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

# Below is an example of a tool that does nothing. Amaze us with your creativity !

@tool
def resolve_gene(query: str) -> dict:
    """Return HGNC symbol, Ensembl ID, canonical coords (GRCh37/38), synonyms."""

@tool
def resolve_variant(query: str, assembly: str) -> dict:
    """Return rsID, position, liftover if needed, nearest genes."""

@tool
def query_gwas_associations(
    gene_id: str | None = None, rsid: str | None = None,
    region: tuple | None = None, trait_efo: str | None = None,
    pval_max: float = 5e-8
) -> list[dict]:
    """GWAS Catalog hits with study metadata."""

@tool
def query_finemap_and_ld(rsid: str, ancestry: str) -> dict:
    """Credible set, PP, LD partners via OTG + LDlink."""

@tool
def annotate_variant(rsid: str) -> dict:
    """VEP consequence, gnomAD AF."""

@tool
def enrich_traits_with_efo(trait_labels: list[str]) -> list[dict]:
    """Map to EFO terms and parents for grouping."""

@tool
def collate_and_rank(records: list[dict]) -> dict:
    """Merge, score, aggregate, and return final payload with provenance."""


@tool
def get_current_time_in_timezone(timezone: str) -> str:
    """A tool that fetches the current local time in a specified timezone.
    Args:
        timezone: A string representing a valid timezone (e.g., 'America/New_York').
    """
    try:
        # Create timezone object
        tz = pytz.timezone(timezone)
        # Get current time in that timezone
        local_time = datetime.datetime.now(tz).strftime("%Y-%m-%d %H:%M:%S")
        return f"The current local time in {timezone} is: {local_time}"
    except Exception as e:
        return f"Error fetching time for timezone '{timezone}': {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,
)


# Import tool from Hub
image_generation_tool = load_tool("agents-course/text-to-image", trust_remote_code=True)

with open("prompts.yaml", 'r') as stream:
    prompt_templates = yaml.safe_load(stream)
    
agent = CodeAgent(
    model=model,
    tools=[resolve_gene, resolve_variant, query_gwas_associations, query_finemap_and_ld, annotate_variant, enrich_traits_with_efo, collate_and_rank, final_answer], ## add your tools here (don't remove final answer)
    max_steps=6,
    verbosity_level=1,
    grammar=None,
    planning_interval=None,
    name=None,
    description=None,
    prompt_templates=prompt_templates
)


GradioUI(agent).launch()