import { z } from "zod";
import { GraphQLClient } from "../utils/graphql-client.js";
import { ErrorHandler } from "../utils/error-handling.js";
export interface VariantAssertionsToolConfig {
name: string;
description: string;
annotations: {
destructive: boolean;
idempotent: boolean;
cacheable: boolean;
world_interaction: string;
side_effects: string[];
resource_usage: string;
};
}
export class VariantAssertionsTool {
private graphqlClient: GraphQLClient;
private errorHandler: ErrorHandler;
private config: VariantAssertionsToolConfig;
constructor(graphqlClient: GraphQLClient, config: VariantAssertionsToolConfig) {
this.graphqlClient = graphqlClient;
this.errorHandler = new ErrorHandler(graphqlClient);
this.config = config;
}
getToolDefinition() {
return {
name: this.config.name,
description: this.config.description,
inputSchema: {
molecular_profile_id: z.number().optional().describe("CIViC molecular profile ID (numeric)"),
molecular_profile_name: z.string().optional().describe("CIViC molecular profile name (string)")
},
annotations: this.config.annotations
};
}
async execute(params: { molecular_profile_id?: number; molecular_profile_name?: string }) {
const startTime = Date.now();
try {
if (!params.molecular_profile_id && !params.molecular_profile_name) {
throw new Error("Either molecular_profile_id or molecular_profile_name must be provided");
}
const result = await this.getVariantAssertions(params.molecular_profile_id, params.molecular_profile_name);
const executionTime = Date.now() - startTime;
return {
content: [{
type: "text" as const,
text: JSON.stringify(result, null, 2)
}],
_meta: {
tool_type: "variant_assertions",
execution_time_ms: executionTime,
molecular_profile_id: params.molecular_profile_id,
molecular_profile_name: params.molecular_profile_name,
assertion_count: result.data?.molecularProfiles?.nodes?.[0]?.assertions?.nodes?.length || 0,
timestamp: new Date().toISOString()
}
};
} catch (error) {
const executionTime = Date.now() - startTime;
return this.errorHandler.createErrorResponse("Variant assertions retrieval failed", error, executionTime);
}
}
private async getVariantAssertions(molecularProfileId?: number, molecularProfileName?: string): Promise<any> {
let query: string;
let variables: Record<string, any> = {};
if (molecularProfileId) {
query = `
query GetAssertionsByProfileId($id: Int!) {
molecularProfile(id: $id) {
id
name
assertions {
nodes {
id
name
summary
description
assertionType
assertionDirection
significance
status
ampLevel
evidenceItems {
id
name
description
evidenceLevel
evidenceType
significance
status
}
disease {
id
name
displayName
}
therapies {
id
name
}
molecularProfile {
id
name
}
acmgCodes {
code
description
}
}
}
}
}
`;
variables.id = molecularProfileId;
} else if (molecularProfileName) {
query = `
query GetAssertionsByProfileName($name: String!) {
molecularProfiles(name: $name) {
nodes {
id
name
assertions {
nodes {
id
name
summary
description
assertionType
assertionDirection
significance
status
ampLevel
evidenceItems {
id
name
description
evidenceLevel
evidenceType
significance
status
}
disease {
id
name
displayName
}
therapies {
id
name
}
molecularProfile {
id
name
}
acmgCodes {
code
description
}
}
}
}
}
}
`;
variables.name = molecularProfileName;
} else {
throw new Error("Either molecularProfileId or molecularProfileName must be provided");
}
return await this.graphqlClient.executeQuery(query, variables);
}
}
