Ensure FhirContext loads custom resources in the list of resource names (#5073)

* Fix bug by maintaining a separate list of resource types including the custom resources that will be used to validate the Bundle resources.

* Add custom resource types to resource types list and add conditional logic in ValidationDataInitializerSvcImpl to ensure there is no Exception when parsing a custom resource type.

* Add changelog.

* Remove unnecessary change.

* Address code review feedback.

* Address code review feedback.

* Add one more unit test.

* Bump to 6.7.14-SNAPSHOT.
This commit is contained in:
Luke deGruchy 2023-07-12 10:32:09 -04:00 committed by GitHub
parent 52f3ef5992
commit 43694f378c
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
81 changed files with 196 additions and 77 deletions

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -28,6 +28,7 @@ import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.model.api.IElement;
import ca.uhn.fhir.model.api.IFhirVersion;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.annotation.ResourceDef;
import ca.uhn.fhir.model.view.ViewGenerator;
import ca.uhn.fhir.narrative.INarrativeGenerator;
import ca.uhn.fhir.parser.DataFormatException;
@ -71,8 +72,11 @@ import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Objects;
import java.util.Optional;
import java.util.Properties;
import java.util.Set;
import java.util.stream.Collectors;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
@ -111,6 +115,7 @@ public class FhirContext {
private volatile Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> myClassToElementDefinition =
Collections.emptyMap();
private ArrayList<Class<? extends IBase>> myCustomTypes;
private final Set<String> myCustomResourceNames = new HashSet<>();
private volatile Map<String, RuntimeResourceDefinition> myIdToResourceDefinition = Collections.emptyMap();
private volatile boolean myInitialized;
private volatile boolean myInitializing = false;
@ -648,6 +653,7 @@ public class FhirContext {
retVal.add(next.substring("resource.".length()).trim());
}
}
retVal.addAll(myCustomResourceNames);
return retVal;
}
@ -1043,6 +1049,14 @@ public class FhirContext {
}
if (myCustomTypes != null) {
typesToScan.addAll(myCustomTypes);
myCustomResourceNames.addAll(myCustomTypes.stream()
.map(customType -> Optional.ofNullable(customType.getAnnotation(ResourceDef.class))
.map(ResourceDef::name)
.orElse(null)) // This will be caught by the call to ModelScanner
.filter(Objects::nonNull)
.collect(Collectors.toSet()));
myCustomTypes = null;
}

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@ -4,7 +4,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-bom</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<packaging>pom</packaging>
<name>HAPI FHIR BOM</name>
@ -12,7 +12,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
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<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -0,0 +1,4 @@
---
type: fix
issue: 5075
title: "The system was failing to recognize custom resources during transaction processing. This has been fixed."

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@ -11,7 +11,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -4,7 +4,7 @@
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<artifactId>hapi-deployable-pom</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
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<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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@ -5,7 +5,7 @@
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<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -6,7 +6,7 @@
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<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -3,7 +3,7 @@
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<groupId>ca.uhn.hapi.fhir</groupId>
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<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
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<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -5,7 +5,7 @@
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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@ -5,7 +5,7 @@
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@ -5,7 +5,7 @@
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<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -6,7 +6,7 @@
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<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -6,7 +6,7 @@
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<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -6,7 +6,7 @@
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<groupId>ca.uhn.hapi.fhir</groupId>
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<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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@ -6,7 +6,7 @@
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<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
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<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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@ -6,7 +6,7 @@
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<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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@ -5,7 +5,7 @@
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<relativePath>../pom.xml</relativePath>
</parent>

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@ -7,7 +7,7 @@
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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@ -5,7 +5,7 @@
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@ -5,7 +5,7 @@
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -7,7 +7,7 @@
<parent>
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<groupId>ca.uhn.hapi.fhir</groupId>
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@ -7,7 +7,7 @@
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<relativePath>../pom.xml</relativePath>
</parent>
@ -21,7 +21,7 @@
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-caching-api</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
</dependency>
<dependency>

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@ -7,7 +7,7 @@
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<relativePath>../pom.xml</relativePath>
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@ -7,7 +7,7 @@
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<relativePath>../../pom.xml</relativePath>
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@ -5,7 +5,7 @@
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@ -5,7 +5,7 @@
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@ -5,7 +5,7 @@
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<artifactId>hapi-fhir-spring-boot-sample-client-apache</artifactId>

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@ -5,7 +5,7 @@
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@ -5,7 +5,7 @@
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@ -5,7 +5,7 @@
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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@ -5,7 +5,7 @@
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@ -5,7 +5,7 @@
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@ -5,7 +5,7 @@
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@ -5,7 +5,7 @@
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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@ -4,7 +4,7 @@
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<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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@ -5,7 +5,7 @@
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@ -5,7 +5,7 @@
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@ -5,7 +5,7 @@
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</parent>

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@ -0,0 +1,18 @@
package ca.uhn.fhir.context;
import ca.uhn.fhir.model.api.annotation.ResourceDef;
import org.hl7.fhir.r4.model.DomainResource;
import org.hl7.fhir.r4.model.ResourceType;
@ResourceDef(name = "Clock", profile = "http://example.org/StructureDefinition/Clock")
public class Clock extends DomainResource {
@Override
public DomainResource copy() {
return null;
}
@Override
public ResourceType getResourceType() {
return null;
}
}

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@ -0,0 +1,18 @@
package ca.uhn.fhir.context;
import ca.uhn.fhir.model.api.annotation.ResourceDef;
import org.hl7.fhir.r4.model.DomainResource;
import org.hl7.fhir.r4.model.ResourceType;
@ResourceDef(name = "CustomResourceResourceDef", profile = "http://example.org/StructureDefinition/CustomResourceResourceDef")
public class CustomResourceClassName extends DomainResource {
@Override
public DomainResource copy() {
return null;
}
@Override
public ResourceType getResourceType() {
return null;
}
}

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@ -0,0 +1,48 @@
package ca.uhn.fhir.context;
import org.junit.jupiter.api.Test;
import java.util.Set;
import static org.junit.jupiter.api.Assertions.assertThrows;
import static org.junit.jupiter.api.Assertions.assertTrue;
public class FhirContextR4Test {
@Test
void customResourceTypeClassNameAndResourceDefSame() {
final FhirContext fhirContext = FhirContext.forR4();
fhirContext.registerCustomType(Clock.class);
// This is needed in order to trigger scanResourceTypes() which in turn populates the custom resource types in fhirContext.getResourceTypes()
fhirContext.getAllResourceDefinitions();
final Set<String> resourceTypes = fhirContext.getResourceTypes();
assertTrue(resourceTypes.contains("Clock"));
}
@Test
void customResourceTypeClassNameAndResourceDefDifferent() {
final FhirContext fhirContext = FhirContext.forR4();
fhirContext.registerCustomType(CustomResourceClassName.class);
// This is needed in order to trigger scanResourceTypes() which in turn populates the custom resource types in fhirContext.getResourceTypes()
fhirContext.getAllResourceDefinitions();
final Set<String> resourceTypes = fhirContext.getResourceTypes();
assertTrue(resourceTypes.contains("CustomResourceResourceDef"));
}
@Test
void customResourceTypesNoResourceDef() {
final FhirContext fhirContext = FhirContext.forR4();
fhirContext.registerCustomType(NoResourceDef.class);
assertThrows(ConfigurationException.class, () -> fhirContext.getAllResourceDefinitions());
}
}

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@ -0,0 +1,17 @@
package ca.uhn.fhir.context;
import ca.uhn.fhir.model.api.annotation.ResourceDef;
import org.hl7.fhir.r4.model.DomainResource;
import org.hl7.fhir.r4.model.ResourceType;
public class NoResourceDef extends DomainResource {
@Override
public DomainResource copy() {
return null;
}
@Override
public ResourceType getResourceType() {
return null;
}
}

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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@ -9,7 +9,7 @@
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<packaging>pom</packaging>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<name>HAPI-FHIR</name>
<description>An open-source implementation of the FHIR specification in Java.</description>

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@ -7,7 +7,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>

View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>

View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.7.13-SNAPSHOT</version>
<version>6.7.14-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>