fhirsmith 0.3.0 → 0.5.0

package/stats.js

@@ -1,5 +1,6 @@
 const { monitorEventLoopDelay } = require('perf_hooks');
-const {cache} = require("express/lib/application");
+const {Utilities} = require("./library/utilities");
+const escape = require('escape-html');
 
 class ServerStats {
   started = false;
@@ -13,6 +14,7 @@ class ServerStats {
   startTime = Date.now();
   timer;
   cachingModules = [];
+  taskMap = new Map();
 
   constructor() {
     this.timer = setInterval(() => {
@@ -73,6 +75,42 @@ class ServerStats {
     this.requestTime = this.requestTime + tat;
   }
 
+  addTask(name, frequency) {
+    let info = {};
+    this.taskMap.set(name, info);
+    info.frequency = frequency;
+    info.state = "Started";
+  }
+
+  task(name, state) {
+    let info = this.taskMap.get(name);
+    if (info) {
+      info.date = Date.now();
+      info.state = state;
+    }
+  }
+
+  taskDetails() {
+    if (this.taskMap.size == 0) {
+      return "";
+    }
+    let html = '<table class="grid"><tr style="background-color: #EEEEEE"><th colspan="4">Background Tasks</th></tr>';
+    html += "<tr><th>Task</th><th>Status</th><th>Frequency</th><th>Last Seen</th></tr>";
+    for (let m of this.taskMap.keys()) {
+      html += "<tr><td>";
+      html += escape(m);
+      html += "</td><td>";
+      html += escape(this.taskMap.get(m).state);
+      html += "</td><td>";
+      html += this.taskMap.get(m).frequency;
+      html += "</td><td>";
+      html += Utilities.formatDuration(this.taskMap.get(m).date, Date.now());
+      html += "</td></tr>";
+    }
+    html += "</table>";
+    return html;
+  }
+
   finishStats() {
     clearInterval(this.timer);
   }

package/token/token.js

@@ -19,6 +19,7 @@ const GitHubStrategy = require('passport-github2').Strategy;
 const rateLimit = require('express-rate-limit');
 const lusca = require('lusca');
 const folders = require('../library/folder-setup');
+const escape = require('escape-html');
 
 
 const Logger = require('../library/logger');
@@ -325,6 +326,7 @@ class TokenModule {
     this.log.info('OAuth strategies configured:', configuredStrategies);
   }
 
+  // eslint-disable-next-line no-unused-vars
   async handleOAuthCallback(req, provider, profile, tokens) {
     const email = this.extractEmail(profile);
     const name = this.extractName(profile);
@@ -928,6 +930,7 @@ class TokenModule {
     });
   }
 
+  // eslint-disable-next-line no-unused-vars
   async updateKeyLastUsed(keyId, ip = null) {
     return new Promise((resolve, reject) => {
       this.db.run(
@@ -1004,6 +1007,7 @@ class TokenModule {
   }
 
   async logSecurityEvent(userId, eventType, ip, userAgent, details) {
+    // eslint-disable-next-line no-unused-vars
     return new Promise((resolve, reject) => {
       this.db.run(
         'INSERT INTO security_log (user_id, event_type, ip_address, user_agent, details) VALUES (?, ?, ?, ?, ?)',
@@ -1020,14 +1024,15 @@ class TokenModule {
   }
 
   // Content builders
+  // eslint-disable-next-line no-unused-vars
   buildDashboardContent(user, apiKeys, usageStats) {
     let content = `
       <div class="row mb-4">
         <div class="col-12">
           <div class="d-flex justify-content-between align-items-center">
             <div>
-              <h3>Welcome, ${htmlServer.escapeHtml(user.name)}</h3>
-              <p class="text-muted">Email: ${htmlServer.escapeHtml(user.email)} | Provider: ${htmlServer.escapeHtml(user.provider)}</p>
+              <h3>Welcome, ${escape(user.name)}</h3>
+              <p class="text-muted">Email: ${escape(user.email)} | Provider: ${escape(user.provider)}</p>
             </div>
             <form method="POST" action="/token/logout" class="d-inline">
               <button type="submit" class="btn btn-outline-secondary">Logout</button>
@@ -1126,16 +1131,16 @@ class TokenModule {
         
         content += `
           <tr>
-            <td><strong>${htmlServer.escapeHtml(key.name)}</strong></td>
-            <td><code>${htmlServer.escapeHtml(key.key_prefix)}...</code></td>
-            <td><span class="badge bg-secondary">${htmlServer.escapeHtml(scopes)}</span></td>
+            <td><strong>${escape(key.name)}</strong></td>
+            <td><code>${escape(key.key_prefix)}...</code></td>
+            <td><span class="badge bg-secondary">${escape(scopes)}</span></td>
             <td>${new Date(key.created_at).toLocaleDateString()}</td>
             <td>${lastUsed}</td>
             <td>${expires}</td>
             <td><span class="${statusClass}">${status}</span></td>
             <td>
               ${key.is_active ? 
-                `<button class="btn btn-sm btn-danger" onclick="deleteKey(${key.id}, '${htmlServer.escapeHtml(key.name)}')">Delete</button>` :
+                `<button class="btn btn-sm btn-danger" onclick="deleteKey(${key.id}, '${escape(key.name)}')">Delete</button>` :
                 '<span class="text-muted">-</span>'
               }
             </td>
@@ -1176,7 +1181,7 @@ class TokenModule {
       
       content += `
         <div class="alert alert-danger" role="alert">
-          <strong>Error:</strong> ${htmlServer.escapeHtml(errorMessage)}
+          <strong>Error:</strong> ${escape(errorMessage)}
         </div>
       `;
     }
@@ -1252,7 +1257,7 @@ class TokenModule {
       <!DOCTYPE html>
       <html lang="en">
       <head>
-        <title>${htmlServer.escapeHtml(title)} - FHIR Token Server</title>
+        <title>${escape(title)} - FHIR Token Server</title>
         <meta charset="utf-8">
         <meta name="viewport" content="width=device-width, initial-scale=1">
         <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.1.3/dist/css/bootstrap.min.css" rel="stylesheet">
@@ -1263,7 +1268,7 @@ class TokenModule {
           <nav class="mb-4">
             <a href="/" class="text-decoration-none">← Back to Server Home</a>
           </nav>
-          <h1 class="mb-4">${htmlServer.escapeHtml(title)}</h1>
+          <h1 class="mb-4">${escape(title)}</h1>
           ${content}
         </div>
         <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.1.3/dist/js/bootstrap.bundle.min.js"></script>

package/translations/Messages.properties

@@ -1312,7 +1312,8 @@ VS_EXP_IMPORT_UNK_PINNED = Unable to find included value set ''{0}'' version ''{
 VS_EXP_IMPORT_UNK_PINNED_X = Unable to find excluded value set ''{0}'' version ''{1}''
 VS_EXP_IMPORT_UNK_X = Unable to find excluded value set ''{0}''
 Wrong_namespace__expected_ = Wrong namespace - expected ''{0}''
-Wrong_type_for_resource = Wrong type for resource
+Wrong_type_for_resource = Wrong type for resource 
+Wrong_type_for_resource_expected = Wrong type for resource. Expected {0} but found {1} 
 TEXT_LINK_DATA_NOT_FOUND = The target of the textLink data reference ''{0}'' was not found in the resource
 TEXT_LINK_DATA_MULTIPLE_MATCHES = Multiple matching targets for the textLink data reference ''{0}'' were found in the resource
 XHTML_URL_DATA_DATA_INVALID = The data should be valid base64 content for a data: URL: {0}

package/tx/README.md

@@ -4,12 +4,7 @@ The TX module provides FHIR terminology services for CodeSystem, ValueSet, and C
 
 ## Todo
 
-* More work on the HTML interface (external code systems, global functions, render capability statements) 
-* add more tests for the code system providers - filters, extended lookup, designations and languages 
-* more refactoring in validate.js and expand.js 
-* full batch support 
-* check vsac support 
-* get tx tests running in pipelines 
+* Improve batch support 
 
 ## Overview
 
@@ -303,6 +298,22 @@ You can specify a version using the `#` syntax:
 
 If no version is specified, the latest released version is fetched.
 
+#### `url` - FHIR Packages from Direct URLs
+
+Loads a FHIR package directly from a tarball URL instead of the FHIR package registry. Useful for packages hosted on CI build servers, branches, or other locations.
+
+Use `url/cs` to load only CodeSystem resources from the package (same as `npm/cs`).
+
+```yaml
+# Load a package from a CI build server
+- url:https://example.com/my-package/package.tgz
+
+# Load a code-systems-only package from a URL
+- url/cs:https://example.com/my-codesystems/package.tgz
+```
+
+The URL must point to a `.tgz` file in standard FHIR NPM package format. Downloaded packages are cached locally by URL.
+
 ### Default Marker (`!`)
 
 When multiple versions of the same code system are loaded, append `!` to mark one as the default:

package/tx/cs/cs-api.js

@@ -11,6 +11,11 @@ const {VersionUtilities} = require("../../library/version-utilities");
 
 class FilterExecutionContext {
   filters = [];
+  forIterate = false;
+
+  constructor(forIterate) {
+    this.forIterate = forIterate;
+  }
 }
 
 class CodeSystemProvider {
@@ -122,6 +127,17 @@ class CodeSystemProvider {
   isNotClosed() {
     return false;
   }
+
+  /**
+   * returns true if the code system is case sensitive when comparing codes.
+   * this is true by default
+   *
+   * @returns {boolean}
+   */
+  isCaseSensitive() {
+    return true;
+  }
+
   /**
    * @param {Languages} languages language specification
    * @returns {boolean} defined properties for the code system
@@ -489,7 +505,7 @@ class CodeSystemProvider {
    * @param {boolean} iterate true if the conceptSets that result from this will be iterated, and false if they'll be used to locate a single code
    * @returns {FilterExecutionContext} filter (or null, it no use for this)
    * */
-  async getPrepContext(iterate) { return new FilterExecutionContext(); }
+  async getPrepContext(iterate) { return new FilterExecutionContext(iterate); }
 
   /**
    * executes a text search filter (whatever that means) and returns a FilterConceptSet
@@ -662,6 +678,8 @@ class CodeSystemProvider {
   valueSet() {
     return null;
   }
+
+
 }
 
 class CodeSystemFactoryProvider {

package/tx/cs/cs-base.js

@@ -0,0 +1,77 @@
+const {CodeSystemProvider} = require("./cs-api");
+
+class BaseCSServices extends CodeSystemProvider {
+
+  _addProperty(params, type, name, value, language = null) {
+
+    const property = {
+      name: type,
+      part: [
+        {name: 'code', valueCode: name},
+        {name: 'value', valueString: value}
+      ]
+    };
+
+    if (language) {
+      property.part.push({name: 'language', valueCode: language});
+    }
+
+    params.push(property);
+  }
+
+
+  _addCodeProperty(params, type, name, value, language = null, description = null) {
+
+    const property = {
+      name: type,
+      part: [
+        {name: 'code', valueCode: name},
+        {name: 'value', valueCode: value}
+      ]
+    };
+
+    if (language) {
+      property.part.push({name: 'language', valueCode: language});
+    }
+    if (description) {
+      property.part.push({name: 'description', valueString: description});
+    }
+
+    params.push(property);
+    return property;
+  }
+
+  _addStringProperty(params, type, name, value, language = null) {
+
+    const property = {
+      name: type,
+      part: [
+        {name: 'code', valueCode: name},
+        {name: 'value', valueString: value}
+      ]
+    };
+
+    if (language) {
+      property.part.push({name: 'language', valueCode: language});
+    }
+
+    params.push(property);
+    return property;
+  }
+
+
+  // Helper to check if a property should be included
+  _hasProp = (props, name, defaultValue = true) => {
+    if (!props || props.length === 0) {
+      return defaultValue;
+    }
+    const lowerName = name.toLowerCase();
+    return props.some(p =>
+      p.toLowerCase() === lowerName || p === '*'
+    );
+  };
+}
+
+module.exports = {
+  BaseCSServices
+};

package/tx/cs/cs-country.js

@@ -578,6 +578,52 @@ class CountryCodeFactoryProvider extends CodeSystemFactoryProvider {
       ['ZM', 'Zambia'],
       ['ZW', 'Zimbabwe'],
 
+      // ISO 3166-1 User-assigned code elements
+      // These codes are reserved for user assignment and will never be used for country names
+      // See: https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2#User-assigned_code_elements
+      ['AA', 'User-assigned'],
+      ['QM', 'User-assigned'],
+      ['QN', 'User-assigned'],
+      ['QO', 'User-assigned'],
+      ['QP', 'User-assigned'],
+      ['QQ', 'User-assigned'],
+      ['QR', 'User-assigned'],
+      ['QS', 'User-assigned'],
+      ['QT', 'User-assigned'],
+      ['QU', 'User-assigned'],
+      ['QV', 'User-assigned'],
+      ['QW', 'User-assigned'],
+      ['QX', 'User-assigned'],
+      ['QY', 'User-assigned'],
+      ['QZ', 'User-assigned'],
+      ['XA', 'User-assigned'],
+      ['XB', 'User-assigned'],
+      ['XC', 'User-assigned'],
+      ['XD', 'User-assigned'],
+      ['XE', 'User-assigned'],
+      ['XF', 'User-assigned'],
+      ['XG', 'User-assigned'],
+      ['XH', 'User-assigned'],
+      ['XI', 'User-assigned'],
+      ['XJ', 'User-assigned'],
+      ['XK', 'Kosovo'],
+      ['XL', 'User-assigned'],
+      ['XM', 'User-assigned'],
+      ['XN', 'User-assigned'],
+      ['XO', 'User-assigned'],
+      ['XP', 'User-assigned'],
+      ['XQ', 'User-assigned'],
+      ['XR', 'User-assigned'],
+      ['XS', 'User-assigned'],
+      ['XT', 'User-assigned'],
+      ['XU', 'User-assigned'],
+      ['XV', 'User-assigned'],
+      ['XW', 'User-assigned'],
+      ['XX', 'Unknown'],
+      ['XY', 'User-assigned'],
+      ['XZ', 'International Waters'],
+      ['ZZ', 'Unknown or Invalid Territory'],
+
       // 3-letter codes
       ['ABW', 'Aruba'],
       ['AFG', 'Afghanistan'],

package/tx/cs/cs-cpt.js

@@ -1,8 +1,9 @@
 const sqlite3 = require('sqlite3').verbose();
 const assert = require('assert');
 const { CodeSystem } = require('../library/codesystem');
-const { CodeSystemProvider, FilterExecutionContext, CodeSystemFactoryProvider } = require('./cs-api');
+const { FilterExecutionContext, CodeSystemFactoryProvider } = require('./cs-api');
 const {validateArrayParameter} = require("../../library/utilities");
+const {BaseCSServices} = require("./cs-base");
 
 class CPTConceptDesignation {
   constructor(kind, value) {
@@ -108,7 +109,7 @@ class CPTPrep extends FilterExecutionContext {
   }
 }
 
-class CPTServices extends CodeSystemProvider {
+class CPTServices extends BaseCSServices {
   constructor(opContext, supplements, db, sharedData) {
     super(opContext, supplements);
     this.db = db;
@@ -224,6 +225,9 @@ class CPTServices extends CodeSystemProvider {
 
   }
 
+  isNotClosed() {
+    return true;
+  }
   async extendLookup(ctxt, props, params) {
     validateArrayParameter(props, 'props', String);
     validateArrayParameter(params, 'params', Object);
@@ -255,7 +259,7 @@ class CPTServices extends CodeSystemProvider {
       }
     } else if (ctxt instanceof CPTConcept) {
       // Add designations
-      if (this.#hasProp(props, 'designation', true)) {
+      if (this._hasProp(props, 'designation', true)) {
         for (const d of ctxt.designations) {
           this.#addProperty(params, 'designation', d.kind, d.value, 'en');
         }
@@ -263,7 +267,7 @@ class CPTServices extends CodeSystemProvider {
 
       // Add properties
       for (const p of ctxt.properties) {
-        if (this.#hasProp(props, p.name, true)) {
+        if (this._hasProp(props, p.name, true)) {
           this.#addProperty(params, 'property', p.name, p.value);
         }
       }
@@ -545,7 +549,7 @@ class CPTServices extends CodeSystemProvider {
     if (concept) {
       return concept;
     }
-    return `Code ${code} is not in the specified filter`;
+    return null;
   }
 
   async filterCheck(filterContext, set, concept) {

package/tx/cs/cs-cs.js

@@ -1,10 +1,11 @@
 const { CodeSystem}  = require("../library/codesystem");
-const { CodeSystemFactoryProvider, CodeSystemProvider, FilterExecutionContext }  = require( "./cs-api");
+const { CodeSystemFactoryProvider, FilterExecutionContext }  = require( "./cs-api");
 const { VersionUtilities }  = require("../../library/version-utilities");
 const { Language }  = require ("../../library/languages");
 const { validateOptionalParameter, getValuePrimitive, validateArrayParameter} = require("../../library/utilities");
 const {Issue} = require("../library/operation-outcome");
 const {Extensions} = require("../library/extensions");
+const {BaseCSServices} = require("./cs-base");
 
 /**
  * Context class for FHIR CodeSystem provider concepts
@@ -101,7 +102,7 @@ class FhirCodeSystemProviderFilterContext {
   }
 }
 
-class FhirCodeSystemProvider extends CodeSystemProvider {
+class FhirCodeSystemProvider extends BaseCSServices {
   /**
    * @param {CodeSystem} codeSystem - The primary CodeSystem
    * @param {CodeSystem[]} supplements - Array of supplement CodeSystems
@@ -385,6 +386,10 @@ class FhirCodeSystemProvider extends CodeSystemProvider {
     return ctxt ? (ctxt.concept.definition || null) : null;
   }
 
+  isCaseSensitive() {
+    return !this.codeSystem.caseInsensitive();
+  }
+
   /**
    * @param {string|FhirCodeSystemProviderContext} context - Code or context
    * @returns {Promise<boolean>} If the concept is abstract
@@ -642,6 +647,15 @@ class FhirCodeSystemProvider extends CodeSystemProvider {
     return extensions.length > 0 ? extensions : null;
   }
 
+  getPropertyDefinition(cs, code) {
+    for (let p of cs.property || []) {
+      if (code == p.code) {
+        return p;
+      }
+    }
+    return undefined;
+  }
+
   /**
    * @param {string|FhirCodeSystemProviderContext} context - Code or context
    * @returns {Promise<Object[]|null>} Properties, if any
@@ -656,16 +670,20 @@ class FhirCodeSystemProvider extends CodeSystemProvider {
     const properties = [];
 
     // Add properties from main concept
-    if (ctxt.concept.property && Array.isArray(ctxt.concept.property)) {
-      properties.push(...ctxt.concept.property);
+    for (let p of ctxt.concept.property || []) {
+      let pd = this.getPropertyDefinition(this.codeSystem.jsonObj, p.code);
+      properties.push({ ...p, definition: pd });
     }
 
     // Add properties from supplements
     if (this.supplements) {
       for (const supplement of this.supplements) {
         const supplementConcept = supplement.getConceptByCode(ctxt.code);
-        if (supplementConcept && supplementConcept.property && Array.isArray(supplementConcept.property)) {
-          properties.push(...supplementConcept.property);
+        if (supplementConcept) {
+          for (let p of supplementConcept.property || []) {
+            let pd = this.getPropertyDefinition(supplement.jsonObj, p.code);
+            properties.push({...p, definition: pd});
+          }
         }
       }
     }
@@ -886,12 +904,8 @@ class FhirCodeSystemProvider extends CodeSystemProvider {
       return;
     }
 
-    // Set abstract status
-    if (!params.find(p => p.name == "abstract") && await this.isAbstract(ctxt)) {
-      params.push({ name: 'property', part: [ { name: 'code', valueCode: 'abstract' }, { name: 'value', valueBoolean: true } ]});
-    }
     // Add properties if requested (or by default)
-    if (!props || props.length === 0 || props.includes('*') || props.includes('property')) {
+    if (this._hasProp(props, 'property', true)) {
       const properties = await this.properties(ctxt);
       if (properties) {
         for (const property of properties) {
@@ -920,7 +934,7 @@ class FhirCodeSystemProvider extends CodeSystemProvider {
     }
 
     // Add parent if requested and exists
-    if (!props || props.length === 0 || props.includes('*') || props.includes('parent')) {
+    if (this._hasProp(props, 'parent', true)) {
       const parentCode = await this.parent(ctxt);
       if (parentCode) {
         let parts = [];
@@ -932,7 +946,7 @@ class FhirCodeSystemProvider extends CodeSystemProvider {
     }
 
     // Add children if requested
-    if (!props || props.length === 0 || props.includes('*') || props.includes('child')) {
+    if (this._hasProp(props, 'child', true)) {
       const children = this.codeSystem.getChildren(ctxt.code);
       if (children.length > 0) {
         for (const childCode of children) {

package/tx/cs/cs-db.js

@@ -5,19 +5,6 @@ const { Language, Languages} = require('../../library/languages');
 const { CodeSystemProvider, CodeSystemFactoryProvider} = require('./cs-api');
 const { validateOptionalParameter, validateArrayParameter} = require("../../library/utilities");
 
-/**
- * SQL Tables:
- *
- *   Metadata: Name, Value
- *   Concepts: ConceptKey, Code, Display, Definition, Parent
- *   Closure: ParentKey, ChildKey
- *   DesignationUses: DesignationUseKey, System, Version, Code, Display
- *   Languages: LanguageKey, LanguageCode
- *   Designations: ConceptKey, LanguageKey, DesignationUseKey, Value
- *   PropertyDefinitions: PropertyDefinitionKey, Code, Uri, Description, Type
- *   Properties: PropertyKey, PropertyDefinitionKey, Value, System, Version, Display
- */
-
 class CachedDesignation {
   constructor(display, language, use) {
     this.display = display;