Examples with IridaToolParameter ca.corefacility.bioinformatics.irida.model.workflow.description.IridaToolParameter used on opensource projects

Example 6 with IridaToolParameter

use of ca.corefacility.bioinformatics.irida.model.workflow.description.IridaToolParameter in project irida by phac-nml.

the class AnalysisParameterServiceGalaxyTest method testPrepareParametersOverrideMultipleLevelMultipleParameterSuccess.

/**
 * Tests preparing workflow parameters with multiple levels, multiple
 * parameters and overriding with custom value successfully.
 *
 * @throws IridaWorkflowParameterException
 */
@Test
public void testPrepareParametersOverrideMultipleLevelMultipleParameterSuccess() throws IridaWorkflowParameterException {
    IridaToolParameter iridaToolParameter = new IridaToolParameter("galaxy-tool1", "level1.parameter1");
    IridaToolParameter iridaToolParameter2 = new IridaToolParameter("galaxy-tool1", "level1.parameter2");
    IridaWorkflowParameter parameter1 = new IridaWorkflowParameter("parameter1", "0", Lists.newArrayList(iridaToolParameter, iridaToolParameter2));
    List<IridaWorkflowParameter> iridaWorkflowParameters = Lists.newArrayList(parameter1);
    when(iridaWorkflowDescription.getParameters()).thenReturn(iridaWorkflowParameters);
    Map<String, String> parameters = Maps.newHashMap();
    parameters.put("parameter1", "1");
    WorkflowInputsGalaxy workflowInputsGalaxy = analysisParameterService.prepareAnalysisParameters(parameters, iridaWorkflow);
    assertNotNull("workflowInputsGalaxy is null", workflowInputsGalaxy);
    WorkflowInputs workflowInputs = workflowInputsGalaxy.getInputsObject();
    Map<Object, Map<String, Object>> workflowParameters = workflowInputs.getParameters();
    Map<String, Object> tool1Parameters = workflowParameters.get("galaxy-tool1");
    assertNotNull("parameters for galaxy-tool1 should not be null", tool1Parameters);
    assertEquals("parameter not properly defined", ImmutableMap.of("level1", ImmutableMap.of("parameter1", "1", "parameter2", "1")), tool1Parameters);
}

Example 7 with IridaToolParameter

use of ca.corefacility.bioinformatics.irida.model.workflow.description.IridaToolParameter in project irida by phac-nml.

the class AnalysisParameterServiceGalaxyTest method setup.

@Before
public void setup() {
    MockitoAnnotations.initMocks(this);
    analysisParameterService = new AnalysisParameterServiceGalaxy();
    when(iridaWorkflow.getWorkflowDescription()).thenReturn(iridaWorkflowDescription);
    IridaToolParameter iridaToolParameter = new IridaToolParameter("galaxy-tool1", "parameter1");
    IridaWorkflowParameter parameter1 = new IridaWorkflowParameter("parameter1", "0", Lists.newArrayList(iridaToolParameter));
    List<IridaWorkflowParameter> iridaWorkflowParameters = Lists.newArrayList(parameter1);
    when(iridaWorkflowDescription.getParameters()).thenReturn(iridaWorkflowParameters);
    when(iridaWorkflowDescription.acceptsParameters()).thenReturn(true);
}

Example 8 with IridaToolParameter

use of ca.corefacility.bioinformatics.irida.model.workflow.description.IridaToolParameter in project irida by phac-nml.

the class IridaWorkflowLoaderServiceIT method buildTestDescription.

private IridaWorkflowDescription buildTestDescription(UUID id, String name, String version, String sequenceReadsSingle, String sequenceReadsPaired, boolean requiresSingleSample) throws MalformedURLException {
    List<IridaWorkflowOutput> outputs = new LinkedList<>();
    outputs.add(new IridaWorkflowOutput("output1", "output1.txt"));
    outputs.add(new IridaWorkflowOutput("output2", "output2.txt"));
    List<IridaWorkflowToolRepository> tools = new LinkedList<>();
    IridaWorkflowToolRepository workflowTool = new IridaWorkflowToolRepository("sam_to_bam", "devteam", new URL("http://toolshed.g2.bx.psu.edu/"), "8176b2575aa1");
    tools.add(workflowTool);
    List<IridaWorkflowParameter> parameters = new LinkedList<>();
    IridaToolParameter tool1 = new IridaToolParameter("irida.corefacility.ca/galaxy-shed/repos/irida/test-tool/0.1", "a");
    IridaToolParameter tool2 = new IridaToolParameter("irida.corefacility.ca/galaxy-shed/repos/irida/test-tool/0.1", "b");
    IridaWorkflowParameter parameter1 = new IridaWorkflowParameter("test-parameter", "1", Lists.newArrayList(tool1, tool2));
    parameters.add(parameter1);
    IridaWorkflowDescription iridaWorkflow = new IridaWorkflowDescription(id, name, version, AnalysisType.DEFAULT, new IridaWorkflowInput(sequenceReadsSingle, sequenceReadsPaired, "reference", requiresSingleSample), outputs, tools, parameters);
    return iridaWorkflow;
}