app.py

# --- Imports ---
import spaces
import gradio as gr
from transformers import pipeline
import os

# --- Load Model ---
pipe = pipeline(model="InstaDeepAI/ChatNT", trust_remote_code=True)

# --- Logs ---
log_file = "logs.txt"

class Log:
    def __init__(self, log_file):
        self.log_file = log_file

    def __call__(self):
        if not os.path.exists(self.log_file):
            return ""
        with open(self.log_file, "r") as f:
            return f.read()

# --- Main Function ---
@spaces.GPU
def run_chatnt(dna_text, fasta_file, custom_question):
    with open(log_file, "a") as log:
        log.write("Request started\n\n")

    # Read DNA sequence from text field or file
    dna_sequence = ""
    if dna_text and dna_text.strip():
        dna_sequence = dna_text.strip().replace("\n", "")
    elif fasta_file is not None:
        with open(fasta_file.name, "r") as f:
            file_content = f.read()
        lines = file_content.splitlines()
        sequence = ""
        for line in lines:
            line = line.strip()
            if not line or line.startswith(">"):
                continue
            sequence += line
        dna_sequence = sequence

    dna_sequences = []
    if dna_sequence:
        dna_sequences.append(dna_sequence)

    with open(log_file, "a") as log:
        log.write(f"DNA sequences found: {dna_sequences}\n")

    # Check DNA sequences count
    if len(dna_sequences) > 1:
        return "You must use only one DNA sequence."

    if not custom_question or custom_question.strip() == "":
        return "Please provide a question."

    # Build prompt
    num_placeholders = custom_question.count("<DNA>")

    if len(dna_sequences) == 0:
        english_sequence = custom_question
    else:
        if num_placeholders == 0:
            return "Your question must include the <DNA> token at the position where the DNA sequence should be inserted."
        elif num_placeholders == 1:
            english_sequence = custom_question
        else:
            return "You can only provide one DNA sequence, so you must use exactly one <DNA> placeholder."

    with open(log_file, "a") as log:
        log.write(f"Initial user question: {custom_question}\n")
        log.write(f"Full english prompt: {english_sequence}\n")
        log.write("Calling model\n")

    output = pipe(
        inputs={
            "english_sequence": english_sequence,
            "dna_sequences": dna_sequences
        }
    )

    if len(dna_sequences) == 0:
        return f"{output}\n\nNote: Careful, you did not provide any DNA sequence."

    with open(log_file, "a") as log:
        log.write(f"Output: {output}\n")

    return output

# --- Gradio Interface ---
css = """
.gradio-container { font-family: sans-serif; }
.gr-button { color: white; border-color: black; background: black; }
footer { display: none !important; }
"""

with gr.Blocks(css=css) as demo:
    gr.Markdown("# 🧬 ChatNT: A Multimodal Conversational Agent for DNA, RNA and Protein Tasks")

    with gr.Row():
        with gr.Column(scale=1):
            dna_text = gr.Textbox(
                label="Paste your DNA sequence",
                placeholder="ATGCATGCATGC...",
                lines=4
            )

            fasta_file = gr.File(
                label="Or upload your FASTA file",
                file_types=[".fasta", ".fa", ".txt"]
            )

            custom_question = gr.Textbox(
                label="English Question",
                placeholder="e.g., Does this sequence <DNA> contain a donor splice site?"
            )

            submit_btn = gr.Button("Run Query", variant="primary")

        with gr.Row():
            output = gr.Textbox(label="Answer", lines=6)

    submit_btn.click(
        run_chatnt,
        inputs=[dna_text, fasta_file, custom_question],
        outputs=output,
    )

    gr.Markdown("""
**Note:**  
✅ You must use **exactly one DNA sequence** (either paste it or upload a file).  
✅ Your question must include the `<DNA>` token **exactly once** at the position where the DNA will be inserted.  
Example: *"Does this sequence `<DNA>` contain a donor splice site?"*
    """)

    with gr.Accordion("Logs", open=True):
        log_display = Log(log_file)
        gr.Markdown(log_display)

# --- Launch ---
if __name__ == "__main__":
    demo.queue()
    demo.launch(debug=True, show_error=True)