import json, subprocess, base64
from io import BytesIO
from pptx import Presentation
from pptx.util import Inches, Pt, Emu
from pptx.dml.color import RGBColor
from pptx.enum.text import PP_ALIGN, MSO_ANCHOR
from pptx.util import Inches, Pt

# ── Color palette ──────────────────────────────────────────────────────────────
DARK_BLUE   = RGBColor(0x0D, 0x3B, 0x66)   # deep navy
MED_BLUE    = RGBColor(0x15, 0x78, 0xC2)   # accent blue
LIGHT_BLUE  = RGBColor(0xD6, 0xEA, 0xF8)   # pale bg
WHITE       = RGBColor(0xFF, 0xFF, 0xFF)
GOLD        = RGBColor(0xF4, 0xD0, 0x3F)
DARK_TEXT   = RGBColor(0x1A, 0x1A, 0x2E)
RED_ACCENT  = RGBColor(0xC0, 0x39, 0x2B)
GREEN_ACCENT= RGBColor(0x1E, 0x8B, 0x4C)

# ── Image URLs ─────────────────────────────────────────────────────────────────
IMAGE_URLS = [
    "https://cdn.orris.care/cdss_images/49d38cde9a3992651593182476968ceb171b1e0388a71f199f66da0054691e9f.png",  # mechanism diagram
    "https://cdn.orris.care/cdss_images/8426b25c5dec7b4f22e4a4f723295873648a2634e18dfa0fbd624bf7989e52a2.png",  # EM image
    "https://cdn.orris.care/cdss_images/pmc_clinical_VQA_14f7bd8cd4cde816d7111c7f43998f25b6a4a7698b26c13ca0da5be5df07a870.jpg",  # histopathology
]

print("Fetching images...")
raw = subprocess.check_output(["python", "/tmp/skills/shared/scripts/fetch_images.py"] + IMAGE_URLS)
imgs = json.loads(raw)
img_data = []
for img in imgs:
    if img["base64"]:
        mime, b64 = img["base64"].split(";base64,", 1)
        img_data.append(BytesIO(base64.b64decode(b64)))
    else:
        img_data.append(None)
print(f"Loaded {sum(1 for x in img_data if x)} images")

# ── Helpers ────────────────────────────────────────────────────────────────────
prs = Presentation()
prs.slide_width  = Inches(13.333)
prs.slide_height = Inches(7.5)
blank = prs.slide_layouts[6]

def add_rect(slide, x, y, w, h, fill_rgb, alpha=None):
    from pptx.oxml.ns import qn
    shape = slide.shapes.add_shape(1, Inches(x), Inches(y), Inches(w), Inches(h))
    shape.line.fill.background()
    fill = shape.fill
    fill.solid()
    fill.fore_color.rgb = fill_rgb
    return shape

def add_text(slide, text, x, y, w, h, size, bold=False, color=WHITE,
             align=PP_ALIGN.LEFT, wrap=True, italic=False, anchor=MSO_ANCHOR.TOP):
    tb = slide.shapes.add_textbox(Inches(x), Inches(y), Inches(w), Inches(h))
    tf = tb.text_frame
    tf.word_wrap = wrap
    tf.vertical_anchor = anchor
    tf.margin_left = 0; tf.margin_right = 0
    tf.margin_top = 0;  tf.margin_bottom = 0
    p = tf.paragraphs[0]
    p.alignment = align
    run = p.add_run()
    run.text = text
    run.font.size  = Pt(size)
    run.font.bold  = bold
    run.font.italic = italic
    run.font.color.rgb = color
    run.font.name  = "Calibri"
    return tb

def add_multiline(slide, lines, x, y, w, h, size, color=DARK_TEXT,
                  bold_first=False, line_spacing=1.15, bullet=True):
    """lines = list of (text, bold) tuples or plain strings"""
    tb = slide.shapes.add_textbox(Inches(x), Inches(y), Inches(w), Inches(h))
    tf = tb.text_frame
    tf.word_wrap = True
    tf.margin_left  = Pt(4)
    tf.margin_right = Pt(4)
    tf.margin_top   = Pt(2)
    tf.margin_bottom= Pt(2)
    first = True
    for item in lines:
        if isinstance(item, tuple):
            text, bold = item
        else:
            text, bold = item, False
        if first:
            p = tf.paragraphs[0]
            first = False
        else:
            p = tf.add_paragraph()
        from pptx.util import Pt as Pt2
        p.space_after = Pt2(3)
        run = p.add_run()
        prefix = "• " if bullet else ""
        run.text = prefix + text
        run.font.size  = Pt(size)
        run.font.bold  = bold
        run.font.color.rgb = color
        run.font.name  = "Calibri"
    return tb

def add_image(slide, img_io, x, y, w, h=None):
    if img_io is None:
        return
    img_io.seek(0)
    if h:
        slide.shapes.add_picture(img_io, Inches(x), Inches(y), Inches(w), Inches(h))
    else:
        slide.shapes.add_picture(img_io, Inches(x), Inches(y), Inches(w))

def header_bar(slide, title, subtitle=None):
    """Blue header bar at top of slide"""
    add_rect(slide, 0, 0, 13.333, 1.2, DARK_BLUE)
    add_rect(slide, 0, 1.2, 13.333, 0.08, GOLD)
    add_text(slide, title, 0.3, 0.1, 12.5, 0.8, 32, bold=True,
             color=WHITE, align=PP_ALIGN.LEFT, anchor=MSO_ANCHOR.MIDDLE)
    if subtitle:
        add_text(slide, subtitle, 0.3, 0.82, 12.5, 0.4, 14,
                 color=GOLD, align=PP_ALIGN.LEFT)

def footer(slide, text="Pertussis | Bordetella pertussis | Apurba Sastry's Medical Microbiology"):
    add_rect(slide, 0, 7.2, 13.333, 0.3, DARK_BLUE)
    add_text(slide, text, 0.3, 7.2, 12.5, 0.3, 10, color=RGBColor(0xAA,0xCC,0xFF),
             align=PP_ALIGN.CENTER, anchor=MSO_ANCHOR.MIDDLE)

# ══════════════════════════════════════════════════════════════════════════════
# SLIDE 1 – Title
# ══════════════════════════════════════════════════════════════════════════════
slide = prs.slides.add_slide(blank)
add_rect(slide, 0, 0, 13.333, 7.5, DARK_BLUE)
add_rect(slide, 0, 2.8, 13.333, 2.4, MED_BLUE)
add_rect(slide, 0, 2.75, 13.333, 0.08, GOLD)
add_rect(slide, 0, 5.12, 13.333, 0.08, GOLD)

add_text(slide, "PERTUSSIS", 0.5, 1.0, 12.3, 1.5, 72, bold=True,
         color=WHITE, align=PP_ALIGN.CENTER, anchor=MSO_ANCHOR.MIDDLE)
add_text(slide, "Whooping Cough", 0.5, 2.4, 12.3, 0.6, 28,
         color=GOLD, align=PP_ALIGN.CENTER)
add_text(slide, "Causative Agent: Bordetella pertussis", 0.5, 2.95, 12.3, 0.7, 22,
         color=WHITE, align=PP_ALIGN.CENTER, anchor=MSO_ANCHOR.MIDDLE)
add_text(slide, "Gram-negative coccobacillus | Strict aerobe | Non-motile | No animal reservoir",
         0.5, 3.55, 12.3, 0.5, 15, color=LIGHT_BLUE, align=PP_ALIGN.CENTER)
add_text(slide, "As per Apurba Sastry's Essentials of Medical Microbiology",
         0.5, 5.3, 12.3, 0.5, 13, color=GOLD, align=PP_ALIGN.CENTER, italic=True)
add_text(slide, "Microbiology | MBBS Second Professional",
         0.5, 6.8, 12.3, 0.5, 13, color=RGBColor(0xAA,0xCC,0xFF), align=PP_ALIGN.CENTER)

# ══════════════════════════════════════════════════════════════════════════════
# SLIDE 2 – Bacteriology & Culture
# ══════════════════════════════════════════════════════════════════════════════
slide = prs.slides.add_slide(blank)
add_rect(slide, 0, 0, 13.333, 7.5, RGBColor(0xF4,0xF6,0xFF))
header_bar(slide, "Bacteriology & Cultural Characteristics")
footer(slide)

# Left panel
add_rect(slide, 0.3, 1.45, 5.8, 5.5, WHITE)
add_rect(slide, 0.3, 1.45, 5.8, 0.45, MED_BLUE)
add_text(slide, "MORPHOLOGY & BIOLOGY", 0.35, 1.47, 5.7, 0.4, 13, bold=True,
         color=WHITE, anchor=MSO_ANCHOR.MIDDLE)
add_multiline(slide, [
    ("Gram-negative coccobacillus (0.5–1.0 µm)", True),
    ("Morphologically similar to Haemophilus", False),
    ("Strict aerobe", True),
    ("Non-motile, non-sporing", False),
    ("Capsule present in virulent phase", False),
    ("Oxidase positive, catalase positive", False),
    ("Nitrate, citrate, urea – NEGATIVE", False),
    ("NO known animal reservoir", True),
    ("Survives only briefly outside human host", False),
], 0.4, 2.0, 5.6, 4.8, 13.5, color=DARK_TEXT)

# Right panel
add_rect(slide, 6.4, 1.45, 6.6, 5.5, WHITE)
add_rect(slide, 6.4, 1.45, 6.6, 0.45, MED_BLUE)
add_text(slide, "CULTURE REQUIREMENTS", 6.45, 1.47, 6.5, 0.4, 13, bold=True,
         color=WHITE, anchor=MSO_ANCHOR.MIDDLE)
add_multiline(slide, [
    ("Media: Bordet-Gengou (BG) medium", True),
    ("   Potato-blood-glycerol agar + penicillin G", False),
    ("Preferred: Regan-Lowe charcoal medium", True),
    ("   Charcoal + horse blood + cephalexin + amphotericin B", False),
    ("   Longer shelf life than BG", False),
    ("Incubation: 35–37°C, 3–7 days (aerobic, moist)", False),
    ("Colonies: Small, shiny 'mercury droplet' / bisected pearl", True),
    ("Identified by immunofluorescence staining", False),
    ("Charcoal/blood neutralises inhibitory compounds", False),
], 6.5, 2.0, 6.4, 4.8, 13.5, color=DARK_TEXT)

# ══════════════════════════════════════════════════════════════════════════════
# SLIDE 3 – Virulence Factors
# ══════════════════════════════════════════════════════════════════════════════
slide = prs.slides.add_slide(blank)
add_rect(slide, 0, 0, 13.333, 7.5, RGBColor(0xF0,0xF4,0xFF))
header_bar(slide, "Virulence Factors", "BvgA/BvgS Two-Component Regulatory System controls all virulence genes")
footer(slide)

# 6 factor boxes in 2 rows × 3 cols
factors = [
    ("Pertussis Toxin (PT)", MED_BLUE,
     "A-B toxin (A1 + B5 oligomer)\n• ADP-ribosylates Giα → ↑cAMP\n• Causes: Lymphocytosis, histamine\n  sensitization, ↑insulin secretion\n• Immunosuppression of macrophages\n• KEY exam toxin"),
    ("Filamentous Hemagglutinin (FHA)", RGBColor(0x11,0x6A,0xA0),
     "Primary adhesin\n• Binds RGD integrin sequences on\n  ciliated epithelium\n• Secreted outside bacterial cell\n• Present in ALL acellular vaccines"),
    ("Tracheal Cytotoxin (TCT)", RED_ACCENT,
     "Peptidoglycan disaccharide fragment\n• Not BvgA/BvgS regulated\n• Induces IL-1 & Nitric Oxide in\n  ciliated cells\n• Destroys & extrudes ciliated cells\n• Causes denuded mucosa → cough"),
    ("Adenylate Cyclase Toxin (ACT/CyaA)", RGBColor(0x7D,0x3C,0x98),
     "Binds CR3 (CD11b) on phagocytes\n• Activated by calmodulin inside cell\n• Supraphysiologic ↑cAMP\n• Inhibits oxidative burst, chemotaxis\n• Kills neutrophils & macrophages"),
    ("Pertactin (Prn)", GREEN_ACCENT,
     "Outer membrane protein (~69 kDa)\n• Adhesin – binds integrins\n• KEY vaccine antigen\n• Pertactin-deficient strains\n  emerging due to vaccine pressure"),
    ("Fimbriae / Pili (FIM 2, FIM 3)", RGBColor(0xD3,0x54,0x00),
     "Surface appendages\n• Adhesins for ciliated epithelium\n• Role in tracheal colonization\n• Present in some acellular\n  vaccine formulations"),
]

cols = [0.25, 4.55, 8.85]
rows = [1.45, 4.35]
box_w, box_h = 4.0, 2.7

for i, (name, color, desc) in enumerate(factors):
    r, c = divmod(i, 3)
    x = cols[c]
    y = rows[r]
    add_rect(slide, x, y, box_w, box_h, WHITE)
    add_rect(slide, x, y, box_w, 0.42, color)
    add_text(slide, name, x+0.1, y+0.02, box_w-0.2, 0.38, 11.5, bold=True,
             color=WHITE, anchor=MSO_ANCHOR.MIDDLE, wrap=True)
    # desc as plain textbox
    tb = slide.shapes.add_textbox(Inches(x+0.1), Inches(y+0.5), Inches(box_w-0.2), Inches(box_h-0.6))
    tf = tb.text_frame; tf.word_wrap = True
    tf.margin_left = 0; tf.margin_right = 0; tf.margin_top = 0; tf.margin_bottom = 0
    for j, line in enumerate(desc.split("\n")):
        p = tf.paragraphs[0] if j == 0 else tf.add_paragraph()
        run = p.add_run(); run.text = line
        run.font.size = Pt(11); run.font.name = "Calibri"
        run.font.color.rgb = DARK_TEXT
        run.font.bold = (j == 0)

# ══════════════════════════════════════════════════════════════════════════════
# SLIDE 4 – Pathogenesis with diagram image
# ══════════════════════════════════════════════════════════════════════════════
slide = prs.slides.add_slide(blank)
add_rect(slide, 0, 0, 13.333, 7.5, RGBColor(0xF8,0xF9,0xFF))
header_bar(slide, "Pathogenesis of Pertussis", "Non-invasive disease — all pathology mediated by toxins")
footer(slide)

# Steps on left
add_rect(slide, 0.25, 1.45, 7.2, 5.7, WHITE)
steps = [
    ("Step 1 – Attachment", "B. pertussis attaches to ciliated bronchial epithelium via FHA, pertactin, fimbriae & PT binding subunit (B oligomer)"),
    ("Step 2 – Toxin Production", "Bacteria immobilize cilia, then secrete TCT (destroys ciliated cells via IL-1/NO) and ACT (kills macrophages/neutrophils via ↑cAMP)"),
    ("Step 3 – Epithelial Destruction", "Ciliated cells progressively extruded → denuded mucosa without ciliary blanket → impaired mucociliary clearance → PERSISTENT COUGH"),
    ("Step 4 – PT Absorption", "PT absorbed into bloodstream → systemic effects: lymphocytosis, histamine sensitization, ↑insulin secretion, immune paralysis"),
    ("KEY POINT", "B. pertussis does NOT invade tissue or bloodstream — disease is ENTIRELY toxin-mediated"),
]
y_pos = 1.55
for title, body in steps:
    is_key = title == "KEY POINT"
    bg = RGBColor(0xFF,0xF3,0xCD) if is_key else LIGHT_BLUE
    tc = RED_ACCENT if is_key else MED_BLUE
    add_rect(slide, 0.3, y_pos, 7.1, 0.25, tc)
    add_text(slide, title, 0.35, y_pos, 7.0, 0.24, 11, bold=True,
             color=WHITE, anchor=MSO_ANCHOR.MIDDLE)
    add_rect(slide, 0.3, y_pos+0.25, 7.1, 0.68, bg)
    tb = slide.shapes.add_textbox(Inches(0.4), Inches(y_pos+0.27), Inches(6.9), Inches(0.64))
    tf = tb.text_frame; tf.word_wrap = True
    tf.margin_left=0;tf.margin_right=0;tf.margin_top=0;tf.margin_bottom=0
    p=tf.paragraphs[0]; run=p.add_run(); run.text=body
    run.font.size=Pt(11.5); run.font.name="Calibri"; run.font.color.rgb=DARK_TEXT
    y_pos += 1.06

# Right: mechanism diagram image
add_text(slide, "Cellular mechanism of epithelial destruction", 7.7, 1.45, 5.3, 0.35, 11.5,
         bold=True, color=MED_BLUE, align=PP_ALIGN.CENTER)
if img_data[0]:
    img_data[0].seek(0)
    slide.shapes.add_picture(img_data[0], Inches(7.6), Inches(1.85), Inches(5.4), Inches(3.6))

add_text(slide, "↑ B. pertussis attaches to cilia → toxin secretion (PT, AC, TCT) → ciliated cell extrusion",
         7.6, 5.5, 5.4, 0.5, 10, color=RGBColor(0x55,0x55,0x55),
         align=PP_ALIGN.CENTER, italic=True, wrap=True)

# EM image below
if img_data[1]:
    img_data[1].seek(0)
    slide.shapes.add_picture(img_data[1], Inches(7.6), Inches(5.1), Inches(2.5), Inches(1.9))
add_text(slide, "SEM: B. pertussis (large arrow)\nattached to cilia (small arrow)", 10.2, 5.1, 2.9, 0.9,
         9.5, color=DARK_TEXT, wrap=True, italic=True)

# ══════════════════════════════════════════════════════════════════════════════
# SLIDE 5 – Clinical Stages
# ══════════════════════════════════════════════════════════════════════════════
slide = prs.slides.add_slide(blank)
add_rect(slide, 0, 0, 13.333, 7.5, RGBColor(0xF0,0xF8,0xFF))
header_bar(slide, "Clinical Features — Three Stages of Pertussis")
footer(slide)

stages = [
    ("1. CATARRHAL STAGE", "1–2 weeks", MED_BLUE, [
        "Profuse mucoid rhinorrhea",
        "Low-grade fever, malaise, sneezing",
        "Anorexia",
        "⚠ MOST COMMUNICABLE STAGE",
        "Indistinguishable from common cold",
        "Large no. of organisms in nasopharynx",
    ]),
    ("2. PAROXYSMAL STAGE", "2–4+ weeks", RED_ACCENT, [
        "Paroxysmal coughing (15–25 rapid coughs)",
        "Followed by INSPIRATORY WHOOP",
        "Post-tussive vomiting",
        "Cyanosis during severe episodes",
        "Apnea in infants (instead of whoop)",
        "MARKED LYMPHOCYTOSIS (15,000–100,000/µL)",
    ]),
    ("3. CONVALESCENT STAGE", "Weeks–months", GREEN_ACCENT, [
        "Gradual resolution of paroxysms",
        "Cough decreases in frequency & severity",
        "Intercurrent infections may trigger recurrence",
        "Immunity develops (not lifelong)",
        "Second attacks tend to be mild",
        "",
    ]),
]

x_starts = [0.25, 4.6, 8.95]
for i, (title, duration, color, bullets) in enumerate(stages):
    x = x_starts[i]
    add_rect(slide, x, 1.45, 4.1, 5.6, WHITE)
    add_rect(slide, x, 1.45, 4.1, 0.6, color)
    add_text(slide, title, x+0.1, 1.47, 3.9, 0.35, 13, bold=True,
             color=WHITE, anchor=MSO_ANCHOR.MIDDLE)
    add_text(slide, f"Duration: {duration}", x+0.1, 1.82, 3.9, 0.25, 11,
             color=GOLD if color==MED_BLUE else WHITE, anchor=MSO_ANCHOR.MIDDLE)
    add_multiline(slide, bullets, x+0.15, 2.15, 3.8, 4.8, 12.5, color=DARK_TEXT)

# Incubation period note
add_rect(slide, 0.25, 7.05, 12.8, 0.2, GOLD)
add_text(slide, "Incubation period: 7–10 days   |   Communicability: Highest in catarrhal stage", 
         0.3, 7.05, 12.7, 0.2, 11, color=DARK_TEXT, align=PP_ALIGN.CENTER, anchor=MSO_ANCHOR.MIDDLE)

# ══════════════════════════════════════════════════════════════════════════════
# SLIDE 6 – Laboratory Diagnosis
# ══════════════════════════════════════════════════════════════════════════════
slide = prs.slides.add_slide(blank)
add_rect(slide, 0, 0, 13.333, 7.5, RGBColor(0xF8,0xFB,0xFF))
header_bar(slide, "Laboratory Diagnosis", "Specimen: Nasopharyngeal swab (deep posterior) — NOT throat swab")
footer(slide)

# Table header
add_rect(slide, 0.25, 1.45, 12.8, 0.5, MED_BLUE)
for text, xpos, width in [("TEST", 0.3, 2.5), ("SPECIMEN / TIMING", 2.85, 3.0), ("DETAILS", 5.9, 4.5), ("NOTE", 10.45, 2.5)]:
    add_text(slide, text, xpos, 1.47, width, 0.45, 12, bold=True, color=WHITE, anchor=MSO_ANCHOR.MIDDLE)

rows_data = [
    ("Culture\n(Gold Standard)", "NP swab\nCatarrhal / early\nparoxysmal phase",
     "Bordet-Gengou OR Regan-Lowe medium\nIncubate 35–37°C, 3–7 days aerobically",
     "Specific but insensitive;\nbest in early disease", LIGHT_BLUE),
    ("PCR (NAAT)\n[Most sensitive]", "NP swab\nAny stage (best\nin first 3 wks)",
     "Detects B. pertussis-specific DNA\nMore sensitive than culture",
     "Test of choice in\nlater stages", RGBColor(0xE8,0xF8,0xE8)),
    ("DFA (Direct\nFluorescent Ab)", "NP swab\nEarly disease",
     "Immunofluorescence on direct smear\nRapid but low sensitivity (~50%)",
     "Declining use;\nnot recommended alone", LIGHT_BLUE),
    ("Serology\n(Anti-PT IgG)", "Serum\nLater disease\n(>3 wks)", 
     "Single high titer OR 4-fold rise in paired samples\nUseful in adolescents & adults",
     "Not useful acutely;\ngood for epidemiology", RGBColor(0xE8,0xF8,0xE8)),
    ("CBC (Blood\nCount)", "Blood\nParoxysmal phase",
     "Marked LYMPHOCYTOSIS (not neutrophilia)\nWBC 15,000–100,000/µL",
     "Hallmark diagnostic\nclue; due to PT effect", LIGHT_BLUE),
]

y = 1.95
for test, spec, detail, note, bg in rows_data:
    add_rect(slide, 0.25, y, 12.8, 0.8, bg)
    for text, xpos, width in [(test, 0.3, 2.45), (spec, 2.85, 2.95), (detail, 5.9, 4.45), (note, 10.45, 2.5)]:
        tb = slide.shapes.add_textbox(Inches(xpos), Inches(y+0.02), Inches(width), Inches(0.76))
        tf = tb.text_frame; tf.word_wrap = True
        tf.margin_left=Pt(3);tf.margin_right=Pt(2);tf.margin_top=Pt(2);tf.margin_bottom=Pt(2)
        for j, line in enumerate(text.split("\n")):
            p = tf.paragraphs[0] if j==0 else tf.add_paragraph()
            run=p.add_run(); run.text=line
            run.font.size=Pt(11); run.font.name="Calibri"; run.font.color.rgb=DARK_TEXT
            run.font.bold=(j==0 and test==text)
    y += 0.82

# Histopath image
if img_data[2]:
    img_data[2].seek(0)
    slide.shapes.add_picture(img_data[2], Inches(10.5), Inches(5.55), Inches(2.6), Inches(1.7))
add_text(slide, "Histopathology: mucopurulent\nexudate in nasal cavity\n(H&E stain, B. pertussis model)",
         8.0, 5.65, 2.4, 1.55, 9.5, color=DARK_TEXT, italic=True, wrap=True)

# ══════════════════════════════════════════════════════════════════════════════
# SLIDE 7 – Treatment & Vaccination
# ══════════════════════════════════════════════════════════════════════════════
slide = prs.slides.add_slide(blank)
add_rect(slide, 0, 0, 13.333, 7.5, RGBColor(0xF4,0xF8,0xF4))
header_bar(slide, "Treatment, Prophylaxis & Vaccination")
footer(slide)

# Left: Treatment
add_rect(slide, 0.25, 1.45, 6.0, 5.7, WHITE)
add_rect(slide, 0.25, 1.45, 6.0, 0.42, GREEN_ACCENT)
add_text(slide, "TREATMENT", 0.3, 1.47, 5.9, 0.38, 14, bold=True, color=WHITE, anchor=MSO_ANCHOR.MIDDLE)
add_multiline(slide, [
    ("Drug of Choice: AZITHROMYCIN", True),
    ("  • 5-day course; preferred in all ages especially infants", False),
    ("Alternatives:", True),
    ("  • Clarithromycin", False),
    ("  • Erythromycin (avoid in neonates <1 month →", False),
    ("    risk of infantile hypertrophic pyloric stenosis)", False),
    ("  • TMP-SMX (if macrolide-intolerant)", False),
    ("Timing matters:", True),
    ("  • Catarrhal phase: eradicates organism, shortens illness", False),
    ("  • Paroxysmal phase: reduces communicability only,", False),
    ("    does NOT shorten clinical illness", False),
    ("Chemoprophylaxis:", True),
    ("  • Azithromycin for ALL close contacts", False),
    ("  • Regardless of vaccination status", False),
], 0.35, 1.95, 5.8, 5.1, 12.5, color=DARK_TEXT)

# Right: Vaccination
add_rect(slide, 6.5, 1.45, 6.6, 5.7, WHITE)
add_rect(slide, 6.5, 1.45, 6.6, 0.42, MED_BLUE)
add_text(slide, "VACCINATION", 6.55, 1.47, 6.5, 0.38, 14, bold=True, color=WHITE, anchor=MSO_ANCHOR.MIDDLE)
add_multiline(slide, [
    ("Acellular Pertussis Vaccine (DTaP) contains:", True),
    ("  ✓ Pertussis toxoid (PT) — ALL formulations", True),
    ("  ✓ Filamentous hemagglutinin (FHA)", True),
    ("  ✓ Pertactin (Prn) — most formulations", False),
    ("  ✓ Fimbriae (FIM 2, 3) — some formulations", False),
    ("Indian Schedule (DPT): 6, 10, 14 weeks + boosters", True),
    ("Tdap booster: Adolescents 11–12 years", False),
    ("Maternal Tdap: 27–36 weeks pregnancy", True),
    ("  → Passive IgG to protect newborns", False),
    ("Whole-cell (DTwP) vs Acellular (DTaP):", True),
    ("  • DTwP: TH1/TH17 response, longer-lasting", False),
    ("  • DTaP: TH2-biased, wanes in 2–4 years", False),
    ("  • DTwP reduces mucosal carriage better", False),
    ("  • DTaP: safer, less reactogenic", False),
], 6.6, 1.95, 6.4, 5.1, 12.5, color=DARK_TEXT)

# ══════════════════════════════════════════════════════════════════════════════
# SLIDE 8 – Exam Key Points Summary
# ══════════════════════════════════════════════════════════════════════════════
slide = prs.slides.add_slide(blank)
add_rect(slide, 0, 0, 13.333, 7.5, DARK_BLUE)
add_rect(slide, 0, 0, 13.333, 1.3, RGBColor(0x0A,0x29,0x4A))
add_rect(slide, 0, 1.28, 13.333, 0.07, GOLD)
add_text(slide, "HIGH-YIELD EXAM POINTS", 0.3, 0.1, 12.7, 1.1, 34, bold=True,
         color=WHITE, align=PP_ALIGN.CENTER, anchor=MSO_ANCHOR.MIDDLE)
add_text(slide, "As per Apurba Sastry's Essentials of Medical Microbiology", 0.3, 0.95, 12.7, 0.35,
         14, color=GOLD, align=PP_ALIGN.CENTER, italic=True)

points = [
    ("No animal reservoir", "B. pertussis is EXCLUSIVELY a human pathogen — classic Apurba Sastry MCQ point"),
    ("Most communicable stage", "CATARRHAL stage — maximum organisms in nasopharynx"),
    ("Hallmark lab finding", "LYMPHOCYTOSIS (not neutrophilia) — due to Pertussis Toxin effect on Giα"),
    ("Specimen of choice", "NASOPHARYNGEAL SWAB — deep posterior; NOT throat swab"),
    ("Best diagnostic test", "PCR/NAAT — most sensitive & specific; preferred in later stages"),
    ("Drug of choice", "AZITHROMYCIN — 5 days; preferred in infants; reduces communicability"),
    ("Acellular vaccine must contain", "PT toxoid + FHA (minimum); also pertactin + fimbriae in most"),
    ("PT mechanism", "ADP-ribosylates Giα protein → ↑cAMP → lymphocytosis + immune paralysis"),
    ("TCT effect", "Destroys ciliated cells via IL-1/NO → denuded mucosa → persistent cough"),
    ("BvgA/BvgS system", "Two-component regulator — adhesins expressed FIRST, then toxins"),
]

col1 = points[:5]
col2 = points[5:]
for col_pts, x_base in [(col1, 0.25), (col2, 6.85)]:
    y = 1.45
    for key, val in col_pts:
        add_rect(slide, x_base, y, 6.3, 0.98, RGBColor(0x12,0x3A,0x60))
        add_rect(slide, x_base, y, 0.18, 0.98, GOLD)
        add_text(slide, key, x_base+0.25, y+0.03, 5.9, 0.35, 12.5, bold=True,
                 color=GOLD, anchor=MSO_ANCHOR.TOP)
        add_text(slide, val, x_base+0.25, y+0.38, 5.9, 0.55, 11.5,
                 color=LIGHT_BLUE, wrap=True)
        y += 1.05

footer(slide)

# ══════════════════════════════════════════════════════════════════════════════
# SAVE
# ══════════════════════════════════════════════════════════════════════════════
out_path = "/tmp/workspace/pertussis-ppt/Pertussis_Microbiology_Apurba_Sastry.pptx"
buf = BytesIO()
prs.save(buf)
with open(out_path, "wb") as f:
    f.write(buf.getvalue())
print(f"Saved: {out_path}")
print(f"Slides: {len(prs.slides)}")

import json, subprocess, base64
from io import BytesIO
from pptx import Presentation
from pptx.util import Inches, Pt, Emu
from pptx.dml.color import RGBColor
from pptx.enum.text import PP_ALIGN, MSO_ANCHOR

# ── Palette ────────────────────────────────────────────────────────────────────
NAVY        = RGBColor(0x07, 0x28, 0x48)
TEAL        = RGBColor(0x00, 0x7B, 0x83)
LIGHT_TEAL  = RGBColor(0xCC, 0xEE, 0xF0)
WHITE       = RGBColor(0xFF, 0xFF, 0xFF)
GOLD        = RGBColor(0xF4, 0xC84F & 0xFF, 0x1C)
GOLD        = RGBColor(0xF4, 0xC8, 0x1C)
DARK_TEXT   = RGBColor(0x1A, 0x1A, 0x2E)
RED         = RGBColor(0xC0, 0x39, 0x2B)
GREEN       = RGBColor(0x1E, 0x8B, 0x4C)
ORANGE      = RGBColor(0xD3, 0x54, 0x00)
PURPLE      = RGBColor(0x6C, 0x35, 0x83)
SLATE       = RGBColor(0xF2, 0xF6, 0xF9)

IMAGE_URLS = [
    "https://cdn.orris.care/cdss_images/pmc_clinical_VQA_a275dd96400386e3b831d1ca96d2632a9c58248fe673745f3ccb780ddc731c8e.jpg",  # 0 variants infographic
    "https://cdn.orris.care/cdss_images/pmc_clinical_VQA_fcb36cd84ce86f7b40d0dfdcdca0ba3298be5b8a11584709c9d70613e467c402.jpg",  # 1 ACE2 entry diagram
    "https://cdn.orris.care/cdss_images/pmc_clinical_VQA_d20b515184651d3f841bf40f1e14c472f29711aa98ecd92f15ae87f0d8d7f715.jpg",  # 2 CT scan progression
    "https://cdn.orris.care/cdss_images/pmc_clinical_VQA_39f3bd9dabd1415d09d3506206509e052fea54ec3c71e7e6dc6dd79f5f2486e5.jpg",  # 3 EM + IHC lung
    "https://cdn.orris.care/cdss_images/pmc_clinical_VQA_fdeeaac10ea9f4f92b6dc6da0e47133760ce1655cfbc5599b7bd1794e72aae7a.jpg",  # 4 cytokine storm diagram
]

print("Fetching images...")
raw = subprocess.check_output(["python", "/tmp/skills/shared/scripts/fetch_images.py"] + IMAGE_URLS)
imgs = json.loads(raw)
img_data = []
for img in imgs:
    if img["base64"]:
        mime, b64 = img["base64"].split(";base64,", 1)
        img_data.append(BytesIO(base64.b64decode(b64)))
    else:
        img_data.append(None)
print(f"Loaded {sum(1 for x in img_data if x)}/{len(img_data)} images")

# ── Setup ──────────────────────────────────────────────────────────────────────
prs = Presentation()
prs.slide_width  = Inches(13.333)
prs.slide_height = Inches(7.5)
blank = prs.slide_layouts[6]

# ── Helper functions ──────────────────────────────────────────────────────────
def rect(slide, x, y, w, h, color):
    s = slide.shapes.add_shape(1, Inches(x), Inches(y), Inches(w), Inches(h))
    s.line.fill.background()
    s.fill.solid()
    s.fill.fore_color.rgb = color
    return s

def txt(slide, text, x, y, w, h, size, bold=False, color=WHITE,
        align=PP_ALIGN.LEFT, italic=False, anchor=MSO_ANCHOR.TOP, wrap=True):
    tb = slide.shapes.add_textbox(Inches(x), Inches(y), Inches(w), Inches(h))
    tf = tb.text_frame
    tf.word_wrap = wrap
    tf.vertical_anchor = anchor
    tf.margin_left = 0; tf.margin_right = 0
    tf.margin_top = 0;  tf.margin_bottom = 0
    p = tf.paragraphs[0]
    p.alignment = align
    r = p.add_run()
    r.text = text
    r.font.size   = Pt(size)
    r.font.bold   = bold
    r.font.italic = italic
    r.font.color.rgb = color
    r.font.name   = "Calibri"
    return tb

def bullets(slide, lines, x, y, w, h, size, color=DARK_TEXT, use_bullet=True):
    tb = slide.shapes.add_textbox(Inches(x), Inches(y), Inches(w), Inches(h))
    tf = tb.text_frame
    tf.word_wrap = True
    tf.margin_left  = Pt(3)
    tf.margin_right = Pt(3)
    tf.margin_top   = Pt(2)
    tf.margin_bottom= Pt(2)
    first = True
    for item in lines:
        bold = False
        if isinstance(item, tuple):
            text, bold = item
        else:
            text = item
        p = tf.paragraphs[0] if first else tf.add_paragraph()
        first = False
        p.space_after = Pt(2)
        r = p.add_run()
        r.text = ("• " if use_bullet else "") + text
        r.font.size  = Pt(size)
        r.font.bold  = bold
        r.font.color.rgb = color
        r.font.name  = "Calibri"
    return tb

def header(slide, title, subtitle=None):
    rect(slide, 0, 0, 13.333, 1.25, NAVY)
    rect(slide, 0, 1.25, 13.333, 0.07, GOLD)
    txt(slide, title, 0.35, 0.1, 12.6, 0.85, 32, bold=True,
        color=WHITE, align=PP_ALIGN.LEFT, anchor=MSO_ANCHOR.MIDDLE)
    if subtitle:
        txt(slide, subtitle, 0.35, 0.88, 12.6, 0.38, 13,
            color=GOLD, align=PP_ALIGN.LEFT, italic=True)

def footer(slide, note="COVID-19 | SARS-CoV-2 | As per Apurba Sastry's Essentials of Medical Microbiology"):
    rect(slide, 0, 7.22, 13.333, 0.28, NAVY)
    txt(slide, note, 0.3, 7.22, 12.7, 0.28, 10, color=RGBColor(0xAA,0xCC,0xFF),
        align=PP_ALIGN.CENTER, anchor=MSO_ANCHOR.MIDDLE)

def add_pic(slide, img_io, x, y, w, h=None):
    if img_io is None: return
    img_io.seek(0)
    if h:
        slide.shapes.add_picture(img_io, Inches(x), Inches(y), Inches(w), Inches(h))
    else:
        slide.shapes.add_picture(img_io, Inches(x), Inches(y), Inches(w))

def label(slide, text, x, y, w, h, bg, fg=WHITE, size=11):
    rect(slide, x, y, w, h, bg)
    txt(slide, text, x+0.05, y, w-0.1, h, size, bold=True, color=fg,
        align=PP_ALIGN.CENTER, anchor=MSO_ANCHOR.MIDDLE)

# ══════════════════════════════════════════════════════════════════════════════
# SLIDE 1 — Title
# ══════════════════════════════════════════════════════════════════════════════
s = prs.slides.add_slide(blank)
rect(s, 0, 0, 13.333, 7.5, NAVY)
rect(s, 0, 2.5, 13.333, 2.6, TEAL)
rect(s, 0, 2.44, 13.333, 0.09, GOLD)
rect(s, 0, 5.0,  13.333, 0.09, GOLD)

txt(s, "COVID-19", 0.5, 0.55, 12.3, 1.6, 80, bold=True,
    color=WHITE, align=PP_ALIGN.CENTER, anchor=MSO_ANCHOR.MIDDLE)
txt(s, "Coronavirus Disease 2019", 0.5, 2.0, 12.3, 0.55, 26,
    color=GOLD, align=PP_ALIGN.CENTER)
txt(s, "Causative Agent: SARS-CoV-2  |  β-Coronavirus  |  Enveloped, +ssRNA Virus",
    0.5, 2.6, 12.3, 0.55, 19, color=WHITE, align=PP_ALIGN.CENTER,
    anchor=MSO_ANCHOR.MIDDLE)
txt(s, "Single-Stranded RNA Virus  |  Genome: ~30 kb (largest RNA virus genome)",
    0.5, 3.15, 12.3, 0.45, 15, color=LIGHT_TEAL, align=PP_ALIGN.CENTER)
txt(s, "Declared WHO Pandemic: March 11, 2020",
    0.5, 3.62, 12.3, 0.4, 14, color=GOLD, align=PP_ALIGN.CENTER)
txt(s, "As per Apurba Sastry's Essentials of Medical Microbiology",
    0.5, 5.2, 12.3, 0.45, 14, color=GOLD, align=PP_ALIGN.CENTER, italic=True)
txt(s, "Microbiology  |  MBBS Second Professional",
    0.5, 5.7, 12.3, 0.4, 13, color=RGBColor(0xAA,0xCC,0xFF), align=PP_ALIGN.CENTER)

# ══════════════════════════════════════════════════════════════════════════════
# SLIDE 2 — Taxonomy, Structure & Morphology
# ══════════════════════════════════════════════════════════════════════════════
s = prs.slides.add_slide(blank)
rect(s, 0, 0, 13.333, 7.5, SLATE)
header(s, "Taxonomy, Structure & Morphology of SARS-CoV-2")
footer(s)

# Left: Taxonomy & classification
rect(s, 0.25, 1.45, 5.9, 5.7, WHITE)
rect(s, 0.25, 1.45, 5.9, 0.42, NAVY)
txt(s, "TAXONOMY & CLASSIFICATION", 0.3, 1.47, 5.8, 0.38, 12.5, bold=True,
    color=WHITE, anchor=MSO_ANCHOR.MIDDLE)
bullets(s, [
    ("Family: Coronaviridae", True),
    ("Subfamily: Coronavirinae", False),
    ("Genus: Betacoronavirus (β-CoV)", True),
    ("Sub-genus: Sarbecovirus", False),
    ("Species: SARS-CoV-2 (novel coronavirus)", True),
    "",
    ("Other β-CoVs: SARS-CoV-1, MERS-CoV", True),
    ("Shares ~80% genome identity with SARS-CoV-1", False),
    ("Shares ~50% genome identity with MERS-CoV", False),
    "",
    ("Animal reservoir: Horseshoe bats (presumed)", True),
    ("Possible intermediate host before human spread", False),
], 0.35, 1.95, 5.7, 5.1, 12.5, color=DARK_TEXT)

# Right: Structural proteins
rect(s, 6.4, 1.45, 6.65, 5.7, WHITE)
rect(s, 6.4, 1.45, 6.65, 0.42, TEAL)
txt(s, "VIRAL STRUCTURE — 4 STRUCTURAL PROTEINS", 6.45, 1.47, 6.55, 0.38, 12.5,
    bold=True, color=WHITE, anchor=MSO_ANCHOR.MIDDLE)

struct_items = [
    ("S — Spike Glycoprotein", TEAL,
     "Most important; has RBD (Receptor Binding Domain)\nBinds ACE2 receptor on host cells\nS1 subunit: binds ACE2 | S2 subunit: membrane fusion\nCleaved by TMPRSS2 & cathepsin L\nTarget of ALL vaccines & monoclonal antibodies"),
    ("N — Nucleocapsid Protein", NAVY,
     "Surrounds the RNA genome\nHelical nucleocapsid\nTarget of antigen (rapid) diagnostic tests"),
    ("M — Membrane Protein", RGBColor(0x1E,0x8B,0x4C),
     "Most abundant structural protein\nMaintains viral shape\nCentral organizer of assembly"),
    ("E — Envelope Protein", ORANGE,
     "Small, involved in viral assembly\nPlays role in pathogenesis\nIon channel activity"),
]
y_s = 1.95
for name, col, desc in struct_items:
    rect(s, 6.45, y_s, 6.5, 0.28, col)
    txt(s, name, 6.5, y_s, 6.4, 0.27, 12, bold=True, color=WHITE, anchor=MSO_ANCHOR.MIDDLE)
    tb = s.shapes.add_textbox(Inches(6.5), Inches(y_s+0.3), Inches(6.4), Inches(0.8))
    tf = tb.text_frame; tf.word_wrap = True
    tf.margin_left=Pt(2);tf.margin_right=Pt(2);tf.margin_top=Pt(1);tf.margin_bottom=Pt(1)
    for j, line in enumerate(desc.split("\n")):
        p = tf.paragraphs[0] if j==0 else tf.add_paragraph()
        r = p.add_run(); r.text = "• " + line
        r.font.size=Pt(11); r.font.name="Calibri"; r.font.color.rgb=DARK_TEXT
    y_s += 1.2

# ══════════════════════════════════════════════════════════════════════════════
# SLIDE 3 — Epidemiology & Transmission
# ══════════════════════════════════════════════════════════════════════════════
s = prs.slides.add_slide(blank)
rect(s, 0, 0, 13.333, 7.5, RGBColor(0xF0,0xF4,0xFF))
header(s, "Epidemiology & Transmission",
       "First reported: Wuhan, Hubei province, China — December 2019 | WHO Pandemic declared: March 11, 2020")
footer(s)

# Timeline box
rect(s, 0.25, 1.42, 7.1, 5.75, WHITE)
rect(s, 0.25, 1.42, 7.1, 0.42, NAVY)
txt(s, "EPIDEMIOLOGY TIMELINE", 0.3, 1.44, 7.0, 0.38, 13, bold=True,
    color=WHITE, anchor=MSO_ANCHOR.MIDDLE)

timeline = [
    ("Dec 2019", "Cluster of viral pneumonia cases in Wuhan, China", TEAL),
    ("Jan 11-12, 2020", "Genomic sequence of SARS-CoV-2 published by Chinese scientists", NAVY),
    ("Jan 20-21, 2020", "Human-to-human transmission confirmed; 1st US case (Washington State)", ORANGE),
    ("Feb 2020", "Spread to Asia, North America, Europe, Middle East, Africa", RGBColor(0x6C,0x35,0x83)),
    ("Mar 11, 2020", "WHO declared COVID-19 a PANDEMIC — 219 countries & territories affected", RED),
    ("Ongoing", "Variants emerging: Alpha, Beta, Gamma, Delta (India), Omicron", RGBColor(0x1E,0x8B,0x4C)),
]
y_t = 1.92
for date, event, col in timeline:
    rect(s, 0.3, y_t, 1.6, 0.7, col)
    txt(s, date, 0.32, y_t, 1.56, 0.7, 10.5, bold=True, color=WHITE,
        align=PP_ALIGN.CENTER, anchor=MSO_ANCHOR.MIDDLE, wrap=True)
    rect(s, 1.92, y_t, 5.3, 0.7, RGBColor(0xF8,0xF9,0xFF))
    txt(s, event, 2.0, y_t+0.05, 5.1, 0.6, 11.5, color=DARK_TEXT, wrap=True)
    y_t += 0.8

# Right: Transmission box
rect(s, 7.55, 1.42, 5.5, 5.75, WHITE)
rect(s, 7.55, 1.42, 5.5, 0.42, TEAL)
txt(s, "TRANSMISSION", 7.6, 1.44, 5.4, 0.38, 13, bold=True,
    color=WHITE, anchor=MSO_ANCHOR.MIDDLE)
bullets(s, [
    ("Route: Respiratory droplets (primary)", True),
    ("  Coughing/sneezing → droplets land on\n  nose, eyes, face of another person", False),
    ("Aerosol transmission also demonstrated", True),
    ("  Fine respiratory droplets can be inhaled", False),
    ("Fomite transmission (indirect)", True),
    ("  Hand-to-face after touching contaminated\n  surfaces", False),
    ("UNIQUE FEATURE:", True),
    ("  Asymptomatic infected persons transmit virus", False),
    ("Viral stability on surfaces:", True),
    ("  Aerosol: 2–4 hours", False),
    ("  Plastic: 72 hours", False),
    ("  Steel: 48 hours", False),
    ("  Cardboard: 24 hours", False),
    ("  Copper: 8 hours", False),
], 7.65, 1.92, 5.3, 5.1, 12, color=DARK_TEXT)

# Variant infographic image
# (will be on slide 5 to save space)

# ══════════════════════════════════════════════════════════════════════════════
# SLIDE 4 — Pathogenesis (with ACE2 entry image)
# ══════════════════════════════════════════════════════════════════════════════
s = prs.slides.add_slide(blank)
rect(s, 0, 0, 13.333, 7.5, RGBColor(0xF8,0xF9,0xFF))
header(s, "Pathogenesis of COVID-19",
       "Non-cytopathic initially; damage = viral + immune-mediated (cytokine storm)")
footer(s)

# Steps column
steps = [
    (TEAL,   "Step 1 — Entry",
     "Respiratory tract → nasopharyngeal/oropharyngeal cells are initial targets. Spike RBD binds ACE2 receptor."),
    (NAVY,   "Step 2 — S protein cleavage",
     "Cellular TMPRSS2 & cathepsin L cleave S1/S2. S2 mediates viral envelope fusion with cell membrane → endosomal entry."),
    (ORANGE, "Step 3 — Replication",
     "Viral genome released in cytoplasm → translated into polyprotein → cleaved by host & viral proteases into RdRp, ExoN, and nonstructural proteins. Subgenomic RNAs → structural proteins."),
    (PURPLE, "Step 4 — Assembly & Release",
     "Virus assembled in cytoplasm; acquires envelope from ER-Golgi membranes (with Spike, M, E proteins); released by exocytosis."),
    (RED,    "Step 5 — Immune Response & Damage",
     "IFN-I suppressed by SARS-CoV-2 NSPs. Proinflammatory cytokines (IL-1β, IL-6, TNF-α) → cytokine storm in severe cases → ARDS, DIC, multi-organ failure."),
]
y_p = 1.45
for col, title, body in steps:
    rect(s, 0.25, y_p, 7.2, 0.27, col)
    txt(s, title, 0.3, y_p, 7.1, 0.26, 11.5, bold=True, color=WHITE, anchor=MSO_ANCHOR.MIDDLE)
    rect(s, 0.25, y_p+0.27, 7.2, 0.72, RGBColor(0xF0,0xF4,0xFF))
    tb = s.shapes.add_textbox(Inches(0.35), Inches(y_p+0.3), Inches(7.0), Inches(0.67))
    tf = tb.text_frame; tf.word_wrap = True
    tf.margin_left=Pt(2);tf.margin_right=Pt(2);tf.margin_top=Pt(1);tf.margin_bottom=Pt(1)
    p = tf.paragraphs[0]; r = p.add_run(); r.text = body
    r.font.size=Pt(11); r.font.name="Calibri"; r.font.color.rgb=DARK_TEXT
    y_p += 1.04

# Right: ACE2 entry image
txt(s, "SARS-CoV-2 Viral Entry via ACE2 Receptor", 7.65, 1.45, 5.4, 0.38, 11.5,
    bold=True, color=TEAL, align=PP_ALIGN.CENTER)
add_pic(s, img_data[1], 7.6, 1.85, 5.45, 3.3)
txt(s, "Spike RBD → ACE2 binding → TMPRSS2 cleavage → membrane fusion → viral entry",
    7.6, 5.18, 5.4, 0.45, 10, color=RGBColor(0x55,0x55,0x55),
    italic=True, align=PP_ALIGN.CENTER, wrap=True)

# Cytokine storm image
txt(s, "Cytokine Storm Cascade:", 7.65, 5.68, 5.4, 0.3, 11, bold=True, color=RED, align=PP_ALIGN.CENTER)
add_pic(s, img_data[4], 7.6, 5.98, 5.45, 1.22)

# ══════════════════════════════════════════════════════════════════════════════
# SLIDE 5 — Variants + ACE2 target organs
# ══════════════════════════════════════════════════════════════════════════════
s = prs.slides.add_slide(blank)
rect(s, 0, 0, 13.333, 7.5, SLATE)
header(s, "SARS-CoV-2 Variants & ACE2 Target Organs",
       "Mutations in Spike RBD → ↑ACE2 affinity → ↑infectivity & transmissibility")
footer(s)

# Left: variants table
rect(s, 0.25, 1.45, 6.5, 5.7, WHITE)
rect(s, 0.25, 1.45, 6.5, 0.42, NAVY)
txt(s, "VARIANTS OF CONCERN (VOC)", 0.3, 1.47, 6.4, 0.38, 13, bold=True,
    color=WHITE, anchor=MSO_ANCHOR.MIDDLE)

# Table header row
for text, xp, wp in [("VARIANT", 0.3, 1.5), ("PANGO", 1.82, 1.4), ("ORIGIN", 3.25, 1.6), ("KEY FEATURES", 4.87, 1.75)]:
    rect(s, xp, 1.95, wp, 0.35, TEAL)
    txt(s, text, xp+0.05, 1.95, wp-0.1, 0.35, 10.5, bold=True, color=WHITE,
        align=PP_ALIGN.CENTER, anchor=MSO_ANCHOR.MIDDLE)

variants = [
    ("Alpha (α)",   "B.1.1.7",  "UK",          "↑transmissibility; N501Y mutation",        RGBColor(0xE8,0xF4,0xFF)),
    ("Beta (β)",    "B.1.351",  "S. Africa",   "Immune escape; E484K mutation",             WHITE),
    ("Gamma (γ)",   "P.1",      "Brazil",      "Similar to Beta; E484K + K417T",            RGBColor(0xE8,0xF4,0xFF)),
    ("Delta (δ)",   "B.1.617.2","India",       "P681R mutation; very high transmissibility",WHITE),
    ("Omicron (ο)", "B.1.1.529","S. Africa",   ">30 spike mutations; high immune escape;\nhigh transmission, lower severity", RGBColor(0xE8,0xF4,0xFF)),
    ("D614G",       "Multiple", "Global",      "First dominant mutation; ↑viral load in\nupper RT; ↑human-to-human spread", WHITE),
]
y_v = 2.35
for var, pango, origin, feat, bg in variants:
    row_h = 0.65 if "\n" in feat else 0.52
    for text, xp, wp in [(var, 0.3, 1.5), (pango, 1.82, 1.4), (origin, 3.25, 1.6)]:
        rect(s, xp, y_v, wp, row_h, bg)
        txt(s, text, xp+0.05, y_v+0.02, wp-0.1, row_h-0.04, 11,
            color=DARK_TEXT, anchor=MSO_ANCHOR.MIDDLE, align=PP_ALIGN.CENTER, wrap=True)
    rect(s, 4.87, y_v, 1.75, row_h, bg)
    tb = s.shapes.add_textbox(Inches(4.92), Inches(y_v+0.02), Inches(1.65), Inches(row_h-0.04))
    tf = tb.text_frame; tf.word_wrap=True
    tf.margin_left=Pt(2);tf.margin_right=Pt(2);tf.margin_top=Pt(1);tf.margin_bottom=Pt(1)
    for j, line in enumerate(feat.split("\n")):
        p = tf.paragraphs[0] if j==0 else tf.add_paragraph()
        r = p.add_run(); r.text = line
        r.font.size=Pt(10); r.font.name="Calibri"; r.font.color.rgb=DARK_TEXT
    y_v += row_h + 0.03

# Right: variants infographic image + ACE2 target organs
txt(s, "SARS-CoV-2 Variant Evolution & Structure", 7.0, 1.45, 6.1, 0.38, 11.5,
    bold=True, color=NAVY, align=PP_ALIGN.CENTER)
add_pic(s, img_data[0], 6.95, 1.85, 6.1, 3.4)

# ACE2 organ targets
rect(s, 6.95, 5.35, 6.1, 1.8, WHITE)
rect(s, 6.95, 5.35, 6.1, 0.32, TEAL)
txt(s, "ACE2 RECEPTOR — TARGET ORGANS", 7.0, 5.37, 6.0, 0.28, 11, bold=True,
    color=WHITE, anchor=MSO_ANCHOR.MIDDLE)
bullets(s, [
    ("Lungs (alveolar type II cells) — PRIMARY target", True),
    ("Heart (myocardial cells)", False),
    ("Kidneys (tubular cells)", False),
    ("Intestine (enterocytes, cholangiocytes)", False),
    ("Blood vessels (endothelial cells)", False),
    ("Brain, testes, bladder urothelial cells", False),
], 7.0, 5.72, 6.0, 1.35, 11, color=DARK_TEXT)

# ══════════════════════════════════════════════════════════════════════════════
# SLIDE 6 — Clinical Features
# ══════════════════════════════════════════════════════════════════════════════
s = prs.slides.add_slide(blank)
rect(s, 0, 0, 13.333, 7.5, RGBColor(0xF0,0xF8,0xFF))
header(s, "Clinical Features of COVID-19",
       "Incubation period: 2–14 days (median 5–6 days)  |  Symptom onset: within ~11.5 days")
footer(s)

# 3 severity columns
sev_data = [
    ("MILD / MODERATE\n(~80% of cases)", TEAL, [
        ("Fever or chills", False),
        ("Dry cough", True),
        ("Shortness of breath", False),
        ("Fatigue, myalgia", False),
        ("Headache", False),
        ("Anosmia / Ageusia", True),
        ("  (Loss of smell/taste — ~10%)", False),
        ("Sore throat, rhinorrhea", False),
        ("Nausea, vomiting, diarrhea", False),
        ("Maculopapular / urticarial rash", False),
    ]),
    ("SEVERE\n(~15% of cases)", ORANGE, [
        ("Persistent breathlessness", True),
        ("Chest pain/pressure", True),
        ("Viral pneumonia", True),
        ("Hypoxemia (SpO₂ <94%)", False),
        ("New confusion / altered sensorium", False),
        ("Bluish lips or face (cyanosis)", False),
        ("Inability to stay awake", False),
        ("Ground-glass opacities on CT", True),
        ("High D-dimer, elevated CRP, LDH", False),
    ]),
    ("CRITICAL\n(~5% of cases)", RED, [
        ("ARDS — Acute Respiratory Distress Syndrome", True),
        ("Septic shock", False),
        ("Multi-organ dysfunction", True),
        ("Cytokine storm", True),
        ("Pulmonary hypertension", False),
        ("Thrombosis (large & small vessels)", True),
        ("DIC (Disseminated Intravascular\n Coagulation)", False),
        ("Neurological: stroke, encephalopathy", False),
        ("Myocarditis, pericardial effusion", False),
    ]),
]
x_c = [0.25, 4.6, 8.95]
for i, (title, color, pts) in enumerate(sev_data):
    x = x_c[i]
    rect(s, x, 1.45, 4.1, 5.65, WHITE)
    rect(s, x, 1.45, 4.1, 0.62, color)
    txt(s, title, x+0.1, 1.47, 3.9, 0.58, 13.5, bold=True,
        color=WHITE, align=PP_ALIGN.CENTER, anchor=MSO_ANCHOR.MIDDLE, wrap=True)
    bullets(s, pts, x+0.15, 2.12, 3.8, 4.9, 12.5, color=DARK_TEXT)

# Risk factors footer strip
rect(s, 0.25, 7.05, 12.8, 0.22, RGBColor(0xFF,0xF0,0xD0))
txt(s, "Risk factors for severe disease: Age >60 yrs, Obesity, Diabetes, HTN, CVD, CKD, Malignancy, Immunocompromise",
    0.3, 7.05, 12.7, 0.22, 10.5, color=DARK_TEXT,
    align=PP_ALIGN.CENTER, anchor=MSO_ANCHOR.MIDDLE)

# ══════════════════════════════════════════════════════════════════════════════
# SLIDE 7 — Special Conditions: Long COVID, MIS-C, CT findings
# ══════════════════════════════════════════════════════════════════════════════
s = prs.slides.add_slide(blank)
rect(s, 0, 0, 13.333, 7.5, SLATE)
header(s, "Complications, Long COVID & Imaging Findings")
footer(s)

# Left panel: special conditions
rect(s, 0.25, 1.45, 6.2, 5.7, WHITE)

rect(s, 0.25, 1.45, 6.2, 0.38, RED)
txt(s, "LONG COVID / PASC (Post-Acute Sequelae of SARS-CoV-2)", 0.3, 1.47, 6.1, 0.34, 11.5,
    bold=True, color=WHITE, anchor=MSO_ANCHOR.MIDDLE)
bullets(s, [
    ("Fatigue, body aches, shortness of breath", False),
    ("Brain fog (difficulty concentrating)", False),
    ("Inability to exercise, headache, sleep disturbance", False),
    ("May last weeks to months after acute illness", False),
    ("Possible chronic damage: lungs, heart, kidneys, brain", True),
], 0.35, 1.88, 5.9, 1.5, 12, color=DARK_TEXT)

rect(s, 0.25, 3.44, 6.2, 0.35, PURPLE)
txt(s, "MIS-C — Multisystem Inflammatory Syndrome in Children", 0.3, 3.45, 6.1, 0.32, 11.5,
    bold=True, color=WHITE, anchor=MSO_ANCHOR.MIDDLE)
bullets(s, [
    ("Post-COVID inflammatory syndrome in children", False),
    ("Features: myocarditis, shock", False),
    ("Similar to Kawasaki disease — coronary artery aneurysms", True),
    ("Managed with IVIG + steroids", False),
], 0.35, 3.84, 5.9, 1.1, 12, color=DARK_TEXT)

rect(s, 0.25, 4.98, 6.2, 0.35, ORANGE)
txt(s, "OTHER COMPLICATIONS", 0.3, 4.99, 6.1, 0.32, 11.5, bold=True,
    color=WHITE, anchor=MSO_ANCHOR.MIDDLE)
bullets(s, [
    ("Bacterial superinfections (secondary pneumonia)", False),
    ("Guillain-Barré syndrome (acute flaccid myelitis)", True),
    ("Stroke, encephalopathy, peripheral neuropathy", False),
    ("Pulmonary fibrosis (post-ARDS)", False),
    ("Thromboembolism (PE, DVT)", True),
], 0.35, 5.38, 5.9, 1.72, 12, color=DARK_TEXT)

# Right: CT scan image
txt(s, "CT Chest — COVID-19 Pneumonia Progression", 6.65, 1.45, 6.4, 0.38, 11.5,
    bold=True, color=NAVY, align=PP_ALIGN.CENTER)
add_pic(s, img_data[2], 6.6, 1.85, 6.45, 3.5)
txt(s, "Day 1: Peripheral consolidations  |  Day 5: Peak ground-glass opacities  |  Day 10: Resolution",
    6.6, 5.38, 6.45, 0.42, 10, color=RGBColor(0x44,0x44,0x44),
    italic=True, align=PP_ALIGN.CENTER, wrap=True)

# IHC/EM image below
add_pic(s, img_data[3], 6.6, 5.82, 3.2, 1.38)
txt(s, "IHC + EM: SARS-CoV-2\nnucleoprotein in alveolar\nhyaline membranes (DAD)",
    9.82, 5.85, 3.2, 1.3, 9.5, color=DARK_TEXT, italic=True, wrap=True)

# ══════════════════════════════════════════════════════════════════════════════
# SLIDE 8 — Laboratory Diagnosis
# ══════════════════════════════════════════════════════════════════════════════
s = prs.slides.add_slide(blank)
rect(s, 0, 0, 13.333, 7.5, RGBColor(0xF8,0xFB,0xFF))
header(s, "Laboratory Diagnosis of COVID-19",
       "Specimen: Nasopharyngeal swab (NPS) — preferred  |  Also: oropharyngeal swab, BAL, sputum")
footer(s)

# Table
rect(s, 0.25, 1.45, 12.8, 0.45, NAVY)
for text, xp, wp in [("TEST", 0.3, 3.0), ("SPECIMEN", 3.35, 2.5), ("DETAILS", 5.9, 4.7), ("NOTE", 10.65, 2.25)]:
    txt(s, text, xp, 1.47, wp, 0.41, 12, bold=True, color=WHITE,
        align=PP_ALIGN.CENTER, anchor=MSO_ANCHOR.MIDDLE)

rows = [
    ("RT-PCR\n(Gold Standard)", "NPS/OPS\nBAL, sputum", "Detects SARS-CoV-2 RNA (genes: RdRp, E, N, ORF1ab)\nMost sensitive & specific; results in 4–6 hrs", "Test of choice\nfor active infection", RGBColor(0xE0,0xF0,0xFF)),
    ("Rapid Antigen Test\n(RAT)", "NPS\nNasal swab", "Detects nucleocapsid (N) protein\nResults in 15–30 minutes; less sensitive\nConfirm negatives by RT-PCR if high suspicion", "Point-of-care;\nscreen & triage", WHITE),
    ("BioFire RP2.1 Panel\n(NAT-based)", "NPS", "Nucleic acid–based multiplex panel\nDetects 15 viral + 4 bacterial pathogens\nIncludes common cold CoVs + SARS-CoV-2\nFDA emergency use authorization", "Useful in ICU/\nrespiratory panels", RGBColor(0xE0,0xF0,0xFF)),
    ("Serology\n(Antibody Test)", "Serum/Blood", "Detects anti-Spike or anti-N IgG/IgM\nNOT for diagnosing current infection\nUseful for: seroprevalence, past exposure, vaccine response", "Epidemiology &\nsurveillance only", WHITE),
    ("CBC (Blood Count)", "Blood", "Lymphopenia (hallmark of severe COVID-19)\nNeutrophilia in severe/bacterial co-infection\nElevated D-dimer, CRP, LDH, ferritin in severe disease", "Lymphopenia =\nbad prognostic sign", RGBColor(0xE0,0xF0,0xFF)),
]
y_t = 1.95
for test, spec, detail, note, bg in rows:
    rh = 0.82
    for text, xp, wp in [(test, 0.3, 3.0), (spec, 3.35, 2.5), (detail, 5.9, 4.7), (note, 10.65, 2.25)]:
        rect(s, xp, y_t, wp, rh, bg)
        tb = s.shapes.add_textbox(Inches(xp+0.05), Inches(y_t+0.03), Inches(wp-0.1), Inches(rh-0.06))
        tf = tb.text_frame; tf.word_wrap=True
        tf.margin_left=Pt(2);tf.margin_right=Pt(2);tf.margin_top=Pt(1);tf.margin_bottom=Pt(1)
        for j, line in enumerate(text.split("\n")):
            p = tf.paragraphs[0] if j==0 else tf.add_paragraph()
            r = p.add_run(); r.text = line
            r.font.size=Pt(11); r.font.name="Calibri"; r.font.color.rgb=DARK_TEXT
            r.font.bold=(j==0 and text==test)
    y_t += rh + 0.02

# ══════════════════════════════════════════════════════════════════════════════
# SLIDE 9 — Treatment & Prevention
# ══════════════════════════════════════════════════════════════════════════════
s = prs.slides.add_slide(blank)
rect(s, 0, 0, 13.333, 7.5, RGBColor(0xF2,0xFB,0xF4))
header(s, "Treatment, Prevention & Vaccination")
footer(s)

# Left: Treatment
rect(s, 0.25, 1.45, 6.0, 5.7, WHITE)
rect(s, 0.25, 1.45, 6.0, 0.38, GREEN)
txt(s, "TREATMENT", 0.3, 1.47, 5.9, 0.34, 14, bold=True, color=WHITE, anchor=MSO_ANCHOR.MIDDLE)
bullets(s, [
    ("Antivirals:", True),
    ("  Remdesivir — RNA-dependent RNA polymerase inhibitor;", False),
    ("  approved for hospitalized patients", False),
    ("  Molnupiravir / Paxlovid (nirmatrelvir+ritonavir) —", False),
    ("  oral antivirals for high-risk outpatients", False),
    ("Anti-inflammatory:", True),
    ("  Dexamethasone — reduces mortality in severe cases", False),
    ("  requiring supplemental oxygen / ventilation", False),
    ("Monoclonal Antibodies (mAb):", True),
    ("  Target: Spike glycoprotein", False),
    ("  Bamlanivimab, Casirivimab + Imdevimab", False),
    ("  For high-risk patients (FDA EUA)", False),
    ("Supportive / ICU Care:", True),
    ("  Supplemental O₂, prone positioning,", False),
    ("  Intubation & mechanical ventilation (critical)", False),
    ("  Anticoagulation for thromboprophylaxis", False),
    ("  Current guidelines: covid19treatmentguidelines.nih.gov", False),
], 0.35, 1.9, 5.8, 5.1, 12, color=DARK_TEXT)

# Right: Vaccines
rect(s, 6.5, 1.45, 6.6, 5.7, WHITE)
rect(s, 6.5, 1.45, 6.6, 0.38, NAVY)
txt(s, "VACCINES & PREVENTION", 6.55, 1.47, 6.5, 0.34, 14, bold=True,
    color=WHITE, anchor=MSO_ANCHOR.MIDDLE)
bullets(s, [
    ("Vaccine types authorized:", True),
    ("  1. mRNA vaccines — Pfizer-BioNTech (BNT162b2),", False),
    ("     Moderna (mRNA-1273)", False),
    ("     Encode SARS-CoV-2 Spike glycoprotein", True),
    ("     2-dose primary series + booster", False),
    ("  2. Viral vector vaccine — J&J/Janssen", False),
    ("     Replication-incompetent adenovirus vector", False),
    ("     Encodes Spike protein", False),
    ("  3. Protein subunit — Novavax (NVX-CoV2373)", False),
    ("     Recombinant spike + Matrix-M adjuvant", False),
    "",
    ("Preventive measures:", True),
    ("  Wear mask / face shield", False),
    ("  Social distancing (6 feet from others)", False),
    ("  Avoid crowded, poorly ventilated places", False),
    ("  Hand wash with soap & water", False),
    ("  Hand sanitizer with ≥60% ethanol", True),
    ("  Disinfect frequently touched surfaces", False),
    ("  Cover cough/sneeze", False),
], 6.6, 1.9, 6.4, 5.1, 12, color=DARK_TEXT)

# ══════════════════════════════════════════════════════════════════════════════
# SLIDE 10 — High-Yield Exam Summary
# ══════════════════════════════════════════════════════════════════════════════
s = prs.slides.add_slide(blank)
rect(s, 0, 0, 13.333, 7.5, NAVY)
rect(s, 0, 0, 13.333, 1.28, RGBColor(0x05,0x1C,0x35))
rect(s, 0, 1.25, 13.333, 0.07, GOLD)
txt(s, "HIGH-YIELD EXAM POINTS — COVID-19", 0.3, 0.1, 12.7, 0.95, 32, bold=True,
    color=WHITE, align=PP_ALIGN.CENTER, anchor=MSO_ANCHOR.MIDDLE)
txt(s, "As per Apurba Sastry's Essentials of Medical Microbiology  |  MBBS Exam Ready",
    0.3, 0.95, 12.7, 0.33, 13, color=GOLD, align=PP_ALIGN.CENTER, italic=True)

points = [
    ("Causative agent", "SARS-CoV-2 — β-Coronavirus, enveloped, +ssRNA (~30 kb)"),
    ("Classification", "Family: Coronaviridae | Genus: Betacoronavirus | Sub-genus: Sarbecovirus"),
    ("Structural proteins", "Spike (S), Nucleocapsid (N), Membrane (M), Envelope (E)"),
    ("Receptor binding", "Spike RBD → ACE2 receptor | Cleaved by TMPRSS2 & Cathepsin L"),
    ("Unique feature", "Asymptomatic transmission — patients spread virus without symptoms"),
    ("Viral stability", "Aerosol: 2–4 h | Plastic: 72 h | Steel: 48 h | Cardboard: 24 h | Copper: 8 h"),
    ("Gold standard Dx", "RT-PCR (NPS) — detects viral RNA; RdRp / E / N / ORF1ab genes"),
    ("Hallmark lab finding", "Lymphopenia (not neutrophilia) — bad prognostic marker in severe COVID"),
    ("Treatment (antiviral)", "Remdesivir (RdRp inhibitor) + Dexamethasone (anti-inflammatory)"),
    ("Vaccine target", "ALL COVID vaccines target the Spike glycoprotein"),
]
col1, col2 = points[:5], points[5:]
for col_pts, x_base in [(col1, 0.25), (col2, 6.85)]:
    y = 1.42
    for key, val in col_pts:
        rect(s, x_base, y, 6.3, 0.99, RGBColor(0x0E,0x3A,0x62))
        rect(s, x_base, y, 0.17, 0.99, GOLD)
        txt(s, key, x_base+0.24, y+0.03, 5.9, 0.34, 12.5, bold=True, color=GOLD)
        txt(s, val, x_base+0.24, y+0.38, 5.9, 0.57, 11.5,
            color=LIGHT_TEAL, wrap=True)
        y += 1.04

footer(s)

# ══════════════════════════════════════════════════════════════════════════════
# SAVE
# ══════════════════════════════════════════════════════════════════════════════
out = "/tmp/workspace/covid-ppt/COVID19_SARS_CoV2_Apurba_Sastry.pptx"
buf = BytesIO()
prs.save(buf)
with open(out, "wb") as f:
    f.write(buf.getvalue())
print(f"Saved: {out}")
print(f"Slides: {len(prs.slides)}")