mtdna_backend.py

import gradio as gr
from collections import Counter
import csv
import os
from functools import lru_cache
#import app
from mtdna_classifier import classify_sample_location 
import data_preprocess, model, pipeline
import subprocess
import json
import pandas as pd
import io
import re
import tempfile
import gspread
from oauth2client.service_account import ServiceAccountCredentials
from io import StringIO
import hashlib
import threading

# @lru_cache(maxsize=3600)
# def classify_sample_location_cached(accession):
#     return classify_sample_location(accession)

#@lru_cache(maxsize=3600)
def pipeline_classify_sample_location_cached(accession,stop_flag=None, save_df=None):
    print("inside pipeline_classify_sample_location_cached, and [accession] is ", [accession])
    print("len of save df: ", len(save_df))
    return pipeline.pipeline_with_gemini([accession],stop_flag=stop_flag, save_df=save_df)    

# Count and suggest final location
# def compute_final_suggested_location(rows):
#     candidates = [
#         row.get("Predicted Location", "").strip()
#         for row in rows
#         if row.get("Predicted Location", "").strip().lower() not in ["", "sample id not found", "unknown"]
#     ] + [
#         row.get("Inferred Region", "").strip()
#         for row in rows
#         if row.get("Inferred Region", "").strip().lower() not in  ["", "sample id not found", "unknown"]
#     ]

#     if not candidates:
#         return Counter(), ("Unknown", 0)
#     # Step 1: Combine into one string and split using regex to handle commas, line breaks, etc.
#     tokens = []
#     for item in candidates:
#         # Split by comma, whitespace, and newlines
#         parts = re.split(r'[\s,]+', item)
#         tokens.extend(parts)

#     # Step 2: Clean and normalize tokens
#     tokens = [word.strip() for word in tokens if word.strip().isalpha()]  # Keep only alphabetic tokens

#     # Step 3: Count
#     counts = Counter(tokens)

#     # Step 4: Get most common
#     top_location, count = counts.most_common(1)[0]
#     return counts, (top_location, count)

# Store feedback (with required fields)

def store_feedback_to_google_sheets(accession, answer1, answer2, contact=""):
    if not answer1.strip() or not answer2.strip():
        return "⚠️ Please answer both questions before submitting."

    try:
        # ✅ Step: Load credentials from Hugging Face secret
        creds_dict = json.loads(os.environ["GCP_CREDS_JSON"])
        scope = ["https://spreadsheets.google.com/feeds", "https://www.googleapis.com/auth/drive"]
        creds = ServiceAccountCredentials.from_json_keyfile_dict(creds_dict, scope)

        # Connect to Google Sheet
        client = gspread.authorize(creds)
        sheet = client.open("feedback_mtdna").sheet1  # make sure sheet name matches

        # Append feedback
        sheet.append_row([accession, answer1, answer2, contact])
        return "✅ Feedback submitted. Thank you!"

    except Exception as e:
        return f"❌ Error submitting feedback: {e}"

# helper function to extract accessions
def extract_accessions_from_input(file=None, raw_text=""):
    print(f"RAW TEXT RECEIVED: {raw_text}")
    accessions = []
    seen = set()
    if file:
        try:
            if file.name.endswith(".csv"):
                df = pd.read_csv(file)
            elif file.name.endswith(".xlsx"):
                df = pd.read_excel(file)
            else:
                return [], "Unsupported file format. Please upload CSV or Excel."
            for acc in df.iloc[:, 0].dropna().astype(str).str.strip():
                if acc not in seen:
                    accessions.append(acc)
                    seen.add(acc)
        except Exception as e:
            return [], f"Failed to read file: {e}"

    if raw_text:
        text_ids = [s.strip() for s in re.split(r"[\n,;\t]", raw_text) if s.strip()]
        for acc in text_ids:
            if acc not in seen:
                accessions.append(acc)
                seen.add(acc)

    return list(accessions), None
# ✅ Add a new helper to backend: `filter_unprocessed_accessions()`
def get_incomplete_accessions(file_path):
    df = pd.read_excel(file_path)

    incomplete_accessions = []
    for _, row in df.iterrows():
        sample_id = str(row.get("Sample ID", "")).strip()

        # Skip if no sample ID
        if not sample_id:
            continue

        # Drop the Sample ID and check if the rest is empty
        other_cols = row.drop(labels=["Sample ID"], errors="ignore")
        if other_cols.isna().all() or (other_cols.astype(str).str.strip() == "").all():
            # Extract the accession number from the sample ID using regex
            match = re.search(r"\b[A-Z]{2,4}\d{4,}", sample_id)
            if match:
                incomplete_accessions.append(match.group(0))
    print(len(incomplete_accessions))
    return incomplete_accessions

# GOOGLE_SHEET_NAME = "known_samples"
# USAGE_DRIVE_FILENAME = "user_usage_log.json"

def summarize_results(accession, stop_flag=None):
    # Early bail
    if stop_flag is not None and stop_flag.value:
        print(f"🛑 Skipping {accession} before starting.")
        return []
    # try cache first
    cached = check_known_output(accession)
    if cached:
        print(f"✅ Using cached result for {accession}")
        return [[
            cached["Sample ID"] or "unknown",
            cached["Predicted Country"] or "unknown",
            cached["Country Explanation"] or "unknown",
            cached["Predicted Sample Type"] or "unknown",
            cached["Sample Type Explanation"] or "unknown",
            cached["Sources"] or "No Links",
            cached["Time cost"]
        ]]
    # only run when nothing in the cache  
    try:
        print("try gemini pipeline: ",accession)
        # ✅ Load credentials from Hugging Face secret
        creds_dict = json.loads(os.environ["GCP_CREDS_JSON"])
        scope = ['https://spreadsheets.google.com/feeds', 'https://www.googleapis.com/auth/drive']
        creds = ServiceAccountCredentials.from_json_keyfile_dict(creds_dict, scope)
        client = gspread.authorize(creds)

        spreadsheet = client.open("known_samples")
        sheet = spreadsheet.sheet1

        data = sheet.get_all_values()
        if not data:
            print("⚠️ Google Sheet 'known_samples' is empty.")
            return None

        save_df = pd.DataFrame(data[1:], columns=data[0])
        print("before pipeline, len of save df: ", len(save_df))
        outputs = pipeline_classify_sample_location_cached(accession, stop_flag, save_df)
        if stop_flag is not None and stop_flag.value:
            print(f"🛑 Skipped {accession} mid-pipeline.")
            return []
        # outputs = {'KU131308': {'isolate':'BRU18',
        # 'country': {'brunei': ['ncbi',
        # 'rag_llm-The text mentions "BRU18 Brunei Borneo" in a table listing various samples, and it is not described as ancient or archaeological.']},
        # 'sample_type': {'modern': 
        # ['rag_llm-The text mentions "BRU18 Brunei Borneo" in a table listing various samples, and it is not described as ancient or archaeological.']},
        # 'query_cost': 9.754999999999999e-05,
        # 'time_cost': '24.776 seconds',
        # 'source': ['https://doi.org/10.1007/s00439-015-1620-z',
        # 'https://static-content.springer.com/esm/art%3A10.1007%2Fs00439-015-1620-z/MediaObjects/439_2015_1620_MOESM1_ESM.pdf',
        # 'https://static-content.springer.com/esm/art%3A10.1007%2Fs00439-015-1620-z/MediaObjects/439_2015_1620_MOESM2_ESM.xls']}}
    except Exception as e:
        return []#, f"Error: {e}", f"Error: {e}", f"Error: {e}"

    if accession not in outputs:
        print("no accession in output ", accession)
        return []#, "Accession not found in results.", "Accession not found in results.", "Accession not found in results."

    row_score = []
    rows = []
    save_rows = []
    for key in outputs:
        pred_country, pred_sample, country_explanation, sample_explanation = "unknown","unknown","unknown","unknown" 
        for section, results in outputs[key].items():
          if section == "country" or section =="sample_type":
            pred_output = []#"\n".join(list(results.keys()))
            output_explanation = ""
            for result, content in results.items():
              if len(result) == 0:  result = "unknown"
              if len(content) == 0: output_explanation = "unknown"
              else:
                output_explanation += 'Method: ' + "\nMethod: ".join(content)  + "\n"
              pred_output.append(result)
            pred_output = "\n".join(pred_output)    
            if section == "country":
              pred_country, country_explanation = pred_output, output_explanation
            elif section == "sample_type":
              pred_sample, sample_explanation = pred_output, output_explanation    
          if outputs[key]["isolate"].lower()!="unknown":
            label = key + "(Isolate: " + outputs[key]["isolate"] + ")"
          else: label = key  
        if len(outputs[key]["source"]) == 0:  outputs[key]["source"] = ["No Links"]
        row = {
            "Sample ID": label or "unknown",
            "Predicted Country": pred_country or "unknown",
            "Country Explanation": country_explanation or "unknown",
            "Predicted Sample Type":pred_sample or "unknown",
            "Sample Type Explanation":sample_explanation or "unknown",
            "Sources": "\n".join(outputs[key]["source"]) or "No Links",
            "Time cost": outputs[key]["time_cost"]
        }
        #row_score.append(row)
        rows.append(list(row.values()))

        save_row = {
            "Sample ID": label or "unknown",
            "Predicted Country": pred_country or "unknown",
            "Country Explanation": country_explanation or "unknown",
            "Predicted Sample Type":pred_sample or "unknown",
            "Sample Type Explanation":sample_explanation or "unknown",
            "Sources": "\n".join(outputs[key]["source"]) or "No Links",
            "Query_cost": outputs[key]["query_cost"] or "",
            "Time cost": outputs[key]["time_cost"] or "",
            "file_chunk":outputs[key]["file_chunk"] or "",
            "file_all_output":outputs[key]["file_all_output"] or ""
        }
        #row_score.append(row)
        save_rows.append(list(save_row.values()))

    # #location_counts, (final_location, count) = compute_final_suggested_location(row_score)
    # summary_lines = [f"### 🧭 Location Summary:\n"]
    # summary_lines += [f"- **{loc}**: {cnt} times" for loc, cnt in location_counts.items()]
    # summary_lines.append(f"\n**Final Suggested Location:** 🗺️ **{final_location}** (mentioned {count} times)")
    # summary = "\n".join(summary_lines)

    # save the new running sample to known excel file
    # try:
    #   df_new = pd.DataFrame(save_rows, columns=["Sample ID", "Predicted Country", "Country Explanation", "Predicted Sample Type", "Sample Type Explanation", "Sources", "Query_cost","Time cost"])
    #   if os.path.exists(KNOWN_OUTPUT_PATH):
    #       df_old = pd.read_excel(KNOWN_OUTPUT_PATH)
    #       df_combined = pd.concat([df_old, df_new]).drop_duplicates(subset="Sample ID")
    #   else:
    #       df_combined = df_new
    #   df_combined.to_excel(KNOWN_OUTPUT_PATH, index=False)
    # except Exception as e:
    #   print(f"⚠️ Failed to save known output: {e}")
    # try:
    #     df_new = pd.DataFrame(save_rows, columns=[
    #         "Sample ID", "Predicted Country", "Country Explanation", 
    #         "Predicted Sample Type", "Sample Type Explanation", 
    #         "Sources", "Query_cost", "Time cost"
    #     ])
    
    #     # ✅ Google Sheets API setup
    #     creds_dict = json.loads(os.environ["GCP_CREDS_JSON"])
    #     scope = ['https://spreadsheets.google.com/feeds', 'https://www.googleapis.com/auth/drive']
    #     creds = ServiceAccountCredentials.from_json_keyfile_dict(creds_dict, scope)
    #     client = gspread.authorize(creds)
    
    #     # ✅ Open the known_samples sheet
    #     spreadsheet = client.open("known_samples")  # Replace with your sheet name
    #     sheet = spreadsheet.sheet1
    
    #     # ✅ Read old data
    #     existing_data = sheet.get_all_values()
    #     if existing_data:
    #         df_old = pd.DataFrame(existing_data[1:], columns=existing_data[0])
    #     else:
    #         df_old = pd.DataFrame(columns=df_new.columns)
    
    #     # ✅ Combine and remove duplicates
    #     df_combined = pd.concat([df_old, df_new], ignore_index=True).drop_duplicates(subset="Sample ID")
    
    #     # ✅ Clear and write back
    #     sheet.clear()
    #     sheet.update([df_combined.columns.values.tolist()] + df_combined.values.tolist())
    
    # except Exception as e:
    #     print(f"⚠️ Failed to save known output to Google Sheets: {e}")
    try:
        # Prepare as DataFrame
        df_new = pd.DataFrame(save_rows, columns=[
            "Sample ID", "Predicted Country", "Country Explanation",
            "Predicted Sample Type", "Sample Type Explanation",
            "Sources", "Query_cost", "Time cost", "file_chunk", "file_all_output"
        ])

        # ✅ Setup Google Sheets
        creds_dict = json.loads(os.environ["GCP_CREDS_JSON"])
        scope = ['https://spreadsheets.google.com/feeds', 'https://www.googleapis.com/auth/drive']
        creds = ServiceAccountCredentials.from_json_keyfile_dict(creds_dict, scope)
        client = gspread.authorize(creds)
        spreadsheet = client.open("known_samples")
        sheet = spreadsheet.sheet1

        # ✅ Read existing data
        existing_data = sheet.get_all_values()
    
        if existing_data:
            df_old = pd.DataFrame(existing_data[1:], columns=existing_data[0])
            
        else:
            
            df_old = pd.DataFrame(columns=[
                "Sample ID", "Actual_country", "Actual_sample_type", "Country Explanation",
                "Match_country", "Match_sample_type", "Predicted Country", "Predicted Sample Type",
                "Query_cost", "Sample Type Explanation", "Sources", "Time cost", "file_chunk", "file_all_output"
            ])


        # ✅ Index by Sample ID
        df_old.set_index("Sample ID", inplace=True)
        df_new.set_index("Sample ID", inplace=True)

        # ✅ Update only matching fields
        update_columns = [
            "Predicted Country", "Predicted Sample Type", "Country Explanation",
            "Sample Type Explanation", "Sources", "Query_cost", "Time cost", "file_chunk", "file_all_output"
        ]
        for idx, row in df_new.iterrows():
            if idx not in df_old.index:
                df_old.loc[idx] = ""  # new row, fill empty first
            for col in update_columns:
                if pd.notna(row[col]) and row[col] != "":
                    df_old.at[idx, col] = row[col]

        # ✅ Reset and write back
        df_old.reset_index(inplace=True)
        sheet.clear()
        sheet.update([df_old.columns.values.tolist()] + df_old.values.tolist())
        print("✅ Match results saved to known_samples.")

    except Exception as e:
        print(f"❌ Failed to update known_samples: {e}")

        
    return rows#, summary, labelAncient_Modern, explain_label

# save the batch input in excel file
# def save_to_excel(all_rows, summary_text, flag_text, filename):
#     with pd.ExcelWriter(filename) as writer:
#         # Save table
#         df_new = pd.DataFrame(all_rows, columns=["Sample ID", "Predicted Country", "Country Explanation", "Predicted Sample Type", "Sample Type Explanation", "Sources", "Time cost"])
#         df.to_excel(writer, sheet_name="Detailed Results", index=False)
#         try:
#           df_old = pd.read_excel(filename)
#         except:
#           df_old = pd.DataFrame([[]], columns=["Sample ID", "Predicted Country", "Country Explanation", "Predicted Sample Type", "Sample Type Explanation", "Sources", "Time cost"])
#         df_combined = pd.concat([df_old, df_new]).drop_duplicates(subset="Sample ID")
#         # if os.path.exists(filename):
#         #   df_old = pd.read_excel(filename)
#         #   df_combined = pd.concat([df_old, df_new]).drop_duplicates(subset="Sample ID")
#         # else:
#         #     df_combined = df_new
#         df_combined.to_excel(filename, index=False)
#           # # Save summary
#         # summary_df = pd.DataFrame({"Summary": [summary_text]})
#         # summary_df.to_excel(writer, sheet_name="Summary", index=False)
        
#         # # Save flag
#         # flag_df = pd.DataFrame({"Flag": [flag_text]})
#         # flag_df.to_excel(writer, sheet_name="Ancient_Modern_Flag", index=False)
# def save_to_excel(all_rows, summary_text, flag_text, filename):
#     df_new = pd.DataFrame(all_rows, columns=[
#         "Sample ID", "Predicted Country", "Country Explanation", 
#         "Predicted Sample Type", "Sample Type Explanation", 
#         "Sources", "Time cost"
#     ])

#     try:
#         if os.path.exists(filename):
#             df_old = pd.read_excel(filename)
#         else:
#             df_old = pd.DataFrame(columns=df_new.columns)
#     except Exception as e:
#         print(f"⚠️ Warning reading old Excel file: {e}")
#         df_old = pd.DataFrame(columns=df_new.columns)

#     #df_combined = pd.concat([df_new, df_old], ignore_index=True).drop_duplicates(subset="Sample ID", keep="first")
#     df_old.set_index("Sample ID", inplace=True)
#     df_new.set_index("Sample ID", inplace=True)

#     df_old.update(df_new)  # <-- update matching rows in df_old with df_new content

#     df_combined = df_old.reset_index()

#     try:
#         df_combined.to_excel(filename, index=False)
#     except Exception as e:
#         print(f"❌ Failed to write Excel file {filename}: {e}")
def save_to_excel(all_rows, summary_text, flag_text, filename, is_resume=False):
    df_new = pd.DataFrame(all_rows, columns=[
        "Sample ID", "Predicted Country", "Country Explanation", 
        "Predicted Sample Type", "Sample Type Explanation", 
        "Sources", "Time cost"
    ])

    if is_resume and os.path.exists(filename):
        try:
            df_old = pd.read_excel(filename)
        except Exception as e:
            print(f"⚠️ Warning reading old Excel file: {e}")
            df_old = pd.DataFrame(columns=df_new.columns)

        # Set index and update existing rows
        df_old.set_index("Sample ID", inplace=True)
        df_new.set_index("Sample ID", inplace=True)
        df_old.update(df_new)

        df_combined = df_old.reset_index()
    else:
        # If not resuming or file doesn't exist, just use new rows
        df_combined = df_new

    try:
        df_combined.to_excel(filename, index=False)
    except Exception as e:
        print(f"❌ Failed to write Excel file {filename}: {e}")


# save the batch input in JSON file
def save_to_json(all_rows, summary_text, flag_text, filename):
    output_dict = {
        "Detailed_Results": all_rows#,  # <-- make sure this is a plain list, not a DataFrame
        # "Summary_Text": summary_text,
        # "Ancient_Modern_Flag": flag_text
    }

    # If all_rows is a DataFrame, convert it
    if isinstance(all_rows, pd.DataFrame):
        output_dict["Detailed_Results"] = all_rows.to_dict(orient="records")

    with open(filename, "w") as external_file:
        json.dump(output_dict, external_file, indent=2)

# save the batch input in Text file
def save_to_txt(all_rows, summary_text, flag_text, filename):
    if isinstance(all_rows, pd.DataFrame):
        detailed_results = all_rows.to_dict(orient="records")
    output = ""
    #output += ",".join(list(detailed_results[0].keys())) + "\n\n"
    output += ",".join([str(k) for k in detailed_results[0].keys()]) + "\n\n"
    for r in detailed_results:
      output += ",".join([str(v) for v in r.values()]) + "\n\n"
    with open(filename, "w") as f:
        f.write("=== Detailed Results ===\n")
        f.write(output + "\n")

        # f.write("\n=== Summary ===\n")
        # f.write(summary_text + "\n")
        
        # f.write("\n=== Ancient/Modern Flag ===\n")
        # f.write(flag_text + "\n")

def save_batch_output(all_rows, output_type, summary_text=None, flag_text=None):
    tmp_dir = tempfile.mkdtemp()

    #html_table = all_rows.value  # assuming this is stored somewhere

    # Parse back to DataFrame
    #all_rows = pd.read_html(all_rows)[0]  # [0] because read_html returns a list
    all_rows = pd.read_html(StringIO(all_rows))[0]
    print(all_rows)

    if output_type == "Excel":
        file_path = f"{tmp_dir}/batch_output.xlsx"
        save_to_excel(all_rows, summary_text, flag_text, file_path)
    elif output_type == "JSON":
        file_path = f"{tmp_dir}/batch_output.json"
        save_to_json(all_rows, summary_text, flag_text, file_path)
        print("Done with JSON")
    elif output_type == "TXT":
        file_path = f"{tmp_dir}/batch_output.txt"
        save_to_txt(all_rows, summary_text, flag_text, file_path)
    else:
        return gr.update(visible=False)  # invalid option
    
    return gr.update(value=file_path, visible=True)
# save cost by checking the known outputs

# def check_known_output(accession):
#     if not os.path.exists(KNOWN_OUTPUT_PATH):
#         return None

#     try:
#         df = pd.read_excel(KNOWN_OUTPUT_PATH)
#         match = re.search(r"\b[A-Z]{2,4}\d{4,}", accession)
#         if match:
#           accession = match.group(0)
          
#         matched = df[df["Sample ID"].str.contains(accession, case=False, na=False)]
#         if not matched.empty:
#             return matched.iloc[0].to_dict()  # Return the cached row
#     except Exception as e:
#         print(f"⚠️ Failed to load known samples: {e}")
#         return None

# def check_known_output(accession):
#     try:
#         # ✅ Load credentials from Hugging Face secret
#         creds_dict = json.loads(os.environ["GCP_CREDS_JSON"])
#         scope = ['https://spreadsheets.google.com/feeds', 'https://www.googleapis.com/auth/drive']
#         creds = ServiceAccountCredentials.from_json_keyfile_dict(creds_dict, scope)
#         client = gspread.authorize(creds)

#         # ✅ Open the known_samples sheet
#         spreadsheet = client.open("known_samples")  # Replace with your sheet name
#         sheet = spreadsheet.sheet1

#         # ✅ Read all rows
#         data = sheet.get_all_values()
#         if not data:
#             return None

#         df = pd.DataFrame(data[1:], columns=data[0])  # Skip header row

#         # ✅ Normalize accession pattern
#         match = re.search(r"\b[A-Z]{2,4}\d{4,}", accession)
#         if match:
#             accession = match.group(0)

#         matched = df[df["Sample ID"].str.contains(accession, case=False, na=False)]
#         if not matched.empty:
#             return matched.iloc[0].to_dict()

#     except Exception as e:
#         print(f"⚠️ Failed to load known samples from Google Sheets: {e}")
#         return None
def check_known_output(accession):
    print("inside check known output function")
    try:
        # ✅ Load credentials from Hugging Face secret
        creds_dict = json.loads(os.environ["GCP_CREDS_JSON"])
        scope = ['https://spreadsheets.google.com/feeds', 'https://www.googleapis.com/auth/drive']
        creds = ServiceAccountCredentials.from_json_keyfile_dict(creds_dict, scope)
        client = gspread.authorize(creds)

        spreadsheet = client.open("known_samples")
        sheet = spreadsheet.sheet1

        data = sheet.get_all_values()
        if not data:
            print("⚠️ Google Sheet 'known_samples' is empty.")
            return None

        df = pd.DataFrame(data[1:], columns=data[0])
        if "Sample ID" not in df.columns:
            print("❌ Column 'Sample ID' not found in Google Sheet.")
            return None
        
        match = re.search(r"\b[A-Z]{2,4}\d{4,}", accession)
        if match:
            accession = match.group(0)

        matched = df[df["Sample ID"].str.contains(accession, case=False, na=False)]
        if not matched.empty:
            #return matched.iloc[0].to_dict()
            row = matched.iloc[0]
            country = row.get("Predicted Country", "").strip().lower()
            sample_type = row.get("Predicted Sample Type", "").strip().lower()

            if country and country != "unknown" and sample_type and sample_type != "unknown":
                return row.to_dict()
            else:
                print(f"⚠️ Accession {accession} found but country/sample_type is unknown or empty.")
                return None
        else:
            print(f"🔍 Accession {accession} not found in known_samples.")
            return None

    except Exception as e:
        import traceback
        print("❌ Exception occurred during check_known_output:")
        traceback.print_exc()
        return None


def hash_user_id(user_input):
    return hashlib.sha256(user_input.encode()).hexdigest()

# ✅ Load and save usage count

# def load_user_usage():
#     if not os.path.exists(USER_USAGE_TRACK_FILE):
#         return {}

#     try:
#         with open(USER_USAGE_TRACK_FILE, "r") as f:
#             content = f.read().strip()
#             if not content:
#                 return {}  # file is empty
#             return json.loads(content)
#     except (json.JSONDecodeError, ValueError):
#         print("⚠️ Warning: user_usage.json is corrupted or invalid. Resetting.")
#         return {}  # fallback to empty dict
# def load_user_usage():
#     try:
#         creds_dict = json.loads(os.environ["GCP_CREDS_JSON"])
#         scope = ['https://spreadsheets.google.com/feeds', 'https://www.googleapis.com/auth/drive']
#         creds = ServiceAccountCredentials.from_json_keyfile_dict(creds_dict, scope)
#         client = gspread.authorize(creds)

#         sheet = client.open("user_usage_log").sheet1
#         data = sheet.get_all_records()  # Assumes columns: email, usage_count

#         usage = {}
#         for row in data:
#             email = row.get("email", "").strip().lower()
#             count = int(row.get("usage_count", 0))
#             if email:
#                 usage[email] = count
#         return usage
#     except Exception as e:
#         print(f"⚠️ Failed to load user usage from Google Sheets: {e}")
#         return {}
# def load_user_usage():
#     try:
#         parent_id = pipeline.get_or_create_drive_folder("mtDNA-Location-Classifier")
#         iterate3_id = pipeline.get_or_create_drive_folder("iterate3", parent_id=parent_id)

#         found = pipeline.find_drive_file("user_usage_log.json", parent_id=iterate3_id)
#         if not found:
#             return {}  # not found, start fresh

#         #file_id = found[0]["id"]
#         file_id = found
#         content = pipeline.download_drive_file_content(file_id)
#         return json.loads(content.strip()) if content.strip() else {}

#     except Exception as e:
#         print(f"⚠️ Failed to load user_usage_log.json from Google Drive: {e}")
#         return {}
def load_user_usage():
    try:
        creds_dict = json.loads(os.environ["GCP_CREDS_JSON"])
        scope = ['https://spreadsheets.google.com/feeds', 'https://www.googleapis.com/auth/drive']
        creds = ServiceAccountCredentials.from_json_keyfile_dict(creds_dict, scope)
        client = gspread.authorize(creds)

        sheet = client.open("user_usage_log").sheet1
        data = sheet.get_all_values()
        print("data: ", data)
        print("🧪 Raw header row from sheet:", data[0])
        print("🧪 Character codes in each header:")
        for h in data[0]:
            print([ord(c) for c in h])

        if not data or len(data) < 2:
            print("⚠️ Sheet is empty or missing rows.")
            return {}

        headers = [h.strip().lower() for h in data[0]]
        if "email" not in headers or "usage_count" not in headers:
            print("❌ Header format incorrect. Must have 'email' and 'usage_count'.")
            return {}
            
        permitted_index = headers.index("permitted_samples") if "permitted_samples" in headers else None
        df = pd.DataFrame(data[1:], columns=headers)

        usage = {}
        permitted = {}
        for _, row in df.iterrows():
            email = row.get("email", "").strip().lower()
            try:
                #count = int(row.get("usage_count", 0))
                try:
                    count = int(float(row.get("usage_count", 0)))
                except Exception:
                    print(f"⚠️ Invalid usage_count for {email}: {row.get('usage_count')}")
                    count = 0

                if email:
                    usage[email] = count
                    if permitted_index is not None:
                        try:
                            permitted_count = int(float(row.get("permitted_samples", 50)))
                            permitted[email] = permitted_count
                        except:
                            permitted[email] = 50
                        
            except ValueError:
                print(f"⚠️ Invalid usage_count for {email}: {row.get('usage_count')}")
        return usage, permitted

    except Exception as e:
        print(f"❌ Error in load_user_usage: {e}")
        return {}, {}



# def save_user_usage(usage):
#     with open(USER_USAGE_TRACK_FILE, "w") as f:
#         json.dump(usage, f, indent=2)

# def save_user_usage(usage_dict):
#     try:
#         creds_dict = json.loads(os.environ["GCP_CREDS_JSON"])
#         scope = ['https://spreadsheets.google.com/feeds', 'https://www.googleapis.com/auth/drive']
#         creds = ServiceAccountCredentials.from_json_keyfile_dict(creds_dict, scope)
#         client = gspread.authorize(creds)

#         sheet = client.open("user_usage_log").sheet1
#         sheet.clear()  # clear old contents first

#         # Write header + rows
#         rows = [["email", "usage_count"]] + [[email, count] for email, count in usage_dict.items()]
#         sheet.update(rows)
#     except Exception as e:
#         print(f"❌ Failed to save user usage to Google Sheets: {e}")
# def save_user_usage(usage_dict):
#     try:
#         parent_id = pipeline.get_or_create_drive_folder("mtDNA-Location-Classifier")
#         iterate3_id = pipeline.get_or_create_drive_folder("iterate3", parent_id=parent_id)

#         import tempfile
#         tmp_path = os.path.join(tempfile.gettempdir(), "user_usage_log.json")
#         print("💾 Saving this usage dict:", usage_dict)
#         with open(tmp_path, "w") as f:
#             json.dump(usage_dict, f, indent=2)

#         pipeline.upload_file_to_drive(tmp_path, "user_usage_log.json", iterate3_id)

#     except Exception as e:
#         print(f"❌ Failed to save user_usage_log.json to Google Drive: {e}")
# def save_user_usage(usage_dict):
#     try:
#         creds_dict = json.loads(os.environ["GCP_CREDS_JSON"])
#         scope = ['https://spreadsheets.google.com/feeds', 'https://www.googleapis.com/auth/drive']
#         creds = ServiceAccountCredentials.from_json_keyfile_dict(creds_dict, scope)
#         client = gspread.authorize(creds)

#         spreadsheet = client.open("user_usage_log")
#         sheet = spreadsheet.sheet1

#         # Step 1: Convert new usage to DataFrame
#         df_new = pd.DataFrame(list(usage_dict.items()), columns=["email", "usage_count"])
#         df_new["email"] = df_new["email"].str.strip().str.lower()

#         # Step 2: Load existing data
#         existing_data = sheet.get_all_values()
#         print("🧪 Sheet existing_data:", existing_data)

#         # Try to load old data
#         if existing_data and len(existing_data[0]) >= 1:
#             df_old = pd.DataFrame(existing_data[1:], columns=existing_data[0])

#             # Fix missing columns
#             if "email" not in df_old.columns:
#                 df_old["email"] = ""
#             if "usage_count" not in df_old.columns:
#                 df_old["usage_count"] = 0

#             df_old["email"] = df_old["email"].str.strip().str.lower()
#             df_old["usage_count"] = pd.to_numeric(df_old["usage_count"], errors="coerce").fillna(0).astype(int)
#         else:
#             df_old = pd.DataFrame(columns=["email", "usage_count"])

#         # Step 3: Merge
#         df_combined = pd.concat([df_old, df_new], ignore_index=True)
#         df_combined = df_combined.groupby("email", as_index=False).sum()

#         # Step 4: Write back
#         sheet.clear()
#         sheet.update([df_combined.columns.tolist()] + df_combined.astype(str).values.tolist())
#         print("✅ Saved user usage to user_usage_log sheet.")

#     except Exception as e:
#         print(f"❌ Failed to save user usage to Google Sheets: {e}")
def save_user_usage(usage_dict):
    try:
        creds_dict = json.loads(os.environ["GCP_CREDS_JSON"])
        scope = ['https://spreadsheets.google.com/feeds', 'https://www.googleapis.com/auth/drive']
        creds = ServiceAccountCredentials.from_json_keyfile_dict(creds_dict, scope)
        client = gspread.authorize(creds)

        spreadsheet = client.open("user_usage_log")
        sheet = spreadsheet.sheet1

        # Build new df
        df_new = pd.DataFrame(list(usage_dict.items()), columns=["email", "usage_count"])
        df_new["email"] = df_new["email"].str.strip().str.lower()
        df_new["usage_count"] = pd.to_numeric(df_new["usage_count"], errors="coerce").fillna(0).astype(int)

        # Read existing data
        existing_data = sheet.get_all_values()
        if existing_data and len(existing_data[0]) >= 2:
            df_old = pd.DataFrame(existing_data[1:], columns=existing_data[0])
            df_old["email"] = df_old["email"].str.strip().str.lower()
            df_old["usage_count"] = pd.to_numeric(df_old["usage_count"], errors="coerce").fillna(0).astype(int)
        else:
            df_old = pd.DataFrame(columns=["email", "usage_count"])

        # ✅ Overwrite specific emails only
        df_old = df_old.set_index("email")
        for email, count in usage_dict.items():
            email = email.strip().lower()
            df_old.loc[email, "usage_count"] = count
        df_old = df_old.reset_index()

        # Save
        sheet.clear()
        sheet.update([df_old.columns.tolist()] + df_old.astype(str).values.tolist())
        print("✅ Saved user usage to user_usage_log sheet.")

    except Exception as e:
        print(f"❌ Failed to save user usage to Google Sheets: {e}")




# def increment_usage(user_id, num_samples=1):
#     usage = load_user_usage()
#     if user_id not in usage:
#         usage[user_id] = 0
#     usage[user_id] += num_samples
#     save_user_usage(usage)
#     return usage[user_id]
# def increment_usage(email: str, count: int):
#     usage = load_user_usage()
#     email_key = email.strip().lower()
#     usage[email_key] = usage.get(email_key, 0) + count
#     save_user_usage(usage)
#     return usage[email_key]
def increment_usage(email: str, count: int = 1):
    usage, permitted = load_user_usage()
    email_key = email.strip().lower()
    #usage[email_key] = usage.get(email_key, 0) + count
    current = usage.get(email_key, 0)
    new_value = current + count
    max_allowed = permitted.get(email_key) or 50
    usage[email_key] = max(current, new_value)  # ✅ Prevent overwrite with lower
    print(f"🧪 increment_usage saving: {email_key=} {current=} + {count=} => {usage[email_key]=}")
    print("max allow is: ", max_allowed)
    save_user_usage(usage)
    return usage[email_key], max_allowed


# run the batch
def summarize_batch(file=None, raw_text="", resume_file=None, user_email="", 
                    stop_flag=None, output_file_path=None, 
                    limited_acc=50, yield_callback=None):
    if user_email:
      limited_acc += 10
    accessions, error = extract_accessions_from_input(file, raw_text)
    if error:
        #return [], "", "", f"Error: {error}"
        return [], f"Error: {error}", 0, "", ""
    if resume_file:
      accessions = get_incomplete_accessions(resume_file)
    tmp_dir = tempfile.mkdtemp()
    if not output_file_path:
      if resume_file:
        output_file_path = os.path.join(tmp_dir, resume_file) 
      else:  
        output_file_path = os.path.join(tmp_dir, "batch_output_live.xlsx")

    all_rows = []
    # all_summaries = []
    # all_flags = []
    progress_lines = []
    warning = ""
    if len(accessions) > limited_acc:  
      accessions = accessions[:limited_acc]
      warning = f"Your number of accessions is more than the {limited_acc}, only handle first {limited_acc} accessions"
    for i, acc in enumerate(accessions):
        if stop_flag and stop_flag.value:
            line = f"🛑 Stopped at {acc} ({i+1}/{len(accessions)})"
            progress_lines.append(line)
            if yield_callback:
              yield_callback(line)
            print("🛑 User requested stop.")
            break
        print(f"[{i+1}/{len(accessions)}] Processing {acc}")
        try:
            # rows, summary, label, explain = summarize_results(acc)
            rows = summarize_results(acc)
            all_rows.extend(rows)
            # all_summaries.append(f"**{acc}**\n{summary}")
            # all_flags.append(f"**{acc}**\n### 🏺 Ancient/Modern Flag\n**{label}**\n\n_Explanation:_ {explain}")
            #save_to_excel(all_rows, summary_text="", flag_text="", filename=output_file_path)
            save_to_excel(all_rows, summary_text="", flag_text="", filename=output_file_path, is_resume=bool(resume_file))
            line = f"✅ Processed {acc} ({i+1}/{len(accessions)})"
            progress_lines.append(line)
            if yield_callback:
              yield_callback(f"✅ Processed {acc} ({i+1}/{len(accessions)})")
        except Exception as e:
            print(f"❌ Failed to process {acc}: {e}")
            continue
            #all_summaries.append(f"**{acc}**: Failed - {e}")
        #progress_lines.append(f"✅ Processed {acc} ({i+1}/{len(accessions)})")
        limited_acc -= 1
    """for row in all_rows:
          source_column = row[2]  # Assuming the "Source" is in the 3rd column (index 2)
          
          if source_column.startswith("http"):  # Check if the source is a URL
              # Wrap it with HTML anchor tags to make it clickable
              row[2] = f'<a href="{source_column}" target="_blank" style="color: blue; text-decoration: underline;">{source_column}</a>'"""
    if not warning:
      warning = f"You only have {limited_acc} left"
    if user_email.strip():
        user_hash = hash_user_id(user_email)
        total_queries = increment_usage(user_hash, len(all_rows))
    else:
        total_queries = 0
    yield_callback("✅ Finished!")

    # summary_text = "\n\n---\n\n".join(all_summaries)
    # flag_text = "\n\n---\n\n".join(all_flags)
    #return all_rows, summary_text, flag_text, gr.update(visible=True), gr.update(visible=False)
    #return all_rows, gr.update(visible=True), gr.update(visible=False)
    return all_rows, output_file_path, total_queries, "\n".join(progress_lines), warning