Program: 188992
Project: 188992
Buggy source:
protected SampleInfo generateSampleInfo(String prettyName,String projectCode,String individualNumber,String librarySourceTemplateType,String tissueOrigin,String tissueType,String libraryType,String librarySizeCode,String barcode,Integer organismId,String targetedResequencing,String tissuePreparation) throws Exception {
  if (individualNumber == null || individualNumber.isEmpty() || projectCode == null || projectCode.isEmpty()) {
    throw new Exception("String_Node_Str" + projectCode + "String_Node_Str"+ individualNumber);
  }
  SampleInfo sa=new SampleInfo();
  sa.setIndividualNumber(individualNumber);
  sa.setProjectCode(projectCode);
  if (libraryType == null || libraryType.isEmpty()) {
    libraryType=choiceOf(prettyName,"String_Node_Str",libraryTypeList,this.lity);
    this.lity=libraryType;
  }
  if (librarySourceTemplateType == null || librarySourceTemplateType.isEmpty()) {
    librarySourceTemplateType=choiceOf(prettyName,"String_Node_Str",librarySourceTemplateTypeList,this.lstety);
    this.lstety=librarySourceTemplateType;
  }
  if (targetedResequencing == null || targetedResequencing.isEmpty()) {
    targetedResequencing=choiceOf(prettyName,"String_Node_Str",targetedResequencingList,this.tare);
    this.tare=targetedResequencing;
  }
  if (tissueOrigin == null || tissueOrigin.isEmpty()) {
    tissueOrigin=choiceOf(prettyName,"String_Node_Str",tissueOriginList,this.tior);
    if (tissueOrigin.isEmpty()) {
      tissueOrigin="String_Node_Str";
    }
 else {
      this.tior=tissueOrigin;
    }
  }
  if (tissueType == null || tissuePreparation.isEmpty()) {
    tissuePreparation=choiceOf(prettyName,"String_Node_Str",tissuePreparationList,this.tipr);
    this.tipr=tissuePreparation;
  }
  if (tissueType == null || tissueType.isEmpty()) {
    tissueType=choiceOf(prettyName,"String_Node_Str",tissueTypeList,this.tity);
    if (tissueType.isEmpty()) {
      tissueType="String_Node_Str";
    }
 else {
      this.tity=tissueType;
    }
  }
  if (librarySizeCode == null || librarySizeCode.isEmpty() || !StringUtils.isNumeric(librarySizeCode)) {
    Integer lSize=ConsoleAdapter.getInstance().promptInteger("String_Node_Str",this.lSize);
    if (lSize <= 0) {
      librarySizeCode="String_Node_Str";
    }
 else {
      this.lSize=lSize;
      librarySizeCode=lSize.toString();
    }
  }
  StringBuilder name=new StringBuilder();
  name.append(projectCode).append("String_Node_Str").append(individualNumber);
  name.append("String_Node_Str").append(tissueOrigin).append("String_Node_Str").append(tissueType).append("String_Node_Str").append(libraryType).append("String_Node_Str");
  name.append(librarySizeCode).append("String_Node_Str").append(librarySourceTemplateType);
  sa.setName(name.toString());
  sa.setTissueOrigin(tissueOrigin);
  sa.setTissuePreparation(tissuePreparation);
  sa.setTissueType(tissueType);
  if (barcode == null || barcode.isEmpty()) {
    barcode=ConsoleAdapter.getInstance().promptString("String_Node_Str","String_Node_Str");
  }
  sa.setBarcode(barcode);
  if (organismId == null || organismId <= 0) {
    List<Organism> organisms=new ArrayList<Organism>(metadata.getOrganisms());
    for (int i=0; i < organisms.size(); i++) {
      Log.stdout(i + "String_Node_Str" + organisms.get(i).toString());
    }
    organismId=ConsoleAdapter.getInstance().promptInteger("String_Node_Str",31);
  }
  sa.setOrganismId(organismId);
  return sa;
}

Fixed version (ground truth):
protected SampleInfo generateSampleInfo(String prettyName,String projectCode,String individualNumber,String librarySourceTemplateType,String tissueOrigin,String tissueType,String libraryType,String librarySizeCode,String barcode,Integer organismId,String targetedResequencing,String tissuePreparation) throws Exception {
  if (individualNumber == null || individualNumber.isEmpty() || projectCode == null || projectCode.isEmpty()) {
    throw new Exception("String_Node_Str" + projectCode + "String_Node_Str"+ individualNumber);
  }
  SampleInfo sa=new SampleInfo();
  sa.setIndividualNumber(individualNumber);
  sa.setProjectCode(projectCode);
  if (libraryType == null || libraryType.isEmpty()) {
    libraryType=choiceOf(prettyName,"String_Node_Str",libraryTypeList,this.lity);
    this.lity=libraryType;
  }
  if (librarySourceTemplateType == null || librarySourceTemplateType.isEmpty()) {
    librarySourceTemplateType=choiceOf(prettyName,"String_Node_Str",librarySourceTemplateTypeList,this.lstety);
    this.lstety=librarySourceTemplateType;
  }
  if (targetedResequencing == null || targetedResequencing.isEmpty()) {
    targetedResequencing=choiceOf(prettyName,"String_Node_Str",targetedResequencingList,this.tare);
    this.tare=targetedResequencing;
  }
  if (tissueOrigin == null || tissueOrigin.isEmpty()) {
    tissueOrigin=choiceOf(prettyName,"String_Node_Str",tissueOriginList,this.tior);
    if (tissueOrigin.isEmpty()) {
      tissueOrigin="String_Node_Str";
    }
 else {
      this.tior=tissueOrigin;
    }
  }
  if (tissuePreparation == null || tissuePreparation.isEmpty()) {
    tissuePreparation=choiceOf(prettyName,"String_Node_Str",tissuePreparationList,this.tipr);
    this.tipr=tissuePreparation;
  }
  if (tissueType == null || tissueType.isEmpty()) {
    tissueType=choiceOf(prettyName,"String_Node_Str",tissueTypeList,this.tity);
    if (tissueType.isEmpty()) {
      tissueType="String_Node_Str";
    }
 else {
      this.tity=tissueType;
    }
  }
  if (librarySizeCode == null || librarySizeCode.isEmpty() || !StringUtils.isNumeric(librarySizeCode)) {
    Integer lSize=ConsoleAdapter.getInstance().promptInteger("String_Node_Str",this.lSize);
    if (lSize <= 0) {
      librarySizeCode="String_Node_Str";
    }
 else {
      this.lSize=lSize;
      librarySizeCode=lSize.toString();
    }
  }
  StringBuilder name=new StringBuilder();
  name.append(projectCode).append("String_Node_Str").append(individualNumber);
  name.append("String_Node_Str").append(tissueOrigin).append("String_Node_Str").append(tissueType).append("String_Node_Str").append(libraryType).append("String_Node_Str");
  name.append(librarySizeCode).append("String_Node_Str").append(librarySourceTemplateType);
  sa.setName(name.toString());
  sa.setTissueOrigin(tissueOrigin);
  sa.setTissuePreparation(tissuePreparation);
  sa.setTissueType(tissueType);
  if (barcode == null || barcode.isEmpty()) {
    barcode=ConsoleAdapter.getInstance().promptString("String_Node_Str","String_Node_Str");
  }
  sa.setBarcode(barcode);
  if (organismId == null || organismId <= 0) {
    List<Organism> organisms=new ArrayList<Organism>(metadata.getOrganisms());
    for (int i=0; i < organisms.size(); i++) {
      Log.stdout(i + "String_Node_Str" + organisms.get(i).toString());
    }
    organismId=ConsoleAdapter.getInstance().promptInteger("String_Node_Str",31);
  }
  sa.setOrganismId(organismId);
  return sa;
}