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[BI-2632] Germplasm download from single list no longer working #463

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Merged
davedrp merged 2 commits into from
Jun 9, 2025
Merged

[BI-2632] Germplasm download from single list no longer working #463

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2b6b3a1
[BI-2632] restore the @Get("/programs/{programId}/germplasm/lists/{li…
davedrp May 8, 2025
3f37b4f
[BI-2632] Added test for exporting a Germplasm List
davedrp May 22, 2025
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19 changes: 19 additions & 0 deletions src/main/java/org/breedinginsight/brapi/v2/BrAPIGermplasmController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -221,6 +221,25 @@ public HttpResponse<Response<DataResponse<List<BrAPIGermplasm>>>> getGermplasm(
return HttpResponse.status(HttpStatus.UNPROCESSABLE_ENTITY, "Error parsing requested date format");
}
}
@Get("/programs/{programId}/germplasm/lists/{listDbId}/export{?fileExtension}")
@Produces(value = "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet")
@ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.PROGRAM_SCOPED_ROLES})
public HttpResponse<StreamedFile> germplasmListExport(
@PathVariable("programId") UUID programId, @PathVariable("listDbId") String listDbId, @QueryValue(defaultValue = "XLSX") String fileExtension) {
String downloadErrorMessage = "An error occurred while generating the download file. Contact the development team at bidevteam@cornell.edu.";
try {
FileType extension = Enum.valueOf(FileType.class, fileExtension);
DownloadFile germplasmListFile = germplasmService.exportGermplasmList(programId, listDbId, extension);
HttpResponse<StreamedFile> germplasmListExport = HttpResponse.ok(germplasmListFile.getStreamedFile()).header(HttpHeaders.CONTENT_DISPOSITION, "attachment;filename="+germplasmListFile.getFileName()+extension.getExtension());
return germplasmListExport;
}
catch (Exception e) {
log.info(e.getMessage(), e);
e.printStackTrace();
HttpResponse response = HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, downloadErrorMessage).contentType(MediaType.TEXT_PLAIN).body(downloadErrorMessage);
return response;
}
}

@Get("/programs/{programId}/germplasm/export{?fileExtension,list}")
@Produces(value = "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet")
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37 changes: 37 additions & 0 deletions src/test/java/org/breedinginsight/brapi/v2/GermplasmControllerIntegrationTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -25,16 +25,22 @@
import org.breedinginsight.model.Program;
import org.breedinginsight.model.Species;
import org.breedinginsight.services.SpeciesService;
import org.breedinginsight.utilities.FileUtil;
import org.breedinginsight.utilities.response.mappers.GermplasmQueryMapper;
import org.jooq.DSLContext;
import org.junit.jupiter.api.*;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.CsvSource;
import tech.tablesaw.api.Table;

import javax.inject.Inject;
import java.io.ByteArrayInputStream;
import java.io.File;
import java.time.OffsetDateTime;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.Objects;

import static io.micronaut.http.HttpRequest.GET;
import static io.micronaut.http.HttpRequest.POST;
Expand Down Expand Up @@ -237,7 +243,38 @@ public void getAllGermplasmListsSuccess() {
}
}
}
@ParameterizedTest
@CsvSource(value = {"CSV", "XLSX", "XLS"})
@SneakyThrows
public void germplasmListExport(String extension) {
String programId = validProgram.getId().toString();
String germplasmListDbId = fetchGermplasmListDbId(programId);

// Build the endpoint to get germplasm by germplasm list.
String endpoint = String.format("/programs/%s/germplasm/lists/%s/export?fileExtension=%s", programId, germplasmListDbId, extension);

// Get germplasm by list.
Flowable<HttpResponse<byte[]>> call = client.exchange(
GET(endpoint).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 download = Table.create();
if (extension.equals("CSV")) {
download = FileUtil.parseTableFromCsv(bodyStream);
}
if (extension.equals("XLS") || extension.equals("XLSX")) {
download = FileUtil.parseTableFromExcel(bodyStream, 0);
}
int dataSize = download.rowCount();
assertEquals(3, dataSize, "Wrong number of germplasm were returned");
}
@Test
@SneakyThrows
public void getAllGermplasmByListSuccess() {
Expand Down
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