Coverage for biobb_model/model/common.py: 36%

1"""Common functions for package biobb_model.model""" 

2 

3import logging 

4from typing import Optional, Union 

5 

6from biobb_common.tools import file_utils as fu 

7 

8 

9def modeller_installed( 

10 out_log: Optional[logging.Logger] = None, 

11 global_log: Optional[logging.Logger] = None, 

12) -> bool: 

13 try: 

14 import modeller # type: ignore 

15 from modeller import automodel 

16 

17 fu.log( 

18 f"Modeller is installed in your environment. Modeller version: {modeller.__version__}", 

19 out_log, 

20 global_log, 

21 ) 

22 fu.log(f"Modeller automodel class: {automodel.automodel}", local_log=out_log) 

23 except ImportError: 

24 fu.log( 

25 "Modeller is not installed in your environment.\nPlease install it by typing:\n\nconda install -c salilab modeller\n", 

26 out_log, 

27 global_log, 

28 ) 

29 return False 

30 

31 return True 

32 

33 

34# TODO: Move this function to biobb_common.tools.file_utils 

35def _from_string_to_list(input_data: Optional[Union[str, list[str]]]) -> list[str]: 

36 """ 

37 Converts a string to a list, splitting by commas or spaces. If the input is already a list, returns it as is. 

38 Returns an empty list if input_data is None. 

39 

40 Parameters: 

41 input_data (str, list, or None): The string, list, or None value to convert. 

42 

43 Returns: 

44 list: A list of string elements or an empty list if input_data is None. 

45 """ 

46 if input_data is None: 

47 return [] 

48 

49 if isinstance(input_data, list): 

50 # If input is already a list, return it 

51 return input_data 

52 

53 # If input is a string, determine the delimiter based on presence of commas 

54 delimiter = "," if "," in input_data else " " 

55 items = input_data.split(delimiter) 

56 

57 # Remove whitespace from each item and ignore empty strings 

58 processed_items = [item.strip() for item in items if item.strip()] 

59 

60 return processed_items