biocontext-mcp 0.5.0__tar.gz

biocontext_mcp-0.5.0/.dockerignore

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+.git/
+.venv/
+__pycache__/
+*.py[cod]
+dist/
+build/
+*.egg-info/
+.cache/
+*.db
+*.sqlite*
+.pytest_cache/
+.coverage
+htmlcov/
+PRD/

biocontext_mcp-0.5.0/.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Bug report
+description: Create a report to help us improve BioContext
+labels: ["bug"]
+body:
+  - type: markdown
+    attributes:
+      value: Thanks for taking the time to report a bug!
+  - type: input
+    id: version
+    attributes:
+      label: BioContext Version
+      description: What version of BioContext are you using? (e.g., `biocontext --version`)
+    validations:
+      required: true
+  - type: textarea
+    id: description
+    attributes:
+      label: Bug Description
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+  - type: textarea
+    id: reproduction
+    attributes:
+      label: Steps To Reproduce
+      description: Steps or Python code snippet to reproduce the behavior.
+      placeholder: |
+        ```python
+        import asyncio
+        from biocontext.resolver import EntityResolver
+        async def run():
+            r = EntityResolver()
+            res = await r.resolve("...")
+        asyncio.run(run())
+        ```
+    validations:
+      required: true
+  - type: textarea
+    id: expected
+    attributes:
+      label: Expected Behavior
+      description: What did you expect to happen?
+    validations:
+      required: true
+  - type: textarea
+    id: logs
+    attributes:
+      label: Relevant Log Output or Traceback
+      render: shell

biocontext_mcp-0.5.0/.github/ISSUE_TEMPLATE/feature_request.yml

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+name: Feature request
+description: Suggest an idea or new database adapter for BioContext
+labels: ["enhancement"]
+body:
+  - type: markdown
+    attributes:
+      value: Thank you for suggesting a feature or new data adapter!
+  - type: textarea
+    id: problem
+    attributes:
+      label: Problem Statement
+      description: Is your feature request related to a specific biological database or workflow gap?
+    validations:
+      required: true
+  - type: textarea
+    id: solution
+    attributes:
+      label: Proposed Solution / Adapter
+      description: Describe the solution you'd like (e.g. adding WormBase adapter for C. elegans).
+    validations:
+      required: true
+  - type: textarea
+    id: alternatives
+    attributes:
+      label: Alternatives Considered
+      description: Any alternative solutions or workarounds you've considered.

biocontext_mcp-0.5.0/.github/pull_request_template.md

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+## Summary of Changes
+<!-- Provide a brief description of what this PR introduces or fixes. -->
+
+## Related Issues
+<!-- Link related issues, e.g. Closes #4 or Relates to #2 -->
+
+## Type of Change
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] Documentation update
+- [ ] Refactoring / Adapter migration
+
+## Checklist
+- [ ] My code follows the code style and guidelines of this project ([CONTRIBUTING.md](CONTRIBUTING.md)).
+- [ ] I have added tests that prove my fix is effective or that my feature works.
+- [ ] All new and existing tests pass locally (`uv run pytest`).
+- [ ] I have updated the documentation / docstrings accordingly.

biocontext_mcp-0.5.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "latest"
+
+      - name: Set up Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: uv sync
+
+      - name: Run full test suite
+        run: uv run pytest tests/ -v
+
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "latest"
+
+      - name: Verify package build
+        run: uv build

biocontext_mcp-0.5.0/.gitignore

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+# Python-generated files
+__pycache__/
+*.py[oc]
+build/
+dist/
+wheels/
+*.egg-info
+
+# Virtual environments
+.venv/
+
+# Caches and local data
+.cache/
+*.db
+*.sqlite
+*.sqlite3
+.pytest_cache/
+.coverage
+htmlcov/
+
+# Specification & internal documents
+PRD/

biocontext_mcp-0.5.0/CITATION.cff

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+cff-version: 1.2.0
+message: "If you use BioContext in your research, please cite it as below."
+authors:
+  - family-names: "Nandatama"
+    given-names: "Engki"
+    orcid: "https://orcid.org/0009-0003-7308-3900"
+title: "BioContext: Authoritative Biological Entity Resolution & Contextual Intelligence Framework"
+version: 0.5.0
+date-released: 2026-09-28
+url: "https://github.com/CORE-Lab-Research/biocontext"
+repository-code: "https://github.com/CORE-Lab-Research/biocontext"
+license: Apache-2.0
+keywords:
+  - bioinformatics
+  - genomics
+  - entity-resolution
+  - model-context-protocol
+  - mcp
+  - hgnc
+  - ncbi
+  - uniprot

biocontext_mcp-0.5.0/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders at [research@engkinandatama.my.id](mailto:research@engkinandatama.my.id).
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant](https://www.contributor-covenant.org),
+version 2.1, available at
+https://www.contributor-covenant.org/version/2/1/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder](https://github.com/mozilla/diversity).

biocontext_mcp-0.5.0/CONTRIBUTING.md

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+# Contributing to BioContext
+
+Thank you for your interest in contributing to BioContext! We welcome contributions from researchers, bioinformaticians, and software engineers.
+
+Please read our [Code of Conduct](CODE_OF_CONDUCT.md) and [Security Policy](SECURITY.md) before participating in our community.
+
+---
+
+## Getting Started
+
+### Prerequisites
+- Python 3.11 or higher
+- [uv](https://docs.astral.sh/uv/) (recommended package installer and resolver) or `pip`
+- Git
+
+### Development Setup
+
+1. Fork the repository on GitHub and clone your fork:
+   ```bash
+   git clone https://github.com/<your-username>/biocontext.git
+   cd biocontext
+   ```
+
+2. Add the upstream repository remote:
+   ```bash
+   git remote add upstream https://github.com/CORE-Lab-Research/biocontext.git
+   ```
+
+3. Create a virtual environment and install dependencies with development tools:
+   ```bash
+   uv sync
+   ```
+
+---
+
+## Architecture & Code Organization
+
+```
+src/biocontext/
+├── base.py       # BaseBioAdapter abstract class, SQLiteCache, AsyncRateLimiter
+├── config.py     # ClientConfig, RateLimitConfig, CLI_COMMANDS_REGISTRY
+├── schemas.py    # Pydantic v2 domain models (GeneEntity, ProteinEntity, GOAnnotation, PathwayContext)
+├── adapters.py   # Database adapters (HGNC, NCBI, UniProt, Ensembl, MGI, QuickGO, Reactome)
+├── resolver.py   # EntityResolver multi-authority resolution engine & batch engine
+├── server.py     # FastMCP tool-calling interface for AI agents
+├── cli.py        # CLI subcommand parsers and argument handlers
+└── logging.py    # Structured logging formatted to stderr
+```
+
+---
+
+## How to Build a New Biological Adapter
+
+BioContext follows an extensible adapter pattern. To connect a new biological database:
+
+### Step 1: Subclass `BaseBioAdapter`
+All adapters must inherit from `BaseBioAdapter` in [`base.py`](file:///home/nanda/projects/biocontext/src/biocontext/base.py):
+
+```python
+from typing import Optional, Dict, Any
+import httpx
+from biocontext.base import BaseBioAdapter, SQLiteCache
+from biocontext.config import ClientConfig, RateLimitConfig
+
+class MyNewBioAdapter(BaseBioAdapter):
+    """Adapter for MyNewDatabase REST API."""
+    BASE_URL = "https://api.mynewdatabase.org"
+
+    def __init__(self, cache: Optional[SQLiteCache] = None, email: Optional[str] = None):
+        super().__init__(name="MyNewDatabase", cache=cache)
+        self.email = ClientConfig.get_email(email)
+        self.headers = ClientConfig.get_headers(self.email)
+
+    async def fetch_data(self, query_id: str) -> Optional[Dict[str, Any]]:
+        # 1. Check SQLite cache
+        cache_key = f"record:{query_id.upper()}"
+        cached = self.cache.get("mynewdb", cache_key)
+        if cached:
+            return cached
+
+        # 2. Query external API with rate limiting & error handling
+        url = f"{self.BASE_URL}/records/{query_id}"
+        async with httpx.AsyncClient(timeout=10.0) as client:
+            resp = await client.get(url, headers=self.headers)
+            if resp.status_code != 200:
+                return None
+            data = resp.json()
+
+        # 3. Store in cache & return
+        self.cache.set("mynewdb", cache_key, data)
+        return data
+```
+
+### Step 2: Define Strongly-Typed Schemas
+Add domain models in [`schemas.py`](file:///home/nanda/projects/biocontext/src/biocontext/schemas.py) using Pydantic v2:
+```python
+class MyEntity(BaseModel):
+    id: str
+    name: str
+    provenance: str = "MyNewDatabase"
+```
+
+### Step 3: Wire into `EntityResolver` and `server.py`
+1. Instantiate the adapter in `EntityResolver.__init__()` ([`resolver.py`](file:///home/nanda/projects/biocontext/src/biocontext/resolver.py)).
+2. Expose an MCP tool in `server.py` decorated with `@mcp.tool()` for AI clients.
+3. Register the CLI subcommand in `config.py` and `cli.py`.
+
+---
+
+## Testing & Quality Assurance
+
+All contributions must pass existing tests and include tests for new functionality.
+
+1. **Run the full test suite**:
+   ```bash
+   uv run pytest tests/ -v
+   ```
+
+2. **Run specific test suites**:
+   ```bash
+   # Core resolver & schemas
+   uv run pytest tests/test_resolver.py -v
+
+   # Biological benchmark accuracy (50 curated test cases)
+   uv run pytest tests/test_benchmark.py -v
+
+   # High-throughput batch processing engine
+   uv run pytest tests/test_batch_processing.py -v
+
+   # Functional annotations & Pathways
+   uv run pytest tests/test_go_adapter.py tests/test_reactome_adapter.py -v
+
+   # MCP Server tool execution
+   uv run pytest tests/test_server.py -v
+   ```
+
+3. **Verify CLI subcommands**:
+   ```bash
+   uv run biocontext --help
+   uv run biocontext resolve TP53
+   uv run biocontext batch TP53 EGFR BRCA1
+   uv run biocontext annotate TP53
+   uv run biocontext pathway TP53
+   ```
+
+---
+
+## Commit Guidelines
+
+We follow the [Conventional Commits](https://www.conventionalcommits.org/) convention:
+
+- `feat(scope): add new feature or adapter`
+- `fix(scope): fix bug or error handling`
+- `docs: update documentation or README`
+- `test: add or update test suites`
+- `refactor: code changes without altering external behavior`
+
+**Git Hygiene Notice**: Do not add AI attribution trailers (e.g. `Co-Authored-By: <AI>`) in commit messages.
+
+---
+
+## Pull Request Process
+
+1. Ensure all tests pass locally (`uv run pytest tests/`).
+2. Push your topic branch to your fork:
+   ```bash
+   git push origin feat/your-feature-name
+   ```
+3. Open a Pull Request against the `main` branch of `CORE-Lab-Research/biocontext`.
+4. Fill out the PR template describing the purpose of the change, test results, and any relevant issue references.
+5. Maintainers will review your PR and coordinate merging.

biocontext_mcp-0.5.0/Dockerfile

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+# syntax=docker/dockerfile:1
+FROM python:3.12-slim-bookworm
+
+ENV PYTHONUNBUFFERED=1 \
+    PYTHONDONTWRITEBYTECODE=1 \
+    PIP_NO_CACHE_DIR=1 \
+    BIOCONTEXT_CACHE_PATH=/data/biocontext_cache.db
+
+WORKDIR /app
+
+# Install system dependencies
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    curl \
+    ca-certificates \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install uv for fast, reliable dependency management
+COPY --from=ghcr.io/astral-sh/uv:0.6.14 /uv /uvx /bin/
+
+# Copy dependency specifications first for layer caching
+COPY pyproject.toml README.md ./
+
+# Install python dependencies without the project first
+RUN uv pip install --system -r pyproject.toml
+
+# Copy project source code
+COPY src/ ./src/
+
+# Install biocontext package
+RUN uv pip install --system -e .
+
+# Create cache data directory
+RUN mkdir -p /data
+
+VOLUME ["/data"]
+
+EXPOSE 8000
+
+# Default entrypoint runs the MCP server via stdio
+ENTRYPOINT ["biocontext"]
+CMD ["serve"]