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[BI-1129] View Germplasm List #222

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Merged
dmeidlin merged 7 commits into from
Nov 14, 2022
Merged

[BI-1129] View Germplasm List #222

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dc24277
add controller for GET germplasm list by dbid
dmeidlin Oct 11, 2022
3b1edfd
add queryparams to endpoint signature
dmeidlin Oct 11, 2022
887b9ae
fix list records controller
dmeidlin Oct 11, 2022
5b4012e
add germplasm service method to fetch germplasm by list dbid
dmeidlin Oct 11, 2022
200cffc
add germplasm importEntryNumber as sort and filter fields
dmeidlin Oct 20, 2022
a2f8acc
fix possible null pointer runtime exception
dmeidlin Nov 7, 2022
4ca5a93
fix nonNull check in GermplasmService
dmeidlin Nov 8, 2022
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18 changes: 18 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 @@ -32,6 +32,7 @@
import org.breedinginsight.brapi.v2.model.request.query.GermplasmQuery;
import org.breedinginsight.brapi.v2.model.response.mappers.GermplasmQueryMapper;
import org.breedinginsight.brapi.v2.services.BrAPIGermplasmService;
import org.breedinginsight.brapps.importer.model.base.Germplasm;
import org.breedinginsight.brapps.importer.model.exports.FileType;
import org.breedinginsight.daos.ProgramDAO;
import org.breedinginsight.model.DownloadFile;
Expand Down Expand Up @@ -102,6 +103,23 @@ public HttpResponse<Response<DataResponse<List<BrAPIGermplasm>>>> getGermplasm(
}
}

@Get("/${micronaut.bi.api.version}/programs/{programId}/germplasm/lists/{listDbId}/records{?queryParams*}")
@Produces(MediaType.APPLICATION_JSON)
@ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
public HttpResponse<Response<DataResponse<List<BrAPIGermplasm>>>> getGermplasmListRecords(
@PathVariable("programId") UUID programId,
@PathVariable("listDbId") String listId,
@QueryValue @QueryValid(using = GermplasmQueryMapper.class) @Valid GermplasmQuery queryParams) {
try {
List<BrAPIGermplasm> germplasm = germplasmService.getGermplasmByList(programId, listId);
SearchRequest searchRequest = queryParams.constructSearchRequest();
return ResponseUtils.getBrapiQueryResponse(germplasm, germplasmQueryMapper, queryParams, searchRequest);
} catch (Exception e) {
log.info(e.getMessage(), e);
return HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error retrieving germplasm list records");
}
}

@Get("/${micronaut.bi.api.version}/programs/{programId}/germplasm/lists/{listDbId}/export{?fileExtension}")
@Produces(value = "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet")
@ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
Expand Down
4 changes: 4 additions & 0 deletions src/main/java/org/breedinginsight/brapi/v2/model/request/query/GermplasmQuery.java
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Expand Up @@ -13,6 +13,7 @@
@Getter
@Introspected
public class GermplasmQuery extends BrapiQuery {
private String importEntryNumber;
private String accessionNumber;
private String defaultDisplayName;
private String breedingMethod;
Expand All @@ -26,6 +27,9 @@ public class GermplasmQuery extends BrapiQuery {

public SearchRequest constructSearchRequest() {
List<FilterRequest> filters = new ArrayList<>();
if (!StringUtils.isBlank(getImportEntryNumber())) {
filters.add(constructFilterRequest("importEntryNumber", getImportEntryNumber()));
}
if (!StringUtils.isBlank(getAccessionNumber())) {
filters.add(constructFilterRequest("accessionNumber", getAccessionNumber()));
}
Expand Down
4 changes: 4 additions & 0 deletions src/main/java/org/breedinginsight/brapi/v2/model/response/mappers/GermplasmQueryMapper.java
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Expand Up @@ -24,6 +24,10 @@ public class GermplasmQueryMapper extends AbstractQueryMapper {

public GermplasmQueryMapper() {
fields = Map.ofEntries(
Map.entry("importEntryNumber", (germplasm) ->
germplasm.getAdditionalInfo() != null && germplasm.getAdditionalInfo().has(BrAPIAdditionalInfoFields.GERMPLASM_IMPORT_ENTRY_NUMBER) ?
germplasm.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GERMPLASM_IMPORT_ENTRY_NUMBER).getAsString() :
null),
Map.entry("accessionNumber", BrAPIGermplasm::getAccessionNumber),
Map.entry("defaultDisplayName", BrAPIGermplasm::getDefaultDisplayName),
Map.entry("breedingMethod", (germplasm) ->
Expand Down
11 changes: 11 additions & 0 deletions src/main/java/org/breedinginsight/brapi/v2/services/BrAPIGermplasmService.java
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Expand Up @@ -11,6 +11,7 @@
import org.brapi.v2.model.core.BrAPIListTypes;
import org.brapi.v2.model.core.response.BrAPIListDetails;
import org.brapi.v2.model.core.response.BrAPIListsListResponse;
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;
Expand Down Expand Up @@ -151,6 +152,16 @@ public List<Map<String, Object>> processData(List<BrAPIGermplasm> germplasm){
return processedData;
}

public List<BrAPIGermplasm> getGermplasmByList(UUID programId, String listId) throws ApiException {
// get list germplasm names
BrAPIListsSingleResponse listResponse = brAPIListDAO.getListById(listId, programId);
if(Objects.nonNull(listResponse) && Objects.nonNull(listResponse.getResult())) {
List<String> germplasmNames = listResponse.getResult().getData();

// get list BrAPI germplasm variables
return germplasmDAO.getGermplasmByRawName(germplasmNames, programId);
} else throw new ApiException();
}
public DownloadFile exportGermplasmList(UUID programId, String listId, FileType fileExtension) throws ApiException, IOException {
List<Column> columns = GermplasmFileColumns.getOrderedColumns();

Expand Down