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Update app.py
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app.py
CHANGED
@@ -1,793 +1,793 @@
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import gradio as gr
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import mtdna_backend
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import json
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import data_preprocess, model, pipeline
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import os
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import hashlib
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import threading
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# Gradio UI
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#stop_flag = gr.State(value=False)
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class StopFlag:
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def __init__(self):
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self.value = False
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global_stop_flag = StopFlag() # Shared between run + stop
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with open("offer.html", "r", encoding="utf-8") as f:
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pricing_html = f.read()
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with gr.Blocks() as interface:
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with gr.Tab("CURIOUS ABOUT THIS PRODUCT?"):
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gr.HTML(value=pricing_html)
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with gr.Tab("𧬠Classifier"):
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gr.Markdown("# 𧬠mtDNA Location Classifier (MVP)")
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#inputMode = gr.Radio(choices=["Single Accession", "Batch Input"], value="Single Accession", label="Choose Input Mode")
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user_email = gr.Textbox(label="π§ Your email (used to track free quota)")
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usage_display = gr.Markdown("", visible=False)
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# with gr.Group() as single_input_group:
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# single_accession = gr.Textbox(label="Enter Single Accession (e.g., KU131308)")
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# with gr.Group(visible=False) as batch_input_group:
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# raw_text = gr.Textbox(label="𧬠Paste Accession Numbers (e.g., MF362736.1,MF362738.1,KU131308,MW291678)")
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# resume_file = gr.File(label="ποΈ Previously saved Excel output (optional)", file_types=[".xlsx"], interactive=True)
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# gr.HTML("""<a href="https://drive.google.com/file/d/1t-TFeIsGVu5Jh3CUZS-VE9jQWzNFCs_c/view?usp=sharing" download target="_blank">Download Example CSV Format</a>""")
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# gr.HTML("""<a href="https://docs.google.com/spreadsheets/d/1lKqPp17EfHsshJGZRWEpcNOZlGo3F5qU/edit?usp=sharing&ouid=112390323314156876153&rtpof=true&sd=true" download target="_blank">Download Example Excel Format</a>""")
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# file_upload = gr.File(label="π Or Upload CSV/Excel File", file_types=[".csv", ".xlsx"], interactive=True, elem_id="file-upload-box")
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raw_text = gr.Textbox(label="π§ Input Accession Number(s) (single (KU131308) or comma-separated (e.g., MF362736.1,MF362738.1,KU131308,MW291678))")
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#resume_file = gr.File(label="ποΈ Previously saved Excel output (optional)", file_types=[".xlsx"], interactive=True)
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gr.HTML("""<a href="https://docs.google.com/spreadsheets/d/1lKqPp17EfHsshJGZRWEpcNOZlGo3F5qU/edit?usp=sharing" download target="_blank">Download Example Excel Format</a>""")
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file_upload = gr.File(label="π Or Upload CSV/Excel File", file_types=[".csv", ".xlsx"], interactive=True)
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with gr.Row():
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run_button = gr.Button("π Submit and Classify")
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stop_button = gr.Button("β Stop Batch", visible=True)
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reset_button = gr.Button("π Reset")
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status = gr.Markdown(visible=False)
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with gr.Group(visible=False) as results_group:
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# with gr.Accordion("Open to See the Result", open=False) as results:
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# with gr.Row():
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# output_summary = gr.Markdown(elem_id="output-summary")
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# output_flag = gr.Markdown(elem_id="output-flag")
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# gr.Markdown("---")
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with gr.Accordion("Open to See the Output Table", open=False) as table_accordion:
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output_table = gr.HTML(render=True)
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#with gr.Row():
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#output_type = gr.Dropdown(choices=["Excel", "JSON", "TXT"], label="Select Output Format", value="Excel")
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#download_button = gr.Button("β¬οΈ Download Output")
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#download_file = gr.File(label="Download File Here",visible=False)
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report_button = gr.Button("Report")
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report_textbox = gr.Textbox(
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label="Describe the issue",
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lines=4,
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placeholder="e.g. DQ981467: it gives me unknown when I can in fact search it on NCBI \n DQ981467:
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visible=False)
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submit_report_button = gr.Button("Submit", visible=False)
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status_report = gr.Markdown(visible=False)
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download_file = gr.File(label="Download File Here", visible=False, interactive=True)
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progress_box = gr.Textbox(label="Live Processing Log", lines=20, interactive=False)
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gr.Markdown("---")
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gr.Markdown("### π¬ Feedback (required)")
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q1 = gr.Textbox(label="1οΈβ£ Was the inferred location accurate or helpful? Please explain.")
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q2 = gr.Textbox(label="2οΈβ£ What would improve your experience with this tool?")
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contact = gr.Textbox(label="π§ Your email or institution (optional)")
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submit_feedback = gr.Button("β
Submit Feedback")
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feedback_status = gr.Markdown()
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# Functions
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# def toggle_input_mode(mode):
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# if mode == "Single Accession":
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# return gr.update(visible=True), gr.update(visible=False)
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# else:
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# return gr.update(visible=False), gr.update(visible=True)
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def classify_with_loading():
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return gr.update(value="β³ Please wait... processing...",visible=True) # Show processing message
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# def classify_dynamic(single_accession, file, text, resume, email, mode):
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# if mode == "Single Accession":
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# return classify_main(single_accession) + (gr.update(visible=False),)
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# else:
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# #return summarize_batch(file, text) + (gr.update(visible=False),) # Hide processing message
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# return classify_mulAcc(file, text, resume) + (gr.update(visible=False),) # Hide processing message
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# Logging helpers defined early to avoid NameError
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# def classify_dynamic(single_accession, file, text, resume, email, mode):
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# if mode == "Single Accession":
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# return classify_main(single_accession) + (gr.update(value="", visible=False),)
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# else:
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# return classify_mulAcc(file, text, resume, email, log_callback=real_time_logger, log_collector=log_collector)
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# for single accession
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# def classify_main(accession):
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# #table, summary, labelAncient_Modern, explain_label = mtdna_backend.summarize_results(accession)
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# table = mtdna_backend.summarize_results(accession)
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# #flag_output = f"### πΊ Ancient/Modern Flag\n**{labelAncient_Modern}**\n\n_Explanation:_ {explain_label}"
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# return (
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# #table,
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# make_html_table(table),
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# # summary,
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# # flag_output,
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# gr.update(visible=True),
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# gr.update(visible=False),
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# gr.update(visible=False)
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# )
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#stop_flag = gr.State(value=False)
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#stop_flag = StopFlag()
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# def stop_batch(stop_flag):
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# stop_flag.value = True
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# return gr.update(value="β Stopping...", visible=True), stop_flag
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def stop_batch():
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global_stop_flag.value = True
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return gr.update(value="β Stopping...", visible=True)
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# def threaded_batch_runner(file, text, email):
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# global_stop_flag.value = False
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# log_lines = []
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# def update_log(line):
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# log_lines.append(line)
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# yield (
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# gr.update(visible=False), # output_table (not yet)
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# gr.update(visible=False), # results_group
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# gr.update(visible=False), # download_file
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# gr.update(visible=False), # usage_display
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# gr.update(value="β³ Still processing...", visible=True), # status
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# gr.update(value="\n".join(log_lines)) # progress_box
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# )
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# # Start a dummy update to say "Starting..."
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# yield from update_log("π Starting batch processing...")
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# rows, file_path, count, final_log, warning = mtdna_backend.summarize_batch(
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# file=file,
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# raw_text=text,
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# resume_file=None,
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# user_email=email,
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# stop_flag=global_stop_flag,
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# yield_callback=lambda line: (yield from update_log(line))
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# )
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# html = make_html_table(rows)
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# file_update = gr.update(value=file_path, visible=True) if os.path.exists(file_path) else gr.update(visible=False)
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# usage_or_warning_text = f"**{count}** samples used by this email." if email.strip() else warning
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# yield (
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# html,
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# gr.update(visible=True), # results_group
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# file_update, # download_file
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# gr.update(value=usage_or_warning_text, visible=True),
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# gr.update(value="β
Done", visible=True),
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# gr.update(value=final_log)
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# )
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# def threaded_batch_runner(file=None, text="", email=""):
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# print("π§ EMAIL RECEIVED:", email)
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# import tempfile
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# from mtdna_backend import (
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# extract_accessions_from_input,
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# summarize_results,
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# save_to_excel,
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# hash_user_id,
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# increment_usage,
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# )
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# import os
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# global_stop_flag.value = False # reset stop flag
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# tmp_dir = tempfile.mkdtemp()
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# output_file_path = os.path.join(tmp_dir, "batch_output_live.xlsx")
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# limited_acc = 50 + (10 if email.strip() else 0)
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# # Step 1: Parse input
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# accessions, error = extract_accessions_from_input(file, text)
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# print(accessions)
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# if error:
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# yield (
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# "", # output_table
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# gr.update(visible=False), # results_group
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# gr.update(visible=False), # download_file
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# "", # usage_display
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# "β Error", # status
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# str(error) # progress_box
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# )
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# return
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# total = len(accessions)
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# if total > limited_acc:
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# accessions = accessions[:limited_acc]
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# warning = f"β οΈ Only processing first {limited_acc} accessions."
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# else:
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# warning = f"β
All {total} accessions will be processed."
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# all_rows = []
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# processed_accessions = 0 # β
tracks how many accessions were processed
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# email_tracked = False
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# log_lines = []
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# # Step 2: Loop through accessions
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# for i, acc in enumerate(accessions):
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# if global_stop_flag.value:
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# log_lines.append(f"π Stopped at {acc} ({i+1}/{total})")
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# usage_text = ""
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# if email.strip() and not email_tracked:
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# # user_hash = hash_user_id(email)
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# # usage_count = increment_usage(user_hash, len(all_rows))
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# print("print(processed_accessions at stop) ",processed_accessions)
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# usage_count = increment_usage(email, processed_accessions)
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# email_tracked = True
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# usage_text = f"**{usage_count}** samples used by this email. Ten more samples are added first (you now have 60 limited accessions), then wait we will contact you via this email."
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# else:
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# usage_text = f"The limited accession is 50. The user has used {processed_accessions}, and only {50-processed_accessions} left."
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# yield (
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# make_html_table(all_rows),
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# gr.update(visible=True),
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# gr.update(value=output_file_path, visible=True),
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# gr.update(value=usage_text, visible=True),
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# "π Stopped",
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# "\n".join(log_lines)
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# )
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# return
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# log_lines.append(f"[{i+1}/{total}] Processing {acc}")
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# yield (
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# make_html_table(all_rows),
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# gr.update(visible=True),
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# gr.update(visible=False),
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# "",
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# "β³ Processing...",
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# "\n".join(log_lines)
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# )
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# try:
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# print(acc)
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# rows = summarize_results(acc)
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# all_rows.extend(rows)
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# processed_accessions += 1 # β
count only successful accessions
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# save_to_excel(all_rows, "", "", output_file_path, is_resume=False)
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# log_lines.append(f"β
Processed {acc} ({i+1}/{total})")
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# except Exception as e:
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# log_lines.append(f"β Failed to process {acc}: {e}")
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# yield (
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# make_html_table(all_rows),
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# gr.update(visible=True),
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# gr.update(visible=False),
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# "",
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# "β³ Processing...",
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# "\n".join(log_lines)
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# )
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# # Final update
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# usage_text = ""
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# if email.strip() and not email_tracked:
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# # user_hash = hash_user_id(email)
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# # usage_count = increment_usage(user_hash, len(all_rows))
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# print("print(processed_accessions final) ",processed_accessions)
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# usage_count = increment_usage(email, processed_accessions)
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# usage_text = f"**{usage_count}** samples used by this email. Ten more samples are added first (you now have 60 limited accessions), then wait we will contact you via this email."
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# elif not email.strip():
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# usage_text = f"The limited accession is 50. The user has used {processed_accessions}, and only {50-processed_accessions} left."
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# yield (
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# make_html_table(all_rows),
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# gr.update(visible=True),
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# gr.update(value=output_file_path, visible=True),
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# gr.update(value=usage_text, visible=True),
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# "β
Done",
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# "\n".join(log_lines)
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# )
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def threaded_batch_runner(file=None, text="", email=""):
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print("π§ EMAIL RECEIVED:", repr(email))
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import tempfile
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from mtdna_backend import (
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extract_accessions_from_input,
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summarize_results,
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save_to_excel,
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increment_usage,
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)
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import os
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global_stop_flag.value = False # reset stop flag
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tmp_dir = tempfile.mkdtemp()
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output_file_path = os.path.join(tmp_dir, "batch_output_live.xlsx")
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#output_file_path = "/mnt/data/batch_output_live.xlsx"
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all_rows = []
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processed_accessions = 0 # β
track successful accessions
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email_tracked = False
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log_lines = []
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if not email.strip():
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output_file_path = None#"Write your email so that you can download the outputs."
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log_lines.append("π₯ Provide your email to receive a downloadable Excel report and get 20 more free queries.")
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limited_acc = 30
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if email.strip():
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usage_count, max_allowed = increment_usage(email, processed_accessions)
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if int(usage_count) >= int(max_allowed):
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log_lines.append("β You have reached your quota. Please contact us to unlock more.")
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# Minimal blank yield to trigger UI rendering
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yield (
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make_html_table([]),
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gr.update(visible=True),
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gr.update(visible=False),
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gr.update(value="", visible=True),
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"βοΈ Quota limit",
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"βοΈ Quota limit"
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)
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# Actual warning frame
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yield (
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make_html_table([]),
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gr.update(visible=False),
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gr.update(visible=False),
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gr.update(value="β You have reached your quota. Please contact us to unlock more.", visible=True),
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"β Quota Exceeded",
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"\n".join(log_lines)
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)
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return
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limited_acc = int(max_allowed-usage_count)
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# Step 1: Parse input
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accessions, error = extract_accessions_from_input(file, text)
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print("π§ͺ Accessions received:", accessions)
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if error:
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yield (
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"", # output_table
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gr.update(visible=False), # results_group
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gr.update(visible=False), # download_file
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"", # usage_display
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"β Error", # status
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str(error) # progress_box
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)
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return
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total = len(accessions)
|
355 |
-
if total > limited_acc:
|
356 |
-
accessions = accessions[:limited_acc]
|
357 |
-
warning = f"β οΈ Only processing first {limited_acc} accessions."
|
358 |
-
else:
|
359 |
-
warning = f"β
All {total} accessions will be processed."
|
360 |
-
|
361 |
-
# all_rows = []
|
362 |
-
# processed_accessions = 0 # β
track successful accessions
|
363 |
-
# email_tracked = False
|
364 |
-
# log_lines = []
|
365 |
-
# if not email.strip():
|
366 |
-
# output_file_path = None#"Write your email so that you can download the outputs."
|
367 |
-
# log_lines.append("π₯ Provide your email to receive a downloadable Excel report and get 20 more free queries.")
|
368 |
-
# if email.strip():
|
369 |
-
# usage_count, max_allowed = increment_usage(email, processed_accessions)
|
370 |
-
# if int(usage_count) > int(max_allowed):
|
371 |
-
# log_lines.append("β You have reached your quota. Please contact us to unlock more.")
|
372 |
-
|
373 |
-
# # Minimal blank yield to trigger UI rendering
|
374 |
-
# yield (
|
375 |
-
# make_html_table([]),
|
376 |
-
# gr.update(visible=True),
|
377 |
-
# gr.update(visible=False),
|
378 |
-
# gr.update(value="", visible=True),
|
379 |
-
# "βοΈ Quota limit",
|
380 |
-
# "βοΈ Quota limit"
|
381 |
-
# )
|
382 |
-
|
383 |
-
# # Actual warning frame
|
384 |
-
# yield (
|
385 |
-
# make_html_table([]),
|
386 |
-
# gr.update(visible=False),
|
387 |
-
# gr.update(visible=False),
|
388 |
-
# gr.update(value="β You have reached your quota. Please contact us to unlock more.", visible=True),
|
389 |
-
# "β Quota Exceeded",
|
390 |
-
# "\n".join(log_lines)
|
391 |
-
# )
|
392 |
-
# return
|
393 |
-
|
394 |
-
|
395 |
-
# Step 2: Loop through accessions
|
396 |
-
for i, acc in enumerate(accessions):
|
397 |
-
if global_stop_flag.value:
|
398 |
-
log_lines.append(f"π Stopped at {acc} ({i+1}/{total})")
|
399 |
-
usage_text = ""
|
400 |
-
|
401 |
-
if email.strip() and not email_tracked:
|
402 |
-
print(f"π§ͺ increment_usage at STOP: {email=} {processed_accessions=}")
|
403 |
-
usage_count, max_allowed = increment_usage(email, processed_accessions)
|
404 |
-
email_tracked = True
|
405 |
-
usage_text = f"**{usage_count}**/{max_allowed} allowed samples used by this email."
|
406 |
-
#Ten more samples are added first (you now have 60 limited accessions), then wait we will contact you via this email."
|
407 |
-
else:
|
408 |
-
usage_text = f"The limited accession is 30. The user has used {processed_accessions}, and only {30 - processed_accessions} left."
|
409 |
-
|
410 |
-
yield (
|
411 |
-
make_html_table(all_rows),
|
412 |
-
gr.update(visible=True),
|
413 |
-
#gr.update(value=output_file_path, visible=True),
|
414 |
-
gr.update(value=output_file_path, visible=bool(output_file_path)),
|
415 |
-
gr.update(value=usage_text, visible=True),
|
416 |
-
"π Stopped",
|
417 |
-
"\n".join(log_lines)
|
418 |
-
)
|
419 |
-
return
|
420 |
-
|
421 |
-
log_lines.append(f"[{i+1}/{total}] Processing {acc}")
|
422 |
-
yield (
|
423 |
-
make_html_table(all_rows),
|
424 |
-
gr.update(visible=True),
|
425 |
-
gr.update(visible=False),
|
426 |
-
"",
|
427 |
-
"β³ Processing...",
|
428 |
-
"\n".join(log_lines)
|
429 |
-
)
|
430 |
-
|
431 |
-
try:
|
432 |
-
print("π Processing accession:", acc)
|
433 |
-
rows = summarize_results(acc)
|
434 |
-
all_rows.extend(rows)
|
435 |
-
processed_accessions += 1 # β
only count success
|
436 |
-
if email.strip():
|
437 |
-
save_to_excel(all_rows, "", "", output_file_path, is_resume=False)
|
438 |
-
log_lines.append(f"β
Processed {acc} ({i+1}/{total})")
|
439 |
-
except Exception as e:
|
440 |
-
log_lines.append(f"β Failed to process {acc}: {e}")
|
441 |
-
|
442 |
-
yield (
|
443 |
-
make_html_table(all_rows),
|
444 |
-
gr.update(visible=True),
|
445 |
-
gr.update(visible=False),
|
446 |
-
"",
|
447 |
-
"β³ Processing...",
|
448 |
-
"\n".join(log_lines)
|
449 |
-
)
|
450 |
-
|
451 |
-
# Step 3: Final usage update
|
452 |
-
usage_text = ""
|
453 |
-
if email.strip() and not email_tracked:
|
454 |
-
print(f"π§ͺ increment_usage at END: {email=} {processed_accessions=}")
|
455 |
-
usage_count, max_allowed = increment_usage(email, processed_accessions)
|
456 |
-
email_tracked = True
|
457 |
-
usage_text = f"**{usage_count}**/{max_allowed} allowed samples used by this email."
|
458 |
-
#Ten more samples are added first (you now have 60 limited accessions), then wait we will contact you via this email."
|
459 |
-
elif not email.strip():
|
460 |
-
usage_text = f"The limited accession is 30. The user has used {processed_accessions}, and only {30 - processed_accessions} left."
|
461 |
-
|
462 |
-
yield (
|
463 |
-
make_html_table(all_rows),
|
464 |
-
gr.update(visible=True),
|
465 |
-
#gr.update(value=output_file_path, visible=True),
|
466 |
-
gr.update(value=output_file_path, visible=bool(output_file_path)),
|
467 |
-
gr.update(value=usage_text, visible=True),
|
468 |
-
"β
Done",
|
469 |
-
"\n".join(log_lines)
|
470 |
-
)
|
471 |
-
|
472 |
-
# SUBMIT REPORT UI
|
473 |
-
# 1. Google Sheets setup
|
474 |
-
def get_worksheet(sheet_name="Report"):
|
475 |
-
import os, json
|
476 |
-
import gspread
|
477 |
-
from oauth2client.service_account import ServiceAccountCredentials
|
478 |
-
try:
|
479 |
-
creds_dict = json.loads(os.environ["GCP_CREDS_JSON"])
|
480 |
-
scope = ["https://spreadsheets.google.com/feeds", "https://www.googleapis.com/auth/drive"]
|
481 |
-
creds = ServiceAccountCredentials.from_json_keyfile_dict(creds_dict, scope)
|
482 |
-
client = gspread.authorize(creds)
|
483 |
-
sheet = client.open(sheet_name).sheet1
|
484 |
-
return sheet
|
485 |
-
except Exception as e:
|
486 |
-
print(f"β Error loading Google Sheet '{sheet_name}':", e)
|
487 |
-
return None
|
488 |
-
|
489 |
-
# 2. Submit function to send report to the Google Sheet
|
490 |
-
def submit_report(report_text,user_email=""):
|
491 |
-
try:
|
492 |
-
sheet = get_worksheet()
|
493 |
-
# β
Parse the report_text (each line like 'ACCESSION: message')
|
494 |
-
lines = report_text.strip().split('\n')
|
495 |
-
user = ""
|
496 |
-
if user_email.strip():
|
497 |
-
user = user_email
|
498 |
-
for line in lines:
|
499 |
-
if ':' in line:
|
500 |
-
accession, message = line.split(':', 1)
|
501 |
-
sheet.append_row([accession.strip(), message.strip(), user.strip()])
|
502 |
-
return "β
Report submitted successfully!"
|
503 |
-
except Exception as e:
|
504 |
-
return f"β Error submitting report: {str(e)}"
|
505 |
-
def show_report_ui():
|
506 |
-
return gr.update(visible=True), gr.update(visible=True), gr.update(visible=False)
|
507 |
-
|
508 |
-
def handle_submission(text,user_email):
|
509 |
-
msg = submit_report(text, user_email)
|
510 |
-
return gr.update(value=msg, visible=True), gr.update(visible=False), gr.update(visible=False)
|
511 |
-
# def threaded_batch_runner(file=None, text="", email=""):
|
512 |
-
# global_stop_flag.value = False
|
513 |
-
|
514 |
-
# # Dummy test output that matches expected schema
|
515 |
-
# return (
|
516 |
-
# "<div>β
Dummy output table</div>", # HTML string
|
517 |
-
# gr.update(visible=True), # Group visibility
|
518 |
-
# gr.update(visible=False), # Download file
|
519 |
-
# "**0** samples used.", # Markdown
|
520 |
-
# "β
Done", # Status string
|
521 |
-
# "Processing finished." # Progress string
|
522 |
-
# )
|
523 |
-
|
524 |
-
|
525 |
-
# def classify_mulAcc(file, text, resume, email, log_callback=None, log_collector=None):
|
526 |
-
# stop_flag.value = False
|
527 |
-
# return threaded_batch_runner(file, text, resume, email, status, stop_flag, log_callback=log_callback, log_collector=log_collector)
|
528 |
-
|
529 |
-
|
530 |
-
def make_html_table(rows):
|
531 |
-
# html = """
|
532 |
-
# <div style='overflow-x: auto; padding: 10px;'>
|
533 |
-
# <div style='max-height: 400px; overflow-y: auto; border: 1px solid #444; border-radius: 8px;'>
|
534 |
-
# <table style='width:100%; border-collapse: collapse; table-layout: auto; font-size: 14px; color: #f1f1f1; background-color: #1e1e1e;'>
|
535 |
-
# <thead style='position: sticky; top: 0; background-color: #2c2c2c; z-index: 1;'>
|
536 |
-
# <tr>
|
537 |
-
# """
|
538 |
-
html = """
|
539 |
-
<div style='overflow-x: auto; padding: 10px;'>
|
540 |
-
<div style='max-height: 400px; overflow-y: auto; border: 1px solid #ccc; border-radius: 8px;'>
|
541 |
-
<table style='width:100%; border-collapse: collapse; table-layout: auto; font-size: 14px; color: inherit; background-color: inherit;'>
|
542 |
-
"""
|
543 |
-
|
544 |
-
headers = ["Sample ID", "Predicted Country", "Country Explanation", "Predicted Sample Type", "Sample Type Explanation", "Sources", "Time cost"]
|
545 |
-
html += "".join(
|
546 |
-
f"<th style='padding: 10px; border: 1px solid #555; text-align: left; white-space: nowrap;'>{h}</th>"
|
547 |
-
for h in headers
|
548 |
-
)
|
549 |
-
html += "</tr></thead><tbody>"
|
550 |
-
|
551 |
-
for row in rows:
|
552 |
-
html += "<tr>"
|
553 |
-
for i, col in enumerate(row):
|
554 |
-
header = headers[i]
|
555 |
-
style = "padding: 10px; border: 1px solid #555; vertical-align: top;"
|
556 |
-
|
557 |
-
# For specific columns like Haplogroup, force nowrap
|
558 |
-
if header in ["Country Explanation", "Sample Type Explanation"]:
|
559 |
-
style += " max-width: 400px; word-wrap: break-word; white-space: normal;"
|
560 |
-
elif header in ["Sample ID", "Predicted Country", "Predicted Sample Type", "Time cost"]:
|
561 |
-
style += " white-space: nowrap; text-overflow: ellipsis; max-width: 200px; overflow: hidden;"
|
562 |
-
|
563 |
-
# if header == "Sources" and isinstance(col, str) and col.strip().lower().startswith("http"):
|
564 |
-
# col = f"<a href='{col}' target='_blank' style='color: #4ea1f3; text-decoration: underline;'>{col}</a>"
|
565 |
-
|
566 |
-
#html += f"<td style='{style}'>{col}</td>"
|
567 |
-
if header == "Sources" and isinstance(col, str):
|
568 |
-
links = [f"<a href='{url.strip()}' target='_blank' style='color: #4ea1f3; text-decoration: underline;'>{url.strip()}</a>" for url in col.strip().split("\n") if url.strip()]
|
569 |
-
col = "- "+"<br>- ".join(links)
|
570 |
-
elif isinstance(col, str):
|
571 |
-
# lines = []
|
572 |
-
# for line in col.split("\n"):
|
573 |
-
# line = line.strip()
|
574 |
-
# if not line:
|
575 |
-
# continue
|
576 |
-
# if line.lower().startswith("rag_llm-"):
|
577 |
-
# content = line[len("rag_llm-"):].strip()
|
578 |
-
# line = f"{content} (Method: RAG_LLM)"
|
579 |
-
# lines.append(f"- {line}")
|
580 |
-
col = col.replace("\n", "<br>")
|
581 |
-
#col = col.replace("\t", " ")
|
582 |
-
#col = "<br>".join(lines)
|
583 |
-
|
584 |
-
html += f"<td style='{style}'>{col}</td>"
|
585 |
-
html += "</tr>"
|
586 |
-
|
587 |
-
html += "</tbody></table></div></div>"
|
588 |
-
return html
|
589 |
-
|
590 |
-
|
591 |
-
# def reset_fields():
|
592 |
-
# global_stop_flag.value = False # π‘ Add this to reset the flag
|
593 |
-
# return (
|
594 |
-
# #gr.update(value=""), # single_accession
|
595 |
-
# gr.update(value=""), # raw_text
|
596 |
-
# gr.update(value=None), # file_upload
|
597 |
-
# #gr.update(value=None), # resume_file
|
598 |
-
# #gr.update(value="Single Accession"), # inputMode
|
599 |
-
# gr.update(value=[], visible=True), # output_table
|
600 |
-
# # gr.update(value="", visible=True), # output_summary
|
601 |
-
# # gr.update(value="", visible=True), # output_flag
|
602 |
-
# gr.update(visible=False), # status
|
603 |
-
# gr.update(visible=False), # results_group
|
604 |
-
# gr.update(value="", visible=False), # usage_display
|
605 |
-
# gr.update(value="", visible=False), # progress_box
|
606 |
-
# )
|
607 |
-
def reset_fields():
|
608 |
-
global_stop_flag.value = False # Reset the stop flag
|
609 |
-
|
610 |
-
return (
|
611 |
-
gr.update(value=""), # raw_text
|
612 |
-
gr.update(value=None), # file_upload
|
613 |
-
gr.update(value=[], visible=True), # output_table
|
614 |
-
gr.update(value="", visible=True), # status β reset and make visible again
|
615 |
-
gr.update(visible=False), # results_group
|
616 |
-
gr.update(value="", visible=True), # usage_display β reset and make visible again
|
617 |
-
gr.update(value="", visible=True), # progress_box β reset AND visible!
|
618 |
-
# report-related reset below
|
619 |
-
gr.update(value="", visible=False), # report_textbox
|
620 |
-
gr.update(visible=False), # submit_report_button
|
621 |
-
gr.update(value="", visible=False), # status_report
|
622 |
-
)
|
623 |
-
#inputMode.change(fn=toggle_input_mode, inputs=inputMode, outputs=[single_input_group, batch_input_group])
|
624 |
-
#run_button.click(fn=classify_with_loading, inputs=[], outputs=[status])
|
625 |
-
# run_button.click(
|
626 |
-
# fn=classify_dynamic,
|
627 |
-
# inputs=[single_accession, file_upload, raw_text, resume_file,user_email,inputMode],
|
628 |
-
# outputs=[output_table,
|
629 |
-
# #output_summary, output_flag,
|
630 |
-
# results_group, download_file, usage_display,status, progress_box]
|
631 |
-
# )
|
632 |
-
|
633 |
-
# run_button.click(
|
634 |
-
# fn=threaded_batch_runner,
|
635 |
-
# #inputs=[file_upload, raw_text, resume_file, user_email],
|
636 |
-
# inputs=[file_upload, raw_text, user_email],
|
637 |
-
# outputs=[output_table, results_group, download_file, usage_display, status, progress_box]
|
638 |
-
# )
|
639 |
-
# run_button.click(
|
640 |
-
# fn=threaded_batch_runner,
|
641 |
-
# inputs=[file_upload, raw_text, user_email],
|
642 |
-
# outputs=[output_table, results_group, download_file, usage_display, status, progress_box],
|
643 |
-
# every=0.5 # <-- this tells Gradio to expect streaming
|
644 |
-
# )
|
645 |
-
# output_table = gr.HTML()
|
646 |
-
# results_group = gr.Group(visible=False)
|
647 |
-
# download_file = gr.File(visible=False)
|
648 |
-
# usage_display = gr.Markdown(visible=False)
|
649 |
-
# status = gr.Markdown(visible=False)
|
650 |
-
# progress_box = gr.Textbox(visible=False)
|
651 |
-
|
652 |
-
# run_button.click(
|
653 |
-
# fn=threaded_batch_runner,
|
654 |
-
# inputs=[file_upload, raw_text, user_email],
|
655 |
-
# outputs=[output_table, results_group, download_file, usage_display, status, progress_box],
|
656 |
-
# every=0.5, # streaming enabled
|
657 |
-
# show_progress="full"
|
658 |
-
# )
|
659 |
-
|
660 |
-
# interface.stream(
|
661 |
-
# fn=threaded_batch_runner,
|
662 |
-
# inputs=[file_upload, raw_text, user_email],
|
663 |
-
# outputs=[output_table, results_group, download_file, usage_display, status, progress_box],
|
664 |
-
# trigger=run_button,
|
665 |
-
# every=0.5,
|
666 |
-
# show_progress="full",
|
667 |
-
# )
|
668 |
-
interface.queue() # No arguments here!
|
669 |
-
|
670 |
-
run_button.click(
|
671 |
-
fn=threaded_batch_runner,
|
672 |
-
inputs=[file_upload, raw_text, user_email],
|
673 |
-
outputs=[output_table, results_group, download_file, usage_display, status, progress_box],
|
674 |
-
concurrency_limit=1, # β
correct in Gradio 5.x
|
675 |
-
queue=True, # β
ensure the queue is used
|
676 |
-
#every=0.5
|
677 |
-
)
|
678 |
-
|
679 |
-
|
680 |
-
|
681 |
-
|
682 |
-
stop_button.click(fn=stop_batch, inputs=[], outputs=[status])
|
683 |
-
|
684 |
-
# reset_button.click(
|
685 |
-
# #fn=reset_fields,
|
686 |
-
# fn=lambda: (
|
687 |
-
# gr.update(value=""), gr.update(value=""), gr.update(value=None), gr.update(value=None), gr.update(value="Single Accession"),
|
688 |
-
# gr.update(value=[], visible=True), gr.update(visible=False), gr.update(visible=False), gr.update(value="", visible=False), gr.update(value="", visible=False)
|
689 |
-
# ),
|
690 |
-
# inputs=[],
|
691 |
-
# outputs=[
|
692 |
-
# single_accession, raw_text, file_upload, resume_file,inputMode,
|
693 |
-
# output_table,# output_summary, output_flag,
|
694 |
-
# status, results_group, usage_display, progress_box
|
695 |
-
# ]
|
696 |
-
# )
|
697 |
-
#stop_button.click(fn=lambda sf: (gr.update(value="β Stopping...", visible=True), setattr(sf, "value", True) or sf), inputs=[gr.State(stop_flag)], outputs=[status, gr.State(stop_flag)])
|
698 |
-
|
699 |
-
reset_button.click(
|
700 |
-
fn=reset_fields,
|
701 |
-
inputs=[],
|
702 |
-
#outputs=[raw_text, file_upload, resume_file, output_table, status, results_group, usage_display, progress_box]
|
703 |
-
outputs=[raw_text, file_upload, output_table, status, results_group, usage_display, progress_box,
|
704 |
-
report_textbox,
|
705 |
-
submit_report_button,
|
706 |
-
status_report]
|
707 |
-
)
|
708 |
-
|
709 |
-
# download_button.click(
|
710 |
-
# fn=mtdna_backend.save_batch_output,
|
711 |
-
# #inputs=[output_table, output_summary, output_flag, output_type],
|
712 |
-
# inputs=[output_table, output_type],
|
713 |
-
# outputs=[download_file])
|
714 |
-
|
715 |
-
# submit_feedback.click(
|
716 |
-
# fn=mtdna_backend.store_feedback_to_google_sheets,
|
717 |
-
# inputs=[single_accession, q1, q2, contact], outputs=feedback_status
|
718 |
-
# )
|
719 |
-
report_button.click(fn=show_report_ui, outputs=[report_textbox, submit_report_button, status_report])
|
720 |
-
submit_report_button.click(fn=handle_submission, inputs=[report_textbox, user_email], outputs=[status_report, report_textbox, submit_report_button])
|
721 |
-
|
722 |
-
submit_feedback.click(
|
723 |
-
fn=mtdna_backend.store_feedback_to_google_sheets,
|
724 |
-
inputs=[raw_text, q1, q2, contact],
|
725 |
-
outputs=[feedback_status]
|
726 |
-
)
|
727 |
-
gr.HTML("""
|
728 |
-
<style>
|
729 |
-
body, html {
|
730 |
-
background-color: #121212 !important;
|
731 |
-
color: #ffffff !important;
|
732 |
-
}
|
733 |
-
|
734 |
-
.gradio-container, .gr-block, .gr-box, textarea, input, select, .prose, .prose * {
|
735 |
-
background-color: #1e1e1e !important;
|
736 |
-
color: #ffffff !important;
|
737 |
-
border-color: #333 !important;
|
738 |
-
}
|
739 |
-
|
740 |
-
textarea::placeholder,
|
741 |
-
input::placeholder {
|
742 |
-
color: #aaa !important;
|
743 |
-
}
|
744 |
-
|
745 |
-
button {
|
746 |
-
background-color: #2d2d2d !important;
|
747 |
-
color: #fff !important;
|
748 |
-
border: 1px solid #444 !important;
|
749 |
-
}
|
750 |
-
|
751 |
-
a {
|
752 |
-
color: #4ea1f3 !important;
|
753 |
-
}
|
754 |
-
</style>
|
755 |
-
""")
|
756 |
-
|
757 |
-
# # Custom CSS styles
|
758 |
-
# gr.HTML("""
|
759 |
-
# <style>
|
760 |
-
# /* Ensures both sections are equally spaced with the same background size */
|
761 |
-
# #output-summary, #output-flag {
|
762 |
-
# background-color: #f0f4f8; /* Light Grey for both */
|
763 |
-
# padding: 20px;
|
764 |
-
# border-radius: 10px;
|
765 |
-
# margin-top: 10px;
|
766 |
-
# width: 100%; /* Ensure full width */
|
767 |
-
# min-height: 150px; /* Ensures both have a minimum height */
|
768 |
-
# box-sizing: border-box; /* Prevents padding from increasing size */
|
769 |
-
# display: flex;
|
770 |
-
# flex-direction: column;
|
771 |
-
# justify-content: space-between;
|
772 |
-
# }
|
773 |
-
|
774 |
-
# /* Specific background colors */
|
775 |
-
# #output-summary {
|
776 |
-
# background-color: #434a4b;
|
777 |
-
# }
|
778 |
-
|
779 |
-
# #output-flag {
|
780 |
-
# background-color: #141616;
|
781 |
-
# }
|
782 |
-
|
783 |
-
# /* Ensuring they are in a row and evenly spaced */
|
784 |
-
# .gradio-row {
|
785 |
-
# display: flex;
|
786 |
-
# justify-content: space-between;
|
787 |
-
# width: 100%;
|
788 |
-
# }
|
789 |
-
# </style>
|
790 |
-
# """)
|
791 |
-
|
792 |
-
|
793 |
interface.launch(share=True,debug=True)
|
|
|
1 |
+
import gradio as gr
|
2 |
+
import mtdna_backend
|
3 |
+
import json
|
4 |
+
import data_preprocess, model, pipeline
|
5 |
+
import os
|
6 |
+
import hashlib
|
7 |
+
import threading
|
8 |
+
# Gradio UI
|
9 |
+
#stop_flag = gr.State(value=False)
|
10 |
+
class StopFlag:
|
11 |
+
def __init__(self):
|
12 |
+
self.value = False
|
13 |
+
global_stop_flag = StopFlag() # Shared between run + stop
|
14 |
+
|
15 |
+
with open("offer.html", "r", encoding="utf-8") as f:
|
16 |
+
pricing_html = f.read()
|
17 |
+
|
18 |
+
with gr.Blocks() as interface:
|
19 |
+
with gr.Tab("CURIOUS ABOUT THIS PRODUCT?"):
|
20 |
+
gr.HTML(value=pricing_html)
|
21 |
+
with gr.Tab("𧬠Classifier"):
|
22 |
+
gr.Markdown("# 𧬠mtDNA Location Classifier (MVP)")
|
23 |
+
#inputMode = gr.Radio(choices=["Single Accession", "Batch Input"], value="Single Accession", label="Choose Input Mode")
|
24 |
+
user_email = gr.Textbox(label="π§ Your email (used to track free quota)")
|
25 |
+
usage_display = gr.Markdown("", visible=False)
|
26 |
+
|
27 |
+
# with gr.Group() as single_input_group:
|
28 |
+
# single_accession = gr.Textbox(label="Enter Single Accession (e.g., KU131308)")
|
29 |
+
|
30 |
+
# with gr.Group(visible=False) as batch_input_group:
|
31 |
+
# raw_text = gr.Textbox(label="𧬠Paste Accession Numbers (e.g., MF362736.1,MF362738.1,KU131308,MW291678)")
|
32 |
+
# resume_file = gr.File(label="ποΈ Previously saved Excel output (optional)", file_types=[".xlsx"], interactive=True)
|
33 |
+
# gr.HTML("""<a href="https://drive.google.com/file/d/1t-TFeIsGVu5Jh3CUZS-VE9jQWzNFCs_c/view?usp=sharing" download target="_blank">Download Example CSV Format</a>""")
|
34 |
+
# gr.HTML("""<a href="https://docs.google.com/spreadsheets/d/1lKqPp17EfHsshJGZRWEpcNOZlGo3F5qU/edit?usp=sharing&ouid=112390323314156876153&rtpof=true&sd=true" download target="_blank">Download Example Excel Format</a>""")
|
35 |
+
# file_upload = gr.File(label="π Or Upload CSV/Excel File", file_types=[".csv", ".xlsx"], interactive=True, elem_id="file-upload-box")
|
36 |
+
raw_text = gr.Textbox(label="π§ Input Accession Number(s) (single (KU131308) or comma-separated (e.g., MF362736.1,MF362738.1,KU131308,MW291678))")
|
37 |
+
#resume_file = gr.File(label="ποΈ Previously saved Excel output (optional)", file_types=[".xlsx"], interactive=True)
|
38 |
+
gr.HTML("""<a href="https://docs.google.com/spreadsheets/d/1lKqPp17EfHsshJGZRWEpcNOZlGo3F5qU/edit?usp=sharing" download target="_blank">Download Example Excel Format</a>""")
|
39 |
+
file_upload = gr.File(label="π Or Upload CSV/Excel File", file_types=[".csv", ".xlsx"], interactive=True)
|
40 |
+
|
41 |
+
with gr.Row():
|
42 |
+
run_button = gr.Button("π Submit and Classify")
|
43 |
+
stop_button = gr.Button("β Stop Batch", visible=True)
|
44 |
+
reset_button = gr.Button("π Reset")
|
45 |
+
|
46 |
+
status = gr.Markdown(visible=False)
|
47 |
+
|
48 |
+
with gr.Group(visible=False) as results_group:
|
49 |
+
# with gr.Accordion("Open to See the Result", open=False) as results:
|
50 |
+
# with gr.Row():
|
51 |
+
# output_summary = gr.Markdown(elem_id="output-summary")
|
52 |
+
# output_flag = gr.Markdown(elem_id="output-flag")
|
53 |
+
|
54 |
+
# gr.Markdown("---")
|
55 |
+
|
56 |
+
with gr.Accordion("Open to See the Output Table", open=False) as table_accordion:
|
57 |
+
output_table = gr.HTML(render=True)
|
58 |
+
#with gr.Row():
|
59 |
+
#output_type = gr.Dropdown(choices=["Excel", "JSON", "TXT"], label="Select Output Format", value="Excel")
|
60 |
+
#download_button = gr.Button("β¬οΈ Download Output")
|
61 |
+
#download_file = gr.File(label="Download File Here",visible=False)
|
62 |
+
report_button = gr.Button("Report")
|
63 |
+
report_textbox = gr.Textbox(
|
64 |
+
label="Describe the issue",
|
65 |
+
lines=4,
|
66 |
+
placeholder="e.g. DQ981467: it gives me unknown when I can in fact search it on NCBI \n DQ981467: cannot find the result in batch output when the live processing did show already processed",
|
67 |
+
visible=False)
|
68 |
+
submit_report_button = gr.Button("Submit", visible=False)
|
69 |
+
status_report = gr.Markdown(visible=False)
|
70 |
+
|
71 |
+
download_file = gr.File(label="Download File Here", visible=False, interactive=True)
|
72 |
+
progress_box = gr.Textbox(label="Live Processing Log", lines=20, interactive=False)
|
73 |
+
|
74 |
+
gr.Markdown("---")
|
75 |
+
|
76 |
+
gr.Markdown("### π¬ Feedback (required)")
|
77 |
+
q1 = gr.Textbox(label="1οΈβ£ Was the inferred location accurate or helpful? Please explain.")
|
78 |
+
q2 = gr.Textbox(label="2οΈβ£ What would improve your experience with this tool?")
|
79 |
+
contact = gr.Textbox(label="π§ Your email or institution (optional)")
|
80 |
+
submit_feedback = gr.Button("β
Submit Feedback")
|
81 |
+
feedback_status = gr.Markdown()
|
82 |
+
|
83 |
+
# Functions
|
84 |
+
# def toggle_input_mode(mode):
|
85 |
+
# if mode == "Single Accession":
|
86 |
+
# return gr.update(visible=True), gr.update(visible=False)
|
87 |
+
# else:
|
88 |
+
# return gr.update(visible=False), gr.update(visible=True)
|
89 |
+
|
90 |
+
def classify_with_loading():
|
91 |
+
return gr.update(value="β³ Please wait... processing...",visible=True) # Show processing message
|
92 |
+
|
93 |
+
# def classify_dynamic(single_accession, file, text, resume, email, mode):
|
94 |
+
# if mode == "Single Accession":
|
95 |
+
# return classify_main(single_accession) + (gr.update(visible=False),)
|
96 |
+
# else:
|
97 |
+
# #return summarize_batch(file, text) + (gr.update(visible=False),) # Hide processing message
|
98 |
+
# return classify_mulAcc(file, text, resume) + (gr.update(visible=False),) # Hide processing message
|
99 |
+
# Logging helpers defined early to avoid NameError
|
100 |
+
|
101 |
+
|
102 |
+
# def classify_dynamic(single_accession, file, text, resume, email, mode):
|
103 |
+
# if mode == "Single Accession":
|
104 |
+
# return classify_main(single_accession) + (gr.update(value="", visible=False),)
|
105 |
+
# else:
|
106 |
+
# return classify_mulAcc(file, text, resume, email, log_callback=real_time_logger, log_collector=log_collector)
|
107 |
+
|
108 |
+
# for single accession
|
109 |
+
# def classify_main(accession):
|
110 |
+
# #table, summary, labelAncient_Modern, explain_label = mtdna_backend.summarize_results(accession)
|
111 |
+
# table = mtdna_backend.summarize_results(accession)
|
112 |
+
# #flag_output = f"### πΊ Ancient/Modern Flag\n**{labelAncient_Modern}**\n\n_Explanation:_ {explain_label}"
|
113 |
+
# return (
|
114 |
+
# #table,
|
115 |
+
# make_html_table(table),
|
116 |
+
# # summary,
|
117 |
+
# # flag_output,
|
118 |
+
# gr.update(visible=True),
|
119 |
+
# gr.update(visible=False),
|
120 |
+
# gr.update(visible=False)
|
121 |
+
# )
|
122 |
+
|
123 |
+
#stop_flag = gr.State(value=False)
|
124 |
+
#stop_flag = StopFlag()
|
125 |
+
|
126 |
+
# def stop_batch(stop_flag):
|
127 |
+
# stop_flag.value = True
|
128 |
+
# return gr.update(value="β Stopping...", visible=True), stop_flag
|
129 |
+
def stop_batch():
|
130 |
+
global_stop_flag.value = True
|
131 |
+
return gr.update(value="β Stopping...", visible=True)
|
132 |
+
|
133 |
+
# def threaded_batch_runner(file, text, email):
|
134 |
+
# global_stop_flag.value = False
|
135 |
+
# log_lines = []
|
136 |
+
|
137 |
+
# def update_log(line):
|
138 |
+
# log_lines.append(line)
|
139 |
+
# yield (
|
140 |
+
# gr.update(visible=False), # output_table (not yet)
|
141 |
+
# gr.update(visible=False), # results_group
|
142 |
+
# gr.update(visible=False), # download_file
|
143 |
+
# gr.update(visible=False), # usage_display
|
144 |
+
# gr.update(value="β³ Still processing...", visible=True), # status
|
145 |
+
# gr.update(value="\n".join(log_lines)) # progress_box
|
146 |
+
# )
|
147 |
+
|
148 |
+
# # Start a dummy update to say "Starting..."
|
149 |
+
# yield from update_log("π Starting batch processing...")
|
150 |
+
|
151 |
+
# rows, file_path, count, final_log, warning = mtdna_backend.summarize_batch(
|
152 |
+
# file=file,
|
153 |
+
# raw_text=text,
|
154 |
+
# resume_file=None,
|
155 |
+
# user_email=email,
|
156 |
+
# stop_flag=global_stop_flag,
|
157 |
+
# yield_callback=lambda line: (yield from update_log(line))
|
158 |
+
# )
|
159 |
+
|
160 |
+
# html = make_html_table(rows)
|
161 |
+
# file_update = gr.update(value=file_path, visible=True) if os.path.exists(file_path) else gr.update(visible=False)
|
162 |
+
# usage_or_warning_text = f"**{count}** samples used by this email." if email.strip() else warning
|
163 |
+
|
164 |
+
# yield (
|
165 |
+
# html,
|
166 |
+
# gr.update(visible=True), # results_group
|
167 |
+
# file_update, # download_file
|
168 |
+
# gr.update(value=usage_or_warning_text, visible=True),
|
169 |
+
# gr.update(value="β
Done", visible=True),
|
170 |
+
# gr.update(value=final_log)
|
171 |
+
# )
|
172 |
+
|
173 |
+
# def threaded_batch_runner(file=None, text="", email=""):
|
174 |
+
# print("π§ EMAIL RECEIVED:", email)
|
175 |
+
# import tempfile
|
176 |
+
# from mtdna_backend import (
|
177 |
+
# extract_accessions_from_input,
|
178 |
+
# summarize_results,
|
179 |
+
# save_to_excel,
|
180 |
+
# hash_user_id,
|
181 |
+
# increment_usage,
|
182 |
+
# )
|
183 |
+
# import os
|
184 |
+
|
185 |
+
# global_stop_flag.value = False # reset stop flag
|
186 |
+
|
187 |
+
# tmp_dir = tempfile.mkdtemp()
|
188 |
+
# output_file_path = os.path.join(tmp_dir, "batch_output_live.xlsx")
|
189 |
+
# limited_acc = 50 + (10 if email.strip() else 0)
|
190 |
+
|
191 |
+
# # Step 1: Parse input
|
192 |
+
# accessions, error = extract_accessions_from_input(file, text)
|
193 |
+
# print(accessions)
|
194 |
+
# if error:
|
195 |
+
# yield (
|
196 |
+
# "", # output_table
|
197 |
+
# gr.update(visible=False), # results_group
|
198 |
+
# gr.update(visible=False), # download_file
|
199 |
+
# "", # usage_display
|
200 |
+
# "β Error", # status
|
201 |
+
# str(error) # progress_box
|
202 |
+
# )
|
203 |
+
# return
|
204 |
+
|
205 |
+
# total = len(accessions)
|
206 |
+
# if total > limited_acc:
|
207 |
+
# accessions = accessions[:limited_acc]
|
208 |
+
# warning = f"β οΈ Only processing first {limited_acc} accessions."
|
209 |
+
# else:
|
210 |
+
# warning = f"β
All {total} accessions will be processed."
|
211 |
+
|
212 |
+
# all_rows = []
|
213 |
+
# processed_accessions = 0 # β
tracks how many accessions were processed
|
214 |
+
# email_tracked = False
|
215 |
+
# log_lines = []
|
216 |
+
|
217 |
+
# # Step 2: Loop through accessions
|
218 |
+
# for i, acc in enumerate(accessions):
|
219 |
+
# if global_stop_flag.value:
|
220 |
+
# log_lines.append(f"π Stopped at {acc} ({i+1}/{total})")
|
221 |
+
# usage_text = ""
|
222 |
+
# if email.strip() and not email_tracked:
|
223 |
+
# # user_hash = hash_user_id(email)
|
224 |
+
# # usage_count = increment_usage(user_hash, len(all_rows))
|
225 |
+
# print("print(processed_accessions at stop) ",processed_accessions)
|
226 |
+
# usage_count = increment_usage(email, processed_accessions)
|
227 |
+
# email_tracked = True
|
228 |
+
# usage_text = f"**{usage_count}** samples used by this email. Ten more samples are added first (you now have 60 limited accessions), then wait we will contact you via this email."
|
229 |
+
# else:
|
230 |
+
# usage_text = f"The limited accession is 50. The user has used {processed_accessions}, and only {50-processed_accessions} left."
|
231 |
+
# yield (
|
232 |
+
# make_html_table(all_rows),
|
233 |
+
# gr.update(visible=True),
|
234 |
+
# gr.update(value=output_file_path, visible=True),
|
235 |
+
# gr.update(value=usage_text, visible=True),
|
236 |
+
# "π Stopped",
|
237 |
+
# "\n".join(log_lines)
|
238 |
+
# )
|
239 |
+
# return
|
240 |
+
|
241 |
+
# log_lines.append(f"[{i+1}/{total}] Processing {acc}")
|
242 |
+
# yield (
|
243 |
+
# make_html_table(all_rows),
|
244 |
+
# gr.update(visible=True),
|
245 |
+
# gr.update(visible=False),
|
246 |
+
# "",
|
247 |
+
# "β³ Processing...",
|
248 |
+
# "\n".join(log_lines)
|
249 |
+
# )
|
250 |
+
|
251 |
+
# try:
|
252 |
+
# print(acc)
|
253 |
+
# rows = summarize_results(acc)
|
254 |
+
# all_rows.extend(rows)
|
255 |
+
# processed_accessions += 1 # β
count only successful accessions
|
256 |
+
# save_to_excel(all_rows, "", "", output_file_path, is_resume=False)
|
257 |
+
# log_lines.append(f"β
Processed {acc} ({i+1}/{total})")
|
258 |
+
# except Exception as e:
|
259 |
+
# log_lines.append(f"β Failed to process {acc}: {e}")
|
260 |
+
|
261 |
+
# yield (
|
262 |
+
# make_html_table(all_rows),
|
263 |
+
# gr.update(visible=True),
|
264 |
+
# gr.update(visible=False),
|
265 |
+
# "",
|
266 |
+
# "β³ Processing...",
|
267 |
+
# "\n".join(log_lines)
|
268 |
+
# )
|
269 |
+
|
270 |
+
# # Final update
|
271 |
+
# usage_text = ""
|
272 |
+
|
273 |
+
# if email.strip() and not email_tracked:
|
274 |
+
# # user_hash = hash_user_id(email)
|
275 |
+
# # usage_count = increment_usage(user_hash, len(all_rows))
|
276 |
+
# print("print(processed_accessions final) ",processed_accessions)
|
277 |
+
# usage_count = increment_usage(email, processed_accessions)
|
278 |
+
# usage_text = f"**{usage_count}** samples used by this email. Ten more samples are added first (you now have 60 limited accessions), then wait we will contact you via this email."
|
279 |
+
# elif not email.strip():
|
280 |
+
# usage_text = f"The limited accession is 50. The user has used {processed_accessions}, and only {50-processed_accessions} left."
|
281 |
+
# yield (
|
282 |
+
# make_html_table(all_rows),
|
283 |
+
# gr.update(visible=True),
|
284 |
+
# gr.update(value=output_file_path, visible=True),
|
285 |
+
# gr.update(value=usage_text, visible=True),
|
286 |
+
# "β
Done",
|
287 |
+
# "\n".join(log_lines)
|
288 |
+
# )
|
289 |
+
|
290 |
+
def threaded_batch_runner(file=None, text="", email=""):
|
291 |
+
print("π§ EMAIL RECEIVED:", repr(email))
|
292 |
+
import tempfile
|
293 |
+
from mtdna_backend import (
|
294 |
+
extract_accessions_from_input,
|
295 |
+
summarize_results,
|
296 |
+
save_to_excel,
|
297 |
+
increment_usage,
|
298 |
+
)
|
299 |
+
import os
|
300 |
+
|
301 |
+
global_stop_flag.value = False # reset stop flag
|
302 |
+
|
303 |
+
tmp_dir = tempfile.mkdtemp()
|
304 |
+
output_file_path = os.path.join(tmp_dir, "batch_output_live.xlsx")
|
305 |
+
#output_file_path = "/mnt/data/batch_output_live.xlsx"
|
306 |
+
all_rows = []
|
307 |
+
processed_accessions = 0 # β
track successful accessions
|
308 |
+
email_tracked = False
|
309 |
+
log_lines = []
|
310 |
+
if not email.strip():
|
311 |
+
output_file_path = None#"Write your email so that you can download the outputs."
|
312 |
+
log_lines.append("π₯ Provide your email to receive a downloadable Excel report and get 20 more free queries.")
|
313 |
+
limited_acc = 30
|
314 |
+
if email.strip():
|
315 |
+
usage_count, max_allowed = increment_usage(email, processed_accessions)
|
316 |
+
if int(usage_count) >= int(max_allowed):
|
317 |
+
log_lines.append("β You have reached your quota. Please contact us to unlock more.")
|
318 |
+
|
319 |
+
# Minimal blank yield to trigger UI rendering
|
320 |
+
yield (
|
321 |
+
make_html_table([]),
|
322 |
+
gr.update(visible=True),
|
323 |
+
gr.update(visible=False),
|
324 |
+
gr.update(value="", visible=True),
|
325 |
+
"βοΈ Quota limit",
|
326 |
+
"βοΈ Quota limit"
|
327 |
+
)
|
328 |
+
|
329 |
+
# Actual warning frame
|
330 |
+
yield (
|
331 |
+
make_html_table([]),
|
332 |
+
gr.update(visible=False),
|
333 |
+
gr.update(visible=False),
|
334 |
+
gr.update(value="β You have reached your quota. Please contact us to unlock more.", visible=True),
|
335 |
+
"β Quota Exceeded",
|
336 |
+
"\n".join(log_lines)
|
337 |
+
)
|
338 |
+
return
|
339 |
+
limited_acc = int(max_allowed-usage_count)
|
340 |
+
# Step 1: Parse input
|
341 |
+
accessions, error = extract_accessions_from_input(file, text)
|
342 |
+
print("π§ͺ Accessions received:", accessions)
|
343 |
+
if error:
|
344 |
+
yield (
|
345 |
+
"", # output_table
|
346 |
+
gr.update(visible=False), # results_group
|
347 |
+
gr.update(visible=False), # download_file
|
348 |
+
"", # usage_display
|
349 |
+
"β Error", # status
|
350 |
+
str(error) # progress_box
|
351 |
+
)
|
352 |
+
return
|
353 |
+
|
354 |
+
total = len(accessions)
|
355 |
+
if total > limited_acc:
|
356 |
+
accessions = accessions[:limited_acc]
|
357 |
+
warning = f"β οΈ Only processing first {limited_acc} accessions."
|
358 |
+
else:
|
359 |
+
warning = f"β
All {total} accessions will be processed."
|
360 |
+
|
361 |
+
# all_rows = []
|
362 |
+
# processed_accessions = 0 # β
track successful accessions
|
363 |
+
# email_tracked = False
|
364 |
+
# log_lines = []
|
365 |
+
# if not email.strip():
|
366 |
+
# output_file_path = None#"Write your email so that you can download the outputs."
|
367 |
+
# log_lines.append("π₯ Provide your email to receive a downloadable Excel report and get 20 more free queries.")
|
368 |
+
# if email.strip():
|
369 |
+
# usage_count, max_allowed = increment_usage(email, processed_accessions)
|
370 |
+
# if int(usage_count) > int(max_allowed):
|
371 |
+
# log_lines.append("β You have reached your quota. Please contact us to unlock more.")
|
372 |
+
|
373 |
+
# # Minimal blank yield to trigger UI rendering
|
374 |
+
# yield (
|
375 |
+
# make_html_table([]),
|
376 |
+
# gr.update(visible=True),
|
377 |
+
# gr.update(visible=False),
|
378 |
+
# gr.update(value="", visible=True),
|
379 |
+
# "βοΈ Quota limit",
|
380 |
+
# "βοΈ Quota limit"
|
381 |
+
# )
|
382 |
+
|
383 |
+
# # Actual warning frame
|
384 |
+
# yield (
|
385 |
+
# make_html_table([]),
|
386 |
+
# gr.update(visible=False),
|
387 |
+
# gr.update(visible=False),
|
388 |
+
# gr.update(value="β You have reached your quota. Please contact us to unlock more.", visible=True),
|
389 |
+
# "β Quota Exceeded",
|
390 |
+
# "\n".join(log_lines)
|
391 |
+
# )
|
392 |
+
# return
|
393 |
+
|
394 |
+
|
395 |
+
# Step 2: Loop through accessions
|
396 |
+
for i, acc in enumerate(accessions):
|
397 |
+
if global_stop_flag.value:
|
398 |
+
log_lines.append(f"π Stopped at {acc} ({i+1}/{total})")
|
399 |
+
usage_text = ""
|
400 |
+
|
401 |
+
if email.strip() and not email_tracked:
|
402 |
+
print(f"π§ͺ increment_usage at STOP: {email=} {processed_accessions=}")
|
403 |
+
usage_count, max_allowed = increment_usage(email, processed_accessions)
|
404 |
+
email_tracked = True
|
405 |
+
usage_text = f"**{usage_count}**/{max_allowed} allowed samples used by this email."
|
406 |
+
#Ten more samples are added first (you now have 60 limited accessions), then wait we will contact you via this email."
|
407 |
+
else:
|
408 |
+
usage_text = f"The limited accession is 30. The user has used {processed_accessions}, and only {30 - processed_accessions} left."
|
409 |
+
|
410 |
+
yield (
|
411 |
+
make_html_table(all_rows),
|
412 |
+
gr.update(visible=True),
|
413 |
+
#gr.update(value=output_file_path, visible=True),
|
414 |
+
gr.update(value=output_file_path, visible=bool(output_file_path)),
|
415 |
+
gr.update(value=usage_text, visible=True),
|
416 |
+
"π Stopped",
|
417 |
+
"\n".join(log_lines)
|
418 |
+
)
|
419 |
+
return
|
420 |
+
|
421 |
+
log_lines.append(f"[{i+1}/{total}] Processing {acc}")
|
422 |
+
yield (
|
423 |
+
make_html_table(all_rows),
|
424 |
+
gr.update(visible=True),
|
425 |
+
gr.update(visible=False),
|
426 |
+
"",
|
427 |
+
"β³ Processing...",
|
428 |
+
"\n".join(log_lines)
|
429 |
+
)
|
430 |
+
|
431 |
+
try:
|
432 |
+
print("π Processing accession:", acc)
|
433 |
+
rows = summarize_results(acc)
|
434 |
+
all_rows.extend(rows)
|
435 |
+
processed_accessions += 1 # β
only count success
|
436 |
+
if email.strip():
|
437 |
+
save_to_excel(all_rows, "", "", output_file_path, is_resume=False)
|
438 |
+
log_lines.append(f"β
Processed {acc} ({i+1}/{total})")
|
439 |
+
except Exception as e:
|
440 |
+
log_lines.append(f"β Failed to process {acc}: {e}")
|
441 |
+
|
442 |
+
yield (
|
443 |
+
make_html_table(all_rows),
|
444 |
+
gr.update(visible=True),
|
445 |
+
gr.update(visible=False),
|
446 |
+
"",
|
447 |
+
"β³ Processing...",
|
448 |
+
"\n".join(log_lines)
|
449 |
+
)
|
450 |
+
|
451 |
+
# Step 3: Final usage update
|
452 |
+
usage_text = ""
|
453 |
+
if email.strip() and not email_tracked:
|
454 |
+
print(f"π§ͺ increment_usage at END: {email=} {processed_accessions=}")
|
455 |
+
usage_count, max_allowed = increment_usage(email, processed_accessions)
|
456 |
+
email_tracked = True
|
457 |
+
usage_text = f"**{usage_count}**/{max_allowed} allowed samples used by this email."
|
458 |
+
#Ten more samples are added first (you now have 60 limited accessions), then wait we will contact you via this email."
|
459 |
+
elif not email.strip():
|
460 |
+
usage_text = f"The limited accession is 30. The user has used {processed_accessions}, and only {30 - processed_accessions} left."
|
461 |
+
|
462 |
+
yield (
|
463 |
+
make_html_table(all_rows),
|
464 |
+
gr.update(visible=True),
|
465 |
+
#gr.update(value=output_file_path, visible=True),
|
466 |
+
gr.update(value=output_file_path, visible=bool(output_file_path)),
|
467 |
+
gr.update(value=usage_text, visible=True),
|
468 |
+
"β
Done",
|
469 |
+
"\n".join(log_lines)
|
470 |
+
)
|
471 |
+
|
472 |
+
# SUBMIT REPORT UI
|
473 |
+
# 1. Google Sheets setup
|
474 |
+
def get_worksheet(sheet_name="Report"):
|
475 |
+
import os, json
|
476 |
+
import gspread
|
477 |
+
from oauth2client.service_account import ServiceAccountCredentials
|
478 |
+
try:
|
479 |
+
creds_dict = json.loads(os.environ["GCP_CREDS_JSON"])
|
480 |
+
scope = ["https://spreadsheets.google.com/feeds", "https://www.googleapis.com/auth/drive"]
|
481 |
+
creds = ServiceAccountCredentials.from_json_keyfile_dict(creds_dict, scope)
|
482 |
+
client = gspread.authorize(creds)
|
483 |
+
sheet = client.open(sheet_name).sheet1
|
484 |
+
return sheet
|
485 |
+
except Exception as e:
|
486 |
+
print(f"β Error loading Google Sheet '{sheet_name}':", e)
|
487 |
+
return None
|
488 |
+
|
489 |
+
# 2. Submit function to send report to the Google Sheet
|
490 |
+
def submit_report(report_text,user_email=""):
|
491 |
+
try:
|
492 |
+
sheet = get_worksheet()
|
493 |
+
# β
Parse the report_text (each line like 'ACCESSION: message')
|
494 |
+
lines = report_text.strip().split('\n')
|
495 |
+
user = ""
|
496 |
+
if user_email.strip():
|
497 |
+
user = user_email
|
498 |
+
for line in lines:
|
499 |
+
if ':' in line:
|
500 |
+
accession, message = line.split(':', 1)
|
501 |
+
sheet.append_row([accession.strip(), message.strip(), user.strip()])
|
502 |
+
return "β
Report submitted successfully!"
|
503 |
+
except Exception as e:
|
504 |
+
return f"β Error submitting report: {str(e)}"
|
505 |
+
def show_report_ui():
|
506 |
+
return gr.update(visible=True), gr.update(visible=True), gr.update(visible=False)
|
507 |
+
|
508 |
+
def handle_submission(text,user_email):
|
509 |
+
msg = submit_report(text, user_email)
|
510 |
+
return gr.update(value=msg, visible=True), gr.update(visible=False), gr.update(visible=False)
|
511 |
+
# def threaded_batch_runner(file=None, text="", email=""):
|
512 |
+
# global_stop_flag.value = False
|
513 |
+
|
514 |
+
# # Dummy test output that matches expected schema
|
515 |
+
# return (
|
516 |
+
# "<div>β
Dummy output table</div>", # HTML string
|
517 |
+
# gr.update(visible=True), # Group visibility
|
518 |
+
# gr.update(visible=False), # Download file
|
519 |
+
# "**0** samples used.", # Markdown
|
520 |
+
# "β
Done", # Status string
|
521 |
+
# "Processing finished." # Progress string
|
522 |
+
# )
|
523 |
+
|
524 |
+
|
525 |
+
# def classify_mulAcc(file, text, resume, email, log_callback=None, log_collector=None):
|
526 |
+
# stop_flag.value = False
|
527 |
+
# return threaded_batch_runner(file, text, resume, email, status, stop_flag, log_callback=log_callback, log_collector=log_collector)
|
528 |
+
|
529 |
+
|
530 |
+
def make_html_table(rows):
|
531 |
+
# html = """
|
532 |
+
# <div style='overflow-x: auto; padding: 10px;'>
|
533 |
+
# <div style='max-height: 400px; overflow-y: auto; border: 1px solid #444; border-radius: 8px;'>
|
534 |
+
# <table style='width:100%; border-collapse: collapse; table-layout: auto; font-size: 14px; color: #f1f1f1; background-color: #1e1e1e;'>
|
535 |
+
# <thead style='position: sticky; top: 0; background-color: #2c2c2c; z-index: 1;'>
|
536 |
+
# <tr>
|
537 |
+
# """
|
538 |
+
html = """
|
539 |
+
<div style='overflow-x: auto; padding: 10px;'>
|
540 |
+
<div style='max-height: 400px; overflow-y: auto; border: 1px solid #ccc; border-radius: 8px;'>
|
541 |
+
<table style='width:100%; border-collapse: collapse; table-layout: auto; font-size: 14px; color: inherit; background-color: inherit;'>
|
542 |
+
"""
|
543 |
+
|
544 |
+
headers = ["Sample ID", "Predicted Country", "Country Explanation", "Predicted Sample Type", "Sample Type Explanation", "Sources", "Time cost"]
|
545 |
+
html += "".join(
|
546 |
+
f"<th style='padding: 10px; border: 1px solid #555; text-align: left; white-space: nowrap;'>{h}</th>"
|
547 |
+
for h in headers
|
548 |
+
)
|
549 |
+
html += "</tr></thead><tbody>"
|
550 |
+
|
551 |
+
for row in rows:
|
552 |
+
html += "<tr>"
|
553 |
+
for i, col in enumerate(row):
|
554 |
+
header = headers[i]
|
555 |
+
style = "padding: 10px; border: 1px solid #555; vertical-align: top;"
|
556 |
+
|
557 |
+
# For specific columns like Haplogroup, force nowrap
|
558 |
+
if header in ["Country Explanation", "Sample Type Explanation"]:
|
559 |
+
style += " max-width: 400px; word-wrap: break-word; white-space: normal;"
|
560 |
+
elif header in ["Sample ID", "Predicted Country", "Predicted Sample Type", "Time cost"]:
|
561 |
+
style += " white-space: nowrap; text-overflow: ellipsis; max-width: 200px; overflow: hidden;"
|
562 |
+
|
563 |
+
# if header == "Sources" and isinstance(col, str) and col.strip().lower().startswith("http"):
|
564 |
+
# col = f"<a href='{col}' target='_blank' style='color: #4ea1f3; text-decoration: underline;'>{col}</a>"
|
565 |
+
|
566 |
+
#html += f"<td style='{style}'>{col}</td>"
|
567 |
+
if header == "Sources" and isinstance(col, str):
|
568 |
+
links = [f"<a href='{url.strip()}' target='_blank' style='color: #4ea1f3; text-decoration: underline;'>{url.strip()}</a>" for url in col.strip().split("\n") if url.strip()]
|
569 |
+
col = "- "+"<br>- ".join(links)
|
570 |
+
elif isinstance(col, str):
|
571 |
+
# lines = []
|
572 |
+
# for line in col.split("\n"):
|
573 |
+
# line = line.strip()
|
574 |
+
# if not line:
|
575 |
+
# continue
|
576 |
+
# if line.lower().startswith("rag_llm-"):
|
577 |
+
# content = line[len("rag_llm-"):].strip()
|
578 |
+
# line = f"{content} (Method: RAG_LLM)"
|
579 |
+
# lines.append(f"- {line}")
|
580 |
+
col = col.replace("\n", "<br>")
|
581 |
+
#col = col.replace("\t", " ")
|
582 |
+
#col = "<br>".join(lines)
|
583 |
+
|
584 |
+
html += f"<td style='{style}'>{col}</td>"
|
585 |
+
html += "</tr>"
|
586 |
+
|
587 |
+
html += "</tbody></table></div></div>"
|
588 |
+
return html
|
589 |
+
|
590 |
+
|
591 |
+
# def reset_fields():
|
592 |
+
# global_stop_flag.value = False # π‘ Add this to reset the flag
|
593 |
+
# return (
|
594 |
+
# #gr.update(value=""), # single_accession
|
595 |
+
# gr.update(value=""), # raw_text
|
596 |
+
# gr.update(value=None), # file_upload
|
597 |
+
# #gr.update(value=None), # resume_file
|
598 |
+
# #gr.update(value="Single Accession"), # inputMode
|
599 |
+
# gr.update(value=[], visible=True), # output_table
|
600 |
+
# # gr.update(value="", visible=True), # output_summary
|
601 |
+
# # gr.update(value="", visible=True), # output_flag
|
602 |
+
# gr.update(visible=False), # status
|
603 |
+
# gr.update(visible=False), # results_group
|
604 |
+
# gr.update(value="", visible=False), # usage_display
|
605 |
+
# gr.update(value="", visible=False), # progress_box
|
606 |
+
# )
|
607 |
+
def reset_fields():
|
608 |
+
global_stop_flag.value = False # Reset the stop flag
|
609 |
+
|
610 |
+
return (
|
611 |
+
gr.update(value=""), # raw_text
|
612 |
+
gr.update(value=None), # file_upload
|
613 |
+
gr.update(value=[], visible=True), # output_table
|
614 |
+
gr.update(value="", visible=True), # status β reset and make visible again
|
615 |
+
gr.update(visible=False), # results_group
|
616 |
+
gr.update(value="", visible=True), # usage_display β reset and make visible again
|
617 |
+
gr.update(value="", visible=True), # progress_box β reset AND visible!
|
618 |
+
# report-related reset below
|
619 |
+
gr.update(value="", visible=False), # report_textbox
|
620 |
+
gr.update(visible=False), # submit_report_button
|
621 |
+
gr.update(value="", visible=False), # status_report
|
622 |
+
)
|
623 |
+
#inputMode.change(fn=toggle_input_mode, inputs=inputMode, outputs=[single_input_group, batch_input_group])
|
624 |
+
#run_button.click(fn=classify_with_loading, inputs=[], outputs=[status])
|
625 |
+
# run_button.click(
|
626 |
+
# fn=classify_dynamic,
|
627 |
+
# inputs=[single_accession, file_upload, raw_text, resume_file,user_email,inputMode],
|
628 |
+
# outputs=[output_table,
|
629 |
+
# #output_summary, output_flag,
|
630 |
+
# results_group, download_file, usage_display,status, progress_box]
|
631 |
+
# )
|
632 |
+
|
633 |
+
# run_button.click(
|
634 |
+
# fn=threaded_batch_runner,
|
635 |
+
# #inputs=[file_upload, raw_text, resume_file, user_email],
|
636 |
+
# inputs=[file_upload, raw_text, user_email],
|
637 |
+
# outputs=[output_table, results_group, download_file, usage_display, status, progress_box]
|
638 |
+
# )
|
639 |
+
# run_button.click(
|
640 |
+
# fn=threaded_batch_runner,
|
641 |
+
# inputs=[file_upload, raw_text, user_email],
|
642 |
+
# outputs=[output_table, results_group, download_file, usage_display, status, progress_box],
|
643 |
+
# every=0.5 # <-- this tells Gradio to expect streaming
|
644 |
+
# )
|
645 |
+
# output_table = gr.HTML()
|
646 |
+
# results_group = gr.Group(visible=False)
|
647 |
+
# download_file = gr.File(visible=False)
|
648 |
+
# usage_display = gr.Markdown(visible=False)
|
649 |
+
# status = gr.Markdown(visible=False)
|
650 |
+
# progress_box = gr.Textbox(visible=False)
|
651 |
+
|
652 |
+
# run_button.click(
|
653 |
+
# fn=threaded_batch_runner,
|
654 |
+
# inputs=[file_upload, raw_text, user_email],
|
655 |
+
# outputs=[output_table, results_group, download_file, usage_display, status, progress_box],
|
656 |
+
# every=0.5, # streaming enabled
|
657 |
+
# show_progress="full"
|
658 |
+
# )
|
659 |
+
|
660 |
+
# interface.stream(
|
661 |
+
# fn=threaded_batch_runner,
|
662 |
+
# inputs=[file_upload, raw_text, user_email],
|
663 |
+
# outputs=[output_table, results_group, download_file, usage_display, status, progress_box],
|
664 |
+
# trigger=run_button,
|
665 |
+
# every=0.5,
|
666 |
+
# show_progress="full",
|
667 |
+
# )
|
668 |
+
interface.queue() # No arguments here!
|
669 |
+
|
670 |
+
run_button.click(
|
671 |
+
fn=threaded_batch_runner,
|
672 |
+
inputs=[file_upload, raw_text, user_email],
|
673 |
+
outputs=[output_table, results_group, download_file, usage_display, status, progress_box],
|
674 |
+
concurrency_limit=1, # β
correct in Gradio 5.x
|
675 |
+
queue=True, # β
ensure the queue is used
|
676 |
+
#every=0.5
|
677 |
+
)
|
678 |
+
|
679 |
+
|
680 |
+
|
681 |
+
|
682 |
+
stop_button.click(fn=stop_batch, inputs=[], outputs=[status])
|
683 |
+
|
684 |
+
# reset_button.click(
|
685 |
+
# #fn=reset_fields,
|
686 |
+
# fn=lambda: (
|
687 |
+
# gr.update(value=""), gr.update(value=""), gr.update(value=None), gr.update(value=None), gr.update(value="Single Accession"),
|
688 |
+
# gr.update(value=[], visible=True), gr.update(visible=False), gr.update(visible=False), gr.update(value="", visible=False), gr.update(value="", visible=False)
|
689 |
+
# ),
|
690 |
+
# inputs=[],
|
691 |
+
# outputs=[
|
692 |
+
# single_accession, raw_text, file_upload, resume_file,inputMode,
|
693 |
+
# output_table,# output_summary, output_flag,
|
694 |
+
# status, results_group, usage_display, progress_box
|
695 |
+
# ]
|
696 |
+
# )
|
697 |
+
#stop_button.click(fn=lambda sf: (gr.update(value="β Stopping...", visible=True), setattr(sf, "value", True) or sf), inputs=[gr.State(stop_flag)], outputs=[status, gr.State(stop_flag)])
|
698 |
+
|
699 |
+
reset_button.click(
|
700 |
+
fn=reset_fields,
|
701 |
+
inputs=[],
|
702 |
+
#outputs=[raw_text, file_upload, resume_file, output_table, status, results_group, usage_display, progress_box]
|
703 |
+
outputs=[raw_text, file_upload, output_table, status, results_group, usage_display, progress_box,
|
704 |
+
report_textbox,
|
705 |
+
submit_report_button,
|
706 |
+
status_report]
|
707 |
+
)
|
708 |
+
|
709 |
+
# download_button.click(
|
710 |
+
# fn=mtdna_backend.save_batch_output,
|
711 |
+
# #inputs=[output_table, output_summary, output_flag, output_type],
|
712 |
+
# inputs=[output_table, output_type],
|
713 |
+
# outputs=[download_file])
|
714 |
+
|
715 |
+
# submit_feedback.click(
|
716 |
+
# fn=mtdna_backend.store_feedback_to_google_sheets,
|
717 |
+
# inputs=[single_accession, q1, q2, contact], outputs=feedback_status
|
718 |
+
# )
|
719 |
+
report_button.click(fn=show_report_ui, outputs=[report_textbox, submit_report_button, status_report])
|
720 |
+
submit_report_button.click(fn=handle_submission, inputs=[report_textbox, user_email], outputs=[status_report, report_textbox, submit_report_button])
|
721 |
+
|
722 |
+
submit_feedback.click(
|
723 |
+
fn=mtdna_backend.store_feedback_to_google_sheets,
|
724 |
+
inputs=[raw_text, q1, q2, contact],
|
725 |
+
outputs=[feedback_status]
|
726 |
+
)
|
727 |
+
gr.HTML("""
|
728 |
+
<style>
|
729 |
+
body, html {
|
730 |
+
background-color: #121212 !important;
|
731 |
+
color: #ffffff !important;
|
732 |
+
}
|
733 |
+
|
734 |
+
.gradio-container, .gr-block, .gr-box, textarea, input, select, .prose, .prose * {
|
735 |
+
background-color: #1e1e1e !important;
|
736 |
+
color: #ffffff !important;
|
737 |
+
border-color: #333 !important;
|
738 |
+
}
|
739 |
+
|
740 |
+
textarea::placeholder,
|
741 |
+
input::placeholder {
|
742 |
+
color: #aaa !important;
|
743 |
+
}
|
744 |
+
|
745 |
+
button {
|
746 |
+
background-color: #2d2d2d !important;
|
747 |
+
color: #fff !important;
|
748 |
+
border: 1px solid #444 !important;
|
749 |
+
}
|
750 |
+
|
751 |
+
a {
|
752 |
+
color: #4ea1f3 !important;
|
753 |
+
}
|
754 |
+
</style>
|
755 |
+
""")
|
756 |
+
|
757 |
+
# # Custom CSS styles
|
758 |
+
# gr.HTML("""
|
759 |
+
# <style>
|
760 |
+
# /* Ensures both sections are equally spaced with the same background size */
|
761 |
+
# #output-summary, #output-flag {
|
762 |
+
# background-color: #f0f4f8; /* Light Grey for both */
|
763 |
+
# padding: 20px;
|
764 |
+
# border-radius: 10px;
|
765 |
+
# margin-top: 10px;
|
766 |
+
# width: 100%; /* Ensure full width */
|
767 |
+
# min-height: 150px; /* Ensures both have a minimum height */
|
768 |
+
# box-sizing: border-box; /* Prevents padding from increasing size */
|
769 |
+
# display: flex;
|
770 |
+
# flex-direction: column;
|
771 |
+
# justify-content: space-between;
|
772 |
+
# }
|
773 |
+
|
774 |
+
# /* Specific background colors */
|
775 |
+
# #output-summary {
|
776 |
+
# background-color: #434a4b;
|
777 |
+
# }
|
778 |
+
|
779 |
+
# #output-flag {
|
780 |
+
# background-color: #141616;
|
781 |
+
# }
|
782 |
+
|
783 |
+
# /* Ensuring they are in a row and evenly spaced */
|
784 |
+
# .gradio-row {
|
785 |
+
# display: flex;
|
786 |
+
# justify-content: space-between;
|
787 |
+
# width: 100%;
|
788 |
+
# }
|
789 |
+
# </style>
|
790 |
+
# """)
|
791 |
+
|
792 |
+
|
793 |
interface.launch(share=True,debug=True)
|