Examples with HistoryContents com.github.jmchilton.blend4j.galaxy.beans.HistoryContents used on opensource projects

Example 6 with HistoryContents

use of com.github.jmchilton.blend4j.galaxy.beans.HistoryContents 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);
}

Example 7 with HistoryContents

use of com.github.jmchilton.blend4j.galaxy.beans.HistoryContents in project irida by phac-nml.

the class Util method getIdForFileInHistory.

/**
 * Given a file within a Galaxy history, finds the id of that file.
 * @param filename  The name of the file within a history.
 * @param historyId  The id of the history.
 * @param galaxyInstance  The GalaxyInstance to use for connections.
 * @return  The id of the file in this history, or null if no such file.
 */
public static String getIdForFileInHistory(String filename, String historyId, GalaxyInstance galaxyInstance) {
    String dataId = null;
    List<HistoryContents> historyContentsList = galaxyInstance.getHistoriesClient().showHistoryContents(historyId);
    for (HistoryContents contents : historyContentsList) {
        if (filename.equals(contents.getName())) {
            dataId = contents.getId();
            break;
        }
    }
    return dataId;
}

Example 8 with HistoryContents

use of com.github.jmchilton.blend4j.galaxy.beans.HistoryContents in project irida by phac-nml.

the class GalaxyHistoriesServiceTest method testFileToHistoryFailFindDataset.

/**
 * Tests failing to find a Dataset object after uploading a file to a history.
 * @throws UploadException
 * @throws GalaxyDatasetException
 */
@Test(expected = GalaxyDatasetNotFoundException.class)
public void testFileToHistoryFailFindDataset() throws UploadException, GalaxyDatasetException {
    String filename = dataFile.toFile().getName();
    History createdHistory = new History();
    createdHistory.setId(HISTORY_ID);
    List<HistoryContents> historyContentsList = buildHistoryContentsList(filename, DATA_ID);
    when(toolsClient.uploadRequest(any(FileUploadRequest.class))).thenReturn(okayResponse);
    when(historiesClient.showHistoryContents(HISTORY_ID)).thenReturn(historyContentsList);
    galaxyHistory.fileToHistory(dataFile, FILE_TYPE, createdHistory);
}

Example 9 with HistoryContents

use of com.github.jmchilton.blend4j.galaxy.beans.HistoryContents in project irida by phac-nml.

the class GalaxyHistoriesServiceTest method testFileToHistorySuccess.

/**
 * Tests uploading a file to a history.
 * @throws UploadException
 * @throws GalaxyDatasetException
 */
@Test
public void testFileToHistorySuccess() throws UploadException, GalaxyDatasetException {
    String filename = dataFile.toFile().getName();
    History createdHistory = new History();
    Dataset dataset = new Dataset();
    createdHistory.setId(HISTORY_ID);
    List<HistoryContents> historyContentsList = buildHistoryContentsList(filename, DATA_ID);
    when(toolsClient.uploadRequest(any(FileUploadRequest.class))).thenReturn(okayResponse);
    when(historiesClient.showHistoryContents(HISTORY_ID)).thenReturn(historyContentsList);
    when(historiesClient.showDataset(HISTORY_ID, DATA_ID)).thenReturn(dataset);
    assertEquals(dataset, galaxyHistory.fileToHistory(dataFile, FILE_TYPE, createdHistory));
}

Example 10 with HistoryContents

use of com.github.jmchilton.blend4j.galaxy.beans.HistoryContents in project irida by phac-nml.

the class GalaxyHistoriesServiceTest method buildHistoryContentsList.

private List<HistoryContents> buildHistoryContentsList(String filename, String id) {
    HistoryContents datasetHistoryContent = new HistoryContents();
    datasetHistoryContent.setName(filename);
    datasetHistoryContent.setId(id);
    List<HistoryContents> datasetHistoryContents = new ArrayList<HistoryContents>();
    datasetHistoryContents.add(datasetHistoryContent);
    return Arrays.asList(datasetHistoryContent);
}