studiograph 1.3.47 → 1.3.48-beta.0

package/dist/services/vector-service.js

@@ -18,22 +18,111 @@
 import { join } from 'path';
 import { existsSync, readFileSync, writeFileSync, mkdirSync } from 'fs';
 import * as lancedb from '@lancedb/lancedb';
+import { tryResolve } from '../core/secrets/read-flip.js';
 const VOYAGE_API_URL = 'https://api.voyageai.com/v1/embeddings';
 const VOYAGE_MODEL = 'voyage-3';
 const VECTOR_DIM = 1024;
 const TABLE_NAME = 'entities';
 export class VectorService {
     dbPath;
-    voyageApiKey;
+    /**
+     * Legacy fallback key passed via constructor for tests or for early-
+     * boot code paths that run before the secrets store is initialized.
+     * Live calls prefer `tryResolve('voyage.api_key')` so values written
+     * to the store via the UI / CLI take effect without a restart.
+     */
+    fallbackVoyageApiKey;
+    workspaceRoot;
     db;
     table;
     lastIndexedPath;
     initialized = false;
-    constructor(dbPath, voyageApiKey) {
+    // ── Operator-visible health (surfaced via /api/health/dirty) ──
+    // Tracked here, not at the call sites, because every fire-and-forget
+    // upsert/delete in graph.ts catches its own promise to avoid blocking
+    // writes — the operator needs a single rolled-up signal instead of
+    // grepping logs for `[vector] index failed`.
+    failureCount = 0;
+    inFlight = 0;
+    lastFailureAt = null;
+    lastFailure = null;
+    constructor(dbPath, voyageApiKey, workspaceRoot) {
         this.dbPath = dbPath;
-        this.voyageApiKey = voyageApiKey;
+        this.fallbackVoyageApiKey = voyageApiKey;
+        this.workspaceRoot = workspaceRoot;
         this.lastIndexedPath = join(dbPath, 'last-indexed.json');
     }
+    /**
+     * Resolve the Voyage API key fresh on each call: store > constructor
+     * fallback. Lets the operator flip the key via UI / CLI without a
+     * server restart.
+     */
+    get voyageApiKey() {
+        const fromStore = tryResolve('voyage.api_key');
+        return fromStore ?? this.fallbackVoyageApiKey;
+    }
+    /** Begin tracking an in-flight op. Pair with `recordSuccess`/`recordFailure`. */
+    beginOp() { this.inFlight++; }
+    recordSuccess() {
+        if (this.inFlight > 0)
+            this.inFlight--;
+    }
+    recordFailure(op, entity, err) {
+        if (this.inFlight > 0)
+            this.inFlight--;
+        this.failureCount++;
+        this.lastFailureAt = new Date().toISOString();
+        this.lastFailure = {
+            op,
+            entity,
+            error: err instanceof Error ? err.message : String(err),
+        };
+    }
+    /**
+     * Snapshot for /api/health. Healthy = the last op succeeded (or none have
+     * run yet) AND there is no abnormal in-flight backlog. The failure count
+     * is informational; a single transient Voyage 503 shouldn't permanently
+     * mark the service unhealthy, but operators can see the trend.
+     */
+    getHealth() {
+        return {
+            healthy: this.lastFailure === null,
+            failureCount: this.failureCount,
+            inFlight: this.inFlight,
+            lastFailureAt: this.lastFailureAt,
+            lastFailure: this.lastFailure,
+            embeddingsEnabled: !!this.voyageApiKey,
+        };
+    }
+    /**
+     * For asset entities backed by a PDF, the binary's extracted text
+     * lives in a sidecar at `<workspace>/.studiograph/assets-text/asset/<id>.txt`
+     * (written at upload time by `uploadAsset`). Returns the contents so
+     * `buildEntityText` can fold the PDF into the embedding/FTS input. The
+     * markdown body of an asset entity is intentionally light — without
+     * this, PDF assets would be effectively invisible to RAG.
+     *
+     * Best-effort: missing sidecar / read errors return null. Asset stays
+     * indexed by frontmatter alone.
+     */
+    readPdfSidecar(entity) {
+        if (!this.workspaceRoot)
+            return null;
+        if (entity.entityType !== 'asset')
+            return null;
+        if (entity.data.asset_kind !== 'pdf')
+            return null;
+        const path = join(this.workspaceRoot, '.studiograph', 'assets-text', 'asset', `${entity.id}.txt`);
+        try {
+            if (!existsSync(path))
+                return null;
+            const text = readFileSync(path, 'utf-8').trim();
+            return text || null;
+        }
+        catch {
+            return null;
+        }
+    }
     /**
      * Open/create the LanceDB table and ensure the FTS index exists.
      * Call once before using the service.
@@ -75,7 +164,7 @@ export class VectorService {
     async upsert(repoName, entity) {
         await this.init();
         const id = `${repoName}/${entity.entityType}/${entity.id}`;
-        const text = buildEntityText(entity);
+        const text = buildEntityText(entity, this.readPdfSidecar(entity) ?? undefined);
         const vector = this.voyageApiKey
             ? await this.generateEmbedding(text)
             : null;
@@ -98,15 +187,20 @@ export class VectorService {
     /**
      * Bulk upsert — used by `studiograph index`. Batches Voyage API calls.
      */
-    async upsertMany(repoName, entities) {
+    async upsertMany(repoName, entities, opts = {}) {
         await this.init();
         if (entities.length === 0)
             return;
-        const texts = entities.map(e => buildEntityText(e));
+        const texts = entities.map(e => buildEntityText(e, this.readPdfSidecar(e) ?? undefined));
         // Batch embeddings (Voyage supports up to 128 per request)
         let vectors = new Array(entities.length).fill(null);
         if (this.voyageApiKey) {
-            vectors = await this.generateEmbeddingsBatch(texts);
+            vectors = await this.generateEmbeddingsBatch(texts, opts.onProgress);
+        }
+        else {
+            // No embedding step — report the whole batch as "done" once so
+            // progress UIs that wait on at least one callback don't sit at 0%.
+            opts.onProgress?.(entities.length, entities.length);
         }
         const records = entities.map((entity, i) => ({
             id: `${repoName}/${entity.entityType}/${entity.id}`,
@@ -131,6 +225,26 @@ export class VectorService {
         const id = `${repoName}/${entityType}/${entityId}`;
         await this.table.delete(`id = '${id.replace(/'/g, "''")}'`);
     }
+    /**
+     * Remove an entity by `(repo, id)` alone, without needing its type.
+     *
+     * Used by the serve-boot incremental indexer: when git diff reports a
+     * deletion, the file is gone from disk so its type can't be resolved
+     * from frontmatter. The vector store has a discrete `entity_id` column
+     * so we can match on `repo + entity_id` without falling back to a LIKE
+     * pattern on the synthetic id.
+     *
+     * Safe across type renames: a single id that legitimately had two type
+     * rows (e.g. type changed mid-edit and both old + new still exist) gets
+     * both wiped — which is the right behavior for incremental rebuild
+     * since the next upsert recreates the current type's row.
+     */
+    async deleteByRepoAndId(repoName, entityId) {
+        await this.init();
+        const r = repoName.replace(/'/g, "''");
+        const e = entityId.replace(/'/g, "''");
+        await this.table.delete(`repo = '${r}' AND entity_id = '${e}'`);
+    }
     /**
      * Search the index.
      * Uses hybrid search (vector + FTS) when Voyage key is configured, FTS only otherwise.
@@ -188,9 +302,13 @@ export class VectorService {
         }
     }
     /**
-     * Record the current time as the last index time for a repo.
+     * Record the last index time for a repo.
+     *
+     * Production callers omit `isoTimestamp` and the current time is used.
+     * Tests pass an explicit ISO timestamp so they can rewind the clock and
+     * assert the git-log `--since` window picks up the right commits.
      */
-    setLastIndexedTime(repoName) {
+    setLastIndexedTime(repoName, isoTimestamp) {
         mkdirSync(this.dbPath, { recursive: true });
         let data = {};
         if (existsSync(this.lastIndexedPath)) {
@@ -199,7 +317,7 @@ export class VectorService {
             }
             catch { /* ignore */ }
         }
-        data[repoName] = new Date().toISOString();
+        data[repoName] = isoTimestamp ?? new Date().toISOString();
         writeFileSync(this.lastIndexedPath, JSON.stringify(data, null, 2) + '\n');
     }
     /** Whether Voyage AI embeddings are enabled (Tier 2). */
@@ -211,10 +329,11 @@ export class VectorService {
         const results = await this.generateEmbeddingsBatch([text]);
         return results[0] ?? new Array(VECTOR_DIM).fill(0);
     }
-    async generateEmbeddingsBatch(texts) {
+    async generateEmbeddingsBatch(texts, onProgress) {
         // Voyage supports up to 128 inputs per request
         const BATCH_SIZE = 128;
         const all = [];
+        const total = texts.length;
         for (let i = 0; i < texts.length; i += BATCH_SIZE) {
             const batch = texts.slice(i, i + BATCH_SIZE);
             const response = await fetch(VOYAGE_API_URL, {
@@ -231,6 +350,7 @@ export class VectorService {
             }
             const json = await response.json();
             all.push(...json.data.map(d => d.embedding));
+            onProgress?.(all.length, total);
         }
         return all;
     }
@@ -249,7 +369,7 @@ export async function reindexWorkspace(workspacePath, repos, onProgress) {
     const { homedir } = await import('os');
     const userConfig = loadUserConfig();
     const dbPath = userConfig.vector_db_path || join(homedir(), '.studiograph', 'vector');
-    const vectorService = new VectorService(dbPath, userConfig.voyage_api_key);
+    const vectorService = new VectorService(dbPath, userConfig.voyage_api_key, workspacePath);
     await vectorService.init();
     const log = onProgress ?? (() => { });
     let total = 0;
@@ -277,13 +397,151 @@ export async function reindexWorkspace(workspacePath, repos, onProgress) {
     }
     return total;
 }
+export async function incrementalReindexWorkspace(workspaceManager, repos, workspacePath, opts = {}) {
+    const vectorService = workspaceManager.vectorService;
+    if (!vectorService) {
+        return { total: 0, fresh: false };
+    }
+    const log = opts.log ?? (() => { });
+    const { execFileSync } = await import('child_process');
+    let total = 0;
+    let anyFreshRepo = false;
+    const staleEntities = [];
+    // Pre-pass: figure out the total first-time entity count so the
+    // progress callback has a stable denominator. Cheap — `graph.list()`
+    // doesn't re-read files, it returns the in-memory graph state the
+    // workspace manager already maintains.
+    let firstTimeTotal = 0;
+    if (opts.onFirstTimeProgress) {
+        for (const repo of repos) {
+            if (vectorService.getLastIndexedTime(repo.name))
+                continue;
+            try {
+                firstTimeTotal += workspaceManager.getGraph(repo.name).list().length;
+            }
+            catch {
+                // tolerate per-repo failure; the real loop below will log it
+            }
+        }
+    }
+    let firstTimeDone = 0;
+    for (const repo of repos) {
+        const lastIndexed = vectorService.getLastIndexedTime(repo.name);
+        // Per-repo first-time index. Catches three cases:
+        //   1. Very first `serve` boot (every repo missing a timestamp).
+        //   2. New folder added between serve boots (existing workspace +
+        //      new repo with no timestamp). Pre-fix this was skipped here
+        //      and never indexed unless the operator ran a full reindex.
+        //   3. Vector DB rebuilt from scratch but workspace has existing
+        //      folders.
+        if (!lastIndexed) {
+            try {
+                const graph = workspaceManager.getGraph(repo.name);
+                const entities = graph.list();
+                if (entities.length > 0) {
+                    await vectorService.upsertMany(repo.name, entities, {
+                        onProgress: (batchDone) => {
+                            opts.onFirstTimeProgress?.(firstTimeDone + batchDone, firstTimeTotal);
+                        },
+                    });
+                    firstTimeDone += entities.length;
+                    total += entities.length;
+                }
+                vectorService.setLastIndexedTime(repo.name);
+                anyFreshRepo = true;
+            }
+            catch (err) {
+                log(`failed to index ${repo.name}: ${err instanceof Error ? err.message : 'unknown'}`);
+            }
+            continue;
+        }
+        // Established repo — diff git log since the last index timestamp and
+        // collect a list of stale (repo, id) tuples to upsert / delete below.
+        const repoPath = join(workspacePath, repo.path);
+        if (!existsSync(repoPath))
+            continue;
+        try {
+            const output = execFileSync('git', ['log', `--since=${lastIndexed}`, '--name-status', '--format=', '--', '*.md'], { cwd: repoPath, encoding: 'utf-8', stdio: 'pipe' }).trim();
+            if (!output)
+                continue;
+            for (const line of output.split('\n')) {
+                // Accept any markdown path. Layouts in the wild:
+                //   - flat:    `entity-id.md`
+                //   - typed:   `<type>/entity-id.md`
+                //   - nested:  `folder/sub/entity-id.md`
+                // STU-131 normalized on flat for new entities; older typed layouts
+                // and arbitrary nested folders still appear in mixed repos. Entity
+                // type lives in frontmatter (resolved via graph.getById for
+                // upserts; not needed for deletes since we now match by `(repo,
+                // entity_id)` columns). Pre-fix this regex required exactly one
+                // slash with a `\w+` type segment and missed all three layouts,
+                // plus hyphenated types like `case-study`.
+                const m = line.match(/^([AMD])\s+(.+\.md)$/);
+                if (!m)
+                    continue;
+                const [, status, path] = m;
+                // basename minus `.md`. Entity IDs are unique within a repo.
+                const id = path.split('/').pop().replace(/\.md$/, '');
+                if (!id)
+                    continue;
+                staleEntities.push({ repoName: repo.name, entityId: id, deleted: status === 'D' });
+            }
+        }
+        catch (err) {
+            log(`failed to diff ${repo.name}: ${err instanceof Error ? err.message : 'unknown'}`);
+        }
+    }
+    if (staleEntities.length === 0) {
+        // Nothing changed via git diff. If we did first-time work above, that
+        // counts as a fresh run; otherwise this was a no-op incremental boot.
+        return { total, fresh: anyFreshRepo };
+    }
+    // Dedupe: if an entity appears multiple times (e.g. M then D), the last
+    // entry wins. Order matters — git log is newest-first by default, so we
+    // reverse before reducing to get the newest state per (repo, id).
+    const seen = new Map();
+    for (const item of staleEntities.slice().reverse()) {
+        seen.set(`${item.repoName}/${item.entityId}`, item);
+    }
+    for (const item of seen.values()) {
+        try {
+            if (item.deleted) {
+                // Delete by (repo, id) — type isn't recoverable from a deleted file.
+                // The new column-based matcher in vectorService handles it without
+                // a frontmatter lookup.
+                await vectorService.deleteByRepoAndId(item.repoName, item.entityId);
+            }
+            else {
+                const graph = workspaceManager.getGraph(item.repoName);
+                const entity = graph.getById(item.entityId);
+                await vectorService.upsert(item.repoName, entity);
+                total++;
+            }
+        }
+        catch {
+            // Entity may have been deleted then re-created; safe to skip.
+        }
+    }
+    // Stamp every repo we touched. Empty-diff repos already had a timestamp
+    // (we skipped the rebuild path) — re-stamping is cheap and keeps the
+    // "since" window tight for the next boot.
+    for (const repo of repos) {
+        vectorService.setLastIndexedTime(repo.name);
+    }
+    return { total, fresh: anyFreshRepo };
+}
 // ─── Helpers ─────────────────────────────────────────────────────────────────
 /**
  * Build a text representation of an entity for FTS/embedding.
  * Combines entity type, key frontmatter fields, and markdown body.
+ *
+ * `extraText` is appended after the body — used by VectorService to
+ * fold PDF sidecar text into asset-entity embeddings. Kept as a plain
+ * string parameter (not file IO) so this stays pure and unit-testable.
+ *
  * Exported for testing.
  */
-export function buildEntityText(entity) {
+export function buildEntityText(entity, extraText) {
     const parts = [];
     // Entity type and ID as context
     parts.push(`${entity.entityType}: ${entity.data.name || entity.id}`);
@@ -317,6 +575,11 @@ export function buildEntityText(entity) {
         if (plainText)
             parts.push(plainText);
     }
+    if (extraText) {
+        const trimmed = extraText.trim();
+        if (trimmed)
+            parts.push(trimmed);
+    }
     return parts.join('\n');
 }
 //# sourceMappingURL=vector-service.js.map

package/dist/services/vector-service.js.map

@@ -1 +1 @@
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package/dist/services/workspace-access.d.ts

@@ -0,0 +1,106 @@
+/**
+ * Workspace access service — the single architectural boundary through which
+ * routes resolve a graph (or read an entity) for an identified user.
+ *
+ * Why this exists as a service, not a helper:
+ *   The helpers in `access-control.ts` are correct but opt-in — a route that
+ *   forgets to call `hasRepoAccess()` before `workspaceManager.getGraph()`
+ *   silently bypasses access control. After a security audit flagged this as
+ *   an architectural risk, we moved the "give me a graph for repo X as user U"
+ *   resolution behind this service so the act of getting a graph IS the
+ *   access check. There is no method on this surface that returns a graph
+ *   without first running the check; bypassing it requires reaching past
+ *   the service to `WorkspaceManager.getGraph()` directly, which is what
+ *   review now looks for.
+ *
+ * Routes should call `graphForRead`/`graphForWrite`/`graphForAdmin` instead
+ * of `workspaceManager.getGraph(repo)`. The few internal callers that still
+ * need raw graph access (SessionManager, YjsManager, vector indexer, etc.)
+ * are not user-facing transports and operate with the workspace's own
+ * identity, not a request user — they are explicitly out of scope for this
+ * boundary.
+ */
+import type { WorkspaceManager } from '../core/workspace-manager.js';
+import type { BaseGraphManager, EntityFile } from '../core/graph.js';
+import type { EntityType } from '../core/validation.js';
+import type { AuthService, AuthUser } from './auth-service.js';
+export type AccessMode = 'read' | 'write' | 'admin';
+/**
+ * Thrown when an identified user attempts to resolve a graph or read an
+ * entity in a folder they cannot access. The route layer maps `kind` to an
+ * HTTP status: `not_found` → 404 (don't leak existence to non-members),
+ * `forbidden` → 403 (caller can see the folder but lacks the requested role).
+ */
+export declare class AccessDeniedError extends Error {
+    readonly kind: 'not_found' | 'forbidden';
+    readonly repoName: string;
+    readonly code: "ACCESS_DENIED";
+    constructor(kind: 'not_found' | 'forbidden', repoName: string, message: string);
+}
+export declare class WorkspaceAccessService {
+    private readonly workspaceManager;
+    private readonly authService;
+    constructor(workspaceManager: WorkspaceManager, authService: AuthService);
+    /**
+     * Resolve a graph for read. Identified users without read access get a
+     * not_found denial — we deliberately mirror the "folder doesn't exist"
+     * 404 path so non-members can't probe folder existence by status code.
+     * Unidentified callers (API key / open mode) skip the check, matching
+     * legacy web behavior.
+     */
+    graphForRead(user: AuthUser | undefined, repoName: string): BaseGraphManager;
+    /**
+     * Resolve a graph for write (create / update / delete entities, move
+     * folders, etc.). A caller who can read but not write gets a forbidden
+     * denial so the UI can render an actionable role-required message.
+     */
+    graphForWrite(user: AuthUser | undefined, repoName: string): BaseGraphManager;
+    /**
+     * Resolve a graph for folder-admin operations (delete folder, rename
+     * folder, manage members). Workspace owners are admins on shared folders
+     * but NOT on private/solo folders — see `isFolderAdminOrOwner` for the
+     * full rule. This is enforced separately because some operations (renaming
+     * a folder) are catastrophic if a regular editor can perform them.
+     */
+    graphForAdmin(user: AuthUser | undefined, repoName: string): BaseGraphManager;
+    /**
+     * Read a single entity through the access boundary. Provided as a
+     * convenience so routes that just need an entity body don't have to
+     * resolve the graph and call `.get()` themselves — every such call site
+     * was a place a future refactor could accidentally bypass enforcement.
+     */
+    readEntity(user: AuthUser | undefined, repoName: string, entityType: EntityType, entityId: string): EntityFile;
+    /** List repos the user may read. Wraps the helper for symmetry. */
+    listReadableRepos(user: AuthUser | undefined): {
+        name: string;
+        path: string;
+        display_name?: string | undefined;
+        type?: string | undefined;
+        description?: string | undefined;
+        personal?: boolean | undefined;
+        owner_id?: number | undefined;
+        sync?: {
+            source: string;
+            entity_type?: string | undefined;
+            filter?: Record<string, any> | undefined;
+        }[] | undefined;
+    }[];
+    /** Set of entity IDs visible to the user across their accessible folders. */
+    listAccessibleEntityIds(user: AuthUser | undefined): Set<string> | null;
+    /** Filter a wikilink list to only entities the caller can access. */
+    filterWikilinks(wikilinks: string[], accessibleIds: Set<string> | null): string[];
+    /** Boolean check — for routes that need a 404/200 branch without a graph. */
+    canRead(user: AuthUser | undefined, repoName: string): boolean;
+    /** Boolean check — for routes that need a 403/200 branch without a graph. */
+    canWrite(user: AuthUser | undefined, repoName: string): boolean;
+    /** Boolean check — for routes that need a 403/200 branch without a graph. */
+    canAdmin(user: AuthUser | undefined, repoName: string): boolean;
+}
+/**
+ * Map an AccessDeniedError to an HTTP reply. Routes catch the error at the
+ * top of each handler and call this — keeps the per-route boilerplate to
+ * a single try/catch instead of two checks per access kind.
+ */
+export declare function sendAccessDenied(reply: {
+    status: (n: number) => any;
+}, err: AccessDeniedError): any;