Examples of net.sf.pipet.api.ModuleDefinition

net.sf.pipet.api.ModuleDefinition
A module definition which can be part of a pipeline setup. A module definition object represents a global definition of a PipeT module which uses
- a {@link ModuleInterface} to access the module;
- a {@link CachePolicy} to prevent subsequent repetitive calls to the ModuleInterface, and
- export paths to say how the module can be accessed remotely.
In addition, a ModuleDefinition has attributes which represent the module's custom parameter values.

    int of_before = test_open_files ? getOpenFiles(messenger) : 0;
    
    SimulationModuleData data = new SimulationModuleData(atts, input, output, messenger);


    ModuleInterface modif = ModuleLoader.loadModuleInterface(mod_uri, cfg);
    ModuleDefinition mod = ModuleDefinition.create(cfg.getRootModule(), mod_uri, modif, null, null);
    
    ModuleInstance instance = mod.getInterface().createInstance(data, messenger);
    data.close(instance.run());


    Assert.assertEquals(String.format("Exit status of %s.", mod.getInterfaceSpecification()), status, data.getStatus());
    if (test_content)
      data.testModuleOutput();


    int of_after = test_open_files ? getOpenFiles(messenger) : 0;

View Full Code Here

    selectionChanged(null);
  }
  
  public void moduleCollectionAction(ModuleCollectionView.ActionEvent evt)
  {
    ModuleDefinition mod = evt.getModule();
    
    switch(evt.getAction())
    {
    case ModuleCollectionView.ActionEvent.SELECTION_CHANGED:
      selectionChanged(mod);

View Full Code Here

        return 0;
      }
      
      if (command.printModuleInfo())
      {
        ModuleDefinition mod = command.getModule();
        if (mod == null)
        {
          command.getMessenger().fatal("Missing argument.");
          return -1;
        }
        
        try
        {
          System.out.println("URL: "+mod.getInterfaceSpecification());
          System.out.println("Title: "+mod.getTitle());
          System.out.println("Description: "+mod.getDescription());
          System.out.println("Input pipes: "+getPipeTypes(mod.getInputPipeTypes()));
          System.out.println("Output pipes: "+getPipeTypes(mod.getOutputPipeTypes()));
          System.out.println("Global parameters: "+getParameters(mod.getGlobalParameters()));
          System.out.println("Pipeline parameters: "+getParameters(mod.getPipelineParameters()));
          System.out.println("Runtime parameters: "+getParameters(mod.getRuntimeParameters()));
          return 0;
        }
        catch (ResourceException e)
        {
          command.getMessenger().fatal("Module error.", e);

View Full Code Here

    public Object getValueAt(int rowIndex, int columnIndex)
    {
      if (modlocal == null)
        return null;
      
      ModuleDefinition mod = modlocal.get(rowIndex);
      try {
        return getColumnValue(mod, columnIndex);
      } catch (ResourceException e) {
        return "?";
      }

View Full Code Here

  public ModuleInstance getJob()
    throws PipetError
  {
    try
    {
      ModuleDefinition mod = getModule();
      if (mod == null)
        return null;
      else
        return mod.getInterface().createInstance(createModuleData(), msgr);
    }
    catch (Exception e)
    {
      throw new PipetError(e.toString());
    }

View Full Code Here

          input_pipes.put(kv.getKey(), Collections.<InputStream>singleton(System.in));
        else
          input_pipes.put(kv.getKey(), Collections.<InputStream>singleton(new FileInputStream(kv.getValue())));
      }
      
      ModuleDefinition mod = getModule();
      for (String pipe : mod.getInputPipeTypes().keySet())
      {
        if (!input_pipes.containsKey(pipe))
          msgr.warn("Unconnected input pipe: "+pipe);
      }

View Full Code Here

          output_pipes.put(kv.getKey(), System.out);
        else
          output_pipes.put(kv.getKey(), new FileOutputStream(kv.getValue()));
      }


      ModuleDefinition mod = getModule();
      for (String pipe : mod.getOutputPipeTypes().keySet())
      {
        if (!output_pipes.containsKey(pipe))
          msgr.warn("Unconnected output pipe: "+pipe);
      }

View Full Code Here

    {
      //if (mod.isSatisfied(pipeline.getProvidedLayers()) && !mod.conflicts(pipeline.getProvidedLayers()))
        eligible.add(mod);
    }
    
    ModuleDefinition moddef = (ModuleDefinition)JOptionPane.showInputDialog(null,
      "Add module:",
      "Select module",
      JOptionPane.PLAIN_MESSAGE,
      null,
      eligible.toArray(new ModuleDefinition[] {}),

View Full Code Here

  }
  
  @Override
  protected void newModuleDialog()
  {
    ModuleDefinition mod = ModuleDefinitionDialog.defineNewModule(cfg, app.getMessageReporter());
    if (mod == null)
      return;
    
    cfg.addModule(mod);
  }

View Full Code Here

  {
    Vector<ModuleDefinition> runmods = new Vector<ModuleDefinition>();
    for (ModuleDefinition pipelinemod : pipeline.getModules())
    {
      reporter.debug("setup module: "+pipelinemod.getTitle());
      ModuleDefinition mod = ModuleDefinition.create(pipelinemod);
      if (data_access != null)
        addAttributes(mod, data_access.getAttributes());
      if (parameters != null)
        addAttributes(mod, parameters);
      mod.setValue(ModuleInterface.ATT_PIPELINE_NAME, new UntypedValue(pipeline.getName()));
      try
      {
        ModuleConfigurator modconf = mod.getInterface().getRuntimeConfigurator(interface_type);
        if (modconf == null || modconf.configure(mod, new Vector<ModuleDefinition>(pipeline.getModules()), reporter))
          runmods.add(mod);
        else
        {
          reporter.debug(String.format("Configuration of %s failed.", mod.toString()));
          return false;
        }
      }
      catch (ResourceException e)
      {
        reporter.debug(String.format("Resource not loaded: %s.", mod.toString()));
        return false;
      }
    }
    
    try

View Full Code Here

0 1

TOP

Related Classes of net.sf.pipet.api.ModuleDefinition

net.sf.pipet.app.PipetCommand

net.sf.pipet.app.RunPipeline

net.sf.pipet.config.ConfigurationV0Parser

net.sf.pipet.engine.PipelineJob

net.sf.pipet.engine.PipelineJob$ModuleWrapper

net.sf.pipet.gui.ModuleCollectionTableView$ModuleTableModel

net.sf.pipet.gui.ModuleListTab

net.sf.pipet.gui.ModuleManager

net.sf.pipet.gui.PipelineView

net.sf.pipet.test.PipelineSimulator

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.