Package LONI.tree.workflow

Examples of LONI.tree.workflow.Pipeline

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  }
 
  public static void LoniToGalaxy(String path, String output){
    System.out.println(path);
    System.out.println("> "+output);
    Pipeline P;
    try {
      LoniToGalaxyConverter glc;
      glc = new LoniToGalaxyConverter();
     
      P = LoniSpecification.getXMLParser().parse(new File(path));
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  }
 
  public static void LoniToLoni(String path, String output){
    System.out.println(path);
    System.out.println("> "+output);
    Pipeline P;
    try {
      P = LoniSpecification.getXMLParser().parse(new File(path));
     
     
      try {
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      System.out.println("Before parsing...");
      workflow = TavernaSpecification.getXMLParser().parse(new File(inputPath));
      System.out.println("After parsing...");
      TavernaToLoniConverter tlc = new TavernaToLoniConverter();
      System.out.println("After creating a Tav to Loni converter...");
      Pipeline pipeline = (Pipeline) tlc.visit(workflow);
      System.out.println("After creating the Pipeline object via visit(Workflow)...");
      LoniSpecification.getXMLGenerator().generate(pipeline, outputPath);
      System.out.println("After generating output file...");
   
    } catch (FileNotFoundException e) {
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    System.out.println("==="+path+"===");
    Workflow G;
    try {
      G = TavernaSpecification.getXMLParser().parse(new File(path));
      TavernaToLoniConverter tlc = new TavernaToLoniConverter();
      Pipeline p = (Pipeline) tlc.visit(G);
      try {
        LoniSpecification.getXMLGenerator().generate(p, output);
      } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
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public class JohnTestLoniToTaverna {

  public static void TestLoniXML (String path, String output) {
    System.out.println("==="+path + ">" + output+"===");
    Pipeline p;
    try {
      p = LoniSpecification.getXMLParser().parse(new File(path));
     
      try {
        LoniSpecification.getXMLGenerator().generate(p, output);
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    }
  }
 
  public static void TestLoniToTav (String path, String output) {
    System.out.println("==="+path + ">" + output+"===");
    Pipeline p;
    try {
      p = LoniSpecification.getXMLParser().parse(new File(path));
      LoniToTavernaConverter l2t = new LoniToTavernaConverter();
      Workflow workflow= (Workflow) l2t.visit(p);
      try {
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    }
  }
 
  public static void TestLoniXML (String path, String output) {
    System.out.println("==="+path + ">" + output+"===");
    Pipeline p;
    try {
      p = LoniSpecification.getXMLParser().parse(new File(path));
     
      try {
        LoniSpecification.getXMLGenerator().generate(p, output);
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    }
  }
   
  public static void TestLoniToTaverna (String path, String output) {
      System.out.println("==="+path + ">" + output+"===");
      Pipeline p;
      try {
        p = LoniSpecification.getXMLParser().parse(new File(path));
        LoniToTavernaConverter l2t = new LoniToTavernaConverter();
        Workflow workflow= (Workflow) l2t.visit(p);
        try {
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Related Classes of LONI.tree.workflow.Pipeline

  • CLInterface.PipelineConverter
  • Galaxy.Visitor.Local.GalaxyToLoniWorkflowConverter
  • Galaxy.Visitor.Webservice.GalaxyToLoniWorkflowConverter
  • LONI.tree.GraphObject.ModuleGroup
  • Taverna.Visitor.TavernaToLoniConverter
  • Test.ChrisTestSpecifications
  • Test.GalaxyTestSuite
  • Test.JohnnyTestTavToLoni
  • Test.JohnTestLoniToTaverna
  • Test.NickTestTavToPipe
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