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BI-1922 (Add ability to download all germplasm in a program) #311

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Merged
davedrp merged 3 commits into from
Nov 17, 2023
Merged

BI-1922 (Add ability to download all germplasm in a program) #311

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7572924
[BI-1922] Can download Germplasm
davedrp Oct 25, 2023
819a0f9
[BI-1922] addess 'problems' identified by InelliJ
davedrp Oct 30, 2023
e0cf886
[BI-1922] better error handeling
davedrp Nov 17, 2023
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19 changes: 19 additions & 0 deletions src/main/java/org/breedinginsight/brapi/v2/GermplasmController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -157,6 +157,25 @@ public HttpResponse<StreamedFile> germplasmListExport(
}
}

@Get("/programs/{programId}/germplasm/export{?fileExtension}")
@Produces(value = "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet")
@ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
public HttpResponse<StreamedFile> germplasmExport(
@PathVariable("programId") UUID programId, @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.exportGermplasm(programId, extension);
HttpResponse<StreamedFile> germplasmExport = HttpResponse.ok(germplasmListFile.getStreamedFile()).header(HttpHeaders.CONTENT_DISPOSITION, "attachment;filename="+germplasmListFile.getFileName()+extension.getExtension());
return germplasmExport;
}
catch (Exception e) {
log.error(e.getMessage(), e);
HttpResponse response = HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, downloadErrorMessage).contentType(MediaType.TEXT_PLAIN).body(downloadErrorMessage);
return response;
}
}

@Get("/programs/{programId}" + BrapiVersion.BRAPI_V2 + "/germplasm/{germplasmId}")
@Produces(MediaType.APPLICATION_JSON)
@ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
Expand Down
85 changes: 37 additions & 48 deletions src/main/java/org/breedinginsight/brapi/v2/services/BrAPIGermplasmService.java
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Original file line number Diff line number Diff line change
@@ -1,25 +1,21 @@
package org.breedinginsight.brapi.v2.services;

import io.micronaut.context.annotation.Property;
import io.micronaut.http.HttpRequest;
import io.micronaut.http.server.exceptions.InternalServerException;
import io.micronaut.http.server.types.files.StreamedFile;
import org.brapi.client.v2.model.exceptions.ApiException;
import org.brapi.v2.model.BrAPIExternalReference;
import lombok.extern.slf4j.Slf4j;
import org.brapi.v2.model.core.BrAPIListSummary;
import org.brapi.v2.model.core.BrAPIListTypes;
import org.brapi.v2.model.core.request.BrAPIListNewRequest;
import org.brapi.v2.model.core.response.BrAPIListDetails;
import org.brapi.v2.model.core.response.BrAPIListsSingleResponse;
import org.brapi.v2.model.germ.BrAPIGermplasm;
import org.brapi.v2.model.germ.BrAPIGermplasmSynonyms;
import org.breedinginsight.brapi.v2.constants.BrAPIAdditionalInfoFields;
import org.breedinginsight.brapps.importer.daos.BrAPIListDAO;
import org.breedinginsight.brapps.importer.model.exports.FileType;
import org.breedinginsight.brapps.importer.services.ExternalReferenceSource;
import org.breedinginsight.model.Column;
import org.breedinginsight.model.DownloadFile;
import org.breedinginsight.model.Pedigree;
import org.breedinginsight.model.Program;
import org.breedinginsight.services.ProgramService;
import org.breedinginsight.services.exceptions.DoesNotExistException;
Expand All @@ -28,7 +24,6 @@
import org.breedinginsight.services.writers.ExcelWriter;
import org.breedinginsight.brapi.v2.dao.BrAPIGermplasmDAO;
import org.breedinginsight.brapps.importer.model.ImportUpload;
import org.breedinginsight.utilities.Utilities;

import javax.inject.Inject;
import javax.inject.Singleton;
Expand Down Expand Up @@ -77,39 +72,6 @@ public Optional<BrAPIGermplasm> getGermplasmByDBID(UUID programId, String germpl
return germplasmDAO.getGermplasmByDBID(germplasmId, programId);
}

public List<BrAPIListSummary> getGermplasmListsByProgramId(UUID programId, HttpRequest<String> request) throws DoesNotExistException, ApiException {

if (!programService.exists(programId)) {
throw new DoesNotExistException("Program does not exist");
}

Optional<Program> optionalProgram = programService.getById(programId);
if(optionalProgram.isPresent()) {
Program program = optionalProgram.get();

List<BrAPIListSummary> germplasmLists = brAPIListDAO.getListByTypeAndExternalRef(BrAPIListTypes.GERMPLASM, programId, Utilities.generateReferenceSource(referenceSource, ExternalReferenceSource.PROGRAMS), programId);

for (BrAPIListSummary germplasmList: germplasmLists) {
String listName = germplasmList.getListName();
String newListName = removeAppendedKey(listName, program.getKey());
germplasmList.setListName(newListName);

//Retrieve germplasm details to get list owner name
//Due to listOwnerName not being stored in breedbase
BrAPIListDetails listData = brAPIListDAO.getListById(germplasmList.getListDbId(), programId).getResult();
List<String> germplasmNames = listData.getData().subList(0,1);
List<BrAPIGermplasm> germplasm = germplasmDAO.getGermplasmByRawName(germplasmNames, programId);
String createdBy = germplasm.get(0).getAdditionalInfo().getAsJsonObject("createdBy").get("userName").getAsString();
germplasmList.setListOwnerName(createdBy);
}

return germplasmLists;
}
else {
throw new DoesNotExistException("Program does not exist");
}
}

public List<Map<String, Object>> processListData(List<BrAPIGermplasm> germplasm, UUID germplasmListId){
List<Map<String, Object>> processedData = new ArrayList<>();

Expand Down Expand Up @@ -164,7 +126,7 @@ public List<Map<String, Object>> processListData(List<BrAPIGermplasm> germplasm,
// Synonyms
if (germplasmEntry.getSynonyms() != null && !germplasmEntry.getSynonyms().isEmpty()) {
String joinedSynonyms = germplasmEntry.getSynonyms().stream()
.map(synonym -> synonym.getSynonym())
.map(BrAPIGermplasmSynonyms::getSynonym)
.collect(Collectors.joining(";"));
row.put("Synonyms", joinedSynonyms);
}
Expand All @@ -191,6 +153,38 @@ public List<BrAPIGermplasm> getGermplasmByList(UUID programId, String listDbId)
return germplasm;
} else throw new ApiException();
}
public DownloadFile exportGermplasm(UUID programId, FileType fileExtension) throws IllegalArgumentException, ApiException, IOException {
List<Column> columns = GermplasmFileColumns.getOrderedColumns();

//Retrieve germplasm list data
List<BrAPIGermplasm> germplasm = germplasmDAO.getGermplasm(programId);
germplasm.sort(Comparator.comparingInt(germ -> Integer.parseInt(germ.getAccessionNumber())));

// make file Name
DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd:hh-mm-ssZ");
String timestamp = formatter.format(OffsetDateTime.now());
StringBuilder fileNameSB = new StringBuilder();
Optional<Program> optionalProgram = programService.getById(programId);
if (optionalProgram.isPresent()) {
Program program = optionalProgram.get();
fileNameSB.append( program.getName() );
fileNameSB.append("_");
}
String fileName = fileNameSB.append("germplasm").append("_").append(timestamp).toString();

StreamedFile downloadFile;
//Convert list data to List<Map<String, Object>> data to pass into file writer
List<Map<String, Object>> processedData = processListData(germplasm, new UUID(0,0));

if (fileExtension == FileType.CSV){
downloadFile = CSVWriter.writeToDownload(columns, processedData, fileExtension);
} else {
downloadFile = ExcelWriter.writeToDownload("Data", columns, processedData, fileExtension);
}

return new DownloadFile(fileName, downloadFile);
}

public DownloadFile exportGermplasmList(UUID programId, String listId, FileType fileExtension) throws IllegalArgumentException, ApiException, IOException {
List<Column> columns = GermplasmFileColumns.getOrderedColumns();

Expand Down Expand Up @@ -219,7 +213,7 @@ public DownloadFile exportGermplasmList(UUID programId, String listId, FileType
if (fileExtension == FileType.CSV){
downloadFile = CSVWriter.writeToDownload(columns, processedData, fileExtension);
} else {
downloadFile = ExcelWriter.writeToDownload("Germplasm Import", columns, processedData, fileExtension);
downloadFile = ExcelWriter.writeToDownload("Data", columns, processedData, fileExtension);
}

return new DownloadFile(fileName, downloadFile);
Expand All @@ -229,7 +223,7 @@ public UUID getGermplasmListId(BrAPIListDetails listData) {
if(Objects.nonNull(listData.getExternalReferences()) && hasListExternalReference(listData.getExternalReferences())) {
return UUID.fromString(listData.getExternalReferences().stream()
.filter(e -> referenceSource.concat("/lists").equals(e.getReferenceSource()))
.map(e -> e.getReferenceID()).findAny().orElse("00000000-0000-0000-000000000000"));
.map(BrAPIExternalReference::getReferenceID).findAny().orElse("00000000-0000-0000-000000000000"));
} else {
return new UUID(0,0);
}
Expand All @@ -239,7 +233,7 @@ public UUID getGermplasmListId(BrAPIListNewRequest importList) {
if(Objects.nonNull(importList.getExternalReferences()) && hasListExternalReference(importList.getExternalReferences())) {
return UUID.fromString(importList.getExternalReferences().stream()
.filter(e -> referenceSource.concat("/lists").equals(e.getReferenceSource()))
.map(e -> e.getReferenceID()).findAny().orElse("00000000-0000-0000-000000000000"));
.map(BrAPIExternalReference::getReferenceID).findAny().orElse("00000000-0000-0000-000000000000"));
} else {
return new UUID(0,0);
}
Expand Down Expand Up @@ -306,11 +300,6 @@ public List<BrAPIGermplasm> updateBrAPIGermplasm(List<BrAPIGermplasm> putBrAPIGe
return germplasmDAO.updateBrAPIGermplasm(putBrAPIGermplasmList, programId, upload);
}

public List<BrAPIGermplasm> importBrAPIGermplasm(List<BrAPIGermplasm> postBrAPIGermplasmList, List<BrAPIGermplasm> putBrAPIGermplasmList,
UUID programId, ImportUpload upload) throws ApiException {
return germplasmDAO.createBrAPIGermplasm(postBrAPIGermplasmList, programId, upload);
}

public List<BrAPIGermplasm> getRawGermplasmByAccessionNumber(ArrayList<String> germplasmAccessionNumbers, UUID programId) throws ApiException {
List<BrAPIGermplasm> germplasmList = germplasmDAO.getRawGermplasm(programId);
List<BrAPIGermplasm> resultGermplasm = new ArrayList<>();
Expand Down