app.py

from smolagents import CodeAgent,DuckDuckGoSearchTool, HfApiModel,load_tool,tool
import datetime
import requests
import pytz
import yaml
from tools.final_answer import FinalAnswerTool

from Gradio_UI import GradioUI
import xml.etree.ElementTree as ET

base_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"

@tool
def get_gene_id(organism:str, gene:int) -> str: 
    """A tool that gets the gene ID from an organism with the provided gene name
    Args:
        organism: the name of the organism
        gene: the name of the gene
    """
    search_params = {
        "db": "gene",
        "term": f"{gene}[Gene Name] AND {organism}[Organism]",
        "retmode": "xml",
    }
    esearch_url = base_url + "esearch.fcgi"
    esearch_response = requests.get(esearch_url, params=search_params)
    esearch_tree = ET.fromstring(esearch_response.text)
    id_list = esearch_tree.find("IdList")
    
    if id_list is None or len(id_list) == 0:
        return "Gene not found."

    return id_list.find("Id").text

@tool
def get_gene_location(gene_id:str) -> str:
    """A tool that gets the gene location from a gene ID
    Args:
        gene_id: the gene ID
    """
    efetch_url = base_url + "efetch.fcgi"
    fetch_params = {
        "db": "gene",
        "id": gene_id,
        "retmode": "xml",
    }
    efetch_response = requests.get(efetch_url, params=fetch_params)
    fetch_tree = ET.fromstring(efetch_response.text)

    # Parse XML to extract chromosome, start, end
    try:
        chr_elem = fetch_tree.find(".//Gene-ref_maploc")
        chromosome = chr_elem.text if chr_elem is not None else "Unknown"

        interval = fetch_tree.find(".//Seq-interval")
        start = int(interval.find("Seq-interval_from").text) + 1
        end = int(interval.find("Seq-interval_to").text) + 1

        strand_elem = interval.find("Seq-interval_strand/Na-strand/value")
        strand = strand_elem.text if strand_elem is not None else "unknown"

        return {
            "chromosome": chromosome,
            "start": start,
            "end": end,
            "strand": strand
        }
    except Exception as e:
        return "Error parsing gene location:", str(e)

final_answer = FinalAnswerTool()

# If the agent does not answer, the model is overloaded, please use another model or the following Hugging Face Endpoint that also contains qwen2.5 coder:
# model_id='https://pflgm2locj2t89co.us-east-1.aws.endpoints.huggingface.cloud' 

model = HfApiModel(
    max_tokens=2096,
    temperature=0.5,
    model_id='Qwen/Qwen2.5-Coder-32B-Instruct',# it is possible that this model may be overloaded
    custom_role_conversions=None,
)

with open("prompts.yaml", 'r') as stream:
    prompt_templates = yaml.safe_load(stream)
    
agent = CodeAgent(
    model=model,
    tools=[final_answer, get_gene_id, get_gene_location],
    max_steps=6,
    verbosity_level=1,
    grammar=None,
    planning_interval=None,
    name=None,
    description=None,
    prompt_templates=prompt_templates
)


GradioUI(agent).launch()