Examples with SingleEndSequenceFile ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile used on opensource projects

Example 91 with SingleEndSequenceFile

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile in project irida by phac-nml.

the class PipelineController method ajaxStartPipeline.

// ************************************************************************************************
// AJAX
// ************************************************************************************************
/**
 * Launch a pipeline
 *
 * @param locale     the locale that the browser is using for the current request.
 * @param parameters DTO of pipeline start parameters
 * @return a JSON response with the status and any messages.
 */
@RequestMapping(value = "/ajax/start", method = RequestMethod.POST)
@ResponseBody
public Map<String, Object> ajaxStartPipeline(Locale locale, @RequestBody final PipelineStartParameters parameters) {
    try {
        IridaWorkflow flow = workflowsService.getIridaWorkflow(parameters.getWorkflowId());
        IridaWorkflowDescription description = flow.getWorkflowDescription();
        // The pipeline needs to have a name.
        String name = parameters.getName();
        if (Strings.isNullOrEmpty(name)) {
            return ImmutableMap.of("error", messageSource.getMessage("workflow.no-name-provided", null, locale));
        }
        // Check to see if a reference file is required.
        Long ref = parameters.getRef();
        if (description.requiresReference() && ref == null) {
            return ImmutableMap.of("error", messageSource.getMessage("pipeline.error.no-reference.pipeline-start", null, locale));
        }
        // Get a list of the files to submit
        List<SingleEndSequenceFile> singleEndFiles = new ArrayList<>();
        List<SequenceFilePair> sequenceFilePairs = new ArrayList<>();
        List<Long> single = parameters.getSingle();
        if (single != null) {
            Iterable<SequencingObject> readMultiple = sequencingObjectService.readMultiple(single);
            readMultiple.forEach(f -> {
                if (!(f instanceof SingleEndSequenceFile)) {
                    throw new IllegalArgumentException("file " + f.getId() + " not a SingleEndSequenceFile");
                }
                singleEndFiles.add((SingleEndSequenceFile) f);
            });
            // Check the single files for duplicates in a sample, throws SampleAnalysisDuplicateException
            sequencingObjectService.getUniqueSamplesForSequencingObjects(Sets.newHashSet(singleEndFiles));
        }
        List<Long> paired = parameters.getPaired();
        if (paired != null) {
            Iterable<SequencingObject> readMultiple = sequencingObjectService.readMultiple(paired);
            readMultiple.forEach(f -> {
                if (!(f instanceof SequenceFilePair)) {
                    throw new IllegalArgumentException("file " + f.getId() + " not a SequenceFilePair");
                }
                sequenceFilePairs.add((SequenceFilePair) f);
            });
            // Check the pair files for duplicates in a sample, throws SampleAnalysisDuplicateException
            sequencingObjectService.getUniqueSamplesForSequencingObjects(Sets.newHashSet(sequenceFilePairs));
        }
        // Get the pipeline parameters
        Map<String, String> params = new HashMap<>();
        IridaWorkflowNamedParameters namedParameters = null;
        Map<String, Object> selectedParameters = parameters.getSelectedParameters();
        if (selectedParameters != null) {
            try {
                final String selectedParametersId = selectedParameters.get("id").toString();
                if (!DEFAULT_WORKFLOW_PARAMETERS_ID.equals(selectedParametersId) && !CUSTOM_UNSAVED_WORKFLOW_PARAMETERS_ID.equals(selectedParametersId)) {
                    // this means that a named parameter set was selected
                    // and unmodified, so load up that named parameter set
                    // to pass along.
                    namedParameters = namedParameterService.read(Long.valueOf(selectedParametersId));
                } else {
                    @SuppressWarnings("unchecked") final List<Map<String, String>> unnamedParameters = (List<Map<String, String>>) selectedParameters.get("parameters");
                    for (final Map<String, String> parameter : unnamedParameters) {
                        params.put(parameter.get("name"), parameter.get("value"));
                    }
                }
            } catch (Exception e) {
                return ImmutableMap.of("parameterError", messageSource.getMessage("pipeline.parameters.error", null, locale));
            }
        }
        List<Project> projectsToShare = new ArrayList<>();
        List<Long> sharedProjects = parameters.getSharedProjects();
        if (sharedProjects != null && !sharedProjects.isEmpty()) {
            projectsToShare = Lists.newArrayList(projectService.readMultiple(sharedProjects));
        }
        String analysisDescription = parameters.getDescription();
        Boolean writeResultsToSamples = parameters.getWriteResultsToSamples();
        if (description.getInputs().requiresSingleSample()) {
            analysisSubmissionService.createSingleSampleSubmission(flow, ref, singleEndFiles, sequenceFilePairs, params, namedParameters, name, analysisDescription, projectsToShare, writeResultsToSamples);
        } else {
            analysisSubmissionService.createMultipleSampleSubmission(flow, ref, singleEndFiles, sequenceFilePairs, params, namedParameters, name, analysisDescription, projectsToShare, writeResultsToSamples);
        }
    } catch (IridaWorkflowNotFoundException e) {
        logger.error("Cannot find IridaWorkflow [" + parameters.getWorkflowId() + "]", e);
        return ImmutableMap.of("pipelineError", messageSource.getMessage("pipeline.error.invalid-pipeline", null, locale));
    } catch (DuplicateSampleException e) {
        logger.error("Multiple files for Sample found", e);
        return ImmutableMap.of("pipelineError", messageSource.getMessage("pipeline.error.duplicate-samples", null, locale));
    }
    return ImmutableMap.of("success", true);
}

Example 92 with SingleEndSequenceFile

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile in project irida by phac-nml.

the class GzipFileProcessorTest method testExceptionBehaviours.

@Test(expected = FileProcessorException.class)
public void testExceptionBehaviours() throws IOException {
    final SequenceFile sf = constructSequenceFile();
    // compress the file, update the sequence file reference
    Path uncompressed = sf.getFile();
    Path compressed = Files.createTempFile(null, ".gz");
    GZIPOutputStream out = new GZIPOutputStream(Files.newOutputStream(compressed));
    Files.copy(uncompressed, out);
    out.close();
    sf.setFile(compressed);
    SingleEndSequenceFile so = new SingleEndSequenceFile(sf);
    when(sequenceFileRepository.save(any(SequenceFile.class))).thenThrow(new RuntimeException());
    fileProcessor.process(so);
}

Example 93 with SingleEndSequenceFile

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile in project irida by phac-nml.

the class GzipFileProcessorTest method handleCompressedFileWithGzExtension.

@Test
public void handleCompressedFileWithGzExtension() throws IOException {
    // the file processor should decompress the file, then update the
    // sequence file in the database.
    SequenceFile sf = constructSequenceFile();
    SequenceFile sfUpdated = new SequenceFile();
    sfUpdated.setFile(sf.getFile());
    final Long id = 1L;
    sf.setId(id);
    // compress the file, update the sequence file reference
    Path uncompressed = sf.getFile();
    Path compressed = Files.createTempFile(null, ".gz");
    GZIPOutputStream out = new GZIPOutputStream(Files.newOutputStream(compressed));
    Files.copy(uncompressed, out);
    out.close();
    when(sequenceFileRepository.save(sf)).thenReturn(sfUpdated);
    SingleEndSequenceFile so = new SingleEndSequenceFile(sf);
    sf.setFile(compressed);
    fileProcessor.process(so);
    ArgumentCaptor<SequenceFile> argument = ArgumentCaptor.forClass(SequenceFile.class);
    verify(sequenceFileRepository).save(argument.capture());
    SequenceFile modified = argument.getValue();
    verify(sequenceFileRepository).save(sf);
    String uncompressedFileContents = new String(Files.readAllBytes(modified.getFile()));
    assertEquals("uncompressed file and file in database should be the same.", FILE_CONTENTS, uncompressedFileContents);
    Files.delete(uncompressed);
    assertTrue("Original compressed file should not have been deleted.", Files.exists(compressed));
    Files.delete(compressed);
}

Example 94 with SingleEndSequenceFile

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile in project irida by phac-nml.

the class AnalysisSubmissionRepositoryIT method setup.

/**
 * Sets up objects for test.
 *
 * @throws IOException
 */
@Before
public void setup() throws IOException {
    singleEndFile = (SingleEndSequenceFile) objectRepository.findOne(2L);
    sequenceFile = singleEndFile.getFileWithId(1L);
    assertNotNull(sequenceFile);
    Set<SequencingObject> singleFiles = Sets.newHashSet(singleEndFile);
    SingleEndSequenceFile singleEndFile2 = (SingleEndSequenceFile) objectRepository.findOne(3L);
    SequenceFile sequenceFile2 = singleEndFile2.getFileWithId(2L);
    assertNotNull(sequenceFile2);
    Set<SequencingObject> singleFiles2 = Sets.newHashSet(singleEndFile2);
    sequenceFilePair = (SequenceFilePair) objectRepository.findOne(1L);
    assertNotNull(sequenceFilePair);
    referenceFile = referenceFileRepository.findOne(1L);
    assertNotNull(referenceFile);
    referenceFile2 = referenceFileRepository.findOne(2L);
    submitter1 = userRepository.findOne(1L);
    submitter2 = userRepository.findOne(2L);
    analysisSubmission = AnalysisSubmission.builder(workflowId).name(analysisName).inputFiles(singleFiles).referenceFile(referenceFile).build();
    analysisSubmission.setRemoteAnalysisId(analysisId);
    analysisSubmission.setAnalysisState(AnalysisState.SUBMITTING);
    analysisSubmission.setSubmitter(submitter1);
    analysisSubmission.setAnalysisCleanedState(AnalysisCleanedState.NOT_CLEANED);
    analysisSubmission2 = AnalysisSubmission.builder(workflowId).name(analysisName2).inputFiles(singleFiles2).referenceFile(referenceFile).build();
    analysisSubmission2.setRemoteAnalysisId(analysisId2);
    analysisSubmission2.setAnalysisState(AnalysisState.SUBMITTING);
    analysisSubmission2.setSubmitter(submitter2);
    analysisSubmission2.setAnalysisCleanedState(AnalysisCleanedState.NOT_CLEANED);
    analysisSubmission2b = AnalysisSubmission.builder(workflowId).name(analysisName2).inputFiles(singleFiles2).referenceFile(referenceFile2).build();
    analysisSubmission2b.setRemoteAnalysisId(analysisId2);
    analysisSubmission2b.setAnalysisState(AnalysisState.SUBMITTING);
    analysisSubmission2b.setSubmitter(submitter2);
    analysisSubmission2b.setAnalysisCleanedState(AnalysisCleanedState.NOT_CLEANED);
}

Example 95 with SingleEndSequenceFile

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile in project irida by phac-nml.

the class SequencingObjectConcatenatorFactoryTest method testGetConcatenatorSingleCollection.

@Test
public void testGetConcatenatorSingleCollection() {
    Set<SingleEndSequenceFile> fileSet = Sets.newHashSet(new SingleEndSequenceFile(null));
    SequencingObjectConcatenator<?> concatenator = SequencingObjectConcatenatorFactory.getConcatenator(fileSet);
    assertTrue(concatenator instanceof SingleEndSequenceFileConcatenator);
}