Initial commit — clean history (removed large test files, browser profiles, Medidata/Clario downloads)
This commit is contained in:
@@ -0,0 +1,489 @@
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"""
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download_report.py
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NAHRAZENO skriptem download_edc_datalistings.py
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Původně: stahování Data Listing reportů pro studii MDD3003 (CZE).
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"""
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import os
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import sys
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from datetime import datetime, timedelta
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from pathlib import Path
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from dotenv import load_dotenv
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from playwright.sync_api import sync_playwright, TimeoutError as PWTimeout
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import tkinter as tk
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from tkinter import simpledialog
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load_dotenv(Path(__file__).parent / ".env")
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USERNAME = os.getenv("IMEDIDATA_USERNAME", "vladimir.buzalka")
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PASSWORD = os.getenv("IMEDIDATA_PASSWORD", "")
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DOWNLOAD_DIR = Path(__file__).parent / "downloads"
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AUTH_FILE = Path(__file__).parent / "auth.json"
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AUTH_MAX_AGE_DAYS = 7
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LOGIN_URL = "https://login.imedidata.com/login"
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SELECT_ROLE_URL = (
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"https://jnjja.mdsol.com/MedidataRave/SelectRole.aspx"
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"?client_division_uuid=e5de55d5-a414-4bd1-9abe-18e96fd5475d"
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"&study_group_uuid=b0793ca6-33ec-44e8-883b-6fc1a4b671c4"
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"&studygroup_id=107981"
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)
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STUDY_NAME = "42847922MDD3003"
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SITE_GROUP = "CZE"
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FORM_NAMES = [
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"Date of Visit",
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"Vital Signs",
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"Interim Investigator Signature",
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]
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REPORT_ID = 92 # _EDC Std Rpt - Data Listing (Data Stream)
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# ---------------------------------------------------------------------------
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# Helpers
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# ---------------------------------------------------------------------------
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def auth_valid():
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if not AUTH_FILE.exists():
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return False
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age = datetime.now() - datetime.fromtimestamp(AUTH_FILE.stat().st_mtime)
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return age < timedelta(days=AUTH_MAX_AGE_DAYS)
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def wait_load(page, extra_ms=1000):
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"""Čeká na 'load' event + extra pauza. Rave nikdy nedosáhne networkidle."""
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try:
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page.wait_for_load_state("load", timeout=20_000)
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except PWTimeout:
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pass
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page.wait_for_timeout(extra_ms)
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def dbg(page, label):
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print(f"[{label}] URL: {page.url}")
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# ---------------------------------------------------------------------------
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# Login
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# ---------------------------------------------------------------------------
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def _ask_otp_popup():
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"""Zobrazí GUI dialog pro zadání OKTA OTP kódu."""
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root = tk.Tk()
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root.withdraw()
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root.lift()
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root.attributes("-topmost", True)
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otp = simpledialog.askstring(
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"OKTA MFA",
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"Zadej OTP kód z OKTA (6 číslic):",
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parent=root,
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)
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root.destroy()
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return (otp or "").strip()
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def do_login(page, context):
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print("Přihlašuji se do iMedidata...")
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page.goto(LOGIN_URL)
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wait_load(page, 500)
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dbg(page, "login-page")
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# Pole username a password mají jméno session[username] / session[password]
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page.wait_for_selector('input[name="session[username]"]', timeout=10_000)
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page.fill('input[name="session[username]"]', USERNAME)
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page.fill('input[name="session[password]"]', PASSWORD)
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page.click('button[type="submit"]')
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# Čekáme na přesměrování — může jít přes OKTA nebo rovnou na home
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wait_load(page, 2000)
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dbg(page, "after-signin")
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# OKTA MFA?
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if _okta_mfa_present(page):
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print("\n*** OKTA MFA vyžadována! ***")
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otp = _ask_otp_popup()
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if not otp:
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print("CHYBA: OTP nebylo zadáno.")
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sys.exit(1)
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_fill_otp(page, otp)
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# Čekáme na zpracování OTP a redirect zpět na iMedidata
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wait_load(page, 3000)
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dbg(page, "after-otp")
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# Počkáme až budeme na home.imedidata.com
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try:
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page.wait_for_url("**/home.imedidata.com**", timeout=30_000)
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except PWTimeout:
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dbg(page, "wait-home-timeout")
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dbg(page, "final-login")
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if "home.imedidata.com" not in page.url:
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print("CHYBA: Přihlášení se nezdařilo! Zkontroluj heslo nebo OKTA kód.")
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input("Zmáčkni Enter pro ukončení...")
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sys.exit(1)
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context.storage_state(path=str(AUTH_FILE))
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print("Session uložena do auth.json")
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def _okta_mfa_present(page):
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if "okta" in page.url.lower():
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return True
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for sel in [
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'input[name="answer"]',
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'input[name*="otp"]',
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'input[name*="code"]',
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'input[placeholder*="code" i]',
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]:
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if page.query_selector(sel):
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return True
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return False
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def _fill_otp(page, otp):
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for sel in [
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'input[name="answer"]',
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'input[name*="otp"]',
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'input[name*="code"]',
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'input[type="tel"]',
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'input[placeholder*="code" i]',
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]:
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el = page.query_selector(sel)
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if el:
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el.fill(otp)
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page.keyboard.press("Enter")
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return
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# Záložní: zkusíme první viditelný text input
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page.keyboard.type(otp)
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page.keyboard.press("Enter")
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# ---------------------------------------------------------------------------
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# Navigace po přihlášení
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# ---------------------------------------------------------------------------
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def go_to_select_role(page):
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"""Přejde na SelectRole stránku a vrátí True pokud jsme tam skutečně."""
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print(f"Navigace na SelectRole...")
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try:
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page.goto(SELECT_ROLE_URL)
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except Exception:
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# Rave dělá server-side redirect (ERR_ABORTED) — zkontrolujeme URL až po načtení
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pass
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wait_load(page, 1500)
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dbg(page, "select-role")
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return "login" not in page.url.lower() and "okta" not in page.url.lower()
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def select_role(page):
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"""Vybere Site Manager a klikne Continue."""
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print("Vybírám roli Site Manager...")
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# Počkáme na select element
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try:
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page.wait_for_selector("select", timeout=10_000)
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except PWTimeout:
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dbg(page, "no-select-found")
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return
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# Najdeme select s option Site Manager
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selects = page.query_selector_all("select")
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found = False
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for sel_el in selects:
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opts = sel_el.query_selector_all("option")
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for opt in opts:
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txt = (opt.inner_text() or "").strip()
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if "site manager" in txt.lower():
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sel_el.select_option(label=txt)
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found = True
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print(f" Vybráno: '{txt}'")
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break
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if found:
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break
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if not found:
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print(" VAROVÁNÍ: Option 'Site Manager' nenalezena, zkouším kliknout na text...")
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try:
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page.get_by_text("Site Manager", exact=False).first.click()
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except Exception as e:
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print(f" {e}")
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# Klikneme Continue
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for btn_sel in [
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'input[value="Continue"]',
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'input[type="submit"]',
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'button:has-text("Continue")',
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'button[type="submit"]',
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]:
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try:
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btn = page.query_selector(btn_sel)
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if btn:
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btn.click()
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break
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except Exception:
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continue
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wait_load(page, 2000)
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dbg(page, "after-role")
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def navigate_to_reporter(page):
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print("Klikám na Reporter...")
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try:
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page.wait_for_selector('a:has-text("Reporter")', timeout=15_000)
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page.click('a:has-text("Reporter")')
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wait_load(page, 1500)
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dbg(page, "reporter")
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except PWTimeout:
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dbg(page, "reporter-not-found")
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raise
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def open_report(page):
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print(f"Klikám na report ID={REPORT_ID} (Data Listing - Data Stream)...")
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selector = f'a[href="PromptsPage.aspx?ReportID={REPORT_ID}"]'
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try:
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page.wait_for_selector(selector, timeout=15_000)
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page.click(selector)
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wait_load(page, 2000)
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dbg(page, "report-opened")
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except PWTimeout:
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dbg(page, "report-not-found")
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raise
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# ---------------------------------------------------------------------------
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# Parametry reportu
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# ---------------------------------------------------------------------------
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def set_study_param(page):
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"""Rozbalí Study panel a vybere 42847922MDD3003."""
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print(f" Parametr Study: {STUDY_NAME}")
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page.click('#PromptsBox_st_ShowHideBtn')
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page.wait_for_timeout(1500)
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# Checkbox index 0 = 42847922MDD3003 (ověřeno dříve)
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page.wait_for_selector('#PromptsBox_st_FrontEndCBList_0', timeout=10_000)
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cb = page.locator('#PromptsBox_st_FrontEndCBList_0')
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if not cb.is_checked():
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cb.check()
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wait_load(page, 3000)
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dbg(page, "after-study")
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def set_site_group_param(page):
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"""Rozbalí Site Group, vybere CZE a zaškrtne Include Sub Site Groups."""
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print(f" Parametr Site Group: {SITE_GROUP}")
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# Rozbalit Site Group panel
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page.click('#PromptsBox_sg_ShowHideBtn')
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page.wait_for_timeout(1500)
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# Vybrat CZE a spustit change event (jinak postback nepřijde)
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page.wait_for_selector('#PromptsBox_sg_List', timeout=10_000)
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page.select_option('#PromptsBox_sg_List', label=SITE_GROUP)
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page.evaluate("document.querySelector('#PromptsBox_sg_List').dispatchEvent(new Event('change', {bubbles:true}))")
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wait_load(page, 2000)
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# Include Sub Site Groups
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print(" Include Sub Site Groups: zapnuto")
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cb = page.locator('#PromptsBox_sg_CheckBox')
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if not cb.is_checked():
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cb.check()
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page.evaluate("document.querySelector('#PromptsBox_sg_CheckBox').dispatchEvent(new Event('change', {bubbles:true}))")
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wait_load(page, 2000)
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# Zavřít panel = potvrzení výběru, spustí postback pro Form
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page.click('#PromptsBox_sg_ShowHideBtn')
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wait_load(page, 3000)
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dbg(page, "after-site-group")
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def set_form_param(page, form_name):
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"""Rozbalí Form panel (pokud je zavřený) a zaškrtne formulář.
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Panel je SingleSelection=1, takže nový výběr automaticky odznačí předchozí."""
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print(f" Parametr Form: {form_name}")
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# Otevřít panel jen pokud je zavřený (kontrola přes style.display)
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is_closed = page.locator('#PromptsBox_fm2_div').evaluate('el => el.style.display') == 'none'
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if is_closed:
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page.click('#PromptsBox_fm2_ShowHideBtn')
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page.wait_for_timeout(2000)
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# Po předchozím stažení je panel v "locked" módu.
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# 1. klik na tužku → vymaže výběr, tlačítko se změní na oko
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# 2. klik na oko → načte seznam všech formulářů
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if page.locator('#PromptsBox_fm2_PageModeBtn').is_visible():
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page.click('#PromptsBox_fm2_PageModeBtn') # tužka → oko
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page.wait_for_timeout(1000)
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page.click('#PromptsBox_fm2_PageModeBtn') # oko → načte formuláře
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page.wait_for_timeout(2000)
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# Vyhledat formulář — klik zajistí focus, Enter spustí ajaxSelectionGridSearchBoxOnKeypress
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search = page.locator('#PromptsBox_fm2_SearchTxt')
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search.wait_for(state='visible', timeout=10_000)
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search.click()
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search.fill(form_name)
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search.press('Enter')
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||||
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# Počkáme až AJAX přepíše DOM se seznamem výsledků
|
||||
cb_locator = page.locator('input[id^="PromptsBox_fm2_FrontEndCBList_"]').first
|
||||
try:
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||||
cb_locator.wait_for(state='visible', timeout=8_000)
|
||||
except PWTimeout:
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print(f" VAROVÁNÍ: '{form_name}' nenalezen nebo timeout!")
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return
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||||
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||||
# SingleSelection=1: klik na nový checkbox automaticky odznačí předchozí
|
||||
# Locator se vyhodnotí čerstvě — žádný stale element handle
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||||
if not cb_locator.is_checked():
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||||
cb_locator.click()
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print(f" '{form_name}' zaškrtnuto")
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||||
wait_load(page, 500)
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||||
|
||||
|
||||
# ---------------------------------------------------------------------------
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||||
# Submit a download
|
||||
# ---------------------------------------------------------------------------
|
||||
|
||||
def submit_and_download(page, context, form_name):
|
||||
print("Odesílám report (čekám na nové okno)...")
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||||
|
||||
with context.expect_page() as new_page_info:
|
||||
page.locator('input[value="Submit Report"], button:has-text("Submit Report")').first.click()
|
||||
|
||||
new_page = new_page_info.value
|
||||
new_page.wait_for_url(lambda url: url != 'about:blank', timeout=30_000)
|
||||
# Čekáme až se zobrazí Download File — stránka nejdřív ukazuje "Loading"
|
||||
print(" Čekám na vygenerování reportu...")
|
||||
new_page.wait_for_selector(
|
||||
'input[value="Download File"], button:has-text("Download File")',
|
||||
timeout=300_000 # až 5 minut pro velké reporty
|
||||
)
|
||||
new_page.wait_for_timeout(500)
|
||||
dbg(new_page, "download-window")
|
||||
|
||||
# Nastavení parametrů stahování
|
||||
print(" Nastavuji parametry stahování...")
|
||||
|
||||
# Separator: čárka (default)
|
||||
sep = new_page.query_selector('input[name*="Separator"], input[name*="separator"]')
|
||||
if sep:
|
||||
sep.fill(',')
|
||||
|
||||
# File type: .csv
|
||||
# Formulář je v iframu — najdeme správný frame
|
||||
target_frame = new_page.main_frame
|
||||
for frame in new_page.frames:
|
||||
if frame.query_selector('select') or frame.query_selector('input[value="Download File"]'):
|
||||
target_frame = frame
|
||||
print(f" Frame nalezen: {frame.url}")
|
||||
break
|
||||
|
||||
# File type: .csv (application/vnd.ms-excel)
|
||||
for sel in target_frame.query_selector_all('select'):
|
||||
for opt in sel.query_selector_all('option'):
|
||||
val = opt.get_attribute('value') or ''
|
||||
txt = opt.inner_text() or ''
|
||||
if 'vnd.ms-excel' in val or 'vnd.ms-excel' in txt:
|
||||
sel.select_option(value=val)
|
||||
print(" File type: .csv (application/vnd.ms-excel)")
|
||||
break
|
||||
|
||||
# Export type: attachment
|
||||
for sel in target_frame.query_selector_all('select'):
|
||||
for opt in sel.query_selector_all('option'):
|
||||
if 'attachment' in (opt.get_attribute('value') or '').lower():
|
||||
sel.select_option(value='attachment')
|
||||
break
|
||||
|
||||
# Save as Unicode: necháme nezaškrtnuté (default)
|
||||
|
||||
timestamp = datetime.now().strftime("%Y-%m-%d_%H-%M")
|
||||
form_slug = form_name.replace(" ", "")
|
||||
filename = f"{timestamp}_EDC_MDD3003_{form_slug}_DataListing.csv"
|
||||
output_path = DOWNLOAD_DIR / filename
|
||||
|
||||
print("Stahuji CSV...")
|
||||
with new_page.expect_download(timeout=60_000) as dl_info:
|
||||
btn = target_frame.query_selector('input[value="Download File"], button:has-text("Download File")')
|
||||
if btn:
|
||||
btn.click()
|
||||
else:
|
||||
new_page.locator('input[value="Download File"], button:has-text("Download File")').first.click()
|
||||
|
||||
download = dl_info.value
|
||||
download.save_as(str(output_path))
|
||||
print(f"\nHotovo! Soubor uložen: {output_path}")
|
||||
|
||||
try:
|
||||
new_page.close()
|
||||
print("Stahovací okno zavřeno.")
|
||||
except Exception:
|
||||
pass
|
||||
|
||||
return output_path
|
||||
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
# Hlavní flow
|
||||
# ---------------------------------------------------------------------------
|
||||
|
||||
def run():
|
||||
if not PASSWORD:
|
||||
print("Chyba: nastav IMEDIDATA_PASSWORD v souboru .env")
|
||||
sys.exit(1)
|
||||
|
||||
DOWNLOAD_DIR.mkdir(exist_ok=True)
|
||||
|
||||
with sync_playwright() as p:
|
||||
browser = p.chromium.launch(headless=False, slow_mo=200)
|
||||
ctx_kwargs = {"accept_downloads": True}
|
||||
|
||||
use_saved = auth_valid()
|
||||
if use_saved:
|
||||
print("Načítám uloženou session (auth.json)...")
|
||||
ctx_kwargs["storage_state"] = str(AUTH_FILE)
|
||||
|
||||
context = browser.new_context(**ctx_kwargs)
|
||||
page = context.new_page()
|
||||
|
||||
# Přejdeme na SelectRole
|
||||
logged_in = go_to_select_role(page)
|
||||
|
||||
if not logged_in:
|
||||
if use_saved:
|
||||
print("Session expirovala, mažu auth.json a přihlašuji znovu...")
|
||||
AUTH_FILE.unlink(missing_ok=True)
|
||||
do_login(page, context)
|
||||
go_to_select_role(page)
|
||||
|
||||
# Krok 4: výběr role → přiřadí session ID
|
||||
select_role(page)
|
||||
|
||||
# Krok 5: Reporter
|
||||
navigate_to_reporter(page)
|
||||
|
||||
# Krok 6: otevření reportu
|
||||
open_report(page)
|
||||
|
||||
# Krok 7: nastavení parametrů (Study a Site Group jednou, Form v smyčce)
|
||||
print("Nastavuji parametry reportu...")
|
||||
set_study_param(page)
|
||||
set_site_group_param(page)
|
||||
|
||||
# Krok 8: smyčka přes formuláře
|
||||
for form_name in FORM_NAMES:
|
||||
print(f"\n=== Stahuji formulář: {form_name} ===")
|
||||
set_form_param(page, form_name)
|
||||
submit_and_download(page, context, form_name)
|
||||
|
||||
browser.close()
|
||||
print("Prohlížeč zavřen.")
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
run()
|
||||
@@ -0,0 +1,440 @@
|
||||
"""
|
||||
download_uco3001.py
|
||||
NAHRAZENO skriptem download_edc_datalistings.py
|
||||
|
||||
Původně: stahování Data Listing reportů (ReportID=92) pro studii UCO3001.
|
||||
"""
|
||||
|
||||
import os
|
||||
import sys
|
||||
from datetime import datetime, timedelta
|
||||
from pathlib import Path
|
||||
from dotenv import load_dotenv
|
||||
from playwright.sync_api import sync_playwright, TimeoutError as PWTimeout
|
||||
import tkinter as tk
|
||||
from tkinter import simpledialog
|
||||
|
||||
load_dotenv(Path(__file__).parent / ".env")
|
||||
|
||||
USERNAME = os.getenv("IMEDIDATA_USERNAME", "vladimir.buzalka")
|
||||
PASSWORD = os.getenv("IMEDIDATA_PASSWORD", "")
|
||||
DOWNLOAD_DIR = Path(__file__).parent / "downloads"
|
||||
AUTH_FILE = Path(__file__).parent / "auth.json"
|
||||
AUTH_MAX_AGE_DAYS = 7
|
||||
|
||||
LOGIN_URL = "https://login.imedidata.com/login"
|
||||
SELECT_ROLE_URL = (
|
||||
"https://jnjja.mdsol.com/MedidataRave/SelectRole.aspx"
|
||||
"?client_division_uuid=e5de55d5-a414-4bd1-9abe-18e96fd5475d"
|
||||
"&study_group_uuid=b0793ca6-33ec-44e8-883b-6fc1a4b671c4"
|
||||
"&studygroup_id=107981"
|
||||
)
|
||||
|
||||
STUDY_SEARCH = "77242113UCO3001" # hledáme podle podřetězce v názvu studie
|
||||
REPORT_ID = 92 # _EDC Std Rpt - Data Listing (Data Stream)
|
||||
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
# Helpers
|
||||
# ---------------------------------------------------------------------------
|
||||
|
||||
def auth_valid():
|
||||
if not AUTH_FILE.exists():
|
||||
return False
|
||||
age = datetime.now() - datetime.fromtimestamp(AUTH_FILE.stat().st_mtime)
|
||||
return age < timedelta(days=AUTH_MAX_AGE_DAYS)
|
||||
|
||||
|
||||
def wait_load(page, extra_ms=1000):
|
||||
try:
|
||||
page.wait_for_load_state("load", timeout=20_000)
|
||||
except PWTimeout:
|
||||
pass
|
||||
page.wait_for_timeout(extra_ms)
|
||||
|
||||
|
||||
def dbg(page, label):
|
||||
print(f"[{label}] URL: {page.url}")
|
||||
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
# Login
|
||||
# ---------------------------------------------------------------------------
|
||||
|
||||
def _ask_otp_popup():
|
||||
root = tk.Tk()
|
||||
root.withdraw()
|
||||
root.lift()
|
||||
root.attributes("-topmost", True)
|
||||
otp = simpledialog.askstring("OKTA MFA", "Zadej OTP kód z OKTA (6 číslic):", parent=root)
|
||||
root.destroy()
|
||||
return (otp or "").strip()
|
||||
|
||||
|
||||
def do_login(page, context):
|
||||
print("Přihlašuji se do iMedidata...")
|
||||
page.goto(LOGIN_URL)
|
||||
wait_load(page, 500)
|
||||
page.wait_for_selector('input[name="session[username]"]', timeout=10_000)
|
||||
page.fill('input[name="session[username]"]', USERNAME)
|
||||
page.fill('input[name="session[password]"]', PASSWORD)
|
||||
page.click('button[type="submit"]')
|
||||
wait_load(page, 2000)
|
||||
dbg(page, "after-signin")
|
||||
|
||||
if _okta_mfa_present(page):
|
||||
print("\n*** OKTA MFA vyžadována! ***")
|
||||
otp = _ask_otp_popup()
|
||||
if not otp:
|
||||
print("CHYBA: OTP nebylo zadáno.")
|
||||
sys.exit(1)
|
||||
_fill_otp(page, otp)
|
||||
wait_load(page, 3000)
|
||||
|
||||
try:
|
||||
page.wait_for_url("**/home.imedidata.com**", timeout=30_000)
|
||||
except PWTimeout:
|
||||
dbg(page, "wait-home-timeout")
|
||||
|
||||
if "home.imedidata.com" not in page.url:
|
||||
print("CHYBA: Přihlášení se nezdařilo!")
|
||||
sys.exit(1)
|
||||
|
||||
context.storage_state(path=str(AUTH_FILE))
|
||||
print("Session uložena do auth.json")
|
||||
|
||||
|
||||
def _okta_mfa_present(page):
|
||||
if "okta" in page.url.lower():
|
||||
return True
|
||||
for sel in ['input[name="answer"]', 'input[name*="otp"]',
|
||||
'input[name*="code"]', 'input[placeholder*="code" i]']:
|
||||
if page.query_selector(sel):
|
||||
return True
|
||||
return False
|
||||
|
||||
|
||||
def _fill_otp(page, otp):
|
||||
for sel in ['input[name="answer"]', 'input[name*="otp"]',
|
||||
'input[name*="code"]', 'input[type="tel"]', 'input[placeholder*="code" i]']:
|
||||
el = page.query_selector(sel)
|
||||
if el:
|
||||
el.fill(otp)
|
||||
page.keyboard.press("Enter")
|
||||
return
|
||||
page.keyboard.type(otp)
|
||||
page.keyboard.press("Enter")
|
||||
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
# Navigace
|
||||
# ---------------------------------------------------------------------------
|
||||
|
||||
def go_to_select_role(page):
|
||||
print("Navigace na SelectRole...")
|
||||
try:
|
||||
page.goto(SELECT_ROLE_URL)
|
||||
except Exception:
|
||||
pass
|
||||
wait_load(page, 1500)
|
||||
dbg(page, "select-role")
|
||||
return "login" not in page.url.lower() and "okta" not in page.url.lower()
|
||||
|
||||
|
||||
def select_role(page):
|
||||
print("Vybírám roli Site Manager...")
|
||||
try:
|
||||
page.wait_for_selector("select", timeout=10_000)
|
||||
except PWTimeout:
|
||||
return
|
||||
|
||||
for sel_el in page.query_selector_all("select"):
|
||||
for opt in sel_el.query_selector_all("option"):
|
||||
txt = (opt.inner_text() or "").strip()
|
||||
if "site manager" in txt.lower():
|
||||
sel_el.select_option(label=txt)
|
||||
print(f" Vybráno: '{txt}'")
|
||||
break
|
||||
|
||||
for btn_sel in ['input[value="Continue"]', 'input[type="submit"]',
|
||||
'button:has-text("Continue")', 'button[type="submit"]']:
|
||||
btn = page.query_selector(btn_sel)
|
||||
if btn:
|
||||
btn.click()
|
||||
break
|
||||
|
||||
wait_load(page, 2000)
|
||||
dbg(page, "after-role")
|
||||
|
||||
|
||||
def navigate_to_reporter(page):
|
||||
print("Klikám na Reporter...")
|
||||
page.wait_for_selector('a:has-text("Reporter")', timeout=15_000)
|
||||
page.click('a:has-text("Reporter")')
|
||||
wait_load(page, 1500)
|
||||
dbg(page, "reporter")
|
||||
|
||||
|
||||
def open_report(page):
|
||||
print(f"Otevírám report ID={REPORT_ID} (Data Listing - Data Stream)...")
|
||||
selector = f'a[href="PromptsPage.aspx?ReportID={REPORT_ID}"]'
|
||||
page.wait_for_selector(selector, timeout=15_000)
|
||||
page.click(selector)
|
||||
wait_load(page, 2000)
|
||||
dbg(page, "report-opened")
|
||||
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
# Parametry reportu
|
||||
# ---------------------------------------------------------------------------
|
||||
|
||||
def set_study_param(page):
|
||||
"""Rozbalí Study panel a vybere studii podle podřetězce STUDY_SEARCH."""
|
||||
print(f" Parametr Study: hledám '{STUDY_SEARCH}'...")
|
||||
|
||||
page.click('#PromptsBox_st_ShowHideBtn')
|
||||
page.wait_for_timeout(1500)
|
||||
|
||||
# Projdeme checkboxy a hledáme label obsahující STUDY_SEARCH
|
||||
page.wait_for_selector('input[id^="PromptsBox_st_FrontEndCBList_"]', timeout=10_000)
|
||||
checkboxes = page.query_selector_all('input[id^="PromptsBox_st_FrontEndCBList_"]')
|
||||
|
||||
found = False
|
||||
for cb in checkboxes:
|
||||
cb_id = cb.get_attribute("id")
|
||||
# Label je ve stejné <td> nebo sousední — hledáme přes JS innerText rodiče
|
||||
label_text = page.evaluate(
|
||||
"""id => {
|
||||
const el = document.getElementById(id);
|
||||
if (!el) return '';
|
||||
const row = el.closest('tr') || el.closest('td') || el.parentElement;
|
||||
return row ? row.innerText : '';
|
||||
}""",
|
||||
cb_id
|
||||
)
|
||||
print(f" [{cb_id}] label: {label_text.strip()[:80]}")
|
||||
if STUDY_SEARCH.upper() in label_text.upper():
|
||||
if not page.locator(f"#{cb_id}").is_checked():
|
||||
page.locator(f"#{cb_id}").check()
|
||||
print(f" Nalezeno a zaškrtnuto: '{label_text.strip()}'")
|
||||
found = True
|
||||
break
|
||||
|
||||
if not found:
|
||||
# Záloha: zkusíme index 0 a varujeme
|
||||
print(f" VAROVÁNÍ: Studie '{STUDY_SEARCH}' nenalezena! Zkouším index 0...")
|
||||
cb0 = page.locator('#PromptsBox_st_FrontEndCBList_0')
|
||||
if not cb0.is_checked():
|
||||
cb0.check()
|
||||
|
||||
wait_load(page, 3000)
|
||||
dbg(page, "after-study")
|
||||
|
||||
|
||||
def set_site_group_param(page, country: str):
|
||||
"""Rozbalí Site Group, vybere zadanou zemi a zaškrtne Include Sub Site Groups."""
|
||||
print(f" Parametr Site Group: {country}")
|
||||
|
||||
page.click('#PromptsBox_sg_ShowHideBtn')
|
||||
page.wait_for_timeout(1500)
|
||||
|
||||
page.wait_for_selector('#PromptsBox_sg_List', timeout=10_000)
|
||||
page.select_option('#PromptsBox_sg_List', label=country)
|
||||
page.evaluate(
|
||||
"document.querySelector('#PromptsBox_sg_List').dispatchEvent(new Event('change', {bubbles:true}))"
|
||||
)
|
||||
wait_load(page, 2000)
|
||||
|
||||
cb = page.locator('#PromptsBox_sg_CheckBox')
|
||||
if not cb.is_checked():
|
||||
cb.check()
|
||||
page.evaluate(
|
||||
"document.querySelector('#PromptsBox_sg_CheckBox').dispatchEvent(new Event('change', {bubbles:true}))"
|
||||
)
|
||||
wait_load(page, 2000)
|
||||
|
||||
# Zavřít panel = potvrzení → spustí postback pro Form
|
||||
page.click('#PromptsBox_sg_ShowHideBtn')
|
||||
wait_load(page, 3000)
|
||||
dbg(page, "after-site-group")
|
||||
|
||||
|
||||
def set_form_param(page, form_name: str):
|
||||
"""Vybere formulář v Form panelu."""
|
||||
print(f" Parametr Form: {form_name}")
|
||||
|
||||
is_closed = page.locator('#PromptsBox_fm2_div').evaluate('el => el.style.display') == 'none'
|
||||
if is_closed:
|
||||
page.click('#PromptsBox_fm2_ShowHideBtn')
|
||||
page.wait_for_timeout(2000)
|
||||
|
||||
if page.locator('#PromptsBox_fm2_PageModeBtn').is_visible():
|
||||
page.click('#PromptsBox_fm2_PageModeBtn')
|
||||
page.wait_for_timeout(1000)
|
||||
page.click('#PromptsBox_fm2_PageModeBtn')
|
||||
page.wait_for_timeout(2000)
|
||||
|
||||
search = page.locator('#PromptsBox_fm2_SearchTxt')
|
||||
search.wait_for(state='visible', timeout=10_000)
|
||||
search.click()
|
||||
search.fill(form_name)
|
||||
page.wait_for_timeout(2000)
|
||||
search.press('Enter')
|
||||
page.wait_for_timeout(2000)
|
||||
|
||||
cb_locator = page.locator('input[id^="PromptsBox_fm2_FrontEndCBList_"]').first
|
||||
try:
|
||||
cb_locator.wait_for(state='visible', timeout=8_000)
|
||||
except PWTimeout:
|
||||
print(f" VAROVÁNÍ: '{form_name}' nenalezen!")
|
||||
return
|
||||
|
||||
if not cb_locator.is_checked():
|
||||
cb_locator.click()
|
||||
print(f" '{form_name}' zaškrtnuto")
|
||||
page.wait_for_timeout(2000)
|
||||
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
# Submit a download
|
||||
# ---------------------------------------------------------------------------
|
||||
|
||||
def submit_and_download(page, context, form_name: str, country: str | None):
|
||||
print("Odesílám report...")
|
||||
|
||||
with context.expect_page() as new_page_info:
|
||||
page.locator('input[value="Submit Report"], button:has-text("Submit Report")').first.click()
|
||||
|
||||
new_page = new_page_info.value
|
||||
new_page.wait_for_url(lambda url: url != 'about:blank', timeout=30_000)
|
||||
|
||||
print(" Čekám na vygenerování reportu (max 5 min)...")
|
||||
new_page.wait_for_selector(
|
||||
'input[value="Download File"], button:has-text("Download File")',
|
||||
timeout=300_000
|
||||
)
|
||||
new_page.wait_for_timeout(500)
|
||||
dbg(new_page, "download-window")
|
||||
|
||||
# Najdeme správný frame
|
||||
target_frame = new_page.main_frame
|
||||
for frame in new_page.frames:
|
||||
if frame.query_selector('select') or frame.query_selector('input[value="Download File"]'):
|
||||
target_frame = frame
|
||||
break
|
||||
|
||||
# File type: .csv (application/vnd.ms-excel)
|
||||
for sel in target_frame.query_selector_all('select'):
|
||||
for opt in sel.query_selector_all('option'):
|
||||
val = opt.get_attribute('value') or ''
|
||||
if 'vnd.ms-excel' in val:
|
||||
sel.select_option(value=val)
|
||||
print(" File type: .csv (application/vnd.ms-excel)")
|
||||
break
|
||||
|
||||
# Export type: attachment
|
||||
for sel in target_frame.query_selector_all('select'):
|
||||
for opt in sel.query_selector_all('option'):
|
||||
if 'attachment' in (opt.get_attribute('value') or '').lower():
|
||||
sel.select_option(value='attachment')
|
||||
break
|
||||
|
||||
timestamp = datetime.now().strftime("%Y-%m-%d_%H-%M")
|
||||
country_slug = country if country else "ALL"
|
||||
form_slug = form_name.replace(" ", "").replace("/", "-").replace("(", "").replace(")", "")
|
||||
filename = f"{timestamp}_EDC_UCO3001_{country_slug}_{form_slug}_DataListing.csv"
|
||||
output_path = DOWNLOAD_DIR / filename
|
||||
|
||||
print("Stahuji CSV...")
|
||||
with new_page.expect_download(timeout=60_000) as dl_info:
|
||||
btn = target_frame.query_selector('input[value="Download File"], button:has-text("Download File")')
|
||||
if btn:
|
||||
btn.click()
|
||||
else:
|
||||
new_page.locator('input[value="Download File"], button:has-text("Download File")').first.click()
|
||||
|
||||
dl_info.value.save_as(str(output_path))
|
||||
print(f"\nHotovo! Soubor uložen: {output_path}")
|
||||
|
||||
try:
|
||||
new_page.close()
|
||||
except Exception:
|
||||
pass
|
||||
|
||||
return output_path
|
||||
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
# Hlavní funkce
|
||||
# ---------------------------------------------------------------------------
|
||||
|
||||
def download_datalisting_reports_3001(form_name: str, country: str | None = None):
|
||||
"""
|
||||
Stáhne Data Listing report pro studii UCO3001.
|
||||
|
||||
Args:
|
||||
form_name: Název formuláře, např. "Trial Disposition (Completion / Discontinuation)"
|
||||
country: Kód site group, např. "CZE". Pokud None, filtr země se nenastaví (všechny).
|
||||
"""
|
||||
if not PASSWORD:
|
||||
print("Chyba: nastav IMEDIDATA_PASSWORD v souboru .env")
|
||||
sys.exit(1)
|
||||
|
||||
DOWNLOAD_DIR.mkdir(exist_ok=True)
|
||||
|
||||
with sync_playwright() as p:
|
||||
browser = p.chromium.launch(headless=False, slow_mo=200)
|
||||
ctx_kwargs = {"accept_downloads": True}
|
||||
|
||||
use_saved = auth_valid()
|
||||
if use_saved:
|
||||
print("Načítám uloženou session (auth.json)...")
|
||||
ctx_kwargs["storage_state"] = str(AUTH_FILE)
|
||||
|
||||
context = browser.new_context(**ctx_kwargs)
|
||||
page = context.new_page()
|
||||
|
||||
logged_in = go_to_select_role(page)
|
||||
|
||||
if not logged_in:
|
||||
if use_saved:
|
||||
print("Session expirovala, přihlašuji znovu...")
|
||||
AUTH_FILE.unlink(missing_ok=True)
|
||||
do_login(page, context)
|
||||
go_to_select_role(page)
|
||||
|
||||
select_role(page)
|
||||
navigate_to_reporter(page)
|
||||
open_report(page)
|
||||
|
||||
print("\nNastavuji parametry reportu...")
|
||||
set_study_param(page)
|
||||
|
||||
if country:
|
||||
set_site_group_param(page, country)
|
||||
else:
|
||||
print(" Parametr Site Group: přeskočen (všechny země)")
|
||||
|
||||
print(f"\n=== Stahuji formulář: {form_name} ===")
|
||||
set_form_param(page, form_name)
|
||||
output = submit_and_download(page, context, form_name, country)
|
||||
|
||||
browser.close()
|
||||
print("Prohlížeč zavřen.")
|
||||
return output
|
||||
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
# CLI
|
||||
# ---------------------------------------------------------------------------
|
||||
|
||||
if __name__ == "__main__":
|
||||
# Příklady spuštění:
|
||||
# python download_uco3001.py
|
||||
# python download_uco3001.py CZE
|
||||
|
||||
country_arg = sys.argv[1] if len(sys.argv) > 1 else None
|
||||
download_datalisting_reports_3001(
|
||||
form_name="Trial Disposition (Completion / Discontinuation)",
|
||||
country=country_arg,
|
||||
)
|
||||
@@ -0,0 +1,451 @@
|
||||
"""
|
||||
Import EDC CSV reportů do MongoDB.
|
||||
|
||||
Použití:
|
||||
python edc_import.py report.csv
|
||||
python edc_import.py reports/*.csv
|
||||
python edc_import.py report.csv --host mongodb://192.168.1.100:27017 --db klinicka_studie
|
||||
"""
|
||||
|
||||
import argparse
|
||||
import csv
|
||||
import glob
|
||||
import logging
|
||||
import os
|
||||
import re
|
||||
import sys
|
||||
from datetime import datetime, timezone
|
||||
from pathlib import Path
|
||||
|
||||
from pymongo import MongoClient, ASCENDING
|
||||
from pymongo.errors import PyMongoError
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
# Logging
|
||||
# ---------------------------------------------------------------------------
|
||||
logging.basicConfig(
|
||||
level=logging.INFO,
|
||||
format="%(asctime)s %(levelname)s %(message)s",
|
||||
handlers=[
|
||||
logging.FileHandler("edc_import.log", encoding="utf-8"),
|
||||
logging.StreamHandler(open(sys.stdout.fileno(), mode="w", encoding="utf-8", closefd=False)),
|
||||
],
|
||||
)
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
# Mapování pevných CSV sloupců na MongoDB cesty
|
||||
# ---------------------------------------------------------------------------
|
||||
FIXED_FIELDS = {
|
||||
"StudyName": "study",
|
||||
"SiteGroupName": "site.group",
|
||||
"SiteID": "site.id",
|
||||
"SiteNumber": "site.number",
|
||||
"Site": "site.name",
|
||||
"SubjectID": "subject.id",
|
||||
"Subject": "subject.label",
|
||||
"CRFVersionID": "form.crfVersionId",
|
||||
"InstanceID": "form.instanceId",
|
||||
"InstanceName": "form.instanceName",
|
||||
"FolderSeq": "form.folderSeq",
|
||||
"Page": "form.page",
|
||||
"RecordID": "form.recordId",
|
||||
"RecordPosition": "form.recordPosition",
|
||||
"LastModifiedDate": "lastModified",
|
||||
"PrintDateTime": "importedAt",
|
||||
}
|
||||
|
||||
# Sloupce, které jdou do _meta (ostatní administrativní)
|
||||
META_FIELDS = {"RunUser", "VersionNumber", "FilterField"}
|
||||
|
||||
# Pole, která se převedou na int
|
||||
INT_FIELDS = {"Elapsed days"}
|
||||
|
||||
# Formáty datumů, které zkusíme parsovat
|
||||
DATE_FORMATS = [
|
||||
"%d %b %Y %H:%M:%S", # 20 MAY 2026 12:06:18
|
||||
"%d %b %Y %H:%M:%S:%f", # 10 Aug 2025 18:13:22:080 (EDC query dates)
|
||||
"%Y%m%d %H:%M:%S.%f", # 20250810 18:13:22.080 (sortable query dates)
|
||||
"%Y-%m-%d %H:%M:%S", # 2026-05-20 12:06:28
|
||||
"%Y-%m-%dT%H:%M:%S",
|
||||
"%Y-%m-%dT%H:%M:%S.%fZ",
|
||||
"%d/%m/%Y %H:%M:%S",
|
||||
"%m/%d/%Y %H:%M:%S",
|
||||
"%m/%d/%Y %I:%M:%S %p", # 5/20/2026 1:23:27 PM
|
||||
]
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
# QueryDetails — detekce a mapování
|
||||
# ---------------------------------------------------------------------------
|
||||
QUERY_DETAIL_MARKER = "QueryID(ReQry)"
|
||||
|
||||
QUERY_META_FIELDS = {
|
||||
"StudyParameter", "SiteGroupParameter", "SiteNumberParameter", "SiteParameter",
|
||||
"SubjectParameter", "SubjectStatusParameter", "FolderParameter", "FormParameter",
|
||||
"FieldParameter", "MarkingGroupParameter", "QueryStatusParameter",
|
||||
"IncludeInactivePagesParameter", "PageSDVParameter", "PageFrozenParameter",
|
||||
"PageLockedParameter", "StartDateParameter", "EndDateParameter",
|
||||
"MilestoneParameter", "ReportTypeParameter", "VersionNumber", "TimeZone",
|
||||
"RunUser", "ErrorString",
|
||||
# Sortable dates — redundantní, parsujeme z hlavních sloupců
|
||||
"OpenedDateSrtble", "AnsweredDateSrtble", "ClosedDateSrtble",
|
||||
# Agregátní počty — jdou do meta
|
||||
"VisitSiteLevel", "VisitCountryLevel", "VisitStudyLevel",
|
||||
"PageSubjectLevel", "PageSiteLevel", "PageCountryLevel", "PageStudyLevel",
|
||||
"Queries (Op/Ans/SDV)",
|
||||
}
|
||||
|
||||
|
||||
def is_query_details(fieldnames: list[str]) -> bool:
|
||||
return QUERY_DETAIL_MARKER in fieldnames
|
||||
|
||||
|
||||
def map_query_row(row: dict, source_file: str) -> dict:
|
||||
"""Přemapuje řádek QueryDetails reportu na MongoDB dokument."""
|
||||
|
||||
def val(col: str) -> str:
|
||||
return (row.get(col) or "").strip()
|
||||
|
||||
def int_or_none(col: str):
|
||||
v = val(col)
|
||||
if v == "":
|
||||
return None
|
||||
try:
|
||||
return int(v)
|
||||
except ValueError:
|
||||
return v
|
||||
|
||||
def date_or_str(col: str):
|
||||
v = val(col)
|
||||
if not v:
|
||||
return None
|
||||
parsed = parse_date(v)
|
||||
return parsed if parsed else v
|
||||
|
||||
meta = {k: row[k].strip() for k in QUERY_META_FIELDS if row.get(k, "").strip()}
|
||||
|
||||
doc = {
|
||||
"study": val("StudyParameter"),
|
||||
"site": {
|
||||
"group": val("Country/Region"),
|
||||
"number": val("Site Number"),
|
||||
"name": val("Sites"),
|
||||
},
|
||||
"subject": {
|
||||
"label": val("Subjects"),
|
||||
"status": val("Subject Status"),
|
||||
},
|
||||
"visit": val("Visits"),
|
||||
"page": val("Pages"),
|
||||
"recordPosition": int_or_none("RecordPosition"),
|
||||
"field": val("Field"),
|
||||
"queryGroup": val("Query Group"),
|
||||
"queryId": val(QUERY_DETAIL_MARKER),
|
||||
"queryStatus": val("QueryStatus"),
|
||||
"openedBy": val("Opened By"),
|
||||
"openedDate": date_or_str("Opened Date"),
|
||||
"answeredBy": val("Answered By") or None,
|
||||
"answeredDate": date_or_str("Answered Date"),
|
||||
"closedBy": val("Closed By") or None,
|
||||
"closedDate": date_or_str("Closed Date"),
|
||||
"daysNotYetClosed": int_or_none("DaysNotYetClosed"),
|
||||
"daysToAnswer": int_or_none("Days to Answer"),
|
||||
"daysToClose": int_or_none("Days to Close"),
|
||||
"queryText": val("QueryText"),
|
||||
"answerText": val("Answer Text (if any)") or None,
|
||||
"importedAt": date_or_str("PrintDateTime"),
|
||||
"sourceFile": source_file,
|
||||
"_meta": meta,
|
||||
}
|
||||
|
||||
# Odstraň None hodnoty z top-level (ne z nested)
|
||||
return {k: v for k, v in doc.items() if v is not None or k in ("queryId",)}
|
||||
|
||||
|
||||
def ensure_query_indexes(collection) -> None:
|
||||
collection.create_index([("queryId", ASCENDING)], unique=True, sparse=True)
|
||||
collection.create_index([("subject.label", ASCENDING)])
|
||||
collection.create_index([("site.number", ASCENDING)])
|
||||
collection.create_index([("queryStatus", ASCENDING)])
|
||||
collection.create_index([("openedDate", ASCENDING)])
|
||||
|
||||
|
||||
def ensure_snapshot_indexes(collection) -> None:
|
||||
"""Indexy pro queries_snapshots — unikátní kombinace queryId + snapshotDate."""
|
||||
collection.create_index(
|
||||
[("queryId", ASCENDING), ("snapshotDate", ASCENDING)],
|
||||
unique=True,
|
||||
)
|
||||
collection.create_index([("snapshotDate", ASCENDING)])
|
||||
collection.create_index([("queryStatus", ASCENDING)])
|
||||
collection.create_index([("site.number", ASCENDING)])
|
||||
collection.create_index([("subject.label", ASCENDING)])
|
||||
|
||||
|
||||
def extract_snapshot_date(filename: str) -> str:
|
||||
"""
|
||||
Vytáhne datum ze jména souboru.
|
||||
'2026-05-20_15-23_EDC_MDD3003_QueryDetails.csv' → '2026-05-20'
|
||||
Fallback: dnešní datum.
|
||||
"""
|
||||
stem = Path(filename).name
|
||||
match = re.match(r"(\d{4}-\d{2}-\d{2})", stem)
|
||||
if match:
|
||||
return match.group(1)
|
||||
return datetime.now(timezone.utc).strftime("%Y-%m-%d")
|
||||
|
||||
|
||||
def parse_date(value: str) -> str | None:
|
||||
"""Pokusí se převést string na ISO 8601; jinak vrátí None."""
|
||||
value = value.strip()
|
||||
for fmt in DATE_FORMATS:
|
||||
try:
|
||||
dt = datetime.strptime(value, fmt)
|
||||
return dt.replace(tzinfo=timezone.utc).isoformat()
|
||||
except ValueError:
|
||||
continue
|
||||
return None
|
||||
|
||||
|
||||
def set_nested(doc: dict, path: str, value: str) -> None:
|
||||
"""Nastaví hodnotu v nested dict podle tečkové cesty, např. 'site.id'."""
|
||||
parts = path.split(".")
|
||||
for part in parts[:-1]:
|
||||
doc = doc.setdefault(part, {})
|
||||
doc[parts[-1]] = value
|
||||
|
||||
|
||||
def collection_name_from_filename(filename: str) -> str:
|
||||
"""
|
||||
Odvodí název kolekce z názvu souboru.
|
||||
'2026-05-20_15-09_EDC_MDD3003_InterimInvestigatorSignature_DataListing.csv' → 'MDD3003_InterimInvestigatorSignature'
|
||||
'2026-05-20_15-23_EDC_MDD3003_QueryDetails.csv' → 'MDD3003_QueryDetails'
|
||||
"""
|
||||
stem = Path(filename).stem
|
||||
# Se suffixem _DataListing
|
||||
match = re.search(r"EDC_(.+?)_DataListing", stem, re.IGNORECASE)
|
||||
if match:
|
||||
return match.group(1)
|
||||
# Bez suffixu _DataListing (např. QueryDetails)
|
||||
match = re.search(r"EDC_(.+)$", stem, re.IGNORECASE)
|
||||
if match:
|
||||
return match.group(1)
|
||||
return stem
|
||||
|
||||
|
||||
def map_row(row: dict, source_file: str) -> dict:
|
||||
"""Přemapuje jeden CSV řádek na MongoDB dokument."""
|
||||
doc: dict = {}
|
||||
meta: dict = {}
|
||||
fields: dict = {}
|
||||
|
||||
# Zjisti všechny klíče pro FieldNValue/FieldNLabel
|
||||
field_keys = set(row.keys())
|
||||
|
||||
for col, value in row.items():
|
||||
value = value.strip() if value else ""
|
||||
|
||||
# Pevná pole
|
||||
if col in FIXED_FIELDS:
|
||||
path = FIXED_FIELDS[col]
|
||||
|
||||
if path == "form.folderSeq":
|
||||
try:
|
||||
value = int(value)
|
||||
except (ValueError, TypeError):
|
||||
pass
|
||||
elif path == "form.recordPosition":
|
||||
try:
|
||||
value = int(value)
|
||||
except (ValueError, TypeError):
|
||||
pass
|
||||
elif path in ("lastModified", "importedAt"):
|
||||
parsed = parse_date(value)
|
||||
value = parsed if parsed else value
|
||||
|
||||
set_nested(doc, path, value)
|
||||
continue
|
||||
|
||||
# Meta pole
|
||||
if col in META_FIELDS:
|
||||
if value:
|
||||
meta[col] = value
|
||||
continue
|
||||
|
||||
# FieldNLabel / FieldNValue jsou zpracovány níže
|
||||
if re.match(r"^Field\d+(Value|Label)$", col):
|
||||
continue
|
||||
|
||||
# Zbývající neznámé pevné sloupce také do meta
|
||||
if not re.match(r"^Field\d+", col):
|
||||
if value:
|
||||
meta[col] = value
|
||||
|
||||
# Zpracuj páry Field1Value/Field1Label ... Field300Value/Field300Label
|
||||
n = 1
|
||||
while True:
|
||||
val_key = f"Field{n}Value"
|
||||
lbl_key = f"Field{n}Label"
|
||||
if val_key not in field_keys and lbl_key not in field_keys:
|
||||
break
|
||||
label = (row.get(lbl_key) or "").strip()
|
||||
value = (row.get(val_key) or "").strip()
|
||||
if label and value:
|
||||
# Pokus o převod čísel
|
||||
if label in INT_FIELDS:
|
||||
try:
|
||||
fields[label] = int(value)
|
||||
except ValueError:
|
||||
fields[label] = value
|
||||
else:
|
||||
# Pokus o datum
|
||||
parsed = parse_date(value)
|
||||
fields[label] = parsed if parsed else value
|
||||
n += 1
|
||||
|
||||
doc["fields"] = fields
|
||||
doc["sourceFile"] = source_file
|
||||
if meta:
|
||||
doc["_meta"] = meta
|
||||
|
||||
return doc
|
||||
|
||||
|
||||
def ensure_indexes(collection) -> None:
|
||||
collection.create_index([("form.recordId", ASCENDING)], unique=True, sparse=True)
|
||||
collection.create_index([("subject.id", ASCENDING)])
|
||||
collection.create_index([("site.id", ASCENDING)])
|
||||
collection.create_index([("study", ASCENDING)])
|
||||
collection.create_index([("lastModified", ASCENDING)])
|
||||
|
||||
|
||||
def import_file(
|
||||
csv_path: str,
|
||||
collection,
|
||||
snapshot_col=None,
|
||||
snapshot_date: str | None = None,
|
||||
) -> tuple[int, int, int]:
|
||||
"""
|
||||
Importuje jeden CSV soubor. Vrátí (inserted, updated, errors).
|
||||
snapshot_col: pokud je zadán, pro QueryDetails se zapíše i daily snapshot.
|
||||
"""
|
||||
inserted = updated = errors = 0
|
||||
source_file = Path(csv_path).name
|
||||
|
||||
with open(csv_path, encoding="utf-8", newline="") as f:
|
||||
reader = csv.DictReader(f, delimiter=",", quotechar='"')
|
||||
query_mode = is_query_details(reader.fieldnames or [])
|
||||
|
||||
for line_no, row in enumerate(reader, start=2):
|
||||
try:
|
||||
if query_mode:
|
||||
doc = map_query_row(row, source_file)
|
||||
upsert_key = {"queryId": doc["queryId"]}
|
||||
|
||||
# Snapshot — upsert na (queryId, snapshotDate)
|
||||
if snapshot_col is not None and snapshot_date:
|
||||
snap_doc = {**doc, "snapshotDate": snapshot_date}
|
||||
snapshot_col.update_one(
|
||||
{"queryId": doc["queryId"], "snapshotDate": snapshot_date},
|
||||
{"$set": snap_doc},
|
||||
upsert=True,
|
||||
)
|
||||
else:
|
||||
doc = map_row(row, source_file)
|
||||
record_id = doc.get("form", {}).get("recordId")
|
||||
upsert_key = {"form.recordId": record_id} if record_id else None
|
||||
|
||||
if upsert_key:
|
||||
result = collection.update_one(
|
||||
upsert_key,
|
||||
{"$set": doc},
|
||||
upsert=True,
|
||||
)
|
||||
if result.upserted_id:
|
||||
inserted += 1
|
||||
else:
|
||||
updated += 1
|
||||
else:
|
||||
collection.insert_one(doc)
|
||||
inserted += 1
|
||||
|
||||
except PyMongoError as e:
|
||||
errors += 1
|
||||
log.error("Řádek %d v %s: MongoDB chyba: %s", line_no, csv_path, e)
|
||||
except Exception as e:
|
||||
errors += 1
|
||||
log.error("Řádek %d v %s: %s", line_no, csv_path, e)
|
||||
|
||||
return inserted, updated, errors
|
||||
|
||||
|
||||
def main() -> None:
|
||||
parser = argparse.ArgumentParser(description="Import EDC CSV reportů do MongoDB")
|
||||
parser.add_argument("files", nargs="+", help="CSV soubory nebo glob vzor")
|
||||
parser.add_argument("--host", default="mongodb://192.168.1.76:27017", help="MongoDB URI")
|
||||
parser.add_argument("--db", default="edc", help="Název databáze")
|
||||
args = parser.parse_args()
|
||||
|
||||
# Rozbal glob vzory (důležité na Windows kde shell sám neglobuje)
|
||||
paths: list[str] = []
|
||||
for pattern in args.files:
|
||||
expanded = glob.glob(pattern)
|
||||
paths.extend(expanded if expanded else [pattern])
|
||||
|
||||
if not paths:
|
||||
log.error("Žádné soubory nenalezeny.")
|
||||
sys.exit(1)
|
||||
|
||||
client = MongoClient(args.host, serverSelectionTimeoutMS=5000)
|
||||
try:
|
||||
client.admin.command("ping")
|
||||
except Exception as e:
|
||||
log.error("Nelze se připojit k MongoDB (%s): %s", args.host, e)
|
||||
sys.exit(1)
|
||||
|
||||
db = client[args.db]
|
||||
|
||||
total_inserted = total_updated = total_errors = 0
|
||||
|
||||
for csv_path in paths:
|
||||
if not os.path.isfile(csv_path):
|
||||
log.warning("Soubor neexistuje, přeskakuji: %s", csv_path)
|
||||
continue
|
||||
|
||||
# Detekuj typ souboru a vyber kolekci + indexy
|
||||
with open(csv_path, encoding="utf-8", newline="") as f:
|
||||
fieldnames = csv.DictReader(f).fieldnames or []
|
||||
if is_query_details(fieldnames):
|
||||
col_name = "queries"
|
||||
collection = db[col_name]
|
||||
ensure_query_indexes(collection)
|
||||
snapshot_col = db["queries_snapshots"]
|
||||
ensure_snapshot_indexes(snapshot_col)
|
||||
snapshot_date = extract_snapshot_date(csv_path)
|
||||
log.info("Importuji: %s → %s.%s + queries_snapshots [%s]",
|
||||
csv_path, args.db, col_name, snapshot_date)
|
||||
else:
|
||||
col_name = collection_name_from_filename(csv_path)
|
||||
collection = db[col_name]
|
||||
ensure_indexes(collection)
|
||||
snapshot_col = None
|
||||
snapshot_date = None
|
||||
log.info("Importuji: %s → %s.%s", csv_path, args.db, col_name)
|
||||
|
||||
inserted, updated, errors = import_file(
|
||||
csv_path, collection, snapshot_col, snapshot_date
|
||||
)
|
||||
total_inserted += inserted
|
||||
total_updated += updated
|
||||
total_errors += errors
|
||||
log.info(" nové: %d aktualizované: %d chyby: %d", inserted, updated, errors)
|
||||
|
||||
log.info("=" * 60)
|
||||
log.info("Celkem — nové: %d aktualizované: %d chyby: %d",
|
||||
total_inserted, total_updated, total_errors)
|
||||
|
||||
client.close()
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
main()
|
||||
Reference in New Issue
Block a user