genesis/api_clients/chembl_api.py

# genesis/api_clients/chembl_api.py
import os
import requests
from typing import Dict, List, Optional

CHEMBL_BASE = "https://www.ebi.ac.uk/chembl/api/data/"
CHEMBL_API_KEY = os.getenv("CHEMBL_API_KEY")  # Optional if you have API key

# -------------------------
# Core Request Helper
# -------------------------
def chembl_request(endpoint: str, params: Dict) -> Dict:
    """
    Helper to make ChEMBL API requests.
    """
    url = f"{CHEMBL_BASE}{endpoint}"
    headers = {"Accept": "application/json"}
    if CHEMBL_API_KEY:
        headers["Authorization"] = f"Bearer {CHEMBL_API_KEY}"
    r = requests.get(url, headers=headers, params=params)
    r.raise_for_status()
    return r.json()

# -------------------------
# Search Molecules
# -------------------------
def search_molecule(query: str, max_results: int = 10) -> List[Dict]:
    """
    Search for molecules in ChEMBL by name or ChEMBL ID.
    """
    data = chembl_request("molecule/search", {"q": query, "limit": max_results})
    return data.get("molecules", [])

def get_molecule_details(chembl_id: str) -> Dict:
    """
    Get detailed molecule info by ChEMBL ID.
    """
    return chembl_request(f"molecule/{chembl_id}", {})

def get_molecule_image(chembl_id: str) -> str:
    """
    Get image (SVG) of a molecule structure.
    """
    return f"https://www.ebi.ac.uk/chembl/api/data/image/{chembl_id}.svg"

# -------------------------
# Targets
# -------------------------
def search_target(query: str, max_results: int = 10) -> List[Dict]:
    """
    Search for biological targets in ChEMBL.
    """
    data = chembl_request("target/search", {"q": query, "limit": max_results})
    return data.get("targets", [])

def get_target_details(chembl_id: str) -> Dict:
    """
    Get detailed target info from ChEMBL.
    """
    return chembl_request(f"target/{chembl_id}", {})

# -------------------------
# Bioactivity
# -------------------------
def get_bioactivity_for_molecule(chembl_id: str, max_results: int = 20) -> List[Dict]:
    """
    Get bioactivity data for a molecule.
    """
    data = chembl_request("activity", {"molecule_chembl_id": chembl_id, "limit": max_results})
    return data.get("activities", [])

def get_bioactivity_for_target(chembl_id: str, max_results: int = 20) -> List[Dict]:
    """
    Get bioactivity data for a biological target.
    """
    data = chembl_request("activity", {"target_chembl_id": chembl_id, "limit": max_results})
    return data.get("activities", [])

# -------------------------
# Assays
# -------------------------
def get_assays_for_molecule(chembl_id: str, max_results: int = 20) -> List[Dict]:
    """
    Get assay data for a molecule.
    """
    data = chembl_request("assay", {"molecule_chembl_id": chembl_id, "limit": max_results})
    return data.get("assays", [])

# -------------------------
# Integration Helpers
# -------------------------
def molecule_to_gene_links(chembl_id: str) -> List[Dict]:
    """
    Crosslink molecule targets to gene symbols for integration with NCBI.
    """
    targets = get_bioactivity_for_molecule(chembl_id)
    gene_links = []
    for t in targets:
        if "target_chembl_id" in t:
            target_info = get_target_details(t["target_chembl_id"])
            gene_links.append({
                "target_id": t["target_chembl_id"],
                "gene_symbol": target_info.get("target_components", [{}])[0].get("accession", ""),
                "organism": target_info.get("organism", "")
            })
    return gene_links

# -------------------------
# Alias for Pipeline
# -------------------------
def get_molecule_data(query: str) -> Dict:
    """
    High-level function for the pipeline:
    Searches for molecule and returns first hit with details, image, and bioactivity.
    """
    results = search_molecule(query, max_results=1)
    if not results:
        return {}
    
    chembl_id = results[0].get("molecule_chembl_id")
    details = get_molecule_details(chembl_id)
    image_url = get_molecule_image(chembl_id)
    bioactivity = get_bioactivity_for_molecule(chembl_id)
    
    return {
        "chembl_id": chembl_id,
        "details": details,
        "image_url": image_url,
        "bioactivity": bioactivity
    }