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revert GET list data objects from ListController
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,6 @@ | ||
| package org.breedinginsight.brapi.v2; | ||
|
|
||
| import com.drew.lang.annotations.Nullable; | ||
| import io.micronaut.context.annotation.Property; | ||
| import io.micronaut.http.HttpHeaders; | ||
| import io.micronaut.http.HttpResponse; | ||
|
|
@@ -19,10 +20,11 @@ | |
| import org.brapi.v2.model.BrAPIIndexPagination; | ||
| import org.brapi.v2.model.BrAPIMetadata; | ||
| import org.brapi.v2.model.BrAPIStatus; | ||
| import org.brapi.v2.model.core.BrAPITrial; | ||
| import org.brapi.v2.model.germ.*; | ||
| import org.brapi.v2.model.germ.request.BrAPIGermplasmSearchRequest; | ||
| import org.brapi.v2.model.germ.response.*; | ||
| import org.brapi.v2.model.germ.response.BrAPIGermplasmListResponse; | ||
| import org.brapi.v2.model.germ.response.BrAPIGermplasmPedigreeResponse; | ||
| import org.brapi.v2.model.germ.response.BrAPIGermplasmProgenyResponse; | ||
| import org.breedinginsight.api.auth.ProgramSecured; | ||
| import org.breedinginsight.api.auth.ProgramSecuredRoleGroup; | ||
| import org.breedinginsight.api.model.v1.request.query.SearchRequest; | ||
|
|
@@ -33,27 +35,25 @@ | |
| import org.breedinginsight.brapi.v2.constants.BrAPIAdditionalInfoFields; | ||
| import org.breedinginsight.brapi.v2.dao.BrAPIGermplasmDAO; | ||
| import org.breedinginsight.brapi.v2.model.request.query.GermplasmQuery; | ||
| import org.breedinginsight.brapps.importer.services.ExternalReferenceSource; | ||
| import org.breedinginsight.model.Program; | ||
| import org.breedinginsight.services.ProgramService; | ||
| import org.breedinginsight.utilities.Utilities; | ||
| import org.breedinginsight.utilities.response.mappers.GermplasmQueryMapper; | ||
| import org.breedinginsight.brapi.v2.services.BrAPIGermplasmService; | ||
| import org.breedinginsight.brapps.importer.model.exports.FileType; | ||
| import org.breedinginsight.daos.ProgramDAO; | ||
| import org.breedinginsight.model.DownloadFile; | ||
| import org.breedinginsight.model.GermplasmGenotype; | ||
| import org.breedinginsight.model.Program; | ||
| import org.breedinginsight.services.ProgramService; | ||
| import org.breedinginsight.services.brapi.BrAPIEndpointProvider; | ||
| import org.breedinginsight.services.exceptions.AuthorizationException; | ||
| import org.breedinginsight.services.exceptions.DoesNotExistException; | ||
| import org.breedinginsight.services.geno.GenotypeService; | ||
| import org.breedinginsight.utilities.Utilities; | ||
| import org.breedinginsight.utilities.response.ResponseUtils; | ||
| import org.breedinginsight.utilities.response.mappers.GermplasmQueryMapper; | ||
|
|
||
| import javax.inject.Inject; | ||
| import javax.validation.Valid; | ||
| import java.util.*; | ||
| import java.util.regex.Pattern; | ||
| import java.util.stream.Collectors; | ||
|
|
||
| @Slf4j | ||
| @Controller("/${micronaut.bi.api.version}") | ||
|
|
@@ -222,15 +222,17 @@ public HttpResponse<Response<DataResponse<List<BrAPIGermplasm>>>> getGermplasm( | |
| } | ||
| } | ||
|
|
||
| @Get("/programs/{programId}/germplasm/export{?fileExtension}") | ||
| @Get("/programs/{programId}/germplasm/export{?fileExtension,list}") | ||
| @Produces(value = "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet") | ||
| @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.PROGRAM_SCOPED_ROLES}) | ||
| public HttpResponse<StreamedFile> germplasmExport( | ||
| @PathVariable("programId") UUID programId, @QueryValue(defaultValue = "XLSX") String fileExtension) { | ||
| @PathVariable("programId") UUID programId, | ||
| @QueryValue(defaultValue = "XLSX") String fileExtension, | ||
| @QueryValue Optional<String> list) { | ||
| String downloadErrorMessage = "An error occurred while generating the download file. Contact the development team at [email protected]."; | ||
| try { | ||
| FileType extension = Enum.valueOf(FileType.class, fileExtension); | ||
| DownloadFile germplasmListFile = germplasmService.exportGermplasm(programId, extension); | ||
| DownloadFile germplasmListFile = list.isEmpty() ? germplasmService.exportGermplasm(programId, extension) : germplasmService.exportGermplasmList(programId, list.get(), extension); | ||
| HttpResponse<StreamedFile> germplasmExport = HttpResponse.ok(germplasmListFile.getStreamedFile()).header(HttpHeaders.CONTENT_DISPOSITION, "attachment;filename="+germplasmListFile.getFileName()+extension.getExtension()); | ||
| return germplasmExport; | ||
| } | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,10 +1,10 @@ | ||
| package org.breedinginsight.brapi.v2; | ||
|
|
||
| import io.micronaut.core.beans.BeanIntrospection; | ||
| import io.micronaut.core.beans.BeanProperty; | ||
| import io.micronaut.http.*; | ||
| import io.micronaut.http.HttpRequest; | ||
| import io.micronaut.http.HttpResponse; | ||
| import io.micronaut.http.HttpStatus; | ||
| import io.micronaut.http.MediaType; | ||
| import io.micronaut.http.annotation.*; | ||
| import io.micronaut.http.server.types.files.StreamedFile; | ||
| import io.micronaut.security.annotation.Secured; | ||
| import io.micronaut.security.rules.SecurityRule; | ||
| import lombok.extern.slf4j.Slf4j; | ||
|
|
@@ -18,27 +18,19 @@ | |
| import org.breedinginsight.api.model.v1.response.Response; | ||
| import org.breedinginsight.api.model.v1.validators.QueryValid; | ||
| import org.breedinginsight.brapi.v1.controller.BrapiVersion; | ||
| import org.breedinginsight.brapi.v1.model.request.query.BrapiQuery; | ||
| import org.breedinginsight.brapi.v2.model.request.query.ListQuery; | ||
| import org.breedinginsight.brapi.v2.services.BrAPIListService; | ||
| import org.breedinginsight.brapps.importer.model.exports.FileType; | ||
| import org.breedinginsight.model.DownloadFile; | ||
| import org.breedinginsight.model.Program; | ||
| import org.breedinginsight.model.delta.DeltaListDetails; | ||
| import org.breedinginsight.services.ProgramService; | ||
| import org.breedinginsight.services.exceptions.DoesNotExistException; | ||
| import org.breedinginsight.utilities.response.ResponseUtils; | ||
| import org.breedinginsight.utilities.response.mappers.AbstractQueryMapper; | ||
| import org.breedinginsight.utilities.response.mappers.ListQueryMapper; | ||
|
|
||
| import javax.inject.Inject; | ||
| import javax.validation.ConstraintViolation; | ||
| import javax.validation.Valid; | ||
| import javax.validation.Validator; | ||
| import java.util.List; | ||
| import java.util.Set; | ||
| import java.util.UUID; | ||
| import java.util.stream.Collectors; | ||
|
|
||
| @Slf4j | ||
| @Controller("/${micronaut.bi.api.version}/programs/{programId}" + BrapiVersion.BRAPI_V2) | ||
|
|
@@ -105,7 +97,7 @@ public HttpResponse<Response<DataResponse<Object>>> deleteListById( | |
| @PathVariable("programId") UUID programId, | ||
| @PathVariable("listDbId") String listDbId, | ||
| HttpRequest<Void> request | ||
| ) throws DoesNotExistException, ApiException { | ||
| ) { | ||
| boolean hardDelete = false; | ||
| if (request.getParameters().contains("hardDelete")) { | ||
| String paramValue = request.getParameters().get("hardDelete"); | ||
|
|
@@ -119,110 +111,4 @@ public HttpResponse<Response<DataResponse<Object>>> deleteListById( | |
| return HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error retrieving germplasm list records"); | ||
| } | ||
| } | ||
|
|
||
| @Get("/lists/{listDbId}") | ||
| @Produces(MediaType.APPLICATION_JSON) | ||
| @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.PROGRAM_SCOPED_ROLES}) | ||
| @SuppressWarnings("unchecked") | ||
| public <T extends BrapiQuery, U> HttpResponse<Response<DataResponse<List<U>>>> getListById( | ||
| @PathVariable("programId") UUID programId, | ||
| @PathVariable("listDbId") String listDbId, | ||
| HttpRequest<?> request) { | ||
| try { | ||
| // Get the list from the BrAPI service | ||
| DeltaListDetails details = brapiListService.getDeltaListDetails(listDbId, programId); | ||
|
|
||
| // Get a new instance of BrAPI query matching the type of list contents | ||
| T queryParams = (T) details.getQuery(); | ||
|
|
||
| // Bind query parameters to the object | ||
| bindQueryParams(queryParams, request); | ||
|
|
||
| // Perform standard bean validation | ||
| Set<ConstraintViolation<Object>> violations = validator.validate(queryParams); | ||
| if (!violations.isEmpty()) { | ||
| List<String> errorMessages = violations.stream() | ||
| .map(ConstraintViolation::getMessage) | ||
| .collect(Collectors.toList()); | ||
| log.info(String.join(", ", errorMessages)); | ||
| return HttpResponse.status(HttpStatus.BAD_REQUEST, "Error with list contents search parameters"); | ||
| } | ||
|
|
||
| // Fetch the list contents from the BrAPI service | ||
| List<U> listContentsBrAPIObjects = (List<U>) details.getDataObjects(); | ||
|
|
||
| // Construct a search request for sorting the list contents | ||
| SearchRequest searchRequest = details.constructSearchRequest(queryParams); | ||
|
|
||
| // Get the map used to connect query sorting keys to contents object values | ||
| AbstractQueryMapper contentsQueryMapper = details.getQueryMapper(); | ||
|
|
||
| return ResponseUtils.getBrapiQueryResponse(listContentsBrAPIObjects, contentsQueryMapper, queryParams, searchRequest); | ||
| } catch (Exception e) { | ||
| log.info(e.getMessage(), e); | ||
| return HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error retrieving list records"); | ||
| } | ||
| } | ||
|
|
||
| @Get("/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 [email protected]."; | ||
| try { | ||
| // Get the list from the BrAPI service | ||
| DeltaListDetails details = brapiListService.getDeltaListDetails(listDbId, programId); | ||
|
|
||
| FileType extension = Enum.valueOf(FileType.class, fileExtension); | ||
| DownloadFile listContentsFile = details.exportListObjects(extension); | ||
| return HttpResponse.ok(listContentsFile.getStreamedFile()).header(HttpHeaders.CONTENT_DISPOSITION, "attachment;filename="+listContentsFile.getFileName()+extension.getExtension()); | ||
| } | ||
| 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; | ||
| } | ||
| } | ||
|
|
||
| private void bindQueryParams(BrapiQuery queryParams, HttpRequest<?> request) { | ||
| BeanIntrospection<BrapiQuery> introspection = BeanIntrospection.getIntrospection(BrapiQuery.class); | ||
| for (BeanProperty<BrapiQuery, Object> property : introspection.getBeanProperties()) { | ||
| String paramName = property.getName(); | ||
| if (request.getParameters().contains(paramName)) { | ||
| String paramValue = request.getParameters().get(paramName); | ||
| Object convertedValue; | ||
| Class<?> propertyType = property.getType(); | ||
|
|
||
| if (propertyType.isEnum()) { | ||
| convertedValue = convertToEnum(paramValue, (Class<? extends Enum<?>>) propertyType); | ||
| } else { | ||
| convertedValue = convertValue(paramValue, propertyType); | ||
| } | ||
|
|
||
| property.set(queryParams, convertedValue); | ||
| } | ||
| } | ||
| } | ||
|
|
||
| private <T extends Enum<T>> T convertToEnum(String value, Class<? extends Enum<?>> enumClass) { | ||
| if (value == null) { | ||
| return null; | ||
| } | ||
| return Enum.valueOf((Class<T>) enumClass, value.toUpperCase()); | ||
| } | ||
|
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||
|
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||
| // Convert, if necessary, the values of query parameters to match the type defined for the fields in the BrapiQuery class | ||
| private Object convertValue(String value, Class<?> targetType) { | ||
| // Implement type conversion logic here | ||
| // Other list content types might need more complex logic | ||
| if (targetType == String.class) return value; | ||
| if (targetType == Integer.class) return Integer.parseInt(value); | ||
| if (targetType == Long.class) return Long.parseLong(value); | ||
| if (targetType == Boolean.class) return Boolean.parseBoolean(value); | ||
| // Add more type conversions as needed | ||
| return value; | ||
| } | ||
| } | ||
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