#!/usr/bin/env bun
/**
* CDC WONDER Mortality Database Updater
* Source ID: DS-00005
* API: https://wonder.cdc.gov/controller/datarequest/
* Update Frequency: Annual (final data); Quarterly (provisional data)
*
* NOTE: CDC WONDER uses XML-based request/response format
*/
import { appendFileSync, writeFileSync, readFileSync } from 'fs';
import { join } from 'path';
// Configuration
const CONFIG = {
sourceId: 'DS-00005',
sourceName: 'CDC WONDER Mortality Database',
apiEndpoint: 'https://wonder.cdc.gov/controller/datarequest/D176', // Underlying Cause of Death database
dataDir: './data',
logFile: './update.log',
sourceFile: './source.md',
// Query configurations for key crisis indicators
queries: {
drugOverdose: {
name: 'Drug Overdose Deaths',
// ICD-10 codes: X40-X44 (unintentional), X60-X64 (suicide), X85 (homicide), Y10-Y14 (undetermined)
icd10Codes: ['X40', 'X41', 'X42', 'X43', 'X44', 'X60', 'X61', 'X62', 'X63', 'X64', 'X85', 'Y10', 'Y11', 'Y12', 'Y13', 'Y14'],
},
opioid: {
name: 'Opioid-Specific Deaths',
// ICD-10 codes: T40.0-T40.4, T40.6 (opioid involvement)
icd10Codes: ['T40.0', 'T40.1', 'T40.2', 'T40.3', 'T40.4', 'T40.6'],
},
suicide: {
name: 'Suicide Deaths',
// ICD-10 codes: X60-X84 (intentional self-harm), Y87.0, U03
icd10Codes: ['X60', 'X61', 'X62', 'X63', 'X64', 'X65', 'X66', 'X67', 'X68', 'X69',
'X70', 'X71', 'X72', 'X73', 'X74', 'X75', 'X76', 'X77', 'X78', 'X79',
'X80', 'X81', 'X82', 'X83', 'X84', 'Y87.0', 'U03'],
},
allCause: {
name: 'All-Cause Mortality',
icd10Codes: [], // Empty = all causes
},
},
// Rate limiting
requestDelayMs: 2000, // Conservative: 1 request every 2 seconds
maxRetries: 3,
};
// Types
interface LogEntry {
timestamp: string;
level: 'INFO' | 'WARNING' | 'ERROR';
message: string;
}
interface MortalityRecord {
state?: string;
county?: string;
year: string;
deaths: number;
population?: number;
crudeRate?: number;
ageAdjustedRate?: number;
[key: string]: any;
}
interface UpdateSummary {
success: boolean;
timestamp: string;
queriesExecuted: number;
recordsProcessed: number;
errors: string[];
}
// Logging utility
function log(level: LogEntry['level'], message: string): void {
const timestamp = new Date().toISOString();
const logLine = `[${timestamp}] ${level}: ${message}\n`;
console.log(logLine.trim());
appendFileSync(CONFIG.logFile, logLine);
}
// Sleep utility for rate limiting
const sleep = (ms: number) => new Promise(resolve => setTimeout(resolve, ms));
// Generate XML request body for CDC WONDER API
function generateXMLRequest(queryType: keyof typeof CONFIG.queries, startYear = '2015', endYear = '2023'): string {
const query = CONFIG.queries[queryType];
// Base XML structure for CDC WONDER API
// This is a simplified example - full queries can be more complex
// Documentation: https://wonder.cdc.gov/wonder/help/WONDER-API.html
let xml = `
true
D176.V9
D176.V27
D176.M1
D176.M2
D176.M3
`;
// Add year filter
xml += `
`;
for (let year = parseInt(startYear); year <= parseInt(endYear); year++) {
xml += `
${year}`;
}
xml += `
`;
// Add ICD-10 code filter if specific causes requested
if (query.icd10Codes.length > 0) {
xml += `
`;
for (const code of query.icd10Codes) {
xml += `
${code}`;
}
xml += `
`;
}
xml += `
${query.name}
300
false
true
`;
return xml;
}
// Parse XML response from CDC WONDER API
function parseXMLResponse(xmlString: string): MortalityRecord[] {
const records: MortalityRecord[] = [];
try {
// NOTE: This is a simplified parser. In production, use a proper XML parser library
// like 'fast-xml-parser' or 'xml2js'
// For now, we'll use regex-based parsing (not ideal but works for demo)
// Extract data rows (between tags)
const rowRegex = /(.*?)<\/r>/gs;
const rows = xmlString.match(rowRegex);
if (!rows) {
log('WARNING', 'No data rows found in XML response');
return records;
}
for (const row of rows) {
// Extract cell values (between tags)
const cellRegex = /(.*?)<\/c>/g;
const cells: string[] = [];
let match;
while ((match = cellRegex.exec(row)) !== null) {
cells.push(match[1]);
}
// Map cells to record structure
// Typical structure: [State, Year, Deaths, Population, Crude Rate]
if (cells.length >= 3) {
const record: MortalityRecord = {
state: cells[0] || 'Unknown',
year: cells[1] || 'Unknown',
deaths: parseInt(cells[2]) || 0,
};
// Optional fields
if (cells[3]) record.population = parseInt(cells[3]);
if (cells[4]) record.crudeRate = parseFloat(cells[4]);
records.push(record);
}
}
log('INFO', `Parsed ${records.length} records from XML response`);
return records;
} catch (error) {
log('ERROR', `Failed to parse XML response: ${error instanceof Error ? error.message : String(error)}`);
return records;
}
}
// Fetch data from CDC WONDER API with retry logic
async function fetchCDCData(queryType: keyof typeof CONFIG.queries, retryCount = 0): Promise {
try {
log('INFO', `Fetching data for: ${CONFIG.queries[queryType].name}`);
const xmlRequest = generateXMLRequest(queryType);
const response = await fetch(CONFIG.apiEndpoint, {
method: 'POST',
headers: {
'Content-Type': 'application/xml',
'Accept': 'application/xml',
},
body: xmlRequest,
});
if (!response.ok) {
if (response.status === 429 && retryCount < CONFIG.maxRetries) {
log('WARNING', `Rate limit hit for ${queryType}. Retrying in 60s (attempt ${retryCount + 1}/${CONFIG.maxRetries})`);
await sleep(60000);
return fetchCDCData(queryType, retryCount + 1);
}
throw new Error(`HTTP ${response.status}: ${response.statusText}`);
}
const xmlResponse = await response.text();
// Check for API error messages in XML
if (xmlResponse.includes('') || xmlResponse.includes('Error')) {
throw new Error('API returned error in XML response');
}
const records = parseXMLResponse(xmlResponse);
log('INFO', `Successfully fetched ${records.length} records for ${queryType}`);
return records;
} catch (error) {
const errorMsg = `Failed to fetch ${queryType}: ${error instanceof Error ? error.message : String(error)}`;
log('ERROR', errorMsg);
if (retryCount < CONFIG.maxRetries) {
log('INFO', `Retrying ${queryType} (attempt ${retryCount + 1}/${CONFIG.maxRetries})`);
await sleep(5000 * (retryCount + 1)); // Exponential backoff
return fetchCDCData(queryType, retryCount + 1);
}
throw new Error(errorMsg);
}
}
// Transform API data to Substrate pipe-delimited format
function transformToSubstrateFormat(data: MortalityRecord[], queryType: string): string {
const queryName = CONFIG.queries[queryType as keyof typeof CONFIG.queries].name;
// Header
const lines = [`RECORD ID | QUERY TYPE | STATE | YEAR | DEATHS | POPULATION | CRUDE RATE | AGE ADJUSTED RATE`];
lines.push('-'.repeat(120));
// Data rows
for (const record of data) {
const recordId = `DS-00005-${queryType}-${record.state?.replace(/\s+/g, '_')}-${record.year}`;
const state = record.state || 'Unknown';
const year = record.year || 'Unknown';
const deaths = record.deaths || 0;
const population = record.population || 'N/A';
const crudeRate = record.crudeRate || 'N/A';
const ageAdjustedRate = record.ageAdjustedRate || 'N/A';
lines.push(`${recordId} | ${queryName} | ${state} | ${year} | ${deaths} | ${population} | ${crudeRate} | ${ageAdjustedRate}`);
}
return lines.join('\n');
}
// Update source.md metadata fields
function updateSourceMetadata(summary: UpdateSummary): void {
try {
let sourceContent = readFileSync(CONFIG.sourceFile, 'utf-8');
const timestamp = summary.timestamp;
// Update Last Updated field
sourceContent = sourceContent.replace(
/\*\*Last Updated:\*\* \d{4}-\d{2}-\d{2}/g,
`**Last Updated:** ${timestamp.split('T')[0]}`
);
// Update Record Created if not present
if (!sourceContent.includes('**Record Created:**')) {
sourceContent = sourceContent.replace(
/^## Bibliographic Information/m,
`**Record Created:** ${timestamp.split('T')[0]}\n\n## Bibliographic Information`
);
}
// Update Last Access Test in Review Log
sourceContent = sourceContent.replace(
/\*\*Last Access Test:\*\* \d{4}-\d{2}-\d{2}/g,
`**Last Access Test:** ${timestamp.split('T')[0]} (API tested successfully)`
);
writeFileSync(CONFIG.sourceFile, sourceContent);
log('INFO', 'Updated source.md metadata');
} catch (error) {
log('ERROR', `Failed to update source.md: ${error instanceof Error ? error.message : String(error)}`);
}
}
// Main update function
async function updateCDCWONDER(): Promise {
const startTime = new Date();
log('INFO', '=== Update Started ===');
log('INFO', `Source: ${CONFIG.sourceName}`);
log('INFO', `Source ID: ${CONFIG.sourceId}`);
const summary: UpdateSummary = {
success: false,
timestamp: startTime.toISOString(),
queriesExecuted: 0,
recordsProcessed: 0,
errors: [],
};
try {
// Check API availability
log('INFO', 'Checking API availability...');
const healthCheck = await fetch('https://wonder.cdc.gov/', { method: 'HEAD' });
if (!healthCheck.ok) {
throw new Error('CDC WONDER website unreachable');
}
log('INFO', 'API endpoint is available');
// Execute queries for each indicator
const allData: { [key: string]: MortalityRecord[] } = {};
const queryTypes = Object.keys(CONFIG.queries) as Array;
for (const queryType of queryTypes) {
try {
const queryData = await fetchCDCData(queryType);
allData[queryType] = queryData;
summary.queriesExecuted++;
summary.recordsProcessed += queryData.length;
// Rate limiting between queries
await sleep(CONFIG.requestDelayMs);
} catch (error) {
const errorMsg = `Failed to fetch ${queryType}: ${error instanceof Error ? error.message : String(error)}`;
summary.errors.push(errorMsg);
log('ERROR', errorMsg);
// Continue with other queries
}
}
// Save raw JSON for each query
for (const [queryType, records] of Object.entries(allData)) {
const rawJsonPath = join(CONFIG.dataDir, `${queryType}_latest.json`);
writeFileSync(rawJsonPath, JSON.stringify(records, null, 2));
log('INFO', `Saved raw data to ${rawJsonPath}`);
}
// Transform and save pipe-delimited format for each query
for (const [queryType, records] of Object.entries(allData)) {
const transformedData = transformToSubstrateFormat(records, queryType);
const transformedPath = join(CONFIG.dataDir, `${queryType}_latest.txt`);
writeFileSync(transformedPath, transformedData);
log('INFO', `Saved transformed data to ${transformedPath}`);
}
// Create combined dataset
const combinedRecords = Object.values(allData).flat();
const combinedJsonPath = join(CONFIG.dataDir, 'all_queries_latest.json');
writeFileSync(combinedJsonPath, JSON.stringify(combinedRecords, null, 2));
log('INFO', `Saved combined data to ${combinedJsonPath}`);
// Update source.md metadata
updateSourceMetadata(summary);
summary.success = summary.errors.length === 0;
// Log summary
log('INFO', '=== Update Summary ===');
log('INFO', `Timestamp: ${summary.timestamp}`);
log('INFO', `Queries Executed: ${summary.queriesExecuted}/${queryTypes.length}`);
log('INFO', `Records Processed: ${summary.recordsProcessed}`);
log('INFO', `Errors: ${summary.errors.length}`);
if (summary.errors.length > 0) {
log('WARNING', `Update completed with ${summary.errors.length} error(s)`);
} else {
log('INFO', '=== Update Completed Successfully ===');
}
return summary;
} catch (error) {
const errorMsg = `Fatal error during update: ${error instanceof Error ? error.message : String(error)}`;
log('ERROR', errorMsg);
summary.errors.push(errorMsg);
summary.success = false;
return summary;
}
}
// Execute if run directly
if (import.meta.main) {
updateCDCWONDER()
.then(summary => {
process.exit(summary.success ? 0 : 1);
})
.catch(error => {
log('ERROR', `Unhandled error: ${error}`);
process.exit(1);
});
}
export { updateCDCWONDER, CONFIG as CDC_WONDER_CONFIG };