First slice AK HIV changes (cqframework#491)

* Fix codesystem parsing bug in accelerator kit processor. * Added extension handling for test case example builder. --------- Co-authored-by: ZackAustin <[email protected]>
echicoine-icf · Nov 29, 2023 · 103bba8 · 103bba8
1 parent a3e7544
commit 103bba8
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Showing 3 changed files with 38 additions and 12 deletions.
diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/acceleratorkit/CanonicalResourceAtlas.java b/tooling/src/main/java/org/opencds/cqf/tooling/acceleratorkit/CanonicalResourceAtlas.java
@@ -1,9 +1,6 @@
 package org.opencds.cqf.tooling.acceleratorkit;
 
-import org.hl7.fhir.r4.model.ConceptMap;
-import org.hl7.fhir.r4.model.CodeSystem;
-import org.hl7.fhir.r4.model.StructureDefinition;
-import org.hl7.fhir.r4.model.ValueSet;
+import org.hl7.fhir.r4.model.*;
 
 public class CanonicalResourceAtlas {
     private CanonicalResourceProvider<StructureDefinition> structureDefinitions;
@@ -41,4 +38,13 @@ public CanonicalResourceAtlas setConceptMaps(CanonicalResourceProvider<ConceptMa
         this.conceptMaps = conceptMaps;
         return this;
     }
+
+    private CanonicalResourceProvider<StructureDefinition> extensions;
+    public CanonicalResourceProvider<StructureDefinition> getExtensions() {
+        return extensions;
+    }
+    public CanonicalResourceAtlas setExtensions(CanonicalResourceProvider<StructureDefinition> extensions) {
+        this.extensions = extensions;
+        return this;
+    }
 }
diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/acceleratorkit/ExampleBuilder.java b/tooling/src/main/java/org/opencds/cqf/tooling/acceleratorkit/ExampleBuilder.java
@@ -7,10 +7,7 @@
 import java.time.Instant;
 import java.time.LocalDate;
 import java.time.LocalDateTime;
-import java.util.Date;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 import java.util.concurrent.atomic.AtomicReference;
 
 public class ExampleBuilder {
@@ -378,7 +375,14 @@ private void visitElement(StructureDefinition sd, List<ElementDefinition> eds, A
             extension.setValue((Type)elementValue);
             elementValue = extension;
         }
-        value.setProperty(getElementName(ed.getPath()), elementValue);
+        if (!elementName.equals("extension")) {
+            value.setProperty(getElementName(ed.getPath()), elementValue);
+        }
+        else {
+            Extension subExtension = (Extension) ((Extension) elementValue).getValue();
+            subExtension.setUrl(((Extension) elementValue).getUrl());
+            value.setProperty(getElementName(ed.getPath()), subExtension);
+        }
 
         index.set(index.get() + 1);
         while (index.get() < eds.size()) {
@@ -677,6 +681,21 @@ else if (value instanceof CodeableConcept) {
                         .setDisplay("Example");
             }
         }
+        else if (value instanceof Extension) {
+            if (ed.getType("Extension") != null && ed.getType("Extension").getProfile() != null && atlas != null && atlas.getValueSets() != null && atlas.getExtensions() != null) {
+                StructureDefinition sdExtension = atlas.getExtensions().getByCanonicalUrlWithVersion(ed.getType("Extension").getProfile().get(0).getValue());
+                ElementDefinition extensionElement = sdExtension.getDifferential().getElement().stream()
+                    .filter(x -> x.hasBinding() && x.getBinding().hasValueSetElement()).findFirst().get();
+
+                Type extensionValue = null;
+                if (extensionElement.getType("CodeableConcept") != null) {
+                    extensionValue = new CodeableConcept();
+                }
+
+                generateValue(sdExtension, extensionElement, extensionValue, givenValue);
+                value.addExtension(new Extension().setUrl(extensionElement.getShort()).setValue(extensionValue));
+            }
+        }
     }
 
     private void buildElements(StructureDefinition sd, Resource r, Map<String, Object> elementValues) {

diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/acceleratorkit/Processor.java b/tooling/src/main/java/org/opencds/cqf/tooling/acceleratorkit/Processor.java
@@ -575,14 +575,14 @@ private String getCodeComments(Row row, HashMap<String, Integer> colIds, String
     }
 
     private String getCodeSystemCommentColName(String codeSystem) {
-        switch (codeSystem) {
+        switch (codeSystem.toUpperCase()) {
             case "ICD-10": return "ICD-10Comments";
             case "ICD-11": return "ICD-11Comments";
             case "ICHI": return "ICHIComments";
             case "ICF": return "ICFComments";
             case "SNOMED-CT": return "SNOMEDComments";
             case "LOINC": return "LOINCComments";
-            case "RXNorm": return "RXNormComments";
+            case "RXNORM": return "RXNormComments";
             case "CPT": return "CPTComments";
             case "HCPCS": return "HCPCSComments";
             case "NDC": return "NDCComments";
@@ -2549,7 +2549,8 @@ private CanonicalResourceAtlas getAtlas() {
                     new CanonicalResourceAtlas()
                             .setValueSets(new InMemoryCanonicalResourceProvider<ValueSet>(this.valueSets))
                             .setCodeSystems(new InMemoryCanonicalResourceProvider<CodeSystem>(this.codeSystems))
-                            .setConceptMaps(new InMemoryCanonicalResourceProvider<ConceptMap>(this.conceptMaps.values()));
+                            .setConceptMaps(new InMemoryCanonicalResourceProvider<ConceptMap>(this.conceptMaps.values()))
+                            .setExtensions(new InMemoryCanonicalResourceProvider<StructureDefinition>(this.extensions));
         }
         return atlas;
     }