Merge branch 'master' into ValueSet-display-names

org.hl7.fhir.convertors/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>3.7.37-SNAPSHOT</version>
+        <version>3.7.38-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

org.hl7.fhir.dstu2/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>3.7.37-SNAPSHOT</version>
+		<version>3.7.38-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

org.hl7.fhir.dstu2016may/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>3.7.37-SNAPSHOT</version>
+		<version>3.7.38-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

org.hl7.fhir.dstu3/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>3.7.37-SNAPSHOT</version>
+        <version>3.7.38-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

org.hl7.fhir.r4/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>3.7.37-SNAPSHOT</version>
+		<version>3.7.38-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

org.hl7.fhir.r5/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>3.7.37-SNAPSHOT</version>
+		<version>3.7.38-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java

@@ -800,8 +800,12 @@ public abstract class BaseWorkerContext implements IWorkerContext {
   public Resource fetchResourceById(String type, String uri) {
     synchronized (lock) {
       String[] parts = uri.split("\\/");
-      if (!Utilities.noString(type) && parts.length == 1)
+      if (!Utilities.noString(type) && parts.length == 1) {
-        return allResourcesById.get(type).get(parts[0]);
+        if (allResourcesById.containsKey(type))
+          return allResourcesById.get(type).get(parts[0]);
+        else
+          return null;
+      }
       if (parts.length >= 2) {
         if (!Utilities.noString(type))
           if (!type.equals(parts[parts.length-2])) 

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/Constants.java

@@ -59,4 +59,5 @@ public class Constants {
   public final static String BUILD_ID = "e0e3caf9ba";
   public final static String DATE = "Thu Dec 13 14:07:26 AEDT 2018";
   public final static String URI_REGEX = "((http|https)://([A-Za-z0-9\\\\\\.\\:\\%\\$]*\\/)*)?(Account|ActivityDefinition|AdverseEvent|AllergyIntolerance|Appointment|AppointmentResponse|AuditEvent|Basic|Binary|BiologicallyDerivedProduct|BodyStructure|Bundle|CapabilityStatement|CarePlan|CareTeam|CatalogEntry|ChargeItem|ChargeItemDefinition|Claim|ClaimResponse|ClinicalImpression|CodeSystem|Communication|CommunicationRequest|CompartmentDefinition|Composition|ConceptMap|Condition|Consent|Contract|Coverage|CoverageEligibilityRequest|CoverageEligibilityResponse|DetectedIssue|Device|DeviceDefinition|DeviceMetric|DeviceRequest|DeviceUseStatement|DiagnosticReport|DocumentManifest|DocumentReference|EffectEvidenceSynthesis|Encounter|Endpoint|EnrollmentRequest|EnrollmentResponse|EpisodeOfCare|EventDefinition|Evidence|EvidenceVariable|ExampleScenario|ExplanationOfBenefit|FamilyMemberHistory|Flag|Goal|GraphDefinition|Group|GuidanceResponse|HealthcareService|ImagingStudy|Immunization|ImmunizationEvaluation|ImmunizationRecommendation|ImplementationGuide|InsurancePlan|Invoice|Library|Linkage|List|Location|Measure|MeasureReport|Media|Medication|MedicationAdministration|MedicationDispense|MedicationKnowledge|MedicationRequest|MedicationStatement|MedicinalProduct|MedicinalProductAuthorization|MedicinalProductContraindication|MedicinalProductIndication|MedicinalProductIngredient|MedicinalProductInteraction|MedicinalProductManufactured|MedicinalProductPackaged|MedicinalProductPharmaceutical|MedicinalProductUndesirableEffect|MessageDefinition|MessageHeader|MolecularSequence|NamingSystem|NutritionOrder|Observation|ObservationDefinition|OperationDefinition|OperationOutcome|Organization|OrganizationAffiliation|Patient|PaymentNotice|PaymentReconciliation|Person|PlanDefinition|Practitioner|PractitionerRole|Procedure|Provenance|Questionnaire|QuestionnaireResponse|RelatedPerson|RequestGroup|ResearchDefinition|ResearchElementDefinition|ResearchStudy|ResearchSubject|RiskAssessment|RiskEvidenceSynthesis|Schedule|SearchParameter|ServiceRequest|Slot|Specimen|SpecimenDefinition|StructureDefinition|StructureMap|Subscription|Substance|SubstanceNucleicAcid|SubstancePolymer|SubstanceProtein|SubstanceReferenceInformation|SubstanceSourceMaterial|SubstanceSpecification|SupplyDelivery|SupplyRequest|Task|TerminologyCapabilities|TestReport|TestScript|ValueSet|VerificationResult|VisionPrescription)\\/[A-Za-z0-9\\-\\.]{1,64}(\\/_history\\/[A-Za-z0-9\\-\\.]{1,64})?";
+  public final static String LOCAL_REF_REGEX = "(Account|ActivityDefinition|AdverseEvent|AllergyIntolerance|Appointment|AppointmentResponse|AuditEvent|Basic|Binary|BiologicallyDerivedProduct|BodyStructure|Bundle|CapabilityStatement|CarePlan|CareTeam|CatalogEntry|ChargeItem|ChargeItemDefinition|Claim|ClaimResponse|ClinicalImpression|CodeSystem|Communication|CommunicationRequest|CompartmentDefinition|Composition|ConceptMap|Condition|Consent|Contract|Coverage|CoverageEligibilityRequest|CoverageEligibilityResponse|DetectedIssue|Device|DeviceDefinition|DeviceMetric|DeviceRequest|DeviceUseStatement|DiagnosticReport|DocumentManifest|DocumentReference|EffectEvidenceSynthesis|Encounter|Endpoint|EnrollmentRequest|EnrollmentResponse|EpisodeOfCare|EventDefinition|Evidence|EvidenceVariable|ExampleScenario|ExplanationOfBenefit|FamilyMemberHistory|Flag|Goal|GraphDefinition|Group|GuidanceResponse|HealthcareService|ImagingStudy|Immunization|ImmunizationEvaluation|ImmunizationRecommendation|ImplementationGuide|InsurancePlan|Invoice|Library|Linkage|List|Location|Measure|MeasureReport|Media|Medication|MedicationAdministration|MedicationDispense|MedicationKnowledge|MedicationRequest|MedicationStatement|MedicinalProduct|MedicinalProductAuthorization|MedicinalProductContraindication|MedicinalProductIndication|MedicinalProductIngredient|MedicinalProductInteraction|MedicinalProductManufactured|MedicinalProductPackaged|MedicinalProductPharmaceutical|MedicinalProductUndesirableEffect|MessageDefinition|MessageHeader|MolecularSequence|NamingSystem|NutritionOrder|Observation|ObservationDefinition|OperationDefinition|OperationOutcome|Organization|OrganizationAffiliation|Patient|PaymentNotice|PaymentReconciliation|Person|PlanDefinition|Practitioner|PractitionerRole|Procedure|Provenance|Questionnaire|QuestionnaireResponse|RelatedPerson|RequestGroup|ResearchDefinition|ResearchElementDefinition|ResearchStudy|ResearchSubject|RiskAssessment|RiskEvidenceSynthesis|Schedule|SearchParameter|ServiceRequest|Slot|Specimen|SpecimenDefinition|StructureDefinition|StructureMap|Subscription|Substance|SubstanceNucleicAcid|SubstancePolymer|SubstanceProtein|SubstanceReferenceInformation|SubstanceSourceMaterial|SubstanceSpecification|SupplyDelivery|SupplyRequest|Task|TerminologyCapabilities|TestReport|TestScript|ValueSet|VerificationResult|VisionPrescription)\\/[A-Za-z0-9\\-\\.]{1,64}";
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/DomainResource.java

@@ -447,47 +447,59 @@ Modifier extensions SHALL NOT change the meaning of any elements on Resource or
 
 // added from java-adornments.txt:
 
-  public void checkNoModifiers(String noun, String verb) throws FHIRException {
+      public void checkNoModifiers(String noun, String verb) throws FHIRException {
         if (hasModifierExtension()) {
           throw new FHIRException("Found unknown Modifier Exceptions on "+noun+" doing "+verb);
         }
+
+      }
+
+      public void addExtension(String url, Type value) {
+        Extension ex = new Extension();
+        ex.setUrl(url);
+        ex.setValue(value);
+        getExtension().add(ex);    
+      }
+
+
+
+
+      public boolean hasExtension(String url) {
+        for (Extension e : getExtension())
+          if (url.equals(e.getUrl()))
+            return true;
+        return false;
+      }
+
+      public Extension getExtensionByUrl(String theUrl) {
+        org.apache.commons.lang3.Validate.notBlank(theUrl, "theUrl must not be blank or null");
+        ArrayList<Extension> retVal = new ArrayList<Extension>();
+        for (Extension next : getExtension()) {
+          if (theUrl.equals(next.getUrl())) {
+            retVal.add(next);
+          }
+        }
+        if (retVal.size() == 0)
+          return null;
+        else {
+          org.apache.commons.lang3.Validate.isTrue(retVal.size() == 1, "Url "+theUrl+" must have only one match");
+          return retVal.get(0);
+        }
+      }
+
+
+      public Resource getContained(String ref) {
+        if (ref == null)
+          return null;
         
-  }
+        if (ref.startsWith("#"))
-
+          ref = ref.substring(1);
-  public void addExtension(String url, Type value) {
+        for (Resource r : getContained()) {
-    Extension ex = new Extension();
+          if (r.getId().equals(ref)) 
-    ex.setUrl(url);
+            return r;
-    ex.setValue(value);
+        }
-    getExtension().add(ex);    
+        return null;
-  }
+      }
-  
-
-
-
-  public boolean hasExtension(String url) {
-    for (Extension e : getExtension())
-      if (url.equals(e.getUrl()))
-        return true;
-    return false;
-    }
-    
-       public Extension getExtensionByUrl(String theUrl) {
-     org.apache.commons.lang3.Validate.notBlank(theUrl, "theUrl must not be blank or null");
-     ArrayList<Extension> retVal = new ArrayList<Extension>();
-     for (Extension next : getExtension()) {
-       if (theUrl.equals(next.getUrl())) {
-         retVal.add(next);
-       }
-     }
-     if (retVal.size() == 0)
-       return null;
-     else {
-       org.apache.commons.lang3.Validate.isTrue(retVal.size() == 1, "Url "+theUrl+" must have only one match");
-       return retVal.get(0);
-     }
-   }
-  
-
 
 // end addition
 

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/StructureDefinition.java

@@ -3885,6 +3885,5 @@ public class StructureDefinition extends MetadataResource {
    */
   public static final ca.uhn.fhir.model.api.Include INCLUDE_BASE = new ca.uhn.fhir.model.api.Include("StructureDefinition:base").toLocked();
 
-
 }
 

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/NarrativeGenerator.java

@@ -3369,7 +3369,7 @@ public class NarrativeGenerator implements INarrativeGenerator {
     return "??Lang";
   }
  
-  private boolean addDefineRowToTable(XhtmlNode t, ConceptDefinitionComponent c, int i, boolean hasHierarchy, boolean hasDisplay, boolean comment, boolean version, boolean deprecated, List<UsedConceptMap> maps, String system, CodeSystem cs, String lang) {
+  private boolean addDefineRowToTable(XhtmlNode t, ConceptDefinitionComponent c, int i, boolean hasHierarchy, boolean hasDisplay, boolean comment, boolean version, boolean deprecated, List<UsedConceptMap> maps, String system, CodeSystem cs, String lang) throws FHIRFormatError, DefinitionException, IOException {
     boolean hasExtensions = false;
     XhtmlNode tr = t.tr();
     XhtmlNode td = tr.td();
@@ -3417,7 +3417,10 @@ public class NarrativeGenerator implements INarrativeGenerator {
     if (c != null && 
         c.hasDefinitionElement()) {
       if (lang == null) {
-        td.addText(c.getDefinition());
+        if (hasMarkdownInDefinitions(cs))
+          addMarkdown(td, c.getDefinition());
+        else
+          td.addText(c.getDefinition());
       } else if (lang.equals("*")) {
         boolean sl = false;
         for (ConceptDefinitionDesignationComponent cd : c.getDesignation()) 
@@ -3534,6 +3537,10 @@ public class NarrativeGenerator implements INarrativeGenerator {
   }
 
 
+  private boolean hasMarkdownInDefinitions(CodeSystem cs) {
+    return ToolingExtensions.readBoolExtension(cs, "http://hl7.org/fhir/StructureDefinition/codesystem-use-markdown");
+  }
+
   private String makeAnchor(String codeSystem, String code) {
     String s = codeSystem+'-'+code;
     StringBuilder b = new StringBuilder();

org.hl7.fhir.utilities/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>3.7.37-SNAPSHOT</version>
+        <version>3.7.38-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

org.hl7.fhir.validation.cli/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>3.7.37-SNAPSHOT</version>
+        <version>3.7.38-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

org.hl7.fhir.validation/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>3.7.37-SNAPSHOT</version>
+        <version>3.7.38-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r4/validation/InstanceValidator.java

@@ -2759,12 +2759,12 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
         vs = null;
       }
       if (vs != null) {
-        if (rule(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), vs.hasCompose() && !vs.hasExpansion(), "CodeSystem "+url+" has a 'all system' value set of "+vsu+", but it is an expansion"))
+        warning(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), vs.hasCompose() && !vs.hasExpansion(), "CodeSystem "+url+" has a 'all system' value set of "+vsu+", and contains an expansion");
-          if (rule(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), vs.getCompose().getInclude().size() == 1, "CodeSystem "+url+" has a 'all system' value set of "+vsu+", but doesn't have a single include"))
+        if (rule(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), vs.getCompose().getInclude().size() == 0, "CodeSystem "+url+" has a 'all system' value set of "+vsu+", but doesn't have an include"))
-            if (rule(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), vs.getCompose().getInclude().get(0).getSystem().equals(url), "CodeSystem "+url+" has a 'all system' value set of "+vsu+", but doesn't have a matching system ("+vs.getCompose().getInclude().get(0).getSystem()+")")) {
+          if (rule(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), vs.getCompose().getInclude().get(0).getSystem().equals(url), "CodeSystem "+url+" has a 'all system' value set of "+vsu+", but doesn't have a matching system ("+vs.getCompose().getInclude().get(0).getSystem()+")")) {
-              rule(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), !vs.getCompose().getInclude().get(0).hasValueSet()
+            if (rule(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), !vs.getCompose().getInclude().get(0).hasValueSet() && !vs.getCompose().getInclude().get(0).hasConcept(), "CodeSystem "+url+" has a 'all system' value set of "+vsu+", but the include has extra details"))
-                   && !vs.getCompose().getInclude().get(0).hasConcept() && !vs.getCompose().getInclude().get(0).hasFilter(), "CodeSystem "+url+" has a 'all system' value set of "+vsu+", but the include has extra details");
+              warning(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), !vs.getCompose().getInclude().get(0).hasFilter(), "CodeSystem "+url+" has a 'all system' value set of "+vsu+", but the include involves filters");
-            }
+          }
       } 
     } // todo... try getting the value set the other way...
   }

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/InstanceValidator.java

@@ -392,11 +392,11 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
           if (!ok)
             errors.add(new ValidationMessage(Source.InstanceValidator, IssueType.UNKNOWN, path, "Profile mismatch on type for "+profile.getProfile()+": the profile constrains "+sd.getType()+" but the element is "+element.fhirType(), IssueSeverity.ERROR));
         } else 
-          addProfile(errors, profile.getProfile(), profile.isError(), path, element);          
+          addProfile(errors, profile.getProfile(), profile.isError(), path, element, sd);          
       }
     }
     
-    public boolean addProfile(List<ValidationMessage> errors, String profile, boolean error, String path, Element element) {
+    public boolean addProfile(List<ValidationMessage> errors, String profile, boolean error, String path, Element element, StructureDefinition containingProfile) {
       String effectiveProfile = profile;
       String version = null;
       if (profile.contains("|")) {
@@ -404,10 +404,22 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
         version = profile.substring(profile.indexOf('|')+1);
       }
       StructureDefinition sd = null;
-      if (providedProfiles != null)
+      if (profile.startsWith("#")) {
-        sd = providedProfiles.fetch(effectiveProfile);
+        if (!rule(errors, IssueType.INVALID, element.line(), element.col(), path, sd != null, "StructureDefinition reference \"{0}\" is local, but there is not local context", profile)) {
-      if (sd == null)
+          return false;
-        sd = context.fetchResource(StructureDefinition.class, effectiveProfile);
+        }
+          
+        if (containingProfile.hasUserData("container"))
+          containingProfile = (StructureDefinition) containingProfile.getUserData("container");
+        sd = (StructureDefinition) containingProfile.getContained(profile);
+        if (sd != null)
+          sd.setUserData("container", containingProfile);
+      } else {
+        if (providedProfiles != null)
+          sd = providedProfiles.fetch(effectiveProfile);
+        if (sd == null)
+          sd = context.fetchResource(StructureDefinition.class, effectiveProfile);
+      }
       
       if (warningOrError(error, errors, IssueType.INVALID, element.line(), element.col(), path, sd != null, "StructureDefinition reference \"{0}\" could not be resolved", profile)) {
         if (rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, version==null || (sd.getVersion()!=null && sd.getVersion().equals(version)), 
@@ -1180,7 +1192,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
         String p = stack.addToLiteralPath("meta", "profile", ":" + Integer.toString(i));
         if (rule(errors, IssueType.INVALID, element.line(), element.col(), p, !Utilities.noString(ref), "StructureDefinition reference invalid")) {
           long t = System.nanoTime();
-          resourceProfiles.addProfile(errors, ref, errorForUnknownProfiles, p, element);
+          resourceProfiles.addProfile(errors, ref, errorForUnknownProfiles, p, element, null);
           i++;
         }
       }
@@ -1859,7 +1871,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
                 b.append(bt);
                 ok = bt.equals(ft);
                 if (ok && we!=null && pol.checkValid()) {
-                  doResourceProfile(hostContext, we, pr, errors, stack.push(we, -1, null, null), path, element);
+                  doResourceProfile(hostContext, we, pr, errors, stack.push(we, -1, null, null), path, element, profile);
                 }
               } else
                 ok = true; // suppress following check
@@ -1909,8 +1921,8 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     }
   }
 
-  private void doResourceProfile(ValidatorHostContext hostContext, Element resource, String profile, List<ValidationMessage> errors, NodeStack stack, String path, Element element) throws FHIRException, IOException {
+  private void doResourceProfile(ValidatorHostContext hostContext, Element resource, String profile, List<ValidationMessage> errors, NodeStack stack, String path, Element element, StructureDefinition containingProfile) throws FHIRException, IOException {
-    ResourceProfiles resourceProfiles = addResourceProfile(errors, resource, profile, path, element, stack);
+    ResourceProfiles resourceProfiles = addResourceProfile(errors, resource, profile, path, element, stack, containingProfile);
     if (resourceProfiles.isProcessed()) {
       start(hostContext, errors, resource, resource, null, stack);
     }
@@ -1925,9 +1937,9 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     return resourceProfiles;
   }
 
-  private ResourceProfiles addResourceProfile(List<ValidationMessage> errors, Element resource, String profile, String path, Element element, NodeStack stack) {
+  private ResourceProfiles addResourceProfile(List<ValidationMessage> errors, Element resource, String profile, String path, Element element, NodeStack stack, StructureDefinition containingProfile) {
     ResourceProfiles resourceProfiles = getResourceProfiles(resource, stack);
-    resourceProfiles.addProfile(errors, profile, errorForUnknownProfiles, path, element);
+    resourceProfiles.addProfile(errors, profile, errorForUnknownProfiles, path, element, containingProfile);
     return resourceProfiles;
   }
 

org.hl7.fhir.validation/src/test/resources/validation-examples/manifest.json

@@ -561,14 +561,21 @@
           "errorCount": 16
         }
       },
-       "patient-translated-codes.xml" : {
+      "patient-translated-codes.xml" : {
         "errorCount": 0,
         "warningCount": 4,
         "profile" : {
           "source" : "patient-translated-codes.profile.xml", 
           "errorCount": 0,
           "warningCount": 0
-        }
+      },
+      "patient-contained-org.xml" : {
+         "errorCount": 0,
+         "profile" : {
+           "source" : "patient-contained-org-profile.xml", 
+           "errorCount": 1
+         }
+        } 
       }
     }
 	}

org.hl7.fhir.validation/src/test/resources/validation-examples/patient-contained-org-profile.xml

@@ -0,0 +1,48 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<StructureDefinition xmlns="http://hl7.org/fhir">
+  <id value="patient-contained-org-profile"/>
+  <contained>
+    <StructureDefinition>
+      <id value="gp"/>
+      <url value="http://hl7.org/fhir/patient-contained-org-org-profile"/>
+      <name value="PatientContainedOrgOrg"/>
+      <status value="draft"/>
+      <kind value="resource"/>
+      <abstract value="false"/>
+      <type value="Organization"/>
+      <baseDefinition value="http://hl7.org/fhir/StructureDefinition/Organization"/>
+      <derivation value="constraint"/>
+      <differential>
+        <element id="Organization">
+          <path value="Organization"/>
+        </element>
+        <element id="Organization.name">
+          <path value="Organization.name"/>
+          <min value="1"/>
+        </element>
+      </differential>
+    </StructureDefinition>
+  </contained>
+  <url value="http://hl7.org/fhir/StructureDefinition/patient-contained-gp-profile"/>
+  <name value="PatientContainedOrgProfile"/>
+  <status value="draft"/>
+  <description value="Test profile to confirm that targetProfiles on references are enforced against contained resources"/>
+  <kind value="resource"/>
+  <abstract value="false"/>
+  <type value="Patient"/>
+  <baseDefinition value="http://hl7.org/fhir/StructureDefinition/Patient"/>
+  <derivation value="constraint"/>
+  <differential>
+    <element id="Patient">
+      <path value="Patient"/>
+    </element>
+    <element id="Patient.generalPractitioner">
+      <path value="Patient.generalPractitioner"/>
+      <type>
+        <code value="Reference"/>
+        <targetProfile value="#gp"/>
+        <aggregation value="contained"/>
+      </type>
+    </element>
+  </differential>
+</StructureDefinition>

org.hl7.fhir.validation/src/test/resources/validation-examples/patient-contained-org.xml

@@ -0,0 +1,20 @@
+<Patient xmlns="http://hl7.org/fhir">
+	<id value="patient-error-gender"/>
+	<text>
+		<status value="generated"/>
+		<div xmlns="http://www.w3.org/1999/xhtml">
+      Check that profile validation checks contained resources - should fail because Organization is missing 'name' which is required by profile
+    </div>
+	</text>
+	<contained>
+    <Organization>
+      <id value="gp"/>
+      <identifier>
+        <value value="123"/>
+      </identifier>
+    </Organization>
+  </contained>
+  <generalPractitioner>
+    <reference value="#gp"/>
+  </generalPractitioner>
+</Patient>

pom.xml

@@ -13,7 +13,7 @@
 	each other. It is fine to bump the point version of this POM without affecting
 	HAPI FHIR.
 	-->
-	<version>3.7.37-SNAPSHOT</version>
+	<version>3.7.38-SNAPSHOT</version>
 
 	<properties>
 		<hapi_fhir_version>3.7.0-SNAPSHOT</hapi_fhir_version>

release.bat

@@ -4,25 +4,25 @@ REM make sure you are committed
 @echo off
 echo ..
 echo =====================================================================
-echo upgrade and release fhir.core from 3.7.36-SNAPSHOT to 3.7.37-SNAPSHOT
+echo upgrade and release fhir.core from 3.7.37-SNAPSHOT to 3.7.38-SNAPSHOT
 echo =====================================================================
 echo ..
 echo check versions and make sure committed...
 pause
 
-call mvn versions:set -DnewVersion=3.7.37-SNAPSHOT
+call mvn versions:set -DnewVersion=3.7.38-SNAPSHOT
 call git commit -a -m "Release new version"
 call git push origin master
-call "C:\tools\fnr.exe" --cl --dir "C:\work\org.hl7.fhir\build" --fileMask "*.java" --includeSubDirectories --find "3.7.36-SNAPSHOT" --replace "3.7.37-SNAPSHOT"
+call "C:\tools\fnr.exe" --cl --dir "C:\work\org.hl7.fhir\build" --fileMask "*.java" --includeSubDirectories --find "3.7.37-SNAPSHOT" --replace "3.7.38-SNAPSHOT"
-call "C:\tools\fnr.exe" --cl --dir "C:\work\org.hl7.fhir\fhir-ig-publisher" --fileMask "*.xml" --includeSubDirectories --find "3.7.36-SNAPSHOT" --replace "3.7.37-SNAPSHOT"
+call "C:\tools\fnr.exe" --cl --dir "C:\work\org.hl7.fhir\fhir-ig-publisher" --fileMask "*.xml" --includeSubDirectories --find "3.7.37-SNAPSHOT" --replace "3.7.38-SNAPSHOT"
-call "C:\tools\fnr.exe" --cl --dir "C:\work\org.hl7.fhir\build" --fileMask "*.xml" --find "3.7.36-SNAPSHOT" --replace "3.7.37-SNAPSHOT"
+call "C:\tools\fnr.exe" --cl --dir "C:\work\org.hl7.fhir\build" --fileMask "*.xml" --find "3.7.37-SNAPSHOT" --replace "3.7.38-SNAPSHOT"
 call mvn deploy
-copy org.hl7.fhir.validation.cli\target\org.hl7.fhir.validation.cli-3.7.37-SNAPSHOT.jar ..\latest-ig-publisher\org.hl7.fhir.validator.jar
+copy org.hl7.fhir.validation.cli\target\org.hl7.fhir.validation.cli-3.7.38-SNAPSHOT.jar ..\latest-ig-publisher\org.hl7.fhir.validator.jar
 cd ..\latest-ig-publisher
-call git commit -a -m "Release new version 3.7.37-SNAPSHOT"
+call git commit -a -m "Release new version 3.7.38-SNAPSHOT"
 call git push origin master
 cd ..\org.hl7.fhir.core
-call python c:\tools\zulip-api\zulip\zulip\send.py --stream committers/notification --subject "java core" -m "New Java Core v3.7.37-SNAPSHOT released. New Validator at https://oss.sonatype.org/service/local/artifact/maven/redirect?r=snapshots&g=ca.uhn.hapi.fhir&a=org.hl7.fhir.validation.cli&v=3.7.37-SNAPSHOT&e=jar, and also deployed at https://fhir.github.io/latest-ig-publisher/org.hl7.fhir.validator.jar" --config-file zuliprc
+call python c:\tools\zulip-api\zulip\zulip\send.py --stream committers/notification --subject "java core" -m "New Java Core v3.7.38-SNAPSHOT released. New Validator at https://oss.sonatype.org/service/local/artifact/maven/redirect?r=snapshots&g=ca.uhn.hapi.fhir&a=org.hl7.fhir.validation.cli&v=3.7.38-SNAPSHOT&e=jar, and also deployed at https://fhir.github.io/latest-ig-publisher/org.hl7.fhir.validator.jar" --config-file zuliprc
 
 echo ===============================================================
 echo all done