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[BI-3048] - Exp Collaborator FB Endpoints: /germplasm #558

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[BI-3048] - Exp Collaborator FB Endpoints: /germplasm #558

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24 changes: 22 additions & 2 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 @@ -26,7 +26,9 @@
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.ProgramSecuredRole;
import org.breedinginsight.api.auth.ProgramSecuredRoleGroup;
import org.breedinginsight.api.auth.SecurityService;
import org.breedinginsight.api.model.v1.request.query.SearchRequest;
import org.breedinginsight.api.model.v1.response.DataResponse;
import org.breedinginsight.api.model.v1.response.Response;
Expand All @@ -41,7 +43,9 @@
import org.breedinginsight.model.DownloadFile;
import org.breedinginsight.model.GermplasmGenotype;
import org.breedinginsight.model.Program;
import org.breedinginsight.model.ProgramUser;
import org.breedinginsight.services.ProgramService;
import org.breedinginsight.services.ProgramUserService;
import org.breedinginsight.services.brapi.BrAPIEndpointProvider;
import org.breedinginsight.services.exceptions.AuthorizationException;
import org.breedinginsight.services.exceptions.DoesNotExistException;
Expand Down Expand Up @@ -71,6 +75,8 @@ public class BrAPIGermplasmController {

private final BrAPIEndpointProvider brAPIEndpointProvider;

private final SecurityService securityService;
private final ProgramUserService programUserService;

@Inject
public BrAPIGermplasmController(@Property(name = "brapi.server.reference-source") String referenceSource,
Expand All @@ -80,7 +86,9 @@ public BrAPIGermplasmController(@Property(name = "brapi.server.reference-source"
BrAPIGermplasmDAO germplasmDAO,
GenotypeService genoService,
BrAPIEndpointProvider brAPIEndpointProvider,
ProgramService programService) {
ProgramService programService,
SecurityService securityService,
ProgramUserService programUserService) {
this.referenceSource = referenceSource;
this.germplasmService = germplasmService;
this.germplasmQueryMapper = germplasmQueryMapper;
Expand All @@ -89,6 +97,8 @@ public BrAPIGermplasmController(@Property(name = "brapi.server.reference-source"
this.genoService = genoService;
this.brAPIEndpointProvider = brAPIEndpointProvider;
this.programService = programService;
this.securityService = securityService;
this.programUserService = programUserService;
}

// NOTE: bypasses cache and makes api request directly to brapi service
Expand Down Expand Up @@ -196,7 +206,8 @@ private void batchProcessGermplasm(List<BrAPIGermplasm> germplasmList, String pr

@Get("/programs/{programId}" + BrapiVersion.BRAPI_V2 + "/germplasm{?queryParams*}")
@Produces(MediaType.APPLICATION_JSON)
@ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.PROGRAM_SCOPED_ROLES})
@ProgramSecured(roles = {ProgramSecuredRole.SYSTEM_ADMIN, ProgramSecuredRole.READ_ONLY, ProgramSecuredRole.PROGRAM_ADMIN
,ProgramSecuredRole.EXPERIMENTAL_COLLABORATOR })
public HttpResponse<Response<DataResponse<List<BrAPIGermplasm>>>> getGermplasm(
@PathVariable("programId") UUID programId,
@QueryValue @QueryValid(using = GermplasmQueryMapper.class) @Valid GermplasmQuery queryParams) {
Expand All @@ -209,6 +220,15 @@ public HttpResponse<Response<DataResponse<List<BrAPIGermplasm>>>> getGermplasm(
germplasmQueryMapper.setDateDisplayFormat(dateFormatParam);
}

//If experimental collaborator, 403 error should be returned
//Handled this way due to FieldBook field import involving a germplasm endpoint call
Optional<ProgramUser> experimentalCollaborator = programUserService.getIfExperimentalCollaborator(programId, securityService.getUser().getId());
if (experimentalCollaborator.isPresent()) {
log.info("Experimental Collaborator cannot retrieve germplasm");
return HttpResponse.status(HttpStatus.FORBIDDEN, "Experimental Collaborator cannot retrieve germplasm");

}

// Fetch all germplasm in the program unless a list id is supplied to return only germplasm in that collection
List<BrAPIGermplasm> germplasm = queryParams.getListDbId() == null ? germplasmService.getGermplasm(programId) : germplasmService.getGermplasmByList(programId, queryParams.getListDbId());
SearchRequest searchRequest = queryParams.constructSearchRequest();
Expand Down
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