old_contents: import os
  import sys
  import tempfile
  
  POLYDATA='POLYDATA'
  
  def asbool( val ):
      return str( val ).lower() in [ 'yes', 'true' ]
  
  def get_format_and_type( galaxy_ext ):
      # Define the output file format and type.
      format = None
      datatype = None
      if galaxy_ext in [ 'vtkascii', 'vtkbinary' ]:
          format = 'vtk'
      elif galaxy_ext in [ 'plyascii', 'plybinary' ]:
          format = 'ply'
      if galaxy_ext in [ 'vtkascii', 'plyascii' ]:
          datatype = 'ascii'
      elif galaxy_ext in [ 'vtkbinary', 'plybinary' ]:
          datatype = 'binary'
      return format, datatype
  
  def get_input_file_path( tmp_dir, input_file, format ):
      """
      iCqSol uses file extensions (e.g., .ply, .vtk) when reading and
      writing files, so the Galaxy dataset naming convention of
      setting all file extensions as .dat must be handled.
      """
      file_path = get_temporary_file_path( tmp_dir, format )
      # Remove the file so we can create a symlink.
      os.remove( file_path )
      os.symlink( input_file, file_path )
      return file_path
  
  def get_temp_dir( prefix='tmp-vtk-', dir=None ):
      """
      Return a temporary directory.
      """
      return tempfile.mkdtemp( prefix=prefix, dir=dir )
  
  def get_tempfilename( dir=None, suffix=None ):
      """
      Return a temporary file name.
      """
      fd, name = tempfile.mkstemp( suffix=suffix, dir=dir )
      os.close( fd )
  
  def get_temporary_file_path( tmp_dir, file_extension ):
      """
      Return the path to a temporary file with a valid VTK format
      file extension.
      """
      return get_tempfilename( tmp_dir, file_extension )
  
  def stop_err( msg ):
      sys.stderr.write( "%s\n" % msg )
      sys.exit()
  
new_contents: import os
  import sys
  import tempfile
  
  POLYDATA='POLYDATA'
  
  def asbool( val ):
      return str( val ).lower() in [ 'yes', 'true' ]
  
  def get_format_and_type( galaxy_ext ):
      # Define the output file format and type.
      format = None
      datatype = None
      if galaxy_ext in [ 'vtkascii', 'vtkbinary' ]:
          format = 'vtk'
      elif galaxy_ext in [ 'plyascii', 'plybinary' ]:
          format = 'ply'
      if galaxy_ext in [ 'vtkascii', 'plyascii' ]:
          datatype = 'ascii'
      elif galaxy_ext in [ 'vtkbinary', 'plybinary' ]:
          datatype = 'binary'
      return format, datatype
  
  def get_input_file_path( tmp_dir, input_file, format ):
      """
      iCqSol uses file extensions (e.g., .ply, .vtk) when reading and
      writing files, so the Galaxy dataset naming convention of
      setting all file extensions as .dat must be handled.
      """
      file_path = get_temporary_file_path( tmp_dir, format )
      # Remove the file so we can create a symlink.
      os.remove( file_path )
      os.symlink( input_file, file_path )
      return file_path
  
  def get_temp_dir( prefix='tmp-vtk-', dir=None ):
      """
      Return a temporary directory.
      """
      return tempfile.mkdtemp( prefix=prefix, dir=dir )
  
  def get_tempfilename( dir=None, suffix=None ):
      """
      Return a temporary file name.
      """
      fd, name = tempfile.mkstemp( suffix=suffix, dir=dir )
      os.close( fd )
      return name
  
  def get_temporary_file_path( tmp_dir, file_extension ):
      """
      Return the path to a temporary file with a valid VTK format
      file extension.
      """
      return get_tempfilename( tmp_dir, file_extension )
  
  def stop_err( msg ):
      sys.stderr.write( "%s\n" % msg )
      sys.exit()
  
subject: Fix for getting temp file