import { z } from "zod";
import { GraphQLClient } from "../utils/graphql-client.js";
import { ErrorHandler } from "../utils/error-handling.js";
export interface VariantEvidenceToolConfig {
name: string;
description: string;
annotations: {
destructive: boolean;
idempotent: boolean;
cacheable: boolean;
world_interaction: string;
side_effects: string[];
resource_usage: string;
};
}
export class VariantEvidenceTool {
private graphqlClient: GraphQLClient;
private errorHandler: ErrorHandler;
private config: VariantEvidenceToolConfig;
constructor(graphqlClient: GraphQLClient, config: VariantEvidenceToolConfig) {
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)"),
limit: z.number().max(50).default(10).describe("Maximum number of evidence items to return (max 50, default 10)")
},
annotations: this.config.annotations
};
}
async execute(params: { molecular_profile_id?: number; molecular_profile_name?: string; limit?: number }) {
const startTime = Date.now();
const limit = params.limit ?? 10;
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.getVariantEvidence(params.molecular_profile_id, params.molecular_profile_name, limit);
const executionTime = Date.now() - startTime;
return {
content: [{
type: "text" as const,
text: JSON.stringify(result, null, 2)
}],
_meta: {
tool_type: "variant_evidence",
execution_time_ms: executionTime,
molecular_profile_id: params.molecular_profile_id,
molecular_profile_name: params.molecular_profile_name,
evidence_count: result.data?.evidenceItems?.nodes?.length || 0,
limit_requested: limit,
timestamp: new Date().toISOString()
}
};
} catch (error) {
const executionTime = Date.now() - startTime;
return this.errorHandler.createErrorResponse("Variant evidence retrieval failed", error, executionTime);
}
}
private async getVariantEvidence(molecularProfileId?: number, molecularProfileName?: string, limit: number = 10): Promise<any> {
let query: string;
let variables: Record<string, any> = { first: Math.min(limit, 50) };
if (molecularProfileId) {
query = `
query GetEvidenceByProfileId($profileId: Int!, $first: Int!) {
evidenceItems(molecularProfileId: $profileId, first: $first) {
totalCount
nodes {
id
name
description
evidenceLevel
evidenceType
significance
evidenceDirection
status
source {
id
sourceType
citation
publicationDate
}
disease {
id
name
displayName
doid
}
therapies {
id
name
ncitId
}
molecularProfile {
id
name
}
variantOrigin
}
pageInfo {
hasNextPage
hasPreviousPage
}
}
}
`;
variables.profileId = molecularProfileId;
} else if (molecularProfileName) {
query = `
query GetEvidenceByProfileName($profileName: String!, $first: Int!) {
molecularProfiles(name: $profileName) {
nodes {
id
name
evidenceItems(first: $first) {
totalCount
nodes {
id
name
description
evidenceLevel
evidenceType
significance
evidenceDirection
status
source {
id
sourceType
citation
publicationDate
}
disease {
id
name
displayName
doid
}
therapies {
id
name
ncitId
}
molecularProfile {
id
name
}
variantOrigin
}
pageInfo {
hasNextPage
hasPreviousPage
}
}
}
}
}
`;
variables.profileName = molecularProfileName;
} else {
throw new Error("Either molecularProfileId or molecularProfileName must be provided");
}
return await this.graphqlClient.executeQuery(query, variables);
}
}
