Examples with InvalidFileRefException bio.terra.service.dataset.exception.InvalidFileRefException used on opensource projects

Example 1 with InvalidFileRefException

use of bio.terra.service.dataset.exception.InvalidFileRefException in project jade-data-repo by DataBiosphere.

the class IngestValidateRefsStep method doStep.

@Override
public StepResult doStep(FlightContext context) throws InterruptedException {
    Dataset dataset = IngestUtils.getDataset(context, datasetService);
    Table table = IngestUtils.getDatasetTable(context, dataset);
    String stagingTableName = IngestUtils.getStagingTableName(context);
    // For each fileref column, scan the staging table and build an array of file ids
    // Then probe the file system to validate that the file exists and is part
    // of this dataset. We check all ids and return one complete error.
    List<String> invalidRefIds = new ArrayList<>();
    for (Column column : table.getColumns()) {
        if (StringUtils.equalsIgnoreCase(column.getType(), "FILEREF")) {
            List<String> refIdArray = bigQueryPdao.getRefIds(dataset, stagingTableName, column);
            List<String> badRefIds = fileDao.validateRefIds(dataset, refIdArray);
            if (badRefIds != null) {
                invalidRefIds.addAll(badRefIds);
            }
        }
    }
    int invalidIdCount = invalidRefIds.size();
    if (invalidIdCount != 0) {
        // Made a string buffer to appease findbugs; it saw + in the loop and said "bad!"
        StringBuffer errorMessage = new StringBuffer("Invalid file ids found during ingest (");
        List<String> errorDetails = new ArrayList<>();
        int count = 0;
        for (String badId : invalidRefIds) {
            errorDetails.add(badId);
            count++;
            if (count > MAX_ERROR_REF_IDS) {
                errorMessage.append(MAX_ERROR_REF_IDS + "out of ");
                break;
            }
        }
        errorMessage.append(invalidIdCount + " returned in details)");
        throw new InvalidFileRefException(errorMessage.toString(), errorDetails);
    }
    return StepResult.getStepResultSuccess();
}