fhirsmith 0.5.5 → 0.5.6

package/CHANGELOG.md

@@ -5,6 +5,18 @@ All notable changes to the Health Intersections Node Server will be documented i
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v0.5.6] - 2026-02-26
+
+### Changed
+- Added content to TerminologyCapabilities.codeSystem
+- fix LOINC list filter handling
+- Improve Diagnostic Logging
+- Add icd-9-cm parser
+
+### Tx Conformance Statement
+
+FHIRsmith 0.5.5 passed all 1382 HL7 terminology service tests (modes tx.fhir.org,omop,general,snomed, tests v1.9.0, runner v6.8.1)
+
 ## [v0.5.5] - 2026-02-26
 
 ### Changed

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "fhirsmith",
-  "version": "0.5.5",
+  "version": "0.5.6",
   "description": "A Node.js server that provides a collection of tools to serve the FHIR ecosystem",
   "main": "server.js",
   "engines": {

package/tx/cs/cs-api.js

@@ -785,6 +785,10 @@ class CodeSystemFactoryProvider {
    */
   version() { throw new Error("Must override"); }
 
+  content() {
+    return "complete";
+  }
+
   getPartialVersion() {
     let ver = this.version();
     if (ver && VersionUtilities.isSemVer(ver)) {

package/tx/cs/cs-loinc.js

@@ -670,7 +670,7 @@ class LoincServices extends BaseCSServices {
       sql = `SELECT DISTINCT TargetKey as Key FROM Relationships
              WHERE RelationshipTypeKey = ${this.relationships.get('Answer')}
                AND SourceKey IN (SELECT CodeKey FROM Codes WHERE Code = '${this.#sqlWrapString(value)}')
-             ORDER BY SourceKey ASC`;
+             ORDER BY TargetKey ASC`;
       lsql = `SELECT COUNT(DISTINCT TargetKey) FROM Relationships
               WHERE RelationshipTypeKey = ${this.relationships.get('Answer')}
                 AND SourceKey IN (SELECT CodeKey FROM Codes WHERE Code = '${this.#sqlWrapString(value)}')

package/tx/library/renderer.js

@@ -22,18 +22,17 @@ class Renderer {
   displayCoded(...args) {
     if (args.length === 1) {
       const arg = args[0];
-      if (arg.systemUri !== undefined && arg.version !== undefined && arg.code !== undefined && arg.display !== undefined) {
+      if (arg instanceof CodeSystemProvider) {
+        return arg.system() + "|" + arg.version();
+      } else  if (arg.system !== undefined && arg.version !== undefined && arg.code !== undefined && arg.display !== undefined) {
         // It's a Coding
         return this.displayCodedCoding(arg);
       } else if (arg.coding !== undefined || arg.text) {
         // It's a CodeableConcept
         return this.displayCodedCodeableConcept(arg);
-      } else if (arg.systemUri !== undefined && arg.version !== undefined) {
+      } else if (arg.system !== undefined && arg.version !== undefined) {
         // It's a CodeSystemProvider
         return this.displayCodedProvider(arg);
-      } else if (arg instanceof CodeSystemProvider) {
-        let cs = arg;
-        return cs.system() + "|" + cs.version();
       }
     } else if (args.length === 2) {
       return this.displayCodedSystemVersion(args[0], args[1]);
@@ -46,7 +45,7 @@ class Renderer {
   }
 
   displayCodedProvider(system) {
-    let result = system.systemUri + '|' + system.version;
+    let result = system.system + '|' + system.version;
     if (system.sourcePackage) {
       result = result + ' (from ' + system.sourcePackage + ')';
     }
@@ -70,7 +69,7 @@ class Renderer {
   }
 
   displayCodedCoding(code) {
-    return this.displayCodedSystemVersionCodeDisplay(code.systemUri, code.version, code.code, code.display);
+    return this.displayCodedSystemVersionCodeDisplay(code.system, code.version, code.code, code.display);
   }
 
   displayCodedCodeableConcept(code) {
@@ -90,12 +89,12 @@ class Renderer {
 
   displayValueSetInclude(inc) {
     let result;
-    if (inc.systemUri) {
-      result = '(' + inc.systemUri + ')';
-      if (inc.hasConcepts) {
+    if (inc.system) {
+      result = '(' + inc.system + ')';
+      if (inc.concept) {
         result = result + '(';
         let first = true;
-        for (const cc of inc.concepts) {
+        for (const cc of inc.concept) {
           if (first) {
             first = false;
           } else {
@@ -105,23 +104,23 @@ class Renderer {
         }
         result = result + ')';
       }
-      if (inc.hasFilters) {
+      if (inc.filter) {
         result = result + '(';
         let first = true;
-        for (const ci of inc.filters) {
+        for (const ci of inc.filter) {
           if (first) {
             first = false;
           } else {
             result = result + ',';
           }
-          result = result + ci.prop + ci.op + ci.value;
+          result = result + ci.property + ci.op + ci.value;
         }
         result = result + ')';
       }
     } else {
       result = '(';
       let first = true;
-      for (const s of inc.valueSets || []) {
+      for (const s of inc.valueSet || []) {
         if (first) {
           first = false;
         } else {
@@ -1557,6 +1556,10 @@ class Renderer {
             // No versions specified
             await this.renderLink(li, cs.uri);
           }
+          let content = cs.content || Extensions.readString(cs, "http://hl7.org/fhir/4.0/StructureDefinition/extension-TerminologyCapabilities.codeSystem.content");
+          if (content && content != "complete") {
+            li.tx(" (" + content + ")");
+          }
         }
       }
     }

package/tx/workers/expand.js

@@ -632,7 +632,7 @@ class ValueSetExpander {
           } else if (cs.contentMode() === 'supplement') {
             throw new Issue('error', 'business-rule', null, null, 'The code system definition for ' + cset.system + ' defines a supplement, so this expansion cannot be performed', 'invalid');
           } else {
-            this.addParamUri(exp, cs.contentMode(), cs.system + '|' + cs.version);
+            this.addParamUri(exp, cs.contentMode(), cs.system() + '|' + cs.version());
             Extensions.addString(exp, "http://hl7.org/fhir/StructureDefinition/valueset-unclosed",
               "This extension is based on a fragment of the code system " + cset.system);
           }

package/tx/workers/metadata.js

@@ -325,9 +325,10 @@ class MetadataHandler {
       for (const cs of provider.codeSystems.values()) {
         const url = cs.url || (cs.jsonObj && cs.jsonObj.url);
         const version = cs.version || (cs.jsonObj && cs.jsonObj.version);
+        const content = cs.content || cs.jsonObj.content;
 
         if (url) {
-          this.addCodeSystemEntry(seenSystems, url, version);
+          this.addCodeSystemEntry(seenSystems, url, version, content);
         }
       }
     }
@@ -339,7 +340,7 @@ class MetadataHandler {
         const version = factory.version();
 
         if (url) {
-          this.addCodeSystemEntry(seenSystems, url, version);
+          this.addCodeSystemEntry(seenSystems, url, version, factory.content());
         }
       }
     }
@@ -357,13 +358,16 @@ class MetadataHandler {
    * @param {string} url - Code system URL
    * @param {string} version - Code system version (may be null)
    */
-  addCodeSystemEntry(seenSystems, url, version) {
+  addCodeSystemEntry(seenSystems, url, version, content) {
     if (!seenSystems.has(url)) {
       // Create new entry
       const entry = { uri: url };
       if (version) {
         entry.version = [{ code: version }];
       }
+      if (content) {
+        entry.content = content;
+      }
       seenSystems.set(url, entry);
     } else if (version) {
       // Add version to existing entry
@@ -371,6 +375,9 @@ class MetadataHandler {
       if (!entry.version) {
         entry.version = [];
       }
+      if (content) {
+        entry.content = content;
+      }
       // Check if version already exists
       if (!entry.version.some(v => v.code === version)) {
         entry.version.push({ code: version });

package/tx/workers/validate.js

@@ -44,6 +44,7 @@ class ValueSetChecker {
   valueSet;
   params;
   others = new Map();
+  indentCount = 0;
 
   constructor(worker, valueSet, params) {
     validateParameter(worker, "worker", TerminologyWorker);
@@ -302,8 +303,8 @@ class ValueSetChecker {
       this.seeValueSet();
       this.worker.opContext.addNote(this.valueSet, 'Analysing ' + this.valueSet.vurl + ' for validation purposes', this.indentCount);
       if (this.indentCount === 0) {
-        this.worker.opContext.addNote(this.valueSet, 'Parameters: ' + this.params.summary, this.indentCount);
-        let vrs = this.params.verSummary;
+        this.worker.opContext.addNote(this.valueSet, 'Parameters: ' + this.params.summary(), this.indentCount);
+        let vrs = this.params.verSummary();
         if (vrs) {
           this.worker.opContext.addNote(this.valueSet, 'Version Rules: ' + vrs, this.indentCount);
         }
@@ -1731,7 +1732,7 @@ class ValueSetChecker {
     let list = [];
     for (let filter of cset.filter) {
       let s = cset.filter.length > 1 ? "(" : "";
-      s = filter.prop+" "+filter.op+" "+filter.value;
+      s = filter.property+" "+filter.op+" "+filter.value;
       s = s + (cset.filter.length > 1 ? ")" : "");
       list.push(s)
     }

package/tx/workers/worker.js

@@ -316,7 +316,7 @@ class TerminologyWorker {
       for (const ext of supplementExtensions) {
         const supplementUrl = ext.valueString || ext.valueUri;
         if (supplementUrl && !cs.hasSupplement(this.opContext, supplementUrl)) {
-          throw new TerminologyError(`ValueSet depends on supplement '${supplementUrl}' on ${cs.systemUri} that is not known`);
+          throw new TerminologyError(`ValueSet depends on supplement '${supplementUrl}' on ${cs.system} that is not known`);
         }
       }
     }

package/tx/xversion/xv-terminologyCapabilities.js

@@ -1,4 +1,5 @@
 const {VersionUtilities} = require("../../library/version-utilities");
+const {Extensions} = require("../library/extensions");
 
 /**
  * Converts input TerminologyCapabilities to R5 format (modifies input object for performance)
@@ -14,7 +15,17 @@ function terminologyCapabilitiesToR5(jsonObj, sourceVersion) {
   }
 
   if (VersionUtilities.isR4Ver(sourceVersion)) {
-    // R4 to R5: No major structural changes needed for TerminologyCapabilities
+    for (const cs of jsonObj.codeSystem || []) {
+      if (cs.content) {
+        let cnt = Extensions.readString("http://hl7.org/fhir/5.0/StructureDefinition/extension-TerminologyCapabilities.codeSystem.content");
+        if (cnt) {
+          delete cs.extensions;
+          cs.content = cnt;
+        }
+      }
+    }
+
+
     return jsonObj;
   }
 
@@ -125,6 +136,15 @@ function terminologyCapabilitiesR5ToR4(r5Obj) {
   if (r5Obj.versionAlgorithmCoding) {
     delete r5Obj.versionAlgorithmCoding;
   }
+  for (const cs of r5Obj.codeSystem || []) {
+    if (cs.content) {
+      if (!cs.extension) {
+        cs.extension = [];
+      }
+      cs.extension.push({"url" : "http://hl7.org/fhir/5.0/StructureDefinition/extension-TerminologyCapabilities.codeSystem.content", valueCode : cs.content});
+      delete cs.content;
+    }
+  }
 
   return r5Obj;
 }

package/utilities/icd9cm-parser.js

@@ -0,0 +1,313 @@
+#!/usr/bin/env node
+/**
+ * parse-icd9.js
+ * Parses an ICD-9-CM text file into a FHIR R4 CodeSystem resource.
+ *
+ * Usage:
+ *   node parse-icd9.js <input-file> [output-file]
+ *
+ * File format observed:
+ *
+ *   GROUP HEADERS (two forms):
+ *     [Roman numeral.  ]DISPLAY (NNN-NNN)          <- top-level chapter
+ *     DISPLAY (NNN-NNN)                             <- sub-chapter / block
+ *
+ *   ICD-9 CONCEPT HEADERS:
+ *     NNN[.D...]<whitespace>DISPLAY
+ *     (code is left-aligned; display follows after one or more spaces/tabs)
+ *
+ *   CONTINUATION / ANNOTATION LINES:
+ *     Lines that are neither a group header nor a code header and are not
+ *     blank.  They belong to the most recently opened concept.
+ *     Keyword prefixes  Includes:  Excludes:  Note:  start a named section.
+ *     Subsequent indented lines continue that section.
+ */
+
+'use strict';
+
+const fs   = require('fs');
+const path = require('path');
+
+// ── helpers ──────────────────────────────────────────────────────────────────
+
+function normalise(str) {
+  return str.replace(/[ \t]+/g, ' ').trim();
+}
+
+// Group header: optional roman-numeral prefix + display text + (NNN-NNN)
+// Also handles V-code ranges like (V01-V91) and E-code ranges (E800-E999)
+const GROUP_HDR = /^(?:[IVXLCDM]+\.\s+)?(.*?)\s+\(([A-Z]?\d{1,3}-[A-Z]?\d{1,3})\)\s*$/;
+
+// ICD-9 / V-code / E-code concept header: code at column 0, then 1+ spaces, then display
+const CODE_HDR = /^([A-Z]?\d{2,3}(?:\.\d+)?)\s+(\S.*)/;
+
+function isGroupHeader(line) {
+  return GROUP_HDR.test(line.trim());
+}
+
+function isCodeHeader(line) {
+  // Must start at column 0 (no leading whitespace)
+  return /^[A-Z]?\d/.test(line) && CODE_HDR.test(line);
+}
+
+function parseGroupHeader(line) {
+  const m = line.trim().match(GROUP_HDR);
+  if (!m) return null;
+  return { code: m[2], display: normalise(m[1]) };
+}
+
+function parseCodeHeader(line) {
+  const m = line.match(CODE_HDR);
+  if (!m) return null;
+  return { code: m[1].trim(), display: normalise(m[2]) };
+}
+
+// ── block collection ──────────────────────────────────────────────────────────
+
+/**
+ * Walk lines and emit raw blocks.
+ * Each block = { type: 'group'|'icd9', lines: string[] }
+ * The first line is the header; subsequent lines are body lines (still raw).
+ */
+function collectBlocks(lines) {
+  const blocks = [];
+  let current = null;
+
+  const flush = () => { if (current) { blocks.push(current); current = null; } };
+
+  for (const raw of lines) {
+    const trimmed = raw.trim();
+
+    if (!trimmed) {
+      // blank line - keep current open; annotations can span blank lines
+      continue;
+    }
+
+    if (isGroupHeader(trimmed)) {
+      flush();
+      current = { type: 'group', lines: [trimmed] };
+    } else if (isCodeHeader(raw)) {
+      flush();
+      current = { type: 'icd9', lines: [raw] };
+    } else {
+      // continuation / annotation
+      if (current) current.lines.push(raw);
+      // lines before the first recognised header are silently dropped
+    }
+  }
+  flush();
+  return blocks;
+}
+
+// ── block -> record ────────────────────────────────────────────────────────────
+
+/**
+ * Given a list of body lines (after the header), split into named sections.
+ * Returns { description, includes, excludes, note } - each a plain string or undefined.
+ */
+function parseSections(bodyLines) {
+  const lines = bodyLines.map(normalise).filter(Boolean);
+
+  const sections = { description: [], includes: [], excludes: [], note: [] };
+  let cur = 'description';
+
+  for (const line of lines) {
+    if (/^includes?:/i.test(line)) {
+      cur = 'includes';
+      const rest = line.replace(/^includes?:\s*/i, '').trim();
+      if (rest) sections.includes.push(rest);
+    } else if (/^excludes?:/i.test(line)) {
+      cur = 'excludes';
+      const rest = line.replace(/^excludes?:\s*/i, '').trim();
+      if (rest) sections.excludes.push(rest);
+    } else if (/^note:/i.test(line)) {
+      cur = 'note';
+      const rest = line.replace(/^note:\s*/i, '').trim();
+      if (rest) sections.note.push(rest);
+    } else {
+      sections[cur].push(line);
+    }
+  }
+
+  const join = arr => arr.join(' ').replace(/\s+/g, ' ').trim() || undefined;
+  return {
+    description : join(sections.description),
+    includes    : join(sections.includes),
+    excludes    : join(sections.excludes),
+    note        : join(sections.note),
+  };
+}
+
+function parseBlock(block) {
+  let header;
+  if (block.type === 'group') {
+    header = parseGroupHeader(block.lines[0]);
+  } else {
+    header = parseCodeHeader(block.lines[0]);
+  }
+  if (!header) return null;
+
+  const sections = parseSections(block.lines.slice(1));
+
+  return {
+    code    : header.code,
+    display : header.display,
+    isGroup : block.type === 'group',
+    ...sections,
+  };
+}
+
+// ── hierarchy ─────────────────────────────────────────────────────────────────
+
+/**
+ * Find the best (narrowest) parent for a given code from codes already seen.
+ * Parents always precede children in the source file.
+ */
+function findParent(code, seenCodes) {
+  const isRange = /^[A-Z]?\d{1,3}-[A-Z]?\d{1,3}$/.test(code);
+
+  // Helper: strip leading letter and parse int
+  const numOf = s => parseInt(s.replace(/^[A-Z]/, ''), 10);
+
+  if (isRange) {
+    const [loStr, hiStr] = code.split('-');
+    const lo = numOf(loStr), hi = numOf(hiStr);
+    let best = null, bestSpan = Infinity;
+    for (const c of seenCodes) {
+      if (!/^[A-Z]?\d{1,3}-[A-Z]?\d{1,3}$/.test(c) || c === code) continue;
+      const [pLo, pHi] = c.split('-').map(numOf);
+      if (pLo <= lo && pHi >= hi) {
+        const span = pHi - pLo;
+        if (span < bestSpan) { best = c; bestSpan = span; }
+      }
+    }
+    return best;
+  }
+
+  // Decimal code e.g. "002.1" -> try "002"
+  const dotIdx = code.indexOf('.');
+  if (dotIdx !== -1) {
+    for (let len = code.length - 1; len >= dotIdx; len--) {
+      const candidate = code.substring(0, len);
+      if (seenCodes.includes(candidate)) return candidate;
+    }
+    const base = code.substring(0, dotIdx);
+    if (seenCodes.includes(base)) return base;
+  }
+
+  // Integer code e.g. "002" -> find narrowest containing range
+  const num = numOf(code);
+  let best = null, bestSpan = Infinity;
+  for (const c of seenCodes) {
+    if (!/^[A-Z]?\d{1,3}-[A-Z]?\d{1,3}$/.test(c)) continue;
+    const [pLo, pHi] = c.split('-').map(numOf);
+    if (pLo <= num && pHi >= num) {
+      const span = pHi - pLo;
+      if (span < bestSpan) { best = c; bestSpan = span; }
+    }
+  }
+  return best;
+}
+
+// ── FHIR CodeSystem builder ───────────────────────────────────────────────────
+
+function buildFhirCodeSystem(records) {
+  const byCode    = new Map(records.map(r => [r.code, r]));
+  const parentOf  = new Map();
+  const seenCodes = [];
+
+  for (const r of records) {
+    parentOf.set(r.code, findParent(r.code, seenCodes));
+    seenCodes.push(r.code);
+  }
+
+  const childrenOf = new Map();
+  for (const r of records) {
+    const p = parentOf.get(r.code);
+    if (p) {
+      if (!childrenOf.has(p)) childrenOf.set(p, []);
+      childrenOf.get(p).push(r.code);
+    }
+  }
+
+  function buildConcept(code) {
+    const r       = byCode.get(code);
+    const concept = { code: r.code, display: r.display };
+
+    const props = [];
+    if (r.isGroup)     props.push({ code: 'notSelectable', valueBoolean: true });
+    if (r.description) props.push({ code: 'description',   valueString: r.description });
+    if (r.includes)    props.push({ code: 'includes',      valueString: r.includes });
+    if (r.excludes)    props.push({ code: 'excludes',      valueString: r.excludes });
+    if (r.note)        props.push({ code: 'note',          valueString: r.note });
+    if (props.length)  concept.property = props;
+
+    const kids = childrenOf.get(code);
+    if (kids?.length)  concept.concept = kids.map(buildConcept);
+
+    return concept;
+  }
+
+  const roots = records.filter(r => !parentOf.get(r.code));
+
+  return {
+    resourceType     : 'CodeSystem',
+    id               : 'icd-9-cm',
+    url              : 'http://hl7.org/fhir/sid/icd-9-cm',
+    version          : '2015',
+    name             : 'ICD9CM',
+    title            : 'International Classification of Diseases, 9th Revision, Clinical Modification',
+    status           : 'active',
+    content          : 'complete',
+    hierarchyMeaning : 'is-a',
+    property         : [
+      {
+        code        : 'notSelectable',
+        uri         : 'http://hl7.org/fhir/concept-properties#notSelectable',
+        description : 'Grouping code not intended for direct coding',
+        type        : 'boolean',
+      },
+      { code: 'description', description: 'Additional descriptive text', type: 'string' },
+      { code: 'includes',    description: 'Inclusion notes',             type: 'string' },
+      { code: 'excludes',    description: 'Exclusion notes',             type: 'string' },
+      { code: 'note',        description: 'Additional notes',            type: 'string' },
+    ],
+    concept: roots.map(r => buildConcept(r.code)),
+  };
+}
+
+// ── main ──────────────────────────────────────────────────────────────────────
+
+function countAll(concepts) {
+  if (!concepts) return 0;
+  return concepts.reduce((n, c) => n + 1 + countAll(c.concept), 0);
+}
+
+function main() {
+  const [,, inputFile, outputFile] = process.argv;
+  if (!inputFile) {
+    console.error('Usage: node parse-icd9.js <input-file> [output-file]');
+    process.exit(1);
+  }
+
+  const outFile = outputFile || path.join(path.dirname(inputFile), 'icd9-cm.json');
+
+  const text  = fs.readFileSync(inputFile, 'utf8');
+  const lines = text.split(/\r?\n/);
+  console.log(`Read ${lines.length} lines`);
+
+  const blocks  = collectBlocks(lines);
+  console.log(`Collected ${blocks.length} blocks`);
+
+  const records = blocks.map(parseBlock).filter(Boolean);
+  const groups  = records.filter(r => r.isGroup).length;
+  console.log(`Parsed ${records.length} records  (${groups} groups, ${records.length - groups} codes)`);
+
+  const cs = buildFhirCodeSystem(records);
+  console.log(`CodeSystem has ${countAll(cs.concept)} concepts`);
+
+  fs.writeFileSync(outFile, JSON.stringify(cs, null, 2), 'utf8');
+  console.log(`Written -> ${outFile}`);
+}
+
+main();