Socrates/apps/web/lib/db/repo.ts

// Project + model persistence layer.
//
// Stores the full SysMLModel as a JSON snapshot per version, plus a changelog
// of applied ops. Reads return the latest snapshot; writes apply ops
// server-side and write a new snapshot + changelog row atomically.

import { prisma } from "./client";
import { applyOps } from "../sync/applyOps";
import { fromFixture } from "../sysml/fromFixture";
import { aristotleFixture } from "../fixtures/aristotle";
import { fixtureToDoc } from "../../components/text-canvas/fixtureToDoc";
import type { SysMLModel } from "../sysml/model";
import type { ModelOp } from "../sync/ops";

export interface LoadResult {
  model: SysMLModel;
  version: number;
}

export class ProjectNotFoundError extends Error {
  readonly projectId: string;
  constructor(projectId: string) {
    super(`Project "${projectId}" not found`);
    this.projectId = projectId;
    this.name = "ProjectNotFoundError";
  }
}

export async function loadProject(projectId: string): Promise<LoadResult> {
  // Auto-seed Aristotle ONLY for the literal "aristotle" id (the fixture demo).
  // Any other unknown id is an honest 404 — we don't want to silently spawn
  // a fake project from the wrong fixture.
  if (projectId === "aristotle") {
    await ensureAristotleSeeded();
  }
  const snapshot = await prisma.modelSnapshot.findFirst({
    where: { projectId },
    orderBy: { version: "desc" },
  });
  if (!snapshot) throw new ProjectNotFoundError(projectId);
  return {
    model: JSON.parse(snapshot.json) as SysMLModel,
    version: snapshot.version,
  };
}

export interface ApplyResult {
  applied: boolean;
  model: SysMLModel;
  version: number;
  idMapping: Record<string, string>;
  errors: Array<{ opIndex: number; code: string; message: string }>;
}

export async function applyOpsToProject(
  projectId: string,
  ops: ModelOp[],
  expectedVersion: number | undefined,
  reason?: string
): Promise<ApplyResult> {
  return prisma.$transaction(async tx => {
    const latest = await tx.modelSnapshot.findFirst({
      where: { projectId },
      orderBy: { version: "desc" },
    });
    if (!latest) throw new Error(`No snapshot for project ${projectId}`);

    if (expectedVersion !== undefined && expectedVersion !== latest.version) {
      // Optimistic-concurrency miss; caller must resync.
      return {
        applied: false,
        model: JSON.parse(latest.json) as SysMLModel,
        version: latest.version,
        idMapping: {},
        errors: [{ opIndex: -1, code: "VERSION_MISMATCH", message: `Expected version ${expectedVersion}, server is ${latest.version}` }],
      };
    }

    const currentModel = JSON.parse(latest.json) as SysMLModel;
    const result = applyOps(currentModel, ops);
    if (!result.applied) {
      return {
        applied: false,
        model: currentModel,
        version: latest.version,
        idMapping: {},
        errors: result.errors,
      };
    }

    const newVersion = latest.version + 1;
    await tx.modelSnapshot.create({
      data: {
        projectId,
        version: newVersion,
        json: JSON.stringify(result.model),
      },
    });
    await tx.changelogEntry.create({
      data: {
        projectId,
        version: newVersion,
        ops: JSON.stringify(ops),
        reason,
      },
    });

    return {
      applied: true,
      model: result.model,
      version: newVersion,
      idMapping: result.idMapping,
      errors: [],
    };
  });
}

/** Replace the project's SysML model wholesale. Used by the Analyze model
 *  pass — the analyzer has already merged with the current model so we just
 *  persist the result as a fresh snapshot. */
export async function replaceModel(
  projectId: string,
  model: SysMLModel,
  reason: string
): Promise<{ version: number }> {
  return prisma.$transaction(async tx => {
    const latest = await tx.modelSnapshot.findFirst({
      where: { projectId },
      orderBy: { version: "desc" },
    });
    const newVersion = (latest?.version ?? 0) + 1;
    await tx.modelSnapshot.create({
      data: { projectId, version: newVersion, json: JSON.stringify(model) },
    });
    await tx.changelogEntry.create({
      data: { projectId, version: newVersion, ops: JSON.stringify([]), reason },
    });
    return { version: newVersion };
  });
}

// ─── Seeding ─────────────────────────────────────────────────────────────

/** Idempotent: ensure the literal "aristotle" demo project + initial snapshot
 *  + opening thread exist. Used both by the editor route on first /editor/aristotle
 *  load and by the seed page so users always have at least one project to look at. */
export async function ensureAristotleSeeded(): Promise<void> {
  const projectId = "aristotle";
  const existing = await prisma.project.findUnique({ where: { id: projectId } });
  const snapCount = existing
    ? await prisma.modelSnapshot.count({ where: { projectId } })
    : 0;
  const docExisting = existing
    ? await prisma.narrativeDocument.findUnique({ where: { projectId } })
    : null;
  if (existing && snapCount > 0 && docExisting) return;

  const seedModel = fromFixture(aristotleFixture);
  await prisma.project.upsert({
    where: { id: projectId },
    update: {},
    create: {
      id: projectId,
      name: aristotleFixture.project.name,
      scope: aristotleFixture.project.scope,
      tagline: aristotleFixture.project.tagline,
    },
  });
  if (snapCount === 0) {
    await prisma.modelSnapshot.create({
      data: { projectId, version: 1, json: JSON.stringify(seedModel) },
    });
  }
  if (!docExisting) {
    // Persist the fixture narrative as the canonical document so Analyze has
    // something to chew on for the demo project. Users edit it in the editor
    // after that.
    const doc = fixtureToDoc(aristotleFixture);
    await prisma.narrativeDocument.create({
      data: { projectId, version: 1, doc: JSON.stringify(doc) },
    });
  }
}

// ─── Project list + create-from-seed ────────────────────────────────────

export interface ProjectSummary {
  id: string;
  name: string;
  scope: string;
  tagline: string;
  updatedAt: Date;
  latestVersion: number;
}

export async function listProjects(): Promise<ProjectSummary[]> {
  const rows = await prisma.project.findMany({
    orderBy: { updatedAt: "desc" },
    include: { snapshots: { orderBy: { version: "desc" }, take: 1, select: { version: true } } },
  });
  return rows.map(r => ({
    id: r.id,
    name: r.name,
    scope: r.scope,
    tagline: r.tagline,
    updatedAt: r.updatedAt,
    latestVersion: r.snapshots[0]?.version ?? 0,
  }));
}

export interface CreateProjectInput {
  name: string;
  scope: string;
  tagline: string;
  model: SysMLModel;
}

export async function createProjectFromSeed(input: CreateProjectInput): Promise<{ projectId: string; version: number }> {
  const id = await uniqueProjectId(input.name);
  await prisma.$transaction(async tx => {
    await tx.project.create({
      data: {
        id,
        name: input.name,
        scope: input.scope,
        tagline: input.tagline,
      },
    });
    await tx.modelSnapshot.create({
      data: {
        projectId: id,
        version: 1,
        json: JSON.stringify(input.model),
      },
    });
    await tx.socratesThread.create({
      data: {
        projectId: id,
        title: `Active thread · ${input.name}`,
        status: "open",
      },
    });
  });
  return { projectId: id, version: 1 };
}

async function uniqueProjectId(name: string): Promise<string> {
  const base =
    name
      .toLowerCase()
      .replace(/[^a-z0-9]+/g, "-")
      .replace(/^-+|-+$/g, "")
      .slice(0, 40) || "project";
  let candidate = base;
  let n = 2;
  while (await prisma.project.findUnique({ where: { id: candidate } })) {
    candidate = `${base}-${n}`;
    n++;
  }
  return candidate;
}

// ─── Findings (M8) ───────────────────────────────────────────────────────

import type { Finding as DetectedFinding } from "../llm/detect";

export interface StoredFinding {
  id: string;
  kind: string;
  text: string;
  linkedElementIds: string[];
  confidence: number;
  severity: string | null;
  validationCode: string | null;
  /// "suggested" | "accepted" | "deprecated" | "dismissed" | "resolved".
  /// Legacy value "open" is treated equivalently to "accepted".
  status: string;
  pinned: boolean;
  modelVersion: number;
  provider: string | null;
  llmModel: string | null;
  createdAt: Date;
}

/** Findings the user should currently see (suggested / accepted / deprecated).
 *  Excludes dismissed and resolved. */
export async function listVisibleFindings(projectId: string): Promise<StoredFinding[]> {
  const rows = await prisma.finding.findMany({
    where: {
      projectId,
      status: { in: ["suggested", "accepted", "deprecated", "open"] },
    },
    orderBy: [{ kind: "asc" }, { createdAt: "desc" }],
  });
  return rows.map(rowToFinding);
}

/** @deprecated kept for compat; prefer listVisibleFindings. */
export async function listOpenFindings(projectId: string): Promise<StoredFinding[]> {
  return listVisibleFindings(projectId);
}

/** Findings the user has discarded (dismissed or resolved). Used by the
 *  Discarded drawer in FindingsPane so the user can recover or audit them. */
export async function listDiscardedFindings(projectId: string): Promise<StoredFinding[]> {
  const rows = await prisma.finding.findMany({
    where: {
      projectId,
      status: { in: ["dismissed", "resolved"] },
    },
    orderBy: [{ kind: "asc" }, { createdAt: "desc" }],
  });
  return rows.map(rowToFinding);
}

/** Reactivate a finding that was previously dismissed or resolved. Sets
 *  status back to "accepted" + clears any pin so the next merge can re-assess. */
export async function restoreFinding(findingId: string): Promise<StoredFinding | null> {
  const cur = await prisma.finding.findUnique({ where: { id: findingId } });
  if (!cur) return null;
  const row = await prisma.finding.update({
    where: { id: findingId },
    data: { status: "accepted", pinned: false },
  });
  return rowToFinding(row);
}

/**
 * Merge analyzer-detected findings as a *review*. Identity is the
 * `suggestionKey` (kind + normalized-text for LLM findings, validationCode +
 * elementId for cross-validation findings). Pre-existing rows from before
 * merge-with-review use status="open"; we treat them as accepted.
 */
export async function mergeFindingsSuggestion(
  projectId: string,
  findings: DetectedFinding[],
  modelVersion: number,
  provider: string,
  llmModel: string
): Promise<StoredFinding[]> {
  return prisma.$transaction(async tx => {
    const existing = await tx.finding.findMany({ where: { projectId } });
    const existingByKey = new Map<string, (typeof existing)[number]>();
    for (const e of existing) {
      const key = e.suggestionKey ?? findingKey(e);
      existingByKey.set(key, e);
    }

    const incomingByKey = new Map<string, { f: DetectedFinding; key: string }>();
    for (const f of findings) {
      const key = findingKey(f);
      if (!incomingByKey.has(key)) incomingByKey.set(key, { f, key });
    }

    // Phase 1 — incoming findings.
    for (const [key, { f }] of incomingByKey.entries()) {
      const prior = existingByKey.get(key);
      if (!prior) {
        await tx.finding.create({
          data: {
            projectId,
            kind: f.kind,
            text: f.text,
            linkedElementIds: JSON.stringify(f.linkedElementIds),
            confidence: f.confidence,
            severity: f.severity ?? null,
            validationCode: f.validationCode ?? null,
            status: "suggested",
            pinned: false,
            suggestionKey: key,
            modelVersion,
            provider,
            llmModel,
          },
        });
      } else {
        // The user has decided about this one already (dismissed/resolved/
        // accepted) — leave the decision intact, just refresh detector
        // metadata. If it had been deprecated, flip back to suggested.
        const nextStatus =
          prior.status === "deprecated" ? "suggested" : prior.status;
        await tx.finding.update({
          where: { id: prior.id },
          data: {
            text: f.text,
            linkedElementIds: JSON.stringify(f.linkedElementIds),
            confidence: f.confidence,
            severity: f.severity ?? prior.severity,
            validationCode: f.validationCode ?? prior.validationCode,
            status: nextStatus,
            modelVersion,
            provider,
            llmModel,
            suggestionKey: key,
          },
        });
      }
    }

    // Phase 2 — findings the detector didn't see this run.
    for (const e of existing) {
      const key = e.suggestionKey ?? findingKey(e);
      if (incomingByKey.has(key)) continue;
      // Never reviewed AND analyzer dropped it → quietly delete.
      if (e.status === "suggested") {
        await tx.finding.delete({ where: { id: e.id } });
        continue;
      }
      // Accepted/open and unpinned → mark deprecated (still re-decidable).
      if ((e.status === "accepted" || e.status === "open") && !e.pinned) {
        await tx.finding.update({
          where: { id: e.id },
          data: { status: "deprecated" },
        });
      }
      // dismissed / resolved / pinned → leave alone.
    }

    return (await tx.finding.findMany({
      where: {
        projectId,
        status: { in: ["suggested", "accepted", "deprecated", "open"] },
      },
      orderBy: [{ kind: "asc" }, { createdAt: "desc" }],
    })).map(rowToFinding);
  });
}

export type FindingDecision = "keep" | "discard" | "resolve";

/** Apply a user decision to a finding.
 *
 *   keep    — confirms the finding as a real thing the user is tracking.
 *             From "suggested" → "accepted" (visible). From "deprecated" →
 *             "accepted" + pinned (so re-detection doesn't re-deprecate).
 *   discard — "dismissed". Stops surfacing AND tells future merges to skip it.
 *   resolve — "resolved". Like dismiss but signals "I fixed it."
 */
export async function setFindingDecision(
  findingId: string,
  decision: FindingDecision
): Promise<StoredFinding | null> {
  const cur = await prisma.finding.findUnique({ where: { id: findingId } });
  if (!cur) return null;
  let nextStatus: string;
  let pinned = cur.pinned;
  if (decision === "keep") {
    nextStatus = "accepted";
    if (cur.status === "deprecated") pinned = true;
  } else if (decision === "discard") {
    nextStatus = "dismissed";
  } else {
    nextStatus = "resolved";
  }
  const row = await prisma.finding.update({
    where: { id: findingId },
    data: { status: nextStatus, pinned },
  });
  return rowToFinding(row);
}

export async function dismissFinding(findingId: string): Promise<void> {
  // Back-compat with the legacy "dismiss" route.
  await setFindingDecision(findingId, "discard");
}

/** Stable identity for a finding suggestion. LLM findings: kind + text;
 *  cross-validation findings: validationCode + first linkedElement (which
 *  is the element id or `term:<id>` sentinel). */
function findingKey(f: {
  kind: string;
  text: string;
  validationCode?: string | null;
  linkedElementIds: string | string[];
}): string {
  const codes = (f.validationCode ?? "").trim();
  if (codes) {
    const ids = Array.isArray(f.linkedElementIds)
      ? f.linkedElementIds
      : safeStringArray(f.linkedElementIds);
    const first = ids[0] ?? "";
    return `${codes}:${first}`;
  }
  return `${f.kind}:${(f.text ?? "").trim().toLowerCase().replace(/\s+/g, " ")}`;
}

interface FindingRow {
  id: string;
  kind: string;
  text: string;
  linkedElementIds: string;
  confidence: number;
  severity: string | null;
  validationCode: string | null;
  status: string;
  pinned: boolean;
  modelVersion: number;
  provider: string | null;
  llmModel: string | null;
  createdAt: Date;
}

function rowToFinding(row: FindingRow): StoredFinding {
  let linked: string[] = [];
  try {
    const parsed = JSON.parse(row.linkedElementIds);
    if (Array.isArray(parsed)) linked = parsed.filter((x): x is string => typeof x === "string");
  } catch {
    linked = [];
  }
  // Legacy "open" rows map to "accepted" for the new lifecycle.
  const status = row.status === "open" ? "accepted" : row.status;
  return {
    id: row.id,
    kind: row.kind,
    text: row.text,
    linkedElementIds: linked,
    confidence: row.confidence,
    severity: row.severity,
    validationCode: row.validationCode,
    status,
    pinned: !!row.pinned,
    modelVersion: row.modelVersion,
    provider: row.provider,
    llmModel: row.llmModel,
    createdAt: row.createdAt,
  };
}

// ─── Socrates threads ────────────────────────────────────────────────────

export async function getActiveThread(projectId: string): Promise<{ id: string; title: string | null; messages: Array<{ id: string; role: string; content: string; createdAt: Date }> } | null> {
  const thread = await prisma.socratesThread.findFirst({
    where: { projectId, status: "open" },
    orderBy: { updatedAt: "desc" },
    include: { messages: { orderBy: { createdAt: "asc" } } },
  });
  if (!thread) return null;
  return {
    id: thread.id,
    title: thread.title,
    messages: thread.messages.map(m => ({
      id: m.id,
      role: m.role,
      content: m.content,
      createdAt: m.createdAt,
    })),
  };
}

// ─── Narrative document ──────────────────────────────────────────────────

export interface StoredDocument {
  doc: unknown;
  version: number;
  updatedAt: Date;
}

export async function loadDocument(projectId: string): Promise<StoredDocument | null> {
  const row = await prisma.narrativeDocument.findUnique({ where: { projectId } });
  if (!row) return null;
  let doc: unknown = null;
  try {
    doc = JSON.parse(row.doc);
  } catch {
    doc = null;
  }
  return { doc, version: row.version, updatedAt: row.updatedAt };
}

export async function saveDocument(projectId: string, doc: unknown): Promise<StoredDocument> {
  const json = JSON.stringify(doc);
  const row = await prisma.narrativeDocument.upsert({
    where: { projectId },
    create: { projectId, doc: json, version: 1 },
    update: { doc: json, version: { increment: 1 } },
  });
  return { doc, version: row.version, updatedAt: row.updatedAt };
}

// ─── Taxonomy ────────────────────────────────────────────────────────────

export type TermStatus = "accepted" | "suggested" | "deprecated";

export interface StoredTerm {
  id: string;
  parentId: string | null;
  label: string;
  definition: string | null;
  synonyms: string[];
  linkedBlockId: string | null;
  modelVersion: number;
  /// Review state (see prisma/schema.prisma comment).
  status: TermStatus;
  /// User explicitly preserved → don't re-deprecate on next merge.
  pinned: boolean;
  /// User authored/edited the definition → future Analyze runs skip it.
  definitionPinned: boolean;
}

export interface DetectedTerm {
  id?: string; // optional, allows analyzer to keep stable ids across runs
  parentLabel?: string | null;
  label: string;
  definition?: string | null;
  synonyms?: string[];
}

export async function listTerms(projectId: string): Promise<StoredTerm[]> {
  const rows = await prisma.taxonomyTerm.findMany({
    where: { projectId },
    orderBy: [{ parentId: "asc" }, { label: "asc" }],
  });
  return rows.map(rowToTerm);
}

export interface MergeTaxonomyResult {
  added: StoredTerm[];
  deprecated: StoredTerm[];
  kept: StoredTerm[];
  all: StoredTerm[];
}

/**
 * Merge analyzer output into the project's taxonomy as a *review* — never a
 * destructive replace. Existing user-accepted terms are preserved; terms the
 * analyzer didn't see are flagged "deprecated" (unless `pinned`); brand-new
 * terms are inserted as "suggested." The user can then keep or discard each
 * pending change via setTermDecision.
 *
 * Behaviour by case (matched on lowercased label):
 *   - existing accepted, in incoming → label/synonyms/definition gently
 *     updated (synonyms unioned; definition only filled when previously
 *     empty), status stays "accepted".
 *   - existing suggested, in incoming → updated and stays "suggested".
 *   - existing deprecated, in incoming → flips back to "suggested" so the
 *     user can re-decide (the analyzer changed its mind).
 *   - existing accepted, NOT in incoming, NOT pinned → flipped to
 *     "deprecated".
 *   - existing accepted, NOT in incoming, pinned → left alone.
 *   - existing suggested, NOT in incoming → deleted (user never reviewed and
 *     analyzer no longer believes; quietly drop).
 *   - new label not in existing → inserted as "suggested".
 */
export async function mergeTaxonomySuggestion(
  projectId: string,
  terms: DetectedTerm[],
  modelVersion: number
): Promise<MergeTaxonomyResult> {
  return prisma.$transaction(async tx => {
    const existing = await tx.taxonomyTerm.findMany({ where: { projectId } });
    const existingByLabel = new Map(existing.map(e => [e.label.toLowerCase(), e]));

    const incomingByLabel = new Map<string, DetectedTerm>();
    for (const t of terms) {
      const k = t.label.trim().toLowerCase();
      if (k && !incomingByLabel.has(k)) incomingByLabel.set(k, t);
    }

    const addedIds = new Set<string>();
    const deprecatedIds = new Set<string>();

    // Phase 1 — handle each incoming term.
    for (const [k, t] of incomingByLabel.entries()) {
      const prior = existingByLabel.get(k);
      if (!prior) {
        // Truly new → suggested.
        const created = await tx.taxonomyTerm.create({
          data: {
            projectId,
            parentId: null, // patched in phase 3
            label: t.label,
            definition: t.definition ?? null,
            synonyms: JSON.stringify(t.synonyms ?? []),
            linkedBlockId: null,
            modelVersion,
            status: "suggested",
            pinned: false,
          },
        });
        addedIds.add(created.id);
      } else {
        // Existing — gentle update + status transitions.
        const mergedSynonyms = mergeSynonyms(safeStringArray(prior.synonyms), t.synonyms ?? []);
        // Definition pin: when the user has authored/edited the definition
        // by hand, the analyzer's emit is dropped on the floor. Otherwise
        // the gentle-update rule applies (existing wins; LLM only fills in
        // when prior was empty).
        const newDefinition = prior.definitionPinned
          ? prior.definition
          : prior.definition || t.definition || null;
        const nextStatus =
          prior.status === "deprecated" ? "suggested" : prior.status;

        await tx.taxonomyTerm.update({
          where: { id: prior.id },
          data: {
            // Don't change the canonical label spelling — that would alter
            // the user-facing identity. (Analyzer can rephrase tomorrow.)
            definition: newDefinition,
            synonyms: JSON.stringify(mergedSynonyms),
            modelVersion,
            status: nextStatus,
          },
        });
        if (nextStatus === "suggested" && prior.status !== "suggested") addedIds.add(prior.id);
      }
    }

    // Phase 2 — terms the analyzer didn't see this run.
    for (const e of existing) {
      const k = e.label.toLowerCase();
      if (incomingByLabel.has(k)) continue;
      if (e.status === "suggested") {
        // Never reviewed and analyzer dropped it — quiet delete.
        await tx.taxonomyTerm.delete({ where: { id: e.id } });
        continue;
      }
      if (e.status === "accepted" && !e.pinned) {
        await tx.taxonomyTerm.update({
          where: { id: e.id },
          data: { status: "deprecated" },
        });
        deprecatedIds.add(e.id);
      }
      // pinned/deprecated/accepted-pinned → leave as is.
    }

    // Phase 3 — re-resolve parent pointers from analyzer payload (label-based).
    const allRows = await tx.taxonomyTerm.findMany({ where: { projectId } });
    const labelToId = new Map(allRows.map(r => [r.label.toLowerCase(), r.id]));
    for (const [k, t] of incomingByLabel.entries()) {
      const childId = labelToId.get(k);
      if (!childId) continue;
      const parentLabel = t.parentLabel?.toLowerCase();
      const parentId = parentLabel ? labelToId.get(parentLabel) ?? null : null;
      // Only update when the parent actually changes — keeps the field stable
      // when the user has manually re-parented (future feature).
      const cur = allRows.find(r => r.id === childId);
      if (cur && cur.parentId !== parentId && childId !== parentId) {
        await tx.taxonomyTerm.update({ where: { id: childId }, data: { parentId } });
      }
    }

    const finalRows = await tx.taxonomyTerm.findMany({
      where: { projectId },
      orderBy: [{ parentId: "asc" }, { label: "asc" }],
    });
    const allTerms = finalRows.map(rowToTerm);

    return {
      added: allTerms.filter(t => addedIds.has(t.id)),
      deprecated: allTerms.filter(t => deprecatedIds.has(t.id)),
      kept: allTerms.filter(t => !addedIds.has(t.id) && !deprecatedIds.has(t.id)),
      all: allTerms,
    };
  });
}

export type TermDecision = "keep" | "discard";

/**
 * Apply a user decision to a pending (suggested or deprecated) term.
 *
 *   - keep    → status="accepted". For deprecated terms also sets pinned=true
 *               so the next merge doesn't re-deprecate them.
 *   - discard → row deleted.
 *
 * Returns the resulting StoredTerm, or null if the row was deleted.
 */
export async function setTermDecision(
  termId: string,
  decision: TermDecision
): Promise<StoredTerm | null> {
  if (decision === "discard") {
    await prisma.taxonomyTerm.delete({ where: { id: termId } });
    return null;
  }
  const cur = await prisma.taxonomyTerm.findUnique({ where: { id: termId } });
  if (!cur) return null;
  const pinned = cur.status === "deprecated" ? true : cur.pinned;
  const row = await prisma.taxonomyTerm.update({
    where: { id: termId },
    data: { status: "accepted", pinned },
  });
  return rowToTerm(row);
}

function mergeSynonyms(prev: string[], incoming: string[]): string[] {
  const seen = new Set<string>();
  const out: string[] = [];
  for (const s of [...prev, ...incoming]) {
    const k = s.trim().toLowerCase();
    if (!k || seen.has(k)) continue;
    seen.add(k);
    out.push(s.trim());
  }
  return out;
}

/** Patch glossary definitions onto existing terms (label-keyed). The
 *  glossary analyze pass runs after taxonomy and just enriches it. Skips
 *  terms whose definition the user has pinned (manually authored/edited)
 *  AND skips terms that already have a definition — gentle update only. */
export async function applyGlossaryDefinitions(
  projectId: string,
  defs: Array<{ label: string; definition: string }>
): Promise<void> {
  const map = new Map(defs.map(d => [d.label.toLowerCase(), d.definition]));
  const rows = await prisma.taxonomyTerm.findMany({
    where: { projectId },
    select: { id: true, label: true, definition: true, definitionPinned: true },
  });
  for (const r of rows) {
    if (r.definitionPinned) continue;
    if (r.definition && r.definition.length > 0) continue;
    const def = map.get(r.label.toLowerCase());
    if (def) {
      await prisma.taxonomyTerm.update({ where: { id: r.id }, data: { definition: def } });
    }
  }
}

/**
 * Set a term's definition by user action. Non-empty input is treated as a
 * manual edit and pins the definition (subsequent Analyze runs leave it
 * alone). An empty/whitespace input clears the definition AND the pin —
 * the "Reset to AI suggestion" path, after which the next Analyze fills
 * the definition from prose like a fresh term.
 */
export async function setTermDefinition(
  termId: string,
  definition: string | null
): Promise<StoredTerm | null> {
  const trimmed = (definition ?? "").trim();
  if (trimmed.length === 0) {
    const row = await prisma.taxonomyTerm.update({
      where: { id: termId },
      data: { definition: null, definitionPinned: false },
    });
    return rowToTerm(row);
  }
  const row = await prisma.taxonomyTerm.update({
    where: { id: termId },
    data: { definition: trimmed, definitionPinned: true },
  });
  return rowToTerm(row);
}

export async function linkTermToBlock(termId: string, blockId: string | null): Promise<void> {
  await prisma.taxonomyTerm.update({
    where: { id: termId },
    data: { linkedBlockId: blockId },
  });
}

interface TermRow {
  id: string;
  parentId: string | null;
  label: string;
  definition: string | null;
  synonyms: string;
  linkedBlockId: string | null;
  modelVersion: number;
  status: string;
  pinned: boolean;
  definitionPinned: boolean;
}

function rowToTerm(row: TermRow): StoredTerm {
  let synonyms: string[] = [];
  try {
    const parsed = JSON.parse(row.synonyms);
    if (Array.isArray(parsed)) synonyms = parsed.filter((s): s is string => typeof s === "string");
  } catch {
    /* keep [] */
  }
  const status: TermStatus =
    row.status === "suggested" || row.status === "deprecated" ? row.status : "accepted";
  return {
    id: row.id,
    parentId: row.parentId,
    label: row.label,
    definition: row.definition,
    synonyms,
    linkedBlockId: row.linkedBlockId,
    modelVersion: row.modelVersion,
    status,
    pinned: !!row.pinned,
    definitionPinned: !!row.definitionPinned,
  };
}

// ─── Requirements ────────────────────────────────────────────────────────

export type RequirementStatus = "accepted" | "suggested" | "deprecated";

export interface StoredRequirement {
  id: string;
  tag: string;
  text: string;
  tracedToIds: string[];
  unsupported: boolean;
  modelVersion: number;
  /// Term this requirement is conceptually about (T2 integration). Null when
  /// the analyzer / promote-action didn't pick a term anchor.
  linkedTermId: string | null;
  status: RequirementStatus;
  pinned: boolean;
}

export interface DetectedRequirement {
  tag: string;
  text: string;
  tracedToIds?: string[];
  unsupported?: boolean;
  linkedTermId?: string | null;
}

export async function listRequirements(projectId: string): Promise<StoredRequirement[]> {
  const rows = await prisma.requirementEntry.findMany({
    where: { projectId },
    orderBy: { tag: "asc" },
  });
  return rows.map(rowToRequirement);
}

/**
 * Merge analyzer output into the project's requirements as a *review*.
 * Same shape as mergeTaxonomySuggestion: never destructive, surfaces new
 * suggestions and deprecated rows for the user to keep or discard.
 *
 * Identity match is by **normalized text** (lowercased, whitespace-collapsed).
 * Tags (REQ-NNN) aren't stable across runs because the analyzer renumbers,
 * so text-equality is the safer key.
 */
export async function mergeRequirementsSuggestion(
  projectId: string,
  reqs: DetectedRequirement[],
  modelVersion: number
): Promise<StoredRequirement[]> {
  return prisma.$transaction(async tx => {
    const existing = await tx.requirementEntry.findMany({ where: { projectId } });
    const existingByKey = new Map(existing.map(e => [normalizeText(e.text), e]));

    const incomingByKey = new Map<string, DetectedRequirement>();
    for (const r of reqs) {
      const k = normalizeText(r.text);
      if (k && !incomingByKey.has(k)) incomingByKey.set(k, r);
    }

    // Phase 1 — handle each incoming requirement.
    for (const [k, r] of incomingByKey.entries()) {
      const prior = existingByKey.get(k);
      if (!prior) {
        await tx.requirementEntry.create({
          data: {
            projectId,
            tag: r.tag,
            text: r.text,
            tracedToIds: JSON.stringify(r.tracedToIds ?? []),
            unsupported: r.unsupported ?? (r.tracedToIds ?? []).length === 0,
            modelVersion,
            linkedTermId: r.linkedTermId ?? null,
            status: "suggested",
            pinned: false,
          },
        });
      } else {
        const nextStatus =
          prior.status === "deprecated" ? "suggested" : prior.status;
        await tx.requirementEntry.update({
          where: { id: prior.id },
          data: {
            // Refresh the analyzer-derived fields; preserve the canonical text
            // (matched-on key) and user-set state.
            tag: r.tag || prior.tag,
            tracedToIds: JSON.stringify(r.tracedToIds ?? safeStringArray(prior.tracedToIds)),
            unsupported: r.unsupported ?? (r.tracedToIds ?? []).length === 0,
            modelVersion,
            linkedTermId: r.linkedTermId ?? prior.linkedTermId ?? null,
            status: nextStatus,
          },
        });
      }
    }

    // Phase 2 — requirements analyzer didn't see.
    for (const e of existing) {
      const k = normalizeText(e.text);
      if (incomingByKey.has(k)) continue;
      if (e.status === "suggested") {
        await tx.requirementEntry.delete({ where: { id: e.id } });
        continue;
      }
      if ((e.status === "accepted" || e.status === "open") && !e.pinned) {
        await tx.requirementEntry.update({
          where: { id: e.id },
          data: { status: "deprecated" },
        });
      }
    }

    const finalRows = await tx.requirementEntry.findMany({
      where: { projectId },
      orderBy: { tag: "asc" },
    });
    return finalRows.map(rowToRequirement);
  });
}

export type RequirementDecision = "keep" | "discard";

export async function setRequirementDecision(
  reqId: string,
  decision: RequirementDecision
): Promise<StoredRequirement | null> {
  if (decision === "discard") {
    await prisma.requirementEntry.delete({ where: { id: reqId } });
    return null;
  }
  const cur = await prisma.requirementEntry.findUnique({ where: { id: reqId } });
  if (!cur) return null;
  const pinned = cur.status === "deprecated" ? true : cur.pinned;
  const row = await prisma.requirementEntry.update({
    where: { id: reqId },
    data: { status: "accepted", pinned },
  });
  return rowToRequirement(row);
}

interface RequirementRow {
  id: string;
  tag: string;
  text: string;
  tracedToIds: string;
  unsupported: boolean;
  modelVersion: number;
  linkedTermId: string | null;
  status: string;
  pinned: boolean;
}

function rowToRequirement(r: RequirementRow): StoredRequirement {
  const status: RequirementStatus =
    r.status === "suggested" || r.status === "deprecated" ? r.status : "accepted";
  return {
    id: r.id,
    tag: r.tag,
    text: r.text,
    tracedToIds: safeStringArray(r.tracedToIds),
    unsupported: r.unsupported,
    modelVersion: r.modelVersion,
    linkedTermId: r.linkedTermId ?? null,
    status,
    pinned: !!r.pinned,
  };
}

function normalizeText(s: string): string {
  return s.trim().toLowerCase().replace(/\s+/g, " ");
}

function safeStringArray(s: string): string[] {
  try {
    const parsed = JSON.parse(s);
    if (Array.isArray(parsed)) return parsed.filter((x): x is string => typeof x === "string");
  } catch {
    /* fall through */
  }
  return [];
}

// ─── Analysis runs ───────────────────────────────────────────────────────

export type AnalysisSection =
  | "concepts"
  | "model"
  | "requirements"
  | "assumptions"
  | "risks"
  | "inconsistencies"
  | "all";

/** Back-compat: callers (older clients, scripts) may still pass "taxonomy" or
 *  "glossary". Both map to the unified "concepts" pass. */
export function normalizeAnalysisSection(s: string): AnalysisSection {
  if (s === "taxonomy" || s === "glossary") return "concepts";
  if (
    s === "concepts" ||
    s === "model" ||
    s === "requirements" ||
    s === "assumptions" ||
    s === "risks" ||
    s === "inconsistencies" ||
    s === "all"
  ) {
    return s;
  }
  throw new Error(`Unknown analysis section: ${s}`);
}

export interface StoredAnalysisRun {
  id: string;
  section: AnalysisSection;
  status: "running" | "succeeded" | "failed";
  startedAt: Date;
  finishedAt: Date | null;
  modelVersion: number;
  inputTokens: number | null;
  outputTokens: number | null;
  errorMessage: string | null;
}

export async function startAnalysisRun(
  projectId: string,
  section: AnalysisSection,
  modelVersion: number
): Promise<string> {
  const row = await prisma.analysisRun.create({
    data: { projectId, section, status: "running", modelVersion },
  });
  return row.id;
}

export async function finishAnalysisRun(
  runId: string,
  patch: { status: "succeeded" | "failed"; inputTokens?: number; outputTokens?: number; errorMessage?: string }
): Promise<void> {
  await prisma.analysisRun.update({
    where: { id: runId },
    data: {
      status: patch.status,
      finishedAt: new Date(),
      inputTokens: patch.inputTokens ?? null,
      outputTokens: patch.outputTokens ?? null,
      errorMessage: patch.errorMessage ?? null,
    },
  });
}

export async function listLatestAnalysisRuns(projectId: string): Promise<Record<string, StoredAnalysisRun>> {
  const rows = await prisma.analysisRun.findMany({
    where: { projectId },
    orderBy: { startedAt: "desc" },
  });
  const latest: Record<string, StoredAnalysisRun> = {};
  for (const r of rows) {
    if (latest[r.section]) continue;
    latest[r.section] = {
      id: r.id,
      section: r.section as AnalysisSection,
      status: r.status as StoredAnalysisRun["status"],
      startedAt: r.startedAt,
      finishedAt: r.finishedAt,
      modelVersion: r.modelVersion,
      inputTokens: r.inputTokens,
      outputTokens: r.outputTokens,
      errorMessage: r.errorMessage,
    };
  }
  return latest;
}