adding test ordered code to bulk upload api (#6166)

* adding test ordered code to bulk upload api * adding test ordered code to the bulk upload guide
CDCgov · Jul 25, 2023 · a3bc03f · a3bc03f
1 parent 9def755
commit a3bc03f
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Showing 9 changed files with 206 additions and 9 deletions.
diff --git a/backend/src/main/java/gov/cdc/usds/simplereport/api/model/filerow/TestResultRow.java b/backend/src/main/java/gov/cdc/usds/simplereport/api/model/filerow/TestResultRow.java
@@ -94,6 +94,7 @@ public class TestResultRow implements FileRow {
   final ValueOrError orderingFacilityPhoneNumber;
   final ValueOrError comment;
   final ValueOrError testResultStatus;
+  final ValueOrError testOrderedCode;
 
   static final String PATIENT_LAST_NAME = "patient_last_name";
   static final String PATIENT_FIRST_NAME = "patient_first_name";
@@ -351,6 +352,7 @@ public TestResultRow(Map<String, String> rawRow) {
             rawRow, "ordering_facility_phone_number", isRequired("ordering_facility_phone_number"));
     comment = getValue(rawRow, "comment", isRequired("comment"));
     testResultStatus = getValue(rawRow, "test_result_status", isRequired("test_result_status"));
+    testOrderedCode = getValue(rawRow, "test_ordered_code", isRequired("test_ordered_code"));
   }
 
   private List<FeedbackMessage> validateDeviceModelAndTestPerformedCode(

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
@@ -282,7 +282,7 @@ private Bundle convertRowToFhirBundle(TestResultRow row, UUID orgId) {
     String testKitNameId = null;
     String manufacturer = null;
     String diseaseName = null;
-    String testOrderLoinc = null;
+    String testOrderedCode = row.getTestOrderedCode().getValue();
 
     UUID deviceId = uuidGenerator.randomUUID();
     var testPerformedCode = row.getTestPerformedCode().getValue();
@@ -317,7 +317,10 @@ private Bundle convertRowToFhirBundle(TestResultRow row, UUID orgId) {
               .map(SupportedDisease::getName)
               .orElse(null);
 
-      testOrderLoinc = MultiplexUtils.inferMultiplexTestOrderLoinc(deviceTypeDiseaseEntries);
+      testOrderedCode =
+          StringUtils.isEmpty(testOrderedCode)
+              ? MultiplexUtils.inferMultiplexTestOrderLoinc(deviceTypeDiseaseEntries)
+              : testOrderedCode;
     } else {
       log.info(
           "No device found for model ("
@@ -327,6 +330,9 @@ private Bundle convertRowToFhirBundle(TestResultRow row, UUID orgId) {
               + ")");
     }
 
+    // code was not passed via api or inferred above: defaulting to the test performed code.
+    testOrderedCode = StringUtils.isEmpty(testOrderedCode) ? testPerformedCode : testOrderedCode;
+
     var device = fhirConverter.convertToDevice(manufacturer, modelName, deviceId.toString());
 
     var specimen =
@@ -385,7 +391,7 @@ private Bundle convertRowToFhirBundle(TestResultRow row, UUID orgId) {
     var serviceRequest =
         fhirConverter.convertToServiceRequest(
             ServiceRequest.ServiceRequestStatus.COMPLETED,
-            testOrderLoinc,
+            testOrderedCode,
             uuidGenerator.randomUUID().toString(),
             orderTestDate);
 

diff --git a/backend/src/test/java/gov/cdc/usds/simplereport/service/TestResultUploadServiceTest.java b/backend/src/test/java/gov/cdc/usds/simplereport/service/TestResultUploadServiceTest.java
@@ -416,6 +416,7 @@ void uploadService_processCsv_translatesSpecimenNameToSNOMED() {
     var headerCount = Arrays.stream(rows[0].split(",")).toList().size();
     var row = rows[1];
 
+    // if the last column is optional and empty/null this fails when it shouldn't
     assertThat(row.split(",")).hasSize(headerCount);
     assertThat(rows[1]).contains("000111222");
   }

diff --git a/backend/src/test/java/gov/cdc/usds/simplereport/utils/BulkUploadResultsToFhirTest.java b/backend/src/test/java/gov/cdc/usds/simplereport/utils/BulkUploadResultsToFhirTest.java
@@ -1,6 +1,7 @@
 package gov.cdc.usds.simplereport.utils;
 
 import static gov.cdc.usds.simplereport.test_util.JsonTestUtils.assertJsonNodesEqual;
+import static gov.cdc.usds.simplereport.validators.CsvValidatorUtils.getIteratorForCsv;
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.mockito.ArgumentMatchers.any;
@@ -17,6 +18,7 @@
 import gov.cdc.usds.simplereport.service.ResultsUploaderCachingService;
 import gov.cdc.usds.simplereport.test_util.TestDataBuilder;
 import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
@@ -31,6 +33,7 @@
 import org.hl7.fhir.r4.model.DiagnosticReport;
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Organization;
+import org.hl7.fhir.r4.model.ServiceRequest;
 import org.hl7.fhir.r4.model.Specimen;
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.BeforeEach;
@@ -92,9 +95,77 @@ void convertExistingCsv_success() {
     assertThat(resourceUrls).hasSize(14);
   }
 
+  @Test
+  void allFieldsCsv_TestOrderedCodeMapped() throws IOException {
+    byte[] input = loadCsv("testResultUpload/test-results-upload-all-fields.csv").readAllBytes();
+
+    var serializedBundles =
+        sut.convertToFhirBundles(new ByteArrayInputStream(input), UUID.randomUUID());
+    var mappingIterator = getIteratorForCsv(new ByteArrayInputStream(input));
+
+    int index = 0;
+    while (mappingIterator.hasNext()) {
+      var csvRow = mappingIterator.next();
+      var inputOrderedCode = csvRow.get("test_ordered_code");
+      var inputPerformedCode = csvRow.get("test_performed_code");
+
+      var bundle = serializedBundles.get(index++);
+      var deserializedBundle = (Bundle) parser.parseResource(bundle);
+
+      var serviceRequestEntry =
+          deserializedBundle.getEntry().stream()
+              .filter(entry -> entry.getFullUrl().contains("ServiceRequest/"))
+              .findFirst()
+              .orElseThrow(
+                  () -> new AssertionError("Expected to find ServiceRequest, but not found"));
+      var serviceRequest = (ServiceRequest) serviceRequestEntry.getResource();
+
+      var mappedCode = serviceRequest.getCode().getCoding().stream().findFirst().get().getCode();
+
+      // value is mapped
+      assertThat(mappedCode).isEqualTo(inputOrderedCode);
+      // value is not defaulted to performed code
+      assertThat(inputOrderedCode).isNotEqualTo(inputPerformedCode);
+    }
+  }
+
+  @Test
+  void validCsv_TestOrderedCodeDefaultedToPerformedCode() throws IOException {
+    byte[] input = loadCsv("testResultUpload/test-results-upload-valid.csv").readAllBytes();
+
+    var serializedBundles =
+        sut.convertToFhirBundles(new ByteArrayInputStream(input), UUID.randomUUID());
+    var mappingIterator = getIteratorForCsv(new ByteArrayInputStream(input));
+
+    int index = 0;
+    while (mappingIterator.hasNext()) {
+      var csvRow = mappingIterator.next();
+      var inputOrderedCode = csvRow.get("test_ordered_code");
+      var inputPerformedCode = csvRow.get("test_performed_code");
+
+      var bundle = serializedBundles.get(index++);
+      var deserializedBundle = (Bundle) parser.parseResource(bundle);
+
+      var serviceRequestEntry =
+          deserializedBundle.getEntry().stream()
+              .filter(entry -> entry.getFullUrl().contains("ServiceRequest/"))
+              .findFirst()
+              .orElseThrow(
+                  () -> new AssertionError("Expected to find ServiceRequest, but not found"));
+      var serviceRequest = (ServiceRequest) serviceRequestEntry.getResource();
+
+      var mappedCode = serviceRequest.getCode().getCoding().stream().findFirst().get().getCode();
+
+      // when supplied orderedCode is empty
+      assertThat(inputOrderedCode).isEmpty();
+      // value is defaulted to performed code
+      assertThat(mappedCode).isEqualTo(inputPerformedCode);
+    }
+  }
+
   @Test
   void convertExistingCsv_aoeQuestionsMapped() {
-    InputStream input = loadCsv("testResultUpload/test-results-upload-aoe.csv");
+    InputStream input = loadCsv("testResultUpload/test-results-upload-all-fields.csv");
     var serializedBundles = sut.convertToFhirBundles(input, UUID.randomUUID());
 
     var asymptomaticEntry = serializedBundles.get(0);

diff --git a/backend/src/test/resources/testResultUpload/test-results-upload-all-fields.csv b/backend/src/test/resources/testResultUpload/test-results-upload-all-fields.csv
@@ -0,0 +1,3 @@
+patient_id,patient_last_name,patient_first_name,patient_middle_name,patient_street,patient_street2,patient_city,patient_state,patient_zip_code,patient_county,patient_phone_number,patient_dob,patient_gender,patient_race,patient_ethnicity,patient_preferred_language,patient_email,accession_number,equipment_model_name,test_performed_code,test_result,order_test_date,specimen_collection_date,testing_lab_specimen_received_date,test_result_date,date_result_released,specimen_type,ordering_provider_id,ordering_provider_last_name,ordering_provider_first_name,ordering_provider_middle_name,ordering_provider_street,ordering_provider_street2,ordering_provider_city,ordering_provider_state,ordering_provider_zip_code,ordering_provider_phone_number,testing_lab_clia,testing_lab_name,testing_lab_street,testing_lab_street2,testing_lab_city,testing_lab_state,testing_lab_zip_code,testing_lab_phone_number,pregnant,employed_in_healthcare,symptomatic_for_disease,illness_onset_date,resident_congregate_setting,residence_type,hospitalized,icu,ordering_facility_name,ordering_facility_street,ordering_facility_street2,ordering_facility_city,ordering_facility_state,ordering_facility_zip_code,ordering_facility_phone_number,comment,test_result_status,test_ordered_code
+1234,Doe,Jane,Jingleheimer,123 Main St,Suite 401,Birmingham,AL,35226,Jefferson,205-999-2800,1/20/1962,F,White,Not Hispanic or Latino,Eng,test@test.com,123,ID NOW,94534-5,Detected,12/20/2021 14:00,12/20/2021 14:00,12/20/2021 14:00,12/20/2021 14:00,12/20/2021 14:00,Nasal Swab,1013012657,Smith MD,John,Smitty,400 Main Street,Suite 401,Birmingham,AL,35228,205-888-2000,01D1058442,My Urgent Care,400 Main Street,Suite 401,Birmingham,AL,35228,205-888-2000,N,N,N,01/01/1901,N,22232009,N,N,My Urgent Care,400 Main Street,Suite 100,Birmingham,AL,35228,205-888-2000,Test Comment,C,94534-1
+5678,Doe,John,Jingleheimer,333 Elm St,Suite 401,Hoover,AL,35244,Shelby,205-222-2000,11/1/2001,MALE,BLACK OR AFRICAN AMERICAN,NOT HISPANIC OR LATINO,Spa,myemail@email.com,05be96ef-949f-4f46-9c07-2675e8abf412,BD Veritor System for Rapid Detection of SARS-CoV-2*,94558-4,NOT DETECTED,12/21/2021 17:00,12/21/2021 17:00,12/21/2021 17:00,12/21/2021 17:00,12/21/2021 17:00,ANTERIOR NARES SWAB,1013012657,Smith MD,John,Smitty,400 Main Street,Suite 401,Birmingham,AL,35228,205-888-2000,01D1058442,My Urgent Care,400 Main Street,Suite 401,Birmingham,AL,35228,205-888-2000,NO,YES,Y,01/01/2020,Y,HOSTEL,NO,NO,My Urgent Care,400 Main Street,Suite 100,Birmingham,AL,35228,205-888-2000,testy mctesterson,F,94534-2
diff --git a/backend/src/test/resources/testResultUpload/test-results-upload-aoe.csv b/backend/src/test/resources/testResultUpload/test-results-upload-aoe.csv
diff --git a/backend/src/test/resources/testResultUpload/test-results-upload-valid.csv b/backend/src/test/resources/testResultUpload/test-results-upload-valid.csv
@@ -1,2 +1,2 @@
-patient_id,patient_last_name,patient_first_name,patient_middle_name,patient_street,patient_street2,patient_city,patient_state,patient_zip_code,patient_county,patient_phone_number,patient_dob,patient_gender,patient_race,patient_ethnicity,patient_preferred_language,patient_email,accession_number,equipment_model_name,test_performed_code,test_result,order_test_date,specimen_collection_date,testing_lab_specimen_received_date,test_result_date,date_result_released,specimen_type,ordering_provider_id,ordering_provider_last_name,ordering_provider_first_name,ordering_provider_middle_name,ordering_provider_street,ordering_provider_street2,ordering_provider_city,ordering_provider_state,ordering_provider_zip_code,ordering_provider_phone_number,testing_lab_clia,testing_lab_name,testing_lab_street,testing_lab_street2,testing_lab_city,testing_lab_state,testing_lab_zip_code,testing_lab_phone_number,pregnant,employed_in_healthcare,symptomatic_for_disease,illness_onset_date,resident_congregate_setting,residence_type,hospitalized,icu,ordering_facility_name,ordering_facility_street,ordering_facility_street2,ordering_facility_city,ordering_facility_state,ordering_facility_zip_code,ordering_facility_phone_number,comment,test_result_status
-1234,Doe,Jane,,123 Main St,,Birmingham,AL,35226,Jefferson,205-999-2800,1/20/1962,F,White,Not Hispanic or Latino,,,123,ID NOW,94534-5,Detected,12/20/2021 14:00,12/21/2021 14:00,12/22/2021 14:00,12/23/2021 14:00,12/24/2021 14:00,Nasal Swab,1013012657,Smith MD,John,,400 Main Street,,Birmingham,AL,35228,205-888-2000,01D1058442,My Testing Lab,300 North Street,,Birmingham,AL,35228,205-888-2000,N,N,N,,N,,N,N,My Urgent Care,400 Main Street,Suite 100,Birmingham,AL,35228,205-888-2000,Test Comment,F
+patient_id,patient_last_name,patient_first_name,patient_middle_name,patient_street,patient_street2,patient_city,patient_state,patient_zip_code,patient_county,patient_phone_number,patient_dob,patient_gender,patient_race,patient_ethnicity,patient_preferred_language,patient_email,accession_number,equipment_model_name,test_performed_code,test_result,order_test_date,specimen_collection_date,testing_lab_specimen_received_date,test_result_date,date_result_released,specimen_type,ordering_provider_id,ordering_provider_last_name,ordering_provider_first_name,ordering_provider_middle_name,ordering_provider_street,ordering_provider_street2,ordering_provider_city,ordering_provider_state,ordering_provider_zip_code,ordering_provider_phone_number,testing_lab_clia,testing_lab_name,testing_lab_street,testing_lab_street2,testing_lab_city,testing_lab_state,testing_lab_zip_code,testing_lab_phone_number,pregnant,employed_in_healthcare,symptomatic_for_disease,illness_onset_date,resident_congregate_setting,residence_type,hospitalized,icu,ordering_facility_name,ordering_facility_street,ordering_facility_street2,ordering_facility_city,ordering_facility_state,ordering_facility_zip_code,ordering_facility_phone_number,comment,test_ordered_code,test_result_status
+1234,Doe,Jane,,123 Main St,,Birmingham,AL,35226,Jefferson,205-999-2800,1/20/1962,F,White,Not Hispanic or Latino,,,123,ID NOW,94534-5,Detected,12/20/2021 14:00,12/21/2021 14:00,12/22/2021 14:00,12/23/2021 14:00,12/24/2021 14:00,Nasal Swab,1013012657,Smith MD,John,,400 Main Street,,Birmingham,AL,35228,205-888-2000,01D1058442,My Testing Lab,300 North Street,,Birmingham,AL,35228,205-888-2000,N,N,N,,N,,N,N,My Urgent Care,400 Main Street,Suite 100,Birmingham,AL,35228,205-888-2000,Test Comment,,F
diff --git a/frontend/src/app/testResults/uploads/__snapshots__/CsvSchemaDocumentation.test.tsx.snap b/frontend/src/app/testResults/uploads/__snapshots__/CsvSchemaDocumentation.test.tsx.snap
@@ -2210,6 +2210,108 @@ exports[`CsvSchemaDocumentation tests CsvSchemaDocumentation matches snapshot 1`
               </ul>
             </div>
           </div>
+          <div
+            class="rs-documentation__values margin-top-6"
+          >
+            <h5
+              class="margin-bottom-2"
+              data-testid="header"
+              id="test_ordered_code"
+            >
+              Test ordered LOINC code
+              <span
+                class="text-normal bg-white border-1px border-base font-body-3xs padding-x-1 padding-y-05 text-base margin-left-2 text-bottom"
+              >
+                Optional
+              </span>
+            </h5>
+            <div
+              class="margin-bottom-3"
+              data-testid="subheader"
+            />
+            <div
+              class="grid-row margin-bottom-05"
+              data-testid="column-header"
+            >
+              <div
+                class="grid-col-4 text-base"
+              >
+                Column header
+              </div>
+              <div
+                class="grid-col-auto"
+              >
+                <code>
+                  test_ordered_code
+                </code>
+              </div>
+            </div>
+            <div
+              class="grid-row margin-bottom-05 border-base-lighter border-top-1px padding-top-1"
+              data-testid="format"
+            >
+              <div
+                class="grid-col-4 text-base"
+              >
+                Format
+              </div>
+              <div
+                class="grid-col-8 prime-ul margin-top-0"
+              >
+                00000-0
+              </div>
+            </div>
+            <div
+              class="grid-row margin-bottom-05 border-base-lighter border-top-1px padding-top-1"
+              data-testid="examples"
+            >
+              <div
+                class="grid-col-4 text-base"
+              >
+                Example
+                s
+              </div>
+              <ul
+                class="grid-col-8 prime-ul margin-top-0"
+              >
+                <li
+                  class="bullet-list"
+                >
+                  <em>
+                    94534-5
+                  </em>
+                </li>
+                <li
+                  class="bullet-list"
+                >
+                  <em>
+                    94558-4
+                  </em>
+                </li>
+                <li
+                  class="bullet-list"
+                >
+                  <em>
+                    97097-0
+                  </em>
+                </li>
+                <li
+                  class="bullet-list"
+                >
+                  <em>
+                    94507-1
+                  </em>
+                </li>
+                <li
+                  class="bullet-list"
+                >
+                  <em>
+                    94508-9
+                  </em>
+                </li>
+              </ul>
+            </div>
+          </div>
           <div
             class="rs-documentation__values margin-top-6"
           >

diff --git a/frontend/src/app/testResults/uploads/schemaBuilder.ts b/frontend/src/app/testResults/uploads/schemaBuilder.ts
@@ -244,6 +244,21 @@ export const schemaBuilder = (facilityId: string | null) => {
                   `Find your device on the ${deviceCodeLookupLink}, then copy the value for this field.`,
                 ],
               },
+              {
+                name: "Test ordered LOINC code",
+                colHeader: "test_ordered_code",
+                required: false,
+                requested: false,
+                format: "00000-0",
+                examples: [
+                  "94534-5",
+                  "94558-4",
+                  "97097-0",
+                  "94507-1",
+                  "94508-9",
+                ],
+                description: [],
+              },
               {
                 name: "Test result",
                 colHeader: "test_result",