fhirsmith 0.5.6 → 0.7.0

package/tx/cs/cs-api.js

@@ -774,12 +774,19 @@ class CodeSystemFactoryProvider {
   }
 
   /**
-   * @returns {string} uri for the code system
+   * @returns {string} name for the code system
    */
   name() {
     throw new Error("Must override");
   }
 
+  /**
+   * @returns {string} name for the code system, without version information
+   */
+  nameBase() {
+    return this.name();
+  }
+
   /**
    * @returns {string} version for the code system
    */
@@ -796,6 +803,16 @@ class CodeSystemFactoryProvider {
     }
     return ver;
   }
+
+  /**
+   * the version parameter might not be the same as version() once
+   * all matching rules are done
+   * @param version
+   */
+  describeVersion(version) {
+    return "v"+version;
+  }
+
 /**
    * @returns {number} how many times the factory has been asked to construct a provider
    */

package/tx/cs/cs-base.js

@@ -72,6 +72,7 @@ class BaseCSServices extends CodeSystemProvider {
   };
 }
 
+
 module.exports = {
   BaseCSServices
 };

package/tx/cs/cs-loinc.js

@@ -203,9 +203,12 @@ class LoincServices extends BaseCSServices {
     // Use language-aware display logic
     if (this.opContext.langs && !this.opContext.langs.isEnglishOrNothing()) {
       const displays = await this.#getDisplaysForContext(ctxt, this.opContext.langs);
+      const requestedLanguages = Array.isArray(this.opContext.langs.languages)
+        ? this.opContext.langs.languages
+        : (Array.isArray(this.opContext.langs.langs) ? this.opContext.langs.langs : []);
 
       // Try to find exact language match
-      for (const lang of this.opContext.langs.langs) {
+      for (const lang of requestedLanguages) {
         for (const display of displays) {
           if (lang.matches(display.language, true)) {
             return display.value;
@@ -214,7 +217,7 @@ class LoincServices extends BaseCSServices {
       }
 
       // Try partial language match
-      for (const lang of this.opContext.langs.langs) {
+      for (const lang of requestedLanguages) {
         for (const display of displays) {
           if (lang.matches(display.language, false)) {
             return display.value;

package/tx/cs/cs-provider-api.js

@@ -20,7 +20,13 @@ class AbstractCodeSystemProvider {
   }
 
   /**
-  * Returns the list of CodeSystems this provider provides
+   * Returns the list of CodeSystems this provider provides. This is called once at start up.
+   * The code systems should be fully loaded; lazy loading code systems is not considered good
+   * for engineering.
+   *
+   *
+   * Note that unlike value sets, which are accessed from the provider on the fly, code systems
+   * are all preloaded into the kernel (e.g. provider) at start up
    *
   * @param {string} fhirVersion - The FHIRVersion in scope - if relevant (there's always a stated version, though R5 is always used)
   * @param {string} context - The client's stated context - if provided.
@@ -32,6 +38,24 @@ class AbstractCodeSystemProvider {
     throw new Error('listCodeSystems must be implemented by AbstractCodeSystemProvider subclass');
   }
 
+  /**
+   * This is called once a minute to update the code system list that the provider maintains.
+   *
+   * return an object that has three Map<String, CodeSystem>: {added, changed, deleted}
+   *
+   * these use the same key as the
+   *
+   * code systems are identified by url and version
+   *
+   * @param fhirVersion
+   * @param context
+   * @returns {Promise<null>}
+   */
+  // eslint-disable-next-line no-unused-vars
+  async getCodeSystemChanges(fhirVersion, context){
+    return null;
+  }
+
   async close() {
 
   }

package/tx/cs/cs-provider-list.js

@@ -7,7 +7,7 @@ class ListCodeSystemProvider extends AbstractCodeSystemProvider {
   /**
    * {Map<String, CodeSystem>} A list of code system factories that contains all the preloaded native code systems
    */
-  codeSystems = new Map();
+  codeSystems = [];
 
   /**
    * ensure that the ids on the code systems are unique, if they are
@@ -17,7 +17,7 @@ class ListCodeSystemProvider extends AbstractCodeSystemProvider {
    */
   // eslint-disable-next-line no-unused-vars
   assignIds(ids) {
-    for (const cs of this.codeSystems.values()) {
+    for (const cs of this.codeSystems) {
       if (!cs.id || ids.has("CodeSystem/"+cs.id)) {
         cs.id = ""+ids.size;
       }

package/tx/cs/cs-rxnorm.js

@@ -3,7 +3,7 @@ const assert = require('assert');
 const { CodeSystem } = require('../library/codesystem');
 const { CodeSystemProvider, CodeSystemFactoryProvider } = require('./cs-api');
 const {Designations} = require("../library/designations");
-const {validateArrayParameter} = require("../../library/utilities");
+const {validateArrayParameter, formatDateMMDDYYYY} = require("../../library/utilities");
 
 // Context for RxNorm concepts
 class RxNormConcept {
@@ -806,9 +806,16 @@ class RxNormTypeServicesFactory extends CodeSystemFactoryProvider {
   }
 
   id() {
-    return this.name();
+    return this.name()+"-"+this.version();
   }
 
+  describeVersion(version) {
+    try {
+      return formatDateMMDDYYYY(version);
+    } catch (error) {
+      return "v" + version;
+    }
+  }
 }
 
 // Specific RxNorm implementation

package/tx/cs/cs-snomed.js

@@ -11,6 +11,7 @@ const {
 } = require('../sct/expressions');
 const {DesignationUse} = require("../library/designations");
 const {BaseCSServices} = require("./cs-base");
+const {formatDateMMDDYYYY} = require("../../library/utilities");
 
 // Context kinds matching Pascal enum
 const SnomedProviderContextKind = {
@@ -1262,11 +1263,25 @@ class SnomedServicesFactory extends CodeSystemFactoryProvider {
     return `SCT ${getEditionCode(this._sharedData.edition)}`;
   }
 
+  nameBase() {
+    return `SCT`;
+  }
+
   id() {
-    return "SCT"+this.version();
+    const match = this.version().match(/^http:\/\/snomed\.info\/sct\/(\d+)(?:\/version\/(\d{8}))?$/);
+    return "SCT-"+match[1]+"-"+match[2];
   }
-}
 
+  describeVersion(version) {
+    const match = version.match(/^http:\/\/snomed\.info\/sct\/(\d+)(?:\/version\/(\d{8}))?$/);
+    if (!match) return version;
+
+    const edition = getEditionName(match[1]);
+    if (!match[2]) return edition;
+
+    return edition + ' ' + formatDateMMDDYYYY(match[2].substring(4, 6) + match[2].substring(6, 8) + match[2].substring(0, 4));
+  }
+}
 
 function getEditionName(edition) {
   const editionMap = {

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/canonical-resource.js

@@ -111,7 +111,12 @@ class CanonicalResource {
       const fmt = this.versionAlgorithm() || other.versionAlgorithm() || this.guessVersionAlgorithmFromVersion(this.version);
       switch (fmt) {
         case 'semver':
-          return VersionUtilities.isThisOrLater(other.version, this.version, VersionPrecision.PATCH);
+          try {
+            return VersionUtilities.isThisOrLater(other.version, this.version, VersionPrecision.PATCH);
+          } catch (error) {
+            // other is not semver. Not much we can do
+            return false;
+          }
         case 'date':
           return this.dateIsMoreRecent(this.version, other.version);
         case 'integer':

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

@@ -147,6 +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);
@@ -339,7 +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();
@@ -419,7 +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();
@@ -898,18 +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');
@@ -935,10 +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)
@@ -1117,12 +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
@@ -1566,6 +1594,52 @@ class Renderer {
 
     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 };