old_contents: #!/usr/bin/env python
  
  """export_all_data.py - script for exporting all available data"""
  
  import os
  import argparse
  
  from collectionbatchtool import *
  
  
  def export_all_data(
          config_file, output_dir=None,
          drop_empty_columns=False, quiet=True):
      """
      Export data from Specify to CSV files.
  
      Parameters
      ----------
      output_dir : str
          Path to the output directory.
      """
      apply_user_settings(config_file) 
      output_dir = output_dir if output_dir else ''
      for tabledataset_subclass in TableDataset.__subclasses__():
          instance = tabledataset_subclass()
          if instance.database_query.count() > 0:  # no files without data
              instance.from_database(quiet=quiet)
              filename = instance.model.__name__.lower() + '.csv'
              filepath = os.path.join(output_dir, filename)
              instance.to_csv(
                  filepath,
                  update_sourceid=True,
                  drop_empty_columns=drop_empty_columns,
                  quiet=quiet)
  
  
  if __name__ == '__main__':
      parser = argparse.ArgumentParser(
          description='A command-line script to export Specify data.')
      parser.add_argument(
          'config_file', type=argparse.FileType('rU'),
          help='path to a config-file')
      parser.add_argument(
          'output_dir', default='.', nargs='?',
          help='path to output directory')
      parser.add_argument(
          '-d', '--drop-empty-columns', dest='drop_empty_columns',
          action='store_true', help='drop columns without data')
      parser.add_argument(
          '-v', '--verbose', action='store_true')
      args = parser.parse_args()
   
      if not os.path.isdir(args.output_dir):
          msg = "%d is not valid directory" % args.output_dir
          raise argparse.ArgumentTypeError(msg)
      
      quiet = False if args.verbose else True
   
      export_all_data(
          args.config_file.name,
          output_dir=args.output_dir,
          drop_empty_columns=args.drop_empty_columns,
          quiet=quiet)
  
new_contents: #!/usr/bin/env python
  
  """
  export_all_data.py - script for exporting available data.
  """
  
  import os
  import argparse
  
  from collectionbatchtool import *
  
  
  def export_all_data(
          config_file, output_dir=None,
          drop_empty_columns=False, quiet=True):
      """
      Export data from Specify to CSV files.
  
      Parameters
      ----------
      output_dir : str
          Path to the output directory.
      """
      apply_user_settings(config_file) 
      output_dir = output_dir if output_dir else ''
      for tabledataset_subclass in TableDataset.__subclasses__():
          instance = tabledataset_subclass()
          if instance.database_query.count() > 0:  # no files without data
              instance.from_database(quiet=quiet)
              filename = instance.model.__name__.lower() + '.csv'
              filepath = os.path.join(output_dir, filename)
              instance.to_csv(
                  filepath,
                  update_sourceid=True,
                  drop_empty_columns=drop_empty_columns,
                  quiet=quiet)
  
  
  if __name__ == '__main__':
      parser = argparse.ArgumentParser(
          description='A command-line script to export Specify data.')
      parser.add_argument(
          'config_file', type=argparse.FileType('rU'),
          help='path to a config-file')
      parser.add_argument(
          'output_dir', default='.', nargs='?',
          help='path to output directory')
      parser.add_argument(
          '-d', '--drop-empty-columns', dest='drop_empty_columns',
          action='store_true', help='drop columns without data')
      parser.add_argument(
          '-v', '--verbose', action='store_true')
      args = parser.parse_args()
   
      if not os.path.isdir(args.output_dir):
          msg = "%d is not valid directory" % args.output_dir
          raise argparse.ArgumentTypeError(msg)
      
      quiet = False if args.verbose else True
   
      export_all_data(
          args.config_file.name,
          output_dir=args.output_dir,
          drop_empty_columns=args.drop_empty_columns,
          quiet=quiet)
  
subject: Fix typo