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[BI-2317] System Admin Must Retain Full Read Access To All Programs #405

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Merged
dmeidlin merged 2 commits into from
Sep 20, 2024
Merged

[BI-2317] System Admin Must Retain Full Read Access To All Programs #405

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004179e
fix service method for fetching program user collaborators to allow f…
dmeidlin Sep 18, 2024
899576c
refactor for clarity
dmeidlin Sep 19, 2024
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32 changes: 13 additions & 19 deletions src/main/java/org/breedinginsight/brapi/v2/BrAPIStudiesController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -95,42 +95,36 @@ public HttpResponse<Response<DataResponse<List<BrAPIStudy>>>> getStudies(
@PathVariable("programId") UUID programId,
@QueryValue @QueryValid(using = StudyQueryMapper.class) @Valid StudyQuery queryParams) {
try {
Optional<Program> program = programService.getById(programId);
if (program.isEmpty()) { return HttpResponse.notFound(); }

queryParams.setSortField(studyQueryMapper.getDefaultSortField());
queryParams.setSortOrder(studyQueryMapper.getDefaultSortOrder());
SearchRequest searchRequest = queryParams.constructSearchRequest();
log.debug("fetching studies for program: " + programId);
List<BrAPIStudy> studies;

// If the program user is an experimental collaborator, filter results for only authorized studies.
Optional<ProgramUser> experimentalCollaborator = programUserService.getIfExperimentalCollaborator(programId, securityService.getUser().getId());
// If the program user is an experimental collaborator, filter results.
if (experimentalCollaborator.isPresent()) {
Optional<Program> program = programService.getById(programId);
if (program.isEmpty()) {
return HttpResponse.notFound();
}

List<UUID> experimentIds = experimentalCollaboratorService.getAuthorizedExperimentIds(experimentalCollaborator.get().getId());
studies = studyService.getStudiesByExperimentIds(program.get(), experimentIds)
List<UUID> authorizedExperimentIds = experimentalCollaboratorService.getAuthorizedExperimentIds(experimentalCollaborator.get().getId());
List<BrAPIStudy> authorizedStudies = studyService.getStudiesByExperimentIds(program.get(), authorizedExperimentIds)
.stream()
.peek(this::setDbIds)
.collect(Collectors.toList());
} else {
studies = studyService.getStudies(programId)
return ResponseUtils.getBrapiQueryResponse(authorizedStudies, studyQueryMapper, queryParams, searchRequest);
}

List<BrAPIStudy> studies = studyService.getStudies(programId)
.stream()
.peek(this::setDbIds)
.collect(Collectors.toList());
}

queryParams.setSortField(studyQueryMapper.getDefaultSortField());
queryParams.setSortOrder(studyQueryMapper.getDefaultSortOrder());
SearchRequest searchRequest = queryParams.constructSearchRequest();
return ResponseUtils.getBrapiQueryResponse(studies, studyQueryMapper, queryParams, searchRequest);
} catch (ApiException e) {
log.info(e.getMessage(), e);
return HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error retrieving study");
} catch (IllegalArgumentException e) {
log.info(e.getMessage(), e);
return HttpResponse.status(HttpStatus.UNPROCESSABLE_ENTITY, "Error parsing requested date format");
} catch (DoesNotExistException e) {
log.info(e.getMessage(), e);
return HttpResponse.status(HttpStatus.NOT_FOUND, e.getMessage());
}
}

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18 changes: 8 additions & 10 deletions src/main/java/org/breedinginsight/brapi/v2/BrAPITrialsController.java
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Expand Up @@ -95,23 +95,21 @@ public HttpResponse<Response<DataResponse<List<BrAPITrial>>>> getExperiments(
@PathVariable("programId") UUID programId,
@QueryValue @QueryValid(using = ExperimentQueryMapper.class) @Valid ExperimentQuery queryParams) {
try {
List<BrAPITrial> experiments = new ArrayList<>();
Optional<Program> program = programService.getById(programId);
if (program.isEmpty()) { return HttpResponse.notFound(); }

SearchRequest searchRequest = queryParams.constructSearchRequest();
log.debug("fetching trials for program: " + programId);

// If the program user is an experimental collaborator, filter results for only authorized experiments.
Optional<ProgramUser> experimentalCollaborator = programUserService.getIfExperimentalCollaborator(programId, securityService.getUser().getId());
// If the program user is an experimental collaborator, filter results.
if (experimentalCollaborator.isPresent()) {
Optional<Program> program = programService.getById(programId);
if (program.isEmpty()) {
return HttpResponse.notFound();
}
List<UUID> experimentIds = experimentalCollaboratorService.getAuthorizedExperimentIds(experimentalCollaborator.get().getId());
experiments = experimentService.getTrialsByExperimentIds(program.get(), experimentIds).stream().peek(this::setDbIds).collect(Collectors.toList());
} else {
experiments = experimentService.getExperiments(programId).stream().peek(this::setDbIds).collect(Collectors.toList());
List<BrAPITrial> authorizedExperiments = experimentService.getTrialsByExperimentIds(program.get(), experimentIds).stream().peek(this::setDbIds).collect(Collectors.toList());
return ResponseUtils.getBrapiQueryResponse(authorizedExperiments, experimentQueryMapper, queryParams, searchRequest);
}

SearchRequest searchRequest = queryParams.constructSearchRequest();
List<BrAPITrial> experiments = experimentService.getExperiments(programId).stream().peek(this::setDbIds).collect(Collectors.toList());
return ResponseUtils.getBrapiQueryResponse(experiments, experimentQueryMapper, queryParams, searchRequest);
} catch (ApiException e) {
log.info(e.getMessage(), e);
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17 changes: 7 additions & 10 deletions src/main/java/org/breedinginsight/services/ProgramUserService.java
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@mlm483 mlm483 Sep 19, 2024

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This is much nicer, thanks.

Original file line number Diff line number Diff line change
Expand Up @@ -281,16 +281,13 @@ public boolean existsAndActive(UUID programId, UUID userId) {
* @param userId the user ID.
* @return an Optional that unwraps to a program user if it is an Experimental Collaborator, Optional.empty() otherwise.
*/
public Optional<ProgramUser> getIfExperimentalCollaborator(UUID programId, UUID userId) throws DoesNotExistException {
Optional<ProgramUser> programUser = getProgramUserbyId(programId, userId);
if (programUser.isEmpty()) {
throw new DoesNotExistException("Program User does not exist");
}
boolean isExperimentalCollaborator = programUser.get().getRoles().stream().anyMatch(x -> ProgramSecuredRole.getEnum(x.getDomain()).equals(ProgramSecuredRole.EXPERIMENTAL_COLLABORATOR));
if (isExperimentalCollaborator) {
return programUser;
}
return Optional.empty();
public Optional<ProgramUser> getIfExperimentalCollaborator(UUID programId, UUID userId) {
return getProgramUserbyId(programId, userId)
.flatMap(user -> user.getRoles().stream()
.anyMatch(role -> ProgramSecuredRole.getEnum(role.getDomain()).equals(ProgramSecuredRole.EXPERIMENTAL_COLLABORATOR))
? Optional.of(user)
: Optional.empty()
);
}

public List<ProgramUser> getProgramUsersByRole(UUID programId, UUID roleId) throws DoesNotExistException {
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