// Atlas · Sample data
// Pre-baked content for the prototype.

const SAMPLE_BRIEF = `We need a technology landscape on antisense oligonucleotide (ASO) and siRNA technologies in animal health, focused on companion animals (dogs, cats) and large livestock.

Key questions to answer:
• Who are the leading players (companies + academic groups) driving innovation in antisense therapeutics, with a specific lens on veterinary and animal-health applications?
• What major industry–academic collaborations are active in the antisense space that are relevant to veterinary translation?
• What are the current applications - approved, in-development, and preclinical - of antisense technologies in veterinary medicine?

Parameters to capture for every company/program identified:
- Modality (ASO gapmer, splice-switching, GalNAc-siRNA, LNP-siRNA, miRNA inhibitor)
- Indication & target species
- Development stage (preclinical, IND-enabling, in-life pilot, regulatory)
- Lead investigator or commercial partner
- Funding source / sponsor and any disclosed deal value
- Most recent peer-reviewed citation (PubMed PMID preferred)

Audience is our internal R&D and science team, assume strong molecular-biology background, no need to define basic terms. Date range last 10 years. Global geographic scope. Please err on the side of including translational evidence even when veterinary-specific data is thin.

I've attached two reference docs the agents should mirror in tone and depth: last quarter's Aducanumab landscape and the LNP delivery scouting brief.`;

const SAMPLE_TOPIC = "Antisense oligonucleotide (ASO) and siRNA technologies in animal health";

const PARSED_QUESTIONS = [
  "Who are the key players (companies, research institutions) driving innovation in antisense therapeutics, with a focus on animal-health applications?",
  "What are the major industry–academic collaborations in the antisense field relevant to veterinary translation?",
  "What are the current applications of antisense technologies in veterinary medicine - approved, in-development, and preclinical-stage programs?",
];

const PARSED_PARAMETERS = [
  "Modality (ASO gapmer · splice-switching · GalNAc-siRNA · LNP-siRNA · miRNA inhibitor)",
  "Indication & target species",
  "Development stage (preclinical → regulatory)",
  "Lead investigator or commercial partner",
  "Funding source / sponsor + disclosed deal value",
  "Most recent peer-reviewed citation (PubMed PMID preferred)",
];

const SAMPLE_ATTACHMENTS = [
  { name: "Q1-aducanumab-landscape.pdf", kind: "pdf", size: "4.2 MB" },
  { name: "lnp-delivery-scouting.docx",   kind: "docx", size: "1.1 MB" },
];

const REPORT_TYPES = [
  {
    id: "tech",
    title: "Technology Landscape",
    desc: "A dual-lens view of a technology area: what the science says and who is building it. Maps the development stage of each approach and the players advancing it, from companies to research institutions.",
    icon: "network",
  },
  {
    id: "company",
    title: "Company Intelligence",
    desc: "A structured map of who is active in a market: startups, established players, spin-offs, and partnerships. Each entry is profiled on stage, funding, focus, and strategic fit.",
    icon: "building",
  },
  {
    id: "lit",
    title: "Literature Review",
    desc: "Systematic review of peer-reviewed research on a topic. Returns a structured synthesis of what the literature says, where the evidence converges, and where gaps remain.",
    icon: "bookOpen",
  },
  {
    id: "position",
    title: "Competitive Position",
    desc: "An asset-level competitive map anchored on your company or technology. Profiles competitor and pipeline assets side-by-side: modality, development stage, regulatory pathway, and performance. Includes white space analysis and strategic recommendations.",
    icon: "target",
  },
];

const FORMATS = [
  { id: "pdf",  label: "PDF",         ext: ".pdf",  icon: "pdf" },
  { id: "docx", label: "Word",        ext: ".docx", icon: "doc" },
  { id: "md",   label: "Markdown",    ext: ".md",   icon: "doc" },
];

const AUDIENCES = [
  "Internal R&D / science team",
  "Executive leadership",
  "Academic / research institution",
  "External client / partner",
  "Other",
];

// — Outline (reshaped as flat chapter list with prose blurbs) —————
const SAMPLE_OUTLINE = [
  {
    id: "ch1", num: "I",
    title: "Framing & Methodology",
    blurb: "An <em>opening chapter</em> orienting the reader to scope, search strategy, and how to read the maturity assessment that closes the report.",
    sources: 6, entries: 2, length: "≈ 4 slides",
    status: "approved",
  },
  {
    id: "ch2", num: "II",
    title: "The Antisense Toolkit",
    blurb: "Side-by-side characterisation of the three modalities in scope (ASO gapmers, splice-switching ASOs, and siRNA platforms) with chemistry, delivery routes, and the lead human-drug exemplar for each.",
    sources: 24, entries: 3, length: "≈ 7 slides",
    status: "approved",
  },
  {
    id: "ch3", num: "III",
    title: "Translation into Veterinary Medicine",
    blurb: "Where the science actually lands in animals: companion-animal pilots, livestock work, and the open question of whether GalNAc and LNP delivery transfers across species.",
    sources: 18, entries: 4, length: "≈ 9 slides",
    status: "needs-review",
  },
  {
    id: "ch4", num: "IV",
    title: "Players & Programs",
    blurb: "Profiles of the platform leaders (Ionis, Alnylam, Sarepta), the specialist next tier, and the academic groups running veterinary-first programs; each with pipeline, indications, and animal-health relevance scored.",
    sources: 31, entries: 5, length: "≈ 12 slides",
    status: "needs-review",
  },
  {
    id: "ch5", num: "V",
    title: "Collaborations & Deal Flow",
    blurb: "Industry–academic partnerships and industry–industry deals from 2020–2026, filtered for those that touch a veterinary indication or transferable platform.",
    sources: 14, entries: 2, length: "≈ 5 slides",
    status: "approved",
  },
  {
    id: "ch6", num: "VI",
    title: "Maturity Assessment & Take-aways",
    blurb: "Each modality plotted on the <em>7-stage maturity grid</em>, followed by a synthesis chapter that answers the three brief questions in plain language.",
    sources: 9, entries: 3, length: "≈ 6 slides",
    status: "approved",
  },
];

// — Agent pipeline ——————————————————————————————————
const AGENT_PIPELINE = [
  { id: "rev",   name: "Review Agent",       sub: "scope review",       icon: "checkSmall" },
  { id: "out",   name: "Outline Agent",      sub: "fact-check + outline", icon: "list" },
  { id: "spec",  name: "Tech Specialist",    sub: "coordinator",         icon: "diamond" },
  { id: "sub1",  name: "Subagent 1/4",       sub: "ASO platforms",       icon: "search" },
  { id: "sub2",  name: "Subagent 2/4",       sub: "siRNA platforms",     icon: "search" },
  { id: "sub3",  name: "Subagent 3/4",       sub: "vet. translation",    icon: "search" },
  { id: "sub4",  name: "Subagent 4/4",       sub: "companies & deals",   icon: "search" },
  { id: "syn",   name: "Synthesizer",        sub: "dedupe + structure",  icon: "layers" },
  { id: "rev2",  name: "Review Agent",       sub: "research review",     icon: "checkSmall" },
  { id: "ref",   name: "Reference Agent",    sub: "citation validation", icon: "link" },
  { id: "wri",   name: "Writing Agent",      sub: "drafting sections",   icon: "edit" },
];

const CONSOLE_FEED = [
  { kind: "rule" },
  { kind: "head", agent: "ORCHESTRATOR", phase: "Scope confirmed" },
  { kind: "rule" },
  { kind: "info", text: "Parsed brief into 3 questions, 6 capture parameters, 2 reference attachments." },
  { kind: "info", text: "Scope written to output/2026-05-04_aso-animal-health/scope.md" },
  { kind: "info", text: "Forwarding to Review Agent for scope approval." },
  { kind: "blank" },
  { kind: "rule" },
  { kind: "head", agent: "REVIEW AGENT", phase: "Scope review" },
  { kind: "rule" },
  { kind: "ok", text: "Report type: Technology Landscape" },
  { kind: "ok", text: "Topic: ASO/siRNA in animal health: specific and bounded" },
  { kind: "ok", text: "Capture parameters: 6 fields confirmed for every entry" },
  { kind: "ok", text: "Reference docs: 2 attached, parsed and indexed" },
  { kind: "ok", text: "Output format: PowerPoint (.pptx)" },
  { kind: "info", text: "Note: Date range defaulting to 2016–2026 (last 10 years)" },
  { kind: "blank" },
  { kind: "status", text: "STATUS: APPROVED. Proceeding to research phase." },
  { kind: "rule" },
  { kind: "blank" },
  { kind: "rule" },
  { kind: "head", agent: "TECH LANDSCAPE SPECIALIST", phase: "Research phase" },
  { kind: "rule" },
  { kind: "info", text: "Spawning 4 research subagents with distinct search angles:" },
  { kind: "running", text: "Subagent 1/4 · ASO platforms (gapmer, splice-switching) → PubMed + companies" },
  { kind: "running", text: "Subagent 2/4 · siRNA platforms (GalNAc, LNP) → PubMed + companies" },
  { kind: "running", text: "Subagent 3/4 · veterinary translation evidence → PubMed + sponsored programs" },
  { kind: "running", text: "Subagent 4/4 · industry deals & university partnerships → web search" },
  { kind: "blank" },
  { kind: "info", text: "[Subagent 1/4] 4/10 searches complete · 9 relevant papers · 3 companies" },
  { kind: "info", text: "[Subagent 2/4] 6/10 searches complete · 14 relevant papers · 6 companies" },
  { kind: "info", text: "[Subagent 3/4] 3/10 searches complete · 5 papers · 1 academic group" },
  { kind: "info", text: "[Subagent 4/4] 7/10 searches complete · 11 deals identified · 4 partnerships" },
  { kind: "blank" },
  { kind: "live", text: "Streaming live results. Subagents will continue until all 10 searches each are complete." },
];

const SAMPLE_COMMENTS = [
  {
    id: "c1",
    author: "You",
    avatar: "BC",
    kind: "user",
    target: "§ IV.1 Ionis Pharmaceuticals · ¶2",
    body: "Can we add the latest 2025 collaboration with Boehringer Ingelheim for the veterinary program? It came up in their Q1 earnings.",
    time: "just now",
    status: "Open",
  },
  {
    id: "c2",
    author: "Writing Agent",
    avatar: "WA",
    kind: "agent",
    target: "§ IV.1 Ionis Pharmaceuticals · ¶2",
    body: "Located the announcement (Ionis Q1 2025 earnings, 6 May press release). Drafting an addition: \"In Q1 2025, Ionis announced a strategic collaboration with Boehringer Ingelheim Animal Health to evaluate two undisclosed ASO candidates in companion-animal indications.\" Will source from the press release. Apply?",
    time: "in progress",
    status: "Awaiting approval",
  },
  {
    id: "c3",
    author: "You",
    avatar: "BC",
    kind: "user",
    target: "§ II.1 Antisense Oligonucleotides",
    body: "The mechanism description is too dense for our audience. Can you simplify to two sentences and move the chemistry detail to an appendix?",
    time: "5m ago",
    status: "Resolved",
  },
];

window.ATLAS_DATA = {
  SAMPLE_BRIEF, SAMPLE_TOPIC, PARSED_QUESTIONS, PARSED_PARAMETERS, SAMPLE_ATTACHMENTS,
  REPORT_TYPES, FORMATS, AUDIENCES,
  SAMPLE_OUTLINE, AGENT_PIPELINE, CONSOLE_FEED, SAMPLE_COMMENTS,
};
window.COMPASS_DATA = window.ATLAS_DATA; // back-compat for any leftover refs