2026 02 gg various fixes

tx/README.md

@@ -26,6 +26,8 @@ Add the `tx` section to your `config.json`:
       "enabled": true,
       "librarySource": "/path/to/library.yml",
       "cacheTimeout": 30,
+      "internalLimit" : 10000,
+      "externalLimit" : 1000,
       "expansionCacheSize": 1000,
       "expansionCacheMemoryThreshold": 0,
       "endpoints": [
@@ -57,14 +59,16 @@ Add the `tx` section to your `config.json`:
 
 ### Configuration Options
 
-| Option | Type | Required | Description |
-|--------|------|----------|-------------|
-| `enabled` | boolean | Yes | Whether the module is enabled |
-| `cacheTimeout` | integer | No | How many minutes to keep client side caches (for cache-id parameter). Default: 30 |
-| `expansionCacheSize` | integer | No | Maximum number of expanded ValueSets to cache. Default: 1000 |
-| `expansionCacheMemoryThreshold` | integer | No | Heap memory usage in MB that triggers evicting oldest half of expansion cache. 0 = disabled. Default: 0 |
-| `librarySource` | string | Yes | Path to the YAML file that defines the terminology sources to load |
-| `endpoints` | array | Yes | List of endpoint configurations (at least one required) |
+| Option                          | Type    | Required | Description                                                                                             |
+|---------------------------------|---------|----------|---------------------------------------------------------------------------------------------------------|
+| `enabled`                       | boolean | Yes      | Whether the module is enabled                                                                           |
+| `cacheTimeout`                  | integer | No       | How many minutes to keep client side caches (for cache-id parameter). Default: 30                       |
+| `expansionCacheSize`            | integer | No       | Maximum number of expanded ValueSets to cache. Default: 1000                                            |
+| `expansionCacheMemoryThreshold` | integer | No       | Heap memory usage in MB that triggers evicting oldest half of expansion cache. 0 = disabled. Default: 0 |
+| `librarySource`                 | string  | Yes      | Path to the YAML file that defines the terminology sources to load                                      |
+| `internalLimit`                 | integer | No       | Largest number of codes in internal expansions                                                          |
+| `externalLimit`                 | integer | No       | Largest number of codes the server will return in an expansion                                          |
+| `endpoints`                     | array   | Yes      | List of endpoint configurations (at least one required)                                                 |
 
 ### Endpoint Configuration
 

tx/cs/cs-api.js

@@ -812,6 +812,32 @@ class CodeSystemFactoryProvider {
     return null;
   }
 
+  /**
+   * If the data available to the provider includes the definition of some supplements,
+   * then the provider has to declare them to the server by overriding this method. The
+   * method returns a list of CodeSystem resources, with jsonObj provided. The jsonObj
+   * in this case must include the correct metadata, with content = supplement, but need
+   * not include any actual content (which might be anticipated to be large). If the
+   * server sees a CodeSystem supplement with no content that comes from a provider
+   * then the server will use fillOutSupplement to ask for the details to be populated
+   * if a client has done something that means the server needs it (mostly, it doesn't)
+   *
+   * @returns {CodeSystem[]}
+   */
+  async registerSupplements() {
+    return [];
+  }
+
+  /**
+   * see comemnts for registerSupplements()
+   *
+   * @param {CodeSystem} supplement - the supplement to flesh out
+   * @returns void
+   */
+  async fillOutSupplement(supplement) {
+    // nothing
+  }
+
   /**
    * build and return a known concept map from the URL, if there is one.
    *

tx/cs/cs-country.js

@@ -22,7 +22,6 @@ class CountryCodeServices extends CodeSystemProvider {
     super(opContext, supplements);
     this.codes = codes || [];
     this.codeMap = codeMap || new Map();
-    this.supplements = [];
   }
 
   // Metadata methods

tx/cs/cs-rxnorm.js

@@ -748,6 +748,9 @@ class RxNormTypeServicesFactory extends CodeSystemFactoryProvider {
             if (d.includes('_')) {
               d = d.substring(d.lastIndexOf('_') + 1);
             }
+            if (d.includes('-')) {
+              d = d.substring(0, d.lastIndexOf('-'));
+            }
             if (/^\d+$/.test(d)) {
               version = d;
             }

tx/html/tx-template.html

@@ -89,6 +89,7 @@
             <a href="[%endpoint-path%]/metadata" style="color: gold">Capability Statement</a>  &nbsp;|&nbsp;
             <a href="[%endpoint-path%]/metadata?mode=terminology" style="color: gold">Terminology Capabilities</a>  &nbsp;|&nbsp;
             <a href="[%endpoint-path%]/op.html" style="color: gold">Operations</a>  &nbsp;|&nbsp;
+            <a href="[%endpoint-path%]/problems.html" style="color: gold">Problems</a>  &nbsp;|&nbsp;
   &nbsp;
 		</div>
 		</div>

tx/library.js

@@ -758,6 +758,7 @@ class Library {
       cmp.close();
     }
   }
+
 }
 
 module.exports = { Library };

tx/problems.js

@@ -0,0 +1,68 @@
+
+class ProblemFinder {
+
+  constructor() {
+    this.map = new Map();
+  }
+
+  async scanValueSets(provider) {
+    let unknownVersions = {};  // system -> Set of versions not known to the server
+    for (let vsp of provider.valueSetProviders) {
+      let list = await vsp.listAllValueSets();
+      for (let url of list) {
+        let vs = await vsp.fetchValueSet(url);
+        if (vs && vs.jsonObj.compose) {
+          await this.scanValueSet(vs.jsonObj.compose, unknownVersions, vs.jsonObj.status != 'retired');
+        }
+      }
+    }
+    // Filter to only versions the server doesn't know about
+    for (const [system, vset] of Object.entries(unknownVersions)) {
+      for (let v of [...vset]) {
+        if (await provider.hasCsVersion(system, v)) {
+          vset.delete(v);
+        }
+      }
+      if (vset.size === 0) {
+        delete unknownVersions[system];
+      }
+    }
+    return this.unknownVersionsHtml(unknownVersions);
+  }
+
+  unknownVersionsHtml(unknownVersions) {
+    const entries = Object.entries(unknownVersions || {});
+    if (entries.length === 0) {
+      return '<p>No unknown system versions found.</p>';
+    }
+    entries.sort((a, b) => a[0].localeCompare(b[0]));
+    let html = '<table class="grid"><thead><tr><th>System</th><th>Unknown Versions</th></tr></thead><tbody>';
+    for (const [system, vset] of entries) {
+      const versions = [...vset].sort((a, b) => a.localeCompare(b)).join('<br/>');
+      html += `<tr><td>${system}</td><td>${versions}</td></tr>`;
+    }
+    html += '</tbody></table>';
+    return html;
+  }
+
+  async scanValueSet(compose, versions, active) {
+    for (let inc of compose.include || []) {
+      if (inc.system) {
+        if (active && inc.version) {
+          this.seeVersion(versions, inc.system, inc.version);
+        }
+      }
+    }
+  }
+
+  seeVersion(versions, system, version) {
+    let set = versions[system];
+    if (set == null) {
+      set = new Set();
+      versions[system] = set;
+    }
+    set.add(version);
+  }
+}
+
+module.exports = ProblemFinder;

tx/provider.js

@@ -399,6 +399,20 @@ class Provider {
     return null;
   }
 
+  async hasCsVersion(system, version) {
+    for (let cs of this.codeSystems.values()) {
+      if (cs.url == system && cs.version == version) {
+        return true;
+      }
+    }
+    for (let cp of this.codeSystemFactories.values()) {
+      if (cp.system() == system && cp.version() == version) {
+        return true;
+      }
+    }
+    return false;
+  }
+
 }
 
 module.exports = { Provider };

tx/tx.fhir.org.yml

@@ -26,6 +26,7 @@ sources:
   - snomed:sct_nl_20240930.cache
   - snomed:sct_uk_20230412.cache
   - snomed:sct_us_20230301.cache
+  - snomed:sct_us_20240301.cache
   - snomed:sct_us_20250901.cache
   - snomed:sct_test_20250814.cache
   - cpt:CodeSystem-cpt.db|cpt-2023-fragment-0.1.db

tx/tx.js

@@ -20,7 +20,7 @@ const packageJson = require("../package.json");
 // Import workers
 const ReadWorker = require('./workers/read');
 const SearchWorker = require('./workers/search');
-const { ExpandWorker } = require('./workers/expand');
+const { ExpandWorker, INTERNAL_DEFAULT_LIMIT, EXTERNAL_DEFAULT_LIMIT} = require('./workers/expand');
 const { ValidateWorker } = require('./workers/validate');
 const TranslateWorker = require('./workers/translate');
 const LookupWorker = require('./workers/lookup');
@@ -49,6 +49,7 @@ const {convertResourceToR5} = require("./xversion/xv-resource");
 const ClosureWorker = require("./workers/closure");
 const {BundleXML} = require("./xml/bundle-xml");
 const ConceptUsageTracker = require("./usage-tracker");
+const ProblemFinder = require("./problems");
 // const {writeFileSync} = require("fs");
 
 class TXModule {
@@ -620,7 +621,7 @@ class TXModule {
     router.get('/ValueSet/\\$expand', async (req, res) => {
       const start = Date.now();
       try {
-        let worker = new ExpandWorker(req.txOpContext, this.log, req.txProvider, this.languages, this.i18n);
+        let worker = new ExpandWorker(req.txOpContext, this.log, req.txProvider, this.languages, this.i18n, this.internalLimit(req), this.externalLimit(req));
         await worker.handle(req, res, this.log);
       } finally {
         this.countRequest('$expand', Date.now() - start);
@@ -629,7 +630,7 @@ class TXModule {
     router.post('/ValueSet/\\$expand', async (req, res) => {
       const start = Date.now();
       try {
-        let worker = new ExpandWorker(req.txOpContext, this.log, req.txProvider, this.languages, this.i18n);
+        let worker = new ExpandWorker(req.txOpContext, this.log, req.txProvider, this.languages, this.i18n, this.internalLimit(req), this.externalLimit(req));
         await worker.handle(req, res, this.log);
       } finally {
         this.countRequest('$expand', Date.now() - start);
@@ -784,7 +785,7 @@ class TXModule {
     router.get('/ValueSet/:id/\\$expand', async (req, res) => {
       const start = Date.now();
       try {
-        let worker = new ExpandWorker(req.txOpContext, this.log, req.txProvider, this.languages, this.i18n);
+        let worker = new ExpandWorker(req.txOpContext, this.log, req.txProvider, this.languages, this.i18n, this.internalLimit(req), this.externalLimit(req));
         await worker.handleInstance(req, res, this.log);
       } finally {
         this.countRequest('$expand', Date.now() - start);
@@ -793,7 +794,7 @@ class TXModule {
     router.post('/ValueSet/:id/\\$expand', async (req, res) => {
       const start = Date.now();
       try {
-        let worker = new ExpandWorker(req.txOpContext, this.log, req.txProvider, this.languages, this.i18n);
+        let worker = new ExpandWorker(req.txOpContext, this.log, req.txProvider, this.languages, this.i18n, this.internalLimit(req), this.externalLimit(req));
         await worker.handleInstance(req, res, this.log);
       } finally {
         this.countRequest('$expand', Date.now() - start);
@@ -893,6 +894,20 @@ class TXModule {
       }
     });
 
+    router.get('/problems.html', async (req, res) => {
+      const start = Date.now();
+      try {
+        let txhtml = new TxHtmlRenderer(new Renderer(req.txOpContext, req.txProvider), this.liquid);
+        const problemFinder = new ProblemFinder();
+        const content = await problemFinder.scanValueSets(req.txProvider);
+        const html = await txhtml.renderPage('Problems', '<h3>ValueSet dependencies on unknown CodeSystem/Versions</h3>'+content, req.txEndpoint, req.txStartTime);
+        res.setHeader('Content-Type', 'text/html');
+        res.send(html);
+      } finally {
+        this.countRequest('problems', Date.now() - start);
+      }
+    });
+
     // Metadata / CapabilityStatement
     router.get('/metadata', async (req, res) => {
       const start = Date.now();
@@ -1083,6 +1098,16 @@ class TXModule {
     }
   }
 
+  internalLimit(req) {
+    let isTest = req.header("User-Agent") == 'Tools/Java';
+    if (this.config.internalLimit && !isTest) return this.config.internalLimit; else return INTERNAL_DEFAULT_LIMIT;
+  }
+
+  externalLimit(req) {
+    let isTest = req.header("User-Agent") == 'Tools/Java';
+    if (this.config.internalLimit && !isTest) return this.config.externalLimit; else return EXTERNAL_DEFAULT_LIMIT;
+  }
+
 }
 
 module.exports = TXModule;

tx/usage-tracker.js

@@ -21,10 +21,13 @@ class ConceptUsageTracker {
     return c;
   }
 
-  async scanValueSet(compose) {
+  async scanValueSet(compose, versions, active) {
     let ok = false;
     for (let inc of compose.include || []) {
       if (inc.system) {
+        if (active && inc.version) {
+          this.seeVersion(versions, inc.system, inc.version);
+        }
         for (let c of inc.concept || []) {
           if (c.code) {
             ok = true;
@@ -53,6 +56,15 @@ class ConceptUsageTracker {
   usages(system) {
     return this.map.get(system) || null;
   }
+
+  seeVersion(versions, system, version) {
+    let set = versions[system];
+    if (set == null) {
+      set = new Set();
+      versions[system] = set;
+    }
+    set.add(version);
+  }
 }
 
 module.exports = ConceptUsageTracker;