Ensure that parent structuredefinitions are snapshotted before (#2005)

* Ensure that parent structuredefinitions are snapshotted before
snapshotting child

* Add changelog

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_1_0/2005-snapshot-parents-first.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 2005
+title: When generating a snapshot for a StructureDefinition that extends another non-base StructureDefinition, if the parent
+   SD did not have a snapshot itself, the child snapshot would be empty. This has been corrected.

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4StructureDefinitionTest.java

@@ -13,6 +13,7 @@ import org.junit.jupiter.api.Test;
 import java.io.IOException;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 @SuppressWarnings({"unchecked", "deprecation"})
 public class FhirResourceDaoR4StructureDefinitionTest extends BaseJpaR4Test {
@@ -47,5 +48,24 @@ public class FhirResourceDaoR4StructureDefinitionTest extends BaseJpaR4Test {
 	}
 
 
+	/**
+	 * Make sure that if one SD extends another SD, and the parent SD hasn't been snapshotted itself, the child can
+	 * be snapshotted.
+	 */
+	@Test
+	public void testGenerateSnapshotChained() throws IOException {
+		StructureDefinition sd = loadResourceFromClasspath(StructureDefinition.class, "/r4/StructureDefinition-kfdrc-patient.json");
+		myStructureDefinitionDao.update(sd);
+
+		StructureDefinition sd2 = loadResourceFromClasspath(StructureDefinition.class, "/r4/StructureDefinition-kfdrc-patient-no-phi.json");
+		myStructureDefinitionDao.update(sd2);
+
+		StructureDefinition snapshotted = myStructureDefinitionDao.generateSnapshot(sd2, null, null, null);
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(snapshotted));
+
+		assertTrue(snapshotted.getSnapshot().getElement().size() > 0);
+	}
+
+
 
 }

hapi-fhir-jpaserver-base/src/test/resources/r4/StructureDefinition-kfdrc-patient-no-phi.json

@@ -0,0 +1,62 @@
+{
+  "resourceType": "StructureDefinition",
+  "id": "kfdrc-patient-no-phi",
+  "url": "http://fhir.kids-first.io/StructureDefinition/kfdrc-patient-no-phi",
+  "version": "0.1.0",
+  "name": "kfdrc-patient-no-phi",
+  "title": "Kids First DRC Patient without Protected Health Information",
+  "status": "draft",
+  "fhirVersion": "4.0.0",
+  "kind": "resource",
+  "abstract": false,
+  "type": "Patient",
+  "baseDefinition": "http://fhir.kids-first.io/StructureDefinition/kfdrc-patient",
+  "derivation": "constraint",
+  "differential": {
+    "element": [
+      {
+        "id": "Patient",
+        "path": "Patient"
+      },
+      {
+        "id": "Patient.name",
+        "path": "Patient.name",
+        "max": "0"
+      },
+      {
+        "id": "Patient.telecom",
+        "path": "Patient.telecom",
+        "max": "0"
+      },
+      {
+        "id": "Patient.birthDate",
+        "path": "Patient.birthDate",
+        "max": "0"
+      },
+      {
+        "id": "Patient.deceased[x]",
+        "path": "Patient.deceased[x]",
+        "type" : [
+          {
+            "code" : "boolean"
+          }
+        ]
+      },
+      {
+        "id": "Patient.address",
+        "path": "Patient.address",
+        "max": "0"
+      },
+      {
+        "id": "Patient.photo",
+        "path": "Patient.photo",
+        "max": "0"
+      },
+      {
+        "id": "Patient.contact",
+        "path": "Patient.contact",
+        "max": "0"
+      }
+    ]
+  }
+}

hapi-fhir-jpaserver-base/src/test/resources/r4/StructureDefinition-kfdrc-patient.json

@@ -0,0 +1,100 @@
+{
+  "resourceType": "StructureDefinition",
+  "id": "kfdrc-patient",
+  "url": "http://fhir.kids-first.io/StructureDefinition/kfdrc-patient",
+  "version": "0.1.0",
+  "name": "kfdrc-patient",
+  "title": "Kids First DRC Patient",
+  "status": "draft",
+  "fhirVersion": "4.0.0",
+  "kind": "resource",
+  "abstract": false,
+  "type": "Patient",
+  "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Patient",
+  "derivation": "constraint",
+  "differential": {
+    "element": [
+      {
+        "id": "Patient",
+        "path": "Patient"
+      },
+      {
+        "id": "Patient.extension",
+        "path": "Patient.extension",
+        "slicing": {
+          "discriminator": [
+            {
+              "type": "value",
+              "path": "url"
+            }
+          ],
+          "ordered": false,
+          "rules": "open"
+        }
+      },
+      {
+        "id": "Patient.extension:us-core-ethnicity",
+        "path": "Patient.extension",
+        "sliceName": "us-core-ethnicity",
+        "sliceIsConstraining": false,
+        "short": "US Core Ethnicity Extension",
+        "definition": "Concepts classifying the person into a named category of humans sharing common history, traits, geographical origin or nationality.  The ethnicity codes used to represent these concepts are based upon the [CDC ethnicity and Ethnicity Code Set Version 1.0](http://www.cdc.gov/phin/resources/vocabulary/index.html) which includes over 900 concepts for representing race and ethnicity of which 43 reference ethnicity.  The ethnicity concepts are grouped by and pre-mapped to the 2 OMB ethnicity categories: - Hispanic or Latino - Not Hispanic or Latino.",
+        "min": 0,
+        "max": "1",
+        "type": [
+          {
+            "code": "Extension",
+            "profile": [
+              "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity"
+            ]
+          }
+        ],
+        "mustSupport": true,
+        "isModifier": false
+      },
+      {
+        "id": "Patient.extension:us-core-race",
+        "path": "Patient.extension",
+        "sliceName": "us-core-race",
+        "short": "US Core Race Extension",
+        "definition": "Concepts classifying the person into a named category of humans sharing common history, traits, geographical origin or nationality.  The race codes used to represent these concepts are based upon the [CDC Race and Ethnicity Code Set Version 1.0](http://www.cdc.gov/phin/resources/vocabulary/index.html) which includes over 900 concepts for representing race and ethnicity of which 921 reference race.  The race concepts are grouped by and pre-mapped to the 5 OMB race categories:\n\n   - American Indian or Alaska Native\n   - Asian\n   - Black or African American\n   - Native Hawaiian or Other Pacific Islander\n   - White.",
+        "min": 0,
+        "max": "1",
+        "type": [
+          {
+            "code": "Extension",
+            "profile": [
+              "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race"
+            ]
+          }
+        ],
+        "mustSupport": true,
+        "isModifier": false
+      },
+      {
+        "id": "Patient.extension:species",
+        "path": "Patient.extension",
+        "sliceName": "species",
+        "short": "Species",
+        "definition": "Species of the KF DRC Patient.",
+        "min": 0,
+        "max": "1",
+        "type": [
+          {
+            "code": "Extension",
+            "profile": [
+              "http://fhir.kids-first.io/StructureDefinition/species"
+            ]
+          }
+        ],
+        "mustSupport": true,
+        "isModifier": false,
+        "binding": {
+          "strength": "required",
+          "description": "Species of the Participant.",
+          "valueSet": "http://fhir.kids-first.io/ValueSet/species"
+        }
+      }
+    ]
+  }
+}

hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/SnapshotGeneratingValidationSupport.java

@@ -12,6 +12,7 @@ import org.hl7.fhir.common.hapi.validation.validator.VersionSpecificWorkerContex
 import org.hl7.fhir.common.hapi.validation.validator.VersionTypeConverterDstu3;
 import org.hl7.fhir.common.hapi.validation.validator.VersionTypeConverterR4;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r5.conformance.ProfileUtilities;
 import org.hl7.fhir.r5.context.IWorkerContext;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.slf4j.Logger;
@@ -90,10 +91,17 @@ public class SnapshotGeneratingValidationSupport implements IValidationSupport {
 
 			org.hl7.fhir.r5.model.StructureDefinition baseCanonical = (org.hl7.fhir.r5.model.StructureDefinition) converter.toCanonical(base);
 
+			if (baseCanonical.getSnapshot().getElement().isEmpty()) {
+				// If the base definition also doesn't have a snapshot, generate that first
+				theValidationSupportContext.getRootValidationSupport().generateSnapshot(theValidationSupportContext, base, null, null, null);
+				baseCanonical = (org.hl7.fhir.r5.model.StructureDefinition) converter.toCanonical(base);
+			}
+
 			ArrayList<ValidationMessage> messages = new ArrayList<>();
 			org.hl7.fhir.r5.conformance.ProfileUtilities.ProfileKnowledgeProvider profileKnowledgeProvider = new ProfileKnowledgeWorkerR5(myCtx);
 			IWorkerContext context = new VersionSpecificWorkerContextWrapper(theValidationSupportContext, converter);
-			new org.hl7.fhir.r5.conformance.ProfileUtilities(context, messages, profileKnowledgeProvider).generateSnapshot(baseCanonical, inputCanonical, theUrl, theWebUrl, theProfileName);
+			ProfileUtilities profileUtilities = new ProfileUtilities(context, messages, profileKnowledgeProvider);
+			profileUtilities.generateSnapshot(baseCanonical, inputCanonical, theUrl, theWebUrl, theProfileName);
 
 			switch (theInput.getStructureFhirVersionEnum()) {
 				case DSTU3: