Add optional argument for making clone of predefined resources

src/fhirdefs/FHIRDefinitions.ts

@@ -35,8 +35,12 @@ export class FHIRDefinitions extends BaseFHIRDefinitions implements Fishable {
     return flatten(Array.from(this.supplementalFHIRDefinitions.keys()));
   }
 
-  allPredefinedResources(): any[] {
-    return Array.from(this.predefinedResources.values()).map(v => cloneDeep(v));
+  allPredefinedResources(makeClone = true): any[] {
+    if (makeClone) {
+      return Array.from(this.predefinedResources.values()).map(v => cloneDeep(v));
+    } else {
+      return Array.from(this.predefinedResources.values());
+    }
   }
 
   add(definition: any): void {
@@ -81,7 +85,7 @@ export class FHIRDefinitions extends BaseFHIRDefinitions implements Fishable {
     const resource = this.fishForFHIR(item, ...types);
     if (
       resource &&
-      this.allPredefinedResources().find(
+      this.allPredefinedResources(false).find(
         predefResource =>
           predefResource.id === resource.id &&
           predefResource.resourceType === resource.resourceType &&

src/fhirtypes/ElementDefinition.ts

@@ -774,11 +774,12 @@ export class ElementDefinition {
 
   getSlices() {
     if (this.sliceName) {
-      return this.structDef.elements.filter(
+      // this.parent() should never be undefined if this element has a sliceName, but code defensively just in case
+      return (this.parent()?.children(true) ?? this.structDef.elements).filter(
         e => e.id !== this.id && e.path === this.path && e.id.startsWith(`${this.id}/`)
       );
     } else {
-      return this.structDef.elements.filter(
+      return (this.parent()?.children(true) ?? this.structDef.elements).filter(
         e => e.id !== this.id && e.path === this.path && e.id.startsWith(`${this.id}:`)
       );
     }
@@ -898,12 +899,14 @@ export class ElementDefinition {
     const slicedElement = this.slicedElement();
     if (slicedElement) {
       const parentSlice = this.findParentSlice();
-      const sliceSiblings = this.structDef.elements.filter(
-        el =>
-          this !== el &&
-          slicedElement === el.slicedElement() &&
-          parentSlice === el.findParentSlice()
-      );
+      const sliceSiblings = this.parent()
+        .children(true)
+        .filter(
+          el =>
+            this !== el &&
+            slicedElement === el.slicedElement() &&
+            parentSlice === el.findParentSlice()
+        );
       const newParentMin = min + sliceSiblings.reduce((sum, el) => sum + el.min, 0);
       // if this is a reslice, the parent element will also be a slice of the sliced element.
       // if this is not a reslice, the parent element is the sliced element.
@@ -985,8 +988,9 @@ export class ElementDefinition {
           return parentNameParts.slice(0, i + 1).join('/');
         })
         .reverse();
+      const elementsToSearch = this.parent()?.children(true) ?? this.structDef.elements;
       for (const parentName of potentialParentNames) {
-        const potentialParent = this.structDef.elements.find(el => {
+        const potentialParent = elementsToSearch.find(el => {
           return el.sliceName === parentName && el.slicedElement() === slicedElement;
         });
         if (potentialParent) {
@@ -2586,7 +2590,9 @@ export class ElementDefinition {
    */
   slicedElement(): ElementDefinition | undefined {
     if (this.sliceName) {
-      return this.structDef.elements.find(e => e.id === this.id.slice(0, this.id.lastIndexOf(':')));
+      return (this.parent()?.children(true) ?? this.structDef.elements).find(
+        e => e.id === this.id.slice(0, this.id.lastIndexOf(':'))
+      );
     }
   }
 

src/utils/Processing.ts

@@ -543,7 +543,7 @@ export function writeFHIRResources(
   logger.info('Exporting FHIR resources as JSON...');
   let count = 0;
   const skippedResources: string[] = [];
-  const predefinedResources = defs.allPredefinedResources();
+  const predefinedResources = defs.allPredefinedResources(false);
   const writeResources = (
     resources: {
       getFileName: () => string;