Package uk.ac.ebi.fgpt.conan.model

Examples of uk.ac.ebi.fgpt.conan.model.ConanProcess

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    catch (IOException e) {
      e.printStackTrace();
      fail();
    }

    ConanProcess process = new LocalGzipProcess();
    Map<ConanParameter, String> processParams = new HashMap<ConanParameter, String>();
    Map<String, String> inputParams = new HashMap<String, String>();
    inputParams.put("compression", "9");
    inputParams.put("file", testFile.getAbsolutePath());
    ProcessUtils.extractConanParameters(processParams, inputParams, process);

    try {
      process.execute(processParams);
    }
    catch (ProcessExecutionException e) {
      e.printStackTrace();
      fail();
    }
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  @Test
  public void testGunzip() {
    File file = new File(testFile.getAbsolutePath()+".gz");

    ConanProcess process = new LocalGunzipProcess();
    Map<ConanParameter, String> processParams = new HashMap<ConanParameter, String>();
    Map<String, String> inputParams = new HashMap<String, String>();
    inputParams.put("file", file.getAbsolutePath());
    ProcessUtils.extractConanParameters(processParams, inputParams, process);

    try {
      process.execute(processParams);
    }
    catch (ProcessExecutionException e) {
      e.printStackTrace();
      fail();
    }
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  }

  public void generateAndAddPipeline(PipelineRequest request) {
    List<ConanProcess> conanProcesses = new ArrayList<ConanProcess>();
    for (String processName : request.getProcesses()) {
      ConanProcess conanProcess = getConanProcessService().getProcess(processName);
      conanProcesses.add(conanProcess);
    }

    conanPipelineService.createPipeline(request.getName(),
                                        conanProcesses,
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Related Classes of uk.ac.ebi.fgpt.conan.model.ConanProcess

  • uk.ac.bbsrc.tgac.miso.analysis.manager.AnalysisRequestManager
  • uk.ac.bbsrc.tgac.miso.analysis.tgac.test.LocalTask
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