@atoms-tech/atoms-mcp 0.1.0

package/dist/server.js

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+/**
+ * ATOMS MCP Server — Tool registration and initialization.
+ *
+ * Registers all 10 tools with the MCP SDK using server.registerTool().
+ * Tools are implemented in separate files under src/tools/.
+ *
+ * Naming: atoms_{action}_{resource} (snake_case with service prefix)
+ * Server name: atoms-mcp-server (follows {service}-mcp-server convention)
+ */
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import { z } from "zod";
+import { logAudit, startTimer } from "./middleware/audit.js";
+import { checkRateLimit } from "./middleware/rate-limiter.js";
+import { getClient, getUserId } from "./db/client.js";
+import { formatErrorResult, rateLimitError } from "./tools/_base.js";
+import { randomUUID } from "crypto";
+export const server = new McpServer({
+    name: "atoms-mcp-server",
+    version: "0.1.0",
+});
+// Session ID for grouping tool calls in audit log
+const SESSION_ID = randomUUID();
+const CLIENT_NAME = process.env.ATOMS_CLIENT_NAME ?? "unknown";
+/**
+ * Wrap a tool handler with rate limiting + audit logging.
+ * This is the middleware pipeline for every tool call.
+ */
+function withMiddleware(toolName, handler) {
+    return async (params) => {
+        // Rate limit check
+        let userId;
+        try {
+            await getClient(); // ensure auth
+            userId = getUserId();
+        }
+        catch {
+            // Auth will fail inside the handler with proper error
+            return handler(params);
+        }
+        const rateCheck = checkRateLimit(userId);
+        if (!rateCheck.allowed) {
+            return formatErrorResult(rateLimitError(rateCheck.retryAfterSeconds));
+        }
+        // Execute with timing
+        const elapsed = startTimer();
+        let status = "success";
+        let errorMsg;
+        try {
+            const result = await handler(params);
+            // Detect error responses
+            const resultObj = result;
+            if (resultObj?.isError === true) {
+                status = "error";
+                const content = resultObj?.content;
+                if (content?.[0]?.text) {
+                    try {
+                        const parsed = JSON.parse(content[0].text);
+                        errorMsg = parsed.message;
+                    }
+                    catch { /* not JSON */ }
+                }
+            }
+            return result;
+        }
+        catch (err) {
+            status = "error";
+            errorMsg = err instanceof Error ? err.message : String(err);
+            throw err;
+        }
+        finally {
+            // Fire-and-forget audit log
+            const entry = {
+                tool_name: toolName,
+                params: params,
+                status,
+                duration_ms: elapsed(),
+                error_msg: errorMsg,
+                project_id: params.project_id,
+                session_id: SESSION_ID,
+                client_name: CLIENT_NAME,
+            };
+            try {
+                const client = await getClient();
+                logAudit(client, userId, entry);
+            }
+            catch { /* non-fatal */ }
+        }
+    };
+}
+/** Expose session ID for change_history writes */
+export function getMcpSessionId() {
+    return SESSION_ID;
+}
+// ---------------------------------------------------------------------------
+// Tool Registration — Entry Point
+// ---------------------------------------------------------------------------
+server.registerTool("atoms_list_projects", {
+    title: "List ATOMS Projects",
+    description: `List all projects the authenticated user has access to.
+
+This is the ENTRY POINT tool. Call this first to discover project IDs,
+then use those IDs with all other tools.
+
+Args: None
+
+Returns:
+  { status: "success", data: [{ id, name, description, org_id, created_at }] }
+
+Examples:
+  - "What projects do I have?" → atoms_list_projects()
+  - "Show my projects" → atoms_list_projects()
+
+Workflow:
+  atoms_list_projects → atoms_list_items(project_id) → atoms_get_item(project_id, item_id)`,
+    inputSchema: {},
+    annotations: {
+        readOnlyHint: true,
+        destructiveHint: false,
+        idempotentHint: true,
+        openWorldHint: false,
+    },
+}, withMiddleware("atoms_list_projects", async () => {
+    const { listProjectsHandler } = await import("./tools/list-projects.js");
+    return listProjectsHandler();
+}));
+// ---------------------------------------------------------------------------
+// Tool Registration — Phase 2 (Read Tools)
+// ---------------------------------------------------------------------------
+server.registerTool("atoms_list_items", {
+    title: "List ATOMS Items",
+    description: `List items in an ATOMS project with optional type/domain/level filters.
+
+This is the primary ENTRY POINT for discovering items. Use it to browse
+project contents before drilling into specific items with atoms_get_item.
+
+Args:
+  - project_id (string, UUID): The project to list items from
+  - type (string, optional): Filter: requirement|test-case|note|table
+  - domain (string, optional): Filter by domain tag
+  - level (string, optional): Filter by level (System, Subsystem, Component)
+  - limit (number, optional): Max results, 1-200 (default 50)
+  - offset (number, optional): Pagination offset (default 0)
+
+Returns:
+  { status: "success", data: [{ id, title, type, status, domains, level }], meta: { total_count, limit, offset, has_more } }
+
+Examples:
+  - "Show me all requirements" → atoms_list_items(project_id, type="requirement")
+  - "What test cases exist?" → atoms_list_items(project_id, type="test-case")
+
+Errors:
+  - "Project not found" → verify project_id
+  - "Access denied" → check org membership`,
+    inputSchema: {
+        project_id: z.string().uuid("Must be a valid project UUID")
+            .describe("UUID of the project"),
+        type: z.enum(["requirement", "test-case", "note", "table"]).optional()
+            .describe("Filter by item type"),
+        domain: z.string().optional()
+            .describe("Filter by domain tag (e.g., 'Safety', 'Performance')"),
+        level: z.string().optional()
+            .describe("Filter by level (System, Subsystem, Component)"),
+        limit: z.number().int().min(1).max(200).default(50)
+            .describe("Max results (default 50, max 200)"),
+        offset: z.number().int().min(0).default(0)
+            .describe("Pagination offset (default 0)"),
+    },
+    annotations: {
+        readOnlyHint: true,
+        destructiveHint: false,
+        idempotentHint: true,
+        openWorldHint: false,
+    },
+}, withMiddleware("atoms_list_items", async (params) => {
+    const { listItemsHandler } = await import("./tools/list-items.js");
+    return listItemsHandler(params);
+}));
+server.registerTool("atoms_get_item", {
+    title: "Get ATOMS Item Details",
+    description: `Get full details of a single item including relationships, test history, and ownership.
+
+Use after atoms_list_items or atoms_search to drill into a specific item.
+
+Args:
+  - project_id (string, UUID): The project containing the item
+  - item_id (string): Item ID (e.g., "REQ-00001", "TC-00050")
+
+Returns:
+  Full WorkItem with relationships, test runs, ownership, metadata.
+
+Examples:
+  - "Show me requirement REQ-00001" → atoms_get_item(project_id, "REQ-00001")
+  - "Get test case details" → atoms_get_item(project_id, "TC-00050")`,
+    inputSchema: {
+        project_id: z.string().uuid().describe("UUID of the project"),
+        item_id: z.string().min(1).max(20).describe("Item ID (e.g., REQ-00001)"),
+    },
+    annotations: {
+        readOnlyHint: true,
+        destructiveHint: false,
+        idempotentHint: true,
+        openWorldHint: false,
+    },
+}, withMiddleware("atoms_get_item", async (params) => {
+    const { getItemHandler } = await import("./tools/get-item.js");
+    return getItemHandler(params);
+}));
+server.registerTool("atoms_search", {
+    title: "Search ATOMS Items",
+    description: `Full-text search across items in a project. Searches title, body, and summary.
+
+Alternative entry point to atoms_list_items when you know what you're looking for.
+
+Args:
+  - project_id (string, UUID): The project to search in
+  - query (string): Search text (max 1000 chars)
+  - type (string, optional): Filter by type
+  - limit (number, optional): Max results, 1-100 (default 25)
+
+Returns:
+  Matching items with @basic fields, ranked by relevance.
+
+Examples:
+  - "Find braking requirements" → atoms_search(project_id, "braking system")
+  - "Search for safety tests" → atoms_search(project_id, "safety", type="test-case")`,
+    inputSchema: {
+        project_id: z.string().uuid().describe("UUID of the project"),
+        query: z.string().min(1).max(1000).describe("Search text"),
+        type: z.enum(["requirement", "test-case", "note", "table"]).optional()
+            .describe("Filter by item type"),
+        limit: z.number().int().min(1).max(100).default(25)
+            .describe("Max results (default 25, max 100)"),
+    },
+    annotations: {
+        readOnlyHint: true,
+        destructiveHint: false,
+        idempotentHint: true,
+        openWorldHint: false,
+    },
+}, withMiddleware("atoms_search", async (params) => {
+    const { searchHandler } = await import("./tools/search.js");
+    return searchHandler(params);
+}));
+server.registerTool("atoms_get_coverage", {
+    title: "Get Test Coverage Report",
+    description: `Find requirements without linked test cases (coverage gaps).
+
+Essential for compliance reporting in safety-critical industries.
+
+Args:
+  - project_id (string, UUID): The project to analyze
+  - domain (string, optional): Filter by domain
+  - level (string, optional): Filter by level
+
+Returns:
+  { covered, uncovered, total, coverage_percent, uncovered_items: [...] }
+
+Examples:
+  - "What's our test coverage?" → atoms_get_coverage(project_id)
+  - "Safety coverage gaps?" → atoms_get_coverage(project_id, domain="Safety")`,
+    inputSchema: {
+        project_id: z.string().uuid().describe("UUID of the project"),
+        domain: z.string().optional().describe("Filter by domain tag"),
+        level: z.string().optional().describe("Filter by level"),
+    },
+    annotations: {
+        readOnlyHint: true,
+        destructiveHint: false,
+        idempotentHint: true,
+        openWorldHint: false,
+    },
+}, withMiddleware("atoms_get_coverage", async (params) => {
+    const { getCoverageHandler } = await import("./tools/get-coverage.js");
+    return getCoverageHandler(params);
+}));
+server.registerTool("atoms_get_history", {
+    title: "Get Item Change History",
+    description: `Audit trail for an item — who changed what, when, and whether it was human or AI.
+
+Shows actor attribution (user vs mcp_claude) and session grouping.
+
+Args:
+  - project_id (string, UUID): The project containing the item
+  - item_id (string): Item ID
+  - limit (number, optional): Max entries (default 20, max 100)
+
+Returns:
+  Change entries with actor, session_id, event_type, changed_at, fields_changed.`,
+    inputSchema: {
+        project_id: z.string().uuid().describe("UUID of the project"),
+        item_id: z.string().min(1).max(20).describe("Item ID"),
+        limit: z.number().int().min(1).max(100).default(20)
+            .describe("Max entries (default 20)"),
+    },
+    annotations: {
+        readOnlyHint: true,
+        destructiveHint: false,
+        idempotentHint: true,
+        openWorldHint: false,
+    },
+}, withMiddleware("atoms_get_history", async (params) => {
+    const { getHistoryHandler } = await import("./tools/get-history.js");
+    return getHistoryHandler(params);
+}));
+server.registerTool("atoms_export_mermaid", {
+    title: "Export Mermaid Diagram",
+    description: `Generate a Mermaid diagram of the requirement/test hierarchy.
+
+Output is paste-ready for markdown docs. Shows parent-child relationships
+and requirement-to-test-case verification links.
+
+Args:
+  - project_id (string, UUID): The project to visualize
+  - root_item_id (string, optional): Start node (default: all roots)
+  - depth (number, optional): Max depth (default 3, max 10)
+  - include_tests (boolean, optional): Show test case links (default true)
+
+Returns:
+  Mermaid graph string.`,
+    inputSchema: {
+        project_id: z.string().uuid().describe("UUID of the project"),
+        root_item_id: z.string().optional().describe("Root item ID to start from"),
+        depth: z.number().int().min(1).max(10).default(3).describe("Max depth"),
+        include_tests: z.boolean().default(true).describe("Include test case links"),
+    },
+    annotations: {
+        readOnlyHint: true,
+        destructiveHint: false,
+        idempotentHint: true,
+        openWorldHint: false,
+    },
+}, withMiddleware("atoms_export_mermaid", async (params) => {
+    const { exportMermaidHandler } = await import("./tools/export-mermaid.js");
+    return exportMermaidHandler(params);
+}));
+// ---------------------------------------------------------------------------
+// Tool Registration — Phase 3 (Write Tools)
+// ---------------------------------------------------------------------------
+server.registerTool("atoms_create_item", {
+    title: "Create ATOMS Item",
+    description: `Create a new requirement, test case, or note in a project.
+
+Requires editor or admin role. Changes are logged with AI actor attribution.
+
+Args:
+  - project_id (string, UUID): Target project
+  - type (string): requirement|test-case|note
+  - title (string): Item title (max 500 chars)
+  - body (string, optional): Rich text body
+  - summary (string, optional): Brief summary
+  - domains (string[], optional): Domain tags
+  - level (string, optional): System|Subsystem|Component
+  - parent_ids (string[], optional): Parent item IDs to link
+
+Returns:
+  Created item with generated ID (e.g., "REQ-00058")
+
+Side effects:
+  - Logs to change_history with actor='mcp_claude'
+  - Creates relationships if parent_ids provided`,
+    inputSchema: {
+        project_id: z.string().uuid().describe("UUID of the target project"),
+        type: z.enum(["requirement", "test-case", "note"]).describe("Item type"),
+        title: z.string().min(1).max(500).describe("Item title"),
+        body: z.string().optional().describe("Rich text body"),
+        summary: z.string().optional().describe("Brief summary"),
+        domains: z.array(z.string()).optional().describe("Domain tags"),
+        level: z.string().optional().describe("System|Subsystem|Component"),
+        parent_ids: z.array(z.string()).optional().describe("Parent item IDs to link"),
+    },
+    annotations: {
+        readOnlyHint: false,
+        destructiveHint: false,
+        idempotentHint: false,
+        openWorldHint: false,
+    },
+}, withMiddleware("atoms_create_item", async (params) => {
+    const { createItemHandler } = await import("./tools/create-item.js");
+    return createItemHandler(params);
+}));
+server.registerTool("atoms_update_item", {
+    title: "Update ATOMS Item",
+    description: `Update an existing item's fields. Only provided fields are changed.
+
+Requires editor or admin role. Logs old/new data diff to change history.
+
+Args:
+  - project_id (string, UUID): Project containing the item
+  - item_id (string): Item to update
+  - title, body, summary, domains, level, status: Fields to update (all optional)
+
+Returns:
+  Updated item.`,
+    inputSchema: {
+        project_id: z.string().uuid().describe("UUID of the project"),
+        item_id: z.string().min(1).max(20).describe("Item ID to update"),
+        title: z.string().min(1).max(500).optional().describe("New title"),
+        body: z.string().optional().describe("New body"),
+        summary: z.string().optional().describe("New summary"),
+        domains: z.array(z.string()).optional().describe("New domain tags"),
+        level: z.string().optional().describe("New level"),
+        status: z.enum(["passed", "failed", "blocked", "not-run"]).optional()
+            .describe("Test case status"),
+    },
+    annotations: {
+        readOnlyHint: false,
+        destructiveHint: false,
+        idempotentHint: true,
+        openWorldHint: false,
+    },
+}, withMiddleware("atoms_update_item", async (params) => {
+    const { updateItemHandler } = await import("./tools/update-item.js");
+    return updateItemHandler(params);
+}));
+server.registerTool("atoms_delete_item", {
+    title: "Delete ATOMS Item",
+    description: `Soft-delete an item (sets deleted_at, preserves for audit trail).
+
+Requires editor or admin role. The item is never truly removed.
+
+Args:
+  - project_id (string, UUID): Project containing the item
+  - item_id (string): Item to delete
+
+Returns:
+  Confirmation with deleted item summary.`,
+    inputSchema: {
+        project_id: z.string().uuid().describe("UUID of the project"),
+        item_id: z.string().min(1).max(20).describe("Item ID to soft-delete"),
+    },
+    annotations: {
+        readOnlyHint: false,
+        destructiveHint: true,
+        idempotentHint: true,
+        openWorldHint: false,
+    },
+}, withMiddleware("atoms_delete_item", async (params) => {
+    const { deleteItemHandler } = await import("./tools/delete-item.js");
+    return deleteItemHandler(params);
+}));
+server.registerTool("atoms_link_items", {
+    title: "Link ATOMS Items",
+    description: `Add or remove relationships between items.
+
+Supports: parent, child, related, verifies, verified_by.
+Updates both items' JSONB data and the shadow table.
+
+Args:
+  - project_id (string, UUID): Project containing both items
+  - from_id (string): Source item
+  - to_id (string): Target item
+  - type (string): parent|child|related|verifies|verified_by
+  - action (string): add|remove
+
+Returns:
+  Updated relationship state for both items.`,
+    inputSchema: {
+        project_id: z.string().uuid().describe("UUID of the project"),
+        from_id: z.string().min(1).max(20).describe("Source item ID"),
+        to_id: z.string().min(1).max(20).describe("Target item ID"),
+        type: z.enum(["parent", "child", "related", "verifies", "verified_by"])
+            .describe("Relationship type"),
+        action: z.enum(["add", "remove"]).describe("Add or remove the relationship"),
+    },
+    annotations: {
+        readOnlyHint: false,
+        destructiveHint: false,
+        idempotentHint: true,
+        openWorldHint: false,
+    },
+}, withMiddleware("atoms_link_items", async (params) => {
+    const { linkItemsHandler } = await import("./tools/link-items.js");
+    return linkItemsHandler(params);
+}));
+server.registerTool("atoms_record_test_result", {
+    title: "Record Test Result",
+    description: `Record a pass/fail/blocked result for a test case.
+
+Appends to the test results history. Use atoms_get_item to see all results.
+
+Args:
+  - project_id (string, UUID): Project containing the test case
+  - item_id (string): Test case ID (e.g., "TC-00001")
+  - result (string): passed|failed|blocked|not-run
+  - note (string, optional): Reason or comment for this result
+
+Returns:
+  Recorded result with timestamp.
+
+Side effects:
+  - Appends to test_results table
+  - Logs to change_history with actor='mcp_claude'`,
+    inputSchema: {
+        project_id: z.string().uuid().describe("UUID of the project"),
+        item_id: z.string().min(1).max(20).describe("Test case ID (e.g., TC-00001)"),
+        result: z.enum(["passed", "failed", "blocked", "not-run"])
+            .describe("Test result"),
+        note: z.string().max(1000).optional()
+            .describe("Reason or comment for this result"),
+    },
+    annotations: {
+        readOnlyHint: false,
+        destructiveHint: false,
+        idempotentHint: false,
+        openWorldHint: false,
+    },
+}, withMiddleware("atoms_record_test_result", async (params) => {
+    const { recordTestResultHandler } = await import("./tools/record-test-result.js");
+    return recordTestResultHandler(params);
+}));
+//# sourceMappingURL=server.js.map

package/dist/server.js.map

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package/dist/tools/_base.d.ts

@@ -0,0 +1,58 @@
+/**
+ * Shared error handling and response formatting for all MCP tools.
+ *
+ * Every error MUST include `next_steps` — actionable guidance for the LLM.
+ * This is the #1 pattern from the Polarion MCP that improves agent reliability.
+ */
+import type { ToolError, ToolSuccess, PaginationMeta } from "../types/responses.js";
+/** Maximum response size in characters. Truncate with clear message if exceeded. */
+export declare const CHARACTER_LIMIT = 25000;
+export declare function success<T>(data: T, meta?: PaginationMeta): ToolSuccess<T>;
+export declare function paginationMeta(totalCount: number, limit: number, offset: number): PaginationMeta;
+export declare function errorResponse(message: string, nextSteps: string[]): ToolError;
+export declare function notFoundError(resource: string, id: string): ToolError;
+export declare function accessDeniedError(role: string): ToolError;
+export declare function validationError(message: string): ToolError;
+export declare function authError(): ToolError;
+export declare function rateLimitError(retryAfterSeconds: number): ToolError;
+export declare function dbError(message: string): ToolError;
+/**
+ * Format a tool result as JSON string + structuredContent for the MCP SDK.
+ * Applies CHARACTER_LIMIT truncation if needed.
+ */
+export declare function formatToolResult<T>(result: ToolSuccess<T> | ToolError): {
+    content: {
+        type: "text";
+        text: string;
+    }[];
+    structuredContent: {
+        data: any[];
+        meta: {
+            truncated: boolean;
+            truncation_message: string;
+            total_count?: number | undefined;
+            limit?: number | undefined;
+            offset?: number | undefined;
+            has_more?: boolean | undefined;
+        };
+        status: "success";
+    };
+} | {
+    content: {
+        type: "text";
+        text: string;
+    }[];
+    structuredContent: ToolError | ToolSuccess<T>;
+};
+/**
+ * Format an error result for the MCP SDK.
+ */
+export declare function formatErrorResult(error: ToolError): {
+    content: {
+        type: "text";
+        text: string;
+    }[];
+    structuredContent: ToolError;
+    isError: boolean;
+};
+//# sourceMappingURL=_base.d.ts.map

package/dist/tools/_base.d.ts.map

@@ -0,0 +1 @@
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