Package Taverna.Tree.DataFlowImpl

Examples of Taverna.Tree.DataFlowImpl.Datalinks

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  // data modules have a 0-indexed order attribute specifying what position they take on
  // the command line.
  int order;
 
  public TavernaContext() {
    this.datalinks = new Datalinks();
    this.order = 0;
  }
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    String name = moduleGroup.getName();
    AnnotatedGranularDepthInputPorts inputPorts = new AnnotatedGranularDepthInputPorts();
    AnnotatedGranularDepthOutputPorts outputPorts = new AnnotatedGranularDepthOutputPorts();
    Processors processors = new Processors();
    Conditions conditions = new Conditions();
    Datalinks datalinks = (Datalinks) visit(pipeline.getConnections());
    Annotations annotations = new Annotations();
    String id = UUID.randomUUID().toString();
    String role = "top";
   
    dataflow = new Dataflow(name, inputPorts, outputPorts, processors, conditions, datalinks, annotations, id, role);
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  /**
   * Visits Connections in Loni Pipeline xml file to create corresponding Datalinks in Taverna.
   */
    public Object visit(Connections connections){
      Datalinks datalinks = new Datalinks();
     
      // For each connection in between modules, create a corresponding Datalink for Taverna workflow.
      for (Connection c : connections.getConnections())
      {
          Link src = null;
          Link snk = null;
        String source[] = c.getSource().split("\\.");
        for(GraphObject module : moduleGroup.getModules())
        {
          if(source[0].equals(module.getId())){
            src = module.getSource(source[1]);
          }
        }
        String sink[] = c.getSink().split("\\.");
        for(GraphObject module : moduleGroup.getModules())
        {
          if(sink[0].equals(module.getId())){
            snk = module.getSink(sink[1]);
          }
        }
        DataLink datalink = new DataLink(snk, src);
        datalinks.addDataLink(datalink);
      }
      return datalinks;
    }
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    dataModule.getFileTypes().addFileType(new FileType(TavernaType,"",""));
    // Figure out whether the data module will have inputs or outputs by going through the
    // DataLinks and figuring out if one of their source or sink names matches the
    // ports name. Then you can generate inputs or outputs for the data module depending
    // on what you need
    Datalinks dl = tavernaContext.getDatalinks();
    List<DataLink> datalinks = dl.getDataLinks();
   
    String inputPortName = port.getName();
    String datalinkPortName = "";
    String sourceLinkType = "";
    String sourcePort = "";
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Related Classes of Taverna.Tree.DataFlowImpl.Datalinks

  • LONI.visitor.LoniToTavernaConverter
  • Taverna.util.TavernaContext
  • Taverna.Visitor.DataFlowImplConverter
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