fhirsmith 0.18.1 → 1.0.0

package/tx/html/status-tasks.liquid

@@ -0,0 +1,25 @@
+{%- comment -%}
+  The background tasks under the graphs (stats.taskSummary): one line naming those at work, those
+  whose last run failed (each is a problem in the status line, with its state) and the idle ones,
+  then a row for each at work. Styles are in status-line.liquid; every task is under "More".
+{%- endcomment -%}
+<section class="fs-status fs-status-jobs" aria-labelledby="fs-status-jobs-title">
+  <div class="fs-status-jobs-head">
+    <h{{ level }} id="fs-status-jobs-title">Background tasks</h{{ level }}>
+    <span class="fs-status-idle">
+      {%- if tasks.working.size == 0 %}none at work{% else %}{{ tasks.working.size }} at work{% endif -%}
+      {%- if tasks.failed.size > 0 %} · {{ tasks.failed.size }} failed, under Problems: {{ tasks.failed | join: ', ' | escape }}{% endif -%}
+      {%- if tasks.idle.size > 0 %} · {{ tasks.idle.size }} idle: {{ tasks.idle | join: ', ' | escape }}{% endif -%}
+    </span>
+  </div>
+  {%- if tasks.working.size > 0 %}
+  <table>
+    <thead><tr><th>Task</th><th>Status</th><th>Frequency</th><th>Last seen</th></tr></thead>
+    <tbody>
+    {%- for t in tasks.working %}
+      <tr><td>{{ t.name | escape }}</td><td>{{ t.state | escape }}</td><td>{{ t.frequency | escape }}</td><td>{{ t.ago | escape }}</td></tr>
+    {%- endfor %}
+    </tbody>
+  </table>
+  {%- endif %}
+</section>

package/tx/html/tx-template.html

@@ -83,8 +83,6 @@
 		<div id="stripe"> </div>
 		<div class="container">
 		<div style="background-color: #ad1f2f; padding: 6px; color: white;">
-  <a href="http://www.hl7.org/fhir" style="color: gold" title="Fast Healthcare Interoperability Resources - Home Page"><img border="0" src="/icon-fhir-16.png" style="vertical-align: text-bottom"/> <b>FHIR</b></a> [%fhir-version%] &copy; HL7.org &nbsp;|&nbsp;
-  <a href="https://github.com/HealthIntersections/FHIRsmith/blob/main/README.md" style="color: gold"><img border="0" src="/FHIRsmith16.png" style="vertical-align: text-bottom"/> FHIRsmith</a> [%ver%] &nbsp;|&nbsp;
   <a href="/" style="color: gold"> Server Home</a> &nbsp;|&nbsp;
   <a href="[%endpoint-path%]" style="color: gold">TX Home</a>  &nbsp;|&nbsp;
             <a href="[%endpoint-path%]/metadata" style="color: gold">Capability Statement</a>  &nbsp;|&nbsp;
@@ -105,7 +103,7 @@
             	<div class="inner-wrapper">
  <div class="col-12">
 
-  <h2><img border="0" src="/FHIRsmith32.png" style="vertical-align: text-bottom"/> TX: [%title%] </h2>
+     <h2><a href="https://github.com/HealthIntersections/FHIRsmith/blob/main/README.md" title="FHIRsmith [%ver%]"><img border="0" src="/FHIRsmith32.png" alt="FHIRsmith Logo" style="vertical-align: text-bottom"/></a> TX: [%title%] </h2>
 
 [%content%]
 
@@ -121,8 +119,7 @@
 		<div class="container">
 			<div class="inner-wrapper">
 				<p>
-                    <a href="http://www.hl7.org/fhir" style="color: gold" title="Fast Healthcare Interoperability Resources - Home Page"><img border="0" src="/icon-fhir-16.png" style="vertical-align: text-bottom"/> <b>FHIR</b></a> v[%fhir-version%] &copy; HL7.org 2011+.  &nbsp;|&nbsp;
-                    <a href="https://github.com/HealthIntersections/FHIRsmith/blob/main/README.md" style="color: gold"><img border="0" src="/FHIRsmith16.png" style="vertical-align: text-bottom"/> FHIRsmith</a>  [%ver%]  &copy; HealthIntersections.com.au 2023+ &nbsp;|&nbsp;
+                    <a href="https://github.com/HealthIntersections/FHIRsmith/blob/main/README.md" style="color: gold"><img border="0" src="/FHIRsmith16.png" alt="FHIRsmith Logo" style="vertical-align: text-bottom"/> FHIRsmith</a>  [%ver%]  &copy; HealthIntersections.com.au 2023+ &nbsp;|&nbsp;
                     &nbsp; ([%ms%] ms)
                     [%sponsorMessage%]
         </p>

package/tx/importers/atc-to-fhir.js

@@ -1,5 +1,6 @@
 const fs = require('fs');
 const { XMLParser } = require('fast-xml-parser');
+const terminal = require('./terminal');
 
 // Configuration
 const ATC_FILE = process.argv[2] || '2025_ATC.xml';
@@ -147,21 +148,21 @@ function buildConcept(atcRow, dddMap) {
 
 // Main conversion function
 function convertATCtoFHIR(atcFile, dddFile) {
-    console.log(`Parsing ${atcFile}...`);
+    terminal.log(`Parsing ${atcFile}...`);
     const atcParsed = parseXML(atcFile);
     const atcRows = extractRows(atcParsed);
-    console.log(`  Found ${atcRows.length} ATC codes`);
+    terminal.log(`  Found ${atcRows.length} ATC codes`);
     
-    console.log(`Parsing ${dddFile}...`);
+    terminal.log(`Parsing ${dddFile}...`);
     const dddParsed = parseXML(dddFile);
     const dddRows = extractRows(dddParsed);
-    console.log(`  Found ${dddRows.length} DDD entries`);
+    terminal.log(`  Found ${dddRows.length} DDD entries`);
     
-    console.log('Building DDD lookup map...');
+    terminal.log('Building DDD lookup map...');
     const dddMap = buildDDDMap(dddRows);
-    console.log(`  ${dddMap.size} codes have DDD data`);
+    terminal.log(`  ${dddMap.size} codes have DDD data`);
     
-    console.log('Building FHIR CodeSystem...');
+    terminal.log('Building FHIR CodeSystem...');
     
     const codeSystem = {
         resourceType: 'CodeSystem',
@@ -256,7 +257,7 @@ function convertATCtoFHIR(atcFile, dddFile) {
                 parent.concept.push(concept);
             } else {
                 // Parent not found, add to root (shouldn't happen with valid data)
-                console.warn(`Warning: Parent ${parentCode} not found for ${code}`);
+                terminal.warn(`Warning: Parent ${parentCode} not found for ${code}`);
                 rootConcepts.push(concept);
             }
         }
@@ -265,7 +266,7 @@ function convertATCtoFHIR(atcFile, dddFile) {
     codeSystem.concept = rootConcepts;
     codeSystem.count = conceptMap.size;
     
-    console.log(`  Generated ${conceptMap.size} concepts in nested hierarchy`);
+    terminal.log(`  Generated ${conceptMap.size} concepts in nested hierarchy`);
     
     return codeSystem;
 }
@@ -274,19 +275,19 @@ function convertATCtoFHIR(atcFile, dddFile) {
 try {
     const codeSystem = convertATCtoFHIR(ATC_FILE, DDD_FILE);
     
-    console.log(`Writing to ${OUTPUT_FILE}...`);
+    terminal.log(`Writing to ${OUTPUT_FILE}...`);
     fs.writeFileSync(OUTPUT_FILE, JSON.stringify(codeSystem, null, 2));
-    console.log('Done!');
+    terminal.log('Done!');
 
     const totalConcepts = countConcepts(codeSystem.concept);
     const withDDD = countWithDDD(codeSystem.concept);
-    console.log(`\nStatistics:`);
-    console.log(`  Total concepts: ${totalConcepts}`);
-    console.log(`  Top-level concepts: ${codeSystem.concept.length}`);
-    console.log(`  Concepts with DDD data: ${withDDD}`);
+    terminal.log(`\nStatistics:`);
+    terminal.log(`  Total concepts: ${totalConcepts}`);
+    terminal.log(`  Top-level concepts: ${codeSystem.concept.length}`);
+    terminal.log(`  Concepts with DDD data: ${withDDD}`);
     
 } catch (error) {
-    console.error('Error:', error.message);
+    terminal.error('Error:', error.message);
     process.exit(1);
 }
 

package/tx/importers/export-icd11-codesystem.js

@@ -24,6 +24,7 @@ const crypto = require('crypto');
 const Database = require('better-sqlite3');
 const { Command } = require('commander');
 const { axisLabel } = require('../cs/icd11-expressions');
+const terminal = require('./terminal');
 
 const TOOL_VERSION = '1.0.0';
 const SCHEMA_NS = 'http://id.who.int/icd/schema';
@@ -141,7 +142,7 @@ class CodeSystemExporter {
   constructor(opts) {
     this.opts = opts;
     this.db = new Database(opts.src, { readonly: true });
-    this.log = (...a) => console.log(...a);
+    this.log = (...a) => terminal.log(...a);
   }
 
   meta(key) {
@@ -861,7 +862,7 @@ function main(argv) {
 
 if (require.main === module) {
   main(process.argv).catch(e => {
-    console.error(`\nexport failed: ${e && e.stack || e}`);
+    terminal.error(`\nexport failed: ${e && e.stack || e}`);
     process.exit(1);
   });
 }

package/tx/importers/import-icd11.js

@@ -26,6 +26,7 @@ const fs = require('fs');
 const path = require('path');
 const Database = require('better-sqlite3');
 const { Command } = require('commander');
+const terminal = require('./terminal');
 
 const TOOL_VERSION = '1.0.0';
 const WHO = 'http://id.who.int';
@@ -341,8 +342,8 @@ class Icd11Importer {
     this.native = stripTrailingSlash(opts.native);
     this.fhir = opts.fhir ? stripTrailingSlash(opts.fhir) : null;
     this.fetcher = new Fetcher(opts);
-    this.log = (...a) => console.log(...a);
-    this.warn = (...a) => console.warn(...a);
+    this.log = (...a) => terminal.log(...a);
+    this.warn = (...a) => terminal.warn(...a);
   }
 
   headers(lang) {
@@ -892,7 +893,7 @@ function main(argv) {
 
 if (require.main === module) {
   main(process.argv).catch(e => {
-    console.error(`\nimport failed: ${e && e.stack || e}`);
+    terminal.error(`\nimport failed: ${e && e.stack || e}`);
     process.exit(1);
   });
 }

package/tx/importers/import-loinc.module.js

@@ -5,6 +5,7 @@ const path = require('path');
 const readline = require('readline');
 const { csvRecords } = require('./csv-records');
 const chalk = require('chalk');
+const terminal = require('./terminal');
 
 class LoincModule extends BaseTerminologyModule {
   constructor() {
@@ -109,7 +110,7 @@ class LoincModule extends BaseTerminologyModule {
     } catch (error) {
       this.logError(`Import command failed: ${error.message}`);
       if (options.verbose) {
-        console.error(error.stack);
+        terminal.error(error.stack);
       }
       throw error;
     }
@@ -119,17 +120,17 @@ class LoincModule extends BaseTerminologyModule {
     const inquirer = require('inquirer');
     const chalk = require('chalk');
 
-    console.log(chalk.cyan(`\n📋 ${this.getName()} Import Configuration:`));
-    console.log(`  Source: ${chalk.white(config.source)}`);
-    console.log(`  Destination: ${chalk.white(config.dest)}`);
-    console.log(`  Version: ${chalk.white(config.version)}`);
-    console.log(`  Main Only: ${chalk.white(config.mainOnly ? 'Yes' : 'No')}`);
-    console.log(`  Create Indexes: ${chalk.white(config.createIndexes ? 'Yes' : 'No')}`);
-    console.log(`  Overwrite: ${chalk.white(config.overwrite ? 'Yes' : 'No')}`);
-    console.log(`  Verbose: ${chalk.white(config.verbose ? 'Yes' : 'No')}`);
+    terminal.log(chalk.cyan(`\n📋 ${this.getName()} Import Configuration:`));
+    terminal.log(`  Source: ${chalk.white(config.source)}`);
+    terminal.log(`  Destination: ${chalk.white(config.dest)}`);
+    terminal.log(`  Version: ${chalk.white(config.version)}`);
+    terminal.log(`  Main Only: ${chalk.white(config.mainOnly ? 'Yes' : 'No')}`);
+    terminal.log(`  Create Indexes: ${chalk.white(config.createIndexes ? 'Yes' : 'No')}`);
+    terminal.log(`  Overwrite: ${chalk.white(config.overwrite ? 'Yes' : 'No')}`);
+    terminal.log(`  Verbose: ${chalk.white(config.verbose ? 'Yes' : 'No')}`);
 
     if (config.estimatedDuration) {
-      console.log(`  Estimated Duration: ${chalk.white(config.estimatedDuration)}`);
+      terminal.log(`  Estimated Duration: ${chalk.white(config.estimatedDuration)}`);
     }
 
     const { confirmed } = await inquirer.prompt({
@@ -144,7 +145,7 @@ class LoincModule extends BaseTerminologyModule {
 
   async runImportWithoutConfigSaving(config) {
     try {
-      console.log(chalk.blue.bold(`🏥 Starting ${this.getName()} Import...\n`));
+      terminal.log(chalk.blue.bold(`🏥 Starting ${this.getName()} Import...\n`));
 
       // Pre-flight checks
       this.logInfo('Running pre-flight checks...');
@@ -163,7 +164,7 @@ class LoincModule extends BaseTerminologyModule {
       this.stopProgress();
       this.logError(`${this.getName()} import failed: ${error.message}`);
       if (config.verbose) {
-        console.error(error.stack);
+        terminal.error(error.stack);
       }
       process.exit(1);
     }
@@ -186,14 +187,14 @@ class LoincModule extends BaseTerminologyModule {
       const stats = await this.validateLoincDirectory(options.source);
 
       this.logSuccess('Directory validation passed');
-      console.log(`  Main codes file: ${stats.mainCodesFound ? 'Found' : 'Missing'}`);
-      console.log(`  Parts file: ${stats.partsFound ? 'Found' : 'Missing'}`);
-      console.log(`  Language variants: ${stats.languageVariants.length} found`);
-      console.log(`  Estimated main codes: ${stats.estimatedCodes.toLocaleString()}`);
+      terminal.log(`  Main codes file: ${stats.mainCodesFound ? 'Found' : 'Missing'}`);
+      terminal.log(`  Parts file: ${stats.partsFound ? 'Found' : 'Missing'}`);
+      terminal.log(`  Language variants: ${stats.languageVariants.length} found`);
+      terminal.log(`  Estimated main codes: ${stats.estimatedCodes.toLocaleString()}`);
 
       if (stats.warnings.length > 0) {
         this.logWarning('Validation warnings:');
-        stats.warnings.forEach(warning => console.log(`    ${warning}`));
+        stats.warnings.forEach(warning => terminal.log(`    ${warning}`));
       }
 
     } catch (error) {
@@ -215,15 +216,15 @@ class LoincModule extends BaseTerminologyModule {
       const stats = await this.getDatabaseStats(dbPath);
 
       this.logSuccess('Database status:');
-      console.log(`  Version: ${stats.version}`);
-      console.log(`  Total Codes: ${stats.codeCount.toLocaleString()}`);
-      console.log(`  Main LOINC Codes: ${stats.mainCodeCount.toLocaleString()}`);
-      console.log(`  Parts: ${stats.partCount.toLocaleString()}`);
-      console.log(`  Answer Lists: ${stats.answerListCount.toLocaleString()}`);
-      console.log(`  Languages: ${stats.languageCount.toLocaleString()}`);
-      console.log(`  Relationships: ${stats.relationshipCount.toLocaleString()}`);
-      console.log(`  Database Size: ${stats.sizeGB.toFixed(2)} GB`);
-      console.log(`  Last Modified: ${stats.lastModified}`);
+      terminal.log(`  Version: ${stats.version}`);
+      terminal.log(`  Total Codes: ${stats.codeCount.toLocaleString()}`);
+      terminal.log(`  Main LOINC Codes: ${stats.mainCodeCount.toLocaleString()}`);
+      terminal.log(`  Parts: ${stats.partCount.toLocaleString()}`);
+      terminal.log(`  Answer Lists: ${stats.answerListCount.toLocaleString()}`);
+      terminal.log(`  Languages: ${stats.languageCount.toLocaleString()}`);
+      terminal.log(`  Relationships: ${stats.relationshipCount.toLocaleString()}`);
+      terminal.log(`  Database Size: ${stats.sizeGB.toFixed(2)} GB`);
+      terminal.log(`  Last Modified: ${stats.lastModified}`);
 
     } catch (error) {
       this.logError(`Status check failed: ${error.message}`);
@@ -446,7 +447,7 @@ class LoincModule extends BaseTerminologyModule {
       db.serialize(() => {
         indexes.forEach(sql => {
           db.run(sql, (err) => {
-            if (err) console.warn(`Index creation warning: ${err.message}`);
+            if (err) terminal.warn(`Index creation warning: ${err.message}`);
           });
         });
       });
@@ -579,7 +580,7 @@ class LoincDataMigrator {
   }
 
   async migrate(sourceDir, destFile, version = 'unknown', options = {}) {
-    if (options.verbose) console.log('Starting LOINC data migration...');
+    if (options.verbose) terminal.log('Starting LOINC data migration...');
 
     const destDir = path.dirname(destFile);
     if (!fs.existsSync(destDir)) {
@@ -591,11 +592,21 @@ class LoincDataMigrator {
     }
 
     const db = new sqlite3.Database(destFile);
+    // Run every statement in submission order, and the whole import as one transaction:
+    // without it each INSERT autocommits and waits on its own fsync (~10 ms each), which
+    // made even the small test fixture take minutes
+    db.serialize();
+    const exec = (sql) => new Promise((resolve, reject) => db.exec(sql, (err) => err ? reject(err) : resolve()));
 
     try {
+      await exec('BEGIN');
+
       // Initialize tracking variables
       this.codeKey = 0;
       this.relKey = 0;
+      this.relSeen = new Set();
+      this.axisParts = new Map(); // term key -> { COMPONENT: part key, ... } (see processLanguage)
+      this.partNamesSeen = new Set();
       this.descKey = 0;
       this.propKey = 0;
       this.propValueKey = 0;
@@ -667,14 +678,15 @@ class LoincDataMigrator {
         }
       }
 
-      if (options.verbose) console.log('LOINC data migration completed successfully');
+      await exec('COMMIT');
+      if (options.verbose) terminal.log('LOINC data migration completed successfully');
     } finally {
       await this.closeDatabase(db, options.verbose);
     }
   }
 
   async createTables(db, version, verbose = true) {
-    if (verbose) console.log('Creating database tables...');
+    if (verbose) terminal.log('Creating database tables...');
 
     const tableSQL = [
       `CREATE TABLE Config (
@@ -775,7 +787,7 @@ class LoincDataMigrator {
         });
 
         this.insertInitialData(db, version);
-        if (verbose) console.log('Database tables created');
+        if (verbose) terminal.log('Database tables created');
         resolve();
       });
     });
@@ -826,7 +838,8 @@ class LoincDataMigrator {
     // Description types
     const descriptionTypes = [
       [1, 'LONG_COMMON_NAME'], [2, 'SHORTNAME'], [3, 'ConsumerName'],
-      [4, 'RELATEDNAMES2'], [5, 'DisplayName'], [6, 'LinguisticVariantDisplayName']
+      [4, 'RELATEDNAMES2'], [5, 'DisplayName'], [6, 'LinguisticVariantDisplayName'],
+      [7, 'PartName']
     ];
     descriptionTypes.forEach(([key, desc]) => {
       db.run('INSERT INTO DescriptionTypes (DescriptionTypeKey, Description) VALUES (?, ?)', [key, desc]);
@@ -869,11 +882,11 @@ class LoincDataMigrator {
   }
 
   async processLanguageVariants(db, sourceDir, step, options) {
-    if (options.verbose) console.log('Processing Language Variants...');
+    if (options.verbose) terminal.log('Processing Language Variants...');
 
     const filePath = path.join(sourceDir, 'AccessoryFiles/LinguisticVariants/LinguisticVariants.csv');
     if (!fs.existsSync(filePath)) {
-      if (options.verbose) console.warn(`Language variants file not found: ${filePath}`);
+      if (options.verbose) terminal.warn(`Language variants file not found: ${filePath}`);
       return;
     }
 
@@ -900,7 +913,7 @@ class LoincDataMigrator {
   }
 
   async processParts(db, sourceDir, step, options) {
-    if (options.verbose) console.log('Processing Parts...');
+    if (options.verbose) terminal.log('Processing Parts...');
 
     const filePath = path.join(sourceDir, 'AccessoryFiles/PartFile/Part.csv');
     const rl = csvRecords(filePath);
@@ -928,7 +941,7 @@ class LoincDataMigrator {
       this.updateProgress(remaining);
     }
 
-    if (options.verbose) console.log(`  Processed ${processedCount} parts`);
+    if (options.verbose) terminal.log(`  Processed ${processedCount} parts`);
   }
 
   async processPartItem(db, items) {
@@ -952,7 +965,7 @@ class LoincDataMigrator {
   }
 
   async processCodes(db, sourceDir, step, options) {
-    if (options.verbose) console.log('Processing Main Codes...');
+    if (options.verbose) terminal.log('Processing Main Codes...');
 
     const filePath = path.join(sourceDir, 'LoincTable/Loinc.csv');
     const rl = csvRecords(filePath);
@@ -980,7 +993,7 @@ class LoincDataMigrator {
       this.updateProgress(remaining);
     }
 
-    if (options.verbose) console.log(`  Processed ${processedCount} main codes`);
+    if (options.verbose) terminal.log(`  Processed ${processedCount} main codes`);
   }
 
   async processCodeItem(db, items) {
@@ -1002,6 +1015,7 @@ class LoincDataMigrator {
     const clsCode = this.partNames.get('CLASS.' + items[7]);
     if (clsCode && this.codes.has(clsCode)) {
       this.addRelationship(db, codeKey, this.codes.get(clsCode).key, this.rels.get('CLASS'));
+      this.#noteAxisPart(codeKey, 'CLASS', this.codes.get(clsCode).key);
     }
 
     // Add properties
@@ -1026,11 +1040,11 @@ class LoincDataMigrator {
   async processConsumerNames(db, sourceDir, step, options) {
     const filePath = path.join(sourceDir, 'AccessoryFiles/ConsumerName/ConsumerName.csv');
     if (!fs.existsSync(filePath)) {
-      if (options.verbose) console.warn(`Consumer names file not found: ${filePath}`);
+      if (options.verbose) terminal.warn(`Consumer names file not found: ${filePath}`);
       return;
     }
 
-    if (options.verbose) console.log('Processing Consumer Names...');
+    if (options.verbose) terminal.log('Processing Consumer Names...');
 
     const rl = csvRecords(filePath);
 
@@ -1061,11 +1075,11 @@ class LoincDataMigrator {
   async processLists(db, sourceDir, step, options) {
     const filePath = path.join(sourceDir, 'AccessoryFiles/AnswerFile/AnswerList.csv');
     if (!fs.existsSync(filePath)) {
-      if (options.verbose) console.warn(`Answer lists file not found: ${filePath}`);
+      if (options.verbose) terminal.warn(`Answer lists file not found: ${filePath}`);
       return;
     }
 
-    if (options.verbose) console.log('Processing Answer Lists...');
+    if (options.verbose) terminal.log('Processing Answer Lists...');
 
     const rl = csvRecords(filePath);
 
@@ -1113,6 +1127,12 @@ class LoincDataMigrator {
     }
 
     const answerCode = removeQuotes(items[6]);
+    if (!answerCode) {
+      // an externally defined answer list (ExtDefinedYN = Y: ICD-10, RxNorm, ...) has one row with
+      // no AnswerStringId. The list is a code; the row names no answer, so there is nothing to add
+      // (it used to become a single Answer code '' shared by all 65 such lists)
+      return;
+    }
     let answerCodeKey;
 
     if (this.codes.has(answerCode)) {
@@ -1141,11 +1161,11 @@ class LoincDataMigrator {
   async processPartMappings(db, sourceDir, step, options) {
     const filePath = path.join(sourceDir, 'AccessoryFiles/PartFile/PartRelatedCodeMapping.csv');
     if (!fs.existsSync(filePath)) {
-      if (options.verbose) console.warn(`Part mapping file not found: ${filePath}`);
+      if (options.verbose) terminal.warn(`Part mapping file not found: ${filePath}`);
       return;
     }
 
-    if (options.verbose) console.log('Processing Part Mappings...');
+    if (options.verbose) terminal.log('Processing Part Mappings...');
 
     const rl = csvRecords(filePath);
 
@@ -1180,11 +1200,11 @@ class LoincDataMigrator {
   async processIeeeMappings(db, sourceDir, step, options) {
     const filePath = path.join(sourceDir, 'AccessoryFiles/LoincIeeeMedicalDeviceCodeMappingTable/LoincIeeeMedicalDeviceCodeMappingTable.csv');
     if (!fs.existsSync(filePath)) {
-      if (options.verbose) console.warn(`IEEE mapping file not found: ${filePath}`);
+      if (options.verbose) terminal.warn(`IEEE mapping file not found: ${filePath}`);
       return;
     }
 
-    if (options.verbose) console.log('Processing IEEE Mappings...');
+    if (options.verbose) terminal.log('Processing IEEE Mappings...');
 
     const rl = csvRecords(filePath);
 
@@ -1240,11 +1260,11 @@ class LoincDataMigrator {
   async processPartLinks(db, sourceDir, step, options) {
     const filePath = path.join(sourceDir, 'AccessoryFiles/PartFile/LoincPartLink_Primary.csv');
     if (!fs.existsSync(filePath)) {
-      if (options.verbose) console.warn(`Part links file not found: ${filePath}`);
+      if (options.verbose) terminal.warn(`Part links file not found: ${filePath}`);
       return;
     }
 
-    if (options.verbose) console.log('Processing Part Links...');
+    if (options.verbose) terminal.log('Processing Part Links...');
 
     const rl = csvRecords(filePath);
 
@@ -1269,6 +1289,9 @@ class LoincDataMigrator {
           this.rels.get(relType),
           this.statii.get(status) || 0
         );
+        if (LINGUISTIC_VARIANT_AXES.includes(relType)) {
+          this.#noteAxisPart(this.codes.get(sourceCode).key, relType, this.codes.get(targetCode).key);
+        }
       }
       processedCount++;
 
@@ -1286,11 +1309,11 @@ class LoincDataMigrator {
   async processListLinks(db, sourceDir, step, options) {
     const filePath = path.join(sourceDir, 'AccessoryFiles/AnswerFile/LoincAnswerListLink.csv');
     if (!fs.existsSync(filePath)) {
-      if (options.verbose) console.warn(`List links file not found: ${filePath}`);
+      if (options.verbose) terminal.warn(`List links file not found: ${filePath}`);
       return;
     }
 
-    if (options.verbose) console.log('Processing List Links...');
+    if (options.verbose) terminal.log('Processing List Links...');
 
     const rl = csvRecords(filePath);
 
@@ -1343,7 +1366,7 @@ class LoincDataMigrator {
       throw new Error(`Required file missing: ${filePath}`);
     }
 
-    if (options.verbose) console.log('Processing Hierarchy...');
+    if (options.verbose) terminal.log('Processing Hierarchy...');
 
     const rl = csvRecords(filePath);
 
@@ -1407,7 +1430,7 @@ class LoincDataMigrator {
   }
 
   async processPropertyValues(db, step, options) {
-    if (options.verbose) console.log('Processing Property Values...');
+    if (options.verbose) terminal.log('Processing Property Values...');
 
     for (const [value, key] of this.propValues) {
       db.run('INSERT INTO PropertyValues (PropertyValueKey, Value) VALUES (?, ?)', [key, value]);
@@ -1415,7 +1438,7 @@ class LoincDataMigrator {
   }
 
   async storeClosureTable(db, step, options) {
-    if (options.verbose) console.log('Storing Closure Table...');
+    if (options.verbose) terminal.log('Storing Closure Table...');
 
     let count = 0;
     for (const codeInfo of this.codeList) {
@@ -1440,7 +1463,7 @@ class LoincDataMigrator {
   }
 
   async processLanguage(db, sourceDir, step, langCode, options) {
-    if (options.verbose) console.log(`Processing Language ${langCode}...`);
+    if (options.verbose) terminal.log(`Processing Language ${langCode}...`);
 
     const langKey = this.langs.get(langCode);
     if (!langKey) return;
@@ -1450,7 +1473,7 @@ class LoincDataMigrator {
     const filePath = path.join(sourceDir, 'AccessoryFiles/LinguisticVariants', fileName);
 
     if (!fs.existsSync(filePath)) {
-      if (options.verbose) console.warn(`Language file not found: ${filePath}`);
+      if (options.verbose) terminal.warn(`Language file not found: ${filePath}`);
       return;
     }
 
@@ -1472,6 +1495,24 @@ class LoincDataMigrator {
       this.addDescription(db, codeKey, langKey, this.dTypes.get('SHORTNAME'), items[8]);
       this.addDescription(db, codeKey, langKey, this.dTypes.get('LinguisticVariantDisplayName'), items[11]);
 
+      // The axis columns (COMPONENT ... CLASS) translate the term's Parts. Each becomes a
+      // PartName designation on the Part the term links to for that axis - for some languages
+      // (ko-KR, most of fr-CA) these are the only translations LOINC has. Each distinct name once
+      const axes = this.axisParts.get(codeKey);
+      if (axes) {
+        LINGUISTIC_VARIANT_AXES.forEach((axis, i) => {
+          const value = items[i + 1] ? items[i + 1].trim() : '';
+          const partKey = axes[axis];
+          if (value && partKey) {
+            const id = partKey + '|' + langKey + '|' + value;
+            if (!this.partNamesSeen.has(id)) {
+              this.partNamesSeen.add(id);
+              this.addDescription(db, partKey, langKey, this.dTypes.get('PartName'), value);
+            }
+          }
+        });
+      }
+
       processedCount++;
 
       if (processedCount % 100 === 0) {
@@ -1485,6 +1526,15 @@ class LoincDataMigrator {
     }
   }
 
+  #noteAxisPart(termKey, axis, partKey) {
+    let axes = this.axisParts.get(termKey);
+    if (!axes) {
+      axes = {};
+      this.axisParts.set(termKey, axes);
+    }
+    axes[axis] = partKey;
+  }
+
   addDescription(db, codeKey, languageKey, descriptionType, value) {
     if (!value) return;
 
@@ -1508,6 +1558,14 @@ class LoincDataMigrator {
 
   addRelationship(db, sourceKey, targetKey, relationshipType, statusKey = 0) {
     if (!relationshipType) return;
+    // each relationship once: the source files repeat some (a part under the same parent on
+    // two paths in ComponentHierarchyBySystem, the same answer list linked more than once)
+    if (!this.relSeen) {
+      this.relSeen = new Set();
+    }
+    const id = relationshipType + '|' + sourceKey + '|' + targetKey;
+    if (this.relSeen.has(id)) return;
+    this.relSeen.add(id);
 
     this.relKey++;
     db.run('INSERT INTO Relationships (RelationshipKey, RelationshipTypeKey, SourceKey, TargetKey, StatusKey) VALUES (?, ?, ?, ?, ?)',
@@ -1528,7 +1586,7 @@ class LoincDataMigrator {
     return new Promise((resolve) => {
       db.close((err) => {
         if (err && verbose) {
-          console.error('Error closing database:', err);
+          terminal.error('Error closing database:', err);
         }
         resolve();
       });
@@ -1537,6 +1595,10 @@ class LoincDataMigrator {
 }
 
 // Property name mappings from Pascal code
+// The axis columns of a LinguisticVariant file, in file order (columns 1 to 7), named as the
+// term's relationships to its Parts are
+const LINGUISTIC_VARIANT_AXES = ['COMPONENT', 'PROPERTY', 'TIME_ASPCT', 'SYSTEM', 'SCALE_TYP', 'METHOD_TYP', 'CLASS'];
+
 const KNOWN_PROPERTY_NAMES = [
   'AskAtOrderEntry', 'AssociatedObservations', 'CHANGE_REASON_PUBLIC', 'CHNG_TYPE', 'CLASS', 'CLASSTYPE', 'COMMON_ORDER_RANK', 'COMMON_TEST_RANK', 'COMPONENT', 'CONSUMER_NAME',
   'DefinitionDescription', 'DisplayName', 'EXAMPLE_UCUM_UNITS', 'EXAMPLE_UNITS', 'EXMPL_ANSWERS', 'EXTERNAL_COPYRIGHT_LINK', 'EXTERNAL_COPYRIGHT_NOTICE', 'FORMULA',