@equationalapplications/core-llm-wiki 4.14.1 → 4.15.0

package/dist/index.mjs

@@ -1,6 +1,6 @@
-import { __privateAdd, EmbeddingService, SearchService, JobManager, PromptService, IngestionService, MaintenanceService, ImportExportService, RetrievalService, WriteService, __privateGet, __privateSet, normalizeSourceRef, normalizeSourceHash, generateId } from './chunk-24ANTHZB.mjs';
-export { HOOK_TIMEOUT_MARKER, PromptService, PrunePartialFailureError, WikiBusyError, parseEmbedding } from './chunk-24ANTHZB.mjs';
-import { buildConceptDocument, buildLogMd, buildIndexMd, buildRootIndexMd } from '@equationalapplications/core-okf';
+import { __privateAdd, EmbeddingService, SearchService, JobManager, PromptService, IngestionService, MaintenanceService, ImportExportService, RetrievalService, WriteService, __privateGet, __privateSet, normalizeSourceRef, normalizeSourceHash, generateId } from './chunk-J4GBC6CP.mjs';
+export { HOOK_TIMEOUT_MARKER, PromptService, PrunePartialFailureError, WikiBusyError, parseEmbedding } from './chunk-J4GBC6CP.mjs';
+import { buildConceptDocument, buildLogMd, buildIndexMd, buildRootIndexMd, parseConcept, extractMarkdownLinks, parseLogMd } from '@equationalapplications/core-okf';
 
 // src/db/schema.ts
 async function setupDatabase(db, prefix) {
@@ -21,7 +21,8 @@ async function setupDatabase(db, prefix) {
       access_count INTEGER NOT NULL DEFAULT 0,
       deleted_at INTEGER,
       embedding TEXT,
-      embedding_blob BLOB
+      embedding_blob BLOB,
+      okf_type TEXT
     );
 
     CREATE INDEX IF NOT EXISTS ${prefix}entries_entity_idx ON ${prefix}entries(entity_id);
@@ -38,11 +39,24 @@ async function setupDatabase(db, prefix) {
       created_at INTEGER NOT NULL,
       updated_at INTEGER NOT NULL,
       resolved_at INTEGER,
-      deleted_at INTEGER
+      deleted_at INTEGER,
+      okf_type TEXT
     );
 
     CREATE INDEX IF NOT EXISTS ${prefix}tasks_entity_idx ON ${prefix}tasks(entity_id, status);
 
+    CREATE TABLE IF NOT EXISTS ${prefix}edges (
+      id TEXT PRIMARY KEY,
+      entity_id TEXT NOT NULL,
+      source_id TEXT NOT NULL,
+      target_id TEXT NOT NULL,
+      edge_type TEXT NOT NULL,
+      created_at INTEGER NOT NULL,
+      UNIQUE(entity_id, source_id, target_id, edge_type)
+    );
+
+    CREATE INDEX IF NOT EXISTS ${prefix}edges_entity_idx ON ${prefix}edges(entity_id);
+
     CREATE TABLE IF NOT EXISTS ${prefix}events (
       id TEXT PRIMARY KEY,
       entity_id TEXT NOT NULL,
@@ -143,6 +157,32 @@ var MIGRATIONS = [
           ON ${prefix}outbox (entity_id, created_at);
       `);
     }
+  },
+  {
+    version: 5,
+    description: "Add okf_type to entries/tasks for OKF type fidelity; create edges table for OKF graph import",
+    run: async (db, prefix) => {
+      for (const table of ["entries", "tasks"]) {
+        const cols = await db.getAllAsync(
+          `PRAGMA table_info(${prefix}${table})`
+        );
+        if (!cols.some((c) => c.name === "okf_type")) {
+          await db.execAsync(`ALTER TABLE ${prefix}${table} ADD COLUMN okf_type TEXT`);
+        }
+      }
+      await db.execAsync(`
+        CREATE TABLE IF NOT EXISTS ${prefix}edges (
+          id TEXT PRIMARY KEY,
+          entity_id TEXT NOT NULL,
+          source_id TEXT NOT NULL,
+          target_id TEXT NOT NULL,
+          edge_type TEXT NOT NULL,
+          created_at INTEGER NOT NULL,
+          UNIQUE(entity_id, source_id, target_id, edge_type)
+        );
+        CREATE INDEX IF NOT EXISTS ${prefix}edges_entity_idx ON ${prefix}edges (entity_id);
+      `);
+    }
   }
 ];
 for (let i = 1; i < MIGRATIONS.length; i++) {
@@ -194,7 +234,8 @@ function mapRowToFact(row) {
     updated_at: Number(row.updated_at),
     last_accessed_at: row.last_accessed_at === null || row.last_accessed_at === void 0 ? null : Number(row.last_accessed_at),
     deleted_at: row.deleted_at != null ? Number(row.deleted_at) : null,
-    access_count: Number(row.access_count ?? 0)
+    access_count: Number(row.access_count ?? 0),
+    okf_type: row.okf_type ?? null
   };
 }
 function normalizeEmbeddingBlobValue(blob) {
@@ -367,8 +408,8 @@ var EntryRepository = class extends BaseRepository {
       `INSERT INTO ${this.prefix}entries (
         id, entity_id, title, body, tags, confidence, source_type,
         source_hash, source_ref, created_at, updated_at, last_accessed_at, access_count,
-        deleted_at, embedding_blob, embedding
-      ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+        deleted_at, embedding_blob, embedding, okf_type
+      ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
       ON CONFLICT(id) DO UPDATE SET
         entity_id = excluded.entity_id,
         title = excluded.title,
@@ -384,7 +425,8 @@ var EntryRepository = class extends BaseRepository {
         access_count = excluded.access_count,
         deleted_at = excluded.deleted_at,
         embedding_blob = excluded.embedding_blob,
-        embedding = NULL`,
+        embedding = NULL,
+        okf_type = excluded.okf_type`,
       [
         fact.id,
         fact.entity_id,
@@ -401,7 +443,8 @@ var EntryRepository = class extends BaseRepository {
         fact.access_count,
         fact.deleted_at ?? null,
         embeddingBlob ?? null,
-        null
+        null,
+        fact.okf_type ?? null
       ]
     );
     return result;
@@ -966,7 +1009,8 @@ function mapRowToTask(row) {
     created_at: Number(row.created_at),
     updated_at: Number(row.updated_at),
     resolved_at: row.resolved_at != null ? Number(row.resolved_at) : null,
-    deleted_at: row.deleted_at != null ? Number(row.deleted_at) : null
+    deleted_at: row.deleted_at != null ? Number(row.deleted_at) : null,
+    okf_type: row.okf_type ?? null
   };
 }
 var TaskRepository = class extends BaseRepository {
@@ -1068,8 +1112,8 @@ var TaskRepository = class extends BaseRepository {
     await executor.runAsync(
       `INSERT INTO ${this.prefix}tasks (
         id, entity_id, description, status, priority,
-        created_at, updated_at, resolved_at, deleted_at
-      ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)
+        created_at, updated_at, resolved_at, deleted_at, okf_type
+      ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
       ON CONFLICT(id) DO UPDATE SET
         entity_id = excluded.entity_id,
         description = excluded.description,
@@ -1077,7 +1121,8 @@ var TaskRepository = class extends BaseRepository {
         priority = excluded.priority,
         updated_at = excluded.updated_at,
         resolved_at = excluded.resolved_at,
-        deleted_at = excluded.deleted_at`,
+        deleted_at = excluded.deleted_at,
+        okf_type = excluded.okf_type`,
       [
         task.id,
         task.entity_id,
@@ -1087,7 +1132,8 @@ var TaskRepository = class extends BaseRepository {
         task.created_at,
         now,
         task.resolved_at ?? null,
-        task.deleted_at ?? null
+        task.deleted_at ?? null,
+        task.okf_type ?? null
       ]
     );
   }
@@ -1309,6 +1355,53 @@ var EventRepository = class extends BaseRepository {
   }
 };
 
+// src/repositories/EdgeRepository.ts
+var EdgeRepository = class extends BaseRepository {
+  /**
+   * Insert an edge, silently skipping on primary-key or uniqueness conflicts.
+   * Throws when the insert was skipped due to an id collision with a different edge tuple.
+   */
+  async addIgnoreDuplicate(edge, tx) {
+    const executor = this.getExecutor(tx);
+    const result = await executor.runAsync(
+      `INSERT OR IGNORE INTO ${this.prefix}edges (id, entity_id, source_id, target_id, edge_type, created_at)
+       VALUES (?, ?, ?, ?, ?, ?)`,
+      [edge.id, edge.entity_id, edge.source_id, edge.target_id, edge.edge_type, edge.created_at]
+    );
+    if (result.changes > 0) return;
+    const existing = await executor.getFirstAsync(
+      `SELECT entity_id, source_id, target_id, edge_type FROM ${this.prefix}edges WHERE id = ?`,
+      [edge.id]
+    );
+    if (!existing) return;
+    if (String(existing.entity_id) !== edge.entity_id || String(existing.source_id) !== edge.source_id || String(existing.target_id) !== edge.target_id || String(existing.edge_type) !== edge.edge_type) {
+      throw new Error(
+        `Edge id collision: ${JSON.stringify(edge.id)} already exists with a different (entity_id, source_id, target_id, edge_type) tuple`
+      );
+    }
+  }
+  async getByEntityId(entityId, tx) {
+    const executor = this.getExecutor(tx);
+    const rows = await executor.getAllAsync(
+      `SELECT * FROM ${this.prefix}edges WHERE entity_id = ? ORDER BY created_at ASC`,
+      [entityId]
+    );
+    return rows.map((row) => ({
+      id: String(row.id),
+      entity_id: String(row.entity_id),
+      source_id: String(row.source_id),
+      target_id: String(row.target_id),
+      edge_type: String(row.edge_type),
+      created_at: Number(row.created_at)
+    }));
+  }
+  /** Hard delete — edges have no soft-delete concept, only presence/absence. `tx` is REQUIRED. */
+  async bulkDeleteByEntityId(entityId, tx) {
+    const executor = this.getExecutor(tx);
+    await executor.runAsync(`DELETE FROM ${this.prefix}edges WHERE entity_id = ?`, [entityId]);
+  }
+};
+
 // src/repositories/MetadataRepository.ts
 var MetadataRepository = class extends BaseRepository {
   // CHECKPOINTS TABLE METHODS
@@ -1428,6 +1521,7 @@ var WikiMemory = class {
     this.entryRepo = new EntryRepository(db, this.prefix, this.outboxRepo);
     this.taskRepo = new TaskRepository(db, this.prefix, this.outboxRepo);
     this.eventRepo = new EventRepository(db, this.prefix);
+    this.edgeRepo = new EdgeRepository(db, this.prefix);
     this.metadataRepo = new MetadataRepository(db, this.prefix);
     this.embeddingService = new EmbeddingService(this.db, this.options, this.entryRepo, this.metadataRepo);
     this.searchService = new SearchService(this.entryRepo);
@@ -1461,6 +1555,7 @@ var WikiMemory = class {
       this.entryRepo,
       this.taskRepo,
       this.eventRepo,
+      this.edgeRepo,
       this.metadataRepo,
       this.searchService,
       this.jobManager,
@@ -1921,7 +2016,7 @@ function formatMemoryDump(dump) {
 }
 function factFrontmatter(f) {
   return {
-    type: "fact",
+    type: f.okf_type ?? "fact",
     title: f.title,
     tags: f.tags,
     timestamp: new Date(f.updated_at).toISOString(),
@@ -1939,7 +2034,7 @@ function factFrontmatter(f) {
 }
 function taskFrontmatter(t) {
   return {
-    type: "task",
+    type: t.okf_type ?? "task",
     title: t.description,
     timestamp: new Date(t.updated_at).toISOString(),
     id: t.id,
@@ -2014,6 +2109,227 @@ function formatOkfBundle(dump) {
   });
   return { files };
 }
+var CONFIDENCE_VALUES = /* @__PURE__ */ new Set(["certain", "inferred", "tentative"]);
+var SOURCE_TYPES = /* @__PURE__ */ new Set([
+  "user_stated",
+  "librarian_inferred",
+  "user_confirmed",
+  "immutable_document"
+]);
+var TASK_STATUSES = /* @__PURE__ */ new Set(["pending", "in_progress", "done", "abandoned"]);
+var EVENT_TYPES = /* @__PURE__ */ new Set(["observation", "decision", "action", "outcome"]);
+function basenameMd(filePath) {
+  const name = filePath.slice(filePath.lastIndexOf("/") + 1);
+  return name.endsWith(".md") ? name.slice(0, -3) : name;
+}
+function isConceptFile(filePath) {
+  if (!filePath.endsWith(".md")) return false;
+  if (filePath.endsWith("/index.md") || filePath === "index.md") return false;
+  if (filePath.endsWith("/log.md") || filePath === "log.md") return false;
+  return true;
+}
+function isStructuralPath(filePath) {
+  return filePath.endsWith("/index.md") || filePath === "index.md" || filePath.endsWith("/log.md") || filePath === "log.md";
+}
+function posixDirname(filePath) {
+  const idx = filePath.lastIndexOf("/");
+  return idx === -1 ? "" : filePath.slice(0, idx);
+}
+function resolveRelativePath(fromFile, linkPath) {
+  const baseDir = posixDirname(fromFile);
+  const segments = [...baseDir ? baseDir.split("/") : [], ...linkPath.split("/")];
+  const resolved = [];
+  for (const seg of segments) {
+    if (seg === "" || seg === ".") continue;
+    if (seg === "..") {
+      resolved.pop();
+      continue;
+    }
+    resolved.push(seg);
+  }
+  return resolved.join("/");
+}
+function addPathAliases(map, filePath, resolvedId) {
+  map.set(filePath, resolvedId);
+  const withoutDot = filePath.replace(/^\.\//, "");
+  if (withoutDot !== filePath) map.set(withoutDot, resolvedId);
+  const entityRelative = filePath.replace(/^entities\/[^/]+\//, "");
+  if (entityRelative !== filePath) {
+    map.set(entityRelative, resolvedId);
+    map.set(`./${entityRelative}`, resolvedId);
+  }
+}
+function lookupResolvedId(map, path) {
+  const normalized = path.replace(/^\.\//, "");
+  return map.get(path) ?? map.get(normalized) ?? map.get(`./${normalized}`);
+}
+function stripLinkSuffix(linkPath) {
+  const hashIdx = linkPath.indexOf("#");
+  const queryIdx = linkPath.indexOf("?");
+  if (hashIdx === -1 && queryIdx === -1) return linkPath;
+  const cut = hashIdx === -1 ? queryIdx : queryIdx === -1 ? hashIdx : Math.min(hashIdx, queryIdx);
+  return linkPath.slice(0, cut);
+}
+function resolveRoute(filePath, frontmatterType, options) {
+  if (options?.typeMapping && Object.prototype.hasOwnProperty.call(options.typeMapping, frontmatterType)) {
+    return options.typeMapping[frontmatterType];
+  }
+  if (filePath.includes("/facts/")) return "fact";
+  if (filePath.includes("/tasks/")) return "task";
+  return options?.defaultSchema ?? "fact";
+}
+function parseFrontmatterTimestamp(value, fallback) {
+  if (typeof value === "number" && Number.isFinite(value)) return value;
+  if (typeof value === "string") {
+    const parsed = Date.parse(value);
+    if (Number.isFinite(parsed)) return parsed;
+  }
+  return fallback;
+}
+function unescapeLogSummary(summary) {
+  return summary.replace(/\\\]/g, "]").replace(/\\\[/g, "[").replace(/\\\\/g, "\\");
+}
+var LOG_LINE_PATTERN = /^\(([^)]+)\)\s*(?:\[((?:\\.|[^\]])*)\]\(([^)]+)\)|(.+))$/;
+function parseLogEntryText(text) {
+  const match = LOG_LINE_PATTERN.exec(text.trim());
+  if (!match) return null;
+  const [, rawType, linkedSummary, linkPath, plainSummary] = match;
+  const event_type = EVENT_TYPES.has(rawType) ? rawType : "observation";
+  if (linkPath) {
+    return { event_type, summary: unescapeLogSummary(linkedSummary), linkPath };
+  }
+  return { event_type, summary: (plainSummary ?? "").trim() };
+}
+function frontmatterToFact(entityId, id, frontmatter, body, now) {
+  const created_at = parseFrontmatterTimestamp(frontmatter.created_at, now);
+  const updated_at = parseFrontmatterTimestamp(
+    frontmatter.timestamp,
+    parseFrontmatterTimestamp(frontmatter.updated_at, now)
+  );
+  return {
+    id,
+    entity_id: entityId,
+    title: typeof frontmatter.title === "string" ? frontmatter.title : "",
+    body,
+    tags: Array.isArray(frontmatter.tags) ? frontmatter.tags.filter((t) => typeof t === "string") : [],
+    confidence: CONFIDENCE_VALUES.has(String(frontmatter.confidence)) ? frontmatter.confidence : "tentative",
+    source_type: SOURCE_TYPES.has(String(frontmatter.source_type)) ? frontmatter.source_type : "user_stated",
+    source_hash: typeof frontmatter.source_hash === "string" ? frontmatter.source_hash : null,
+    source_ref: typeof frontmatter.resource === "string" ? frontmatter.resource : null,
+    created_at,
+    updated_at,
+    last_accessed_at: frontmatter.last_accessed_at != null ? parseFrontmatterTimestamp(frontmatter.last_accessed_at, now) : null,
+    access_count: typeof frontmatter.access_count === "number" ? frontmatter.access_count : 0,
+    deleted_at: frontmatter.deleted_at != null ? parseFrontmatterTimestamp(frontmatter.deleted_at, 0) : null,
+    okf_type: frontmatter.type
+  };
+}
+function frontmatterToTask(entityId, id, frontmatter, now) {
+  const created_at = parseFrontmatterTimestamp(frontmatter.created_at, now);
+  const updated_at = parseFrontmatterTimestamp(
+    frontmatter.timestamp,
+    parseFrontmatterTimestamp(frontmatter.updated_at, now)
+  );
+  return {
+    id,
+    entity_id: entityId,
+    description: typeof frontmatter.title === "string" ? frontmatter.title : "",
+    status: TASK_STATUSES.has(String(frontmatter.status)) ? frontmatter.status : "pending",
+    priority: typeof frontmatter.priority === "number" ? frontmatter.priority : 0,
+    created_at,
+    updated_at,
+    resolved_at: frontmatter.resolved_at != null ? parseFrontmatterTimestamp(frontmatter.resolved_at, now) : null,
+    deleted_at: frontmatter.deleted_at != null ? parseFrontmatterTimestamp(frontmatter.deleted_at, 0) : null,
+    okf_type: frontmatter.type
+  };
+}
+function findLogMdPath(files) {
+  return files.find((f) => f.path.endsWith("/log.md") || f.path === "log.md")?.path;
+}
+function parseOkfBundle(entityId, files, options) {
+  const now = Date.now();
+  const pathToResolvedId = /* @__PURE__ */ new Map();
+  for (const file of files) {
+    if (!isConceptFile(file.path)) continue;
+    const { frontmatter } = parseConcept(file.content);
+    const route = resolveRoute(file.path, frontmatter.type ?? "", options);
+    if (route === "ignore") continue;
+    const resolvedId = typeof frontmatter.id === "string" && frontmatter.id ? frontmatter.id : basenameMd(file.path);
+    addPathAliases(pathToResolvedId, file.path, resolvedId);
+  }
+  const facts = [];
+  const tasks = [];
+  const edges = [];
+  let logContent = null;
+  const logMdPath = findLogMdPath(files);
+  for (const file of files) {
+    if (file.path.endsWith("/log.md") || file.path === "log.md") {
+      logContent = file.content;
+      continue;
+    }
+    if (!isConceptFile(file.path)) continue;
+    const { frontmatter, body } = parseConcept(file.content);
+    const route = resolveRoute(file.path, frontmatter.type ?? "", options);
+    if (route === "ignore") continue;
+    const resolvedId = typeof frontmatter.id === "string" && frontmatter.id ? frontmatter.id : basenameMd(file.path);
+    if (route === "fact") {
+      facts.push(frontmatterToFact(entityId, resolvedId, frontmatter, body, now));
+    } else {
+      tasks.push(frontmatterToTask(entityId, resolvedId, frontmatter, now));
+    }
+    const seenEdges = /* @__PURE__ */ new Set();
+    for (const link of extractMarkdownLinks(body)) {
+      const strippedPath = stripLinkSuffix(link.path);
+      const directTargetId = lookupResolvedId(pathToResolvedId, strippedPath);
+      const resolvedTargetPath = resolveRelativePath(file.path, strippedPath);
+      if (isStructuralPath(strippedPath) || isStructuralPath(resolvedTargetPath)) continue;
+      const targetId = directTargetId ?? lookupResolvedId(pathToResolvedId, resolvedTargetPath);
+      if (!targetId) continue;
+      const edgeKey = `${resolvedId}\0${targetId}\0${link.text}`;
+      if (seenEdges.has(edgeKey)) continue;
+      seenEdges.add(edgeKey);
+      edges.push({
+        id: generateId(),
+        entity_id: entityId,
+        source_id: resolvedId,
+        target_id: targetId,
+        edge_type: link.text,
+        created_at: now
+      });
+    }
+  }
+  const events = [];
+  if (logContent != null) {
+    const logPath = logMdPath ?? `entities/${entityId}/log.md`;
+    for (const entry of parseLogMd(logContent)) {
+      const parsed = parseLogEntryText(entry.text);
+      if (!parsed) continue;
+      let related_entry_id = null;
+      if (parsed.linkPath) {
+        const targetPath = resolveRelativePath(logPath, stripLinkSuffix(parsed.linkPath));
+        if (!isStructuralPath(targetPath) && targetPath.includes("/facts/")) {
+          related_entry_id = lookupResolvedId(pathToResolvedId, targetPath) ?? null;
+        }
+      }
+      const created_at = (/* @__PURE__ */ new Date(`${entry.date}T00:00:00.000Z`)).getTime();
+      if (!Number.isFinite(created_at)) continue;
+      events.push({
+        id: generateId("evt_"),
+        entity_id: entityId,
+        event_type: parsed.event_type,
+        summary: parsed.summary,
+        related_entry_id,
+        created_at
+      });
+    }
+  }
+  return {
+    generatedAt: now,
+    entities: {
+      [entityId]: { facts, tasks, events, edges }
+    }
+  };
+}
 
 // src/librarianPrompt.ts
 var DEFAULT_LIBRARIAN_SYNTHESIS_PROMPT = `You are a careful memory synthesis assistant.
@@ -2059,6 +2375,6 @@ function createWiki(db, options) {
   return new WikiMemory(db, options);
 }
 
-export { DEFAULT_LIBRARIAN_SYNTHESIS_PROMPT, WikiMemory, createWiki, formatContext, formatMemoryDump, formatOkfBundle, hydrateLibrarianPrompt, mapLibrarianOptionsToReadOptions, validateLibrarianPromptTemplate };
+export { DEFAULT_LIBRARIAN_SYNTHESIS_PROMPT, WikiMemory, createWiki, formatContext, formatMemoryDump, formatOkfBundle, hydrateLibrarianPrompt, mapLibrarianOptionsToReadOptions, parseOkfBundle, validateLibrarianPromptTemplate };
 //# sourceMappingURL=index.mjs.map
 //# sourceMappingURL=index.mjs.map