z230

Covance_UCO3001/create_report.py

@@ -22,14 +22,19 @@ assert csv_files, "CSV file not found!"
 csv_file = csv_files[0]
 print(f"Source csv:  {csv_file}")
 
-# Delete old output report if exists
+kit_csv_files = glob.glob(src_dir + "sponsor-study-36940-kit-inventory-on-hand-expiration.csv")
-today = date.today().strftime("%Y-%m-%d")
+assert kit_csv_files, "Kit inventory CSV not found!"
-out_filename = f"{today} 77242113UCO3001 Speciment Inventory report.xlsx"
+kit_csv_file = kit_csv_files[0]
-out_path = out_dir + out_filename
+print(f"Kit csv:     {kit_csv_file}")
 
-for old in glob.glob(out_dir + "*77242113UCO3001 Speciment Inventory report*.xlsx"):
+eq_csv_files = glob.glob(src_dir + "sponsor-study-36940-activity-reports-documents-equery.csv")
-    os.remove(old)
+assert eq_csv_files, "eQuery CSV not found!"
-    print(f"Deleted old: {old}")
+eq_csv_file = eq_csv_files[0]
+print(f"eQuery csv:  {eq_csv_file}")
+
+timestamp = datetime.now().strftime("%Y-%m-%d_%H%M%S")
+out_filename = f"{timestamp} 77242113UCO3001 CZE Labcorp samples and kit inventory report.xlsx"
+out_path = out_dir + out_filename
 
 # Copy source file to output — preserves all formatting perfectly
 shutil.copy2(src_file, out_path)
@@ -52,10 +57,8 @@ def fmt_date(val):
         return datetime.strptime(val, '%d-%b-%Y')
     return pd.to_datetime(val).to_pydatetime()
 
-# Get Container Receipt Date + Excel row for patient+specimen from given visit dataframe
 OK_STATUSES = {'Received', 'In Inventory', 'Shipped'}
 
-# Excel row = pandas df index + 2 (row 1 header, data from row 2)
 def get_specimen_info(visit_df, patient, specimen_type=None):
     rows = visit_df[visit_df['Patient No.'] == patient]
     if specimen_type:
@@ -66,7 +69,6 @@ def get_specimen_info(visit_df, patient, specimen_type=None):
     row = rows.iloc[0]
     return fmt_date(row['Container Receipt Date']), rows.index[0] + 2
 
-# Get Container Receipt Date + Excel row by Container Label Line 1 code and visit code
 def get_label_info(patient, label_code, visit_code):
     rows = df[(df['Patient No.'] == patient) &
               (df['Protocol Visit Code'] == visit_code) &
@@ -87,32 +89,47 @@ for col in src_ws.columns:
     max_len = max((len(str(cell.value)) if cell.value is not None else 0) for cell in col)
     src_ws.column_dimensions[get_column_letter(col[0].column)].width = min(max_len + 2, 50)
 
-# Create analysis sheet
+# ── Styly ────────────────────────────────────────────────────────────────────
+thin            = Side(style='thin')
+border          = Border(left=thin, right=thin, top=thin, bottom=thin)
+header_fill     = PatternFill("solid", fgColor="4472C4")
+header_font     = Font(name='Calibri', bold=True, size=11, color="FFFFFF")
+data_font       = Font(name='Calibri', size=11)
+date_font_link  = Font(name='Calibri', size=11, color="000000", underline='single')
+yes_fill        = PatternFill("solid", fgColor="E2EFDA")
+no_fill         = PatternFill("solid", fgColor="FFE7E7")
+sum_header_font = Font(name='Calibri', bold=True, size=11, color="000000")
+sum_total_font  = Font(name='Calibri', bold=True, size=11)
+zero_font       = Font(name='Calibri', size=11, color="BFBFBF")
+zero_red_font   = Font(name='Calibri', size=11, color="C00000")
+dark_blue_fill  = PatternFill("solid", fgColor="203764")
+orange_fill     = PatternFill("solid", fgColor="FFF2CC")
+green_fill      = PatternFill("solid", fgColor="E2EFDA")
+total_fill      = PatternFill("solid", fgColor="D9E1F2")
+exp_fill        = PatternFill("solid", fgColor="FFE7E7")
+ok_fill         = PatternFill("solid", fgColor="E2EFDA")
+
+# ── List: Přehled vzorků ──────────────────────────────────────────────────────
 analysis_ws = out_wb.create_sheet("Přehled vzorků")
 
-thin = Side(style='thin')
-border = Border(left=thin, right=thin, top=thin, bottom=thin)
-
-# Column definitions: (header, width)
-# No "Visit code" column
 columns = [
     ("Investigator Name",   24),
     ("Číslo pacienta",      20),
-    ("Máme biopsii SM11",   20),  # col 3  → SCREENING C:E
+    ("Máme biopsii SM11",   20),
     ("Máme RNA",            16),
     ("Máme Cryostor",       16),
-    ("DNA",                 14),  # col 6  → no group
+    ("DNA",                 14),
-    ("PLASMPK I-0 TROUGH",  18),  # col 7  → RANDOMIZACE I-0 G:L
+    ("PLASMPK I-0 TROUGH",  18),
     ("PLASMA PK I-0 PEAK",  18),
     ("SERUM ADA I-0 PRE",   18),
     ("SM06/SERUM BIOM",     16),
     ("SM07/WB RNA",         14),
     ("SM10/FECAL",          14),
-    ("PLASMPK I-2 TROUGH",  18),  # col 13 → I-2 M:P
+    ("PLASMPK I-2 TROUGH",  18),
     ("PLASMA PK I-2 PEAK",  18),
     ("SERUM ADA I-2 PRE",   18),
     ("STOOL I-2",           12),
-    ("PLASMPK I-4 TROUGH",  18),  # col 17 → I-4 Q:V
+    ("PLASMPK I-4 TROUGH",  18),
     ("PLASMA PK I-4 PEAK",  18),
     ("SERUM ADA I-4 PRE",   18),
     ("SM06/SERUM BIOM",     16),
@@ -120,9 +137,8 @@ columns = [
     ("STOOL I-4",           12),
 ]
 
-# Row 1 — group headers
+group_font   = Font(name='Calibri', bold=True, size=11)
-group_font  = Font(name='Calibri', bold=True, size=11)
+group_fill   = PatternFill("solid", fgColor="FFFFFF")
-group_fill  = PatternFill("solid", fgColor="FFFFFF")  # white, same as user's theme=0
 group_border = Border(left=thin, right=thin, top=thin, bottom=thin)
 
 groups = [
@@ -138,18 +154,13 @@ for start_col, end_col, label in groups:
     cell.fill = group_fill
     cell.alignment = Alignment(horizontal='center', vertical='center')
     cell.border = group_border
-    # apply border to all merged cells
     for c in range(start_col, end_col + 1):
         analysis_ws.cell(row=1, column=c).border = group_border
 
 analysis_ws.row_dimensions[1].height = 20
 
-# Row 2 — column headers
+for col_idx, (hdr, width) in enumerate(columns, 1):
-header_fill = PatternFill("solid", fgColor="4472C4")
+    cell = analysis_ws.cell(row=2, column=col_idx, value=hdr)
-header_font = Font(name='Calibri', bold=True, size=11, color="FFFFFF")
-
-for col_idx, (header, width) in enumerate(columns, 1):
-    cell = analysis_ws.cell(row=2, column=col_idx, value=header)
     cell.font = header_font
     cell.fill = header_fill
     cell.border = border
@@ -157,21 +168,11 @@ for col_idx, (header, width) in enumerate(columns, 1):
     analysis_ws.column_dimensions[get_column_letter(col_idx)].width = width
 
 analysis_ws.row_dimensions[2].height = 30
-
-# Freeze first 2 columns and first 2 rows
 analysis_ws.freeze_panes = "C3"
 
-# Data rows start at row 3
-date_font_link = Font(name='Calibri', size=11, color="000000", underline='single')
-yes_fill = PatternFill("solid", fgColor="E2EFDA")
-no_fill  = PatternFill("solid", fgColor="FFE7E7")
-data_font = Font(name='Calibri', size=11)
-
 src_sheet_name = out_wb.sheetnames[0]
 pat_sheet_name = "Seznam pacientů"
 
-# Build patient → first Excel row in "Seznam pacientů" (header=row1, data from row2)
-# pat_df is built later, but we need sorted order — pre-sort here too
 _csv_df_pre = pd.read_csv(csv_file, encoding='utf-8')
 _pat_pre = _csv_df_pre[['SiteNumber', 'Subject', 'Field4Value']].copy()
 _pat_pre['Field4Value'] = _pat_pre['Field4Value'].apply(lambda v: datetime.strptime(str(v).strip(), '%d %b %Y') if pd.notna(v) else None)
@@ -180,9 +181,8 @@ patient_row_map = {}
 for i, row in _pat_pre.iterrows():
     pat = row['Subject']
     if pat not in patient_row_map:
-        patient_row_map[pat] = i + 2  # +1 for 1-based, +1 for header row
+        patient_row_map[pat] = i + 2
 
-# Only patients with any BXSCR record
 bxscr_patients = sorted(bxscr['Patient No.'].dropna().unique())
 
 for row_idx, patient in enumerate(bxscr_patients, 3):
@@ -208,7 +208,6 @@ for row_idx, patient in enumerate(bxscr_patients, 3):
     sm074,   sm074_row   = get_label_info(patient, 'SM07/WB RNA',          'I-4')
     stool4,  stool4_row  = get_label_info(patient, 'STOOL I-4',            'I-4')
 
-    # col 1-2: plain text, col 3+: (date, excel_row) tuples
     row_data = [investigator, patient,
                 (sm11, sm11_row), (rna, rna_row), (cryo, cryo_row), (dna_date, dna_row),
                 (trough, trough_row), (peak, peak_row), (ada, ada_row),
@@ -239,9 +238,8 @@ for row_idx, patient in enumerate(bxscr_patients, 3):
         cell.border = border
         cell.alignment = Alignment(horizontal='center', vertical='center')
 
-# ── Seznam pacientů sheet ────────────────────────────────────────────────────
+# ── List: Seznam pacientů ─────────────────────────────────────────────────────
 csv_df = pd.read_csv(csv_file, encoding='utf-8')
-
 patients_ws = out_wb.create_sheet("Seznam pacientů")
 
 pat_columns = [
@@ -252,7 +250,6 @@ pat_columns = [
     ("Typ návštěvy",   16),
 ]
 
-# Header row
 for col_idx, (col_name, width) in enumerate(pat_columns, 1):
     cell = patients_ws.cell(row=1, column=col_idx, value=col_name)
     cell.font = header_font
@@ -264,8 +261,7 @@ for col_idx, (col_name, width) in enumerate(pat_columns, 1):
 patients_ws.row_dimensions[1].height = 30
 patients_ws.freeze_panes = "A2"
 
-# Prepare and sort data
+def parse_date_edcstd(val):
-def parse_date(val):
     if pd.isna(val) or str(val).strip() == '':
         return None
     try:
@@ -274,10 +270,9 @@ def parse_date(val):
         return None
 
 pat_df = csv_df[['SiteNumber', 'Subject', 'InstanceName', 'Field4Value', 'Field5Value']].copy()
-pat_df['Field4Value'] = pat_df['Field4Value'].apply(parse_date)
+pat_df['Field4Value'] = pat_df['Field4Value'].apply(parse_date_edcstd)
 pat_df = pat_df.sort_values(['SiteNumber', 'Subject', 'Field4Value']).reset_index(drop=True)
 
-# Data rows
 for row_idx, row in enumerate(pat_df.itertuples(index=False), 2):
     for col_idx, value in enumerate(row, 1):
         cell = patients_ws.cell(row=row_idx, column=col_idx, value=value)
@@ -287,7 +282,244 @@ for row_idx, row in enumerate(pat_df.itertuples(index=False), 2):
         if col_idx == 4 and value is not None:
             cell.number_format = 'DD-MMM-YYYY'
 
+# ── Kit inventory — načtení a příprava dat ────────────────────────────────────
+kit_df_raw = pd.read_csv(kit_csv_file, encoding="utf-8")
+cze = kit_df_raw[kit_df_raw["Country"] == "CZE"].copy()
+
+def parse_kit_date(val):
+    if pd.isna(val):
+        return None
+    try:
+        return datetime.strptime(str(val).strip(), "%b %d, %Y")
+    except:
+        return None
+
+cze["Shipped Date"]    = cze["Shipped Date"].apply(parse_kit_date)
+cze["Expiration Date"] = cze["Expiration Date"].apply(parse_kit_date)
+cze = cze.sort_values(["Site", "Kit Type", "Expiration Date"]).reset_index(drop=True)
+
+today_dt = datetime.combine(date.today(), datetime.min.time())
+
+def bucket(exp_date):
+    if exp_date is None:
+        return None
+    return "soon" if (exp_date - today_dt).days <= 30 else "ok"
+
+cze["_bucket"] = cze["Expiration Date"].apply(bucket)
+
+kit_order = sorted(cze["Kit Type"].unique(), key=lambda x: (str(x).lstrip("T-").zfill(5), str(x)))
+kit_desc  = cze.drop_duplicates("Kit Type").set_index("Kit Type")["Description"].to_dict()
+kit_sites = sorted(cze["Site"].unique())
+
+# ── Pomocná funkce pro souhrnné tabulky ───────────────────────────────────────
+def write_summary_table(ws, current_row, title, rows_data, col_a_header):
+    for c in range(1, 5):
+        cell = ws.cell(row=current_row, column=c)
+        cell.fill = dark_blue_fill
+        cell.border = border
+    ws.cell(row=current_row, column=1, value=title).font = Font(name='Calibri', bold=True, size=12, color="FFFFFF")
+    ws.cell(row=current_row, column=1).alignment = Alignment(horizontal="left", vertical="center")
+    ws.merge_cells(start_row=current_row, start_column=1, end_row=current_row, end_column=4)
+    ws.row_dimensions[current_row].height = 22
+    current_row += 1
+
+    for col_idx, (h, f) in enumerate(zip(
+        [col_a_header, "Description", "Expiruje do 30 dní", "Expiruje později"],
+        [header_fill, header_fill, orange_fill, green_fill]
+    ), 1):
+        cell = ws.cell(row=current_row, column=col_idx, value=h)
+        cell.font = sum_header_font
+        cell.fill = f
+        cell.border = border
+        cell.alignment = Alignment(horizontal="center", vertical="center", wrap_text=True)
+    ws.row_dimensions[current_row].height = 28
+    current_row += 1
+
+    totals = [0, 0]
+    for col_a, col_b, n_soon, n_ok in rows_data:
+        totals[0] += n_soon
+        totals[1] += n_ok
+        all_zero  = (n_soon == 0 and n_ok == 0)
+        row_vals  = [col_a, col_b, n_soon, n_ok]
+        row_fills = [None, None,
+                     orange_fill if n_soon > 0 else None,
+                     green_fill  if n_ok   > 0 else None]
+        for col_idx, (val, rfill) in enumerate(zip(row_vals, row_fills), 1):
+            cell = ws.cell(row=current_row, column=col_idx, value=val)
+            if col_idx >= 3 and val == 0:
+                cell.font = zero_red_font if all_zero else zero_font
+            else:
+                cell.font = data_font
+            cell.border = border
+            cell.alignment = Alignment(horizontal="center" if col_idx >= 2 else "left", vertical="center")
+            if rfill:
+                cell.fill = rfill
+        current_row += 1
+
+    for col_idx, val in enumerate(["CELKEM", "", totals[0], totals[1]], 1):
+        cell = ws.cell(row=current_row, column=col_idx, value=val)
+        cell.font = sum_total_font
+        cell.fill = total_fill
+        cell.border = border
+        cell.alignment = Alignment(horizontal="center" if col_idx >= 2 else "left", vertical="center")
+    current_row += 2
+    return current_row
+
+# ── List: Kit Inventory CZE ───────────────────────────────────────────────────
+kit_ws = out_wb.create_sheet("Kit Inventory CZE")
+
+listing_columns = [
+    ("Project No.",        14),
+    ("Region",             10),
+    ("Country",            10),
+    ("Site",               38),
+    ("Kit Type",           12),
+    ("Description",        22),
+    ("Accession",          18),
+    ("Shipped Date",       16),
+    ("Expiration Date",    16),
+    ("Days to Expiration", 20),
+]
+
+for col_idx, (hdr, width) in enumerate(listing_columns, 1):
+    cell = kit_ws.cell(row=1, column=col_idx, value=hdr)
+    cell.font = header_font
+    cell.fill = header_fill
+    cell.border = border
+    cell.alignment = Alignment(horizontal="center", vertical="center", wrap_text=True)
+    kit_ws.column_dimensions[get_column_letter(col_idx)].width = width
+
+kit_ws.row_dimensions[1].height = 30
+kit_ws.freeze_panes = "A2"
+
+for row_idx, row in enumerate(cze.itertuples(index=False), 2):
+    days = row[9]
+    for col_idx, (col_name, _) in enumerate(listing_columns, 1):
+        value = row[col_idx - 1]
+        cell = kit_ws.cell(row=row_idx, column=col_idx, value=value)
+        cell.font = data_font
+        cell.border = border
+        cell.alignment = Alignment(horizontal="center", vertical="center")
+        if col_name in ("Shipped Date", "Expiration Date") and value is not None:
+            cell.number_format = "DD-MMM-YYYY"
+        if col_name == "Days to Expiration":
+            cell.fill = exp_fill if (pd.notna(days) and days <= 60) else ok_fill
+
+kit_ws.auto_filter.ref = f"A1:{get_column_letter(len(listing_columns))}1"
+
+# ── List: Přehled po centrech ─────────────────────────────────────────────────
+ctr_ws = out_wb.create_sheet("Přehled po centrech")
+ctr_ws.column_dimensions["A"].width = 22
+ctr_ws.column_dimensions["B"].width = 24
+ctr_ws.column_dimensions["C"].width = 22
+ctr_ws.column_dimensions["D"].width = 20
+
+current_row = 1
+for site in kit_sites:
+    site_df = cze[cze["Site"] == site]
+    rows_data = []
+    for kit in kit_order:
+        desc        = kit_desc.get(kit, "")
+        kit_site_df = site_df[site_df["Kit Type"] == kit]
+        n_soon = (kit_site_df["_bucket"] == "soon").sum()
+        n_ok   = (kit_site_df["_bucket"] == "ok").sum()
+        rows_data.append((f"{kit} — {desc}", desc, n_soon, n_ok))
+    current_row = write_summary_table(ctr_ws, current_row, site, rows_data, "Kit Type")
+
+# ── List: Přehled po typech kitů ──────────────────────────────────────────────
+sum_ws = out_wb.create_sheet("Přehled po typech")
+sum_ws.column_dimensions["A"].width = 38
+sum_ws.column_dimensions["B"].width = 22
+sum_ws.column_dimensions["C"].width = 22
+sum_ws.column_dimensions["D"].width = 20
+
+current_row = 1
+for kit in kit_order:
+    desc   = kit_desc.get(kit, "")
+    kit_df = cze[cze["Kit Type"] == kit]
+    rows_data = []
+    for site in sorted(kit_df["Site"].unique()):
+        site_df = kit_df[kit_df["Site"] == site]
+        n_soon = (site_df["_bucket"] == "soon").sum()
+        n_ok   = (site_df["_bucket"] == "ok").sum()
+        rows_data.append((site, desc, n_soon, n_ok))
+    current_row = write_summary_table(sum_ws, current_row, f"Kit Type {kit} — {desc}", rows_data, "Centrum")
+
+# ── List: eQueries ───────────────────────────────────────────────────────────
+eq_df = pd.read_csv(eq_csv_file, encoding="utf-8")
+eq_cze = eq_df[eq_df["Country"] == "CZECH REPUBLIC"].copy()
+
+status_order = {"Open": 0, "Response Received": 1, "Closed": 2}
+eq_cze["_status_order"] = eq_cze["Status"].map(status_order).fillna(99)
+eq_cze = eq_cze.sort_values(["_status_order", "Site"]).reset_index(drop=True)
+
+def parse_eq_date(val):
+    if pd.isna(val):
+        return None
+    for fmt in ("%b %d, %Y %I:%M %p", "%b %d, %Y %I:%M %p"):
+        try:
+            return datetime.strptime(str(val).strip(), fmt)
+        except:
+            pass
+    try:
+        return datetime.strptime(str(val).strip().split(" 12:00")[0], "%b %d, %Y")
+    except:
+        return None
+
+eq_ws = out_wb.create_sheet("eQueries")
+
+eq_columns = [
+    ("Site",                  36),
+    ("Subject",               14),
+    ("Visit",                 20),
+    ("Visit Collection Date", 20),
+    ("Accession",             16),
+    ("eQueryId",              12),
+    ("Issue Type",            30),
+    ("Status",                18),
+    ("Create Date",           20),
+    ("Response Date Time",    20),
+    ("Time Before Response",  20),
+    ("User Name",             20),
+]
+
+status_fills = {
+    "Open":              PatternFill("solid", fgColor="FFE7E7"),
+    "Response Received": PatternFill("solid", fgColor="FFF2CC"),
+    "Closed":            PatternFill("solid", fgColor="E2EFDA"),
+}
+
+for col_idx, (hdr, width) in enumerate(eq_columns, 1):
+    cell = eq_ws.cell(row=1, column=col_idx, value=hdr)
+    cell.font = header_font
+    cell.fill = header_fill
+    cell.border = border
+    cell.alignment = Alignment(horizontal="center", vertical="center", wrap_text=True)
+    eq_ws.column_dimensions[get_column_letter(col_idx)].width = width
+
+eq_ws.row_dimensions[1].height = 30
+eq_ws.freeze_panes = "A2"
+
+for row_idx, row in enumerate(eq_cze.itertuples(index=False), 2):
+    status = row[eq_cze.columns.get_loc("Status")]
+    rfill  = status_fills.get(status)
+    for col_idx, (col_name, _) in enumerate(eq_columns, 1):
+        value = row[eq_cze.columns.get_loc(col_name)]
+        if col_name in ("Visit Collection Date", "Create Date", "Response Date Time"):
+            value = parse_eq_date(value)
+        cell = eq_ws.cell(row=row_idx, column=col_idx, value=value)
+        cell.font = data_font
+        cell.border = border
+        cell.alignment = Alignment(horizontal="center" if col_idx > 1 else "left", vertical="center")
+        if col_name in ("Visit Collection Date", "Create Date", "Response Date Time") and value:
+            cell.number_format = "DD-MMM-YYYY HH:MM"
+        if rfill:
+            cell.fill = rfill
+
+eq_ws.auto_filter.ref = f"A1:{get_column_letter(len(eq_columns))}1"
+
 out_wb.save(out_path)
 print(f"Saved: {out_path}")
-print(f"Patients with BXSCR: {len(bxscr_patients)}")
+print(f"Patients with BXSCR: {len(bxscr_patients)}, All unique patients: {len(all_patients)}")
-print(f"All unique patients: {len(all_patients)}")
+print(f"CZE kit rows: {len(cze)}, Kit types: {len(kit_order)}, Sites: {len(kit_sites)}")
+print(f"CZE eQueries: {len(eq_cze)} (Open: {(eq_cze['Status']=='Open').sum()}, Response Received: {(eq_cze['Status']=='Response Received').sum()}, Closed: {(eq_cze['Status']=='Closed').sum()})")