fhirsmith 0.8.0 → 0.8.3

package/root-bare-template.html

@@ -9,9 +9,6 @@
   <meta content="http://hl7.org/fhir" name="author"/>
   <meta charset="utf-8" http-equiv="X-UA-Compatible" content="IE=edge" />
 
-  <link rel="stylesheet" href="/fhir.css"/>
-
-
     <!-- Bootstrap core CSS -->
   <link rel="stylesheet" href="/assets/css/bootstrap.css"/>
   <link rel="stylesheet" href="/assets/css/bootstrap-fhir.css"/>

package/security.md

@@ -29,4 +29,7 @@ A typical NGINX configuration would be:
   limit_conn perip 50;
   limit_conn perserver 500;
 ```
+## SSL
+
+This server doesn't provide SSL support - use an NGINX reverse proxy for that.
 

package/server.js

@@ -11,6 +11,7 @@ const express = require('express');
 const path = require('path');
 const fs = require('fs');
 const os = require('os');
+const v8 = require('v8');
 const folders = require('./library/folder-setup');  // <-- ADD: load early
 const { statSync, readdirSync } = require('fs');
 const escape = require('escape-html');
@@ -41,8 +42,8 @@ serverLog.info(`Data directory: ${folders.dataDir()}`);
 serverLog.info(`========================================`);
 
 const activeModules = config.modules ? Object.keys(config.modules)
-  .filter(mod => config.modules[mod].enabled)
-  .join(', ') : [];
+    .filter(mod => config.modules[mod].enabled)
+    .join(', ') : [];
 serverLog.info(`Loaded Configuration. Active modules = ${activeModules}`);
 
 // Import modules
@@ -541,20 +542,21 @@ app.get('/dashboard', async (req, res) => {
 
     // Memory usage
     const memUsage = process.memoryUsage();
-    const heapUsedPCT =  (memUsage.heapUsed * 100) / memUsage.heapTotal;
-    const freeMemMB = (os.freemem() / 1024 / 1024).toFixed(0);
-    const totalMemMB = (os.totalmem() / 1024 / 1024).toFixed(0);
-    const usedMemPCT = 100 - ((freeMemMB * 100) / totalMemMB);
+    const heapStats = v8.getHeapStatistics();
+    const nodeMemPCT = (memUsage.heapUsed * 100) / heapStats.heap_size_limit;  // % of Node.js memory limit used
+    const totalMemBytes = os.totalmem();
+    const freeMemBytes = os.freemem();
+    const sysMemPCT = ((totalMemBytes - freeMemBytes) * 100) / totalMemBytes;  // % of system memory used
     const fstats = fs.statfsSync(folders.logsDir());
-    const diskPCT = (fstats.bavail * 100) / fstats.blocks;
+    const diskPCT = 100 - ((fstats.bavail * 100) / fstats.blocks);  // % of disk used
 
-    let content = '';
-    content += '<table border="1">';
+    let content = '<style>table.grid{margin-bottom:10px;border:1px solid black;margin-right:auto}table.grid th,table.grid td{border:1px solid silver;padding:3px 7px 2px;font-size:12px;line-height:1.4em;font-family:verdana;vertical-align:top}table.grid th{font-weight:bold}table.grid td{font-weight:normal}</style>';
+    content += '<table class="grid">';
     content += '<tr>';
     content += `<td><strong>Uptime:</strong> ${escape(uptimeStr)}</td>`;
     content += `<td><strong>Request Count:</strong> ${stats.requestCount} (static: ${stats.staticRequestCount})</td>`;
-    content += `<td style="background-color:${pctColor(usedMemPCT)}"><strong>Memory:</strong> ${usedMemPCT.toFixed(0)}%</td>`;
-    content += `<td style="background-color:${pctColor(heapUsedPCT)}"><strong>Heap:</strong> ${heapUsedPCT.toFixed(0)}%</td>`;
+    content += `<td style="background-color:${pctColor(nodeMemPCT)}"><strong>Node Memory:</strong> ${nodeMemPCT.toFixed(0)}%</td>`;
+    content += `<td style="background-color:${pctColor(sysMemPCT)}"><strong>System Memory:</strong> ${sysMemPCT.toFixed(0)}%</td>`;
     content += `<td style="background-color:${pctColor(diskPCT)}"><strong>Disk:</strong> ${diskPCT.toFixed(0)}%</td>`;
     content += '</tr>';
     content += '</table>';
@@ -590,9 +592,12 @@ app.get('/dashboard', async (req, res) => {
 });
 
 function pctColor(pct) {
-  const r = Math.round(pct * 2.55);
-  const g = Math.round((100 - pct) * 2.55);
-  return `rgb(${r}, ${g}, 100)`;  // the 100 keeps it pastel/light
+  // Gradient from green (#deffe0) at 0% to red (#ffd3d1) at 100%
+  const t = Math.max(0, Math.min(100, pct)) / 100;
+  const r = Math.round(222 + 33 * t);   // 222 -> 255
+  const g = Math.round(255 - 44 * t);   // 255 -> 211
+  const b = Math.round(224 - 15 * t);   // 224 -> 209
+  return `rgb(${r}, ${g}, ${b})`;
 }
 
 // Health check endpoint
@@ -659,10 +664,10 @@ function getLogStats() {
     const limitInfo = `${maxFiles} files × ${maxSize} each`;
 
     return '<tr>'
-      + `<td><strong>Existing Logs:</strong> ${files.length} (${sizeMB} MB)</td>`
-      + `<td><strong>Retention Policy:</strong> ${limitInfo}</td>`
-      + diskInfo
-      + '</tr>';
+        + `<td><strong>Existing Logs:</strong> ${files.length} (${sizeMB} MB)</td>`
+        + `<td><strong>Retention Policy:</strong> ${limitInfo}</td>`
+        + diskInfo
+        + '</tr>';
   } catch (e) {
     return `<tr><td colspan="3"><strong>Logs:</strong> unable to read (${e.message})</td></tr>`;
   }
@@ -793,12 +798,12 @@ async function serveFhirsmithHome(req, res) {
       endpoints: {
         health: '/health',
         ...Object.fromEntries(
-          Object.keys(enabledModules)
-            .filter(m => m !== 'tx')
-            .map(m => [
-              m,
-              m === 'vcl' ? '/VCL' : `/${m}`
-            ])
+            Object.keys(enabledModules)
+                .filter(m => m !== 'tx')
+                .map(m => [
+                  m,
+                  m === 'vcl' ? '/VCL' : `/${m}`
+                ])
         ),
         // Add TX endpoints separately
         ...(enabledModules.tx ? {

package/shl/readme.md

@@ -0,0 +1,27 @@
+To generate a certificate:
+
+```shell
+# Generate EC P-256 private key
+openssl ecparam -name prime256v1 -genkey -noout -out private-key.pem
+
+# Extract the public key / self-signed cert
+openssl req -new -x509 -key private-key.pem -out public-key.pem -days 3650 \
+  -subj "/CN=fhirsmith-shl"
+  
+node -e "
+const crypto = require('crypto');
+const fs = require('fs');
+const key = crypto.createPrivateKey(fs.readFileSync('private-key.pem'));
+const jwk = key.export({format:'jwk'});
+const thumbprint = crypto.createHash('sha256')
+  .update(JSON.stringify({crv:jwk.crv,kty:jwk.kty,x:jwk.x,y:jwk.y}))
+  .digest('base64url');
+console.log('kid: '+thumbprint);
+"
+
+```
+
+Config: 
+
+All files will be in {data}/shl. the file paths in the config are relative to 
+that location

package/shl/shl.js

@@ -396,14 +396,8 @@ class SHLModule {
 
   loadCertificates() {
     try {
-      const certPath = path.resolve(__dirname, this.config.certificates.certFile);
-      const keyPath = path.resolve(__dirname, this.config.certificates.keyFile);
-
-      // Validate paths to prevent directory traversal
-      if (!certPath.startsWith(path.resolve(__dirname)) ||
-        !keyPath.startsWith(path.resolve(__dirname))) {
-        throw new Error('Certificate paths outside allowed directory');
-      }
+      const certPath = folders.filePath('shl', this.config.certificates.certFile);
+      const keyPath = folders.filePath('shl', this.config.certificates.keyFile);
 
       const certPem = fs.readFileSync(certPath, 'utf8');
       const keyPem = fs.readFileSync(keyPath, 'utf8');

package/stats.js

@@ -118,7 +118,7 @@ class ServerStats {
     if (this.taskMap.size == 0) {
       return "";
     }
-    let html = '<table class="grid">';
+    let html = '<table class="grid" >';
     html += "<tr><th>Background Task</th><th>Status</th><th>Frequency</th><th>Last Seen</th></tr>";
     for (let m of this.taskMap.keys()) {
       let mm = this.taskMap.get(m);

package/tx/cs/cs-api.js

@@ -673,11 +673,13 @@ class CodeSystemProvider {
   /**
    * register the concept maps that are implicitly defined as part of the code system
    *
+   * @param {ConceptMap} map the map (this will have been returned from findImplicitConceptMap)
    * @param {Coding} coding the coding to translate
-   * @param {String} target
-   * @returns {CodeTranslation[]} the list of translations
+   * @param {String} target the target code system
+   * @param {boolean} reverse - if the translation is being run backwards
+   * @returns {CodeTranslation[]} the list of translations, each CodeTranslation has map, code, system, version, display, and relationship
    */
-  async getTranslations(coding, target) { return null;}
+  async getTranslations(map, coding, target, reverse) { return null;}
 
   // ==== Parameter checking methods =========
   _ensureLanguages(param) {
@@ -853,7 +855,7 @@ class CodeSystemFactoryProvider {
   }
 
   /**
-   * see comemnts for registerSupplements()
+   * see comments for registerSupplements()
    *
    * @param {CodeSystem} supplement - the supplement to flesh out
    * @returns void
@@ -865,6 +867,8 @@ class CodeSystemFactoryProvider {
   /**
    * build and return a known concept map from the URL, if there is one.
    *
+   * the conceptmap is never visible to a user; if it has an implicitSource, then
+   * provider.getTranslations will be called when it's actually used
    * @param url
    * @param version
    * @returns {ConceptMap}

package/tx/cs/cs-omop.js

@@ -660,8 +660,10 @@ class OMOPServices extends BaseCSServices {
   }
 
   // Translation support
-  async getTranslations(coding, target) {
-    
+  async getTranslations(map, coding, target) {
+    if (map == null) {
+      return;
+    }
 
     const vocabId = getVocabId(target);
     if (vocabId === -1) {
@@ -680,7 +682,7 @@ class OMOPServices extends BaseCSServices {
           reject(err);
         } else {
           const translations = rows.map(row => ({
-            uri: target,
+            system: target,
             code: row.concept_code,
             display: row.concept_name,
             relationship: 'equivalent',

package/tx/cs/cs-rxnorm.js

@@ -395,24 +395,24 @@ class RxNormServices extends CodeSystemProvider {
       } else if (this.rels.includes(prop)) {
         if (value.startsWith('CUI:')) {
           const cui = value.substring(4);
-          sql = `AND (${this.getCodeField()} IN (SELECT ${this.getCodeField()} FROM rxnconso WHERE RXCUI IN (SELECT RXCUI1 FROM rxnrel WHERE REL = $rel AND RXCUI2 = $cui2)))`;
+          sql = `AND (${this.getCodeField()} IN (SELECT ${this.getCodeField()} FROM rxnconso WHERE RXCUI IN (SELECT RXCUI2 FROM rxnrel WHERE REL = $rel AND RXCUI1 = $cui2)))`;
           params.rel = this.#sqlWrapString(prop);
           params.cui2 = this.#sqlWrapString(cui);
         } else if (value.startsWith('AUI:')) {
           const aui = value.substring(4);
-          sql = `AND (${this.getCodeField()} IN (SELECT ${this.getCodeField()} FROM rxnconso WHERE RXAUI IN (SELECT RXAUI1 FROM rxnrel WHERE REL = $rel AND RXAUI2 = $aui2)))`;
+          sql = `AND (${this.getCodeField()} IN (SELECT ${this.getCodeField()} FROM rxnconso WHERE RXAUI IN (SELECT RXAUI2 FROM rxnrel WHERE REL = $rel AND RXAUI1 = $aui2)))`;
           params.rel = this.#sqlWrapString(prop);
           params.aui2 = this.#sqlWrapString(aui);
         }
       } else if (this.reltypes.includes(prop)) {
         if (value.startsWith('CUI:')) {
           const cui = value.substring(4);
-          sql = `AND (${this.getCodeField()} IN (SELECT ${this.getCodeField()} FROM rxnconso WHERE RXCUI IN (SELECT RXCUI1 FROM rxnrel WHERE RELA = $rela AND RXCUI2 = $cui2)))`;
+          sql = `AND (${this.getCodeField()} IN (SELECT ${this.getCodeField()} FROM rxnconso WHERE RXCUI IN (SELECT RXCUI2 FROM rxnrel WHERE RELA = $rela AND RXCUI1 = $cui2)))`;
           params.rela = this.#sqlWrapString(prop);
           params.cui2 = this.#sqlWrapString(cui);
         } else if (value.startsWith('AUI:')) {
           const aui = value.substring(4);
-          sql = `AND (${this.getCodeField()} IN (SELECT ${this.getCodeField()} FROM rxnconso WHERE RXAUI IN (SELECT RXAUI1 FROM rxnrel WHERE RELA = $rela AND RXAUI2 = $aui2)))`;
+          sql = `AND (${this.getCodeField()} IN (SELECT ${this.getCodeField()} FROM rxnconso WHERE RXAUI IN (SELECT RXAUI2 FROM rxnrel WHERE RELA = $rela AND RXAUI1 = $aui2)))`;
           params.rela = this.#sqlWrapString(prop);
           params.aui2 = this.#sqlWrapString(aui);
         }
@@ -498,8 +498,6 @@ class RxNormServices extends CodeSystemProvider {
   }
 
   async filterSize(filterContext, set) {
-    
-
     if (!set.executed) {
       await this.#executeFilter(set);
     }

package/tx/cs/cs-snomed.js

@@ -12,6 +12,7 @@ const {
 const {DesignationUse} = require("../library/designations");
 const {BaseCSServices} = require("./cs-base");
 const {formatDateMMDDYYYY} = require("../../library/utilities");
+const {ConceptMap} = require("../library/conceptmap");
 
 // Context kinds matching Pascal enum
 const SnomedProviderContextKind = {
@@ -1213,6 +1214,64 @@ class SnomedProvider extends BaseCSServices {
            (cd.use.code === '900000000000013009' || cd.use.code === '900000000000003001');
   }
 
+  async getTranslations(map, coding, target, reverse) {
+    if (!map || (target && target !== this.system()) || reverse) {
+      return [];
+    }
+    let ref = this.sct.concepts.findConcept(map.id);
+    if (!ref.found) {
+      return [];
+    }
+    let rref = this.sct.refSetIndex.getRefSetByConcept(ref.index);
+    if (rref == -1) {
+      return [];
+    }
+    let refSetRecord = this.sct.refSetIndex.getReferenceSet(rref);
+    let members = this.sct.refSetMembers.getMembers(refSetRecord.membersByRef);
+    let srcConcept = this.sct.concepts.findConcept(coding.code);
+    if (!srcConcept.found) {
+      return [];
+    }
+
+    let result = [];
+    let L = 0;
+    let H = members.length - 1;
+    while (L <= H) {
+      const I = Math.floor((L + H) / 2);
+      const ref = members[I].ref;
+      if (ref < srcConcept.index) {
+        L = I + 1;
+      } else if (ref > srcConcept.index) {
+        H = I - 1;
+      } else {
+        // Found — but scan left for first match in case of duplicates
+        let first = I;
+        while (first > 0 && members[first - 1].ref === srcConcept.index) {
+          first--;
+        }
+        // Process all matching members
+        for (let i = first; i < members.length && members[i].ref === srcConcept.index; i++) {
+          let values = this.sct.refs.getReferences(members[i].values);
+          if (values && values.length >= 1) {
+            let tgtId = String(this.sct.concepts.getConceptId(values[0]));
+            let ct = {
+              map: map.vurl,
+              code: tgtId,
+              system: this.system(),
+              version : this.version(),
+              display: await this.display(tgtId),
+              relationship: map.jsonObj.relationship
+            }
+            result.push(ct);
+          }
+        }
+        break;
+      }
+    }
+
+    return result;
+  }
+
 }
 
 /**
@@ -1339,7 +1398,7 @@ class SnomedServicesFactory extends CodeSystemFactoryProvider {
         return null;
       }
       let rref = this.snomedServices.refSetIndex.getRefSetByConcept(ref.index);
-      if (rref == 0) {
+      if (rref == -1) {
         return null;
       }
       return {
@@ -1448,6 +1507,59 @@ class SnomedServicesFactory extends CodeSystemFactoryProvider {
 
     return edition + ' ' + formatDateMMDDYYYY(match[2].substring(4, 6) + match[2].substring(6, 8) + match[2].substring(0, 4));
   }
+
+  async findImplicitConceptMap(url, version) {
+    if (version && (version !== this.version())) {
+      return null;
+    }
+    if (!url || !url.startsWith(this.system()+"?fhir_cm=")) {
+      return null;
+    }
+    let id = url.substring(url.indexOf("=")+1);
+    if (['900000000000523009', '900000000000526001', '900000000000527005', '900000000000530003'].includes(id)) {
+      let name = '';
+      let relationship = '';
+      switch (id) {
+        case '900000000000523009':
+          name = 'POSSIBLY EQUIVALENT TO';
+          relationship = 'inexact';
+          break;
+        case '900000000000526001':
+          name = 'REPLACED BY';
+          relationship = 'equivalent';
+          break;
+        case '900000000000527005':
+          name = 'SAME AS';
+          relationship = 'equal';
+          break;
+        case '900000000000530003':
+          name = 'ALTERNATIVE';
+          relationship = 'inexact';
+          break;
+      }
+      let cm = {
+        resourceType: 'ConceptMap',
+        internalSource : this,
+        relationship: relationship,
+        id : id,
+        url: `${this.system}?fhir_cm=${id}`,
+        version: this.version(),
+        name: `SNOMED CT ${name} Concept Map`,
+        description: `The concept map implicitly defined by the ${name} Association Reference Set`,
+        copyright: 'This value set includes content from SNOMED CT, which is copyright © 2002+ International Health Terminology Standards Development Organisation (SNOMED International), and distributed by agreement between SNOMED International and HL7',
+        status: 'active',
+        sourceUri: `${this.system}?fhir_vs`,
+        targetUri: `${this.system}?fhir_vs`,
+        group: [{
+          source: 'http://snomed.info/sct',
+          target: 'http://snomed.info/sct'
+        }]
+      }
+      return new ConceptMap(cm);
+    } else {
+      return null;
+    }
+  }
 }
 
 function getEditionName(edition) {

package/tx/data/cs-de.json

@@ -0,0 +1,186 @@
+{
+  "resourceType" : "CodeSystem",
+  "language" : "de",
+  "id" : "de-multi",
+  "url" : "http://hl7.org/fhir/test/CodeSystem/de-multi",
+  "name" : "TestCodeSystemMultiLangDE",
+  "title" : "Testcodesystem mit mehreren Sprachen",
+  "title:en" : "Test Code System with Multiple Languages",
+  "_title" : {
+    "extension" : [{
+      "url" : "http://hl7.org/fhir/StructureDefinition/translation",
+      "extension" : [{
+        "url" : "lang",
+        "valueCode" : "en"
+      },{
+        "url" : "content",
+        "valueString" : "Test Code System with Multiple Languages"
+      }]
+    }]
+  },
+  "status" : "active",
+  "experimental" : false,
+  "date" : "2023-04-01",
+  "publisher" : "FHIR Project",
+  "caseSensitive" : true,
+  "content" : "complete",
+  "concept" : [{
+    "code" : "code1",
+    "display" : "Anzeige 1",
+    "definition" : "Mein erster Code",
+    "definition:en" : "My first code",
+    "_definition" : {
+      "extension" : [{
+        "url" : "http://hl7.org/fhir/StructureDefinition/translation",
+        "extension" : [{
+          "url" : "lang",
+          "valueCode" : "en"
+        },{
+          "url" : "content",
+          "valueString" : "My first code"
+        }]
+      }]
+    },
+    "designation" : [{
+      "language" : "en",
+      "value" : "Display 1"
+    }]
+  },
+  {
+    "code" : "code2",
+    "display" : "Anzeige 2",
+    "definition" : "Mein zweiter Code, mit Kindern",
+    "definition:en" : "My second code, with children",
+    "_definition" : {
+      "extension" : [{
+        "url" : "http://hl7.org/fhir/StructureDefinition/translation",
+        "extension" : [{
+          "url" : "lang",
+          "valueCode" : "en"
+        },{
+          "url" : "content",
+          "valueString" : "My second code, with children"
+        }]
+      }]
+    },
+    "designation" : [{
+      "language" : "de-CH",
+      "value" : "Anzeige 2"
+    },{
+      "language" : "es",
+      "value" : "Mostrar 2"
+    },{
+      "language" : "en",
+      "value" : "Display 2"
+    }],
+    "concept" : [{
+      "code" : "code2a",
+      "display" : "Anzeige 2a",
+      "definition" : "Mein erster Second-Level-Code",
+      "definition:en" : "My first second level code",
+      "_definition" : {
+        "extension" : [{
+          "url" : "http://hl7.org/fhir/StructureDefinition/translation",
+          "extension" : [{
+            "url" : "lang",
+            "valueCode" : "en"
+          },{
+            "url" : "content",
+            "valueString" : "My first second level code"
+          }]
+        }]
+      },
+      "designation" : [{
+        "language" : "en",
+        "value" : "Display 2a"
+      },{
+        "language" : "es",
+        "value" : "Mostrar 2a"
+      }],
+      "concept" : [{
+        "code" : "code2aI",
+        "display" : "Anzeige 2aI",
+        "definition" : "Mein erster Third-Level-Code",
+        "definition:en" : "My first third level code",
+        "_definition" : {
+          "extension" : [{
+            "url" : "http://hl7.org/fhir/StructureDefinition/translation",
+            "extension" : [{
+              "url" : "lang",
+              "valueCode" : "en"
+            },{
+              "url" : "content",
+              "valueString" : "My first third level code"
+            }]
+          }]
+        },
+        "designation" : [{
+          "language" : "es",
+          "value" : "Mostrar 2aI"
+        }]
+      },
+      {
+        "code" : "code2aII",
+        "display" : "Anzeige 2aII",
+        "definition" : "Mein zweiter Third-Level-Code",
+        "definition:en" : "My second third level code",
+        "_definition" : {
+          "extension" : [{
+            "url" : "http://hl7.org/fhir/StructureDefinition/translation",
+            "extension" : [{
+              "url" : "lang",
+              "valueCode" : "en"
+            },{
+              "url" : "content",
+              "valueString" : "My second third level code"
+            }]
+          }]
+        }
+      }]
+    },
+    {
+      "code" : "code2b",
+      "display" : "Anzeige 2b",
+      "definition" : "Mein zweiter Second-Level-Code",
+      "definition:en" : "My second second level code",
+      "_definition" : {
+        "extension" : [{
+          "url" : "http://hl7.org/fhir/StructureDefinition/translation",
+          "extension" : [{
+            "url" : "lang",
+            "valueCode" : "en"
+          },{
+            "url" : "content",
+            "valueString" : "My second second level code"
+          }]
+        }]
+      },
+      "designation" : [{
+        "language" : "en",
+        "value" : "Display 2b"
+      }]
+    }]
+  },
+  {
+    "code" : "code3",
+    "display" : "Anzeige 3",
+    "definition" : "Mein Third-Level-Code",
+    "definition:en" : "My Third Level Code",
+    "_definition" : {
+      "extension" : [{
+        "url" : "http://hl7.org/fhir/StructureDefinition/translation",
+        "extension" : [{
+          "url" : "lang",
+          "valueCode" : "en"
+        },{
+          "url" : "content",
+          "valueString" : "My Third Level Code"
+        }]
+      }]
+    },
+    "designation" : [{
+      "language" : "en",
+      "value" : "Display 3"
+    }]
+  }]
+}