fhirsmith 0.8.3 → 0.8.5

package/tx/cs/cs-snomed.js

@@ -355,7 +355,7 @@ class SnomedServices {
     return result;
   }
 
-  filterIn(id) {
+  filterChildOf(id = true) {
     const result = new SnomedFilterContext();
     const conceptResult = this.concepts.findConcept(id);
 
@@ -363,12 +363,62 @@ class SnomedServices {
       throw new Error(`The SNOMED CT Concept ${id} is not known`);
     }
 
-    const refSetIndex = this.getConceptRefSet(conceptResult.index, false);
-    if (refSetIndex === 0) {
-      throw new Error(`The SNOMED CT Concept ${id} is not a reference set`);
+    const descendants = this.getConceptChildren(conceptResult.index);
+
+    result.descendants = descendants;
+
+    return result;
+  }
+
+
+  filterGeneralizes(id = true) {
+    const result = new SnomedFilterContext();
+    const conceptResult = this.concepts.findConcept(id);
+
+    if (!conceptResult.found) {
+      throw new Error(`The SNOMED CT Concept ${id} is not known`);
+    }
+
+    let ancestors = new Set();
+    let parents = this.getConceptParents(conceptResult.index);
+    let isNew = true;
+    while (isNew) {
+      isNew = false;
+      let np = [];
+      for (let parent of parents) {
+        if (!ancestors.has(parent)) {
+          isNew = true;
+          ancestors.add(parent);
+          np.push(...this.getConceptParents(parent));
+        }
+      }
+      parents = np;
     }
 
-    result.members = this.refSetMembers.getMembers(refSetIndex) || [];
+    result.descendants = [...ancestors];
+
+    return result;
+  }
+
+
+  filterIn(idList) {
+    const result = new SnomedFilterContext();
+    let members = [];
+    for (let id of idList.split(',')) {
+      const conceptResult = this.concepts.findConcept(id);
+
+      if (!conceptResult.found) {
+        throw new Error(`The SNOMED CT Concept ${id} is not known`);
+      }
+
+      const refSetIndex = this.getConceptRefSet(conceptResult.index, false);
+      if (refSetIndex === 0) {
+        members.push(conceptResult.index);
+      } else {
+        members.push(...this.refSetMembers.getMembers(refSetIndex));
+      }
+    }
+    result.members = members;
     return result;
   }
 
@@ -775,6 +825,13 @@ class SnomedProvider extends BaseCSServices {
     const ctxt = await this.#ensureContext(context);
     if (ctxt) {
       if (!(ctxt instanceof SnomedExpressionContext) || ctxt.expression?.concepts.length == 1) {
+        const time = this.sct.concepts.getConcept(ctxt.getReference()).effectiveTime;
+        const pascalEpoch = new Date(1899, 11, 30);
+        const date = new Date(pascalEpoch.getTime() + time * 86400000);
+        const dateStr = date.toISOString().slice(0, 10);
+        this._addDateTimeProperty(params, 'property', 'effectiveTime', dateStr);
+
+
         const parents = this.sct.getConceptParents(ctxt.getReference());
         for (let parentRef of parents) {
           const code = this.sct.getConceptId(parentRef);
@@ -792,7 +849,7 @@ class SnomedProvider extends BaseCSServices {
         const moduleId = this.sct.concepts.getModuleId(ctxt.getReference());
         if (moduleId) {
           const code = this.sct.getConceptId(moduleId);
-          this._addCodeProperty(params, 'property', 'module', code, null, null);
+          this._addCodeProperty(params, 'property', 'module', code, null, this.sct.getDisplayName(moduleId));
         }
 
         const relationships = this.sct.getConceptRelationships(ctxt.getReference());
@@ -838,9 +895,20 @@ class SnomedProvider extends BaseCSServices {
   async doesFilter(prop, op, value) {
     if (prop === 'concept') {
       const id = this.sct.stringToIdOrZero(value);
-      if (id !== 0n && ['=', 'is-a', 'descendent-of', 'in'].includes(op)) {
+      if (id !== 0n && ['=', 'is-a', 'descendent-of', 'in', 'generalizes', 'child-of'].includes(op)) {
         return this.sct.conceptExists(value);
       }
+      if (op === 'in' && value.includes(',')) {
+        let ok = true;
+        for (const idStr of value.split(',')) {
+          const id = this.sct.stringToIdOrZero(idStr);
+          if (id === 0n) {
+            ok = false;
+            break;
+          }
+        }
+        return ok;
+      }
     }
     if (prop === 'inactive') {
       return op === '=' && ['true', 'false'].includes(value);
@@ -874,7 +942,7 @@ class SnomedProvider extends BaseCSServices {
 
     if (prop === 'concept') {
       const id = this.sct.stringToIdOrZero(value);
-      if (id === 0n) {
+      if (id === 0n && op !== 'in') {
         throw new Error(`Invalid concept ID: ${value}`);
       }
 
@@ -891,8 +959,16 @@ class SnomedProvider extends BaseCSServices {
           filterContext.filters.push(this.sct.filterIsA(id, false));
           return null;
         }
+        case 'child-of': {
+          filterContext.filters.push(this.sct.filterChildOf(id));
+          return null;
+        }
+        case 'generalizes': {
+          filterContext.filters.push(this.sct.filterGeneralizes(id, false));
+          return null;
+        }
         case 'in': {
-          filterContext.filters.push(this.sct.filterIn(id));
+          filterContext.filters.push(this.sct.filterIn(value));
           return null;
         }
         default:
@@ -1121,7 +1197,7 @@ class SnomedProvider extends BaseCSServices {
     if (set.propProp || set.propValue) {
       for (let i = 0; i < this.sct.concepts.count(); i++) {
         let concept = this.sct.concepts.getConceptByCount(i);
-        const relationships = this.sct.getConceptRelationships(concept.getReference());
+        const relationships = this.sct.getConceptRelationships(concept.index);
         for (let relationshipRef of relationships) {
           const relationship = this.sct.relationships.getRelationship(relationshipRef);
           if (set.propProp === relationship.relType && set.propValue === relationship.target) {
@@ -1560,6 +1636,11 @@ class SnomedServicesFactory extends CodeSystemFactoryProvider {
       return null;
     }
   }
+
+  webSource() {
+    return this.version();
+  }
+
 }
 
 function getEditionName(edition) {

package/tx/html/tx-template.html

@@ -126,9 +126,12 @@
 	</div>
 
       <!-- JS and analytics only. -->
-<script src="/assets/js/respond.min.js"/>
-<script src="/assets/js/fhir.js"/>
+<script src="/assets/js/respond.min.js"> </script>
+<script src="/assets/js/fhir.js"> </script>
+  <script src="/assets/js/clipboard.min.js"> </script>
+  <script src="/assets/js/clipboard-btn.js"> </script>
 
 </body>
 
 </html>
+

package/tx/library/codesystem.js

@@ -2,6 +2,7 @@ const { Language } = require("../../library/languages");
 const {CanonicalResource} = require("./canonical-resource");
 const {codeSystemFromR5, codeSystemToR5} = require("../xversion/xv-codesystem");
 const {getValuePrimitive} = require("../../library/utilities");
+const {VersionUtilities} = require("../../library/version-utilities");
 
 const CodeSystemContentMode = Object.freeze({
   Complete: 'complete',
@@ -614,12 +615,31 @@ class CodeSystem extends CanonicalResource {
   }
 
   isLangPack() {
+    // todo: this is a temporary work around until fhir.tx.support.r4#0.37.0 is released that properly marks this as a language pack
+    if (this.jsonObj.url === 'https://terminology.dhp.uz/fhir/CodeSystem/loinc-supplement-uz') {
+      return true;
+    }
     return (this.jsonObj.extension || []).find(x => x.url == 'http://hl7.org/fhir/StructureDefinition/codesystem-supplement-type' && getValuePrimitive(x) == 'lang-pack');
   }
 
   isPropUri(code, uri) {
     return (this.jsonObj.property || []).find(x => x.code == code && x.uri == uri);
   }
+
+  isSupplementFor(url, version) {
+    if (this.jsonObj.content !== 'supplement') {
+      return false;
+    }
+    let suppU = this.jsonObj.supplements;
+    if (suppU == url) {
+      return true;
+    }
+    if (suppU.startsWith(url + '|')) {
+      let suppV = suppU.substring(suppU.indexOf('|') + 1);
+      return VersionUtilities.versionMatchesByAlgorithm(suppV, version, VersionUtilities.guessVersionAlgorithmFromVersion(version));
+    }
+    return false;
+  }
 }
 
 module.exports = { CodeSystem, CodeSystemContentMode };

package/tx/library/designations.js

@@ -404,6 +404,15 @@ class Designations {
     // }
   }
 
+  hasAnyDisplay(value) {
+    for (let designation of this.designations) {
+      if (designation.value === value) {
+        return true;
+      }
+    }
+    return false;
+  }
+
   /**
    * Check if a display value exists with specified matching criteria
    */
@@ -551,7 +560,7 @@ class Designations {
   /**
    * Find the preferred designation for given language preferences
    */
-  preferredDesignation(langList = null) {
+  preferredDesignation(langList = null, supplements = null) {
     if (this.designations.length === 0) {
       return null;
     }
@@ -560,24 +569,39 @@ class Designations {
       // No language list, prefer base designations
       for (const cd of this.designations) {
         if (this._isPreferred(cd) && cd.isActive()) {
+          if (supplements && cd.source) {
+            supplements.add(cd.source);
+          }
           return cd;
         }
       }
       for (const cd of this.designations) {
         if (this.isDisplay(cd) && cd.isActive()) {
+          if (supplements && cd.source) {
+            supplements.add(cd.source);
+          }
           return cd;
         }
       }
       for (const cd of this.designations) {
         if (this.isDisplay(cd)) {
+          if (supplements && cd.source) {
+            supplements.add(cd.source);
+          }
           return cd;
         }
       }
       for (const cd of this.designations) {
         if (this._isPreferred(cd)) {
+          if (supplements && cd.source) {
+            supplements.add(cd.source);
+          }
           return cd;
         }
       }
+      if (supplements && this.designations[0].source) {
+        supplements.add(this.designations[0].source);
+      }
       return this.designations[0];
     }
 
@@ -589,16 +613,25 @@ class Designations {
       for (const matchType of matchTypes) {
         for (const cd of this.designations) {
           if (this._langMatches(lang, cd.language, matchType) && this.isDisplay(cd)) {
+            if (supplements && cd.source) {
+              supplements.add(cd.source);
+            }
             return cd;
           }
         }
         for (const cd of this.designations) {
           if (this._langMatches(lang, cd.language, matchType) && this._isPreferred(cd)) {
+            if (supplements && cd.source) {
+              supplements.add(cd.source);
+            }
             return cd;
           }
         }
         for (const cd of this.designations) {
           if (this._langMatches(lang, cd.language, matchType)) {
+            if (supplements && cd.source) {
+              supplements.add(cd.source);
+            }
             return cd;
           }
         }
@@ -606,6 +639,9 @@ class Designations {
     }
     for (const cd of this.designations) {
       if (!cd.language && this.isDisplay(cd)) {
+        if (supplements && cd.source) {
+          supplements.add(cd.source);
+        }
         return cd;
       }
     }

package/tx/library/renderer.js

@@ -141,8 +141,8 @@ class Renderer {
     this.renderMetadataLastUpdated(res, tbl);
     this.renderMetadataSource(res, tbl);
     this.renderProperty(tbl, 'TEST_PLAN_LANG', res.language);
-    this.renderProperty(tbl, 'GENERAL_DEFINING_URL', res.url);
-    this.renderProperty(tbl, 'GENERAL_VER', res.version);
+    this.renderPropertyCopy(tbl, 'GENERAL_DEFINING_URL', res.url);
+    this.renderPropertyCopy(tbl, 'GENERAL_VER', res.version);
     this.renderProperty(tbl, 'GENERAL_NAME', res.name);
     this.renderProperty(tbl, 'GENERAL_TITLE', res.title);
     this.renderProperty(tbl, 'GENERAL_STATUS', res.status);
@@ -150,9 +150,10 @@ class Renderer {
     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);
+    this.renderPropertyCopy(tbl, 'GENERAL_COPYRIGHT', res.copyright);
     this.renderProperty(tbl, 'EXT_FMM_LEVEL', Extensions.readString(res, 'http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm'));
     this.renderProperty(tbl, 'PAT_PERIOD', res.effectivePeriod);
+    this.renderPropertyLink(tbl, 'WEB_SOURCE', Extensions.readString(res, 'http://hl7.org/fhir/StructureDefinition/web-source'));
 
     // capability statement things
     this.renderProperty(tbl, 'Kind', res.kind);
@@ -253,15 +254,32 @@ class Renderer {
     }
   }
 
-  async renderPropertyLink(tbl, msgId, value) {
+  renderPropertyCopy(tbl, msgId, value) {
     if (value) {
       let tr = tbl.tr();
       tr.td().b().tx(this.translate(msgId));
-      const linkinfo = await this.linkResolver.resolveURL(this.opContext, value);
-      if (linkinfo) {
-        tr.td().ah(linkinfo.link).tx(linkinfo.description);
+      if (value instanceof Object) {
+        tr.td().tx("todo");
       } else {
-        tr.td().tx(value);
+        let td = tr.td();
+        let span = td.span("copy-text");
+        span.tx(value);
+        let btn = span.button();
+        btn.attr("class", "btn-copy");
+        btn.attr("data-clipboard-text", value);
+        btn.attr("data-original-title", this.translate('GENERAL_COPY'));
+      }
+    }
+  }
+
+  renderPropertyLink(tbl, msgId, value) {
+    if (value) {
+      let tr = tbl.tr();
+      tr.td().b().tx(this.translate(msgId));
+      if (value instanceof Object) {
+        tr.td().tx("todo");
+      } else {
+        tr.td().ah(value).tx(value);
       }
     }
   }

package/tx/provider.js

@@ -107,6 +107,36 @@ class Provider {
     return null;
   }
 
+  loadSupplements(url, version, statedSupplements) {
+    let supplements = new Map();
+    for (let csp of this.codeSystemFactories.values()) {
+      csp.listSupplements(supplements, url, version, statedSupplements);
+    }
+    for (let cs of this.codeSystems.values()) {
+      if (cs.isSupplementFor(url, version)) {
+        if (cs.isLangPack() || this.isStatedSupplement(cs, statedSupplements)) {
+          supplements.set(cs.vurl, cs);
+        }
+      }
+    }
+    return [...supplements.values()];
+  }
+
+  isStatedSupplement(cs, statedSupplements) {
+    if (statedSupplements == null) {
+      return false;
+    }
+    for (let suppU of statedSupplements) {
+      if (suppU === cs.url) {
+        return true;
+      }
+      if (suppU.startsWith(cs.url+"|")) {
+        let suppV = suppU.substring(suppU.indexOf('|') + 1);
+        return VersionUtilities.versionMatchesByAlgorithm(suppV, cs.version, VersionUtilities.guessVersionAlgorithmFromVersion(cs.version));
+      }
+    }
+    return false;
+  }
   /**
    * Create a code system provider from a CodeSystem resource
    * @param {OperationContext} opContext - The code system resource

package/tx/tx.fhir.org.yml

@@ -12,7 +12,7 @@ sources:
   - internal:hgvs
   - ucum:tx/data/ucum-essence.xml
   - loinc:loinc-2.77-a.db
-  - loinc!:loinc-2.81-b.db
+  - loinc!:Loinc_2.82.db
   - rxnorm:rxnorm_03022026.db
   - ndc:ndc-20211101.db
   - unii:unii_20240622.db

package/tx/workers/expand.js

@@ -204,6 +204,7 @@ class ValueSetExpander {
   hasExclusions = false;
   requiredSupplements = new Set();
   usedSupplements = new Set();
+  reportedSupplements = new Set();
   internalLimit = INTERNAL_DEFAULT_LIMIT;
   externalLimit = EXTERNAL_DEFAULT_LIMIT;
 
@@ -339,9 +340,9 @@ class ValueSetExpander {
       const s = this.canonical(system, version);
       this.addParamUri(expansion, 'used-codesystem', s);
       if (cs != null) {
-        const ts = cs.listSupplements();
+        const ts = cs.listSupplements(false);
         for (const vs of ts) {
-          this.addParamUri(expansion, 'used-supplement', vs);
+          this.reportedSupplements.add(vs);
         }
       }
     }
@@ -415,7 +416,7 @@ class ValueSetExpander {
       }
 
       // display and designations
-      const pref = displays.preferredDesignation(this.params.workingLanguages());
+      const pref = displays.preferredDesignation(this.params.workingLanguages(), this.reportedSupplements);
       if (pref && pref.value) {
         n.display = pref.value;
       }
@@ -426,6 +427,9 @@ class ValueSetExpander {
             if (!n.designation) {
               n.designation = [];
             }
+            if (t.source) {
+              this.reportedSupplements.add(t.source);
+            }
             n.designation.push(t.asObject());
           }
         }
@@ -490,9 +494,9 @@ class ValueSetExpander {
       const s = this.canonical(system, version);
       this.addParamUri(expansion, 'used-codesystem', s);
       if (cs) {
-        const ts= cs.listSupplements();
+        const ts= cs.listSupplements(false);
         for (const vs of ts) {
-          this.addParamUri(expansion, 'used-supplement', vs);
+          this.reportedSupplements.add(vs);
         }
       }
     }
@@ -813,7 +817,7 @@ class ValueSetExpander {
           this.worker.opContext.log('iterate concepts done');
         }
 
-        if (cset.filter) {
+        if (cset.filter && cset.filter.length > 0) {
           this.worker.opContext.log('prepare filters');
           const fcl = cset.filter;
           const prep = await cs.getPrepContext(true);
@@ -1040,10 +1044,9 @@ class ValueSetExpander {
     if (expansion) {
       const vs = this.canonical(await cs.system(), await cs.version());
       this.addParamUri(expansion, 'used-codesystem', vs);
-      const ts = cs.listSupplements();
+      const ts = cs.listSupplements(false);
       for (const v of ts) {
-        this.worker.deadCheck('processCodeAndDescendants');
-        this.addParamUri(expansion, 'used-supplement', v);
+        this.reportedSupplements.add(v);
       }
     }
 
@@ -1081,10 +1084,9 @@ class ValueSetExpander {
     if (expansion) {
       const vs = this.canonical(await cs.system(), await cs.version());
       this.addParamUri(expansion, 'used-codesystem', vs);
-      const ts= cs.listSupplements();
+      const ts= cs.listSupplements(false);
       for (const v of ts) {
-        this.worker.deadCheck('processCodeAndDescendants');
-        this.addParamUri(expansion, 'used-supplement', v);
+        this.reportedSupplements.add(v);
       }
     }
 
@@ -1303,6 +1305,11 @@ class ValueSetExpander {
       }
     }
 
+    const ts = this.reportedSupplements;
+    for (const v of ts) {
+      this.addParamUri(exp, 'used-supplement', v);
+    }
+
     this.worker.opContext.log('finish up');
 
     let list;

package/tx/workers/lookup.js

@@ -149,14 +149,15 @@ class LookupWorker extends TerminologyWorker {
 
       // check supplements
       const used = new Set();
-      this.checkSupplements(csProvider, null, txp.supplements, used);
+      const reported = new Set();
+      this.checkSupplements(csProvider, null, txp.supplements, used, reported);
       const unused = new Set([...txp.supplements].filter(s => !used.has(s)));
       if (unused.size > 0) {
         throw new Issue('error', 'not-found', null, 'VALUESET_SUPPLEMENT_MISSING', this.i18n.translatePlural(unused.size, 'VALUESET_SUPPLEMENT_MISSING', txp.HTTPLanguages, [[...unused].join(',')]), 'not-found').handleAsOO(400);
       }
 
       // Perform the lookup
-      const result = await this.doLookup(csProvider, code, txp);
+      const result = await this.doLookup(csProvider, code, txp, reported);
       return res.status(200).json(result);
     } catch (error) {
       this.log.error(error);
@@ -242,9 +243,10 @@ class LookupWorker extends TerminologyWorker {
    * @param {CodeSystemProvider} csProvider - CodeSystem provider
    * @param {string} code - Code to look up
    * @param {Object} params - Parsed parameters
+   * @param {Set} reportedSupplements - Set of supplements that are to be reported
    * @returns {Object} Parameters resource with lookup result
    */
-  async doLookup(csProvider, code, params) {
+  async doLookup(csProvider, code, params, reportedSupplements) {
     this.deadCheck('doLookup');
 
     await this.checkSupplements(csProvider, null, params.supplements);
@@ -352,6 +354,12 @@ class LookupWorker extends TerminologyWorker {
           this.deadCheck('doLookup-designations');
           const designationParts = [];
 
+          if (designation.supplement) {
+            designationParts.push({
+              name: 'source',
+              valueCanonical: designation.supplement.vurl
+            });
+          }
           if (designation.language) {
             designationParts.push({
               name: 'language',
@@ -382,6 +390,14 @@ class LookupWorker extends TerminologyWorker {
     // Let the provider add additional properties
     await csProvider.extendLookup(ctxt, params.properties || [], responseParams);
 
+    if (reportedSupplements) {
+      for (const supplement of reportedSupplements) {
+        responseParams.push({
+          name: 'used-supplement',
+          valueCanonical: supplement
+        });
+      }
+    }
     return {
       resourceType: 'Parameters',
       parameter: responseParams

package/tx/workers/read.js

@@ -90,11 +90,15 @@ class ReadWorker extends TerminologyWorker {
           resourceType: "CodeSystem",
           id: "x-" + cs.id(),
           url: cs.system(),
+          version: cs.version(),
           name: cs.name(),
           status: "active",
           description: "This is a place holder for the code system which is fully supported through internal means (not by this code system)",
           content: "not-present"
         }
+        if (cs.webSource()) {
+          json.extension = [{ url: "http://hl7.org/fhir/StructureDefinition/web-source", valueUrl : cs.webSource()}];
+        }
         if (cs.version()) {
           json.version = cs.version();
         }