FM2-411: Added support for instance level $everything operation on Pa…

…tients in R4 (#360)
openmrs · Jul 22, 2021 · 4be5f0e · 4be5f0e
1 parent 7c48ebd
commit 4be5f0e
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Showing 9 changed files with 208 additions and 3 deletions.
diff --git a/api/src/main/java/org/openmrs/module/fhir2/FhirConstants.java b/api/src/main/java/org/openmrs/module/fhir2/FhirConstants.java
@@ -307,4 +307,6 @@ private FhirConstants() {
 	public static final String LASTN_OBSERVATION_SEARCH_HANDLER = "lastn.observation.search.handler";
 
 	public static final String LASTN_ENCOUNTERS_SEARCH_HANDLER = "lastn.encounters.search.handler";
+
+	public static final String EVERYTHING_SEARCH_HANDLER = "everything.search.handler";
 }
diff --git a/api/src/main/java/org/openmrs/module/fhir2/api/FhirPatientService.java b/api/src/main/java/org/openmrs/module/fhir2/api/FhirPatientService.java
@@ -21,6 +21,7 @@
 import ca.uhn.fhir.rest.param.DateRangeParam;
 import ca.uhn.fhir.rest.param.StringAndListParam;
 import ca.uhn.fhir.rest.param.TokenAndListParam;
+import ca.uhn.fhir.rest.param.TokenParam;
 import org.hl7.fhir.r4.model.Identifier;
 import org.hl7.fhir.r4.model.Patient;
 import org.openmrs.PatientIdentifierType;
@@ -41,4 +42,6 @@ IBundleProvider searchForPatients(StringAndListParam name, StringAndListParam gi
 	        TokenAndListParam deceased, StringAndListParam city, StringAndListParam state, StringAndListParam postalCode,
 	        StringAndListParam country, TokenAndListParam id, DateRangeParam lastUpdated, SortSpec sort,
 	        HashSet<Include> revIncludes);
+
+	IBundleProvider getPatientEverything(TokenParam identifier);
 }
diff --git a/api/src/main/java/org/openmrs/module/fhir2/api/impl/FhirPatientServiceImpl.java b/api/src/main/java/org/openmrs/module/fhir2/api/impl/FhirPatientServiceImpl.java
@@ -22,6 +22,7 @@
 import ca.uhn.fhir.rest.param.DateRangeParam;
 import ca.uhn.fhir.rest.param.StringAndListParam;
 import ca.uhn.fhir.rest.param.TokenAndListParam;
+import ca.uhn.fhir.rest.param.TokenParam;
 import lombok.AccessLevel;
 import lombok.Getter;
 import lombok.Setter;
@@ -106,4 +107,26 @@ public IBundleProvider searchForPatients(StringAndListParam name, StringAndListP
 
 		return searchQuery.getQueryResults(theParams, dao, translator, searchQueryInclude);
 	}
+
+	@Override
+	@Transactional(readOnly = true)
+	public IBundleProvider getPatientEverything(TokenParam patientId) {
+		SearchParameterMap theParams = new SearchParameterMap().addParameter(FhirConstants.EVERYTHING_SEARCH_HANDLER, "")
+		        .addParameter(FhirConstants.COMMON_SEARCH_HANDLER, FhirConstants.ID_PROPERTY,
+		            new TokenAndListParam().addAnd(patientId));
+
+		HashSet<Include> revIncludes = new HashSet<>();
+
+		revIncludes.add(new Include(FhirConstants.OBSERVATION + ":" + FhirConstants.INCLUDE_PATIENT_PARAM));
+		revIncludes.add(new Include(FhirConstants.ALLERGY_INTOLERANCE + ":" + FhirConstants.INCLUDE_PATIENT_PARAM));
+		revIncludes.add(new Include(FhirConstants.DIAGNOSTIC_REPORT + ":" + FhirConstants.INCLUDE_PATIENT_PARAM));
+		revIncludes.add(new Include(FhirConstants.ENCOUNTER + ":" + FhirConstants.INCLUDE_PATIENT_PARAM));
+		revIncludes.add(new Include(FhirConstants.MEDICATION_REQUEST + ":" + FhirConstants.INCLUDE_PATIENT_PARAM));
+		revIncludes.add(new Include(FhirConstants.SERVICE_REQUEST + ":" + FhirConstants.INCLUDE_PATIENT_PARAM));
+		revIncludes.add(new Include(FhirConstants.PROCEDURE_REQUEST + ":" + FhirConstants.INCLUDE_PATIENT_PARAM));
+
+		theParams.addParameter(FhirConstants.REVERSE_INCLUDE_SEARCH_HANDLER, revIncludes);
+
+		return searchQuery.getQueryResults(theParams, dao, translator, searchQueryInclude);
+	}
 }
diff --git a/api/src/main/java/org/openmrs/module/fhir2/api/search/SearchQuery.java b/api/src/main/java/org/openmrs/module/fhir2/api/search/SearchQuery.java
@@ -10,9 +10,11 @@
 package org.openmrs.module.fhir2.api.search;
 
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.server.SimpleBundleProvider;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.openmrs.Auditable;
 import org.openmrs.OpenmrsObject;
+import org.openmrs.module.fhir2.FhirConstants;
 import org.openmrs.module.fhir2.api.FhirGlobalPropertyService;
 import org.openmrs.module.fhir2.api.dao.FhirDao;
 import org.openmrs.module.fhir2.api.search.param.SearchParameterMap;
@@ -37,10 +39,20 @@ public class SearchQuery<T extends OpenmrsObject & Auditable, U extends IBaseRes
 	 *
 	 * @param theParams search params.
 	 * @param dao generic dao
-	 * @param translator generic translator
+	 * @param translator generic translator In case of $everything operation, package the results in
+	 *            SimpleBundleProvider to include count of _include and _revinclude resources in the
+	 *            total resources count and prevent paging
 	 * @return IBundleProvider
 	 */
 	public IBundleProvider getQueryResults(SearchParameterMap theParams, O dao, V translator, W searchQueryInclude) {
+		if (!theParams.getParameters(FhirConstants.EVERYTHING_SEARCH_HANDLER).isEmpty()) {
+			SimpleBundleProvider result = new SimpleBundleProvider(
+			        new SearchQueryBundleProvider<>(theParams, dao, translator, globalPropertyService, searchQueryInclude)
+			                .getAllResources());
+
+			result.setPreferredPageSize(result.size());
+			return result;
+		}
 		return new SearchQueryBundleProvider<>(theParams, dao, translator, globalPropertyService, searchQueryInclude);
 	}
 }
diff --git a/api/src/main/java/org/openmrs/module/fhir2/providers/r4/PatientFhirResourceProvider.java b/api/src/main/java/org/openmrs/module/fhir2/providers/r4/PatientFhirResourceProvider.java
@@ -17,11 +17,13 @@
 import java.util.List;
 
 import ca.uhn.fhir.model.api.Include;
+import ca.uhn.fhir.model.valueset.BundleTypeEnum;
 import ca.uhn.fhir.rest.annotation.Create;
 import ca.uhn.fhir.rest.annotation.Delete;
 import ca.uhn.fhir.rest.annotation.History;
 import ca.uhn.fhir.rest.annotation.IdParam;
 import ca.uhn.fhir.rest.annotation.IncludeParam;
+import ca.uhn.fhir.rest.annotation.Operation;
 import ca.uhn.fhir.rest.annotation.OptionalParam;
 import ca.uhn.fhir.rest.annotation.Read;
 import ca.uhn.fhir.rest.annotation.ResourceParam;
@@ -34,6 +36,7 @@
 import ca.uhn.fhir.rest.param.DateRangeParam;
 import ca.uhn.fhir.rest.param.StringAndListParam;
 import ca.uhn.fhir.rest.param.TokenAndListParam;
+import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.server.IResourceProvider;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
@@ -143,4 +146,22 @@ public IBundleProvider searchPatients(@OptionalParam(name = Patient.SP_NAME) Str
 		return patientService.searchForPatients(name, given, family, identifier, gender, birthDate, deathDate, deceased,
 		    city, state, postalCode, country, id, lastUpdated, sort, revIncludes);
 	}
+
+	/**
+	 * The $everything operation fetches all the information related the specified patient
+	 * 
+	 * @param patientId The id of the patient
+	 * @return a bundle of resources which reference to or are referenced from the patient
+	 */
+	@Operation(name = "everything", idempotent = true, type = Patient.class, bundleType = BundleTypeEnum.SEARCHSET)
+	public IBundleProvider getPatientEverything(@IdParam IdType patientId) {
+
+		if (patientId == null || patientId.getIdPart() == null || patientId.getIdPart().isEmpty()) {
+			return null;
+		}
+
+		TokenParam patientReference = new TokenParam().setValue(patientId.getIdPart());
+
+		return patientService.getPatientEverything(patientReference);
+	}
 }
diff --git a/api/src/test/java/org/openmrs/module/fhir2/api/impl/FhirPatientServiceImplTest.java b/api/src/test/java/org/openmrs/module/fhir2/api/impl/FhirPatientServiceImplTest.java
@@ -794,6 +794,43 @@ public void searchForPatients_shouldNotAddRelatedResourcesToResultListForEmptyRe
 		assertThat(resultList.size(), greaterThanOrEqualTo(1));
 	}
 
+	@Test
+	public void getPatientEverything_shouldReturnAllInformationAboutSpecifiedPatient() {
+		TokenParam patientId = new TokenParam().setValue(PATIENT_UUID);
+
+		SearchParameterMap theParams = new SearchParameterMap()
+		        .addParameter(FhirConstants.EVERYTHING_SEARCH_HANDLER, "")
+		        .addParameter(FhirConstants.COMMON_SEARCH_HANDLER, FhirConstants.ID_PROPERTY, patientId);
+
+		HashSet<Include> revIncludes = new HashSet<>();
+
+		revIncludes.add(new Include(FhirConstants.OBSERVATION + ":" + FhirConstants.INCLUDE_PATIENT_PARAM));
+		revIncludes.add(new Include(FhirConstants.ALLERGY_INTOLERANCE + ":" + FhirConstants.INCLUDE_PATIENT_PARAM));
+		revIncludes.add(new Include(FhirConstants.DIAGNOSTIC_REPORT + ":" + FhirConstants.INCLUDE_PATIENT_PARAM));
+		revIncludes.add(new Include(FhirConstants.ENCOUNTER + ":" + FhirConstants.INCLUDE_PATIENT_PARAM));
+		revIncludes.add(new Include(FhirConstants.MEDICATION_REQUEST + ":" + FhirConstants.INCLUDE_PATIENT_PARAM));
+		revIncludes.add(new Include(FhirConstants.SERVICE_REQUEST + ":" + FhirConstants.INCLUDE_PATIENT_PARAM));
+		revIncludes.add(new Include(FhirConstants.PROCEDURE_REQUEST + ":" + FhirConstants.INCLUDE_PATIENT_PARAM));
+
+		theParams.addParameter(FhirConstants.REVERSE_INCLUDE_SEARCH_HANDLER, revIncludes);
+
+		when(dao.getSearchResultUuids(any())).thenReturn(Collections.singletonList(PATIENT_UUID));
+		when(dao.getSearchResults(any(), any())).thenReturn(Collections.singletonList(patient));
+		when(searchQuery.getQueryResults(any(), any(), any(), any())).thenReturn(
+		    new SearchQueryBundleProvider<>(theParams, dao, patientTranslator, globalPropertyService, searchQueryInclude));
+
+		when(patientTranslator.toFhirResource(patient)).thenReturn(fhirPatient);
+
+		IBundleProvider results = patientService.getPatientEverything(patientId);
+
+		List<IBaseResource> resultList = get(results);
+
+		assertThat(results, notNullValue());
+		assertThat(resultList, not(empty()));
+		assertThat(resultList.size(), greaterThanOrEqualTo(1));
+
+	}
+
 	private List<IBaseResource> get(IBundleProvider results) {
 		return results.getResources(0, 10);
 	}

diff --git a/api/src/test/java/org/openmrs/module/fhir2/api/search/PatientSearchQueryTest.java b/api/src/test/java/org/openmrs/module/fhir2/api/search/PatientSearchQueryTest.java
@@ -174,6 +174,10 @@ private List<Patient> get(IBundleProvider results) {
 		        .map(it -> (Patient) it).collect(Collectors.toList());
 	}
 
+	private List<IBaseResource> getAllResources(IBundleProvider results) {
+		return results.getAllResources();
+	}
+
 	@Test
 	public void searchForPatients_shouldSearchForPatientsByName() {
 		SearchParameterMap theParams = new SearchParameterMap().addParameter(FhirConstants.NAME_SEARCH_HANDLER, "name",
@@ -1154,4 +1158,34 @@ public void shouldReturnCollectionOfPatientsSortedByCountry() {
 		}
 	}
 
+	@Test
+	public void searchForPatient_shouldReturnPatientEverything() {
+		TokenAndListParam patientId = new TokenAndListParam().addAnd(new TokenParam().setValue(PATIENT_OTHER2_UUID));
+
+		SearchParameterMap theParams = new SearchParameterMap()
+		        .addParameter(FhirConstants.EVERYTHING_SEARCH_HANDLER, "")
+		        .addParameter(FhirConstants.COMMON_SEARCH_HANDLER, FhirConstants.ID_PROPERTY, patientId);
+
+		HashSet<Include> revIncludes = new HashSet<>();
+
+		revIncludes.add(new Include(FhirConstants.OBSERVATION + ":" + FhirConstants.INCLUDE_PATIENT_PARAM));
+		revIncludes.add(new Include(FhirConstants.ALLERGY_INTOLERANCE + ":" + FhirConstants.INCLUDE_PATIENT_PARAM));
+		revIncludes.add(new Include(FhirConstants.DIAGNOSTIC_REPORT + ":" + FhirConstants.INCLUDE_PATIENT_PARAM));
+		revIncludes.add(new Include(FhirConstants.ENCOUNTER + ":" + FhirConstants.INCLUDE_PATIENT_PARAM));
+		revIncludes.add(new Include(FhirConstants.MEDICATION_REQUEST + ":" + FhirConstants.INCLUDE_PATIENT_PARAM));
+		revIncludes.add(new Include(FhirConstants.SERVICE_REQUEST + ":" + FhirConstants.INCLUDE_PATIENT_PARAM));
+		revIncludes.add(new Include(FhirConstants.PROCEDURE_REQUEST + ":" + FhirConstants.INCLUDE_PATIENT_PARAM));
+
+		theParams.addParameter(FhirConstants.REVERSE_INCLUDE_SEARCH_HANDLER, revIncludes);
+
+		IBundleProvider results = search(theParams);
+
+		assertThat(results, notNullValue());
+		assertThat(results.size(), equalTo(15));
+
+		List<IBaseResource> resultList = getAllResources(results);
+
+		assertThat(resultList.size(), equalTo(15));
+	}
+
 }
diff --git a/api/src/test/java/org/openmrs/module/fhir2/providers/r4/PatientFhirResourceProviderTest.java b/api/src/test/java/org/openmrs/module/fhir2/providers/r4/PatientFhirResourceProviderTest.java
@@ -18,6 +18,7 @@
 import static org.hamcrest.Matchers.not;
 import static org.hamcrest.Matchers.notNullValue;
 import static org.hamcrest.Matchers.nullValue;
+import static org.mockito.ArgumentMatchers.any;
 import static org.mockito.ArgumentMatchers.isNull;
 import static org.mockito.Mockito.when;
 import static org.mockito.hamcrest.MockitoHamcrest.argThat;
@@ -58,7 +59,6 @@
 import org.openmrs.module.fhir2.FhirConstants;
 import org.openmrs.module.fhir2.api.FhirPatientService;
 import org.openmrs.module.fhir2.providers.BaseFhirProvenanceResourceTest;
-import org.openmrs.module.fhir2.providers.r3.MockIBundleProvider;
 
 @RunWith(MockitoJUnitRunner.class)
 public class PatientFhirResourceProviderTest extends BaseFhirProvenanceResourceTest<Patient> {
@@ -528,7 +528,47 @@ public void searchForPatients_shouldNotAddResourcesForEmptyRevInclude() {
 		assertThat(((Patient) resultList.iterator().next()).getId(), equalTo(PATIENT_UUID));
 	}
 
+	@Test
+	public void searchForPatients_shouldReturnPatientEverything() {
+		when(patientService.getPatientEverything(any()))
+		        .thenReturn(new MockIBundleProvider<>(Collections.singletonList(patient), 10, 1));
+
+		IBundleProvider results = resourceProvider.getPatientEverything(new IdType(PATIENT_UUID));
+
+		List<IBaseResource> resultList = getAllResources(results);
+
+		assertThat(resultList, notNullValue());
+		assertThat(resultList.size(), equalTo(1));
+		assertThat(resultList.get(0).fhirType(), equalTo(FhirConstants.PATIENT));
+		assertThat(((Patient) resultList.iterator().next()).getId(), equalTo(PATIENT_UUID));
+	}
+
+	@Test
+	public void searchForPatients_shouldReturnNullForPatientEverythingWhenIdParamIsMissing() {
+		IBundleProvider results = resourceProvider.getPatientEverything(null);
+
+		assertThat(results, nullValue());
+	}
+
+	@Test
+	public void searchForPatients_shouldReturnNullForPatientEverythingWhenIdPartIsMissingInIdParam() {
+		IBundleProvider results = resourceProvider.getPatientEverything(new IdType());
+
+		assertThat(results, nullValue());
+	}
+
+	@Test
+	public void searchForPatients_shouldReturnNullPatientEverythingWhenIdPartIsEmptyInIdParam() {
+		IBundleProvider results = resourceProvider.getPatientEverything(new IdType(""));
+
+		assertThat(results, nullValue());
+	}
+
 	private List<IBaseResource> getResources(IBundleProvider result) {
 		return result.getResources(0, 10);
 	}
+
+	private List<IBaseResource> getAllResources(IBundleProvider result) {
+		return result.getAllResources();
+	}
 }
diff --git a/...c/test/java/org/openmrs/module/fhir2/providers/r4/PatientFhirResourceProviderWebTest.java b/...c/test/java/org/openmrs/module/fhir2/providers/r4/PatientFhirResourceProviderWebTest.java
@@ -42,10 +42,12 @@
 import ca.uhn.fhir.rest.param.DateRangeParam;
 import ca.uhn.fhir.rest.param.StringAndListParam;
 import ca.uhn.fhir.rest.param.TokenAndListParam;
+import ca.uhn.fhir.rest.param.TokenParam;
 import lombok.AccessLevel;
 import lombok.Getter;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.time.DateUtils;
+import org.hamcrest.MatcherAssert;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Coding;
@@ -63,7 +65,6 @@
 import org.openmrs.module.fhir2.FhirConstants;
 import org.openmrs.module.fhir2.api.FhirPatientService;
 import org.openmrs.module.fhir2.api.util.FhirUtils;
-import org.openmrs.module.fhir2.providers.r3.MockIBundleProvider;
 import org.springframework.mock.web.MockHttpServletResponse;
 
 @RunWith(MockitoJUnitRunner.class)
@@ -105,6 +106,9 @@ public class PatientFhirResourceProviderWebTest extends BaseFhirR4ResourceProvid
 	@Captor
 	private ArgumentCaptor<HashSet<Include>> includeArgumentCaptor;
 
+	@Captor
+	private ArgumentCaptor<TokenParam> tokenCaptor;
+
 	@Before
 	public void setup() throws ServletException {
 		resourceProvider = new PatientFhirResourceProvider();
@@ -772,4 +776,33 @@ public void deletePatient_shouldDeletePatient() throws Exception {
 		assertThat(response.getContentType(), equalTo(FhirMediaTypes.JSON.toString()));
 	}
 
+	@Test
+	public void getPatientEverything_shouldHandlePatientId() throws Exception {
+		verifyEverythingOperation("/Patient/" + PATIENT_UUID + "/$everything?");
+
+		verify(patientService).getPatientEverything(tokenCaptor.capture());
+
+		assertThat(tokenCaptor.getValue(), notNullValue());
+		assertThat(tokenCaptor.getValue().getValue(), equalTo(PATIENT_UUID));
+	}
+
+	private void verifyEverythingOperation(String uri) throws Exception {
+		Patient patient = new Patient();
+		patient.setId(PATIENT_UUID);
+
+		when(patientService.getPatientEverything(any()))
+		        .thenReturn(new MockIBundleProvider<>(Collections.singletonList(patient), 10, 1));
+
+		MockHttpServletResponse response = get(uri).accept(FhirMediaTypes.JSON).go();
+
+		MatcherAssert.assertThat(response, isOk());
+		MatcherAssert.assertThat(response.getContentType(), equalTo(FhirMediaTypes.JSON.toString()));
+
+		Bundle results = readBundleResponse(response);
+		assertThat(results.getEntry(), notNullValue());
+		assertThat(results.getEntry(), not(empty()));
+		assertThat(results.getEntry().get(0).getResource(), notNullValue());
+		assertThat(results.getEntry().get(0).getResource().getIdElement().getIdPart(), equalTo(PATIENT_UUID));
+	}
+
 }