NIAD-3148 - Immunizations outside of consultation are mapped to Obser…

…vation (#752) * [NIAD-3148] Add method to TestUtility.java `getEhrFolderComponent` * [NIAD-3148] Add method to TestUtility.java `getEhrFolderComponent` * [NIAD-3148] Add some unit tests for current logic * [NIAD-3148] Remove redundant test file * [NIAD-3148] Initial refactor of DatabaseImmunizationChecker.java * [NIAD-3148] Create DatabaseImmunizationCheckerTest * [NIAD-3148] Create utility to create CD values * [NIAD-3148] Add functionality to create-database-postgres.sql to join the description ID and concept ID * [NIAD-3148] Method signature renamed to `getImmunizationSnomedUsingConceptOrDescriptionId` * [NIAD-3148] Address problem with test-load-immunization-codes.sh * Add DirtiesContext to DatabaseImmunizationCheckerIT * [NIAD-3148] Address PR to #752 (comment) * [NIAD-3148] Address PR comments https://github.com/NHSDigital/nia-patient-switching-standard-adaptor/pull/752/files#r1710239250 and https://github.com/NHSDigital/nia-patient-switching-standard-adaptor/pull/752/files#r1710234310 * [NIAD-3148] Address PR comment https://github.com/NHSDigital/nia-patient-switching-standard-adaptor/pull/752/files#r1710219516 * [NIAD-3148] Update CHANGELOG.md * [NIAD-3148] Update CHANGELOG.md --------- Co-authored-by: MartinWheelerMT <[email protected]>
NHSDigital · Aug 12, 2024 · fccd428 · fccd428
1 parent 58e6022
commit fccd428
Show file tree

Hide file tree

Showing 14 changed files with 495 additions and 51 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -20,6 +20,9 @@ corresponding FHIR resource will now be [appropriately populated][nopat-docs].
     corresponding FHIR resource will now be [appropriately populated][nopat-docs].
 * If a `bloodPressure` record includes a `confidentialityCode`, the `meta.security` field of the
     corresponding FHIR resource will now be [appropriately populated][nopat-docs].
+* Addressed a bug in the PS adaptor where immunizations were incorrectly mapped to observations. 
+The adaptor now verifies the Snomed CT ID against both the Concept ID and the Description ID, ensuring 
+that immunizations are correctly identified when a match is found.
 
 ### Fixed
 * Resolved issue where the SNOMED import script would reject a password containing a '%' character.

diff --git a/db-connector/src/main/java/uk/nhs/adaptors/connector/dao/ImmunizationSnomedCTDao.java b/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("snomedId") String snomedId);
 
     @SqlQuery("verify_immunizations_loaded")
     @UseClasspathSqlLocator

diff --git a/db-connector/src/main/java/uk/nhs/adaptors/connector/mapper/ImmunizationSnomedCTMapper.java b/db-connector/src/main/java/uk/nhs/adaptors/connector/mapper/ImmunizationSnomedCTMapper.java
@@ -11,10 +11,13 @@
 
 @Component
 public class ImmunizationSnomedCTMapper implements RowMapper<ImmunizationSnomedCT> {
+    private static final String COLUMN_NAME = "concept_or_description_id";
+
     @Override
     public ImmunizationSnomedCT map(ResultSet rs, StatementContext ctx) throws SQLException {
+        final String conceptOrDescriptionId = rs.getString(COLUMN_NAME);
         return ImmunizationSnomedCT.builder()
-            .conceptId(rs.getString("conceptId"))
+            .snomedId(conceptOrDescriptionId)
             .build();
     }
-}
+}
diff --git a/db-connector/src/main/java/uk/nhs/adaptors/connector/model/ImmunizationSnomedCT.java b/db-connector/src/main/java/uk/nhs/adaptors/connector/model/ImmunizationSnomedCT.java
@@ -8,5 +8,5 @@
 @Setter
 @Builder
 public class ImmunizationSnomedCT {
-    private String conceptId;
+    private String snomedId;
 }
diff --git a/.../uk/nhs/adaptors/connector/dao/ImmunizationSnomedCTDao/select_immunization_concept_id.sql b/.../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.concept_or_description_id FROM "snomedct".immunization_codes i WHERE i.concept_or_description_id = :snomedId;
diff --git a/...ces/uk/nhs/adaptors/connector/dao/ImmunizationSnomedCTDao/verify_immunizations_loaded.sql b/...ces/uk/nhs/adaptors/connector/dao/ImmunizationSnomedCTDao/verify_immunizations_loaded.sql
@@ -1,9 +1,9 @@
 -- 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.concept_or_description_id) = 16 -- total number of codes
 FROM "snomedct".immunization_codes i
-WHERE i.conceptid IN (
+WHERE i.concept_or_description_id IN (
                       '787859002', '127785005', '304250009', '90351000119108','713404003','2997511000001102',
                       '308101000000104','1036721000000101', '1373691000000102', '945831000000105', '542931000000103',
                       '735981009', '90640007', '571631000119106', '764141000000106', '170399005'

diff --git a/...rc/integrationTest/java/uk/nhs/adaptors/pss/translator/DatabaseImmunizationCheckerIT.java b/...rc/integrationTest/java/uk/nhs/adaptors/pss/translator/DatabaseImmunizationCheckerIT.java
@@ -0,0 +1,61 @@
+package uk.nhs.adaptors.pss.translator;
+
+import org.hl7.v3.CD;
+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.annotation.DirtiesContext;
+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;
+
+@SpringBootTest
+@DirtiesContext
+@ExtendWith(SpringExtension.class)
+class DatabaseImmunizationCheckerIT {
+    private static final String SNOMED_CODE_SYSTEM_OID = "2.16.840.1.113883.2.1.3.2.4.15";
+    private static final String DISPLAY_NAME = "Influenza vaccination";
+
+    @Autowired
+    private DatabaseImmunizationChecker databaseImmunizationChecker;
+
+    @Test
+    void When_Immunization_With_SnomedDescriptionId_Expect_True() {
+        final String immunizationDescriptionSnomedId = "142934010";
+        final CD cd = getCdForSnomedId(immunizationDescriptionSnomedId);
+        final RCMRMT030101UKObservationStatement observationStatement =
+            new RCMRMT030101UKObservationStatement();
+
+        observationStatement.setCode(cd);
+
+        final boolean result = databaseImmunizationChecker.isImmunization(observationStatement);
+
+        assertThat(result).isTrue();
+    }
+
+    @Test
+    void When_Immunization_With_SnomedConceptId_Expect_True() {
+        final String immunizationConceptSnomedId = "86198006";
+        final CD cd = getCdForSnomedId(immunizationConceptSnomedId);
+        final RCMRMT030101UKObservationStatement observationStatement =
+            new RCMRMT030101UKObservationStatement();
+
+        observationStatement.setCode(cd);
+
+        final boolean result = databaseImmunizationChecker.isImmunization(observationStatement);
+
+        assertThat(result).isTrue();
+    }
+
+    private CD getCdForSnomedId(String snomedId) {
+        return createCd(
+            snomedId,
+            SNOMED_CODE_SYSTEM_OID,
+            DISPLAY_NAME
+        );
+    }
+}
diff --git a/...slator/src/main/java/uk/nhs/adaptors/pss/translator/util/DatabaseImmunizationChecker.java b/...slator/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;
     }
-}
+}
diff --git a/gp2gp-translator/src/test/java/uk/nhs/adaptors/pss/translator/TestUtility.java b/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> getEhrFolderComponents(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.";
 

diff --git a/...or/src/test/java/uk/nhs/adaptors/pss/translator/util/DatabaseImmunizationCheckerTest.java b/...or/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.getEhrFolderComponents;
+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()
+            .snomedId(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()
+            .snomedId(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 = getEhrFolderComponents(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);
+    }
+}
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		SELECT i.conceptid FROM "snomedct".immunization_codes i WHERE conceptid = :conceptId;
		SELECT i.concept_or_description_id FROM "snomedct".immunization_codes i WHERE i.concept_or_description_id = :snomedId;