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

Example 56 with SequenceFilePair

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFilePair 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 57 with SequenceFilePair

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

the class SequencingObjectConcatenatorFactoryTest method testGetConcatenatorPairCollection.

@Test
public void testGetConcatenatorPairCollection() {
    Set<SequenceFilePair> fileSet = Sets.newHashSet(new SequenceFilePair());
    SequencingObjectConcatenator<?> concatenator = SequencingObjectConcatenatorFactory.getConcatenator(fileSet);
    assertTrue(concatenator instanceof SequenceFilePairConcatenator);
}

Example 58 with SequenceFilePair

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

the class SequencingObjectConcatenatorFactoryTest method testGetConcatenatorMixedError.

@Test(expected = IllegalArgumentException.class)
public void testGetConcatenatorMixedError() {
    Set<SequencingObject> fileSet = Sets.newHashSet(new SequenceFilePair(), new SingleEndSequenceFile(null));
    SequencingObjectConcatenatorFactory.getConcatenator(fileSet);
}

Example 59 with SequenceFilePair

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

the class AssemblyFileProcessorTest method testAssemblyDisabled.

@Test
public void testAssemblyDisabled() {
    Long sequenceFileId = 1L;
    SequenceFilePair pair = new SequenceFilePair();
    Sample sample = new Sample();
    Project project = new Project();
    project.setAssembleUploads(false);
    when(objectRepository.findOne(sequenceFileId)).thenReturn(pair);
    when(ssoRepository.getSampleForSequencingObject(pair)).thenReturn(new SampleSequencingObjectJoin(sample, pair));
    when(psjRepository.getProjectForSample(sample)).thenReturn(ImmutableList.of(new ProjectSampleJoin(project, sample, true)));
    assertFalse("processor should not want to assemble file", processor.shouldProcessFile(sequenceFileId));
    verifyZeroInteractions(submissionRepository);
}