fhirsmith 0.18.0 → 0.18.2

package/tx/importers/csv-records.js

@@ -0,0 +1,35 @@
+const fs = require('fs');
+const readline = require('readline');
+
+/**
+ * Yields the records of a CSV file one at a time, as text.
+ *
+ * A quoted field can contain a line break (LOINC 2.83's ComponentHierarchyBySystem.csv has one
+ * in a CODE_TEXT), so a record that ends inside quotes is joined to the next line until the
+ * quotes balance. An escaped quote ("") counts twice, so it doesn't upset the count.
+ */
+async function* csvRecords(filePath) {
+  const rl = readline.createInterface({
+    input: fs.createReadStream(filePath),
+    crlfDelay: Infinity
+  });
+
+  let pending = null;
+  let quotes = 0;
+  for await (const line of rl) {
+    pending = pending === null ? line : pending + '\n' + line;
+    for (let i = 0; i < line.length; i++) {
+      if (line.charCodeAt(i) === 34) quotes++;
+    }
+    if (quotes % 2 === 0) {
+      yield pending;
+      pending = null;
+      quotes = 0;
+    }
+  }
+  if (pending !== null) {
+    yield pending;
+  }
+}
+
+module.exports = { csvRecords };

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

@@ -3,6 +3,7 @@ const fs = require('fs');
 const sqlite3 = require('sqlite3').verbose();
 const path = require('path');
 const readline = require('readline');
+const { csvRecords } = require('./csv-records');
 const chalk = require('chalk');
 
 class LoincModule extends BaseTerminologyModule {
@@ -291,7 +292,10 @@ class LoincModule extends BaseTerminologyModule {
     // Translations are a different case: a main-only import is a legitimate thing to want,
     // and their absence costs designations, not correctness
     const optionalFiles = [
-      'AccessoryFiles/LinguisticVariants/LinguisticVariants.csv'
+      'AccessoryFiles/LinguisticVariants/LinguisticVariants.csv',
+      // the external code mappings: their absence costs maps to other code systems, nothing else
+      'AccessoryFiles/PartFile/PartRelatedCodeMapping.csv',
+      'AccessoryFiles/LoincIeeeMedicalDeviceCodeMappingTable/LoincIeeeMedicalDeviceCodeMappingTable.csv'
     ];
 
     const warnings = [];
@@ -428,6 +432,11 @@ class LoincModule extends BaseTerminologyModule {
       'CREATE INDEX IF NOT EXISTS idx_descriptions_type ON Descriptions(DescriptionTypeKey)',
       'CREATE INDEX IF NOT EXISTS idx_descriptions_code_type ON Descriptions(CodeKey, DescriptionTypeKey)',
 
+      // External mapping indexes
+      'CREATE INDEX IF NOT EXISTS idx_externalcodes_code ON ExternalCodes(System, Code)',
+      'CREATE INDEX IF NOT EXISTS idx_externalmappings_code ON ExternalMappings(CodeKey)',
+      'CREATE INDEX IF NOT EXISTS idx_externalmappings_target ON ExternalMappings(ExternalCodeKey)',
+
       // Closure table indexes
       'CREATE INDEX IF NOT EXISTS idx_closure_ancestor ON Closure(AncestorKey)',
       'CREATE INDEX IF NOT EXISTS idx_closure_descendent ON Closure(DescendentKey)'
@@ -506,7 +515,9 @@ class LoincDataMigratorWithProgress {
       'AccessoryFiles/AnswerFile/AnswerList.csv',
       'AccessoryFiles/PartFile/LoincPartLink_Primary.csv',
       'AccessoryFiles/AnswerFile/LoincAnswerListLink.csv',
-      'AccessoryFiles/ComponentHierarchyBySystem/ComponentHierarchyBySystem.csv'
+      'AccessoryFiles/ComponentHierarchyBySystem/ComponentHierarchyBySystem.csv',
+      'AccessoryFiles/PartFile/PartRelatedCodeMapping.csv',
+      'AccessoryFiles/LoincIeeeMedicalDeviceCodeMappingTable/LoincIeeeMedicalDeviceCodeMappingTable.csv'
     ];
 
     // Count main files
@@ -599,6 +610,10 @@ class LoincDataMigrator {
       this.props = new Map();
       this.propValues = new Map();
       this.partNames = new Map();
+      this.extCodeKey = 0;
+      this.extCodes = new Map(); // system|version|code -> ExternalCodeKey
+      this.extMapKey = 0;
+      this.extMaps = new Set(); // codeKey|ExternalCodeKey
 
       // Create tables and initial data
       await this.createTables(db, version, options.verbose);
@@ -631,6 +646,10 @@ class LoincDataMigrator {
       this.updateProgress(0, 'List Links');
       await this.processListLinks(db, sourceDir, 8, options);
 
+      this.updateProgress(0, 'External Mappings');
+      await this.processPartMappings(db, sourceDir, 9, options);
+      await this.processIeeeMappings(db, sourceDir, 9, options);
+
       this.updateProgress(0, 'Hierarchy');
       await this.processHierarchy(db, sourceDir, 9, options);
 
@@ -719,6 +738,21 @@ class LoincDataMigrator {
                                      DescriptionTypeKey INTEGER NOT NULL,
                                      Value TEXT NOT NULL
        )`,
+      // Codes in other code systems that LOINC codes map to (one row per system|version|code)
+      `CREATE TABLE ExternalCodes (
+                                     ExternalCodeKey INTEGER NOT NULL PRIMARY KEY,
+                                     System TEXT NOT NULL,
+                                     Version TEXT NULL,
+                                     Code TEXT NOT NULL,
+                                     Display TEXT NULL
+       )`,
+      // LOINC code (Codes.CodeKey) -> ExternalCodes, with a ConceptMap equivalence (R4 codes)
+      `CREATE TABLE ExternalMappings (
+                                        ExternalMappingKey INTEGER NOT NULL PRIMARY KEY,
+                                        CodeKey INTEGER NOT NULL,
+                                        ExternalCodeKey INTEGER NOT NULL,
+                                        Equivalence TEXT NOT NULL
+       )`,
       `CREATE TABLE Closure (
                                 AncestorKey INTEGER NOT NULL,
                                 DescendentKey INTEGER NOT NULL,
@@ -843,10 +877,7 @@ class LoincDataMigrator {
       return;
     }
 
-    const rl = readline.createInterface({
-      input: fs.createReadStream(filePath),
-      crlfDelay: Infinity
-    });
+    const rl = csvRecords(filePath);
 
     let lineCount = 0;
     for await (const line of rl) {
@@ -872,10 +903,7 @@ class LoincDataMigrator {
     if (options.verbose) console.log('Processing Parts...');
 
     const filePath = path.join(sourceDir, 'AccessoryFiles/PartFile/Part.csv');
-    const rl = readline.createInterface({
-      input: fs.createReadStream(filePath),
-      crlfDelay: Infinity
-    });
+    const rl = csvRecords(filePath);
 
     let lineCount = 0;
     let processedCount = 0;
@@ -927,10 +955,7 @@ class LoincDataMigrator {
     if (options.verbose) console.log('Processing Main Codes...');
 
     const filePath = path.join(sourceDir, 'LoincTable/Loinc.csv');
-    const rl = readline.createInterface({
-      input: fs.createReadStream(filePath),
-      crlfDelay: Infinity
-    });
+    const rl = csvRecords(filePath);
 
     let lineCount = 0;
     let processedCount = 0;
@@ -1007,10 +1032,7 @@ class LoincDataMigrator {
 
     if (options.verbose) console.log('Processing Consumer Names...');
 
-    const rl = readline.createInterface({
-      input: fs.createReadStream(filePath),
-      crlfDelay: Infinity
-    });
+    const rl = csvRecords(filePath);
 
     let lineCount = 0;
     let processedCount = 0;
@@ -1045,10 +1067,7 @@ class LoincDataMigrator {
 
     if (options.verbose) console.log('Processing Answer Lists...');
 
-    const rl = readline.createInterface({
-      input: fs.createReadStream(filePath),
-      crlfDelay: Infinity
-    });
+    const rl = csvRecords(filePath);
 
     let lineCount = 0;
     let processedCount = 0;
@@ -1058,7 +1077,7 @@ class LoincDataMigrator {
       lineCount++;
       if (lineCount === 1) continue;
 
-      const items = csvSplit(line, 11);
+      const items = csvSplit(line, 15);
       if (items.length < 11) continue;
 
       await this.processListItem(db, items, currentList);
@@ -1111,6 +1130,111 @@ class LoincDataMigrator {
 
     this.addRelationship(db, listCodeKey, answerCodeKey, this.rels.get('Answer'));
     this.addRelationship(db, answerCodeKey, listCodeKey, this.rels.get('AnswerList'));
+
+    // ExtCodeId (11), ExtCodeDisplayName (12), ExtCodeSystem (13), ExtCodeSystemVersion (14).
+    // The file carries no equivalence for these; an answer and its external code are the same thing
+    if (items[11] && items[13]) {
+      this.addExternalMapping(db, answerCodeKey, items[13], items[14], items[11], items[12], 'equivalent');
+    }
+  }
+
+  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}`);
+      return;
+    }
+
+    if (options.verbose) console.log('Processing Part Mappings...');
+
+    const rl = csvRecords(filePath);
+
+    // PartNumber, PartName, PartTypeName, ExtCodeId, ExtCodeDisplayName, ExtCodeSystem,
+    // Equivalence, ContentOrigin, ExtCodeSystemVersion, ExtCodeSystemCopyrightNotice
+    let lineCount = 0;
+    let processedCount = 0;
+    for await (const line of rl) {
+      lineCount++;
+      if (lineCount === 1) continue;
+
+      const items = csvSplit(line, 10);
+      const partCode = items[0];
+      const system = items[5];
+      // RadLex mappings are not simple code-to-code maps; not handled yet
+      if (!items[3] || !system || system === 'http://www.radlex.org' || !this.codes.has(partCode)) continue;
+
+      this.addExternalMapping(db, this.codes.get(partCode).key, system, items[8], items[3], items[4], items[6] || 'equivalent');
+      processedCount++;
+
+      if (processedCount % 100 === 0) {
+        this.updateProgress(100);
+      }
+    }
+
+    const remaining = processedCount % 100;
+    if (remaining > 0) {
+      this.updateProgress(remaining);
+    }
+  }
+
+  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}`);
+      return;
+    }
+
+    if (options.verbose) console.log('Processing IEEE Mappings...');
+
+    const rl = csvRecords(filePath);
+
+    // LOINC_NUM, LOINC_LONG_COMMON_NAME, IEEE_CF_CODE10, IEEE_REFID, EQUIVALENCE
+    // The code is the CF_CODE10 (as used in FHIR, e.g. 150456); the REFID is its display.
+    let lineCount = 0;
+    let processedCount = 0;
+    for await (const line of rl) {
+      lineCount++;
+      if (lineCount === 1) continue;
+
+      const items = csvSplit(line, 5);
+      const loincCode = items[0];
+      if (!items[2] || !this.codes.has(loincCode)) continue;
+
+      this.addExternalMapping(db, this.codes.get(loincCode).key, 'urn:iso:std:iso:11073:10101', null,
+        items[2], items[3], ieeeEquivalence(items[4]));
+      processedCount++;
+
+      if (processedCount % 100 === 0) {
+        this.updateProgress(100);
+      }
+    }
+
+    const remaining = processedCount % 100;
+    if (remaining > 0) {
+      this.updateProgress(remaining);
+    }
+  }
+
+  addExternalMapping(db, codeKey, system, version, code, display, equivalence) {
+    system = normaliseExternalSystem(system);
+    version = version || null;
+    const targetId = system + '|' + (version || '') + '|' + code;
+    let extKey = this.extCodes.get(targetId);
+    if (!extKey) {
+      this.extCodeKey++;
+      extKey = this.extCodeKey;
+      this.extCodes.set(targetId, extKey);
+      db.run('INSERT INTO ExternalCodes (ExternalCodeKey, System, Version, Code, Display) VALUES (?, ?, ?, ?, ?)',
+        [extKey, system, version, code, display || null]);
+    }
+
+    // the same answer appears once per answer list it's in
+    const mapId = codeKey + '|' + extKey;
+    if (this.extMaps.has(mapId)) return;
+    this.extMaps.add(mapId);
+    this.extMapKey++;
+    db.run('INSERT INTO ExternalMappings (ExternalMappingKey, CodeKey, ExternalCodeKey, Equivalence) VALUES (?, ?, ?, ?)',
+      [this.extMapKey, codeKey, extKey, equivalence]);
   }
 
   async processPartLinks(db, sourceDir, step, options) {
@@ -1122,10 +1246,7 @@ class LoincDataMigrator {
 
     if (options.verbose) console.log('Processing Part Links...');
 
-    const rl = readline.createInterface({
-      input: fs.createReadStream(filePath),
-      crlfDelay: Infinity
-    });
+    const rl = csvRecords(filePath);
 
     let lineCount = 0;
     let processedCount = 0;
@@ -1171,10 +1292,7 @@ class LoincDataMigrator {
 
     if (options.verbose) console.log('Processing List Links...');
 
-    const rl = readline.createInterface({
-      input: fs.createReadStream(filePath),
-      crlfDelay: Infinity
-    });
+    const rl = csvRecords(filePath);
 
     let lineCount = 0;
     let processedCount = 0;
@@ -1227,10 +1345,7 @@ class LoincDataMigrator {
 
     if (options.verbose) console.log('Processing Hierarchy...');
 
-    const rl = readline.createInterface({
-      input: fs.createReadStream(filePath),
-      crlfDelay: Infinity
-    });
+    const rl = csvRecords(filePath);
 
     let lineCount = 0;
     let processedCount = 0;
@@ -1258,7 +1373,7 @@ class LoincDataMigrator {
   async processHierarchyItem(db, items) {
     const pathCode = items[3];
     const parentPath = items[2];
-    const description = items[4];
+    const description = items[4].trim();
 
     if (!this.codes.has(pathCode)) {
       this.codeKey++;
@@ -1339,10 +1454,7 @@ class LoincDataMigrator {
       return;
     }
 
-    const rl = readline.createInterface({
-      input: fs.createReadStream(filePath),
-      crlfDelay: Infinity
-    });
+    const rl = csvRecords(filePath);
 
     let lineCount = 0;
     let processedCount = 0;
@@ -1488,6 +1600,29 @@ function adjustPropName(s) {
   throw new Error(`Unknown Property Name: ${s}`);
 }
 
+// LOINC names some code systems with something other than their FHIR URI. The others not yet
+// known ('CMS LCDS', 'Unicode') are left as LOINC has them
+const EXTERNAL_SYSTEM_URIS = {
+  'CMS/HCPCS': 'http://www.cms.gov/Medicare/Coding/HCPCSReleaseCodeSets',
+  'https://www.cdc.gov/phin': 'urn:oid:2.16.840.1.113883.6.238' // CDC Race & Ethnicity
+};
+
+function normaliseExternalSystem(system) {
+  return EXTERNAL_SYSTEM_URIS[system] || system;
+}
+
+// The IEEE table states equivalence from the LOINC side ('broader' = the LOINC code is broader,
+// e.g. Glucose in Serum or Plasma -> MDC_CONC_GLU_VENOUS_PLASMA). ConceptMap equivalence is stated
+// from the target side, so broader/narrower swap to narrower/wider.
+function ieeeEquivalence(s) {
+  switch (s) {
+    case 'broader': return 'narrower';
+    case 'narrower': return 'wider';
+    case '': return 'equivalent';
+    default: return s;
+  }
+}
+
 function descClassType(s) {
   const types = {
     '1': 'Laboratory class',
@@ -1539,5 +1674,6 @@ function removeQuotes(str) {
 
 module.exports = {
   LoincModule,
-  LoincDataMigrator
+  LoincDataMigrator,
+  normaliseExternalSystem
 };

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

@@ -1136,6 +1136,12 @@ class SnomedImporter {
       // Step 10: Read relationships
       await this.readRelationships();
 
+      // Step 10a: Read alternate identifiers (e.g. the LOINC codes of the LOINC Extension)
+      await this.readIdentifiers();
+
+      // Step 10b: Read concrete value relationships (sct2_RelationshipConcreteValues)
+      await this.readConcreteValues();
+
       // Step 11: Link concepts
       this.linkConcepts();
 
@@ -1165,6 +1171,8 @@ class SnomedImporter {
       concepts: [],
       descriptions: [],
       relationships: [],
+      identifiers: [],
+      concreteValues: [],
       refsetDirectories: []
     };
 
@@ -1218,6 +1226,10 @@ class SnomedImporter {
       } else if (firstLine.startsWith('id\teffectiveTime\tactive\tmoduleId\tsourceId\tdestinationId\trelationshipGroup\ttypeId\tcharacteristicTypeId\tmodifierId') &&
           !filePath.includes('StatedRelationship')) {
         files.relationships.push(filePath);
+      } else if (files.identifiers && firstLine.startsWith('alternateIdentifier\teffectiveTime\tactive\tmoduleId\tidentifierSchemeId\treferencedComponentId')) {
+        files.identifiers.push(filePath);
+      } else if (files.concreteValues && firstLine.startsWith('id\teffectiveTime\tactive\tmoduleId\tsourceId\tvalue\trelationshipGroup\ttypeId\tcharacteristicTypeId\tmodifierId')) {
+        files.concreteValues.push(filePath);
       }
     } catch (error) {
       console.log(`DEBUG: Error reading file ${filePath}: ${error.message}`);
@@ -1726,6 +1738,108 @@ class SnomedImporter {
     return /^\d+$/.test(str);
   }
 
+  /**
+   * Read the alternate identifier files (sct2_Identifier). Each active row gives a
+   * concept a code in another scheme - the LOINC Extension, for instance, gives each
+   * of its concepts its LOINC code (scheme 30051010000102 |LOINC code identifier|).
+   * Kept as [scheme, module, code, conceptId] for the concepts in this edition; where
+   * a row appears more than once (Full files, or base + extension) the latest wins.
+   */
+  async readIdentifiers() {
+    const rows = new Map(); // scheme|code|concept -> {effectiveTime, active, row}
+    for (const file of this.files.identifiers || []) {
+      const rl = readline.createInterface({
+        input: fs.createReadStream(file),
+        crlfDelay: Infinity
+      });
+      let lineCount = 0;
+      for await (const line of rl) {
+        lineCount++;
+        if (lineCount === 1 || !line) continue;
+        const parts = line.split('\t');
+        if (parts.length < 6) continue;
+        const [code, effectiveTime, active, moduleId, schemeId, conceptId] = parts.map(p => p.trim());
+        const key = schemeId + '|' + code + '|' + conceptId;
+        const prior = rows.get(key);
+        if (!prior || prior.effectiveTime <= effectiveTime) {
+          rows.set(key, { effectiveTime, active: active === '1', row: [schemeId, moduleId, code, conceptId] });
+        }
+      }
+    }
+    this.identifiers = [];
+    let missing = 0;
+    for (const r of rows.values()) {
+      if (!r.active) continue;
+      let known = false;
+      try {
+        known = this.conceptMap.has(BigInt(r.row[3]));
+      } catch {
+        known = false;
+      }
+      if (known) {
+        this.identifiers.push(r.row);
+      } else {
+        missing++;
+      }
+    }
+    this.identifiers.sort((a, b) => (a.join('|') < b.join('|') ? -1 : 1));
+    if (this.identifiers.length > 0 || missing > 0) {
+      console.log(`Alternate identifiers: ${this.identifiers.length}${missing ? ` (${missing} for concepts not in this edition, ignored)` : ''}`);
+    }
+  }
+
+  /**
+   * Read the concrete value relationship files (sct2_RelationshipConcreteValues_*):
+   * the numeric and string attribute values of concepts (strength, count of base of
+   * active ingredient, ...). Kept as rows [sourceId, typeId, group, value] - the value
+   * as written in RF2 ("#500", "#5.5", "\"text\"", "true") - for the ECL evaluator;
+   * they are not relationships to concepts, so they do not join the relationship
+   * table. Only active, inferred rows; where a row appears more than once the latest
+   * effectiveTime wins.
+   */
+  async readConcreteValues() {
+    const rows = new Map(); // id -> {effectiveTime, active, row}
+    for (const file of this.files.concreteValues || []) {
+      const rl = readline.createInterface({
+        input: fs.createReadStream(file),
+        crlfDelay: Infinity
+      });
+      let lineCount = 0;
+      for await (const line of rl) {
+        lineCount++;
+        if (lineCount === 1 || !line) continue;
+        const parts = line.split('\t');
+        if (parts.length < 10) continue;
+        const [id, effectiveTime, active, , sourceId, value, group, typeId, characteristicTypeId] = parts.map(p => p.trim());
+        if (characteristicTypeId !== '900000000000011006') continue; // inferred only
+        const prior = rows.get(id);
+        if (!prior || prior.effectiveTime <= effectiveTime) {
+          rows.set(id, { effectiveTime, active: active === '1', row: [sourceId, typeId, parseInt(group, 10) || 0, value] });
+        }
+      }
+    }
+    this.concreteValues = [];
+    let missing = 0;
+    for (const r of rows.values()) {
+      if (!r.active) continue;
+      let known = false;
+      try {
+        known = this.conceptMap.has(BigInt(r.row[0])) && this.conceptMap.has(BigInt(r.row[1]));
+      } catch {
+        known = false;
+      }
+      if (known) {
+        this.concreteValues.push(r.row);
+      } else {
+        missing++;
+      }
+    }
+    this.concreteValues.sort((a, b) => (a.join('|') < b.join('|') ? -1 : 1));
+    if (this.concreteValues.length > 0 || missing > 0) {
+      console.log(`Concrete values: ${this.concreteValues.length}${missing ? ` (${missing} for concepts not in this edition, ignored)` : ''}`);
+    }
+  }
+
   async readRelationships() {
     // Estimate total lines
     let totalLines = 0;
@@ -2766,8 +2880,15 @@ class SnomedImporter {
 
     progressBar?.update(50);
 
+    const identifiers = this.identifiers || [];
+    const concreteValues = this.concreteValues || [];
     await writer.writeCache({
-      version: '17', // Current version
+      // 17 = the base format; 18 = 17 plus the alternate identifiers; 19 = 18 plus
+      // the concrete value relationships. Each is only used when it has something
+      // to carry, so that caches without them stay readable by older servers.
+      version: concreteValues.length > 0 ? '19' : identifiers.length > 0 ? '18' : '17',
+      identifiers: identifiers,
+      concreteValues: concreteValues,
       versionUri: this.isTesting ? this.config.uri.replace("/sct/", "/xsct/") : this.config.uri,
       versionDate: this.extractDateFromUri(this.config.uri),
 
@@ -2854,6 +2975,15 @@ class SnomedCacheWriter {
     }
     buffers.push(this.writeInteger(data.defaultLanguage));
 
+    if (data.version === '18' || data.version === '19') {
+      // alternate identifiers, as JSON: [[scheme, module, code, conceptId], ...]
+      buffers.push(this.writeBytes(Buffer.from(JSON.stringify(data.identifiers || []), 'utf8')));
+    }
+    if (data.version === '19') {
+      // concrete value relationships, as JSON: [[sourceId, typeId, group, value], ...]
+      buffers.push(this.writeBytes(Buffer.from(JSON.stringify(data.concreteValues || []), 'utf8')));
+    }
+
     // Write to file
     const finalBuffer = Buffer.concat(buffers);
     await fs.promises.writeFile(this.filePath, finalBuffer);

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

@@ -2,6 +2,7 @@ const { BaseTerminologyModule } = require('./tx-import-base');
 const fs = require('fs');
 const path = require('path');
 const readline = require('readline');
+const { csvRecords } = require('./csv-records');
 const chalk = require('chalk');
 
 class LoincSubsetModule extends BaseTerminologyModule {
@@ -716,6 +717,16 @@ class LoincSubsetProcessor {
         dest: 'AccessoryFiles/ComponentHierarchyBySystem/ComponentHierarchyBySystem.csv',
         handler: 'processHierarchy'
       },
+      {
+        source: 'AccessoryFiles/PartFile/PartRelatedCodeMapping.csv',
+        dest: 'AccessoryFiles/PartFile/PartRelatedCodeMapping.csv',
+        handler: 'processFirstColumnCodes'
+      },
+      {
+        source: 'AccessoryFiles/LoincIeeeMedicalDeviceCodeMappingTable/LoincIeeeMedicalDeviceCodeMappingTable.csv',
+        dest: 'AccessoryFiles/LoincIeeeMedicalDeviceCodeMappingTable/LoincIeeeMedicalDeviceCodeMappingTable.csv',
+        handler: 'processFirstColumnCodes'
+      },
       {
         source: 'AccessoryFiles/LinguisticVariants/LinguisticVariants.csv',
         dest: 'AccessoryFiles/LinguisticVariants/LinguisticVariants.csv',
@@ -787,7 +798,8 @@ class LoincSubsetProcessor {
       path.join(destDir, 'AccessoryFiles/ConsumerName'),
       path.join(destDir, 'AccessoryFiles/AnswerFile'),
       path.join(destDir, 'AccessoryFiles/ComponentHierarchyBySystem'),
-      path.join(destDir, 'AccessoryFiles/LinguisticVariants')
+      path.join(destDir, 'AccessoryFiles/LinguisticVariants'),
+      path.join(destDir, 'AccessoryFiles/LoincIeeeMedicalDeviceCodeMappingTable')
     ];
 
     for (const dir of dirs) {
@@ -879,6 +891,16 @@ class LoincSubsetProcessor {
     });
   }
 
+  // keep the rows whose first column (the LOINC code or part) is in the subset
+  async processFirstColumnCodes(sourcePath, destPath) {
+    await this.processFileWithFilter(sourcePath, destPath, (line, lineNum) => {
+      if (lineNum === 1) return true; // Keep header
+
+      const items = this.csvSplit(line, 1);
+      return this.targetCodes.has(this.removeQuotes(items[0]));
+    });
+  }
+
   async processAnswerLists(sourcePath, destPath) {
     await this.processFileWithFilter(sourcePath, destPath, (line, lineNum) => {
       if (lineNum === 1) return true; // Keep header
@@ -1002,13 +1024,10 @@ class LoincSubsetProcessor {
       return;
     }
 
-    const readStream = fs.createReadStream(sourcePath);
     const writeStream = fs.createWriteStream(destPath);
 
-    const rl = readline.createInterface({
-      input: readStream,
-      crlfDelay: Infinity
-    });
+    // records, not lines: a quoted field can hold a line break
+    const rl = csvRecords(sourcePath);
 
     let lineNum = 0;
     let includedLines = 0;

package/tx/library/codesystem.js

@@ -649,7 +649,10 @@ class CodeSystem extends CanonicalResource {
     if (this.jsonObj.url === 'https://terminology.dhp.uz/fhir/CodeSystem/loinc-supplement-uz') {
       return true;
     }
-    return (this.jsonObj.extension || []).find(x => x.url == 'http://hl7.org/fhir/StructureDefinition/codesystem-supplement-type' && getValuePrimitive(x) == 'lang-pack');
+    // a global language pack is used whether or not it is referenced. The code was 'lang-pack'
+    // until Oct 2026; it is still accepted, so that supplements marked the old way keep working
+    return (this.jsonObj.extension || []).find(x => x.url == 'http://hl7.org/fhir/StructureDefinition/codesystem-supplement-type'
+      && ['global-lang-pack', 'lang-pack'].includes(getValuePrimitive(x)));
   }
 
   isPropUri(code, uri) {