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barhodes wants to merge 9 commits into from
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Use HAPI Repository interface #654

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1ea91dc
Use HAPI Repository interface
barhodes Apr 10, 2025
a3c3de7
cleanup
barhodes Apr 10, 2025
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spotless
barhodes Apr 10, 2025
f401f3b
cleanup
barhodes Apr 10, 2025
57a5f43
cleanup
barhodes Apr 11, 2025
a9f5f60
cleanup
barhodes Apr 11, 2025
2ee5e15
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barhodes Apr 11, 2025
2b7a430
Use HAPI classes (wip)
barhodes Apr 17, 2025
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barhodes Apr 17, 2025
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4 changes: 2 additions & 2 deletions cqf-fhir-api/src/main/java/org/opencds/cqf/fhir/api/Repository.java
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Expand Up @@ -7,7 +7,6 @@
import ca.uhn.fhir.rest.server.exceptions.ForbiddenOperationException;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.NotImplementedOperationException;
import com.google.common.annotations.Beta;
import java.util.Collections;
import java.util.List;
import java.util.Map;
Expand All @@ -18,6 +17,7 @@
import org.hl7.fhir.instance.model.api.IIdType;

/**
* @deprecated
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@lukedegruchy lukedegruchy Apr 11, 2025

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Where did this requirement come from?

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@barhodes barhodes Apr 11, 2025

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We've been working towards moving this interface down into HAPI for awhile now. That happened with the 8.0.0 release.

* <p>
* NOTE: This API is still incubating. In particular, we're looking at ways to provide a fluent
* pattern for it. The intent is to eventually promote it up to the HAPI FHIR core once all
Expand Down Expand Up @@ -67,7 +67,7 @@
*
* @see <a href="https://www.hl7.org/fhir/http.html">FHIR REST API</a>
*/
@Beta
@Deprecated(since = "3.20.0", forRemoval = true)
public interface Repository {

// CRUD starts here
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2 changes: 1 addition & 1 deletion ...mark/src/test/java/org/opencds/cqf/fhir/benchmark/ActivityDefinitionProcessorFactory.java
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@@ -1,6 +1,6 @@
package org.opencds.cqf.fhir.benchmark;

import org.opencds.cqf.fhir.api.Repository;
import ca.uhn.fhir.repository.Repository;
import org.opencds.cqf.fhir.cr.activitydefinition.ActivityDefinitionProcessor;
import org.opencds.cqf.fhir.utility.repository.operations.IActivityDefinitionProcessor;
import org.opencds.cqf.fhir.utility.repository.operations.IActivityDefinitionProcessorFactory;
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2 changes: 1 addition & 1 deletion cqf-fhir-benchmark/src/test/java/org/opencds/cqf/fhir/benchmark/measure/r4/Measure.java
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Expand Up @@ -3,13 +3,13 @@
import static org.opencds.cqf.fhir.test.Resources.getResourcePath;

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.repository.Repository;
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@lukedegruchy lukedegruchy Apr 11, 2025

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What happens if we need to update this interface? Will we now have to wait at least one more release cycle to propagate it to clinical-reasoning + cdr-cr? Meaning, with a dependency sequence of hapi-fhir <- clinical-reasoning <- cdr-cr.

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@barhodes barhodes Apr 11, 2025

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Yes, and we already have that dependency for the models. Ideally this interface will not be changing often, if at all.

import java.nio.file.Paths;
import java.time.ZonedDateTime;
import java.util.function.Supplier;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.MeasureReport;
import org.opencds.cqf.fhir.api.Repository;
import org.opencds.cqf.fhir.cql.engine.retrieve.RetrieveSettings.SEARCH_FILTER_MODE;
import org.opencds.cqf.fhir.cql.engine.retrieve.RetrieveSettings.TERMINOLOGY_FILTER_MODE;
import org.opencds.cqf.fhir.cql.engine.terminology.TerminologySettings.VALUESET_EXPANSION_MODE;
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2 changes: 1 addition & 1 deletion ...hmark/src/test/java/org/opencds/cqf/fhir/benchmark/plandefinition/TestPlanDefinition.java
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Expand Up @@ -17,6 +17,7 @@

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.repository.Repository;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
Expand All @@ -36,7 +37,6 @@
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.json.JSONException;
import org.opencds.cqf.cql.engine.model.ModelResolver;
import org.opencds.cqf.fhir.api.Repository;
import org.opencds.cqf.fhir.benchmark.TestOperationProvider;
import org.opencds.cqf.fhir.benchmark.helpers.DataRequirementsLibrary;
import org.opencds.cqf.fhir.benchmark.helpers.GeneratedPackage;
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2 changes: 1 addition & 1 deletion ...nchmark/src/test/java/org/opencds/cqf/fhir/benchmark/questionnaire/TestQuestionnaire.java
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Expand Up @@ -3,6 +3,7 @@
import static org.opencds.cqf.fhir.test.Resources.getResourcePath;

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.repository.Repository;
import java.nio.file.Paths;
import java.util.List;
import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
Expand All @@ -12,7 +13,6 @@
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.opencds.cqf.fhir.api.Repository;
import org.opencds.cqf.fhir.cql.EvaluationSettings;
import org.opencds.cqf.fhir.cql.engine.retrieve.RetrieveSettings.SEARCH_FILTER_MODE;
import org.opencds.cqf.fhir.cql.engine.retrieve.RetrieveSettings.TERMINOLOGY_FILTER_MODE;
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2 changes: 1 addition & 1 deletion cqf-fhir-cql/src/main/java/org/opencds/cqf/fhir/cql/Engines.java
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Expand Up @@ -3,6 +3,7 @@
import static com.google.common.base.Preconditions.checkNotNull;

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.repository.Repository;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
Expand All @@ -24,7 +25,6 @@
import org.opencds.cqf.cql.engine.fhir.converter.FhirTypeConverterFactory;
import org.opencds.cqf.cql.engine.retrieve.RetrieveProvider;
import org.opencds.cqf.cql.engine.terminology.TerminologyProvider;
import org.opencds.cqf.fhir.api.Repository;
import org.opencds.cqf.fhir.cql.cql2elm.content.RepositoryFhirLibrarySourceProvider;
import org.opencds.cqf.fhir.cql.cql2elm.util.LibraryVersionSelector;
import org.opencds.cqf.fhir.cql.engine.parameters.CqlFhirParametersConverter;
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2 changes: 1 addition & 1 deletion cqf-fhir-cql/src/main/java/org/opencds/cqf/fhir/cql/LibraryEngine.java
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Expand Up @@ -3,6 +3,7 @@
import static java.util.Objects.requireNonNull;

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.repository.Repository;
import ca.uhn.fhir.util.ParametersUtil;
import com.google.common.collect.Lists;
import jakarta.annotation.Nullable;
Expand All @@ -22,7 +23,6 @@
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.opencds.cqf.cql.engine.execution.CqlEngine;
import org.opencds.cqf.cql.engine.execution.EvaluationResult;
import org.opencds.cqf.fhir.api.Repository;
import org.opencds.cqf.fhir.cql.engine.parameters.CqlFhirParametersConverter;
import org.opencds.cqf.fhir.cql.engine.parameters.CqlParameterDefinition;
import org.opencds.cqf.fhir.utility.Canonicals;
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2 changes: 1 addition & 1 deletion ...in/java/org/opencds/cqf/fhir/cql/cql2elm/content/RepositoryFhirLibrarySourceProvider.java
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Expand Up @@ -3,11 +3,11 @@
import static java.util.Objects.requireNonNull;

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.repository.Repository;
import java.util.ArrayList;
import org.hl7.elm.r1.VersionedIdentifier;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.opencds.cqf.fhir.api.Repository;
import org.opencds.cqf.fhir.cql.cql2elm.util.LibraryVersionSelector;
import org.opencds.cqf.fhir.utility.adapter.IAdapterFactory;
import org.opencds.cqf.fhir.utility.iterable.BundleIterable;
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2 changes: 1 addition & 1 deletion ...ql/src/main/java/org/opencds/cqf/fhir/cql/engine/retrieve/RepositoryRetrieveProvider.java
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Expand Up @@ -4,6 +4,7 @@

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.repository.Repository;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
Expand All @@ -14,7 +15,6 @@
import org.opencds.cqf.cql.engine.runtime.Code;
import org.opencds.cqf.cql.engine.runtime.Interval;
import org.opencds.cqf.cql.engine.terminology.TerminologyProvider;
import org.opencds.cqf.fhir.api.Repository;
import org.opencds.cqf.fhir.utility.iterable.BundleMappingIterable;

public class RepositoryRetrieveProvider extends BaseRetrieveProvider {
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2 changes: 1 addition & 1 deletion .../main/java/org/opencds/cqf/fhir/cql/engine/terminology/RepositoryTerminologyProvider.java
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Expand Up @@ -4,6 +4,7 @@

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.fhirpath.IFhirPath;
import ca.uhn.fhir.repository.Repository;
import ca.uhn.fhir.util.BundleUtil;
import java.util.Collections;
import java.util.Comparator;
Expand All @@ -19,7 +20,6 @@
import org.opencds.cqf.cql.engine.terminology.CodeSystemInfo;
import org.opencds.cqf.cql.engine.terminology.TerminologyProvider;
import org.opencds.cqf.cql.engine.terminology.ValueSetInfo;
import org.opencds.cqf.fhir.api.Repository;
import org.opencds.cqf.fhir.cql.engine.terminology.TerminologySettings.VALUESET_EXPANSION_MODE;
import org.opencds.cqf.fhir.cql.engine.terminology.TerminologySettings.VALUESET_PRE_EXPANSION_MODE;
import org.opencds.cqf.fhir.utility.FhirPathCache;
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2 changes: 1 addition & 1 deletion cqf-fhir-cql/src/test/java/org/opencds/cqf/fhir/cql/LibraryEngineTests.java
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Expand Up @@ -7,6 +7,7 @@
import static org.opencds.cqf.fhir.utility.r4.Parameters.part;

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.repository.Repository;
import java.io.ByteArrayInputStream;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
Expand All @@ -27,7 +28,6 @@
import org.hl7.fhir.r4.model.Task;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.opencds.cqf.fhir.api.Repository;
import org.opencds.cqf.fhir.utility.CqfExpression;
import org.opencds.cqf.fhir.utility.repository.ig.IgRepository;

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5 changes: 3 additions & 2 deletions ...t/java/org/opencds/cqf/fhir/cql/engine/terminology/RepositoryTerminologyProviderTest.java
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Expand Up @@ -8,13 +8,14 @@
import static org.mockito.Mockito.when;

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.repository.Repository;
import java.util.Map;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.ValueSet;
import org.junit.jupiter.api.Test;
import org.opencds.cqf.cql.engine.runtime.Code;
import org.opencds.cqf.cql.engine.terminology.TerminologyProvider;
import org.opencds.cqf.cql.engine.terminology.ValueSetInfo;
import org.opencds.cqf.fhir.api.Repository;

class RepositoryTerminologyProviderTest {

Expand Down Expand Up @@ -75,7 +76,7 @@ Repository mockRepositoryWithValueSet(ValueSet valueSet) {
when(mockRepository.fhirContext()).thenReturn(FhirContext.forR4Cached());
Bundle bundle = new Bundle();
bundle.addEntry().setFullUrl(valueSet.getUrl()).setResource(valueSet);
when(mockRepository.search(any(), any(), any(), isNull())).thenReturn(bundle);
when(mockRepository.search(any(), any(), any(Map.class), isNull())).thenReturn(bundle);
return mockRepository;
}

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2 changes: 1 addition & 1 deletion cqf-fhir-cr-cli/src/main/java/org/opencds/cqf/fhir/cr/cli/command/CqlCommand.java
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Expand Up @@ -2,6 +2,7 @@

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.repository.Repository;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.List;
Expand All @@ -20,7 +21,6 @@
import org.hl7.fhir.r5.context.IWorkerContext.ILoggingService;
import org.opencds.cqf.cql.engine.execution.EvaluationResult;
import org.opencds.cqf.cql.engine.execution.ExpressionResult;
import org.opencds.cqf.fhir.api.Repository;
import org.opencds.cqf.fhir.cql.CqlOptions;
import org.opencds.cqf.fhir.cql.Engines;
import org.opencds.cqf.fhir.cql.EvaluationSettings;
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4 changes: 2 additions & 2 deletions cqf-fhir-cr-cli/src/test/java/org/opencds/cqf/fhir/cr/cli/CliTest.java
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Expand Up @@ -410,8 +410,8 @@ void qICoreSupplementalDataElements() {
output.contains(
"SDE Race=[Code { code: 1586-7, system: urn:oid:2.16.840.1.113883.6.238, version: null, display: Shoshone }, Code { code: 2036-2, system: urn:oid:2.16.840.1.113883.6.238, version: null, display: Filipino }, Code { code: 1735-0, system: urn:oid:2.16.840.1.113883.6.238, version: null, display: Alaska Native }]"));
assertTrue(output.contains("SDE Payer=[Tuple {\n" + " code: Concept {\n"
+ "\tCode { code: 59, system: urn:oid:2.16.840.1.113883.3.221.5, version: null, display: Other Private Insurance }\n"
+ "}\n" + " period: Interval[2011-05-23, 2012-05-23]\n" + "}]"));
+ "\tCode { code: 59, system: urn:oid:2.16.840.1.113883.3.221.5, version: null, display: Other Private Insurance }\n"
+ "}\n" + " period: Interval[2011-05-23, 2012-05-23]\n" + "}]"));
assertTrue(
output.contains(
"SDE Sex=Code { code: M, system: http://hl7.org/fhir/v3/AdministrativeGender, version: null, display: Male }"));
Expand Down
2 changes: 1 addition & 1 deletion cqf-fhir-cr-hapi/src/main/java/org/opencds/cqf/fhir/cr/hapi/cdshooks/CdsCrService.java
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Expand Up @@ -11,6 +11,7 @@
import static org.opencds.cqf.fhir.cr.hapi.cdshooks.CdsCrConstants.CDS_PARAMETER_USER_ID;

import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.repository.Repository;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.cdshooks.CdsServiceRequestJson;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
Expand All @@ -36,7 +37,6 @@
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.opencds.cqf.fhir.api.Repository;
import org.opencds.cqf.fhir.utility.BundleHelper;
import org.opencds.cqf.fhir.utility.Canonicals;
import org.opencds.cqf.fhir.utility.Constants;
Expand Down
2 changes: 1 addition & 1 deletion cqf-fhir-cr-hapi/src/main/java/org/opencds/cqf/fhir/cr/hapi/cdshooks/CdsCrUtils.java
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@@ -1,8 +1,8 @@
package org.opencds.cqf.fhir.cr.hapi.cdshooks;

import ca.uhn.fhir.repository.Repository;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.opencds.cqf.fhir.api.Repository;

public class CdsCrUtils {

Expand Down
2 changes: 1 addition & 1 deletion cqf-fhir-cr-hapi/src/main/java/org/opencds/cqf/fhir/cr/hapi/cdshooks/ICdsCrService.java
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Expand Up @@ -2,14 +2,14 @@

import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.model.api.IModelJson;
import ca.uhn.fhir.repository.Repository;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.cdshooks.CdsServiceRequestJson;
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceResponseJson;
import java.util.Collections;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.opencds.cqf.fhir.api.Repository;

public interface ICdsCrService {
IBaseParameters encodeParams(CdsServiceRequestJson json);
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2 changes: 1 addition & 1 deletion ...api/src/main/java/org/opencds/cqf/fhir/cr/hapi/cdshooks/discovery/CrDiscoveryService.java
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Expand Up @@ -5,13 +5,13 @@
import static org.opencds.cqf.fhir.utility.Constants.CRMI_EFFECTIVE_DATA_REQUIREMENTS;

import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.repository.Repository;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceJson;
import java.util.ArrayList;
import java.util.List;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.opencds.cqf.fhir.api.Repository;
import org.opencds.cqf.fhir.cr.hapi.cdshooks.CdsCrUtils;
import org.opencds.cqf.fhir.utility.SearchHelper;
import org.opencds.cqf.fhir.utility.VersionUtilities;
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11 changes: 0 additions & 11 deletions cqf-fhir-cr-hapi/src/main/java/org/opencds/cqf/fhir/cr/hapi/common/IRepositoryFactory.java
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12 changes: 0 additions & 12 deletions ...ain/java/org/opencds/cqf/fhir/cr/hapi/common/RepositoryFactoryForRepositoryInterface.java
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4 changes: 2 additions & 2 deletions cqf-fhir-cr-hapi/src/main/java/org/opencds/cqf/fhir/cr/hapi/config/CrCdsHooksConfig.java
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Expand Up @@ -3,6 +3,8 @@
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.cache.IResourceChangeListenerRegistry;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.repository.Repository;
import ca.uhn.fhir.rest.api.server.IRepositoryFactory;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.hapi.fhir.cdshooks.api.ICdsConfigService;
import ca.uhn.hapi.fhir.cdshooks.svc.CdsServiceRegistryImpl;
Expand All @@ -12,7 +14,6 @@
import java.lang.reflect.InvocationTargetException;
import java.util.Optional;
import org.hl7.fhir.instance.model.api.IIdType;
import org.opencds.cqf.fhir.api.Repository;
import org.opencds.cqf.fhir.cr.hapi.cdshooks.CdsCrServiceRegistry;
import org.opencds.cqf.fhir.cr.hapi.cdshooks.CdsServiceInterceptor;
import org.opencds.cqf.fhir.cr.hapi.cdshooks.ICdsCrService;
Expand All @@ -22,7 +23,6 @@
import org.opencds.cqf.fhir.cr.hapi.cdshooks.discovery.ICdsCrDiscoveryServiceRegistry;
import org.opencds.cqf.fhir.cr.hapi.cdshooks.discovery.ICrDiscoveryService;
import org.opencds.cqf.fhir.cr.hapi.cdshooks.discovery.ICrDiscoveryServiceFactory;
import org.opencds.cqf.fhir.cr.hapi.common.IRepositoryFactory;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.context.annotation.Bean;
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1 change: 1 addition & 0 deletions cqf-fhir-cr-hapi/src/main/java/org/opencds/cqf/fhir/cr/hapi/config/CrProcessorConfig.java
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@@ -1,5 +1,6 @@
package org.opencds.cqf.fhir.cr.hapi.config;

import ca.uhn.fhir.rest.api.server.IRepositoryFactory;
import org.opencds.cqf.fhir.cql.EvaluationSettings;
import org.opencds.cqf.fhir.cr.activitydefinition.ActivityDefinitionProcessor;
import org.opencds.cqf.fhir.cr.hapi.common.*;
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11 changes: 2 additions & 9 deletions cqf-fhir-cr-hapi/src/main/java/org/opencds/cqf/fhir/cr/hapi/config/RepositoryConfig.java
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@@ -1,10 +1,9 @@
package org.opencds.cqf.fhir.cr.hapi.config;

import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.repository.HapiFhirRepository;
import ca.uhn.fhir.rest.api.server.IRepositoryFactory;
import ca.uhn.fhir.rest.server.RestfulServer;
import org.opencds.cqf.fhir.cr.hapi.common.IRepositoryFactory;
import org.opencds.cqf.fhir.cr.hapi.common.RepositoryFactoryForRepositoryInterface;
import org.opencds.cqf.fhir.cr.hapi.repo.HapiFhirRepository;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;

Expand All @@ -15,10 +14,4 @@ public class RepositoryConfig {
IRepositoryFactory repositoryFactory(DaoRegistry daoRegistry, RestfulServer restfulServer) {
return rd -> new HapiFhirRepository(daoRegistry, rd, restfulServer);
}

@Bean
RepositoryFactoryForRepositoryInterface repositoryFactoryForInterface(
DaoRegistry daoRegistry, RestfulServer restfulServer) {
return rd -> new HapiFhirRepository(daoRegistry, rd, restfulServer);
}
}
2 changes: 1 addition & 1 deletion cqf-fhir-cr-hapi/src/main/java/org/opencds/cqf/fhir/cr/hapi/config/dstu3/CrDstu3Config.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,10 @@

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.rest.api.server.IRepositoryFactory;
import ca.uhn.fhir.rest.server.RestfulServer;
import java.util.Arrays;
import java.util.Map;
import org.opencds.cqf.fhir.cr.hapi.common.IRepositoryFactory;
import org.opencds.cqf.fhir.cr.hapi.config.CrBaseConfig;
import org.opencds.cqf.fhir.cr.hapi.config.ProviderLoader;
import org.opencds.cqf.fhir.cr.hapi.config.ProviderSelector;
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