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

Example 1 with GalaxyDatasetException

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

the class AnalysisWorkspaceServiceGalaxyTest method testGetAnalysisResultsFail.

/**
 * Tests failure to get analysis results from Galaxy due to failure to get a
 * dataset
 *
 * @throws IridaWorkflowNotFoundException
 * @throws IOException
 * @throws ExecutionManagerException
 * @throws IridaWorkflowAnalysisTypeException
 */
@Test(expected = GalaxyDatasetException.class)
public void testGetAnalysisResultsFail() throws IridaWorkflowNotFoundException, IridaWorkflowAnalysisTypeException, ExecutionManagerException, IOException {
    submission = AnalysisSubmission.builder(workflowId).name("my analysis").inputFiles(singleInputFiles).referenceFile(referenceFile).build();
    submission.setRemoteWorkflowId(WORKFLOW_ID);
    submission.setRemoteAnalysisId(HISTORY_ID);
    when(iridaWorkflowsService.getIridaWorkflow(workflowId)).thenReturn(iridaWorkflowSingle);
    when(galaxyHistoriesService.getDatasetForFileInHistory(output1Filename, HISTORY_ID)).thenThrow(new GalaxyDatasetException());
    workflowPreparation.getAnalysisResults(submission);
}

Example 2 with GalaxyDatasetException

use of ca.corefacility.bioinformatics.irida.exceptions.galaxy.GalaxyDatasetException 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);
}