Program: 188803
Project: 188803
Buggy source:
@Override public Report execute(IndexService index,ModelService model,StorageService storage,List<AIP> list) throws PluginException {
  for (  AIP aip : list) {
    LOGGER.debug("String_Node_Str" + aip.getId());
    for (    String representationID : aip.getRepresentationIds()) {
      LOGGER.debug("String_Node_Str" + representationID + "String_Node_Str"+ aip.getId());
      try {
        Path data=Files.createTempDirectory("String_Node_Str");
        StorageService tempStorage=new FileStorageService(data);
        StoragePath representationPath=ModelUtils.getRepresentationPath(aip.getId(),representationID);
        tempStorage.copy(storage,representationPath,representationPath);
        String siegfriedOutput=SiegfriedPluginUtils.runSiegfriedOnPath(data.resolve(representationPath.asString()));
        final JSONObject obj=new JSONObject(siegfriedOutput);
        JSONArray files=(JSONArray)obj.get("String_Node_Str");
        List<org.roda.core.model.File> updatedFiles=new ArrayList<org.roda.core.model.File>();
        for (int i=0; i < files.length(); i++) {
          JSONObject fileObject=files.getJSONObject(i);
          String fileName=fileObject.getString("String_Node_Str");
          fileName=fileName.substring(fileName.lastIndexOf(File.separatorChar) + 1);
          long fileSize=fileObject.getLong("String_Node_Str");
          Path p=Files.createTempFile("String_Node_Str","String_Node_Str");
          Files.write(p,fileObject.toString().getBytes());
          Binary resource=(Binary)FSUtils.convertPathToResource(p.getParent(),p);
          LOGGER.debug("String_Node_Str" + aip.getId() + "String_Node_Str"+ representationID+ "String_Node_Str"+ fileName+ "String_Node_Str");
          try {
            model.createOtherMetadata(aip.getId(),representationID,fileName + "String_Node_Str","String_Node_Str",resource);
          }
 catch (          ModelServiceException e1) {
            e1.printStackTrace();
          }
          p.toFile().delete();
          JSONArray matches=(JSONArray)fileObject.get("String_Node_Str");
          if (matches.length() > 0) {
            for (int j=0; j < matches.length(); j++) {
              JSONObject match=(JSONObject)matches.get(j);
              if (match.getString("String_Node_Str").equalsIgnoreCase("String_Node_Str")) {
                String pronom=match.getString("String_Node_Str");
                String mime=match.getString("String_Node_Str");
                String version=match.getString("String_Node_Str");
                String extension="String_Node_Str";
                if (fileName.contains("String_Node_Str")) {
                  extension=fileName.substring(fileName.lastIndexOf('.'));
                }
                System.out.println(fileName + "String_Node_Str" + pronom+ "String_Node_Str"+ mime);
                try {
                  org.roda.core.model.File f=model.retrieveFile(aip.getId(),representationID,fileName);
                  FileFormat ff=new org.roda.core.data.v2.FileFormat();
                  ff.setPronom(pronom);
                  ff.setMimeType(mime);
                  ff.setVersion(version);
                  ff.setCreatedDate(new Date());
                  ff.setExtension(extension);
                  f.setFileFormat(ff);
                  f.setSize(fileSize);
                  updatedFiles.add(f);
                }
 catch (                ModelServiceException e) {
                  e.printStackTrace();
                }
              }
            }
          }
        }
        model.updateFileFormats(updatedFiles);
        FSUtils.deletePath(data);
      }
 catch (      StorageServiceException|PluginException|IOException|ModelServiceException e) {
        e.printStackTrace();
        LOGGER.error("String_Node_Str" + aip.getId() + "String_Node_Str"+ e.getMessage());
      }
    }
  }
  return null;
}

Fixed version (ground truth):
@Override public Report execute(IndexService index,ModelService model,StorageService storage,List<AIP> list) throws PluginException {
  for (  AIP aip : list) {
    LOGGER.debug("String_Node_Str" + aip.getId());
    for (    String representationID : aip.getRepresentationIds()) {
      LOGGER.debug("String_Node_Str" + representationID + "String_Node_Str"+ aip.getId());
      try {
        Path data=Files.createTempDirectory("String_Node_Str");
        StorageService tempStorage=new FileStorageService(data);
        StoragePath representationPath=ModelUtils.getRepresentationPath(aip.getId(),representationID);
        tempStorage.copy(storage,representationPath,representationPath);
        String siegfriedOutput=SiegfriedPluginUtils.runSiegfriedOnPath(data.resolve(representationPath.asString()));
        final JSONObject obj=new JSONObject(siegfriedOutput);
        JSONArray files=(JSONArray)obj.get("String_Node_Str");
        List<org.roda.core.model.File> updatedFiles=new ArrayList<org.roda.core.model.File>();
        for (int i=0; i < files.length(); i++) {
          JSONObject fileObject=files.getJSONObject(i);
          String fileName=fileObject.getString("String_Node_Str");
          fileName=fileName.substring(fileName.lastIndexOf(File.separatorChar) + 1);
          long fileSize=fileObject.getLong("String_Node_Str");
          Path p=Files.createTempFile("String_Node_Str","String_Node_Str");
          Files.write(p,fileObject.toString().getBytes());
          Binary resource=(Binary)FSUtils.convertPathToResource(p.getParent(),p);
          LOGGER.debug("String_Node_Str" + aip.getId() + "String_Node_Str"+ representationID+ "String_Node_Str"+ fileName+ "String_Node_Str");
          model.createOtherMetadata(aip.getId(),representationID,fileName + "String_Node_Str","String_Node_Str",resource);
          p.toFile().delete();
          JSONArray matches=(JSONArray)fileObject.get("String_Node_Str");
          if (matches.length() > 0) {
            for (int j=0; j < matches.length(); j++) {
              JSONObject match=(JSONObject)matches.get(j);
              if (match.getString("String_Node_Str").equalsIgnoreCase("String_Node_Str")) {
                String pronom=match.getString("String_Node_Str");
                String mime=match.getString("String_Node_Str");
                String version=match.getString("String_Node_Str");
                String extension="String_Node_Str";
                if (fileName.contains("String_Node_Str")) {
                  extension=fileName.substring(fileName.lastIndexOf('.'));
                }
                System.out.println(fileName + "String_Node_Str" + pronom+ "String_Node_Str"+ mime);
                try {
                  org.roda.core.model.File f=model.retrieveFile(aip.getId(),representationID,fileName);
                  FileFormat ff=new org.roda.core.data.v2.FileFormat();
                  ff.setPronom(pronom);
                  ff.setMimeType(mime);
                  ff.setVersion(version);
                  ff.setCreatedDate(new Date());
                  ff.setExtension(extension);
                  f.setFileFormat(ff);
                  f.setSize(fileSize);
                  updatedFiles.add(f);
                }
 catch (                RequestNotValidException|AuthorizationDeniedException e) {
                  LOGGER.error("String_Node_Str" + e.getMessage(),e);
                }
              }
            }
          }
        }
        model.updateFileFormats(updatedFiles);
        FSUtils.deletePath(data);
      }
 catch (      PluginException|IOException|ModelServiceException|NotFoundException|GenericException|RequestNotValidException|AuthorizationDeniedException|AlreadyExistsException e) {
        e.printStackTrace();
        LOGGER.error("String_Node_Str" + aip.getId() + "String_Node_Str"+ e.getMessage());
      }
    }
  }
  return null;
}