Ensure that parent structuredefinitions are snapshotted before (#2005)
* Ensure that parent structuredefinitions are snapshotted before snapshotting child * Add changelog
This commit is contained in:
James Agnew
GitHub
parent
20d1ab2fac
commit
6a8e09addf
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@ -0,0 +1,5 @@
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---
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type: fix
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issue: 2005
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title: When generating a snapshot for a StructureDefinition that extends another non-base StructureDefinition, if the parent
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SD did not have a snapshot itself, the child snapshot would be empty. This has been corrected.
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@ -13,6 +13,7 @@ import org.junit.jupiter.api.Test;
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import java.io.IOException;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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@SuppressWarnings({"unchecked", "deprecation"})
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public class FhirResourceDaoR4StructureDefinitionTest extends BaseJpaR4Test {
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@ -47,5 +48,24 @@ public class FhirResourceDaoR4StructureDefinitionTest extends BaseJpaR4Test {
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}
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/**
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* Make sure that if one SD extends another SD, and the parent SD hasn't been snapshotted itself, the child can
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* be snapshotted.
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*/
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@Test
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public void testGenerateSnapshotChained() throws IOException {
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StructureDefinition sd = loadResourceFromClasspath(StructureDefinition.class, "/r4/StructureDefinition-kfdrc-patient.json");
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myStructureDefinitionDao.update(sd);
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StructureDefinition sd2 = loadResourceFromClasspath(StructureDefinition.class, "/r4/StructureDefinition-kfdrc-patient-no-phi.json");
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myStructureDefinitionDao.update(sd2);
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StructureDefinition snapshotted = myStructureDefinitionDao.generateSnapshot(sd2, null, null, null);
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ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(snapshotted));
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assertTrue(snapshotted.getSnapshot().getElement().size() > 0);
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}
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}
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@ -0,0 +1,62 @@
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{
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"resourceType": "StructureDefinition",
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"id": "kfdrc-patient-no-phi",
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"url": "http://fhir.kids-first.io/StructureDefinition/kfdrc-patient-no-phi",
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"version": "0.1.0",
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"name": "kfdrc-patient-no-phi",
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"title": "Kids First DRC Patient without Protected Health Information",
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"status": "draft",
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"fhirVersion": "4.0.0",
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"kind": "resource",
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"abstract": false,
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"type": "Patient",
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"baseDefinition": "http://fhir.kids-first.io/StructureDefinition/kfdrc-patient",
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"derivation": "constraint",
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"differential": {
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"element": [
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{
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"id": "Patient",
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"path": "Patient"
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},
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{
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"id": "Patient.name",
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"path": "Patient.name",
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"max": "0"
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},
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{
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"id": "Patient.telecom",
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"path": "Patient.telecom",
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"max": "0"
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},
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{
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"id": "Patient.birthDate",
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"path": "Patient.birthDate",
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"max": "0"
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},
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{
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"id": "Patient.deceased[x]",
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"path": "Patient.deceased[x]",
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"type" : [
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{
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"code" : "boolean"
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}
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]
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},
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{
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"id": "Patient.address",
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"path": "Patient.address",
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"max": "0"
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},
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{
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"id": "Patient.photo",
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"path": "Patient.photo",
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"max": "0"
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},
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{
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"id": "Patient.contact",
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"path": "Patient.contact",
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"max": "0"
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}
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]
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}
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}
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@ -0,0 +1,100 @@
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{
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"resourceType": "StructureDefinition",
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"id": "kfdrc-patient",
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"url": "http://fhir.kids-first.io/StructureDefinition/kfdrc-patient",
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"version": "0.1.0",
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"name": "kfdrc-patient",
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"title": "Kids First DRC Patient",
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"status": "draft",
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"fhirVersion": "4.0.0",
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"kind": "resource",
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"abstract": false,
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"type": "Patient",
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"baseDefinition": "http://hl7.org/fhir/StructureDefinition/Patient",
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"derivation": "constraint",
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"differential": {
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"element": [
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{
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"id": "Patient",
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"path": "Patient"
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},
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{
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"id": "Patient.extension",
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"path": "Patient.extension",
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"slicing": {
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"discriminator": [
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{
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"type": "value",
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"path": "url"
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}
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],
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"ordered": false,
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"rules": "open"
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}
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},
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{
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"id": "Patient.extension:us-core-ethnicity",
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"path": "Patient.extension",
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"sliceName": "us-core-ethnicity",
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"sliceIsConstraining": false,
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"short": "US Core Ethnicity Extension",
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"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.",
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"min": 0,
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"max": "1",
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"type": [
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{
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"code": "Extension",
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"profile": [
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"http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity"
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]
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}
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],
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"mustSupport": true,
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"isModifier": false
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},
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{
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"id": "Patient.extension:us-core-race",
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"path": "Patient.extension",
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"sliceName": "us-core-race",
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"short": "US Core Race Extension",
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"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.",
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"min": 0,
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"max": "1",
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"type": [
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{
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"code": "Extension",
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"profile": [
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"http://hl7.org/fhir/us/core/StructureDefinition/us-core-race"
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]
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}
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],
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"mustSupport": true,
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"isModifier": false
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},
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{
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"id": "Patient.extension:species",
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"path": "Patient.extension",
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"sliceName": "species",
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"short": "Species",
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"definition": "Species of the KF DRC Patient.",
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"min": 0,
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"max": "1",
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"type": [
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{
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"code": "Extension",
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"profile": [
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"http://fhir.kids-first.io/StructureDefinition/species"
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]
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}
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],
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"mustSupport": true,
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"isModifier": false,
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"binding": {
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"strength": "required",
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"description": "Species of the Participant.",
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"valueSet": "http://fhir.kids-first.io/ValueSet/species"
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}
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}
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]
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}
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}
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@ -12,6 +12,7 @@ import org.hl7.fhir.common.hapi.validation.validator.VersionSpecificWorkerContex
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import org.hl7.fhir.common.hapi.validation.validator.VersionTypeConverterDstu3;
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import org.hl7.fhir.common.hapi.validation.validator.VersionTypeConverterR4;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.r5.conformance.ProfileUtilities;
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import org.hl7.fhir.r5.context.IWorkerContext;
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import org.hl7.fhir.utilities.validation.ValidationMessage;
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import org.slf4j.Logger;
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@ -90,10 +91,17 @@ public class SnapshotGeneratingValidationSupport implements IValidationSupport {
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org.hl7.fhir.r5.model.StructureDefinition baseCanonical = (org.hl7.fhir.r5.model.StructureDefinition) converter.toCanonical(base);
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if (baseCanonical.getSnapshot().getElement().isEmpty()) {
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// If the base definition also doesn't have a snapshot, generate that first
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theValidationSupportContext.getRootValidationSupport().generateSnapshot(theValidationSupportContext, base, null, null, null);
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baseCanonical = (org.hl7.fhir.r5.model.StructureDefinition) converter.toCanonical(base);
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}
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ArrayList<ValidationMessage> messages = new ArrayList<>();
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org.hl7.fhir.r5.conformance.ProfileUtilities.ProfileKnowledgeProvider profileKnowledgeProvider = new ProfileKnowledgeWorkerR5(myCtx);
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IWorkerContext context = new VersionSpecificWorkerContextWrapper(theValidationSupportContext, converter);
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new org.hl7.fhir.r5.conformance.ProfileUtilities(context, messages, profileKnowledgeProvider).generateSnapshot(baseCanonical, inputCanonical, theUrl, theWebUrl, theProfileName);
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ProfileUtilities profileUtilities = new ProfileUtilities(context, messages, profileKnowledgeProvider);
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profileUtilities.generateSnapshot(baseCanonical, inputCanonical, theUrl, theWebUrl, theProfileName);
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switch (theInput.getStructureFhirVersionEnum()) {
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case DSTU3:
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