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UCO3001.ConcomitantTherapy) +Filtr: pouze řádky s SiteGroupName == "CZE" +Historie: při změně fields se stará verze uloží do pole history[] + +Použití: + python import_to_mongo.py # importuje všechny CSV z downloads/ + python import_to_mongo.py downloads/konkretni.csv # jeden soubor +""" + +import csv +import re +import sys +from datetime import datetime, timezone +from pathlib import Path + +from pymongo import MongoClient, ASCENDING + +MONGO_URI = "mongodb://192.168.1.76:27017" +DB_NAME = "edc" +DOWNLOADS_DIR = Path(__file__).parent / "downloads" + +COUNTRY_FILTER = "CZE" + +# --------------------------------------------------------------------------- +# Mapování pevných CSV sloupců +# --------------------------------------------------------------------------- + +FIXED_FIELDS = { + "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", +} + +INT_CAST = {"form.folderSeq", "form.recordPosition"} + +META_FIELDS = { + "StudyName", "SiteGroupParameter", "SiteNumberParameter", "SiteParameter", + "SubjectParameter", "FormParameter", "FieldParameter", "FilterField", + "FilterValue", "StartDateParameter", "EndDateParameter", "RunUser", + "VersionNumber", "PrintDateTime", "TimeZone", "LastModifiedDateSortable", + "StartDateSortable", "EndDateSortable", "ErrorMsg", +} + +DATE_FORMATS = [ + "%d %b %Y %H:%M:%S", + "%d %b %Y %H:%M:%S:%f", + "%d %b %Y", + "%d %B %Y", + "%Y%m%d %H:%M:%S.%f", + "%Y-%m-%d %H:%M:%S", + "%m/%d/%Y %I:%M:%S %p", +] + + +# --------------------------------------------------------------------------- +# Helpers +# --------------------------------------------------------------------------- + +def parse_date(value: str) -> str | 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) -> None: + parts = path.split(".") + for part in parts[:-1]: + doc = doc.setdefault(part, {}) + doc[parts[-1]] = value + + +def extract_snapshot_date(filename: str) -> str: + match = re.match(r"(\d{4}-\d{2}-\d{2})", Path(filename).name) + return match.group(1) if match else datetime.now().strftime("%Y-%m-%d") + + +def parse_collection_name(filename: str) -> str | None: + """ + Z názvu souboru odvodí kolekci ve formátu STUDY.FormName. + Vrátí None pro QueryDetails (mají vlastní flow). + """ + stem = Path(filename).stem + if "QueryDetails" in stem: + return None + match = re.search( + r"EDC_(\w+?)_(?:ALL_|CZE_|[A-Z]{2,3}_)?(.+?)_DataListing", + stem, re.IGNORECASE, + ) + if match: + study, form = match.group(1), match.group(2) + return f"{study}.{form}" + return None + + +# --------------------------------------------------------------------------- +# CSV → dokument +# --------------------------------------------------------------------------- + +def map_row(row: dict) -> dict: + doc: dict = {} + fields: dict = {} + field_keys = set(row.keys()) + + for col, value in row.items(): + value = value.strip() if value else "" + + if col in FIXED_FIELDS: + path = FIXED_FIELDS[col] + if path in INT_CAST: + try: + value = int(value) + except (ValueError, TypeError): + pass + elif path == "lastModified": + parsed = parse_date(value) + value = parsed if parsed else value + set_nested(doc, path, value) + continue + + if col in META_FIELDS: + continue + + if re.match(r"^Field\d+(Value|Label)$", col): + continue + + n = 1 + while True: + val_key = f"Field{n}Value" + lbl_key = f"Field{n}Label" + if val_key not in field_keys and lbl_key not in field_keys: + break + label = (row.get(lbl_key) or "").strip() + value = (row.get(val_key) or "").strip() + if label and value: + parsed = parse_date(value) + fields[label] = parsed if parsed else value + n += 1 + + doc["fields"] = fields + return doc + + +# --------------------------------------------------------------------------- +# Import jednoho souboru +# --------------------------------------------------------------------------- + +def import_file(csv_path: str, db) -> dict: + filename = Path(csv_path).name + col_name = parse_collection_name(filename) + if col_name is None: + print(f" Preskakuji (QueryDetails): {filename}") + return {"skipped": True} + + snapshot_date = extract_snapshot_date(filename) + collection = db[col_name] + + inserted = changed = unchanged = filtered_out = 0 + + with open(csv_path, encoding="utf-8", newline="") as f: + reader = csv.DictReader(f, delimiter=",", quotechar='"') + + for row in reader: + site_group = (row.get("SiteGroupName") or "").strip() + if site_group != COUNTRY_FILTER: + filtered_out += 1 + continue + + doc = map_row(row) + record_id = doc.get("form", {}).get("recordId") + if not record_id: + continue + + doc["sourceFile"] = filename + + existing = collection.find_one({"form.recordId": record_id}) + + if existing is None: + doc["firstSeen"] = snapshot_date + doc["lastSeen"] = snapshot_date + doc["history"] = [] + collection.insert_one(doc) + inserted += 1 + + elif existing.get("fields") != doc["fields"]: + old_entry = { + "date": existing.get("lastSeen", snapshot_date), + "fields": existing["fields"], + } + update_doc = {k: v for k, v in doc.items()} + update_doc["lastSeen"] = snapshot_date + collection.update_one( + {"_id": existing["_id"]}, + { + "$push": {"history": old_entry}, + "$set": update_doc, + }, + ) + changed += 1 + + else: + collection.update_one( + {"_id": existing["_id"]}, + {"$set": {"lastSeen": snapshot_date, "sourceFile": filename}}, + ) + unchanged += 1 + + collection.create_index([("form.recordId", ASCENDING)], unique=True) + collection.create_index([("subject.label", ASCENDING)]) + collection.create_index([("site.number", ASCENDING)]) + + stats = { + "collection": col_name, + "snapshot": snapshot_date, + "inserted": inserted, + "changed": changed, + "unchanged": unchanged, + "filtered_out": filtered_out, + } + print(f" {col_name} [{snapshot_date}]: +{inserted} new, ~{changed} changed, ={unchanged} same, -{filtered_out} non-CZE") + return stats + + +# --------------------------------------------------------------------------- +# Main +# --------------------------------------------------------------------------- + +def main(): + paths: list[Path] = [] + + if len(sys.argv) > 1: + for arg in sys.argv[1:]: + p = Path(arg) + if p.is_file(): + paths.append(p) + else: + print(f"Soubor nenalezen: {arg}") + else: + paths = sorted(DOWNLOADS_DIR.glob("*_DataListing.csv")) + + if not paths: + print("Zadne CSV soubory k importu.") + return + + print(f"Nalezeno {len(paths)} souboru.\n") + + client = MongoClient(MONGO_URI, serverSelectionTimeoutMS=5000) + client.admin.command("ping") + db = client[DB_NAME] + + total = {"inserted": 0, "changed": 0, "unchanged": 0} + + for csv_path in paths: + print(f"Import: {csv_path.name}") + stats = import_file(str(csv_path), db) + if not stats.get("skipped"): + for k in total: + total[k] += stats.get(k, 0) + + client.close() + + print(f"\nCelkem: +{total['inserted']} new, ~{total['changed']} changed, ={total['unchanged']} same") + + +if __name__ == "__main__": + main() diff --git a/Medidata/run_uco3001.py b/Medidata/run_uco3001.py index b4600ab..995066f 100644 --- a/Medidata/run_uco3001.py +++ b/Medidata/run_uco3001.py @@ -3,8 +3,9 @@ from download_uco3001 import download_datalisting_reports_3001 # === Vyber jeden řádek, odkomentuj ho a spusť === # --- Trial Disposition --- -download_datalisting_reports_3001("Trial Disposition (Completion / Discontinuation)") -download_datalisting_reports_3001("Date of Visit") +# download_datalisting_reports_3001("Trial Disposition (Completion / Discontinuation)") +# download_datalisting_reports_3001("Date of Visit") +download_datalisting_reports_3001("Concomitant Therapy", country="CZE") # download_datalisting_reports_3001("Trial Disposition (Completion / Discontinuation)", country="CZE") # --- Date of Visit ---