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

Example 1 with IridaWorkflowToolRepository

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

the class ToolsListExporter method main.

public static void main(String[] args) throws IridaWorkflowNotFoundException, JsonGenerationException, JsonMappingException, IOException {
    if (args.length != 1) {
        throw new RuntimeException("Error: invalid number of arguments \n" + usage);
    }
    Path toolsListOutput = Paths.get(args[0]);
    ObjectMapper mapper = new ObjectMapper(new YAMLFactory());
    Map<AnalysisType, IridaWorkflow> workflows = getDefaultWorkflows();
    Set<IridaWorkflowToolRepository> uniqueToolRepositories = new HashSet<>();
    Map<String, Object> yamlMap = Maps.newHashMap();
    yamlMap.put("api_key", "<Galaxy Admin user API key>");
    yamlMap.put("galaxy_instance", "<IP address for target Galaxy instance>");
    List<Map<String, String>> tools = Lists.newArrayList();
    yamlMap.put("tools", tools);
    List<IridaWorkflow> workflowsSorted = workflows.values().stream().sorted(new Comparator<IridaWorkflow>() {

        @Override
        public int compare(IridaWorkflow o1, IridaWorkflow o2) {
            return o1.getWorkflowDescription().getName().compareTo(o2.getWorkflowDescription().getName());
        }
    }).collect(Collectors.toList());
    for (IridaWorkflow workflow : workflowsSorted) {
        logger.info("Adding tools for workflow " + workflow);
        String workflowName = workflow.getWorkflowDescription().getName();
        String workflowVersion = workflow.getWorkflowDescription().getVersion();
        tools.add(ImmutableMap.of(toolsSectionName, "### Tools for " + workflowName + " v" + workflowVersion + " ###"));
        for (IridaWorkflowToolRepository toolRepository : workflow.getWorkflowDescription().getToolRepositories()) {
            // Append trailing '/' to URL, so it becomes for example
            // http://example.com/galaxy-shed/
            // This is because other software (e.g. bioblend) assume a
            // Galaxy toolshed URL ends with a '/'
            // Otherwise, the end component of the path is stripped (e.g.,
            // becomes http://example.com)
            String toolRepositoryURLString = toolRepository.getUrl().toString();
            if (!toolRepositoryURLString.endsWith("/")) {
                toolRepositoryURLString += "/";
            }
            if (uniqueToolRepositories.contains(toolRepository)) {
                logger.info("Tool defined by " + toolRepository + " already exists, skipping ...");
            } else {
                uniqueToolRepositories.add(toolRepository);
                // @formatter:off
                tools.add(ImmutableMap.<String, String>builder().put("name", toolRepository.getName()).put("owner", toolRepository.getOwner()).put("tool_shed_url", toolRepositoryURLString).put("revision", toolRepository.getRevision()).put("tool_panel_section_id", defaultToolPanelId).build());
            // @formatter:on
            }
        }
    }
    // Bit of a hack, but does the job. Wanted to add a comment in the YAML
    // file for each tool section for readability but no YAML library
    // supports this. Instead, I do some pattern substitute/replace on a
    // special String variable "toolsSectionName" to generate the comments.
    String yaml = replaceAllWithCaptureGroup1(mapper.writeValueAsString(yamlMap), regexPattern, "\n  ", "\n");
    if (yaml.matches(toolsSectionName)) {
        throw new RuntimeException("Error: not all instances of \"" + toolsSectionName + "\" were replaced");
    }
    PrintWriter outputFileWriter = new PrintWriter(toolsListOutput.toFile());
    outputFileWriter.print(yaml);
    outputFileWriter.close();
    logger.info("Wrote tools list to: " + toolsListOutput.toAbsolutePath());
}

Example 2 with IridaWorkflowToolRepository

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

the class IridaWorkflowTestBuilder method buildTestDescription.

/**
 * Builds a {@link IridaWorkflowDescription} with the following information.
 *
 * @param id
 *            The id of the workflow.
 * @param name
 *            The name of the workflow.
 * @param version
 *            The version of the workflow.
 * @param analysisType
 *            The {@link AnalysisType} of the workflow.
 * @param reference
 *            The reference label for the workflow.
 * @param requiresSingleSample
 *            Whether or not this workflow requires a single sample.
 * @return An {@link IridaWorkflowDescription} with the given information.
 * @throws MalformedURLException
 */
public static IridaWorkflowDescription buildTestDescription(UUID id, String name, String version, AnalysisType analysisType, Input input, String reference, 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);
    IridaWorkflowInput workflowInput = null;
    switch(input) {
        case SINGLE:
            workflowInput = new IridaWorkflowInput("sequence_reads", null, reference, requiresSingleSample);
            break;
        case PAIRED:
            workflowInput = new IridaWorkflowInput(null, "sequence_reads_paired", reference, requiresSingleSample);
            break;
        case SINGLE_PAIRED:
            workflowInput = new IridaWorkflowInput("sequence_reads", "sequence_reads_paired", reference, requiresSingleSample);
            break;
    }
    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, workflowInput, outputs, tools, parameters);
    return iridaWorkflow;
}

Example 3 with IridaWorkflowToolRepository

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

the class TestDataFactory method getIridaWorkflow.

public static IridaWorkflow getIridaWorkflow(UUID id) {
    IridaWorkflowInput input = new IridaWorkflowInput();
    List<IridaWorkflowOutput> outputs = ImmutableList.of(new IridaWorkflowOutput());
    List<IridaWorkflowToolRepository> tools = ImmutableList.of();
    List<IridaWorkflowParameter> parameters = ImmutableList.of();
    IridaWorkflowDescription description = new IridaWorkflowDescription(id, "My Workflow", "V1", AnalysisType.DEFAULT, input, outputs, tools, parameters);
    IridaWorkflowStructure structure = new IridaWorkflowStructure(null);
    return new IridaWorkflow(description, structure);
}

Example 4 with IridaWorkflowToolRepository

use of ca.corefacility.bioinformatics.irida.model.workflow.description.IridaWorkflowToolRepository 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;
}