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import os
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import glob
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import datetime
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import pandas as pd
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from openpyxl import Workbook
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from openpyxl.styles import (
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Font, PatternFill, Alignment, Border, Side, GradientFill
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)
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from openpyxl.utils import get_column_letter
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BASE_DIR = os.path.dirname(os.path.abspath(__file__))
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INCOMING_DIR = os.path.join(BASE_DIR, "IncomingSourceReports")
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CREATED_DIR = os.path.join(BASE_DIR, "CreatedReports")
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STUDIES = ["77242113UCO3001", "42847922MDD3003"]
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SOURCE_COLS = [
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"Subject",
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"Investigator",
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"Subject's age collection",
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"Cohort per IRT",
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"IRT Subject Status",
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"Last Recorded IRT Transaction",
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"Next Expected IRT Transaction",
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"Next Expected IRT Transaction Date [Local]",
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]
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DISPLAY_HEADERS = [
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"Subject",
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"Investigator",
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"Věk",
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"Cohort",
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"Status",
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"Last IRT",
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"Next Visit",
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"Next Date",
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]
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COL_WIDTHS = [14, 22, 6, 12, 14, 12, 12, 13]
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# ── Styles ───────────────────────────────────────────────────────────────────
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HEADER_FILL = PatternFill("solid", fgColor="1F4E79")
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HEADER_FONT = Font(name="Arial", bold=True, color="FFFFFF", size=10)
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NORMAL_FONT = Font(name="Arial", size=10)
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BOLD_FONT = Font(name="Arial", bold=True, size=10)
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STRIKE_FONT = Font(name="Arial", size=10, strike=True, color="999999")
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ADOLESC_FONT = Font(name="Arial", bold=True, size=10)
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THIN = Side(style="thin", color="CCCCCC")
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BORDER = Border(left=THIN, right=THIN, top=THIN, bottom=THIN)
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EVEN_FILL = PatternFill("solid", fgColor="EBF3FB")
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ODD_FILL = PatternFill("solid", fgColor="FFFFFF")
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CENTER = Alignment(horizontal="center", vertical="center", wrap_text=False)
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LEFT = Alignment(horizontal="left", vertical="center", wrap_text=False)
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def unique_path(directory, stem):
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path = os.path.join(directory, f"{stem}.xlsx")
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if not os.path.exists(path):
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return path
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time_tag = datetime.datetime.now().strftime("%H%M")
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return os.path.join(directory, f"{stem} {time_tag}.xlsx")
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def find_latest_source(study):
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pattern = os.path.join(INCOMING_DIR, f"* {study} Subject Summary Report.xlsx")
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files = sorted(
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[f for f in glob.glob(pattern) if not os.path.basename(f).startswith("~$")],
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key=os.path.getmtime,
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reverse=True,
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)
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if not files:
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raise FileNotFoundError(f"Nenalezen zdrojový soubor pro {study} v {INCOMING_DIR}")
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return files[0]
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def load_source(path):
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raw = pd.read_excel(path, header=None)
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# find header row (row with "Subject" in first cell)
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header_row = None
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for i, row in raw.iterrows():
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if "Subject" in [str(v).strip() for v in row]:
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header_row = i
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break
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if header_row is None:
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raise ValueError("Hlavičkový řádek nenalezen")
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df = pd.read_excel(path, header=header_row)
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return df
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def simplify_cohort(val):
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if pd.isna(val):
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return ""
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val = str(val)
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if "dolescent" in val:
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return "Adolescent"
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if val.startswith("Adult"):
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return "Adult"
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# MDD3003: "Part 1", "Part 2" — keep as-is
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return val
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def format_date(val):
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if pd.isna(val):
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return ""
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if hasattr(val, "strftime"):
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return val.strftime("%Y-%m-%d")
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return str(val)[:10]
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def write_zdroj(wb, df_raw, source_path):
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mtime = datetime.datetime.fromtimestamp(os.path.getmtime(source_path))
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sheet_name = f"ZDROJ ({mtime.strftime('%d%b%Y').upper()})"
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ws = wb.create_sheet(sheet_name)
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ws.sheet_view.showGridLines = True
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# write raw headers + data as plain table
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headers = list(df_raw.columns)
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for c, h in enumerate(headers, 1):
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cell = ws.cell(row=1, column=c, value=h)
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cell.font = Font(name="Arial", bold=True, size=9, color="FFFFFF")
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cell.fill = PatternFill("solid", fgColor="404040")
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cell.alignment = LEFT
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cell.border = BORDER
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ws.column_dimensions[get_column_letter(c)].width = 20
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for r, (_, row) in enumerate(df_raw.iterrows(), 2):
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fill = EVEN_FILL if r % 2 == 0 else ODD_FILL
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for c, col in enumerate(headers, 1):
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val = row[col]
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if pd.isna(val):
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val = ""
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elif hasattr(val, "strftime"):
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val = val.strftime("%Y-%m-%d")
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cell = ws.cell(row=r, column=c, value=val)
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cell.font = Font(name="Arial", size=9)
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cell.fill = fill
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cell.border = BORDER
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cell.alignment = LEFT
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ws.freeze_panes = "A2"
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ws.auto_filter.ref = f"A1:{get_column_letter(len(headers))}1"
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def write_prehled(wb, df_raw, study):
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ws = wb.create_sheet("Přehled")
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ws.sheet_view.showGridLines = False
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ws.sheet_view.showRowColHeaders = True
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# ── title row ────────────────────────────────────────────────────────────
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ws.merge_cells("A1:H1")
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title = ws["A1"]
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title.value = f"Subject Summary — {study} ({datetime.date.today().strftime('%d-%b-%Y')})"
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title.font = Font(name="Arial", bold=True, size=12, color="1F4E79")
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title.alignment = Alignment(horizontal="left", vertical="center")
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ws.row_dimensions[1].height = 22
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# ── header row ───────────────────────────────────────────────────────────
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for c, (h, w) in enumerate(zip(DISPLAY_HEADERS, COL_WIDTHS), 1):
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cell = ws.cell(row=2, column=c, value=h)
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cell.font = HEADER_FONT
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cell.fill = HEADER_FILL
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cell.alignment = CENTER
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cell.border = BORDER
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ws.column_dimensions[get_column_letter(c)].width = w
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ws.row_dimensions[2].height = 18
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# ── build display dataframe ───────────────────────────────────────────────
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display = pd.DataFrame()
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display["Subject"] = df_raw["Subject"].fillna("")
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display["Investigator"]= df_raw["Investigator"].fillna("")
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display["Věk"] = df_raw["Subject's age collection"].apply(
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lambda v: "" if pd.isna(v) else int(v))
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display["Cohort"] = df_raw["Cohort per IRT"].apply(simplify_cohort)
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display["Status"] = df_raw["IRT Subject Status"].fillna("")
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display["Last IRT"] = df_raw["Last Recorded IRT Transaction"].fillna("—")
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display["Next Visit"] = df_raw["Next Expected IRT Transaction"].fillna("—")
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display["Next Date"] = df_raw["Next Expected IRT Transaction Date [Local]"].apply(format_date)
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display = display.sort_values("Subject").reset_index(drop=True)
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# ── data rows ────────────────────────────────────────────────────────────
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for r_idx, row in display.iterrows():
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excel_row = r_idx + 3 # row 1=title, row 2=header
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status = str(row["Status"])
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is_failed = "Screen Failed" in status or "Discontinued" in status
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is_randomized = "Randomized" in status
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is_adolescent = row["Cohort"] == "Adolescent"
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fill = EVEN_FILL if r_idx % 2 == 0 else ODD_FILL
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values = [
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row["Subject"], row["Investigator"], row["Věk"],
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row["Cohort"], row["Status"], row["Last IRT"],
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row["Next Visit"], row["Next Date"],
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]
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for c_idx, val in enumerate(values, 1):
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cell = ws.cell(row=excel_row, column=c_idx, value=val if val != "" else None)
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cell.fill = fill
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cell.border = BORDER
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# alignment
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cell.alignment = CENTER if c_idx in (3,) else LEFT
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# font logic
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if is_failed:
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cell.font = STRIKE_FONT
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elif c_idx == 5 and is_randomized:
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cell.font = BOLD_FONT
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elif c_idx == 4 and is_adolescent:
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cell.font = ADOLESC_FONT
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else:
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cell.font = NORMAL_FONT
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ws.row_dimensions[excel_row].height = 16
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ws.freeze_panes = "A3"
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last_data_row = len(display) + 2
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ws.auto_filter.ref = f"A2:H{last_data_row}"
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def write_next_visits(wb, df_raw, study):
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ws = wb.create_sheet("Next Visits")
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ws.sheet_view.showGridLines = False
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# title
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ws.merge_cells("A1:D1")
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title = ws["A1"]
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title.value = f"Next Expected Visits — {study} ({datetime.date.today().strftime('%d-%b-%Y')})"
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title.font = Font(name="Arial", bold=True, size=12, color="1F4E79")
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title.alignment = Alignment(horizontal="left", vertical="center")
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ws.row_dimensions[1].height = 22
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# headers
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nv_headers = ["Subject", "Investigator", "Next Visit", "Datum"]
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nv_widths = [14, 22, 26, 13]
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for c, (h, w) in enumerate(zip(nv_headers, nv_widths), 1):
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cell = ws.cell(row=2, column=c, value=h)
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cell.font = HEADER_FONT
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cell.fill = HEADER_FILL
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cell.alignment = CENTER
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cell.border = BORDER
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ws.column_dimensions[get_column_letter(c)].width = w
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ws.row_dimensions[2].height = 18
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# data — only rows with a Next Date, exclude Screen Failed / Discontinued
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df = pd.DataFrame()
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df["Subject"] = df_raw["Subject"].fillna("")
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df["Investigator"]= df_raw["Investigator"].fillna("")
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df["Next Visit"] = df_raw["Next Expected IRT Transaction"].fillna("")
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df["Datum"] = df_raw["Next Expected IRT Transaction Date [Local]"]
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df["Status"] = df_raw["IRT Subject Status"].fillna("")
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df = df[df["Datum"].notna()]
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df = df[~df["Status"].str.contains("Screen Failed|Discontinued", na=False)]
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df = df.sort_values("Datum").reset_index(drop=True)
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for r_idx, row in df.iterrows():
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excel_row = r_idx + 3
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fill = EVEN_FILL if r_idx % 2 == 0 else ODD_FILL
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datum_val = row["Datum"]
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datum_str = datum_val.strftime("%Y-%m-%d") if hasattr(datum_val, "strftime") else str(datum_val)[:10]
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values = [row["Subject"], row["Investigator"], row["Next Visit"], datum_str]
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for c_idx, val in enumerate(values, 1):
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cell = ws.cell(row=excel_row, column=c_idx, value=val if val != "" else None)
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cell.fill = fill
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cell.border = BORDER
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cell.font = NORMAL_FONT
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cell.alignment = LEFT
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ws.row_dimensions[excel_row].height = 16
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ws.freeze_panes = "A3"
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last_data_row = len(df) + 2
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ws.auto_filter.ref = f"A2:D{last_data_row}"
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def create_report(study):
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source_path = find_latest_source(study)
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print(f"[{study}] Čtu: {os.path.basename(source_path)}")
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df_raw = load_source(source_path)
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wb = Workbook()
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wb.remove(wb.active) # remove default sheet
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write_prehled(wb, df_raw, study)
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write_next_visits(wb, df_raw, study)
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write_zdroj(wb, df_raw, source_path)
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today = datetime.date.today().strftime("%Y-%m-%d")
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out_path = unique_path(CREATED_DIR, f"{today} {study} Subject Summary")
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wb.save(out_path)
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print(f"[{study}] Uloženo: {out_path}")
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return out_path
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def main():
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os.makedirs(CREATED_DIR, exist_ok=True)
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for study in STUDIES:
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try:
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create_report(study)
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except FileNotFoundError as e:
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print(f"[{study}] PŘESKOČENO: {e}")
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print("\nHotovo.")
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main()
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