private List<String> getSamplesFromIndividuals(MyResources<Individual> resource) throws CatalogDBException { // Look for all the samples belonging to the individual Query query = new Query() .append(IndividualDBAdaptor.QueryParams.STUDY_UID.key(), resource.getStudy().getUid()) .append(IndividualDBAdaptor.QueryParams.UID.key(), resource.getResourceList().stream().map(Individual::getUid) .collect(Collectors.toList())); QueryResult<Individual> individualQueryResult = individualDBAdaptor.get(query, new QueryOptions(QueryOptions.INCLUDE, IndividualDBAdaptor.QueryParams.SAMPLES.key())); List<String> sampleIds = new ArrayList<>(); for (Individual individual : individualQueryResult.getResult()) { sampleIds.addAll(individual.getSamples().stream().map(Sample::getId).collect(Collectors.toList())); } return sampleIds; }
authorizationManager.checkCanAssignOrSeePermissions(resource.getStudy().getUid(), resource.getUser()); checkMembers(resource.getStudy().getUid(), members); .map(String::valueOf) .collect(Collectors.toList()); return authorizationManager.setAcls(resource.getStudy().getUid(), resource.getResourceList().stream() .map(Panel::getUid) .collect(Collectors.toList()), members, permissions, allPanelPermissions, Entity.PANEL); case ADD: return authorizationManager.addAcls(resource.getStudy().getUid(), resource.getResourceList().stream() .map(Panel::getUid) .collect(Collectors.toList()), members, permissions, Entity.PANEL);
authorizationManager.checkCanAssignOrSeePermissions(resource.getStudy().getUid(), resource.getUser()); checkMembers(resource.getStudy().getUid(), members); .map(String::valueOf) .collect(Collectors.toList()); return authorizationManager.setAcls(resource.getStudy().getUid(), resource.getResourceList().stream().map(Family::getUid) .collect(Collectors.toList()), members, permissions, allFamilyPermissions, Entity.FAMILY); case ADD: return authorizationManager.addAcls(resource.getStudy().getUid(), resource.getResourceList().stream().map(Family::getUid) .collect(Collectors.toList()), members, permissions, Entity.FAMILY); case REMOVE:
.append(JobDBAdaptor.QueryParams.STUDY_UID.key(), resource.getStudy().getUid()) .append(JobDBAdaptor.QueryParams.INPUT_UID.key(), resourceList) .append(JobDBAdaptor.QueryParams.STATUS_NAME.key(), Constants.ALL_STATUS); .append(JobDBAdaptor.QueryParams.STUDY_UID.key(), resource.getStudy().getUid()) .append(JobDBAdaptor.QueryParams.OUTPUT_UID.key(), resourceList) .append(JobDBAdaptor.QueryParams.STATUS_NAME.key(), Constants.ALL_STATUS); .append(JobDBAdaptor.QueryParams.STUDY_UID.key(), resource.getStudy().getUid()) .append(JobDBAdaptor.QueryParams.OUT_DIR_UID.key(), resourceList) .append(JobDBAdaptor.QueryParams.STATUS_NAME.key(), Constants.ALL_STATUS); .append(FileDBAdaptor.QueryParams.STUDY_UID.key(), resource.getStudy().getUid()) .append(FileDBAdaptor.QueryParams.STATUS_NAME.key(), GET_NON_DELETED_FILES); QueryResult<File> fileQueryResult = fileDBAdaptor.get(query, QueryOptions.empty());
MyResources<File> resource = getUids(fileList, studyStr, sessionId); List<File> fileFolderIdList = resource.getResourceList(); long studyId = resource.getStudy().getUid(); String userId = resource.getUser(); outDir = smartResolutor(resource.getStudy().getUid(), outDirPath, resource.getUser()); } catch (CatalogException e) { logger.warn("'{}' does not exist. Trying to create the output directory.", outDirPath); attributes.put(IndexDaemon.INDEX_TYPE, indexDaemonType); attributes.putIfNotNull(Job.OPENCGA_OUTPUT_DIR, outDirPath); attributes.putIfNotNull(Job.OPENCGA_STUDY, resource.getStudy().getFqn());
authorizationManager.checkCanAssignOrSeePermissions(resource.getStudy().getUid(), resource.getUser()); checkMembers(resource.getStudy().getUid(), members); .map(String::valueOf) .collect(Collectors.toList()); queryResults = authorizationManager.setAcls(resource.getStudy().getUid(), resource.getResourceList().stream() .map(Sample::getUid).collect(Collectors.toList()), members, permissions, allSamplePermissions, Entity.SAMPLE); queryResults = authorizationManager.addAcls(resource.getStudy().getUid(), resource.getResourceList().stream() .map(Sample::getUid).collect(Collectors.toList()), members, permissions, Entity.SAMPLE); if (sampleAclParams.isPropagate()) {
authorizationManager.checkCanAssignOrSeePermissions(resource.getStudy().getUid(), resource.getUser()); checkMembers(resource.getStudy().getUid(), members); .map(String::valueOf) .collect(Collectors.toList()); queryResults = authorizationManager.setAcls(resource.getStudy().getUid(), resource.getResourceList().stream() .map(Individual::getUid).collect(Collectors.toList()), members, permissions, allIndividualPermissions, Entity.INDIVIDUAL); queryResults = authorizationManager.addAcls(resource.getStudy().getUid(), resource.getResourceList().stream() .map(Individual::getUid).collect(Collectors.toList()), members, permissions, Entity.INDIVIDUAL); if (aclParams.isPropagate()) {
authorizationManager.checkCanAssignOrSeePermissions(resource.getStudy().getUid(), resource.getUser()); checkMembers(resource.getStudy().getUid(), members); .map(String::valueOf) .collect(Collectors.toList()); return authorizationManager.setAcls(resource.getStudy().getUid(), resource.getResourceList().stream().map(File::getUid) .collect(Collectors.toList()), members, permissions, allFilePermissions, Entity.FILE); case ADD: return authorizationManager.addAcls(resource.getStudy().getUid(), resource.getResourceList().stream().map(File::getUid) .collect(Collectors.toList()), members, permissions, Entity.FILE); case REMOVE:
authorizationManager.checkCanAssignOrSeePermissions(resource.getStudy().getUid(), resource.getUser()); checkMembers(resource.getStudy().getUid(), members); .map(String::valueOf) .collect(Collectors.toList()); return authorizationManager.setAcls(resource.getStudy().getUid(), resource.getResourceList().stream() .map(ClinicalAnalysis::getUid) .collect(Collectors.toList()), members, permissions, allClinicalPermissions, Entity.CLINICAL_ANALYSIS); case ADD: return authorizationManager.addAcls(resource.getStudy().getUid(), resource.getResourceList().stream() .map(ClinicalAnalysis::getUid) .collect(Collectors.toList()), members, permissions, Entity.CLINICAL_ANALYSIS);
authorizationManager.checkCanAssignOrSeePermissions(resource.getStudy().getUid(), resource.getUser()); checkMembers(resource.getStudy().getUid(), members); .map(String::valueOf) .collect(Collectors.toList()); return authorizationManager.setAcls(resource.getStudy().getUid(), resource.getResourceList().stream().map(Job::getUid) .collect(Collectors.toList()), members, permissions, allJobPermissions, Entity.JOB); case ADD: return authorizationManager.addAcls(resource.getStudy().getUid(), resource.getResourceList().stream().map(Job::getUid) .collect(Collectors.toList()), members, permissions, Entity.JOB); case REMOVE:
authorizationManager.checkCanAssignOrSeePermissions(resource.getStudy().getUid(), resource.getUser()); members = Collections.emptyList(); checkMembers(resource.getStudy().getUid(), members); authorizationManager.checkNotAssigningPermissionsToAdminsGroup(members); .map(String::valueOf) .collect(Collectors.toList()); return authorizationManager.setAcls(resource.getStudy().getUid(), resource.getResourceList().stream().map(Cohort::getUid) .collect(Collectors.toList()), members, permissions, allCohortPermissions, Entity.COHORT); case ADD: return authorizationManager.addAcls(resource.getStudy().getUid(), resource.getResourceList().stream().map(Cohort::getUid) .collect(Collectors.toList()), members, permissions, Entity.COHORT);
AbstractManager.MyResources<File> resource = catalogManager.getFileManager().getUids(fileIdStrs, studyIdStr, sessionId); files = resource.getResourceList(); study = resource.getStudy();