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[DT-2757] Ensure institutional Certification files are saved on appropriate dataset updates #2771

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[DT-2757] Ensure institutional Certification files are saved on appropriate dataset updates #2771

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354820c
Ensure institutional Certification files are saved on appropriate dat…
otchet-broad Dec 19, 2025
96ef8ae
Save **insert** files when inserting a new dataset as part of a study…
otchet-broad Dec 22, 2025
833867e
fix: sonar lint.
otchet-broad Dec 22, 2025
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25 changes: 15 additions & 10 deletions src/main/java/org/broadinstitute/consent/http/service/DatasetRegistrationService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -128,7 +128,7 @@ public Study updateStudyFromRegistration(
convertConsentGroupToDatasetProperties(cg));
DatasetServiceDAO.DatasetUpdate update =
createDatasetUpdate(
cg.getDatasetId(), user, datasetUpdate, files, uploadedFileCache);
cg.getDatasetId(), user, datasetUpdate, files, uploadedFileCache, idx);
datasetUpdates.add(update);
} catch (Exception e) {
logException(e);
Expand Down Expand Up @@ -267,7 +267,7 @@ public Dataset updateDataset(

try {
DatasetServiceDAO.DatasetUpdate datasetUpdates =
createDatasetUpdate(datasetId, user, update, files, uploadedFileCache);
createDatasetUpdate(datasetId, user, update, files, uploadedFileCache, 0);

// Update or create the objects in the database
datasetServiceDAO.updateDataset(datasetUpdates);
Expand Down Expand Up @@ -324,13 +324,14 @@ private DatasetServiceDAO.DatasetUpdate createDatasetUpdate(
User user,
DatasetUpdate datasetUpdate,
Map<String, FormDataBodyPart> files,
Map<String, BlobId> uploadedFileCache)
Map<String, BlobId> uploadedFileCache,
int idx)
throws IOException {

List<DatasetProperty> props = datasetUpdate.getDatasetProperties();

List<FileStorageObject> fileStorageObjects =
uploadFilesForDatasetUpdate(files, uploadedFileCache, user);
uploadFilesForDatasetUpdate(files, uploadedFileCache, user, idx);

return new DatasetServiceDAO.DatasetUpdate(
datasetId,
Expand Down Expand Up @@ -407,17 +408,21 @@ private List<FileStorageObject> uploadFilesForDataset(
}

private List<FileStorageObject> uploadFilesForDatasetUpdate(
Map<String, FormDataBodyPart> files, Map<String, BlobId> uploadedFileCache, User user)
Map<String, FormDataBodyPart> files,
Map<String, BlobId> uploadedFileCache,
User user,
int idx)
throws IOException {
List<FileStorageObject> updateDatasetFSOs = new ArrayList<>();

if (files.containsKey(String.format(NIH_INSTITUTIONAL_CERTIFICATION_NAME, 0))) {
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@otchet-broad otchet-broad Dec 19, 2025 •
edited
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This is the core of the bug. When multiple datasets are updated, we can have multiple files submitted. Assuming the files key was always consentGroups[**0**].nihInstitutionalCertificationFile is incorrect. The update payload might be just a change for consentGroup[5], or a case where multiple consentGroup entries are updated at the same time.

Given this bug I've made https://broadworkbench.atlassian.net/browse/DT-2759

String fileKey = String.format(NIH_INSTITUTIONAL_CERTIFICATION_NAME, idx);
FormDataBodyPart fileToUpdate = files.get(fileKey);
if (fileToUpdate != null) {
updateDatasetFSOs.add(
uploadFile(
files,
uploadedFileCache,
user,
String.format(NIH_INSTITUTIONAL_CERTIFICATION_NAME, 0),
fileKey,
FileCategory.NIH_INSTITUTIONAL_CERTIFICATION));
}

Expand All @@ -440,8 +445,8 @@ private List<FileStorageObject> uploadFilesForStudy(
Map<String, FormDataBodyPart> files, Map<String, BlobId> uploadedFileCache, User user)
throws IOException {
List<FileStorageObject> studyFSOs = new ArrayList<>();

if (files.containsKey(ALTERNATIVE_DATA_SHARING_PLAN_NAME)) {
FormDataBodyPart alternateSharingPlanFile = files.get(ALTERNATIVE_DATA_SHARING_PLAN_NAME);
if (alternateSharingPlanFile != null) {
studyFSOs.add(
uploadFile(
files,
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/org/broadinstitute/consent/http/service/dao/DatasetServiceDAO.java
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Original file line number Diff line number Diff line change
Expand Up @@ -256,7 +256,7 @@ public Study updateStudy(
studyUpdate.userId,
datasetUpdate.dacId,
datasetUpdate.props,
studyUpdate.files,
datasetUpdate.files,
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@otchet-broad otchet-broad Dec 22, 2025

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Passing the studyUpdate files into the dataset updates (and inserts ~L271) was also problematic. The files would be uploaded to GCS but the FSOs wouldn't be recorded.

false);
}
for (DatasetServiceDAO.DatasetInsert insert : datasetInserts) {
Expand All @@ -268,7 +268,7 @@ public Study updateStudy(
insert.dataUse,
studyUpdate.userId,
insert.props,
studyUpdate.files);
insert.files);
}
handle.commit();
});
Expand Down
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