Examples with AnalysisOutputFile ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisOutputFile used on opensource projects

Example 11 with AnalysisOutputFile

use of ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisOutputFile in project irida by phac-nml.

the class AnalysisServiceTest method testCreateAnalysisWithMultipleOutputFile.

@Test
public void testCreateAnalysisWithMultipleOutputFile() throws IOException {
    Path outputFile1 = Files.createTempFile(null, null);
    Path outputFile2 = Files.createTempFile(null, null);
    Path outputFile3 = Files.createTempFile(null, null);
    AnalysisOutputFile report1 = new AnalysisOutputFile(outputFile1, "", "", null);
    AnalysisOutputFile report2 = new AnalysisOutputFile(outputFile2, "", "", null);
    AnalysisOutputFile report3 = new AnalysisOutputFile(outputFile3, "", "", null);
    Map<String, AnalysisOutputFile> analysisOutputFiles = new ImmutableMap.Builder<String, AnalysisOutputFile>().put("tree", report1).put("matrix", report2).put("table", report3).build();
    Analysis analysis = new Analysis("something", analysisOutputFiles, AnalysisType.PHYLOGENOMICS);
    analysisService.create(analysis);
    verify(analysisOutputFileRepository, times(3)).save(any(AnalysisOutputFile.class));
    verify(analysisRepository).save(analysis);
}

Example 12 with AnalysisOutputFile

use of ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisOutputFile in project irida by phac-nml.

the class AnalysisServiceImplIT method testCreatePhylogenomicsAnalysis.

@Test
@WithMockUser(username = "admin", roles = "ADMIN")
public void testCreatePhylogenomicsAnalysis() throws IOException {
    Path treePath = Files.createTempFile(null, null);
    Path tablePath = Files.createTempFile(null, null);
    Path matrixPath = Files.createTempFile(null, null);
    Map<String, String> params = new HashMap<>();
    params.put("param", "value");
    ToolExecution toolExecutionTree = new ToolExecution(null, "ls", "1.0", "executionManagerId", params, "/bin/ls -lrth");
    ToolExecution toolExecutionTable = new ToolExecution(null, "ls", "1.0", "executionManagerId", params, "/bin/ls -lrth");
    ToolExecution toolExecutionMatrix = new ToolExecution(null, "ls", "1.0", "executionManagerId", params, "/bin/ls -lrth");
    AnalysisOutputFile tree = new AnalysisOutputFile(treePath, "internal-galaxy-tree-identifier", "", toolExecutionTree);
    AnalysisOutputFile table = new AnalysisOutputFile(tablePath, "internal-galaxy-table-identifier", "", toolExecutionTable);
    AnalysisOutputFile matrix = new AnalysisOutputFile(matrixPath, "internal-galaxy-matrix-identifier", "", toolExecutionMatrix);
    Map<String, AnalysisOutputFile> analysisOutputFiles = new ImmutableMap.Builder<String, AnalysisOutputFile>().put("tree", tree).put("matrix", matrix).put("table", table).build();
    Analysis pipeline = new Analysis(EXECUTION_MANAGER_ID, analysisOutputFiles, AnalysisType.PHYLOGENOMICS);
    // make sure that we're not falsely putting the files into the correct
    // directory in the first place.
    assertFalse("file was stored in the wrong directory.", pipeline.getAnalysisOutputFile(TREE_KEY).getFile().startsWith(outputFileBaseDirectory));
    assertFalse("file was stored in the wrong directory.", pipeline.getAnalysisOutputFile(MATRIX_KEY).getFile().startsWith(outputFileBaseDirectory));
    assertFalse("file was stored in the wrong directory.", pipeline.getAnalysisOutputFile(TABLE_KEY).getFile().startsWith(outputFileBaseDirectory));
    Analysis analysis = analysisService.create(pipeline);
    // make sure that we put the analysis output files into the correct
    // directory.
    assertEquals("returned analysis was of the wrong type.", AnalysisType.PHYLOGENOMICS, analysis.getAnalysisType());
    assertTrue("file was stored in the wrong directory.", analysis.getAnalysisOutputFile(TREE_KEY).getFile().startsWith(outputFileBaseDirectory));
    assertTrue("file was stored in the wrong directory.", analysis.getAnalysisOutputFile(MATRIX_KEY).getFile().startsWith(outputFileBaseDirectory));
    assertTrue("file was stored in the wrong directory.", analysis.getAnalysisOutputFile(TABLE_KEY).getFile().startsWith(outputFileBaseDirectory));
}

Example 13 with AnalysisOutputFile

use of ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisOutputFile in project irida by phac-nml.

the class TestDataFactory method constructAnalysisOutputFile.

private static AnalysisOutputFile constructAnalysisOutputFile(String name, Long id) {
    if (id == null) {
        id = 1L;
    }
    ToolExecution toolExecution = new ToolExecution(1L, null, "testTool", "0.0.12", "executionManagersId", ImmutableMap.of());
    final AnalysisOutputFile of = new AnalysisOutputFile(Paths.get(FAKE_FILE_PATH.replace("{name}", name)), "", FAKE_EXECUTION_MANAGER_ID, toolExecution);
    final DirectFieldAccessor dfa = new DirectFieldAccessor(of);
    dfa.setPropertyValue("id", id);
    return of;
}

Example 14 with AnalysisOutputFile

use of ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisOutputFile in project irida by phac-nml.

the class AnalysisWorkspaceServiceGalaxy method getAnalysisResults.

/**
 * {@inheritDoc}
 */
@Override
public Analysis getAnalysisResults(AnalysisSubmission analysisSubmission) throws ExecutionManagerException, IridaWorkflowNotFoundException, IOException, IridaWorkflowAnalysisTypeException {
    checkNotNull(analysisSubmission, "analysisSubmission is null");
    checkNotNull(analysisSubmission.getWorkflowId(), "workflowId is null");
    checkNotNull(analysisSubmission.getRemoteWorkflowId(), "remoteWorkflowId is null");
    Path outputDirectory = Files.createTempDirectory("analysis-output");
    logger.trace("Created temporary directory " + outputDirectory + " for analysis output files");
    IridaWorkflow iridaWorkflow = iridaWorkflowsService.getIridaWorkflow(analysisSubmission.getWorkflowId());
    String analysisId = analysisSubmission.getRemoteAnalysisId();
    Map<String, IridaWorkflowOutput> outputsMap = iridaWorkflow.getWorkflowDescription().getOutputsMap();
    String labelPrefix = getLabelPrefix(analysisSubmission, iridaWorkflow);
    Map<String, AnalysisOutputFile> analysisOutputFiles = Maps.newHashMap();
    for (String analysisOutputName : outputsMap.keySet()) {
        String outputFileName = outputsMap.get(analysisOutputName).getFileName();
        Dataset outputDataset = galaxyHistoriesService.getDatasetForFileInHistory(outputFileName, analysisId);
        AnalysisOutputFile analysisOutput = buildOutputFile(analysisId, labelPrefix, outputDataset, outputDirectory);
        analysisOutputFiles.put(analysisOutputName, analysisOutput);
    }
    AnalysisType analysisType = iridaWorkflow.getWorkflowDescription().getAnalysisType();
    return new Analysis(analysisId, analysisOutputFiles, analysisType);
}

Example 15 with AnalysisOutputFile

use of ca.corefacility.bioinformatics.irida.model.workflow.analysis.AnalysisOutputFile in project irida by phac-nml.

the class RESTAnalysisSubmissionController method getAnalysisOutputFile.

/**
 * Get an analysis output file for a given submission
 *
 * @param submissionId
 *            The {@link AnalysisSubmission} id
 * @param fileType
 *            The {@link AnalysisOutputFile} type as defined in the
 *            {@link Analysis} subclass
 * @return {@link ModelMap} containing the {@link AnalysisOutputFile}
 */
@RequestMapping("/{submissionId}/analysis/file/{fileType}")
public ModelMap getAnalysisOutputFile(@PathVariable Long submissionId, @PathVariable String fileType) {
    ModelMap model = new ModelMap();
    AnalysisSubmission read = analysisSubmissionService.read(submissionId);
    if (read.getAnalysisState() != AnalysisState.COMPLETED) {
        throw new EntityNotFoundException("Analysis is not completed");
    }
    AnalysisOutputFile analysisOutputFile = read.getAnalysis().getAnalysisOutputFile(fileType);
    analysisOutputFile.add(linkTo(methodOn(RESTAnalysisSubmissionController.class).getAnalysisOutputFile(submissionId, fileType)).withSelfRel());
    model.addAttribute(RESOURCE_NAME, analysisOutputFile);
    return model;
}