FhirParseService refactoring

Author: ORybak5

service/src/intTest/java/uk/nhs/adaptors/gp2gp/common/task/BaseTaskTest.java

@@ -1,5 +1,6 @@
 package uk.nhs.adaptors.gp2gp.common.task;
 
+import ca.uhn.fhir.context.FhirContext;
 import org.junit.jupiter.api.extension.ExtendWith;
 import org.springframework.boot.test.context.SpringBootTest;
 import org.springframework.boot.test.mock.mockito.MockBean;
@@ -17,7 +18,7 @@
 @SuppressWarnings("checkstyle:VisibilityModifier")
 public abstract class BaseTaskTest {
     public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
-    public static final FhirParseService FHIR_PARSE_SERVICE = new FhirParseService();
+    public static final FhirParseService FHIR_PARSE_SERVICE = new FhirParseService(FhirContext.forDstu3());
 
     @MockBean
     protected TaskDispatcher taskDispatcher;

service/src/main/java/uk/nhs/adaptors/gp2gp/common/service/FhirParseService.java

@@ -10,7 +10,12 @@
 
 @Service
 public class FhirParseService {
-    private final IParser jsonParser = prepareParser();
+
+    private final IParser jsonParser;
+
+    public FhirParseService(FhirContext fhirContext) {
+        this.jsonParser = prepareParser(fhirContext);
+    }
 
     public <T extends IBaseResource> T parseResource(String body, Class<T> fhirClass) {
         try {
@@ -20,10 +25,9 @@ public <T extends IBaseResource> T parseResource(String body, Class<T> fhirClass
         }
     }
 
-    private IParser prepareParser() {
-        FhirContext ctx = FhirContext.forDstu3();
-        ctx.newJsonParser();
-        ctx.setParserErrorHandler(new StrictErrorHandler());
-        return ctx.newJsonParser();
+    private IParser prepareParser(FhirContext fhirContext) {
+        fhirContext.newJsonParser();
+        fhirContext.setParserErrorHandler(new StrictErrorHandler());
+        return fhirContext.newJsonParser();
     }
 }

service/src/main/java/uk/nhs/adaptors/gp2gp/transformJsonToXmlTool/TransformJsonToXml.java

@@ -12,6 +12,7 @@
 import java.util.List;
 import java.util.stream.Collectors;
 
+import ca.uhn.fhir.context.FhirContext;
 import org.apache.commons.io.FilenameUtils;
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.dstu3.model.Identifier;
@@ -116,7 +117,7 @@ private List<InputFile> getFiles() throws UnreadableJsonFileException, NoJsonFil
     final String mapJsonToXml(String jsonAsStringInput) {
         String hl7TranslatedResponse;
         try {
-            final Bundle bundle = new FhirParseService().parseResource(jsonAsStringInput, Bundle.class);
+            final Bundle bundle = new FhirParseService(FhirContext.forDstu3()).parseResource(jsonAsStringInput, Bundle.class);
 
             messageContext.initialize(bundle);
 

service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/AgentDirectoryMapperTest.java

@@ -10,6 +10,7 @@
 
 import java.io.IOException;
 
+import ca.uhn.fhir.context.FhirContext;
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.dstu3.model.ResourceType;
 import org.junit.jupiter.api.AfterEach;
@@ -56,7 +57,7 @@ public void setUp() {
         lenient().when(agentPersonMapper.mapAgentPerson(any(), any())).thenAnswer(answerWithObjectId());
 
         agentDirectoryMapper = new AgentDirectoryMapper(messageContext, agentPersonMapper);
-        fhirParseService = new FhirParseService();
+        fhirParseService = new FhirParseService(FhirContext.forDstu3());
     }
 
     private Answer<String> answerWithObjectId() {

service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/AgentDirectoryTest.java

@@ -9,6 +9,7 @@
 import java.util.Map;
 import java.util.Optional;
 
+import ca.uhn.fhir.context.FhirContext;
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.dstu3.model.ResourceType;
 import org.junit.jupiter.api.BeforeEach;
@@ -44,7 +45,7 @@ public void setUp() throws IOException {
         lenient().when(randomIdGeneratorService.createNewId()).thenReturn(GENERATED_ID_1, GENERATED_ID_2);
 
         String jsonInput = ResourceTestFileUtils.getFileContent(INPUT_BUNDLE);
-        inputBundle = new FhirParseService().parseResource(jsonInput, Bundle.class);
+        inputBundle = new FhirParseService(FhirContext.forDstu3()).parseResource(jsonInput, Bundle.class);
     }
 
     @Test

service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/AgentPersonMapperTest.java

@@ -6,6 +6,7 @@
 import java.io.IOException;
 import java.util.stream.Stream;
 
+import ca.uhn.fhir.context.FhirContext;
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.dstu3.model.Organization;
 import org.hl7.fhir.dstu3.model.Practitioner;
@@ -52,7 +53,7 @@ public void setUp() {
         when(randomIdGeneratorService.createNewId()).thenReturn(TEST_ID);
         messageContext = new MessageContext(randomIdGeneratorService);
         agentPersonMapper = new AgentPersonMapper(messageContext);
-        fhirParseService = new FhirParseService();
+        fhirParseService = new FhirParseService(FhirContext.forDstu3());
     }
 
     @ParameterizedTest
@@ -149,12 +150,12 @@ private static Stream<Arguments> readPractitionerRoleTests() {
 
     private static Practitioner getPractitionerResource() throws IOException {
         String jsonPractitioner = ResourceTestFileUtils.getFileContent(PRACTITIONER);
-        return new FhirParseService().parseResource(jsonPractitioner, Practitioner.class);
+        return new FhirParseService(FhirContext.forDstu3()).parseResource(jsonPractitioner, Practitioner.class);
     }
 
     private static Organization getOrganizationResource() throws IOException {
         String jsonOrganization = ResourceTestFileUtils.getFileContent(ORGANIZATION);
-        return new FhirParseService().parseResource(jsonOrganization, Organization.class);
+        return new FhirParseService(FhirContext.forDstu3()).parseResource(jsonOrganization, Organization.class);
     }
 
     @AfterEach

service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/AllergyStructureMapperTest.java

@@ -15,6 +15,7 @@
 import java.util.Optional;
 import java.util.stream.Stream;
 
+import ca.uhn.fhir.context.FhirContext;
 import org.hl7.fhir.dstu3.model.AllergyIntolerance;
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.dstu3.model.CodeableConcept;
@@ -198,7 +199,7 @@ public void setUp() throws IOException {
             .thenReturn(Optional.empty());
 
         var bundleInput = ResourceTestFileUtils.getFileContent(INPUT_JSON_BUNDLE);
-        Bundle bundle = new FhirParseService().parseResource(bundleInput, Bundle.class);
+        Bundle bundle = new FhirParseService(FhirContext.forDstu3()).parseResource(bundleInput, Bundle.class);
         messageContext = new MessageContext(randomIdGeneratorService);
         messageContext.initialize(bundle);
         List.of(ResourceType.Patient, ResourceType.Device)
@@ -265,7 +266,7 @@ public void When_ConfidentialityServiceReturnsEmptyOptional_Expect_MessageDoesNo
 
     private static AllergyIntolerance parseAllergyIntoleranceFromJsonFile(String filepath) {
         final var jsonInput = ResourceTestFileUtils.getFileContent(filepath);
-        return new FhirParseService().parseResource(jsonInput, AllergyIntolerance.class);
+        return new FhirParseService(FhirContext.forDstu3()).parseResource(jsonInput, AllergyIntolerance.class);
     }
 
 }

service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/BloodPressureMapperTest.java

@@ -1,5 +1,6 @@
 package uk.nhs.adaptors.gp2gp.ehr.mapper;
 
+import ca.uhn.fhir.context.FhirContext;
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.dstu3.model.CodeableConcept;
 import org.hl7.fhir.dstu3.model.Observation;
@@ -59,6 +60,7 @@ public class BloodPressureMapperTest {
     private static final String INPUT_BLOOD_PRESSURE_WITH_CODEABLE_CONCEPTS = "blood-pressure-with-codeable-concepts.json";
     private static final String EXPECTED_BLOOD_PRESSURE_WITH_CODEABLE_CONCEPTS = "blood-pressure-with-codeable-concepts.xml";
     private static final String INPUT_BLOOD_PRESSURE_WITH_NO_CODEABLE_CONCEPTS = "blood-pressure-with-no-codeable-concepts.json";
+    private FhirContext fhirCtx = FhirContext.forDstu3();
 
     @Mock
     private RandomIdGeneratorService randomIdGeneratorService;
@@ -92,7 +94,7 @@ public void When_MappingEmptyObservation_Expect_CompoundStatementXmlReturned() t
         var jsonInput = ResourceTestFileUtils.getFileContent(BLOOD_PRESSURE_FILE_LOCATION + INPUT_EMPTY_OBSERVATION);
         var expectedOutput = ResourceTestFileUtils.getFileContent(BLOOD_PRESSURE_FILE_LOCATION + EXPECTED_EMPTY_OBSERVATION);
 
-        Observation observation = new FhirParseService().parseResource(jsonInput, Observation.class);
+        Observation observation = new FhirParseService(fhirCtx).parseResource(jsonInput, Observation.class);
         var outputMessage = bloodPressureMapper.mapBloodPressure(observation, false);
 
         assertThat(outputMessage).isEqualTo(expectedOutput);
@@ -106,7 +108,7 @@ public void When_MappingBloodPressureWithNestedTrue_Expect_CompoundStatementXmlR
         var jsonInput = ResourceTestFileUtils.getFileContent(BLOOD_PRESSURE_FILE_LOCATION + INPUT_BLOOD_PRESSURE_WITH_DATA);
         var expectedOutput = ResourceTestFileUtils.getFileContent(BLOOD_PRESSURE_FILE_LOCATION + EXPECTED_NESTED_BLOOD_PRESSURE);
 
-        Observation observation = new FhirParseService().parseResource(jsonInput, Observation.class);
+        Observation observation = new FhirParseService(fhirCtx).parseResource(jsonInput, Observation.class);
         var outputMessage = bloodPressureMapper.mapBloodPressure(observation, true);
 
         assertThat(outputMessage).isEqualToIgnoringWhitespace(expectedOutput);
@@ -121,7 +123,7 @@ public void When_MappingBloodPressure_Expect_CompoundStatementXmlReturned(String
         var jsonInput = ResourceTestFileUtils.getFileContent(BLOOD_PRESSURE_FILE_LOCATION + inputJson);
         var expectedOutput = ResourceTestFileUtils.getFileContent(BLOOD_PRESSURE_FILE_LOCATION + outputXml);
 
-        Observation observation = new FhirParseService().parseResource(jsonInput, Observation.class);
+        Observation observation = new FhirParseService(fhirCtx).parseResource(jsonInput, Observation.class);
         var outputMessage = bloodPressureMapper.mapBloodPressure(observation, false);
 
         assertThat(outputMessage)
@@ -157,7 +159,7 @@ public void When_MappingBloodPressureWithCodeableConcepts_Expect_CompoundStateme
             messageContext, randomIdGeneratorService, new StructuredObservationValueMapper(),
             codeableConceptCdMapper, new ParticipantMapper());
 
-        Observation observation = new FhirParseService().parseResource(jsonInput, Observation.class);
+        Observation observation = new FhirParseService(fhirCtx).parseResource(jsonInput, Observation.class);
         var outputMessage = bloodPressureMapper.mapBloodPressure(observation, true);
 
         assertThat(outputMessage).isEqualToIgnoringWhitespace(expectedOutput);
@@ -172,7 +174,7 @@ public void When_MappingBloodPressureWithNoCodeableConcepts_Expect_Exception() t
             messageContext, randomIdGeneratorService, new StructuredObservationValueMapper(),
             codeableConceptCdMapper, new ParticipantMapper());
 
-        Observation observation = new FhirParseService().parseResource(jsonInput, Observation.class);
+        Observation observation = new FhirParseService(fhirCtx).parseResource(jsonInput, Observation.class);
 
         assertThrows(EhrMapperException.class, ()
             -> bloodPressureMapper.mapBloodPressure(observation, true));

service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/CodeableConceptCdMapperTest.java

@@ -5,6 +5,7 @@
 import java.io.IOException;
 import java.util.stream.Stream;
 
+import ca.uhn.fhir.context.FhirContext;
 import org.hl7.fhir.dstu3.model.AllergyIntolerance;
 import org.hl7.fhir.dstu3.model.Condition;
 import org.hl7.fhir.dstu3.model.Medication;
@@ -68,7 +69,7 @@ private static Stream<Arguments> getTestArgumentsForTopicRelatedProblem() {
 
     @BeforeEach
     public void setUp() {
-        fhirParseService = new FhirParseService();
+        fhirParseService = new FhirParseService(FhirContext.forDstu3());
         codeableConceptCdMapper = new CodeableConceptCdMapper();
     }
 

service/src/test/java/uk/nhs/adaptors/gp2gp/ehr/mapper/ConditionLinkSetMapperTest.java

@@ -1,5 +1,6 @@
 package uk.nhs.adaptors.gp2gp.ehr.mapper;
 
+import ca.uhn.fhir.context.FhirContext;
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.dstu3.model.CodeableConcept;
 import org.hl7.fhir.dstu3.model.Condition;
@@ -131,7 +132,7 @@ class ConditionLinkSetMapperTest {
     @BeforeEach
     void setUp() throws IOException {
         var bundleInput = ResourceTestFileUtils.getFileContent(TEST_FILES_DIRECTORY + INPUT_JSON_BUNDLE);
-        final Bundle bundle = new FhirParseService().parseResource(bundleInput, Bundle.class);
+        final Bundle bundle = new FhirParseService(FhirContext.forDstu3()).parseResource(bundleInput, Bundle.class);
         inputBundle = new InputBundle(bundle);
 
         lenient().when(codeableConceptCdMapper.mapCodeableConceptToCd(any(CodeableConcept.class)))