fhirsmith 0.7.3 → 0.7.5

package/tx/cs/cs-snomed.js

@@ -1275,7 +1275,7 @@ class SnomedServicesFactory extends CodeSystemFactoryProvider {
 
   id() {
     const match = this.version().match(/^http:\/\/snomed\.info\/sct\/(\d+)(?:\/version\/(\d{8}))?$/);
-    return "SCT-"+match[1]+"-"+match[2];
+    return match && match[1] && match[2] ? "SCT-"+match[1]+"-"+match[2] : null;
   }
 
   describeVersion(version) {

package/tx/cs/cs-uri.js

@@ -21,7 +21,7 @@ class UriServices extends CodeSystemProvider {
   }
 
   version() {
-    return 'n/a';
+    return null;
   }
 
   description() {
@@ -182,7 +182,7 @@ class UriServicesFactory extends CodeSystemFactoryProvider {
   }
 
   defaultVersion() {
-    return 'n/a';
+    return null;
   }
 
   system() {
@@ -190,7 +190,7 @@ class UriServicesFactory extends CodeSystemFactoryProvider {
   }
 
   version() {
-    return 'n/a';
+    return null;
   }
 
   // eslint-disable-next-line no-unused-vars

package/tx/library.js

@@ -34,6 +34,7 @@ const {VSACValueSetProvider} = require("./vs/vs-vsac");
 const { OCLCodeSystemProvider, OCLSourceCodeSystemFactory } = require('./ocl/cs-ocl');
 const { OCLValueSetProvider } = require('./ocl/vs-ocl');
 const { OCLConceptMapProvider } = require('./ocl/cm-ocl');
+const {UriServicesFactory} = require("./cs/cs-uri");
 
 /**
  * This class holds all the loaded content ready for processing
@@ -100,6 +101,7 @@ class Library {
     this.conceptMapProviders = [];
     this.oclProviderSets = new Map();
     this.oclConfig = {};
+    this.ignored = new Set();
 
     // Create package manager for FHIR packages
     const packageServers = ['https://packages2.fhir.org/packages'];
@@ -160,6 +162,7 @@ class Library {
     const config = yaml.parse(yamlContent);
     this.baseUrl = config.base.url;
     this.oclConfig = config.ocl && typeof config.ocl === 'object' ? config.ocl : {};
+    this.ignored = new Set(Array.isArray(config.ignored) ? config.ignored : []);
 
     this.log.info('Fetching Data from '+this.baseUrl);
 
@@ -287,7 +290,7 @@ class Library {
       case 'ocl':
         await this.loadOcl(details, isDefault, mode);
         break;
-        
+
       default:
         throw new Error(`Unknown source type: ${type}`);
     }
@@ -454,6 +457,12 @@ class Library {
         this.registerProvider('internal', hgvs);
         break;
       }
+      case "urls" : {
+        const urls = new UriServicesFactory(this.i18n);
+        await urls.load();
+        this.registerProvider('internal', urls);
+        break;
+      }
       case "vsac" : {
         if (!this.vsacCfg || !this.vsacCfg.apiKey) {
           throw new Error("Unable to load VSAC provider unless vsacCfg is provided in the configuration");
@@ -560,6 +569,17 @@ class Library {
     this.registerProvider(omopFN, omop, isDefault);
   }
 
+  /**
+   * Returns true if the given url/version should be excluded from npm/url package loading.
+   * Matches against the ignored list using either plain url or url#version.
+   */
+  #isIgnored(url, version) {
+    if (this.ignored.size === 0) return false;
+    if (this.ignored.has(url)) return true;
+    if (version && this.ignored.has(`${url}#${version}`)) return true;
+    return false;
+  }
+
   async loadNpm(packageManager, details, isDefault, mode, csOnly) {
     // Parse packageId and version from details (e.g., "hl7.terminology.r4#6.0.2")
     let packageId = details;
@@ -584,6 +604,10 @@ class Library {
     let csc = 0;
     for (const resource of resources) {
       const cs = new CodeSystem(await contentLoader.loadFile(resource, contentLoader.fhirVersion()));
+      if (this.#isIgnored(cs.url, cs.version)) {
+        this.log.info(`Ignoring CodeSystem ${cs.url}${cs.version ? '#' + cs.version : ''} (excluded by config)`);
+        continue;
+      }
       cs.sourcePackage = contentLoader.pid();
       cp.codeSystems.push(cs);
       csc++;
@@ -618,6 +642,10 @@ class Library {
     let csc = 0;
     for (const resource of resources) {
       const cs = new CodeSystem(await contentLoader.loadFile(resource, contentLoader.fhirVersion()));
+      if (this.#isIgnored(cs.url, cs.version)) {
+        this.log.info(`Ignoring CodeSystem ${cs.url}${cs.version ? '#' + cs.version : ''} (excluded by config)`);
+        continue;
+      }
       cs.sourcePackage = contentLoader.pid();
       cp.codeSystems.set(cs.url, cs);
       cp.codeSystems.set(cs.vurl, cs);
@@ -898,4 +926,4 @@ class Library {
 
 }
 
-module.exports = { Library };
+module.exports = { Library };

package/tx/tx.fhir.org.yml

@@ -8,6 +8,7 @@ sources:
   - internal:areacode
   - internal:mimetypes
   - internal:usstates
+  - internal:urls
   - internal:hgvs
   - ucum:tx/data/ucum-essence.xml
   - loinc:loinc-2.77-a.db
@@ -39,3 +40,6 @@ sources:
   - npm:us.cdc.phinvads
   - npm:hl7.fhir.uv.sdc
   - internal:vsac
+
+ignored:
+  - urn:iso:std:iso:3166#20210120

package/tx/tx.js

@@ -196,6 +196,9 @@ class TXModule {
     }
 
     this.log.info(`TX module initialized with ${config.endpoints.length} endpoint(s)`);
+
+    // Self-test: verify metadata generation works for each endpoint before accepting traffic
+    await this.selfTest();
   }
 
   /**
@@ -388,8 +391,8 @@ class TXModule {
       }
 
       if (contentType.includes('application/json') ||
-          contentType.includes('application/fhir+json') ||
-          contentType.includes('application/json+fhir')) {
+        contentType.includes('application/fhir+json') ||
+        contentType.includes('application/json+fhir')) {
 
         // If body is a Buffer, parse it
         if (Buffer.isBuffer(req.body)) {
@@ -731,11 +734,11 @@ class TXModule {
     router.get('/CodeSystem/:id/\\$validate-code', async (req, res) => {
       const start = Date.now();
       try {
-      let worker = new ValidateWorker(req.txOpContext, this.log, req.txProvider, this.languages, this.i18n);
+        let worker = new ValidateWorker(req.txOpContext, this.log, req.txProvider, this.languages, this.i18n);
         await worker.handleCodeSystemInstance(req, res, this.log);
-    } finally {
-      this.countRequest('$validate', Date.now() - start);
-    }
+      } finally {
+        this.countRequest('$validate', Date.now() - start);
+      }
     });
     router.post('/CodeSystem/:id/\\$validate-code', async (req, res) => {
       const start = Date.now();
@@ -745,7 +748,7 @@ class TXModule {
       } finally {
         this.countRequest('$validate', Date.now() - start);
       }
-      
+
     });
 
     // ValueSet/[id]/$validate-code
@@ -964,6 +967,79 @@ class TXModule {
     });
   }
 
+  /**
+   * Self-test: exercise CapabilityStatement and TerminologyCapabilities generation
+   * for each endpoint immediately after startup, throwing on any failure.
+   */
+  async selfTest() {
+    this.log.info('Running startup self-test for metadata endpoints...');
+
+    for (const endpointInfo of this.endpoints) {
+      const label = `${endpointInfo.path} (FHIR v${endpointInfo.fhirVersion})`;
+
+      // Build a minimal mock req/res that captures what metadataHandler.handle() produces
+      const makeMockReqRes = (mode) => {
+        const captured = { data: null, status: 200 };
+
+        const req = {
+          method: 'GET',
+          query: { mode },
+          headers: {},
+          // eslint-disable-next-line no-unused-vars
+          get: (name) => null,
+          txEndpoint: endpointInfo,
+          txProvider: endpointInfo.provider,
+        };
+
+        const res = {
+          statusCode: 200,
+          status(code) { captured.status = code; return this; },
+          setHeader() { return this; },
+          json(data) { captured.data = data; return this; },
+          send(data) { captured.data = data; return this; },
+        };
+
+        return { req, res, captured };
+      };
+
+      // Test 1: CapabilityStatement  (/metadata with no mode, or mode=full)
+      try {
+        const { req, res, captured } = makeMockReqRes(undefined);
+        await this.metadataHandler.handle(req, res);
+        if (!captured.data) {
+          throw new Error('No response data returned');
+        }
+        const rt = captured.data.resourceType;
+        if (rt !== 'CapabilityStatement') {
+          throw new Error(`Expected CapabilityStatement, got ${rt}`);
+        }
+        this.log.info(`  [OK] CapabilityStatement for ${label}`);
+      } catch (err) {
+        this.log.error(`  [FAIL] CapabilityStatement for ${label}: ${err.message}`);
+        throw new Error(`Startup self-test failed (CapabilityStatement, ${label}): ${err.message}`);
+      }
+
+      // Test 2: TerminologyCapabilities  (/metadata?mode=terminology)
+      try {
+        const { req, res, captured } = makeMockReqRes('terminology');
+        await this.metadataHandler.handle(req, res);
+        if (!captured.data) {
+          throw new Error('No response data returned');
+        }
+        const rt = captured.data.resourceType;
+        if (rt !== 'TerminologyCapabilities') {
+          throw new Error(`Expected TerminologyCapabilities, got ${rt}`);
+        }
+        this.log.info(`  [OK] TerminologyCapabilities for ${label}`);
+      } catch (err) {
+        this.log.error(`  [FAIL] TerminologyCapabilities for ${label}: ${err.message}`);
+        throw new Error(`Startup self-test failed (TerminologyCapabilities, ${label}): ${err.message}`);
+      }
+    }
+
+    this.log.info('Startup self-test passed.');
+  }
+
   /**
    * Build an OperationOutcome for errors
    */
@@ -1077,21 +1153,21 @@ class TXModule {
   ec = 0;
 
   checkProperJson() { // jsonStr) {
-  //   const errors = [];
-  //   if (jsonStr.includes("[]")) errors.push("Found [] in json");
-  //   if (jsonStr.includes('""')) errors.push('Found "" in json');
-  //
-  //   if (errors.length > 0) {
-  //     this.ec++;
-  //     const filename = `/Users/grahamegrieve/temp/tx-err-log/err${this.ec}.json`;
-  //     writeFileSync(filename, jsonStr);
-  //     throw new Error(errors.join('; '));
-  //   }
+                      //   const errors = [];
+                      //   if (jsonStr.includes("[]")) errors.push("Found [] in json");
+                      //   if (jsonStr.includes('""')) errors.push('Found "" in json');
+                      //
+                      //   if (errors.length > 0) {
+                      //     this.ec++;
+                      //     const filename = `/Users/grahamegrieve/temp/tx-err-log/err${this.ec}.json`;
+                      //     writeFileSync(filename, jsonStr);
+                      //     throw new Error(errors.join('; '));
+                      //   }
   }
 
   transformResourceForVersion(data, fhirVersion) {
     if (fhirVersion == "5.0" || !data.resourceType) {
-        return data;
+      return data;
     }
     switch (data.resourceType) {
       case "CodeSystem": return codeSystemFromR5(data, fhirVersion);

package/tx/workers/validate.js

@@ -1389,17 +1389,22 @@ class ValueSetChecker {
     let hd = list.hasDisplay(this.params.workingLanguages(), null, c.display, false, DisplayCheckingStyle.CASE_INSENSITIVE)
     if (!hd.found) {
       let baseMsg;
-      if (hd.difference === DisplayDifference.Normalized) {
+      let severity = this.dispWarning();
+      if (list.userDefined) {
+        baseMsg = 'Display_Name_Not_Fixed_use_Supplement';
+        severity = 'information';
+      } else if (hd.difference === DisplayDifference.Normalized) {
         baseMsg = 'Display_Name_WS_for__should_be_one_of__instead_of';
       } else {
         baseMsg = 'Display_Name_for__should_be_one_of__instead_of';
       }
-      let mid = baseMsg;
       let dc = list.displayCount(this.params.workingLanguages(), null, true);
-      let severity = this.dispWarning();
-      if (dc === 0) {
-        severity = 'warning';
-        dc = list.displayCount(this.params.workingLanguages(), null, false);
+      let mid = baseMsg;
+      if (severity !== 'information') {
+        if (dc === 0) {
+          severity = 'warning';
+          dc = list.displayCount(this.params.workingLanguages(), null, false);
+        }
       }
 
       let m, ds;

package/tx/workers/worker.js

@@ -276,12 +276,9 @@ class TerminologyWorker {
         if (this.hasSupplement(cs, supplements)) {
           continue;
         }
-        // Handle exact URL match (no version specified in supplements)
+        // Handle exact URL match (no version specified in supplements field)
         if (supplementsUrl === url) {
-          // If we're looking for a specific version, only include if no version in supplements URL
-          if (!version) {
-            supplements.push(cs);
-          }
+          supplements.push(cs);
           continue;
         }
 

package/xig/xig.js

@@ -1241,13 +1241,14 @@ function buildAdditionalForm(queryParams) {
     }
   }
 
+
   // Add text search field and package filter field
   html += `Text: <input type="text" name="text" value="${escape(text || '')}" class="" style="width: 200px;"/> `;
   html += `Package: <input type="text" name="pkg" value="${escape(pkg || '')}" placeholder="e.g. hl7.fhir.us" class="" style="width: 200px;"/> `;
 
   // Add submit button with 'only used' checkbox immediately before it
   const onlyUsedChecked = onlyUsed === 'true' ? ' checked' : '';
-  html += `<input type="checkbox" name="onlyUsed" value="true"${onlyUsedChecked}/> Only Used `;
+  html += `<input type="checkbox" name="onlyUsed" value="true"${onlyUsedChecked}/> Only Show Used `;
   html += '<input type="submit" value="Search" style="color:rgb(89, 137, 241)"/>';
 
   html += '</form>';
@@ -2747,11 +2748,14 @@ function buildDependencyTable(dependencies) {
       }
       currentType = dep.ResourceType;
       html += '<table class="table table-bordered">';
-      html += `<tr style="background-color: #eeeeee"><td colspan="2"><strong>${escape(currentType)}</strong></td></tr>`;
+      html += `<tr style="background-color: #eeeeee"><td colspan="3"><strong>${escape(currentType)}</strong></td></tr>`;
     }
 
     html += '<tr>';
 
+    // Package column
+    html += `<td>${escape(dep.PID || '')}</td>`;
+
     // Build the link to the resource detail page
     const packagePid = dep.PID.replace(/#/g, '|'); // Convert # to | for URL
     const resourceUrl = `/xig/resource/${encodeURIComponent(packagePid)}/${encodeURIComponent(dep.ResourceType)}/${encodeURIComponent(dep.Id)}`;