@codified/cli 0.3.9 → 0.4.1

package/dist/__tests__/integration.test.d.ts

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+export {};
+//# sourceMappingURL=integration.test.d.ts.map

package/dist/__tests__/integration.test.d.ts.map

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+{"version":3,"file":"integration.test.d.ts","sourceRoot":"","sources":["../../src/__tests__/integration.test.ts"],"names":[],"mappings":""}

package/dist/__tests__/integration.test.js

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+import { describe, it, expect, beforeAll, afterAll } from "vitest";
+let pool;
+let testProjectId;
+const DEFAULT_PROJECT_ID = "00000000-0000-0000-0000-000000000000";
+beforeAll(async () => {
+    process.env.DATABASE_URL =
+        process.env.DATABASE_URL ??
+            "postgresql://codify:codify@localhost:5432/codify";
+    const pg = await import("pg");
+    pool = new pg.default.Pool({ connectionString: process.env.DATABASE_URL });
+    // Create a test project
+    const result = await pool.query("INSERT INTO projects (name, description) VALUES ($1, $2) RETURNING id", ["test-isolation-" + Date.now(), "Test project for isolation tests"]);
+    testProjectId = result.rows[0].id;
+    // Insert test nodes in the test project
+    await pool.query(`INSERT INTO nodes (id, type, layer, properties, metadata, confidence, freshness, source_system, source_reference, project_id)
+     VALUES (gen_random_uuid(), 'Decision', 'permanent', '{"title": "Test Auth Decision", "description": "test auth decision"}', '{}', 0.8, 1.0, 'test', 'test', $1)`, [testProjectId]);
+    await pool.query(`INSERT INTO nodes (id, type, layer, properties, metadata, confidence, freshness, source_system, source_reference, project_id)
+     VALUES (gen_random_uuid(), 'Gap', 'permanent', '{"title": "Test Gap", "severity": "high", "description": "test gap"}', '{}', 0.8, 1.0, 'test', 'test', $1)`, [testProjectId]);
+});
+afterAll(async () => {
+    await pool.query("DELETE FROM nodes WHERE project_id = $1", [testProjectId]);
+    await pool.query("DELETE FROM projects WHERE id = $1", [testProjectId]);
+    await pool.end();
+});
+describe("Project Isolation", () => {
+    it("nodes in test project are not visible from default project", async () => {
+        const result = await pool.query(`SELECT * FROM nodes WHERE project_id = $1 AND properties::text ILIKE '%Test Auth Decision%'`, [DEFAULT_PROJECT_ID]);
+        expect(result.rows.length).toBe(0);
+    });
+    it("nodes in test project are visible when querying that project", async () => {
+        const result = await pool.query(`SELECT * FROM nodes WHERE project_id = $1 AND properties::text ILIKE '%Test Auth Decision%'`, [testProjectId]);
+        expect(result.rows.length).toBe(1);
+    });
+    it("gaps in test project are isolated", async () => {
+        const defaultGaps = await pool.query(`SELECT * FROM nodes WHERE project_id = $1 AND type = 'Gap' AND properties::text ILIKE '%Test Gap%'`, [DEFAULT_PROJECT_ID]);
+        expect(defaultGaps.rows.length).toBe(0);
+        const testGaps = await pool.query(`SELECT * FROM nodes WHERE project_id = $1 AND type = 'Gap' AND properties::text ILIKE '%Test Gap%'`, [testProjectId]);
+        expect(testGaps.rows.length).toBe(1);
+    });
+});
+describe("Search Keyword Splitting", () => {
+    beforeAll(async () => {
+        await pool.query(`INSERT INTO nodes (id, type, layer, properties, metadata, confidence, freshness, source_system, source_reference, project_id)
+       VALUES (gen_random_uuid(), 'CodeArtifact', 'permanent', '{"title": "Authentication Middleware Handler", "description": "handles auth middleware"}', '{}', 0.8, 1.0, 'test', 'test', $1)`, [testProjectId]);
+    });
+    it("search splits multi-word queries into keywords", async () => {
+        const result = await pool.query(`SELECT * FROM nodes WHERE project_id = $1 AND properties::text ILIKE '%auth%' AND properties::text ILIKE '%middleware%'`, [testProjectId]);
+        expect(result.rows.length).toBeGreaterThanOrEqual(1);
+    });
+    it("keyword splitting finds results that exact phrase would miss", async () => {
+        // "middleware authentication" as a phrase doesn't appear in "Authentication Middleware Handler"
+        // but splitting into keywords "middleware" + "authentication" finds it via AND
+        const phraseResult = await pool.query(`SELECT * FROM nodes WHERE project_id = $1 AND properties::text ILIKE '%middleware authentication handler xyz%'`, [testProjectId]);
+        expect(phraseResult.rows.length).toBe(0);
+        // But splitting "middleware" AND "authentication" works
+        const splitResult = await pool.query(`SELECT * FROM nodes WHERE project_id = $1 AND properties::text ILIKE '%middleware%' AND properties::text ILIKE '%authentication%'`, [testProjectId]);
+        expect(splitResult.rows.length).toBeGreaterThanOrEqual(1);
+    });
+});
+describe("Metabolism Audit", () => {
+    let testNodeId;
+    beforeAll(async () => {
+        // Get a node ID from the test project for audit events
+        const nodeResult = await pool.query(`SELECT id FROM nodes WHERE project_id = $1 LIMIT 1`, [testProjectId]);
+        testNodeId = nodeResult.rows[0].id;
+        // Insert test audit events
+        await pool.query(`INSERT INTO metabolism_audit (event_type, node_ids, action, reason, metadata)
+       VALUES ($1, $2, $3, $4, $5)`, [
+            "metabolism.decay.applied",
+            [testNodeId],
+            "decayed",
+            "Node freshness below threshold",
+            JSON.stringify({ oldFreshness: 0.8, newFreshness: 0.6 }),
+        ]);
+        await pool.query(`INSERT INTO metabolism_audit (event_type, node_ids, action, reason, metadata)
+       VALUES ($1, $2, $3, $4, $5)`, [
+            "metabolism.gate.promoted",
+            [testNodeId],
+            "promoted",
+            "High confidence node promoted to permanent",
+            JSON.stringify({ confidence: 0.95 }),
+        ]);
+        await pool.query(`INSERT INTO metabolism_audit (event_type, node_ids, action, reason, metadata)
+       VALUES ($1, $2, $3, $4, $5)`, [
+            "metabolism.prune.archived",
+            [testNodeId],
+            "pruned",
+            "Stale node archived after 90 days",
+            JSON.stringify({}),
+        ]);
+    });
+    afterAll(async () => {
+        await pool.query(`DELETE FROM metabolism_audit WHERE node_ids @> $1`, [[testNodeId]]);
+    });
+    it("audit events are queryable by action type", async () => {
+        const result = await pool.query(`SELECT * FROM metabolism_audit WHERE action = $1 AND node_ids @> $2`, ["decayed", [testNodeId]]);
+        expect(result.rows.length).toBe(1);
+        expect(result.rows[0].reason).toBe("Node freshness below threshold");
+    });
+    it("audit events are filterable by time range", async () => {
+        const recent = await pool.query(`SELECT * FROM metabolism_audit WHERE created_at > NOW() - INTERVAL '1 hour' AND node_ids @> $1`, [[testNodeId]]);
+        expect(recent.rows.length).toBe(3);
+        const future = await pool.query(`SELECT * FROM metabolism_audit WHERE created_at > NOW() + INTERVAL '1 hour' AND node_ids @> $1`, [[testNodeId]]);
+        expect(future.rows.length).toBe(0);
+    });
+});
+describe("Markdown Connector SourceRef", () => {
+    it("document sourceRef format uses doc: prefix", async () => {
+        // Insert a node with a document sourceRef
+        await pool.query(`INSERT INTO nodes (id, type, layer, properties, metadata, confidence, freshness, source_system, source_reference, project_id)
+       VALUES (gen_random_uuid(), 'Decision', 'permanent', '{"title": "Use PostgreSQL ADR", "description": "ADR-003: Use PostgreSQL for graph storage"}', '{}', 0.9, 1.0, 'markdown', 'doc:docs/adr/003-use-postgresql.md', $1)`, [testProjectId]);
+        // Verify sourceRef dedup would match
+        const result = await pool.query(`SELECT * FROM nodes WHERE source_reference = $1 AND project_id = $2`, ["doc:docs/adr/003-use-postgresql.md", testProjectId]);
+        expect(result.rows.length).toBe(1);
+        expect(result.rows[0].properties.title).toBe("Use PostgreSQL ADR");
+        expect(result.rows[0].source_system).toBe("markdown");
+    });
+    it("document nodes are searchable alongside git nodes", async () => {
+        const result = await pool.query(`SELECT * FROM nodes WHERE project_id = $1 AND properties::text ILIKE '%PostgreSQL%'`, [testProjectId]);
+        expect(result.rows.length).toBeGreaterThanOrEqual(1);
+    });
+});
+describe("Export/Import Round-Trip", () => {
+    it("export and import preserves data", async () => {
+        // Count nodes in the test project
+        const countBefore = await pool.query(`SELECT count(*) as cnt FROM nodes WHERE project_id = $1 AND superseded_by IS NULL`, [testProjectId]);
+        const originalCount = parseInt(countBefore.rows[0].cnt, 10);
+        expect(originalCount).toBeGreaterThan(0);
+        // Export nodes
+        const exported = await pool.query(`SELECT * FROM nodes WHERE project_id = $1 AND superseded_by IS NULL`, [testProjectId]);
+        const rows = exported.rows;
+        // Delete all nodes from the test project
+        await pool.query("DELETE FROM nodes WHERE project_id = $1", [
+            testProjectId,
+        ]);
+        // Verify deletion
+        const countAfterDelete = await pool.query(`SELECT count(*) as cnt FROM nodes WHERE project_id = $1`, [testProjectId]);
+        expect(parseInt(countAfterDelete.rows[0].cnt, 10)).toBe(0);
+        // Re-insert exported nodes
+        for (const row of rows) {
+            await pool.query(`INSERT INTO nodes (id, type, layer, properties, metadata, confidence, freshness, source_system, source_reference, project_id)
+         VALUES ($1, $2, $3, $4, $5, $6, $7, $8, $9, $10)`, [
+                row.id,
+                row.type,
+                row.layer,
+                row.properties,
+                row.metadata,
+                row.confidence,
+                row.freshness,
+                row.source_system,
+                row.source_reference,
+                row.project_id,
+            ]);
+        }
+        // Count again
+        const countAfterImport = await pool.query(`SELECT count(*) as cnt FROM nodes WHERE project_id = $1 AND superseded_by IS NULL`, [testProjectId]);
+        expect(parseInt(countAfterImport.rows[0].cnt, 10)).toBe(originalCount);
+        // Verify specific property is preserved
+        const verify = await pool.query(`SELECT properties FROM nodes WHERE project_id = $1 AND properties::text ILIKE '%Test Auth Decision%'`, [testProjectId]);
+        expect(verify.rows.length).toBe(1);
+        expect(verify.rows[0].properties.title).toBe("Test Auth Decision");
+    });
+});
+//# sourceMappingURL=integration.test.js.map

package/dist/__tests__/integration.test.js.map

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package/dist/commands/add.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"add.d.ts","sourceRoot":"","sources":["../../src/commands/add.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAuMpC,eAAO,MAAM,UAAU,SAwBQ,CAAC"}
+{"version":3,"file":"add.d.ts","sourceRoot":"","sources":["../../src/commands/add.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAwMpC,eAAO,MAAM,UAAU,SAwBQ,CAAC"}

package/dist/commands/add.js

@@ -1,7 +1,7 @@
 // codify add — record context into the graph from the terminal
 import { Command } from "commander";
 import { randomUUID } from "node:crypto";
-import { loadProjectConfig } from "../lib/config.js";
+import { loadProjectConfig, getProjectId } from "../lib/config.js";
 // --- Color helpers (ANSI escape codes) ---
 const RESET = "\x1b[0m";
 const BOLD = "\x1b[1m";
@@ -43,6 +43,7 @@ async function insertNode(typeDef, title, opts) {
             console.error("  ERROR: Cannot connect to PostgreSQL. Run 'codify init' first.\n");
             process.exit(1);
         }
+        const projectId = getProjectId();
         const nodeId = randomUUID();
         const tags = opts.tags ? opts.tags.split(",").map((t) => t.trim()).filter(Boolean) : [];
         const properties = {
@@ -53,8 +54,8 @@ async function insertNode(typeDef, title, opts) {
             properties.description = opts.description;
         }
         // Insert the node
-        await pool.query(`INSERT INTO nodes (id, type, layer, confidence, freshness, source_system, source_reference, source_agent_id, source_reliability, properties, tags)
-       VALUES ($1, $2, 'permanent', 0.8, 1.0, 'cli', 'codify-add', 'user', 0.8, $3, $4)`, [nodeId, typeDef.type, JSON.stringify(properties), tags]);
+        await pool.query(`INSERT INTO nodes (id, type, layer, confidence, freshness, source_system, source_reference, source_agent_id, source_reliability, properties, tags, project_id)
+       VALUES ($1, $2, 'permanent', 0.8, 1.0, 'cli', 'codify-add', 'user', 0.8, $3, $4, $5)`, [nodeId, typeDef.type, JSON.stringify(properties), tags, projectId]);
         // If --link is provided, also create an edge
         if (opts.link) {
             const edgeType = opts.linkType ?? "relates_to";

package/dist/commands/add.js.map

@@ -1 +1 @@
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package/dist/commands/audit.d.ts

@@ -0,0 +1,3 @@
+import { Command } from "commander";
+export declare const auditCommand: Command;
+//# sourceMappingURL=audit.d.ts.map

package/dist/commands/audit.d.ts.map

@@ -0,0 +1 @@
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package/dist/commands/audit.js

@@ -0,0 +1,291 @@
+// codify audit — show metabolism audit trail
+import { Command } from "commander";
+import { loadProjectConfig, getProjectId } from "../lib/config.js";
+// --- ANSI color helpers ---
+const RESET = "\x1b[0m";
+const BOLD = "\x1b[1m";
+const DIM = "\x1b[2m";
+const GREEN = "\x1b[32m";
+const YELLOW = "\x1b[33m";
+const RED = "\x1b[31m";
+const CYAN = "\x1b[36m";
+const MAGENTA = "\x1b[35m";
+// --- Duration parsing ---
+/**
+ * Parse a duration string like "7d", "1h", "24h", "30m" into milliseconds.
+ */
+function parseDuration(input) {
+    const match = input.match(/^(\d+)(d|h|m)$/);
+    if (!match)
+        return null;
+    const value = parseInt(match[1], 10);
+    const unit = match[2];
+    switch (unit) {
+        case "d":
+            return value * 24 * 60 * 60 * 1000;
+        case "h":
+            return value * 60 * 60 * 1000;
+        case "m":
+            return value * 60 * 1000;
+        default:
+            return null;
+    }
+}
+/**
+ * Resolve a cutoff date from the --since flag.
+ * Default: 24 hours ago.
+ */
+function resolveCutoff(since) {
+    const ms = parseDuration(since);
+    if (ms === null) {
+        console.error(`\n  ERROR: Invalid duration "${since}". Use formats like 24h, 7d, 30m.\n`);
+        process.exit(1);
+    }
+    return new Date(Date.now() - ms);
+}
+/**
+ * Map an action to its display color.
+ */
+function actionColor(action) {
+    switch (action) {
+        case "promoted":
+            return GREEN;
+        case "decayed":
+            return YELLOW;
+        case "pruned":
+            return RED;
+        case "gate_rejected":
+            return RED;
+        case "merged":
+            return CYAN;
+        case "evolved":
+            return MAGENTA;
+        default:
+            return DIM;
+    }
+}
+/**
+ * Map an action to an icon prefix.
+ */
+function actionIcon(action) {
+    switch (action) {
+        case "promoted":
+            return "+";
+        case "decayed":
+            return "~";
+        case "pruned":
+            return "x";
+        case "gate_rejected":
+            return "!";
+        case "merged":
+            return "=";
+        case "evolved":
+            return "^";
+        default:
+            return "*";
+    }
+}
+/**
+ * Format a timestamp for display (HH:MM:SS).
+ */
+function formatTime(date) {
+    return date.toLocaleTimeString("en-US", {
+        hour12: false,
+        hour: "2-digit",
+        minute: "2-digit",
+        second: "2-digit",
+    });
+}
+/**
+ * Truncate a string, adding "..." if needed.
+ */
+function truncate(str, maxLen) {
+    if (str.length <= maxLen)
+        return str;
+    return str.slice(0, maxLen - 3) + "...";
+}
+// --- Command definition ---
+export const auditCommand = new Command("audit")
+    .description("Show metabolism audit trail — what the graph auto-maintained")
+    .option("--action <type>", "Filter by action type (e.g. promoted, decayed, pruned, gate_rejected)")
+    .option("--since <duration>", "Time range (e.g. 7d, 1h, 24h, 30m)", "24h")
+    .option("--limit <n>", "Maximum events to show", "100")
+    .option("--json", "Output structured JSON")
+    .action(async (opts) => {
+    try {
+        await loadProjectConfig();
+        const { getPool, closePool } = await import("@codify/graph");
+        const pool = getPool();
+        try {
+            await pool.query("SELECT 1");
+        }
+        catch {
+            console.error("  ERROR: Cannot connect to PostgreSQL. Run 'codify init' first.\n");
+            process.exit(1);
+        }
+        const projectId = getProjectId();
+        const cutoff = resolveCutoff(opts.since);
+        const limit = parseInt(opts.limit, 10);
+        if (isNaN(limit) || limit < 1) {
+            console.error("\n  ERROR: --limit must be a positive integer.\n");
+            process.exit(1);
+        }
+        // --- Build query ---
+        const conditions = ["ma.created_at >= $1"];
+        const params = [cutoff.toISOString()];
+        let paramIdx = 2;
+        if (opts.action) {
+            conditions.push(`ma.action = $${paramIdx++}`);
+            params.push(opts.action);
+        }
+        // Scope to project: only include audit events whose node_ids overlap
+        // with nodes belonging to this project. Events with empty node_ids
+        // (system-level) are also included.
+        conditions.push(`(ma.node_ids = '{}' OR EXISTS (
+          SELECT 1 FROM nodes n
+          WHERE n.id = ANY(ma.node_ids::uuid[]) AND n.project_id = $${paramIdx++}
+        ))`);
+        params.push(projectId);
+        // Check if the table exists first
+        try {
+            await pool.query("SELECT 1 FROM information_schema.tables WHERE table_name = 'metabolism_audit' LIMIT 1");
+        }
+        catch {
+            // table doesn't exist at all — show empty state
+            printEmptyState(opts.since);
+            await closePool();
+            return;
+        }
+        const tableCheck = await pool.query("SELECT EXISTS (SELECT 1 FROM information_schema.tables WHERE table_name = 'metabolism_audit') as exists");
+        if (!tableCheck.rows[0].exists) {
+            printEmptyState(opts.since);
+            await closePool();
+            return;
+        }
+        const result = await pool.query(`SELECT ma.id, ma.event_type, ma.node_ids, ma.action, ma.reason,
+                ma.metadata, ma.created_at
+         FROM metabolism_audit ma
+         WHERE ${conditions.join(" AND ")}
+         ORDER BY ma.created_at DESC
+         LIMIT $${paramIdx}`, [...params, limit]);
+        if (result.rows.length === 0) {
+            printEmptyState(opts.since);
+            await closePool();
+            return;
+        }
+        // --- Resolve node titles ---
+        // Collect all unique node_ids across all events
+        const allNodeIds = new Set();
+        for (const row of result.rows) {
+            for (const nid of row.node_ids) {
+                allNodeIds.add(nid);
+            }
+        }
+        // Batch-fetch node titles
+        const titleMap = new Map();
+        if (allNodeIds.size > 0) {
+            const nodeIdsArray = [...allNodeIds];
+            const titleResult = await pool.query(`SELECT id, properties, metadata FROM nodes
+           WHERE id = ANY($1::uuid[])`, [nodeIdsArray]);
+            for (const row of titleResult.rows) {
+                const props = row.properties ?? {};
+                const meta = row.metadata ?? {};
+                const title = props.title ??
+                    meta.title ??
+                    props.name ??
+                    meta.name ??
+                    null;
+                if (title) {
+                    titleMap.set(row.id, title);
+                }
+            }
+        }
+        // Build enriched events
+        const events = result.rows.map((row) => {
+            const nodeTitles = new Map();
+            for (const nid of row.node_ids) {
+                nodeTitles.set(nid, titleMap.get(nid) ?? nid.slice(0, 8));
+            }
+            return { ...row, node_titles: nodeTitles };
+        });
+        // --- JSON output ---
+        if (opts.json) {
+            const jsonEvents = events.map((ev) => ({
+                id: ev.id,
+                event_type: ev.event_type,
+                action: ev.action,
+                reason: ev.reason,
+                node_ids: ev.node_ids,
+                node_titles: Object.fromEntries(ev.node_titles),
+                metadata: ev.metadata,
+                created_at: ev.created_at,
+            }));
+            console.log(JSON.stringify({
+                since: opts.since,
+                cutoff: cutoff.toISOString(),
+                count: events.length,
+                events: jsonEvents,
+            }, null, 2));
+            await closePool();
+            return;
+        }
+        // --- Pretty output: group by action ---
+        const actionGroups = new Map();
+        for (const ev of events) {
+            const existing = actionGroups.get(ev.action);
+            if (existing) {
+                existing.push(ev);
+            }
+            else {
+                actionGroups.set(ev.action, [ev]);
+            }
+        }
+        // Sort action groups by count descending
+        const sortedActions = [...actionGroups.entries()].sort((a, b) => b[1].length - a[1].length);
+        console.log(`\n  ${BOLD}Codify — Metabolism Audit (last ${opts.since})${RESET}\n`);
+        // Summary line
+        const summaryParts = [];
+        for (const [action, group] of sortedActions) {
+            const color = actionColor(action);
+            summaryParts.push(`${color}${group.length} ${action}${RESET}`);
+        }
+        console.log(`  ${events.length} events: ${summaryParts.join(", ")}\n`);
+        // Display each group
+        for (const [action, group] of sortedActions) {
+            const color = actionColor(action);
+            const icon = actionIcon(action);
+            console.log(`  ${color}${BOLD}${action.toUpperCase()}${RESET} ${DIM}(${group.length})${RESET}`);
+            for (const ev of group) {
+                const created = new Date(ev.created_at);
+                const timeStr = formatTime(created);
+                const dateStr = created.toISOString().slice(0, 10);
+                // Build node label
+                const nodeLabels = [...ev.node_titles.values()]
+                    .map((t) => truncate(t, 50))
+                    .join(", ");
+                const reasonStr = ev.reason ? ` -- ${truncate(ev.reason, 60)}` : "";
+                console.log(`    ${color}${icon}${RESET} ${DIM}${dateStr} ${timeStr}${RESET}  ${nodeLabels || DIM + "(no nodes)" + RESET}${DIM}${reasonStr}${RESET}`);
+            }
+            console.log("");
+        }
+        // Footer
+        console.log(`  ${DIM}Flags: --action <type>  --since <duration>  --limit <n>  --json${RESET}`);
+        console.log("");
+        await closePool();
+    }
+    catch (err) {
+        const message = err instanceof Error ? err.message : String(err);
+        if (message.includes("ECONNREFUSED")) {
+            console.error("\n  ERROR: Cannot connect to Codify services.");
+            console.error("  Run 'codify init' to start the infrastructure.\n");
+        }
+        else {
+            console.error(`\n  ERROR: ${message}\n`);
+        }
+        process.exit(1);
+    }
+});
+function printEmptyState(since) {
+    console.log(`\n  No metabolism events in the last ${since}. The graph maintains itself automatically when \`codify start\` is running.\n`);
+}
+//# sourceMappingURL=audit.js.map

package/dist/commands/audit.js.map

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package/dist/commands/bootstrap.d.ts.map

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