job.getParams().put("outdir", path.toString()); job.getParams().put("path", dbAdaptorFactory.getCatalogFileDBAdaptor().get(job.getOutDir().getUid(), QueryOptions.empty()).first().getId()); } catch (CatalogDBException e) { "L", "log-level", "merge", "o", "outdir", "overwrite-annotations", "path", "queue", "s", "study", "transform", "transformed-files", "resume", "load-split-data")); buildCommandLine(job.getParams(), commandLine, knownParams); } else { commandLine.append(" alignment index"); for (Map.Entry<String, String> param : job.getParams().entrySet()) { commandLine.append(' '); commandLine.append("--").append(param.getKey());
public int execute(Job job) throws CatalogException, AnalysisExecutionException { return execute(job.getToolId(), job.getExecution(), catalogManager.getJobManager().getStudyId(job.getUid()), job.getParams()); }
Map<String, String> params = new HashMap<>(job.getParams()); List<Param> inputParams = toolManager.getInputParams(tool, execution); QueryOptions options = new QueryOptions(QueryOptions.INCLUDE, FileDBAdaptor.QueryParams.URI.key());
job.setOutput(ParamUtils.defaultObject(job.getOutput(), Collections.emptyList())); job.setExecution(ParamUtils.defaultObject(job.getExecution(), "")); job.setParams(ParamUtils.defaultObject(job.getParams(), HashMap::new)); job.setResourceManagerAttributes(ParamUtils.defaultObject(job.getResourceManagerAttributes(), HashMap::new)); job.setAttributes(ParamUtils.defaultObject(job.getAttributes(), HashMap::new));