z230

Covance/import_equeries_to_mysql.py

@@ -0,0 +1,182 @@
+"""
+Import Covance eQuery CSV do MySQL tabulky covance_equeries.
+Strategie: versioning — každý import = nový import_id.
+"""
+
+import os
+import glob
+import datetime
+
+import numpy as np
+import pandas as pd
+import mysql.connector
+
+import db_config
+
+STUDY      = "42847922MDD3003"
+SOURCE_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), "SourceData")
+
+
+# ── type converters ──────────────────────────────────────────────────────────
+
+def _py(val):
+    if isinstance(val, np.generic):
+        return val.item()
+    return val
+
+def to_str(val):
+    val = _py(val)
+    if val is None:
+        return None
+    if isinstance(val, float) and (val != val):
+        return None
+    s = str(val).strip()
+    return None if s.lower() in ("nan", "nat", "none", "") else s
+
+def to_int(val):
+    val = _py(val)
+    try:
+        v = float(val)
+        return None if (v != v) else int(v)
+    except (TypeError, ValueError):
+        return None
+
+def to_datetime(val):
+    val = _py(val)
+    if val is None:
+        return None
+    if isinstance(val, float) and (val != val):
+        return None
+    try:
+        if pd.isna(val):
+            return None
+    except (TypeError, ValueError):
+        pass
+    if isinstance(val, pd.Timestamp):
+        return None if pd.isna(val) else val.to_pydatetime()
+    if isinstance(val, datetime.datetime):
+        return val
+    if isinstance(val, datetime.date):
+        return datetime.datetime(val.year, val.month, val.day)
+    s = str(val).strip()
+    if not s or s.lower() in ("nat", "nan", "none", ""):
+        return None
+    for fmt in ("%b %d, %Y %I:%M %p", "%b %d, %Y",
+                "%Y-%m-%d %H:%M:%S", "%Y-%m-%d"):
+        try:
+            return datetime.datetime.strptime(s, fmt)
+        except ValueError:
+            pass
+    return None
+
+
+# ── DB helpers ───────────────────────────────────────────────────────────────
+
+def get_conn():
+    return mysql.connector.connect(
+        host=db_config.DB_HOST, port=db_config.DB_PORT,
+        user=db_config.DB_USER, password=db_config.DB_PASSWORD,
+        database=db_config.DB_NAME,
+    )
+
+def insert_import(cursor, study, source_file):
+    cursor.execute(
+        "INSERT INTO iwrs_import (study, imported_at, source_file, report_type) VALUES (%s, %s, %s, %s)",
+        (study, datetime.datetime.now(), source_file, "covance_equeries"),
+    )
+    return cursor.lastrowid
+
+
+# ── parser ───────────────────────────────────────────────────────────────────
+
+def find_csv(study):
+    pattern = os.path.join(SOURCE_DIR, f"Protocol {study} *equery*.csv")
+    files = glob.glob(pattern)
+    if not files:
+        raise FileNotFoundError(f"Nenalezen CSV soubor: {pattern}")
+    return sorted(files)[-1]
+
+def parse_site(site_str):
+    """'CZ10004 - Dr. Erik Herman'  →  ('CZ10004', 'Dr. Erik Herman')"""
+    if not site_str:
+        return None, None
+    parts = site_str.split(" - ", 1)
+    code = parts[0].strip()
+    name = parts[1].strip() if len(parts) > 1 else None
+    return code, name
+
+def parse_csv(path):
+    df = pd.read_csv(path, dtype=str)
+    # odstraň metadata řádky (eQueryId není číslo)
+    df = df[pd.to_numeric(df["eQueryId"], errors="coerce").notna()].copy()
+
+    rows = []
+    for _, r in df.iterrows():
+        site_code, investigator_name = parse_site(to_str(r.get("Site")))
+        rows.append({
+            "site_code":             site_code,
+            "investigator_name":     investigator_name,
+            "country":               to_str(r.get("Country")),
+            "visit":                 to_str(r.get("Visit")),
+            "visit_collection_date": to_datetime(r.get("Visit Collection Date")),
+            "accession":             to_str(r.get("Accession")),
+            "subject":               to_str(r.get("Subject")),
+            "equery_id":             to_int(r.get("eQueryId")),
+            "create_date":           to_datetime(r.get("Create Date")),
+            "response_datetime":     to_datetime(r.get("Response Date Time")),
+            "issue_type":            to_str(r.get("Issue Type")),
+            "status":                to_str(r.get("Status")),
+            "time_before_response":  to_str(r.get("Time Before Response")),
+            "user_name":             to_str(r.get("User Name")),
+            "email":                 to_str(r.get("Email")),
+            "study_role":            to_str(r.get("Study Role")),
+        })
+    return rows
+
+
+# ── insert ───────────────────────────────────────────────────────────────────
+
+def insert_equeries(cursor, import_id, rows):
+    sql = """INSERT INTO covance_equeries
+        (import_id, study, site_code, investigator_name, country,
+         visit, visit_collection_date, accession, subject, equery_id,
+         create_date, response_datetime, issue_type, status,
+         time_before_response, user_name, email, study_role)
+        VALUES (%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s)"""
+    for r in rows:
+        cursor.execute(sql, (
+            import_id, STUDY,
+            r["site_code"], r["investigator_name"], r["country"],
+            r["visit"], r["visit_collection_date"], r["accession"],
+            r["subject"], r["equery_id"],
+            r["create_date"], r["response_datetime"],
+            r["issue_type"], r["status"],
+            r["time_before_response"], r["user_name"],
+            r["email"], r["study_role"],
+        ))
+
+
+# ── main ─────────────────────────────────────────────────────────────────────
+
+def main():
+    csv_path = find_csv(STUDY)
+    print(f"Soubor: {os.path.basename(csv_path)}")
+
+    rows = parse_csv(csv_path)
+    print(f"Načteno řádků: {len(rows)}")
+
+    conn = get_conn()
+    cursor = conn.cursor()
+
+    import_id = insert_import(cursor, STUDY, os.path.basename(csv_path))
+    print(f"import_id = {import_id}")
+
+    insert_equeries(cursor, import_id, rows)
+    conn.commit()
+    cursor.close()
+    conn.close()
+
+    print(f"Hotovo — {len(rows)} eQuery záznamů importováno.")
+
+
+main()