fhirsmith 0.7.5 → 0.8.0

package/tx/html/dash-metrics.liquid

@@ -0,0 +1,147 @@
+<div style="display: flex; gap: 20px; margin-bottom: 20px;">
+  <div style="flex: 1;">
+    <h6>Memory Usage (Heap Used)</h6>
+    <canvas id="memoryChart" height="200"></canvas>
+  </div>
+  <div style="flex: 1;">
+    <h6>Turnaround Time</h6>
+    <canvas id="tatChart" height="200"></canvas>
+  </div>
+  <div style="flex: 1;">
+    <h6>Requests per Minute</h6>
+    <canvas id="requestChart" height="200"></canvas>
+  </div>
+</div>
+
+<script src="https://cdn.jsdelivr.net/npm/chart.js"></script>
+<script>
+(function() {
+  const historyData = {{ historyJson }};
+  const startTime = {{ startTime }};
+
+  function formatTime(timestamp) {
+    const d = new Date(timestamp);
+    return d.toLocaleTimeString([], { hour: '2-digit', minute: '2-digit' });
+  }
+
+  function formatMB(bytes) {
+    return (bytes / 1024 / 1024).toFixed(1);
+  }
+
+  function formatDuration(ms) {
+    const hours = ms / 3600000;
+    if (hours < 1) {
+      return Math.round(ms / 60000) + 'm ago';
+    }
+    return hours.toFixed(1) + 'h ago';
+  }
+
+  const chartOptions = {
+    responsive: false,
+    maintainAspectRatio: false,
+    scales: {
+      x: {
+        ticks: {
+          maxTicksAuto: 6
+        }
+      },
+      y: {
+        beginAtZero: true
+      }
+    },
+    plugins: {
+      legend: {
+        display: false
+      }
+    }
+  };
+
+  // Memory chart
+  new Chart(document.getElementById('memoryChart'), {
+    type: 'line',
+    data: {
+      labels: historyData.map(d => formatTime(d.time)),
+      datasets: [{
+        data: historyData.map(d => parseFloat(formatMB(d.mem))),
+        borderColor: '#007bff',
+        backgroundColor: 'rgba(0, 123, 255, 0.1)',
+        fill: true,
+        tension: 0.3,
+        pointRadius: 2
+      }]
+    },
+    options: {
+      ...chartOptions,
+      scales: {
+        ...chartOptions.scales,
+        y: {
+          ...chartOptions.scales.y,
+          title: {
+            display: true,
+            text: 'MB (𝚫 from start)'
+          }
+        }
+      }
+    }
+  });
+
+
+  // Tat chart
+  new Chart(document.getElementById('tatChart'), {
+    type: 'line',
+    data: {
+      labels: historyData.map(d => formatTime(d.time)),
+      datasets: [{
+        data: historyData.map(d => d.tat),
+        borderColor: '#7b7b7b',
+        backgroundColor: 'rgba(123, 123, 123, 0.1)',
+        fill: true,
+        tension: 0.3,
+        pointRadius: 2
+      }]
+    },
+    options: {
+      ...chartOptions,
+      scales: {
+        ...chartOptions.scales,
+        y: {
+          ...chartOptions.scales.y,
+          title: {
+            display: true,
+            text: 'ms'
+          }
+        }
+      }
+    }
+  });
+
+  // Requests chart
+  new Chart(document.getElementById('requestChart'), {
+    type: 'line',
+    data: {
+      labels: historyData.map(d => formatTime(d.time)),
+      datasets: [{
+        data: historyData.map(d => d.rpm.toFixed(2)),
+        borderColor: '#28a745',
+        backgroundColor: 'rgba(40, 167, 69, 0.1)',
+        fill: true,
+        tension: 0.3,
+        pointRadius: 2
+      }]
+    },
+    options: {
+      ...chartOptions,
+      scales: {
+        ...chartOptions.scales,
+        y: {
+          ...chartOptions.scales.y,
+          title: {
+            display: true,
+            text: 'req/min'
+          }
+        }
+      }
+    }
+  });
+})();
+</script>

package/tx/importers/import-rxnorm.module.js

@@ -428,7 +428,8 @@ class RxNormModule extends BaseTerminologyModule {
       'CREATE INDEX IF NOT EXISTS idx_rxnrel_rel ON RXNREL(REL)',
       'CREATE INDEX IF NOT EXISTS idx_rxnrel_rela ON RXNREL(RELA)',
       'CREATE INDEX IF NOT EXISTS X_RXNSTY_2 ON RXNSTY(TUI)',
-      'CREATE INDEX IF NOT EXISTS idx_rxnstems_stem_cui ON RXNSTEMS(stem, CUI)'
+      'CREATE INDEX IF NOT EXISTS idx_rxnstems_stem_cui ON RXNSTEMS(stem, CUI)',
+      'CREATE INDEX IF NOT EXISTS idx_rxnstems_cui_stem ON RXNSTEMS(CUI, stem)'
     ];
 
     return new Promise((resolve, reject) => {
@@ -779,7 +780,7 @@ class RxNormImporter {
     if (this.options.verbose) console.log('Generating word stems...');
 
     // Simple English stemmer implementation
-    const stemmer = new SimpleStemmer();
+    var natural = require('natural');
     const stems = new Map();
 
     // Get all RXNORM concepts
@@ -791,7 +792,7 @@ class RxNormImporter {
         rows.forEach(row => {
           const words = this.extractWords(row.STR);
           words.forEach(word => {
-            const stem = stemmer.stem(word.toLowerCase());
+            const stem = natural.PorterStemmer.stem(word.toLowerCase());
             if (stem.length > 0 && stem.length <= 20) {
               if (!stems.has(stem)) {
                 stems.set(stem, new Set());
@@ -864,33 +865,6 @@ class RxNormImporter {
   }
 }
 
-// Simple English stemmer (basic implementation)
-class SimpleStemmer {
-  constructor() {
-    // Common English suffixes to remove
-    this.suffixes = [
-      'ing', 'ly', 'ed', 'ies', 'ied', 'ies', 'ies', 'y', 's',
-      'tion', 'sion', 'ness', 'ment', 'able', 'ible', 'ant', 'ent'
-    ].sort((a, b) => b.length - a.length); // Longest first
-  }
-
-  stem(word) {
-    if (word.length <= 3) return word;
-
-    // Try to remove suffixes
-    for (const suffix of this.suffixes) {
-      if (word.endsWith(suffix) && word.length > suffix.length + 2) {
-        const stem = word.substring(0, word.length - suffix.length);
-        // Basic validation - stem should still be reasonable length
-        if (stem.length >= 3) {
-          return stem;
-        }
-      }
-    }
-
-    return word;
-  }
-}
 
 module.exports = {
   RxNormModule,

package/tx/importers/readme.md

@@ -1,6 +1,8 @@
 # TX-Import: Medical Terminology Import Tool
 
-A comprehensive CLI tool for importing various medical terminology standards into SQLite databases and other formats. The tool supports LOINC, SNOMED CT, UNII, NDC, and provides extensible architecture for additional terminologies.
+A comprehensive CLI tool for importing various medical terminology standards into SQLite databases and other formats
+for use by FHIRsmith. The tool supports LOINC, SNOMED CT, UNII, NDC, and provides extensible architecture for
+additional terminologies.
 
 ## Table of Contents
 

package/tx/library/canonical-resource.js

@@ -64,6 +64,14 @@ class CanonicalResource {
     return this.version ? this.url+'|' + this.version : this.url;
   }
 
+  get vurlOrMsg() {
+    if (this.url) {
+      return this.version ? this.url+'|' + this.version : this.url;
+    } else {
+      return '(unidentified)';
+    }
+  }
+
   get fhirType() {
     return this.jsonObj.resourceType;
   }

package/tx/library/conceptmap.js

@@ -132,7 +132,9 @@ class ConceptMap extends CanonicalResource {
 
     let all = this.canonicalMatches(targetScope, this.targetScope);
     for (const g of this.jsonObj.group || []) {
-      if (all || (this.canonicalMatches(vurl, g.source) && this.canonicalMatches(targetSystem, g.target) )) {
+      const sourceOk = this.canonicalMatches(vurl, g.source);
+      const targetOk = !targetSystem || this.canonicalMatches(targetSystem, g.target);
+      if (all || (sourceOk && targetOk)) {
         for (const em of g.element || []) {
           if (em.code === coding.code) {
             let match = {

package/tx/library/designations.js

@@ -1,6 +1,6 @@
 const { LanguagePartType, Languages, Language, LanguageDefinitions} = require('../../library/languages');
 const {validateParameter, validateOptionalParameter, validateArrayParameter} = require("../../library/utilities");
-
+const natural = require('natural');
 /**
  * Display checking modes for concept designations
  */
@@ -26,6 +26,7 @@ class SearchFilterText {
 
     this.filter = filter ? filter.toLowerCase() : null;
     this.stems = [];
+    this.stemmer = natural.PorterStemmer;
     if (filter) {
       this._process();
     }
@@ -59,7 +60,7 @@ class SearchFilterText {
           i++;
         }
         const word = value.substring(j, i).toLowerCase();
-        const stemmed = this._stem(word);
+        const stemmed = this.stemmer.stem(word);
 
         if (this._find(stemmed)) {
           if (returnRating) {
@@ -142,7 +143,7 @@ class SearchFilterText {
           i++;
         }
         const word = this.filter.substring(j, i);
-        this.stems.push(this._stem(word));
+        this.stems.push(this.stemmer.stem(word.toLowerCase()));
       } else {
         i++;
       }
@@ -155,11 +156,6 @@ class SearchFilterText {
     return /[0-9a-zA-Z]/.test(char);
   }
 
-  _stem(word) {
-    // Simple stemming - in practice you'd want a proper stemmer
-    return word.toLowerCase();
-  }
-
   _find(stem) {
     // Binary search
     let left = 0;

package/tx/library/renderer.js

@@ -1800,12 +1800,12 @@ class Renderer {
       if (elem.noMap) {
         const nomapComment = Extensions.readString(elem, 'http://hl7.org/fhir/StructureDefinition/conceptmap-nomap-comment');
         if (!hasComment) {
-          tr.td().colspan("2").style("background-color: #efefef").tx("(not mapped)");
+          tr.td().setAttribute('colspan',"2").style("background-color: #efefef").tx("(not mapped)");
         } else if (nomapComment) {
-          tr.td().colspan("2").style("background-color: #efefef").tx("(not mapped)");
+          tr.td().setAttribute('colspan',"2").style("background-color: #efefef").tx("(not mapped)");
           tr.td().style("background-color: #efefef").tx(nomapComment);
         } else {
-          tr.td().colspan("3").style("background-color: #efefef").tx("(not mapped)");
+          tr.td().setAttribute('colspan',"3").style("background-color: #efefef").tx("(not mapped)");
         }
       } else {
         let first = true;
@@ -1858,16 +1858,16 @@ class Renderer {
     let tr = tbl.tr();
     const sourceColCount = 1 + Object.keys(sources).length - 1; // code + dependsOn attributes
     const targetColCount = 1 + Object.keys(targets).length - 1; // code + product attributes
-    tr.td().colspan(String(sourceColCount + 1)).b().tx(this.translate('CONC_MAP_SRC_DET'));
+    tr.td().setAttribute('colspan', String(sourceColCount + 1)).b().tx(this.translate('CONC_MAP_SRC_DET'));
     if (hasRelationships) {
       tr.td().b().tx(this.translate('CONC_MAP_REL'));
     }
-    tr.td().colspan(String(targetColCount + 1)).b().tx(this.translate('CONC_MAP_TRGT_DET'));
+    tr.td().setAttribute('colspan', String(targetColCount + 1)).b().tx(this.translate('CONC_MAP_TRGT_DET'));
     if (hasComment) {
       tr.td().b().tx(this.translate('GENERAL_COMMENT'));
     }
     if (hasProperties) {
-      tr.td().colspan(String(Object.keys(props).length)).b().tx(this.translate('GENERAL_PROPS'));
+      tr.td().setAttribute('colspan', String(Object.keys(props).length)).b().tx(this.translate('GENERAL_PROPS'));
     }
 
     // Second header row: actual column headers
@@ -1944,10 +1944,10 @@ class Renderer {
 
         const nomapComment = Extensions.readString(elem, 'http://hl7.org/fhir/StructureDefinition/conceptmap-nomap-comment');
         if (nomapComment) {
-          tr.td().colspan("3").style("background-color: #efefef").tx("(not mapped)");
+          tr.td().setAttribute('colspan',"3").style("background-color: #efefef").tx("(not mapped)");
           tr.td().style("background-color: #efefef").tx(nomapComment);
         } else {
-          tr.td().colspan("4").style("background-color: #efefef").tx("(not mapped)");
+          tr.td().setAttribute('colspan',"4").style("background-color: #efefef").tx("(not mapped)");
         }
       } else {
         let first = true;
@@ -2072,7 +2072,7 @@ class Renderer {
   async renderCSDetailsLink(tr, url, span2) {
     const td = tr.td();
     if (span2) {
-      td.colspan("2");
+      td.setAttribute('colspan',"2");
     }
     td.b().tx(this.translate('CONC_MAP_CODES'));
     td.tx(" " + this.translate('CONC_MAP_FRM') + " ");

package/tx/library.js

@@ -65,7 +65,8 @@ class Library {
    */
   conceptMapProviders;
 
-  contentSources = [];
+  packageSources = [];
+  externalSources = [];
 
   baseUrl = null;
   cacheFolder = null;
@@ -360,6 +361,9 @@ class Library {
       const codeSystemProvider = new OCLCodeSystemProvider(config);
       const valueSetProvider = new OCLValueSetProvider(config);
       const conceptMapProvider = new OCLConceptMapProvider(config);
+      this.externalSources.push(codeSystemProvider);
+      this.externalSources.push(valueSetProvider);
+      this.externalSources.push(conceptMapProvider);
       providerSet = {
         config,
         codeSystemProvider,
@@ -470,6 +474,7 @@ class Library {
         let vsac = new VSACValueSetProvider(this.vsacCfg, this.stats);
         vsac.initialize();
         this.valueSetProviders.push(vsac);
+        this.externalSources.push(vsac);
         //const mem = process.memoryUsage();
         let time = Math.floor(Date.now() - this.lastTime).toString().padStart(5)+" ";
         let system = "vsac".padEnd(50);
@@ -597,7 +602,7 @@ class Library {
     const contentLoader = new PackageContentLoader(fullPackagePath);
     await contentLoader.initialize();
 
-    this.contentSources.push(contentLoader.id()+"#"+contentLoader.version());
+    this.packageSources.push(contentLoader.id()+"#"+contentLoader.version());
 
     let cp = new ListCodeSystemProvider();
     const resources = await contentLoader.getResourcesByType("CodeSystem");
@@ -635,7 +640,7 @@ class Library {
     const contentLoader = new PackageContentLoader(fullPackagePath);
     await contentLoader.initialize();
 
-    this.contentSources.push(contentLoader.id()+"#"+contentLoader.version());
+    this.packageSources.push(contentLoader.id()+"#"+contentLoader.version());
 
     let cp = new ListCodeSystemProvider();
     const resources = await contentLoader.getResourcesByType("CodeSystem");
@@ -847,7 +852,8 @@ class Library {
     provider.lastTime = this.lastTime;
     provider.lastMemory = this.lastMemory;
     provider.totalDownloaded = this.totalDownloaded;
-    provider.contentSources = this.contentSources;
+    provider.packageSources = this.packageSources;
+    provider.externalSources = this.externalSources;
 
 
     // Now add the existing value set providers after the FHIR core packages