notebook
This commit is contained in:
+11
-365
@@ -4,7 +4,7 @@ Kompletní pipeline pro Drugs:
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2. IP destruction (per košík, přeskočí již existující soubory)
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3. Shipments report (jeden soubor na studii, přepisuje)
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4. Shipment details (per zásilka CZ, vždy přepisuje)
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5. Import do MySQL
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5. Import do MongoDB (studie.iwrs_shipments / iwrs_shipment_items / iwrs_inventory / iwrs_destruction)
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Spusť tento skript — zpracuje obě studie automaticky.
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"""
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@@ -14,12 +14,11 @@ import glob
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import re
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import datetime
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import numpy as np
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import sys
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import pandas as pd
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from playwright.sync_api import sync_playwright
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import mysql.connector
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import db_config
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import import_to_mongo as drugs_mongo
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BASE_URL = "https://janssen.4gclinical.com"
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EMAIL = "vbuzalka@its.jnj.com"
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@@ -42,357 +41,6 @@ SITES = {
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BASE_DIR = os.path.dirname(os.path.abspath(__file__))
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# ── type converters ──────────────────────────────────────────────────────────
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def _py(val):
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if isinstance(val, np.generic):
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return val.item()
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return val
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def to_date(val):
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val = _py(val)
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if val is None:
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return None
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if isinstance(val, float) and (val != val):
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return None
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try:
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if pd.isna(val):
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return None
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except (TypeError, ValueError):
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pass
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if isinstance(val, pd.Timestamp):
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return None if pd.isna(val) else val.date()
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if isinstance(val, datetime.datetime):
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return val.date()
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if isinstance(val, datetime.date):
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return val
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s = str(val).strip()
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if not s or s.lower() in ("nat", "nan", "none", ""):
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return None
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for fmt in ("%Y-%m-%d", "%d-%b-%Y", "%d-%m-%Y", "%Y-%m-%d %H:%M:%S"):
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try:
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return datetime.datetime.strptime(s, fmt).date()
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except ValueError:
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pass
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return None
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def to_int(val):
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val = _py(val)
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try:
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v = float(val)
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return None if (v != v) else int(v)
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except (TypeError, ValueError):
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return None
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def to_str(val):
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val = _py(val)
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if val is None:
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return None
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if isinstance(val, float) and (val != val):
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return None
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s = str(val).strip()
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return None if s.lower() in ("nan", "nat", "none", "") else s
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# ── DB helpers ───────────────────────────────────────────────────────────────
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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 insert_import(cursor, study, source_label):
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cursor.execute(
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"INSERT INTO iwrs_import (study, imported_at, source_file, report_type) VALUES (%s, %s, %s, %s)",
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(study, datetime.datetime.now(), source_label, "drugs"),
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)
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return cursor.lastrowid
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def basket_already_imported(cursor, study, basket_id):
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cursor.execute(
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"SELECT 1 FROM iwrs_destruction WHERE study=%s AND basket_id=%s LIMIT 1",
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(study, str(basket_id)),
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)
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return cursor.fetchone() is not None
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# ── parsery ──────────────────────────────────────────────────────────────────
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def parse_shipments_report(study):
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path = os.path.join(BASE_DIR, f"xls_shipments_{study}", f"shipments_report_{study}.xlsx")
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if not os.path.exists(path):
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print(f" CHYBÍ: {path}")
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return []
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raw = pd.read_excel(path, header=None)
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header_row = None
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for i, row in raw.iterrows():
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if "Shipment ID" 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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return []
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df = pd.read_excel(path, header=header_row).dropna(how="all")
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df = df[df["Location"].astype(str).str.contains("Czech", na=False, case=False)]
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col = df.columns.tolist()
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rows = []
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for _, r in df.iterrows():
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rows.append({
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"shipment_id": to_str(r["Shipment ID"]),
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"status": to_str(r["IRT Shipment Status"]),
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"type": to_str(r["Type"]),
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"ship_from": to_str(r["Shipment From"]),
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"ship_to_site": to_str(r["Ship To:"]),
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"location": to_str(r["Location"]),
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"request_date": to_date(r["Request Date"]),
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"shipped_date": to_date(r["Shipped Date"]),
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"received_date": to_date(r["Received Date"]) if "Received Date" in col else None,
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"received_by": to_str(r["Received by"]) if "Received by" in col else None,
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"delivered_date_utc": to_date(r["Delivered Date [UTC]"]) if "Delivered Date [UTC]" in col else None,
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"delivery_recipient": to_str(r["Delivery Recipient"]) if "Delivery Recipient" in col else None,
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"delivery_details": to_str(r["Delivery Details"]) if "Delivery Details" in col else None,
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"cancelled_date": to_date(r["Cancelled Date"]) if "Cancelled Date" in col else None,
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"total_medication_ids": to_int(r["Total Medication IDs"]) if "Total Medication IDs" in col else None,
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"tracking_no": to_str(r["Tracking #"]) if "Tracking #" in col else None,
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"shipping_category": to_str(r["Shipping Category"]) if "Shipping Category" in col else None,
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"expected_arrival": to_date(r["Expected Arrival"]) if "Expected Arrival" in col else None,
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})
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return rows
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def parse_shipment_details(study):
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detail_dir = os.path.join(BASE_DIR, f"xls_shipment_details_{study}")
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files = sorted(glob.glob(os.path.join(detail_dir, "shipment_details_*.xlsx")))
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rows = []
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for path in files:
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m = re.search(r"shipment_details_(.+)\.xlsx", os.path.basename(path))
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shipment_id = m.group(1) if m else "UNKNOWN"
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raw = pd.read_excel(path, header=None)
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header_row = None
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for i, row in raw.iterrows():
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if "Medication ID" 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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continue
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df = pd.read_excel(path, header=header_row).dropna(how="all")
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for _, r in df.iterrows():
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med_desc = (to_str(r.get("Medication Description"))
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or to_str(r.get("Medication ID Description")))
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med_type = (to_str(r.get("Medication type"))
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or to_str(r.get("Medication ID type")))
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rows.append({
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"shipment_id": shipment_id,
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"destination_location": to_str(r.get("Destination Location")),
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"shipment_status": to_str(r.get("IRT Shipment Status")),
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"shipment_type": to_str(r.get("Type")),
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"destination_site": to_str(r.get("Destination Site")),
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"investigator": to_str(r.get("Investigator")),
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"medication_description": med_desc,
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"medication_type": med_type,
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"medication_id": to_str(r.get("Medication ID")),
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"packaged_lot_no": to_str(r.get("Packaged Lot number")),
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"packaged_lot_description": to_str(r.get("Packaged Lot description")),
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"container_id": to_str(r.get("Container ID")),
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"quantity": to_int(r.get("Quantity of Medication IDs")),
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"expiration_date": to_date(r.get("Expiration Date")),
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"item_status": to_str(r.get("Status")),
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})
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return rows
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def parse_inventory(study):
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inv_dir = os.path.join(BASE_DIR, f"xls_reports_{study}")
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files = sorted(glob.glob(os.path.join(inv_dir, "onsite_inventory_detail_*.xlsx")))
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rows = []
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for path in files:
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raw = pd.read_excel(path, header=None)
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site = investigator = location = None
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header_row = None
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for i, row in raw.iterrows():
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first = str(row.iloc[0]).strip() if pd.notna(row.iloc[0]) else ""
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if first.startswith("Site:"):
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site = first.replace("Site:", "").strip()
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elif first.startswith("Investigator:"):
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investigator = first.replace("Investigator:", "").strip()
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elif first.startswith("Location:"):
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location = first.replace("Location:", "").strip()
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if first in ("Medication", "Medication ID") and header_row is None:
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header_row = i
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if header_row is None:
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continue
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df = pd.read_excel(path, header=header_row).dropna(how="all")
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df = df.rename(columns={df.columns[0]: "medication_id"})
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for _, r in df.iterrows():
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rows.append({
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"site": site,
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"investigator": investigator,
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"location": location,
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"medication_id": to_str(r["medication_id"]),
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"packaged_lot_no": to_str(r.get("Packaged Lot number")),
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"original_expiration_date": to_date(r.get("Original Expiration Date when Packaged Lot was Added")),
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"expiration_date": to_date(r.get("Expiration date")),
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"received_date": to_date(r.get("Received Date")),
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"receipt_user": to_str(r.get("Shipment Receipt User")),
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"subject_identifier": to_str(r.get("Subject Identifier")),
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"quantity_assigned": to_int(r.get("Quantity Assigned")),
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"irt_transaction": to_str(r.get("IRT Transaction")),
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"date_assigned": to_date(r.get("Date Assigned")),
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"assignment_user": to_str(r.get("Assignment User")),
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"dispensation_status": to_str(r.get("Dispensation Status")),
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"dispensing_date": to_date(r.get("Dispensing date") or r.get("Dispensing Date")),
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"quantity_dispensed": to_int(r.get("Quantity Dispensed")),
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"dispensing_user": to_str(r.get("Dispensing User")),
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"quantity_returned": to_int(r.get("Quantity Returned")),
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"date_returned": to_date(r.get("Date Returned")),
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"return_user": to_str(r.get("Return User")),
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})
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return rows
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def parse_destruction_files(study):
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dest_dir = os.path.join(BASE_DIR, f"xls_ip_destruction_{study}")
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files = sorted(glob.glob(os.path.join(dest_dir, "ip_destruction_basket_*.xlsx")))
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baskets = []
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for path in files:
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raw = pd.read_excel(path, header=None)
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meta = {}
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header_row = None
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for i, row in raw.iterrows():
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first = str(row.iloc[0]).strip() if pd.notna(row.iloc[0]) else ""
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for key, attr in [
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("Investigator Name:", "investigator"),
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("Site ID:", "site_id"),
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("Location:", "location"),
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("Basket ID:", "basket_id"),
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("Drug Destruction Created Date:", "destruction_date"),
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]:
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if first.startswith(key):
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meta[attr] = first.replace(key, "").strip()
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if first == "Medication ID Description" and header_row is None:
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header_row = i
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if header_row is None:
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continue
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df = pd.read_excel(path, header=header_row).dropna(how="all")
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items = []
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for _, r in df.iterrows():
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items.append({
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"medication_description": to_str(r.get("Medication ID Description")),
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"medication_id": to_str(r.get("Medication ID")),
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"packaged_lot_description": to_str(r.get("Packaged Lot description")),
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"comments": to_str(r.get("Comments")),
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})
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baskets.append({
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"site_id": meta.get("site_id"),
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"investigator": meta.get("investigator"),
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"location": meta.get("location"),
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"basket_id": meta.get("basket_id"),
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"destruction_date": to_date(meta.get("destruction_date")),
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"items": items,
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})
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return baskets
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# ── insertery ────────────────────────────────────────────────────────────────
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def insert_shipments(cursor, import_id, study, rows):
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sql = """INSERT INTO iwrs_shipments
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(import_id, study, shipment_id, status, type, ship_from, ship_to_site,
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location, request_date, shipped_date, received_date, received_by,
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delivered_date_utc, delivery_recipient, delivery_details, cancelled_date,
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total_medication_ids, tracking_no, shipping_category, expected_arrival)
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VALUES (%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s)"""
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for r in rows:
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cursor.execute(sql, (
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import_id, study, r["shipment_id"], r["status"], r["type"],
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r["ship_from"], r["ship_to_site"], r["location"],
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r["request_date"], r["shipped_date"], r["received_date"],
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r["received_by"], r["delivered_date_utc"], r["delivery_recipient"],
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r["delivery_details"], r["cancelled_date"], r["total_medication_ids"],
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r["tracking_no"], r["shipping_category"], r["expected_arrival"],
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))
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def insert_shipment_items(cursor, import_id, study, rows):
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sql = """INSERT INTO iwrs_shipment_items
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(import_id, study, shipment_id, destination_location, shipment_status,
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shipment_type, destination_site, investigator, medication_description,
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medication_type, medication_id, packaged_lot_no, packaged_lot_description,
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container_id, quantity, expiration_date, item_status)
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VALUES (%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s)"""
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for r in rows:
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cursor.execute(sql, (
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import_id, study, r["shipment_id"], r["destination_location"],
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r["shipment_status"], r["shipment_type"], r["destination_site"],
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r["investigator"], r["medication_description"], r["medication_type"],
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r["medication_id"], r["packaged_lot_no"], r["packaged_lot_description"],
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r["container_id"], r["quantity"], r["expiration_date"], r["item_status"],
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))
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def insert_inventory(cursor, import_id, study, rows):
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sql = """INSERT INTO iwrs_inventory
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(import_id, study, site, investigator, location, medication_id,
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packaged_lot_no, original_expiration_date, expiration_date, received_date,
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receipt_user, subject_identifier, quantity_assigned, irt_transaction,
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date_assigned, assignment_user, dispensation_status, dispensing_date,
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quantity_dispensed, dispensing_user, quantity_returned, date_returned, return_user)
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VALUES (%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s)"""
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for r in rows:
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cursor.execute(sql, (
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import_id, study, r["site"], r["investigator"], r["location"],
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r["medication_id"], r["packaged_lot_no"], r["original_expiration_date"],
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r["expiration_date"], r["received_date"], r["receipt_user"],
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r["subject_identifier"], r["quantity_assigned"], r["irt_transaction"],
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r["date_assigned"], r["assignment_user"], r["dispensation_status"],
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r["dispensing_date"], r["quantity_dispensed"], r["dispensing_user"],
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r["quantity_returned"], r["date_returned"], r["return_user"],
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))
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def insert_destruction(cursor, study, baskets):
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sql = """INSERT IGNORE INTO iwrs_destruction
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(study, site_id, investigator, location, basket_id, destruction_date,
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medication_description, medication_id, packaged_lot_description, comments)
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VALUES (%s,%s,%s,%s,%s,%s,%s,%s,%s,%s)"""
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skipped = imported = 0
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for b in baskets:
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if basket_already_imported(cursor, study, b["basket_id"]):
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skipped += 1
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continue
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for item in b["items"]:
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cursor.execute(sql, (
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study, b["site_id"], b["investigator"], b["location"],
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b["basket_id"], b["destruction_date"],
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item["medication_description"], item["medication_id"],
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item["packaged_lot_description"], item["comments"],
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))
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imported += 1
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return imported, skipped
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def import_study(study):
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print(f"\n Parsování dat pro {study}...")
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shipments = parse_shipments_report(study)
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items = parse_shipment_details(study)
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inventory = parse_inventory(study)
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baskets = parse_destruction_files(study)
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print(f" Zásilky: {len(shipments)} | Položky: {len(items)} | Sklad: {len(inventory)} | Destrukce: {len(baskets)} košíků")
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conn = get_conn()
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cursor = conn.cursor()
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import_id = insert_import(cursor, study, f"drugs_{study}")
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print(f" import_id = {import_id}")
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insert_shipments(cursor, import_id, study, shipments)
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insert_shipment_items(cursor, import_id, study, items)
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insert_inventory(cursor, import_id, study, inventory)
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dest_imported, dest_skipped = insert_destruction(cursor, study, baskets)
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conn.commit()
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cursor.close()
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conn.close()
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print(f" Destrukce: {dest_imported} nových | {dest_skipped} košíků přeskočeno")
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|
||||
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# ── login ────────────────────────────────────────────────────────────────────
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||||
|
||||
@@ -577,19 +225,17 @@ def main():
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finally:
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browser.close()
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||||
|
||||
# ── Import do MySQL ───────────────────────────────────────────────────────
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||||
# ── Import do MongoDB ─────────────────────────────────────────────────────
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||||
print(f"\n{'='*60}")
|
||||
print("IMPORT DO MySQL")
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print("IMPORT DO MongoDB")
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print(f"{'='*60}")
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||||
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for study in STUDIES:
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print(f"\n[{study}]")
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try:
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import_study(study)
|
||||
except Exception as e:
|
||||
import traceback
|
||||
print(f" CHYBA při importu: {e}")
|
||||
traceback.print_exc()
|
||||
try:
|
||||
drugs_mongo.run(STUDIES)
|
||||
except Exception as e:
|
||||
import traceback
|
||||
print(f" CHYBA při importu: {e}")
|
||||
traceback.print_exc()
|
||||
|
||||
print(f"\n{'='*60}")
|
||||
print("Vše hotovo.")
|
||||
|
||||
Reference in New Issue
Block a user