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

Example 11 with Library

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

the class GalaxyHistoriesServiceIT method testFilesToLibraryToHistoryFailNoLibrary.

/**
 * Tests failure to upload a list of files to a Galaxy history through a Library (no library).
 *
 * @throws UploadException
 * @throws GalaxyDatasetException
 */
@Test(expected = UploadException.class)
public void testFilesToLibraryToHistoryFailNoLibrary() throws UploadException, GalaxyDatasetException {
    History history = galaxyHistory.newHistoryForWorkflow();
    Library library = buildEmptyLibrary("testFilesToLibraryToHistoryFail");
    library.setId("invalid");
    galaxyHistory.filesToLibraryToHistory(Sets.newHashSet(dataFile), FILE_TYPE, history, library, DataStorage.LOCAL);
}

Example 12 with Library

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

the class GalaxyLibrariesServiceIT method testDeleteLibrarySuccess.

/**
 * Tests successfully deleting a data library.
 *
 * @throws ExecutionManagerException
 */
@Test
public void testDeleteLibrarySuccess() throws ExecutionManagerException {
    Library library = buildEmptyLibrary("testDeleteLibrarySuccess");
    Map<Path, String> datasetsMap = galaxyLibrariesService.filesToLibraryWait(ImmutableSet.of(dataFile), FILE_TYPE, library, DataStorage.LOCAL);
    String datasetId = datasetsMap.get(dataFile);
    assertNotNull("Dataset not uploaded correctly", librariesClient.showDataset(library.getId(), datasetId));
    // Note: I cannot do much more to test deleting a library beyond making
    // sure no exception is thrown.
    // The Galaxy API still provides access to libraries even when deleted,
    // but sets a deleted status.
    // The status is not available in blend4j right now.
    galaxyLibrariesService.deleteLibrary(library.getId());
}

Example 13 with Library

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

the class GalaxyLibrariesServiceIT method testFilesToLibraryWaitSuccess.

/**
 * Tests successful upload of a list of files to a Galaxy Library.
 *
 * @throws UploadException
 * @throws GalaxyDatasetException
 */
@Test
public void testFilesToLibraryWaitSuccess() throws UploadException, GalaxyDatasetException {
    Library library = buildEmptyLibrary("testFilesToLibraryWaitSuccess");
    Map<Path, String> datasetsMap = galaxyLibrariesService.filesToLibraryWait(Sets.newHashSet(dataFile, dataFile2), FILE_TYPE, library, DataStorage.LOCAL);
    assertNotNull(datasetsMap);
    assertEquals(2, datasetsMap.size());
    String datasetId1 = datasetsMap.get(dataFile);
    String datasetId2 = datasetsMap.get(dataFile2);
    LibraryDataset actualDataset1 = localGalaxy.getGalaxyInstanceAdmin().getLibrariesClient().showDataset(library.getId(), datasetId1);
    assertNotNull(actualDataset1);
    LibraryDataset actualDataset2 = localGalaxy.getGalaxyInstanceAdmin().getLibrariesClient().showDataset(library.getId(), datasetId2);
    assertNotNull(actualDataset2);
}

Example 14 with Library

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

the class GalaxyLibrariesServiceIT method testFileToLibraryFailure.

/**
 * Tests failure to upload of a file to a Galaxy Library.
 *
 * @throws UploadException
 * @throws GalaxyDatasetException
 */
@Test(expected = UploadException.class)
public void testFileToLibraryFailure() throws UploadException, GalaxyDatasetException {
    Library library = buildEmptyLibrary("testFileToLibraryFailure");
    library.setId("invalid");
    galaxyLibrariesService.fileToLibrary(dataFile, FILE_TYPE, library, DataStorage.LOCAL);
}

Example 15 with Library

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

the class GalaxyLibrariesServiceIT method testFilesToLibraryWaitFailTimeout.

/**
 * Tests failure to upload to a library due to a timeout issue.
 *
 * @throws UploadException
 * @throws GalaxyDatasetException
 */
@Test(expected = UploadTimeoutException.class)
public void testFilesToLibraryWaitFailTimeout() throws UploadException, GalaxyDatasetException {
    galaxyLibrariesService = new GalaxyLibrariesService(librariesClient, 1, 2, 1);
    Library library = buildEmptyLibrary("testFilesToLibraryWaitFailTimeout");
    galaxyLibrariesService.filesToLibraryWait(Sets.newHashSet(dataFile, dataFile2), FILE_TYPE, library, DataStorage.LOCAL);
}