Add test date to Observation.issued for single-entry and bulk upload (#…

…5982) * Add test date to Observation.issued for single-entry and bulk upload * also force time zones to make fhir converter easier to test * also fix rounding of test date to start of day * using system default time zone for now but should look into what time zone to infer for dates in bulk upload
CDCgov · Jun 16, 2023 · e4df864 · e4df864
1 parent f1f93ed
commit e4df864
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Showing 9 changed files with 77 additions and 26 deletions.
diff --git a/backend/src/main/java/gov/cdc/usds/simplereport/api/converter/ConvertToObservationProps.java b/backend/src/main/java/gov/cdc/usds/simplereport/api/converter/ConvertToObservationProps.java
@@ -1,6 +1,7 @@
 package gov.cdc.usds.simplereport.api.converter;
 
 import gov.cdc.usds.simplereport.db.model.auxiliary.TestCorrectionStatus;
+import java.util.Date;
 import lombok.Builder;
 import lombok.Getter;
 
@@ -17,4 +18,5 @@ public class ConvertToObservationProps {
   private String testkitNameId;
   private String equipmentUid;
   private String deviceModel;
+  private Date issued;
 }
diff --git a/backend/src/main/java/gov/cdc/usds/simplereport/api/converter/FhirConverter.java b/backend/src/main/java/gov/cdc/usds/simplereport/api/converter/FhirConverter.java
@@ -33,6 +33,7 @@
 import static gov.cdc.usds.simplereport.api.converter.FhirConstants.UNIVERSAL_ID_SYSTEM;
 import static gov.cdc.usds.simplereport.api.converter.FhirConstants.YESNO_CODE_SYSTEM;
 
+import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
 import com.google.i18n.phonenumbers.NumberParseException;
 import com.google.i18n.phonenumbers.PhoneNumberUtil;
 import com.google.i18n.phonenumbers.PhoneNumberUtil.PhoneNumberFormat;
@@ -489,7 +490,8 @@ public List<Observation> convertToObservation(
       Set<Result> results,
       DeviceType deviceType,
       TestCorrectionStatus correctionStatus,
-      String correctionReason) {
+      String correctionReason,
+      Date resultDate) {
     return results.stream()
         .map(
             result -> {
@@ -515,7 +517,8 @@ public List<Observation> convertToObservation(
                   correctionReason,
                   testkitNameId,
                   equipmentUid,
-                  deviceType.getModel());
+                  deviceType.getModel(),
+                  resultDate);
             })
         .collect(Collectors.toList());
   }
@@ -534,7 +537,8 @@ public Observation convertToObservation(
       String correctionReason,
       String testkitNameId,
       String equipmentUid,
-      String deviceModel) {
+      String deviceModel,
+      Date resultDate) {
     if (result != null && result.getDisease() != null) {
 
       return convertToObservation(
@@ -550,6 +554,7 @@ public Observation convertToObservation(
               .testkitNameId(testkitNameId)
               .equipmentUid(equipmentUid)
               .deviceModel(deviceModel)
+              .issued(resultDate)
               .build());
     }
     return null;
@@ -582,6 +587,9 @@ public Observation convertToObservation(ConvertToObservationProps props) {
         .addInterpretation()
         .addCoding(convertToAbnormalFlagInterpretation(props.getResultCode()));
 
+    observation.setIssued(props.getIssued());
+    observation.getIssuedElement().setTimeZoneZulu(true).setPrecision(TemporalPrecisionEnum.SECOND);
+
     return observation;
   }
 
@@ -793,7 +801,7 @@ public DiagnosticReport convertToDiagnosticReport(
     var diagnosticReport =
         new DiagnosticReport()
             .setStatus(status)
-            .setEffective(new DateTimeType(dateTested))
+            .setEffective(new DateTimeType(dateTested).setTimeZoneZulu(true))
             .setIssued(dateUpdated);
 
     // Allows EffectiveDateTimeType to be mocked during tests
@@ -834,7 +842,8 @@ public Bundle createFhirBundle(
                     testEvent.getResults(),
                     testEvent.getDeviceType(),
                     testEvent.getCorrectionStatus(),
-                    testEvent.getReasonForCorrection()))
+                    testEvent.getReasonForCorrection(),
+                    testEvent.getDateTested()))
             .aoeObservations(
                 convertToAOEObservations(
                     testEvent.getInternalId().toString(), testEvent.getSurveyData()))

diff --git a/backend/src/main/java/gov/cdc/usds/simplereport/utils/BulkUploadResultsToFhir.java b/backend/src/main/java/gov/cdc/usds/simplereport/utils/BulkUploadResultsToFhir.java
@@ -25,8 +25,10 @@
 import gov.cdc.usds.simplereport.service.ResultsUploaderDeviceValidationService;
 import java.io.InputStream;
 import java.time.LocalDate;
+import java.time.LocalDateTime;
 import java.time.format.DateTimeFormatter;
 import java.time.format.DateTimeParseException;
+import java.time.temporal.TemporalAccessor;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.HashMap;
@@ -127,6 +129,17 @@ private Bundle convertRowToFhirBundle(TestResultRow row, UUID orgId) {
     DateTimeFormatter dateTimeFormatter = DateTimeFormatter.ofPattern("M/d/yyyy[ HH:mm]");
 
     var testEventId = row.getAccessionNumber().getValue();
+
+    LocalDateTime testResultDate;
+    TemporalAccessor temporalAccessor =
+        dateTimeFormatter.parseBest(
+            row.getTestResultDate().getValue(), LocalDateTime::from, LocalDate::from);
+    if (temporalAccessor instanceof LocalDateTime) {
+      testResultDate = (LocalDateTime) temporalAccessor;
+    } else {
+      testResultDate = ((LocalDate) temporalAccessor).atStartOfDay();
+    }
+
     var patientAddr =
         new StreetAddress(
             row.getPatientStreet().getValue(),
@@ -309,6 +322,9 @@ private Bundle convertRowToFhirBundle(TestResultRow row, UUID orgId) {
                     .testkitNameId(testKitNameId)
                     .equipmentUid(equipmentUid)
                     .deviceModel(row.getEquipmentModelName().getValue())
+                    .issued(
+                        Date.from(
+                            testResultDate.atZone(zoneIdGenerator.getSystemZoneId()).toInstant()))
                     .build()));
 
     LocalDate symptomOnsetDate = null;
@@ -336,13 +352,12 @@ private Bundle convertRowToFhirBundle(TestResultRow row, UUID orgId) {
             testOrderLoinc,
             uuidGenerator.randomUUID().toString());
 
-    var testDate = LocalDate.parse(row.getTestResultDate().getValue(), dateTimeFormatter);
     var diagnosticReport =
         fhirConverter.convertToDiagnosticReport(
             mapTestResultStatusToFhirValue(row.getTestResultStatus().getValue()),
             testPerformedCode,
             testEventId,
-            Date.from(testDate.atStartOfDay(zoneIdGenerator.getSystemZoneId()).toInstant()),
+            Date.from(testResultDate.atZone(zoneIdGenerator.getSystemZoneId()).toInstant()),
             dateGenerator.newDate());
 
     return fhirConverter.createFhirBundle(

diff --git a/backend/src/test/java/gov/cdc/usds/simplereport/api/converter/FhirConverterTest.java b/backend/src/test/java/gov/cdc/usds/simplereport/api/converter/FhirConverterTest.java
@@ -609,6 +609,7 @@ void convertToObservation_Strings_valid() {
                 .testkitNameId("testKitName")
                 .equipmentUid("equipmentUid")
                 .deviceModel("modelName")
+                .issued(Date.from(Instant.parse("2023-06-10T23:15:00.00Z")))
                 .build());
 
     assertThat(actual.getId()).isEqualTo("id-123");
@@ -625,6 +626,7 @@ void convertToObservation_Strings_valid() {
         .isEqualTo("resultCode");
     assertThat(actual.getNote()).isEmpty();
     assertThat(actual.getMethod().getCodingFirstRep().getDisplay()).isEqualTo("modelName");
+    assertThat(actual.getIssued()).isEqualTo("2023-06-10T23:15:00.00Z");
   }
 
   @Test
@@ -642,7 +644,8 @@ void convertToObservation_Result_valid() {
             null,
             "testkitName",
             "equipmentUid",
-            "modelName");
+            "modelName",
+            Date.from(Instant.parse("2023-06-10T23:15:00.00Z")));
 
     assertThat(actual.getId()).isEqualTo(internalId.toString());
     assertThat(actual.getStatus().getDisplay()).isEqualTo(ObservationStatus.FINAL.getDisplay());
@@ -657,6 +660,7 @@ void convertToObservation_Result_valid() {
         .isEqualTo("260373001");
     assertThat(actual.getNote()).isEmpty();
     assertThat(actual.getMethod().getCodingFirstRep().getDisplay()).isEqualTo("modelName");
+    assertThat(actual.getIssued()).isEqualTo("2023-06-10T23:15:00.00Z");
   }
 
   @Test
@@ -674,7 +678,8 @@ void convertToObservation_Result_correction() {
             "Oopsy Daisy",
             "testkitName",
             "equipmentUid",
-            "modelName");
+            "modelName",
+            new Date());
 
     assertThat(actual.getId()).isEqualTo(internalId.toString());
     assertThat(actual.getStatus().getDisplay()).isEqualTo(ObservationStatus.CORRECTED.getDisplay());
@@ -697,7 +702,8 @@ void convertToObservation_Result_removeWithoutReason() {
             null,
             "testkitName",
             "equipmentUid",
-            "modelName");
+            "modelName",
+            new Date());
 
     assertThat(actual.getId()).isEqualTo(internalId.toString());
     assertThat(actual.getStatus().getDisplay())
@@ -716,7 +722,8 @@ void convertToObservation_Result_null() {
             null,
             "testkitName",
             "equipmentUid",
-            "modelName");
+            "modelName",
+            new Date());
 
     assertThat(actual).isNull();
   }
@@ -733,7 +740,8 @@ void convertToObservation_Result_nullDisease() {
             null,
             "testkitName",
             "equipmentUid",
-            "modelName");
+            "modelName",
+            new Date());
 
     assertThat(actual).isNull();
   }
@@ -765,7 +773,11 @@ void convertToObservation_Result_matchesJson() throws IOException {
 
     var actual =
         fhirConverter.convertToObservation(
-            Set.of(covidResult, fluResult), device, TestCorrectionStatus.ORIGINAL, null);
+            Set.of(covidResult, fluResult),
+            device,
+            TestCorrectionStatus.ORIGINAL,
+            null,
+            Date.from(Instant.parse("2023-06-10T23:15:00.00Z")));
 
     assertThat(actual).hasSize(2);
     String covidSerialized =
@@ -815,7 +827,11 @@ void convertToObservation_Result_correctionMatchesJson() throws IOException {
 
     var actual =
         fhirConverter.convertToObservation(
-            Set.of(result), device, TestCorrectionStatus.CORRECTED, "woops");
+            Set.of(result),
+            device,
+            TestCorrectionStatus.CORRECTED,
+            "woops",
+            Date.from(Instant.parse("2023-06-10T23:15:00.00Z")));
 
     String actualSerialized = parser.encodeResourceToString(actual.get(0));
     var expectedSerialized1 =
@@ -936,7 +952,8 @@ void convertToDiagnosticReport_TestEvent_matchesJson() throws IOException {
             StandardCharsets.UTF_8);
     expectedSerialized =
         expectedSerialized.replace(
-            "$EFFECTIVE_DATE_TIME_TESTED", new DateTimeType(date).getValueAsString());
+            "$EFFECTIVE_DATE_TIME_TESTED",
+            new DateTimeType(date).setTimeZoneZulu(true).getValueAsString());
 
     JSONAssert.assertEquals(expectedSerialized, actualSerialized, true);
   }
@@ -953,8 +970,8 @@ void convertToDiagnosticReport_Strings_valid() {
     assertThat(actual.getCode().getCoding()).hasSize(1);
     assertThat(actual.getCode().getCodingFirstRep().getSystem()).isEqualTo("http://loinc.org");
     assertThat(actual.getCode().getCodingFirstRep().getCode()).isEqualTo("95422-2");
-    assertThat(((DateTimeType) actual.getEffective()).getAsV3())
-        .isEqualTo(new DateTimeType(date).getAsV3());
+    assertThat(((DateTimeType) actual.getEffective()).getValueAsString())
+        .isEqualTo(new DateTimeType(date).setTimeZoneZulu(true).getValueAsString());
     assertThat((actual.getIssued())).isEqualTo(date);
   }
 
@@ -1461,7 +1478,8 @@ void createFhirBundle_TestEvent_matchesJson() throws IOException {
     expectedSerialized = expectedSerialized.replace("$PROVENANCE_ID", provenanceId);
     expectedSerialized =
         expectedSerialized.replace(
-            "$EFFECTIVE_DATE_TIME_TESTED", new DateTimeType(dateTested).getValueAsString());
+            "$EFFECTIVE_DATE_TIME_TESTED",
+            new DateTimeType(dateTested).setTimeZoneZulu(true).getValueAsString());
     expectedSerialized =
         expectedSerialized.replace(
             "$PROVENANCE_RECORDED_DATE",

diff --git a/backend/src/test/resources/fhir/bundle.json b/backend/src/test/resources/fhir/bundle.json
@@ -450,7 +450,8 @@
               }
             }
           ]
-        }
+        },
+        "issued": "$EFFECTIVE_DATE_TIME_TESTED"
       }
     },
     {
@@ -522,7 +523,8 @@
               }
             }
           ]
-        }
+        },
+        "issued": "$EFFECTIVE_DATE_TIME_TESTED"
       }
     },
     {
@@ -594,7 +596,8 @@
               }
             }
           ]
-        }
+        },
+        "issued": "$EFFECTIVE_DATE_TIME_TESTED"
       }
     },
     {

diff --git a/backend/src/test/resources/fhir/observationCorrection.json b/backend/src/test/resources/fhir/observationCorrection.json
@@ -51,5 +51,6 @@
     {
       "text": "Corrected Result: woops"
     }
-  ]
+  ],
+  "issued": "2023-06-10T23:15:00Z"
 }
diff --git a/backend/src/test/resources/fhir/observationCovid.json b/backend/src/test/resources/fhir/observationCovid.json
@@ -51,5 +51,6 @@
         }
       }
     ]
-  }
+  },
+  "issued": "2023-06-10T23:15:00Z"
 }
diff --git a/backend/src/test/resources/fhir/observationFlu.json b/backend/src/test/resources/fhir/observationFlu.json
@@ -51,5 +51,6 @@
         }
       }
     ]
-  }
+  },
+  "issued": "2023-06-10T23:15:00Z"
 }
diff --git a/backend/src/test/resources/testResultUpload/test-results-upload-valid-as-fhir.json b/backend/src/test/resources/testResultUpload/test-results-upload-valid-as-fhir.json
@@ -116,7 +116,7 @@
         "subject": {
           "reference": "Patient/1234"
         },
-        "effectiveDateTime": "2021-12-20T00:00:00Z",
+        "effectiveDateTime": "2021-12-20T14:00:00Z",
         "issued": "2023-05-24T19:33:06.472Z",
         "specimen": [
           {
@@ -486,7 +486,8 @@
         },
         "device": {
           "reference": "Device/00000000-0000-0000-0000-000000000003"
-        }
+        },
+        "issued": "2021-12-20T14:00:00Z"
       }
     },
     {