fhirsmith 0.5.5 → 0.6.0

package/tx/html/codesystem-operations.liquid

@@ -1,25 +1,18 @@
-<div class="operations" style="margin-top: 20px;">
-  <button type="button" class="btn btn-sm btn-outline-secondary" onclick="toggleOperations('{{ opsId }}')">Show Operations</button>
-  <div id="{{ opsId }}" style="display: none; margin-top: 10px;">
+<div class="operation-form" style="margin-bottom: 15px;">
+  <strong>Lookup</strong>
+  <form method="get" action="$lookup" style="display: inline-block; margin-left: 10px;">
+    <input type="hidden" name="system" value="{{ url }}"/>
+    <input type="text" name="code" placeholder="Code" required size="20"/>
+    <button type="submit" class="btn btn-sm btn-primary">Lookup</button>
+  </form>
+</div>
 
-    <div class="operation-form" style="margin-bottom: 15px;">
-      <strong>Lookup</strong>
-      <form method="get" action="$lookup" style="display: inline-block; margin-left: 10px;">
-        <input type="hidden" name="system" value="{{ url }}"/>
-        <input type="text" name="code" placeholder="Code" required size="20"/>
-        <button type="submit" class="btn btn-sm btn-primary">Lookup</button>
-      </form>
-    </div>
-
-    <div class="operation-form" style="margin-bottom: 15px;">
-      <strong>Subsumes</strong>
-      <form method="get" action="$subsumes" style="display: inline-block; margin-left: 10px;">
-        <input type="hidden" name="system" value="{{ url }}"/>
-        <input type="text" name="codeA" placeholder="Code A" required size="15"/>
-        <input type="text" name="codeB" placeholder="Code B" required size="15"/>
-        <button type="submit" class="btn btn-sm btn-primary">Subsumes</button>
-      </form>
-    </div>
-
-  </div>
-</div>
+<div class="operation-form" style="margin-bottom: 15px;">
+  <strong>Subsumes</strong>
+  <form method="get" action="$subsumes" style="display: inline-block; margin-left: 10px;">
+    <input type="hidden" name="system" value="{{ url }}"/>
+    <input type="text" name="codeA" placeholder="Code A" required size="15"/>
+    <input type="text" name="codeB" placeholder="Code B" required size="15"/>
+    <button type="submit" class="btn btn-sm btn-primary">Subsumes</button>
+  </form>
+</div>

package/tx/html/valueset-operations.liquid

@@ -1,54 +1,48 @@
-<div class="operations" style="margin-top: 20px;">
-  <button type="button" class="btn btn-sm btn-outline-secondary" onclick="toggleOperations('{{ opsId }}')">Show Operations</button>
-  <div id="{{ opsId }}" style="display: none; margin-top: 10px;">
 
-    <div class="operation-form" style="margin-bottom: 15px;">
-      <strong>Expand</strong>
-      <form method="get" action="$expand" style="margin-left: 10px; margin-top: 5px;">
-        <input type="hidden" name="url" value="{{ url }}"/>
-        <table class="grid" cellpadding="0" cellspacing="0">
-          <tr>
-            <td>Filter: <input type="text" name="filter" size="20"/></td>
-            <td>Language: <input type="text" name="displayLanguage" size="10"/></td>
-          </tr>
-          <tr>
-            <td colspan="2">
-              <input type="checkbox" name="includeDesignations" id="expand_desig" value="true"/>
-              <label for="expand_desig">Include Designations</label>
-              <input type="checkbox" name="activeOnly" id="expand_active" value="true"/>
-              <label for="expand_active">Active Only</label>
-            </td>
-          </tr>
-        </table>
-        <button type="submit" class="btn btn-sm btn-primary">Expand</button>
-      </form>
-    </div>
+<div class="operation-form" style="margin-bottom: 15px;">
+  <strong>Expand</strong>
+  <form method="get" action="$expand" style="margin-left: 10px; margin-top: 5px;">
+    <input type="hidden" name="url" value="{{ url }}"/>
+    <table class="grid" cellpadding="0" cellspacing="0">
+      <tr>
+        <td>Filter: <input type="text" name="filter" size="20"/></td>
+        <td>Language: <input type="text" name="displayLanguage" size="10"/></td>
+      </tr>
+      <tr>
+        <td colspan="2">
+          <input type="checkbox" name="includeDesignations" id="expand_desig" value="true"/>
+          <label for="expand_desig">Include Designations</label>
+          <input type="checkbox" name="activeOnly" id="expand_active" value="true"/>
+          <label for="expand_active">Active Only</label>
+        </td>
+      </tr>
+    </table>
+    <button type="submit" class="btn btn-sm btn-primary">Expand</button>
+  </form>
+</div>
 
-    <div class="operation-form" style="margin-bottom: 15px;">
-      <strong>Validate Code (ValueSet)</strong>
-      <form method="get" action="$validate-code" style="margin-left: 10px; margin-top: 5px;">
-        <input type="hidden" name="url" value="{{ url }}"/>
-        <input type="hidden" name="inferSystem" id="{{ inferSystemId }}" value="true"/>
-        <table class="grid" cellpadding="0" cellspacing="0">
-          <tr>
-            <td>System: <input type="text" name="system" id="{{ vcSystemId }}" size="30" onchange="updateInferSystem('{{ vcSystemId }}', '{{ inferSystemId }}')"/></td>
-            <td>Version: <input type="text" name="version" size="10"/></td>
-          </tr>
-          <tr>
-            <td>Code: <input type="text" name="code" size="20" required/></td>
-            <td>Display: <input type="text" name="display" size="20"/></td>
-          </tr>
-          <tr>
-            <td>Language: <input type="text" name="displayLanguage" size="10"/></td>
-            <td>
-              <input type="checkbox" name="abstract" value="true"/>
-              <label>Abstract</label>
-            </td>
-          </tr>
-        </table>
-        <button type="submit" class="btn btn-sm btn-primary">Validate Code</button>
-      </form>
-    </div>
-
-  </div>
-</div>
+<div class="operation-form" style="margin-bottom: 15px;">
+  <strong>Validate Code (ValueSet)</strong>
+  <form method="get" action="$validate-code" style="margin-left: 10px; margin-top: 5px;">
+    <input type="hidden" name="url" value="{{ url }}"/>
+    <input type="hidden" name="inferSystem" id="{{ inferSystemId }}" value="true"/>
+    <table class="grid" cellpadding="0" cellspacing="0">
+      <tr>
+        <td>System: <input type="text" name="system" id="{{ vcSystemId }}" size="30" onchange="updateInferSystem('{{ vcSystemId }}', '{{ inferSystemId }}')"/></td>
+        <td>Version: <input type="text" name="version" size="10"/></td>
+      </tr>
+      <tr>
+        <td>Code: <input type="text" name="code" size="20" required/></td>
+        <td>Display: <input type="text" name="display" size="20"/></td>
+      </tr>
+      <tr>
+        <td>Language: <input type="text" name="displayLanguage" size="10"/></td>
+        <td>
+          <input type="checkbox" name="abstract" value="true"/>
+          <label>Abstract</label>
+        </td>
+      </tr>
+    </table>
+    <button type="submit" class="btn btn-sm btn-primary">Validate Code</button>
+  </form>
+</div>

package/tx/library/codesystem.js

@@ -33,7 +33,12 @@ class CodeSystem extends CanonicalResource {
     // Convert to R5 format internally (modifies input for performance)
     this.jsonObj = codeSystemToR5(this.jsonObj, fhirVersion);
     if (!noMaps) {
-      this.validate();
+      try {
+        this.validate();
+      } catch (e) {
+        const id = this.jsonObj?.url ? `${this.jsonObj.url}|${this.jsonObj.version || ''}` : this.jsonObj?.name || 'unknown';
+        throw new Error(`${e.message} (in ${id})`);
+      }
       this.buildMaps();
     }
   }

package/tx/library/renderer.js

@@ -22,18 +22,17 @@ class Renderer {
   displayCoded(...args) {
     if (args.length === 1) {
       const arg = args[0];
-      if (arg.systemUri !== undefined && arg.version !== undefined && arg.code !== undefined && arg.display !== undefined) {
+      if (arg instanceof CodeSystemProvider) {
+        return arg.system() + "|" + arg.version();
+      } else  if (arg.system !== undefined && arg.version !== undefined && arg.code !== undefined && arg.display !== undefined) {
         // It's a Coding
         return this.displayCodedCoding(arg);
       } else if (arg.coding !== undefined || arg.text) {
         // It's a CodeableConcept
         return this.displayCodedCodeableConcept(arg);
-      } else if (arg.systemUri !== undefined && arg.version !== undefined) {
+      } else if (arg.system !== undefined && arg.version !== undefined) {
         // It's a CodeSystemProvider
         return this.displayCodedProvider(arg);
-      } else if (arg instanceof CodeSystemProvider) {
-        let cs = arg;
-        return cs.system() + "|" + cs.version();
       }
     } else if (args.length === 2) {
       return this.displayCodedSystemVersion(args[0], args[1]);
@@ -46,7 +45,7 @@ class Renderer {
   }
 
   displayCodedProvider(system) {
-    let result = system.systemUri + '|' + system.version;
+    let result = system.system + '|' + system.version;
     if (system.sourcePackage) {
       result = result + ' (from ' + system.sourcePackage + ')';
     }
@@ -70,7 +69,7 @@ class Renderer {
   }
 
   displayCodedCoding(code) {
-    return this.displayCodedSystemVersionCodeDisplay(code.systemUri, code.version, code.code, code.display);
+    return this.displayCodedSystemVersionCodeDisplay(code.system, code.version, code.code, code.display);
   }
 
   displayCodedCodeableConcept(code) {
@@ -90,12 +89,12 @@ class Renderer {
 
   displayValueSetInclude(inc) {
     let result;
-    if (inc.systemUri) {
-      result = '(' + inc.systemUri + ')';
-      if (inc.hasConcepts) {
+    if (inc.system) {
+      result = '(' + inc.system + ')';
+      if (inc.concept) {
         result = result + '(';
         let first = true;
-        for (const cc of inc.concepts) {
+        for (const cc of inc.concept) {
           if (first) {
             first = false;
           } else {
@@ -105,23 +104,23 @@ class Renderer {
         }
         result = result + ')';
       }
-      if (inc.hasFilters) {
+      if (inc.filter) {
         result = result + '(';
         let first = true;
-        for (const ci of inc.filters) {
+        for (const ci of inc.filter) {
           if (first) {
             first = false;
           } else {
             result = result + ',';
           }
-          result = result + ci.prop + ci.op + ci.value;
+          result = result + ci.property + ci.op + ci.value;
         }
         result = result + ')';
       }
     } else {
       result = '(';
       let first = true;
-      for (const s of inc.valueSets || []) {
+      for (const s of inc.valueSet || []) {
         if (first) {
           first = false;
         } else {
@@ -148,6 +147,7 @@ class Renderer {
     this.renderProperty(tbl, 'GENERAL_TITLE', res.title);
     this.renderProperty(tbl, 'GENERAL_STATUS', res.status);
     this.renderPropertyMD(tbl, 'GENERAL_DEFINITION', res.description);
+    this.renderPropertyMD(tbl, 'GENERAL_PURPOSE', res.purpose);
     this.renderProperty(tbl, 'CANON_REND_PUBLISHER', res.publisher);
     this.renderProperty(tbl, 'CANON_REND_COMMITTEE', Extensions.readString(res, 'http://hl7.org/fhir/StructureDefinition/structuredefinition-wg'));
     this.renderProperty(tbl, 'GENERAL_COPYRIGHT', res.copyright);
@@ -340,7 +340,7 @@ class Renderer {
     }
     if (vs.expansion) {
       div_.h2().tx("Expansion");
-      await this.renderExpansion(div_.table("grid"), vs, tbl);
+      await this.renderExpansion(div_, vs, tbl);
     }
 
     return div_.toString();
@@ -420,7 +420,7 @@ class Renderer {
         li.tx(this.translate('VALUE_SET_ALL_CODES_DEF')+" ");
         await this.renderLink(li,inc.system+(inc.version ? "|"+inc.version : ""));
       } else if (inc.concept) {
-        li.tx(this.translate('VALUE_SET_THESE_CODES_DEF'));
+        li.tx(this.translate('VALUE_SET_THESE_CODES_DEF')+" ");
         await this.renderLink(li,inc.system+(inc.version ? "|"+inc.version : ""));
         li.tx(":");
         const ul = li.ul();
@@ -899,18 +899,45 @@ class Renderer {
     return count;
   }
 
+  async renderVSExpansion(vs, showProps) {
+    let div_ = div();
+    let tbl;
+    if (showProps) {
+      div_.h2().tx("Expansion Properties");
+      tbl = div_.table("grid");
+    } else {
+      tbl = div(); // dummy
+    }
+    await this.renderExpansion(div_.table("grid"), vs, tbl);
+    return div_.toString();
+  }
+
   async renderExpansion(x, vs, tbl) {
     this.renderProperty(tbl, 'Expansion Identifier', vs.expansion.identifier);
     this.renderProperty(tbl, 'Expansion Timestamp', vs.expansion.timestamp);
     this.renderProperty(tbl, 'Expansion Total', vs.expansion.total);
     this.renderProperty(tbl, 'Expansion Offset', vs.expansion.offset);
+    const warnings = [];
+    const warningNames = new Set(['deprecated', 'withdrawn', 'retired', 'experimental', 'draft']);
+    const useds = [];
+    const usedNames = new Set(['codesystem', 'valueset', 'supplement']);
     for (let p of vs.expansion.parameter || []) {
-      if( getValueName(p) === 'valueUri' || getValueName(p) === 'valueCanonical') {
+      if (p.name.startsWith('warning-') && warningNames.has(p.name.substring(8))) {
+        warnings.push(p);
+      } else if (p.name.startsWith('used-') && usedNames.has(p.name.substring(5))) {
+        useds.push(p);
+      } else if( getValueName(p) === 'valueUri' || getValueName(p) === 'valueCanonical') {
         await this.renderPropertyLink(tbl, "Parameter: " + p.name, getValuePrimitive(p));
       } else {
         this.renderProperty(tbl, "Parameter: " + p.name, getValuePrimitive(p));
       }
     }
+    if (useds.length > 0) {
+      await this.renderUsed(x, useds);
+    }
+    if (warnings.length > 0) {
+      await this.renderWarnings(x, warnings);
+    }
 
     if (!vs.expansion.contains || vs.expansion.contains.length === 0) {
       x.para().i().tx('No concepts in expansion');
@@ -936,10 +963,10 @@ class Renderer {
     }
     headerRow.th().tx(this.translate('TX_DISPLAY'));
     if (columnInfo.hasAbstract) {
-      headerRow.th().tx('Abstract');
+      headerRow.th().tx(this.translate('Abstract'));
     }
     if (columnInfo.hasInactive) {
-      headerRow.th().tx('Inactive');
+      headerRow.th().tx(this.translate('VALUE_SET_INACTIVE'));
     }
 
     // Property columns (from expansion.property definitions)
@@ -1118,12 +1145,12 @@ class Renderer {
 
     // Abstract column
     if (columnInfo.hasAbstract) {
-      tr.td().tx(contains.abstract === true ? 'true' : '');
+      tr.td().tx(contains.abstract === true ? 'abstract' : '');
     }
 
     // Inactive column
     if (columnInfo.hasInactive) {
-      tr.td().tx(contains.inactive === true ? 'true' : '');
+      tr.td().tx(contains.inactive === true ? this.translate('VALUE_SET_INACT') : '');
     }
 
     // Property columns
@@ -1557,12 +1584,62 @@ class Renderer {
             // No versions specified
             await this.renderLink(li, cs.uri);
           }
+          let content = cs.content || Extensions.readString(cs, "http://hl7.org/fhir/4.0/StructureDefinition/extension-TerminologyCapabilities.codeSystem.content");
+          if (content && content != "complete") {
+            li.tx(" (" + content + ")");
+          }
         }
       }
     }
 
     return div_.toString();
   }
+
+  async renderWarnings(x, warnings) {
+    await this.renderWarningsForStatus(x, 'deprecated', warnings);
+    await this.renderWarningsForStatus(x, 'withdrawn', warnings);
+    await this.renderWarningsForStatus(x, 'retired', warnings);
+    await this.renderWarningsForStatus(x, 'experimental', warnings);
+    await this.renderWarningsForStatus(x, 'draft', warnings);
+  }
+
+  async renderWarningsForStatus(x, name, warnings) {
+    const wl = warnings.filter(item => item.name == 'warning-'+name);
+    if (wl && wl.length > 0) {
+      x.para().tx(`This ValueSet depends on the following ${name} ValueSets: `);
+      let ul = x.ul();
+      for (const w of wl) {
+        const linkinfo = await this.linkResolver.resolveURL(this.opContext, getValuePrimitive(w));
+        if (linkinfo) {
+          ul.li().ah(linkinfo.link).tx(linkinfo.description);
+        } else {
+          ul.li().code().tx(getValuePrimitive(w));
+        }
+      }
+    }
+  }
+
+  async renderUsed(x, list) {
+    x.para().tx(`This ValueSet depends on the following items:`);
+    let ul = x.ul();
+    await this.renderUsedForType(ul, 'codesystem', 'CodeSystem', list);
+    await this.renderUsedForType(ul, 'valueset', 'ValueSet', list);
+    await this.renderUsedForType(ul, 'supplement', 'Supplement', list);
+  }
+
+  async renderUsedForType(ul, name, title, list) {
+    const wl = list.filter(item => item.name == 'used-' + name);
+    for (const w of wl) {
+      const li = ul.li();
+      li.tx(title+": ");
+      const linkinfo = await this.linkResolver.resolveURL(this.opContext, getValuePrimitive(w));
+      if (linkinfo) {
+        li.ah(linkinfo.link).tx(linkinfo.description);
+      } else {
+        li.code().tx(getValuePrimitive(w));
+      }
+    }
+  }
 }
 
 module.exports = { Renderer };

package/tx/library.js

@@ -158,7 +158,12 @@ class Library {
     this.log.info('Fetching Data from '+this.baseUrl);
 
     for (const source of config.sources) {
-      await this.processSource(source, this.packageManager, "fetch");
+      try {
+        await this.processSource(source, this.packageManager, "fetch");
+      } catch (error) {
+        console.error(`Failed to fetch source '${source}': ${error.message}`);
+        throw error;
+      }
     }
 
     this.log.info("Downloaded "+((this.totalDownloaded + this.packageManager.totalDownloaded)/ 1024)+" kB");
@@ -167,13 +172,23 @@ class Library {
     this.#logSystemHeader();
 
     for (const source of config.sources) {
-      await this.processSource(source, this.packageManager, "cs");
+      try {
+        await this.processSource(source, this.packageManager, "cs");
+      } catch (error) {
+        console.error(`Failed to load code systems from '${source}': ${error.message}`);
+        throw error;
+      }
     }
     this.log.info('Loading Packages');
     this.#logPackagesHeader();
 
     for (const source of config.sources) {
-      await this.processSource(source, this.packageManager, "npm");
+      try {
+        await this.processSource(source, this.packageManager, "npm");
+      } catch (error) {
+        console.error(`Failed to load package '${source}': ${error.message}`);
+        throw error;
+      }
     }
 
     const endMemory = process.memoryUsage();

package/tx/provider.js

@@ -153,6 +153,7 @@ class Provider {
   }
 
   getCodeSystemById(opContext, id) {
+
     // Search through codeSystems map for matching id
     for (const cs of this.codeSystems.values()) {
       if (opContext) opContext.deadCheck('getCodeSystemById');
@@ -318,9 +319,10 @@ class Provider {
       factory = this.codeSystemFactories.get(vurlMM);
     }
     if (factory != null) {
+      let vdesc = version == null ? "" : factory.describeVersion(version);
       return {
-        link: this.path+"/CodeSystem/"+factory.id(),
-        description: factory.name()+(version ? " v"+version : "")
+        link: this.path+"/CodeSystem/x-"+factory.id(),
+        description: factory.nameBase()+' '+vdesc
       };
     }
     let cs = this.codeSystems.get(vurl);

package/tx/sct/expressions.js

@@ -1469,7 +1469,7 @@ class SnomedExpressionServices {
   /**
    * Validate concept reference
    */
-  checkConcept(concept, limit) {
+  checkConcept(concept, limits) {
     if (concept.code) {
       const conceptId = BigInt(concept.code);
       const result = this.concepts.findConcept(conceptId);
@@ -1480,13 +1480,24 @@ class SnomedExpressionServices {
         throw new Error(`Concept ${concept.code} not found`);
       }
     }
-    if (limit && concept.reference) {
-      // if a limit is specified, then the concept has to be a specialization of that.
-      let parentRef = this.concepts.findConcept(limit);
-      let descendentsRef = this.concepts.getAllDesc(parentRef.index);
-      const descendants = this.refs.getReferences(descendentsRef);
-      if (descendants && !descendants.includes(concept.reference)) {
-        throw new Error(`Concept ${concept.code} is not valid in this context (must be a ${limit})`);
+    if (limits && concept.reference) {
+      // if a limit is specified, then the concept has to be a specialization of one of them.
+      let ok = false;
+      for (const limit of limits) {
+        let parentRef = this.concepts.findConcept(limit);
+        let descendentsRef = this.concepts.getAllDesc(parentRef.index);
+        const descendants = this.refs.getReferences(descendentsRef);
+        if (descendants && descendants.includes(concept.reference)) {
+          ok = true;
+          break;
+        }
+      }
+      if (!ok) {
+        if (limits.length == 1) {
+          throw new Error(`Concept ${concept.code} is not valid in this context (must be a ${limits[0]})`);
+        } else {
+          throw new Error(`Concept ${concept.code} is not valid in this context (must be a descendent of one of ${limits})`);
+        }
       }
     }
 
@@ -1615,7 +1626,7 @@ class SnomedExpressionServices {
    * Validate refinement
    */
   checkRefinement(refinement) {
-    this.checkConcept(refinement.name, '410662002');
+    this.checkConcept(refinement.name, ['410662002', '106237007']);
     this.checkExpression(refinement.value);
   }