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issue #2777 - bulkdata authz enforcement in fhir-smart #2785

Merged
merged 9 commits into from
Oct 22, 2021
Merged

issue #2777 - bulkdata authz enforcement in fhir-smart #2785

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543e9f5
issue #2777 - bulkdata authz enforcement in fhir-smart
lmsurpre Sep 20, 2021
8aef9e0
Guard MyInterceptor methods from interactions from other tests
lmsurpre Sep 21, 2021
ff520bf
issue #2777 - intercept the other bulkdata operations as well
lmsurpre Sep 22, 2021
adcd131
post-merge updates
lmsurpre Oct 18, 2021
c9a3784
fix javadoc for new FHIRPersistenceInterceptorMgr
lmsurpre Oct 19, 2021
4e62a94
Introduce fhir-server-spi
lmsurpre Oct 19, 2021
cae989f
update META-INF/services names to match the new spi packages
lmsurpre Oct 19, 2021
a866d19
Merge pull request #2870 from IBM/fhir-server-spi
lmsurpre Oct 21, 2021
a8d616f
Updates per PR review
lmsurpre Oct 22, 2021
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2 changes: 1 addition & 1 deletion ...ver/src/main/java/com/ibm/fhir/cql/engine/server/retrieve/ServerFHIRRetrieveProvider.java
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Expand Up @@ -26,7 +26,7 @@
import com.ibm.fhir.model.resource.Resource;
import com.ibm.fhir.persistence.SingleResourceResult;
import com.ibm.fhir.search.SearchConstants;
import com.ibm.fhir.server.operation.spi.FHIRResourceHelpers;
import com.ibm.fhir.server.spi.operation.FHIRResourceHelpers;

/**
* This is an implementation of a retrieve provider for the CQL Engine that uses
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2 changes: 1 addition & 1 deletion ...c/main/java/com/ibm/fhir/cql/engine/server/terminology/ServerFHIRTerminologyProvider.java
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Expand Up @@ -22,7 +22,7 @@
import com.ibm.fhir.model.type.Uri;
import com.ibm.fhir.model.type.code.ResourceType;
import com.ibm.fhir.persistence.SingleResourceResult;
import com.ibm.fhir.server.operation.spi.FHIRResourceHelpers;
import com.ibm.fhir.server.spi.operation.FHIRResourceHelpers;
import com.ibm.fhir.term.service.FHIRTermService;
import com.ibm.fhir.term.service.LookupOutcome;
import com.ibm.fhir.term.service.ValidationOutcome;
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2 changes: 1 addition & 1 deletion ...src/test/java/com/ibm/fhir/cql/engine/server/retrieve/ServerFHIRRetrieveProviderTest.java
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import com.ibm.fhir.model.type.code.BundleType;
import com.ibm.fhir.persistence.SingleResourceResult;
import com.ibm.fhir.persistence.exception.FHIRPersistenceResourceNotFoundException;
import com.ibm.fhir.server.operation.spi.FHIRResourceHelpers;
import com.ibm.fhir.server.spi.operation.FHIRResourceHelpers;

public class ServerFHIRRetrieveProviderTest {

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2 changes: 1 addition & 1 deletion ...st/java/com/ibm/fhir/cql/engine/server/terminology/ServerFHIRTerminologyProviderTest.java
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Expand Up @@ -36,7 +36,7 @@
import com.ibm.fhir.model.type.Uri;
import com.ibm.fhir.model.type.code.PublicationStatus;
import com.ibm.fhir.persistence.SingleResourceResult;
import com.ibm.fhir.server.operation.spi.FHIRResourceHelpers;
import com.ibm.fhir.server.spi.operation.FHIRResourceHelpers;
import com.ibm.fhir.term.service.FHIRTermService;
import com.ibm.fhir.term.service.LookupOutcome;
import com.ibm.fhir.term.service.ValidationOutcome;
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9 changes: 8 additions & 1 deletion cql/operation/fhir-operation-apply/pom.xml
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Expand Up @@ -15,8 +15,15 @@
<dependencies>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>fhir-server</artifactId>
<artifactId>fhir-server-spi</artifactId>
<version>${project.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>fhir-persistence</artifactId>
<version>${project.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>jakarta.ws.rs</groupId>
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8 changes: 4 additions & 4 deletions ...ation/fhir-operation-apply/src/main/java/com/ibm/fhir/operation/apply/ApplyOperation.java
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Expand Up @@ -45,10 +45,10 @@
import com.ibm.fhir.model.type.code.IssueSeverity;
import com.ibm.fhir.model.type.code.IssueType;
import com.ibm.fhir.registry.FHIRRegistry;
import com.ibm.fhir.server.operation.spi.AbstractOperation;
import com.ibm.fhir.server.operation.spi.FHIROperationContext;
import com.ibm.fhir.server.operation.spi.FHIRResourceHelpers;
import com.ibm.fhir.server.util.FHIROperationUtil;
import com.ibm.fhir.server.spi.operation.AbstractOperation;
import com.ibm.fhir.server.spi.operation.FHIROperationContext;
import com.ibm.fhir.server.spi.operation.FHIROperationUtil;
import com.ibm.fhir.server.spi.operation.FHIRResourceHelpers;

/**
* <code>$apply</code> is an operation specific to PlanDefinition.
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0 ...m.fhir.server.operation.spi.FHIROperation → ...m.fhir.server.spi.operation.FHIROperation
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4 changes: 3 additions & 1 deletion cql/operation/fhir-operation-cpg/pom.xml
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Expand Up @@ -28,12 +28,14 @@
<groupId>com.ibm.fhir</groupId>
<artifactId>fhir-model</artifactId>
<version>${project.version}</version>
<scope>provided</scope>
</dependency>

<dependency>
<groupId>com.ibm.fhir</groupId>
<artifactId>fhir-server</artifactId>
<artifactId>fhir-server-spi</artifactId>
<version>${project.version}</version>
<scope>provided</scope>
</dependency>

<dependency>
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4 changes: 2 additions & 2 deletions ...ion/fhir-operation-cpg/src/main/java/com/ibm/fhir/operation/cpg/AbstractCqlOperation.java
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import com.ibm.fhir.model.resource.Library;
import com.ibm.fhir.model.resource.Parameters;
import com.ibm.fhir.model.resource.Parameters.Parameter;
import com.ibm.fhir.server.operation.spi.AbstractOperation;
import com.ibm.fhir.server.operation.spi.FHIRResourceHelpers;
import com.ibm.fhir.server.spi.operation.AbstractOperation;
import com.ibm.fhir.server.spi.operation.FHIRResourceHelpers;

public abstract class AbstractCqlOperation extends AbstractOperation {

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4 changes: 2 additions & 2 deletions cql/operation/fhir-operation-cpg/src/main/java/com/ibm/fhir/operation/cpg/CqlOperation.java
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import com.ibm.fhir.model.type.code.PublicationStatus;
import com.ibm.fhir.model.type.code.RelatedArtifactType;
import com.ibm.fhir.registry.FHIRRegistry;
import com.ibm.fhir.server.operation.spi.FHIROperationContext;
import com.ibm.fhir.server.operation.spi.FHIRResourceHelpers;
import com.ibm.fhir.server.spi.operation.FHIROperationContext;
import com.ibm.fhir.server.spi.operation.FHIRResourceHelpers;

public class CqlOperation extends AbstractCqlOperation {

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4 changes: 2 additions & 2 deletions ...fhir-operation-cpg/src/main/java/com/ibm/fhir/operation/cpg/LibraryEvaluateOperation.java
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Expand Up @@ -31,8 +31,8 @@
import com.ibm.fhir.model.type.code.ResourceType;
import com.ibm.fhir.persistence.SingleResourceResult;
import com.ibm.fhir.registry.FHIRRegistry;
import com.ibm.fhir.server.operation.spi.FHIROperationContext;
import com.ibm.fhir.server.operation.spi.FHIRResourceHelpers;
import com.ibm.fhir.server.spi.operation.FHIROperationContext;
import com.ibm.fhir.server.spi.operation.FHIRResourceHelpers;

public class LibraryEvaluateOperation extends AbstractCqlOperation {

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0 ...m.fhir.server.operation.spi.FHIROperation → ...m.fhir.server.spi.operation.FHIROperation
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4 changes: 2 additions & 2 deletions ...fhir-operation-cpg/src/test/java/com/ibm/fhir/operation/cpg/AbstractCqlOperationTest.java
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Expand Up @@ -33,8 +33,8 @@
import com.ibm.fhir.model.resource.Resource;
import com.ibm.fhir.model.type.code.OperationKind;
import com.ibm.fhir.model.type.code.PublicationStatus;
import com.ibm.fhir.server.operation.spi.FHIROperationContext;
import com.ibm.fhir.server.operation.spi.FHIRResourceHelpers;
import com.ibm.fhir.server.spi.operation.FHIROperationContext;
import com.ibm.fhir.server.spi.operation.FHIRResourceHelpers;

public class AbstractCqlOperationTest extends BaseCqlOperationTest<AbstractCqlOperation> {

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29 changes: 18 additions & 11 deletions ...eration/fhir-operation-cpg/src/test/java/com/ibm/fhir/operation/cpg/CqlOperationTest.java
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Expand Up @@ -10,8 +10,6 @@
import static com.ibm.fhir.cql.helpers.ModelHelper.concept;
import static com.ibm.fhir.cql.helpers.ModelHelper.fhirboolean;
import static com.ibm.fhir.cql.helpers.ModelHelper.fhirstring;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.fail;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.ArgumentMatchers.anyBoolean;
import static org.mockito.ArgumentMatchers.anyString;
Expand All @@ -20,12 +18,14 @@
import static org.mockito.Mockito.mockStatic;
import static org.mockito.Mockito.spy;
import static org.mockito.Mockito.when;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.fail;

import javax.ws.rs.core.MultivaluedMap;

import org.testng.annotations.Test;
import org.mockito.MockedStatic;
import org.testng.annotations.Test;

import com.ibm.fhir.cql.Constants;
import com.ibm.fhir.cql.helpers.LibraryHelper;
Expand All @@ -45,8 +45,8 @@
import com.ibm.fhir.model.type.code.EncounterStatus;
import com.ibm.fhir.model.type.code.IssueType;
import com.ibm.fhir.registry.FHIRRegistry;
import com.ibm.fhir.server.operation.spi.FHIROperationContext;
import com.ibm.fhir.server.operation.spi.FHIRResourceHelpers;
import com.ibm.fhir.server.spi.operation.FHIROperationContext;
import com.ibm.fhir.server.spi.operation.FHIRResourceHelpers;

public class CqlOperationTest extends BaseCqlOperationTest<CqlOperation> {

Expand All @@ -63,8 +63,15 @@ public void testInlineExpression() throws Exception {
String encounterCode = "office-visit";
Coding reason = coding(codesystem, encounterCode);

Encounter encounter =
Encounter.builder().reasonCode(concept(reason)).status(EncounterStatus.FINISHED).clazz(reason).period(Period.builder().start(DateTime.now()).end(DateTime.now()).build()).build();
Encounter encounter = Encounter.builder()
.reasonCode(concept(reason))
.status(EncounterStatus.FINISHED)
.clazz(reason)
.period(Period.builder()
.start(DateTime.now())
.end(DateTime.now())
.build())
.build();

String expression = "[Encounter] e where e.status = 'finished'";

Expand All @@ -85,7 +92,7 @@ public void testInlineExpression() throws Exception {

// when(mockRegistry.getResource(javastring(fhirHelpers.getUrl()), Library.class)).thenReturn(fhirHelpers);

FHIROperationContext ctx = FHIROperationContext.createSystemOperationContext();
FHIROperationContext ctx = FHIROperationContext.createSystemOperationContext(null);
Parameters result = getOperation().doInvoke(ctx, null, null, null, parameters, resourceHelper);
assertNotNull(result);

Expand Down Expand Up @@ -136,7 +143,7 @@ public void testInlineExpressionWithIncludes() throws Exception {
canonical = ModelHelper.canonical(modelInfo.getUrl(), modelInfo.getVersion());
when(mockRegistry.getResource(canonical.getValue(), Library.class)).thenReturn(modelInfo);

FHIROperationContext ctx = FHIROperationContext.createSystemOperationContext();
FHIROperationContext ctx = FHIROperationContext.createSystemOperationContext("cql");
getOperation().doInvoke(ctx, null, null, null, parameters, resourceHelper);
}
}
Expand All @@ -158,7 +165,7 @@ public void testInlineExpressionInvalid() throws Exception {
FHIRRegistry mockRegistry = spy(FHIRRegistry.class);
staticRegistry.when(FHIRRegistry::getInstance).thenReturn(mockRegistry);

FHIROperationContext ctx = FHIROperationContext.createSystemOperationContext();
FHIROperationContext ctx = FHIROperationContext.createSystemOperationContext("cql");
getOperation().doInvoke(ctx, null, null, null, parameters, resourceHelper);
fail("Missing expected Exception");
} catch (FHIROperationException fex) {
Expand Down Expand Up @@ -189,7 +196,7 @@ public void testInlineExpressionWithDebug() throws Exception {
FHIRRegistry mockRegistry = spy(FHIRRegistry.class);
staticRegistry.when(FHIRRegistry::getInstance).thenReturn(mockRegistry);

FHIROperationContext ctx = FHIROperationContext.createSystemOperationContext();
FHIROperationContext ctx = FHIROperationContext.createSystemOperationContext("cql");
Parameters result = getOperation().doInvoke(ctx, null, null, null, parameters, resourceHelper);

assertNotNull(result);
Expand Down
2 changes: 1 addition & 1 deletion ...-operation-cpg/src/test/java/com/ibm/fhir/operation/cpg/LibraryEvaluateOperationTest.java
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Expand Up @@ -42,7 +42,7 @@
import com.ibm.fhir.model.type.code.EncounterStatus;
import com.ibm.fhir.model.type.code.ProcedureStatus;
import com.ibm.fhir.registry.FHIRRegistry;
import com.ibm.fhir.server.operation.spi.FHIRResourceHelpers;
import com.ibm.fhir.server.spi.operation.FHIRResourceHelpers;

public class LibraryEvaluateOperationTest extends BaseCqlOperationTest<LibraryEvaluateOperation> {

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9 changes: 9 additions & 0 deletions cql/operation/fhir-operation-cqf/pom.xml
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Expand Up @@ -34,12 +34,21 @@
<groupId>com.ibm.fhir</groupId>
<artifactId>fhir-model</artifactId>
<version>${project.version}</version>
<scope>provided</scope>
</dependency>

<dependency>
<groupId>com.ibm.fhir</groupId>
<artifactId>fhir-server-spi</artifactId>
<version>${project.version}</version>
<scope>provided</scope>
</dependency>

<dependency>
<groupId>com.ibm.fhir</groupId>
<artifactId>fhir-search</artifactId>
<version>${project.version}</version>
<scope>provided</scope>
</dependency>

<dependency>
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8 changes: 4 additions & 4 deletions ...ation-cqf/src/main/java/com/ibm/fhir/operation/cqf/AbstractDataRequirementsOperation.java
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Expand Up @@ -24,10 +24,10 @@
import com.ibm.fhir.model.type.RelatedArtifact;
import com.ibm.fhir.model.type.code.PublicationStatus;
import com.ibm.fhir.model.type.code.RelatedArtifactType;
import com.ibm.fhir.server.operation.spi.AbstractOperation;
import com.ibm.fhir.server.operation.spi.FHIROperationContext;
import com.ibm.fhir.server.operation.spi.FHIRResourceHelpers;
import com.ibm.fhir.server.util.FHIROperationUtil;
import com.ibm.fhir.server.spi.operation.AbstractOperation;
import com.ibm.fhir.server.spi.operation.FHIROperationContext;
import com.ibm.fhir.server.spi.operation.FHIROperationUtil;
import com.ibm.fhir.server.spi.operation.FHIRResourceHelpers;

public abstract class AbstractDataRequirementsOperation extends AbstractOperation {
public static final String PARAM_OUT_RETURN = "return";
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4 changes: 2 additions & 2 deletions ...fhir-operation-cqf/src/main/java/com/ibm/fhir/operation/cqf/AbstractMeasureOperation.java
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Expand Up @@ -45,8 +45,8 @@
import com.ibm.fhir.model.resource.Patient;
import com.ibm.fhir.model.type.Date;
import com.ibm.fhir.registry.FHIRRegistry;
import com.ibm.fhir.server.operation.spi.AbstractOperation;
import com.ibm.fhir.server.operation.spi.FHIRResourceHelpers;
import com.ibm.fhir.server.spi.operation.AbstractOperation;
import com.ibm.fhir.server.spi.operation.FHIRResourceHelpers;

public abstract class AbstractMeasureOperation extends AbstractOperation {

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6 changes: 3 additions & 3 deletions ...ration/fhir-operation-cqf/src/main/java/com/ibm/fhir/operation/cqf/CareGapsOperation.java
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Expand Up @@ -34,9 +34,9 @@
import com.ibm.fhir.model.type.code.ResourceType;
import com.ibm.fhir.registry.FHIRRegistry;
import com.ibm.fhir.search.SearchConstants;
import com.ibm.fhir.server.operation.spi.FHIROperationContext;
import com.ibm.fhir.server.operation.spi.FHIRResourceHelpers;
import com.ibm.fhir.server.util.FHIROperationUtil;
import com.ibm.fhir.server.spi.operation.FHIROperationContext;
import com.ibm.fhir.server.spi.operation.FHIROperationUtil;
import com.ibm.fhir.server.spi.operation.FHIRResourceHelpers;

public class CareGapsOperation extends AbstractMeasureOperation {

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6 changes: 3 additions & 3 deletions ...fhir-operation-cqf/src/main/java/com/ibm/fhir/operation/cqf/EvaluateMeasureOperation.java
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Expand Up @@ -27,9 +27,9 @@
import com.ibm.fhir.model.type.code.ResourceType;
import com.ibm.fhir.persistence.SingleResourceResult;
import com.ibm.fhir.registry.FHIRRegistry;
import com.ibm.fhir.server.operation.spi.FHIROperationContext;
import com.ibm.fhir.server.operation.spi.FHIRResourceHelpers;
import com.ibm.fhir.server.util.FHIROperationUtil;
import com.ibm.fhir.server.spi.operation.FHIROperationContext;
import com.ibm.fhir.server.spi.operation.FHIROperationUtil;
import com.ibm.fhir.server.spi.operation.FHIRResourceHelpers;

public class EvaluateMeasureOperation extends AbstractMeasureOperation {

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4 changes: 2 additions & 2 deletions ...ration-cqf/src/main/java/com/ibm/fhir/operation/cqf/LibraryDataRequirementsOperation.java
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Expand Up @@ -18,8 +18,8 @@
import com.ibm.fhir.model.type.code.ResourceType;
import com.ibm.fhir.persistence.SingleResourceResult;
import com.ibm.fhir.registry.FHIRRegistry;
import com.ibm.fhir.server.operation.spi.FHIROperationContext;
import com.ibm.fhir.server.operation.spi.FHIRResourceHelpers;
import com.ibm.fhir.server.spi.operation.FHIROperationContext;
import com.ibm.fhir.server.spi.operation.FHIRResourceHelpers;

public class LibraryDataRequirementsOperation extends AbstractDataRequirementsOperation {

Expand Down
4 changes: 2 additions & 2 deletions ...r-operation-cqf/src/main/java/com/ibm/fhir/operation/cqf/MeasureCollectDataOperation.java
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Expand Up @@ -25,8 +25,8 @@
import com.ibm.fhir.model.util.ModelSupport.ElementInfo;
import com.ibm.fhir.persistence.SingleResourceResult;
import com.ibm.fhir.registry.FHIRRegistry;
import com.ibm.fhir.server.operation.spi.FHIROperationContext;
import com.ibm.fhir.server.operation.spi.FHIRResourceHelpers;
import com.ibm.fhir.server.spi.operation.FHIROperationContext;
import com.ibm.fhir.server.spi.operation.FHIRResourceHelpers;

public class MeasureCollectDataOperation extends EvaluateMeasureOperation {

Expand Down
4 changes: 2 additions & 2 deletions ...ration-cqf/src/main/java/com/ibm/fhir/operation/cqf/MeasureDataRequirementsOperation.java
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Expand Up @@ -20,8 +20,8 @@
import com.ibm.fhir.model.type.code.ResourceType;
import com.ibm.fhir.persistence.SingleResourceResult;
import com.ibm.fhir.registry.FHIRRegistry;
import com.ibm.fhir.server.operation.spi.FHIROperationContext;
import com.ibm.fhir.server.operation.spi.FHIRResourceHelpers;
import com.ibm.fhir.server.spi.operation.FHIROperationContext;
import com.ibm.fhir.server.spi.operation.FHIRResourceHelpers;

public class MeasureDataRequirementsOperation extends AbstractDataRequirementsOperation {

Expand Down
8 changes: 4 additions & 4 deletions ...ir-operation-cqf/src/main/java/com/ibm/fhir/operation/cqf/MeasureSubmitDataOperation.java
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Expand Up @@ -21,10 +21,10 @@
import com.ibm.fhir.model.type.code.BundleType;
import com.ibm.fhir.model.type.code.HTTPVerb;
import com.ibm.fhir.registry.FHIRRegistry;
import com.ibm.fhir.server.operation.spi.AbstractOperation;
import com.ibm.fhir.server.operation.spi.FHIROperationContext;
import com.ibm.fhir.server.operation.spi.FHIRResourceHelpers;
import com.ibm.fhir.server.util.FHIROperationUtil;
import com.ibm.fhir.server.spi.operation.AbstractOperation;
import com.ibm.fhir.server.spi.operation.FHIROperationContext;
import com.ibm.fhir.server.spi.operation.FHIROperationUtil;
import com.ibm.fhir.server.spi.operation.FHIRResourceHelpers;

public class MeasureSubmitDataOperation extends AbstractOperation {

Expand Down
0 ...m.fhir.server.operation.spi.FHIROperation → ...m.fhir.server.spi.operation.FHIROperation
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4 changes: 2 additions & 2 deletions ...ation-cqf/src/test/java/com/ibm/fhir/operation/cqf/BaseDataRequirementsOperationTest.java
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Expand Up @@ -45,8 +45,8 @@
import com.ibm.fhir.model.type.code.PublicationStatus;
import com.ibm.fhir.model.type.code.RelatedArtifactType;
import com.ibm.fhir.registry.FHIRRegistry;
import com.ibm.fhir.server.operation.spi.FHIROperationContext;
import com.ibm.fhir.server.operation.spi.FHIRResourceHelpers;
import com.ibm.fhir.server.spi.operation.FHIROperationContext;
import com.ibm.fhir.server.spi.operation.FHIRResourceHelpers;

public abstract class BaseDataRequirementsOperationTest {

Expand Down
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