[JN-1395] adding pre-enroll to export (#1135)

broadinstitute · Oct 9, 2024 · 083d10d · 083d10d
1 parent b3a75d6
commit 083d10d
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Showing 6 changed files with 34 additions and 7 deletions.
diff --git a/core/src/main/java/bio/terra/pearl/core/service/export/EnrolleeExportService.java b/core/src/main/java/bio/terra/pearl/core/service/export/EnrolleeExportService.java
@@ -7,6 +7,7 @@
 import bio.terra.pearl.core.model.participant.Enrollee;
 import bio.terra.pearl.core.model.participant.EnrolleeRelation;
 import bio.terra.pearl.core.model.search.EnrolleeSearchExpressionResult;
+import bio.terra.pearl.core.model.study.StudyEnvironment;
 import bio.terra.pearl.core.model.study.StudyEnvironmentConfig;
 import bio.terra.pearl.core.model.survey.StudyEnvironmentSurvey;
 import bio.terra.pearl.core.model.survey.Survey;
@@ -21,8 +22,10 @@
 import bio.terra.pearl.core.service.search.EnrolleeSearchExpression;
 import bio.terra.pearl.core.service.search.EnrolleeSearchOptions;
 import bio.terra.pearl.core.service.study.StudyEnvironmentConfigService;
+import bio.terra.pearl.core.service.study.StudyEnvironmentService;
 import bio.terra.pearl.core.service.study.StudyEnvironmentSurveyService;
 import bio.terra.pearl.core.service.survey.SurveyResponseService;
+import bio.terra.pearl.core.service.survey.SurveyService;
 import bio.terra.pearl.core.service.workflow.ParticipantTaskService;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import lombok.extern.slf4j.Slf4j;
@@ -41,6 +44,8 @@ public class EnrolleeExportService {
     private final AnswerDao answerDao;
     private final SurveyQuestionDefinitionDao surveyQuestionDefinitionDao;
     private final StudyEnvironmentSurveyService studyEnvironmentSurveyService;
+    private final SurveyService surveyService;
+    private final StudyEnvironmentService studyEnvironmentService;
     private final SurveyResponseService surveyResponseService;
     private final ParticipantTaskService participantTaskService;
     private final KitRequestService kitRequestService;
@@ -55,7 +60,7 @@ public EnrolleeExportService(ProfileService profileService,
                                  AnswerDao answerDao,
                                  SurveyQuestionDefinitionDao surveyQuestionDefinitionDao,
                                  StudyEnvironmentSurveyService studyEnvironmentSurveyService,
-                                 SurveyResponseService surveyResponseService,
+                                 SurveyService surveyService, StudyEnvironmentService studyEnvironmentService, SurveyResponseService surveyResponseService,
                                  ParticipantTaskService participantTaskService,
                                  KitRequestService kitRequestService,
                                  ParticipantUserService participantUserService,
@@ -67,6 +72,8 @@ public EnrolleeExportService(ProfileService profileService,
         this.answerDao = answerDao;
         this.surveyQuestionDefinitionDao = surveyQuestionDefinitionDao;
         this.studyEnvironmentSurveyService = studyEnvironmentSurveyService;
+        this.surveyService = surveyService;
+        this.studyEnvironmentService = studyEnvironmentService;
         this.surveyResponseService = surveyResponseService;
         this.participantTaskService = participantTaskService;
         this.kitRequestService = kitRequestService;
@@ -163,6 +170,21 @@ public List<ModuleFormatter> generateModuleInfos(ExportOptions exportOptions, UU
      * If multiple versions of a survey have been attached, those will be consolidated into a single ModuleExportInfo
      */
     protected List<SurveyFormatter> generateSurveyModules(ExportOptions exportOptions, UUID studyEnvironmentId, List<EnrolleeExportData> enrolleeExportData) {
+        List<SurveyFormatter> moduleFormatters = new ArrayList<>();
+        // now add the pre-enrollment survey (if it exists)
+        StudyEnvironment studyEnvironment = studyEnvironmentService.find(studyEnvironmentId).orElseThrow();
+        if (studyEnvironment.getPreEnrollSurveyId() != null) {
+            Survey preEnrollSurvey = surveyService.find(studyEnvironment.getPreEnrollSurveyId()).orElseThrow();
+            List<SurveyQuestionDefinition> preEnrollSurveyQuestionDefinitions = surveyQuestionDefinitionDao.findAllBySurveyIds(List.of(preEnrollSurvey.getId()));
+            moduleFormatters.add(new SurveyFormatter(
+                    exportOptions,
+                    preEnrollSurvey.getStableId(),
+                    List.of(preEnrollSurvey),
+                    preEnrollSurveyQuestionDefinitions,
+                    enrolleeExportData,
+                    objectMapper));
+        }
+
         // get all surveys that have ever been attached to the StudyEnvironment, including inactive ones
         List<StudyEnvironmentSurvey> configuredSurveys = studyEnvironmentSurveyService.findAllByStudyEnvIdWithSurvey(studyEnvironmentId, null);
         Map<String, List<StudyEnvironmentSurvey>> configuredSurveysByStableId = configuredSurveys.stream().collect(
@@ -177,7 +199,7 @@ protected List<SurveyFormatter> generateSurveyModules(ExportOptions exportOption
                 .toList();
 
         // create one moduleExportInfo for each survey stableId.
-        List<SurveyFormatter> moduleFormatters = new ArrayList<>();
+
         for (Map.Entry<String, List<StudyEnvironmentSurvey>> surveysOfStableId : sortedCfgSurveysByStableId) {
             List<Survey> surveys = surveysOfStableId.getValue().stream().map(StudyEnvironmentSurvey::getSurvey).toList();
             List<SurveyQuestionDefinition> surveyQuestionDefinitions = surveyQuestionDefinitionDao.findAllBySurveyIds(surveys.stream().map(Survey::getId).toList());
@@ -189,14 +211,12 @@ protected List<SurveyFormatter> generateSurveyModules(ExportOptions exportOption
                     enrolleeExportData,
                     objectMapper));
         }
-
         return moduleFormatters;
     }
 
     protected List<EnrolleeExportData> loadEnrolleesForExport(StudyEnvironmentConfig config,
                                                               List<Enrollee> enrollees) {
 
-
         // for now, load each enrollee individually.  Later we'll want more sophisticated batching strategies
         return enrollees
                 .stream()

diff --git a/core/src/main/java/bio/terra/pearl/core/service/study/StudyEnvironmentService.java b/core/src/main/java/bio/terra/pearl/core/service/study/StudyEnvironmentService.java
@@ -23,6 +23,7 @@
 import bio.terra.pearl.core.service.participant.FamilyEnrolleeService;
 import bio.terra.pearl.core.service.participant.FamilyService;
 import bio.terra.pearl.core.service.workflow.ParticipantDataChangeService;
+import org.springframework.context.annotation.Lazy;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
 
@@ -64,7 +65,7 @@ public StudyEnvironmentService(StudyEnvironmentDao studyEnvironmentDao,
                                    FamilyEnrolleeService familyEnrolleeService,
                                    EnrolleeRelationService enrolleeRelationService,
                                    ParticipantDataChangeService participantDataChangeService,
-                                   ExportIntegrationService exportIntegrationService) {
+                                   @Lazy ExportIntegrationService exportIntegrationService) {
         super(studyEnvironmentDao);
         this.studyEnvironmentSurveyDao = studyEnvironmentSurveyDao;
         this.studyEnvironmentConfigService = studyEnvironmentConfigService;

diff --git a/populate/src/test/java/bio/terra/pearl/populate/PopulateDemoTest.java b/populate/src/test/java/bio/terra/pearl/populate/PopulateDemoTest.java
@@ -201,6 +201,12 @@ private void checkExportContent(UUID sandboxEnvironmentId) throws Exception {
         List<Map<String, String>> exportData = enrolleeExportService.generateExportMaps(enrolleeExportData, moduleInfos);
 
         assertThat(exportData, hasSize(13));
+        // confirm pre-enroll questions are included
+        Map<String, String> salkMap = exportData.stream().filter(map -> "HDSALK".equals(map.get("enrollee.shortcode")))
+                .findFirst().get();
+        assertThat(salkMap.get("hd_hd_preenroll.hd_hd_preenroll_livesInUS"), equalTo("Yes"));
+
+
         Map<String, String> oldVersionMap = exportData.stream().filter(map -> "HDVERS".equals(map.get("enrollee.shortcode")))
                 .findFirst().get();
         assertThat(oldVersionMap.get("account.username"), equalTo("oldversion@test.com"));

diff --git a/...c/study/export/ExportDataControl.test.tsx → ...src/study/export/ExportDataModal.test.tsx b/...c/study/export/ExportDataControl.test.tsx → ...src/study/export/ExportDataModal.test.tsx
diff --git a/ui-admin/src/study/export/ExportDataModal.tsx b/ui-admin/src/study/export/ExportDataModal.tsx
@@ -39,7 +39,7 @@ const DEFAULT_EXPORT_OPTS: ExportOptions = {
   excludeModules: []
 }
 
-const MODULE_EXCLUDE_OPTIONS: Record<string, string> = { surveys: 'Surveys' }
+const MODULE_EXCLUDE_OPTIONS: Record<string, string> = { surveys: 'Surveys', profile: 'Profile', account: 'Account' }
 
 /** form for configuring and downloading enrollee data */
 const ExportDataModal = ({ studyEnvContext, show, setShow }: {studyEnvContext: StudyEnvContextT, show: boolean,

diff --git a/ui-admin/src/study/export/integrations/ExportIntegrationList.tsx b/ui-admin/src/study/export/integrations/ExportIntegrationList.tsx
@@ -120,7 +120,7 @@ export default function ExportIntegrationList({ studyEnvContext }:
         <Button variant="secondary" onClick={() => {
           setShowCreateModal(false)
           setNewIntegration(DEFAULT_EXPORT_INTEGRATION)
-        }}>Create</Button>
+        }}>Cancel</Button>
       </Modal.Footer>
     </Modal>