nanohub-remote 0.2.0

A set of tools to run nanohub web apis

Nanohub remote

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A set of tools/apps to run on nanohub

Installation

pip install nanohub-remote

Usage

Basic Authentication

import nanohubremote as nr

# Option 1: OAuth Password Grant (requires web application)
auth_data = {
  'client_id': 'XXXXXXXX',
  'client_secret': 'XXXXXXXX',
  'grant_type': 'password',
  'username': 'your_username',
  'password': 'your_password'
}

# Option 2: Personal Access Token (recommended)
auth_data = {
  'grant_type': 'personal_token',
  'token': 'your_personal_token'
}

# to get username and password, register on nanohub.org (https://nanohub.org/register/)
# to get client id and secret, create a web application (https://nanohub.org/developer/api/applications/new), use "https://127.0.0.1" as Redirect URL
# to get a personal token, go to https://nanohub.org/developer/api/tokens

# Create a session
session = nr.Session(auth_data)

# Or use as a context manager (recommended - automatically cleans up resources)
with nr.Session(auth_data) as session:
    # Your code here
    pass

Session Configuration

The Session class supports advanced configuration options:

session = nr.Session(
    auth_data,
    url="https://nanohub.org/api",  # Custom API URL
    timeout=10,                       # Request timeout in seconds (default: 5)
    max_retries=5,                    # Maximum retries for failed requests (default: 3)
    pool_connections=20,              # Connection pool size (default: 10)
    pool_maxsize=20                   # Max pool size (default: 10)
)

HTTP Methods

The Session class provides methods for all standard HTTP verbs:

with nr.Session(auth_data) as session:
    # GET request
    response = session.requestGet('tools/list')
    tools = response.json()

    # POST request with form data
    response = session.requestPost('endpoint', data={'key': 'value'})

    # POST request with JSON
    response = session.requestPost('endpoint', json={'key': 'value'})

    # PUT request
    response = session.requestPut('resource/123', json={'status': 'updated'})

    # DELETE request
    response = session.requestDelete('resource/123')

    # PATCH request
    response = session.requestPatch('resource/123', json={'field': 'new_value'})

Features

• Connection Pooling: Reuses HTTP connections for better performance
• Automatic Retries: Automatically retries failed requests (configurable)
• Token Management: Handles OAuth token refresh automatically
• Context Manager: Use with statement for automatic resource cleanup
• Persistent Headers: Headers are maintained across all requests

Development

Running Tests

# Install development dependencies
pip install -r requirements-dev.txt

# Run all tests
pytest

# Run with coverage
pytest --cov=nanohubremote --cov-report=html

# Run specific test file
pytest tests/test_session.py

See tests/README.md for detailed testing documentation.

Available Nanohub Points

Tools

TOOLNAME = '' # valid Nanoohub tool name e.g. pntoy
tool = nr.Tool(auth_data)

# Get Available input parameters
params = tool.getToolParameters(TOOLNAME)

# Submit a simulation experiment
job_id = tool.submitTool(params)

# Check Status
status = tool.checkStatus(job_id['job_id'])

# Get Results
results = tool.getResults(job_id['job_id'])

# Submit an wait for results
results = tool.submitTool(params, wait_results=True)

Sim2Ls

TOOLNAME = '' # valid Nanoohub tool name e.g. pntoy
s2l = nr.Sim2L(auth_data)

# Get Available input parameters
params = s2l.getToolParameters(TOOLNAME)

# Submit a simulation experiment
job_id = s2l.submitTool(params)

# Check Status
status = s2l.checkStatus(job_id['job_id'])

# Get Results
results = s2l.getResults(job_id['job_id'])

# Submit an wait for results
results = s2l.submitTool(params, wait_results=True)