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