Restructured availability time value mappings (#602)

* Restructured availability time value mappings
* Changed source value for availabilityTime from onsetDate to assertedDate
* Corrected test data.
* Removed Line Break

Author: Alex-Nita

service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/AllergyStructureExtractor.java

@@ -59,6 +59,13 @@ public static String extractOnsetDate(AllergyIntolerance allergyIntolerance) {
         return StringUtils.EMPTY;
     }
 
+    public static String extractAssertedDate(AllergyIntolerance allergyIntolerance) {
+        if (allergyIntolerance.hasAssertedDateElement() && allergyIntolerance.getAssertedDateElement().hasValue()) {
+            return toHl7Format(allergyIntolerance.getAssertedDateElement());
+        }
+        return StringUtils.EMPTY;
+    }
+
     public static String extractReaction(AllergyIntolerance.AllergyIntoleranceReactionComponent reactionComponent,
         AtomicInteger reactionCount) {
         String reaction = String.format(REACTION, reactionCount.getAndIncrement());

service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/mapper/AllergyStructureMapper.java

@@ -2,6 +2,7 @@
 
 import static uk.nhs.adaptors.gp2gp.ehr.mapper.AllergyStructureExtractor.extractOnsetDate;
 import static uk.nhs.adaptors.gp2gp.ehr.mapper.AllergyStructureExtractor.extractReaction;
+import static uk.nhs.adaptors.gp2gp.ehr.mapper.AllergyStructureExtractor.extractAssertedDate;
 import static uk.nhs.adaptors.gp2gp.ehr.utils.DateFormatUtil.toTextFormat;
 import static uk.nhs.adaptors.gp2gp.ehr.utils.ExtensionMappingUtils.filterExtensionByUrl;
 
@@ -124,11 +125,10 @@ private String buildCode(AllergyIntolerance allergyIntolerance) {
     }
 
     private String buildAvailabilityTime(AllergyIntolerance allergyIntolerance) {
-        return Optional.of(allergyIntolerance)
-            .filter(AllergyIntolerance::hasOnsetDateTimeType)
-            .map(AllergyIntolerance::getOnsetDateTimeType)
-            .map(DateFormatUtil::toHl7Format)
-            .orElse(StringUtils.EMPTY);
+
+        var availabilityTime = extractAssertedDate(allergyIntolerance);
+
+        return StatementTimeMappingUtils.prepareAvailabilityTimeForAllergyIntolerance(availabilityTime);
     }
 
     private String buildEffectiveTime(AllergyIntolerance allergyIntolerance) {

service/src/main/java/uk/nhs/adaptors/gp2gp/ehr/utils/StatementTimeMappingUtils.java

@@ -117,6 +117,14 @@ public static String prepareEffectiveTimeForAllergyIntolerance(String onsetDate)
         }
     }
 
+    public static String prepareAvailabilityTimeForAllergyIntolerance(String date) {
+        if (!date.isEmpty()) {
+            return String.format(AVAILABILITY_TIME_VALUE_TEMPLATE, date);
+        }
+
+        return DEFAULT_AVAILABILITY_TIME_VALUE;
+    }
+
     public static String prepareEffectiveTimeForMedicationRequest(MedicationRequest medicationRequest) {
         final var dispenseRequest = medicationRequest.getDispenseRequest();
         if (dispenseRequest.hasValidityPeriod() && dispenseRequest.getValidityPeriod().hasStart()) {

service/src/main/resources/templates/ehr_allergy_structure_template.mustache

@@ -6,7 +6,7 @@
         <effectiveTime>
             {{{effectiveTime}}}
         </effectiveTime>
-        <availabilityTime {{#availabilityTime}}value="{{availabilityTime}}"{{/availabilityTime}}{{^availabilityTime}}nullFlavor="UNK"{{/availabilityTime}} />
+        {{{availabilityTime}}}
         <component typeCode="COMP" contextConductionInd="true">
             <ObservationStatement classCode="OBS" moodCode="ENV">
                 <id root="{{observationId}}"/>
@@ -15,7 +15,7 @@
                 <effectiveTime>
                     {{{effectiveTime}}}
                 </effectiveTime>
-                <availabilityTime {{#availabilityTime}}value="{{availabilityTime}}"{{/availabilityTime}}{{^availabilityTime}}nullFlavor="UNK"{{/availabilityTime}} />
+                {{{availabilityTime}}}
                 <pertinentInformation typeCode="PERT">
                     <sequenceNumber value="+1"/>
                     <pertinentAnnotation classCode="OBS" moodCode="EVN">

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

@@ -70,6 +70,8 @@ public class AllergyStructureMapperTest {
         + "example-allergy-intolerance-resource-20.json";
     private static final String INPUT_JSON_WITHOUT_END_DATE = TEST_FILE_DIRECTORY
         + "example-allergy-intolerance-resource-without-endDate.json";
+    private static final String INPUT_JSON_WITHOUT_ASSERTED_DATE = TEST_FILE_DIRECTORY
+            + "example-allergy-intolerance-resource-without-assertedDate.json";
     private static final String INPUT_JSON_WITH_VALID_RECORDER_NO_ASSERTER = TEST_FILE_DIRECTORY
         + "example-allergy-intolerance-resource-21.json";
     private static final String INPUT_JSON_WITH_INVALID_RECORDER_NO_ASSERTER = TEST_FILE_DIRECTORY
@@ -108,6 +110,8 @@ public class AllergyStructureMapperTest {
     private static final String OUTPUT_XML_USES_END_DATE = TEST_FILE_DIRECTORY + "expected-output-allergy-structure-17.xml";
     private static final String OUTPUT_XML_USES_NO_END_DATE = TEST_FILE_DIRECTORY
         + "expected-output-allergy-structure-without-endDate.xml";
+    private static final String OUTPUT_XML_USES_NO_ASSERTED_DATE = TEST_FILE_DIRECTORY
+            + "expected-output-allergy-structure-without-assertedDate.xml";
     private static final String OUTPUT_XML_USES_RECORDER_AS_PERFORMER = TEST_FILE_DIRECTORY
         + "expected-output-allergy-structure-17.xml";
     private static final String OUTPUT_XML_USES_NO_AUTHOR_OR_PERFORMER = TEST_FILE_DIRECTORY
@@ -151,6 +155,7 @@ private static Stream<Arguments> resourceFileParams() {
             Arguments.of(INPUT_JSON_WITH_RELATED_PERSON_ASSERTER_NAME_TEXT, OUTPUT_XML_USES_RELATED_PERSON_ASSERTER),
             Arguments.of(INPUT_JSON_WITH_RELATED_PERSON_ASSERTER_NO_NAME, OUTPUT_XML_USES_RELATED_PERSON_ASSERTER_NO_NAME),
             Arguments.of(INPUT_JSON_WITHOUT_END_DATE, OUTPUT_XML_USES_NO_END_DATE),
+            Arguments.of(INPUT_JSON_WITHOUT_ASSERTED_DATE, OUTPUT_XML_USES_NO_ASSERTED_DATE),
             Arguments.of(INPUT_JSON_WITH_VALID_RECORDER_NO_ASSERTER, OUTPUT_XML_USES_RECORDER_AS_FALLBACK_ASSERTER),
             Arguments.of(INPUT_JSON_WITH_INVALID_RECORDER_NO_ASSERTER, OUTPUT_XML_USES_NO_AUTHOR_OR_PERFORMER),
             Arguments.of(INPUT_JSON_WITH_VALID_RECORDER_RELATED_PERSON_ASSERTER,

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

@@ -245,7 +245,7 @@ public void When_MappingJsonBody_Expect_OnlyOneConsultationResource() throws IOE
             getGpcStructuredTaskDefinition,
             bundle);
         String output = ehrExtractMapper.mapEhrExtractToXml(ehrExtractTemplateParameters);
-        assertThat(output).isEqualTo(expectedJsonToXmlContent);
+        assertThat(output).isEqualToIgnoringWhitespace(expectedJsonToXmlContent);
     }
 
     @Test

service/src/test/resources/ehr/mapper/allergy/example-allergy-intolerance-resource-without-assertedDate.json

@@ -0,0 +1,12 @@
+{
+    "resourceType": "AllergyIntolerance",
+    "id": "230D3D37-99E3-450A-AE88-B5AB802B7137",
+    "onsetDateTime": "1978-12-31",
+    "clinicalStatus": "resolved",
+    "category": [
+        "medication"
+    ],
+    "code": {
+        "text": "test"
+    }
+}

service/src/test/resources/ehr/mapper/allergy/expected-output-allergy-structure-1.xml

@@ -6,7 +6,7 @@
         <effectiveTime>
             <center value="19781231"/>
         </effectiveTime>
-        <availabilityTime value="19781231" />
+        <availabilityTime value="20100114095757"/>
         <component typeCode="COMP" contextConductionInd="true">
             <ObservationStatement classCode="OBS" moodCode="ENV">
                 <id root="394559384658936"/>
@@ -15,7 +15,7 @@
                 <effectiveTime>
                     <center value="19781231"/>
                 </effectiveTime>
-                <availabilityTime value="19781231" />
+                <availabilityTime value="20100114095757"/>
                 <pertinentInformation typeCode="PERT">
                     <sequenceNumber value="+1"/>
                     <pertinentAnnotation classCode="OBS" moodCode="EVN">

service/src/test/resources/ehr/mapper/allergy/expected-output-allergy-structure-10.xml

@@ -6,7 +6,7 @@
         <effectiveTime>
             <center value="20200724"/>
         </effectiveTime>
-        <availabilityTime value="20200724" />
+        <availabilityTime value="20200724133829"/>
         <component typeCode="COMP" contextConductionInd="true">
             <ObservationStatement classCode="OBS" moodCode="ENV">
                 <id root="394559384658936"/>
@@ -15,7 +15,7 @@
                 <effectiveTime>
                     <center value="20200724"/>
                 </effectiveTime>
-                <availabilityTime value="20200724" />
+                <availabilityTime value="20200724133829"/>
                 <pertinentInformation typeCode="PERT">
                     <sequenceNumber value="+1"/>
                     <pertinentAnnotation classCode="OBS" moodCode="EVN">

service/src/test/resources/ehr/mapper/allergy/expected-output-allergy-structure-11.xml

@@ -6,7 +6,7 @@
         <effectiveTime>
             <center value="20100114"/>
         </effectiveTime>
-        <availabilityTime value="20100114" />
+        <availabilityTime value="20100114095728"/>
         <component typeCode="COMP" contextConductionInd="true">
             <ObservationStatement classCode="OBS" moodCode="ENV">
                 <id root="394559384658936"/>
@@ -15,7 +15,7 @@
                 <effectiveTime>
                     <center value="20100114"/>
                 </effectiveTime>
-                <availabilityTime value="20100114" />
+                <availabilityTime value="20100114095728"/>
                 <pertinentInformation typeCode="PERT">
                     <sequenceNumber value="+1"/>
                     <pertinentAnnotation classCode="OBS" moodCode="EVN">