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Example 6 with GalaxyLibrariesService

use of ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyLibrariesService 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);
}
Also used : Library(com.github.jmchilton.blend4j.galaxy.beans.Library) GalaxyLibrariesService(ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyLibrariesService) Test(org.junit.Test)

Example 7 with GalaxyLibrariesService

use of ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyLibrariesService in project irida by phac-nml.

the class AnalysisWorkspaceServiceGalaxyIT method setup.

/**
 * Sets up variables for testing.
 *
 * @throws URISyntaxException
 * @throws IOException
 * @throws IridaWorkflowLoadException
 */
@Before
public void setup() throws URISyntaxException, IOException, IridaWorkflowLoadException {
    Assume.assumeFalse(WindowsPlatformCondition.isWindows());
    Path sequenceFilePathReal = Paths.get(DatabaseSetupGalaxyITService.class.getResource("testData1.fastq").toURI());
    Path referenceFilePathReal = Paths.get(DatabaseSetupGalaxyITService.class.getResource("testReference.fasta").toURI());
    Path tempDir = Files.createTempDirectory(rootTempDirectory, "workspaceServiceGalaxyTest");
    sequenceFilePathA = tempDir.resolve("testDataA_R1_001.fastq");
    Files.copy(sequenceFilePathReal, sequenceFilePathA, StandardCopyOption.REPLACE_EXISTING);
    sequenceFilePath2A = tempDir.resolve("testDataA_R2_001.fastq");
    Files.copy(sequenceFilePathReal, sequenceFilePath2A, StandardCopyOption.REPLACE_EXISTING);
    sequenceFilePathB = tempDir.resolve("testDataB_R1_001.fastq");
    Files.copy(sequenceFilePathReal, sequenceFilePathB, StandardCopyOption.REPLACE_EXISTING);
    sequenceFilePath2B = tempDir.resolve("testDataB_R2_001.fastq");
    Files.copy(sequenceFilePathReal, sequenceFilePath2B, StandardCopyOption.REPLACE_EXISTING);
    sequenceFilePath3 = tempDir.resolve("testData3_R1_001.fastq");
    Files.copy(sequenceFilePathReal, sequenceFilePath3, StandardCopyOption.REPLACE_EXISTING);
    referenceFilePath = Files.createTempFile("testReference", ".fasta");
    Files.delete(referenceFilePath);
    Files.copy(referenceFilePathReal, referenceFilePath);
    singleFileSet = Sets.newHashSet(new SingleEndSequenceFile(new SequenceFile(sequenceFilePathA)));
    GalaxyInstance galaxyInstanceAdmin = localGalaxy.getGalaxyInstanceAdmin();
    HistoriesClient historiesClient = galaxyInstanceAdmin.getHistoriesClient();
    ToolsClient toolsClient = galaxyInstanceAdmin.getToolsClient();
    LibrariesClient librariesClient = galaxyInstanceAdmin.getLibrariesClient();
    GalaxyLibrariesService galaxyLibrariesService = new GalaxyLibrariesService(librariesClient, LIBRARY_POLLING_TIME, LIBRARY_TIMEOUT, 1);
    galaxyHistoriesService = new GalaxyHistoriesService(historiesClient, toolsClient, galaxyLibrariesService);
    pairSequenceFiles1A = new ArrayList<>();
    pairSequenceFiles1A.add(sequenceFilePathA);
    pairSequenceFiles2A = new ArrayList<>();
    pairSequenceFiles2A.add(sequenceFilePath2A);
    pairSequenceFiles1AB = new ArrayList<>();
    pairSequenceFiles1AB.add(sequenceFilePathA);
    pairSequenceFiles1AB.add(sequenceFilePathB);
    pairSequenceFiles2AB = new ArrayList<>();
    pairSequenceFiles2AB.add(sequenceFilePath2A);
    pairSequenceFiles2AB.add(sequenceFilePath2B);
}
Also used : Path(java.nio.file.Path) GalaxyHistoriesService(ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyHistoriesService) SequenceFile(ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile) SingleEndSequenceFile(ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile) ToolsClient(com.github.jmchilton.blend4j.galaxy.ToolsClient) LibrariesClient(com.github.jmchilton.blend4j.galaxy.LibrariesClient) GalaxyInstance(com.github.jmchilton.blend4j.galaxy.GalaxyInstance) SingleEndSequenceFile(ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile) HistoriesClient(com.github.jmchilton.blend4j.galaxy.HistoriesClient) GalaxyLibrariesService(ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyLibrariesService) Before(org.junit.Before)

Aggregations

GalaxyLibrariesService (ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyLibrariesService)7 Before (org.junit.Before)4 GalaxyHistoriesService (ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyHistoriesService)3 Library (com.github.jmchilton.blend4j.galaxy.beans.Library)3 Test (org.junit.Test)3 GalaxyProjectName (ca.corefacility.bioinformatics.irida.model.upload.galaxy.GalaxyProjectName)2 HistoriesClient (com.github.jmchilton.blend4j.galaxy.HistoriesClient)2 LibrariesClient (com.github.jmchilton.blend4j.galaxy.LibrariesClient)2 ToolsClient (com.github.jmchilton.blend4j.galaxy.ToolsClient)2 SequenceFile (ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile)1 SingleEndSequenceFile (ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile)1 GalaxyWorkflowService (ca.corefacility.bioinformatics.irida.pipeline.upload.galaxy.GalaxyWorkflowService)1 GalaxyInstance (com.github.jmchilton.blend4j.galaxy.GalaxyInstance)1 Path (java.nio.file.Path)1