antclient 1.1.2

Lightweight Python client for Anthive REST API - query single-cell expression databases

Anthive Client

Lightweight Python client for the Anthive REST API - query single-cell expression databases with ease.

Features

• Lightweight: Only requires requests library
• Optional pandas support: Install pandas for DataFrame output
• Pyodide-compatible: Runs in JupyterLite / browser environments
• Type hints: Full type annotations for IDE support
• Auto-detection: Works in standard Python, Pyodide, and Streamlit
• Comprehensive: Complete API coverage including gene statistics

Installation

From PyPI

# Basic installation
pip install antclient

# With pandas support for DataFrames
pip install antclient[pandas]

From Source

# Clone repository
git clone https://github.com/anthive/anthive4.git
cd anthive4

# Install
pip install -e .

# Or just copy the single file
cp antclient.py /path/to/your/project/

Quick Start

from antclient import AnthiveClient
from anthelper import find_database, find_metadata

# Connect to API (auto-detects URL in Pyodide/browser)
client = AnthiveClient()

# Browse available datasets
find_database(client, "brain")          # search by keyword
find_metadata(client, "LC5/SPM")        # list obs columns

# Get database info and detect best layer
info = client.get_database_info("LC5/SPM")
layer = 'data' if 'data' in info['layers'] else info['layers'][0]

# Search genes
genes = client.search_genes("LC5/SPM", q="Apoe", limit=10)

# Get per-gene statistics (fast — no full cell download)
stats = client.get_gene_stats("LC5/SPM", ["Apoe", "Actb"], format='dataframe')
print(stats[["gene", "pct_nonzero", "mean", "median_nonzero"]])

# Get cell data as DataFrame
df = client.get_cells(
    "LC5/SPM",
    genes=["Apoe", "Trem2"],
    metadata=["genotype", "cell_type"],
    layer=layer,
    format='dataframe'
)
print(df.head())

Usage Examples

Database Discovery

# List all databases
databases = client.get_databases()

# Get as DataFrame
df = client.get_databases(format='dataframe')

# Force refresh from disk
databases = client.get_databases(refresh=True)

# Get specific database info
info = client.get_database_info("Voet2025/slide_st.counts")
print(f"Title: {info['title']}")
print(f"Layers: {info['layers']}")
print(f"Embeddings: {info['embeddings']}")

Gene Operations

# Search genes
genes = client.search_genes("mydb", q="CD", limit=20)

# Case-sensitive search
genes = client.search_genes("mydb", q="Cd4", case_sensitive=True)

# Get gene info
info = client.get_gene_info("mydb", "CD4")

# Get all genes (careful - may be large!)
all_genes = client.get_all_genes("mydb")

Gene Statistics (lightweight — no full cell download)

# Single gene
stats = client.get_gene_stats("mydb", "APOE")
# Returns list of dicts: gene, layer, n_cells, n_nonzero, pct_nonzero,
#   mean, std (all cells), mean_nonzero, std_nonzero, median_nonzero,
#   q10_nonzero, q90_nonzero, max

# Multiple genes as DataFrame
df = client.get_gene_stats("mydb", ["APOE", "CLU", "ACTB"],
                           layer="data", format='dataframe')
print(df[["gene", "pct_nonzero", "mean", "median_nonzero"]])

Cell Data Retrieval

# Get expression data for specific genes
result = client.get_cells(
    "mydb",
    genes=["CD4", "CD8"],
    limit=100
)

# Get with metadata
result = client.get_cells(
    "mydb",
    genes=["CD4"],
    metadata=["cell_type", "tissue"]
)

# Get all metadata
result = client.get_cells(
    "mydb",
    genes=["CD4"],
    metadata="*"  # or metadata=["*"]
)

# With filters
result = client.get_cells(
    "mydb",
    genes=["CD4"],
    metadata=["cell_type", "n_counts"],
    filters=[
        "cell_type:T-cell",
        "n_counts:1000,5000"  # range filter
    ]
)

# Get as DataFrame
df = client.get_cells(
    "mydb",
    genes=["CD4", "CD8"],
    metadata=["cell_type"],
    format='dataframe'
)

# Export to CSV
csv_data = client.get_cells(
    "mydb",
    genes=["CD4"],
    format='csv'
)

# Export to Parquet
parquet_bytes = client.get_cells(
    "mydb",
    genes=["CD4"],
    format='parquet'
)

Embeddings

# List available embeddings
embeddings = client.get_embeddings("mydb")

# Get UMAP coordinates
umap = client.get_embedding_data("mydb", "Umap", n_dims=2, limit=1000)

# Get as DataFrame
df = client.get_embedding_data("mydb", "Umap", format='dataframe')

# Get all dimensions
pca = client.get_embedding_data("mydb", "Pca", n_dims=0)  # 0 = all

Metadata Operations

# List metadata fields
fields = client.get_metadata_fields("mydb")
print(f"Numerical fields: {fields['numerical']}")
print(f"Categorical fields: {fields['categorical']}")

# List layers
layers = client.get_layers("mydb")

SQL Queries

# Execute raw SQL
result = client.execute_sql(
    "mydb",
    "SELECT cell_name, celltype FROM obscat LIMIT 10"
)

# Get as DataFrame
df = client.execute_sql(
    "mydb",
    "SELECT * FROM obsnum WHERE n_counts > 5000",
    format='dataframe'
)

# With limit
result = client.execute_sql(
    "mydb",
    "SELECT * FROM cells",
    limit=100
)

Server Monitoring (Phase 2)

# Check server health
health = client.get_health()
print(f"Status: {health['status']}")

# Get performance metrics
metrics = client.get_metrics()
print(f"Cache hit rate: {metrics['connection_pool']['hit_rate']:.2%}")
print(f"Uptime: {metrics['uptime_seconds']} seconds")

Admin Operations

# Rescan databases
result = client.rescan_databases()
print(f"Databases: {result['previous_count']} -> {result['current_count']}")
print(f"Added: {result['added']}")
print(f"Removed: {result['removed']}")

Advanced Usage

Environment Variables

# Set default API URL
export ANTHIVE_API_URL="http://myserver:8080"

# Client will auto-detect from environment
client = AnthiveClient()  # Uses ANTHIVE_API_URL

Pyodide/Browser Integration

// In browser JavaScript, set global variable
window.ANTHIVE_API_URL = "https://api.example.com";

# In Pyodide Python
from antclient import AnthiveClient

# Auto-detects from window.location or ANTHIVE_API_URL global
client = AnthiveClient()

Streamlit Integration

The client automatically uses Streamlit's caching when available:

import streamlit as st
from antclient import AnthiveClient

# Cached automatically in Streamlit
client = AnthiveClient("http://localhost:8080")
databases = client.get_databases()  # Cached for 60s

st.dataframe(databases)

Custom Timeout

# Set custom timeout
client = AnthiveClient("http://localhost:8080", timeout=60)

API Reference

AnthiveClient

Constructor:

• AnthiveClient(base_url=None, timeout=30)

Info Methods:

• get_root() - API root information
• get_health() - Server health status
• get_metrics() - Performance metrics (Phase 2)

Database Methods:

• get_databases(refresh=False, format='list') - List databases
• get_database_info(db_id) - Database details
• list_database_ids() - Get database IDs only

Gene Methods:

• search_genes(db_id, q='', limit=100, case_sensitive=False) - Search genes
• get_gene_info(db_id, gene_id) - Gene details
• get_all_genes(db_id) - All genes (may be large!)
• get_gene_stats(db_id, genes, layer='X', format='json') - Per-gene statistics

Metadata Methods:

• get_layers(db_id) - List layers
• get_metadata_fields(db_id) - List metadata fields
• get_embeddings(db_id) - List embeddings

Data Methods:

• get_cells(db_id, genes=None, metadata=None, layer='X', filters=None, limit=None, format='json') - Get cell data
• get_embedding_data(db_id, embedding_id, n_dims=2, limit=None, format='json') - Get embeddings

Query Methods:

• execute_sql(db_id, query, limit=None, format='json') - Execute SQL

Admin Methods:

• rescan_databases() - Force database rescan

Error Handling

import requests

try:
    result = client.get_database_info("nonexistent")
except requests.HTTPError as e:
    if e.response.status_code == 404:
        print("Database not found")
    elif e.response.status_code == 503:
        print("Server unavailable")
    else:
        print(f"Error: {e}")

Development

Testing

# Install dev dependencies
pip install -e .[dev]

# Run tests (when test suite is created)
pytest tests/

# Check code style
black antclient.py
flake8 antclient.py

Building for PyPI

cd antclient
./build_pypi.sh            # copies README, builds, checks

# Upload (requires PyPI credentials)
uvx twine upload --repository testpypi dist/*   # test first
uvx twine upload dist/*                          # production

anthelper — Jupyter Notebook Helpers

The companion anthelper module ships with antclient and provides pretty-printing helpers for interactive use:

from anthelper import find_database, find_metadata

# Browse available datasets (sorted by year, up to 20)
find_database(client)
find_database(client, "alzheimer")   # filter by keyword

# List obs columns for a dataset
find_metadata(client, "LC5/SPM")
find_metadata(client, "LC5/SPM", "cell")   # filter column names

anthelper is designed for Jupyter / JupyterLite but works in any Python environment.

Requirements

Required:

• Python >= 3.9
• requests >= 2.25.0

Optional:

• pandas >= 1.3.0 (for format='dataframe' support)

Compatibility

• Python: 3.9, 3.10, 3.11, 3.12
• Environments: Standard Python, Pyodide, Streamlit
• API: Anthive REST API v2.0 (Phase 2)

License

MIT License - see LICENSE file for details

Contributing

Contributions welcome! Please open an issue or pull request on GitHub.

Support

• Issues: https://github.com/anthive/anthive4/issues
• Documentation: https://github.com/anthive/anthive4
• API Documentation: http://your-server:8080/docs

Changelog

1.0.0 (2026-02-24)

• Initial release for Anthive REST API v2.0 (Phase 2)
• Single-file lightweight client
• Full API coverage
• Optional pandas support
• Pyodide compatible
• Streamlit caching support