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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() |