def is_valid_cmd_args(self, cmd_arg_string):
"""
Given a yap command argument string,
if enable is set to yes, validates the command arguments
Returns true if it is valid,a warning message if a basename is found in
one of the arguments, false otherwise.
If enable is set to no, returns true
A command argument is valid if all paths or basenames contained in it
exist in system
"""
if self.enable != "yes":
return True # True is default when disabled
# strip starting and trailing spaces
cmd_arg_string = cmd_arg_string.strip()
if len(cmd_arg_string) <= 0:
return True # return True if empty string
# find all file names and paths in argument string
path_ops = yap_path_checks()
cmd_arg_items = path_ops.extract_files_and_paths(cmd_arg_string)
# return True if no files/paths in command arguments
if len(cmd_arg_items) <= 0:
return True
# check if all files and paths exist in command argument
return self.is_valid_cmd_paths(
cmd_arg_items,
path_ops.valid_path_or_link,
path_ops.basename_exists)
def is_valid_cmd_args(self, cmd_arg_string):
"""
Given a yap command argument string,
if enable is set to yes, validates the command arguments
Returns true if it is valid,a warning message if a basename is found in
one of the arguments, false otherwise.
If enable is set to no, returns true
A command argument is valid if all paths or basenames contained in it
exist in system
"""
if self.enable != "yes":
return True # True is default when disabled
# strip starting and trailing spaces
cmd_arg_string = cmd_arg_string.strip()
if len(cmd_arg_string) <= 0:
return True # return True if empty string
# find all file names and paths in argument string
path_ops = yap_path_checks()
cmd_arg_items = path_ops.extract_files_and_paths(cmd_arg_string)
# return True if no files/paths in command arguments
if len(cmd_arg_items) <= 0:
return True
# check if all files and paths exist in command argument
return self.is_valid_cmd_paths(cmd_arg_items,
path_ops.valid_path_or_link,
path_ops.basename_exists)
def check_files_when_postproc_only(
self,
postprocess_cmd_arr,
input_files_path):
"""
When run postprocess alone, check if needed file of given
input_file_type exists in given input_directory.
"""
path_check = yap_path_checks() # new object of yap_path_checks
for post_cmd in postprocess_cmd_arr:
# each command in postprocess
file_info = post_cmd[1]
command_name = post_cmd[2][0][0]
found = 'not check'
# file_info e.g.:
# ['input_file_type *queryname*.sam',
# 'input_directory aligner_output']
for info in file_info:
# get input_file_type and input_directory
if info.startswith("input_file_type"):
l = len('input_file_type')
input_file_type = info[l:].strip()
if info.startswith("input_directory"):
l = len("input_directory")
input_directory = info[l:].strip()
if input_directory == 'aligner_output':
# when the input_directory is 'aligner_output',
# check if the required input_file_type
# exists in the input_directory
input_directory = input_files_path.split(';')
found = \
path_check.file_or_basename_exist_in_any(
input_directory,
input_file_type)
if found == 'files_found' or found == 'not check':
pass
elif found == 'basename found':
warning_string = "Warning: basename found " + \
"instead of filename in " + \
" input file type. Please" + \
" make sure that command '" + \
command_name + "' can work with" + \
"basenames."
self.warning_list.append(warning_string)
elif found == 'not found':
self.error_list.append("Error: required file " +
input_file_type + " not exists" +
" in aligner_output directory.")
def check_files_when_postproc_only(self, postprocess_cmd_arr,
input_files_path):
"""
When run postprocess alone, check if needed file of given
input_file_type exists in given input_directory.
"""
path_check = yap_path_checks() # new object of yap_path_checks
for post_cmd in postprocess_cmd_arr:
# each command in postprocess
file_info = post_cmd[1]
command_name = post_cmd[2][0][0]
found = 'not check'
# file_info e.g.:
# ['input_file_type *queryname*.sam',
# 'input_directory aligner_output']
for info in file_info:
# get input_file_type and input_directory
if info.startswith("input_file_type"):
l = len('input_file_type')
input_file_type = info[l:].strip()
if info.startswith("input_directory"):
l = len("input_directory")
input_directory = info[l:].strip()
if input_directory == 'aligner_output':
# when the input_directory is 'aligner_output',
# check if the required input_file_type
# exists in the input_directory
input_directory = input_files_path.split(';')
found = \
path_check.file_or_basename_exist_in_any(
input_directory,
input_file_type)
if found == 'files_found' or found == 'not check':
pass
elif found == 'basename found':
warning_string = "Warning: basename found " + \
"instead of filename in " + \
" input file type. Please" + \
" make sure that command '" + \
command_name + "' can work with" + \
"basenames."
self.warning_list.append(warning_string)
elif found == 'not found':
self.error_list.append("Error: required file " +
input_file_type + " not exists" +
" in aligner_output directory.")
def check_exe(self, command):
"""
Given a command string,
Retuns true if command is executable, false otherwise
"""
# expand environment variables in command
command = os.path.expandvars(command)
if command in self.exceptions_list:
return True # true for all exceptions
# find path of the given command exectuable
find_exe_result = distutils.spawn.find_executable(command)
if find_exe_result is None:
return False # not an executable
# check if executable path exists (applies only when full path is
# given)
path_checker = yap_path_checks()
if path_checker.valid_path_or_link(find_exe_result):
# return true if execute is set on executable file
return os.access(find_exe_result, os.X_OK)
else:
return False # return false if executable does not exist
def check_exe(self, command):
"""
Given a command string,
Retuns true if command is executable, false otherwise
"""
# expand environment variables in command
command = os.path.expandvars(command)
if command in self.exceptions_list:
return True # true for all exceptions
# find path of the given command exectuable
find_exe_result = distutils.spawn.find_executable(command)
if find_exe_result is None:
return False # not an executable
# check if executable path exists (applies only when full path is
# given)
path_checker = yap_path_checks()
if path_checker.valid_path_or_link(find_exe_result):
# return true if execute is set on executable file
return os.access(find_exe_result, os.X_OK)
else:
return False # return false if executable does not exist
