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gui.py
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gui.py
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# -*- coding: utf-8 -*-
"""
@Time ： 2024/1/15 11:45
@Auth ： Juexiao Zhou
@File ：app.py
@IDE ：PyCharm
@Page: www.joshuachou.ink
"""
import argparse
import os
from src.agent import Agent
import gradio as gr
import time
import yaml
import subprocess
import sys
def parse_args():
parser = argparse.ArgumentParser(description="AutoBA-GUI v0.1")
parser.add_argument('--port', type=int, default=5904)
args = parser.parse_args()
return args
def gradio_reset():
return None, None, None
def get_an_example():
_input_file_path_description = "./experiments/case1.1/data/SRR1234567_R1.fastq.gz: Paired-end Illumina WGS reads, forward\n" \
"./experiments/case1.1/data/SRR1234567_R2.fastq.gz: Paired-end Illumina WGS reads, reverse\n" \
"./experiments/case1.1/data/TruSeq3-PE.fa: Adapter sequences for trimming\n" \
"./experiments/case1.1/data/Reference.fasta: Reference genome for the organism under study in FASTA format"
_input_outoput_path = "./experiments/case1.1/output"
_input_goal = "To perform genome assembly using paired-end WGS data"
return _input_file_path_description, _input_outoput_path, _input_goal
def print_to_textbox(*args, **kwargs):
global HISTORY
text = " ".join(map(str, args)) + "\n"
if len(HISTORY) > 100:
HISTORY = HISTORY[1:]
HISTORY.append(text)
else:
HISTORY.append(text)
def run(input_file_path_description, input_outoput_path, input_goal, model_engine, openai_api, execute):
AIAgent = Agent(initial_data_list=input_file_path_description.split('\n'),
output_dir=input_outoput_path,
initial_goal_description=input_goal,
model_engine=model_engine,
openai_api=openai_api,
execute=execute,
blacklist='STAR,java,perl,annovar',
gui_mode=False)
AIAgent.run()
return 'Job Finished!'
if __name__ == '__main__':
args = parse_args()
# model_folder = args.model_root
# model_files = [os.path.join(model_folder, f) for f in os.listdir(model_folder) if os.path.isfile(os.path.join(model_folder, f))]
FORCE_STOP = False
HISTORY = []
with gr.Blocks() as demo:
gr.Markdown("""<h1 align="center">AutoBA-GUI v0.1</h1>""")
gr.Markdown("""<h3>An AI Agent for Fully Automated Multi-omic Analyses</h3>""")
with gr.Row():
with gr.Column():
input_file_path_description = gr.TextArea(
label="File path and description",
placeholder="Enter the absolute file path and file description in the following format, e.g.: \n"
"/data/SRR1234567_R1.fastq.gz: Paired-end Illumina WGS reads, forward\n"
"/data/SRR1234567_R2.fastq.gz: Paired-end Illumina WGS reads, reverse\n"
"/data/TruSeq3-PE.fa: Adapter sequences for trimming\n"
"/data/Reference.fasta: Reference genome for the organism under study in FASTA format",
max_lines=999999,
container=True,
)
input_outoput_path = gr.TextArea(
label="Output path",
placeholder="Enter absolute output path, e.g.: \n"
"/output",
max_lines=999999,
container=True,
)
input_goal = gr.TextArea(
label="Goal",
placeholder="Describe your goal for analysis, e.g.: \n"
"To perform genome assembly using paired-end WGS data",
max_lines=999999,
container=True,
)
local_model_engines = ['codellama-7bi',
'codellama-13bi',
'codellama-34bi',
'llama2-7bc',
'llama2-13bc',
'llama2-70bc']
gpt_model_engines = ['gpt-3.5-turbo',
'gpt-4',
'gpt-3.5-turbo-1106',
'gpt-4-0613',
'gpt-4-32k-0613',
'gpt-4-1106-preview']
model_engines = local_model_engines + gpt_model_engines
with gr.Row():
model_engine = gr.Dropdown(
label="Select model engine",
choices=model_engines,
value='gpt-4-1106-preview',
max_choices=1,
container=True,
interactive=True
)
openai_api = gr.Textbox(
label="OpenAI API",
placeholder="sk-xxxxx. Leave it empty for local version ",
max_lines=1,
container=True,
interactive=True
)
execute = gr.Checkbox(
label="Execute Code",
value=False,
visible=True
)
with gr.Row():
example_button = gr.Button(
value="Get an example",
interactive=True,
variant="primary"
)
upload_button = gr.Button(
value="Run",
interactive=True,
variant="primary"
)
#clear = gr.Button("Restart")
with gr.Row():
with gr.Column():
gr.Markdown('### Check command line for realtime outputs')
output_log = gr.TextArea(
label="Check command line for realtime outputs",
max_lines=5,
container=True,
lines=5,
)
gr.Markdown("""This site was created by King Abdullah University of Science and Technology (KAUST).""")
click_event = upload_button.click(run,
[input_file_path_description, input_outoput_path, input_goal, model_engine, openai_api,
execute],
[output_log])
example_button.click(get_an_example,
[],
[input_file_path_description, input_outoput_path, input_goal])
demo.launch(share=True, server_port=args.port, server_name='0.0.0.0')