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[HIE-2] client registry Patient search flow implementation
[HIE-2] define ihe-pix operation and start implementation of getCRPatient [HIE-2] adding config options for default system and get patient endpoint [HIE-2] drop format param and change targetSystems to OR [HIE-2] move targetSystem param logic to controller [HIE-2] change to OperationParam in getCRPatient provider method cleanup, adding comments, refactoring Patient parsing
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6 changes: 6 additions & 0 deletions
6
api/src/main/java/org/openmrs/module/clientregistry/ClientRegistryTransactionType.java
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| @@ -0,0 +1,6 @@ | ||
| package org.openmrs.module.clientregistry; | ||
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| public enum ClientRegistryTransactionType { | ||
| FHIR, | ||
| HL7 | ||
| } |
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14
api/src/main/java/org/openmrs/module/clientregistry/api/CRPatientService.java
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| package org.openmrs.module.clientregistry.api; | ||
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| import ca.uhn.fhir.rest.server.exceptions.InternalErrorException; | ||
| import org.hl7.fhir.r4.model.Patient; | ||
| import org.openmrs.module.fhir2.api.search.param.PatientSearchParams; | ||
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| import java.util.List; | ||
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| public interface CRPatientService { | ||
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| List<Patient> getCRPatient(String sourceIdentifier, String sourceIdentifierSystem, List<String> extraTargetSystems); | ||
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| List<Patient> searchCRForPatients(PatientSearchParams patientSearchParams); | ||
| } |
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67 changes: 67 additions & 0 deletions
67
api/src/main/java/org/openmrs/module/clientregistry/api/impl/FhirCRPatientServiceImpl.java
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| @@ -0,0 +1,67 @@ | ||
| package org.openmrs.module.clientregistry.api.impl; | ||
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| import ca.uhn.fhir.rest.client.api.IGenericClient; | ||
| import ca.uhn.fhir.rest.gclient.IQuery; | ||
| import org.hl7.fhir.instance.model.api.IBaseBundle; | ||
| import org.hl7.fhir.r4.model.Bundle; | ||
| import org.hl7.fhir.r4.model.Patient; | ||
| import org.openmrs.module.clientregistry.ClientRegistryConfig; | ||
| import org.openmrs.module.clientregistry.api.CRPatientService; | ||
| import org.openmrs.module.clientregistry.providers.FhirCRConstants; | ||
| import org.openmrs.module.fhir2.FhirConstants; | ||
| import org.openmrs.module.fhir2.api.search.param.PatientSearchParams; | ||
| import org.springframework.beans.factory.annotation.Autowired; | ||
| import org.springframework.stereotype.Component; | ||
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| import java.util.List; | ||
| import java.util.stream.Collectors; | ||
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| @Component | ||
| public class FhirCRPatientServiceImpl implements CRPatientService { | ||
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| @Autowired | ||
| private IGenericClient fhirClient; | ||
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| @Autowired | ||
| private ClientRegistryConfig config; | ||
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| /** | ||
| * Constructs a $ihe-pix fhir client call to an external Client Registry returning any patients that match the given | ||
| * identifier and target systems. | ||
| */ | ||
| @Override | ||
| public List<Patient> getCRPatient(String sourceIdentifier, String sourceIdentifierSystem, List<String> extraTargetSystems) { | ||
| // construct and send request to external client registry | ||
| IQuery<IBaseBundle> crRequest = fhirClient | ||
| .search() | ||
| .byUrl( | ||
| String.format("%s/%s", config.getClientRegistryServerUrl(), config.getClientRegistryGetPatientEndpoint())) | ||
| .where( | ||
| FhirCRConstants.SOURCE_IDENTIFIER_PARAM.exactly().systemAndIdentifier(sourceIdentifierSystem, | ||
| sourceIdentifier)); | ||
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| if (!extraTargetSystems.isEmpty()) { | ||
| crRequest.and(FhirCRConstants.TARGET_SYSTEM_PARAM.matches().values(extraTargetSystems)); | ||
| } | ||
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| Bundle patientBundle = crRequest.returnBundle(Bundle.class).execute(); | ||
| return parseCRPatientSearchResults(patientBundle); | ||
| } | ||
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| @Override | ||
| public List<Patient> searchCRForPatients(PatientSearchParams patientSearchParams) { | ||
| return null; | ||
| } | ||
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| /** | ||
| * Filter and parse out fhir patients from Client Registry Patient Search results | ||
| */ | ||
| private List<Patient> parseCRPatientSearchResults(Bundle patientBundle) { | ||
| return patientBundle | ||
| .getEntry() | ||
| .stream() | ||
| .filter(entry -> entry.hasType(FhirConstants.PATIENT)) | ||
| .map(entry -> (Patient) entry.getResource()) | ||
| .collect(Collectors.toList()); | ||
| } | ||
| } |
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26
api/src/main/java/org/openmrs/module/clientregistry/providers/FhirCRConstants.java
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| @@ -0,0 +1,26 @@ | ||
| package org.openmrs.module.clientregistry.providers; | ||
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| import ca.uhn.fhir.model.api.annotation.SearchParamDefinition; | ||
| import ca.uhn.fhir.rest.gclient.StringClientParam; | ||
| import ca.uhn.fhir.rest.gclient.TokenClientParam; | ||
| import ca.uhn.fhir.rest.gclient.UriClientParam; | ||
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| public class FhirCRConstants { | ||
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| public static final String IHE_PIX_OPERATION = "$ihe-pix"; | ||
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| @SearchParamDefinition(name = "sourceIdentifier", path = "Patient.sourceIdentifier", description = "A patient identifier used to find cross-matching identifiers in client registry", type = "token") | ||
| public static final String SOURCE_IDENTIFIER = "sourceIdentifier"; | ||
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| public static final TokenClientParam SOURCE_IDENTIFIER_PARAM = new TokenClientParam("sourceIdentifier"); | ||
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| @SearchParamDefinition(name = "targetSystem", path = "Patient.targetSystem", description = "Assigning Authorities for the Patient Identifier Domains from which the returned identifiers shall be selected", type = "token") | ||
| public static final String TARGET_SYSTEM = "targetSystem"; | ||
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| public static final UriClientParam TARGET_SYSTEM_PARAM = new UriClientParam("targetSystem"); | ||
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| @SearchParamDefinition(name = "_format", path = "Patient.targetSystem", description = "Assigning Authorities for the Patient Identifier Domains from which the returned identifiers shall be selected", type = "token") | ||
| public static final String _FORMAT = "_FORMAT"; | ||
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| public static final StringClientParam _FORMAT_PARAM = new StringClientParam("_format"); | ||
| } |
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102
...in/java/org/openmrs/module/clientregistry/providers/r4/FhirCRPatientResourceProvider.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,102 @@ | ||
| package org.openmrs.module.clientregistry.providers.r4; | ||
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| import ca.uhn.fhir.model.valueset.BundleTypeEnum; | ||
| import ca.uhn.fhir.rest.annotation.Search; | ||
| import ca.uhn.fhir.rest.param.StringParam; | ||
| import ca.uhn.fhir.rest.param.StringOrListParam; | ||
| import ca.uhn.fhir.rest.server.IResourceProvider; | ||
| import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException; | ||
| import ca.uhn.fhir.rest.server.exceptions.NotImplementedOperationException; | ||
| import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException; | ||
| import lombok.Setter; | ||
| import org.hl7.fhir.instance.model.api.IBaseResource; | ||
| import org.hl7.fhir.r4.model.Patient; | ||
| import ca.uhn.fhir.rest.annotation.Operation; | ||
| import ca.uhn.fhir.rest.annotation.OperationParam; | ||
| import org.openmrs.module.clientregistry.ClientRegistryConfig; | ||
| import org.openmrs.module.clientregistry.api.ClientRegistryManager; | ||
| import org.openmrs.module.clientregistry.providers.FhirCRConstants; | ||
| import org.openmrs.module.fhir2.api.annotations.R4Provider; | ||
| import org.springframework.beans.factory.annotation.Autowired; | ||
| import org.springframework.stereotype.Component; | ||
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| import java.util.Collections; | ||
| import java.util.List; | ||
| import java.util.Objects; | ||
| import java.util.stream.Collectors; | ||
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| import static lombok.AccessLevel.PACKAGE; | ||
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| @Component("crPatientFhirR4ResourceProvider") | ||
| @R4Provider | ||
| @Setter(PACKAGE) | ||
| public class FhirCRPatientResourceProvider implements IResourceProvider { | ||
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| @Autowired | ||
| private ClientRegistryManager clientRegistryManager; | ||
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| @Autowired | ||
| private ClientRegistryConfig config; | ||
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| @Override | ||
| public Class<? extends IBaseResource> getResourceType() { | ||
| return Patient.class; | ||
| } | ||
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| /** | ||
| * FHIR endpoint to get Patient references from external client registry Example request: GET | ||
| * [fhirbase]/Patient/$ihe-pix?sourceIdentifier=1234[&targetSystem=system1,system2] | ||
| * | ||
| * @param sourceIdentifierParam patient identifier | ||
| * @param targetSystemsParam (optional) Patient assigning authorities (ie systems) from which | ||
| * the returned identifiers shall be selected. Use module defined default if not | ||
| * provided. | ||
| * @return OpenMRS Patient corresponding to identifier (TODO this might change to a list of | ||
| * identifier references returned by CR) | ||
| */ | ||
| @Operation(name = FhirCRConstants.IHE_PIX_OPERATION, idempotent=true, type = Patient.class, bundleType = BundleTypeEnum.SEARCHSET) | ||
| public List<Patient> getCRPatientById( | ||
| @OperationParam(name = FhirCRConstants.SOURCE_IDENTIFIER) StringParam sourceIdentifierParam, | ||
| @OperationParam(name = FhirCRConstants.TARGET_SYSTEM) StringOrListParam targetSystemsParam | ||
| ) { | ||
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| if (sourceIdentifierParam == null || sourceIdentifierParam.getValue() == null) { | ||
| throw new InvalidRequestException("sourceIdentifier must be specified"); | ||
| } | ||
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| List<String> targetSystems = targetSystemsParam == null | ||
| ? Collections.emptyList() | ||
| : targetSystemsParam.getValuesAsQueryTokens().stream().filter(Objects::nonNull).map(StringParam::getValue).collect(Collectors.toList()); | ||
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| // If no targetSystem provided, use config defined default. Otherwise, take first targetSystem provided and | ||
| // include in sourceIdentifier token. Remaining targetSystems included in targetSystem param passed to CR | ||
| String sourceIdentifierSystem; | ||
| if (targetSystems.isEmpty()) { | ||
| sourceIdentifierSystem = config.getClientRegistryDefaultPatientIdentifierSystem(); | ||
| } else { | ||
| sourceIdentifierSystem = targetSystems.get(0); | ||
| targetSystems.remove(0); | ||
| } | ||
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| if (sourceIdentifierSystem == null || sourceIdentifierSystem.isEmpty()) { | ||
| throw new InvalidRequestException("ClientRegistry module does not have a default target system assigned " + | ||
| "via the defaultPatientIdentifierSystem property. At least one targetSystem must be provided in " + | ||
| "the request"); | ||
| } | ||
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| List<Patient> patients = clientRegistryManager.getPatientService().getCRPatient( | ||
| sourceIdentifierParam.getValue(), sourceIdentifierSystem, targetSystems | ||
| ); | ||
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| if (patients.isEmpty()) { | ||
| throw new ResourceNotFoundException("No Client Registry patients found."); | ||
| } | ||
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| return patients; | ||
| } | ||
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| @Search | ||
| public List<Patient> searchClientRegistryPatients() { | ||
| throw new NotImplementedOperationException("search client registry is not yet implemented"); | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -35,13 +35,37 @@ | |
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| <!-- Required Global Properties --> | ||
| <globalProperty> | ||
| <property>@MODULE_ID@.serverUrl</property> | ||
| <defaultValue>http://localhost:5001/CR/fhir/</defaultValue> | ||
| <property>@MODULE_ID@.clientRegistryServerUrl</property> | ||
| <defaultValue>http://localhost:5001/CR/fhir</defaultValue> | ||
| <description> | ||
| Base URL for the Client Registry Server | ||
| </description> | ||
| </globalProperty> | ||
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| <globalProperty> | ||
| <property>@[email protected]</property> | ||
| <defaultValue>Patient/$ihe-pix</defaultValue> | ||
| <description> | ||
| Client registry endpoint implementing the Patient identifier cross-reference transaction (ITI-83) | ||
| </description> | ||
| </globalProperty> | ||
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| <globalProperty> | ||
| <property>@[email protected]</property> | ||
| <defaultValue></defaultValue> | ||
| <description> | ||
| Default system from which the Patient identifiers will be returned, if no system provided in requests | ||
| </description> | ||
| </globalProperty> | ||
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| <globalProperty> | ||
| <property>@[email protected]</property> | ||
| <defaultValue>fhir</defaultValue> | ||
| <description> | ||
| Transaction method supported by the Client Registry. Currently supporting fhir or hl7. | ||
| </description> | ||
| </globalProperty> | ||
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| <globalProperty> | ||
| <property>@[email protected]</property> | ||
| <defaultValue>openmrs</defaultValue> | ||
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