365 lines
14 KiB
Python
365 lines
14 KiB
Python
import sys
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import os
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import mysql.connector
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import pandas as pd
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from datetime import date
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from pathlib import Path
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from openpyxl import load_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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sys.path.insert(0, os.path.join(os.path.dirname(os.path.abspath(__file__)), ".."))
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import db_config
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STUDY = "42847922MDD3003"
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# STUDY = "77242113UCO3001"
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BASE_DIR = Path(os.path.dirname(os.path.abspath(__file__)))
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OUTPUT_DIR = BASE_DIR / "output"
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OUTPUT_FILE = OUTPUT_DIR / f"{date.today().strftime('%Y-%m-%d')} {STUDY} CZ IWRS overview.xlsx"
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DATE_COLUMNS = {
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"Orig Exp Date", "Exp Date", "Rcv Date",
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"Date Asgn", "Disp Date", "Date Ret", "Destroyed", "Max Visit Date",
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}
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COLUMN_WIDTHS = {
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"Site": 14,
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"Med ID": 10,
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"Lot No.": 12,
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"Orig Exp Date": 16,
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"Exp Date": 14,
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"Rcv Date": 14,
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"Rcpt User": 22,
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"Subject ID": 14,
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"Qty Asgn": 9,
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"IRT Tx": 8,
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"Date Asgn": 14,
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"Asgn User": 20,
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"Disp Status": 16,
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"Disp Date": 14,
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"Qty Disp": 9,
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"Disp User": 20,
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"Qty Ret": 10,
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"Date Ret": 14,
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"Ret User": 18,
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"Destroyed": 14,
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"Basket No.": 12,
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"Max Visit Date": 16,
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}
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# shipments sheet: kolík kde začínají detail sloupce (1-based, pro format_shipment_sheet)
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N_SHIP_COLS = 9
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# ── DB ────────────────────────────────────────────────────────────────────────
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def get_conn():
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return mysql.connector.connect(
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host=db_config.DB_HOST, port=db_config.DB_PORT,
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user=db_config.DB_USER, password=db_config.DB_PASSWORD,
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database=db_config.DB_NAME,
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)
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def get_latest_import_id(cursor, study):
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cursor.execute(
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"SELECT MAX(import_id) AS mid FROM iwrs_import WHERE study=%s AND report_type='drugs'",
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(study,),
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)
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row = cursor.fetchone()
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mid = row["mid"]
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if mid is None:
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raise RuntimeError(f"Žádná data v MySQL pro studii {study}")
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return mid
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# ── Načítání dat z MySQL ──────────────────────────────────────────────────────
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def load_inventory(cursor, study, import_id):
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"""
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Vrátí DataFrame s inventory + destruction join.
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Sloupce jsou rovnou přejmenované pro downstream funkce.
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"""
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sql = """
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SELECT
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i.site AS Site,
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i.medication_id AS `Med ID`,
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i.packaged_lot_no AS `Lot No.`,
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i.original_expiration_date AS `Orig Exp Date`,
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i.expiration_date AS `Exp Date`,
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i.received_date AS `Rcv Date`,
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i.receipt_user AS `Rcpt User`,
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i.subject_identifier AS `Subject ID`,
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i.quantity_assigned AS `Qty Asgn`,
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i.irt_transaction AS `IRT Tx`,
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i.date_assigned AS `Date Asgn`,
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i.assignment_user AS `Asgn User`,
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i.dispensation_status AS `Disp Status`,
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i.dispensing_date AS `Disp Date`,
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i.quantity_dispensed AS `Qty Disp`,
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i.dispensing_user AS `Disp User`,
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i.quantity_returned AS `Qty Ret`,
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i.date_returned AS `Date Ret`,
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i.return_user AS `Ret User`,
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d.destruction_date AS Destroyed,
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d.basket_id AS `Basket No.`
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FROM iwrs_inventory i
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LEFT JOIN (
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SELECT medication_id,
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ANY_VALUE(basket_id) AS basket_id,
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ANY_VALUE(destruction_date) AS destruction_date
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FROM iwrs_destruction
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WHERE study = %s
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GROUP BY medication_id
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) d ON d.medication_id = i.medication_id
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WHERE i.import_id = %s
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AND i.study = %s
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ORDER BY i.site, i.received_date, i.medication_id
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"""
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cursor.execute(sql, (study, import_id, study))
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rows = cursor.fetchall()
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df = pd.DataFrame(rows)
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for col in DATE_COLUMNS:
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if col in df.columns:
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df[col] = pd.to_datetime(df[col], errors="coerce")
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print(f" Inventory: {len(df)} kitu")
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return df
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def load_shipments(cursor, study, import_id):
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"""
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Vrátí DataFrame se spojenými shipments + items.
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"""
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sql = """
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SELECT
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s.shipment_id AS `Shipment ID`,
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s.status AS `IRT Shipment Status`,
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s.type AS Type,
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s.ship_from AS `Shipment From`,
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s.ship_to_site AS `Ship To:`,
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s.request_date AS `Request Date`,
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s.received_date AS `Received Date`,
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s.received_by AS `Received by`,
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s.expected_arrival AS `Expected Arrival`,
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i.investigator AS Investigator,
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i.medication_description AS `Medication Description`,
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i.medication_id AS `Medication ID`,
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i.packaged_lot_no AS `Packaged Lot number`,
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i.expiration_date AS `Expiration Date`,
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i.item_status AS Status
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FROM iwrs_shipments s
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JOIN iwrs_shipment_items i
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ON i.study = s.study
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AND i.shipment_id = s.shipment_id
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AND i.import_id = %s
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WHERE s.import_id = %s
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AND s.study = %s
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ORDER BY s.ship_to_site, s.shipment_id, i.medication_id
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"""
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cursor.execute(sql, (import_id, import_id, study))
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rows = cursor.fetchall()
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df = pd.DataFrame(rows)
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for col in ("Request Date", "Received Date", "Expiration Date", "Expected Arrival"):
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if col in df.columns:
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df[col] = pd.to_datetime(df[col], errors="coerce")
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print(f" Shipments: {df['Shipment ID'].nunique() if len(df) else 0} zásilek, {len(df)} kitu")
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return df
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# ── Odvozené sheety ───────────────────────────────────────────────────────────
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def build_site_summary(shipments_df):
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STATUS_COLS = ["Available", "Assigned", "Dispensed", "Returned by Subject"]
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pivot = shipments_df.groupby("Ship To:")["Status"].value_counts().unstack(fill_value=0)
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for s in STATUS_COLS:
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if s not in pivot.columns:
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pivot[s] = 0
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pivot = (
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pivot[STATUS_COLS]
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.reset_index()
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.rename(columns={"Ship To:": "Site", "Returned by Subject": "Returned"})
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.sort_values("Site")
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.reset_index(drop=True)
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)
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pivot["Total"] = pivot[["Available", "Assigned", "Dispensed", "Returned"]].sum(axis=1)
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print(f" Site Summary: {len(pivot)} center")
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return pivot
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def build_expired(df):
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today = date.today()
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mask = (
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df["Basket No."].isna() &
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df["Subject ID"].isna() &
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(df["Exp Date"] < pd.Timestamp(today))
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)
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filtered = df[mask].copy().reset_index(drop=True)
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sheet_name = f"Expired as of {today.strftime('%d-%b-%Y')}"
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print(f" Expired: {len(filtered)}")
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return filtered, sheet_name
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def build_assigned_not_dispensed(df):
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mask = df["Subject ID"].notna() & df["Disp Date"].isna()
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filtered = df[mask].copy().reset_index(drop=True)
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print(f" Assigned not dispensed: {len(filtered)}")
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return filtered
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def build_not_returned(df):
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no_ret = df[
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df["Date Ret"].isna() &
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df["Subject ID"].notna() &
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(df["Disp Status"].fillna("").str.upper() != "NOT DISPENSED")
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].copy()
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max_asgn = df.groupby("Subject ID")["Date Asgn"].max().rename("Max Visit Date")
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no_ret = no_ret.join(max_asgn, on="Subject ID")
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filtered = no_ret[no_ret["Date Asgn"] < no_ret["Max Visit Date"]].copy()
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filtered = filtered.drop(columns=["Qty Ret", "Date Ret", "Ret User", "Destroyed", "Basket No."])
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filtered = filtered.reset_index(drop=True)
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print(f" Not returned: {len(filtered)}")
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return filtered
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def build_kits_for_destruction(df):
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mask = (
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df["Basket No."].isna() &
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(df["Date Ret"].notna() | (df["Disp Status"].fillna("").str.upper() == "NOT DISPENSED"))
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)
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filtered = (
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df[mask]
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.copy()
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.sort_values(["Site", "Date Ret"], ascending=[True, True])
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.drop(columns=["Destroyed", "Basket No."])
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.reset_index(drop=True)
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)
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print(f" Kits for destruction: {len(filtered)}")
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return filtered
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# ── Formátování ───────────────────────────────────────────────────────────────
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def format_sheet(ws, header_color, highlight_col=None, highlight_color=None):
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thin = Side(style="thin", color="000000")
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border = Border(left=thin, right=thin, top=thin, bottom=thin)
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header_fill = PatternFill("solid", start_color=header_color)
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header_font = Font(bold=True, color="FFFFFF", name="Arial", size=10)
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row_font = Font(name="Arial", size=10)
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hi_fill = PatternFill("solid", start_color=highlight_color) if highlight_color else None
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headers = [cell.value for cell in ws[1]]
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for cell in ws[1]:
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cell.fill = header_fill
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cell.font = header_font
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cell.alignment = Alignment(horizontal="center", vertical="center", wrap_text=False)
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cell.border = border
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for row in ws.iter_rows(min_row=2, max_row=ws.max_row):
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for cell in row:
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col_name = headers[cell.column - 1] if cell.column <= len(headers) else None
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cell.font = row_font
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cell.border = border
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cell.alignment = Alignment(horizontal="center")
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if col_name in DATE_COLUMNS:
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cell.number_format = "DD-MMM-YYYY"
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if hi_fill and col_name == highlight_col:
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cell.fill = hi_fill
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for cell in ws[1]:
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width = COLUMN_WIDTHS.get(cell.value, 14)
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ws.column_dimensions[get_column_letter(cell.column)].width = width
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ws.auto_filter.ref = ws.dimensions
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ws.freeze_panes = "A2"
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def format_shipment_sheet(ws, header_color_ship, header_color_detail, n_ship_cols):
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thin = Side(style="thin", color="000000")
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border = Border(left=thin, right=thin, top=thin, bottom=thin)
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hfont = Font(bold=True, color="FFFFFF", name="Arial", size=10)
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dfont = Font(name="Arial", size=10)
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fill_ship = PatternFill("solid", start_color=header_color_ship)
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fill_detail = PatternFill("solid", start_color=header_color_detail)
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for cell in ws[1]:
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cell.fill = fill_ship if cell.column <= n_ship_cols else fill_detail
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cell.font = hfont
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cell.alignment = Alignment(horizontal="center", vertical="center", wrap_text=True)
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cell.border = border
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ws.column_dimensions[get_column_letter(cell.column)].width = min(
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len(str(cell.value or "")) + 4, 35
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)
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ws.row_dimensions[1].height = 30
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for row in ws.iter_rows(min_row=2, max_row=ws.max_row):
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for cell in row:
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cell.font = dfont
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cell.border = border
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cell.alignment = Alignment(horizontal="center", vertical="center")
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if cell.value.__class__.__name__ in ("datetime", "date", "Timestamp"):
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cell.number_format = "DD-MMM-YYYY"
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ws.auto_filter.ref = ws.dimensions
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ws.freeze_panes = "A2"
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# ── Main ──────────────────────────────────────────────────────────────────────
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def main():
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OUTPUT_DIR.mkdir(exist_ok=True)
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print(f"\nNačítám data z MySQL pro {STUDY}...")
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conn = get_conn()
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cursor = conn.cursor(dictionary=True)
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import_id = get_latest_import_id(cursor, STUDY)
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print(f" import_id = {import_id}")
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df = load_inventory(cursor, STUDY, import_id)
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shipments_df = load_shipments(cursor, STUDY, import_id)
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cursor.close()
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conn.close()
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expired_df, expired_sheet = build_expired(df)
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assigned_df = build_assigned_not_dispensed(df)
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not_returned_df = build_not_returned(df)
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destruction_df = build_kits_for_destruction(df)
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site_summary_df = build_site_summary(shipments_df)
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with pd.ExcelWriter(OUTPUT_FILE, engine="openpyxl") as writer:
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df.to_excel( writer, index=False, sheet_name="CountryMedicationOverview")
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expired_df.to_excel( writer, index=False, sheet_name=expired_sheet)
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assigned_df.to_excel( writer, index=False, sheet_name="Assigned not dispensed")
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not_returned_df.to_excel( writer, index=False, sheet_name="Not returned")
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destruction_df.to_excel( writer, index=False, sheet_name="Kits for destruction")
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shipments_df.to_excel( writer, index=False, sheet_name="Shipments")
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site_summary_df.to_excel( writer, index=False, sheet_name="Site Summary")
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wb = load_workbook(OUTPUT_FILE)
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ws_main = wb["CountryMedicationOverview"]
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format_sheet(ws_main, header_color="1F4E79")
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new_col_fill = PatternFill("solid", start_color="E2EFDA")
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headers_main = [c.value for c in ws_main[1]]
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for row in ws_main.iter_rows(min_row=2, max_row=ws_main.max_row):
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for cell in row:
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col_name = headers_main[cell.column - 1] if cell.column <= len(headers_main) else None
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if col_name in ("Destroyed", "Basket No."):
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cell.fill = new_col_fill
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format_sheet(wb[expired_sheet], header_color="C00000", highlight_col="Exp Date", highlight_color="FFE0E0")
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format_sheet(wb["Assigned not dispensed"], header_color="833C00", highlight_col="Subject ID", highlight_color="FFF2CC")
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format_sheet(wb["Not returned"], header_color="375623", highlight_col="Max Visit Date", highlight_color="E2EFDA")
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format_sheet(wb["Kits for destruction"], header_color="595959")
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format_shipment_sheet(wb["Shipments"], "1F4E79", "375623", N_SHIP_COLS)
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format_sheet(wb["Site Summary"], header_color="1F4E79")
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wb.save(OUTPUT_FILE)
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print(f"\nUloženo: {OUTPUT_FILE} ({len(df)} řádků, sheety: {wb.sheetnames})")
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if __name__ == "__main__":
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main()
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