@atoms-tech/atoms-mcp 0.1.0

package/dist/tools/_base.js

@@ -0,0 +1,109 @@
+/**
+ * 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.
+ */
+/** Maximum response size in characters. Truncate with clear message if exceeded. */
+export const CHARACTER_LIMIT = 25_000;
+// ---------------------------------------------------------------------------
+// Success helpers
+// ---------------------------------------------------------------------------
+export function success(data, meta) {
+    return { status: "success", data, ...(meta ? { meta } : {}) };
+}
+export function paginationMeta(totalCount, limit, offset) {
+    return {
+        total_count: totalCount,
+        limit,
+        offset,
+        has_more: offset + limit < totalCount,
+    };
+}
+// ---------------------------------------------------------------------------
+// Error helpers
+// ---------------------------------------------------------------------------
+export function errorResponse(message, nextSteps) {
+    return { status: "error", message, next_steps: nextSteps };
+}
+export function notFoundError(resource, id) {
+    return errorResponse(`${resource} '${id}' not found`, [
+        `Verify the ${resource.toLowerCase()} ID is correct`,
+        `Use atoms_list_items or atoms_search to find valid IDs`,
+    ]);
+}
+export function accessDeniedError(role) {
+    return errorResponse(`${role} role cannot modify project data`, [
+        "Contact your org admin to upgrade your role to editor",
+        "Use read-only tools (atoms_list_items, atoms_get_item, atoms_search) instead",
+    ]);
+}
+export function validationError(message) {
+    return errorResponse(`Validation error: ${message}`, [
+        "Check the parameter types and constraints in the tool description",
+        "Ensure all required parameters are provided",
+    ]);
+}
+export function authError() {
+    return errorResponse("Not authenticated. Run 'npx @atoms-tech/atoms-mcp login' first.", [
+        "Run: npx @atoms-tech/atoms-mcp login",
+        "Or set ATOMS_ACCESS_TOKEN environment variable",
+    ]);
+}
+export function rateLimitError(retryAfterSeconds) {
+    return errorResponse("Rate limit exceeded", [
+        `Wait ${retryAfterSeconds} seconds before making more requests`,
+        "Reduce the frequency of tool calls",
+    ]);
+}
+export function dbError(message) {
+    return errorResponse(`Database error: ${message}`, [
+        "This may be a temporary issue — try again",
+        "If the error persists, check that the project_id is valid",
+    ]);
+}
+// ---------------------------------------------------------------------------
+// Response formatting
+// ---------------------------------------------------------------------------
+/**
+ * Format a tool result as JSON string + structuredContent for the MCP SDK.
+ * Applies CHARACTER_LIMIT truncation if needed.
+ */
+export function formatToolResult(result) {
+    const json = JSON.stringify(result, null, 2);
+    if (json.length > CHARACTER_LIMIT) {
+        // If it's a success with array data, truncate the data
+        if (result.status === "success" && Array.isArray(result.data)) {
+            const halfLength = Math.max(1, Math.floor(result.data.length / 2));
+            const truncated = {
+                ...result,
+                data: result.data.slice(0, halfLength),
+                meta: {
+                    ...result.meta,
+                    truncated: true,
+                    truncation_message: `Response truncated from ${result.data.length} to ${halfLength} items. ` +
+                        `Use 'offset' parameter or add filters to see more results.`,
+                },
+            };
+            return {
+                content: [{ type: "text", text: JSON.stringify(truncated, null, 2) }],
+                structuredContent: truncated,
+            };
+        }
+    }
+    return {
+        content: [{ type: "text", text: json }],
+        structuredContent: result,
+    };
+}
+/**
+ * Format an error result for the MCP SDK.
+ */
+export function formatErrorResult(error) {
+    return {
+        content: [{ type: "text", text: JSON.stringify(error, null, 2) }],
+        structuredContent: error,
+        isError: true,
+    };
+}
+//# sourceMappingURL=_base.js.map

package/dist/tools/_base.js.map

@@ -0,0 +1 @@
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package/dist/tools/create-item.d.ts

@@ -0,0 +1,43 @@
+/**
+ * atoms_create_item — Create a new requirement, test case, or note.
+ * Requires editor or admin role. Logs with AI actor attribution.
+ */
+export declare function createItemHandler(params: {
+    project_id: string;
+    type: "requirement" | "test-case" | "note";
+    title: string;
+    body?: string;
+    summary?: string;
+    domains?: string[];
+    level?: string;
+    parent_ids?: string[];
+}): Promise<{
+    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: import("../types/responses.js").ToolError | import("../types/responses.js").ToolSuccess<{
+        id: string;
+        type: "requirement" | "test-case" | "note";
+        title: string;
+        project_id: string;
+    }>;
+}>;
+//# sourceMappingURL=create-item.d.ts.map

package/dist/tools/create-item.d.ts.map

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package/dist/tools/create-item.js

@@ -0,0 +1,118 @@
+/**
+ * atoms_create_item — Create a new requirement, test case, or note.
+ * Requires editor or admin role. Logs with AI actor attribution.
+ */
+import { getClient, getUserId, requireWriteAccess } from "../db/client.js";
+import { generateItemId } from "../db/queries.js";
+import { getMcpSessionId } from "../server.js";
+import { formatToolResult, formatErrorResult, success, accessDeniedError, dbError, authError, } from "./_base.js";
+export async function createItemHandler(params) {
+    try {
+        const client = await getClient();
+        const userId = getUserId();
+        // Check write access
+        try {
+            await requireWriteAccess(client, params.project_id);
+        }
+        catch (err) {
+            if (err instanceof Error && err.message === "VIEWER_ROLE") {
+                return formatErrorResult(accessDeniedError("Viewer"));
+            }
+            throw err;
+        }
+        // Generate next ID (uses SECURITY DEFINER function to avoid collisions)
+        const itemId = await generateItemId(client, params.project_id, params.type);
+        // Build WorkItem data blob
+        const workItem = {
+            id: itemId,
+            type: params.type,
+            title: params.title,
+            summary: params.summary,
+            body: params.body,
+            tags: {
+                domains: params.domains ?? [],
+                level: params.level,
+            },
+            ownership: {
+                primary: null,
+                additional: [],
+            },
+            relationships: {
+                parents: params.parent_ids ?? [],
+                children: [],
+                related: [],
+            },
+            links: [],
+            metadata: {
+                created_at: new Date().toISOString(),
+                created_by: userId,
+                updated_at: new Date().toISOString(),
+                updated_by: userId,
+            },
+        };
+        // Insert to items table
+        const { error: insertErr } = await client
+            .from("items")
+            .insert({
+            id: itemId,
+            project_id: params.project_id,
+            type: params.type,
+            title: params.title,
+            data: workItem,
+            created_by: userId,
+            updated_by: userId,
+        })
+            .select()
+            .single();
+        if (insertErr)
+            throw new Error(insertErr.message);
+        // Dual-write: sync relationships to shadow table
+        if (params.parent_ids && params.parent_ids.length > 0) {
+            const relRows = params.parent_ids.map((parentId) => ({
+                from_id: itemId,
+                to_id: parentId,
+                type: "parent",
+                project_id: params.project_id,
+            }));
+            await client
+                .from("item_relationships")
+                .insert(relRows)
+                .then(({ error }) => {
+                if (error) {
+                    process.stderr.write(`[atoms-mcp] Warning: relationship sync failed: ${error.message}\n`);
+                }
+            });
+        }
+        // Audit: log to change_history with MCP actor
+        await client
+            .from("change_history")
+            .insert({
+            item_id: itemId,
+            project_id: params.project_id,
+            changed_by: userId,
+            event_type: "created",
+            old_data: null,
+            new_data: workItem,
+            actor: "mcp_claude",
+            session_id: getMcpSessionId(),
+        })
+            .then(({ error }) => {
+            if (error) {
+                process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${error.message}\n`);
+            }
+        });
+        return formatToolResult(success({
+            id: itemId,
+            type: params.type,
+            title: params.title,
+            project_id: params.project_id,
+        }));
+    }
+    catch (err) {
+        if (err instanceof Error && err.message.includes("Not authenticated")) {
+            return formatErrorResult(authError());
+        }
+        return formatErrorResult(dbError(err instanceof Error ? err.message : String(err)));
+    }
+}
+//# sourceMappingURL=create-item.js.map

package/dist/tools/create-item.js.map

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package/dist/tools/delete-item.d.ts

@@ -0,0 +1,38 @@
+/**
+ * atoms_delete_item — Soft-delete an item (sets deleted_at, preserves for audit).
+ * Requires editor or admin role.
+ */
+export declare function deleteItemHandler(params: {
+    project_id: string;
+    item_id: string;
+}): Promise<{
+    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: import("../types/responses.js").ToolError | import("../types/responses.js").ToolSuccess<{
+        id: string;
+        title: string;
+        type: string;
+        deleted: boolean;
+        message: string;
+    }>;
+}>;
+//# sourceMappingURL=delete-item.d.ts.map

package/dist/tools/delete-item.d.ts.map

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package/dist/tools/delete-item.js

@@ -0,0 +1,69 @@
+/**
+ * atoms_delete_item — Soft-delete an item (sets deleted_at, preserves for audit).
+ * Requires editor or admin role.
+ */
+import { getClient, getUserId, requireWriteAccess } from "../db/client.js";
+import { getItemById } from "../db/queries.js";
+import { getMcpSessionId } from "../server.js";
+import { formatToolResult, formatErrorResult, success, notFoundError, accessDeniedError, dbError, authError, } from "./_base.js";
+export async function deleteItemHandler(params) {
+    try {
+        const client = await getClient();
+        const userId = getUserId();
+        // Check write access
+        try {
+            await requireWriteAccess(client, params.project_id);
+        }
+        catch (err) {
+            if (err instanceof Error && err.message === "VIEWER_ROLE") {
+                return formatErrorResult(accessDeniedError("Viewer"));
+            }
+            throw err;
+        }
+        // Get existing item
+        const existing = await getItemById(client, params.project_id, params.item_id);
+        if (!existing) {
+            return formatErrorResult(notFoundError("Item", params.item_id));
+        }
+        // Soft delete (set deleted_at, never remove the row)
+        const { error: deleteErr } = await client
+            .from("items")
+            .update({ deleted_at: new Date().toISOString() })
+            .eq("id", params.item_id)
+            .eq("project_id", params.project_id);
+        if (deleteErr)
+            throw new Error(deleteErr.message);
+        // Audit: log deletion to change_history
+        await client
+            .from("change_history")
+            .insert({
+            item_id: params.item_id,
+            project_id: params.project_id,
+            changed_by: userId,
+            event_type: "deleted",
+            old_data: existing.data,
+            new_data: null,
+            actor: "mcp_claude",
+            session_id: getMcpSessionId(),
+        })
+            .then(({ error }) => {
+            if (error) {
+                process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${error.message}\n`);
+            }
+        });
+        return formatToolResult(success({
+            id: params.item_id,
+            title: existing.title,
+            type: existing.type,
+            deleted: true,
+            message: `Item ${params.item_id} soft-deleted. It can still be found in audit logs.`,
+        }));
+    }
+    catch (err) {
+        if (err instanceof Error && err.message.includes("Not authenticated")) {
+            return formatErrorResult(authError());
+        }
+        return formatErrorResult(dbError(err instanceof Error ? err.message : String(err)));
+    }
+}
+//# sourceMappingURL=delete-item.js.map

package/dist/tools/delete-item.js.map

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package/dist/tools/export-mermaid.d.ts

@@ -0,0 +1,36 @@
+/**
+ * atoms_export_mermaid — Generate Mermaid diagram of requirement/test hierarchy.
+ * Output is paste-ready for markdown documentation.
+ */
+export declare function exportMermaidHandler(params: {
+    project_id: string;
+    root_item_id?: string;
+    depth: number;
+    include_tests: boolean;
+}): Promise<{
+    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: import("../types/responses.js").ToolError | import("../types/responses.js").ToolSuccess<{
+        mermaid: string;
+    }>;
+}>;
+//# sourceMappingURL=export-mermaid.d.ts.map

package/dist/tools/export-mermaid.d.ts.map

@@ -0,0 +1 @@
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package/dist/tools/export-mermaid.js

@@ -0,0 +1,125 @@
+/**
+ * atoms_export_mermaid — Generate Mermaid diagram of requirement/test hierarchy.
+ * Output is paste-ready for markdown documentation.
+ */
+import { getClient } from "../db/client.js";
+import { formatToolResult, formatErrorResult, success, dbError, authError, } from "./_base.js";
+export async function exportMermaidHandler(params) {
+    try {
+        const client = await getClient();
+        // Get all items in the project
+        const { data: items, error: itemsErr } = await client
+            .from("items")
+            .select("id, title, type, data")
+            .eq("project_id", params.project_id)
+            .is("deleted_at", null);
+        if (itemsErr)
+            throw new Error(itemsErr.message);
+        if (!items || items.length === 0) {
+            return formatToolResult(success({ mermaid: "graph TD\n  empty[No items in project]" }));
+        }
+        // Get all relationships
+        const { data: rels, error: relsErr } = await client
+            .from("item_relationships")
+            .select("from_id, to_id, type")
+            .eq("project_id", params.project_id);
+        if (relsErr)
+            throw new Error(relsErr.message);
+        const itemMap = new Map();
+        for (const item of items) {
+            itemMap.set(item.id, item);
+        }
+        // Build Mermaid graph
+        const lines = ["graph TD"];
+        const visited = new Set();
+        const edges = new Set();
+        // Find root nodes (items with no parents)
+        const childIds = new Set((rels ?? []).filter((r) => r.type === "child").map((r) => r.to_id));
+        const parentIds = new Set((rels ?? []).filter((r) => r.type === "parent").map((r) => r.from_id));
+        let roots;
+        if (params.root_item_id) {
+            roots = [params.root_item_id];
+        }
+        else {
+            // Items that are not children of anything
+            roots = items
+                .filter((item) => !parentIds.has(item.id))
+                .filter((item) => {
+                if (!params.include_tests && item.type === "test-case")
+                    return false;
+                return true;
+            })
+                .map((item) => item.id);
+        }
+        // BFS to build graph up to depth
+        const queue = roots.map((id) => ({
+            id,
+            depth: 0,
+        }));
+        while (queue.length > 0) {
+            const { id, depth } = queue.shift();
+            if (visited.has(id) || depth > params.depth)
+                continue;
+            visited.add(id);
+            const item = itemMap.get(id);
+            if (!item)
+                continue;
+            // Skip test cases if not included
+            if (!params.include_tests && item.type === "test-case")
+                continue;
+            // Add node
+            const label = sanitizeLabel(item.title);
+            const shape = item.type === "requirement"
+                ? `["${label}"]`
+                : item.type === "test-case"
+                    ? `(["${label}"])`
+                    : `("${label}")`;
+            lines.push(`  ${id}${shape}`);
+            // Add edges from relationships
+            for (const rel of rels ?? []) {
+                if (rel.from_id !== id)
+                    continue;
+                const targetItem = itemMap.get(rel.to_id);
+                if (!targetItem)
+                    continue;
+                if (!params.include_tests && targetItem.type === "test-case")
+                    continue;
+                const edgeKey = `${rel.from_id}-${rel.type}-${rel.to_id}`;
+                if (edges.has(edgeKey))
+                    continue;
+                edges.add(edgeKey);
+                if (rel.type === "child") {
+                    lines.push(`  ${id} --> ${rel.to_id}`);
+                }
+                else if (rel.type === "verified_by") {
+                    lines.push(`  ${id} -.->|verified_by| ${rel.to_id}`);
+                }
+                else if (rel.type === "related") {
+                    lines.push(`  ${id} -.- ${rel.to_id}`);
+                }
+                if (!visited.has(rel.to_id) && depth + 1 <= params.depth) {
+                    queue.push({ id: rel.to_id, depth: depth + 1 });
+                }
+            }
+        }
+        const mermaid = lines.join("\n");
+        return formatToolResult(success({
+            mermaid,
+            node_count: visited.size,
+            edge_count: edges.size,
+        }));
+    }
+    catch (err) {
+        if (err instanceof Error && err.message.includes("Not authenticated")) {
+            return formatErrorResult(authError());
+        }
+        return formatErrorResult(dbError(err instanceof Error ? err.message : String(err)));
+    }
+}
+function sanitizeLabel(title) {
+    return title
+        .replace(/"/g, "'")
+        .replace(/[[\]{}()]/g, "")
+        .substring(0, 50);
+}
+//# sourceMappingURL=export-mermaid.js.map

package/dist/tools/export-mermaid.js.map

@@ -0,0 +1 @@
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package/dist/tools/get-coverage.d.ts

@@ -0,0 +1,34 @@
+/**
+ * atoms_get_coverage — Find requirements without linked test cases.
+ * Essential for compliance reporting in safety-critical industries.
+ */
+import type { CoverageReport } from "../types/responses.js";
+export declare function getCoverageHandler(params: {
+    project_id: string;
+    domain?: string;
+    level?: string;
+}): Promise<{
+    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: import("../types/responses.js").ToolError | import("../types/responses.js").ToolSuccess<CoverageReport>;
+}>;
+//# sourceMappingURL=get-coverage.d.ts.map

package/dist/tools/get-coverage.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"get-coverage.d.ts","sourceRoot":"","sources":["../../src/tools/get-coverage.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAWH,OAAO,KAAK,EAAe,cAAc,EAAE,MAAM,uBAAuB,CAAC;AAEzE,wBAAsB,kBAAkB,CAAC,MAAM,EAAE;IAC/C,UAAU,EAAE,MAAM,CAAC;IACnB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;;;;;;;;;;;;;;;;;;;;;;;GAoCA"}

package/dist/tools/get-coverage.js

@@ -0,0 +1,36 @@
+/**
+ * atoms_get_coverage — Find requirements without linked test cases.
+ * Essential for compliance reporting in safety-critical industries.
+ */
+import { getClient } from "../db/client.js";
+import { getCoverageReport } from "../db/queries.js";
+import { formatToolResult, formatErrorResult, success, dbError, authError, } from "./_base.js";
+export async function getCoverageHandler(params) {
+    try {
+        const client = await getClient();
+        const { covered, uncovered, total } = await getCoverageReport(client, params.project_id, { domain: params.domain, level: params.level });
+        const uncoveredItems = uncovered.map((item) => ({
+            id: item.id,
+            title: item.title,
+            type: item.type,
+            status: item.data?.status,
+            domains: item.data?.tags?.domains ?? [],
+            level: item.data?.tags?.level,
+        }));
+        const report = {
+            covered: covered.length,
+            uncovered: uncovered.length,
+            total,
+            coverage_percent: total > 0 ? Math.round((covered.length / total) * 1000) / 10 : 100,
+            uncovered_items: uncoveredItems,
+        };
+        return formatToolResult(success(report));
+    }
+    catch (err) {
+        if (err instanceof Error && err.message.includes("Not authenticated")) {
+            return formatErrorResult(authError());
+        }
+        return formatErrorResult(dbError(err instanceof Error ? err.message : String(err)));
+    }
+}
+//# sourceMappingURL=get-coverage.js.map