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vladimir.buzalka
2026-06-17 15:05:10 +02:00
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Feasibility/sipiq_import_v1.2.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
sipiq_import_v1.2.py
====================
Verze: 1.2
Datum: 2026-06-17
Autor: Claude Code (pro MUDr. Vladimíra Buzalku)
Změny proti v1.1
----------------
- PROVENANCE: ke každé odpovědi se ukládá `source_exported_at` = datum/čas reportu
podle FILESYSTÉMU (mtime CSV souboru). Mimo content-hash → nezpůsobuje zbytečné
UPDATE; backfilluje se i na "beze změny" cestě. Stará v1.1 ponechána v TRASH.
Změny proti v1.0
----------------
- FOLDER WORKFLOW (v1.1): režim --folder sebere *.csv ve složce, naimportuje (delta)
a přesune do podsložky `Zpracováno`. Default složka =
U:\\PythonProject\\Janssen\\Feasibility\\77242113UCO2001\\ImportSIPIQcompled.
Popis
-----
Import SIPIQ odpovědí (Qualtrics CSV export, studie 77242113UCO3002 / ICONIC DAWN)
do MongoDB db `feasibility`. Dvě kolekce:
* sipiq_questions – slovník dotazníku (1 dok = 1 logická otázka).
* sipiq_responses – 1 dok = 1 odpověď (_id = Qualtrics ResponseId), ploché answers{},
soft-link investigator_oid, delta bookkeeping + history[].
DELTA import (přepíše JEN změněná data): nová->insert; beze změn->jen last_seen_at;
změna->$set jen změněných polí + push do history[].
Použití
-------
python sipiq_import_v1.2.py --dry-run # folder režim, default složka
python sipiq_import_v1.2.py --apply
python sipiq_import_v1.2.py --folder "<cesta>" --apply
python sipiq_import_v1.2.py --csv "<cesta.csv>" --apply # jediný soubor (NEpřesouvá)
Závislosti: pymongo (.venv). Mongo 192.168.1.76:27017, bez auth.
"""
import argparse
import csv
import glob
import hashlib
import json
import os
import re
import shutil
import sys
import unicodedata
from datetime import datetime, timezone
try:
from pymongo import MongoClient
except ImportError:
print("CHYBA: pymongo není nainstalován v aktuálním pythonu.", file=sys.stderr)
raise
MONGO_URI = "mongodb://192.168.1.76:27017"
DB_NAME = "feasibility"
COL_Q = "sipiq_questions"
COL_R = "sipiq_responses"
DEFAULT_FOLDER = r"U:\PythonProject\Janssen\Feasibility\77242113UCO2001\ImportSIPIQcompled"
PROCESSED_SUBDIR = "Zpracováno"
META_COLS = {
"StartDate", "EndDate", "Status", "IPAddress", "Progress", "Duration (in seconds)",
"Finished", "RecordedDate", "ResponseId", "RecipientLastName", "RecipientFirstName",
"RecipientEmail", "ExternalReference", "LocationLatitude", "LocationLongitude",
"DistributionChannel", "UserLanguage",
}
PROMOTE = [
"site_name", "site_address", "site_city", "site_state", "site_postcode", "site_country",
"pi_first_name", "pi_last_name", "pi_phone", "pi_email",
"sdl_site_id", "fire_site_id", "fire_investigator_id", "mailinglist_id",
"survey_generated_by", "Date", "Time",
]
SECTION_BY_QNUM = {}
def _sec(rng, name):
for n in rng:
SECTION_BY_QNUM[n] = name
_sec([2], "J&J Internal Assessment")
_sec([6, 7, 8, 9, 10, 11, 12, 13], "Contact Information")
_sec(range(14, 22), "Confidentiality Statement")
_sec([25, 26, 27], "Interest")
_sec([29, 30, 31, 32, 33, 34], "Protocol Requirements")
_sec([36, 37, 38], "Enrollment")
_sec([40, 41, 42, 43], "Patient Demographics Overview")
_sec([45, 46, 47, 48, 49], "Site Overview")
_sec([51], "Operational Considerations")
_sec([53, 54], "Comments")
_sec([57, 58, 59, 60, 61], "Patient Population")
_sec([63, 64, 65, 66, 67], "Site Experience and Staffing")
_sec([69], "Equipment and Facility Requirements")
_sec([71, 72, 73, 74, 75], "Institutional Review Board, Ethics Committee, and Contracts")
STEM_OVERRIDE = {
"Q31": "At your site, at what line(s) of treatment do you most commonly prescribe "
"vedolizumab for patients with moderately to severely active ulcerative colitis?",
"Q63": "Do you or your site staff have experience in performing the following types of "
"study assessments/procedures?",
"Q64": "The following personnel are required to run the study. "
"Will your site have the following available?",
"Q69": "The following equipment and facilities are required to run the studies. "
"Are these available at your site?",
}
def now_iso():
return datetime.now(timezone.utc).astimezone().isoformat(timespec="seconds")
def file_mtime_iso(path):
return datetime.fromtimestamp(os.path.getmtime(path)).astimezone().isoformat(timespec="seconds")
def strip_accents(s):
if not s:
return ""
return "".join(c for c in unicodedata.normalize("NFKD", s) if not unicodedata.combining(c))
def norm_name(s):
return re.sub(r"\s+", " ", strip_accents(s or "").lower()).strip()
def sanitize_key(qcode):
return qcode.replace("#", "_").replace(".", "_")
def qnum(qcode):
m = re.match(r"Q(\d+)", qcode)
return int(m.group(1)) if m else None
def qbase(qcode):
m = re.match(r"(Q\d+)", qcode)
return m.group(1) if m else qcode
def import_id(h3_cell):
try:
return json.loads(h3_cell).get("ImportId", "")
except Exception:
return h3_cell
def split_text(text):
parts = [p.strip() for p in re.split(r"\s+-\s+", text)]
stem = parts[0]
if len(parts) == 1:
return stem, None
label_parts = [p for p in parts[1:] if p.lower() != "selected choice"]
label_parts = [p for p in label_parts if not re.fullmatch(r"Q\d+#\d+", p)]
return stem, (" - ".join(label_parts) if label_parts else None)
def detect_type(qcode, observed):
has_hash = "#" in qcode
vals = [v for v in observed if v]
yesno = vals and all(v in ("Yes", "No") for v in vals)
numeric = vals and all(re.fullmatch(r"-?\d+(\.\d+)?", v) for v in vals)
if has_hash and yesno:
return "matrix_yesno"
if has_hash and numeric:
return "matrix_percent"
if has_hash:
return "matrix"
if numeric:
return "numeric"
if yesno:
return "yesno"
return "single_or_text"
def load_csv(path):
with open(path, encoding="utf-8-sig", newline="") as fh:
rows = list(csv.reader(fh))
h1, h2, h3 = rows[0], rows[1], rows[2]
data = rows[3:]
cols = [{"i": i, "code": c, "text": t, "qid": import_id(j)}
for i, (c, t, j) in enumerate(zip(h1, h2, h3))]
return cols, data
def col_getter(cols, data):
idx = {c["code"]: c["i"] for c in cols}
def get(row, code):
i = idx.get(code)
return (row[i].strip() if i is not None and i < len(row) else "")
return get, idx
def is_question_col(code):
return bool(re.match(r"Q\d", code))
def build_questions(cols, data):
qcols = [c for c in cols if is_question_col(c["code"])]
observed = {c["code"]: set() for c in qcols}
for row in data:
for c in qcols:
v = (row[c["i"]].strip() if c["i"] < len(row) else "")
if v:
observed[c["code"]].add(v)
groups, order_seen = {}, []
for c in qcols:
base = qbase(c["code"])
if base not in groups:
groups[base] = {"_id": base, "order": c["i"], "qnum": qnum(c["code"]),
"section": SECTION_BY_QNUM.get(qnum(c["code"]), "Other"),
"qids": [], "text": split_text(c["text"])[0],
"items": [], "_obs": set(), "_types": []}
order_seen.append(base)
g = groups[base]
bq = re.match(r"(QID\d+)", c["qid"] or "")
if bq and bq.group(1) not in g["qids"]:
g["qids"].append(bq.group(1))
_, label = split_text(c["text"])
item = {"key": sanitize_key(c["code"]), "qcode": c["code"], "qid": c["qid"]}
if label:
item["label"] = label
g["items"].append(item)
g["_obs"] |= observed[c["code"]]
g["_types"].append(detect_type(c["code"], observed[c["code"]]))
out = []
for n, base in enumerate(order_seen):
g = groups[base]
obs = sorted(g.pop("_obs"))
types = g.pop("_types")
gtype = max(set(types), key=types.count) if types else "single_or_text"
g["type"] = gtype
if gtype in ("yesno", "matrix_yesno"):
g["options"] = ["Yes", "No"]
elif gtype == "single_or_text" and obs and len(obs) <= 12:
g["options"] = obs
else:
g["options"] = []
if base in STEM_OVERRIDE:
g["text"] = STEM_OVERRIDE[base]
g["order"] = n
if len(g["items"]) == 1 and "label" not in g["items"][0]:
g["items"] = []
out.append(g)
return out
def build_response(cols, get, row, source_file):
rid = get(row, "ResponseId")
answers = {}
for c in cols:
if is_question_col(c["code"]):
v = (row[c["i"]].strip() if c["i"] < len(row) else "")
if v:
answers[sanitize_key(c["code"])] = v
meta = {
"start_date": get(row, "StartDate") or None,
"end_date": get(row, "EndDate") or None,
"recorded_date": get(row, "RecordedDate") or None,
"status": get(row, "Status") or None,
"progress": int(get(row, "Progress")) if get(row, "Progress").isdigit() else (get(row, "Progress") or None),
"finished": get(row, "Finished") in ("True", "1", "TRUE"),
"duration_sec": int(get(row, "Duration (in seconds)")) if get(row, "Duration (in seconds)").isdigit() else None,
"user_language": get(row, "UserLanguage") or None,
"distribution_channel": get(row, "DistributionChannel") or None,
"ip_address": get(row, "IPAddress") or None,
"location_lat": get(row, "LocationLatitude") or None,
"location_lng": get(row, "LocationLongitude") or None,
"survey_date": get(row, "Date") or None,
"survey_time": get(row, "Time") or None,
}
doc = {
"_id": rid, "study": "77242113UCO3002",
"site_country": get(row, "site_country") or None,
"site_name": get(row, "site_name") or None,
"site_city": get(row, "site_city") or None,
"site_state": get(row, "site_state") or None,
"site_postcode": get(row, "site_postcode") or None,
"site_address": get(row, "site_address") or None,
"pi_first_name": get(row, "pi_first_name") or None,
"pi_last_name": get(row, "pi_last_name") or None,
"pi_email": (get(row, "pi_email") or "").lower() or None,
"pi_phone": get(row, "pi_phone") or None,
"sdl_site_id": get(row, "sdl_site_id") or None,
"fire_site_id": get(row, "fire_site_id") or None,
"fire_investigator_id": get(row, "fire_investigator_id") or None,
"mailinglist_id": get(row, "mailinglist_id") or None,
"survey_generated_by": get(row, "survey_generated_by") or None,
"recipient_email": (get(row, "RecipientEmail") or "").lower() or None,
"recipient_last_name": get(row, "RecipientLastName") or None,
"recipient_first_name": get(row, "RecipientFirstName") or None,
"meta": meta,
"is_full_sipiq": any(k.startswith(("Q57", "Q58", "Q59", "Q63", "Q66", "Q71")) for k in answers),
"interested": answers.get("Q25"),
"answers": answers,
"investigator_oid": None, "investigator_match": None,
"source_file": source_file,
}
return doc
def content_hash(doc):
payload = {k: doc[k] for k in doc if k not in
("content_sha256", "first_imported_at", "last_seen_at", "last_updated_at",
"history", "investigator_oid", "investigator_match", "source_file",
"source_exported_at")}
return hashlib.sha256(json.dumps(payload, sort_keys=True, ensure_ascii=False,
default=str).encode("utf-8")).hexdigest()
def load_investigators(db):
inv = list(db.investigators.find(
{"zeme": {"$in": ["Czech Republic", "Slovakia"]}},
{"prijmeni": 1, "jmeno": 1, "email": 1, "email2": 1, "zeme": 1, "KROK": 1}))
by_email, by_name = {}, {}
for d in inv:
for ef in ("email", "email2"):
e = (d.get(ef) or "").lower().strip()
if e:
by_email.setdefault(e, d)
nm = norm_name(d.get("prijmeni"))
if nm:
by_name.setdefault((nm, d.get("zeme")), []).append(d)
return inv, by_email, by_name
def soft_link(doc, by_email, by_name):
e = (doc.get("pi_email") or "").lower().strip()
if e and e in by_email:
d = by_email[e]; return d["_id"], f"email:{e}", d
e2 = (doc.get("recipient_email") or "").lower().strip()
if e2 and e2 in by_email:
d = by_email[e2]; return d["_id"], f"recipient_email:{e2}", d
nm = norm_name(doc.get("pi_last_name"))
cand = by_name.get((nm, doc.get("site_country")), [])
if len(cand) == 1:
return cand[0]["_id"], f"prijmeni:{nm}", cand[0]
if len(cand) > 1:
return None, f"prijmeni_ambiguous:{nm}({len(cand)})", None
return None, "NENALEZENO", None
def diff_docs(old, new):
changes = []
def walk(prefix, o, n):
for k in sorted(set((o or {}).keys()) | set((n or {}).keys())):
ov, nv = (o or {}).get(k), (n or {}).get(k)
if isinstance(ov, dict) or isinstance(nv, dict):
walk(f"{prefix}{k}.", ov or {}, nv or {})
elif ov != nv:
changes.append({"key": f"{prefix}{k}", "old": ov, "new": nv})
for field in ("answers", "meta"):
walk(f"{field}.", old.get(field, {}), new.get(field, {}))
for k in ("site_name", "pi_email", "pi_last_name", "interested", "is_full_sipiq"):
if old.get(k) != new.get(k):
changes.append({"key": k, "old": old.get(k), "new": new.get(k)})
return changes
# ---------------------------------------------------------------------------
def process_file(db, csv_path, scope, dry, by_email, by_name):
source_file = os.path.basename(csv_path)
exported_at = file_mtime_iso(csv_path) # datum/čas reportu dle filesystému (mtime)
cols, data = load_csv(csv_path)
get, _ = col_getter(cols, data)
if scope == "czsk":
data = [r for r in data if get(r, "site_country") in ("Czech Republic", "Slovakia")]
print(f"\n########## {source_file} (rozsah={scope}, odpovědí={len(data)}, export={exported_at}) ##########")
cols_all, data_all = load_csv(csv_path)
questions = build_questions(cols_all, data_all)
docs, link_rows = [], []
for r in data:
doc = build_response(cols, get, r, source_file)
oid, how, matched = soft_link(doc, by_email, by_name)
doc["investigator_oid"] = oid
doc["investigator_match"] = how
doc["source_exported_at"] = exported_at
doc["content_sha256"] = content_hash(doc)
docs.append(doc)
link_rows.append((doc, how, matched))
existing = {d["_id"]: d for d in db[COL_R].find({}, {"content_sha256": 1})}
to_insert = [d for d in docs if d["_id"] not in existing]
to_update = [d for d in docs if d["_id"] in existing and existing[d["_id"]].get("content_sha256") != d["content_sha256"]]
unchanged = [d for d in docs if d["_id"] in existing and existing[d["_id"]].get("content_sha256") == d["content_sha256"]]
mk7 = mko = un = 0
for doc, how, m in link_rows:
krok = (m or {}).get("KROK", "")
if m and str(krok).startswith("7"): mk7 += 1
elif m: mko += 1
else: un += 1
print(f" slovník: {len(questions)} otázek | soft-link: KROK7={mk7}, jiný={mko}, nenapárováno={un}")
print(f" delta: INSERT={len(to_insert)}, UPDATE={len(to_update)}, beze změny={len(unchanged)}")
if un:
for doc, how, m in link_rows:
if not m:
print(f" ✗ NENAPÁROVÁNO: {doc.get('pi_last_name')} / {doc.get('pi_email')} ({how})")
if dry:
print(" [DRY-RUN] nezapsáno")
return {"insert": 0, "update": 0, "unchanged": 0, "wrote": False}
for q in questions:
db[COL_Q].replace_one({"_id": q["_id"]}, q, upsert=True)
ts = now_iso()
ni = nu = ns = 0
for d in docs:
cur = db[COL_R].find_one({"_id": d["_id"]})
if cur is None:
d.update({"first_imported_at": ts, "last_seen_at": ts, "last_updated_at": ts, "history": []})
db[COL_R].insert_one(d); ni += 1
elif cur.get("content_sha256") != d["content_sha256"]:
changes = diff_docs(cur, d)
db[COL_R].update_one({"_id": d["_id"]}, {
"$set": {**{k: d[k] for k in d if k != "_id"}, "last_seen_at": ts, "last_updated_at": ts},
"$push": {"history": {"changed_at": ts, "source_file": source_file, "changes": changes}}})
nu += 1
else:
db[COL_R].update_one({"_id": d["_id"]}, {"$set": {
"last_seen_at": ts, "source_file": source_file, "source_exported_at": d["source_exported_at"]}})
ns += 1
print(f" [APPLY] questions upsert={len(questions)} | responses insert={ni}, update={nu}, beze změny={ns}")
return {"insert": ni, "update": nu, "unchanged": ns, "wrote": True}
def move_to_processed(csv_path, folder):
dest_dir = os.path.join(folder, PROCESSED_SUBDIR)
os.makedirs(dest_dir, exist_ok=True)
base = os.path.basename(csv_path)
dest = os.path.join(dest_dir, base)
if os.path.exists(dest):
stem, ext = os.path.splitext(base)
n = 1
while os.path.exists(os.path.join(dest_dir, f"{stem}_{n}{ext}")):
n += 1
dest = os.path.join(dest_dir, f"{stem}_{n}{ext}")
shutil.move(csv_path, dest)
print(f" -> přesunuto do {PROCESSED_SUBDIR}\\{os.path.basename(dest)}")
def main():
ap = argparse.ArgumentParser()
ap.add_argument("--csv", help="jediný soubor (NEpřesouvá)")
ap.add_argument("--folder", default=DEFAULT_FOLDER, help="složka se SIPIQ CSV (přesune do Zpracováno)")
ap.add_argument("--scope", choices=["czsk", "all"], default="czsk")
ap.add_argument("--apply", action="store_true")
ap.add_argument("--dry-run", action="store_true")
args = ap.parse_args()
dry = not args.apply
if args.csv:
files, move_mode, folder = [args.csv], False, None
else:
folder = args.folder
files = sorted(glob.glob(os.path.join(folder, "*.csv")))
move_mode = True
print(f"Složka: {folder}\nNalezeno CSV ke zpracování: {len(files)}")
if not files:
print("Nic ke zpracování (žádné *.csv).")
return
client = MongoClient(MONGO_URI, serverSelectionTimeoutMS=8000)
db = client[DB_NAME]
client.admin.command("ping")
inv, by_email, by_name = load_investigators(db)
print(f"Investigatorů CZ+SK v DB: {len(inv)}")
total = {"insert": 0, "update": 0, "unchanged": 0}
for f in files:
res = process_file(db, f, args.scope, dry, by_email, by_name)
for k in total:
total[k] += res[k]
if move_mode and res["wrote"]:
move_to_processed(f, folder)
print(f"\n=== CELKEM: insert={total['insert']}, update={total['update']}, beze změny={total['unchanged']} ===")
if dry:
print("[DRY-RUN] Nic se nezapsalo ani nepřesunulo. Ostrý běh: --apply")
client.close()
if __name__ == "__main__":
main()