@knowledgine/cli 0.6.1 → 0.6.3

package/dist/commands/doctor.js

@@ -0,0 +1,600 @@
+import { resolve } from "path";
+import { existsSync, statSync, accessSync, constants } from "fs";
+import { resolveDefaultPath, createDatabase, Migrator, KnowledgeRepository, ALL_MIGRATIONS, ModelManager, DEFAULT_MODEL_NAME, } from "@knowledgine/core";
+import { colors, symbols } from "../lib/ui/index.js";
+// Check 1: .knowledgine directory exists
+export function checkKnowledgineDir(knowledgineDir) {
+    if (!existsSync(knowledgineDir)) {
+        return {
+            name: "knowledgine directory",
+            status: "error",
+            message: `.knowledgine directory not found at ${knowledgineDir}`,
+            fix: `knowledgine init --path ${resolve(knowledgineDir, "..")}`,
+        };
+    }
+    return {
+        name: "knowledgine directory",
+        status: "pass",
+        message: ".knowledgine directory exists",
+    };
+}
+// Check 2: Database exists and is readable
+export function checkDatabaseExists(dbPath) {
+    if (!existsSync(dbPath)) {
+        return {
+            name: "database file",
+            status: "error",
+            message: `index.sqlite not found at ${dbPath}`,
+            fix: `knowledgine init --path ${resolve(dbPath, "../..")}`,
+        };
+    }
+    try {
+        accessSync(dbPath, constants.R_OK);
+    }
+    catch {
+        return {
+            name: "database file",
+            status: "error",
+            message: `index.sqlite is not readable (permission denied)`,
+            fix: `chmod 600 ${dbPath}`,
+        };
+    }
+    return {
+        name: "database file",
+        status: "pass",
+        message: "index.sqlite exists and is readable",
+    };
+}
+// Check 3: Database is not empty (0-byte)
+export function checkDatabaseNotEmpty(dbPath) {
+    if (!existsSync(dbPath)) {
+        return {
+            name: "database size",
+            status: "error",
+            message: "index.sqlite not found — cannot check size",
+        };
+    }
+    const stat = statSync(dbPath);
+    if (stat.size === 0) {
+        return {
+            name: "database size",
+            status: "error",
+            message: "index.sqlite is 0 bytes (empty/corrupt file)",
+            fix: `rm ${dbPath} && knowledgine init --path ${resolve(dbPath, "../..")}`,
+        };
+    }
+    return {
+        name: "database size",
+        status: "pass",
+        message: `database file is ${stat.size} bytes`,
+    };
+}
+// Check 4: Database file permissions (should be readable/writable by owner on Unix)
+export function checkDatabasePermissions(dbPath) {
+    if (!existsSync(dbPath)) {
+        return {
+            name: "database permissions",
+            status: "error",
+            message: "index.sqlite not found — cannot check permissions",
+        };
+    }
+    // On Windows, skip permission check
+    if (process.platform === "win32") {
+        return {
+            name: "database permissions",
+            status: "pass",
+            message: "permission check skipped on Windows",
+        };
+    }
+    try {
+        accessSync(dbPath, constants.R_OK | constants.W_OK);
+    }
+    catch {
+        return {
+            name: "database permissions",
+            status: "warning",
+            message: "index.sqlite is not writable by current user",
+            fix: `chmod 600 ${dbPath}`,
+        };
+    }
+    return {
+        name: "database permissions",
+        status: "pass",
+        message: "database file permissions are correct",
+    };
+}
+// Check 5: FTS5 integrity
+export function checkFTS5Integrity(dbPath) {
+    if (!existsSync(dbPath) || statSync(dbPath).size === 0) {
+        return {
+            name: "FTS5 integrity",
+            status: "error",
+            message: "database unavailable — cannot check FTS5 integrity",
+        };
+    }
+    try {
+        const db = createDatabase(dbPath);
+        try {
+            // Check if FTS5 index exists
+            const ftsTable = db
+                .prepare("SELECT name FROM sqlite_master WHERE type='table' AND name='knowledge_notes_fts'")
+                .get();
+            if (!ftsTable) {
+                return {
+                    name: "FTS5 integrity",
+                    status: "warning",
+                    message: "FTS5 index table not found — database may need migration",
+                    fix: `knowledgine init --path ${resolve(dbPath, "../..")}`,
+                };
+            }
+            // Run FTS5 integrity check (special SELECT command, read-only safe)
+            db.prepare("SELECT content FROM knowledge_notes_fts WHERE knowledge_notes_fts MATCH 'a*' LIMIT 1").all();
+            return {
+                name: "FTS5 integrity",
+                status: "pass",
+                message: "FTS5 index integrity check passed",
+            };
+        }
+        finally {
+            db.close();
+        }
+    }
+    catch (error) {
+        const msg = error instanceof Error ? error.message : String(error);
+        return {
+            name: "FTS5 integrity",
+            status: "error",
+            message: `FTS5 integrity check failed: ${msg}`,
+            fix: `knowledgine init --force --path ${resolve(dbPath, "../..")}`,
+        };
+    }
+}
+// Check 6: Embedding model files exist
+export function checkModelFiles() {
+    try {
+        const modelManager = new ModelManager();
+        const available = modelManager.isModelAvailable();
+        if (!available) {
+            return {
+                name: "embedding model",
+                status: "warning",
+                message: `${DEFAULT_MODEL_NAME} model files not found — semantic search unavailable`,
+                fix: "knowledgine upgrade --semantic",
+            };
+        }
+        return {
+            name: "embedding model",
+            status: "pass",
+            message: `${DEFAULT_MODEL_NAME} model files are present`,
+        };
+    }
+    catch (error) {
+        const msg = error instanceof Error ? error.message : String(error);
+        return {
+            name: "embedding model",
+            status: "warning",
+            message: `Could not check model availability: ${msg}`,
+            fix: "knowledgine upgrade --semantic",
+        };
+    }
+}
+// Check 7: Embedding coverage percentage
+export function checkEmbeddingCoverage(dbPath) {
+    if (!existsSync(dbPath) || statSync(dbPath).size === 0) {
+        return {
+            name: "embedding coverage",
+            status: "error",
+            message: "database unavailable — cannot check embedding coverage",
+        };
+    }
+    try {
+        const db = createDatabase(dbPath);
+        try {
+            new Migrator(db, ALL_MIGRATIONS).migrate();
+            const repository = new KnowledgeRepository(db);
+            const stats = repository.getStats();
+            if (stats.totalNotes === 0) {
+                return {
+                    name: "embedding coverage",
+                    status: "pass",
+                    message: "no notes indexed yet",
+                };
+            }
+            const withoutEmbeddings = repository.getNotesWithoutEmbeddingIds().length;
+            const withEmbeddings = stats.totalNotes - withoutEmbeddings;
+            const coverage = Math.round((withEmbeddings / stats.totalNotes) * 100);
+            // Determine correct fix command: if model exists, suggest ingest; otherwise, suggest upgrade
+            const modelManager = new ModelManager();
+            const modelExists = modelManager.isModelAvailable();
+            const fixCommand = modelExists
+                ? "knowledgine ingest --all"
+                : "knowledgine upgrade --semantic";
+            if (coverage === 100) {
+                return {
+                    name: "embedding coverage",
+                    status: "pass",
+                    message: `100% coverage (${withEmbeddings}/${stats.totalNotes} notes have embeddings)`,
+                };
+            }
+            else if (coverage >= 80) {
+                return {
+                    name: "embedding coverage",
+                    status: "pass",
+                    message: `${coverage}% coverage (${withEmbeddings}/${stats.totalNotes} notes have embeddings)`,
+                };
+            }
+            else if (coverage > 0) {
+                return {
+                    name: "embedding coverage",
+                    status: "warning",
+                    message: `${coverage}% coverage — ${withoutEmbeddings} notes missing embeddings`,
+                    fix: fixCommand,
+                };
+            }
+            else {
+                return {
+                    name: "embedding coverage",
+                    status: "warning",
+                    message: "no embeddings generated yet — semantic search is unavailable",
+                    fix: fixCommand,
+                };
+            }
+        }
+        finally {
+            db.close();
+        }
+    }
+    catch (error) {
+        const msg = error instanceof Error ? error.message : String(error);
+        return {
+            name: "embedding coverage",
+            status: "error",
+            message: `Failed to check embedding coverage: ${msg}`,
+        };
+    }
+}
+// Check 8: sqlite-vec extension loadable
+export async function checkSqliteVec(dbPath) {
+    if (!existsSync(dbPath) || statSync(dbPath).size === 0) {
+        return {
+            name: "sqlite-vec extension",
+            status: "warning",
+            message: "database unavailable — cannot check sqlite-vec",
+        };
+    }
+    try {
+        const { loadSqliteVecExtension, createDatabase: createDb } = await import("@knowledgine/core");
+        const db = createDb(dbPath);
+        try {
+            const loaded = await loadSqliteVecExtension(db);
+            if (!loaded) {
+                return {
+                    name: "sqlite-vec extension",
+                    status: "warning",
+                    message: "sqlite-vec extension not available — vector search disabled",
+                    fix: "npm install sqlite-vec  (or reinstall knowledgine)",
+                };
+            }
+            return {
+                name: "sqlite-vec extension",
+                status: "pass",
+                message: "sqlite-vec extension loaded successfully",
+            };
+        }
+        finally {
+            db.close();
+        }
+    }
+    catch (error) {
+        const msg = error instanceof Error ? error.message : String(error);
+        return {
+            name: "sqlite-vec extension",
+            status: "warning",
+            message: `sqlite-vec check failed: ${msg}`,
+        };
+    }
+}
+// Check 9: Stale embeddings (notes modified after embedding was generated)
+export function checkStaleEmbeddings(dbPath) {
+    if (!existsSync(dbPath) || statSync(dbPath).size === 0) {
+        return {
+            name: "stale embeddings",
+            status: "error",
+            message: "database unavailable — cannot check stale embeddings",
+        };
+    }
+    try {
+        const db = createDatabase(dbPath);
+        try {
+            new Migrator(db, ALL_MIGRATIONS).migrate();
+            // Check if embedding_updated_at column exists in the schema
+            const tableInfo = db.prepare("PRAGMA table_info(knowledge_notes)").all();
+            const hasEmbeddingCol = tableInfo.some((col) => col.name === "embedding_updated_at");
+            if (!hasEmbeddingCol) {
+                return {
+                    name: "stale embeddings",
+                    status: "pass",
+                    message: "stale embedding check not applicable (embedding_updated_at column not present)",
+                };
+            }
+            // Count notes where updated_at > embedding_updated_at
+            const staleCount = db
+                .prepare(`SELECT COUNT(*) as count FROM knowledge_notes
+             WHERE embedding_updated_at IS NOT NULL
+               AND updated_at IS NOT NULL
+               AND updated_at > embedding_updated_at`)
+                .get().count;
+            if (staleCount > 0) {
+                return {
+                    name: "stale embeddings",
+                    status: "warning",
+                    message: `${staleCount} notes have stale embeddings (modified after last embedding update)`,
+                    fix: "knowledgine upgrade --semantic",
+                };
+            }
+            return {
+                name: "stale embeddings",
+                status: "pass",
+                message: "no stale embeddings detected",
+            };
+        }
+        finally {
+            db.close();
+        }
+    }
+    catch (error) {
+        const msg = error instanceof Error ? error.message : String(error);
+        return {
+            name: "stale embeddings",
+            status: "warning",
+            message: `Could not check stale embeddings: ${msg}`,
+        };
+    }
+}
+// Check 10: Node.js version >= 20
+export function checkNodeVersion() {
+    const version = process.version; // e.g., "v20.11.0"
+    const match = version.match(/^v(\d+)\./);
+    if (!match) {
+        return {
+            name: "Node.js version",
+            status: "warning",
+            message: `Could not parse Node.js version: ${version}`,
+        };
+    }
+    const major = parseInt(match[1], 10);
+    if (major < 20) {
+        return {
+            name: "Node.js version",
+            status: "error",
+            message: `Node.js ${version} is below required minimum v20`,
+            fix: "nvm install 20 && nvm use 20  (or upgrade Node.js to v20+)",
+        };
+    }
+    return {
+        name: "Node.js version",
+        status: "pass",
+        message: `Node.js ${version} meets minimum requirement (v20+)`,
+    };
+}
+// Check 11: Search latency micro-benchmark (single query)
+export async function checkSearchLatency(dbPath) {
+    if (!existsSync(dbPath) || statSync(dbPath).size === 0) {
+        return {
+            name: "search latency",
+            status: "error",
+            message: "database unavailable — cannot benchmark search",
+        };
+    }
+    try {
+        const db = createDatabase(dbPath);
+        try {
+            new Migrator(db, ALL_MIGRATIONS).migrate();
+            const ftsTable = db
+                .prepare("SELECT name FROM sqlite_master WHERE type='table' AND name='knowledge_notes_fts'")
+                .get();
+            if (!ftsTable) {
+                return {
+                    name: "search latency",
+                    status: "warning",
+                    message: "FTS5 index not found — cannot benchmark search",
+                };
+            }
+            const start = Date.now();
+            db.prepare("SELECT rowid FROM knowledge_notes_fts WHERE knowledge_notes_fts MATCH ? LIMIT 10").all("test");
+            const latencyMs = Date.now() - start;
+            if (latencyMs > 500) {
+                return {
+                    name: "search latency",
+                    status: "warning",
+                    message: `FTS5 search took ${latencyMs}ms — slower than expected (>500ms)`,
+                    fix: "Consider running VACUUM on the database: sqlite3 index.sqlite VACUUM",
+                };
+            }
+            return {
+                name: "search latency",
+                status: "pass",
+                message: `FTS5 search latency: ${latencyMs}ms`,
+            };
+        }
+        finally {
+            db.close();
+        }
+    }
+    catch (error) {
+        const msg = error instanceof Error ? error.message : String(error);
+        return {
+            name: "search latency",
+            status: "warning",
+            message: `Search latency benchmark failed: ${msg}`,
+        };
+    }
+}
+export async function doctorCommand(options) {
+    const rootPath = resolveDefaultPath(options.path);
+    const knowledgineDir = resolve(rootPath, ".knowledgine");
+    const dbPath = resolve(knowledgineDir, "index.sqlite");
+    const results = [];
+    console.error("");
+    console.error(`  ${colors.bold("knowledgine doctor")} — running health checks...`);
+    console.error("");
+    // Run all checks, capturing each independently so one failure doesn't block others
+    try {
+        results.push(checkKnowledgineDir(knowledgineDir));
+    }
+    catch (error) {
+        results.push({
+            name: "knowledgine directory",
+            status: "error",
+            message: `Unexpected error: ${error instanceof Error ? error.message : String(error)}`,
+        });
+    }
+    try {
+        results.push(checkDatabaseExists(dbPath));
+    }
+    catch (error) {
+        results.push({
+            name: "database file",
+            status: "error",
+            message: `Unexpected error: ${error instanceof Error ? error.message : String(error)}`,
+        });
+    }
+    try {
+        results.push(checkDatabaseNotEmpty(dbPath));
+    }
+    catch (error) {
+        results.push({
+            name: "database size",
+            status: "error",
+            message: `Unexpected error: ${error instanceof Error ? error.message : String(error)}`,
+        });
+    }
+    try {
+        results.push(checkDatabasePermissions(dbPath));
+    }
+    catch (error) {
+        results.push({
+            name: "database permissions",
+            status: "error",
+            message: `Unexpected error: ${error instanceof Error ? error.message : String(error)}`,
+        });
+    }
+    try {
+        results.push(checkFTS5Integrity(dbPath));
+    }
+    catch (error) {
+        results.push({
+            name: "FTS5 integrity",
+            status: "error",
+            message: `Unexpected error: ${error instanceof Error ? error.message : String(error)}`,
+        });
+    }
+    try {
+        results.push(checkModelFiles());
+    }
+    catch (error) {
+        results.push({
+            name: "embedding model",
+            status: "error",
+            message: `Unexpected error: ${error instanceof Error ? error.message : String(error)}`,
+        });
+    }
+    try {
+        results.push(checkEmbeddingCoverage(dbPath));
+    }
+    catch (error) {
+        results.push({
+            name: "embedding coverage",
+            status: "error",
+            message: `Unexpected error: ${error instanceof Error ? error.message : String(error)}`,
+        });
+    }
+    try {
+        results.push(await checkSqliteVec(dbPath));
+    }
+    catch (error) {
+        results.push({
+            name: "sqlite-vec extension",
+            status: "error",
+            message: `Unexpected error: ${error instanceof Error ? error.message : String(error)}`,
+        });
+    }
+    try {
+        results.push(checkStaleEmbeddings(dbPath));
+    }
+    catch (error) {
+        results.push({
+            name: "stale embeddings",
+            status: "error",
+            message: `Unexpected error: ${error instanceof Error ? error.message : String(error)}`,
+        });
+    }
+    try {
+        results.push(checkNodeVersion());
+    }
+    catch (error) {
+        results.push({
+            name: "Node.js version",
+            status: "error",
+            message: `Unexpected error: ${error instanceof Error ? error.message : String(error)}`,
+        });
+    }
+    try {
+        results.push(await checkSearchLatency(dbPath));
+    }
+    catch (error) {
+        results.push({
+            name: "search latency",
+            status: "error",
+            message: `Unexpected error: ${error instanceof Error ? error.message : String(error)}`,
+        });
+    }
+    // Auto-fix: attempt to repair issues when --fix is specified
+    if (options.fix) {
+        for (const result of results) {
+            if (result.status !== "pass" && result.fix) {
+                // Auto-fix DB permissions
+                if (result.name === "database permissions" && existsSync(dbPath)) {
+                    try {
+                        const { chmodSync } = await import("fs");
+                        chmodSync(dbPath, 0o600);
+                        result.status = "pass";
+                        result.message = "database file permissions fixed (chmod 600)";
+                        console.error(`  ${symbols.success} ${colors.success(`Fixed: ${result.name}`)}`);
+                    }
+                    catch {
+                        /* non-fatal */
+                    }
+                }
+            }
+        }
+    }
+    // Output: failures first, then success summary
+    const failures = results.filter((r) => r.status !== "pass");
+    const passes = results.filter((r) => r.status === "pass");
+    if (failures.length > 0) {
+        for (const f of failures) {
+            const icon = f.status === "error" ? symbols.error : symbols.warning;
+            const color = f.status === "error" ? colors.error : colors.warning;
+            console.error(`  ${icon} ${color(f.name)}: ${f.message}`);
+            if (f.fix) {
+                console.error(`    Fix: ${colors.hint(f.fix)}`);
+            }
+        }
+        console.error("");
+    }
+    if (passes.length > 0) {
+        const passNames = passes.map((p) => p.name).join(", ");
+        console.error(`  ${symbols.success} ${passes.length} checks passed (${passNames})`);
+    }
+    // Health score: 100 - (errors * 15 + warnings * 5)
+    const errorCount = results.filter((r) => r.status === "error").length;
+    const warningCount = results.filter((r) => r.status === "warning").length;
+    const score = Math.max(0, 100 - errorCount * 15 - warningCount * 5);
+    const scoreColor = score >= 80 ? colors.success : score >= 50 ? colors.warning : colors.error;
+    console.error(`\n  Health Score: ${scoreColor(String(score))}/100`);
+    console.error("");
+    if (errorCount > 0)
+        process.exitCode = 1;
+}
+//# sourceMappingURL=doctor.js.map

package/dist/commands/doctor.js.map

@@ -0,0 +1 @@
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package/dist/commands/explain.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"explain.d.ts","sourceRoot":"","sources":["../../src/commands/explain.ts"],"names":[],"mappings":"AAgBA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAEzC,MAAM,WAAW,qBAAqB;IACpC,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAiTD,wBAAgB,sBAAsB,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CAU7D"}
+{"version":3,"file":"explain.d.ts","sourceRoot":"","sources":["../../src/commands/explain.ts"],"names":[],"mappings":"AAgBA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAEzC,MAAM,WAAW,qBAAqB;IACpC,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAqTD,wBAAgB,sBAAsB,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CAU7D"}

package/dist/commands/explain.js

@@ -7,7 +7,10 @@ function formatDate(iso) {
 function formatPlain(entityName, entityGraph, provenance) {
     const lines = [];
     lines.push(`Entity: ${entityGraph.name}`);
-    lines.push(`Type: ${entityGraph.entityType}`);
+    const typeDisplay = entityGraph.entityType === "unknown"
+        ? `unknown (detected in ${entityGraph.linkedNotes.length} note${entityGraph.linkedNotes.length !== 1 ? "s" : ""}, type not yet classified)`
+        : entityGraph.entityType;
+    lines.push(`Type: ${typeDisplay}`);
     if (entityGraph.description) {
         lines.push(`Description: ${entityGraph.description}`);
     }