hla-compass 1.6.15

Python SDK for HLA-Compass bioinformatics platform - Build powerful modules for immuno-peptidomics analysis

HLA-Compass Python SDK

The official Python SDK for developing modules on the HLA-Compass platform.

Requirements

• Python 3.8 or higher (3.8, 3.9, 3.10, 3.11, 3.12, 3.13 supported)
• pip package manager

Installation

pip install hla-compass

That's it! No extras needed.

Install from Source (Latest Development Version)

# Clone the repository
git clone https://github.com/AlitheaBio/HLA-Compass-platform.git
cd HLA-Compass-platform/sdk/python

# Install in development mode
pip install -e .

Quick Start

# 1. Setup
hla-compass configure --env dev
hla-compass auth login --env dev

# 2. Create module
hla-compass init my-module --interactive
cd my-module

# 3. Develop with hot-reload
hla-compass dev

# 4. Test
hla-compass test --input examples/sample.json

# 5. Publish
hla-compass build --tag my-module:1.0.0
hla-compass publish --env dev --image-ref my-module:1.0.0

Workflow

The SDK follows a simple 5-step workflow:

1. init - Scaffold module from template
2. dev - Develop with hot-reload in Docker
3. validate/test - Validate manifest and test execution
4. build - Create Docker image
5. publish - Sign and register with platform

Each step builds on the previous, ensuring a smooth development experience.

📚 For complete development guide, see: Developer Guide

Ten-Minute Module (Guided)

Step	Command / Code	Why
1	pip install hla-compass	Installs CLI, wizard, dev server, and data helpers in one go so nothing is missing when you scaffold.
2	hla-compass init --interactive	Wizard captures manifest metadata, inputs, and UI choice, emitting backend/frontend scaffolding ready to run.
3	hla-compass validate-module	Runs schema + structure + security checks (and warns if devkit/OpenAPI are out-of-sync) before you spend time testing.
4	python\nfrom hla_compass.testing import ModuleTester\nfrom backend.main import Module\nModuleTester().quickstart(Module, mode="interactive")\n	Spins up a mock context using manifest defaults so you can smoke-test the execute path instantly.
5	Add self.storage.save_json("results/preview.json", payload) inside execute	Storage helper normalises metadata, accepts streams, and raises friendly extras guidance if optional deps (pandas/xlsxwriter) are missing.
6	python\nfrom hla_compass.client import APIClient\nclient = APIClient()\nclient.set_telemetry_callback(print)\n	Hooks the new telemetry callback so each API request logs status/duration/idempotency for troubleshooting.
7	hla-compass doctor	Checks auth, rate-limit env vars, Docker, Node, optional extras, and tells you exactly what to install or export.
8	hla-compass build && hla-compass publish --env dev	Generates MCP descriptor + Docker image, signs manifest, pushes, and registers the module with the chosen environment.

👉 The table above mirrors the expanded walkthrough in SDK Documentation, which adds manifest snippets and deeper commentary.

CLI Commands

Module Management

# Create new module
hla-compass init <name> [options]
# Options: --yes (skip prompts), --template, --type

# Validate module structure
hla-compass validate [--json]  # --json for machine-readable output

# Full validation (schema + structure + security + OpenAPI)
hla-compass validate-module [--strict] [--with-devkit] [--format json]

# Test module (auto-detects local vs remote based on auth)
hla-compass test [--input FILE] [--verbose]

# Test locally without API
hla-compass test --local [--input FILE]

# Test against real API (requires auth)
# Note: Remote mode currently executes locally with API authentication context
# Full remote execution on the platform is on the roadmap
hla-compass test --remote [--input FILE]

# Output as JSON for CI/automation
hla-compass test --json [--input FILE]

# Build container image (local by default)
hla-compass build [--tag TAG] [--push]

# Publish container + MCP descriptor to the platform (signs automatically)
hla-compass publish --env ENV --image-ref IMAGE

# Local devkit docker-compose stack
hla-compass devkit up [--build]
hla-compass devkit status
hla-compass devkit logs [--service postgres] [--follow]
hla-compass devkit down

# List deployed modules
hla-compass list [--env ENV]

# Removed commands (functionality now integrated into publish):
# - hla-compass sign: Signing now happens automatically during publish
# - hla-compass deploy: Use publish instead

Development Server

# Offline dev server (quiet by default)
hla-compass dev

# Stream webpack/aiohttp logs
hla-compass dev --verbose

# Proxy selected routes to the live API (read-only by default)
hla-compass dev --online --env dev --proxy-routes=auth,data

# Serve UI bundle from a custom webpack port
hla-compass dev --frontend-port 3100

Authentication

# Login to platform
hla-compass auth login --env dev

# Logout
hla-compass auth logout

# Register as a developer (self-service)
hla-compass auth register [--env ENV]

CLI Feature Matrix

Command	Description	Status
hla-compass configure	Initialize SDK config and signing keys	Available
hla-compass init	Scaffold a new module from templates	Available
hla-compass validate	Validate module structure and manifest	Available
hla-compass test --local	Run module locally without API	Available
hla-compass test --remote	Run locally with API auth context	Available (executes locally)
hla-compass auth login/logout/status	Authentication flows	Available
hla-compass build	Build Docker image + MCP descriptor (optionally push)	Available
hla-compass publish	Sign and register module with platform	Available
hla-compass list	List deployed modules	Available
hla-compass test	Test module execution (local/remote)	Available
hla-compass sign	Sign a module directory/manifest	Removed (use publish)
hla-compass deploy	Register an existing container image	Removed (use publish)
hla-compass templates list	List module templates	Planned
hla-compass local-services	Start local DB/S3 dev services	Planned

Storage Quick Reference

Helper	Input Types	Output	Notes
save_json(name, data)	dict, list, or serialisable objects	.json artifact	Uses json.dumps(..., default=str) so datetimes survive. [storage.py:120–196]
save_csv(name, dataframe, index=False, compress=False)	pandas DataFrame	.csv text or .csv.gz when compress=True	Requires pandas; metadata coerced to strings automatically; safe against CSV formula injection.
save_excel(name, dataframe)	pandas DataFrame or dict of DataFrames	.xlsx workbook	Raises MissingDependencyError with install guidance when optional extras are missing. [storage.py:224–276]
save_file(name, content, content_type=None, metadata=None)	bytes, str, file-like object	Raw object with MIME detection	Accepts streams, normalises metadata collections to comma-separated strings. [storage.py:79–158]

All helpers return the storage key/URL emitted by the execution environment, so you can echo links in summary payloads without additional plumbing.

Notes:

• --remote test currently executes locally with API authentication context; full remote execution is on the roadmap.
• For end-to-end deployments, prefer the publish path integrated with the platform pipelines.

Testing

Unit Testing

# tests/test_module.py
import pytest
from hla_compass.testing import ModuleTester, MockContext

def test_module_execution():
    tester = ModuleTester()
    
    input_data = {
        'sequence': 'MLLSVPLLL',
        'threshold': 0.5
    }
    
    result = tester.test_local(
        'backend/main.py',
        input_data
    )
    
    assert result['status'] == 'success'
    assert len(result['results']) > 0

Integration Testing

# Test with mock API data
def test_with_mock_data():
    context = MockContext.create(
        api_data={
            'peptides': [
                {'id': '1', 'sequence': 'MLLSVPLLL'},
                {'id': '2', 'sequence': 'SIINFEKL'}
            ]
        }
    )
    
    result = tester.test_local(
        'backend/main.py',
        {'min_length': 8},
        context
    )
    
    assert len(result['results']) == 2

Need to exercise the devkit container or real S3/MinIO buckets? Opt in explicitly so tests don’t accidentally touch production services:

tester.configure_local_devkit(use_real_storage=True)
context = MockContext.create(use_devkit=True, use_real_storage=True)

Performance Testing

# Benchmark module performance
def test_performance():
    tester = ModuleTester()
    
    results = tester.benchmark(
        'backend/main.py',
        input_data,
        iterations=100
    )
    
    assert results['average_time'] < 0.1  # 100ms

Advanced Features

Module Types

Lambda Modules (Quick Analysis)

• Execution time: <15 minutes
• Memory: 128MB - 10GB
• Best for: Simple calculations, data filtering

Fargate Modules (Long Running)

• Execution time: <8 hours
• Memory: 512MB - 30GB
• Best for: Complex pipelines, batch processing

SageMaker Modules (ML Inference)

• GPU support available
• Pre-trained model hosting
• Best for: Machine learning predictions

UI Module Bundles

UI-capable modules ship a React bundle the platform loads dynamically. Keep the generated webpack configuration’s ModuleUI UMD export intact so the host application can mount your UI. When running hla-compass dev, pass --verbose to stream webpack output if the UI fails to load (helpful for diagnosing “ModuleUI UMD not found” and other build issues).

Custom Validation

class MyModule(Module):
    def validate_inputs(self, input_data):
        # Call parent validation
        validated = super().validate_inputs(input_data)
        
        # Custom validation
        sequence = validated.get('sequence', '')
        if not all(aa in 'ACDEFGHIKLMNPQRSTVWY' for aa in sequence):
            raise ValidationError("Invalid amino acids in sequence")
        
        return validated

Best Practices

1. Input Validation: Always validate inputs thoroughly
2. Error Handling: Use try-except blocks and provide clear error messages
3. Logging: Use appropriate logging levels (debug, info, warning, error)
4. Performance: Process data in batches when possible
5. Memory: Stream large results instead of loading all into memory
6. Security: Never hardcode credentials or sensitive data
7. Testing: Write comprehensive tests for all functionality
8. Documentation: Document inputs, outputs, and algorithms clearly

Environment Variables

• HLA_COMPASS_ENV: Default environment (dev, staging, prod) - takes precedence over HLA_ENV
• HLA_ENV: Alternative environment variable (used if HLA_COMPASS_ENV not set)
• HLA_COMPASS_CONFIG_DIR: Configuration directory (default: ~/.hla-compass)
• HLA_COMPASS_LOG_LEVEL: Logging level (DEBUG, INFO, WARNING, ERROR)
• HLA_CORRELATION_ID: Optional global correlation ID propagated as X-Correlation-Id

Troubleshooting

Common Issues

1. Import Errors: Ensure all dependencies are in requirements.txt
2. Timeout Errors: Increase timeout in manifest.json or optimize code
3. Memory Errors: Process data in smaller chunks or increase memory
4. Authentication Errors: Run hla-compass auth login to refresh tokens

Debug Mode

Enable debug logging:

import logging
logging.basicConfig(level=logging.DEBUG)

Request Headers & Tracing

The SDK standardizes outbound request headers and retry behavior.

• Accept: Always application/json (session default)
• User-Agent: hla-compass-sdk/<version> python/<version> os/<platform>
• Content-Type: application/json for JSON requests (per-call)
• X-Request-Id: Unique UUID per HTTP attempt (changes on retry)
• X-Correlation-Id: Optional global correlation ID for cross-service tracing
  • Set environment variable HLA_CORRELATION_ID to propagate a stable value
  • Added to both SDK auth requests and APIClient requests
• Idempotency-Key: Added to POST requests to make retries safe
  • A stable UUID is generated per SDK call and reused across retry attempts
  • Server-side should de-duplicate requests using this key

Retry Policy

• GET/HEAD/OPTIONS: Retries enabled (connection/read) with exponential backoff via urllib3.Retry
• 401 Unauthorized: One automatic token refresh (Auth.refresh_token) and retry
• 429 Too Many Requests: Honors Retry-After (falls back to exponential backoff)
• 5xx Server Errors: Exponential backoff; for POST, retries only when an Idempotency-Key is present (the SDK adds one per call)
• Timeouts/Network errors: Limited retries with backoff for transient connection issues

Tip: For end-to-end traceability, set HLA_CORRELATION_ID in your environment and pass it across your systems.

Deployment Note: SimpleDeployer (Deprecated / Dev-only)

The legacy hla_compass.deployer.SimpleDeployer utility is disabled by default and intended only for local development experiments. It bypasses platform authentication and infrastructure pipelines.

• Disabled by default; to enable explicitly set HLA_ENABLE_SIMPLE_DEPLOYER=1.
• Recommended path: use hla-compass build + hla-compass publish/deploy and the platform’s Serverless/Terraform pipelines.

Support

• Complete Guide: Developer Guide
• Examples: Module Templates
• Issues: GitHub Issues
• Quick Start: Quick Start

License

Copyright © 2024 Alithea Bio. All rights reserved.

Advanced Topics

Data Access (SQL & Storage)

Modules access data via the DataClient, which provides scoped access to specific data catalogs.

from hla_compass.module import Module

class AnalysisModule(Module):
    def execute(self, input_data, context):
        # 1. Execute SQL (Secure, Row-Level Scoped)
        # Queries are executed against the schema for the configured catalog (default: immunopeptidomics)
        query = "SELECT sequence, mass FROM peptides WHERE length > %s LIMIT 10"
        result = self.data.sql.query(query, params=[input_data.get("min_length", 8)])
        
        # 2. Access Storage (Direct S3)
        # Reads directly from the organization's S3 bucket prefix
        # Supports 'polars' or 'pandas' engines
        df = self.data.storage.read_parquet("runs/latest/results.parquet", engine="polars")
        
        return {
            "peptides": result["data"],
            "stats": df.describe().to_dict()
        }

Handling Large Datasets (Streaming Iterators)

When working with large result sets via the APIClient (outside module context), you can still use the client directly:

Example: Iterating peptides in pages of 1,000 and stopping after 100k results

from hla_compass.client import APIClient

client = APIClient()

count = 0
for peptide in client.iter_peptides(
    {"hla_allele": "HLA-A*02:01"},
    page_size=1000,
    max_results=100_000,
):
    # process peptide incrementally
    count += 1

print("processed", count)

Inside a Module, you can access the underlying API client from the data helper to stream safely during execute:

from hla_compass.module import Module

class StreamModule(Module):
    def execute(self, input_data, context):
        assert self.peptides is not None and self.peptides.api is not None

        top = []
        for pep in self.peptides.api.iter_peptides({"sequence": input_data.get("sequence", "%")}, page_size=2000):
            # Example: collect just a small sample to keep memory bounded
            if len(top) < 5000:
                top.append({"sequence": pep["sequence"], "mass": pep.get("mass")})
            else:
                break
        return top

Tips:

• Prefer iter_peptides/iter_proteins/iter_samples for bulk processing.
• Use max_results to enforce hard caps in long-running jobs.
• For DataFrame needs, accumulate to CSV via Storage.save_csv in chunks instead of building a giant list in memory.

Telemetry Callbacks for APIClient

Capture per-request metrics (status, duration, retries, idempotency key presence) with a callback to ease troubleshooting.

import logging
from hla_compass.client import APIClient

log = logging.getLogger(__name__)

def on_api(data):
    # data contains: method, url, status_code, duration_seconds, attempt, max_retries,
    #                rate_limit_wait, params (redacted in logs), idempotency_key, request_id, error
    log.info("API %s %s %.3fs", data["status_code"], data["url"], data["duration_seconds"]) 

client = APIClient()
client.set_telemetry_callback(on_api)
client.get_peptide("pep_123")
print(client.get_rate_limit_state())  # {'max_requests': ..., 'time_window': ..., 'last_wait_seconds': ...}

Environment knobs:

• HLA_RATE_LIMIT_MAX_REQUESTS, HLA_RATE_LIMIT_TIME_WINDOW to tune rate limits
• HLA_CORRELATION_ID to propagate a stable X-Correlation-Id across requests

Auto-generated API Reference (pdoc)

• Browse: SDK Documentation
• Build locally:

bash scripts/docs-generate-python-sdk.sh
open docs/sdk/python/index.html  # macOS, or use your browser to open the file

The script sets PYTHONPATH to include sdk/python and generates docs for the hla_compass package using pdoc.