NIAD-3217 - Send Observation (Test Result) when they do not have a …

…`Specimen` attached to them (#963) --------- Co-authored-by: Alex-Nita <[email protected]> Co-authored-by: Steven McCullagh <[email protected]> Co-authored-by: Alex-Nita <[email protected]> Co-authored-by: Adrian Clay <[email protected]>
NHSDigital · Nov 15, 2024 · a8ce62e · a8ce62e
1 parent 117e72a
commit a8ce62e
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Showing 16 changed files with 203 additions and 48 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,7 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [Unreleased]
 
 ## Added
-
+* When mapping a `DiagnosticReport` which contains a `TestResult` without a `Specimen` attached to it, a new `Specimen` is 
+created to allow the `TestResult` to be mapped correctly.
 * When mapping a `DocumentReference` which contains a `NOPAT` `meta.security` or `NOPAT` `securityLabel` tag the resultant XML for that resource
   will contain a `NOPAT` `confidentialityCode` element.
 * When mapping `AllergyIntolerances` which contain a `NOPAT` `meta.security` tag the resultant XML for that resource

diff --git a/...c/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/diagnosticreport/DiagnosticReportMapper.java b/...c/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/diagnosticreport/DiagnosticReportMapper.java
@@ -8,9 +8,11 @@
 import static uk.nhs.adaptors.gp2gp.ehr.mapper.CommentType.LABORATORY_RESULT_COMMENT;
 import static uk.nhs.adaptors.gp2gp.ehr.mapper.diagnosticreport.ObservationMapper.NARRATIVE_STATEMENT_TEMPLATE;
 
+import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 import java.util.Optional;
+import java.util.function.Predicate;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
@@ -73,13 +75,19 @@ public class DiagnosticReportMapper {
     private final ConfidentialityService confidentialityService;
 
     public String mapDiagnosticReportToCompoundStatement(DiagnosticReport diagnosticReport) {
-        List<Specimen> specimens = fetchSpecimens(diagnosticReport);
         List<Observation> observations = fetchObservations(diagnosticReport);
+        List<Specimen> specimens = fetchSpecimens(diagnosticReport, observations);
         final IdMapper idMapper = messageContext.getIdMapper();
         markObservationsAsProcessed(idMapper, observations);
 
+        List<Observation> observationsExcludingFilingComments = assignDummySpecimensToObservationsWithNoSpecimen(
+                observations.stream()
+                    .filter(Predicate.not(DiagnosticReportMapper::isFilingComment))
+                    .toList(),
+                specimens);
+
         String mappedSpecimens = specimens.stream()
-            .map(specimen -> specimenMapper.mapSpecimenToCompoundStatement(specimen, observations, diagnosticReport))
+            .map(specimen -> specimenMapper.mapSpecimenToCompoundStatement(specimen, observationsExcludingFilingComments, diagnosticReport))
             .collect(Collectors.joining());
 
         String reportLevelNarrativeStatements = prepareReportLevelNarrativeStatements(diagnosticReport, observations);
@@ -113,21 +121,60 @@ private String fetchExtensionId(List<Identifier> identifiers) {
             .orElse(StringUtils.EMPTY);
     }
 
-    private List<Specimen> fetchSpecimens(DiagnosticReport diagnosticReport) {
-        if (!diagnosticReport.hasSpecimen()) {
-            return Collections.singletonList(generateDefaultSpecimen(diagnosticReport));
+    private List<Specimen> fetchSpecimens(DiagnosticReport diagnosticReport, List<Observation> observations) {
+
+        List<Specimen> specimens = new ArrayList<>();
+
+        // At least one specimen is required to exist for any DiagnosticReport, according to the mim
+        if (!diagnosticReport.hasSpecimen() || hasObservationsWithoutSpecimen(observations)) {
+            specimens.add(generateDummySpecimen(diagnosticReport));
         }
 
         var inputBundleHolder = messageContext.getInputBundleHolder();
-        return diagnosticReport.getSpecimen()
+        List<Specimen> nonDummySpecimens = diagnosticReport.getSpecimen()
             .stream()
             .map(specimenReference -> inputBundleHolder.getResource(specimenReference.getReferenceElement()))
             .flatMap(Optional::stream)
             .map(Specimen.class::cast)
             .collect(Collectors.toList());
+
+        specimens.addAll(nonDummySpecimens);
+
+        return specimens;
+
+    }
+
+    private boolean hasObservationsWithoutSpecimen(List<Observation> observations) {
+        return observations
+                .stream()
+                .filter(observation -> !isFilingComment(observation))
+                .anyMatch(observation -> !observation.hasSpecimen());
+    }
+
+    private List<Observation> assignDummySpecimensToObservationsWithNoSpecimen(
+            List<Observation> observations, List<Specimen> specimens) {
+
+        if (!hasObservationsWithoutSpecimen(observations)) {
+            return observations;
+        }
+
+        // The assumption was made that all test results without a specimen will have the same dummy specimen referenced
+        Specimen dummySpecimen = specimens.stream()
+                .filter(specimen -> specimen.getId().contains(DUMMY_SPECIMEN_ID_PREFIX))
+                .toList().getFirst();
+
+        Reference dummySpecimenReference = new Reference(dummySpecimen.getId());
+
+        for (Observation observation : observations) {
+            if (!observation.hasSpecimen() && !isFilingComment(observation)) {
+                observation.setSpecimen(dummySpecimenReference);
+            }
+        }
+
+        return observations;
     }
 
-    private Specimen generateDefaultSpecimen(DiagnosticReport diagnosticReport) {
+    private Specimen generateDummySpecimen(DiagnosticReport diagnosticReport) {
         Specimen specimen = new Specimen();
 
         specimen.setId(DUMMY_SPECIMEN_ID_PREFIX + randomIdGeneratorService.createNewId());

diff --git a/service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/diagnosticreport/SpecimenMapper.java b/service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/diagnosticreport/SpecimenMapper.java
@@ -43,7 +43,6 @@
 import java.util.List;
 import java.util.Objects;
 import java.util.Optional;
-import java.util.function.Predicate;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
@@ -149,7 +148,6 @@ private String mapObservationsAssociatedWithSpecimen(Specimen specimen, List<Obs
         }
 
         return observationsAssociatedWithSpecimen.stream()
-            .filter(Predicate.not(DiagnosticReportMapper::isFilingComment))
             .map(observationMapper::mapObservationToCompoundStatement)
             .collect(Collectors.joining());
     }

diff --git a/...st/java/uk/nhs/adaptors/gp2gp/ehr/mapper/diagnosticreport/DiagnosticReportMapperTest.java b/...st/java/uk/nhs/adaptors/gp2gp/ehr/mapper/diagnosticreport/DiagnosticReportMapperTest.java
@@ -6,6 +6,7 @@
 import static org.mockito.Mockito.when;
 
 import java.io.IOException;
+import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 import java.util.Optional;
@@ -76,7 +77,6 @@ class DiagnosticReportMapperTest {
     private static final String INPUT_JSON_MULTIPLE_CODED_DIAGNOSIS = "diagnostic-report-with-multiple-coded-diagnosis.json";
     private static final String INPUT_JSON_EXTENSION_ID = "diagnostic-report-with-extension-id.json";
     private static final String INPUT_JSON_URN_OID_EXTENSION_ID = "diagnostic-report-with-urn-oid-extension-id.json";
-    private static final String INPUT_JSON_UNRELATED_TEST_RESULT = "diagnostic-report-with-one-specimen-and-one-unrelated-observation.json";
 
     private static final String OUTPUT_XML_REQUIRED_DATA = "diagnostic-report-with-required-data.xml";
     private static final String OUTPUT_XML_STATUS_NARRATIVE = "diagnostic-report-with-status-narrative.xml";
@@ -88,7 +88,6 @@ class DiagnosticReportMapperTest {
     private static final String OUTPUT_XML_MULTIPLE_CODED_DIAGNOSIS = "diagnostic-report-with-multiple-coded-diagnosis.xml";
     private static final String OUTPUT_XML_EXTENSION_ID = "diagnostic-report-with-extension-id.xml";
     private static final String OUTPUT_XML_MULTIPLE_RESULTS = "diagnostic-report-with-multiple-results.xml";
-    private static final String OUTPUT_XML_UNRELATED_TEST_RESULT = "diagnostic-report-with-one-specimen-and-one-unrelated-observation.xml";
 
     @Mock
     private CodeableConceptCdMapper codeableConceptCdMapper;
@@ -293,6 +292,44 @@ void When_DiagnosticReport_With_NoReferencedSpecimenAndFilingCommentWithNoCommen
         assertThat(actualXml).isEqualToIgnoringWhitespace(expectedXml);
     }
 
+    /**
+     * A Diagnosis Report may have an Observation (Test Result) and Specimen. If the result and specimen are not
+     * linked then we need to create a dummy specimen linked to the result.
+     */
+    @Test
+    void When_DiagnosticReport_Has_SpecimenAndUnlinkedTestResult_Expect_ADummySpecimenLinkedToTestResult() {
+        final String diagnosticReportFileName = "diagnostic-report-with-one-specimen-and-one-unrelated-observation.json";
+        final DiagnosticReport diagnosticReport = getDiagnosticReportResourceFromJson(diagnosticReportFileName);
+        final Bundle bundle = getBundleResourceFromJson(INPUT_JSON_BUNDLE);
+        final InputBundle inputBundle = new InputBundle(bundle);
+
+        when(messageContext.getInputBundleHolder()).thenReturn(inputBundle);
+
+        final String actualXml = mapper.mapDiagnosticReportToCompoundStatement(diagnosticReport);
+
+        // This checks that the unlinked test result is given a dummy specimen.
+        assertThat(actualXml).containsIgnoringWhitespaces(
+                "<!-- Mapped Specimen with id: DUMMY-SPECIMEN-5E496953-065B-41F2-9577-BE8F2FBD0757 "
+                        + "with linked Observations: Observation/TestResult-WithoutSpecimenReference-->");
+    }
+
+    @Test
+    void When_DiagnosticReport_Has_SpecimenALinkedTestResultAndAnUnlinkedTestResult_Expect_ASpecimenOnAllTestResults() {
+        final String diagnosticReportFileName =
+                "diagnostic-report-with-one-specimen-one-linked-observation-and-one-unlinked-observation.json";
+        final DiagnosticReport diagnosticReport = getDiagnosticReportResourceFromJson(diagnosticReportFileName);
+        final Bundle bundle = getBundleResourceFromJson(INPUT_JSON_BUNDLE);
+        final InputBundle inputBundle = new InputBundle(bundle);
+        when(messageContext.getInputBundleHolder()).thenReturn(inputBundle);
+
+        final String actualXml = mapper.mapDiagnosticReportToCompoundStatement(diagnosticReport);
+        // This checks that the unlinked test result is given a dummy specimen.
+        assertThat(actualXml).containsIgnoringWhitespaces(
+                "<!-- Mapped Specimen with id: DUMMY-SPECIMEN-5E496953-065B-41F2-9577-BE8F2FBD0757 "
+                        + "with linked Observations: Observation/TestResult-WithoutSpecimenReference-->");
+
+    }
+
     private Bundle getBundleResourceFromJson(String filename) {
         final String filePath = TEST_FILE_DIRECTORY + filename;
         return FileParsingUtility.parseResourceFromJsonFile(filePath, Bundle.class);
@@ -318,8 +355,7 @@ private static Stream<Arguments> resourceFileParams() {
             Arguments.of(INPUT_JSON_CODED_DIAGNOSIS, OUTPUT_XML_CODED_DIAGNOSIS),
             Arguments.of(INPUT_JSON_MULTIPLE_CODED_DIAGNOSIS, OUTPUT_XML_MULTIPLE_CODED_DIAGNOSIS),
             Arguments.of(INPUT_JSON_EXTENSION_ID, OUTPUT_XML_EXTENSION_ID),
-            Arguments.of(INPUT_JSON_URN_OID_EXTENSION_ID, OUTPUT_XML_EXTENSION_ID),
-            Arguments.of(INPUT_JSON_UNRELATED_TEST_RESULT, OUTPUT_XML_UNRELATED_TEST_RESULT)
+            Arguments.of(INPUT_JSON_URN_OID_EXTENSION_ID, OUTPUT_XML_EXTENSION_ID)
         );
     }
 
@@ -341,7 +377,23 @@ private Answer<String> mockIdForReference() {
     private Answer<String> mockSpecimenMapping() {
         return invocation -> {
             Specimen specimen = invocation.getArgument(0);
-            return String.format("<!-- Mapped Specimen with id: %s -->", specimen.getId());
+            List<Observation> observations = invocation.getArgument(1);
+
+            List<String> linkedObservations = new ArrayList<>();
+
+            for (Observation observation : observations) {
+                if (observation.getSpecimen().getReference() != null
+                        && observation.getSpecimen().getReference().equals(specimen.getId())) {
+                    linkedObservations.add(observation.getId());
+                }
+            }
+
+            if (linkedObservations.isEmpty()) {
+                return String.format("<!-- Mapped Specimen with id: %s -->", specimen.getId());
+            }
+            return String.format("<!-- Mapped Specimen with id: %s with linked Observations: %s-->",
+                    specimen.getId(),
+                    String.join(",", linkedObservations));
         };
     }
 }
diff --git a/...src/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-coded-diagnosis.xml b/...src/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-coded-diagnosis.xml
@@ -30,6 +30,6 @@ Status: unknown</text>
         <availabilityTime value="20100225154100"/>
     </NarrativeStatement>
 </component>
-            <!-- Mapped Specimen with id: DUMMY-SPECIMEN-5E496953-065B-41F2-9577-BE8F2FBD0757 -->
+            <!-- Mapped Specimen with id: DUMMY-SPECIMEN-5E496953-065B-41F2-9577-BE8F2FBD0757 with linked Observations: DUMMY-OBSERVATION-5E496953-065B-41F2-9577-BE8F2FBD0757-->
     </CompoundStatement>
 </component>
diff --git a/service/src/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-conclusion.xml b/service/src/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-conclusion.xml
@@ -30,6 +30,6 @@ Status: unknown</text>
         <availabilityTime value="20100225154100"/>
     </NarrativeStatement>
 </component>
-            <!-- Mapped Specimen with id: DUMMY-SPECIMEN-5E496953-065B-41F2-9577-BE8F2FBD0757 -->
+            <!-- Mapped Specimen with id: DUMMY-SPECIMEN-5E496953-065B-41F2-9577-BE8F2FBD0757 with linked Observations: DUMMY-OBSERVATION-5E496953-065B-41F2-9577-BE8F2FBD0757-->
     </CompoundStatement>
 </component>
diff --git a/...ce/src/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-extension-id.xml b/...ce/src/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-extension-id.xml
@@ -21,6 +21,6 @@ Status: unknown</text>
         <availabilityTime value="20100225154100"/>
     </NarrativeStatement>
 </component>
-            <!-- Mapped Specimen with id: DUMMY-SPECIMEN-5E496953-065B-41F2-9577-BE8F2FBD0757 -->
+            <!-- Mapped Specimen with id: DUMMY-SPECIMEN-5E496953-065B-41F2-9577-BE8F2FBD0757 with linked Observations: DUMMY-OBSERVATION-5E496953-065B-41F2-9577-BE8F2FBD0757-->
     </CompoundStatement>
 </component>
diff --git a/...src/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-multi-specimens.xml b/...src/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-multi-specimens.xml
@@ -20,6 +20,9 @@ Status: unknown</text>
         <availabilityTime value="20100225154100"/>
     </NarrativeStatement>
 </component>
-            <!-- Mapped Specimen with id: Specimen/96B93E28-293D-46E7-B4C2-D477EEBF7098-SPEC-0 --><!-- Mapped Specimen with id: Specimen/96B93E28-293D-46E7-B4C2-D477EEBF7098-SPEC-1 --><!-- Mapped Specimen with id: Specimen/96B93E28-293D-46E7-B4C2-D477EEBF7098-SPEC-2 -->
+        <!-- Mapped Specimen with id: DUMMY-SPECIMEN-5E496953-065B-41F2-9577-BE8F2FBD0757 with linked Observations: DUMMY-OBSERVATION-5E496953-065B-41F2-9577-BE8F2FBD0757-->
+        <!-- Mapped Specimen with id: Specimen/96B93E28-293D-46E7-B4C2-D477EEBF7098-SPEC-0 -->
+        <!-- Mapped Specimen with id: Specimen/96B93E28-293D-46E7-B4C2-D477EEBF7098-SPEC-1 -->
+        <!-- Mapped Specimen with id: Specimen/96B93E28-293D-46E7-B4C2-D477EEBF7098-SPEC-2 -->
     </CompoundStatement>
 </component>
diff --git a/...resources/ehr/mapper/diagnosticreport/diagnostic-report-with-multiple-coded-diagnosis.xml b/...resources/ehr/mapper/diagnosticreport/diagnostic-report-with-multiple-coded-diagnosis.xml
@@ -30,6 +30,6 @@ Status: unknown</text>
         <availabilityTime value="20100225154100"/>
     </NarrativeStatement>
 </component>
-            <!-- Mapped Specimen with id: DUMMY-SPECIMEN-5E496953-065B-41F2-9577-BE8F2FBD0757 -->
+        <!-- Mapped Specimen with id: DUMMY-SPECIMEN-5E496953-065B-41F2-9577-BE8F2FBD0757 with linked Observations: DUMMY-OBSERVATION-5E496953-065B-41F2-9577-BE8F2FBD0757-->
     </CompoundStatement>
 </component>
diff --git a/...er/diagnosticreport/diagnostic-report-with-one-specimen-and-one-unrelated-observation.xml b/...er/diagnosticreport/diagnostic-report-with-one-specimen-and-one-unrelated-observation.xml
diff --git a/...gnostic-report-with-one-specimen-one-linked-observation-and-one-unlinked-observation.json b/...gnostic-report-with-one-specimen-one-linked-observation-and-one-unlinked-observation.json
@@ -0,0 +1,45 @@
+{
+  "resourceType": "DiagnosticReport",
+  "id": "96B93E28-293D-46E7-B4C2-D477EEBF7098",
+  "meta": {
+    "profile": [
+      "https://fhir.nhs.uk/STU3/StructureDefinition/CareConnect-GPC-DiagnosticReport-1"
+    ]
+  },
+  "identifier": [
+    {
+      "system": "https://EMISWeb/A82038",
+      "value": "96B93E28-293D-46E7-B4C2-D477EEBF7098"
+    }
+  ],
+  "status": "unknown",
+  "category": {
+    "coding": [
+      {
+        "system": "http://hl7.org/fhir/v2/0074",
+        "code": "PAT",
+        "display": "Pathology (gross & histopath, not surgical)"
+      }
+    ]
+  },
+  "code": {
+    "coding": [
+      {
+        "system": "http://snomed.info/sct",
+        "code": "721981007",
+        "display": "Diagnostic studies report"
+      }
+    ]
+  },
+  "subject": {
+    "reference": "Patient/DAED5527-1985-45D9-993E-C5FF51F36828"
+  },
+  "issued": "2010-02-25T15:41:00+00:00",
+  "specimen": [{
+    "reference": "Specimen/96B93E28-293D-46E7-B4C2-D477EEBF7098-SPEC-0"
+  }],
+  "result": [
+    { "reference": "Observation/B7F05EA7-A1A4-48C0-9C4C-CDB5768796B2" },
+    { "reference": "Observation/TestResult-WithoutSpecimenReference" }
+  ]
+}
diff --git a/...ce/src/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-one-specimen.xml b/...ce/src/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-one-specimen.xml
@@ -20,6 +20,7 @@ Status: unknown</text>
         <availabilityTime value="20100225154100"/>
     </NarrativeStatement>
 </component>
+            <!-- Mapped Specimen with id: DUMMY-SPECIMEN-5E496953-065B-41F2-9577-BE8F2FBD0757 with linked Observations: DUMMY-OBSERVATION-5E496953-065B-41F2-9577-BE8F2FBD0757-->
             <!-- Mapped Specimen with id: Specimen/96B93E28-293D-46E7-B4C2-D477EEBF7098-SPEC-0 -->
     </CompoundStatement>
 </component>
diff --git a/...ice/src/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-participant.xml b/...ice/src/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-participant.xml
@@ -30,7 +30,7 @@ Participants: TEMPLE SOWERBY MEDICAL PRACTICE</text>
         <availabilityTime value="20100225154100"/>
     </NarrativeStatement>
 </component>
-            <!-- Mapped Specimen with id: DUMMY-SPECIMEN-5E496953-065B-41F2-9577-BE8F2FBD0757 -->
+            <!-- Mapped Specimen with id: DUMMY-SPECIMEN-5E496953-065B-41F2-9577-BE8F2FBD0757 with linked Observations: DUMMY-OBSERVATION-5E496953-065B-41F2-9577-BE8F2FBD0757-->
             <Participant typeCode="AUT" contextControlCode="OP">
     <agentRef classCode="AGNT">
         <id root="II-for-Organization/5E496953-065B-41F2-9577-BE8F2FBD0757"/>

diff --git a/...rc/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-status-narrative.xml b/...rc/test/resources/ehr/mapper/diagnosticreport/diagnostic-report-with-status-narrative.xml
@@ -20,6 +20,6 @@ Status: unknown</text>
         <availabilityTime value="20100225154100"/>
     </NarrativeStatement>
 </component>
-            <!-- Mapped Specimen with id: DUMMY-SPECIMEN-5E496953-065B-41F2-9577-BE8F2FBD0757 -->
+            <!-- Mapped Specimen with id: DUMMY-SPECIMEN-5E496953-065B-41F2-9577-BE8F2FBD0757 with linked Observations: DUMMY-OBSERVATION-5E496953-065B-41F2-9577-BE8F2FBD0757-->
     </CompoundStatement>
 </component>
diff --git a/...hr/mapper/diagnosticreport/specimen/expected_output_default_specimen_with_observation.xml b/...hr/mapper/diagnosticreport/specimen/expected_output_default_specimen_with_observation.xml
@@ -31,6 +31,6 @@ Received Date: 2010-02-24 15:41
         <availabilityTime value="20201012143344"/>
     </NarrativeStatement>
 </component>
-            <!-- Mapped Observation with id: Observation/B7F05EA7-A1A4-48C0-9C4C-CDB5768796B2 -->
+            <!-- Mapped Observation with id: Observation/B7F05EA7-A1A4-48C0-9C4C-CDB5768796B2 --><!-- Mapped Observation with id: Observation/B7F05EA7-A1A4-48C0-9C4C-CDB5768796B2-COMM -->
     </CompoundStatement>
 </component>