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

Example 11 with Dataset

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

the class GalaxyHistoriesServiceIT method testFilesToLibraryToHistoryRemoteSuccess.

/**
 * Tests successful upload of a file to a Galaxy history through a Library (where files are remote files).
 *
 * @throws UploadException
 * @throws GalaxyDatasetException
 */
@Test
public void testFilesToLibraryToHistoryRemoteSuccess() throws UploadException, GalaxyDatasetException {
    History history = galaxyHistory.newHistoryForWorkflow();
    Library library = buildEmptyLibrary("testFilesToLibraryToHistorySuccess");
    Map<Path, String> datasetsMap = galaxyHistory.filesToLibraryToHistory(Sets.newHashSet(dataFile, dataFile2), FILE_TYPE, history, library, DataStorage.REMOTE);
    assertNotNull(datasetsMap);
    assertEquals(2, datasetsMap.size());
    String datasetId1 = datasetsMap.get(dataFile);
    String datasetId2 = datasetsMap.get(dataFile2);
    Dataset actualDataset1 = localGalaxy.getGalaxyInstanceAdmin().getHistoriesClient().showDataset(history.getId(), datasetId1);
    assertNotNull(actualDataset1);
    Dataset actualDataset2 = localGalaxy.getGalaxyInstanceAdmin().getHistoriesClient().showDataset(history.getId(), datasetId2);
    assertNotNull(actualDataset2);
}

Example 12 with Dataset

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

the class GalaxyHistoriesServiceIT method testFileToHistory.

/**
 * Tests direct upload of a file to a Galaxy history.
 * @throws UploadException
 * @throws GalaxyDatasetException
 */
@Test
public void testFileToHistory() throws UploadException, GalaxyDatasetException {
    History history = galaxyHistory.newHistoryForWorkflow();
    String filename = dataFile.toFile().getName();
    Dataset actualDataset = galaxyHistory.fileToHistory(dataFile, FILE_TYPE, history);
    assertNotNull(actualDataset);
    String dataId = Util.getIdForFileInHistory(filename, history.getId(), localGalaxy.getGalaxyInstanceAdmin());
    assertEquals(dataId, actualDataset.getId());
}

Example 13 with Dataset

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

the class GalaxyHistoriesServiceIT method testGetDatasetForFileInHistoryFailMultipleDatasets.

/**
 * Tests getting a dataset for a file in the history and failing due to multiple datasets.
 * @throws UploadException
 * @throws GalaxyDatasetException
 */
@Test(expected = GalaxyDatasetException.class)
public void testGetDatasetForFileInHistoryFailMultipleDatasets() throws UploadException, GalaxyDatasetException {
    History history = galaxyHistory.newHistoryForWorkflow();
    Dataset dataset1 = galaxyHistory.fileToHistory(dataFile, InputFileType.FASTQ_SANGER, history);
    galaxyHistory.fileToHistory(dataFile, InputFileType.FASTQ_SANGER, history);
    String datasetName = dataset1.getName();
    galaxyHistory.getDatasetForFileInHistory(datasetName, history.getId());
}

Example 14 with Dataset

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

the class GalaxyHistoriesServiceIT method testGetDatasetForFileInHistorySuccess.

/**
 * Tests getting a dataset for a file in the history.
 * @throws UploadException
 * @throws GalaxyDatasetException
 */
@Test
public void testGetDatasetForFileInHistorySuccess() throws UploadException, GalaxyDatasetException {
    History history = galaxyHistory.newHistoryForWorkflow();
    Dataset dataset = galaxyHistory.fileToHistory(dataFile, InputFileType.FASTQ_SANGER, history);
    String datasetName = dataset.getName();
    Dataset actualDataset = galaxyHistory.getDatasetForFileInHistory(datasetName, history.getId());
    assertEquals("actual output dataset id should equal dataset created id", dataset.getId(), actualDataset.getId());
}

Example 15 with Dataset

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

the class GalaxyHistoriesServiceIT method testConstructCollectionFail.

/**
 * Tests out failure to construct a collection of datasets.
 * @throws ExecutionManagerException
 */
@Test(expected = ExecutionManagerException.class)
public void testConstructCollectionFail() throws ExecutionManagerException {
    History history = galaxyHistory.newHistoryForWorkflow();
    Dataset dataset1 = galaxyHistory.fileToHistory(dataFile, FILE_TYPE, history);
    Dataset datasetInvalid = new Dataset();
    datasetInvalid.setId("invalidId");
    assertNotNull(dataset1);
    String collectionName = "collectionInvalid";
    CollectionDescription description = new CollectionDescription();
    description.setName(collectionName);
    description.setCollectionType(DatasetCollectionType.LIST.toString());
    HistoryDatasetElement element1 = new HistoryDatasetElement();
    element1.setId(dataset1.getId());
    element1.setName(dataset1.getName());
    description.addDatasetElement(element1);
    HistoryDatasetElement elementInvalid = new HistoryDatasetElement();
    elementInvalid.setId(datasetInvalid.getId());
    elementInvalid.setName(datasetInvalid.getName());
    description.addDatasetElement(elementInvalid);
    galaxyHistory.constructCollection(description, history);
}