NIAD-3148 - Immunizations outside of consultation are mapped to Observation

db-connector/src/main/java/uk/nhs/adaptors/connector/dao/ImmunizationSnomedCTDao.java

@@ -9,7 +9,7 @@
 public interface ImmunizationSnomedCTDao {
     @SqlQuery("select_immunization_concept_id")
     @UseClasspathSqlLocator
-    ImmunizationSnomedCT getImmunizationSnomednUsingConceptId(@Bind("conceptId") String conceptId);
+    ImmunizationSnomedCT getImmunizationSnomedUsingConceptOrDescriptionId(@Bind("sctid") String sctId);
 
     @SqlQuery("verify_immunizations_loaded")
     @UseClasspathSqlLocator

db-connector/src/main/resources/uk/nhs/adaptors/connector/dao/ImmunizationSnomedCTDao/select_immunization_concept_id.sql

@@ -1 +1 @@
-SELECT i.conceptid FROM "snomedct".immunization_codes i WHERE conceptid = :conceptId;
+SELECT i.conceptid FROM "snomedct".immunization_codes i WHERE conceptid = :sctid OR descriptionid = :sctid;

db-connector/src/main/resources/uk/nhs/adaptors/connector/dao/ImmunizationSnomedCTDao/verify_immunizations_loaded.sql

@@ -1,7 +1,7 @@
 -- the conceptIds being checked for below represent the immunization root codes and those immunization codes outside
 -- of the root code hierarchy, as described in the snomed-database-loader README.md file
 
-SELECT COUNT(i.conceptid) = 16 -- total number of codes
+SELECT COUNT(DISTINCT i.conceptid) = 16 -- total number of codes
 FROM "snomedct".immunization_codes i
 WHERE i.conceptid IN (
                       '787859002', '127785005', '304250009', '90351000119108','713404003','2997511000001102',

gp2gp-translator/src/integrationTest/java/uk/nhs/adaptors/pss/translator/DatabaseImmunizationCheckerIT.java

@@ -0,0 +1,56 @@
+package uk.nhs.adaptors.pss.translator;
+
+import org.hl7.v3.RCMRMT030101UKObservationStatement;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.test.context.junit.jupiter.SpringExtension;
+import uk.nhs.adaptors.pss.translator.util.DatabaseImmunizationChecker;
+
+import static org.assertj.core.api.Assertions.assertThat;
+import static uk.nhs.adaptors.pss.translator.TestUtility.createCd;
+
+@ExtendWith(SpringExtension.class)
+@SpringBootTest
+class DatabaseImmunizationCheckerIT {
+    private static final String SNOMED_CODE_SYSTEM = "2.16.840.1.113883.2.1.3.2.4.15";
+    private static final String DISPLAY_NAME = "Administration of yellow fever vaccine";
+
+    @Autowired
+    private DatabaseImmunizationChecker databaseImmunizationChecker;
+
+    @Test
+    void When_Immunization_With_SnomedDescriptionId_Expect_True() {
+        final String immunizationDescriptionSnomedId = "67308009";
+        final RCMRMT030101UKObservationStatement observationStatement =
+            new RCMRMT030101UKObservationStatement();
+
+        observationStatement.setCode(createCd(
+            immunizationDescriptionSnomedId,
+            SNOMED_CODE_SYSTEM,
+            DISPLAY_NAME
+        ));
+
+        final boolean result = databaseImmunizationChecker.isImmunization(observationStatement);
+
+        assertThat(result).isTrue();
+    }
+
+    @Test
+    void When_Immunization_With_SnomedConceptId_Expect_True() {
+        final String immunizationConceptSnomedId = "67308009";
+        final RCMRMT030101UKObservationStatement observationStatement =
+            new RCMRMT030101UKObservationStatement();
+
+        observationStatement.setCode(createCd(
+            immunizationConceptSnomedId,
+            SNOMED_CODE_SYSTEM,
+            DISPLAY_NAME
+        ));
+
+        final boolean result = databaseImmunizationChecker.isImmunization(observationStatement);
+
+        assertThat(result).isTrue();
+    }
+}

gp2gp-translator/src/main/java/uk/nhs/adaptors/pss/translator/util/DatabaseImmunizationChecker.java

@@ -6,26 +6,39 @@
 
 import lombok.RequiredArgsConstructor;
 import uk.nhs.adaptors.connector.dao.ImmunizationSnomedCTDao;
-import uk.nhs.adaptors.connector.model.ImmunizationSnomedCT;
 
-@RequiredArgsConstructor(onConstructor = @__(@Autowired))
 @Component
+@RequiredArgsConstructor(onConstructor = @__(@Autowired))
 public class DatabaseImmunizationChecker implements ImmunizationChecker {
     private final ImmunizationSnomedCTDao immunizationSnomedDao;
 
     @Override
     public boolean isImmunization(RCMRMT030101UKObservationStatement observationStatement) {
-        ImmunizationSnomedCT immunizationCode = null;
+        final boolean translationIsPresent = !observationStatement.getCode().getTranslation().isEmpty();
 
-        if (!observationStatement.getCode().getTranslation().isEmpty()) {
-            immunizationCode = immunizationSnomedDao
-                    .getImmunizationSnomednUsingConceptId(observationStatement.getCode().getTranslation().get(0).getCode());
-        }
+        if (translationIsPresent) {
+            final boolean isImmunization = isTranslationCodeImmunization(observationStatement);
 
-        if (immunizationCode == null) {
-            immunizationCode = immunizationSnomedDao.getImmunizationSnomednUsingConceptId(observationStatement.getCode().getCode());
+            if (isImmunization) {
+                return true;
+            }
         }
 
-        return immunizationCode != null;
+        return isCodeImmunization(observationStatement);
+    }
+
+    private boolean isTranslationCodeImmunization(RCMRMT030101UKObservationStatement observationStatement) {
+        final String code = observationStatement.getCode()
+            .getTranslation()
+            .getFirst()
+            .getCode();
+
+        return immunizationSnomedDao.getImmunizationSnomedUsingConceptOrDescriptionId(code) != null;
+    }
+
+    private boolean isCodeImmunization(RCMRMT030101UKObservationStatement observationStatement) {
+        final String code = observationStatement.getCode().getCode();
+
+        return immunizationSnomedDao.getImmunizationSnomedUsingConceptOrDescriptionId(code) != null;
     }
-}
+}

gp2gp-translator/src/test/java/uk/nhs/adaptors/pss/translator/TestUtility.java

@@ -1,19 +1,23 @@
 package uk.nhs.adaptors.pss.translator;
 
+import org.hl7.v3.CD;
 import org.hl7.v3.CV;
+import org.hl7.v3.RCMRMT030101UKComponent3;
 import org.hl7.v3.RCMRMT030101UKEhrComposition;
 import org.hl7.v3.RCMRMT030101UKEhrExtract;
+import org.hl7.v3.RCMRMT030101UKEhrFolder;
 
+import java.util.List;
 import java.util.function.Function;
 
 public final class TestUtility {
     private TestUtility() { }
 
     public static final Function<RCMRMT030101UKEhrExtract, RCMRMT030101UKEhrComposition> GET_EHR_COMPOSITION =
         extract -> extract
-            .getComponent().get(0)
+            .getComponent().getFirst()
             .getEhrFolder()
-            .getComponent().get(0)
+            .getComponent().getFirst()
             .getEhrComposition();
 
     public static CV createCv(String code, String codeSystem, String displayName) {
@@ -28,6 +32,32 @@ public static CV createCv(String code) {
         return createCv(code, "", "");
     }
 
+    public static CD createCd(String code, String codeSystem, String displayName) {
+        final CD cd = new CD();
+        cd.setCode(code);
+        cd.setCodeSystem(codeSystem);
+        cd.setDisplayName(displayName);
+        return cd;
+    }
+
+    /**
+     * An EHR Extract has a cardinality of one to many components, each component (based
+     * of the UK05 schema) can contain one and only one EHR Folder. This utility method provides
+     * a means of extracting ALL components from within a target EHR Folder.
+     * @param extract The EHR Extract.
+     * @param extractComponentIndex The index of the RCMRMT030101UKComponent which houses the EHR Folder.
+     * @return A list of RCMRMT030101UKComponent3.
+     */
+    public static List<RCMRMT030101UKComponent3> getEhrFolderComponent(RCMRMT030101UKEhrExtract extract,
+                                                                       int extractComponentIndex) {
+        final RCMRMT030101UKEhrFolder targetFolder = extract
+            .getComponent()
+            .get(extractComponentIndex)
+            .getEhrFolder();
+
+        return targetFolder.getComponent();
+    }
+
     public static class NoConfidentialityCodePresentException extends RuntimeException {
         private static final String EXCEPTION_MESSAGE = "No confidentiality code is present within the test file.";
 

gp2gp-translator/src/test/java/uk/nhs/adaptors/pss/translator/util/DatabaseImmunizationCheckerTest.java

@@ -0,0 +1,101 @@
+package uk.nhs.adaptors.pss.translator.util;
+
+import jakarta.xml.bind.JAXBException;
+import org.hl7.v3.RCMRMT030101UKComponent3;
+import org.hl7.v3.RCMRMT030101UKEhrExtract;
+import org.hl7.v3.RCMRMT030101UKObservationStatement;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.ArgumentCaptor;
+import org.mockito.Captor;
+import org.mockito.InjectMocks;
+import org.mockito.Mock;
+import org.mockito.junit.jupiter.MockitoExtension;
+import uk.nhs.adaptors.connector.dao.ImmunizationSnomedCTDao;
+import uk.nhs.adaptors.connector.model.ImmunizationSnomedCT;
+import uk.nhs.adaptors.pss.translator.FileFactory;
+
+import java.io.File;
+import java.util.List;
+
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.junit.jupiter.api.Assertions.assertAll;
+import static org.mockito.Mockito.when;
+import static uk.nhs.adaptors.pss.translator.TestUtility.getEhrFolderComponent;
+import static uk.nhs.adaptors.pss.translator.util.XmlUnmarshallUtil.unmarshallFile;
+
+@ExtendWith(MockitoExtension.class)
+class DatabaseImmunizationCheckerTest {
+    @Mock
+    private ImmunizationSnomedCTDao immunizationSnomedCTDao;
+
+    @InjectMocks
+    private DatabaseImmunizationChecker databaseImmunizationChecker;
+
+    @Captor
+    private ArgumentCaptor<String> snomedCtIdCaptor;
+
+    private static final String TEST_FILES_DIRECTORY = "Immunization";
+
+    @Test
+    void When_IsObservationStatementImmunization_With_ImmunizationCode_Expect_True() throws JAXBException {
+        final String expectedCode = "3955997015";
+        final RCMRMT030101UKObservationStatement observationStatement = getObservationStatementFromExtract(
+            "full_valid_immunization_with_no_translation.xml");
+        final ImmunizationSnomedCT immunizationSnomedCT = ImmunizationSnomedCT.builder()
+            .conceptId(expectedCode)
+            .build();
+
+        when(immunizationSnomedCTDao.getImmunizationSnomedUsingConceptOrDescriptionId(
+            snomedCtIdCaptor.capture()
+        )).thenReturn(immunizationSnomedCT);
+
+        final boolean result = databaseImmunizationChecker.isImmunization(observationStatement);
+
+        assertAll(
+            () -> assertThat(result).isTrue(),
+            () -> assertThat(snomedCtIdCaptor.getValue()).isEqualTo(expectedCode)
+        );
+    }
+
+    @Test
+    void When_IsObservationStatementImmunization_With_ImmunizationCodeAndNonImmunizationTranslation_Expect_True() throws JAXBException {
+        final String snomedCode = "142934010";
+        final String readsV2Code = "65E..00";
+        final RCMRMT030101UKObservationStatement observationStatement = getObservationStatementFromExtract(
+            "full_valid_immunization_with_translation.xml"
+        );
+
+        final ImmunizationSnomedCT immunizationSnomedCT = ImmunizationSnomedCT.builder()
+            .conceptId(snomedCode)
+            .build();
+
+        when(immunizationSnomedCTDao.getImmunizationSnomedUsingConceptOrDescriptionId(
+            snomedCtIdCaptor.capture()
+        )).thenReturn(null, immunizationSnomedCT);
+
+        final boolean result = databaseImmunizationChecker.isImmunization(observationStatement);
+
+        assertAll(
+            () -> assertThat(result).isTrue(),
+            () -> assertThat(snomedCtIdCaptor.getAllValues().getFirst()).isEqualTo(readsV2Code),
+            () -> assertThat(snomedCtIdCaptor.getAllValues().get(1)).isEqualTo(snomedCode)
+        );
+    }
+
+    private RCMRMT030101UKObservationStatement getObservationStatementFromExtract(String filename) throws JAXBException {
+        final RCMRMT030101UKEhrExtract ehrExtract = getEhrExtractFromFile(filename);
+        final List<RCMRMT030101UKComponent3> components = getEhrFolderComponent(ehrExtract, 0);
+
+        return components.getFirst()
+            .getEhrComposition()
+            .getComponent()
+            .getFirst()
+            .getObservationStatement();
+    }
+
+    private RCMRMT030101UKEhrExtract getEhrExtractFromFile(String filename) throws JAXBException {
+        final File file = FileFactory.getXmlFileFor(TEST_FILES_DIRECTORY, filename);
+        return unmarshallFile(file, RCMRMT030101UKEhrExtract.class);
+    }
+}