Examples with GalaxyDatasetNotFoundException ca.corefacility.bioinformatics.irida.exceptions.galaxy.GalaxyDatasetNotFoundException used on opensource projects

Example 1 with GalaxyDatasetNotFoundException

use of ca.corefacility.bioinformatics.irida.exceptions.galaxy.GalaxyDatasetNotFoundException in project irida by phac-nml.

the class GalaxyHistoriesService method getDatasetForFileInHistory.

/**
 * Gets a Dataset object for a file with the given name in the given history.
 * @param filename  The name of the file to get a Dataset object for.
 * @param historyId  The history id to look for the dataset.
 * @return The corresponding dataset for the given file name.
 * @throws GalaxyDatasetException If there was an issue when searching for a dataset.
 */
public Dataset getDatasetForFileInHistory(String filename, String historyId) throws GalaxyDatasetException {
    checkNotNull(filename, "filename is null");
    checkNotNull(historyId, "historyId is null");
    List<HistoryContents> historyContentsList = historiesClient.showHistoryContents(historyId);
    List<HistoryContents> matchingHistoryContents = historyContentsList.stream().filter((historyContents) -> filename.equals(historyContents.getName())).collect(Collectors.toList());
    // if more than one matching history item
    if (matchingHistoryContents.size() > 1) {
        String historyIds = "[";
        for (HistoryContents content : matchingHistoryContents) {
            historyIds += content.getId() + ",";
        }
        historyIds += "]";
        throw new GalaxyDatasetException("Found " + matchingHistoryContents.size() + " datasets for file " + filename + ": " + historyIds);
    } else if (matchingHistoryContents.size() == 1) {
        String dataId = matchingHistoryContents.get(0).getId();
        if (dataId != null) {
            Dataset dataset = historiesClient.showDataset(historyId, dataId);
            if (dataset != null) {
                return dataset;
            }
        }
    }
    throw new GalaxyDatasetNotFoundException("dataset for file " + filename + " not found in Galaxy history " + historyId);
}