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JN-1055 import kitrequest data (#911)
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Co-authored-by: Sampath K. Settipalli <[email protected]>
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@ssettipalli
ssettipalli and Sampath K. Settipalli authored May 28, 2024
1 parent 91678c0 commit 0b0c521
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Showing 11 changed files with 295 additions and 64 deletions.
3 changes: 3 additions & 0 deletions core/src/main/java/bio/terra/pearl/core/dao/dataimport/ImportDao.java
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Expand Up @@ -26,5 +26,8 @@ public List<Import> findAllByStudyEnv(UUID studyEnvId) {
return findAllByProperty("study_environment_id", studyEnvId);
}

public void deleteByStudyEnvId(UUID studyEnvId) {
deleteByProperty("study_environment_id", studyEnvId);
}

}
4 changes: 4 additions & 0 deletions core/src/main/java/bio/terra/pearl/core/dao/dataimport/ImportItemDao.java
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Expand Up @@ -24,4 +24,8 @@ public List<ImportItem> findAllByImport(UUID importId) {
return findAllByProperty("import_id", importId);
}

public void deleteByImportId(UUID importId) {
deleteByProperty("import_id", importId);
}

}
3 changes: 3 additions & 0 deletions core/src/main/java/bio/terra/pearl/core/service/dataimport/ImportItemService.java
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Expand Up @@ -55,5 +55,8 @@ public void deleteEnrolleeById(UUID id) {
}
}

public void deleteByImportId(UUID importId) {
dao.deleteByImportId(importId);
}

}
7 changes: 7 additions & 0 deletions core/src/main/java/bio/terra/pearl/core/service/dataimport/ImportService.java
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Expand Up @@ -62,4 +62,11 @@ public void deleteEnrolleesByImportId(UUID id) {
});
}

@Transactional
public void deleteByStudyEnvId(UUID studyEnvironmentId) {
List<Import> imports = dao.findAllByStudyEnv(studyEnvironmentId);
imports.forEach(dataImport -> importItemService.deleteByImportId(dataImport.getId()));
dao.deleteByStudyEnvId(studyEnvironmentId);
}

}
47 changes: 41 additions & 6 deletions core/src/main/java/bio/terra/pearl/core/service/export/EnrolleeImportService.java
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Expand Up @@ -8,7 +8,8 @@
import bio.terra.pearl.core.model.dataimport.ImportItemStatus;
import bio.terra.pearl.core.model.dataimport.ImportStatus;
import bio.terra.pearl.core.model.dataimport.ImportType;
import bio.terra.pearl.core.model.audit.ResponsibleEntity;
import bio.terra.pearl.core.model.kit.KitRequest;
import bio.terra.pearl.core.model.kit.KitType;
import bio.terra.pearl.core.model.participant.Enrollee;
import bio.terra.pearl.core.model.participant.ParticipantUser;
import bio.terra.pearl.core.model.participant.PortalParticipantUser;
Expand All @@ -23,9 +24,12 @@
import bio.terra.pearl.core.service.dataimport.ImportService;
import bio.terra.pearl.core.service.exception.internal.InternalServerException;
import bio.terra.pearl.core.service.export.formatters.module.EnrolleeFormatter;
import bio.terra.pearl.core.service.export.formatters.module.KitRequestFormatter;
import bio.terra.pearl.core.service.export.formatters.module.ParticipantUserFormatter;
import bio.terra.pearl.core.service.export.formatters.module.ProfileFormatter;
import bio.terra.pearl.core.service.export.formatters.module.SurveyFormatter;
import bio.terra.pearl.core.service.kit.KitRequestDto;
import bio.terra.pearl.core.service.kit.KitRequestService;
import bio.terra.pearl.core.service.participant.EnrolleeService;
import bio.terra.pearl.core.service.participant.ParticipantUserService;
import bio.terra.pearl.core.service.participant.PortalParticipantUserService;
Expand Down Expand Up @@ -92,6 +96,7 @@ public class EnrolleeImportService {
private final TimeShiftPopulateDao timeShiftPopulateDao;
private final ImportService importService;
private final ImportItemService importItemService;
private final KitRequestService kitRequestService;
private final char CSV_DELIMITER = ',';
private final char TSV_DELIMITER = '\t';

Expand All @@ -100,7 +105,7 @@ public EnrolleeImportService(RegistrationService registrationService, Enrollment
SurveyResponseService surveyResponseService, ParticipantTaskService participantTaskService, PortalService portalService,
ImportService importService, ImportItemService importItemService, SurveyTaskDispatcher surveyTaskDispatcher,
TimeShiftPopulateDao timeShiftPopulateDao, EnrolleeService enrolleeService, ParticipantUserService participantUserService,
PortalParticipantUserService portalParticipantUserService) {
PortalParticipantUserService portalParticipantUserService, KitRequestService kitRequestService) {
this.registrationService = registrationService;
this.enrollmentService = enrollmentService;
this.profileService = profileService;
Expand All @@ -115,6 +120,7 @@ public EnrolleeImportService(RegistrationService registrationService, Enrollment
this.enrolleeService = enrolleeService;
this.participantUserService = participantUserService;
this.portalParticipantUserService = portalParticipantUserService;
this.kitRequestService = kitRequestService;
}

@Transactional
Expand Down Expand Up @@ -144,7 +150,7 @@ public Import importEnrollees(String portalShortcode, String studyShortcode, Stu
Enrollee enrollee = null;
ImportItem importItem;
try {
enrollee = importEnrollee(portalShortcode, studyShortcode, studyEnv, enrolleeMap, exportOptions);
enrollee = importEnrollee(portalShortcode, studyShortcode, studyEnv, enrolleeMap, exportOptions, adminId);
importItem = ImportItem.builder()
.createdEnrolleeId(enrollee.getId())
.importId(dataImport.getId())
Expand Down Expand Up @@ -204,7 +210,7 @@ public List<Map<String, String>> generateImportMaps(InputStream in, ImportFileFo
}
}

public Enrollee importEnrollee(String portalShortcode, String studyShortcode, StudyEnvironment studyEnv, Map<String, String> enrolleeMap, ExportOptions exportOptions) {
public Enrollee importEnrollee(String portalShortcode, String studyShortcode, StudyEnvironment studyEnv, Map<String, String> enrolleeMap, ExportOptions exportOptions, UUID adminId) {
/** while importing handle update for existing import
if same enrolle: update enrollee
if same participant & same portal.. new enrollee & same profile
Expand All @@ -215,7 +221,6 @@ public Enrollee importEnrollee(String portalShortcode, String studyShortcode, St
DataAuditInfo.systemProcessName(getClass(), "importEnrollee")
).build();

//
ParticipantUserFormatter participantUserFormatter = new ParticipantUserFormatter(exportOptions);
final ParticipantUser participantUserInfo = participantUserFormatter.fromStringMap(studyEnv.getId(), enrolleeMap);

Expand All @@ -226,6 +231,9 @@ public Enrollee importEnrollee(String portalShortcode, String studyShortcode, St
/** now update the profile */
Profile profile = importProfile(enrolleeMap, regResult.profile(), exportOptions, studyEnv, auditInfo);

/** populate kit_requests */
importKitRequests(enrolleeMap, adminId, enrollee);

importSurveyResponses(portalShortcode, enrolleeMap, exportOptions, studyEnv, regResult.portalParticipantUser(), enrollee, auditInfo);

/** restore email */
Expand All @@ -234,6 +242,33 @@ public Enrollee importEnrollee(String portalShortcode, String studyShortcode, St
return enrollee;
}

private void importKitRequests(Map<String, String> enrolleeMap, UUID adminId, Enrollee enrollee) {
new KitRequestFormatter().listFromStringMap(enrolleeMap).stream().map(
kitRequestDto -> kitRequestService.create(convertKitRequestDto(adminId, enrollee, kitRequestDto))).toList();
}

private KitRequest convertKitRequestDto(
UUID adminUserId,
Enrollee enrollee,
KitRequestDto kitRequestDto) {

KitType kitType = kitRequestService.lookupKitTypeByName(kitRequestDto.getKitType().getName());
return KitRequest.builder()
.creatingAdminUserId(adminUserId)
.enrolleeId(enrollee.getId())
.status(kitRequestDto.getStatus())
.sentToAddress(kitRequestDto.getSentToAddress())
.skipAddressValidation(kitRequestDto.isSkipAddressValidation())
.kitTypeId(kitType.getId())
.createdAt(kitRequestDto.getCreatedAt())
.labeledAt(kitRequestDto.getLabeledAt())
.sentAt(kitRequestDto.getSentAt())
.receivedAt(kitRequestDto.getReceivedAt())
.trackingNumber(kitRequestDto.getTrackingNumber())
.returnTrackingNumber(kitRequestDto.getReturnTrackingNumber())
.build();
}

private RegistrationService.RegistrationResult registerIfNeeded(String portalShortcode, StudyEnvironment studyEnv, ParticipantUser participantUserInfo) {
return portalParticipantUserService.findOne(participantUserInfo.getUsername(), portalShortcode, studyEnv.getEnvironmentName())
.map(ppUser -> new RegistrationService.RegistrationResult(
Expand Down Expand Up @@ -322,6 +357,6 @@ protected SurveyResponse importSurveyResponse(UUID portalId, SurveyFormatter for
}
// we're not worrying about dating the response yet
return surveyResponseService.updateResponse(response, new ResponsibleEntity(DataAuditInfo.systemProcessName(getClass(), "importSurveyResponse")),
ppUser, enrollee, relatedTask.getId(), portalId).getResponse();
ppUser, enrollee, relatedTask.getId(), portalId).getResponse();
}
}
17 changes: 0 additions & 17 deletions ...ain/java/bio/terra/pearl/core/service/export/formatters/item/KitRequestTypeFormatter.java
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33 changes: 33 additions & 0 deletions core/src/main/java/bio/terra/pearl/core/service/export/formatters/item/KitTypeFormatter.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,33 @@
package bio.terra.pearl.core.service.export.formatters.item;

import bio.terra.pearl.core.model.kit.KitType;
import bio.terra.pearl.core.service.export.DataValueExportType;
import bio.terra.pearl.core.service.kit.KitRequestDto;
import lombok.extern.slf4j.Slf4j;
import org.apache.commons.beanutils.PropertyUtils;

@Slf4j
public class KitTypeFormatter extends PropertyItemFormatter<KitRequestDto> {
public KitTypeFormatter() {
super("kitType", KitRequestDto.class);
this.baseColumnKey = "kitType";
this.dataType = DataValueExportType.STRING;
}

@Override
public String getExportString(KitRequestDto bean) {
return bean.getKitType().getName();
}

@Override
public void importValueToBean(KitRequestDto bean, String exportString) {
if (exportString != null) {
try {
PropertyUtils.setNestedProperty(bean, getPropertyName(), KitType.builder().name(exportString).build());
} catch (Exception e) {
log.warn("error setting property " + getPropertyName(), e);
}
}
}

}
44 changes: 41 additions & 3 deletions .../main/java/bio/terra/pearl/core/service/export/formatters/module/KitRequestFormatter.java
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Original file line number Diff line number Diff line change
@@ -1,10 +1,13 @@
package bio.terra.pearl.core.service.export.formatters.module;

import bio.terra.pearl.core.model.kit.KitRequestStatus;
import bio.terra.pearl.core.service.export.EnrolleeExportData;
import bio.terra.pearl.core.service.export.formatters.item.KitRequestTypeFormatter;
import bio.terra.pearl.core.service.export.formatters.item.KitTypeFormatter;
import bio.terra.pearl.core.service.export.formatters.item.PropertyItemFormatter;
import bio.terra.pearl.core.service.kit.KitRequestDto;
import org.apache.commons.lang3.StringUtils;

import java.util.ArrayList;
import java.util.Comparator;
import java.util.HashMap;
import java.util.List;
Expand All @@ -14,14 +17,15 @@
public class KitRequestFormatter extends ModuleFormatter<KitRequestDto, PropertyItemFormatter<KitRequestDto>> {
private static final String KIT_REQUEST_MODULE_NAME = "sample_kit";
private static final List<String> KIT_REQUEST_INCLUDED_PROPERTIES =
List.of("status", "sentToAddress", "sentAt", "receivedAt");
List.of("status", "sentToAddress", "sentAt", "receivedAt", "createdAt", "labeledAt",
"trackingNumber", "returnTrackingNumber", "skipAddressValidation");

public KitRequestFormatter() {
itemFormatters = KIT_REQUEST_INCLUDED_PROPERTIES.stream()
.map(propName -> new PropertyItemFormatter<KitRequestDto>(propName, KitRequestDto.class))
.collect(Collectors.toList());
// we have to handle kitType separately because we'll need to match it to the kitType name
itemFormatters.add(new KitRequestTypeFormatter());
itemFormatters.add(new KitTypeFormatter());
moduleName = KIT_REQUEST_MODULE_NAME;
displayName = "Sample kit";
}
Expand All @@ -43,4 +47,38 @@ public Map<String, String> toStringMap(EnrolleeExportData enrolleeData) {
maxNumRepeats = Math.max(maxNumRepeats, sortedKitRequests.size());
return allKitMap;
}

public List<KitRequestDto> listFromStringMap(Map<String, String> enrolleeMap) {
List<KitRequestDto> kitRequests = new ArrayList<>();
int requestNum = 1;
KitRequestDto kitRequestDto = getKitRequestDto(enrolleeMap, requestNum);
while (kitRequestDto != null) {
kitRequests.add(kitRequestDto);
requestNum++;
kitRequestDto = getKitRequestDto(enrolleeMap, requestNum);
}
return kitRequests;
}

private KitRequestDto getKitRequestDto(Map<String, String> enrolleeMap, int requestNum) {
KitRequestDto kitRequestDto = null;
for (PropertyItemFormatter<KitRequestDto> itemFormatter : itemFormatters) {
String columnName = getColumnKey(itemFormatter, false, null, requestNum);
String stringVal = enrolleeMap.get(columnName);
if (StringUtils.isEmpty(stringVal)) {
continue;
}
if (kitRequestDto == null) {
kitRequestDto = new KitRequestDto();
}
if (columnName.contains(".status")) {
//enum lookup
kitRequestDto.setStatus(KitRequestStatus.valueOf(stringVal));
} else {
itemFormatter.importValueToBean(kitRequestDto, stringVal);
}
}
return kitRequestDto;
}

}
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