Examples with NcbiBioSampleFiles ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles used on opensource projects

Example 1 with NcbiBioSampleFiles

use of ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles in project irida by phac-nml.

the class ExportUploadServiceTest method testGetResultsSubmitted.

@SuppressWarnings("unchecked")
@Test
public void testGetResultsSubmitted() throws IOException, UploadException {
    NcbiExportSubmissionService exportSubmissionService = mock(NcbiExportSubmissionService.class);
    NcbiBioSampleFiles sample2 = new NcbiBioSampleFiles();
    sample2.setId("NMLTEST2");
    NcbiBioSampleFiles sample3 = new NcbiBioSampleFiles();
    sample3.setId("NMLTEST3");
    NcbiExportSubmission submission = new NcbiExportSubmission();
    submission.setBioSampleFiles(Lists.newArrayList(sample2, sample3));
    submission.setDirectoryPath("submit/Test/example");
    when(exportSubmissionService.getSubmissionsWithState(any(Set.class))).thenReturn(Lists.newArrayList(submission));
    String report = "<?xml version='1.0' encoding='utf-8'?>\n" + "<SubmissionStatus submission_id=\"SUB189884\" status=\"processing\">\n" + "  <Action action_id=\"SUB189884-nmltest2\" target_db=\"SRA\" status=\"processing\">\n" + "    <Response status=\"processing\"/>\n" + "  </Action>\n" + "  <Action action_id=\"SUB189884-nmltest3\" target_db=\"SRA\" status=\"submitted\"/>\n" + "</SubmissionStatus>\n";
    String ftpHost = "localhost";
    String ftpUser = "test";
    String ftpPassword = "password";
    String baseDirectory = "/home/test/submit/Test";
    String submissionDirectory = baseDirectory + "/example";
    String reportFile = submissionDirectory + "/report.2.xml";
    FakeFtpServer server = new FakeFtpServer();
    server.addUserAccount(new UserAccount(ftpUser, ftpPassword, "/home/test"));
    FileSystem fileSystem = new UnixFakeFileSystem();
    fileSystem.add(new DirectoryEntry(submissionDirectory));
    fileSystem.add(new FileEntry(reportFile, report));
    server.setFileSystem(fileSystem);
    // finds an open port
    server.setServerControlPort(0);
    ExportUploadService exportUploadService = new ExportUploadService(exportSubmissionService, null, new TestEmailController());
    try {
        server.start();
        int ftpPort = server.getServerControlPort();
        exportUploadService.setConnectionDetails(ftpHost, ftpPort, ftpUser, ftpPassword, baseDirectory);
        exportUploadService.updateRunningUploads();
    } finally {
        server.stop();
    }
    assertEquals("sample2 should have processing state", ExportUploadState.PROCESSING, sample2.getSubmissionStatus());
    assertEquals("sample3 should have processing state", ExportUploadState.SUBMITTED, sample3.getSubmissionStatus());
}

Example 2 with NcbiBioSampleFiles

use of ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles in project irida by phac-nml.

the class ExportUploadServiceTest method testGetResultsWithAccession.

@SuppressWarnings("unchecked")
@Test
public void testGetResultsWithAccession() throws IOException, UploadException {
    NcbiExportSubmissionService exportSubmissionService = mock(NcbiExportSubmissionService.class);
    NcbiBioSampleFiles sample2 = new NcbiBioSampleFiles();
    sample2.setId("NMLTEST2");
    NcbiExportSubmission submission = new NcbiExportSubmission();
    submission.setBioSampleFiles(Lists.newArrayList(sample2));
    submission.setDirectoryPath("submit/Test/example");
    String newAccession = "SRR12345";
    when(exportSubmissionService.getSubmissionsWithState(any(Set.class))).thenReturn(Lists.newArrayList(submission));
    String report = "<?xml version='1.0' encoding='utf-8'?>\n" + "<SubmissionStatus submission_id=\"SUB11245\" status=\"processed-ok\">\n" + "  <Action action_id=\"SUB11245-nmltest2\" target_db=\"SRA\" status=\"processed-ok\" notify_submitter=\"true\">\n" + "    <Response status=\"processed-ok\">\n" + "      <Object target_db=\"SRA\" object_id=\"RUN:3119494\" spuid_namespace=\"NML\" spuid=\"nmltest2\" accession=\"" + newAccession + "\" status=\"updated\">\n" + "        <Meta>\n" + "          <SRAStudy>SRP12345</SRAStudy>\n" + "        </Meta>\n" + "      </Object>\n" + "    </Response>\n" + "  </Action>\n" + "</SubmissionStatus>";
    String ftpHost = "localhost";
    String ftpUser = "test";
    String ftpPassword = "password";
    String baseDirectory = "/home/test/submit/Test";
    String submissionDirectory = baseDirectory + "/example";
    String reportFile = submissionDirectory + "/report.2.xml";
    FakeFtpServer server = new FakeFtpServer();
    server.addUserAccount(new UserAccount(ftpUser, ftpPassword, "/home/test"));
    FileSystem fileSystem = new UnixFakeFileSystem();
    fileSystem.add(new DirectoryEntry(submissionDirectory));
    fileSystem.add(new FileEntry(reportFile, report));
    server.setFileSystem(fileSystem);
    // finds an open port
    server.setServerControlPort(0);
    ExportUploadService exportUploadService = new ExportUploadService(exportSubmissionService, null, new TestEmailController());
    try {
        server.start();
        int ftpPort = server.getServerControlPort();
        exportUploadService.setConnectionDetails(ftpHost, ftpPort, ftpUser, ftpPassword, baseDirectory);
        exportUploadService.updateRunningUploads();
    } finally {
        server.stop();
    }
    assertEquals("sample2 should have processing state", ExportUploadState.PROCESSED_OK, sample2.getSubmissionStatus());
    assertEquals("sample2 should have an accession", newAccession, sample2.getAccession());
}

Example 3 with NcbiBioSampleFiles

use of ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles in project irida by phac-nml.

the class ExportUploadServiceTest method createFakeSubmission.

/**
 * Create a fake submission for test uploads
 *
 * @return a {@link NcbiExportSubmission}
 * @throws IOException
 *             if the test file couldn't be created
 */
private NcbiExportSubmission createFakeSubmission() throws IOException {
    NcbiExportSubmission submission = new NcbiExportSubmission();
    submission.setId(1L);
    NcbiBioSampleFiles ncbiBioSampleFiles = new NcbiBioSampleFiles();
    Path tempFile = Files.createTempFile("sequencefile", ".fastq");
    SequenceFile sequenceFile = new SequenceFile(tempFile);
    sequenceFile.setId(1L);
    SingleEndSequenceFile singleFile = new SingleEndSequenceFile(sequenceFile);
    singleFile.setId(1L);
    ncbiBioSampleFiles.setFiles(Lists.newArrayList(singleFile));
    submission.setBioSampleFiles(Lists.newArrayList(ncbiBioSampleFiles));
    return submission;
}

Example 4 with NcbiBioSampleFiles

use of ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles in project irida by phac-nml.

the class NcbiExportSubmissionServceTest method testCreateNoFiles.

@Test(expected = IllegalArgumentException.class)
public void testCreateNoFiles() {
    NcbiBioSampleFiles ncbiBioSampleFiles = new NcbiBioSampleFiles("sample", Lists.newArrayList(), Lists.newArrayList(), null, "library_name", null, null, null, "library_construction_protocol", "namespace");
    NcbiExportSubmission submission = new NcbiExportSubmission(null, null, "bioProjectId", "organization", "ncbiNamespace", new Date(), Lists.newArrayList(ncbiBioSampleFiles));
    service.create(submission);
}

Example 5 with NcbiBioSampleFiles

use of ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles in project irida by phac-nml.

the class NcbiExportSubmissionServceTest method testCreatePairs.

@Test
public void testCreatePairs() {
    SequenceFile sequenceFile = new SequenceFile();
    NcbiBioSampleFiles ncbiBioSampleFiles = new NcbiBioSampleFiles("sample", Lists.newArrayList(), Lists.newArrayList(new SequenceFilePair(sequenceFile, sequenceFile)), null, "library_name", null, null, null, "library_construction_protocol", "namespace");
    NcbiExportSubmission submission = new NcbiExportSubmission(null, null, "bioProjectId", "organization", "ncbiNamespace", new Date(), Lists.newArrayList(ncbiBioSampleFiles));
    service.create(submission);
    verify(repository).save(submission);
}