src/lib/demo-engine.ts

/**
 * Demo conversation engine with Plan Mode and Action Mode.
 *
 * Plan Mode: Deep structured interview for drug hunters — asks the critical
 * questions that determine whether a molecule will succeed in the clinic.
 *
 * Action Mode: AI takes the lead — minimal questions, proactive exploration,
 * autonomous pipeline decisions.
 */

import { BENCHMARKS, MODELS, TARGETS } from "./data";
import type { StreamEvent, PlanProposal, TraceEntry, Artifact, Citation } from "./types";
import {
  createPhyloCampaign,
  submitPhyloJob,
  getPhyloJobStatus,
  estimateToolCost,
} from "./api";
import { resolveToolEndpoint } from "./tool-mapping";

export type AgentMode = "plan" | "action";

type PlanState =
  | "greeting"
  | "ask_target"
  | "ask_indication"
  | "ask_mechanism"
  | "ask_format"
  | "ask_epitope"
  | "ask_affinity"
  | "ask_species"
  | "ask_developability"
  | "ask_route"
  | "ask_competition"
  | "ask_seed"
  | "ask_scale"
  | "show_plan"
  | "confirmed"
  | "free_chat";

type ActionState = "greeting" | "ask_target" | "running" | "free_chat";

interface DemoConversation {
  id: string;
  mode: AgentMode;
  planState: PlanState;
  actionState: ActionState;
  target: string;
  indication: string;
  mechanism: string;
  format: string;
  epitope: string;
  affinity: string;
  species: string;
  developability: string;
  route: string;
  competition: string;
  seed: string;
  scale: string;
  messageCount: number;
}

let _conv: DemoConversation | null = null;

/** Optional scientist-provided input file (PDB/FASTA). Set from the UI. */
let _inputFile: File | null = null;

/** Set the scientist-provided input file for use in executePlan. */
export function demoSetInputFile(file: File | null): void {
  _inputFile = file;
}

export function demoCreateConversation(): string {
  const id = "demo-" + Math.random().toString(36).slice(2, 10);
  _conv = {
    id,
    mode: "plan",
    planState: "greeting",
    actionState: "greeting",
    target: "", indication: "", mechanism: "", format: "", epitope: "",
    affinity: "", species: "", developability: "", route: "", competition: "",
    seed: "", scale: "",
    messageCount: 0,
  };
  return id;
}

export function demoSetMode(mode: AgentMode): void {
  if (_conv) _conv.mode = mode;
}

export function demoGetMode(): AgentMode {
  return _conv?.mode ?? "plan";
}

export function demoGetDesignBrief(): Record<string, string> {
  if (!_conv) return {};
  const b: Record<string, string> = {};
  if (_conv.target) b["Target"] = _conv.target;
  if (_conv.indication) b["Indication"] = _conv.indication;
  if (_conv.mechanism) b["Mechanism"] = _conv.mechanism;
  if (_conv.format) b["Format"] = _conv.format;
  if (_conv.epitope) b["Epitope"] = _conv.epitope;
  if (_conv.affinity) b["Affinity"] = _conv.affinity;
  if (_conv.species) b["Species"] = _conv.species;
  if (_conv.developability) b["Developability"] = _conv.developability;
  if (_conv.route) b["Route"] = _conv.route;
  if (_conv.competition) b["Competition"] = _conv.competition;
  if (_conv.seed) b["Starting point"] = _conv.seed;
  if (_conv.scale) b["Designs"] = _conv.scale;
  return b;
}

export async function demoSendMessage(
  message: string,
  onEvent: (ev: StreamEvent) => void
): Promise<void> {
  if (!_conv) return;
  _conv.messageCount++;
  const msg = message.toLowerCase().trim();

  // Explore queries work in any mode/state
  if (isExploreQuery(msg)) {
    await handleExploreQuery(msg, onEvent);
    return;
  }

  if (_conv.mode === "plan") {
    await handlePlanMode(msg, onEvent);
  } else {
    await handleActionMode(msg, onEvent);
  }
}

// ============================================================
// PLAN MODE — Deep drug design interview
// ============================================================

async function handlePlanMode(msg: string, onEvent: (ev: StreamEvent) => void) {
  switch (_conv!.planState) {
    case "greeting": {
      const target = detectTarget(msg);
      if (target) {
        _conv!.target = target;
        await emitToolCall("lookup_target", { target_name: target }, getTargetData(target), onEvent);
        await streamText(
          `**${target}** — ${getTargetNotes(target)}.\n\nWhat therapeutic indication are you pursuing?\n\n` +
          `- **Oncology** (e.g., solid tumors, hematologic malignancies)\n` +
          `- **Autoimmune / Inflammation**\n` +
          `- **Infectious disease**\n` +
          `- **Other**`,
          onEvent
        );
        _conv!.planState = "ask_indication";
      } else {
        await streamText(
          `Welcome to **Plan Mode**. I will walk you through a structured design brief to make sure we capture everything that matters for your molecule.\n\n` +
          `What is your **target protein**?`,
          onEvent
        );
        _conv!.planState = "ask_target";
      }
      break;
    }
    case "ask_target": {
      const target = detectTarget(msg) || msg.replace(/[^a-zA-Z0-9\-\s]/g, "").trim().toUpperCase();
      _conv!.target = target;
      const known = TARGETS.find((t) => t.name.toLowerCase() === target.toLowerCase());
      if (known) {
        await emitToolCall("lookup_target", { target_name: target }, getTargetData(target), onEvent);
        await streamText(
          `**${target}** — ${known.notes}\n\nWhat therapeutic indication?\n\n- **Oncology**\n- **Autoimmune / Inflammation**\n- **Infectious disease**\n- **Other**`,
          onEvent
        );
      } else {
        await streamText(
          `Noted: **${target}**. No benchmark data yet, but we can design against it.\n\nWhat therapeutic indication?\n\n- **Oncology**\n- **Autoimmune / Inflammation**\n- **Infectious disease**\n- **Other**`,
          onEvent
        );
      }
      _conv!.planState = "ask_indication";
      break;
    }
    case "ask_indication": {
      _conv!.indication = extractChoice(msg, ["oncology", "autoimmune", "inflammation", "infectious", "other"]) || msg.slice(0, 60);
      await streamText(
        `What is the desired **mechanism of action**?\n\n` +
        `- **Blocking / Neutralization** — prevent ligand-receptor interaction\n` +
        `- **Receptor agonism** — activate signaling\n` +
        `- **Internalization / ADC** — deliver payload into cell\n` +
        `- **Cell depletion** — ADCC/CDC to kill target-expressing cells\n` +
        `- **Not sure** — I can advise based on target biology`,
        onEvent
      );
      _conv!.planState = "ask_mechanism";
      break;
    }
    case "ask_mechanism": {
      _conv!.mechanism = extractChoice(msg, ["blocking", "neutralization", "agonism", "internalization", "adc", "depletion", "adcc", "cdc"]) || msg.slice(0, 60);
      const needsFc = ["depletion", "adcc", "cdc", "internalization", "adc"].some((k) => _conv!.mechanism.includes(k));
      await streamText(
        `What **antibody format**?${needsFc ? " (Your mechanism likely needs Fc effector functions.)" : ""}\n\n` +
        `- **VHH** (nanobody) — 15 kDa, great tissue penetration, no Fc\n` +
        `- **scFv** — 27 kDa, no Fc\n` +
        `- **mAb (IgG1)** — full Fc, enables ADCC/CDC\n` +
        `- **mAb (IgG4)** — Fc-silent, blocking only\n` +
        `- **Bispecific** — dual-target engagement`,
        onEvent
      );
      _conv!.planState = "ask_format";
      break;
    }
    case "ask_format": {
      if (msg.includes("vhh") || msg.includes("nanobody")) _conv!.format = "VHH";
      else if (msg.includes("scfv")) _conv!.format = "scFv";
      else if (msg.includes("igg1") || msg.includes("mab")) _conv!.format = "mAb (IgG1)";
      else if (msg.includes("igg4")) _conv!.format = "mAb (IgG4)";
      else if (msg.includes("bispecific")) _conv!.format = "Bispecific";
      else _conv!.format = msg.slice(0, 20);
      await streamText(
        `Do you have a **preferred epitope** or binding site on ${_conv!.target}?\n\n` +
        `- **Orthosteric** — ligand binding site\n` +
        `- **Allosteric** — away from active site\n` +
        `- **Specific residues** — describe them\n` +
        `- **No preference** — let the model explore`,
        onEvent
      );
      _conv!.planState = "ask_epitope";
      break;
    }
    case "ask_epitope": {
      _conv!.epitope = msg.includes("no preference") || msg.includes("no pref") || msg.includes("explore") ? "no preference" : msg.slice(0, 80);
      await streamText(
        `What **affinity** are you targeting?\n\n` +
        `- **< 1 nM** — ultra-high (typical for therapeutic mAbs)\n` +
        `- **1-10 nM** — high (standard for most programs)\n` +
        `- **10-100 nM** — moderate (acceptable for some mechanisms)\n` +
        `- **Any binder first** — optimize affinity later`,
        onEvent
      );
      _conv!.planState = "ask_affinity";
      break;
    }
    case "ask_affinity": {
      _conv!.affinity = extractChoice(msg, ["< 1", "1-10", "10-100", "any binder"]) || msg.slice(0, 30);
      await streamText(
        `What **species cross-reactivity** do you need?\n\n` +
        `- **Human only** — sufficient for early discovery\n` +
        `- **Human + cynomolgus** — needed for tox studies\n` +
        `- **Human + cyno + mouse** — enables mouse efficacy models\n` +
        `- **Not sure**`,
        onEvent
      );
      _conv!.planState = "ask_species";
      break;
    }
    case "ask_species": {
      _conv!.species = extractChoice(msg, ["human only", "cyno", "mouse", "not sure"]) || msg.slice(0, 40);
      await streamText(
        `**Developability** priorities? Select the most critical:\n\n` +
        `- **Low aggregation** — Agmata score < 0.3\n` +
        `- **High expression** — > 1 g/L in CHO\n` +
        `- **Thermostability** — Tm > 70C\n` +
        `- **Low immunogenicity** — high humanness score\n` +
        `- **Balanced** — optimize all equally`,
        onEvent
      );
      _conv!.planState = "ask_developability";
      break;
    }
    case "ask_developability": {
      _conv!.developability = extractChoice(msg, ["aggregation", "expression", "thermostab", "immunogenicity", "balanced"]) || msg.slice(0, 40);
      await streamText(
        `Intended **route of administration**?\n\n` +
        `- **IV** (intravenous) — standard for oncology\n` +
        `- **SC** (subcutaneous) — preferred for chronic dosing\n` +
        `- **Intrathecal** — CNS delivery\n` +
        `- **Inhaled** — respiratory targets\n` +
        `- **Not decided**`,
        onEvent
      );
      _conv!.planState = "ask_route";
      break;
    }
    case "ask_route": {
      _conv!.route = extractChoice(msg, ["iv", "sc", "intrathecal", "inhaled", "not decided"]) || msg.slice(0, 30);
      await streamText(
        `Are there **existing antibodies** against ${_conv!.target} you want to benchmark against or differentiate from?\n\n` +
        `- Name specific antibodies (e.g., trastuzumab, pembrolizumab)\n` +
        `- **None known**\n` +
        `- **Yes, but undisclosed**`,
        onEvent
      );
      _conv!.planState = "ask_competition";
      break;
    }
    case "ask_competition": {
      _conv!.competition = msg.includes("none") ? "none known" : msg.slice(0, 80);
      await streamText(
        `Starting point?\n\n` +
        `- **De novo** — design from scratch against the target structure\n` +
        `- **Seed sequence** — optimize an existing antibody\n` +
        `- **Humanize** — humanize a non-human lead`,
        onEvent
      );
      _conv!.planState = "ask_seed";
      break;
    }
    case "ask_seed": {
      _conv!.seed = msg.includes("novo") || msg.includes("scratch") ? "de novo" : msg.includes("humanize") ? "humanization" : "seed optimization";
      await streamText(
        `How many designs to generate?\n\n- **10** — quick pilot\n- **50** — standard campaign\n- **100+** — comprehensive`,
        onEvent
      );
      _conv!.planState = "ask_scale";
      break;
    }
    case "ask_scale": {
      const match = msg.match(/(\d+)/);
      _conv!.scale = match ? match[1] : "50";
      await showDesignBrief(onEvent);
      _conv!.planState = "show_plan";
      break;
    }
    case "show_plan": {
      if (msg.includes("run") || msg.includes("go") || msg.includes("yes") || msg.includes("ready") || msg.includes("confirm") || msg.includes("start")) {
        await executePlan(onEvent);
        _conv!.planState = "free_chat";
      } else {
        await streamText("What would you like to adjust in the design brief?", onEvent);
      }
      break;
    }
    case "confirmed":
    case "free_chat": {
      await handleFreeChat(msg, onEvent);
      break;
    }
  }
  onEvent({ type: "done" });
}

async function showDesignBrief(onEvent: (ev: StreamEvent) => void) {
  // KB lookups — simulate best-practice retrieval before planning
  await emitKBLookup("antibody design best practices", onEvent);
  await emitKBLookup("benchmark catalog", onEvent);
  await emitKBLookup("target lookup", onEvent);

  await emitTrace({ kind: "thought", label: "Synthesizing design brief from interview answers" }, onEvent);
  await emitToolCall("browse_benchmarks", {}, { count: BENCHMARKS.length }, onEvent);
  await emitToolCall("browse_models", { capability: "full_design" }, { count: MODELS.filter((m) => m.capabilities.includes("full_design")).length }, onEvent);

  const pipeline = _conv!.seed === "de novo"
    ? "RFdiffusion → ProteinMPNN → RF2 (filter) → Chai-1 (score)"
    : "ProteinMPNN (CDR redesign) → RF2 → Chai-1";

  await streamText(
    `Here is your **Design Brief**:\n\n` +
    `| Parameter | Value |\n` +
    `|-----------|-------|\n` +
    `| Target | **${_conv!.target}** |\n` +
    `| Indication | ${_conv!.indication} |\n` +
    `| Mechanism | ${_conv!.mechanism} |\n` +
    `| Format | **${_conv!.format}** |\n` +
    `| Epitope | ${_conv!.epitope} |\n` +
    `| Affinity goal | ${_conv!.affinity} |\n` +
    `| Species cross-rx | ${_conv!.species} |\n` +
    `| Developability | ${_conv!.developability} |\n` +
    `| Route | ${_conv!.route} |\n` +
    `| Competition | ${_conv!.competition} |\n` +
    `| Starting point | ${_conv!.seed} |\n` +
    `| Designs | **${_conv!.scale}** |\n` +
    `| Pipeline | ${pipeline} |\n` +
    `| Scoring | 3-model consensus (Chai-1 + AF2 + Protenix) |\n\n` +
    `Ready to launch this campaign, or want to adjust anything?`,
    onEvent
  );

  // Emit structured plan proposal right before the execute/chat fork
  onEvent({ type: "plan", plan: buildPlanProposal() });
}

async function executePlan(onEvent: (ev: StreamEvent) => void) {
  await emitTrace({ kind: "thought", label: `Launching campaign for ${_conv!.target}` }, onEvent);

  // ---- Determine pipeline tools from the plan ----
  const plan = buildPlanProposal();
  const pipelineTools = plan.steps.flatMap((s) => s.tools);

  try {
    // ---- 1. Create real campaign via Phylo backend ----
    const campaignParams = {
      name: `${_conv!.target}-${_conv!.format}-${Date.now()}`,
      target: _conv!.target,
      modality: _conv!.format || "VHH",
      goal: _conv!.mechanism || "blocking",
      constraints: {
        epitope: _conv!.epitope,
        affinity: _conv!.affinity,
        species: _conv!.species,
        developability: _conv!.developability,
        route: _conv!.route,
        scale: _conv!.scale,
        seed: _conv!.seed,
      },
    };

    const campaign = await createPhyloCampaign(campaignParams);
    const campaignId = campaign.id;

    await emitToolCall(
      "create_campaign",
      campaignParams,
      { campaign_id: campaignId, status: "created" },
      onEvent,
    );
    await emitTrace(
      { kind: "tool_result", label: `campaign_id=${campaignId}`, detail: truncate(JSON.stringify(campaign)) },
      onEvent,
    );

    await streamText(`Campaign **${campaignId}** created on the Innovation Hub.\n\n`, onEvent);

    // ---- 2. Estimate costs for each pipeline tool ----
    for (const tool of pipelineTools) {
      try {
        const endpoint = resolveToolEndpoint(tool);
        const estimate = await estimateToolCost(endpoint);
        await emitToolCall(
          "estimate_cost",
          { endpoint_name: endpoint, gpu_type: "A100" },
          estimate,
          onEvent,
        );
        const costLine = `**${tool}**: ~$${estimate.estimated_usd.toFixed(2)} (${estimate.minutes_used} min on ${estimate.gpu_type})`;
        const alertLine = estimate.cost_alert ? ` -- ${estimate.cost_alert}` : "";
        await streamText(costLine + alertLine + "\n", onEvent);
      } catch {
        // Cost estimation is non-critical — skip silently
        await streamText(`**${tool}**: cost estimate unavailable\n`, onEvent);
      }
    }

    await streamText("\nSubmitting jobs to the GPU cluster...\n\n", onEvent);

    // ---- 3. Submit jobs sequentially ----
    const completedJobs: { tool: string; jobId: string; output: unknown }[] = [];

    for (const tool of pipelineTools) {
      const jobEndpoint = resolveToolEndpoint(tool);
      await emitTrace({ kind: "tool_call", label: tool, detail: `Submitting ${tool} job (${jobEndpoint})` }, onEvent);

      // Use scientist-provided file if available, otherwise build placeholder FASTA
      let inputBlob: Blob;
      let inputFilename: string;
      if (_inputFile) {
        inputBlob = _inputFile;
        inputFilename = _inputFile.name;
      } else {
        const fastaContent = buildMinimalFasta(_conv!.target, _conv!.seed);
        inputBlob = new Blob([fastaContent], { type: "text/plain" });
        inputFilename = "input.fasta";
      }
      const formData = new FormData();
      formData.append("endpoint_name", jobEndpoint);
      formData.append("provider", "runpod");
      formData.append("call_params", JSON.stringify({
        target: _conv!.target,
        format: _conv!.format,
        num_designs: parseInt(_conv!.scale || "50", 10),
      }));
      formData.append("role", "design");
      formData.append("input_file", inputBlob, inputFilename);

      let jobResult;
      try {
        jobResult = await submitPhyloJob(campaignId, formData);
      } catch (err: unknown) {
        const errMsg = err instanceof Error ? err.message : String(err);
        await emitTrace({ kind: "tool_result", label: `${tool} submission failed`, detail: errMsg }, onEvent);
        await streamText(`**${tool}** -- job submission failed: ${errMsg}\n`, onEvent);
        continue;
      }

      const jobId = jobResult.campaign_job_id;
      await emitToolCall(
        "submit_job",
        { campaign_id: campaignId, endpoint_name: jobEndpoint },
        { job_id: jobId, provider: jobResult.provider },
        onEvent,
      );

      await streamText(`**${tool}** job **${jobId}** submitted. Polling for completion...\n`, onEvent);

      // ---- 4. Poll until complete or timeout (10 min) ----
      const POLL_INTERVAL_MS = 5_000;
      const MAX_POLL_MS = 10 * 60 * 1_000;
      const pollStart = Date.now();
      let finalStatus: Awaited<ReturnType<typeof getPhyloJobStatus>> | null = null;

      while (Date.now() - pollStart < MAX_POLL_MS) {
        await sleep(POLL_INTERVAL_MS);
        try {
          const status = await getPhyloJobStatus(jobId);
          const hubStatus = status.hub?.status?.toLowerCase() ?? "";

          if (hubStatus === "completed" || hubStatus === "success" || hubStatus === "done") {
            finalStatus = status;
            break;
          } else if (hubStatus === "failed" || hubStatus === "error") {
            const detail = typeof status.hub?.output_data === "string"
              ? status.hub.output_data
              : JSON.stringify(status.hub?.output_data ?? "unknown error");
            await emitTrace({ kind: "tool_result", label: `${tool} failed`, detail }, onEvent);
            await streamText(`**${tool}** failed: ${detail}\n`, onEvent);
            break;
          }
          // Still running — continue polling
        } catch {
          // Transient poll failure — keep trying
        }
      }

      if (finalStatus) {
        await emitTrace(
          { kind: "tool_result", label: `${tool} completed`, detail: truncate(JSON.stringify(finalStatus.hub)) },
          onEvent,
        );
        await streamText(`**${tool}** completed.\n`, onEvent);

        completedJobs.push({ tool, jobId, output: finalStatus.hub?.output_data });

        // ---- 5. Emit real artifacts ----
        if (finalStatus.artifacts && finalStatus.artifacts.length > 0) {
          for (const art of finalStatus.artifacts) {
            const artifact: Artifact = {
              id: `art-${jobId}-${art.name}`,
              name: art.name,
              bytes: art.bytes ?? 0,
              mime: art.mime ?? "application/octet-stream",
              url: art.url,
              createdAt: Date.now(),
            };
            onEvent({ type: "artifact", artifact });
          }
        }
      } else if (!finalStatus) {
        await streamText(`**${tool}** timed out after 10 minutes.\n`, onEvent);
      }
    }

    // ---- Summary ----
    const successCount = completedJobs.length;
    const totalTools = pipelineTools.length;
    await streamText(
      `\n---\n**Campaign ${campaignId}**: ${successCount}/${totalTools} pipeline steps completed.\n` +
      `Track full progress in the **Campaigns** tab.`,
      onEvent,
    );

    // Emit design brief artifact (always useful even with real backend)
    const designBriefMd = buildDesignBriefMarkdown();
    await emitArtifact("design_brief.md", designBriefMd, "text/markdown", onEvent);
  } catch (err: unknown) {
    // ---- Backend unreachable — fall back to demo mode ----
    const errMsg = err instanceof Error ? err.message : String(err);
    await streamText(
      `> **Backend unreachable** -- showing demo results. (${errMsg})\n\n`,
      onEvent,
    );
    await executePlanDemo(onEvent);
  }
}

/** Original demo-only plan execution — used as fallback when Phylo backend is down. */
async function executePlanDemo(onEvent: (ev: StreamEvent) => void) {
  const campaignId = "camp-" + Math.random().toString(36).slice(2, 8);
  await emitToolCall(
    "plan_campaign",
    { target: _conv!.target, modality: _conv!.format, goal: _conv!.mechanism },
    { campaign_id: campaignId, status: "planned" },
    onEvent,
  );
  await streamText(
    `Campaign **${campaignId}** created (demo mode).\n\n` +
    `Pipeline steps:\n` +
    `1. Generate ${_conv!.scale} backbone structures (RFdiffusion)\n` +
    `2. Design sequences (ProteinMPNN, 2x per backbone)\n` +
    `3. Filter by RF2 iPAE < 10\n` +
    `4. Score with Chai-1 AntiConf > 0.50\n` +
    `5. Rank by 3-model consensus\n\n` +
    `Track progress in the **Campaigns** tab.`,
    onEvent,
  );

  const designBriefMd = buildDesignBriefMarkdown();
  const topDesignsCsv = buildTopDesignsCsv();
  const executionTraceJson = buildExecutionTraceJson();

  await emitArtifact("design_brief.md", designBriefMd, "text/markdown", onEvent);
  await emitArtifact("top_designs.csv", topDesignsCsv, "text/csv", onEvent);
  await emitArtifact("execution_trace.json", executionTraceJson, "application/json", onEvent);
}

/** Build a minimal FASTA string from interview fields for job submission. */
function buildMinimalFasta(target: string, seed: string): string {
  // If the user provided a seed sequence, use it; otherwise use a placeholder
  const placeholder = "MEVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAR";
  const header = `>${target}_design seed=${seed || "de_novo"}`;
  return `${header}\n${placeholder}\n`;
}

// ============================================================
// ACTION MODE — AI takes the lead
// ============================================================

async function handleActionMode(msg: string, onEvent: (ev: StreamEvent) => void) {
  switch (_conv!.actionState) {
    case "greeting": {
      const target = detectTarget(msg);
      if (target) {
        _conv!.target = target;
        await runActionAutonomous(onEvent);
        _conv!.actionState = "free_chat";
      } else {
        await streamText(
          `**Action Mode** — I will handle everything. Just tell me: what is your **target protein**?`,
          onEvent
        );
        _conv!.actionState = "ask_target";
      }
      break;
    }
    case "ask_target": {
      const target = detectTarget(msg) || msg.replace(/[^a-zA-Z0-9\-\s]/g, "").trim().toUpperCase();
      _conv!.target = target;
      await runActionAutonomous(onEvent);
      _conv!.actionState = "free_chat";
      break;
    }
    case "running":
    case "free_chat": {
      await handleFreeChat(msg, onEvent);
      break;
    }
  }
  onEvent({ type: "done" });
}

async function runActionAutonomous(onEvent: (ev: StreamEvent) => void) {
  const target = _conv!.target;

  // KB lookups before planning
  await emitKBLookup("antibody design best practices", onEvent);
  await emitKBLookup("target lookup", onEvent);

  // Step 1: Look up target
  await emitTrace({ kind: "thought", label: `Assessing target ${target}` }, onEvent);
  await emitToolCall("lookup_target", { target_name: target }, getTargetData(target), onEvent);
  const known = TARGETS.find((t) => t.name.toLowerCase() === target.toLowerCase());
  const tClass = known?.target_class || "unknown";

  await streamText(`Analyzing **${target}**...`, onEvent);

  // Step 2: Check benchmarks
  await emitToolCall("browse_benchmarks", {}, { count: BENCHMARKS.length }, onEvent);

  // Step 3: Auto-select format
  const format = tClass === "gpcr" ? "VHH" : "VHH";
  _conv!.format = format;

  // Step 4: Check models
  await emitToolCall("browse_models", { capability: "full_design" }, { count: 1 }, onEvent);

  // Step 5: Auto-build plan
  _conv!.seed = "de novo";
  _conv!.scale = "50";
  _conv!.mechanism = tClass === "gpcr" ? "blocking" : "blocking / neutralization";
  _conv!.indication = "auto-detected";

  const benchmarkData = getTargetBindingData(target);
  let benchmarkNote = "";
  if (benchmarkData.length > 0) {
    const best = benchmarkData.sort((a, b) => (b.hit_rate ?? 0) - (a.hit_rate ?? 0))[0];
    benchmarkNote = `\n\nBest published result: **${best.benchmark}** achieved ${fmtPct(best.hit_rate)} hit rate on ${target}.`;
  }

  await streamText(
    `Here is my recommended plan for **${target}**:\n\n` +
    `| Parameter | Value |\n` +
    `|-----------|-------|\n` +
    `| Target | **${target}** (${tClass}) |\n` +
    `| Format | **${format}** — best hit rates in benchmarks |\n` +
    `| Approach | **De novo** — RFdiffusion → ProteinMPNN → RF2 → Chai-1 |\n` +
    `| Designs | **50** |\n` +
    `| Scoring | 3-model consensus, AntiConf > 0.50 |\n` +
    benchmarkNote +
    `\n\nI selected VHH because it consistently achieves the highest hit rates across published benchmarks (JAM-2: 39%). ` +
    `The de novo pipeline is the most validated approach for new targets.\n\n` +
    `**Ready to launch?** Or switch to Plan Mode for a deeper interview.`,
    onEvent
  );
  onEvent({ type: "citation", citation: { label: "JAM-2 benchmark paper", url: "https://doi.org/10.1101/2024.jam2" } });
  onEvent({ type: "plan", plan: buildPlanProposal() });
}

// ============================================================
// EXPLORE QUERIES (shared)
// ============================================================

function isExploreQuery(msg: string): boolean {
  const kw = ["benchmark", "benchmarks", "compare", "models", "model", "what models", "what benchmarks", "show me", "list", "tell me about", "look up"];
  return kw.some((k) => msg.includes(k));
}

async function handleExploreQuery(msg: string, onEvent: (ev: StreamEvent) => void) {
  // KB lookups for benchmark/model/target questions
  if (msg.includes("benchmark") || msg.includes("model") || msg.includes("target") || msg.includes("compare")) {
    await emitKBLookup("benchmark catalog", onEvent);
    await emitKBLookup("model registry", onEvent);
  }
  if (msg.includes("compare")) {
    const names = extractBenchmarkNames(msg);
    if (names.length >= 2) {
      const rows = names.map((n) => {
        const bm = BENCHMARKS.find((b) => b.source.toLowerCase() === n.toLowerCase());
        return bm ? { source: bm.source, vhh: bm.avg_hit_rate_vhh, mab: bm.avg_hit_rate_mab, designs: bm.total_designs_tested } : { source: n, error: "not found" };
      });
      await emitToolCall("compare_benchmarks", { benchmark_names: names }, { comparison: rows }, onEvent);
      let table = "| Benchmark | VHH Hit Rate | mAb Hit Rate | Designs | Open Source |\n|-----------|:---:|:---:|:---:|:---:|\n";
      for (const bm of BENCHMARKS.filter((b) => names.some((n) => n.toLowerCase() === b.source.toLowerCase()))) {
        table += `| ${bm.source} | ${fmtPct(bm.avg_hit_rate_vhh)} | ${fmtPct(bm.avg_hit_rate_mab)} | ${bm.total_designs_tested} | ${bm.code_available ? "Yes" : "No"} |\n`;
      }
      await streamText(table + `\n**JAM-2** leads on hit rates. **Chai-2** has the best developability. **RFantibody** is validated by cryo-EM.`, onEvent);
      onEvent({ type: "citation", citation: { label: "JAM-2 paper", url: "https://doi.org/10.1101/2024.jam2" } });
      onEvent({ type: "citation", citation: { label: "RFantibody", url: "https://github.com/RosettaCommons/RFantibody" } });
    } else {
      await emitToolCall("browse_benchmarks", {}, { count: BENCHMARKS.length }, onEvent);
      await streamText(`Which benchmarks to compare? Available: ${BENCHMARKS.map((b) => `**${b.source}**`).join(", ")}`, onEvent);
    }
  } else if (msg.includes("benchmark")) {
    await emitToolCall("browse_benchmarks", {}, { count: BENCHMARKS.length }, onEvent);
    let table = "| Benchmark | Date | VHH Hit Rate | Best KD | Designs | Open |\n|-----------|------|:---:|:---:|:---:|:---:|\n";
    for (const bm of BENCHMARKS) {
      table += `| ${bm.source} | ${bm.paper_date} | ${fmtPct(bm.avg_hit_rate_vhh)} | ${bm.best_affinity_pM ? bm.best_affinity_pM + " pM" : "-"} | ${bm.total_designs_tested} | ${bm.code_available ? "Yes" : "No"} |\n`;
    }
    await streamText(`Published antibody design benchmarks:\n\n${table}\n**JAM-2** is current SOTA at 39% VHH hit rate.`, onEvent);
    onEvent({ type: "citation", citation: { label: "JAM-2 paper", url: "https://doi.org/10.1101/2024.jam2" } });
    onEvent({ type: "citation", citation: { label: "Chai-2", url: "https://chaidiscovery.com" } });
  } else if (msg.includes("model")) {
    await emitToolCall("browse_models", {}, { count: MODELS.length }, onEvent);
    let table = "| Model | Source | Capabilities | GPU | Formats |\n|-------|--------|------------|:---:|---------|\n";
    for (const m of MODELS) {
      table += `| ${m.name} | ${m.source} | ${m.capabilities.map((c) => c.replace(/_/g, " ")).join(", ")} | ${m.gpu_required ? m.min_vram_gb + "GB" : "CPU"} | ${m.antibody_formats.join(", ")} |\n`;
    }
    await streamText(`Model registry:\n\n${table}\nDe novo pipeline: **RFdiffusion** → **ProteinMPNN** → **Chai-1/AF2** (scoring).`, onEvent);
    onEvent({ type: "citation", citation: { label: "RFdiffusion", url: "https://github.com/RosettaCommons/RFdiffusion" } });
    onEvent({ type: "citation", citation: { label: "ProteinMPNN", url: "https://github.com/dauparas/ProteinMPNN" } });
    onEvent({ type: "citation", citation: { label: "Chai-1", url: "https://chaidiscovery.com" } });
  } else if (msg.includes("target") || msg.includes("tell me about") || msg.includes("look up")) {
    const target = detectTarget(msg);
    if (target) {
      await emitToolCall("lookup_target", { target_name: target }, getTargetData(target), onEvent);
      const t = TARGETS.find((t) => t.name.toLowerCase() === target.toLowerCase());
      if (t) {
        const bd = getTargetBindingData(target);
        let text = `**${t.name}** — ${t.notes}\n\n- Class: ${t.target_class}\n- PDB: ${t.pdb_id}\n`;
        if (bd.length > 0) {
          text += `\n| Benchmark | Format | Hit Rate | Best KD |\n|-----------|--------|:---:|:---:|\n`;
          for (const d of bd) text += `| ${d.benchmark} | ${d.format} | ${fmtPct(d.hit_rate)} | ${d.best_kd ? d.best_kd + " nM" : "-"} |\n`;
        }
        await streamText(text, onEvent);
      }
    } else {
      await streamText(`Available targets: ${TARGETS.map((t) => `**${t.name}**`).join(", ")}`, onEvent);
    }
  } else {
    await streamText(
      `I can help you explore:\n- **Benchmarks** — "What benchmarks exist?"\n- **Models** — "What models can do full design?"\n- **Targets** — "Tell me about HER2"\n- **Compare** — "Compare JAM-2 and Chai-2"`,
      onEvent
    );
  }
  onEvent({ type: "done" });
}

// ============================================================
// FREE CHAT (shared)
// ============================================================

async function handleFreeChat(msg: string, onEvent: (ev: StreamEvent) => void) {
  if (isExploreQuery(msg)) {
    await handleExploreQuery(msg, onEvent);
    return;
  }
  await streamText(
    `In the full version, I would use the Innovation Hub and FACADS tools here.\n\n` +
    `For now you can:\n- Explore **benchmarks** and **models**\n- **Compare** benchmarks or **look up** targets\n- Start a new design by telling me your target protein`,
    onEvent
  );
  onEvent({ type: "done" });
}

// ============================================================
// UTILITIES
// ============================================================

async function streamText(text: string, onEvent: (ev: StreamEvent) => void): Promise<void> {
  const words = text.split(" ");
  for (let i = 0; i < words.length; i++) {
    onEvent({ type: "text_delta", text: (i === 0 ? "" : " ") + words[i] });
    await sleep(18 + Math.random() * 25);
  }
}

async function emitToolCall(toolName: string, input: Record<string, unknown>, result: unknown, onEvent: (ev: StreamEvent) => void): Promise<void> {
  onEvent({ type: "tool_use", tool: toolName, input });
  await sleep(350 + Math.random() * 250);
  onEvent({ type: "tool_result", tool: toolName, result });
  await sleep(150);
}

function sleep(ms: number): Promise<void> {
  return new Promise((r) => setTimeout(r, ms));
}

function detectTarget(msg: string): string | null {
  for (const t of TARGETS) {
    if (msg.toLowerCase().includes(t.name.toLowerCase())) return t.name;
  }
  return null;
}

function getTargetNotes(name: string): string {
  return TARGETS.find((t) => t.name.toLowerCase() === name.toLowerCase())?.notes || "";
}

function getTargetData(name: string): Record<string, unknown> {
  const t = TARGETS.find((t) => t.name.toLowerCase() === name.toLowerCase());
  if (!t) return { error: "Target not found" };
  return { name: t.name, target_class: t.target_class, pdb_id: t.pdb_id, notes: t.notes, binding_data: getTargetBindingData(name) };
}

function getTargetBindingData(name: string): { benchmark: string; format: string; hit_rate: number | null; best_kd: number | null }[] {
  const results: { benchmark: string; format: string; hit_rate: number | null; best_kd: number | null }[] = [];
  for (const bm of BENCHMARKS) {
    for (const br of bm.binding_results) {
      if (br.target.toLowerCase() === name.toLowerCase()) {
        results.push({ benchmark: bm.source, format: br.antibody_format, hit_rate: br.hit_rate, best_kd: br.best_affinity_nM });
      }
    }
  }
  return results;
}

function extractBenchmarkNames(msg: string): string[] {
  return BENCHMARKS.filter((bm) => msg.toLowerCase().includes(bm.source.toLowerCase())).map((bm) => bm.source);
}

function extractChoice(msg: string, options: string[]): string {
  for (const opt of options) {
    if (msg.includes(opt)) return opt;
  }
  return "";
}

function fmtPct(v: number | null): string {
  return v != null ? `${(v * 100).toFixed(0)}%` : "-";
}

// ============================================================
// v2 EVENT HELPERS
// ============================================================

// ---- Static KB cache ----

interface KBEntry {
  id: string;
  title: string;
  category: string;
  content: string;
}

interface KBData {
  version: string;
  entries: KBEntry[];
}

let _kbCache: KBData | null = null;
let _kbFetchPromise: Promise<KBData | null> | null = null;

/** Keyword map: caller name → terms used for matching KB entries. */
const KB_QUERY_TERMS: Record<string, string[]> = {
  "antibody design best practices": ["design", "cdr", "fc", "bispecific", "engineering"],
  "benchmark catalog": ["scoring", "developability", "assessment", "metrics"],
  "target lookup": ["expression", "immunogenicity", "safety", "production"],
  "model registry": ["format", "bispecific", "fc", "knob"],
};

async function fetchKB(): Promise<KBData | null> {
  if (_kbCache) return _kbCache;
  if (_kbFetchPromise) return _kbFetchPromise;
  _kbFetchPromise = fetch("/kb/antibody-design-practices.json")
    .then((res) => {
      if (!res.ok) return null;
      return res.json() as Promise<KBData>;
    })
    .then((data) => {
      _kbCache = data;
      return data;
    })
    .catch(() => null);
  return _kbFetchPromise;
}

function matchKBEntry(name: string, entries: KBEntry[]): KBEntry | undefined {
  const terms = KB_QUERY_TERMS[name] || name.toLowerCase().split(/\s+/);
  let best: KBEntry | undefined;
  let bestScore = 0;
  for (const entry of entries) {
    const hay = `${entry.title} ${entry.category} ${entry.content}`.toLowerCase();
    let score = 0;
    for (const t of terms) {
      if (hay.includes(t)) score++;
    }
    if (score > bestScore) {
      bestScore = score;
      best = entry;
    }
  }
  return best;
}

async function emitKBLookup(name: string, onEvent: (ev: StreamEvent) => void): Promise<void> {
  const t0 = performance.now();
  const kb = await fetchKB();
  const ms = Math.round(performance.now() - t0);

  if (kb && kb.entries.length > 0) {
    const entry = matchKBEntry(name, kb.entries);
    const label = entry ? entry.title : name;
    onEvent({ type: "kb_lookup", kb: { name: label, ms } });
  } else {
    // Fallback: emit with original name if fetch failed
    onEvent({ type: "kb_lookup", kb: { name, ms: ms || 1 } });
  }
}

async function emitTrace(entry: Omit<TraceEntry, "ts">, onEvent: (ev: StreamEvent) => void): Promise<void> {
  const t: TraceEntry = { ts: Date.now(), ...entry };
  onEvent({ type: "trace", trace: t });
}

function truncate(s: string, n = 400): string {
  return s.length > n ? s.slice(0, n) + "…" : s;
}

async function emitArtifact(
  name: string,
  content: string,
  mime: string,
  onEvent: (ev: StreamEvent) => void
): Promise<void> {
  const id = "art-" + Math.random().toString(36).slice(2, 10);
  const bytes = new TextEncoder().encode(content).length;
  // Demo-mode artifact — the actual content is embedded as a data: URL so the
  // download works fully client-side without requiring the backend to have
  // saved the bytes. When the real backend lands and saveArtifact() is wired
  // up, switch to /api/artifacts/{id} and serve from disk.
  const dataUrl = `data:${mime};base64,${typeof window === "undefined"
    ? Buffer.from(content, "utf8").toString("base64")
    : btoa(unescape(encodeURIComponent(content)))}`;
  const artifact: Artifact = {
    id,
    name,
    bytes,
    mime,
    url: dataUrl,
    createdAt: Date.now(),
  };
  onEvent({ type: "artifact", artifact });
}

function buildPlanProposal(): PlanProposal {
  const seed = _conv!.seed || "de novo";
  const format = _conv!.format || "VHH";
  const target = _conv!.target || "target";

  // Plans use short names that resolve to LIVE Hub endpoints via
  // resolveToolEndpoint() in tool-mapping.ts. Do not reintroduce Biomni
  // research-repro names (RFdiffusion / ProteinMPNN / Protenix) here —
  // those endpoints are not live on hub-api and will 404 at run time.
  const steps = seed === "de novo"
    ? [
        { label: `Generate candidates against ${target}`, tools: ["Ankh"] },
        { label: `Rank by Fc effector profile`, tools: ["CRPS-Fc-DMS", "FcgR2B"] },
        { label: `Predict structure (${format})`, tools: ["Chai-1", "AF2"] },
        { label: "Developability triage", tools: ["Agmata", "PTM"] },
        { label: "FcRn half-life screen", tools: ["FcRn-pH6"] },
      ]
    : seed === "humanization"
    ? [
        { label: "Baseline parent Fc profile", tools: ["FcgR2B", "FcRn-pH6"] },
        { label: "Generate humanised variants", tools: ["Ankh"] },
        { label: "Re-score Fc binding", tools: ["CRPS-Fc-DMS"] },
        { label: "Structural QC", tools: ["Chai-1", "AF2"] },
        { label: "Developability triage", tools: ["Agmata", "PTM"] },
      ]
    : [
        { label: `Variant generation on seed (${format})`, tools: ["D3PM", "Ankh"] },
        { label: "Affinity ranking", tools: ["CRPS-ESM"] },
        { label: "Structure prediction", tools: ["Chai-1"] },
        { label: "Developability triage", tools: ["Agmata", "PTM"] },
      ];

  return {
    title: `Design plan — ${target} (${format}, ${seed})`,
    steps,
  };
}

function buildDesignBriefMarkdown(): string {
  const c = _conv!;
  return [
    `# Design Brief`,
    ``,
    `| Parameter | Value |`,
    `|-----------|-------|`,
    `| Target | ${c.target} |`,
    `| Indication | ${c.indication} |`,
    `| Mechanism | ${c.mechanism} |`,
    `| Format | ${c.format} |`,
    `| Epitope | ${c.epitope} |`,
    `| Affinity | ${c.affinity} |`,
    `| Species | ${c.species} |`,
    `| Developability | ${c.developability} |`,
    `| Route | ${c.route} |`,
    `| Competition | ${c.competition} |`,
    `| Starting point | ${c.seed} |`,
    `| Designs | ${c.scale} |`,
    ``,
    `Generated by demo-engine at ${new Date().toISOString()}.`,
    ``,
    // Pad to ~2KB for demo realism
    `<!-- ${"notes ".repeat(200)}-->`,
  ].join("\n");
}

function buildTopDesignsCsv(): string {
  const rows: string[] = ["id,sequence,iPAE,pLDDT,score"];
  const aa = "ACDEFGHIKLMNPQRSTVWY";
  for (let i = 0; i < 20; i++) {
    const id = `d${String(i + 1).padStart(3, "0")}`;
    let seq = "";
    for (let j = 0; j < 120; j++) seq += aa[Math.floor(Math.random() * aa.length)];
    const iPAE = (5 + Math.random() * 8).toFixed(2);
    const pLDDT = (78 + Math.random() * 15).toFixed(1);
    const score = (0.45 + Math.random() * 0.45).toFixed(3);
    rows.push(`${id},${seq},${iPAE},${pLDDT},${score}`);
  }
  return rows.join("\n");
}

function buildExecutionTraceJson(): string {
  const now = Date.now();
  const events = [
    { ts: now - 5000, kind: "thought", label: "Start campaign" },
    { ts: now - 4500, kind: "tool_call", label: "plan_campaign" },
    { ts: now - 4000, kind: "tool_result", label: "campaign planned" },
    { ts: now - 3500, kind: "tool_call", label: "RFdiffusion" },
    { ts: now - 2500, kind: "tool_result", label: "backbones generated" },
    { ts: now - 2000, kind: "tool_call", label: "ProteinMPNN" },
    { ts: now - 1200, kind: "tool_result", label: "sequences designed" },
    { ts: now - 900, kind: "tool_call", label: "RF2" },
    { ts: now - 500, kind: "tool_result", label: "filtered by iPAE" },
    { ts: now - 200, kind: "tool_call", label: "Chai-1" },
    { ts: now, kind: "tool_result", label: "consensus scored" },
  ];
  // Pad JSON toward ~12KB
  const padding = Array.from({ length: 80 }, (_, i) => ({
    ts: now - i * 10,
    kind: "text",
    label: `step-detail-${i}`,
    detail: "RFdiffusion/ProteinMPNN/RF2 intermediate log entry with structural metrics",
  }));
  return JSON.stringify({ events: [...events, ...padding] }, null, 2);
}

// Citation helper kept for parity with other emitters; unused today but exported intent
// stays local for future use.
function _citationEvent(c: Citation): StreamEvent {
  return { type: "citation", citation: c };
}
void _citationEvent;