Package LONI.tree.workflow

Examples of LONI.tree.workflow.Connections

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   * Convert a Pipeline to a Galaxy Workflow
   */
  public Object visit(Pipeline pipeline) {
    Workflow workflow;
    ModuleGroup mgroup = pipeline.getPipelineModuleGroup();
    Connections conns = pipeline.getConnections();
    GalaxyContext context=  new GalaxyContext();
    context.getDatabase().clear();
    NODE_COUNT = 0;
   
    //convert the module group
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        secret, order, ConverterConfig.GALAXY_OUTPUT_DIR) );
   
    /* Record environmental variable in context for future use*/
    /*TODO: Migrate these globals to some sort of configuration file*/
   
    Connections connections = new Connections();
   
    for(Step s : workflow.getSteps()){
      Pair<GraphObject, LoniEnvironment> dat;
      dat = (Pair<GraphObject, LoniEnvironment>) stepVisitor.visit(s, context);
      connections.addConnections(dat.getElem2().getConnections());
      mgroup.getModules().addAll(dat.getElem2().getModules());
      if(dat.getElem1() != null)
        mgroup.getModules().add(dat.getElem1());
     
    }
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    annotationVisitor = new AnnotationConverter();
    dataFlowImplVisitor = new DataFlowImplConverter();
  }
 
  public Connections getConnections(Dataflow dflow){
    Connections conn = (Connections) dataFlowImplVisitor.visit(dflow.getDatalinks());
    return conn;
  }
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  public Object visit(Workflow workflow){
    Pipeline pipeline;
    String version  = workflow.getVersion();
   
    ModuleGroup moduleGroup;
    Connections connections = getConnections(workflow.getDataflow());
    moduleGroup = (ModuleGroup) visit(workflow.getDataflow());


    pipeline = new Pipeline(version, moduleGroup, connections);
    return pipeline;
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  /*
   * @see Taverna.Visitor.DataFlowImplVisitor#visit(Taverna.Tree.Datalinks)
   */
  public Object visit(Datalinks d){
    this.tavernaContext.setDatalinks(d);
    Connections connections = new Connections();
    Pair<String, String> sourceAndSink;
   
    if(d.getDataLinks() != null){     
      List<DataLink> datalinkList = d.getDataLinks();
      for(DataLink datalink : datalinkList){
        sourceAndSink = (Pair) visit(datalink);
        connections.addConnection(new Connection(sourceAndSink.getElem1(), sourceAndSink.getElem2()));
      }
    } else {
      Printer.log("d.getDataLinks() is null");
    }   
    return connections;
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Related Classes of LONI.tree.workflow.Connections

  • Galaxy.Visitor.Local.GalaxyToLoniWorkflowConverter
  • LONI.visitor.LoniToGalaxyConverter
  • Taverna.Visitor.DataFlowImplConverter
  • Taverna.Visitor.TavernaToLoniConverter
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