utils/pdf_generator.py

"""Downloadable candidate and variant reports."""

from io import BytesIO
from datetime import datetime

from reportlab.lib import colors
from reportlab.lib.enums import TA_CENTER, TA_LEFT
from reportlab.lib.pagesizes import A4
from reportlab.lib.styles import ParagraphStyle
from reportlab.lib.units import cm
from reportlab.platypus import (
    HRFlowable,
    Paragraph,
    SimpleDocTemplate,
    Spacer,
    Table,
    TableStyle,
)

NAVY = colors.HexColor("#1B365D")
TEAL = colors.HexColor("#0E7C7B")
LIGHT = colors.HexColor("#F4F7FB")
WHITE = colors.white
TEXT = colors.HexColor("#111827")
MUTED = colors.HexColor("#4A5568")
GREEN = colors.HexColor("#2F855A")
RED = colors.HexColor("#C53030")
ORANGE = colors.HexColor("#C45C26")


def _styles():
    return {
        "title": ParagraphStyle("t", fontName="Helvetica-Bold", fontSize=16, textColor=NAVY, alignment=TA_CENTER),
        "sub": ParagraphStyle("s", fontName="Helvetica", fontSize=9, textColor=colors.HexColor("#D6E0F0"), alignment=TA_CENTER),
        "h": ParagraphStyle("h", fontName="Helvetica-Bold", fontSize=11, textColor=NAVY, spaceBefore=10, spaceAfter=4),
        "b": ParagraphStyle("b", fontName="Helvetica", fontSize=9, textColor=TEXT, leading=12),
        "small": ParagraphStyle("sm", fontName="Helvetica", fontSize=8, textColor=MUTED, leading=11),
    }


def _header_footer(canvas, doc):
    canvas.saveState()
    canvas.setFillColor(NAVY)
    canvas.rect(0, A4[1] - 52, A4[0], 52, fill=1, stroke=0)
    canvas.setFillColor(TEAL)
    canvas.rect(0, 0, A4[0], 22, fill=1, stroke=0)
    canvas.setFillColor(WHITE)
    canvas.setFont("Helvetica", 8)
    canvas.drawString(1.6 * cm, 8, "TP53 Mutant Discovery Platform  |  Computational prioritization, not clinical proof")
    canvas.restoreState()


def generate_variant_report(variant_row, candidates, structure_row=None, pocket_row=None) -> bytes:
    styles = _styles()
    buf = BytesIO()
    doc = SimpleDocTemplate(
        buf,
        pagesize=A4,
        leftMargin=1.6 * cm,
        rightMargin=1.6 * cm,
        topMargin=2.4 * cm,
        bottomMargin=1.4 * cm,
    )
    hgvs = variant_row.get("hgvs_p", "")
    story = [
        Spacer(1, 6),
        Paragraph("TP53 Variant-to-Compound Discovery Report", styles["title"]),
        Paragraph(f"Project: Lung Cancer  ·  Variant {hgvs}  ·  {datetime.utcnow():%Y-%m-%d}", styles["sub"]),
        Spacer(1, 28),
        Paragraph("Mutation analysis", styles["h"]),
        Paragraph(
            f"<b>{hgvs}</b> &nbsp;|&nbsp; Exon {variant_row.get('exon','')} &nbsp;|&nbsp; "
            f"{variant_row.get('domain','')} &nbsp;|&nbsp; Inferred type: {variant_row.get('type_inferred','')}<br/>"
            f"Source type: {variant_row.get('type_source','')} &nbsp;|&nbsp; Effect: {variant_row.get('effect_source','')}<br/>"
            f"Allele frequency (observation): {variant_row.get('allele_frequency','')} &nbsp;|&nbsp; "
            f"QC: {variant_row.get('qc_flags','')} &nbsp;|&nbsp; Route: {variant_row.get('route','')}<br/>"
            f"Priority score: {variant_row.get('priority_score','')} &nbsp;|&nbsp; "
            f"Hotspot: {variant_row.get('hotspot','')}",
            styles["b"],
        ),
    ]
    if structure_row is not None:
        story += [
            Paragraph("Wild-type versus mutant structure", styles["h"]),
            Paragraph(
                f"ΔΔG proxy: {structure_row.get('ddg_kcal','')} kcal/mol &nbsp;|&nbsp; "
                f"Cα RMSD: {structure_row.get('ca_rmsd_A','')} Å &nbsp;|&nbsp; "
                f"Local RMSD: {structure_row.get('local_rmsd_A','')} Å<br/>"
                f"Pocket volume WT→mut: {structure_row.get('pocket_vol_wt','')} → {structure_row.get('pocket_vol_mut','')} ų &nbsp;|&nbsp; "
                f"Structure quality: {structure_row.get('structure_quality','')}",
                styles["b"],
            ),
        ]
    if pocket_row is not None:
        story += [
            Paragraph("Primary pocket", styles["h"]),
            Paragraph(
                f"{pocket_row.get('pocket_name','')} ({pocket_row.get('pocket_id','')}) &nbsp;|&nbsp; "
                f"Druggability {pocket_row.get('druggability','')} &nbsp;|&nbsp; "
                f"Docking gate: {pocket_row.get('docking_gate','')} &nbsp;|&nbsp; "
                f"Volume Δ {pocket_row.get('volume_delta','')} ų",
                styles["b"],
            ),
        ]
    story.append(Paragraph("Top ranked candidates", styles["h"]))
    header = ["Rank", "Compound", "Status", "Dock mut", "Dock WT", "Sel.", "MD", "ADMET", "Score", "Rec."]
    data = [header]
    use = candidates.sort_values("rank").head(10)
    for _, r in use.iterrows():
        data.append(
            [
                str(int(r["rank"])),
                str(r["name"])[:18],
                str(r["status"])[:10],
                f"{r['dock_mut']:.1f}",
                f"{r['dock_wt']:.1f}",
                f"{r['Sselectivity']:.2f}",
                f"{r['MDstability']:.2f}",
                f"{r['ADMET']:.2f}",
                f"{r['rescue_score']:.2f}",
                str(r["recommendation"]),
            ]
        )
    tbl = Table(data, repeatRows=1)
    tbl.setStyle(
        TableStyle(
            [
                ("BACKGROUND", (0, 0), (-1, 0), NAVY),
                ("TEXTCOLOR", (0, 0), (-1, 0), WHITE),
                ("FONTNAME", (0, 0), (-1, 0), "Helvetica-Bold"),
                ("FONTSIZE", (0, 0), (-1, -1), 7),
                ("BACKGROUND", (0, 1), (-1, -1), LIGHT),
                ("GRID", (0, 0), (-1, -1), 0.3, colors.HexColor("#D1D5DB")),
                ("ALIGN", (0, 0), (-1, -1), "CENTER"),
                ("VALIGN", (0, 0), (-1, -1), "MIDDLE"),
                ("TOPPADDING", (0, 0), (-1, -1), 4),
                ("BOTTOMPADDING", (0, 0), (-1, -1), 4),
            ]
        )
    )
    story += [tbl, Spacer(1, 8)]
    if len(use):
        top = use.iloc[0]
        story += [
            Paragraph("AI recommendation", styles["h"]),
            Paragraph(
                f"Top candidate <b>{top['name']}</b> &nbsp;|&nbsp; Rescue/Opportunity Score {top['rescue_score']:.2f} "
                f"&nbsp;|&nbsp; Confidence {top['confidence']:.2f}<br/>"
                f"Recommendation: <b>{top['recommendation']}</b> &nbsp;|&nbsp; Next: {top['next_experiment']}<br/>"
                f"Reason codes: {top['reason_codes']}",
                styles["b"],
            ),
        ]
    story += [
        Paragraph("Disclaimer", styles["h"]),
        Paragraph(
            "Scores are multi-objective computational estimates for prioritization. "
            "They are not proof of binding, rescue, or clinical efficacy. Experimental assays remain the validation layer.",
            styles["small"],
        ),
    ]
    # dummy title overlay: we already drew header bar in canvas; put title into flow with white space
    doc.build(story, onFirstPage=_header_footer, onLaterPages=_header_footer)
    return buf.getvalue()