use of org.pmiops.workbench.cohortbuilder.ParticipantCriteria 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;
}
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