fhirsmith 0.6.0 → 0.7.0

package/CHANGELOG.md

@@ -5,6 +5,26 @@ 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).
 
+## [v0.7.0] - 2026-03-13
+
+### Added
+- Add support for serving for OCL TX content (h/t Italo Macêdo from the OCL team)
+- Add default configurations (wip)
+
+### Changed
+- Make web-crawlers more robust after tx.fhir.org crash
+- Don't accept NPM packages that have .js code or install scripts
+
+### Fixed 
+- Fix many bugs in expansion and validation for value sets that include two different versions of the same code system
+- Fix CodeSystem search on system parameter to reduce user confusion
+- Fix CodeSystem search such that default search is without any specified source
+- Fix headers sent multiple times error
+
+### Tx Conformance Statement
+
+FHIRsmith passed all 1452 HL7 terminology service tests (modes tx.fhir.org+omop+general+snomed, tests v1.9.1-SNAPSHOT, runner v6.8.2)
+
 ## [v0.6.0] - 2026-03-06
 
 ### Added

package/README.md

@@ -229,6 +229,8 @@ GitHub Actions will automatically:
    - Change description
    ### Fixed
    - Bug fix description
+   ### Tx Conformance Statement
+     {copy content from text-cases-summary.txt}
 ```
 2. Update `package.json` to have the same release version
 

package/configurations/projector.json

@@ -0,0 +1,21 @@
+{
+  "hostName" : "NPM Publisher",
+  "server": {
+    "port": 3001,
+    "cors": {
+      "origin": true,
+      "credentials": true
+    }
+  },
+  "modules": {
+    "npmprojector": {
+      "enabled": false,
+      "fhirVersion": "r4",
+      "basePath": "/us-core",
+      "npm": "hl7.fhir.us.core#7.0.1",
+      "resourceFolders": ["data"],
+      "searchParametersFolder": "data",
+      "debounceMs": 500
+    }
+  }
+}

package/configurations/readme.md

@@ -0,0 +1,5 @@
+This folder contains some basic starter configurations:
+
+* Terminology server: see tx-config.json for a vanilla server that doesn't contain any licensed content
+* NPM web server: see projector.json for a basic configuration to make a package available online
+

package/library/package-manager.js

@@ -380,7 +380,6 @@ class PackageManager {
             return cachedPath;
         }
 
-        console.log("Fetch Package "+packageId+"#"+version);
         // Not in cache, fetch from servers
         const packageData = await this.fetchFromServers(packageId, resolvedVersion);
 
@@ -593,7 +592,6 @@ class PackageManager {
      * @returns {Promise<string>} Path to extracted package folder
      */
     async fetchUrl(url) {
-        console.log("Fetch Package from URL: " + url);
         try {
             const client = new CIBuildClient();
             const packageData = await client.fetchFromUrlSpecific(url);

package/library/version-utilities.js

@@ -1051,6 +1051,91 @@ class VersionUtilities {
             return url;
         }
     }
+
+
+    static isAnInteger(version) {
+        return /^\d+$/.test(version);
+    }
+
+    static appearsToBeDate(version) {
+        if (!version || typeof version !== 'string') return false;
+        // Strip optional time portion (T...) before checking
+        const datePart = version.split('T')[0];
+        return /^\d{4}-?\d{2}(-?\d{2})?$/.test(datePart);
+
+    }
+
+    static guessVersionAlgorithmFromVersion(version) {
+        if (VersionUtilities.isSemVerWithWildcards(version)) {
+            return 'semver';
+        }
+        if (this.appearsToBeDate(version)) {
+            return 'date';
+        }
+        if (this.isAnInteger(version)) {
+            return 'integer';
+        }
+        return 'alpha';
+    }
+
+    static dateIsMoreRecent(date, date2) {
+        return VersionUtilities.normaliseDateString(date) > VersionUtilities.normaliseDateString(date2);
+    }
+
+    static normaliseDateString(date) {
+        // Strip time portion, then remove dashes so all formats compare uniformly as YYYYMMDD or YYYYMM
+        return date.split('T')[0].replace(/-/g, '');
+    }
+
+
+    /**
+     * guesses the correct format, then compares accordingly
+     */
+    static compareVersionsGeneral(version1, version2) {
+        if (version1 && version2) {
+            if (version1 == version2) {
+                return 0;
+            }
+            const fmt1 = VersionUtilities.guessVersionAlgorithmFromVersion(version1);
+            const fmt2 = VersionUtilities.guessVersionAlgorithmFromVersion(version2);
+            if (fmt1 != fmt2) {
+                return version1.localeCompare(version2);
+            }
+            switch (fmt1) {
+                case 'semver': {
+                    let b1 = VersionUtilities.isThisOrLater(version1, version2, VersionPrecision.PATCH);
+                    let b2 = VersionUtilities.isThisOrLater(version2, version1, VersionPrecision.PATCH);
+                    if (b1 && b2) {
+                        return 0;
+                    } else if (b2) {
+                        return 1;
+                    } else {
+                        return -1;
+                    }
+                }
+                case 'date':
+                    if (VersionUtilities.dateIsMoreRecent(version1, version2)) {
+                        return 1;
+                    } else if (VersionUtilities.dateIsMoreRecent(version2, version1)) {
+                        return -1;
+                    } else {
+                        return 0;
+                    }
+                case 'integer':
+                    return parseInt(version1, 10) - parseInt(version2, 10);
+                case 'alpha':
+                    return version1.localeCompare(version2);
+                default:
+                    return version1.localeCompare(version2);
+            }
+        } else if (version1) {
+            return 1;
+        } else if (version2) {
+            return -1;
+        } else {
+            return 0;
+        }
+    }
 }
 
 module.exports = { VersionUtilities, VersionPrecision, SemverParser };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "fhirsmith",
-  "version": "0.6.0",
+  "version": "0.7.0",
   "description": "A Node.js server that provides a collection of tools to serve the FHIR ecosystem",
   "main": "server.js",
   "engines": {

package/packages/package-crawler.js

@@ -9,11 +9,12 @@ const {XMLParser} = require('fast-xml-parser');
 const crypto = require('crypto');
 const fs = require('fs');
 const path = require('path');
+const {debugLog} = require("../tx/operation-context");
 
 class PackageCrawler {
   log;
   packages = new Set();
-  
+
   constructor(config, db, stats) {
     this.config = config;
     this.db = db;
@@ -21,6 +22,7 @@ class PackageCrawler {
     this.totalBytes = 0;
     this.crawlerLog = {};
     this.errors = '';
+    this.abortController = null;
     this.db.run('PRAGMA journal_mode = WAL');
     this.db.run('PRAGMA busy_timeout = 5000');
   }
@@ -28,7 +30,8 @@ class PackageCrawler {
   async crawl(log) {
     this.log = log;
     this.packages.clear();
-    
+    this.abortController = new AbortController();
+
     const startTime = Date.now();
     this.crawlerLog = {
       startTime: new Date().toISOString(),
@@ -54,6 +57,7 @@ class PackageCrawler {
 
       // Process each feed
       for (const feedConfig of masterResponse.feeds) {
+        if (this.abortController?.signal.aborted) break;
         if (!feedConfig.url) {
           this.log.info('Skipping feed with no URL: '+ feedConfig);
           continue;
@@ -71,6 +75,7 @@ class PackageCrawler {
       }
       // process simplifier last
       for (const feedConfig of masterResponse.feeds) {
+        if (this.abortController?.signal.aborted) break;
         if (!feedConfig.url) {
           this.log.info('Skipping feed with no URL: '+ feedConfig);
           continue;
@@ -123,6 +128,7 @@ class PackageCrawler {
       } else {
         const response = await axios.get(url, {
           timeout: 30000,
+          signal: this.abortController?.signal,
           headers: {
             'User-Agent': 'FHIR Package Crawler/1.0'
           }
@@ -130,7 +136,7 @@ class PackageCrawler {
         return response.data;
       }
     } catch (error) {
-      console.log(error);
+      debugLog(error);
       if (error.response && error.response.status === 429) {
         throw new Error(`RATE_LIMITED: Server returned 429 Too Many Requests for ${url}`);
       }
@@ -151,6 +157,7 @@ class PackageCrawler {
       } else {
         const response = await axios.get(url, {
           timeout: 30000,
+          signal: this.abortController?.signal,
           headers: {
             'User-Agent': 'FHIR Package Crawler/1.0'
           }
@@ -165,6 +172,7 @@ class PackageCrawler {
         return parser.parse(response.data);
       }
     } catch (error) {
+      debugLog(error);
       if (error.response && error.response.status === 429) {
         throw new Error(`RATE_LIMITED: Server returned 429 Too Many Requests for ${url}`);
       }
@@ -182,6 +190,7 @@ class PackageCrawler {
         const response = await axios.get(url, {
           timeout: 60000,
           responseType: 'arraybuffer',
+          signal: this.abortController?.signal,
           headers: {
             'User-Agent': 'FHIR Package Crawler/1.0'
           }
@@ -191,6 +200,7 @@ class PackageCrawler {
         return Buffer.from(response.data);
       }
     } catch (error) {
+      debugLog(error);
       if (error.response && error.response.status === 429) {
         throw new Error(`RATE_LIMITED: Server returned 429 Too Many Requests for ${url}`);
       }
@@ -222,6 +232,7 @@ class PackageCrawler {
       this.log.info(`Found ${items.length} items in feed`);
 
       for (let i = 0; i < items.length; i++) {
+        if (this.abortController?.signal.aborted) break;
         try {
           await this.updateItem(url, items[i], i, packageRestrictions, feedLog);
         } catch (itemError) {
@@ -244,7 +255,7 @@ class PackageCrawler {
       }
 
     } catch (error) {
-      console.log(error);
+      debugLog(error);
       // Check if this is a 429 error on feed fetch
       if (error.message.includes('RATE_LIMITED')) {
         this.log.info(`Rate limited while fetching feed ${url}, skipping this feed`);
@@ -302,7 +313,7 @@ class PackageCrawler {
       }
 
       // Check package restrictions
-      if (!this.isPackageAllowed(id, source, packageRestrictions)) {
+      if (!this.isPackageAllowed(id, source, packageRestrictions).allowed) {
         if (!source.includes('simplifier.net')) {
           const error = `The package ${id} is not allowed to come from ${source}`;
           this.log.info(error);
@@ -329,11 +340,12 @@ class PackageCrawler {
 
       // Parse publication date
       let pubDate;
+      let pd;
       try {
         let pd = item.pubDate;
         pubDate = this.parsePubDate(pd);
       } catch (error) {
-        itemLog.error = `Invalid date format '{pd}': ${error.message}`;
+        itemLog.error = `Invalid date format '${pd}': ${error.message}`;
         itemLog.status = 'error';
         return;
       }
@@ -355,7 +367,7 @@ class PackageCrawler {
       itemLog.status = 'Fetched';
 
     } catch (error) {
-      this.log.error(`Exception processing item ${itemLog.guid || index}:`+ error.message);
+      this.log.error(`Exception processing item ${itemLog.guid || index} from ${source}: `+ error.message);
       itemLog.status = 'Exception';
       itemLog.error = error.message;
       if (error.message.includes('RATE_LIMITED')) {
@@ -383,7 +395,7 @@ class PackageCrawler {
 
       if (this.matchesPattern(fixedPackageId, fixedMask)) {
         // This package matches a restriction - check if source is allowed
-        const allowedFeeds = restriction.feeds.map(feed => feed);
+        const allowedFeeds = restriction.feeds.map(feed => fixUrl(feed));
         const feedList = allowedFeeds.join(', ');
 
         for (const allowedFeed of restriction.feeds) {
@@ -485,6 +497,14 @@ class PackageCrawler {
         throw new Error(`NPM Canonical "${canonical}" is not valid from ${source}`);
       }
 
+      const isTemplate = npmPackage.kind === 2; // fhir.template
+      if (npmPackage.hasInstallScripts) {
+        throw new Error(`Package ${idver} rejected: contains install scripts (preinstall/install/postinstall)`);
+      }
+      if (npmPackage.hasJavaScript && !isTemplate) {
+        throw new Error(`Package ${idver} rejected: contains JavaScript files but is not a template package`);
+      }
+
       // Extract URLs from package
       const urls = this.processPackageUrls(npmPackage);
 
@@ -492,7 +512,7 @@ class PackageCrawler {
       await this.commit(packageBuffer, npmPackage, date, guid, id, version, canonical, urls);
 
     } catch (error) {
-      console.log(error);
+      debugLog(error);
       this.log.error(`Error storing package ${guid}:`+ error.message);
       throw error;
     }
@@ -555,6 +575,14 @@ class PackageCrawler {
       }
 
       const packageJson = JSON.parse(files['package.json']);
+      const hasInstallScripts = !!(
+        packageJson.scripts && (
+          packageJson.scripts.preinstall ||
+          packageJson.scripts.install ||
+          packageJson.scripts.postinstall
+        )
+      );
+      const hasJavaScript = Object.keys(files).some(f => f.endsWith('.js') || f.endsWith('.mjs') || f.endsWith('.cjs'));
 
       // Extract basic NPM fields
       const id = packageJson.name || '';
@@ -664,6 +692,8 @@ class PackageCrawler {
         url: homepage,
         dependencies,
         kind,
+        hasInstallScripts,
+        hasJavaScript,
         notForPublication,
         files
       };
@@ -903,6 +933,11 @@ class PackageCrawler {
       return id;
     }
   }
+  shutdown() {
+    if (this.abortController) {
+      this.abortController.abort();
+    }
+  }
 }
 
 module.exports = PackageCrawler;

package/packages/packages.js

@@ -803,6 +803,7 @@ class PackagesModule {
 
   stopCrawlerJob() {
     if (this.crawlerJob) {
+      this.crawler.shutdown();
       this.crawlerJob.stop();
       this.crawlerJob = null;
       pckLog.info('Package crawler job stopped');

package/registry/crawler.js

@@ -9,6 +9,7 @@ const {
   ServerVersionInformation,
 } = require('./model');
 const {Extensions} = require("../tx/library/extensions");
+const {debugLog} = require("../tx/operation-context");
 
 const MASTER_URL = 'https://fhir.github.io/ig-registry/tx-servers.json';
 
@@ -31,6 +32,7 @@ class RegistryCrawler {
     this.errors = [];
     this.totalBytes = 0;
     this.log = console;
+    this.abortController = null;
   }
 
   useLog(logv) {
@@ -48,6 +50,7 @@ class RegistryCrawler {
       this.addLogEntry('warn', 'Crawl already in progress, skipping...');
       return this.currentData;
     }
+    this.abortController = new AbortController();
 
     this.isCrawling = true;
     const startTime = new Date();
@@ -75,6 +78,7 @@ class RegistryCrawler {
       // Process each registry
       const registries = masterJson.registries || [];
       for (const registryConfig of registries) {
+        if (this.abortController?.signal.aborted) break;
         const registry = await this.processRegistry(registryConfig);
         if (registry) {
           newData.registries.push(registry);
@@ -86,7 +90,7 @@ class RegistryCrawler {
       // Update the current data
       this.currentData = newData;
     } catch (error) {
-      console.log(error);
+      debugLog(error);
       this.addLogEntry('error', 'Exception Scanning:', error);
       this.currentData.outcome = `Error: ${error.message}`;
       this.errors.push({
@@ -118,7 +122,7 @@ class RegistryCrawler {
     }
     
     if (!registry.address) {
-      this.addLogEntry('error', `No url provided for ${registry.name, registry.name}`, '');
+      this.addLogEntry('error', `No url provided for ${registry.name}`, '');
       return registry;
     }
     
@@ -134,6 +138,7 @@ class RegistryCrawler {
       // Process each server in the registry
       const servers = registryJson.servers || [];
       for (const serverConfig of servers) {
+        if (this.abortController?.signal.aborted) break;
         const server = await this.processServer(serverConfig, registry.address);
         if (server) {
           registry.servers.push(server);
@@ -141,7 +146,7 @@ class RegistryCrawler {
       }
       
     } catch (error) {
-      console.log(error);
+      debugLog(error);
       registry.error = error.message;
       this.addLogEntry('error', `Exception processing registry ${registry.name}: ${error.message}`, registry.address);
     }
@@ -177,6 +182,7 @@ class RegistryCrawler {
     // Process each FHIR version
     const fhirVersions = serverConfig.fhirVersions || [];
     for (const versionConfig of fhirVersions) {
+      if (this.abortController?.signal.aborted) break;
       const version = await this.processServerVersion(versionConfig, server, serverConfig.exclusions);
       if (version) {
         server.versions.push(version);
@@ -231,7 +237,7 @@ class RegistryCrawler {
       this.addLogEntry('info', `  Server ${version.address}: ${version.lastTat} for ${version.codeSystems.length} CodeSystems and ${version.valueSets.length} ValueSets`);
       
     } catch (error) {
-      console.log(error);
+      debugLog(error);
       const elapsed = Date.now() - startTime;
       this.addLogEntry('error', `Server ${version.address}: Error after ${elapsed}ms: ${error.message}`);
       version.error = error.message;
@@ -276,10 +282,11 @@ class RegistryCrawler {
         });
       }
     } catch (error) {
-      console.log(error);
-      this.addLogEntry('error', `Could not fetch terminology capabilities: ${error.message}`);
+      debugLog(error);
+      this.addLogEntry('error', `Could not fetch terminology capabilities from ${version.address}: ${error.message}`);
     }
-    
+
+    if (this.abortController?.signal.aborted) return;
     // Search for value sets
     await this.fetchValueSets(version, server, exclusions);
   }
@@ -324,8 +331,8 @@ class RegistryCrawler {
         });
       }
     } catch (error) {
-      console.log(error);
-      this.addLogEntry('error', `Could not fetch terminology capabilities: ${error.message}`);
+      debugLog(error);
+      this.addLogEntry('error', `Could not fetch terminology capabilities from ${version.address}: ${error.message}`);
     }
     
     // Search for value sets
@@ -342,14 +349,20 @@ class RegistryCrawler {
    */
   async fetchValueSets(version, server, exclusions) {
     // Initial search URL
+    let count = 0;
     let searchUrl = `${version.address}/ValueSet?_elements=url,version`+(version.address.includes("fhir.org") ? "&_count=200" : "");
     try {
       // Set of URLs to avoid duplicates
       const valueSetUrls = new Set();
 
-
       // Continue fetching while we have a URL
       while (searchUrl) {
+        count++;
+        if (count == 1000) {
+          throw new Error(`Fetch ValueSet loop exceeded 1000 iterations - a logic problem on the server? (${version.address})`);
+        }
+
+        if (this.abortController?.signal.aborted) break;
         this.log.debug(`Fetching value sets from ${searchUrl}`);
         const bundle = await this.fetchJson(searchUrl, server.code);
 
@@ -382,7 +395,7 @@ class RegistryCrawler {
       version.valueSets = Array.from(valueSetUrls).sort();
 
     } catch (error) {
-      console.log(error);
+      debugLog(error);
       this.addLogEntry('error', `Could not fetch value sets: ${error.message} from ${searchUrl}`);
     }
   }
@@ -441,6 +454,7 @@ class RegistryCrawler {
       const response = await axios.get(fetchUrl, {
         timeout: this.config.timeout,
         headers: headers,
+        signal: this.abortController?.signal,
         validateStatus: (status) => status < 500 // Don't throw on 4xx
       });
       
@@ -459,7 +473,7 @@ class RegistryCrawler {
       return response.data;
       
     } catch (error) {
-      console.log(error);
+      debugLog(error);
       if (error.response) {
         throw new Error(`HTTP ${error.response.status}: ${error.response.statusText}`);
       } else if (error.request) {
@@ -603,14 +617,14 @@ class RegistryCrawler {
    * @param {string} level - Filter by log level
    * @returns {Array} Array of log entries
    */
-  getLogs(limit = 100)
+  getLogs(limit = 100, level = null)
   {
     if (!this.logs) {
       return [];
     }
 
     // Filter by level if specified
-    let filteredLogs = this.logs;
+    let filteredLogs = level ? this.logs.filter(entry => entry.level === level) : this.logs;
 
     // Get the latest entries up to the limit
     return filteredLogs.slice(-limit);
@@ -648,6 +662,13 @@ class RegistryCrawler {
     }
     return false;
   }
+
+  shutdown() {
+    if (this.abortController) {
+      this.abortController.abort();
+    }
+  }
+
 }
 
 module.exports = RegistryCrawler;

package/registry/registry.js

@@ -926,6 +926,9 @@ class RegistryModule {
       this.crawlInterval = null;
     }
 
+    if (this.crawler) {
+      this.crawler.shutdown();
+    }
     // Save current data
     if (this.crawler && this.currentData) {
       await this.saveData();

package/server.js

@@ -436,9 +436,11 @@ app.get('/', async (req, res) => {
       const html = htmlServer.renderPage('root', escape(config.hostName) || 'FHIRsmith Server', content, stats);
       res.setHeader('Content-Type', 'text/html');
       res.send(html);
+      return;
     } catch (error) {
       serverLog.error('Error rendering root page:', error);
       htmlServer.sendErrorResponse(res, 'root', error);
+      return;
     }
   }
   return serveFhirsmithHome(req, res);
@@ -623,9 +625,11 @@ async function serveFhirsmithHome(req, res) {
       const html = htmlServer.renderPage('root', escape(config.hostName) || 'FHIRsmith Server', content, stats);
       res.setHeader('Content-Type', 'text/html');
       res.send(html);
+      return;
     } catch (error) {
       serverLog.error('Error rendering root page:', error);
       htmlServer.sendErrorResponse(res, 'root', error);
+      return;
     }
   } else {
     // Return JSON response for API clients

package/tx/README.md

@@ -33,22 +33,22 @@ Add the `tx` section to your `config.json`:
       "endpoints": [
         {
           "path": "/tx/r5",
-          "fhirVersion": 5,
+          "fhirVersion": "5.0",
           "context": null
         },
         {
           "path": "/tx/r4",
-          "fhirVersion": 4,
+          "fhirVersion": "4.0",
           "context": null
         },
         {
           "path": "/tx/r3",
-          "fhirVersion": 3,
+          "fhirVersion": "3.0",
           "context": null
         },
         {
           "path": "/tx/r4/demo",
-          "fhirVersion": 4,
+          "fhirVersion": "4.0",
           "context": "demo"
         }
       ]

package/tx/cs/cs-loinc.js

@@ -203,9 +203,12 @@ class LoincServices extends BaseCSServices {
     // Use language-aware display logic
     if (this.opContext.langs && !this.opContext.langs.isEnglishOrNothing()) {
       const displays = await this.#getDisplaysForContext(ctxt, this.opContext.langs);
+      const requestedLanguages = Array.isArray(this.opContext.langs.languages)
+        ? this.opContext.langs.languages
+        : (Array.isArray(this.opContext.langs.langs) ? this.opContext.langs.langs : []);
 
       // Try to find exact language match
-      for (const lang of this.opContext.langs.langs) {
+      for (const lang of requestedLanguages) {
         for (const display of displays) {
           if (lang.matches(display.language, true)) {
             return display.value;
@@ -214,7 +217,7 @@ class LoincServices extends BaseCSServices {
       }
 
       // Try partial language match
-      for (const lang of this.opContext.langs.langs) {
+      for (const lang of requestedLanguages) {
         for (const display of displays) {
           if (lang.matches(display.language, false)) {
             return display.value;