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<!doctype html> <html lang="en"> <head> <title>Code coverage report for src/mcp-server/tools/definitions/clinicaltrials-analyze-trends.tool.ts</title> <meta charset="utf-8" /> <link rel="stylesheet" href="../../../../prettify.css" /> <link rel="stylesheet" href="../../../../base.css" /> <link rel="shortcut icon" type="image/x-icon" href="../../../../favicon.png" /> <meta name="viewport" content="width=device-width, initial-scale=1" /> <style type='text/css'> .coverage-summary .sorter { background-image: url(../../../../sort-arrow-sprite.png); } </style> </head> <body> <div class='wrapper'> <div class='pad1'> <h1><a href="../../../../index.html">All files</a> / <a href="index.html">src/mcp-server/tools/definitions</a> clinicaltrials-analyze-trends.tool.ts</h1> <div class='clearfix'> <div class='fl pad1y space-right2'> 96.61% Statements 257/266 </div> <div class='fl pad1y space-right2'> 72.34% Branches 34/47 </div> <div class='fl pad1y space-right2'> 75% Functions 3/4 </div> <div class='fl pad1y space-right2'> 96.61% Lines 257/266 </div> </div> Press n or j to go to the next uncovered block, b, p or k for the previous block. <template id="filterTemplate"> <div class="quiet"> Filter: <input type="search" id="fileSearch"> </div> </template> </div> <div class='status-line high'></div> <pre><table class="coverage"> <tr><td class="line-count quiet"><a name='L1'></a><a href='#L1'>1</a> <a name='L2'></a><a href='#L2'>2</a> <a name='L3'></a><a href='#L3'>3</a> <a name='L4'></a><a href='#L4'>4</a> <a name='L5'></a><a href='#L5'>5</a> <a name='L6'></a><a href='#L6'>6</a> <a name='L7'></a><a href='#L7'>7</a> <a name='L8'></a><a href='#L8'>8</a> <a name='L9'></a><a href='#L9'>9</a> <a name='L10'></a><a href='#L10'>10</a> <a name='L11'></a><a href='#L11'>11</a> <a name='L12'></a><a href='#L12'>12</a> <a name='L13'></a><a href='#L13'>13</a> <a name='L14'></a><a href='#L14'>14</a> <a name='L15'></a><a href='#L15'>15</a> <a name='L16'></a><a href='#L16'>16</a> <a 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8x 8x 8x 8x 8x   8x 8x 8x   8x 8x   8x     8x   8x 8x 8x   8x 8x         11x 11x 11x 11x 11x 11x 11x 11x 11x   11x 11x 11x 11x 11x   9x 1x 8x   11x   11x 10x   10x 18x   18x 18x 4x 4x   18x 2x 2x 3x 3x 3x 2x 2x   18x 3x 3x 3x 3x   18x 3x     3x 4x 4x 3x 3x 3x   18x 3x 3x 3x 3x 3x 3x     3x 3x   18x 3x 3x 3x 3x 3x 3x     3x 3x 18x   7x 7x 7x 18x   10x 10x 10x 10x 10x 10x   9x 9x 9x 9x   9x 9x         1x 1x   1x 1x 1x 1x   1x 1x 3x 3x 1x 1x   1x 1x   1x   1x 1x 1x 1x 1x 1x 1x 1x 1x 1x   1x 1x 1x 1x 1x 1x 1x         1x     1x 1x 1x 1x 1x 1x 1x 1x 1x 1x  </td><td class="text"><pre class="prettyprint lang-js">/** * @fileoverview Complete, declarative definition for the 'clinicaltrials_analyze_trends' tool. * Performs statistical analysis on clinical trial data by fetching matching studies and aggregating metrics. * * @module src/mcp-server/tools/definitions/clinicaltrials-analyze-trends.tool */   import type { ContentBlock } from '@modelcontextprotocol/sdk/types.js'; import { container } from 'tsyringe'; import { z } from 'zod';   import { AppConfig, ClinicalTrialsProvider } from '@/container/tokens.js'; import type { SdkContext, ToolAnnotations, ToolDefinition, } from '@/mcp-server/tools/utils/toolDefinition.js'; import { withToolAuth } from '@/mcp-server/transports/auth/lib/withAuth.js'; import type { IClinicalTrialsProvider } from '@/services/clinical-trials-gov/core/IClinicalTrialsProvider.js'; import type { Study } from '@/services/clinical-trials-gov/types.js'; import { JsonRpcErrorCode, McpError } from '@/types-global/errors.js'; import { logger, type RequestContext } from '@/utils/index.js';   /** --------------------------------------------------------- */ /** Programmatic tool name (must be unique). */ const TOOL_NAME = 'clinicaltrials_analyze_trends'; /** --------------------------------------------------------- */   /** Human-readable title used by UIs. */ const TOOL_TITLE = 'Analyze Clinical Trial Trends'; /** --------------------------------------------------------- */   /** * LLM-facing description of the tool. */ const TOOL_DESCRIPTION = 'Performs statistical analysis on clinical trial studies matching search criteria. Aggregates data by status, country, sponsor type, phase, year, or month. May fetch up to 5000 studies.'; /** --------------------------------------------------------- */   /** UI/behavior hints for clients. */ const TOOL_ANNOTATIONS: ToolAnnotations = { readOnlyHint: true, idempotentHint: true, openWorldHint: true, // Accesses external ClinicalTrials.gov API }; /** --------------------------------------------------------- */   /** API call delay to avoid rate limiting */ const API_CALL_DELAY_MS = 250;   /** * A simple promise-based delay function. */ const delay = (ms: number) => new Promise((resolve) => setTimeout(resolve, ms));   // // Schemas (input and output) // --------------------------   /** * Defines the types of analysis that can be performed. */ const AnalysisTypeSchema = z.enum([ 'countByStatus', 'countByCountry', 'countBySponsorType', 'countByPhase', 'countByYear', 'countByMonth', ]);   const InputSchema = z .object({ query: z .string() .optional() .describe( 'General search query for conditions, interventions, sponsors, or other terms.', ), filter: z .string() .optional() .describe( 'Advanced filter expression using the ClinicalTrials.gov filter syntax.', ), analysisType: z .union([ AnalysisTypeSchema.describe('A single analysis type to perform.'), z .array(AnalysisTypeSchema) .min(1) .describe('An array of analysis types to perform.'), ]) .describe( 'Specify one or more analysis types: countByStatus, countByCountry, countBySponsorType, countByPhase, countByYear, or countByMonth.', ), }) .describe('Input parameters for analyzing clinical trial trends.');   const AnalysisResultSchema = z .object({ analysisType: AnalysisTypeSchema.describe( 'The type of analysis performed.', ), totalStudies: z .number() .int() .describe('Total number of studies included in this analysis.'), results: z .record(z.number()) .describe( 'Aggregated counts by category (e.g., status, country, phase).', ), }) .describe('Result of a single analysis type.');   const OutputSchema = z .object({ analysis: z .array(AnalysisResultSchema) .describe('Array of analysis results, one per requested analysis type.'), }) .describe('Trend analysis results for clinical trial studies.');   type AnalyzeTrendsInput = z.infer<typeof InputSchema>; type AnalysisResult = z.infer<typeof AnalysisResultSchema>; type AnalyzeTrendsOutput = z.infer<typeof OutputSchema>;   // // Pure business logic (no try/catch; throw McpError on failure) // -------------------------------------------------------------   /** * Fetches all studies for a given query, handling pagination. * Throws if the total count exceeds the configured limit. */ async function fetchAllStudies( query: string | undefined, filter: string | undefined, appContext: RequestContext, ): Promise<Study[]> { const config = container.resolve< ReturnType<typeof import('@/config/index.js').parseConfig> >(AppConfig); const provider = container.resolve<IClinicalTrialsProvider>( ClinicalTrialsProvider, );   const maxStudies = config.maxStudiesForAnalysis;   logger.debug('Fetching all studies for analysis...', { ...appContext });   // First, make one call to check the total number of studies const initialResponse = await provider.listStudies( { ...(query && { query }), ...(filter && { filter }), pageSize: 1, }, appContext, );   const totalStudies = initialResponse.totalCount ?? 0;   if (totalStudies > maxStudies) { throw new McpError( JsonRpcErrorCode.ValidationError, `The query returned ${totalStudies} studies, which exceeds the limit of ${maxStudies} for analysis. Please provide a more specific query.`, { totalStudies, limit: maxStudies }, ); }   if (totalStudies === 0) { return []; }   // If within limits, proceed to fetch all studies let allStudies: Study[] = []; let pageToken: string | undefined = undefined; let hasMore = true;   while (hasMore) { const pagedStudies = await provider.listStudies( { ...(query && { query }), ...(filter && { filter }), ...(pageToken && { pageToken }), pageSize: 1000, }, appContext, );   if (pagedStudies.studies) { allStudies = allStudies.concat(pagedStudies.studies); }   pageToken = pagedStudies.nextPageToken; hasMore = !!pageToken && allStudies.length < totalStudies;   if (hasMore) { await delay(API_CALL_DELAY_MS); } }   logger.info(`Fetched a total of ${allStudies.length} studies for analysis.`, { ...appContext, });   return allStudies; }   /** * Performs a statistical analysis on a set of clinical trials matching the given criteria. */ async function analyzeTrendsLogic( input: AnalyzeTrendsInput, appContext: RequestContext, _sdkContext: SdkContext, ): Promise<AnalyzeTrendsOutput> { logger.debug('Executing analyzeTrendsLogic', { ...appContext, toolInput: input, });   const allStudies = await fetchAllStudies( input.query, input.filter, appContext, );   const analysisTypes = Array.isArray(input.analysisType) ? input.analysisType : [input.analysisType];   const finalResults: AnalysisResult[] = [];   for (const type of analysisTypes) { const results: Record<string, number> = {};   for (const study of allStudies) { let key: string | undefined;   switch (type) { case 'countByStatus': key = study.protocolSection?.statusModule?.overallStatus ?? 'Unknown'; break;   case 'countByCountry': study.protocolSection?.contactsLocationsModule?.locations?.forEach( (loc) => { const country = loc.country ?? 'Unknown'; results[country] = (results[country] ?? 0) + 1; }, ); continue;   case 'countBySponsorType': key = study.protocolSection?.sponsorCollaboratorsModule?.leadSponsor ?.class ?? 'Unknown'; break;   case 'countByPhase': { const phases = study.protocolSection?.designModule?.phases ?? [ 'Unknown', ]; phases.forEach((phase) => { const phaseKey = phase ?? 'Unknown'; results[phaseKey] = (results[phaseKey] ?? 0) + 1; }); continue; }   case 'countByYear': { const startDate = study.protocolSection?.statusModule?.startDateStruct?.date; if (startDate) { const year = startDate.substring(0, 4); // Extract YYYY from date results[year] = (results[year] ?? 0) + 1; } else { results['Unknown'] = (results['Unknown'] ?? 0) + 1; } continue; }   case 'countByMonth': { const startDate = study.protocolSection?.statusModule?.startDateStruct?.date; if (startDate && startDate.length >= 7) { const yearMonth = startDate.substring(0, 7); // Extract YYYY-MM from date results[yearMonth] = (results[yearMonth] ?? 0) + 1; } else { results['Unknown'] = (results['Unknown'] ?? 0) + 1; } continue; } }   if (key) { results[key] = (results[key] ?? 0) + 1; } }   finalResults.push({ analysisType: type, totalStudies: allStudies.length, results, }); }   logger.info('Successfully completed trend analysis', { ...appContext, analysisCount: finalResults.length, });   return { analysis: finalResults }; }   /** * Formats a concise human-readable summary. */ function responseFormatter(result: AnalyzeTrendsOutput): ContentBlock[] { const analysisCount = result.analysis.length;   const summaries = result.analysis.map((analysis) => { const topEntries = Object.entries(analysis.results) .sort((a, b) => b[1] - a[1]) .slice(0, 10);   const categoryList = topEntries .map(([category, count]) => { const percentage = ((count / analysis.totalStudies) * 100).toFixed(1); return ` • ${category}: ${count} (${percentage}%)`; }) .join('\n');   const more = Object.keys(analysis.results).length > 10 ? ` ...and ${Object.keys(analysis.results).length - 10} more` : '';   return [ `Analysis: ${analysis.analysisType}`, `Total Studies: ${analysis.totalStudies}`, 'Top Categories:', categoryList, more, ] .filter(Boolean) .join('\n'); });   return [ { type: 'text', text: `Completed ${analysisCount} ${analysisCount === 1 ? 'analysis' : 'analyses'}\n\n${summaries.join('\n\n---\n\n')}`, }, ]; }   /** * The complete tool definition for analyzing clinical trial trends. */ export const analyzeTrendsTool: ToolDefinition< typeof InputSchema, typeof OutputSchema > = { name: TOOL_NAME, title: TOOL_TITLE, description: TOOL_DESCRIPTION, inputSchema: InputSchema, outputSchema: OutputSchema, annotations: TOOL_ANNOTATIONS, logic: withToolAuth(['tool:clinicaltrials:read'], analyzeTrendsLogic), responseFormatter, };  </pre></td></tr></table></pre> <div class='push'></div> </div> <div class='footer quiet pad2 space-top1 center small'> Code coverage generated by <a href="https://istanbul.js.org/" target="_blank" rel="noopener noreferrer">istanbul</a> at 2025-10-15T17:09:47.939Z </div> <script src="../../../../prettify.js"></script> <script> window.onload = function () { prettyPrint(); }; </script> <script src="../../../../sorter.js"></script> <script src="../../../../block-navigation.js"></script> </body> </html>

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