Merge pull request hapifhir#1798 from hapifhir/2024-11-gg-pe-code-gen-2

2024 11 gg pe code gen 2

RELEASE_NOTES.md

@@ -1,7 +1,20 @@
 ## Validator Changes
 
-* no changes
+* Fix issue where valdiator not retaining extension context when checking constraint expressions in profiles
+* Validate min-length when found in extension
+* Correct bug parsing json-property-key values with meant validation failed
+* Fix problem validating json-property-key value pairs
+* Fix special case r5 loading of terminology to fix validation error on ExampleScenario
+* Improve handling of JSON format errors
 
 ## Other code changes
 
-* no changes
+* More work on code generation for profiles
+* Render min-length extension on profiles
+* Clone SQL on FHIR engine to R4, and update FHIRPath engine based on R5 current code
+* Update SQL on FHIR engine to allow push as well as pull
+* Change R5 tx server to use http://tx.fhir.org/r5 (instead of /r4)
+* Update output from tx-tester to include release ready statement
+* Fix rendering of Logical Models for polymorphic elements, and rendering target profiles with versions
+* Render contained resources in List resource
+* #1790 - Fix versionFromCanonical returns system instead and systemFromCanonical returns version

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/fhirpath/FHIRPathEngine.java

@@ -3621,11 +3621,35 @@ private TypeDetails evaluateFunctionType(ExecutionTypeContext context, TypeDetai
       ExpressionNode p = exp.getParameters().get(0);
       if (p.getKind() == Kind.Constant && p.getConstant() != null) {
         String url = exp.getParameters().get(0).getConstant().primitiveValue();
-        ExtensionDefinition ed = findExtensionDefinition(focus, url);
-        if (ed != null) {
-          return new TypeDetails(CollectionStatus.ORDERED, new ProfiledType(ed.sd.getUrl()));
+        if (!Utilities.isAbsoluteUrl(url) && focus.hasType("Extension")) {
+          TypeDetails res = new TypeDetails(CollectionStatus.ORDERED);
+          List<String> profiles = focus.getProfiles("Extension");
+          if (profiles != null) {
+            for (String pt : profiles) {
+              String extn = pt.contains("#") ? pt.substring(0, pt.indexOf("#")) : pt;
+              String subExtn = pt.contains("#") ? pt.substring(0, pt.indexOf("#")) : null;
+              StructureDefinition sd = worker.fetchResource(StructureDefinition.class, extn);
+              if (sd != null) {
+                String id = subExtn == null ? "Extension.extension:"+url : subExtn+".extension:"+url;
+                ElementDefinition ed = sd.getSnapshot().getElementById(id);
+                if (ed != null) {
+                  res.addType("Extension", sd.getUrl()+"#"+id);
+                }
+              }
+            }
+          }
+          if (res.isEmpty()) {
+            typeWarnings.add(new IssueMessage(worker.formatMessage(I18nConstants.FHIRPATH_UNKNOWN_EXTENSION, url), I18nConstants.FHIRPATH_UNKNOWN_EXTENSION));            
+          } else {
+            return res;
+          }
         } else {
-          typeWarnings.add(new IssueMessage(worker.formatMessage(I18nConstants.FHIRPATH_UNKNOWN_EXTENSION, url), I18nConstants.FHIRPATH_UNKNOWN_EXTENSION));
+          ExtensionDefinition ed = findExtensionDefinition(focus, url);
+          if (ed != null) {
+            return new TypeDetails(CollectionStatus.ORDERED, new ProfiledType(ed.sd.getUrl()));
+          } else {
+            typeWarnings.add(new IssueMessage(worker.formatMessage(I18nConstants.FHIRPATH_UNKNOWN_EXTENSION, url), I18nConstants.FHIRPATH_UNKNOWN_EXTENSION));
+          }
         }
         return new TypeDetails(CollectionStatus.SINGLETON, "Extension");
       }

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/fhirpath/TypeDetails.java

@@ -593,5 +593,17 @@ public void setChoice(boolean b) {
   public boolean isChoice() {
     return choice;
   }
+  public boolean isEmpty() {
+    return types.isEmpty();
+  }
+  public List<String> getProfiles(String t) {
+    t = ProfiledType.ns(t);
+    for (ProfiledType pt : types) {
+      if (t.equals(pt.uri)) {
+        return pt.getProfiles();
+      }
+    }
+    return new ArrayList<String>();
+  }
 
 }

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/profilemodel/PEBuilder.java

@@ -33,7 +33,9 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
 
 import org.apache.commons.lang3.NotImplementedException;
 import org.hl7.fhir.exceptions.DefinitionException;
+import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r4.conformance.ProfileUtilities;
+import org.hl7.fhir.r4.context.ContextUtilities;
 import org.hl7.fhir.r4.context.IWorkerContext;
 import org.hl7.fhir.r4.fhirpath.FHIRPathEngine;
 import org.hl7.fhir.r4.model.Base;
@@ -44,10 +46,14 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
 import org.hl7.fhir.r4.model.ElementDefinition.ElementDefinitionSlicingDiscriminatorComponent;
 import org.hl7.fhir.r4.model.ElementDefinition.SlicingRules;
 import org.hl7.fhir.r4.model.ElementDefinition.TypeRefComponent;
+import org.hl7.fhir.r4.model.Enumerations.BindingStrength;
 import org.hl7.fhir.r4.model.Resource;
 import org.hl7.fhir.r4.model.ResourceFactory;
 import org.hl7.fhir.r4.model.StructureDefinition;
 import org.hl7.fhir.r4.model.StructureDefinition.TypeDerivationRule;
+import org.hl7.fhir.r4.model.ValueSet;
+import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionContainsComponent;
+import org.hl7.fhir.r4.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
 import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
 import org.hl7.fhir.utilities.Utilities;
 
@@ -110,6 +116,7 @@ public enum PEElementPropertiesPolicy {
 
   private IWorkerContext context;
   private ProfileUtilities pu;
+  private ContextUtilities cu;
   private PEElementPropertiesPolicy elementProps;
   private boolean fixedPropsDefault;
   private FHIRPathEngine fpe;
@@ -124,6 +131,7 @@ public PEBuilder(IWorkerContext context, PEElementPropertiesPolicy elementProps,
     this.elementProps = elementProps;
     this.fixedPropsDefault = fixedPropsDefault;
     pu = new ProfileUtilities(context, null, null);
+    cu = new ContextUtilities(context);
     fpe = new FHIRPathEngine(context, pu);
   }
 
@@ -338,6 +346,9 @@ protected List<PEDefinition> listChildren(boolean allFixed, PEDefinition parent,
       List<PEDefinition> res = new ArrayList<>();
       if (list.size() == 0) {
         profile = context.fetchResource(StructureDefinition.class, url);
+        if (profile == null) {
+          throw new FHIRException("Unable to resolve profile "+url);
+        }
         list = pu.getChildList(profile, profile.getSnapshot().getElementFirstRep());
       }
       if (list.size() > 0) {
@@ -574,20 +585,42 @@ public String makeSliceExpression(StructureDefinition profile, ElementDefinition
         throw new DefinitionException("The discriminator type 'type' is not supported by the PEBuilder");
       case VALUE:
         String path = d.getPath();
-        if (path.contains(".")) {
-          throw new DefinitionException("The discriminator path '"+path+"' is not supported by the PEBuilder");          
-        }
         ElementDefinition ed = getChildElement(profile, definition, path);
         if (ed == null) {
           throw new DefinitionException("The discriminator path '"+path+"' could not be resolved by the PEBuilder");          
         }
-        if (!ed.hasFixed()) {
-          throw new DefinitionException("The discriminator path '"+path+"' has no fixed value - this is not supported by the PEBuilder");          
-        }
-        if (!ed.getFixed().isPrimitive()) {
-          throw new DefinitionException("The discriminator path '"+path+"' has a fixed value that is not a primitive ("+ed.getFixed().fhirType()+") - this is not supported by the PEBuilder");          
+        // three things possible:
+        //  fixed, pattern, or binding
+        if (ed.hasFixed()) {
+          if (!ed.getFixed().isPrimitive()) {
+            throw new DefinitionException("The discriminator path '"+path+"' has a fixed value that is not a primitive ("+ed.getFixed().fhirType()+") - this is not supported by the PEBuilder");          
+          }
+          b.append(path+" = '"+ed.getFixed().primitiveValue()+"'");
+        } else if (ed.hasPattern()) {
+          throw new DefinitionException("The discriminator path '"+path+"' has a pattern on the element '"+ed.getId()+"' - this is not supported by the PEBuilder");
+        } else if (ed.hasBinding()) {
+          if (ed.getBinding().getStrength() != BindingStrength.REQUIRED) {
+            throw new DefinitionException("The discriminator path '"+path+"' has a binding on the element '"+ed.getId()+"' but the strength is not required - this is not supported by the PEBuilder");
+          } else {
+            ValueSet vs = context.fetchResource(ValueSet.class, ed.getBinding().getValueSet());
+            if (vs == null) {
+              throw new DefinitionException("The discriminator path '"+path+"' has a binding on the element '"+ed.getId()+"' but the valueSet '"+ed.getBinding().getValueSet()+"' is not known - this is not supported by the PEBuilder");              
+            }
+            ValueSetExpansionOutcome exp = context.expandVS(vs, true, false);
+            if (exp.isOk()) {
+              CommaSeparatedStringBuilder bs = new CommaSeparatedStringBuilder(" | ");
+              for (ValueSetExpansionContainsComponent cc : exp.getValueset().getExpansion().getContains()) {
+                bs.append("'"+cc.getCode()+"'");
+              }
+              b.append(path+" in ("+bs.toString()+")");
+            } else {
+              throw new DefinitionException("The discriminator path '"+path+"' has a binding on the element '"+ed.getId()+"' but the valueSet '"+ed.getBinding().getValueSet()+"' could not be expanded: "+exp.getError());                            
+            }            
+          }
+        } else {
+          throw new DefinitionException("The discriminator path '"+path+"' has no fixed or pattern value or a binding on the element '"+ed.getId()+"' - this is not supported by the PEBuilder");          
+
         }
-        b.append(path+" = '"+ed.getFixed().primitiveValue()+"'");
         break;
       case NULL:
         throw new DefinitionException("The discriminator type 'null' is not supported by the PEBuilder");
@@ -599,20 +632,33 @@ public String makeSliceExpression(StructureDefinition profile, ElementDefinition
   }
 
   private ElementDefinition getChildElement(StructureDefinition profile, ElementDefinition definition, String path) {
-    List<ElementDefinition> elements = pu.getChildList(profile, definition);
-    if (elements.size() == 0) {
-      profile = definition.getTypeFirstRep().hasProfile() ? context.fetchResource(StructureDefinition.class, definition.getTypeFirstRep().getProfile().get(0).asStringValue()) :
-        context.fetchTypeDefinition(definition.getTypeFirstRep().getWorkingCode());
-      elements = pu.getChildList(profile, profile.getSnapshot().getElementFirstRep());
-    }
-    return getByName(elements, path);
+    String head = path.contains(".") ? path.substring(0, path.indexOf(".")) : path;
+    String tail = path.contains(".") ? path.substring(path.indexOf(".")+1) : null;
+    ElementDefinition focus = definition;
+
+    do {
+      List<ElementDefinition> elements = pu.getChildList(profile, focus);
+      if (elements.size() == 0) {
+        profile = focus.getTypeFirstRep().hasProfile() ? context.fetchResource(StructureDefinition.class, focus.getTypeFirstRep().getProfile().get(0).asStringValue()) :
+          context.fetchTypeDefinition(focus.getTypeFirstRep().getWorkingCode());
+        elements = pu.getChildList(profile, profile.getSnapshot().getElementFirstRep());
+      }
+      focus = getByName(elements, head);
+      if (tail != null) {
+        head = tail.contains(".") ? tail.substring(0, tail.indexOf(".")) : tail;
+        tail = tail.contains(".") ? tail.substring(tail.indexOf(".")+1) : null;
+      } else {
+        head = null;
+      }
+    } while (head != null && focus != null);
+    return focus;
   }
 
   public List<Base> exec(Resource resource, Base data, String fhirpath) {
     return fpe.evaluate(this, resource, resource, data, fhirpath);
   }
 
   public boolean isResource(String name) {
-    return context.getResourceNamesAsSet().contains(name);
+    return cu.isResource(name);
   }
 }

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/profilemodel/PEInstance.java

@@ -299,10 +299,16 @@ public IWorkerContext getContext() {
   }
 
   public Base addChild(String name, Type value) {
-      PEDefinition child = byName(definition.children(), name);
-      Base b = data.setProperty(child.schemaName(), value);
-      return b;
-  }
+    PEDefinition child = byName(definition.children(), name);
+    Base b = data.setProperty(child.schemaName(), value);
+    return b;
+}
+
+  public Base addChild(String name, Resource value) {
+    PEDefinition child = byName(definition.children(), name);
+    Base b = data.setProperty(child.schemaName(), value);
+    return b;
+}
 
   public Base addChild(String name, BackboneElement value) {
       PEDefinition child = byName(definition.children(), name);