|-------------|
+| `get_permissions` | Check subscription tier and domain access |
+| `list_subjects` | List available biological subjects |
+| `set_subject` | Set active subject for personalization tools |
+
+### Personalized Health (10 tools)
+
+| Tool | Description |
+|------|-------------|
+| `get_user_profile` | Personal info linked to the subject |
+| `list_user_variants` | Detected genomic variants |
+| `list_biomarker_readings` | Time-series health data |
+| `create_biomarker_reading` | Log a new biomarker measurement |
+| `list_treatment_logs` | Intervention history |
+| `create_treatment_log` | Log a new treatment |
+| `list_pathway_scores` | Pathway health scores |
+| `list_recommendations` | Personalized treatment suggestions |
+| `upload_genomic_file` | Upload VCF/23andMe file for analysis |
+| `get_processing_status` | Check genomic file processing progress |
+
+### Commercial Intelligence (6 tools)
+
+| Tool | Description |
+|------|-------------|
+| `list_market_organizations` | Pharma/biotech companies |
+| `get_market_organization` | Full company details |
+| `list_patents` | Patent filings and status |
+| `list_development_pipelines` | Clinical trial phases |
+| `list_regulatory_approvals` | FDA/EMA approvals |
+| `list_licensing_agreements` | Commercial partnerships |
+
+## Example Queries
+
+```
+"What drugs target EGFR and are in Phase III?"
+"Show me Novo Nordisk's full portfolio"
+"What variants are associated with Alzheimer's risk?"
+"Compare GLP-1 receptor agonists across companies"
+"Who else is targeting mTOR?"
+"List all therapeutic peptides in the database"
+"What are my detected genomic variants?"
+```
+
+## CLI Commands
+
+| Command | Description |
+|---------|-------------|
+| `nexotype-cli login` | Authenticate with email/password |
+| `nexotype-cli logout` | Delete stored credentials |
+| `nexotype-cli status` | Show current auth status |
+
+## Environment Variables
+
+| Variable | Default | Description |
+|----------|---------|-------------|
+| `NEXOTYPE_API_URL` | `http://localhost:8000` | API server URL |

nexotype_mcp-0.1.0/pyproject.toml

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+[project]
+name = "nexotype-mcp"
+version = "0.1.0"
+description = "Nexotype MCP Server — biomedical knowledge graph for drug discovery, genomics, and market intelligence"
+readme = "README.md"
+license = "MIT"
+authors = [
+    { name = "Robert Radoslav", email = "43938206+rbtrsv@users.noreply.github.com" }
+]
+requires-python = ">=3.12"
+keywords = ["mcp", "nexotype", "biotech", "drug-discovery", "knowledge-graph", "genomics", "ai", "claude", "llm"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Healthcare Industry",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+]
+dependencies = [
+    "click>=8.3.2",
+    "fastmcp>=3.2.3",
+    "httpx>=0.28.1",
+]
+
+[project.urls]
+Homepage = "https://www.nexotype.com"
+Documentation = "https://www.nexotype.com"
+"PyPI" = "https://pypi.org/project/nexotype-mcp/"
+
+[project.scripts]
+nexotype-mcp = "nexotype_mcp.server:main"
+nexotype-cli = "nexotype_mcp.cli:main"
+
+[build-system]
+requires = ["uv_build>=0.8.15,<0.9.0"]
+build-backend = "uv_build"

nexotype_mcp-0.1.0/src/nexotype_mcp/__init__.py

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+# Hello from nexotype-mcp!

nexotype_mcp-0.1.0/src/nexotype_mcp/cli.py

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+"""
+Nexotype CLI — Interactive terminal authentication
+
+Commands:
+  nexotype-cli login    — Login with email/password in terminal
+  nexotype-cli logout   — Delete stored credentials
+  nexotype-cli status   — Show current auth status
+"""
+
+import getpass
+
+import click
+import httpx
+
+from .config import API_BASE_URL, REQUEST_TIMEOUT
+from .credentials import load_credentials, save_credentials, delete_credentials
+
+
+@click.group()
+def main():
+    """Nexotype CLI — Authenticate and manage your Nexotype MCP connection."""
+    pass
+
+
+def _save_and_show(data: dict) -> None:
+    """Save credentials and show orgs. Shared between login flows."""
+    token = data["token"]
+    user = data["data"]["user"]
+    orgs = data["data"]["organizations"]
+
+    # Default to first organization
+    default_org_id = orgs[0]["id"] if orgs else None
+
+    save_credentials({
+        "access_token": token["access_token"],
+        "refresh_token": token["refresh_token"],
+        "organization_id": default_org_id,
+        "user_email": user["email"],
+    })
+
+    click.echo(f"\n✓ Logged in as {user['email']}")
+    click.echo(f"✓ Credentials saved to ~/.nexotype/credentials.json\n")
+
+    if orgs:
+        click.echo("Organizations:")
+        for org in orgs:
+            marker = " (active)" if org["id"] == default_org_id else ""
+            click.echo(f"  {org['id']}. {org['name']} — role: {org['user_role']}{marker}")
+    else:
+        click.echo("Warning: No organizations found. Create one in the Nexotype dashboard.")
+
+
+@main.command()
+def login():
+    """Login to Nexotype with email and password."""
+    email = click.prompt("Email")
+    password = getpass.getpass("Password: ")
+
+    click.echo("Logging in...")
+
+    try:
+        with httpx.Client(timeout=REQUEST_TIMEOUT) as client:
+            r = client.post(
+                f"{API_BASE_URL}/accounts/auth/login",
+                json={"email": email, "password": password},
+            )
+
+            if r.status_code == 401:
+                click.echo("Error: Invalid email or password.", err=True)
+                raise SystemExit(1)
+
+            r.raise_for_status()
+            _save_and_show(r.json())
+
+    except httpx.HTTPStatusError as e:
+        click.echo(f"Error: API returned {e.response.status_code}", err=True)
+        raise SystemExit(1)
+    except httpx.ConnectError:
+        click.echo(f"Error: Cannot connect to {API_BASE_URL}. Is the server running?", err=True)
+        raise SystemExit(1)
+
+
+@main.command()
+def logout():
+    """Delete stored credentials."""
+    delete_credentials()
+    click.echo("✓ Logged out. Credentials deleted.")
+
+
+@main.command()
+def status():
+    """Show current authentication status."""
+    creds = load_credentials()
+    if not creds:
+        click.echo("Not authenticated. Run 'nexotype-cli login' first.")
+        return
+
+    click.echo(f"Email: {creds.get('user_email', 'unknown')}")
+    click.echo(f"Organization ID: {creds.get('organization_id', 'not set')}")
+    click.echo(f"API: {API_BASE_URL}")
+    click.echo(f"Token: {'present' if creds.get('access_token') else 'missing'}")
+    click.echo(f"Refresh token: {'present' if creds.get('refresh_token') else 'missing'}")

nexotype_mcp-0.1.0/src/nexotype_mcp/client.py

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+"""
+Nexotype MCP Server — HTTP Client
+
+Async httpx wrapper that handles:
+- JWT authentication (from ~/.nexotype/credentials.json)
+- Subject context (for personalization tools)
+- Automatic token refresh on 401 responses
+- Multipart file upload for VCF files
+
+Key difference from Finpy: Nexotype backend resolves organization from JWT,
+so no organization_id query param is needed.
+"""
+
+import httpx
+
+from .config import API_BASE_URL, REQUEST_TIMEOUT, UPLOAD_TIMEOUT
+from .credentials import load_credentials, save_credentials
+
+
+class NexotypeClient:
+    """HTTP client for Nexotype API with JWT auth and subject context."""
+
+    def __init__(self) -> None:
+        self.base_url = API_BASE_URL
+        # Subject context — set via set_subject() tool for personalization queries
+        self.subject_id: int | None = None
+
+    def _get_credentials(self) -> dict:
+        """Load credentials or raise descriptive error."""
+        creds = load_credentials()
+        if not creds or not creds.get("access_token"):
+            raise RuntimeError(
+                "Not authenticated. Please run 'nexotype-cli login' in your terminal first."
+            )
+        return creds
+
+    @property
+    def _headers(self) -> dict:
+        """Auth headers from stored credentials."""
+        creds = self._get_credentials()
+        return {"Authorization": f"Bearer {creds['access_token']}"}
+
+    async def _refresh_token(self) -> bool:
+        """Attempt to refresh JWT using refresh_token. Returns True if successful."""
+        creds = load_credentials()
+        if not creds or not creds.get("refresh_token"):
+            return False
+
+        try:
+            async with httpx.AsyncClient(timeout=REQUEST_TIMEOUT) as http:
+                r = await http.post(
+                    f"{self.base_url}/accounts/auth/refresh-token",
+                    json={"refresh_token": creds["refresh_token"]},
+                )
+                if r.status_code == 200:
+                    data = r.json()
+                    creds["access_token"] = data["token"]["access_token"]
+                    creds["refresh_token"] = data["token"]["refresh_token"]
+                    save_credentials(creds)
+                    return True
+        except httpx.HTTPError:
+            pass
+        return False
+
+    async def _request(self, method: str, path: str, **kwargs) -> dict:
+        """Make HTTP request with auto-refresh on 401."""
+        async with httpx.AsyncClient(timeout=REQUEST_TIMEOUT) as http:
+            r = await http.request(
+                method,
+                f"{self.base_url}{path}",
+                headers=self._headers,
+                **kwargs,
+            )
+
+            # Auto-refresh on 401
+            if r.status_code == 401:
+                refreshed = await self._refresh_token()
+                if refreshed:
+                    r = await http.request(
+                        method,
+                        f"{self.base_url}{path}",
+                        headers=self._headers,
+                        **kwargs,
+                    )
+                else:
+                    raise RuntimeError(
+                        "Session expired. Please run 'nexotype-cli login' again."
+                    )
+
+            r.raise_for_status()
+            return r.json()
+
+    async def get(self, path: str, **kwargs) -> dict:
+        """GET request to Nexotype API."""
+        return await self._request("GET", path, **kwargs)
+
+    async def post(self, path: str, data: dict) -> dict:
+        """POST request to Nexotype API."""
+        return await self._request("POST", path, json=data)
+
+    async def put(self, path: str, data: dict) -> dict:
+        """PUT request to Nexotype API."""
+        return await self._request("PUT", path, json=data)
+
+    async def post_file(self, path: str, file_path: str, form_data: dict) -> dict:
+        """
+        POST multipart file upload to Nexotype API.
+        Used for VCF/23andMe genomic file uploads.
+        Longer timeout (120s) for large files.
+        """
+        async with httpx.AsyncClient(timeout=UPLOAD_TIMEOUT) as http:
+            with open(file_path, "rb") as f:
+                files = {"file": (file_path.split("/")[-1], f)}
+                r = await http.post(
+                    f"{self.base_url}{path}",
+                    headers=self._headers,
+                    files=files,
+                    data=form_data,
+                )
+
+            # Auto-refresh on 401
+            if r.status_code == 401:
+                refreshed = await self._refresh_token()
+                if refreshed:
+                    with open(file_path, "rb") as f:
+                        files = {"file": (file_path.split("/")[-1], f)}
+                        r = await http.post(
+                            f"{self.base_url}{path}",
+                            headers=self._headers,
+                            files=files,
+                            data=form_data,
+                        )
+                else:
+                    raise RuntimeError(
+                        "Session expired. Please run 'nexotype-cli login' again."
+                    )
+
+            r.raise_for_status()
+            return r.json()
+
+
+# Singleton instance — shared across all tools
+nexotype = NexotypeClient()

nexotype_mcp-0.1.0/src/nexotype_mcp/config.py

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+"""
+Nexotype MCP Server — Configuration
+
+API base URL is read from NEXOTYPE_API_URL env var.
+Defaults to localhost for development, override for production.
+"""
+
+import os
+
+# API base URL — override with NEXOTYPE_API_URL env var for production
+API_BASE_URL = os.environ.get("NEXOTYPE_API_URL", "http://localhost:8000")
+
+# Credentials file path — where JWT + refresh token are stored locally
+CREDENTIALS_PATH = os.path.expanduser("~/.nexotype/credentials.json")
+
+# HTTP client timeout (seconds) — standard requests
+REQUEST_TIMEOUT = 30.0
+
+# HTTP client timeout (seconds) — file uploads (VCF can be up to 500MB)
+UPLOAD_TIMEOUT = 120.0

nexotype_mcp-0.1.0/src/nexotype_mcp/credentials.py

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+"""
+Nexotype MCP Server — Credentials Management
+
+Reads/writes JWT + refresh token to ~/.nexotype/credentials.json.
+File permissions set to 600 (owner read/write only).
+Password is NEVER stored — only tokens.
+"""
+
+import json
+import os
+from pathlib import Path
+from typing import TypedDict
+
+from .config import CREDENTIALS_PATH
+
+
+class Credentials(TypedDict):
+    access_token: str
+    refresh_token: str
+    organization_id: int | None
+    user_email: str
+
+
+def load_credentials() -> Credentials | None:
+    """Load credentials from ~/.nexotype/credentials.json. Returns None if not found."""
+    path = Path(CREDENTIALS_PATH)
+    if not path.exists():
+        return None
+    try:
+        with open(path) as f:
+            return json.load(f)
+    except (json.JSONDecodeError, KeyError):
+        return None
+
+
+def save_credentials(creds: Credentials) -> None:
+    """Save credentials to ~/.nexotype/credentials.json with chmod 600."""
+    path = Path(CREDENTIALS_PATH)
+    path.parent.mkdir(parents=True, exist_ok=True)
+    with open(path, "w") as f:
+        json.dump(creds, f, indent=2)
+    # Owner read/write only — no group/other access
+    os.chmod(path, 0o600)
+
+
+def delete_credentials() -> None:
+    """Delete credentials file (logout)."""
+    path = Path(CREDENTIALS_PATH)
+    if path.exists():
+        path.unlink()