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 sys
import urllib.parse
import time
import re
import argparse

# Below is an example of a tool that does nothing. Amaze us with your creativity !
@tool
def my_custom_tool(arg1:str, arg2:int)-> str: #it's import to specify the return type
    #Keep this format for the description / args / args description but feel free to modify the tool
    """A tool that does nothing yet [BLAST???]
    Args:
        arg1: the first argument
        arg2: the second argument
    """
    return "What magic will you build ?"

@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)}"


@tool
def run_blast(arguments_string: str) -> str:
    """
    Submits a BLAST job to NCBI and retrieves the results.
    Parses arguments from a string input.  Now accepts a sequence directly, not a file.

    Args:
        arguments_string (str): String containing program, database, and query sequence.
                                 e.g., "blastp nr ATGCGTAGCTAGCTAG...".  Sequence should be directly in the string.

    Returns:
        str: BLAST results in text format on success, or an error message string on failure.
             Possible error messages include:
                "Error: Invalid arguments"
                "Error submitting request: {error_details}"
                "Error: Could not parse RID or RTOE from BLAST response."
                "Search {rid} failed; please report to blast-help@ncbi.nlm.nih.gov."
                "Search {rid} expired."
                "No hits found."
                "Unknown error during polling."
                "Error polling for results: {error_details}"
                "Error retrieving results: {error_details}"
    """

    parser = argparse.ArgumentParser(
        description="Submit and retrieve BLAST jobs from NCBI with a direct sequence input.",
        formatter_class=argparse.RawTextHelpFormatter # To keep help message formatting nice
    )
    parser.add_argument("program", help="BLAST program (e.g., megablast, blastn, blastp, rpsblast, blastx, tblastn, tblastx)")
    parser.add_argument("database", help="BLAST database name")
    parser.add_argument("query_sequence", nargs='+', help="Query sequence (directly input as string)")

    try:
        args = parser.parse_args(arguments_string.split()) # Parse arguments from the input string
    except SystemExit as e: # Catch argparse exit on error and return error string
        if e.code == 2: #  2 is the exit code for incorrect usage in argparse
            return "Error: Invalid arguments. Usage: program database query_sequence"
        else:
            return "Error: Argument parsing failed." # Unexpected argparse error

    program = args.program
    database = args.database
    query_sequence_list = args.query_sequence #  List of strings if sequence is split by spaces
    query_sequence = " ".join(query_sequence_list) # Rejoin if sequence was split by spaces in input string

    if program == "megablast":
        program = "blastn&MEGABLAST=on"
    elif program == "rpsblast":
        program = "blastp&SERVICE=rpsblast"

    encoded_query = urllib.parse.quote(query_sequence) # Encode the sequence directly

    # build the request
    api_url = 'https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi'
    payload = {
        'CMD': 'Put',
        'PROGRAM': program,
        'DATABASE': database,
        'QUERY': encoded_query
    }

    try:
        response = requests.post(api_url, data=payload)
        response.raise_for_status()  # Raise HTTPError for bad responses (4xx or 5xx)
    except requests.exceptions.RequestException as e:
        return f"Error submitting request: {e}"

    response_content = response.text

    rid_match = re.search(r"RID = (.*)", response_content)
    rtoe_match = re.search(r"RTOE = (.*)", response_content)

    if rid_match and rtoe_match:
        rid = rid_match.group(1).strip()
        rtoe = int(rtoe_match.group(1).strip())
    else:
        return "Error: Could not parse RID or RTOE from BLAST response.\nResponse content:\n" + response_content

    time.sleep(rtoe)

    # poll for results
    while True:
        time.sleep(5)
        poll_url = f"{api_url}?CMD=Get&FORMAT_OBJECT=SearchInfo&RID={rid}"
        try:
            response = requests.get(poll_url)
            response.raise_for_status()
        except requests.exceptions.RequestException as e:
            return f"Error polling for results: {e}"

        status_content = response.text

        if re.search(r"\s+Status=WAITING", status_content):
            # print(sys.stderr, "Searching...") # Optional: print to stderr if needed
            continue
        elif re.search(r"\s+Status=FAILED", status_content):
            return f"Search {rid} failed; please report to blast-help@ncbi.nlm.nih.gov."
        elif re.search(r"\s+Status=UNKNOWN", status_content):
            return f"Search {rid} expired."
        elif re.search(r"\s+Status=READY", status_content):
            if re.search(r"\s+ThereAreHits=yes", status_content):
                # print(sys.stderr, "Search complete, retrieving results...") # Optional: print to stderr if needed
                break
            else:
                return "No hits found."
        else:
            # if we get here, something unexpected happened.
            return "Unknown error during polling.\nStatus response content:\n" + status_content

    # retrieve and display results
    result_url = f"{api_url}?CMD=Get&FORMAT_TYPE=Text&RID={rid}"
    try:
        result_response = requests.get(result_url)
        result_response.raise_for_status()
    except requests.exceptions.RequestException as e:
        return f"Error retrieving results: {e}"

    return result_response.text

if __name__ == "__main__":
    if len(sys.argv) < 3:
        print("Usage: python blast_tool.py program database query_sequence", file=sys.stderr)
        print("       query_sequence should be the sequence itself, not a file.", file=sys.stderr)
        sys.exit(1)

    arguments_string = " ".join(sys.argv[1:]) # Reconstruct arguments string from command line
    results = run_blast(arguments_string)

    if results.startswith("Error:"):
        print(results, file=sys.stderr) # Print errors to stderr
        if results == "Error: Invalid arguments. Usage: program database query_sequence":
            sys.exit(1)
        elif results == "No hits found.":
            sys.exit(2)
        elif results.startswith("Search ") and results.endswith("expired."):
            sys.exit(3)
        elif results.startswith("Search ") and results.endswith("failed; please report to blast-help@ncbi.nlm.nih.gov."):
            sys.exit(4)
        else: # Catch-all for other errors
            sys.exit(5)
    else:
        print(results)
        sys.exit(0)


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=[DuckDuckGoSearchTool(),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()