Program: 188437
Project: 188437
Buggy source:
private static <T extends IsRODAObject>List<LinkingIdentifier> runSiegfriedOnRepresentationOrFile(Plugin<T> plugin,ModelService model,String aipId,String representationId,List<String> fileDirectoryPath,String fileId,Path path) throws RequestNotValidException, GenericException, NotFoundException, AuthorizationDeniedException, PluginException {
  List<LinkingIdentifier> sources=new ArrayList<LinkingIdentifier>();
  if (Files.exists(path)) {
    String siegfriedOutput=SiegfriedPluginUtils.runSiegfriedOnPath(path);
    final JsonNode jsonObject=JsonUtils.parseJson(siegfriedOutput);
    final JsonNode files=jsonObject.get("String_Node_Str");
    for (    JsonNode file : files) {
      Path fullFsPath=Paths.get(file.get("String_Node_Str").asText());
      Path relativeFsPath=path.relativize(fullFsPath);
      String jsonFileId=fullFsPath.getFileName().toString();
      List<String> jsonFilePath=new ArrayList<>(fileDirectoryPath);
      if (fileId != null) {
        jsonFilePath.add(fileId);
      }
      for (int j=0; j < relativeFsPath.getNameCount() && StringUtils.isNotBlank(relativeFsPath.getName(j).toString()); j++) {
        jsonFilePath.add(relativeFsPath.getName(j).toString());
      }
      jsonFilePath.remove(jsonFilePath.size() - 1);
      ContentPayload payload=new StringContentPayload(file.toString());
      model.createOrUpdateOtherMetadata(aipId,representationId,jsonFilePath,jsonFileId,SiegfriedPlugin.FILE_SUFFIX,RodaConstants.OTHER_METADATA_TYPE_SIEGFRIED,payload,false);
      sources.add(PluginHelper.getLinkingIdentifier(aipId,representationId,jsonFilePath,jsonFileId,RodaConstants.PRESERVATION_LINKING_OBJECT_SOURCE));
      final JsonNode matches=file.get("String_Node_Str");
      for (      JsonNode match : matches) {
        String format=null;
        String version=null;
        String pronom=null;
        String mime=null;
        if (plugin.getVersion().startsWith("String_Node_Str") || plugin.getVersion().startsWith("String_Node_Str")) {
          if (match.get("String_Node_Str").textValue().equalsIgnoreCase("String_Node_Str")) {
            format=match.get("String_Node_Str").textValue();
            version=match.get("String_Node_Str").textValue();
            pronom=match.get("String_Node_Str").textValue();
            mime=match.get("String_Node_Str").textValue();
          }
        }
 else {
          if (match.get("String_Node_Str").textValue().equalsIgnoreCase("String_Node_Str")) {
            format=match.get("String_Node_Str").textValue();
            version=match.get("String_Node_Str").textValue();
            pronom=match.get("String_Node_Str").textValue();
            mime=match.get("String_Node_Str").textValue();
          }
        }
        PremisV3Utils.updateFormatPreservationMetadata(model,aipId,representationId,jsonFilePath,jsonFileId,format,version,pronom,mime,true);
      }
    }
  }
  return sources;
}

Fixed version (ground truth):
private static <T extends IsRODAObject>List<LinkingIdentifier> runSiegfriedOnRepresentationOrFile(Plugin<T> plugin,ModelService model,String aipId,String representationId,List<String> fileDirectoryPath,String fileId,Path path) throws RequestNotValidException, GenericException, NotFoundException, AuthorizationDeniedException, PluginException {
  List<LinkingIdentifier> sources=new ArrayList<LinkingIdentifier>();
  if (Files.exists(path)) {
    String siegfriedOutput=SiegfriedPluginUtils.runSiegfriedOnPath(path);
    final JsonNode jsonObject=JsonUtils.parseJson(siegfriedOutput);
    final JsonNode files=jsonObject.get("String_Node_Str");
    for (    JsonNode file : files) {
      Path fullFsPath=Paths.get(file.get("String_Node_Str").asText());
      Path relativeFsPath=path.relativize(fullFsPath);
      String jsonFileId=fullFsPath.getFileName().toString();
      List<String> jsonFilePath=new ArrayList<>(fileDirectoryPath);
      if (fileId != null) {
        jsonFilePath.add(fileId);
      }
      for (int j=0; j < relativeFsPath.getNameCount() && StringUtils.isNotBlank(relativeFsPath.getName(j).toString()); j++) {
        jsonFilePath.add(relativeFsPath.getName(j).toString());
      }
      jsonFilePath.remove(jsonFilePath.size() - 1);
      ContentPayload payload=new StringContentPayload(file.toString());
      model.createOrUpdateOtherMetadata(aipId,representationId,jsonFilePath,jsonFileId,SiegfriedPlugin.FILE_SUFFIX,RodaConstants.OTHER_METADATA_TYPE_SIEGFRIED,payload,false);
      sources.add(PluginHelper.getLinkingIdentifier(aipId,representationId,jsonFilePath,jsonFileId,RodaConstants.PRESERVATION_LINKING_OBJECT_SOURCE));
      final JsonNode matches=file.get("String_Node_Str");
      for (      JsonNode match : matches) {
        String format=null;
        String version=null;
        String pronom=null;
        String mime=null;
        String[] pluginVersion=plugin.getVersion().split("String_Node_Str");
        if ("String_Node_Str".equals(pluginVersion[0])) {
          if (Integer.parseInt(pluginVersion[1]) > 4) {
            if (match.get("String_Node_Str").textValue().equalsIgnoreCase("String_Node_Str")) {
              format=match.get("String_Node_Str").textValue();
              version=match.get("String_Node_Str").textValue();
              pronom=match.get("String_Node_Str").textValue();
              mime=match.get("String_Node_Str").textValue();
            }
          }
 else {
            if (match.get("String_Node_Str").textValue().equalsIgnoreCase("String_Node_Str")) {
              format=match.get("String_Node_Str").textValue();
              version=match.get("String_Node_Str").textValue();
              pronom=match.get("String_Node_Str").textValue();
              mime=match.get("String_Node_Str").textValue();
            }
          }
        }
        PremisV3Utils.updateFormatPreservationMetadata(model,aipId,representationId,jsonFilePath,jsonFileId,format,version,pronom,mime,true);
      }
    }
  }
  return sources;
}