Examples with ServerUnavailableException org.pmiops.workbench.exceptions.ServerUnavailableException used on opensource projects

Example 1 with ServerUnavailableException

use of org.pmiops.workbench.exceptions.ServerUnavailableException in project workbench by all-of-us.

the class WorkspaceServiceImpl method updateUserRoles.

@Override
public Workspace updateUserRoles(Workspace workspace, Set<WorkspaceUserRole> userRoleSet) {
    Map<Long, WorkspaceUserRole> userRoleMap = new HashMap<Long, WorkspaceUserRole>();
    for (WorkspaceUserRole userRole : userRoleSet) {
        userRole.setWorkspace(workspace);
        userRoleMap.put(userRole.getUser().getUserId(), userRole);
    }
    ArrayList<WorkspaceACLUpdate> updateACLRequestList = new ArrayList<WorkspaceACLUpdate>();
    Iterator<WorkspaceUserRole> dbUserRoles = workspace.getWorkspaceUserRoles().iterator();
    while (dbUserRoles.hasNext()) {
        WorkspaceUserRole currentUserRole = dbUserRoles.next();
        WorkspaceUserRole mapValue = userRoleMap.get(currentUserRole.getUser().getUserId());
        if (mapValue != null) {
            currentUserRole.setRole(mapValue.getRole());
            userRoleMap.remove(currentUserRole.getUser().getUserId());
        } else {
            // This is how to remove a user from the FireCloud ACL:
            // Pass along an update request with NO ACCESS as the given access level.
            WorkspaceACLUpdate removedUser = new WorkspaceACLUpdate();
            removedUser.setEmail(currentUserRole.getUser().getEmail());
            removedUser.setCanCompute(false);
            removedUser.setCanShare(false);
            removedUser.setAccessLevel(WorkspaceAccessLevel.NO_ACCESS.toString());
            updateACLRequestList.add(removedUser);
            dbUserRoles.remove();
        }
    }
    for (Entry<Long, WorkspaceUserRole> remainingRole : userRoleMap.entrySet()) {
        workspace.getWorkspaceUserRoles().add(remainingRole.getValue());
    }
    for (WorkspaceUserRole currentWorkspaceUser : workspace.getWorkspaceUserRoles()) {
        WorkspaceACLUpdate currentUpdate = new WorkspaceACLUpdate();
        currentUpdate.setEmail(currentWorkspaceUser.getUser().getEmail());
        currentUpdate.setCanCompute(false);
        if (currentWorkspaceUser.getRole() == WorkspaceAccessLevel.OWNER) {
            currentUpdate.setCanShare(true);
            currentUpdate.setAccessLevel(WorkspaceAccessLevel.OWNER.toString());
        } else if (currentWorkspaceUser.getRole() == WorkspaceAccessLevel.WRITER) {
            currentUpdate.setCanShare(false);
            currentUpdate.setAccessLevel(WorkspaceAccessLevel.WRITER.toString());
        } else {
            currentUpdate.setCanShare(false);
            currentUpdate.setAccessLevel(WorkspaceAccessLevel.READER.toString());
        }
        updateACLRequestList.add(currentUpdate);
    }
    try {
        WorkspaceACLUpdateResponseList fireCloudResponse = fireCloudService.updateWorkspaceACL(workspace.getWorkspaceNamespace(), workspace.getFirecloudName(), updateACLRequestList);
        if (fireCloudResponse.getUsersNotFound().size() != 0) {
            String usersNotFound = "";
            for (int i = 0; i < fireCloudResponse.getUsersNotFound().size(); i++) {
                if (i > 0) {
                    usersNotFound += ", ";
                }
                usersNotFound += fireCloudResponse.getUsersNotFound().get(i).getEmail();
            }
            throw new BadRequestException(usersNotFound);
        }
    } catch (ApiException e) {
        if (e.getCode() == 400) {
            throw new BadRequestException(e.getResponseBody());
        } else if (e.getCode() == 404) {
            throw new NotFoundException("Workspace not found.");
        } else if (e.getCode() == 500) {
            throw new ServerErrorException(e);
        } else {
            throw new ServerUnavailableException(e);
        }
    }
    return this.saveWithLastModified(workspace);
}

Example 2 with ServerUnavailableException

use of org.pmiops.workbench.exceptions.ServerUnavailableException in project workbench by all-of-us.

the class CohortMaterializationService method materializeCohort.

public MaterializeCohortResponse materializeCohort(@Nullable CohortReview cohortReview, SearchRequest searchRequest, MaterializeCohortRequest request) {
    long offset = 0L;
    FieldSet fieldSet = request.getFieldSet();
    List<CohortStatus> statusFilter = request.getStatusFilter();
    String paginationToken = request.getPageToken();
    int pageSize = request.getPageSize();
    // TODO: add CDR version ID here
    Object[] paginationParameters = new Object[] { searchRequest, statusFilter };
    if (paginationToken != null) {
        PaginationToken token = PaginationToken.fromBase64(paginationToken);
        if (token.matchesParameters(paginationParameters)) {
            offset = token.getOffset();
        } else {
            throw new BadRequestException(String.format("Use of pagination token %s with new parameter values", paginationToken));
        }
    }
    int limit = pageSize + 1;
    if (statusFilter == null) {
        statusFilter = ALL_STATUSES;
    }
    ParticipantCriteria criteria;
    MaterializeCohortResponse response = new MaterializeCohortResponse();
    if (statusFilter.contains(CohortStatus.NOT_REVIEWED)) {
        Set<Long> participantIdsToExclude;
        if (statusFilter.size() < CohortStatus.values().length) {
            // Find the participant IDs that have statuses which *aren't* in the filter.
            Set<CohortStatus> statusesToExclude = Sets.difference(ImmutableSet.copyOf(CohortStatus.values()), ImmutableSet.copyOf(statusFilter));
            participantIdsToExclude = getParticipantIdsWithStatus(cohortReview, ImmutableList.copyOf(statusesToExclude));
        } else {
            participantIdsToExclude = ImmutableSet.of();
        }
        criteria = new ParticipantCriteria(searchRequest, participantIdsToExclude);
    } else {
        Set<Long> participantIds = getParticipantIdsWithStatus(cohortReview, statusFilter);
        if (participantIds.isEmpty()) {
            // return an empty response.
            return response;
        }
        criteria = new ParticipantCriteria(participantIds);
    }
    TableQueryAndConfig tableQueryAndConfig = getTableQueryAndConfig(fieldSet);
    QueryJobConfiguration jobConfiguration = fieldSetQueryBuilder.buildQuery(criteria, tableQueryAndConfig, limit, offset);
    QueryResult result;
    try {
        result = bigQueryService.executeQuery(bigQueryService.filterBigQueryConfig(jobConfiguration));
    } catch (BigQueryException e) {
        if (e.getCode() == HttpServletResponse.SC_SERVICE_UNAVAILABLE) {
            throw new ServerUnavailableException("BigQuery was temporarily unavailable, try again later", e);
        } else if (e.getCode() == HttpServletResponse.SC_FORBIDDEN) {
            throw new ForbiddenException("Access to the CDR is denied", e);
        } else {
            throw new ServerErrorException(String.format("An unexpected error occurred materializing the cohort with " + "query = (%s), params = (%s)", jobConfiguration.getQuery(), jobConfiguration.getNamedParameters()), e);
        }
    }
    Map<String, Integer> rm = bigQueryService.getResultMapper(result);
    int numResults = 0;
    boolean hasMoreResults = false;
    ArrayList<Object> results = new ArrayList<>();
    for (List<FieldValue> row : result.iterateAll()) {
        if (numResults == pageSize) {
            hasMoreResults = true;
            break;
        }
        Map<String, Object> resultMap = fieldSetQueryBuilder.extractResults(tableQueryAndConfig, row);
        results.add(resultMap);
        numResults++;
    }
    response.setResults(results);
    if (hasMoreResults) {
        // TODO: consider pagination based on cursor / values rather than offset
        PaginationToken token = PaginationToken.of(offset + pageSize, paginationParameters);
        response.setNextPageToken(token.toBase64());
    }
    return response;
}