400 lines
15 KiB
Python
400 lines
15 KiB
Python
# =============================================================================
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# Název: download_lab_reports_v1.1.py
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# Verze: 1.1
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# Datum: 2026-06-16
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# Popis: Stahuje PDF Lab Reports ze xsp.labcorp.com pro studii 77242113UCO3001
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# (interni cislo 36940), filtrovane na 10 ceskych center (CZ),
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# a uklada je PRIMO do MongoDB (db covance, kolekce labreports) —
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# metadata z tabulky + skutecne PDF (inline Binary). Na disk NEUKLADA.
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#
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# Princip stahovani stejny jako download_test_results: Playwright +
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# perzistentni profil, jednorazovy login, klik na "English" ve sloupci
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# Download. PDF bajty se ctou z Playwright temp souboru (download.path()),
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# save_as se nevola -> nic netrvale neni na disku.
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#
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# INKREMENTALNE (stop-at-known): list je Posted DESC (nejnovejsi nahore).
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# Skript jde shora dolu; u kazdeho radku nejdriv precte metadata a
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# spocita record_id. Jakmile narazi na uz ulozeny report, KONCI
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# (vse pod nim je starsi a uz v Mongo je). Korekce vysledku = stejny
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# report znovu vystaveny s NOVYM Posted => novy record_id => stahne se
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# jako novy, puvodni zustava.
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#
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# record_id = "{site}|{subject}|{accession}|{visit}|{posted}"
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# (Posted vc. casu odlisuje reissue).
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#
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# Prepinace:
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# --full projit vsechny radky (bez predcasneho konce); upsertne
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# chybejici / zmenene (rekonciliace).
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# --dry-run nestahuje ani nepise do DB; jen vypise NOVE reporty.
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# --limit N zpracovat max N radku (test).
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# =============================================================================
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from playwright.sync_api import sync_playwright
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from datetime import datetime
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from pymongo import MongoClient, ASCENDING
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from bson.binary import Binary
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import argparse
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import hashlib
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import json
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import os
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import re
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import traceback
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import urllib.parse
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# --- argumenty --------------------------------------------------------------
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parser = argparse.ArgumentParser(description="Stahovani Lab Reports PDF (XSP) do MongoDB.")
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parser.add_argument("--full", action="store_true", help="projit vse (bez stop-at-known)")
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parser.add_argument("--dry-run", action="store_true", help="nestahovat ani nepsat do DB; jen vypsat nove")
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parser.add_argument("--limit", type=int, default=0, help="max N radku (0 = vse)")
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ARGS = parser.parse_args()
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def log(msg):
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print(f"[{datetime.now().strftime('%H:%M:%S')}] {msg}", flush=True)
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# --- konfigurace ------------------------------------------------------------
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EMAIL = "vbuzalka@its.jnj.com"
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PASSWORD = "%zT3Wqfc9)cWua5"
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LOGIN_URL = "https://xsp.labcorp.com/"
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STUDY = "36940"
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STUDY_CODE = "77242113UCO3001"
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MONGO_URI = "mongodb://192.168.1.76:27017"
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DB_NAME = "covance"
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COLLECTION = "labreports"
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# 10 center (interni ID center) — z URL "GO TO LINK".
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SITES = [
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"930539", "930547", "930555", "930556", "930553",
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"930549", "930525", "930536", "930557", "930531",
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]
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_BASE = os.path.dirname(os.path.abspath(__file__))
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PROFILE_DIR = os.path.join(_BASE, "browser_profile")
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def lab_reports_url():
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site_param = json.dumps(SITES, separators=(",", ":"))
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return (f"https://xsp.labcorp.com/sponsor/study/{STUDY}/lab-reports"
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f"?site={urllib.parse.quote(site_param)}")
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# --- formatovani --------------------------------------------------------------
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_MONTHS = {"Jan": "01", "Feb": "02", "Mar": "03", "Apr": "04", "May": "05",
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"Jun": "06", "Jul": "07", "Aug": "08", "Sep": "09", "Oct": "10",
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"Nov": "11", "Dec": "12"}
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def safe(s: str) -> str:
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return re.sub(r'[\\/:*?"<>|]', "", s or "").strip()
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def fmt_date(s: str) -> str:
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"""'Jun 10, 2026' i 'Jun 15, 2026 7:49 PM' -> '2026-06-10'."""
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m = re.match(r"\s*([A-Za-z]{3})\w*\s+(\d{1,2}),\s+(\d{4})", s or "")
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if m and m.group(1)[:3] in _MONTHS:
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return f"{m.group(3)}-{_MONTHS[m.group(1)[:3]]}-{int(m.group(2)):02d}"
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return safe(s)
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def fmt_datetime(s: str) -> str:
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"""'Jun 15, 2026 7:49 PM' -> '2026-06-15 19:49'. Bez casu -> jen datum."""
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s = (s or "").strip()
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for f in ("%b %d, %Y %I:%M %p", "%b %d, %Y %I:%M:%S %p"):
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try:
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return datetime.strptime(s, f).strftime("%Y-%m-%d %H:%M")
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except ValueError:
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pass
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return fmt_date(s)
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def make_record_id(meta: dict) -> str:
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return "|".join([
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meta["site"], meta["subject"], meta["accession"],
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meta["visit"], fmt_datetime(meta["posted"]),
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])
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def build_basename(meta: dict) -> str:
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"""Nazev (kvuli budoucimu materializacnimu skriptu); ulozen jako fileName."""
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return safe(
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f"{STUDY_CODE} {fmt_date(meta['collected'])} {meta['site']} "
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f"{meta['subject']} {meta['visit']} {meta['accession']} "
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f"posted {fmt_date(meta['posted'])}"
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) + ".pdf"
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# --- JS helpery (AG Grid) ---------------------------------------------------
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JS_GRID_INFO = r"""() => {
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const c = document.querySelector('.ag-body-container');
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const r = document.querySelector('.ag-body-container .ag-row');
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const rh = r ? r.getBoundingClientRect().height : 25;
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const ch = c ? parseFloat(c.style.height || '0') : 0;
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return { rowHeight: rh || 25, total: rh ? Math.round(ch / rh) : 0 };
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}"""
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JS_READ_ROW = r"""(idx) => {
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const dedup = s => {
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s = (s || '').replace(/\s+/g, ' ').trim();
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const h = s.slice(0, Math.floor(s.length / 2));
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if (s === h + h) return h;
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const m = s.match(/^(.*?)\s+\1$/);
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if (m) return m[1];
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return s;
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};
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const row = document.querySelector('.ag-body-container .ag-row[row-index="' + idx + '"]');
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if (!row) return null;
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const get = id => {
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const c = row.querySelector('[col-id="' + id + '"]');
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return c ? dedup(c.textContent) : '';
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};
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return {
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type: get('type'),
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subject: get('subjectId'),
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accession: get('accessionNumber'),
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visit: get('visit'),
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collected: get('visitCollectionDate'),
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site: get('siteNum'),
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posted: get('postedDateTime'),
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};
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}"""
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JS_SCROLL_TO = r"""(args) => {
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const [idx, rh] = args;
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const vp = document.querySelector('.ag-body-viewport');
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if (!vp) return;
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vp.scrollTop = Math.max(0, idx * rh - vp.clientHeight / 2);
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}"""
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# --- login ------------------------------------------------------------------
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def login(page):
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log("LOGIN: otviram login stranku...")
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page.goto(LOGIN_URL)
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try:
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page.get_by_label("Email").wait_for(state="visible", timeout=12000)
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except Exception:
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log(f"LOGIN: Email pole se neobjevilo -> session aktivni, login preskocen ({page.url})")
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return
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log("LOGIN: zadavam email...")
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page.get_by_label("Email").fill(EMAIL)
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page.get_by_role("button", name="Next").click()
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log("LOGIN: cekam na pole pro heslo...")
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page.get_by_label("Password").wait_for(state="visible", timeout=30000)
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log("LOGIN: zadavam heslo...")
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page.get_by_label("Password").fill(PASSWORD)
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page.get_by_role("button", name="Verify").click()
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log("LOGIN: cekam na presmerovani po prihlaseni...")
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try:
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page.wait_for_url(lambda url: "code=" not in url or "xsp." in url, timeout=60000)
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except Exception:
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log("LOGIN: wait_for_url vyprsel, pokracuji.")
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page.wait_for_timeout(3000)
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log(f"LOGIN: prihlaseni hotovo ({page.url})")
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def open_grid(page):
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log(f"GRID: navigace na Lab Reports ({len(SITES)} center)...")
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page.goto(lab_reports_url())
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log("GRID: cekam na radky (.ag-row)...")
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page.wait_for_selector(".ag-body-container .ag-row", timeout=120000)
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prev = -1
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for i in range(20):
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info = page.evaluate(JS_GRID_INFO)
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cnt = info["total"]
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log(f" ...kontrola #{i+1}: total={cnt}, rowHeight={info['rowHeight']}")
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if cnt == prev and cnt > 0:
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break
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prev = cnt
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page.wait_for_timeout(2000)
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info = page.evaluate(JS_GRID_INFO)
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log(f"GRID: nacteno, total={info['total']} radku, rowHeight={info['rowHeight']}px.")
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return info["total"], info["rowHeight"]
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def read_row(page, idx, row_height):
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page.evaluate(JS_SCROLL_TO, [idx, row_height])
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page.wait_for_selector(f'.ag-body-container .ag-row[row-index="{idx}"]', timeout=15000)
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page.wait_for_timeout(120)
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meta = page.evaluate(JS_READ_ROW, idx)
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if not meta or not meta.get("subject"):
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raise RuntimeError(f"radek {idx}: nepodarilo se precist metadata")
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return meta
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def download_pdf_bytes(page, idx):
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link = page.locator(
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f'.ag-body-container .ag-row[row-index="{idx}"] a.dl-link',
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has_text="English",
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).first
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with page.expect_download(timeout=60000) as dl:
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link.click()
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path = dl.value.path() # temp soubor Playwrightu
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with open(path, "rb") as f:
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data = f.read()
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return data
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def upsert(col, meta, rid, data, now):
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fields = {
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"Type": meta["type"],
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"Subject": meta["subject"],
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"Accession": meta["accession"],
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"Visit": meta["visit"],
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"Collected Date": meta["collected"],
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"Site Number": meta["site"],
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"Posted": meta["posted"],
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}
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sha = hashlib.sha256(data).hexdigest()
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derived = {
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"study": STUDY,
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"studyCode": STUDY_CODE,
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"type": meta["type"] or "Lab Result",
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"site": meta["site"],
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"subject": meta["subject"],
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"accession": meta["accession"],
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"visit": meta["visit"],
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"collected": fmt_date(meta["collected"]),
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"posted": fmt_datetime(meta["posted"]),
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"fields": fields,
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"fileName": build_basename(meta),
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"pdf": Binary(data),
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"pdfSize": len(data),
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"pdfSha256": sha,
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}
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existing = col.find_one({"record_id": rid}, {"pdfSha256": 1, "fields": 1, "lastSeen": 1})
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if existing is None:
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col.insert_one({"record_id": rid, **derived,
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"firstSeen": now, "lastSeen": now, "history": []})
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return "insert"
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if existing.get("pdfSha256") != sha or existing.get("fields") != fields:
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col.update_one(
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{"_id": existing["_id"]},
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{"$push": {"history": {"date": existing.get("lastSeen"),
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"fields": existing.get("fields"),
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"pdfSha256": existing.get("pdfSha256")}},
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"$set": {**derived, "lastSeen": now}},
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)
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return "update"
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col.update_one({"_id": existing["_id"]}, {"$set": {"lastSeen": now}})
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return "same"
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def main():
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now = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
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log(f"START: studie {STUDY_CODE} ({STUDY}) -> {DB_NAME}.{COLLECTION}, "
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f"{'DRY-RUN' if ARGS.dry_run else 'ZAPIS'}"
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f"{' [FULL]' if ARGS.full else ' [stop-at-known]'}"
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f"{f', limit {ARGS.limit}' if ARGS.limit else ''}.")
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col = None
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existing_ids = set()
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if not ARGS.dry_run:
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client = MongoClient(MONGO_URI, serverSelectionTimeoutMS=5000)
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client.admin.command("ping")
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col = client[DB_NAME][COLLECTION]
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col.create_index([("record_id", ASCENDING)], unique=True)
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for idx_def in (["study"], ["site"], ["subject"], ["accession"],
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["posted"], ["collected"]):
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col.create_index([(idx_def[0], ASCENDING)])
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existing_ids = {d["record_id"] for d in col.find({"study": STUDY}, {"record_id": 1})}
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log(f"START: v Mongo uz je {len(existing_ids)} reportu pro tuto studii.")
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else:
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# i v dry-run nacti existujici, at vime, co je opravdu nove
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try:
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client = MongoClient(MONGO_URI, serverSelectionTimeoutMS=5000)
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client.admin.command("ping")
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existing_ids = {d["record_id"] for d in
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client[DB_NAME][COLLECTION].find({"study": STUDY}, {"record_id": 1})}
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log(f"START: [dry-run] v Mongo je {len(existing_ids)} reportu.")
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except Exception as e:
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log(f"START: [dry-run] Mongo nedostupne ({e!r}), beru vse jako nove.")
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with sync_playwright() as p:
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context = p.chromium.launch_persistent_context(
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user_data_dir=PROFILE_DIR,
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headless=False,
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args=[
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"--disable-blink-features=AutomationControlled",
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"--start-maximized",
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"--disable-restore-session-state",
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"--disable-session-crashed-bubble",
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],
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no_viewport=True,
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user_agent="Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/136.0.0.0 Safari/537.36",
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accept_downloads=True,
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)
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context.add_init_script("Object.defineProperty(navigator, 'webdriver', {get: () => undefined})")
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page = context.new_page()
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log("START: prohlizec spusten.")
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login(page)
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total, row_height = open_grid(page)
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if ARGS.limit:
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total = min(total, ARGS.limit)
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new_cnt = upd_cnt = same_cnt = 0
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failed = []
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stopped = False
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for idx in range(total):
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try:
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meta = read_row(page, idx, row_height)
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except Exception as e:
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failed.append(idx)
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log(f"CHYBA cteni radku {idx}: {e!r} — pokracuji.")
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continue
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rid = make_record_id(meta)
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known = rid in existing_ids
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if known and not ARGS.full:
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log(f">>> Radek {idx+1}/{total}: '{rid}' uz v Mongo "
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f"-> stop-at-known, koncim (zbytek je starsi).")
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stopped = True
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break
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if known and ARGS.full:
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log(f" #{idx}: znamy, [full] preskakuji download.")
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same_cnt += 1
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continue
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# novy report
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if ARGS.dry_run:
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log(f" [DRY] NOVY #{idx}: {build_basename(meta)}")
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new_cnt += 1
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existing_ids.add(rid)
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continue
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try:
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data = download_pdf_bytes(page, idx)
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action = upsert(col, meta, rid, data, now)
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existing_ids.add(rid)
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if action == "insert":
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new_cnt += 1
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log(f" #{idx}: INSERT ({len(data)//1024} KB) {build_basename(meta)}")
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elif action == "update":
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upd_cnt += 1
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log(f" #{idx}: UPDATE {build_basename(meta)}")
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else:
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same_cnt += 1
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except Exception as e:
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failed.append(idx)
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log(f"CHYBA stazeni/zapisu radku {idx}: {e!r} — pokracuji.")
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log(f"KONEC: nove={new_cnt}, update={upd_cnt}, beze zmeny={same_cnt}, "
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f"chyby={len(failed)} {'(stop-at-known)' if stopped else '(projeto vse)'}.")
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if failed:
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log(f"KONEC: SELHALY indexy: {failed}")
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context.close()
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if __name__ == "__main__":
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try:
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main()
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except Exception as e:
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log(f"FATAL: beh spadl: {e!r}")
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traceback.print_exc()
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finally:
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try:
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input("\n[Enter] pro zavreni tohoto okna...")
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except EOFError:
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pass
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