import glob
import os
import shutil
import pandas as pd
from openpyxl import load_workbook
from openpyxl.styles import Font, PatternFill, Border, Side, Alignment
from openpyxl.utils import get_column_letter
from datetime import date, datetime

# Paths
src_dir = os.path.dirname(os.path.abspath(__file__)) + "/"
out_dir = "U:/Dropbox/!!!Days/Downloads Z230/"

# Find source files
src_files = glob.glob(src_dir + "Protocol 77242113UCO3001 - All Samples*.xlsx")
assert src_files, "Source file not found!"
src_file = src_files[0]
print(f"Source xlsx: {src_file}")

csv_files = glob.glob(src_dir + "_EDCStdRpt-DataListing.csv")
assert csv_files, "CSV file not found!"
csv_file = csv_files[0]
print(f"Source csv:  {csv_file}")

kit_csv_files = glob.glob(src_dir + "sponsor-study-36940-kit-inventory-on-hand-expiration.csv")
assert kit_csv_files, "Kit inventory CSV not found!"
kit_csv_file = kit_csv_files[0]
print(f"Kit csv:     {kit_csv_file}")

eq_csv_files = glob.glob(src_dir + "sponsor-study-36940-activity-reports-documents-equery.csv")
assert eq_csv_files, "eQuery CSV not found!"
eq_csv_file = eq_csv_files[0]
print(f"eQuery csv:  {eq_csv_file}")

timestamp = datetime.now().strftime("%Y-%m-%d_%H%M%S")
out_filename = f"{timestamp} 77242113UCO3001 CZE Labcorp samples and kit inventory report.xlsx"
out_path = out_dir + out_filename

# Copy source file to output — preserves all formatting perfectly
shutil.copy2(src_file, out_path)

# Load data with pandas for analysis
df = pd.read_excel(src_file, sheet_name=0, header=0)

# All unique patients
all_patients = sorted(df['Patient No.'].dropna().unique())

# BXSCR and DNA rows
bxscr = df[df['Protocol Visit Code'] == 'BXSCR']
dna   = df[df['Protocol Visit Code'] == 'DNA']

# Parse date value to datetime object
def fmt_date(val):
    if pd.isna(val):
        return None
    if isinstance(val, str):
        return datetime.strptime(val, '%d-%b-%Y')
    return pd.to_datetime(val).to_pydatetime()

OK_STATUSES = {'Received', 'In Inventory', 'Shipped'}

def get_specimen_info(visit_df, patient, specimen_type=None):
    rows = visit_df[visit_df['Patient No.'] == patient]
    if specimen_type:
        rows = rows[rows['Specimen Type'] == specimen_type]
    rows = rows[rows['Sample Status'].isin(OK_STATUSES)]
    if rows.empty:
        return '', None
    row = rows.iloc[0]
    return fmt_date(row['Container Receipt Date']), rows.index[0] + 2

def get_label_info(patient, label_code, visit_code):
    rows = df[(df['Patient No.'] == patient) &
              (df['Protocol Visit Code'] == visit_code) &
              (df['Container Label Line 1'] == label_code)]
    rows = rows[rows['Sample Status'].isin(OK_STATUSES)]
    if rows.empty:
        return '', None
    row = rows.iloc[0]
    return fmt_date(row['Container Receipt Date']), rows.index[0] + 2

# Open copied workbook and add analysis sheet
out_wb = load_workbook(out_path)

# Rename and autofit first sheet
src_ws = out_wb.active
src_ws.title = "Zdroj"
for col in src_ws.columns:
    max_len = max((len(str(cell.value)) if cell.value is not None else 0) for cell in col)
    src_ws.column_dimensions[get_column_letter(col[0].column)].width = min(max_len + 2, 50)

# ── Styly ────────────────────────────────────────────────────────────────────
thin            = Side(style='thin')
border          = Border(left=thin, right=thin, top=thin, bottom=thin)
header_fill     = PatternFill("solid", fgColor="4472C4")
header_font     = Font(name='Calibri', bold=True, size=11, color="FFFFFF")
data_font       = Font(name='Calibri', size=11)
date_font_link  = Font(name='Calibri', size=11, color="000000", underline='single')
yes_fill        = PatternFill("solid", fgColor="E2EFDA")
no_fill         = PatternFill("solid", fgColor="FFE7E7")
sum_header_font = Font(name='Calibri', bold=True, size=11, color="000000")
sum_total_font  = Font(name='Calibri', bold=True, size=11)
zero_font       = Font(name='Calibri', size=11, color="BFBFBF")
zero_red_font   = Font(name='Calibri', size=11, color="C00000")
dark_blue_fill  = PatternFill("solid", fgColor="203764")
orange_fill     = PatternFill("solid", fgColor="FFF2CC")
green_fill      = PatternFill("solid", fgColor="E2EFDA")
total_fill      = PatternFill("solid", fgColor="D9E1F2")
exp_fill        = PatternFill("solid", fgColor="FFE7E7")
ok_fill         = PatternFill("solid", fgColor="E2EFDA")

# ── List: Přehled vzorků ──────────────────────────────────────────────────────
analysis_ws = out_wb.create_sheet("Přehled vzorků")

columns = [
    ("Investigator Name",   24),
    ("Číslo pacienta",      20),
    ("Máme biopsii SM11",   20),
    ("Máme RNA",            16),
    ("Máme Cryostor",       16),
    ("DNA",                 14),
    ("PLASMPK I-0 TROUGH",  18),
    ("PLASMA PK I-0 PEAK",  18),
    ("SERUM ADA I-0 PRE",   18),
    ("SM06/SERUM BIOM",     16),
    ("SM07/WB RNA",         14),
    ("SM10/FECAL",          14),
    ("PLASMPK I-2 TROUGH",  18),
    ("PLASMA PK I-2 PEAK",  18),
    ("SERUM ADA I-2 PRE",   18),
    ("STOOL I-2",           12),
    ("PLASMPK I-4 TROUGH",  18),
    ("PLASMA PK I-4 PEAK",  18),
    ("SERUM ADA I-4 PRE",   18),
    ("SM06/SERUM BIOM",     16),
    ("SM07/WB RNA",         14),
    ("STOOL I-4",           12),
]

group_font   = Font(name='Calibri', bold=True, size=11)
group_fill   = PatternFill("solid", fgColor="FFFFFF")
group_border = Border(left=thin, right=thin, top=thin, bottom=thin)

groups = [
    (3,  5,  "SCREENING"),
    (7,  12, "RANDOMIZACE I-0"),
    (13, 16, "I-2"),
    (17, 22, "I-4"),
]
for start_col, end_col, label in groups:
    analysis_ws.merge_cells(start_row=1, start_column=start_col, end_row=1, end_column=end_col)
    cell = analysis_ws.cell(row=1, column=start_col, value=label)
    cell.font = group_font
    cell.fill = group_fill
    cell.alignment = Alignment(horizontal='center', vertical='center')
    cell.border = group_border
    for c in range(start_col, end_col + 1):
        analysis_ws.cell(row=1, column=c).border = group_border

analysis_ws.row_dimensions[1].height = 20

for col_idx, (hdr, width) in enumerate(columns, 1):
    cell = analysis_ws.cell(row=2, column=col_idx, value=hdr)
    cell.font = header_font
    cell.fill = header_fill
    cell.border = border
    cell.alignment = Alignment(horizontal='center', vertical='center', wrap_text=True)
    analysis_ws.column_dimensions[get_column_letter(col_idx)].width = width

analysis_ws.row_dimensions[2].height = 30
analysis_ws.freeze_panes = "C3"

src_sheet_name = out_wb.sheetnames[0]
pat_sheet_name = "Seznam pacientů"

_csv_df_pre = pd.read_csv(csv_file, encoding='utf-8')
_pat_pre = _csv_df_pre[['SiteNumber', 'Subject', 'Field4Value']].copy()
_pat_pre['Field4Value'] = _pat_pre['Field4Value'].apply(lambda v: datetime.strptime(str(v).strip(), '%d %b %Y') if pd.notna(v) else None)
_pat_pre = _pat_pre.sort_values(['SiteNumber', 'Subject', 'Field4Value']).reset_index(drop=True)
patient_row_map = {}
for i, row in _pat_pre.iterrows():
    pat = row['Subject']
    if pat not in patient_row_map:
        patient_row_map[pat] = i + 2

bxscr_patients = sorted(bxscr['Patient No.'].dropna().unique())

for row_idx, patient in enumerate(bxscr_patients, 3):
    investigator = bxscr[bxscr['Patient No.'] == patient].iloc[0]['Investigator Name']
    sm11, sm11_row    = get_specimen_info(bxscr, patient, 'Tissue , Paraffin Block')
    rna,  rna_row     = get_specimen_info(bxscr, patient, 'Biopsy RNA Later')
    cryo, cryo_row    = get_specimen_info(bxscr, patient, 'Biopsy, Frozen Tissue')
    dna_date, dna_row = get_specimen_info(dna, patient)
    trough,  trough_row  = get_label_info(patient, 'PLASMPK I-0 TROUGH', 'I-0')
    peak,    peak_row    = get_label_info(patient, 'PLASMA PK I-0 PEAK',  'I-0')
    ada,     ada_row     = get_label_info(patient, 'SERUM ADA I-0 PRE',   'I-0')
    sm06,    sm06_row    = get_label_info(patient, 'SM06/SERUM BIOM',     'I-0')
    sm07,    sm07_row    = get_label_info(patient, 'SM07/WB RNA',          'I-0')
    sm10,    sm10_row    = get_label_info(patient, 'SM10/FECAL',           'I-0')
    trough2, trough2_row = get_label_info(patient, 'PLASMPK I-2 TROUGH',  'I-2')
    peak2,   peak2_row   = get_label_info(patient, 'PLASMA PK I-2 PEAK',  'I-2')
    ada2,    ada2_row    = get_label_info(patient, 'SERUM ADA I-2 PRE',   'I-2')
    stool2,  stool2_row  = get_label_info(patient, 'STOOL I-2',            'I-2')
    trough4, trough4_row = get_label_info(patient, 'PLASMPK I-4 TROUGH',  'I-4')
    peak4,   peak4_row   = get_label_info(patient, 'PLASMA PK I-4 PEAK',  'I-4')
    ada4,    ada4_row    = get_label_info(patient, 'SERUM ADA I-4 PRE',   'I-4')
    sm064,   sm064_row   = get_label_info(patient, 'SM06/SERUM BIOM',     'I-4')
    sm074,   sm074_row   = get_label_info(patient, 'SM07/WB RNA',          'I-4')
    stool4,  stool4_row  = get_label_info(patient, 'STOOL I-4',            'I-4')

    row_data = [investigator, patient,
                (sm11, sm11_row), (rna, rna_row), (cryo, cryo_row), (dna_date, dna_row),
                (trough, trough_row), (peak, peak_row), (ada, ada_row),
                (sm06, sm06_row), (sm07, sm07_row), (sm10, sm10_row),
                (trough2, trough2_row), (peak2, peak2_row), (ada2, ada2_row), (stool2, stool2_row),
                (trough4, trough4_row), (peak4, peak4_row), (ada4, ada4_row),
                (sm064, sm064_row), (sm074, sm074_row), (stool4, stool4_row)]

    for col_idx, value in enumerate(row_data, 1):
        if col_idx <= 2:
            cell = analysis_ws.cell(row=row_idx, column=col_idx, value=value)
            if col_idx == 2 and patient in patient_row_map:
                cell.hyperlink = f"#'{pat_sheet_name}'!B{patient_row_map[patient]}"
                cell.font = Font(name='Calibri', size=11, underline='single')
            else:
                cell.font = data_font
        else:
            dt, excel_row = value
            cell = analysis_ws.cell(row=row_idx, column=col_idx, value=dt)
            if dt and excel_row is not None:
                cell.hyperlink = f"#'{src_sheet_name}'!A{excel_row}"
                cell.font = date_font_link
                cell.fill = yes_fill
                cell.number_format = 'DD-MMM-YYYY'
            else:
                cell.font = Font(name='Calibri', size=11, color="C00000")
                cell.fill = no_fill
        cell.border = border
        cell.alignment = Alignment(horizontal='center', vertical='center')

# ── List: Seznam pacientů ─────────────────────────────────────────────────────
csv_df = pd.read_csv(csv_file, encoding='utf-8')
patients_ws = out_wb.create_sheet("Seznam pacientů")

pat_columns = [
    ("Číslo centra",   20),
    ("Číslo pacienta", 20),
    ("Kód návštěvy",   20),
    ("Datum návštěvy", 16),
    ("Typ návštěvy",   16),
]

for col_idx, (col_name, width) in enumerate(pat_columns, 1):
    cell = patients_ws.cell(row=1, column=col_idx, value=col_name)
    cell.font = header_font
    cell.fill = header_fill
    cell.border = border
    cell.alignment = Alignment(horizontal='center', vertical='center', wrap_text=True)
    patients_ws.column_dimensions[get_column_letter(col_idx)].width = width

patients_ws.row_dimensions[1].height = 30
patients_ws.freeze_panes = "A2"

def parse_date_edcstd(val):
    if pd.isna(val) or str(val).strip() == '':
        return None
    try:
        return datetime.strptime(str(val).strip(), '%d %b %Y')
    except:
        return None

pat_df = csv_df[['SiteNumber', 'Subject', 'InstanceName', 'Field4Value', 'Field5Value']].copy()
pat_df['Field4Value'] = pat_df['Field4Value'].apply(parse_date_edcstd)
pat_df = pat_df.sort_values(['SiteNumber', 'Subject', 'Field4Value']).reset_index(drop=True)

for row_idx, row in enumerate(pat_df.itertuples(index=False), 2):
    for col_idx, value in enumerate(row, 1):
        cell = patients_ws.cell(row=row_idx, column=col_idx, value=value)
        cell.font = data_font
        cell.border = border
        cell.alignment = Alignment(horizontal='center', vertical='center')
        if col_idx == 4 and value is not None:
            cell.number_format = 'DD-MMM-YYYY'

# ── Kit inventory — načtení a příprava dat ────────────────────────────────────
kit_df_raw = pd.read_csv(kit_csv_file, encoding="utf-8")
cze = kit_df_raw[kit_df_raw["Country"] == "CZE"].copy()

def parse_kit_date(val):
    if pd.isna(val):
        return None
    try:
        return datetime.strptime(str(val).strip(), "%b %d, %Y")
    except:
        return None

cze["Shipped Date"]    = cze["Shipped Date"].apply(parse_kit_date)
cze["Expiration Date"] = cze["Expiration Date"].apply(parse_kit_date)
cze = cze.sort_values(["Site", "Kit Type", "Expiration Date"]).reset_index(drop=True)

today_dt = datetime.combine(date.today(), datetime.min.time())

def bucket(exp_date):
    if exp_date is None:
        return None
    return "soon" if (exp_date - today_dt).days <= 30 else "ok"

cze["_bucket"] = cze["Expiration Date"].apply(bucket)

kit_order = sorted(cze["Kit Type"].unique(), key=lambda x: (str(x).lstrip("T-").zfill(5), str(x)))
kit_desc  = cze.drop_duplicates("Kit Type").set_index("Kit Type")["Description"].to_dict()
kit_sites = sorted(cze["Site"].unique())

# ── Pomocná funkce pro souhrnné tabulky ───────────────────────────────────────
def write_summary_table(ws, current_row, title, rows_data, col_a_header):
    for c in range(1, 5):
        cell = ws.cell(row=current_row, column=c)
        cell.fill = dark_blue_fill
        cell.border = border
    ws.cell(row=current_row, column=1, value=title).font = Font(name='Calibri', bold=True, size=12, color="FFFFFF")
    ws.cell(row=current_row, column=1).alignment = Alignment(horizontal="left", vertical="center")
    ws.merge_cells(start_row=current_row, start_column=1, end_row=current_row, end_column=4)
    ws.row_dimensions[current_row].height = 22
    current_row += 1

    for col_idx, (h, f) in enumerate(zip(
        [col_a_header, "Description", "Expiruje do 30 dní", "Expiruje později"],
        [header_fill, header_fill, orange_fill, green_fill]
    ), 1):
        cell = ws.cell(row=current_row, column=col_idx, value=h)
        cell.font = sum_header_font
        cell.fill = f
        cell.border = border
        cell.alignment = Alignment(horizontal="center", vertical="center", wrap_text=True)
    ws.row_dimensions[current_row].height = 28
    current_row += 1

    totals = [0, 0]
    for col_a, col_b, n_soon, n_ok in rows_data:
        totals[0] += n_soon
        totals[1] += n_ok
        all_zero  = (n_soon == 0 and n_ok == 0)
        row_vals  = [col_a, col_b, n_soon, n_ok]
        row_fills = [None, None,
                     orange_fill if n_soon > 0 else None,
                     green_fill  if n_ok   > 0 else None]
        for col_idx, (val, rfill) in enumerate(zip(row_vals, row_fills), 1):
            cell = ws.cell(row=current_row, column=col_idx, value=val)
            if col_idx >= 3 and val == 0:
                cell.font = zero_red_font if all_zero else zero_font
            else:
                cell.font = data_font
            cell.border = border
            cell.alignment = Alignment(horizontal="center" if col_idx >= 2 else "left", vertical="center")
            if rfill:
                cell.fill = rfill
        current_row += 1

    for col_idx, val in enumerate(["CELKEM", "", totals[0], totals[1]], 1):
        cell = ws.cell(row=current_row, column=col_idx, value=val)
        cell.font = sum_total_font
        cell.fill = total_fill
        cell.border = border
        cell.alignment = Alignment(horizontal="center" if col_idx >= 2 else "left", vertical="center")
    current_row += 2
    return current_row

# ── List: Kit Inventory CZE ───────────────────────────────────────────────────
kit_ws = out_wb.create_sheet("Kit Inventory CZE")

listing_columns = [
    ("Project No.",        14),
    ("Region",             10),
    ("Country",            10),
    ("Site",               38),
    ("Kit Type",           12),
    ("Description",        22),
    ("Accession",          18),
    ("Shipped Date",       16),
    ("Expiration Date",    16),
    ("Days to Expiration", 20),
]

for col_idx, (hdr, width) in enumerate(listing_columns, 1):
    cell = kit_ws.cell(row=1, column=col_idx, value=hdr)
    cell.font = header_font
    cell.fill = header_fill
    cell.border = border
    cell.alignment = Alignment(horizontal="center", vertical="center", wrap_text=True)
    kit_ws.column_dimensions[get_column_letter(col_idx)].width = width

kit_ws.row_dimensions[1].height = 30
kit_ws.freeze_panes = "A2"

for row_idx, row in enumerate(cze.itertuples(index=False), 2):
    days = row[9]
    for col_idx, (col_name, _) in enumerate(listing_columns, 1):
        value = row[col_idx - 1]
        cell = kit_ws.cell(row=row_idx, column=col_idx, value=value)
        cell.font = data_font
        cell.border = border
        cell.alignment = Alignment(horizontal="center", vertical="center")
        if col_name in ("Shipped Date", "Expiration Date") and value is not None:
            cell.number_format = "DD-MMM-YYYY"
        if col_name == "Days to Expiration":
            cell.fill = exp_fill if (pd.notna(days) and days <= 60) else ok_fill

kit_ws.auto_filter.ref = f"A1:{get_column_letter(len(listing_columns))}1"

# ── List: Přehled po centrech ─────────────────────────────────────────────────
ctr_ws = out_wb.create_sheet("Přehled po centrech")
ctr_ws.column_dimensions["A"].width = 22
ctr_ws.column_dimensions["B"].width = 24
ctr_ws.column_dimensions["C"].width = 22
ctr_ws.column_dimensions["D"].width = 20

current_row = 1
for site in kit_sites:
    site_df = cze[cze["Site"] == site]
    rows_data = []
    for kit in kit_order:
        desc        = kit_desc.get(kit, "")
        kit_site_df = site_df[site_df["Kit Type"] == kit]
        n_soon = (kit_site_df["_bucket"] == "soon").sum()
        n_ok   = (kit_site_df["_bucket"] == "ok").sum()
        rows_data.append((f"{kit} — {desc}", desc, n_soon, n_ok))
    current_row = write_summary_table(ctr_ws, current_row, site, rows_data, "Kit Type")

# ── List: Přehled po typech kitů ──────────────────────────────────────────────
sum_ws = out_wb.create_sheet("Přehled po typech")
sum_ws.column_dimensions["A"].width = 38
sum_ws.column_dimensions["B"].width = 22
sum_ws.column_dimensions["C"].width = 22
sum_ws.column_dimensions["D"].width = 20

current_row = 1
for kit in kit_order:
    desc   = kit_desc.get(kit, "")
    kit_df = cze[cze["Kit Type"] == kit]
    rows_data = []
    for site in sorted(kit_df["Site"].unique()):
        site_df = kit_df[kit_df["Site"] == site]
        n_soon = (site_df["_bucket"] == "soon").sum()
        n_ok   = (site_df["_bucket"] == "ok").sum()
        rows_data.append((site, desc, n_soon, n_ok))
    current_row = write_summary_table(sum_ws, current_row, f"Kit Type {kit} — {desc}", rows_data, "Centrum")

# ── List: eQueries ───────────────────────────────────────────────────────────
eq_df = pd.read_csv(eq_csv_file, encoding="utf-8")
eq_cze = eq_df[eq_df["Country"] == "CZECH REPUBLIC"].copy()

status_order = {"Open": 0, "Response Received": 1, "Closed": 2}
eq_cze["_status_order"] = eq_cze["Status"].map(status_order).fillna(99)
eq_cze = eq_cze.sort_values(["_status_order", "Site"]).reset_index(drop=True)

def parse_eq_date(val):
    if pd.isna(val):
        return None
    for fmt in ("%b %d, %Y %I:%M %p", "%b %d, %Y %I:%M %p"):
        try:
            return datetime.strptime(str(val).strip(), fmt)
        except:
            pass
    try:
        return datetime.strptime(str(val).strip().split(" 12:00")[0], "%b %d, %Y")
    except:
        return None

eq_ws = out_wb.create_sheet("eQueries")

eq_columns = [
    ("Site",                  36),
    ("Subject",               14),
    ("Visit",                 20),
    ("Visit Collection Date", 20),
    ("Accession",             16),
    ("eQueryId",              12),
    ("Issue Type",            30),
    ("Status",                18),
    ("Create Date",           20),
    ("Response Date Time",    20),
    ("Time Before Response",  20),
    ("User Name",             20),
]

status_fills = {
    "Open":              PatternFill("solid", fgColor="FFE7E7"),
    "Response Received": PatternFill("solid", fgColor="FFF2CC"),
    "Closed":            PatternFill("solid", fgColor="E2EFDA"),
}

for col_idx, (hdr, width) in enumerate(eq_columns, 1):
    cell = eq_ws.cell(row=1, column=col_idx, value=hdr)
    cell.font = header_font
    cell.fill = header_fill
    cell.border = border
    cell.alignment = Alignment(horizontal="center", vertical="center", wrap_text=True)
    eq_ws.column_dimensions[get_column_letter(col_idx)].width = width

eq_ws.row_dimensions[1].height = 30
eq_ws.freeze_panes = "A2"

for row_idx, row in enumerate(eq_cze.itertuples(index=False), 2):
    status = row[eq_cze.columns.get_loc("Status")]
    rfill  = status_fills.get(status)
    for col_idx, (col_name, _) in enumerate(eq_columns, 1):
        value = row[eq_cze.columns.get_loc(col_name)]
        if col_name in ("Visit Collection Date", "Create Date", "Response Date Time"):
            value = parse_eq_date(value)
        cell = eq_ws.cell(row=row_idx, column=col_idx, value=value)
        cell.font = data_font
        cell.border = border
        cell.alignment = Alignment(horizontal="center" if col_idx > 1 else "left", vertical="center")
        if col_name in ("Visit Collection Date", "Create Date", "Response Date Time") and value:
            cell.number_format = "DD-MMM-YYYY HH:MM"
        if rfill:
            cell.fill = rfill

eq_ws.auto_filter.ref = f"A1:{get_column_letter(len(eq_columns))}1"

out_wb.save(out_path)
print(f"Saved: {out_path}")
print(f"Patients with BXSCR: {len(bxscr_patients)}, All unique patients: {len(all_patients)}")
print(f"CZE kit rows: {len(cze)}, Kit types: {len(kit_order)}, Sites: {len(kit_sites)}")
print(f"CZE eQueries: {len(eq_cze)} (Open: {(eq_cze['Status']=='Open').sum()}, Response Received: {(eq_cze['Status']=='Response Received').sum()}, Closed: {(eq_cze['Status']=='Closed').sum()})")