Coverage for biobb_amber/sander/common.py: 69%

1#!/usr/bin/env python3 

2 

3""" Common functions for package biobb_amber.sander """ 

4from pathlib import Path, PurePath 

5from biobb_common.tools import file_utils as fu 

6 

7 

8# CHECK INPUT PARAMETERS 

9def check_input_path(path, argument, optional, out_log, classname): 

10 """ Checks input file """ 

11 if optional and not path: 

12 return None 

13 if not Path(path).exists(): 

14 fu.log("Path: " + path) 

15 fu.log("Path " + path + " --- " + classname + ': Unexisting %s file, exiting' % argument, out_log) 

16 raise SystemExit(classname + ': Unexisting %s file' % argument) 

17 file_extension = PurePath(path).suffix 

18 if not is_valid_file(file_extension[1:], argument): 

19 fu.log(classname + ': Format %s in %s file is not compatible' % (file_extension[1:], argument), out_log) 

20 raise SystemExit(classname + ': Format %s in %s file is not compatible' % (file_extension[1:], argument)) 

21 return path 

22 

23 

24def check_output_path(path, argument, optional, out_log, classname): 

25 """ Checks output file """ 

26 if optional and not path: 

27 return None 

28 if PurePath(path).parent and not Path(PurePath(path).parent).exists(): 

29 fu.log(classname + ': Unexisting %s folder, exiting' % argument, out_log) 

30 raise SystemExit(classname + ': Unexisting %s folder' % argument) 

31 file_extension = PurePath(path).suffix 

32 if not is_valid_file(file_extension[1:], argument): 

33 fu.log(classname + ': Format %s in %s file is not compatible' % (file_extension[1:], argument), out_log) 

34 raise SystemExit(classname + ': Format %s in %s file is not compatible' % (file_extension[1:], argument)) 

35 return path 

36 

37 

38def is_valid_file(ext, argument): 

39 """ Checks if file format is compatible """ 

40 formats = { 

41 'input_top_path': ['top', 'prmtop', 'parmtop'], 

42 'input_crd_path': ['crd', 'inpcrd', 'mdcrd', 'rst', 'rst7', 'netcdf', 'nc', 'ncrst'], 

43 'input_mdin_path': ['mdin', 'txt', 'in'], 

44 'input_cpin_path': ['cpin', 'txt', 'in'], 

45 'input_ref_path': ['crd', 'inpcrd', 'mdcrd', 'rst', 'rst7', 'netcdf', 'nc', 'ncrst'], 

46 'output_log_path': ['log', 'out', 'txt', 'o'], 

47 'output_traj_path': ['trj', 'crd', 'mdcrd', 'x', 'netcdf', 'nc'], 

48 'output_rst_path': ['rst', 'rst7', 'netcdf', 'nc', 'ncrst'], 

49 'output_cpout_path': ['cpout'], 

50 'output_cprst_path': ['cprst', 'rst', 'rst7'], 

51 'output_mdinfo_path': ['mdinfo'] 

52 } 

53 return ext in formats[argument]