448 lines
17 KiB
Python
448 lines
17 KiB
Python
"""
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create_report.py
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Verze: 1.4
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Datum: 2026-05-29
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Generuje Excel report (.xlsm) pro studii 77242113UCO3001 z MongoDB databáze Clario.
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Výstup: U:/Dropbox/!!!Days/Downloads Z230/YYYY-MM-DD 77242113UCO3001 Clario Reports.xlsm
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Zdroj dat:
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MongoDB 192.168.1.76, databáze Clario
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Kolekce Clario.MayoScore — skóre Mayo per pacient × visit
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Kolekce Clario.MayoDiary — denní záznamy deníku pacienta
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Listy:
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MayoScore — jeden řádek = pacient × visit
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sloupec „KLIKNI SEM" naviguje na filtrovaný EligibleDays
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řádky I-0 s Modified Mayo < 5 červeně tučně
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MayoDiary — jeden řádek = denní záznam deníku pacienta
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EligibleDays — jeden řádek = jeden eligible day z MayoScore obohacený o data z MayoDiary;
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included/excluded flag, excluded dny šedě na žlutém pozadí
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VBA makro (Worksheet_SelectionChange na listu MayoScore):
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Klik na sloupec „KLIKNI SEM" → přepne na EligibleDays a vyfiltruje záznamy
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pro daného pacienta a visit. Vyžaduje povolení maker při otevření souboru.
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"""
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VERSION = "1.4"
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from datetime import datetime
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from pathlib import Path
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import time
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from pymongo import MongoClient
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from openpyxl import Workbook
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from openpyxl.styles import Font, PatternFill, Alignment, Border, Side
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from openpyxl.utils import get_column_letter
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import xlwings as xw
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# ---------------------------------------------------------------------------
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# Konfigurace
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# ---------------------------------------------------------------------------
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MONGO_URI = "mongodb://192.168.1.76:27017"
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DB_NAME = "Clario"
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OUTPUT_DIR = Path(r"U:\Dropbox\!!!Days\Downloads Z230")
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VISIT_ORDER = ["I-0", "I-2", "I-4", "I-8", "I-12"]
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COLUMNS_SCORE = [
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("KLIKNI SEM", lambda d: "▶ klikni sem"),
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("Site", lambda d: d.get("site", {}).get("name", "")),
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("Subject ID", lambda d: d.get("subject", {}).get("id", "")),
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("Visit", lambda d: d["fields"].get("Visit", "")),
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("Visit Date", lambda d: d["fields"].get("Visit Date", "")),
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("Baseline Stool Frequency", lambda d: _num(d["fields"].get("Baseline Stool Frequency", ""))),
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("Central Endoscopy Score", lambda d: _num(d["fields"].get("Central Endoscopy Score", ""))),
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("PGA Score", lambda d: _num(d["fields"].get("PGA Score", ""))),
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("Stool Frequency Sub-score", lambda d: _num(d["fields"].get("Stool Frequency Sub-score", ""))),
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("Rectal Bleeding Sub-score", lambda d: _num(d["fields"].get("Rectal Bleeding Sub-score", ""))),
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("Partial Mayo Score", lambda d: _num(d["fields"].get("Partial Mayo Score", ""))),
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("Modified Mayo Score", lambda d: _num(d["fields"].get("Modified Mayo Score", ""))),
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("Full Mayo Score", lambda d: _num(d["fields"].get("Full Mayo Score", ""))),
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]
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COLUMNS_DIARY = [
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("Subject ID", lambda d: d.get("subject", {}).get("id", "")),
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("Report Date", lambda d: d["fields"].get("Report Date", "")),
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("Baseline Stool Count", lambda d: _num(d["fields"].get("Baseline Stool Count", ""))),
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("Stool Frequency", lambda d: _num(d["fields"].get("Stool Frequency", ""))),
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("MAYO050", lambda d: d["fields"].get("MAYO050", "")),
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("Not Applicable", lambda d: d["fields"].get("Not Applicable", "")),
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("Constipation", lambda d: d["fields"].get("Constipation", "")),
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("Diarrhea", lambda d: d["fields"].get("Diarrhea", "")),
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("Irregularity", lambda d: d["fields"].get("Irregularity", "")),
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]
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# ---------------------------------------------------------------------------
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# Helpers
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# ---------------------------------------------------------------------------
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def _num(value):
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"""Převede číselný string na int, jinak vrátí původní hodnotu nebo None."""
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if value == "" or value is None:
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return None
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try:
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return int(value)
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except (ValueError, TypeError):
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try:
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return float(value)
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except (ValueError, TypeError):
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return value
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def _visit_sort_key(doc):
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visit = doc["fields"].get("Visit", "")
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try:
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idx = VISIT_ORDER.index(visit)
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except ValueError:
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idx = len(VISIT_ORDER)
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return (doc.get("site", {}).get("name", ""), doc.get("subject", {}).get("id", ""), idx, visit)
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def _iso_to_date(value):
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"""ISO string → Python date pro Excel."""
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if not isinstance(value, str):
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return value
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try:
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return datetime.fromisoformat(value).date()
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except ValueError:
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return value
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# ---------------------------------------------------------------------------
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# Styly
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# ---------------------------------------------------------------------------
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HEADER_FILL = PatternFill("solid", fgColor="1F497D")
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HEADER_FONT = Font(bold=True, color="FFFFFF", size=10)
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CELL_FONT = Font(size=10)
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ALIGN_CTR = Alignment(horizontal="center", vertical="center", wrap_text=False)
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ALIGN_LEFT = Alignment(horizontal="left", vertical="center")
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THIN = Side(style="thin", color="BFBFBF")
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BORDER = Border(left=THIN, right=THIN, top=THIN, bottom=THIN)
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# zebra
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FILL_ODD = PatternFill("solid", fgColor="FFFFFF")
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FILL_EVEN = PatternFill("solid", fgColor="EBF1DE")
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SCORE_COLS = {"Partial Mayo Score", "Modified Mayo Score", "Full Mayo Score"}
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SCORE_FILL = PatternFill("solid", fgColor="FFC7CE") # červená pro skóre ≥ 5 (placeholder — nepoužíváme podmíněné formátování)
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# ---------------------------------------------------------------------------
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# Sestavení sheetu
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# ---------------------------------------------------------------------------
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def _build_sheet(ws, docs, columns, date_cols, center_cols, col_widths, row_font_fn=None):
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headers = [c[0] for c in columns]
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for col_idx, header in enumerate(headers, 1):
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cell = ws.cell(row=1, column=col_idx, value=header)
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cell.font = HEADER_FONT
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cell.fill = HEADER_FILL
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cell.alignment = ALIGN_CTR
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cell.border = BORDER
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ws.row_dimensions[1].height = 28
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for row_idx, doc in enumerate(docs, 2):
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fill = FILL_EVEN if row_idx % 2 == 0 else FILL_ODD
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font = row_font_fn(doc) if row_font_fn else CELL_FONT
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for col_idx, (col_name, getter) in enumerate(columns, 1):
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value = getter(doc)
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if col_name in date_cols and isinstance(value, str):
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value = _iso_to_date(value)
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cell = ws.cell(row=row_idx, column=col_idx, value=value)
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cell.font = font
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cell.fill = fill
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cell.border = BORDER
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cell.alignment = ALIGN_CTR if col_name in center_cols else ALIGN_LEFT
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for col_idx, (col_name, _) in enumerate(columns, 1):
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ws.column_dimensions[get_column_letter(col_idx)].width = col_widths.get(col_name, 14)
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for col_name in date_cols:
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if col_name in headers:
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letter = get_column_letter(headers.index(col_name) + 1)
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for row_idx in range(2, len(docs) + 2):
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ws[f"{letter}{row_idx}"].number_format = "DD-MMM-YYYY"
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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 _score_row_font(doc):
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visit = doc["fields"].get("Visit", "")
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try:
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mod_mayo = int(doc["fields"].get("Modified Mayo Score", ""))
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except (ValueError, TypeError):
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mod_mayo = None
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if visit == "I-0" and mod_mayo is not None and mod_mayo < 5:
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return Font(size=10, bold=True, color="FF0000")
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return CELL_FONT
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def build_mayo_score_sheet(ws, docs):
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_build_sheet(
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ws, docs, COLUMNS_SCORE,
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date_cols={"Visit Date"},
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center_cols={"KLIKNI SEM", "Visit", "Central Endoscopy Score", "PGA Score",
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"Stool Frequency Sub-score", "Rectal Bleeding Sub-score",
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"Partial Mayo Score", "Modified Mayo Score", "Full Mayo Score",
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"Baseline Stool Frequency"},
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col_widths={
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"KLIKNI SEM": 14,
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"Site": 18, "Subject ID": 16, "Visit": 12, "Visit Date": 14,
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"Baseline Stool Frequency": 14, "Central Endoscopy Score": 14,
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"PGA Score": 10, "Stool Frequency Sub-score": 14,
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"Rectal Bleeding Sub-score": 14, "Partial Mayo Score": 14,
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"Modified Mayo Score": 14, "Full Mayo Score": 13,
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},
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row_font_fn=_score_row_font,
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)
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# Speciální styl pro sloupec KLIKNI SEM — vypadá jako tlačítko/odkaz
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link_font = Font(size=10, bold=True, color="FFFFFF")
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link_fill = PatternFill("solid", fgColor="2E75B6")
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for row in range(2, len(docs) + 2):
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cell = ws.cell(row=row, column=1)
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cell.font = link_font
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cell.fill = link_fill
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cell.alignment = ALIGN_CTR
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def build_mayo_diary_sheet(ws, docs):
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_build_sheet(
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ws, docs, COLUMNS_DIARY,
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date_cols={"Report Date"},
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center_cols={"Baseline Stool Count", "Stool Frequency", "Not Applicable",
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"Constipation", "Diarrhea", "Irregularity"},
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col_widths={
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"Subject ID": 16, "Report Date": 14, "Baseline Stool Count": 14,
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"Stool Frequency": 14, "MAYO050": 48, "Not Applicable": 14,
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"Constipation": 14, "Diarrhea": 12, "Irregularity": 14,
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},
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)
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def build_eligible_days_sheet(ws, score_docs, diary_docs):
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# Lookup diary records by (subject_id, date_part YYYY-MM-DD)
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diary_lookup: dict[tuple, dict] = {}
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for d in diary_docs:
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subj = d.get("subject", {}).get("id", "")
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date_iso = d["fields"].get("Report Date", "")
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date_part = date_iso[:10] if date_iso else ""
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if subj and date_part:
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diary_lookup[(subj, date_part)] = d
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headers = [
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"Included", "Subject ID", "Visit", "Visit Date", "Day",
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"Report Date", "Baseline Stool Count", "Stool Frequency",
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"MAYO050", "Not Applicable", "Constipation", "Diarrhea", "Irregularity",
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]
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col_widths = {
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"Included": 10, "Subject ID": 16, "Visit": 10, "Visit Date": 14, "Day": 8,
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"Report Date": 14, "Baseline Stool Count": 14, "Stool Frequency": 14,
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"MAYO050": 48, "Not Applicable": 14, "Constipation": 14,
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"Diarrhea": 12, "Irregularity": 14,
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}
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center_cols = {"Included", "Visit", "Day", "Baseline Stool Count", "Stool Frequency",
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"Not Applicable", "Constipation", "Diarrhea", "Irregularity"}
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date_cols = {"Visit Date", "Report Date"}
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no_fill = PatternFill("solid", fgColor="FFF2CC") # žlutá pro excluded dny
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for col_idx, header in enumerate(headers, 1):
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cell = ws.cell(row=1, column=col_idx, value=header)
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cell.font = HEADER_FONT
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cell.fill = HEADER_FILL
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cell.alignment = ALIGN_CTR
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cell.border = BORDER
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ws.row_dimensions[1].height = 28
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row_idx = 2
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for score_doc in score_docs:
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subj = score_doc.get("subject", {}).get("id", "")
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visit = score_doc["fields"].get("Visit", "")
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visit_date = score_doc["fields"].get("Visit Date", "")
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for n in range(1, 11):
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day_date_iso = score_doc["fields"].get(f"Eligible Day (-{n})")
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if not day_date_iso or day_date_iso == "-":
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continue
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date_part = day_date_iso[:10]
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excl_reason = score_doc["fields"].get(f"Day (-{n}) Excluded Reason(s)", "")
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included = "No" if excl_reason and excl_reason != "-" else "Yes"
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diary = diary_lookup.get((subj, date_part), {})
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df = diary.get("fields", {})
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fill = no_fill if included == "No" else (FILL_EVEN if row_idx % 2 == 0 else FILL_ODD)
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font = Font(size=10, color="808080") if included == "No" else CELL_FONT
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values = [
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included,
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subj,
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visit,
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_iso_to_date(visit_date) if isinstance(visit_date, str) else visit_date,
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f"-{n}",
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_iso_to_date(day_date_iso),
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_num(df.get("Baseline Stool Count", "")),
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_num(df.get("Stool Frequency", "")),
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df.get("MAYO050", ""),
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df.get("Not Applicable", ""),
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df.get("Constipation", ""),
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df.get("Diarrhea", ""),
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df.get("Irregularity", ""),
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]
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for col_idx, (header, value) in enumerate(zip(headers, values), 1):
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cell = ws.cell(row=row_idx, column=col_idx, value=value)
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cell.font = font
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cell.fill = fill
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cell.border = BORDER
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if header in date_cols:
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cell.number_format = "DD-MMM-YYYY"
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cell.alignment = ALIGN_CTR if header in center_cols else ALIGN_LEFT
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row_idx += 1
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for col_idx, header in enumerate(headers, 1):
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ws.column_dimensions[get_column_letter(col_idx)].width = col_widths.get(header, 14)
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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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# ---------------------------------------------------------------------------
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# Timing helper
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# ---------------------------------------------------------------------------
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def _tick(label: str, t0: float) -> float:
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"""Vypíše dobu od t0 a vrátí aktuální čas jako nový t0."""
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elapsed = time.perf_counter() - t0
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print(f" {label:<30} {elapsed:6.2f} s")
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return time.perf_counter()
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# ---------------------------------------------------------------------------
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# Main
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# ---------------------------------------------------------------------------
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def main():
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t_total = time.perf_counter()
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print("Spouštím generování reportu...")
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print()
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# -- 1. MongoDB: připojení + načtení + seřazení --------------------------
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t = time.perf_counter()
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client = MongoClient(MONGO_URI, serverSelectionTimeoutMS=5000)
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client.admin.command("ping")
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db = client[DB_NAME]
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score_docs = list(db["Clario.MayoScore"].find({}))
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diary_docs = list(db["Clario.MayoDiary"].find({}))
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client.close()
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score_docs.sort(key=_visit_sort_key)
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diary_docs.sort(key=lambda d: (
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d.get("subject", {}).get("id", ""),
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d["fields"].get("Report Date", ""),
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))
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t = _tick(f"MongoDB (ping, fetch, sort → {len(score_docs)} + {len(diary_docs)} záznamů)", t)
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# -- 2–4. Tvorba listů ---------------------------------------------------
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wb = Workbook()
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ws_score = wb.active
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ws_score.title = "MayoScore"
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build_mayo_score_sheet(ws_score, score_docs)
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t = _tick("List MayoScore (KLIKNI SEM, zebra, červené I-0, autofilter)", t)
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ws_diary = wb.create_sheet("MayoDiary")
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build_mayo_diary_sheet(ws_diary, diary_docs)
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t = _tick("List MayoDiary (zebra, formátování dat, autofilter)", t)
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ws_days = wb.create_sheet("EligibleDays")
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build_eligible_days_sheet(ws_days, score_docs, diary_docs)
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t = _tick("List EligibleDays (diary lookup, included/excluded flag, autofilter)", t)
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# -- 5. Uložení XLSX -----------------------------------------------------
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OUTPUT_DIR.mkdir(parents=True, exist_ok=True)
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today = datetime.now().strftime("%Y-%m-%d")
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filename = f"{today} 77242113UCO3001 Clario Reports.xlsx"
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output_path = OUTPUT_DIR / filename
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xlsx_path = output_path.with_suffix(".xlsx")
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xlsm_path = output_path.with_suffix(".xlsm")
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wb.save(str(xlsx_path))
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t = _tick("Uložení XLSX (openpyxl, dočasný soubor)", t)
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# -- 6. Injektování VBA --------------------------------------------------
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inject_vba(xlsx_path, xlsm_path)
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xlsx_path.unlink(missing_ok=True)
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_tick("Injektování VBA (xlwings: open → AddFromString → SaveAs .xlsm)", t)
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# -- Souhrn --------------------------------------------------------------
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total = time.perf_counter() - t_total
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print()
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print(f" {'Celkem':<30} {total:6.2f} s")
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print()
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print(f"Uloženo: {xlsm_path}")
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def inject_vba(xlsx_path: Path, xlsm_path: Path) -> None:
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vba_code = '''\
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Private Sub Worksheet_SelectionChange(ByVal Target As Range)
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If Target.Row < 2 Then Exit Sub
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If Target.Rows.Count > 1 Then Exit Sub
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If Target.Column <> 1 Then Exit Sub
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Dim subjectId As String
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Dim visit As String
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subjectId = CStr(Me.Cells(Target.Row, 3).Value)
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visit = CStr(Me.Cells(Target.Row, 4).Value)
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If subjectId = "" Or visit = "" Then Exit Sub
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Dim ws As Worksheet
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On Error Resume Next
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Set ws = ThisWorkbook.Sheets("EligibleDays")
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On Error GoTo 0
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If ws Is Nothing Then Exit Sub
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Application.ScreenUpdating = False
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ws.AutoFilterMode = False
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ws.Range("A1").AutoFilter
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ws.Range("A1").AutoFilter Field:=2, Criteria1:=subjectId
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ws.Range("A1").AutoFilter Field:=3, Criteria1:=visit
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ws.Activate
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ws.Range("A2").Select
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Application.ScreenUpdating = True
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End Sub
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'''
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app = xw.App(visible=False)
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try:
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wb = app.books.open(str(xlsx_path))
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# Najdi VBComponent odpovídající listu "MayoScore" podle tab názvu
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vb_comp = None
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for comp in wb.api.VBProject.VBComponents:
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if comp.Type == 100: # xlSheet
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try:
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if comp.Properties("Name").Value == "MayoScore":
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vb_comp = comp
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break
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except Exception:
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pass
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if vb_comp is None:
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# fallback: první sheet (Sheet1)
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vb_comp = wb.api.VBProject.VBComponents("Sheet1")
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vb_comp.CodeModule.AddFromString(vba_code)
|
||
wb.api.SaveAs(str(xlsm_path), FileFormat=52) # 52 = xlOpenXMLWorkbookMacroEnabled
|
||
wb.close()
|
||
finally:
|
||
app.quit()
|
||
|
||
|
||
if __name__ == "__main__":
|
||
main()
|