fhirsmith 0.5.5 → 0.6.0

package/CHANGELOG.md

@@ -5,6 +5,36 @@ 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).
 
+## [v0.6.0] - 2026-03-06
+
+### Added
+- Add support to packages server for scoped packages
+- Add support for exclusions and content tracking in tx-registry
+- Add support for serving a host
+
+### Changed
+- fix error in SCT expression validation
+- fix null error in search
+- fix search for code systems with uppercase letters in their name
+- rework html interface for CodeSystem and ValueSet
+- further work on publisehr
+
+### Tx Conformance Statement
+
+FHIRsmith passed all 1382 HL7 terminology service tests (modes tx.fhir.org,omop,general,snomed, tests v1.9.0, runner v6.8.2)
+
+## [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/library/html-server.js

@@ -72,7 +72,8 @@ class HtmlServer {
       .replace(/\[%total-packages%\]/g, escape(renderOptions.totalPackages.toLocaleString()))
       .replace(/\[%endpoint-path%\]/g, escape(renderOptions.endpointpath))
       .replace(/\[%fhir-version%\]/g, escape(renderOptions.fhirversion))
-      .replace(/\[%ms%\]/g, escape(renderOptions.processingTime.toString()));
+      .replace(/\[%ms%\]/g, escape(renderOptions.processingTime.toString()))
+      .replace(/\[%about%\]/g, renderOptions.about || '');
     
     // Handle any custom template variables
     if (options.templateVars) {

package/library/package-manager.js

@@ -594,41 +594,46 @@ class PackageManager {
      */
     async fetchUrl(url) {
         console.log("Fetch Package from URL: " + url);
-        const client = new CIBuildClient();
-        const packageData = await client.fetchFromUrlSpecific(url);
-
-        // Extract to a temp location to read package.json for name and version
-        const tempKey = `_url_temp_${Date.now()}`;
-        const tempPath = await this.extractToCache(tempKey, 'url', packageData);
-        const tempFullPath = path.join(this.cacheFolder, tempPath);
-
-        // Read package name and version from the extracted package
-        const pkgJsonPath = path.join(tempFullPath, 'package', 'package.json');
-        const pkgJson = JSON.parse(await fs.readFile(pkgJsonPath, 'utf8'));
-        const packageId = pkgJson.name;
-        const version = pkgJson.version;
-
-        if (!packageId || !version) {
-            throw new Error(`Package at ${url} has no name or version in package.json`);
-        }
+        try {
+            const client = new CIBuildClient();
+            const packageData = await client.fetchFromUrlSpecific(url);
+
+            // Extract to a temp location to read package.json for name and version
+            const tempKey = `_url_temp_${Date.now()}`;
+            const tempPath = await this.extractToCache(tempKey, 'url', packageData);
+            const tempFullPath = path.join(this.cacheFolder, tempPath);
+
+            // Read package name and version from the extracted package
+            const pkgJsonPath = path.join(tempFullPath, 'package', 'package.json');
+            const pkgJson = JSON.parse(await fs.readFile(pkgJsonPath, 'utf8'));
+            const packageId = pkgJson.name;
+            const version = pkgJson.version;
+
+            if (!packageId || !version) {
+                throw new Error(`Package at ${url} has no name or version in package.json`);
+            }
 
-        // Use the same cache key format as npm packages
-        const finalName = `${packageId}#${version}`;
-        const finalPath = path.join(this.cacheFolder, finalName);
+            // Use the same cache key format as npm packages
+            const finalName = `${packageId}#${version}`;
+            const finalPath = path.join(this.cacheFolder, finalName);
 
-        // If it already exists, the same package is already loaded - that's a config error
-        try {
-            await fs.access(finalPath);
-            await fs.rm(tempFullPath, { recursive: true, force: true });
-            throw new Error(`Package ${finalName} already exists in cache. Check library config for duplicates (url: ${url})`);
-        } catch (e) {
-            if (e.message.includes('already exists')) throw e;
-            // Doesn't exist yet, rename temp to final
-            await fs.rename(tempFullPath, finalPath);
-        }
+            // If it already exists, the same package is already loaded - that's a config error
+            try {
+                await fs.access(finalPath);
+                await fs.rm(tempFullPath, { recursive: true, force: true });
+                throw new Error(`Package ${finalName} already exists in cache. Check library config for duplicates (url: ${url})`);
+            } catch (e) {
+                if (e.message.includes('already exists')) throw e;
+                // Doesn't exist yet, rename temp to final
+                await fs.rename(tempFullPath, finalPath);
+            }
 
-        this.totalDownloaded = this.totalDownloaded + packageData.length;
-        return finalName;
+            this.totalDownloaded = this.totalDownloaded + packageData.length;
+            return finalName;
+        } catch (error) {
+            console.error(`Error fetching package from URL ${url}: ${error.message}`);
+            throw error;
+        }
     }
 
     /**

package/library/utilities.js

@@ -274,4 +274,13 @@ class ArrayMatcher {
   }
 }
 
-module.exports = { Utilities, ArrayMatcher, validateParameter, validateOptionalParameter, validateArrayParameter, validateResource, strToBool, getValuePrimitive, getValueDT, getValueName, isAbsoluteUrl };
+const months = ['Jan','Feb','Mar','Apr','May','Jun','Jul','Aug','Sep','Oct','Nov','Dec'];
+
+function formatDateMMDDYYYY(s) {
+  const mm = parseInt(s.substring(0, 2), 10);
+  const dd = s.substring(2, 4);
+  const yyyy = s.substring(4, 8);
+  return dd + '-' + months[mm - 1] + ' ' + yyyy;
+}
+
+module.exports = { Utilities, ArrayMatcher, validateParameter, validateOptionalParameter, validateArrayParameter, validateResource, strToBool, getValuePrimitive, getValueDT, getValueName, isAbsoluteUrl, formatDateMMDDYYYY };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "fhirsmith",
-  "version": "0.5.5",
+  "version": "0.6.0",
   "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

@@ -12,6 +12,7 @@ const path = require('path');
 
 class PackageCrawler {
   log;
+  packages = new Set();
   
   constructor(config, db, stats) {
     this.config = config;
@@ -26,6 +27,7 @@ class PackageCrawler {
 
   async crawl(log) {
     this.log = log;
+    this.packages.clear();
     
     const startTime = Date.now();
     this.crawlerLog = {
@@ -56,15 +58,30 @@ class PackageCrawler {
           this.log.info('Skipping feed with no URL: '+ feedConfig);
           continue;
         }
-        this.stats.task('Package Crawler', 'Running for '+feedConfig.url);
+        try {
+          let url = this.fixUrl(feedConfig.url)
+          if (!url.includes('simplifier')) {
+            this.stats.task('Package Crawler', 'Running for '+feedConfig.url);
+            await this.updateTheFeed(url, this.config.masterUrl,feedConfig.errors ? feedConfig.errors.replace(/\|/g, '@').replace(/_/g, '.') : '', packageRestrictions);
+          }
+        } catch (feedError) {
+          this.log.error(`Failed to process feed ${feedConfig.url}: `+ feedError.message);
+          // Continue with next feed even if this one fails
+        }
+      }
+      // process simplifier last
+      for (const feedConfig of masterResponse.feeds) {
+        if (!feedConfig.url) {
+          this.log.info('Skipping feed with no URL: '+ feedConfig);
+          continue;
+        }
 
         try {
-          await this.updateTheFeed(
-            this.fixUrl(feedConfig.url),
-            this.config.masterUrl,
-            feedConfig.errors ? feedConfig.errors.replace(/\|/g, '@').replace(/_/g, '.') : '',
-            packageRestrictions
-          );
+          let url = this.fixUrl(feedConfig.url)
+          if (url.includes('simplifier')) {
+            this.stats.task('Package Crawler', 'Running for '+feedConfig.url);
+            await this.updateTheFeed(url, this.config.masterUrl,feedConfig.errors ? feedConfig.errors.replace(/\|/g, '@').replace(/_/g, '.') : '', packageRestrictions);
+          }
         } catch (feedError) {
           this.log.error(`Failed to process feed ${feedConfig.url}: `+ feedError.message);
           // Continue with next feed even if this one fails
@@ -100,14 +117,20 @@ class PackageCrawler {
 
   async fetchJson(url) {
     try {
-      const response = await axios.get(url, {
-        timeout: 30000,
-        headers: {
-          'User-Agent': 'FHIR Package Crawler/1.0'
-        }
-      });
-      return response.data;
+      if (url.startsWith("/")) {
+        const content = await fs.promises.readFile(url, "utf8");
+        return JSON.parse(content);
+      } else {
+        const response = await axios.get(url, {
+          timeout: 30000,
+          headers: {
+            'User-Agent': 'FHIR Package Crawler/1.0'
+          }
+        });
+        return response.data;
+      }
     } catch (error) {
+      console.log(error);
       if (error.response && error.response.status === 429) {
         throw new Error(`RATE_LIMITED: Server returned 429 Too Many Requests for ${url}`);
       }
@@ -117,20 +140,30 @@ class PackageCrawler {
 
   async fetchXml(url) {
     try {
-      const response = await axios.get(url, {
-        timeout: 30000,
-        headers: {
-          'User-Agent': 'FHIR Package Crawler/1.0'
-        }
-      });
+      if (url.startsWith("/")) {
+        const content = await fs.promises.readFile(url, 'utf8');
+        const parser = new XMLParser({
+          ignoreAttributes: false,
+          attributeNamePrefix: '@_',
+          textNodeName: '#text'
+        });
+        return parser.parse(content);
+      } else {
+        const response = await axios.get(url, {
+          timeout: 30000,
+          headers: {
+            'User-Agent': 'FHIR Package Crawler/1.0'
+          }
+        });
 
-      const parser = new XMLParser({
-        ignoreAttributes: false,
-        attributeNamePrefix: '@_',
-        textNodeName: '#text'
-      });
+        const parser = new XMLParser({
+          ignoreAttributes: false,
+          attributeNamePrefix: '@_',
+          textNodeName: '#text'
+        });
 
-      return parser.parse(response.data);
+        return parser.parse(response.data);
+      }
     } catch (error) {
       if (error.response && error.response.status === 429) {
         throw new Error(`RATE_LIMITED: Server returned 429 Too Many Requests for ${url}`);
@@ -141,16 +174,22 @@ class PackageCrawler {
 
   async fetchUrl(url) {
     try {
-      const response = await axios.get(url, {
-        timeout: 60000,
-        responseType: 'arraybuffer',
-        headers: {
-          'User-Agent': 'FHIR Package Crawler/1.0'
-        }
-      });
+      if (url.startsWith("/")) {
+        const buffer = await fs.promises.readFile(url);
+        this.totalBytes += buffer.byteLength;
+        return buffer;
+      } else {
+        const response = await axios.get(url, {
+          timeout: 60000,
+          responseType: 'arraybuffer',
+          headers: {
+            'User-Agent': 'FHIR Package Crawler/1.0'
+          }
+        });
 
-      this.totalBytes += response.data.byteLength;
-      return Buffer.from(response.data);
+        this.totalBytes += response.data.byteLength;
+        return Buffer.from(response.data);
+      }
     } catch (error) {
       if (error.response && error.response.status === 429) {
         throw new Error(`RATE_LIMITED: Server returned 429 Too Many Requests for ${url}`);
@@ -166,7 +205,7 @@ class PackageCrawler {
     };
     this.crawlerLog.feeds.push(feedLog);
 
-    this.log.info('Processing feed: '+ url);
+    this.log.info('Processing feed: ' + url);
     const startTime = Date.now();
 
     try {
@@ -195,7 +234,7 @@ class PackageCrawler {
             break; // Stop processing this feed
           }
           // For other errors, log and continue with next item
-          this.log.error(`Error processing item ${i} from ${url}:`+ itemError.message);
+          this.log.error(`Error processing item ${i} from ${url}:` + itemError.message);
         }
       }
 
@@ -205,6 +244,7 @@ class PackageCrawler {
       }
 
     } catch (error) {
+      console.log(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`);
@@ -216,7 +256,7 @@ class PackageCrawler {
 
       feedLog.exception = error.message;
       feedLog.failTime = `${Date.now() - startTime}ms`;
-      this.log.error(`Exception processing feed ${url}:`+ error.message);
+      this.log.error(`Exception processing feed ${url}:` + error.message);
 
       // TODO: Send email notification for non-rate-limit errors
       if (email) {
@@ -275,6 +315,12 @@ class PackageCrawler {
         return;
       }
 
+      if (this.packages.has(id)) {
+        this.log.info(`Ignoring package ${id} because it's already been seen in another feed`);
+        return;
+      }
+      this.packages.add(id);
+
       // Check if already processed
       if (await this.hasStored(guid)) {
         itemLog.status = 'Already Processed';
@@ -301,7 +347,7 @@ class PackageCrawler {
       }
 
       itemLog.url = url;
-      this.log.info('Fetching package: '+ url);
+      this.log.info('Fetching package: ' + url);
 
       const packageContent = await this.fetchUrl(url, 'application/tar+gzip');
       await this.store(source, url, guid, pubDate, packageContent, id, itemLog);
@@ -316,6 +362,7 @@ class PackageCrawler {
         throw error;
       }
     }
+
   }
 
   isPackageAllowed(packageId, source, restrictions) {
@@ -416,18 +463,19 @@ class PackageCrawler {
         itemLog.warning = warning;
       }
 
+      // Validate package data
+      if (!this.isValidPackageId(id)) {
+        throw new Error(`NPM Id "${id}" is not valid from ${source}`);
+      }
+
       // Save to mirror if configured
       if (this.config.mirrorPath) {
-        const filename = `${id}-${version}.tgz`;
+        let fid = this.fixPrefix(id);
+        const filename = `${fid}-${version}.tgz`;
         const filepath = path.join(this.config.mirrorPath, filename);
         fs.writeFileSync(filepath, packageBuffer);
       }
 
-      // Validate package data
-      if (!this.isValidPackageId(id)) {
-        throw new Error(`NPM Id "${id}" is not valid from ${source}`);
-      }
-
       if (!this.isValidSemVersion(version)) {
         throw new Error(`NPM Version "${version}" is not valid from ${source}`);
       }
@@ -444,6 +492,7 @@ class PackageCrawler {
       await this.commit(packageBuffer, npmPackage, date, guid, id, version, canonical, urls);
 
     } catch (error) {
+      console.log(error);
       this.log.error(`Error storing package ${guid}:`+ error.message);
       throw error;
     }
@@ -668,7 +717,7 @@ class PackageCrawler {
 
   isValidPackageId(id) {
     // Simple package ID validation
-    return /^[a-z0-9][a-z0-9._-]*$/.test(id);
+    return /^(@[a-z0-9._-]+\/)?[a-z0-9][a-z0-9._-]*$/.test(id);
   }
 
   isValidSemVersion(version) {
@@ -846,6 +895,14 @@ class PackageCrawler {
       });
     });
   }
+
+  fixPrefix(id) {
+    if (id && id.startsWith("@") && id.includes("/")) {
+      return id.replace("@", "$$").replace("/", "$");
+    } else {
+      return id;
+    }
+  }
 }
 
 module.exports = PackageCrawler;

package/packages/packages.js

@@ -1067,13 +1067,13 @@ class PackagesModule {
         const {id, version} = req.params;
 
         if (!id || !version ||
-          !/^[a-zA-Z0-9._-]+$/.test(id) ||
+          !/^(@[a-z0-9._-]+\/)?[a-zA-Z0-9._-]+$/.test(id) ||
           !/^[a-zA-Z0-9._-]+$/.test(version)) {
-          return res.status(400).json({error: 'Invalid package id or version format'});
+          return res.status(400).json({error: `Invalid package id or version format: ${id}`});
         }
 
         if (id.length > 100 || version.length > 50) {
-          return res.status(400).json({error: 'Package id or version too long'});
+          return res.status(400).json({error: `Package id or version too long: ${id}`});
         }
 
         next();
@@ -1517,7 +1517,7 @@ class PackagesModule {
       // Check if we should redirect to bucket storage
       if (this.config.bucketPath) {
         let bucketUrl = this.getBucketUrl(secure);
-        const redirectUrl = `${bucketUrl}${id}-${version}.tgz`;
+        const redirectUrl = `${bucketUrl}${this.fixPrefix(id)}-${version}.tgz`;
         res.redirect(redirectUrl);
         return;
       }
@@ -1888,7 +1888,7 @@ class PackagesModule {
       table += `<td>${escape(this.codeForKind(pv.Kind))}</td>`;
       table += `<td>${new Date(pv.PubDate).toLocaleDateString()}</td>`;
       table += `<td>${(pv.DownloadCount || 0).toLocaleString()}</td>`;
-      table += `<td><a href="/packages/${escape(id)}/${escape(pv.Version)}" class="btn btn-sm btn-primary">Download</a></td>`;
+      table += `<td><a href="/packages/${encodeURIComponent(id)}/${escape(pv.Version)}" class="btn btn-sm btn-primary">Download</a></td>`;
       table += '</tr>';
     }
 
@@ -2126,8 +2126,8 @@ class PackagesModule {
 
     for (const pkg of results) {
       table += '<tr>';
-      table += `<td><a href="${escape(pkg.url)}">${escape(pkg.name)}</a></td>`;
-      table += `<td>${escape(pkg.version)} (<a href="/packages/${escape(pkg.name)}">all</a>)</td>`;
+      table += `<td><a href="${escape(this.fixPrefix(pkg.url))}">${escape(pkg.name)}</a></td>`;
+      table += `<td>${escape(pkg.version)} (<a href="/packages/${encodeURIComponent(pkg.name)}">all</a>)</td>`;
       table += `<td>${escape(pkg.fhirVersion)}</td>`;
       table += `<td>${escape(pkg.kind)}</td>`;
       table += `<td>${pkg.date ? new Date(pkg.date).toLocaleDateString() : 'N/A'}</td>`;
@@ -2817,6 +2817,13 @@ class PackagesModule {
     return content;
   }
 
+  fixPrefix(id) {
+    if (id && id.startsWith("@") && id.includes("/")) {
+      return id.replace("@", "$$").replace("/", "$");
+    } else {
+      return id;
+    }
+  }
 }
 
 module.exports = PackagesModule;

package/publisher/publisher.js

@@ -91,6 +91,8 @@ class PublisherModule {
                                                id INTEGER PRIMARY KEY AUTOINCREMENT,
                                                name TEXT NOT NULL,
                                                local_folder TEXT NOT NULL,
+                                               history_templates TEXT NOT NULL,
+                                               web_templates TEXT NOT NULL,
                                                server_update_script TEXT NOT NULL,
                                                is_active BOOLEAN DEFAULT 1,
                                                created_at DATETIME DEFAULT CURRENT_TIMESTAMP
@@ -1605,6 +1607,14 @@ class PublisherModule {
         content += '<input type="text" class="form-control" id="local_folder" name="local_folder" required>';
         content += '</div>';
         content += '<div class="col-md-4">';
+        content += '<label for="history_templates" class="form-label">History Templates</label>';
+        content += '<input type="text" class="form-control" id="history_templates" name="history_templates" required>';
+        content += '</div>';
+        content += '<div class="col-md-4">';
+        content += '<label for="web_templates" class="form-label">Web Templates</label>';
+        content += '<input type="text" class="form-control" id="web_templates" name="web_templates" required>';
+        content += '</div>';
+        content += '<div class="col-md-4">';
         content += '<label for="server_update_script" class="form-label">Update Script</label>';
         content += '<input type="text" class="form-control" id="server_update_script" name="server_update_script" required>';
         content += '</div>';
@@ -1631,6 +1641,8 @@ class PublisherModule {
             content += '<tr>';
             content += '<td>' + website.name + '</td>';
             content += '<td><code>' + website.local_folder + '</code></td>';
+            content += '<td><code>' + website.history_templates + '</code></td>';
+            content += '<td><code>' + website.web_templates + '</code></td>';
             content += '<td><code>' + website.server_update_script + '</code></td>';
             content += '<td>' + (website.is_active ? '✓' : '✗') + '</td>';
             content += '<td>' + new Date(website.created_at).toLocaleString() + '</td>';
@@ -1665,12 +1677,12 @@ class PublisherModule {
     const start = Date.now();
     try {
       try {
-        const {name, local_folder, server_update_script} = req.body;
+        const {name, local_folder, history_templates, web_templates, server_update_script} = req.body;
 
         await new Promise((resolve, reject) => {
           this.db.run(
-            'INSERT INTO websites (name, local_folder, server_update_script) VALUES (?, ?, ?)',
-            [name, local_folder, server_update_script],
+            'INSERT INTO websites (name, local_folder, history_templates, web_templates, server_update_script) VALUES (?, ?, ?, ?, ?)',
+            [name, local_folder, history_templates, web_templates, server_update_script],
             function (err) {
               if (err) reject(err);
               else resolve();