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Feature/bi 2948 #551

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d3a2f33
[BI-2948] - Sample Submission Download
HMS17 Aug 27, 2026
c04cf8e
[BI-2948] - Sample Submission Download
HMS17 Aug 27, 2026
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27 changes: 27 additions & 0 deletions src/main/java/org/breedinginsight/api/v1/controller/geno/SampleSubmissionController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -188,6 +188,33 @@ public HttpResponse<StreamedFile> generateDArTFile(@PathVariable UUID programId,
}
}

@Get("/programs/{programId}/submissions/{submissionId}/export")
@ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.PROGRAM_SCOPED_ROLES})
@Produces(value={"text/csv", "application/vnd.ms-excel", "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", "application/octet-stream"})
public HttpResponse<StreamedFile> sampleSubmissionExport(@PathVariable UUID programId, @PathVariable UUID submissionId) {
try {
Optional<Program> program = programService.getById(programId);
if(program.isEmpty()) {
return HttpResponse.notFound();
}
Optional<DownloadFile> downloadFile = sampleSubmissionService.exportSubmission(program.get(), submissionId);
if(downloadFile.isEmpty()) {
return HttpResponse.notFound();
}
HttpResponse<StreamedFile> response = HttpResponse
.ok(downloadFile.get().getStreamedFile())
.header(HttpHeaders.CONTENT_DISPOSITION, "attachment;filename=" + downloadFile.get().getFileName());
return response;
} catch (ApiException e) {
log.error(Utilities.generateApiExceptionLogMessage(e), e);
return HttpResponse.serverError();
} catch (IOException e) {
log.error("Error exporting Sample Submission file", e);
HttpResponse response = HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error exporting Sample Submission file").contentType(MediaType.TEXT_PLAIN).body("Error exporting Sample Submission file");
return response;
}
}

@Get("/programs/{programId}/submissions/{submissionId}/lookup")
@ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.PROGRAM_SCOPED_ROLES})
@Produces(value={"text/csv", "application/vnd.ms-excel", "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", "application/octet-stream"})
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58 changes: 55 additions & 3 deletions src/main/java/org/breedinginsight/services/SampleSubmissionService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -65,6 +65,7 @@
public class SampleSubmissionService {

private static final String COLUMN_GENOTYPE = "Genotype";
public static final String COLUMN_SAMPLE_NAME = "Sample Name";
private static final String VENDOR_NOT_SUBMITTED_STATUS = "NOT SUBMITTED";
private static final String VENDOR_SUBMITTED_STATUS = "SUBMITTED";
private final String referenceSource;
Expand Down Expand Up @@ -214,20 +215,71 @@ public Optional<DownloadFile> generateDArTFile(Program program, UUID submissionI
columns.add(Column.builder().value(SampleSubmissionImport.Columns.TISSUE).dataType(Column.ColumnDataType.STRING).build());
columns.add(Column.builder().value(SampleSubmissionImport.Columns.COMMENTS).dataType(Column.ColumnDataType.STRING).build());

//Sort samples first. May be updated to use BrAPI server sorting after cache removal changes are merged
submission.get().getSamples().sort(Comparator.comparing(BrAPISample::getPlateName)
sortSamples(submission.get().getSamples());

List<Map<String, Object>> rows = new ArrayList<>();
submission.get().getSamples().forEach(sample -> {
Map<String, Object> row = new HashMap<>();
row.put(SampleSubmissionImport.Columns.PLATE_ID, sample.getPlateName());
row.put(SampleSubmissionImport.Columns.ROW, sample.getRow());
row.put(SampleSubmissionImport.Columns.COLUMN, sample.getColumn());
row.put(SampleSubmissionImport.Columns.ORGANISM, sample.getAdditionalInfo().get(BrAPIAdditionalInfoFields.SAMPLE_ORGANISM).getAsString());
row.put(SampleSubmissionImport.Columns.SPECIES, sample.getAdditionalInfo().has(BrAPIAdditionalInfoFields.SAMPLE_SPECIES) ? sample.getAdditionalInfo().get(BrAPIAdditionalInfoFields.SAMPLE_SPECIES).getAsString() : "");
row.put(COLUMN_GENOTYPE, sample.getSampleName());
row.put(SampleSubmissionImport.Columns.TISSUE, sample.getTissueType());
row.put(SampleSubmissionImport.Columns.COMMENTS, sample.getSampleDescription());

rows.add(row);
});


return Optional.of(new DownloadFile(filename, FileUtil.writeToStreamedFile(columns, rows, FileType.CSV, "Data")));
}

//Helper method to sort samples. May be updated to use BrAPI server sorting after cache removal changes are merged
public void sortSamples(List<BrAPISample> samples) {
samples.sort(Comparator.comparing(BrAPISample::getPlateName)
.thenComparing(BrAPISample::getColumn)
.thenComparing(BrAPISample::getRow));
}

public Optional<DownloadFile> exportSubmission(Program program, UUID submissionId) throws ApiException, IOException {
Optional<SampleSubmission> submission = getSampleSubmission(program, submissionId, true);
if (submission.isEmpty()) {
return Optional.empty();
}

DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd_hh-mm-ssZ");
String timestamp = formatter.format(OffsetDateTime.now());
String filename = Utilities.makePortableFilename(String.format("%s_SampleSubmission_%s.csv", submission.get().getName(), timestamp));

List<Column> columns = new ArrayList<>();
columns.add(Column.builder().value(SampleSubmissionImport.Columns.GERMPLASM_NAME).dataType(Column.ColumnDataType.STRING).build());
columns.add(Column.builder().value(SampleSubmissionImport.Columns.GERMPLASM_GID).dataType(Column.ColumnDataType.STRING).build());
columns.add(Column.builder().value(SampleSubmissionImport.Columns.OBS_UNIT_ID).dataType(Column.ColumnDataType.STRING).build());
columns.add(Column.builder().value(COLUMN_SAMPLE_NAME).dataType(Column.ColumnDataType.STRING).build());
columns.add(Column.builder().value(SampleSubmissionImport.Columns.PLATE_ID).dataType(Column.ColumnDataType.STRING).build());
columns.add(Column.builder().value(SampleSubmissionImport.Columns.ROW).dataType(Column.ColumnDataType.STRING).build());
columns.add(Column.builder().value(SampleSubmissionImport.Columns.COLUMN).dataType(Column.ColumnDataType.INTEGER).build());
columns.add(Column.builder().value(SampleSubmissionImport.Columns.ORGANISM).dataType(Column.ColumnDataType.STRING).build());
columns.add(Column.builder().value(SampleSubmissionImport.Columns.SPECIES).dataType(Column.ColumnDataType.STRING).build());
columns.add(Column.builder().value(SampleSubmissionImport.Columns.TISSUE).dataType(Column.ColumnDataType.STRING).build());
columns.add(Column.builder().value(SampleSubmissionImport.Columns.COMMENTS).dataType(Column.ColumnDataType.STRING).build());

sortSamples(submission.get().getSamples());

List<Map<String, Object>> rows = new ArrayList<>();
submission.get().getSamples().forEach(sample -> {
Map<String, Object> row = new HashMap<>();
row.put(SampleSubmissionImport.Columns.GERMPLASM_NAME, sample.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GERMPLASM_NAME).getAsString());
row.put(SampleSubmissionImport.Columns.GERMPLASM_GID, sample.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GID).getAsString());
row.put(SampleSubmissionImport.Columns.OBS_UNIT_ID, sample.getObservationUnitDbId());
row.put(COLUMN_SAMPLE_NAME, sample.getSampleName());
row.put(SampleSubmissionImport.Columns.PLATE_ID, sample.getPlateName());
row.put(SampleSubmissionImport.Columns.ROW, sample.getRow());
row.put(SampleSubmissionImport.Columns.COLUMN, sample.getColumn());
row.put(SampleSubmissionImport.Columns.ORGANISM, sample.getAdditionalInfo().get(BrAPIAdditionalInfoFields.SAMPLE_ORGANISM).getAsString());
row.put(SampleSubmissionImport.Columns.SPECIES, sample.getAdditionalInfo().has(BrAPIAdditionalInfoFields.SAMPLE_SPECIES) ? sample.getAdditionalInfo().get(BrAPIAdditionalInfoFields.SAMPLE_SPECIES).getAsString() : "");
row.put(COLUMN_GENOTYPE, sample.getSampleName());
row.put(SampleSubmissionImport.Columns.TISSUE, sample.getTissueType());
row.put(SampleSubmissionImport.Columns.COMMENTS, sample.getSampleDescription());

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42 changes: 42 additions & 0 deletions ...java/org/breedinginsight/api/v1/controller/SampleSubmissionControllerIntegrationTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -326,6 +326,48 @@ public void testGenerateDArTFile() throws IOException, InterruptedException, Par
assertEquals("Genotype", lookupTable.column(5).name());
assertEquals(Columns.TISSUE, lookupTable.column(6).name());
assertEquals(Columns.COMMENTS, lookupTable.column(7).name());

//Check sorting
assertEquals("valid_1", lookupTable.column(0).get(1));
assertEquals("A1", lookupTable.column(1).get(1));
assertEquals(0, lookupTable.column(2).get(1));
}

@Test
public void testExportSampleSubmission() throws IOException, InterruptedException, ParsingException {
Pair<SampleSubmission, List<Map<String, Object>>> uploadedSubmission = createSubmission(program);

Flowable<HttpResponse<byte[]>> call = client.exchange(
GET(String.format("/programs/%s/submissions/%s/export",
program.getId().toString(), uploadedSubmission.getLeft().getId()))
.cookie(new NettyCookie("phylo-token", "test-registered-user")), byte[].class
);
HttpResponse<byte[]> response = call.blockingFirst();

assertEquals(HttpStatus.OK, response.getStatus());

ByteArrayInputStream bodyStream = new ByteArrayInputStream(Objects.requireNonNull(response.body()));
Table lookupTable = FileUtil.parseTableFromCsv(bodyStream);
assertEquals(11, lookupTable.columnCount());

//Check columns correct
assertEquals(Columns.GERMPLASM_NAME, lookupTable.column(0).name());
assertEquals(Columns.GERMPLASM_GID, lookupTable.column(1).name());
assertEquals(Columns.OBS_UNIT_ID, lookupTable.column(2).name());
assertEquals("Sample Name", lookupTable.column(3).name());
assertEquals(Columns.PLATE_ID, lookupTable.column(4).name());
assertEquals(Columns.ROW, lookupTable.column(5).name());
assertEquals(Columns.COLUMN, lookupTable.column(6).name());
assertEquals(Columns.ORGANISM, lookupTable.column(7).name());
assertEquals(Columns.SPECIES, lookupTable.column(8).name());
assertEquals(Columns.TISSUE, lookupTable.column(9).name());
assertEquals(Columns.COMMENTS, lookupTable.column(10).name());

//Check sorting
assertEquals(2, lookupTable.column(1).get(1));
assertEquals("valid_1", lookupTable.column(4).get(1));
assertEquals("A1", lookupTable.column(5).get(1));
assertEquals(0, lookupTable.column(6).get(1));
}

@Test
Expand Down
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