Merge pull request #2448 from hapifhir/2446-issues-with-placeholder-reference-targets-need-to-be-resolved
Issues with placeholder reference targets have been resolved.
This commit is contained in:
Diederik Muylwyk
GitHub
commit
8f9f46a907
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@ -174,7 +174,7 @@ public interface IGenericClient extends IRestfulClient {
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void unregisterInterceptor(Object theInterceptor);
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/**
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* Fluent method for the "update" operation, which performs a logical delete on a server resource
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* Fluent method for the "update" operation, which updates a resource instance on the server
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*/
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IUpdate update();
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@ -109,8 +109,7 @@ public class HapiExtensions {
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/**
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* URL for boolean extension added to all placeholder resources
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*/
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public static final String EXT_RESOURCE_META_PLACEHOLDER = "http://hapifhir.io/fhir/StructureDefinition/resource-meta-placeholder";
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public static final String EXT_RESOURCE_PLACEHOLDER = "http://hapifhir.io/fhir/StructureDefinition/resource-placeholder";
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/**
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* Non instantiable
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@ -1,5 +1,4 @@
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---
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type: add
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issue: 2332
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title: "All created placeholder resources now have a meta extension with the url http://hapifhir.io/fhir/StructureDefinition/resource-meta-placeholder
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and the value 'true'. Also, terminology storage is now skipped for placeholder ValueSet and ConceptMap resources."
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title: "Terminology storage is now skipped for placeholder ValueSet and ConceptMap resources."
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@ -0,0 +1,5 @@
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---
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type: add
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issue: 2446
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title: "Auto-created placeholder reference targets now have an extension with the URL
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`http://hapifhir.io/fhir/StructureDefinition/resource-meta-placeholder` and a value of `true`."
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@ -0,0 +1,5 @@
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---
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type: change
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issue: 2446
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title: "DaoConfig setting for [Populate Identifier In Auto Created Placeholder Reference Targets](https://hapifhir.io/hapi-fhir/apidocs/hapi-fhir-jpaserver-api/ca/uhn/fhir/jpa/api/config/DaoConfig.html#setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(boolean))
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now defaults to `true`."
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@ -186,9 +186,11 @@ public class DaoConfig {
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private int myPreExpandValueSetsMaxCount = 1000;
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/**
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* Do not change default of {@code true}!
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*
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* @since 4.2.0
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*/
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private boolean myPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets;
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private boolean myPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets = true;
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/**
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* @since 5.0.0
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@ -1069,7 +1071,7 @@ public class DaoConfig {
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* as they are never allowed to be client supplied in HAPI FHIR JPA.
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*
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* All placeholder resources created in this way have a meta extension
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* with the URL {@link HapiExtensions#EXT_RESOURCE_META_PLACEHOLDER} and the value "true".
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* with the URL {@link HapiExtensions#EXT_RESOURCE_PLACEHOLDER} and the value "true".
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* </p>
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*/
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public boolean isAutoCreatePlaceholderReferenceTargets() {
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@ -1093,7 +1095,7 @@ public class DaoConfig {
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* as they are never allowed to be client supplied in HAPI FHIR JPA.
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*
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* All placeholder resources created in this way have a meta extension
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* with the URL {@link HapiExtensions#EXT_RESOURCE_META_PLACEHOLDER} and the value "true".
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* with the URL {@link HapiExtensions#EXT_RESOURCE_PLACEHOLDER} and the value "true".
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* </p>
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*/
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public void setAutoCreatePlaceholderReferenceTargets(boolean theAutoCreatePlaceholderReferenceTargets) {
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@ -1102,7 +1104,7 @@ public class DaoConfig {
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/**
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* When {@link #setAutoCreatePlaceholderReferenceTargets(boolean)} is enabled, if this
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* setting is set to <code>true</code> (default is <code>false</code>) and the source
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* setting is set to <code>true</code> (default is <code>true</code>) and the source
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* reference has an identifier populated, the identifier will be copied to the target
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* resource.
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* <p>
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@ -1144,6 +1146,41 @@ public class DaoConfig {
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* }
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* }
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* </pre>
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* <p>
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* Note that the default for this setting was previously <code>false</code>, and was changed to <code>true</code>
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* in 5.4.0 with consideration to the following:
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* </p>
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* <pre>
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* CP = Auto-Create Placeholder Reference Targets
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* PI = Populate Identifier in Auto-Created Placeholder Reference Targets
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*
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* CP | PI
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* -------
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* F | F <- PI=F is ignored
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* F | T <- PI=T is ignored
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* T | F <- resources may reference placeholder reference targets that are never updated : (
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* T | T <- placeholder reference targets can be updated : )
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* </pre>
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* <p>
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* Where CP=T and PI=F, the following could happen:
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* </p>
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* <ol>
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* <li>
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* Resource instance A is created with a reference to resource instance B. B is a placeholder reference target
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* without an identifier.
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* </li>
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* <li>
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* Resource instance C is conditionally created using a match URL. It is not matched to B although these
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* resources represent the same entity.
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* </li>
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* <li>
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* A continues to reference placeholder B, and does not reference populated C.
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* </li>
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* </ol>
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* <p>
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* There may be cases where configuring this setting to <code>false</code> would be appropriate; however, these are
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* exceptional cases that should be opt-in.
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* </p>
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*
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* @since 4.2.0
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*/
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@ -1153,7 +1190,7 @@ public class DaoConfig {
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/**
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* When {@link #setAutoCreatePlaceholderReferenceTargets(boolean)} is enabled, if this
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* setting is set to <code>true</code> (default is <code>false</code>) and the source
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* setting is set to <code>true</code> (default is <code>true</code>) and the source
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* reference has an identifier populated, the identifier will be copied to the target
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* resource.
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* <p>
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@ -1195,6 +1232,41 @@ public class DaoConfig {
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* }
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* }
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* </pre>
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* <p>
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* Note that the default for this setting was previously <code>false</code>, and was changed to <code>true</code>
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* in 5.4.0 with consideration to the following:
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* </p>
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* <pre>
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* CP = Auto-Create Placeholder Reference Targets
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* PI = Populate Identifier in Auto-Created Placeholder Reference Targets
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*
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* CP | PI
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* -------
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* F | F <- PI=F is ignored
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* F | T <- PI=T is ignored
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* T | F <- resources may reference placeholder reference targets that are never updated : (
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* T | T <- placeholder reference targets can be updated : )
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* </pre>
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* <p>
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* Where CP=T and PI=F, the following could happen:
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* </p>
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* <ol>
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* <li>
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* Resource instance A is created with a reference to resource instance B. B is a placeholder reference target
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* without an identifier.
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* </li>
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* <li>
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* Resource instance C is conditionally created using a match URL. It is not matched to B although these
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* resources represent the same entity.
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* </li>
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* <li>
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* A continues to reference placeholder B, and does not reference populated C.
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* </li>
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* </ol>
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* <p>
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* There may be cases where configuring this setting to <code>false</code> would be appropriate; however, these are
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* exceptional cases that should be opt-in.
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* </p>
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*
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* @since 4.2.0
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*/
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@ -41,7 +41,6 @@ import ca.uhn.fhir.util.HapiExtensions;
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import org.hl7.fhir.instance.model.api.IBase;
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import org.hl7.fhir.instance.model.api.IBaseExtension;
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import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
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import org.hl7.fhir.instance.model.api.IBaseMetaType;
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import org.hl7.fhir.instance.model.api.IBaseReference;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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@ -123,10 +122,9 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver {
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@SuppressWarnings("unchecked")
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T newResource = (T) missingResourceDef.newInstance();
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IBaseMetaType meta = newResource.getMeta();
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if (meta instanceof IBaseHasExtensions) {
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IBaseExtension<?, ?> extension = ((IBaseHasExtensions) meta).addExtension();
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extension.setUrl(HapiExtensions.EXT_RESOURCE_META_PLACEHOLDER);
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if (newResource instanceof IBaseHasExtensions) {
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IBaseExtension<?, ?> extension = ((IBaseHasExtensions) newResource).addExtension();
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extension.setUrl(HapiExtensions.EXT_RESOURCE_PLACEHOLDER);
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extension.setValue(myContext.getPrimitiveBoolean(true));
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}
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@ -119,15 +119,17 @@ import org.hl7.fhir.instance.model.api.IBaseDatatype;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.instance.model.api.IPrimitiveType;
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import org.hl7.fhir.r4.model.BooleanType;
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import org.hl7.fhir.r4.model.CanonicalType;
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import org.hl7.fhir.r4.model.CodeSystem;
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import org.hl7.fhir.r4.model.CodeableConcept;
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import org.hl7.fhir.r4.model.Coding;
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import org.hl7.fhir.r4.model.ConceptMap;
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import org.hl7.fhir.r4.model.DomainResource;
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import org.hl7.fhir.r4.model.Enumerations;
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import org.hl7.fhir.r4.model.Extension;
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import org.hl7.fhir.r4.model.IdType;
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import org.hl7.fhir.r4.model.IntegerType;
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import org.hl7.fhir.r4.model.MetadataResource;
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import org.hl7.fhir.r4.model.StringType;
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import org.hl7.fhir.r4.model.ValueSet;
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import org.hl7.fhir.r4.model.codesystems.ConceptSubsumptionOutcome;
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@ -2122,8 +2124,13 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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}
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}
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private boolean isPlaceholder(MetadataResource theResource) {
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return theResource.getMeta().getExtensionByUrl(HapiExtensions.EXT_RESOURCE_META_PLACEHOLDER) != null;
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private boolean isPlaceholder(DomainResource theResource) {
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boolean retVal = false;
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Extension extension = theResource.getExtensionByUrl(HapiExtensions.EXT_RESOURCE_PLACEHOLDER);
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if (extension != null && extension.hasValue() && extension.getValue() instanceof BooleanType) {
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retVal = ((BooleanType) extension.getValue()).booleanValue();
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}
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return retVal;
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}
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@Override
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@ -7,10 +7,12 @@ import ca.uhn.fhir.rest.param.ReferenceParam;
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import ca.uhn.fhir.rest.param.TokenParam;
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import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
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import ca.uhn.fhir.util.TestUtil;
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import ca.uhn.fhir.util.HapiExtensions;
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import com.google.common.collect.Sets;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.r4.model.AuditEvent;
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import org.hl7.fhir.r4.model.BooleanType;
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import org.hl7.fhir.r4.model.Extension;
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import org.hl7.fhir.r4.model.IdType;
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import org.hl7.fhir.r4.model.Observation;
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import org.hl7.fhir.r4.model.Observation.ObservationStatus;
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@ -18,16 +20,18 @@ import org.hl7.fhir.r4.model.Patient;
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import org.hl7.fhir.r4.model.Reference;
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import org.hl7.fhir.r4.model.Task;
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import org.junit.jupiter.api.AfterEach;
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import org.junit.jupiter.api.AfterAll;
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import org.junit.jupiter.api.Test;
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import java.util.List;
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import static org.hamcrest.CoreMatchers.startsWith;
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import static org.hamcrest.MatcherAssert.assertThat;
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import static org.hamcrest.Matchers.contains;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertFalse;
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import static org.hamcrest.MatcherAssert.assertThat;
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import static org.junit.jupiter.api.Assertions.assertNotNull;
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import static org.junit.jupiter.api.Assertions.assertNull;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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import static org.junit.jupiter.api.Assertions.fail;
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@SuppressWarnings({"ConstantConditions"})
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@ -174,9 +178,54 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
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}
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@Test
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public void testCreatePlaceholderWithMatchUrl_IdentifierNotCopiedByDefault() {
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public void testCreatePlaceholderExtension_WithUpdateToTarget() {
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myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
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// Create an Observation that references a Patient
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Observation obsToCreate = new Observation();
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obsToCreate.setStatus(ObservationStatus.FINAL);
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obsToCreate.getSubject().setReference("Patient/AAA");
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IIdType id = myObservationDao.create(obsToCreate, mySrd).getId();
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// Read the Observation
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Observation createdObs = myObservationDao.read(id);
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ourLog.info("\nObservation created:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
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/*
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* Read the placeholder Patient referenced by the Observation
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* Placeholder extension should exist and be true
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*/
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Patient placeholderPat = myPatientDao.read(new IdType(createdObs.getSubject().getReference()));
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IIdType placeholderPatId = placeholderPat.getIdElement();
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ourLog.info("\nPlaceholder Patient created:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(placeholderPat));
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assertEquals(0, placeholderPat.getIdentifier().size());
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Extension extension = placeholderPat.getExtensionByUrl(HapiExtensions.EXT_RESOURCE_PLACEHOLDER);
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assertNotNull(extension);
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assertTrue(extension.hasValue());
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assertTrue(((BooleanType) extension.getValue()).booleanValue());
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// Update the Patient
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Patient patToUpdate = new Patient();
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patToUpdate.setId("Patient/AAA");
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patToUpdate.addIdentifier().setSystem("http://foo").setValue("123");
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IIdType updatedPatId = myPatientDao.update(patToUpdate).getId();
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/*
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* Read the updated Patient
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* Placeholder extension should not exist
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*/
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Patient updatedPat = myPatientDao.read(updatedPatId);
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ourLog.info("\nUpdated Patient:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(updatedPat));
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assertEquals(1, updatedPat.getIdentifier().size());
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extension = updatedPat.getExtensionByUrl(HapiExtensions.EXT_RESOURCE_PLACEHOLDER);
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assertNull(extension);
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}
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@Test
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public void testCreatePlaceholderWithMatchUrl_IdentifierNotCopied() {
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myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
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myDaoConfig.setAllowInlineMatchUrlReferences(true);
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myDaoConfig.setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(false);
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Observation obsToCreate = new Observation();
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obsToCreate.setStatus(ObservationStatus.FINAL);
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@ -192,12 +241,60 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
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assertEquals(0, patient.getIdentifier().size());
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}
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@Test
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public void testCreatePlaceholderWithMatchUrl_IdentifierCopied_NotPreExisting() {
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public void testCreatePlaceholderWithMatchUrl_IdentifierCopiedByDefault_WithUpdateToTarget() {
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myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
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myDaoConfig.setAllowInlineMatchUrlReferences(true);
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/*
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* Create an Observation that references a Patient
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* Reference is populated with inline match URL and includes identifier
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*/
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Observation obsToCreate = new Observation();
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obsToCreate.setStatus(ObservationStatus.FINAL);
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obsToCreate.getSubject().setReference("Patient?identifier=http://foo|123");
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obsToCreate.getSubject().getIdentifier().setSystem("http://foo").setValue("123");
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IIdType obsId = myObservationDao.create(obsToCreate, mySrd).getId();
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// Read the Observation
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Observation createdObs = myObservationDao.read(obsId);
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ourLog.info("\nObservation created:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
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/*
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* Read the placeholder Patient referenced by the Observation
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* Identifier should be populated since it was provided
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*/
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Patient placeholderPat = myPatientDao.read(new IdType(createdObs.getSubject().getReference()));
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IIdType placeholderPatId = placeholderPat.getIdElement();
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ourLog.info("\nPlaceholder Patient created:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(placeholderPat));
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assertEquals(1, placeholderPat.getIdentifier().size());
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assertEquals(createdObs.getSubject().getReference(), placeholderPatId.toUnqualifiedVersionless().getValueAsString());
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// Conditionally update a Patient with the same identifier
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Patient patToConditionalUpdate = new Patient();
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patToConditionalUpdate.addIdentifier().setSystem("http://foo").setValue("123");
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patToConditionalUpdate.addName().setFamily("Simpson");
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IIdType conditionalUpdatePatId = myPatientDao.update(patToConditionalUpdate, "Patient?identifier=http://foo|123", mySrd).getId();
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// Read the conditionally updated Patient
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Patient conditionalUpdatePat = myPatientDao.read(conditionalUpdatePatId);
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ourLog.info("\nConditionally updated Patient:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conditionalUpdatePat));
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assertEquals(1, conditionalUpdatePat.getIdentifier().size());
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/*
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* Observation should reference conditionally updated Patient
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* ID of placeholder Patient should match ID of conditionally updated Patient
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*/
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createdObs = myObservationDao.read(obsId);
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ourLog.info("\nObservation read after Patient update:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
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assertEquals(createdObs.getSubject().getReference(), conditionalUpdatePatId.toUnqualifiedVersionless().getValueAsString());
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assertEquals(placeholderPatId.toUnqualifiedVersionless().getValueAsString(), conditionalUpdatePatId.toUnqualifiedVersionless().getValueAsString());
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}
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@Test
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public void testCreatePlaceholderWithMatchUrl_IdentifierCopiedByDefault_NotPreExisting() {
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myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
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myDaoConfig.setAllowInlineMatchUrlReferences(true);
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myDaoConfig.setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(true);
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Observation obsToCreate = new Observation();
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||||
obsToCreate.setStatus(ObservationStatus.FINAL);
|
||||
|
|
@ -219,7 +316,6 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
|
|||
public void testCreatePlaceholderWithMatchUrl_IdentifierNotCopiedBecauseNoFieldMatches() {
|
||||
myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
|
||||
myDaoConfig.setAllowInlineMatchUrlReferences(true);
|
||||
myDaoConfig.setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(true);
|
||||
myDaoConfig.setBundleTypesAllowedForStorage(Sets.newHashSet(""));
|
||||
|
||||
AuditEvent eventToCreate = new AuditEvent();
|
||||
|
|
@ -238,7 +334,6 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
|
|||
public void testCreatePlaceholderWithMatchUrl_PreExisting() {
|
||||
myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
|
||||
myDaoConfig.setAllowInlineMatchUrlReferences(true);
|
||||
myDaoConfig.setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(true);
|
||||
|
||||
Patient patient = new Patient();
|
||||
patient.setId("ABC");
|
||||
|
|
|
|||
Loading…
Reference in New Issue