fhirsmith 0.5.5 → 0.6.0

package/tx/tx-html.js

@@ -9,6 +9,15 @@ const htmlServer = require('../library/html-server');
 const Logger = require('../library/logger');
 const packageJson = require("../package.json");
 const escape = require('escape-html');
+const {ExpandWorker} = require("./workers/expand");
+const ValueSet = require("./library/valueset");
+const {CodeSystemXML} = require("./xml/codesystem-xml");
+const {ValueSetXML} = require("./xml/valueset-xml");
+const {BundleXML} = require("./xml/bundle-xml");
+const {CapabilityStatementXML} = require("./xml/capabilitystatement-xml");
+const {TerminologyCapabilitiesXML} = require("./xml/terminologycapabilities-xml");
+const {ParametersXML} = require("./xml/parameters-xml");
+const {OperationOutcomeXML} = require("./xml/operationoutcome-xml");
 
 const txHtmlLog = Logger.getInstance().child({ module: 'tx-html' });
 
@@ -57,10 +66,16 @@ function loadTemplate() {
 class TxHtmlRenderer {
   renderer;
   liquid;
+  languages;
+  i18n;
+  path;
 
-  constructor(renderer, liquid) {
+  constructor(renderer, liquid, languages, i18n, path) {
     this.renderer = renderer;
     this.liquid = liquid;
+    this.languages = languages;
+    this.i18n = i18n;
+    this.path = path;
   }
 
   /**
@@ -85,7 +100,7 @@ class TxHtmlRenderer {
     if (_fmt && typeof _fmt !== 'string') {
       _fmt = null;
     }
-    if (_fmt && _fmt == 'html') {
+    if (_fmt && (_fmt == 'html' || _fmt.startsWith('html/'))) {
       return true;
     }
     if (!_fmt) {
@@ -106,6 +121,14 @@ class TxHtmlRenderer {
     } else {
       const resourceType = json.resourceType || 'Response';
 
+      let pfx = resourceType;
+      if (req.path.includes('$')) {
+        let s = req.path.substring(req.path.indexOf('$') + 1).replace(/[^a-zA-Z].*$/, '');
+        switch (s) {
+          case 'expand': pfx = "Expansion for "+resourceType;
+        }
+      }
+
       if (resourceType === 'Bundle' && json.type === 'searchset') {
         // Extract the resource type being searched from self link or entries
         const selfLink = json.link?.find(l => l.relation === 'self')?.url || '';
@@ -124,11 +147,11 @@ class TxHtmlRenderer {
       }
 
       if (json.id) {
-        return `${resourceType}/${json.id}`;
+        return `${pfx} ${json.id}`;
       }
 
       if (json.name) {
-        return `${resourceType}: ${json.name}`;
+        return `${pfx} ${json.name}`;
       }
 
       return resourceType;
@@ -267,15 +290,27 @@ class TxHtmlRenderer {
       return await this.buildHomePage(req);
     } else {
       try {
+        const _fmt = req?.query?._format || req?.query?.format || req?.body?._format;
+        const op = req ? req.path.includes("$") : false;
         const resourceType = json.resourceType;
 
         switch (resourceType) {
           case 'Parameters':
             return await this.renderParameters(json);
           case 'CodeSystem':
-            return await this.renderCodeSystem(json, inBundle);
-          case 'ValueSet':
-            return await this.renderValueSet(json, inBundle);
+            return await this.renderCodeSystem(json, inBundle, _fmt, op);
+          case 'ValueSet': {
+            let exp = undefined;
+            if (!inBundle && !op && (!_fmt || _fmt == 'html')) {
+              try {
+                let worker = new ExpandWorker(req.txOpContext, this.log, req.txProvider, this.languages, this.i18n);
+                exp = new ValueSet(await worker.handleInternalExpand(json, req));
+              } catch (error) {
+                exp = error;
+              }
+            }
+            return await this.renderValueSet(json, inBundle, _fmt, op, exp);
+          }
           case 'ConceptMap':
             return await this.renderConceptMap(json, inBundle);
           case 'CapabilityStatement':
@@ -575,35 +610,88 @@ class TxHtmlRenderer {
   /**
    * Render CodeSystem resource
    */
-  async renderCodeSystem(json, inBundle) {
-    let html = await this.renderResourceWithNarrative(json, await this.renderer.renderCodeSystem(json));
+  async renderCodeSystem(json, inBundle, _fmt) {
+    if (inBundle) {
+      return await this.renderResourceWithNarrative(json, await this.renderer.renderCodeSystem(json));
+    } else {
+      let html = `<ul class="nav nav-tabs">`;
+      html += this.tab(!_fmt || _fmt == 'html', json.resourceType, json.resourceType, 'html', json.id);
+      html += this.tab(_fmt && _fmt == 'html/json', 'JSON', json.resourceType, 'html/json', json.id);
+      html += this.tab(_fmt && _fmt == 'html/xml', 'XML', json.resourceType, 'html/xml', json.id);
+      html += this.tab(_fmt && _fmt == 'html/narrative', 'Original Narrative', json.resourceType, 'html/narrative', json.id);
+      html += this.tab(_fmt && _fmt == 'html/ops', 'LookUp / Subsumes', json.resourceType, 'html/ops', json.id);
+      html += `</ul>`;
+
+      if (!_fmt || _fmt == 'html') {
+        html += await this.renderResourceWithNarrative(json, await this.renderer.renderCodeSystem(json));
+      } else if (_fmt == "html/json") {
+        html += await this.renderResourceJson(json);
+      } else if (_fmt == "html/xml") {
+        html += await this.renderResourceXml(json);
+      } else if (_fmt == "html/narrative") {
+        html += await this.renderResourceWithNarrative(json, json.text?.div);
+      } else if (_fmt == "html/ops") {
+        html += await this.liquid.renderFile('codesystem-operations', {
+          opsId: this.generateResourceId(),
+          vcSystemId: this.generateResourceId(),
+          inferSystemId: this.generateResourceId(),
+          url: escape(json.url || '')
+        });
+      }
 
-    if (!inBundle) {
-      html += await this.liquid.renderFile('codesystem-operations', {
-        opsId: this.generateResourceId(),
-        url: escape(json.url || '')
-      });
-    }
 
-    return html;
+      return html;
+    }
   }
 
+  tab(b, name, rtype, type, id) {
+    if (b) {
+      return `<li class="active"><a href="#">${name}</a></li>`;
+    } else {
+      return `<li><a href="${this.path}/${rtype}/${id}?_format=${type}">${name}</a></li>`;
+    }
+  }
   /**
    * Render ValueSet resource
    */
-  async renderValueSet(json, inBundle) {
-    let html = await this.renderResourceWithNarrative(json, await this.renderer.renderValueSet(json));
-
-    if (!inBundle) {
-      html += await this.liquid.renderFile('valueset-operations', {
-        opsId: this.generateResourceId(),
-        vcSystemId: this.generateResourceId(),
-        inferSystemId: this.generateResourceId(),
-        url: escape(json.url || '')
-      });
+  async renderValueSet(json, inBundle, _fmt, op, exp) {
+    if (inBundle || op) {
+      return await this.renderResourceWithNarrative(json, await this.renderer.renderValueSet(json));
+    } else {
+      let html = `<ul class="nav nav-tabs">`;
+      html += this.tab(!_fmt || _fmt == 'html', json.resourceType, json.resourceType, 'html', json.id);
+      html += this.tab(_fmt && _fmt == 'html/json', 'JSON', json.resourceType, 'html/json', json.id);
+      html += this.tab(_fmt && _fmt == 'html/xml', 'XML', json.resourceType, 'html/xml', json.id);
+      html += this.tab(_fmt && _fmt == 'html/narrative', 'Original Narrative', json.resourceType, 'html/narrative', json.id);
+      html += this.tab(_fmt && _fmt == 'html/ops', 'Expand / Validate', json.resourceType, 'html/ops', json.id);
+      html += `</ul>`;
+
+      if (!_fmt || _fmt == 'html') {
+        html += await this.renderResourceWithNarrative(json, await this.renderer.renderValueSet(json));
+        if (exp) {
+          html += "<h2>Expansion</h2>";
+          if (exp instanceof ValueSet) {
+            html += await this.renderer.renderVSExpansion(exp.jsonObj, false)
+          } else {
+            html += `<p>Error: `+exp.message+`</p>`;
+          }
+        }
+      } else if (_fmt == "html/json") {
+        html += await this.renderResourceJson(json);
+      } else if (_fmt == "html/xml") {
+        html += await this.renderResourceXml(json);
+      } else if (_fmt == "html/narrative") {
+        html += await this.renderResourceWithNarrative(json, json.text?.div);
+      } else if (_fmt == "html/ops") {
+        html += await this.liquid.renderFile('valueset-operations', {
+          opsId: this.generateResourceId(),
+          vcSystemId: this.generateResourceId(),
+          inferSystemId: this.generateResourceId(),
+          url: escape(json.url || '')
+        });
+      }
+      return html;
     }
-
-    return html;
   }
 
   /**
@@ -1101,9 +1189,7 @@ class TxHtmlRenderer {
    * Render resource with text/div narrative and collapsible JSON source
    */
   async renderResourceWithNarrative(json, rendered) {
-    const resourceId = this.generateResourceId();
-
-    let html = "";
+    let html = '';
 
     // Show text/div narrative if present
     if (rendered) {
@@ -1113,30 +1199,37 @@ class TxHtmlRenderer {
     } else {
       html += '<div class="narrative">(No Narrative)</div>';
     }
-    if (json.text && json.text.div) {
-      // Collapsible JSON source
-      html += '<div class="xhtml">';
-      html += `<button type="button" class="btn btn-sm btn-outline-secondary" onclick="toggleOriginalNarrative('${resourceId}x')">`;
-      html += 'Show Original Narrative</button>';
-      html += `<div id="${resourceId}x" class="original-narrative" style="display: none; margin-top: 10px;">`;
-
-      html += '<div class="narrative">';
-      html += json.text.div;  // Already HTML, render as-is
-      html += '</div>';
-    }
-    html += '</div>';
-    html += '</div>';
 
+    return html;
+  }
 
-    // Collapsible JSON source
-    html += '<div class="json-source">';
-    html += `<button type="button" class="btn btn-sm btn-outline-secondary" onclick="toggleJsonSource('${resourceId}')">`;
-    html += 'Show JSON Source</button>';
-    html += `<div id="${resourceId}" class="json-content" style="display: none; margin-top: 10px;">`;
+  async renderResourceJson(json) {
+    let html = "";
+    html += `<div class="json-content" style="margin-top: 10px;">`;
     html += `<pre>${escape(JSON.stringify(json, null, 2))}</pre>`;
     html += '</div>';
-    html += '</div>';
+    return html;
+  }
+
+  convertResourceToXml(res) {
+    switch (res.resourceType) {
+      case "CodeSystem" : return CodeSystemXML.toXml(res);
+      case "ValueSet" : return ValueSetXML.toXml(res);
+      case "Bundle" : return BundleXML.toXml(res, this.fhirVersion);
+      case "CapabilityStatement" : return CapabilityStatementXML.toXml(res, "R5");
+      case "TerminologyCapabilities" : return TerminologyCapabilitiesXML.toXml(res, "R5");
+      case "Parameters": return ParametersXML.toXml(res, this.fhirVersion);
+      case "OperationOutcome": return OperationOutcomeXML.toXml(res, this.fhirVersion);
+    }
+    throw new Error(`Resource type ${res.resourceType} not supported in XML`);
+  }
 
+  async renderResourceXml(json) {
+    let xml = this.convertResourceToXml(json);
+    let html = "";
+    html += `<div class="xml-content" style="margin-top: 10px;">`;
+    html += `<pre>${escape(xml)}</pre>`;
+    html += '</div>';
     return html;
   }
 

package/tx/tx.js

@@ -300,7 +300,7 @@ class TXModule {
       // Wrap res.json to intercept and convert to HTML if browser requests it, and log the request
       const originalJson = res.json.bind(res);
 
-      let txhtml = new TxHtmlRenderer(new Renderer(opContext, endpointInfo.provider), this.liquid);
+      let txhtml = new TxHtmlRenderer(new Renderer(opContext, endpointInfo.provider), this.liquid, this.languages, this.i18n, endpointInfo.path);
       res.json = async (data) => {
         try {
           const duration = Date.now() - req.txStartTime;
@@ -897,7 +897,7 @@ 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);
+        let txhtml = new TxHtmlRenderer(new Renderer(req.txOpContext, req.txProvider), this.liquid, this.languages, this.i18n, req.txEndpoint.path);
         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);

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);
           }
@@ -1388,17 +1388,28 @@ class ValueSetExpander {
   }
 
   checkCanonicalStatus(exp, vurl, status, standardsStatus, experimental, source) {
+    let sourceStatus = source ? source.status : undefined;
+    let sourceStandardsStatus= source ? Extensions.readString(source, 'http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status') : undefined;
     if (standardsStatus == 'deprecated') {
-      this.addParamUri(exp, 'warning-deprecated', vurl);
+      if (sourceStandardsStatus != 'deprecated') {
+        this.addParamUri(exp, 'warning-deprecated', vurl);
+      }
     } else if (standardsStatus == 'withdrawn') {
-      this.addParamUri(exp, 'warning-withdrawn', vurl);
+      if (sourceStandardsStatus != 'withdrawn') {
+        this.addParamUri(exp, 'warning-withdrawn', vurl);
+      }
     } else if (status == 'retired') {
-      this.addParamUri(exp, 'warning-retired', vurl);
-    } else if (experimental && !source.experimental) {
-      this.addParamUri(exp, 'warning-experimental', vurl)
-    } else if (((status == 'draft') || (standardsStatus == 'draft')) &&
-      !((source.status == 'draft') || (Extensions.readString(source, 'http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status') == 'draft'))) {
-      this.addParamUri(exp, 'warning-draft', vurl)
+      if (sourceStatus != 'retired') {
+        this.addParamUri(exp, 'warning-retired', vurl);
+      }
+    } else if (experimental) {
+      if (!source.experimental) {
+        this.addParamUri(exp, 'warning-experimental', vurl);
+      }
+    } else if (((status == 'draft') || (standardsStatus == 'draft'))) {
+      if (!((source.status == 'draft') || (Extensions.readString(source, 'http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status') == 'draft'))) {
+        this.addParamUri(exp, 'warning-draft', vurl)
+      }
     }
   }
 
@@ -1797,7 +1808,48 @@ class ExpandWorker extends TerminologyWorker {
     req.logInfo = this.usedSources.join("|")+txp.logInfo();
     return res.json(result);
   }
-  
+
+  /**
+   * Handle type-level expand: /ValueSet/$expand
+   * ValueSet identified by url, or provided directly in body
+   */
+  async handleInternalExpand(valueSet, req) {
+    this.deadCheck('expand-internal');
+
+    if (!valueSet.jsonObj) {
+      valueSet = new ValueSet(valueSet);
+    }
+    // Determine how the request is structured
+    let params = null;
+    this.seeSourceVS(valueSet);
+
+    if (req.method === 'POST' && req.body) {
+      if (req.body.resourceType === 'ValueSet') {
+        params = this.queryToParameters(req.query);
+      } else if (req.body.resourceType === 'Parameters') {
+        // Body is a Parameters resource
+        params = req.body;
+      } else {
+        // Assume form body - convert to Parameters
+        params = this.formToParameters(req.body, req.query);
+      }
+    } else {
+      // GET request - convert query to Parameters
+      params = this.queryToParameters(req.query);
+    }
+    this.addHttpParams(req, params);
+
+    // Handle tx-resource and cache-id parameters
+    this.setupAdditionalResources(params);
+    const logExtraOutput = this.findParameter(params, 'logExtraOutput');
+
+    let txp = new TxParameters(this.opContext.i18n.languageDefinitions, this.opContext.i18n, false);
+    txp.readParams(params);
+
+    // Perform the expansion
+    return await this.doExpand(valueSet, txp, logExtraOutput);
+  }
+
   /**
    * Handle instance-level expand: /ValueSet/{id}/$expand
    * ValueSet identified by resource ID

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/search.js

@@ -137,7 +137,7 @@ class SearchWorker extends TerminologyWorker {
     const searchParams = {};
     for (const [key, value] of Object.entries(params)) {
       if (!key.startsWith('_') && value && SearchWorker.ALLOWED_PARAMS.includes(key)) {
-        searchParams[key] = value.toLowerCase();
+        searchParams[key] = key == 'url' ? value : value.toLowerCase();
       }
     }
 
@@ -146,6 +146,9 @@ class SearchWorker extends TerminologyWorker {
 
     for (const [key, cs] of this.provider.codeSystems) {
       this.deadCheck('searchCodeSystems');
+      if (cs.url == 'http://www.cms.gov/Medicare/Coding/HCPCSReleaseCodeSets') {
+        console.log("debug");
+      }
       if (key == cs.vurl) {
         const json = cs.jsonObj;
 
@@ -179,7 +182,7 @@ class SearchWorker extends TerminologyWorker {
             }
           } else if (param === 'url') { // exact match
             const propValue = json.url;
-            if (propValue != searchValue) {
+            if (propValue !== searchValue) {
               isMatch = false;
               break;
             }

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(cs, "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;
 }