z230

Covance/SourceData/Protocol 42847922MDD3003 sponsor-study-35472-activity-reports-documents-equery.csv

@@ -0,0 +1,37 @@
+Site,Country,Visit,Visit Collection Date,Accession,Subject,eQueryId,Create Date,Response Date Time,Issue Type,Status,Time Before Response,User Name,Email,Study Role
+CZ10012 - Dr.Ales Urban,CZECH REPUBLIC,End of Phase/Treatment,"Mar 25, 2026 5:00 PM",6226560888,CZ100120005,2064594,"Mar 27, 2026 9:33 AM","Apr 1, 2026 4:32 PM",VST,Closed,5d,,,
+CZ10012 - Dr.Ales Urban,CZECH REPUBLIC,Part 2 DB Every 12 Weeks,"Mar 6, 2026 2:00 PM",6226560891,CZ100120004,2035331,"Mar 10, 2026 11:18 AM","Mar 10, 2026 12:50 PM",ADT201,Closed,1h 31m,Marcela Sedlackova,marcelasedlackova@seznam.cz,Investigator
+CZ10012 - Dr.Ales Urban,CZECH REPUBLIC,Part 2 OL Induction Day 29,"Jan 2, 2026 12:00 PM",6226976943,CZ100120004,1936950,"Jan 6, 2026 12:29 PM","Jan 9, 2026 8:41 AM",DOB,Closed,2d,Marcela Sedlackova,marcelasedlackova@seznam.cz,Investigator
+CZ10012 - Dr.Ales Urban,CZECH REPUBLIC,End of Phase/Treatment,"Mar 25, 2026 3:00 PM",6226752555,CZ100120006,2064606,"Mar 27, 2026 9:48 AM","Apr 1, 2026 4:32 PM",VST,Closed,5d,,,
+CZ10011 - Dr. Marta Lendlova,CZECH REPUBLIC,Retest,"Dec 11, 2025 9:05 AM",6226935606,CZ100110003,1930555,"Dec 31, 2025 12:41 PM","Jan 3, 2026 5:26 PM","VST, AMT4164",Closed,3d,Marta Lendlova,studie@medipa.org,Investigator
+CZ10011 - Dr. Marta Lendlova,CZECH REPUBLIC,Retest,"Dec 11, 2025 9:05 AM",6226935606,CZ100110003,1908988,"Dec 16, 2025 2:17 PM","Dec 19, 2025 3:55 PM","VST, AMT4164",Closed,3d,Marta Lendlova,studie@medipa.org,Investigator
+CZ10011 - Dr. Marta Lendlova,CZECH REPUBLIC,Part 2 OL Induction Baseline,"Jan 6, 2026 10:11 AM",6227261836,CZ100110006,1943384,"Jan 9, 2026 2:23 PM",,VST,Closed,,,,
+CZ10011 - Dr. Marta Lendlova,CZECH REPUBLIC,Part 2 OL Induction Baseline,"Jan 6, 2026 10:11 AM",6227261836,CZ100110006,1953531,"Jan 16, 2026 7:52 AM",,VST,Closed,,,,
+CZ10011 - Dr. Marta Lendlova,CZECH REPUBLIC,Part 2 OL Induction Baseline,"Jan 6, 2026 10:11 AM",6227261836,CZ100110006,1965291,"Jan 23, 2026 11:05 AM","Jan 26, 2026 6:18 PM",VST,Closed,3d,Marta Lendlova,studie@medipa.org,Investigator
+CZ10011 - Dr. Marta Lendlova,CZECH REPUBLIC,Part 1 Screening,"Jan 21, 2026 10:11 AM",6227542160,CZ100110009,1965641,"Jan 23, 2026 12:41 PM","Jan 26, 2026 6:18 PM",ADT201,Closed,3d,Marta Lendlova,studie@medipa.org,Investigator
+CZ10011 - Dr. Marta Lendlova,CZECH REPUBLIC,Retest,"Apr 10, 2026 8:16 AM",6227542182,CZ100110010,2105984,"Apr 22, 2026 4:51 PM",,"AMT4164, ADT201",Closed,,,,
+CZ10011 - Dr. Marta Lendlova,CZECH REPUBLIC,Retest,"Apr 10, 2026 8:16 AM",6227542182,CZ100110010,2117124,"Apr 29, 2026 5:13 PM",,"AMT4164, ADT201",Open,,,,
+CZ10011 - Dr. Marta Lendlova,CZECH REPUBLIC,Retest,"Apr 10, 2026 8:16 AM",6227542182,CZ100110010,2094889,"Apr 15, 2026 7:25 PM",,"AMT4164, ADT201",Closed,,,,
+CZ10011 - Dr. Marta Lendlova,CZECH REPUBLIC,Part 2 OL Induction Day 29,"Feb 3, 2026 10:23 AM",6226561517,CZ100110006,2040081,"Mar 12, 2026 12:52 PM","Mar 20, 2026 9:35 AM",VST,Closed,7d,Marta Lendlova,studie@medipa.org,Investigator
+CZ10011 - Dr. Marta Lendlova,CZECH REPUBLIC,Part 2 OL Induction Day 29,"Feb 3, 2026 10:23 AM",6226561517,CZ100110006,2015993,"Feb 25, 2026 2:26 PM","Mar 4, 2026 4:37 PM",VST,Closed,7d,Marta Lendlova,studie@medipa.org,Investigator
+CZ10011 - Dr. Marta Lendlova,CZECH REPUBLIC,Part 2 OL Induction Day 29,"Feb 3, 2026 10:23 AM",6226561517,CZ100110006,2005997,"Feb 18, 2026 3:01 PM",,VST,Closed,,,,
+CZ10011 - Dr. Marta Lendlova,CZECH REPUBLIC,Part 2 OL Induction Day 29,"Feb 3, 2026 10:23 AM",6226561517,CZ100110006,1984511,"Feb 5, 2026 10:36 AM","Feb 10, 2026 5:12 PM",VST,Closed,5d,Marta Lendlova,studie@medipa.org,Investigator
+CZ10011 - Dr. Marta Lendlova,CZECH REPUBLIC,End of Phase/Treatment,,6228234300,CZ100110010,2112166,"Apr 27, 2026 1:26 PM",,SCD,Closed,,,,
+CZ10011 - Dr. Marta Lendlova,CZECH REPUBLIC,End of Phase/Treatment,,6228234300,CZ100110010,2124850,"May 5, 2026 1:37 PM",,SCD,Open,,,,
+CZ10008 - Dr.Zdenek Solle,CZECH REPUBLIC,Part 1 Screening,"Aug 5, 2025 11:58 AM",6225351045,CZ100080002,1712216,"Aug 7, 2025 12:05 PM","Aug 7, 2025 12:45 PM",SCT,Closed,40m,Roman Gregar,r.gregar@clintrial.cz,Investigator
+CZ10008 - Dr.Zdenek Solle,CZECH REPUBLIC,Part 2 OL Induction Baseline,"Sep 10, 2025 11:35 AM",6225351056,CZ100080001,1769239,"Sep 15, 2025 5:00 PM","Sep 16, 2025 8:14 AM",SCT,Closed,15h 14m,Roman Gregar,r.gregar@clintrial.cz,Investigator
+CZ10008 - Dr.Zdenek Solle,CZECH REPUBLIC,Early Withdrawal,"Oct 14, 2025 12:30 PM",6225351066,CZ100080004,1817448,"Oct 16, 2025 12:29 PM","Oct 16, 2025 1:37 PM",ADT201,Closed,1h 7m,Barbora Sollova,b.sollova@clintrial.cz,Investigator
+CZ10008 - Dr.Zdenek Solle,CZECH REPUBLIC,Part 2 DB Baseline,"Mar 10, 2026 11:10 AM",6226804962,CZ100080006,2039863,"Mar 12, 2026 12:07 PM","Mar 16, 2026 8:11 AM",VST,Closed,3d,Barbora Sollova,b.sollova@clintrial.cz,Investigator
+CZ10005 - Dr.Lubos Janu,CZECH REPUBLIC,Retest,"Sep 16, 2025 10:00 AM",6225351036,CZ100050001,1776942,"Sep 19, 2025 11:34 AM","Sep 23, 2025 2:21 PM",VST,Closed,4d,,,
+CZ10005 - Dr.Lubos Janu,CZECH REPUBLIC,Retest,"Nov 11, 2025 10:04 AM",6225351037,CZ100050002,1859363,"Nov 13, 2025 12:27 PM","Nov 18, 2025 10:16 AM",ADT201,Closed,4d,,,
+CZ10004 - Dr. Erik Herman,CZECH REPUBLIC,End of Phase/Treatment,"Jan 9, 2026 10:20 AM",6227178908,CZ100040002,1947467,"Jan 13, 2026 10:55 AM","Jan 16, 2026 10:51 AM","PCFCOM, ADT201",Closed,2d,Gabriela Novotna,gnovotna@email.cz,Investigator
+CZ10004 - Dr. Erik Herman,CZECH REPUBLIC,End of Phase/Treatment,"Mar 6, 2026 9:50 AM",6227178911,CZ100040002,2034798,"Mar 10, 2026 12:00 AM","Mar 12, 2026 5:11 PM",ADT201,Closed,2d,Gabriela Novotna,gnovotna@email.cz,Investigator
+CZ10004 - Dr. Erik Herman,CZECH REPUBLIC,Part 1 Screening,"Feb 27, 2026 8:00 AM",6227547329,CZ100040007,2024391,"Mar 3, 2026 12:47 PM","Mar 4, 2026 6:56 PM",PID,Closed,1d,Gabriela Novotna,gnovotna@email.cz,Investigator
+CZ10004 - Dr. Erik Herman,CZECH REPUBLIC,Part 1 DB Baseline,"Feb 27, 2026 11:35 AM",6227547332,CZ100040006,2024264,"Mar 3, 2026 12:10 PM","Mar 4, 2026 6:57 PM",PID,Closed,1d,Gabriela Novotna,gnovotna@email.cz,Investigator
+CZ10004 - Dr. Erik Herman,CZECH REPUBLIC,Part 2 OL Induction Baseline,"Apr 7, 2026 9:45 AM",6227541258,CZ100040005,2083848,"Apr 8, 2026 8:50 PM","Apr 13, 2026 5:16 PM",ADT201,Closed,4d,Erik Herman,erik.herman@seznam.cz,Investigator
+CZ10004 - Dr. Erik Herman,CZECH REPUBLIC,Part 2 DB Week 13,"Apr 7, 2026 8:35 AM",6227541264,CZ100040001,2090583,"Apr 13, 2026 6:24 PM","Apr 28, 2026 2:16 PM","VST, ADT201",Closed,14d,Gabriela Novotna,gnovotna@email.cz,Investigator
+title,value,,,,,,,,,,,,,
+Search,,,,,,,,,,,,,,
+Site,"CZ10005 - Dr.Lubos Janu, CZ10008 - Dr.Zdenek Solle, CZ10011 - Dr. Marta Lendlova, CZ10004 - Dr. Erik Herman, CZ10012 - Dr.Ales Urban",,,,,,,,,,,,,
+Unresponded Only?,FALSE,,,,,,,,,,,,,
+Posted,From  -  To  - ,,,,,,,,,,,,,

Covance/_create_tables_equeries.py

@@ -0,0 +1,49 @@
+"""
+Vytvoří tabulku covance_equeries v databázi studie.
+Spusť jednorázově pro inicializaci.
+"""
+
+import mysql.connector
+import db_config
+
+DDL = """
+CREATE TABLE IF NOT EXISTS covance_equeries (
+    id                    INT AUTO_INCREMENT PRIMARY KEY,
+    import_id             INT NOT NULL,
+    study                 VARCHAR(20)  NOT NULL,
+    site_code             VARCHAR(10),
+    investigator_name     VARCHAR(100),
+    country               VARCHAR(30),
+    visit                 VARCHAR(100),
+    visit_collection_date DATETIME,
+    accession             VARCHAR(20),
+    subject               VARCHAR(20),
+    equery_id             INT,
+    create_date           DATETIME,
+    response_datetime     DATETIME,
+    issue_type            VARCHAR(100),
+    status                VARCHAR(20),
+    time_before_response  VARCHAR(20),
+    user_name             VARCHAR(100),
+    email                 VARCHAR(100),
+    study_role            VARCHAR(50),
+    FOREIGN KEY (import_id) REFERENCES iwrs_import(import_id),
+    INDEX idx_import   (import_id),
+    INDEX idx_site     (site_code),
+    INDEX idx_subject  (subject),
+    INDEX idx_equery   (equery_id),
+    INDEX idx_status   (status)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4;
+"""
+
+conn = 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,
+)
+cursor = conn.cursor()
+cursor.execute(DDL)
+conn.commit()
+cursor.close()
+conn.close()
+print("Tabulka covance_equeries OK.")

Covance/create_report.py

@@ -1,11 +1,13 @@
 """
 Covance samples report pro studii 42847922MDD3003.
-Čte z MySQL (nejnovější import), generuje Excel s 5 listy:
+Čte z MySQL (nejnovější import), generuje Excel s 7 listy:
   1. Přehled      — agregát per pacient+visit (Received / Not Received / Cancelled)
   2. Chybějící    — detail Not Received vzorků
-  3. Kity         — pivot kit inventory: centra × typy kitů
+  3. Kity         — kit inventory: centra × typy kitů s expirací
-  4. ZDROJ        — surová data samples
+  4. eQueries     — přehled eQuery dotazů (Open červeně)
-  5. ZDROJ Kity   — surová data kit inventory
+  5. ZDROJ Vzorky — surová data samples
+  6. ZDROJ Kity   — surová data kit inventory
+  7. ZDROJ eQuery — surová data eQueries
 """
 
 import os
@@ -37,6 +39,7 @@ EVEN_FILL      = PatternFill("solid", fgColor="EBF3FB")
 ODD_FILL       = PatternFill("solid", fgColor="FFFFFF")
 NOTRCV_FILL    = PatternFill("solid", fgColor="FCE4D6")
 CANCELLED_FILL = PatternFill("solid", fgColor="F2F2F2")
+OPEN_FILL      = PatternFill("solid", fgColor="FFC7CE")
 
 CENTER = Alignment(horizontal="center", vertical="center")
 LEFT   = Alignment(horizontal="left",   vertical="center")

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()